diff --git a/.github/CODE_OF_CONDUCT.md b/.github/CODE_OF_CONDUCT.md deleted file mode 100644 index 841ad1e..0000000 --- a/.github/CODE_OF_CONDUCT.md +++ /dev/null @@ -1,132 +0,0 @@ -# Contributor Covenant Code of Conduct - -## Our Pledge - -We as members, contributors, and leaders pledge to make participation in our -community a harassment-free experience for everyone, regardless of age, body -size, visible or invisible disability, ethnicity, sex characteristics, gender -identity and expression, level of experience, education, socioeconomic status, -nationality, personal appearance, race, caste, color, religion, or sexual -identity and orientation. - -We pledge to act and interact in ways that contribute to an open, welcoming, -diverse, inclusive, and healthy community. - -## Our Standards - -Examples of behavior that contributes to a positive environment for our -community include: - -* Demonstrating empathy and kindness toward other people -* Being respectful of differing opinions, viewpoints, and experiences -* Giving and gracefully accepting constructive feedback -* Accepting responsibility and apologizing to those affected by our mistakes, - and learning from the experience -* Focusing on what is best not just for us as individuals, but for the overall - community - -Examples of unacceptable behavior include: - -* The use of sexualized language or imagery, and sexual attention or advances of - any kind -* Trolling, insulting or derogatory comments, and personal or political attacks -* Public or private harassment -* Publishing others' private information, such as a physical or email address, - without their explicit permission -* Other conduct which could reasonably be considered inappropriate in a - professional setting - -## Enforcement Responsibilities - -Community leaders are responsible for clarifying and enforcing our standards of -acceptable behavior and will take appropriate and fair corrective action in -response to any behavior that they deem inappropriate, threatening, offensive, -or harmful. - -Community leaders have the right and responsibility to remove, edit, or reject -comments, commits, code, wiki edits, issues, and other contributions that are -not aligned to this Code of Conduct, and will communicate reasons for moderation -decisions when appropriate. - -## Scope - -This Code of Conduct applies within all community spaces, and also applies when -an individual is officially representing the community in public spaces. -Examples of representing our community include using an official e-mail address, -posting via an official social media account, or acting as an appointed -representative at an online or offline event. - -## Enforcement - -Instances of abusive, harassing, or otherwise unacceptable behavior may be -reported to the community leaders responsible for enforcement at -cjm@berkeleybop.org (Christopher J Mungall). -All complaints will be reviewed and investigated promptly and fairly. - -All community leaders are obligated to respect the privacy and security of the -reporter of any incident. - -## Enforcement Guidelines - -Community leaders will follow these Community Impact Guidelines in determining -the consequences for any action they deem in violation of this Code of Conduct: - -### 1. Correction - -**Community Impact**: Use of inappropriate language or other behavior deemed -unprofessional or unwelcome in the community. - -**Consequence**: A private, written warning from community leaders, providing -clarity around the nature of the violation and an explanation of why the -behavior was inappropriate. A public apology may be requested. - -### 2. Warning - -**Community Impact**: A violation through a single incident or series of -actions. - -**Consequence**: A warning with consequences for continued behavior. No -interaction with the people involved, including unsolicited interaction with -those enforcing the Code of Conduct, for a specified period of time. This -includes avoiding interactions in community spaces as well as external channels -like social media. Violating these terms may lead to a temporary or permanent -ban. - -### 3. Temporary Ban - -**Community Impact**: A serious violation of community standards, including -sustained inappropriate behavior. - -**Consequence**: A temporary ban from any sort of interaction or public -communication with the community for a specified period of time. No public or -private interaction with the people involved, including unsolicited interaction -with those enforcing the Code of Conduct, is allowed during this period. -Violating these terms may lead to a permanent ban. - -### 4. Permanent Ban - -**Community Impact**: Demonstrating a pattern of violation of community -standards, including sustained inappropriate behavior, harassment of an -individual, or aggression toward or disparagement of classes of individuals. - -**Consequence**: A permanent ban from any sort of public interaction within the -community. - -## Attribution - -This Code of Conduct is adapted from the [Contributor Covenant][homepage], -version 2.1, available at -[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1]. - -Community Impact Guidelines were inspired by -[Mozilla's code of conduct enforcement ladder][Mozilla CoC]. - -For answers to common questions about this code of conduct, see the FAQ at -[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at -[https://www.contributor-covenant.org/translations][translations]. - -[homepage]: https://www.contributor-covenant.org -[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html -[Mozilla CoC]: https://github.com/mozilla/diversity -[FAQ]: https://www.contributor-covenant.org/faq -[translations]: https://www.contributor-covenant.org/translations diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md deleted file mode 100644 index 6f9238f..0000000 --- a/.github/CONTRIBUTING.md +++ /dev/null @@ -1,23 +0,0 @@ -# Contributing - -### Code Style - -This project uses [`black`](https://github.com/psf/black) to automatically -enforce a consistent code style. You can apply `black` and other pre-configured -linters with `tox -e lint`. - -This project uses [`flake8`](https://flake8.pycqa.org) and several plugins for -additional checks of documentation style, security issues, good variable -nomenclature, and more ( -see [`tox.ini`](tox.ini) for a list of flake8 plugins). You can check if your -code passes `flake8` with `tox -e flake8`. - -Each of these checks are run on each commit using GitHub Actions as a continuous -integration service. Passing all of them is required for accepting a -contribution. If you're unsure how to address the feedback from one of these -tools, please say so either in the description of your pull request or in a -comment, and we will help you. - -These code style contribution guidelines have been adapted from the -[cthoyt/cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack/blob/main/%7B%7Bcookiecutter.package_name%7D%7D/.github/CODE_OF_CONDUCT.md) -Python package template. diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml deleted file mode 100644 index 08a1267..0000000 --- a/.github/workflows/codespell.yml +++ /dev/null @@ -1,27 +0,0 @@ -# Codespell configuration is within pyproject.toml ---- -name: Codespell - -on: - push: - branches: [main] - pull_request: - types: - - opened - - reopened - - synchronize - - ready_for_review - -permissions: - contents: read - -jobs: - codespell: - name: Check for spelling errors - runs-on: ubuntu-latest - - steps: - - name: Checkout - uses: actions/checkout@v4 - - name: Codespell - uses: codespell-project/actions-codespell@v2 diff --git a/.github/workflows/deploy_documentation.yml b/.github/workflows/deploy_documentation.yml deleted file mode 100644 index 1459043..0000000 --- a/.github/workflows/deploy_documentation.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: Deploy Documentation - -# Controls when the action will run. Triggers the workflow on push -on: - workflow_dispatch: - push: - branches: [ main ] - - paths: - - 'src/linkml_map/datamodel.yaml' - -# A workflow run is made up of one or more jobs that can run sequentially or in parallel -jobs: - build-docs: - # The type of runner that the job will run on - runs-on: ubuntu-latest - - # Steps represent a sequence of tasks that will be executed as part of the job - steps: - - name: Check out repository - uses: actions/checkout@v4 - with: - fetch-depth: 0 - - - name: Install uv - uses: astral-sh/setup-uv@v5 - - - name: Set up Python3 - uses: actions/setup-python@v5 - with: - python-version: 3.12 - - - name: Install dependencies - run: uv sync - - - name: Generate and deploy docs - run: | - mkdir docs - touch docs/.nojekyll - make deploy-gh-doc diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml deleted file mode 100644 index ac11ccf..0000000 --- a/.github/workflows/main.yaml +++ /dev/null @@ -1,76 +0,0 @@ -# Built from: -# https://docs.github.com/en/actions/guides/building-and-testing-python - -name: Build and test - -on: - push: - branches: [ main ] - - pull_request: - types: - - opened - - reopened - - synchronize - - ready_for_review - -jobs: - lint: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: '3.12' - - - name: Install dependencies - run: | - pip install tox - - - name: Check code quality with ruff - run: tox -e lint_stats - - test: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: [ '3.9', '3.10', '3.11', '3.12', '3.13' ] - - steps: - - uses: actions/checkout@v4 - - - uses: ts-graphviz/setup-graphviz@v2 - - - name: Install uv - uses: astral-sh/setup-uv@v5 - - - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - - - name: Install dependencies - run: uv sync - - - name: Generate LinkML-Map Transformation Model artifacts - run: | - # Force regenerate by removing the target file first - rm -f src/linkml_map/datamodel/transformer_model.py - make src/linkml_map/datamodel/transformer_model.py - - # Run tests to make sure everything works - make test - - # Check if there are any changes and commit them - git config --local user.email "action@github.com" - git config --local user.name "GitHub Action" - git add src/ - - # Only commit if there are changes - if ! git diff --cached --quiet; then - git commit -m "Regenerate artifacts from linkml-map transformer_model.yaml" - git push - else - echo "No changes to commit" - fi diff --git a/.github/workflows/pypi-publish.yaml b/.github/workflows/pypi-publish.yaml deleted file mode 100644 index 23b139a..0000000 --- a/.github/workflows/pypi-publish.yaml +++ /dev/null @@ -1,36 +0,0 @@ -name: Publish Python Package - -on: - workflow_dispatch: - release: - types: [created] - -jobs: - build-n-publish: - name: Build and publish Python 🐍 distributions 📦 to PyPI - runs-on: ubuntu-latest - # needs: [test] - environment: release - permissions: - id-token: write - steps: - - uses: actions/checkout@v4 - - - name: Install uv - uses: astral-sh/setup-uv@v5 - - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: '3.12' - - - name: Install dependencies - run: uv sync - - - name: Build source and wheel archives - run: uv build - - - name: Publish - uses: pypa/gh-action-pypi-publish@release/v1 - with: - verbose: true diff --git a/.gitignore b/.gitignore deleted file mode 100644 index 9d5951b..0000000 --- a/.gitignore +++ /dev/null @@ -1,13 +0,0 @@ -*.old -.coverage -coverage.xml -.idea -project/ -tmp/ -site/ -__pycache__ -tests/output/ -dist/* -.vscode -mise.toml - diff --git a/src/linkml_map/cli/__init__.py b/.nojekyll similarity index 100% rename from src/linkml_map/cli/__init__.py rename to .nojekyll diff --git a/404.html b/404.html new file mode 100644 index 0000000..69cf66a --- /dev/null +++ b/404.html @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + +

404

+

Page not found

+ + + +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/AliasedClass/index.html b/AliasedClass/index.html new file mode 100644 index 0000000..77cdaf1 --- /dev/null +++ b/AliasedClass/index.html @@ -0,0 +1,202 @@ + + + + + + + + + + +Class: AliasedClass - LinkML-Map + + + + + + + + + + + + + + + + + + +
+ +

Class: AliasedClass

+

alias-class key value pairs for classes

+

URI: linkmltr:AliasedClass

+
classDiagram + class AliasedClass + AliasedClass : alias + + AliasedClass --> None : alias + + AliasedClass : class_named + + AliasedClass --> None : class_named + + +
+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
alias0..1
String
name of the class to be aliaseddirect
class_named0..1
String
local alias for the classdirect
+

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
ClassDerivationjoinsrangeAliasedClass
+

Identifier and Mapping Information

+

Schema Source

+ +

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selflinkmltr:AliasedClass
nativelinkmltr:AliasedClass
+

LinkML Source

+ +

Direct

+
+
name: AliasedClass
+description: alias-class key value pairs for classes
+from_schema: https://w3id.org/linkml/transformer
+attributes:
+  alias:
+    name: alias
+    description: name of the class to be aliased
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    key: true
+    domain_of:
+    - AliasedClass
+    required: true
+  class_named:
+    name: class_named
+    description: local alias for the class
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    domain_of:
+    - AliasedClass
+
+
+
+

Induced

+
+
name: AliasedClass
+description: alias-class key value pairs for classes
+from_schema: https://w3id.org/linkml/transformer
+attributes:
+  alias:
+    name: alias
+    description: name of the class to be aliased
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    key: true
+    alias: alias
+    owner: AliasedClass
+    domain_of:
+    - AliasedClass
+    required: true
+  class_named:
+    name: class_named
+    description: local alias for the class
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: class_named
+    owner: AliasedClass
+    domain_of:
+    - AliasedClass
+
+
+
+
+
+
+ + + \ No newline at end of file diff --git a/Any/index.html b/Any/index.html new file mode 100644 index 0000000..bd2a84f --- /dev/null +++ b/Any/index.html @@ -0,0 +1,203 @@ + + + + + + + + + + +Class: Any - LinkML-Map + + + + + + + + + + + + + + + + + + +
+ +

Class: Any

+

URI: linkml:Any

+
classDiagram + class Any + +
+ +

Slots

+ + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
ElementDerivationoverridesrangeAny
ClassDerivationoverridesrangeAny
SlotDerivationoverridesrangeAny
EnumDerivationoverridesrangeAny
PermissibleValueDerivationoverridesrangeAny
PrefixDerivationoverridesrangeAny
KeyValvaluerangeAny
CopyDirectiveexcluderangeAny
CopyDirectiveincluderangeAny
CopyDirectiveaddrangeAny
+

Identifier and Mapping Information

+

Schema Source

+ +

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selflinkml:Any
nativelinkmltr:Any
+

LinkML Source

+ +

Direct

+
+
name: Any
+from_schema: https://w3id.org/linkml/transformer
+class_uri: linkml:Any
+
+
+
+

Induced

+
+
name: Any
+from_schema: https://w3id.org/linkml/transformer
+class_uri: linkml:Any
+
+
+
+
+
+
+ + + \ No newline at end of file diff --git a/Boolean/index.html b/Boolean/index.html new file mode 100644 index 0000000..db69c91 --- /dev/null +++ b/Boolean/index.html @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + Type: Boolean - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Type: Boolean

+

A binary (true or false) value

+

URI: xsd:boolean

+ +

Identifier and Mapping Information

+

Schema Source

+ + +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/ClassDerivation/index.html b/ClassDerivation/index.html new file mode 100644 index 0000000..5d3fb1b --- /dev/null +++ b/ClassDerivation/index.html @@ -0,0 +1,546 @@ + + + + + + + + + + +Class: ClassDerivation - LinkML-Map + + + + + + + + + + + + + + + + + + +
+ +

Class: ClassDerivation

+

A specification of how to derive a target class from a source class.

+

URI: linkmltr:ClassDerivation

+
classDiagram + class ClassDerivation + ElementDerivation <|-- ClassDerivation + + ClassDerivation : comments + + ClassDerivation : copy_directives + + ClassDerivation --> CopyDirective : copy_directives + + ClassDerivation : description + + ClassDerivation --> None : description + + ClassDerivation : expression_to_expression_mappings + + ClassDerivation --> KeyVal : expression_to_expression_mappings + + ClassDerivation : expression_to_value_mappings + + ClassDerivation --> KeyVal : expression_to_value_mappings + + ClassDerivation : implements + + ClassDerivation : is_a + + ClassDerivation --> ElementDerivation : is_a + + ClassDerivation : joins + + ClassDerivation --> AliasedClass : joins + + ClassDerivation : mirror_source + + ClassDerivation : mixins + + ClassDerivation --> ElementDerivation : mixins + + ClassDerivation : name + + ClassDerivation --> None : name + + ClassDerivation : overrides + + ClassDerivation --> Any : overrides + + ClassDerivation : populated_from + + ClassDerivation : slot_derivations + + ClassDerivation --> SlotDerivation : slot_derivations + + ClassDerivation : sources + + ClassDerivation : value_mappings + + ClassDerivation --> KeyVal : value_mappings + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
populated_from0..1
ClassReference
Name of the class in the source schemadirect
sources0..*
ClassReference
direct
joins0..*
AliasedClass
Additional classes to be joined to derive instances of the target classdirect
slot_derivations0..*
SlotDerivation
direct
name1..1
String
Name of the element in the target schemaElementDerivation
copy_directives0..*
CopyDirective
ElementDerivation
overrides0..1
Any
overrides source schema slotsElementDerivation
is_a0..1
ElementDerivation
ElementDerivation
mixins0..*
ElementDerivation
ElementDerivation
value_mappings0..*
KeyVal
A mapping table that is applied directly to mappings, in order of precedenceElementDerivation
expression_to_value_mappings0..*
KeyVal
A mapping table in which the keys are expressionsElementDerivation
expression_to_expression_mappings0..*
KeyVal
A mapping table in which the keys and values are expressionsElementDerivation
mirror_source0..1
Boolean
ElementDerivation
description0..1
String
description of the specification componentSpecificationComponent
implements0..*
Uriorcurie
A reference to a specification that this component implementsSpecificationComponent
comments0..*
String
A list of comments about this componentSpecificationComponent
+

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
TransformationSpecificationclass_derivationsrangeClassDerivation
+

Identifier and Mapping Information

+

Schema Source

+ +

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selflinkmltr:ClassDerivation
nativelinkmltr:ClassDerivation
+

LinkML Source

+ +

Direct

+
+
name: ClassDerivation
+description: A specification of how to derive a target class from a source class.
+from_schema: https://w3id.org/linkml/transformer
+is_a: ElementDerivation
+attributes:
+  populated_from:
+    name: populated_from
+    description: Name of the class in the source schema
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    domain_of:
+    - ClassDerivation
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    range: ClassReference
+  sources:
+    name: sources
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    domain_of:
+    - ClassDerivation
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    range: ClassReference
+  joins:
+    name: joins
+    description: Additional classes to be joined to derive instances of the target
+      class
+    comments:
+    - not yet implemented
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    domain_of:
+    - ClassDerivation
+    range: AliasedClass
+    inlined: true
+  slot_derivations:
+    name: slot_derivations
+    from_schema: https://w3id.org/linkml/transformer
+    multivalued: true
+    domain_of:
+    - TransformationSpecification
+    - ClassDerivation
+    range: SlotDerivation
+    inlined: true
+
+
+
+

Induced

+
+
name: ClassDerivation
+description: A specification of how to derive a target class from a source class.
+from_schema: https://w3id.org/linkml/transformer
+is_a: ElementDerivation
+attributes:
+  populated_from:
+    name: populated_from
+    description: Name of the class in the source schema
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: populated_from
+    owner: ClassDerivation
+    domain_of:
+    - ClassDerivation
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    range: ClassReference
+  sources:
+    name: sources
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: sources
+    owner: ClassDerivation
+    domain_of:
+    - ClassDerivation
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    range: ClassReference
+  joins:
+    name: joins
+    description: Additional classes to be joined to derive instances of the target
+      class
+    comments:
+    - not yet implemented
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: joins
+    owner: ClassDerivation
+    domain_of:
+    - ClassDerivation
+    range: AliasedClass
+    inlined: true
+  slot_derivations:
+    name: slot_derivations
+    from_schema: https://w3id.org/linkml/transformer
+    multivalued: true
+    alias: slot_derivations
+    owner: ClassDerivation
+    domain_of:
+    - TransformationSpecification
+    - ClassDerivation
+    range: SlotDerivation
+    inlined: true
+  name:
+    name: name
+    description: Name of the element in the target schema
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    key: true
+    alias: name
+    owner: ClassDerivation
+    domain_of:
+    - ElementDerivation
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    range: string
+    required: true
+  copy_directives:
+    name: copy_directives
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: copy_directives
+    owner: ClassDerivation
+    domain_of:
+    - ElementDerivation
+    range: CopyDirective
+    inlined: true
+  overrides:
+    name: overrides
+    description: overrides source schema slots
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: overrides
+    owner: ClassDerivation
+    domain_of:
+    - ElementDerivation
+    range: Any
+  is_a:
+    name: is_a
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: linkml:is_a
+    alias: is_a
+    owner: ClassDerivation
+    domain_of:
+    - ElementDerivation
+    range: ElementDerivation
+  mixins:
+    name: mixins
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: linkml:mixins
+    multivalued: true
+    alias: mixins
+    owner: ClassDerivation
+    domain_of:
+    - ElementDerivation
+    range: ElementDerivation
+    inlined: false
+  value_mappings:
+    name: value_mappings
+    description: A mapping table that is applied directly to mappings, in order of
+      precedence
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: value_mappings
+    owner: ClassDerivation
+    domain_of:
+    - ElementDerivation
+    range: KeyVal
+    inlined: true
+  expression_to_value_mappings:
+    name: expression_to_value_mappings
+    description: A mapping table in which the keys are expressions
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: expression_to_value_mappings
+    owner: ClassDerivation
+    domain_of:
+    - ElementDerivation
+    range: KeyVal
+    inlined: true
+  expression_to_expression_mappings:
+    name: expression_to_expression_mappings
+    description: A mapping table in which the keys and values are expressions
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: expression_to_expression_mappings
+    owner: ClassDerivation
+    domain_of:
+    - ElementDerivation
+    range: KeyVal
+    inlined: true
+  mirror_source:
+    name: mirror_source
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: mirror_source
+    owner: ClassDerivation
+    domain_of:
+    - ElementDerivation
+    range: boolean
+  description:
+    name: description
+    description: description of the specification component
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: dcterms:description
+    alias: description
+    owner: ClassDerivation
+    domain_of:
+    - SpecificationComponent
+    range: string
+  implements:
+    name: implements
+    description: A reference to a specification that this component implements.
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: implements
+    owner: ClassDerivation
+    domain_of:
+    - SpecificationComponent
+    range: uriorcurie
+  comments:
+    name: comments
+    description: A list of comments about this component. Comments are free text,
+      and may be used to provide additional information about the component, including
+      instructions for its use.
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: rdfs:comment
+    multivalued: true
+    alias: comments
+    owner: ClassDerivation
+    domain_of:
+    - SpecificationComponent
+    range: string
+
+
+
+
+
+
+ + + \ No newline at end of file diff --git a/ClassReference/index.html b/ClassReference/index.html new file mode 100644 index 0000000..e811220 --- /dev/null +++ b/ClassReference/index.html @@ -0,0 +1,94 @@ + + + + + + + + + + + + + + Type: ClassReference - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Type: ClassReference

+

URI: xsd:string

+ +

Identifier and Mapping Information

+

Schema Source

+ + +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/CollectionType/index.html b/CollectionType/index.html new file mode 100644 index 0000000..abc4e5c --- /dev/null +++ b/CollectionType/index.html @@ -0,0 +1,152 @@ + + + + + + + + + + + + + + Enum: CollectionType - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Enum: CollectionType

+

URI: CollectionType

+

Permissible Values

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ValueMeaningDescription
SingleValuedNone
MultiValuedNone
MultiValuedListNone
MultiValuedDictNone
+

Slots

+ + + + + + + + + + + + + +
NameDescription
cast_collection_as
+

Identifier and Mapping Information

+

Schema Source

+ +

LinkML Source

+
+ +
name: CollectionType
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+permissible_values:
+  SingleValued:
+    text: SingleValued
+  MultiValued:
+    text: MultiValued
+  MultiValuedList:
+    text: MultiValuedList
+  MultiValuedDict:
+    text: MultiValuedDict
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/CopyDirective/index.html b/CopyDirective/index.html new file mode 100644 index 0000000..70e8e03 --- /dev/null +++ b/CopyDirective/index.html @@ -0,0 +1,334 @@ + + + + + + + + + + +Class: CopyDirective - LinkML-Map + + + + + + + + + + + + + + + + + + +
+ +

Class: CopyDirective

+

Instructs a Schema Mapper in how to map to a target schema. Not used for data transformation.

+

URI: linkmltr:CopyDirective

+
classDiagram + class CopyDirective + CopyDirective : add + + CopyDirective --> Any : add + + CopyDirective : copy_all + + CopyDirective : element_name + + CopyDirective --> None : element_name + + CopyDirective : exclude + + CopyDirective --> Any : exclude + + CopyDirective : exclude_all + + CopyDirective : include + + CopyDirective --> Any : include + + +
+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
element_name0..1
String
direct
copy_all0..1
Boolean
direct
exclude_all0..1
Boolean
direct
exclude0..1
Any
direct
include0..1
Any
direct
add0..1
Any
direct
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
ElementDerivationcopy_directivesrangeCopyDirective
ClassDerivationcopy_directivesrangeCopyDirective
SlotDerivationcopy_directivesrangeCopyDirective
EnumDerivationcopy_directivesrangeCopyDirective
PermissibleValueDerivationcopy_directivesrangeCopyDirective
PrefixDerivationcopy_directivesrangeCopyDirective
+

Identifier and Mapping Information

+

Schema Source

+ +

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selflinkmltr:CopyDirective
nativelinkmltr:CopyDirective
+

LinkML Source

+ +

Direct

+
+
name: CopyDirective
+description: Instructs a Schema Mapper in how to map to a target schema. Not used
+  for data transformation.
+from_schema: https://w3id.org/linkml/transformer
+status: testing
+attributes:
+  element_name:
+    name: element_name
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    key: true
+    domain_of:
+    - CopyDirective
+    required: true
+  copy_all:
+    name: copy_all
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    domain_of:
+    - CopyDirective
+    range: boolean
+  exclude_all:
+    name: exclude_all
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    domain_of:
+    - CopyDirective
+    range: boolean
+  exclude:
+    name: exclude
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    domain_of:
+    - CopyDirective
+    range: Any
+  include:
+    name: include
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    domain_of:
+    - CopyDirective
+    range: Any
+  add:
+    name: add
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    domain_of:
+    - CopyDirective
+    range: Any
+
+
+
+

Induced

+
+
name: CopyDirective
+description: Instructs a Schema Mapper in how to map to a target schema. Not used
+  for data transformation.
+from_schema: https://w3id.org/linkml/transformer
+status: testing
+attributes:
+  element_name:
+    name: element_name
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    key: true
+    alias: element_name
+    owner: CopyDirective
+    domain_of:
+    - CopyDirective
+    required: true
+  copy_all:
+    name: copy_all
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: copy_all
+    owner: CopyDirective
+    domain_of:
+    - CopyDirective
+    range: boolean
+  exclude_all:
+    name: exclude_all
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: exclude_all
+    owner: CopyDirective
+    domain_of:
+    - CopyDirective
+    range: boolean
+  exclude:
+    name: exclude
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: exclude
+    owner: CopyDirective
+    domain_of:
+    - CopyDirective
+    range: Any
+  include:
+    name: include
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: include
+    owner: CopyDirective
+    domain_of:
+    - CopyDirective
+    range: Any
+  add:
+    name: add
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: add
+    owner: CopyDirective
+    domain_of:
+    - CopyDirective
+    range: Any
+
+
+
+
+
+
+ + + \ No newline at end of file diff --git a/Curie/index.html b/Curie/index.html new file mode 100644 index 0000000..2714d40 --- /dev/null +++ b/Curie/index.html @@ -0,0 +1,101 @@ + + + + + + + + + + + + + + Type: Curie - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Type: Curie

+

a compact URI

+

URI: xsd:string

+ +

Comments

+ +

Identifier and Mapping Information

+

Schema Source

+ + +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/Date/index.html b/Date/index.html new file mode 100644 index 0000000..f8f9934 --- /dev/null +++ b/Date/index.html @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + Type: Date - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Type: Date

+

a date (year, month and day) in an idealized calendar

+

URI: xsd:date

+ +

Identifier and Mapping Information

+

Schema Source

+ + +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/DateOrDatetime/index.html b/DateOrDatetime/index.html new file mode 100644 index 0000000..8aed0b6 --- /dev/null +++ b/DateOrDatetime/index.html @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + Type: DateOrDatetime - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Type: DateOrDatetime

+

Either a date or a datetime

+

URI: linkml:DateOrDatetime

+ +

Identifier and Mapping Information

+

Schema Source

+ + +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/Datetime/index.html b/Datetime/index.html new file mode 100644 index 0000000..27e04be --- /dev/null +++ b/Datetime/index.html @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + Type: Datetime - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Type: Datetime

+

The combination of a date and time

+

URI: xsd:dateTime

+ +

Identifier and Mapping Information

+

Schema Source

+ + +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/Decimal/index.html b/Decimal/index.html new file mode 100644 index 0000000..b669280 --- /dev/null +++ b/Decimal/index.html @@ -0,0 +1,92 @@ + + + + + + + + + + + + + + Type: Decimal - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Type: Decimal

+

A real number with arbitrary precision that conforms to the xsd:decimal specification

+

URI: xsd:decimal

+ +

Identifier and Mapping Information

+

Schema Source

+ + +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/Double/index.html b/Double/index.html new file mode 100644 index 0000000..381c9a8 --- /dev/null +++ b/Double/index.html @@ -0,0 +1,92 @@ + + + + + + + + + + + + + + Type: Double - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Type: Double

+

A real number that conforms to the xsd:double specification

+

URI: xsd:double

+ +

Identifier and Mapping Information

+

Schema Source

+ + +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/ElementDerivation/index.html b/ElementDerivation/index.html new file mode 100644 index 0000000..9e5f2c6 --- /dev/null +++ b/ElementDerivation/index.html @@ -0,0 +1,583 @@ + + + + + + + + + + +Class: ElementDerivation - LinkML-Map + + + + + + + + + + + + + + + + + + +
+ +

Class: ElementDerivation

+

An abstract grouping for classes that provide a specification of how to derive a target element from a source element.

+ +

URI: linkmltr:ElementDerivation

+
classDiagram + class ElementDerivation + SpecificationComponent <|-- ElementDerivation + + + ElementDerivation <|-- ClassDerivation + ElementDerivation <|-- SlotDerivation + ElementDerivation <|-- EnumDerivation + ElementDerivation <|-- PermissibleValueDerivation + ElementDerivation <|-- PrefixDerivation + + + ElementDerivation : comments + + ElementDerivation : copy_directives + + ElementDerivation --> CopyDirective : copy_directives + + ElementDerivation : description + + ElementDerivation --> None : description + + ElementDerivation : expression_to_expression_mappings + + ElementDerivation --> KeyVal : expression_to_expression_mappings + + ElementDerivation : expression_to_value_mappings + + ElementDerivation --> KeyVal : expression_to_value_mappings + + ElementDerivation : implements + + ElementDerivation : is_a + + ElementDerivation --> ElementDerivation : is_a + + ElementDerivation : mirror_source + + ElementDerivation : mixins + + ElementDerivation --> ElementDerivation : mixins + + ElementDerivation : name + + ElementDerivation --> None : name + + ElementDerivation : overrides + + ElementDerivation --> Any : overrides + + ElementDerivation : value_mappings + + ElementDerivation --> KeyVal : value_mappings + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
name0..1
String
Name of the element in the target schemadirect
copy_directives0..*
CopyDirective
direct
overrides0..1
Any
overrides source schema slotsdirect
is_a0..1
ElementDerivation
direct
mixins0..*
ElementDerivation
direct
value_mappings0..*
KeyVal
A mapping table that is applied directly to mappings, in order of precedencedirect
expression_to_value_mappings0..*
KeyVal
A mapping table in which the keys are expressionsdirect
expression_to_expression_mappings0..*
KeyVal
A mapping table in which the keys and values are expressionsdirect
mirror_source0..1
Boolean
direct
description0..1
String
description of the specification componentSpecificationComponent
implements0..*
Uriorcurie
A reference to a specification that this component implementsSpecificationComponent
comments0..*
String
A list of comments about this componentSpecificationComponent
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
ElementDerivationis_arangeElementDerivation
ElementDerivationmixinsrangeElementDerivation
ClassDerivationis_arangeElementDerivation
ClassDerivationmixinsrangeElementDerivation
SlotDerivationis_arangeElementDerivation
SlotDerivationmixinsrangeElementDerivation
EnumDerivationis_arangeElementDerivation
EnumDerivationmixinsrangeElementDerivation
PermissibleValueDerivationis_arangeElementDerivation
PermissibleValueDerivationmixinsrangeElementDerivation
PrefixDerivationis_arangeElementDerivation
PrefixDerivationmixinsrangeElementDerivation
+

Identifier and Mapping Information

+

Schema Source

+ +

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selflinkmltr:ElementDerivation
nativelinkmltr:ElementDerivation
+

LinkML Source

+ +

Direct

+
+
name: ElementDerivation
+description: An abstract grouping for classes that provide a specification of how
+  to  derive a target element from a source element.
+from_schema: https://w3id.org/linkml/transformer
+is_a: SpecificationComponent
+abstract: true
+attributes:
+  name:
+    name: name
+    description: Name of the element in the target schema
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    key: true
+    domain_of:
+    - ElementDerivation
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    required: true
+  copy_directives:
+    name: copy_directives
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    domain_of:
+    - ElementDerivation
+    range: CopyDirective
+    inlined: true
+  overrides:
+    name: overrides
+    description: overrides source schema slots
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    domain_of:
+    - ElementDerivation
+    range: Any
+  is_a:
+    name: is_a
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: linkml:is_a
+    domain_of:
+    - ElementDerivation
+    range: ElementDerivation
+  mixins:
+    name: mixins
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: linkml:mixins
+    multivalued: true
+    domain_of:
+    - ElementDerivation
+    range: ElementDerivation
+    inlined: false
+  value_mappings:
+    name: value_mappings
+    description: A mapping table that is applied directly to mappings, in order of
+      precedence
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    domain_of:
+    - ElementDerivation
+    range: KeyVal
+    inlined: true
+  expression_to_value_mappings:
+    name: expression_to_value_mappings
+    description: A mapping table in which the keys are expressions
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    domain_of:
+    - ElementDerivation
+    range: KeyVal
+    inlined: true
+  expression_to_expression_mappings:
+    name: expression_to_expression_mappings
+    description: A mapping table in which the keys and values are expressions
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    domain_of:
+    - ElementDerivation
+    range: KeyVal
+    inlined: true
+  mirror_source:
+    name: mirror_source
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    domain_of:
+    - ElementDerivation
+    range: boolean
+
+
+
+

Induced

+
+
name: ElementDerivation
+description: An abstract grouping for classes that provide a specification of how
+  to  derive a target element from a source element.
+from_schema: https://w3id.org/linkml/transformer
+is_a: SpecificationComponent
+abstract: true
+attributes:
+  name:
+    name: name
+    description: Name of the element in the target schema
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    key: true
+    alias: name
+    owner: ElementDerivation
+    domain_of:
+    - ElementDerivation
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    required: true
+  copy_directives:
+    name: copy_directives
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: copy_directives
+    owner: ElementDerivation
+    domain_of:
+    - ElementDerivation
+    range: CopyDirective
+    inlined: true
+  overrides:
+    name: overrides
+    description: overrides source schema slots
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: overrides
+    owner: ElementDerivation
+    domain_of:
+    - ElementDerivation
+    range: Any
+  is_a:
+    name: is_a
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: linkml:is_a
+    alias: is_a
+    owner: ElementDerivation
+    domain_of:
+    - ElementDerivation
+    range: ElementDerivation
+  mixins:
+    name: mixins
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: linkml:mixins
+    multivalued: true
+    alias: mixins
+    owner: ElementDerivation
+    domain_of:
+    - ElementDerivation
+    range: ElementDerivation
+    inlined: false
+  value_mappings:
+    name: value_mappings
+    description: A mapping table that is applied directly to mappings, in order of
+      precedence
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: value_mappings
+    owner: ElementDerivation
+    domain_of:
+    - ElementDerivation
+    range: KeyVal
+    inlined: true
+  expression_to_value_mappings:
+    name: expression_to_value_mappings
+    description: A mapping table in which the keys are expressions
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: expression_to_value_mappings
+    owner: ElementDerivation
+    domain_of:
+    - ElementDerivation
+    range: KeyVal
+    inlined: true
+  expression_to_expression_mappings:
+    name: expression_to_expression_mappings
+    description: A mapping table in which the keys and values are expressions
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: expression_to_expression_mappings
+    owner: ElementDerivation
+    domain_of:
+    - ElementDerivation
+    range: KeyVal
+    inlined: true
+  mirror_source:
+    name: mirror_source
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: mirror_source
+    owner: ElementDerivation
+    domain_of:
+    - ElementDerivation
+    range: boolean
+  description:
+    name: description
+    description: description of the specification component
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: dcterms:description
+    alias: description
+    owner: ElementDerivation
+    domain_of:
+    - SpecificationComponent
+    range: string
+  implements:
+    name: implements
+    description: A reference to a specification that this component implements.
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: implements
+    owner: ElementDerivation
+    domain_of:
+    - SpecificationComponent
+    range: uriorcurie
+  comments:
+    name: comments
+    description: A list of comments about this component. Comments are free text,
+      and may be used to provide additional information about the component, including
+      instructions for its use.
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: rdfs:comment
+    multivalued: true
+    alias: comments
+    owner: ElementDerivation
+    domain_of:
+    - SpecificationComponent
+    range: string
+
+
+
+
+
+
+ + + \ No newline at end of file diff --git a/EnumDerivation/index.html b/EnumDerivation/index.html new file mode 100644 index 0000000..050f13a --- /dev/null +++ b/EnumDerivation/index.html @@ -0,0 +1,575 @@ + + + + + + + + + + +Class: EnumDerivation - LinkML-Map + + + + + + + + + + + + + + + + + + +
+ +

Class: EnumDerivation

+

A specification of how to derive the value of a target enum from a source enum

+

URI: linkmltr:EnumDerivation

+
classDiagram + class EnumDerivation + ElementDerivation <|-- EnumDerivation + + EnumDerivation : comments + + EnumDerivation : copy_directives + + EnumDerivation --> CopyDirective : copy_directives + + EnumDerivation : description + + EnumDerivation --> None : description + + EnumDerivation : expr + + EnumDerivation : expression_to_expression_mappings + + EnumDerivation --> KeyVal : expression_to_expression_mappings + + EnumDerivation : expression_to_value_mappings + + EnumDerivation --> KeyVal : expression_to_value_mappings + + EnumDerivation : hide + + EnumDerivation : implements + + EnumDerivation : is_a + + EnumDerivation --> ElementDerivation : is_a + + EnumDerivation : mirror_source + + EnumDerivation : mixins + + EnumDerivation --> ElementDerivation : mixins + + EnumDerivation : name + + EnumDerivation --> None : name + + EnumDerivation : overrides + + EnumDerivation --> Any : overrides + + EnumDerivation : permissible_value_derivations + + EnumDerivation --> PermissibleValueDerivation : permissible_value_derivations + + EnumDerivation : populated_from + + EnumDerivation : sources + + EnumDerivation : value_mappings + + EnumDerivation --> KeyVal : value_mappings + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
name0..1
String
Target enum namedirect
populated_from0..1
EnumReference
Source enum namedirect
sources0..*
EnumReference
direct
expr0..1
String
An expression to be evaluated on the source object to derive the target slotdirect
hide0..1
Boolean
True if this is suppresseddirect
permissible_value_derivations0..*
PermissibleValueDerivation
Instructions on how to derive a set of PVs in the target schemadirect
copy_directives0..*
CopyDirective
ElementDerivation
overrides0..1
Any
overrides source schema slotsElementDerivation
is_a0..1
ElementDerivation
ElementDerivation
mixins0..*
ElementDerivation
ElementDerivation
value_mappings0..*
KeyVal
A mapping table that is applied directly to mappings, in order of precedenceElementDerivation
expression_to_value_mappings0..*
KeyVal
A mapping table in which the keys are expressionsElementDerivation
expression_to_expression_mappings0..*
KeyVal
A mapping table in which the keys and values are expressionsElementDerivation
mirror_source0..1
Boolean
ElementDerivation
description0..1
String
description of the specification componentSpecificationComponent
implements0..*
Uriorcurie
A reference to a specification that this component implementsSpecificationComponent
comments0..*
String
A list of comments about this componentSpecificationComponent
+

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
TransformationSpecificationenum_derivationsrangeEnumDerivation
+

Identifier and Mapping Information

+

Schema Source

+ +

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selflinkmltr:EnumDerivation
nativelinkmltr:EnumDerivation
+

LinkML Source

+ +

Direct

+
+
name: EnumDerivation
+description: A specification of how to derive the value of a target enum from a source
+  enum
+from_schema: https://w3id.org/linkml/transformer
+is_a: ElementDerivation
+attributes:
+  name:
+    name: name
+    description: Target enum name
+    from_schema: https://w3id.org/linkml/transformer
+    key: true
+    domain_of:
+    - ElementDerivation
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    required: true
+  populated_from:
+    name: populated_from
+    description: Source enum name
+    from_schema: https://w3id.org/linkml/transformer
+    domain_of:
+    - ClassDerivation
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    range: EnumReference
+  sources:
+    name: sources
+    from_schema: https://w3id.org/linkml/transformer
+    multivalued: true
+    domain_of:
+    - ClassDerivation
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    range: EnumReference
+  expr:
+    name: expr
+    description: An expression to be evaluated on the source object to derive the
+      target slot. Should be specified using the LinkML expression language.
+    from_schema: https://w3id.org/linkml/transformer
+    domain_of:
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    range: string
+  hide:
+    name: hide
+    description: True if this is suppressed
+    from_schema: https://w3id.org/linkml/transformer
+    domain_of:
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    range: boolean
+  permissible_value_derivations:
+    name: permissible_value_derivations
+    description: Instructions on how to derive a set of PVs in the target schema
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    domain_of:
+    - EnumDerivation
+    range: PermissibleValueDerivation
+    inlined: true
+
+
+
+

Induced

+
+
name: EnumDerivation
+description: A specification of how to derive the value of a target enum from a source
+  enum
+from_schema: https://w3id.org/linkml/transformer
+is_a: ElementDerivation
+attributes:
+  name:
+    name: name
+    description: Target enum name
+    from_schema: https://w3id.org/linkml/transformer
+    key: true
+    alias: name
+    owner: EnumDerivation
+    domain_of:
+    - ElementDerivation
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    required: true
+  populated_from:
+    name: populated_from
+    description: Source enum name
+    from_schema: https://w3id.org/linkml/transformer
+    alias: populated_from
+    owner: EnumDerivation
+    domain_of:
+    - ClassDerivation
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    range: EnumReference
+  sources:
+    name: sources
+    from_schema: https://w3id.org/linkml/transformer
+    multivalued: true
+    alias: sources
+    owner: EnumDerivation
+    domain_of:
+    - ClassDerivation
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    range: EnumReference
+  expr:
+    name: expr
+    description: An expression to be evaluated on the source object to derive the
+      target slot. Should be specified using the LinkML expression language.
+    from_schema: https://w3id.org/linkml/transformer
+    alias: expr
+    owner: EnumDerivation
+    domain_of:
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    range: string
+  hide:
+    name: hide
+    description: True if this is suppressed
+    from_schema: https://w3id.org/linkml/transformer
+    alias: hide
+    owner: EnumDerivation
+    domain_of:
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    range: boolean
+  permissible_value_derivations:
+    name: permissible_value_derivations
+    description: Instructions on how to derive a set of PVs in the target schema
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: permissible_value_derivations
+    owner: EnumDerivation
+    domain_of:
+    - EnumDerivation
+    range: PermissibleValueDerivation
+    inlined: true
+  copy_directives:
+    name: copy_directives
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: copy_directives
+    owner: EnumDerivation
+    domain_of:
+    - ElementDerivation
+    range: CopyDirective
+    inlined: true
+  overrides:
+    name: overrides
+    description: overrides source schema slots
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: overrides
+    owner: EnumDerivation
+    domain_of:
+    - ElementDerivation
+    range: Any
+  is_a:
+    name: is_a
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: linkml:is_a
+    alias: is_a
+    owner: EnumDerivation
+    domain_of:
+    - ElementDerivation
+    range: ElementDerivation
+  mixins:
+    name: mixins
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: linkml:mixins
+    multivalued: true
+    alias: mixins
+    owner: EnumDerivation
+    domain_of:
+    - ElementDerivation
+    range: ElementDerivation
+    inlined: false
+  value_mappings:
+    name: value_mappings
+    description: A mapping table that is applied directly to mappings, in order of
+      precedence
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: value_mappings
+    owner: EnumDerivation
+    domain_of:
+    - ElementDerivation
+    range: KeyVal
+    inlined: true
+  expression_to_value_mappings:
+    name: expression_to_value_mappings
+    description: A mapping table in which the keys are expressions
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: expression_to_value_mappings
+    owner: EnumDerivation
+    domain_of:
+    - ElementDerivation
+    range: KeyVal
+    inlined: true
+  expression_to_expression_mappings:
+    name: expression_to_expression_mappings
+    description: A mapping table in which the keys and values are expressions
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: expression_to_expression_mappings
+    owner: EnumDerivation
+    domain_of:
+    - ElementDerivation
+    range: KeyVal
+    inlined: true
+  mirror_source:
+    name: mirror_source
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: mirror_source
+    owner: EnumDerivation
+    domain_of:
+    - ElementDerivation
+    range: boolean
+  description:
+    name: description
+    description: description of the specification component
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: dcterms:description
+    alias: description
+    owner: EnumDerivation
+    domain_of:
+    - SpecificationComponent
+    range: string
+  implements:
+    name: implements
+    description: A reference to a specification that this component implements.
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: implements
+    owner: EnumDerivation
+    domain_of:
+    - SpecificationComponent
+    range: uriorcurie
+  comments:
+    name: comments
+    description: A list of comments about this component. Comments are free text,
+      and may be used to provide additional information about the component, including
+      instructions for its use.
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: rdfs:comment
+    multivalued: true
+    alias: comments
+    owner: EnumDerivation
+    domain_of:
+    - SpecificationComponent
+    range: string
+
+
+
+
+
+
+ + + \ No newline at end of file diff --git a/EnumReference/index.html b/EnumReference/index.html new file mode 100644 index 0000000..cbb4c1e --- /dev/null +++ b/EnumReference/index.html @@ -0,0 +1,94 @@ + + + + + + + + + + + + + + Type: EnumReference - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Type: EnumReference

+

URI: xsd:string

+ +

Identifier and Mapping Information

+

Schema Source

+ + +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/Float/index.html b/Float/index.html new file mode 100644 index 0000000..ef247a7 --- /dev/null +++ b/Float/index.html @@ -0,0 +1,92 @@ + + + + + + + + + + + + + + Type: Float - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Type: Float

+

A real number that conforms to the xsd:float specification

+

URI: xsd:float

+ +

Identifier and Mapping Information

+

Schema Source

+ + +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/Integer/index.html b/Integer/index.html new file mode 100644 index 0000000..d2040eb --- /dev/null +++ b/Integer/index.html @@ -0,0 +1,92 @@ + + + + + + + + + + + + + + Type: Integer - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Type: Integer

+

An integer

+

URI: xsd:integer

+ +

Identifier and Mapping Information

+

Schema Source

+ + +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/Inverse/index.html b/Inverse/index.html new file mode 100644 index 0000000..71b6f0a --- /dev/null +++ b/Inverse/index.html @@ -0,0 +1,206 @@ + + + + + + + + + + +Class: Inverse - LinkML-Map + + + + + + + + + + + + + + + + + + +
+ +

Class: Inverse

+

Used for back references in mapping to relational model

+

URI: linkmltr:Inverse

+
classDiagram + class Inverse + Inverse : class_name + + Inverse --> None : class_name + + Inverse : slot_name + + Inverse --> None : slot_name + + +
+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
slot_name0..1
String
direct
class_name0..1
String
direct
+

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
SlotDerivationinverse_ofrangeInverse
+

Aliases

+ +

Identifier and Mapping Information

+

Schema Source

+ +

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selflinkmltr:Inverse
nativelinkmltr:Inverse
+

LinkML Source

+ +

Direct

+
+
name: Inverse
+description: Used for back references in mapping to relational model
+from_schema: https://w3id.org/linkml/transformer
+aliases:
+- backref
+- back_references
+attributes:
+  slot_name:
+    name: slot_name
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    domain_of:
+    - Inverse
+  class_name:
+    name: class_name
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    domain_of:
+    - Inverse
+
+
+
+

Induced

+
+
name: Inverse
+description: Used for back references in mapping to relational model
+from_schema: https://w3id.org/linkml/transformer
+aliases:
+- backref
+- back_references
+attributes:
+  slot_name:
+    name: slot_name
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: slot_name
+    owner: Inverse
+    domain_of:
+    - Inverse
+  class_name:
+    name: class_name
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: class_name
+    owner: Inverse
+    domain_of:
+    - Inverse
+
+
+
+
+
+
+ + + \ No newline at end of file diff --git a/Jsonpath/index.html b/Jsonpath/index.html new file mode 100644 index 0000000..e1c9b15 --- /dev/null +++ b/Jsonpath/index.html @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + Type: Jsonpath - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Type: Jsonpath

+

A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.

+

URI: xsd:string

+ +

Identifier and Mapping Information

+

Schema Source

+ + +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/Jsonpointer/index.html b/Jsonpointer/index.html new file mode 100644 index 0000000..dfaf3b4 --- /dev/null +++ b/Jsonpointer/index.html @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + Type: Jsonpointer - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Type: Jsonpointer

+

A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.

+

URI: xsd:string

+ +

Identifier and Mapping Information

+

Schema Source

+ + +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/KeyVal/index.html b/KeyVal/index.html new file mode 100644 index 0000000..37cabec --- /dev/null +++ b/KeyVal/index.html @@ -0,0 +1,305 @@ + + + + + + + + + + +Class: KeyVal - LinkML-Map + + + + + + + + + + + + + + + + + + +
+ +

Class: KeyVal

+

URI: linkmltr:KeyVal

+
classDiagram + class KeyVal + KeyVal : key + + KeyVal --> None : key + + KeyVal : value + + KeyVal --> Any : value + + +
+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
key0..1
String
direct
value0..1
Any
direct
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
TransformationSpecificationprefixesrangeKeyVal
ElementDerivationvalue_mappingsrangeKeyVal
ElementDerivationexpression_to_value_mappingsrangeKeyVal
ElementDerivationexpression_to_expression_mappingsrangeKeyVal
ClassDerivationvalue_mappingsrangeKeyVal
ClassDerivationexpression_to_value_mappingsrangeKeyVal
ClassDerivationexpression_to_expression_mappingsrangeKeyVal
SlotDerivationvalue_mappingsrangeKeyVal
SlotDerivationexpression_to_value_mappingsrangeKeyVal
SlotDerivationexpression_to_expression_mappingsrangeKeyVal
EnumDerivationvalue_mappingsrangeKeyVal
EnumDerivationexpression_to_value_mappingsrangeKeyVal
EnumDerivationexpression_to_expression_mappingsrangeKeyVal
PermissibleValueDerivationvalue_mappingsrangeKeyVal
PermissibleValueDerivationexpression_to_value_mappingsrangeKeyVal
PermissibleValueDerivationexpression_to_expression_mappingsrangeKeyVal
PrefixDerivationvalue_mappingsrangeKeyVal
PrefixDerivationexpression_to_value_mappingsrangeKeyVal
PrefixDerivationexpression_to_expression_mappingsrangeKeyVal
+

Identifier and Mapping Information

+

Schema Source

+ +

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selflinkmltr:KeyVal
nativelinkmltr:KeyVal
+

LinkML Source

+ +

Direct

+
+
name: KeyVal
+from_schema: https://w3id.org/linkml/transformer
+attributes:
+  key:
+    name: key
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    key: true
+    domain_of:
+    - KeyVal
+    required: true
+  value:
+    name: value
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    domain_of:
+    - KeyVal
+    range: Any
+
+
+
+

Induced

+
+
name: KeyVal
+from_schema: https://w3id.org/linkml/transformer
+attributes:
+  key:
+    name: key
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    key: true
+    alias: key
+    owner: KeyVal
+    domain_of:
+    - KeyVal
+    required: true
+  value:
+    name: value
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: value
+    owner: KeyVal
+    domain_of:
+    - KeyVal
+    range: Any
+
+
+
+
+
+
+ + + \ No newline at end of file diff --git a/LICENSE b/LICENSE deleted file mode 100644 index d88c0cc..0000000 --- a/LICENSE +++ /dev/null @@ -1,13 +0,0 @@ -Apache-2.0 - -Licensed under the Apache License, Version 2.0 (the "License"); -you may not use this file except in compliance with the License. -You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - -Unless required by applicable law or agreed to in writing, software -distributed under the License is distributed on an "AS IS" BASIS, -WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -See the License for the specific language governing permissions and -limitations under the License. \ No newline at end of file diff --git a/Makefile b/Makefile deleted file mode 100644 index bf476ba..0000000 --- a/Makefile +++ /dev/null @@ -1,128 +0,0 @@ -MAKEFLAGS += --warn-undefined-variables -SHELL := bash -.SHELLFLAGS := -eu -o pipefail -c -.DEFAULT_GOAL := help -.DELETE_ON_ERROR: -.SUFFIXES: -.SECONDARY: - -RUN = uv run -# get values from about.yaml file -SCHEMA_NAME = $(shell bash ./utils/get-value.sh name) -SOURCE_SCHEMA_PATH = $(shell bash ./utils/get-value.sh source_schema_path) -SRC = src -DEST = project -PYMODEL = $(SRC)/$(SCHEMA_NAME)/datamodel -DOCDIR = docs - -# basename of a YAML file in model/ -.PHONY: all clean - -help: status - @echo "" - @echo "make all -- makes site locally" - @echo "make install -- install dependencies" - @echo "make setup -- initial setup" - @echo "make test -- runs tests" - @echo "make testdoc -- builds docs and runs local test server" - @echo "make deploy -- deploys site" - @echo "make update-packages -- updates dependencies" - @echo "make help -- show this help" - @echo "" - -status: check-config - @echo "Project: $(SCHEMA_NAME)" - @echo "Source: $(SOURCE_SCHEMA_PATH)" - -setup: install gen-project gendoc git-init-add - -install: - uv sync -.PHONY: install - -all: gen-project gendoc -%.yaml: gen-project -deploy: all deploy-gh-doc - -# TODO: make this default -src/linkml_map/datamodel/transformer_model.py: src/linkml_map/datamodel/transformer_model.yaml - # $(RUN) gen-pydantic --pydantic-version 2 $< > $@.tmp && mv $@.tmp $@ - $(RUN) gen-pydantic --template-dir templates/pydantic $< > $@.tmp && mv $@.tmp $@ - -# generates all project files -# TODO: combine pydantic into this step -gen-project: $(PYMODEL) src/linkml_map/datamodel/transformer_model.py - $(RUN) gen-project -X sqltable -d $(DEST) $(SOURCE_SCHEMA_PATH) - -test: test-python doctest -test-python: - $(RUN) pytest -test-project: - $(RUN) gen-project -d tmp $(SOURCE_SCHEMA_PATH) - -check-config: - @(grep my-datamodel about.yaml > /dev/null && printf "\n**Project not configured**:\n\n - Remember to edit 'about.yaml'\n\n" || exit 0) - -convert-examples-to-%: - $(patsubst %, $(RUN) linkml-convert % -s $(SOURCE_SCHEMA_PATH) -C Person, $(shell find src/data/examples -name "*.yaml")) - -examples/%.yaml: src/data/examples/%.yaml - $(RUN) linkml-convert -s $(SOURCE_SCHEMA_PATH) -C Person $< -o $@ -examples/%.json: src/data/examples/%.yaml - $(RUN) linkml-convert -s $(SOURCE_SCHEMA_PATH) -C Person $< -o $@ -examples/%.ttl: src/data/examples/%.yaml - $(RUN) linkml-convert -P EXAMPLE=http://example.org/ -s $(SOURCE_SCHEMA_PATH) -C Person $< -o $@ - -# N.b. this does not update pyproject.toml -# as of Apr 2025, uv does not have this feature -# see https://github.com/astral-sh/uv/issues/6794 -update-packages: - uv sync -U - -# Test documentation locally -serve: mkd-serve - -deploy: mkd-deploy - -# Deploy gh docs -# https://github.com/linkml/linkml/issues/2193 -#deploy-gh-doc: gendoc -deploy-gh-doc: - $(RUN) mkdocs gh-deploy - - - -# Python datamodel -$(PYMODEL): - mkdir -p $@ - -# docs directory -$(DOCDIR): - mkdir -p $@ - -gendoc: $(DOCDIR) - $(RUN) gen-doc -d $(DOCDIR)/schema $(SOURCE_SCHEMA_PATH) --index-name datamodel - -testdoc: gendoc serve - -MKDOCS = $(RUN) mkdocs -mkd-%: - $(MKDOCS) $* $(MKDOCS_ARGS) - -PROJECT_FOLDERS = sqlschema shex shacl protobuf prefixmap owl jsonschema jsonld graphql excel -git-init-add: git-init git-add git-commit git-status -git-init: - git init -git-add: - git add .gitignore .github Makefile LICENSE *.md examples utils about.yaml mkdocs.yml uv.lock project.Makefile pyproject.toml src/linkml/*yaml src/*/datamodel/*py src/data - git add $(patsubst %, project/%, $(PROJECT_FOLDERS)) -git-commit: - git commit -m 'Initial commit' -a -git-status: - git status - -clean: - rm -rf $(DEST) - rm -rf tmp - -include project.Makefile diff --git a/Ncname/index.html b/Ncname/index.html new file mode 100644 index 0000000..4ee96b1 --- /dev/null +++ b/Ncname/index.html @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + Type: Ncname - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Type: Ncname

+

Prefix part of CURIE

+

URI: xsd:string

+ +

Identifier and Mapping Information

+

Schema Source

+ + +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/Nodeidentifier/index.html b/Nodeidentifier/index.html new file mode 100644 index 0000000..9df806f --- /dev/null +++ b/Nodeidentifier/index.html @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + Type: Nodeidentifier - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Type: Nodeidentifier

+

A URI, CURIE or BNODE that represents a node in a model.

+

URI: shex:nonLiteral

+ +

Identifier and Mapping Information

+

Schema Source

+ + +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/Objectidentifier/index.html b/Objectidentifier/index.html new file mode 100644 index 0000000..13b059e --- /dev/null +++ b/Objectidentifier/index.html @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + Type: Objectidentifier - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Type: Objectidentifier

+

A URI or CURIE that represents an object in the model.

+

URI: shex:iri

+ +

Comments

+ +

Identifier and Mapping Information

+

Schema Source

+ + +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/PermissibleValueDerivation/index.html b/PermissibleValueDerivation/index.html new file mode 100644 index 0000000..71bff6e --- /dev/null +++ b/PermissibleValueDerivation/index.html @@ -0,0 +1,544 @@ + + + + + + + + + + +Class: PermissibleValueDerivation - LinkML-Map + + + + + + + + + + + + + + + + + + +
+ +

Class: PermissibleValueDerivation

+

A specification of how to derive the value of a PV from a source enum

+

URI: linkmltr:PermissibleValueDerivation

+
classDiagram + class PermissibleValueDerivation + ElementDerivation <|-- PermissibleValueDerivation + + PermissibleValueDerivation : comments + + PermissibleValueDerivation : copy_directives + + PermissibleValueDerivation --> CopyDirective : copy_directives + + PermissibleValueDerivation : description + + PermissibleValueDerivation --> None : description + + PermissibleValueDerivation : expr + + PermissibleValueDerivation : expression_to_expression_mappings + + PermissibleValueDerivation --> KeyVal : expression_to_expression_mappings + + PermissibleValueDerivation : expression_to_value_mappings + + PermissibleValueDerivation --> KeyVal : expression_to_value_mappings + + PermissibleValueDerivation : hide + + PermissibleValueDerivation : implements + + PermissibleValueDerivation : is_a + + PermissibleValueDerivation --> ElementDerivation : is_a + + PermissibleValueDerivation : mirror_source + + PermissibleValueDerivation : mixins + + PermissibleValueDerivation --> ElementDerivation : mixins + + PermissibleValueDerivation : name + + PermissibleValueDerivation --> None : name + + PermissibleValueDerivation : overrides + + PermissibleValueDerivation --> Any : overrides + + PermissibleValueDerivation : populated_from + + PermissibleValueDerivation : sources + + PermissibleValueDerivation : value_mappings + + PermissibleValueDerivation --> KeyVal : value_mappings + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
name0..1
String
Target permissible value textdirect
expr0..1
String
direct
populated_from0..1
String
Source permissible valuedirect
sources0..*
String
direct
hide0..1
Boolean
direct
copy_directives0..*
CopyDirective
ElementDerivation
overrides0..1
Any
overrides source schema slotsElementDerivation
is_a0..1
ElementDerivation
ElementDerivation
mixins0..*
ElementDerivation
ElementDerivation
value_mappings0..*
KeyVal
A mapping table that is applied directly to mappings, in order of precedenceElementDerivation
expression_to_value_mappings0..*
KeyVal
A mapping table in which the keys are expressionsElementDerivation
expression_to_expression_mappings0..*
KeyVal
A mapping table in which the keys and values are expressionsElementDerivation
mirror_source0..1
Boolean
ElementDerivation
description0..1
String
description of the specification componentSpecificationComponent
implements0..*
Uriorcurie
A reference to a specification that this component implementsSpecificationComponent
comments0..*
String
A list of comments about this componentSpecificationComponent
+

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
EnumDerivationpermissible_value_derivationsrangePermissibleValueDerivation
+

TODOs

+ +

Identifier and Mapping Information

+

Schema Source

+ +

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selflinkmltr:PermissibleValueDerivation
nativelinkmltr:PermissibleValueDerivation
+

LinkML Source

+ +

Direct

+
+
name: PermissibleValueDerivation
+description: A specification of how to derive the value of a PV from a source enum
+todos:
+- this is currently under-specified. We will need boolean combinators to express if-then-else
+from_schema: https://w3id.org/linkml/transformer
+is_a: ElementDerivation
+attributes:
+  name:
+    name: name
+    description: Target permissible value text
+    from_schema: https://w3id.org/linkml/transformer
+    key: true
+    domain_of:
+    - ElementDerivation
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    required: true
+  expr:
+    name: expr
+    from_schema: https://w3id.org/linkml/transformer
+    domain_of:
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    range: string
+  populated_from:
+    name: populated_from
+    description: Source permissible value
+    from_schema: https://w3id.org/linkml/transformer
+    domain_of:
+    - ClassDerivation
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    range: string
+  sources:
+    name: sources
+    from_schema: https://w3id.org/linkml/transformer
+    multivalued: true
+    domain_of:
+    - ClassDerivation
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    range: string
+  hide:
+    name: hide
+    from_schema: https://w3id.org/linkml/transformer
+    domain_of:
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    range: boolean
+
+
+
+

Induced

+
+
name: PermissibleValueDerivation
+description: A specification of how to derive the value of a PV from a source enum
+todos:
+- this is currently under-specified. We will need boolean combinators to express if-then-else
+from_schema: https://w3id.org/linkml/transformer
+is_a: ElementDerivation
+attributes:
+  name:
+    name: name
+    description: Target permissible value text
+    from_schema: https://w3id.org/linkml/transformer
+    key: true
+    alias: name
+    owner: PermissibleValueDerivation
+    domain_of:
+    - ElementDerivation
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    required: true
+  expr:
+    name: expr
+    from_schema: https://w3id.org/linkml/transformer
+    alias: expr
+    owner: PermissibleValueDerivation
+    domain_of:
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    range: string
+  populated_from:
+    name: populated_from
+    description: Source permissible value
+    from_schema: https://w3id.org/linkml/transformer
+    alias: populated_from
+    owner: PermissibleValueDerivation
+    domain_of:
+    - ClassDerivation
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    range: string
+  sources:
+    name: sources
+    from_schema: https://w3id.org/linkml/transformer
+    multivalued: true
+    alias: sources
+    owner: PermissibleValueDerivation
+    domain_of:
+    - ClassDerivation
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    range: string
+  hide:
+    name: hide
+    from_schema: https://w3id.org/linkml/transformer
+    alias: hide
+    owner: PermissibleValueDerivation
+    domain_of:
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    range: boolean
+  copy_directives:
+    name: copy_directives
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: copy_directives
+    owner: PermissibleValueDerivation
+    domain_of:
+    - ElementDerivation
+    range: CopyDirective
+    inlined: true
+  overrides:
+    name: overrides
+    description: overrides source schema slots
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: overrides
+    owner: PermissibleValueDerivation
+    domain_of:
+    - ElementDerivation
+    range: Any
+  is_a:
+    name: is_a
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: linkml:is_a
+    alias: is_a
+    owner: PermissibleValueDerivation
+    domain_of:
+    - ElementDerivation
+    range: ElementDerivation
+  mixins:
+    name: mixins
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: linkml:mixins
+    multivalued: true
+    alias: mixins
+    owner: PermissibleValueDerivation
+    domain_of:
+    - ElementDerivation
+    range: ElementDerivation
+    inlined: false
+  value_mappings:
+    name: value_mappings
+    description: A mapping table that is applied directly to mappings, in order of
+      precedence
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: value_mappings
+    owner: PermissibleValueDerivation
+    domain_of:
+    - ElementDerivation
+    range: KeyVal
+    inlined: true
+  expression_to_value_mappings:
+    name: expression_to_value_mappings
+    description: A mapping table in which the keys are expressions
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: expression_to_value_mappings
+    owner: PermissibleValueDerivation
+    domain_of:
+    - ElementDerivation
+    range: KeyVal
+    inlined: true
+  expression_to_expression_mappings:
+    name: expression_to_expression_mappings
+    description: A mapping table in which the keys and values are expressions
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: expression_to_expression_mappings
+    owner: PermissibleValueDerivation
+    domain_of:
+    - ElementDerivation
+    range: KeyVal
+    inlined: true
+  mirror_source:
+    name: mirror_source
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: mirror_source
+    owner: PermissibleValueDerivation
+    domain_of:
+    - ElementDerivation
+    range: boolean
+  description:
+    name: description
+    description: description of the specification component
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: dcterms:description
+    alias: description
+    owner: PermissibleValueDerivation
+    domain_of:
+    - SpecificationComponent
+    range: string
+  implements:
+    name: implements
+    description: A reference to a specification that this component implements.
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: implements
+    owner: PermissibleValueDerivation
+    domain_of:
+    - SpecificationComponent
+    range: uriorcurie
+  comments:
+    name: comments
+    description: A list of comments about this component. Comments are free text,
+      and may be used to provide additional information about the component, including
+      instructions for its use.
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: rdfs:comment
+    multivalued: true
+    alias: comments
+    owner: PermissibleValueDerivation
+    domain_of:
+    - SpecificationComponent
+    range: string
+
+
+
+
+
+
+ + + \ No newline at end of file diff --git a/PrefixDerivation/index.html b/PrefixDerivation/index.html new file mode 100644 index 0000000..5c263df --- /dev/null +++ b/PrefixDerivation/index.html @@ -0,0 +1,390 @@ + + + + + + + + + + +Class: PrefixDerivation - LinkML-Map + + + + + + + + + + + + + + + + + + +
+ +

Class: PrefixDerivation

+

URI: linkmltr:PrefixDerivation

+
classDiagram + class PrefixDerivation + ElementDerivation <|-- PrefixDerivation + + PrefixDerivation : comments + + PrefixDerivation : copy_directives + + PrefixDerivation --> CopyDirective : copy_directives + + PrefixDerivation : description + + PrefixDerivation --> None : description + + PrefixDerivation : expression_to_expression_mappings + + PrefixDerivation --> KeyVal : expression_to_expression_mappings + + PrefixDerivation : expression_to_value_mappings + + PrefixDerivation --> KeyVal : expression_to_value_mappings + + PrefixDerivation : implements + + PrefixDerivation : is_a + + PrefixDerivation --> ElementDerivation : is_a + + PrefixDerivation : mirror_source + + PrefixDerivation : mixins + + PrefixDerivation --> ElementDerivation : mixins + + PrefixDerivation : name + + PrefixDerivation --> None : name + + PrefixDerivation : overrides + + PrefixDerivation --> Any : overrides + + PrefixDerivation : value_mappings + + PrefixDerivation --> KeyVal : value_mappings + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
name1..1
String
Name of the element in the target schemaElementDerivation
copy_directives0..*
CopyDirective
ElementDerivation
overrides0..1
Any
overrides source schema slotsElementDerivation
is_a0..1
ElementDerivation
ElementDerivation
mixins0..*
ElementDerivation
ElementDerivation
value_mappings0..*
KeyVal
A mapping table that is applied directly to mappings, in order of precedenceElementDerivation
expression_to_value_mappings0..*
KeyVal
A mapping table in which the keys are expressionsElementDerivation
expression_to_expression_mappings0..*
KeyVal
A mapping table in which the keys and values are expressionsElementDerivation
mirror_source0..1
Boolean
ElementDerivation
description0..1
String
description of the specification componentSpecificationComponent
implements0..*
Uriorcurie
A reference to a specification that this component implementsSpecificationComponent
comments0..*
String
A list of comments about this componentSpecificationComponent
+

Identifier and Mapping Information

+

Schema Source

+ +

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selflinkmltr:PrefixDerivation
nativelinkmltr:PrefixDerivation
+

LinkML Source

+ +

Direct

+
+
name: PrefixDerivation
+from_schema: https://w3id.org/linkml/transformer
+is_a: ElementDerivation
+
+
+
+

Induced

+
+
name: PrefixDerivation
+from_schema: https://w3id.org/linkml/transformer
+is_a: ElementDerivation
+attributes:
+  name:
+    name: name
+    description: Name of the element in the target schema
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    key: true
+    alias: name
+    owner: PrefixDerivation
+    domain_of:
+    - ElementDerivation
+    - SlotDerivation
+    - EnumDerivation
+    - PermissibleValueDerivation
+    range: string
+    required: true
+  copy_directives:
+    name: copy_directives
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: copy_directives
+    owner: PrefixDerivation
+    domain_of:
+    - ElementDerivation
+    range: CopyDirective
+    inlined: true
+  overrides:
+    name: overrides
+    description: overrides source schema slots
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: overrides
+    owner: PrefixDerivation
+    domain_of:
+    - ElementDerivation
+    range: Any
+  is_a:
+    name: is_a
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: linkml:is_a
+    alias: is_a
+    owner: PrefixDerivation
+    domain_of:
+    - ElementDerivation
+    range: ElementDerivation
+  mixins:
+    name: mixins
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: linkml:mixins
+    multivalued: true
+    alias: mixins
+    owner: PrefixDerivation
+    domain_of:
+    - ElementDerivation
+    range: ElementDerivation
+    inlined: false
+  value_mappings:
+    name: value_mappings
+    description: A mapping table that is applied directly to mappings, in order of
+      precedence
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: value_mappings
+    owner: PrefixDerivation
+    domain_of:
+    - ElementDerivation
+    range: KeyVal
+    inlined: true
+  expression_to_value_mappings:
+    name: expression_to_value_mappings
+    description: A mapping table in which the keys are expressions
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: expression_to_value_mappings
+    owner: PrefixDerivation
+    domain_of:
+    - ElementDerivation
+    range: KeyVal
+    inlined: true
+  expression_to_expression_mappings:
+    name: expression_to_expression_mappings
+    description: A mapping table in which the keys and values are expressions
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: expression_to_expression_mappings
+    owner: PrefixDerivation
+    domain_of:
+    - ElementDerivation
+    range: KeyVal
+    inlined: true
+  mirror_source:
+    name: mirror_source
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: mirror_source
+    owner: PrefixDerivation
+    domain_of:
+    - ElementDerivation
+    range: boolean
+  description:
+    name: description
+    description: description of the specification component
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: dcterms:description
+    alias: description
+    owner: PrefixDerivation
+    domain_of:
+    - SpecificationComponent
+    range: string
+  implements:
+    name: implements
+    description: A reference to a specification that this component implements.
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: implements
+    owner: PrefixDerivation
+    domain_of:
+    - SpecificationComponent
+    range: uriorcurie
+  comments:
+    name: comments
+    description: A list of comments about this component. Comments are free text,
+      and may be used to provide additional information about the component, including
+      instructions for its use.
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: rdfs:comment
+    multivalued: true
+    alias: comments
+    owner: PrefixDerivation
+    domain_of:
+    - SpecificationComponent
+    range: string
+
+
+
+
+
+
+ + + \ No newline at end of file diff --git a/README.md b/README.md deleted file mode 100644 index 43a1665..0000000 --- a/README.md +++ /dev/null @@ -1,36 +0,0 @@ -# linkml-map - -[![Pyversions](https://img.shields.io/pypi/pyversions/linkml-map.svg)](https://pypi.python.org/pypi/linkml-map) -![](https://github.com/linkml/linkml-map/workflows/Build/badge.svg) -[![PyPi](https://img.shields.io/pypi/v/linkml-map.svg)](https://pypi.python.org/pypi/linkml-map) -[![codecov](https://codecov.io/gh/linkml/linkml-map/branch/main/graph/badge.svg?token=WNQNG986UN)](https://codecov.io/gh/linkml/linkml-map) - -LinkML Map is a framework for specifying and executing mappings between data models. - -Features: - -- YAML-based lightweight syntax -- Python library for executing mappings on data files -- Ability to compile to other frameworks (forthcoming) -- Derivation of target (implicit) schemas, allowing easy customization of data models (*profiling*) -- Simple YAML dictionaries for simple mappings -- Automatic unit conversion -- Use of subset of Python to specify complex mappings -- Visualizations of mappings -- Mappings are reversible (provided all expressions used are reversible) - -For full documentation see: - -- [linkml.io/linkml-map/](https://linkml.io/linkml-map/) - -Status: - -The transformation data model is not yet fully stable, and may be subject to change. -Not all parts of the model are implemented in the reference Python framework. - -## Quickstart - -* [Tutorial Notebook](docs/examples/Tutorial.ipynb) -* [Generated Docs](https://linkml.github.io/linkml-map/) -* [Compliance Suite](https://linkml.github.io/linkml-map/specification/compliance) -* [API Docs](https://linkml.github.io/linkml-map/api/) \ No newline at end of file diff --git a/SerializationSyntaxType/index.html b/SerializationSyntaxType/index.html new file mode 100644 index 0000000..6284cb9 --- /dev/null +++ b/SerializationSyntaxType/index.html @@ -0,0 +1,145 @@ + + + + + + + + + + + + + + Enum: SerializationSyntaxType - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Enum: SerializationSyntaxType

+

URI: SerializationSyntaxType

+

Permissible Values

+ + + + + + + + + + + + + + + + + + + + + + + + + +
ValueMeaningDescription
JSONNone
YAMLNone
TURTLENone
+

Slots

+ + + + + + + + + + + + + +
NameDescription
syntax
+

Identifier and Mapping Information

+

Schema Source

+ +

LinkML Source

+
+ +
name: SerializationSyntaxType
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+permissible_values:
+  JSON:
+    text: JSON
+  YAML:
+    text: YAML
+  TURTLE:
+    text: TURTLE
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/docs/schema/SlotDerivation.md b/SlotDerivation/index.html similarity index 54% rename from docs/schema/SlotDerivation.md rename to SlotDerivation/index.html index 8d8c673..7c4a9cd 100644 --- a/docs/schema/SlotDerivation.md +++ b/SlotDerivation/index.html @@ -1,194 +1,358 @@ - - -# Class: SlotDerivation - - -_A specification of how to derive the value of a target slot from a source slot_ - - - - - -URI: [linkmltr:SlotDerivation](https://w3id.org/linkml/transformer/SlotDerivation) - - - - -```mermaid - classDiagram + + + + + + + + + + +Class: SlotDerivation - LinkML-Map + + + + + + + + + + + + + + + + + + +
+ +

Class: SlotDerivation

+

A specification of how to derive the value of a target slot from a source slot

+

URI: linkmltr:SlotDerivation

+
classDiagram class SlotDerivation - ElementDerivation <|-- SlotDerivation - - SlotDerivation : cast_collection_as - - SlotDerivation --> CollectionType : cast_collection_as - - SlotDerivation : comments - - SlotDerivation : copy_directives - - SlotDerivation --> CopyDirective : copy_directives - - SlotDerivation : derived_from - - SlotDerivation : description - - SlotDerivation --> None : description - - SlotDerivation : dictionary_key - - SlotDerivation : expr - - SlotDerivation : expression_to_expression_mappings - - SlotDerivation --> KeyVal : expression_to_expression_mappings - - SlotDerivation : expression_to_value_mappings - - SlotDerivation --> KeyVal : expression_to_value_mappings - - SlotDerivation : hide - - SlotDerivation : implements - - SlotDerivation : inverse_of - - SlotDerivation --> Inverse : inverse_of - - SlotDerivation : is_a - - SlotDerivation --> ElementDerivation : is_a - - SlotDerivation : mirror_source - - SlotDerivation : mixins - - SlotDerivation --> ElementDerivation : mixins - - SlotDerivation : name - - SlotDerivation --> None : name - - SlotDerivation : overrides - - SlotDerivation --> Any : overrides - - SlotDerivation : populated_from - - SlotDerivation : range - - SlotDerivation : sources - - SlotDerivation : stringification - - SlotDerivation --> StringificationConfiguration : stringification - - SlotDerivation : type_designator - - SlotDerivation : unit_conversion - - SlotDerivation --> UnitConversionConfiguration : unit_conversion - - SlotDerivation : value_mappings - - SlotDerivation --> KeyVal : value_mappings - - -``` - - - - - -## Inheritance -* [SpecificationComponent](SpecificationComponent.md) - * [ElementDerivation](ElementDerivation.md) - * **SlotDerivation** + ElementDerivation <|-- SlotDerivation + SlotDerivation : cast_collection_as + SlotDerivation --> CollectionType : cast_collection_as -## Slots + SlotDerivation : comments -| Name | Cardinality and Range | Description | Inheritance | -| --- | --- | --- | --- | -| [name](name.md) | 0..1
[String](String.md) | Target slot name | direct | -| [populated_from](populated_from.md) | 0..1
[SlotReference](SlotReference.md) | Source slot name | direct | -| [sources](sources.md) | 0..*
[SlotReference](SlotReference.md) | | direct | -| [derived_from](derived_from.md) | 0..*
[SlotReference](SlotReference.md) | Source slots that are used to derive this slot | direct | -| [expr](expr.md) | 0..1
[String](String.md) | An expression to be evaluated on the source object to derive the target slot | direct | -| [range](range.md) | 0..1
[String](String.md) | | direct | -| [unit_conversion](unit_conversion.md) | 0..1
[UnitConversionConfiguration](UnitConversionConfiguration.md) | | direct | -| [inverse_of](inverse_of.md) | 0..1
[Inverse](Inverse.md) | Used to specify a class-slot tuple that is the inverse of the derived/target ... | direct | -| [hide](hide.md) | 0..1
[Boolean](Boolean.md) | True if this is suppressed | direct | -| [type_designator](type_designator.md) | 0..1
[Boolean](Boolean.md) | | direct | -| [cast_collection_as](cast_collection_as.md) | 0..1
[CollectionType](CollectionType.md) | | direct | -| [dictionary_key](dictionary_key.md) | 0..1
[String](String.md) | | direct | -| [stringification](stringification.md) | 0..1
[StringificationConfiguration](StringificationConfiguration.md) | | direct | -| [copy_directives](copy_directives.md) | 0..*
[CopyDirective](CopyDirective.md) | | [ElementDerivation](ElementDerivation.md) | -| [overrides](overrides.md) | 0..1
[Any](Any.md) | overrides source schema slots | [ElementDerivation](ElementDerivation.md) | -| [is_a](is_a.md) | 0..1
[ElementDerivation](ElementDerivation.md) | | [ElementDerivation](ElementDerivation.md) | -| [mixins](mixins.md) | 0..*
[ElementDerivation](ElementDerivation.md) | | [ElementDerivation](ElementDerivation.md) | -| [value_mappings](value_mappings.md) | 0..*
[KeyVal](KeyVal.md) | A mapping table that is applied directly to mappings, in order of precedence | [ElementDerivation](ElementDerivation.md) | -| [expression_to_value_mappings](expression_to_value_mappings.md) | 0..*
[KeyVal](KeyVal.md) | A mapping table in which the keys are expressions | [ElementDerivation](ElementDerivation.md) | -| [expression_to_expression_mappings](expression_to_expression_mappings.md) | 0..*
[KeyVal](KeyVal.md) | A mapping table in which the keys and values are expressions | [ElementDerivation](ElementDerivation.md) | -| [mirror_source](mirror_source.md) | 0..1
[Boolean](Boolean.md) | | [ElementDerivation](ElementDerivation.md) | -| [description](description.md) | 0..1
[String](String.md) | description of the specification component | [SpecificationComponent](SpecificationComponent.md) | -| [implements](implements.md) | 0..*
[Uriorcurie](Uriorcurie.md) | A reference to a specification that this component implements | [SpecificationComponent](SpecificationComponent.md) | -| [comments](comments.md) | 0..*
[String](String.md) | A list of comments about this component | [SpecificationComponent](SpecificationComponent.md) | + SlotDerivation : copy_directives + SlotDerivation --> CopyDirective : copy_directives + SlotDerivation : derived_from + SlotDerivation : description + SlotDerivation --> None : description -## Usages + SlotDerivation : dictionary_key -| used by | used in | type | used | -| --- | --- | --- | --- | -| [TransformationSpecification](TransformationSpecification.md) | [slot_derivations](slot_derivations.md) | range | [SlotDerivation](SlotDerivation.md) | -| [ClassDerivation](ClassDerivation.md) | [slot_derivations](slot_derivations.md) | range | [SlotDerivation](SlotDerivation.md) | + SlotDerivation : expr + SlotDerivation : expression_to_expression_mappings + SlotDerivation --> KeyVal : expression_to_expression_mappings + SlotDerivation : expression_to_value_mappings + SlotDerivation --> KeyVal : expression_to_value_mappings + SlotDerivation : hide -## Identifier and Mapping Information + SlotDerivation : implements + SlotDerivation : inverse_of + SlotDerivation --> Inverse : inverse_of + SlotDerivation : is_a + SlotDerivation --> ElementDerivation : is_a + SlotDerivation : mirror_source + SlotDerivation : mixins -### Schema Source + SlotDerivation --> ElementDerivation : mixins + SlotDerivation : name -* from schema: https://w3id.org/linkml/transformer + SlotDerivation --> None : name + SlotDerivation : overrides + SlotDerivation --> Any : overrides + SlotDerivation : populated_from + SlotDerivation : range -## Mappings + SlotDerivation : sources -| Mapping Type | Mapped Value | -| --- | --- | -| self | linkmltr:SlotDerivation | -| native | linkmltr:SlotDerivation | + SlotDerivation : stringification + SlotDerivation --> StringificationConfiguration : stringification + SlotDerivation : type_designator + SlotDerivation : unit_conversion + SlotDerivation --> UnitConversionConfiguration : unit_conversion -## LinkML Source + SlotDerivation : value_mappings + SlotDerivation --> KeyVal : value_mappings + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
name0..1
String
Target slot namedirect
populated_from0..1
SlotReference
Source slot namedirect
sources0..*
SlotReference
direct
derived_from0..*
SlotReference
Source slots that are used to derive this slotdirect
expr0..1
String
An expression to be evaluated on the source object to derive the target slotdirect
range0..1
String
direct
unit_conversion0..1
UnitConversionConfiguration
direct
inverse_of0..1
Inverse
Used to specify a class-slot tuple that is the inverse of the derived/target ...direct
hide0..1
Boolean
True if this is suppresseddirect
type_designator0..1
Boolean
direct
cast_collection_as0..1
CollectionType
direct
dictionary_key0..1
String
direct
stringification0..1
StringificationConfiguration
direct
copy_directives0..*
CopyDirective
ElementDerivation
overrides0..1
Any
overrides source schema slotsElementDerivation
is_a0..1
ElementDerivation
ElementDerivation
mixins0..*
ElementDerivation
ElementDerivation
value_mappings0..*
KeyVal
A mapping table that is applied directly to mappings, in order of precedenceElementDerivation
expression_to_value_mappings0..*
KeyVal
A mapping table in which the keys are expressionsElementDerivation
expression_to_expression_mappings0..*
KeyVal
A mapping table in which the keys and values are expressionsElementDerivation
mirror_source0..1
Boolean
ElementDerivation
description0..1
String
description of the specification componentSpecificationComponent
implements0..*
Uriorcurie
A reference to a specification that this component implementsSpecificationComponent
comments0..*
String
A list of comments about this componentSpecificationComponent
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
TransformationSpecificationslot_derivationsrangeSlotDerivation
ClassDerivationslot_derivationsrangeSlotDerivation
+

Identifier and Mapping Information

+

Schema Source

+ +

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selflinkmltr:SlotDerivation
nativelinkmltr:SlotDerivation
+

LinkML Source

- -### Direct - +

Direct

-```yaml -name: SlotDerivation +
name: SlotDerivation
 description: A specification of how to derive the value of a target slot from a source
   slot
 from_schema: https://w3id.org/linkml/transformer
@@ -312,14 +476,11 @@
     - SlotDerivation
     range: StringificationConfiguration
 
-```
+
- -### Induced - +

Induced

-```yaml -name: SlotDerivation +
name: SlotDerivation
 description: A specification of how to derive the value of a target slot from a source
   slot
 from_schema: https://w3id.org/linkml/transformer
@@ -594,5 +755,17 @@
     - SpecificationComponent
     range: string
 
-```
-
\ No newline at end of file + + +
+
+
+ + + \ No newline at end of file diff --git a/SlotReference/index.html b/SlotReference/index.html new file mode 100644 index 0000000..55d735e --- /dev/null +++ b/SlotReference/index.html @@ -0,0 +1,94 @@ + + + + + + + + + + + + + + Type: SlotReference - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Type: SlotReference

+

URI: xsd:string

+ +

Identifier and Mapping Information

+

Schema Source

+ + +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/Sparqlpath/index.html b/Sparqlpath/index.html new file mode 100644 index 0000000..8c408d5 --- /dev/null +++ b/Sparqlpath/index.html @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + Type: Sparqlpath - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Type: Sparqlpath

+

A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.

+

URI: xsd:string

+ +

Identifier and Mapping Information

+

Schema Source

+ + +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/SpecificationComponent/index.html b/SpecificationComponent/index.html new file mode 100644 index 0000000..0f9bc34 --- /dev/null +++ b/SpecificationComponent/index.html @@ -0,0 +1,229 @@ + + + + + + + + + + +Class: SpecificationComponent - LinkML-Map + + + + + + + + + + + + + + + + + + +
+ +

Class: SpecificationComponent

+ +

URI: linkmltr:SpecificationComponent

+
classDiagram + class SpecificationComponent + SpecificationComponent <|-- TransformationSpecification + SpecificationComponent <|-- ElementDerivation + + SpecificationComponent : comments + + SpecificationComponent : description + + SpecificationComponent --> None : description + + SpecificationComponent : implements + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
description0..1
String
description of the specification componentdirect
implements0..*
Uriorcurie
A reference to a specification that this component implementsdirect
comments0..*
String
A list of comments about this componentdirect
+

Identifier and Mapping Information

+

Schema Source

+ +

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selflinkmltr:SpecificationComponent
nativelinkmltr:SpecificationComponent
+

LinkML Source

+ +

Direct

+
+
name: SpecificationComponent
+from_schema: https://w3id.org/linkml/transformer
+abstract: true
+attributes:
+  description:
+    name: description
+    description: description of the specification component
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: dcterms:description
+    domain_of:
+    - SpecificationComponent
+  implements:
+    name: implements
+    description: A reference to a specification that this component implements.
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    domain_of:
+    - SpecificationComponent
+    range: uriorcurie
+  comments:
+    name: comments
+    description: A list of comments about this component. Comments are free text,
+      and may be used to provide additional information about the component, including
+      instructions for its use.
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: rdfs:comment
+    multivalued: true
+    domain_of:
+    - SpecificationComponent
+    range: string
+
+
+
+

Induced

+
+
name: SpecificationComponent
+from_schema: https://w3id.org/linkml/transformer
+abstract: true
+attributes:
+  description:
+    name: description
+    description: description of the specification component
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: dcterms:description
+    alias: description
+    owner: SpecificationComponent
+    domain_of:
+    - SpecificationComponent
+  implements:
+    name: implements
+    description: A reference to a specification that this component implements.
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: implements
+    owner: SpecificationComponent
+    domain_of:
+    - SpecificationComponent
+    range: uriorcurie
+  comments:
+    name: comments
+    description: A list of comments about this component. Comments are free text,
+      and may be used to provide additional information about the component, including
+      instructions for its use.
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    slot_uri: rdfs:comment
+    multivalued: true
+    alias: comments
+    owner: SpecificationComponent
+    domain_of:
+    - SpecificationComponent
+    range: string
+
+
+
+
+
+
+ + + \ No newline at end of file diff --git a/String/index.html b/String/index.html new file mode 100644 index 0000000..0da201d --- /dev/null +++ b/String/index.html @@ -0,0 +1,92 @@ + + + + + + + + + + + + + + Type: String - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Type: String

+

A character string

+

URI: xsd:string

+ +

Identifier and Mapping Information

+

Schema Source

+ + +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/StringificationConfiguration/index.html b/StringificationConfiguration/index.html new file mode 100644 index 0000000..71e5ea7 --- /dev/null +++ b/StringificationConfiguration/index.html @@ -0,0 +1,257 @@ + + + + + + + + + + +Class: StringificationConfiguration - LinkML-Map + + + + + + + + + + + + + + + + + + +
+ +

Class: StringificationConfiguration

+

URI: linkmltr:StringificationConfiguration

+
classDiagram + class StringificationConfiguration + StringificationConfiguration : delimiter + + StringificationConfiguration : over_slots + + StringificationConfiguration : reversed + + StringificationConfiguration : syntax + + StringificationConfiguration --> SerializationSyntaxType : syntax + + +
+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
delimiter0..1
String
direct
reversed0..1
Boolean
direct
over_slots0..*
String
direct
syntax0..1
SerializationSyntaxType
direct
+

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
SlotDerivationstringificationrangeStringificationConfiguration
+

Identifier and Mapping Information

+

Schema Source

+ +

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selflinkmltr:StringificationConfiguration
nativelinkmltr:StringificationConfiguration
+

LinkML Source

+ +

Direct

+
+
name: StringificationConfiguration
+from_schema: https://w3id.org/linkml/transformer
+attributes:
+  delimiter:
+    name: delimiter
+    examples:
+    - value: ','
+    - value: '|'
+    - value: ;
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    domain_of:
+    - StringificationConfiguration
+    range: string
+  reversed:
+    name: reversed
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    domain_of:
+    - StringificationConfiguration
+    range: boolean
+  over_slots:
+    name: over_slots
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    domain_of:
+    - StringificationConfiguration
+    range: string
+  syntax:
+    name: syntax
+    examples:
+    - value: json
+    - value: yaml
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    domain_of:
+    - StringificationConfiguration
+    range: SerializationSyntaxType
+
+
+
+

Induced

+
+
name: StringificationConfiguration
+from_schema: https://w3id.org/linkml/transformer
+attributes:
+  delimiter:
+    name: delimiter
+    examples:
+    - value: ','
+    - value: '|'
+    - value: ;
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: delimiter
+    owner: StringificationConfiguration
+    domain_of:
+    - StringificationConfiguration
+    range: string
+  reversed:
+    name: reversed
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: reversed
+    owner: StringificationConfiguration
+    domain_of:
+    - StringificationConfiguration
+    range: boolean
+  over_slots:
+    name: over_slots
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    multivalued: true
+    alias: over_slots
+    owner: StringificationConfiguration
+    domain_of:
+    - StringificationConfiguration
+    range: string
+  syntax:
+    name: syntax
+    examples:
+    - value: json
+    - value: yaml
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: syntax
+    owner: StringificationConfiguration
+    domain_of:
+    - StringificationConfiguration
+    range: SerializationSyntaxType
+
+
+
+
+
+
+ + + \ No newline at end of file diff --git a/Time/index.html b/Time/index.html new file mode 100644 index 0000000..c010ded --- /dev/null +++ b/Time/index.html @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + Type: Time - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Type: Time

+

A time object represents a (local) time of day, independent of any particular day

+

URI: xsd:time

+ +

Identifier and Mapping Information

+

Schema Source

+ + +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/docs/schema/TransformationSpecification.md b/TransformationSpecification/index.html similarity index 50% rename from docs/schema/TransformationSpecification.md rename to TransformationSpecification/index.html index 980c906..715e393 100644 --- a/docs/schema/TransformationSpecification.md +++ b/TransformationSpecification/index.html @@ -1,138 +1,217 @@ - - -# Class: TransformationSpecification - - -_A collection of mappings between source and target classes_ - - - - - -URI: [linkmltr:TransformationSpecification](https://w3id.org/linkml/transformer/TransformationSpecification) - - - - -```mermaid - classDiagram - class TransformationSpecification - SpecificationComponent <|-- TransformationSpecification - - TransformationSpecification : class_derivations - - TransformationSpecification --> ClassDerivation : class_derivations - - TransformationSpecification : comments - - TransformationSpecification : description - - TransformationSpecification --> None : description - - TransformationSpecification : enum_derivations - - TransformationSpecification --> EnumDerivation : enum_derivations - - TransformationSpecification : id - - TransformationSpecification --> None : id - - TransformationSpecification : implements - - TransformationSpecification : prefixes - - TransformationSpecification --> KeyVal : prefixes - - TransformationSpecification : slot_derivations - - TransformationSpecification --> SlotDerivation : slot_derivations - - TransformationSpecification : source_schema - - TransformationSpecification --> None : source_schema - - TransformationSpecification : target_schema + + + + + + + + + + +Class: TransformationSpecification - LinkML-Map + + + + + + + + + + + + + + + + + + +
+ +

Class: TransformationSpecification

+

A collection of mappings between source and target classes

+

URI: linkmltr:TransformationSpecification

+
classDiagram + class TransformationSpecification + SpecificationComponent <|-- TransformationSpecification + TransformationSpecification : class_derivations + TransformationSpecification --> ClassDerivation : class_derivations + TransformationSpecification : comments + TransformationSpecification : description + TransformationSpecification --> None : description -### Schema Source + TransformationSpecification : enum_derivations + TransformationSpecification --> EnumDerivation : enum_derivations -* from schema: https://w3id.org/linkml/transformer + TransformationSpecification : id + TransformationSpecification --> None : id + TransformationSpecification : implements + TransformationSpecification : prefixes + TransformationSpecification --> KeyVal : prefixes -## Mappings + TransformationSpecification : slot_derivations -| Mapping Type | Mapped Value | -| --- | --- | -| self | linkmltr:TransformationSpecification | -| native | linkmltr:TransformationSpecification | + TransformationSpecification --> SlotDerivation : slot_derivations + TransformationSpecification : source_schema + TransformationSpecification --> None : source_schema + TransformationSpecification : target_schema + TransformationSpecification --> None : target_schema -## LinkML Source + TransformationSpecification : title + TransformationSpecification --> None : title + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
id0..1
String
Unique identifier for this transformation specificationdirect
title0..1
String
human readable title for this transformation specificationdirect
prefixes0..*
KeyVal
maps prefixes to URL expansionsdirect
source_schema0..1
String
name of the schema that describes the source (input) objectsdirect
target_schema0..1
String
name of the schema that describes the target (output) objectsdirect
class_derivations0..*
ClassDerivation
Instructions on how to derive a set of classes in the target schema from clas...direct
enum_derivations0..*
EnumDerivation
Instructions on how to derive a set of enums in the target schemadirect
slot_derivations0..*
SlotDerivation
Instructions on how to derive a set of top level slots in the target schemadirect
description0..1
String
description of the specification componentSpecificationComponent
implements0..*
Uriorcurie
A reference to a specification that this component implementsSpecificationComponent
comments0..*
String
A list of comments about this componentSpecificationComponent
+

Identifier and Mapping Information

+

Schema Source

+ +

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selflinkmltr:TransformationSpecification
nativelinkmltr:TransformationSpecification
+

LinkML Source

- -### Direct - +

Direct

-```yaml -name: TransformationSpecification +
name: TransformationSpecification
 description: A collection of mappings between source and target classes
 from_schema: https://w3id.org/linkml/transformer
 is_a: SpecificationComponent
@@ -213,14 +292,11 @@
     inlined: true
 tree_root: true
 
-```
+
- -### Induced - +

Induced

-```yaml -name: TransformationSpecification +
name: TransformationSpecification
 description: A collection of mappings between source and target classes
 from_schema: https://w3id.org/linkml/transformer
 is_a: SpecificationComponent
@@ -353,5 +429,17 @@
     range: string
 tree_root: true
 
-```
-
\ No newline at end of file + + +
+
+
+ + + \ No newline at end of file diff --git a/UnitConversionConfiguration/index.html b/UnitConversionConfiguration/index.html new file mode 100644 index 0000000..05275d7 --- /dev/null +++ b/UnitConversionConfiguration/index.html @@ -0,0 +1,343 @@ + + + + + + + + + + +Class: UnitConversionConfiguration - LinkML-Map + + + + + + + + + + + + + + + + + + +
+ +

Class: UnitConversionConfiguration

+

URI: linkmltr:UnitConversionConfiguration

+
classDiagram + class UnitConversionConfiguration + UnitConversionConfiguration : source_magnitude_slot + + UnitConversionConfiguration --> None : source_magnitude_slot + + UnitConversionConfiguration : source_unit + + UnitConversionConfiguration --> None : source_unit + + UnitConversionConfiguration : source_unit_scheme + + UnitConversionConfiguration : source_unit_slot + + UnitConversionConfiguration --> None : source_unit_slot + + UnitConversionConfiguration : target_magnitude_slot + + UnitConversionConfiguration --> None : target_magnitude_slot + + UnitConversionConfiguration : target_unit + + UnitConversionConfiguration --> None : target_unit + + UnitConversionConfiguration : target_unit_scheme + + UnitConversionConfiguration : target_unit_slot + + UnitConversionConfiguration --> None : target_unit_slot + + +
+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
target_unit0..1
String
direct
target_unit_scheme0..1
String
direct
source_unit0..1
String
direct
source_unit_scheme0..1
String
direct
source_unit_slot0..1
String
direct
source_magnitude_slot0..1
String
direct
target_unit_slot0..1
String
direct
target_magnitude_slot0..1
String
direct
+

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
SlotDerivationunit_conversionrangeUnitConversionConfiguration
+

Identifier and Mapping Information

+

Schema Source

+ +

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selflinkmltr:UnitConversionConfiguration
nativelinkmltr:UnitConversionConfiguration
+

LinkML Source

+ +

Direct

+
+
name: UnitConversionConfiguration
+from_schema: https://w3id.org/linkml/transformer
+attributes:
+  target_unit:
+    name: target_unit
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    domain_of:
+    - UnitConversionConfiguration
+  target_unit_scheme:
+    name: target_unit_scheme
+    examples:
+    - value: ucum
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    domain_of:
+    - UnitConversionConfiguration
+    range: string
+  source_unit:
+    name: source_unit
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    domain_of:
+    - UnitConversionConfiguration
+  source_unit_scheme:
+    name: source_unit_scheme
+    examples:
+    - value: ucum
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    domain_of:
+    - UnitConversionConfiguration
+    range: string
+  source_unit_slot:
+    name: source_unit_slot
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    domain_of:
+    - UnitConversionConfiguration
+  source_magnitude_slot:
+    name: source_magnitude_slot
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    domain_of:
+    - UnitConversionConfiguration
+  target_unit_slot:
+    name: target_unit_slot
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    domain_of:
+    - UnitConversionConfiguration
+  target_magnitude_slot:
+    name: target_magnitude_slot
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    domain_of:
+    - UnitConversionConfiguration
+
+
+
+

Induced

+
+
name: UnitConversionConfiguration
+from_schema: https://w3id.org/linkml/transformer
+attributes:
+  target_unit:
+    name: target_unit
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: target_unit
+    owner: UnitConversionConfiguration
+    domain_of:
+    - UnitConversionConfiguration
+  target_unit_scheme:
+    name: target_unit_scheme
+    examples:
+    - value: ucum
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: target_unit_scheme
+    owner: UnitConversionConfiguration
+    domain_of:
+    - UnitConversionConfiguration
+    range: string
+  source_unit:
+    name: source_unit
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: source_unit
+    owner: UnitConversionConfiguration
+    domain_of:
+    - UnitConversionConfiguration
+  source_unit_scheme:
+    name: source_unit_scheme
+    examples:
+    - value: ucum
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: source_unit_scheme
+    owner: UnitConversionConfiguration
+    domain_of:
+    - UnitConversionConfiguration
+    range: string
+  source_unit_slot:
+    name: source_unit_slot
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: source_unit_slot
+    owner: UnitConversionConfiguration
+    domain_of:
+    - UnitConversionConfiguration
+  source_magnitude_slot:
+    name: source_magnitude_slot
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: source_magnitude_slot
+    owner: UnitConversionConfiguration
+    domain_of:
+    - UnitConversionConfiguration
+  target_unit_slot:
+    name: target_unit_slot
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: target_unit_slot
+    owner: UnitConversionConfiguration
+    domain_of:
+    - UnitConversionConfiguration
+  target_magnitude_slot:
+    name: target_magnitude_slot
+    from_schema: https://w3id.org/linkml/transformer
+    rank: 1000
+    alias: target_magnitude_slot
+    owner: UnitConversionConfiguration
+    domain_of:
+    - UnitConversionConfiguration
+
+
+
+
+
+
+ + + \ No newline at end of file diff --git a/Uri/index.html b/Uri/index.html new file mode 100644 index 0000000..b683027 --- /dev/null +++ b/Uri/index.html @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + Type: Uri - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Type: Uri

+

a complete URI

+

URI: xsd:anyURI

+ +

Comments

+ +

Identifier and Mapping Information

+

Schema Source

+ + +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/Uriorcurie/index.html b/Uriorcurie/index.html new file mode 100644 index 0000000..9ca8d1c --- /dev/null +++ b/Uriorcurie/index.html @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + Type: Uriorcurie - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Type: Uriorcurie

+

a URI or a CURIE

+

URI: xsd:anyURI

+ +

Identifier and Mapping Information

+

Schema Source

+ + +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/about.yaml b/about.yaml deleted file mode 100644 index c0b6dcc..0000000 --- a/about.yaml +++ /dev/null @@ -1,3 +0,0 @@ -name: linkml_map -description: Datamodel for schema transformations -source_schema_path: src/linkml_map/datamodel/transformer_model.yaml diff --git a/add/index.html b/add/index.html new file mode 100644 index 0000000..365c82d --- /dev/null +++ b/add/index.html @@ -0,0 +1,124 @@ + + + + + + + + + + + + + + Slot: add - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: add

+

URI: linkmltr:add

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
CopyDirectiveInstructs a Schema Mapper in how to map to a target schemano
+

Properties

+ +

Identifier and Mapping Information

+

Schema Source

+ +

LinkML Source

+
+ +
name: add
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+alias: add
+owner: CopyDirective
+domain_of:
+- CopyDirective
+range: Any
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/alias/index.html b/alias/index.html new file mode 100644 index 0000000..b83d734 --- /dev/null +++ b/alias/index.html @@ -0,0 +1,132 @@ + + + + + + + + + + + + + + Slot: alias - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: alias

+

name of the class to be aliased

+

URI: linkmltr:alias

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
AliasedClassalias-class key value pairs for classesno
+

Properties

+ +

Identifier and Mapping Information

+

Schema Source

+ +

LinkML Source

+
+ +
name: alias
+description: name of the class to be aliased
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+key: true
+alias: alias
+owner: AliasedClass
+domain_of:
+- AliasedClass
+required: true
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/cast_collection_as/index.html b/cast_collection_as/index.html new file mode 100644 index 0000000..635a314 --- /dev/null +++ b/cast_collection_as/index.html @@ -0,0 +1,124 @@ + + + + + + + + + + + + + + Slot: cast_collection_as - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: cast_collection_as

+

URI: linkmltr:cast_collection_as

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
SlotDerivationA specification of how to derive the value of a target slot from a source slo...no
+

Properties

+ +

Identifier and Mapping Information

+

Schema Source

+ +

LinkML Source

+
+ +
name: cast_collection_as
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+alias: cast_collection_as
+owner: SlotDerivation
+domain_of:
+- SlotDerivation
+range: CollectionType
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/class_derivations/index.html b/class_derivations/index.html new file mode 100644 index 0000000..91030fc --- /dev/null +++ b/class_derivations/index.html @@ -0,0 +1,134 @@ + + + + + + + + + + + + + + Slot: class_derivations - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: class_derivations

+

Instructions on how to derive a set of classes in the target schema from classes in the source schema.

+

URI: linkmltr:class_derivations

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
TransformationSpecificationA collection of mappings between source and target classesno
+

Properties

+ +

Identifier and Mapping Information

+

Schema Source

+ +

LinkML Source

+
+ +
name: class_derivations
+description: Instructions on how to derive a set of classes in the target schema from
+  classes in the source schema.
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+multivalued: true
+alias: class_derivations
+owner: TransformationSpecification
+domain_of:
+- TransformationSpecification
+range: ClassDerivation
+inlined: true
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/class_name/index.html b/class_name/index.html new file mode 100644 index 0000000..8536337 --- /dev/null +++ b/class_name/index.html @@ -0,0 +1,123 @@ + + + + + + + + + + + + + + Slot: class_name - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: class_name

+

URI: linkmltr:class_name

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
InverseUsed for back references in mapping to relational modelno
+

Properties

+ +

Identifier and Mapping Information

+

Schema Source

+ +

LinkML Source

+
+ +
name: class_name
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+alias: class_name
+owner: Inverse
+domain_of:
+- Inverse
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/class_named/index.html b/class_named/index.html new file mode 100644 index 0000000..eb037d0 --- /dev/null +++ b/class_named/index.html @@ -0,0 +1,125 @@ + + + + + + + + + + + + + + Slot: class_named - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: class_named

+

local alias for the class

+

URI: linkmltr:class_named

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
AliasedClassalias-class key value pairs for classesno
+

Properties

+ +

Identifier and Mapping Information

+

Schema Source

+ +

LinkML Source

+
+ +
name: class_named
+description: local alias for the class
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+alias: class_named
+owner: AliasedClass
+domain_of:
+- AliasedClass
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/comments/index.html b/comments/index.html new file mode 100644 index 0000000..c138414 --- /dev/null +++ b/comments/index.html @@ -0,0 +1,170 @@ + + + + + + + + + + + + + + Slot: comments - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: comments

+

A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use.

+

URI: rdfs:comment

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
EnumDerivationA specification of how to derive the value of a target enum from a source enu...no
PermissibleValueDerivationA specification of how to derive the value of a PV from a source enumno
ElementDerivationAn abstract grouping for classes that provide a specification of how to deri...no
PrefixDerivationno
SlotDerivationA specification of how to derive the value of a target slot from a source slo...no
ClassDerivationA specification of how to derive a target class from a source classno
SpecificationComponentno
TransformationSpecificationA collection of mappings between source and target classesno
+

Properties

+ +

Identifier and Mapping Information

+

Schema Source

+ +

LinkML Source

+
+ +
name: comments
+description: A list of comments about this component. Comments are free text, and
+  may be used to provide additional information about the component, including instructions
+  for its use.
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+slot_uri: rdfs:comment
+multivalued: true
+alias: comments
+owner: SpecificationComponent
+domain_of:
+- SpecificationComponent
+range: string
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/copy_all/index.html b/copy_all/index.html new file mode 100644 index 0000000..edb344b --- /dev/null +++ b/copy_all/index.html @@ -0,0 +1,124 @@ + + + + + + + + + + + + + + Slot: copy_all - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: copy_all

+

URI: linkmltr:copy_all

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
CopyDirectiveInstructs a Schema Mapper in how to map to a target schemano
+

Properties

+ +

Identifier and Mapping Information

+

Schema Source

+ +

LinkML Source

+
+ +
name: copy_all
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+alias: copy_all
+owner: CopyDirective
+domain_of:
+- CopyDirective
+range: boolean
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/copy_directives/index.html b/copy_directives/index.html new file mode 100644 index 0000000..f29c692 --- /dev/null +++ b/copy_directives/index.html @@ -0,0 +1,156 @@ + + + + + + + + + + + + + + Slot: copy_directives - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: copy_directives

+

URI: linkmltr:copy_directives

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
EnumDerivationA specification of how to derive the value of a target enum from a source enu...no
ElementDerivationAn abstract grouping for classes that provide a specification of how to deri...no
PrefixDerivationno
SlotDerivationA specification of how to derive the value of a target slot from a source slo...no
ClassDerivationA specification of how to derive a target class from a source classno
PermissibleValueDerivationA specification of how to derive the value of a PV from a source enumno
+

Properties

+ +

Identifier and Mapping Information

+

Schema Source

+ +

LinkML Source

+
+ +
name: copy_directives
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+multivalued: true
+alias: copy_directives
+owner: ElementDerivation
+domain_of:
+- ElementDerivation
+range: CopyDirective
+inlined: true
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/css/ansi-colours.css b/css/ansi-colours.css new file mode 100644 index 0000000..42301ef --- /dev/null +++ b/css/ansi-colours.css @@ -0,0 +1,174 @@ +/*! +* +* IPython notebook +* +*/ +/* CSS font colors for translated ANSI escape sequences */ +/* The color values are a mix of + http://www.xcolors.net/dl/baskerville-ivorylight and + http://www.xcolors.net/dl/euphrasia */ +.ansi-black-fg { + color: #3E424D; +} +.ansi-black-bg { + background-color: #3E424D; +} +.ansi-black-intense-fg { + color: #282C36; +} +.ansi-black-intense-bg { + background-color: #282C36; +} +.ansi-red-fg { + color: #E75C58; +} +.ansi-red-bg { + background-color: #E75C58; +} +.ansi-red-intense-fg { + color: #B22B31; +} +.ansi-red-intense-bg { + background-color: #B22B31; +} +.ansi-green-fg { + color: #00A250; +} +.ansi-green-bg { + background-color: #00A250; +} +.ansi-green-intense-fg { + color: #007427; +} +.ansi-green-intense-bg { + background-color: #007427; +} +.ansi-yellow-fg { + color: #DDB62B; +} +.ansi-yellow-bg { + background-color: #DDB62B; +} +.ansi-yellow-intense-fg { + color: #B27D12; +} +.ansi-yellow-intense-bg { + background-color: #B27D12; +} +.ansi-blue-fg { + color: #208FFB; +} +.ansi-blue-bg { + background-color: #208FFB; +} +.ansi-blue-intense-fg { + color: #0065CA; +} +.ansi-blue-intense-bg { + background-color: #0065CA; +} +.ansi-magenta-fg { + color: #D160C4; +} +.ansi-magenta-bg { + background-color: #D160C4; +} +.ansi-magenta-intense-fg { + color: #A03196; +} +.ansi-magenta-intense-bg { + background-color: #A03196; +} +.ansi-cyan-fg { + color: #60C6C8; +} +.ansi-cyan-bg { + background-color: #60C6C8; +} +.ansi-cyan-intense-fg { + color: #258F8F; +} +.ansi-cyan-intense-bg { + background-color: #258F8F; +} +.ansi-white-fg { + color: #C5C1B4; +} +.ansi-white-bg { + background-color: #C5C1B4; +} +.ansi-white-intense-fg { + color: #A1A6B2; +} +.ansi-white-intense-bg { + background-color: #A1A6B2; +} +.ansi-default-inverse-fg { + color: #FFFFFF; +} +.ansi-default-inverse-bg { + background-color: #000000; +} +.ansi-bold { + font-weight: bold; +} +.ansi-underline { + text-decoration: underline; +} +/* The following styles are deprecated an will be removed in a future version */ +.ansibold { + font-weight: bold; +} +.ansi-inverse { + outline: 0.5px dotted; +} +/* use dark versions for foreground, to improve visibility */ +.ansiblack { + color: black; +} +.ansired { + color: darkred; +} +.ansigreen { + color: darkgreen; +} +.ansiyellow { + color: #c4a000; +} +.ansiblue { + color: darkblue; +} +.ansipurple { + color: darkviolet; +} +.ansicyan { + color: steelblue; +} +.ansigray { + color: gray; +} +/* and light for background, for the same reason */ +.ansibgblack { + background-color: black; +} +.ansibgred { + background-color: red; +} +.ansibggreen { + background-color: green; +} +.ansibgyellow { + background-color: yellow; +} +.ansibgblue { + background-color: blue; +} +.ansibgpurple { + background-color: magenta; +} +.ansibgcyan { + background-color: cyan; +} +.ansibggray { + background-color: gray; +} \ No newline at end of file diff --git a/css/base.css b/css/base.css new file mode 100644 index 0000000..5c8018c --- /dev/null +++ b/css/base.css @@ -0,0 +1,537 @@ +body { + background-color: #f8f8f8; +} + +/*********************************************************************** + Top bar + ***********************************************************************/ + +.navbar { + background-color: #546e7a; + box-shadow: 0 1.5px 3px rgba(0,0,0,.24), 0 3px 8px rgba(0,0,0,.05); + border: none; + border-radius: 0px; + margin-bottom: 0px; + height: 50px; + z-index: 2; +} + +.wm-top-page { + overflow: hidden; +} + +.wm-page-content { + max-width: 700px; + position: relative; +} + +.wm-page-top-frame { display: none; } +.wm-top-page > .wm-page-top-frame { display: block; } +.wm-top-page > .wm-page-content { display: none; } + +.wm-top-brand { + display: inline-block; + float: left; + overflow: visible; + width: 0px; + height: 50px; + color: #fff; + font-size: 18px; + white-space: nowrap; + text-decoration: none; +} + +.wm-top-link, .wm-top-link:hover, .wm-top-link:active, .wm-top-link:visited, .wm-top-link:focus { + color: #fff; + text-decoration: none; +} + +.wm-vcenter:before { + content: ''; + display: inline-block; + height: 100%; + vertical-align: middle; + margin-left: -0.25em; +} + +.wm-vcentered { + display: inline-block; + vertical-align: middle; +} + +.wm-top-title { + display: inline-block; + line-height: 16px; + vertical-align: middle; +} + +.wm-top-logo { + max-height: 100%; +} + +.wm-top-version { + border: 1px solid #ddd; + border-radius: 3px; + padding: 0px 5px; + color: #ddd; + font-size: 8pt; +} + +.wm-top-tool { + height: 50px; + white-space: nowrap; +} + +.wm-top-tool-expanded { + position: absolute; + right: 0px; + padding: inherit; + width: 100%; + background-color: #546e7a; +} + +.wm-top-search { + width: 20rem; +} + +#wm-toc-button { + margin-right: 1rem; + margin-left: 0.5rem; +} + +/*********************************************************************** + Table of contents (side pane) + ***********************************************************************/ + +.wm-toc-pane { + position: absolute; + top: 0px; + padding-top: 70px; + height: 100%; + min-width: 250px; + max-width: 350px; + z-index: 1; + background-color: #f2f2f2; + border-right: 1px solid #e0e0e0; + overflow: auto; + margin-left: 0px; + padding-left: 1rem; + padding-right: 1rem; + padding-bottom: 2rem; + transition: margin-left 0.3s; +} + +.wm-content-pane { + position: absolute; + top: 0px; + padding-top: 50px; + height: 100%; + width: 100%; + z-index: 0; + padding-left: 250px; + transition: padding-left 0.3s; + /* required for iPhone to scroll the contained iframe */ + -webkit-overflow-scrolling: touch; +} + +.wm-toc-pane.wm-toc-dropdown { + position: absolute; + display: block; + top: 0; + left: 0; + margin-left: 0; + height: auto; + box-shadow: 2px 3px 4px 0 grey; +} + +.wm-toc-repo { + margin-top: -15px; + margin-bottom: 5px; + padding-bottom: 5px; + border-bottom: 1px solid #e0e0e0; +} + +.wm-toc-hidden > .wm-toc-pane { + margin-left: -250px; +} + +.wm-toc-hidden > .wm-content-pane { + padding-left: 0px; +} + +.wm-small-show { + display: none; +} + +#wm-search-form { + width: 100%; +} +#wm-search-show { + display: none; +} + +@media (max-width: 600px) { + .wm-small-hide { + display: none; + } + .wm-small-show { + display: block; + } + .wm-small-left { + float: left !important; + } + #wm-search-show { + display: block; + margin-left: 1rem; + } + .wm-top-tool-expanded #wm-search-show { + display: none; + } + .wm-top-search { + display: none; + } + .wm-top-tool-expanded .wm-top-search { + display: table; + width: 100%; + padding: 0px; + } + + .wm-top-page { + overflow: visible; + } + .wm-top-container { + /* This prevents horizontal overflow, but cuts off search results on bigger + * screens, so included in small-screen section */ + overflow-x: hidden; + } + .wm-toc-pane { + display: none; + } + .wm-content-pane { + padding-left: 0px; + overflow: visible; + } +} + +.wm-toctree { + list-style-type: none; + line-height: 16px; + padding-left: 0px; +} + +.wm-toctree a, .wm-toctree a:visited, .wm-toctree a:hover, .wm-toctree a:focus { + color: #546e7a; + text-decoration: none; + outline: none; +} + +.wm-toc-text { + display: block; + padding: 4px; + cursor: pointer; +} + +.wm-toc-lev1 > .wm-toc-text { padding-left: 14px; } +.wm-toc-lev2 > .wm-toc-text { padding-left: 28px; } +.wm-toc-lev3 > .wm-toc-text { padding-left: 42px; } +.wm-toc-lev4 > .wm-toc-text { padding-left: 56px; } +.wm-toc-lev5 > .wm-toc-text { padding-left: 70px; } +.wm-toc-lev6 > .wm-toc-text { padding-left: 84px; } + +.wm-toc-lev1 + .wm-page-toc { margin-left: 14px; } +.wm-toc-lev2 + .wm-page-toc { margin-left: 28px; } +.wm-toc-lev3 + .wm-page-toc { margin-left: 42px; } +.wm-toc-lev4 + .wm-page-toc { margin-left: 56px; } +.wm-toc-lev5 + .wm-page-toc { margin-left: 70px; } +.wm-toc-lev6 + .wm-page-toc { margin-left: 84px; } + +.wm-toc-li-nested { + padding: 0px; + margin: 0px; +} + +.wm-toc-opener > .wm-toc-text::before { + content: "\25B6 \FE0E"; + display: inline-block; + vertical-align: middle; + font-size: 8px; + width: 14px; +} + +.wm-toc-opener.wm-toc-open > .wm-toc-text::before { + content: "\25BC \FE0E"; +} + +.wm-toc-li.wm-current, .wm-toc-li.wm-current:hover { + background-color: #546e7a; + color: white; +} + +.wm-toc-li:hover { + background-color: #e0e0e0; +} + +.wm-toc-li.wm-current a { + color: white; +} + +.wm-toc-li-nested.wm-page-toc { + font-size: 1.2rem; + line-height: 1.2rem; + overflow: hidden; + border-left: 1px solid #546e7a; +} + +.wm-page-toc-opener > .wm-toc-text::after { + content: "\25C4"; + display: inline-block; + float: right; + vertical-align: middle; + font-size: 8px; +} + +.wm-page-toc-opener.wm-page-toc-open > .wm-toc-text::after { + content: "\25BC"; +} + +.wm-page-toc-text { + padding: 2px 2px 2px 1rem; + display: block; + cursor: pointer; +} + +.wm-article { + width: 1px; + min-width: 100%; + height: 100%; + border: none; +} + +.btn:focus, .btn:active:focus, .btn.active:focus, .btn.focus, .btn:active.focus, .btn.active.focus { + outline: none; +} + +.btn-default:focus, .btn-default.focus { + color: #333; + background-color: #fff; + border-color: #ccc; +} + +.btn-default.greybtn { + color: #888; +} + +.wm-article-nav-buttons { + margin: 1rem 0; +} + +.wm-page-content img { + max-width: 100%; + display: inline-block; + padding: 4px; + line-height: 1.428571429; + background-color: #fff; + border: 1px solid #ddd; + border-radius: 4px; + margin: 20px auto 30px auto; +} + +.wm-page-content a { + color: #2fa4e7; +} + +.wm-article-nav { + display: inline-block; + max-width: 48%; + white-space: nowrap; + color: #546e7a; + text-align: right; +} + +.wm-article-nav > .btn-link { + display: block; + padding-left: 0.5rem; + padding-right: 0.5rem; + overflow: hidden; + text-overflow: ellipsis; +} + +.wm-article-nav > a, .wm-article-nav > a:visited, .wm-article-nav > a:hover, .wm-article-nav > a:focus { + color: #546e7a; + text-decoration: none; + outline: none; +} + +/*********************************************************************** + * Dropdown search results + ***********************************************************************/ +#mkdocs-search-results.dropdown-menu { + width: 40rem; + overflow-y: auto; + overflow-x: hidden; + white-space: normal; + max-height: calc(100vh - 60px); + max-width: 90vw; +} + +#mkdocs-search-results { + font-family: "Helvetica Neue",Helvetica,Arial,sans-serif,FontAwesome; +} + +.search-link { + font-size: 1.2rem; +} + +.search-title { + font-weight: bold; + color: #337ab7; + padding-right: 1rem; +} + +.search-text { + color: #666; + overflow: hidden; + text-overflow: ellipsis; +} + +.search-text > b { + color: #000; +} + +.wm-search-page { + list-style: none; + padding: 5px 0; +} + +.wm-search-page > li { + padding: 1rem 0; + border-bottom: 1px solid #ccc; +} + +.wm-search-page .search-link { + font-size: inherit; +} + +.wm-search-page .search-link:hover, .wm-search-page .search-link:active { + text-decoration: none; +} + +.wm-search-page .search-link:hover .search-title { + text-decoration: underline; +} + + + +/*********************************************************************** + * The rest is taken from base.css from mkdocs. + ***********************************************************************/ + +.source-links { + float: right; +} + +h1 { + color: #444; + font-weight: 400; + font-size: 42px; +} + +h2, h3, h4, h5, h6 { + color: #444; + font-weight: 300; +} + +hr { + border-top: 1px solid #aaa; +} + +pre, .rst-content tt { + max-width: 100%; + background: #fff; + border: solid 1px #e1e4e5; + color: #333; + overflow-x: auto; +} + +code.code-large, .rst-content tt.code-large { + font-size: 90%; +} + +code { + padding: 2px 5px; + background: #fff; + border: solid 1px #e1e4e5; + color: #333; + white-space: pre-wrap; + word-wrap: break-word; +} + +pre code { + background: transparent; + border: none; + white-space: pre; + word-wrap: normal; + font-family: monospace,serif; + font-size: 12px; +} + +a code { + color: #2FA4E7; +} + +a:hover code, a:focus code { + color: #157AB5; +} + +footer { + margin-bottom: 10px; + text-align: center; + font-weight: 200; + font-size: smaller; +} + +.modal-dialog { + margin-top: 60px; +} + +.headerlink { + font-family: FontAwesome; + font-size: 14px; + display: none; + padding-left: .5em; +} + +h1:hover .headerlink, h2:hover .headerlink, h3:hover .headerlink, h4:hover .headerlink, h5:hover .headerlink, h6:hover .headerlink{ + display:inline-block; +} + +.admonition { + padding: 15px; + margin-bottom: 20px; + border: 1px solid transparent; + border-radius: 4px; + text-align: left; +} + +.admonition.note { /* csslint allow: adjoining-classes */ + color: #3a87ad; + background-color: #d9edf7; + border-color: #bce8f1; +} + +.admonition.warning { /* csslint allow: adjoining-classes */ + color: #c09853; + background-color: #fcf8e3; + border-color: #fbeed5; +} + +.admonition.danger { /* csslint allow: adjoining-classes */ + color: #b94a48; + background-color: #f2dede; + border-color: #eed3d7; +} + +.admonition-title { + font-weight: bold; + text-align: left; +} diff --git a/css/bootstrap-3.3.7.css b/css/bootstrap-3.3.7.css new file mode 100644 index 0000000..6167622 --- /dev/null +++ b/css/bootstrap-3.3.7.css @@ -0,0 +1,6757 @@ +/*! + * Bootstrap v3.3.7 (http://getbootstrap.com) + * Copyright 2011-2016 Twitter, Inc. + * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE) + */ +/*! normalize.css v3.0.3 | MIT License | github.com/necolas/normalize.css */ +html { + font-family: sans-serif; + -webkit-text-size-adjust: 100%; + -ms-text-size-adjust: 100%; +} +body { + margin: 0; +} +article, +aside, +details, +figcaption, +figure, +footer, +header, +hgroup, +main, +menu, +nav, +section, +summary { + display: block; +} +audio, +canvas, +progress, +video { + display: inline-block; + vertical-align: baseline; +} +audio:not([controls]) { + display: none; + height: 0; +} +[hidden], +template { + display: none; +} +a { + background-color: transparent; +} +a:active, +a:hover { + outline: 0; +} +abbr[title] { + border-bottom: 1px dotted; +} +b, +strong { + font-weight: bold; +} +dfn { + font-style: italic; +} +h1 { + margin: .67em 0; + font-size: 2em; +} +mark { + color: #000; + background: #ff0; +} +small { + font-size: 80%; +} +sub, +sup { + position: relative; + font-size: 75%; + line-height: 0; + vertical-align: baseline; +} +sup { + top: -.5em; +} +sub { + bottom: -.25em; +} +img { + border: 0; +} +svg:not(:root) { + overflow: hidden; +} +figure { + margin: 1em 40px; +} +hr { + height: 0; + -webkit-box-sizing: content-box; + -moz-box-sizing: content-box; + box-sizing: content-box; +} +pre { + overflow: auto; +} +code, +kbd, +pre, +samp { + font-family: monospace, monospace; + font-size: 1em; +} +button, +input, +optgroup, +select, +textarea { + margin: 0; + font: inherit; + color: inherit; +} +button { + overflow: visible; +} +button, +select { + text-transform: none; +} +button, +html input[type="button"], +input[type="reset"], +input[type="submit"] { + -webkit-appearance: button; + cursor: pointer; +} +button[disabled], +html input[disabled] { + cursor: default; +} +button::-moz-focus-inner, +input::-moz-focus-inner { + padding: 0; + border: 0; +} +input { + line-height: normal; +} +input[type="checkbox"], +input[type="radio"] { + -webkit-box-sizing: border-box; + -moz-box-sizing: border-box; + box-sizing: border-box; + padding: 0; +} +input[type="number"]::-webkit-inner-spin-button, +input[type="number"]::-webkit-outer-spin-button { + height: auto; +} +input[type="search"] { + -webkit-box-sizing: content-box; + -moz-box-sizing: content-box; + box-sizing: content-box; + -webkit-appearance: textfield; +} +input[type="search"]::-webkit-search-cancel-button, +input[type="search"]::-webkit-search-decoration { + -webkit-appearance: none; +} +fieldset { + padding: .35em .625em .75em; + margin: 0 2px; + border: 1px solid #c0c0c0; +} +legend { + padding: 0; + border: 0; +} +textarea { + overflow: auto; +} +optgroup { + font-weight: bold; +} +table { + border-spacing: 0; + border-collapse: collapse; +} +td, +th { + padding: 0; +} +/*! Source: https://github.com/h5bp/html5-boilerplate/blob/master/src/css/main.css */ +@media print { + *, + *:before, + *:after { + color: #000 !important; + text-shadow: none !important; + background: transparent !important; + -webkit-box-shadow: none !important; + box-shadow: none !important; + } + a, + a:visited { + text-decoration: underline; + } + a[href]:after { + content: " (" attr(href) ")"; + } + abbr[title]:after { + content: " (" attr(title) ")"; + } + a[href^="#"]:after, + a[href^="javascript:"]:after { + content: ""; + } + pre, + blockquote { + border: 1px solid #999; + + page-break-inside: avoid; + } + thead { + display: table-header-group; + } + tr, + img { + page-break-inside: avoid; + } + img { + max-width: 100% !important; + } + p, + h2, + h3 { + orphans: 3; + widows: 3; + } + h2, + h3 { + page-break-after: avoid; + } + .navbar { + display: none; + } + .btn > .caret, + .dropup > .btn > .caret { + border-top-color: #000 !important; + } + .label { + border: 1px solid #000; + } + .table { + border-collapse: collapse !important; + } + .table td, + .table th { + background-color: #fff !important; + } + .table-bordered th, + .table-bordered td { + border: 1px solid #ddd !important; + } +} +@font-face { + font-family: 'Glyphicons Halflings'; + + src: url('http://github.com/fonts/glyphicons-halflings-regular.eot'); + src: url('http://github.com/fonts/glyphicons-halflings-regular.eot?#iefix') format('embedded-opentype'), url('http://github.com/fonts/glyphicons-halflings-regular.woff2') format('woff2'), url('http://github.com/fonts/glyphicons-halflings-regular.woff') format('woff'), url('http://github.com/fonts/glyphicons-halflings-regular.ttf') format('truetype'), url('http://github.com/fonts/glyphicons-halflings-regular.svg#glyphicons_halflingsregular') format('svg'); +} +.glyphicon { + position: relative; + top: 1px; + display: inline-block; + font-family: 'Glyphicons Halflings'; + font-style: normal; + font-weight: normal; + line-height: 1; + + -webkit-font-smoothing: antialiased; + -moz-osx-font-smoothing: grayscale; +} +.glyphicon-asterisk:before { + content: "\002a"; +} +.glyphicon-plus:before { + content: "\002b"; +} +.glyphicon-euro:before, +.glyphicon-eur:before { + content: "\20ac"; +} +.glyphicon-minus:before { + content: "\2212"; +} +.glyphicon-cloud:before { + content: "\2601"; +} +.glyphicon-envelope:before { + content: "\2709"; +} +.glyphicon-pencil:before { + content: "\270f"; +} +.glyphicon-glass:before { + content: "\e001"; +} +.glyphicon-music:before { + content: "\e002"; +} +.glyphicon-search:before { + content: "\e003"; +} +.glyphicon-heart:before { + content: "\e005"; +} +.glyphicon-star:before { + content: "\e006"; +} +.glyphicon-star-empty:before { + content: "\e007"; +} +.glyphicon-user:before { + content: "\e008"; +} +.glyphicon-film:before { + content: "\e009"; +} +.glyphicon-th-large:before { + content: "\e010"; +} +.glyphicon-th:before { + content: "\e011"; +} +.glyphicon-th-list:before { + content: "\e012"; +} +.glyphicon-ok:before { + content: "\e013"; +} +.glyphicon-remove:before { + content: "\e014"; +} +.glyphicon-zoom-in:before { + content: "\e015"; +} +.glyphicon-zoom-out:before { + content: "\e016"; +} +.glyphicon-off:before { + content: "\e017"; +} +.glyphicon-signal:before { + content: "\e018"; +} +.glyphicon-cog:before { + content: "\e019"; +} +.glyphicon-trash:before { + content: "\e020"; +} +.glyphicon-home:before { + content: "\e021"; +} +.glyphicon-file:before { + content: "\e022"; +} +.glyphicon-time:before { + content: "\e023"; +} +.glyphicon-road:before { + content: "\e024"; +} +.glyphicon-download-alt:before { + content: "\e025"; +} +.glyphicon-download:before { + content: "\e026"; +} +.glyphicon-upload:before { + content: "\e027"; +} +.glyphicon-inbox:before { + content: "\e028"; +} +.glyphicon-play-circle:before { + content: "\e029"; +} +.glyphicon-repeat:before { + content: "\e030"; +} +.glyphicon-refresh:before { + content: "\e031"; +} +.glyphicon-list-alt:before { + content: "\e032"; +} +.glyphicon-lock:before { + content: "\e033"; +} +.glyphicon-flag:before { + content: "\e034"; +} +.glyphicon-headphones:before { + content: "\e035"; +} +.glyphicon-volume-off:before { + content: "\e036"; +} +.glyphicon-volume-down:before { + content: "\e037"; +} +.glyphicon-volume-up:before { + content: "\e038"; +} +.glyphicon-qrcode:before { + content: "\e039"; +} +.glyphicon-barcode:before { + content: "\e040"; +} +.glyphicon-tag:before { + content: "\e041"; +} +.glyphicon-tags:before { + content: "\e042"; +} +.glyphicon-book:before { + content: "\e043"; +} +.glyphicon-bookmark:before { + content: "\e044"; +} +.glyphicon-print:before { + content: "\e045"; +} +.glyphicon-camera:before { + content: "\e046"; +} +.glyphicon-font:before { + content: "\e047"; +} +.glyphicon-bold:before { + content: "\e048"; +} +.glyphicon-italic:before { + content: "\e049"; +} +.glyphicon-text-height:before { + content: "\e050"; +} +.glyphicon-text-width:before { + content: "\e051"; +} +.glyphicon-align-left:before { + content: "\e052"; +} +.glyphicon-align-center:before { + content: "\e053"; +} +.glyphicon-align-right:before { + content: "\e054"; +} +.glyphicon-align-justify:before { + content: "\e055"; +} +.glyphicon-list:before { + content: "\e056"; +} +.glyphicon-indent-left:before { + content: "\e057"; +} +.glyphicon-indent-right:before { + content: "\e058"; +} +.glyphicon-facetime-video:before { + content: "\e059"; +} +.glyphicon-picture:before { + content: "\e060"; +} +.glyphicon-map-marker:before { + content: "\e062"; +} +.glyphicon-adjust:before { + content: "\e063"; +} +.glyphicon-tint:before { + content: "\e064"; +} +.glyphicon-edit:before { + content: "\e065"; +} +.glyphicon-share:before { + content: "\e066"; +} +.glyphicon-check:before { + content: "\e067"; +} +.glyphicon-move:before { + content: "\e068"; +} +.glyphicon-step-backward:before { + content: "\e069"; +} +.glyphicon-fast-backward:before { + content: "\e070"; +} +.glyphicon-backward:before { + content: "\e071"; +} +.glyphicon-play:before { + content: "\e072"; +} +.glyphicon-pause:before { + content: "\e073"; +} +.glyphicon-stop:before { + content: "\e074"; +} +.glyphicon-forward:before { + content: "\e075"; +} +.glyphicon-fast-forward:before { + content: "\e076"; +} +.glyphicon-step-forward:before { + content: "\e077"; +} +.glyphicon-eject:before { + content: "\e078"; +} +.glyphicon-chevron-left:before { + content: "\e079"; +} +.glyphicon-chevron-right:before { + content: "\e080"; +} +.glyphicon-plus-sign:before { + content: "\e081"; +} +.glyphicon-minus-sign:before { + content: "\e082"; +} +.glyphicon-remove-sign:before { + content: "\e083"; +} +.glyphicon-ok-sign:before { + content: "\e084"; +} +.glyphicon-question-sign:before { + content: "\e085"; +} +.glyphicon-info-sign:before { + content: "\e086"; +} +.glyphicon-screenshot:before { + content: "\e087"; +} +.glyphicon-remove-circle:before { + content: "\e088"; +} +.glyphicon-ok-circle:before { + content: "\e089"; +} +.glyphicon-ban-circle:before { + content: "\e090"; +} +.glyphicon-arrow-left:before { + content: "\e091"; +} +.glyphicon-arrow-right:before { + content: "\e092"; +} +.glyphicon-arrow-up:before { + content: "\e093"; +} +.glyphicon-arrow-down:before { + content: "\e094"; +} +.glyphicon-share-alt:before { + content: "\e095"; +} +.glyphicon-resize-full:before { + content: "\e096"; +} +.glyphicon-resize-small:before { + content: "\e097"; +} +.glyphicon-exclamation-sign:before { + content: "\e101"; +} +.glyphicon-gift:before { + content: "\e102"; +} +.glyphicon-leaf:before { + content: "\e103"; +} +.glyphicon-fire:before { + content: "\e104"; +} +.glyphicon-eye-open:before { + content: "\e105"; +} +.glyphicon-eye-close:before { + content: "\e106"; +} +.glyphicon-warning-sign:before { + content: "\e107"; +} +.glyphicon-plane:before { + content: "\e108"; +} +.glyphicon-calendar:before { + content: "\e109"; +} +.glyphicon-random:before { + content: "\e110"; +} +.glyphicon-comment:before { + content: "\e111"; +} +.glyphicon-magnet:before { + content: "\e112"; +} +.glyphicon-chevron-up:before { + content: "\e113"; +} +.glyphicon-chevron-down:before { + content: "\e114"; +} +.glyphicon-retweet:before { + content: "\e115"; +} +.glyphicon-shopping-cart:before { + content: "\e116"; +} +.glyphicon-folder-close:before { + content: "\e117"; +} +.glyphicon-folder-open:before { + content: "\e118"; +} +.glyphicon-resize-vertical:before { + content: "\e119"; +} +.glyphicon-resize-horizontal:before { + content: "\e120"; +} +.glyphicon-hdd:before { + content: "\e121"; +} +.glyphicon-bullhorn:before { + content: "\e122"; +} +.glyphicon-bell:before { + content: "\e123"; +} +.glyphicon-certificate:before { + content: "\e124"; +} +.glyphicon-thumbs-up:before { + content: "\e125"; +} +.glyphicon-thumbs-down:before { + content: "\e126"; +} +.glyphicon-hand-right:before { + content: "\e127"; +} +.glyphicon-hand-left:before { + content: "\e128"; +} +.glyphicon-hand-up:before { + content: "\e129"; +} +.glyphicon-hand-down:before { + content: "\e130"; +} +.glyphicon-circle-arrow-right:before { + content: "\e131"; +} +.glyphicon-circle-arrow-left:before { + content: "\e132"; +} +.glyphicon-circle-arrow-up:before { + content: "\e133"; +} +.glyphicon-circle-arrow-down:before { + content: "\e134"; +} +.glyphicon-globe:before { + content: "\e135"; +} +.glyphicon-wrench:before { + content: "\e136"; +} +.glyphicon-tasks:before { + content: "\e137"; +} +.glyphicon-filter:before { + content: "\e138"; +} +.glyphicon-briefcase:before { + content: "\e139"; +} +.glyphicon-fullscreen:before { + content: "\e140"; +} +.glyphicon-dashboard:before { + content: "\e141"; +} +.glyphicon-paperclip:before { + content: "\e142"; +} +.glyphicon-heart-empty:before { + content: "\e143"; +} +.glyphicon-link:before { + content: "\e144"; +} +.glyphicon-phone:before { + content: "\e145"; +} +.glyphicon-pushpin:before { + content: "\e146"; +} +.glyphicon-usd:before { + content: "\e148"; +} +.glyphicon-gbp:before { + content: "\e149"; +} +.glyphicon-sort:before { + content: "\e150"; +} +.glyphicon-sort-by-alphabet:before { + content: "\e151"; +} +.glyphicon-sort-by-alphabet-alt:before { + content: "\e152"; +} +.glyphicon-sort-by-order:before { + content: "\e153"; +} +.glyphicon-sort-by-order-alt:before { + content: "\e154"; +} +.glyphicon-sort-by-attributes:before { + content: "\e155"; +} +.glyphicon-sort-by-attributes-alt:before { + content: "\e156"; +} +.glyphicon-unchecked:before { + content: "\e157"; +} +.glyphicon-expand:before { + content: "\e158"; +} +.glyphicon-collapse-down:before { + content: "\e159"; +} +.glyphicon-collapse-up:before { + content: "\e160"; +} +.glyphicon-log-in:before { + content: "\e161"; +} +.glyphicon-flash:before { + content: "\e162"; +} +.glyphicon-log-out:before { + content: "\e163"; +} +.glyphicon-new-window:before { + content: "\e164"; +} +.glyphicon-record:before { + content: "\e165"; +} +.glyphicon-save:before { + content: "\e166"; +} +.glyphicon-open:before { + content: "\e167"; +} +.glyphicon-saved:before { + content: "\e168"; +} +.glyphicon-import:before { + content: "\e169"; +} +.glyphicon-export:before { + content: "\e170"; +} +.glyphicon-send:before { + content: "\e171"; +} +.glyphicon-floppy-disk:before { + content: "\e172"; +} +.glyphicon-floppy-saved:before { + content: "\e173"; +} +.glyphicon-floppy-remove:before { + content: "\e174"; +} +.glyphicon-floppy-save:before { + content: "\e175"; +} +.glyphicon-floppy-open:before { + content: "\e176"; +} +.glyphicon-credit-card:before { + content: "\e177"; +} +.glyphicon-transfer:before { + content: "\e178"; +} +.glyphicon-cutlery:before { + content: "\e179"; +} +.glyphicon-header:before { + content: "\e180"; +} +.glyphicon-compressed:before { + content: "\e181"; +} +.glyphicon-earphone:before { + content: "\e182"; +} +.glyphicon-phone-alt:before { + content: "\e183"; +} +.glyphicon-tower:before { + content: "\e184"; +} +.glyphicon-stats:before { + content: "\e185"; +} +.glyphicon-sd-video:before { + content: "\e186"; +} +.glyphicon-hd-video:before { + content: "\e187"; +} +.glyphicon-subtitles:before { + content: "\e188"; +} +.glyphicon-sound-stereo:before { + content: "\e189"; +} +.glyphicon-sound-dolby:before { + content: "\e190"; +} +.glyphicon-sound-5-1:before { + content: "\e191"; +} +.glyphicon-sound-6-1:before { + content: "\e192"; +} +.glyphicon-sound-7-1:before { + content: "\e193"; +} +.glyphicon-copyright-mark:before { + content: "\e194"; +} +.glyphicon-registration-mark:before { + content: "\e195"; +} +.glyphicon-cloud-download:before { + content: "\e197"; +} +.glyphicon-cloud-upload:before { + content: "\e198"; +} +.glyphicon-tree-conifer:before { + content: "\e199"; +} +.glyphicon-tree-deciduous:before { + content: "\e200"; +} +.glyphicon-cd:before { + content: "\e201"; +} +.glyphicon-save-file:before { + content: "\e202"; +} +.glyphicon-open-file:before { + content: "\e203"; +} +.glyphicon-level-up:before { + content: "\e204"; +} +.glyphicon-copy:before { + content: "\e205"; +} +.glyphicon-paste:before { + content: "\e206"; +} +.glyphicon-alert:before { + content: "\e209"; +} +.glyphicon-equalizer:before { + content: "\e210"; +} +.glyphicon-king:before { + content: "\e211"; +} +.glyphicon-queen:before { + content: "\e212"; +} +.glyphicon-pawn:before { + content: "\e213"; +} +.glyphicon-bishop:before { + content: "\e214"; +} +.glyphicon-knight:before { + content: "\e215"; +} +.glyphicon-baby-formula:before { + content: "\e216"; +} +.glyphicon-tent:before { + content: "\26fa"; +} +.glyphicon-blackboard:before { + content: "\e218"; +} +.glyphicon-bed:before { + content: "\e219"; +} +.glyphicon-apple:before { + content: "\f8ff"; +} +.glyphicon-erase:before { + content: "\e221"; +} +.glyphicon-hourglass:before { + content: "\231b"; +} +.glyphicon-lamp:before { + content: "\e223"; +} +.glyphicon-duplicate:before { + content: "\e224"; +} +.glyphicon-piggy-bank:before { + content: "\e225"; +} +.glyphicon-scissors:before { + content: "\e226"; +} +.glyphicon-bitcoin:before { + content: "\e227"; +} +.glyphicon-btc:before { + content: "\e227"; +} +.glyphicon-xbt:before { + content: "\e227"; +} +.glyphicon-yen:before { + content: "\00a5"; +} +.glyphicon-jpy:before { + content: "\00a5"; +} +.glyphicon-ruble:before { + content: "\20bd"; +} +.glyphicon-rub:before { + content: "\20bd"; +} +.glyphicon-scale:before { + content: "\e230"; +} +.glyphicon-ice-lolly:before { + content: "\e231"; +} +.glyphicon-ice-lolly-tasted:before { + content: "\e232"; +} +.glyphicon-education:before { + content: "\e233"; +} +.glyphicon-option-horizontal:before { + content: "\e234"; +} +.glyphicon-option-vertical:before { + content: "\e235"; +} +.glyphicon-menu-hamburger:before { + content: "\e236"; +} +.glyphicon-modal-window:before { + content: "\e237"; +} +.glyphicon-oil:before { + content: "\e238"; +} +.glyphicon-grain:before { + content: "\e239"; +} +.glyphicon-sunglasses:before { + content: "\e240"; +} +.glyphicon-text-size:before { + content: "\e241"; +} +.glyphicon-text-color:before { + content: "\e242"; +} +.glyphicon-text-background:before { + content: "\e243"; +} +.glyphicon-object-align-top:before { + content: "\e244"; +} +.glyphicon-object-align-bottom:before { + content: "\e245"; +} +.glyphicon-object-align-horizontal:before { + content: "\e246"; +} +.glyphicon-object-align-left:before { + content: "\e247"; +} +.glyphicon-object-align-vertical:before { + content: "\e248"; +} +.glyphicon-object-align-right:before { + content: "\e249"; +} +.glyphicon-triangle-right:before { + content: "\e250"; +} +.glyphicon-triangle-left:before { + content: "\e251"; +} +.glyphicon-triangle-bottom:before { + content: "\e252"; +} +.glyphicon-triangle-top:before { + content: "\e253"; +} +.glyphicon-console:before { + content: "\e254"; +} +.glyphicon-superscript:before { + content: "\e255"; +} +.glyphicon-subscript:before { + content: "\e256"; +} +.glyphicon-menu-left:before { + content: "\e257"; +} +.glyphicon-menu-right:before { + content: "\e258"; +} +.glyphicon-menu-down:before { + content: "\e259"; +} +.glyphicon-menu-up:before { + content: "\e260"; +} +* { + -webkit-box-sizing: border-box; + -moz-box-sizing: border-box; + box-sizing: border-box; +} +*:before, +*:after { + -webkit-box-sizing: border-box; + -moz-box-sizing: border-box; + box-sizing: border-box; +} +html { + font-size: 10px; + + -webkit-tap-highlight-color: rgba(0, 0, 0, 0); +} +body { + font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; + font-size: 14px; + line-height: 1.42857143; + color: #333; + background-color: #fff; +} +input, +button, +select, +textarea { + font-family: inherit; + font-size: inherit; + line-height: inherit; +} +a { + color: #337ab7; + text-decoration: none; +} +a:hover, +a:focus { + color: #23527c; + text-decoration: underline; +} +a:focus { + outline: 5px auto -webkit-focus-ring-color; + outline-offset: -2px; +} +figure { + margin: 0; +} +img { + vertical-align: middle; +} +.img-responsive, +.thumbnail > img, +.thumbnail a > img, +.carousel-inner > .item > img, +.carousel-inner > .item > a > img { + display: block; + max-width: 100%; + height: auto; +} +.img-rounded { + border-radius: 6px; +} +.img-thumbnail { + display: inline-block; + max-width: 100%; + height: auto; + padding: 4px; + line-height: 1.42857143; + background-color: #fff; + border: 1px solid #ddd; + border-radius: 4px; + -webkit-transition: all .2s ease-in-out; + -o-transition: all .2s ease-in-out; + transition: all .2s ease-in-out; +} +.img-circle { + border-radius: 50%; +} +hr { + margin-top: 20px; + margin-bottom: 20px; + border: 0; + border-top: 1px solid #eee; +} +.sr-only { + position: absolute; + width: 1px; + height: 1px; + padding: 0; + margin: -1px; + overflow: hidden; + clip: rect(0, 0, 0, 0); + border: 0; +} +.sr-only-focusable:active, +.sr-only-focusable:focus { + position: static; + width: auto; + height: auto; + margin: 0; + overflow: visible; + clip: auto; +} +[role="button"] { + cursor: pointer; +} +h1, +h2, +h3, +h4, +h5, +h6, +.h1, +.h2, +.h3, +.h4, +.h5, +.h6 { + font-family: inherit; + font-weight: 500; + line-height: 1.1; + color: inherit; +} +h1 small, +h2 small, +h3 small, +h4 small, +h5 small, +h6 small, +.h1 small, +.h2 small, +.h3 small, +.h4 small, +.h5 small, +.h6 small, +h1 .small, +h2 .small, +h3 .small, +h4 .small, +h5 .small, +h6 .small, +.h1 .small, +.h2 .small, +.h3 .small, +.h4 .small, +.h5 .small, +.h6 .small { + font-weight: normal; + line-height: 1; + color: #777; +} +h1, +.h1, +h2, +.h2, +h3, +.h3 { + margin-top: 20px; + margin-bottom: 10px; +} +h1 small, +.h1 small, +h2 small, +.h2 small, +h3 small, +.h3 small, +h1 .small, +.h1 .small, +h2 .small, +.h2 .small, +h3 .small, +.h3 .small { + font-size: 65%; +} +h4, +.h4, +h5, +.h5, +h6, +.h6 { + margin-top: 10px; + margin-bottom: 10px; +} +h4 small, +.h4 small, +h5 small, +.h5 small, +h6 small, +.h6 small, +h4 .small, +.h4 .small, +h5 .small, +.h5 .small, +h6 .small, +.h6 .small { + font-size: 75%; +} +h1, +.h1 { + font-size: 36px; +} +h2, +.h2 { + font-size: 30px; +} +h3, +.h3 { + font-size: 24px; +} +h4, +.h4 { + font-size: 18px; +} +h5, +.h5 { + font-size: 14px; +} +h6, +.h6 { + font-size: 12px; +} +p { + margin: 0 0 10px; +} +.lead { + margin-bottom: 20px; + font-size: 16px; + font-weight: 300; + line-height: 1.4; +} +@media (min-width: 768px) { + .lead { + font-size: 21px; + } +} +small, +.small { + font-size: 85%; +} +mark, +.mark { + padding: .2em; + background-color: #fcf8e3; +} +.text-left { + text-align: left; +} +.text-right { + text-align: right; +} +.text-center { + text-align: center; +} +.text-justify { + text-align: justify; +} +.text-nowrap { + white-space: nowrap; +} +.text-lowercase { + text-transform: lowercase; +} +.text-uppercase { + text-transform: uppercase; +} +.text-capitalize { + text-transform: capitalize; +} +.text-muted { + color: #777; +} +.text-primary { + color: #337ab7; +} +a.text-primary:hover, +a.text-primary:focus { + color: #286090; +} +.text-success { + color: #3c763d; +} +a.text-success:hover, +a.text-success:focus { + color: #2b542c; +} +.text-info { + color: #31708f; +} +a.text-info:hover, +a.text-info:focus { + color: #245269; +} +.text-warning { + color: #8a6d3b; +} +a.text-warning:hover, +a.text-warning:focus { + color: #66512c; +} +.text-danger { + color: #a94442; +} +a.text-danger:hover, +a.text-danger:focus { + color: #843534; +} +.bg-primary { + color: #fff; + background-color: #337ab7; +} +a.bg-primary:hover, +a.bg-primary:focus { + background-color: #286090; +} +.bg-success { + background-color: #dff0d8; +} +a.bg-success:hover, +a.bg-success:focus { + background-color: #c1e2b3; +} +.bg-info { + background-color: #d9edf7; +} +a.bg-info:hover, +a.bg-info:focus { + background-color: #afd9ee; +} +.bg-warning { + background-color: #fcf8e3; +} +a.bg-warning:hover, +a.bg-warning:focus { + background-color: #f7ecb5; +} +.bg-danger { + background-color: #f2dede; +} +a.bg-danger:hover, +a.bg-danger:focus { + background-color: #e4b9b9; +} +.page-header { + padding-bottom: 9px; + margin: 40px 0 20px; + border-bottom: 1px solid #eee; +} +ul, +ol { + margin-top: 0; + margin-bottom: 10px; +} +ul ul, +ol ul, +ul ol, +ol ol { + margin-bottom: 0; +} +.list-unstyled { + padding-left: 0; + list-style: none; +} +.list-inline { + padding-left: 0; + margin-left: -5px; + list-style: none; +} +.list-inline > li { + display: inline-block; + padding-right: 5px; + padding-left: 5px; +} +dl { + margin-top: 0; + margin-bottom: 20px; +} +dt, +dd { + line-height: 1.42857143; +} +dt { + font-weight: bold; +} +dd { + margin-left: 0; +} +@media (min-width: 768px) { + .dl-horizontal dt { + float: left; + width: 160px; + overflow: hidden; + clear: left; + text-align: right; + text-overflow: ellipsis; + white-space: nowrap; + } + .dl-horizontal dd { + margin-left: 180px; + } +} +abbr[title], +abbr[data-original-title] { + cursor: help; + border-bottom: 1px dotted #777; +} +.initialism { + font-size: 90%; + text-transform: uppercase; +} +blockquote { + padding: 10px 20px; + margin: 0 0 20px; + font-size: 17.5px; + border-left: 5px solid #eee; +} +blockquote p:last-child, +blockquote ul:last-child, +blockquote ol:last-child { + margin-bottom: 0; +} +blockquote footer, +blockquote small, +blockquote .small { + display: block; + font-size: 80%; + line-height: 1.42857143; + color: #777; +} +blockquote footer:before, +blockquote small:before, +blockquote .small:before { + content: '\2014 \00A0'; +} +.blockquote-reverse, +blockquote.pull-right { + padding-right: 15px; + padding-left: 0; + text-align: right; + border-right: 5px solid #eee; + border-left: 0; +} +.blockquote-reverse footer:before, +blockquote.pull-right footer:before, +.blockquote-reverse small:before, +blockquote.pull-right small:before, +.blockquote-reverse .small:before, +blockquote.pull-right .small:before { + content: ''; +} +.blockquote-reverse footer:after, +blockquote.pull-right footer:after, +.blockquote-reverse small:after, +blockquote.pull-right small:after, +.blockquote-reverse .small:after, +blockquote.pull-right .small:after { + content: '\00A0 \2014'; +} +address { + margin-bottom: 20px; + font-style: normal; + line-height: 1.42857143; +} +code, +kbd, +pre, +samp { + font-family: Menlo, Monaco, Consolas, "Courier New", monospace; +} +code { + padding: 2px 4px; + font-size: 90%; + color: #c7254e; + background-color: #f9f2f4; + border-radius: 4px; +} +kbd { + padding: 2px 4px; + font-size: 90%; + color: #fff; + background-color: #333; + border-radius: 3px; + -webkit-box-shadow: inset 0 -1px 0 rgba(0, 0, 0, .25); + box-shadow: inset 0 -1px 0 rgba(0, 0, 0, .25); +} +kbd kbd { + padding: 0; + font-size: 100%; + font-weight: bold; + -webkit-box-shadow: none; + box-shadow: none; +} +pre { + display: block; + padding: 9.5px; + margin: 0 0 10px; + font-size: 13px; + line-height: 1.42857143; + color: #333; + word-break: break-all; + word-wrap: break-word; + background-color: #f5f5f5; + border: 1px solid #ccc; + border-radius: 4px; +} +pre code { + padding: 0; + font-size: inherit; + color: inherit; + white-space: pre-wrap; + background-color: transparent; + border-radius: 0; +} +.pre-scrollable { + max-height: 340px; + overflow-y: scroll; +} +.container { + padding-right: 15px; + padding-left: 15px; + margin-right: auto; + margin-left: auto; +} +@media (min-width: 768px) { + .container { + width: 750px; + } +} +@media (min-width: 992px) { + .container { + width: 970px; + } +} +@media (min-width: 1200px) { + .container { + width: 1170px; + } +} +.container-fluid { + padding-right: 15px; + padding-left: 15px; + margin-right: auto; + margin-left: auto; +} +.row { + margin-right: -15px; + margin-left: -15px; +} +.col-xs-1, .col-sm-1, .col-md-1, .col-lg-1, .col-xs-2, .col-sm-2, .col-md-2, .col-lg-2, .col-xs-3, .col-sm-3, .col-md-3, .col-lg-3, .col-xs-4, .col-sm-4, .col-md-4, .col-lg-4, .col-xs-5, .col-sm-5, .col-md-5, .col-lg-5, .col-xs-6, .col-sm-6, .col-md-6, .col-lg-6, .col-xs-7, .col-sm-7, .col-md-7, .col-lg-7, .col-xs-8, .col-sm-8, .col-md-8, .col-lg-8, .col-xs-9, .col-sm-9, .col-md-9, .col-lg-9, .col-xs-10, .col-sm-10, .col-md-10, .col-lg-10, .col-xs-11, .col-sm-11, .col-md-11, .col-lg-11, .col-xs-12, .col-sm-12, .col-md-12, .col-lg-12 { + position: relative; + min-height: 1px; + padding-right: 15px; + padding-left: 15px; +} +.col-xs-1, .col-xs-2, .col-xs-3, .col-xs-4, .col-xs-5, .col-xs-6, .col-xs-7, .col-xs-8, .col-xs-9, .col-xs-10, .col-xs-11, .col-xs-12 { + float: left; +} +.col-xs-12 { + width: 100%; +} +.col-xs-11 { + width: 91.66666667%; +} +.col-xs-10 { + width: 83.33333333%; +} +.col-xs-9 { + width: 75%; +} +.col-xs-8 { + width: 66.66666667%; +} +.col-xs-7 { + width: 58.33333333%; +} +.col-xs-6 { + width: 50%; +} +.col-xs-5 { + width: 41.66666667%; +} +.col-xs-4 { + width: 33.33333333%; +} +.col-xs-3 { + width: 25%; +} +.col-xs-2 { + width: 16.66666667%; +} +.col-xs-1 { + width: 8.33333333%; +} +.col-xs-pull-12 { + right: 100%; +} +.col-xs-pull-11 { + right: 91.66666667%; +} +.col-xs-pull-10 { + right: 83.33333333%; +} +.col-xs-pull-9 { + right: 75%; +} +.col-xs-pull-8 { + right: 66.66666667%; +} +.col-xs-pull-7 { + right: 58.33333333%; +} +.col-xs-pull-6 { + right: 50%; +} +.col-xs-pull-5 { + right: 41.66666667%; +} +.col-xs-pull-4 { + right: 33.33333333%; +} +.col-xs-pull-3 { + right: 25%; +} +.col-xs-pull-2 { + right: 16.66666667%; +} +.col-xs-pull-1 { + right: 8.33333333%; +} +.col-xs-pull-0 { + right: auto; +} +.col-xs-push-12 { + left: 100%; +} +.col-xs-push-11 { + left: 91.66666667%; +} +.col-xs-push-10 { + left: 83.33333333%; +} +.col-xs-push-9 { + left: 75%; +} +.col-xs-push-8 { + left: 66.66666667%; +} +.col-xs-push-7 { + left: 58.33333333%; +} +.col-xs-push-6 { + left: 50%; +} +.col-xs-push-5 { + left: 41.66666667%; +} +.col-xs-push-4 { + left: 33.33333333%; +} +.col-xs-push-3 { + left: 25%; +} +.col-xs-push-2 { + left: 16.66666667%; +} +.col-xs-push-1 { + left: 8.33333333%; +} +.col-xs-push-0 { + left: auto; +} +.col-xs-offset-12 { + margin-left: 100%; +} +.col-xs-offset-11 { + margin-left: 91.66666667%; +} +.col-xs-offset-10 { + margin-left: 83.33333333%; +} +.col-xs-offset-9 { + margin-left: 75%; +} +.col-xs-offset-8 { + margin-left: 66.66666667%; +} +.col-xs-offset-7 { + margin-left: 58.33333333%; +} +.col-xs-offset-6 { + margin-left: 50%; +} +.col-xs-offset-5 { + margin-left: 41.66666667%; +} +.col-xs-offset-4 { + margin-left: 33.33333333%; +} +.col-xs-offset-3 { + margin-left: 25%; +} +.col-xs-offset-2 { + margin-left: 16.66666667%; +} +.col-xs-offset-1 { + margin-left: 8.33333333%; +} +.col-xs-offset-0 { + margin-left: 0; +} +@media (min-width: 768px) { + .col-sm-1, .col-sm-2, .col-sm-3, .col-sm-4, .col-sm-5, .col-sm-6, .col-sm-7, .col-sm-8, .col-sm-9, .col-sm-10, .col-sm-11, .col-sm-12 { + float: left; + } + .col-sm-12 { + width: 100%; + } + .col-sm-11 { + width: 91.66666667%; + } + .col-sm-10 { + width: 83.33333333%; + } + .col-sm-9 { + width: 75%; + } + .col-sm-8 { + width: 66.66666667%; + } + .col-sm-7 { + width: 58.33333333%; + } + .col-sm-6 { + width: 50%; + } + .col-sm-5 { + width: 41.66666667%; + } + .col-sm-4 { + width: 33.33333333%; + } + .col-sm-3 { + width: 25%; + } + .col-sm-2 { + width: 16.66666667%; + } + .col-sm-1 { + width: 8.33333333%; + } + .col-sm-pull-12 { + right: 100%; + } + .col-sm-pull-11 { + right: 91.66666667%; + } + .col-sm-pull-10 { + right: 83.33333333%; + } + .col-sm-pull-9 { + right: 75%; + } + .col-sm-pull-8 { + right: 66.66666667%; + } + .col-sm-pull-7 { + right: 58.33333333%; + } + .col-sm-pull-6 { + right: 50%; + } + .col-sm-pull-5 { + right: 41.66666667%; + } + .col-sm-pull-4 { + right: 33.33333333%; + } + .col-sm-pull-3 { + right: 25%; + } + .col-sm-pull-2 { + right: 16.66666667%; + } + .col-sm-pull-1 { + right: 8.33333333%; + } + .col-sm-pull-0 { + right: auto; + } + .col-sm-push-12 { + left: 100%; + } + .col-sm-push-11 { + left: 91.66666667%; + } + .col-sm-push-10 { + left: 83.33333333%; + } + .col-sm-push-9 { + left: 75%; + } + .col-sm-push-8 { + left: 66.66666667%; + } + .col-sm-push-7 { + left: 58.33333333%; + } + .col-sm-push-6 { + left: 50%; + } + .col-sm-push-5 { + left: 41.66666667%; + } + .col-sm-push-4 { + left: 33.33333333%; + } + .col-sm-push-3 { + left: 25%; + } + .col-sm-push-2 { + left: 16.66666667%; + } + .col-sm-push-1 { + left: 8.33333333%; + } + .col-sm-push-0 { + left: auto; + } + .col-sm-offset-12 { + margin-left: 100%; + } + .col-sm-offset-11 { + margin-left: 91.66666667%; + } + .col-sm-offset-10 { + margin-left: 83.33333333%; + } + .col-sm-offset-9 { + margin-left: 75%; + } + .col-sm-offset-8 { + margin-left: 66.66666667%; + } + .col-sm-offset-7 { + margin-left: 58.33333333%; + } + .col-sm-offset-6 { + margin-left: 50%; + } + .col-sm-offset-5 { + margin-left: 41.66666667%; + } + .col-sm-offset-4 { + margin-left: 33.33333333%; + } + .col-sm-offset-3 { + margin-left: 25%; + } + .col-sm-offset-2 { + margin-left: 16.66666667%; + } + .col-sm-offset-1 { + margin-left: 8.33333333%; + } + .col-sm-offset-0 { + margin-left: 0; + } +} +@media (min-width: 992px) { + .col-md-1, .col-md-2, .col-md-3, .col-md-4, .col-md-5, .col-md-6, .col-md-7, .col-md-8, .col-md-9, .col-md-10, .col-md-11, .col-md-12 { + float: left; + } + .col-md-12 { + width: 100%; + } + .col-md-11 { + width: 91.66666667%; + } + .col-md-10 { + width: 83.33333333%; + } + .col-md-9 { + width: 75%; + } + .col-md-8 { + width: 66.66666667%; + } + .col-md-7 { + width: 58.33333333%; + } + .col-md-6 { + width: 50%; + } + .col-md-5 { + width: 41.66666667%; + } + .col-md-4 { + width: 33.33333333%; + } + .col-md-3 { + width: 25%; + } + .col-md-2 { + width: 16.66666667%; + } + .col-md-1 { + width: 8.33333333%; + } + .col-md-pull-12 { + right: 100%; + } + .col-md-pull-11 { + right: 91.66666667%; + } + .col-md-pull-10 { + right: 83.33333333%; + } + .col-md-pull-9 { + right: 75%; + } + .col-md-pull-8 { + right: 66.66666667%; + } + .col-md-pull-7 { + right: 58.33333333%; + } + .col-md-pull-6 { + right: 50%; + } + .col-md-pull-5 { + right: 41.66666667%; + } + .col-md-pull-4 { + right: 33.33333333%; + } + .col-md-pull-3 { + right: 25%; + } + .col-md-pull-2 { + right: 16.66666667%; + } + .col-md-pull-1 { + right: 8.33333333%; + } + .col-md-pull-0 { + right: auto; + } + .col-md-push-12 { + left: 100%; + } + .col-md-push-11 { + left: 91.66666667%; + } + .col-md-push-10 { + left: 83.33333333%; + } + .col-md-push-9 { + left: 75%; + } + .col-md-push-8 { + left: 66.66666667%; + } + .col-md-push-7 { + left: 58.33333333%; + } + .col-md-push-6 { + left: 50%; + } + .col-md-push-5 { + left: 41.66666667%; + } + .col-md-push-4 { + left: 33.33333333%; + } + .col-md-push-3 { + left: 25%; + } + .col-md-push-2 { + left: 16.66666667%; + } + .col-md-push-1 { + left: 8.33333333%; + } + .col-md-push-0 { + left: auto; + } + .col-md-offset-12 { + margin-left: 100%; + } + .col-md-offset-11 { + margin-left: 91.66666667%; + } + .col-md-offset-10 { + margin-left: 83.33333333%; + } + .col-md-offset-9 { + margin-left: 75%; + } + .col-md-offset-8 { + margin-left: 66.66666667%; + } + .col-md-offset-7 { + margin-left: 58.33333333%; + } + .col-md-offset-6 { + margin-left: 50%; + } + .col-md-offset-5 { + margin-left: 41.66666667%; + } + .col-md-offset-4 { + margin-left: 33.33333333%; + } + .col-md-offset-3 { + margin-left: 25%; + } + .col-md-offset-2 { + margin-left: 16.66666667%; + } + .col-md-offset-1 { + margin-left: 8.33333333%; + } + .col-md-offset-0 { + margin-left: 0; + } +} +@media (min-width: 1200px) { + .col-lg-1, .col-lg-2, .col-lg-3, .col-lg-4, .col-lg-5, .col-lg-6, .col-lg-7, .col-lg-8, .col-lg-9, .col-lg-10, .col-lg-11, .col-lg-12 { + float: left; + } + .col-lg-12 { + width: 100%; + } + .col-lg-11 { + width: 91.66666667%; + } + .col-lg-10 { + width: 83.33333333%; + } + .col-lg-9 { + width: 75%; + } + .col-lg-8 { + width: 66.66666667%; + } + .col-lg-7 { + width: 58.33333333%; + } + .col-lg-6 { + width: 50%; + } + .col-lg-5 { + width: 41.66666667%; + } + .col-lg-4 { + width: 33.33333333%; + } + .col-lg-3 { + width: 25%; + } + .col-lg-2 { + width: 16.66666667%; + } + .col-lg-1 { + width: 8.33333333%; + } + .col-lg-pull-12 { + right: 100%; + } + .col-lg-pull-11 { + right: 91.66666667%; + } + .col-lg-pull-10 { + right: 83.33333333%; + } + .col-lg-pull-9 { + right: 75%; + } + .col-lg-pull-8 { + right: 66.66666667%; + } + .col-lg-pull-7 { + right: 58.33333333%; + } + .col-lg-pull-6 { + right: 50%; + } + .col-lg-pull-5 { + right: 41.66666667%; + } + .col-lg-pull-4 { + right: 33.33333333%; + } + .col-lg-pull-3 { + right: 25%; + } + .col-lg-pull-2 { + right: 16.66666667%; + } + .col-lg-pull-1 { + right: 8.33333333%; + } + .col-lg-pull-0 { + right: auto; + } + .col-lg-push-12 { + left: 100%; + } + .col-lg-push-11 { + left: 91.66666667%; + } + .col-lg-push-10 { + left: 83.33333333%; + } + .col-lg-push-9 { + left: 75%; + } + .col-lg-push-8 { + left: 66.66666667%; + } + .col-lg-push-7 { + left: 58.33333333%; + } + .col-lg-push-6 { + left: 50%; + } + .col-lg-push-5 { + left: 41.66666667%; + } + .col-lg-push-4 { + left: 33.33333333%; + } + .col-lg-push-3 { + left: 25%; + } + .col-lg-push-2 { + left: 16.66666667%; + } + .col-lg-push-1 { + left: 8.33333333%; + } + .col-lg-push-0 { + left: auto; + } + .col-lg-offset-12 { + margin-left: 100%; + } + .col-lg-offset-11 { + margin-left: 91.66666667%; + } + .col-lg-offset-10 { + margin-left: 83.33333333%; + } + .col-lg-offset-9 { + margin-left: 75%; + } + .col-lg-offset-8 { + margin-left: 66.66666667%; + } + .col-lg-offset-7 { + margin-left: 58.33333333%; + } + .col-lg-offset-6 { + margin-left: 50%; + } + .col-lg-offset-5 { + margin-left: 41.66666667%; + } + .col-lg-offset-4 { + margin-left: 33.33333333%; + } + .col-lg-offset-3 { + margin-left: 25%; + } + .col-lg-offset-2 { + margin-left: 16.66666667%; + } + .col-lg-offset-1 { + margin-left: 8.33333333%; + } + .col-lg-offset-0 { + margin-left: 0; + } +} +table { + background-color: transparent; +} +caption { + padding-top: 8px; + padding-bottom: 8px; + color: #777; + text-align: left; +} +th { + text-align: left; +} +.table { + width: 100%; + max-width: 100%; + margin-bottom: 20px; +} +.table > thead > tr > th, +.table > tbody > tr > th, +.table > tfoot > tr > th, +.table > thead > tr > td, +.table > tbody > tr > td, +.table > tfoot > tr > td { + padding: 8px; + line-height: 1.42857143; + vertical-align: top; + border-top: 1px solid #ddd; +} +.table > thead > tr > th { + vertical-align: bottom; + border-bottom: 2px solid #ddd; +} +.table > caption + thead > tr:first-child > th, +.table > colgroup + thead > tr:first-child > th, +.table > thead:first-child > tr:first-child > th, +.table > caption + thead > tr:first-child > td, +.table > colgroup + thead > tr:first-child > td, +.table > thead:first-child > tr:first-child > td { + border-top: 0; +} +.table > tbody + tbody { + border-top: 2px solid #ddd; +} +.table .table { + background-color: #fff; +} +.table-condensed > thead > tr > th, +.table-condensed > tbody > tr > th, +.table-condensed > tfoot > tr > th, +.table-condensed > thead > tr > td, +.table-condensed > tbody > tr > td, +.table-condensed > tfoot > tr > td { + padding: 5px; +} +.table-bordered { + border: 1px solid #ddd; +} +.table-bordered > thead > tr > th, +.table-bordered > tbody > tr > th, +.table-bordered > tfoot > tr > th, +.table-bordered > thead > tr > td, +.table-bordered > tbody > tr > td, +.table-bordered > tfoot > tr > td { + border: 1px solid #ddd; +} +.table-bordered > thead > tr > th, +.table-bordered > thead > tr > td { + border-bottom-width: 2px; +} +.table-striped > tbody > tr:nth-of-type(odd) { + background-color: #f9f9f9; +} +.table-hover > tbody > tr:hover { + background-color: #f5f5f5; +} +table col[class*="col-"] { + position: static; + display: table-column; + float: none; +} +table td[class*="col-"], +table th[class*="col-"] { + position: static; + display: table-cell; + float: none; +} +.table > thead > tr > td.active, +.table > tbody > tr > td.active, +.table > tfoot > tr > td.active, +.table > thead > tr > th.active, +.table > tbody > tr > th.active, +.table > tfoot > tr > th.active, +.table > thead > tr.active > td, +.table > tbody > tr.active > td, +.table > tfoot > tr.active > td, +.table > thead > tr.active > th, +.table > tbody > tr.active > th, +.table > tfoot > tr.active > th { + background-color: #f5f5f5; +} +.table-hover > tbody > tr > td.active:hover, +.table-hover > tbody > tr > th.active:hover, +.table-hover > tbody > tr.active:hover > td, +.table-hover > tbody > tr:hover > .active, +.table-hover > tbody > tr.active:hover > th { + background-color: #e8e8e8; +} +.table > thead > tr > td.success, +.table > tbody > tr > td.success, +.table > tfoot > tr > td.success, +.table > thead > tr > th.success, +.table > tbody > tr > th.success, +.table > tfoot > tr > th.success, +.table > thead > tr.success > td, +.table > tbody > tr.success > td, +.table > tfoot > tr.success > td, +.table > thead > tr.success > th, +.table > tbody > tr.success > th, +.table > tfoot > tr.success > th { + background-color: #dff0d8; +} +.table-hover > tbody > tr > td.success:hover, +.table-hover > tbody > tr > th.success:hover, +.table-hover > tbody > tr.success:hover > td, +.table-hover > tbody > tr:hover > .success, +.table-hover > tbody > tr.success:hover > th { + background-color: #d0e9c6; +} +.table > thead > tr > td.info, +.table > tbody > tr > td.info, +.table > tfoot > tr > td.info, +.table > thead > tr > th.info, +.table > tbody > tr > th.info, +.table > tfoot > tr > th.info, +.table > thead > tr.info > td, +.table > tbody > tr.info > td, +.table > tfoot > tr.info > td, +.table > thead > tr.info > th, +.table > tbody > tr.info > th, +.table > tfoot > tr.info > th { + background-color: #d9edf7; +} +.table-hover > tbody > tr > td.info:hover, +.table-hover > tbody > tr > th.info:hover, +.table-hover > tbody > tr.info:hover > td, +.table-hover > tbody > tr:hover > .info, +.table-hover > tbody > tr.info:hover > th { + background-color: #c4e3f3; +} +.table > thead > tr > td.warning, +.table > tbody > tr > td.warning, +.table > tfoot > tr > td.warning, +.table > thead > tr > th.warning, +.table > tbody > tr > th.warning, +.table > tfoot > tr > th.warning, +.table > thead > tr.warning > td, +.table > tbody > tr.warning > td, +.table > tfoot > tr.warning > td, +.table > thead > tr.warning > th, +.table > tbody > tr.warning > th, +.table > tfoot > tr.warning > th { + background-color: #fcf8e3; +} +.table-hover > tbody > tr > td.warning:hover, +.table-hover > tbody > tr > th.warning:hover, +.table-hover > tbody > tr.warning:hover > td, +.table-hover > tbody > tr:hover > .warning, +.table-hover > tbody > tr.warning:hover > th { + background-color: #faf2cc; +} +.table > thead > tr > td.danger, +.table > tbody > tr > td.danger, +.table > tfoot > tr > td.danger, +.table > thead > tr > th.danger, +.table > tbody > tr > th.danger, +.table > tfoot > tr > th.danger, +.table > thead > tr.danger > td, +.table > tbody > tr.danger > td, +.table > tfoot > tr.danger > td, +.table > thead > tr.danger > th, +.table > tbody > tr.danger > th, +.table > tfoot > tr.danger > th { + background-color: #f2dede; +} +.table-hover > tbody > tr > td.danger:hover, +.table-hover > tbody > tr > th.danger:hover, +.table-hover > tbody > tr.danger:hover > td, +.table-hover > tbody > tr:hover > .danger, +.table-hover > tbody > tr.danger:hover > th { + background-color: #ebcccc; +} +.table-responsive { + min-height: .01%; + overflow-x: auto; +} +@media screen and (max-width: 767px) { + .table-responsive { + width: 100%; + margin-bottom: 15px; + overflow-y: hidden; + -ms-overflow-style: -ms-autohiding-scrollbar; + border: 1px solid #ddd; + } + .table-responsive > .table { + margin-bottom: 0; + } + .table-responsive > .table > thead > tr > th, + .table-responsive > .table > tbody > tr > th, + .table-responsive > .table > tfoot > tr > th, + .table-responsive > .table > thead > tr > td, + .table-responsive > .table > tbody > tr > td, + .table-responsive > .table > tfoot > tr > td { + white-space: nowrap; + } + .table-responsive > .table-bordered { + border: 0; + } + .table-responsive > .table-bordered > thead > tr > th:first-child, + .table-responsive > .table-bordered > tbody > tr > th:first-child, + .table-responsive > .table-bordered > tfoot > tr > th:first-child, + .table-responsive > .table-bordered > thead > tr > td:first-child, + .table-responsive > .table-bordered > tbody > tr > td:first-child, + .table-responsive > .table-bordered > tfoot > tr > td:first-child { + border-left: 0; + } + .table-responsive > .table-bordered > thead > tr > th:last-child, + .table-responsive > .table-bordered > tbody > tr > th:last-child, + .table-responsive > .table-bordered > tfoot > tr > th:last-child, + .table-responsive > .table-bordered > thead > tr > td:last-child, + .table-responsive > .table-bordered > tbody > tr > td:last-child, + .table-responsive > .table-bordered > tfoot > tr > td:last-child { + border-right: 0; + } + .table-responsive > .table-bordered > tbody > tr:last-child > th, + .table-responsive > .table-bordered > tfoot > tr:last-child > th, + .table-responsive > .table-bordered > tbody > tr:last-child > td, + .table-responsive > .table-bordered > tfoot > tr:last-child > td { + border-bottom: 0; + } +} +fieldset { + min-width: 0; + padding: 0; + margin: 0; + border: 0; +} +legend { + display: block; + width: 100%; + padding: 0; + margin-bottom: 20px; + font-size: 21px; + line-height: inherit; + color: #333; + border: 0; + border-bottom: 1px solid #e5e5e5; +} +label { + display: inline-block; + max-width: 100%; + margin-bottom: 5px; + font-weight: bold; +} +input[type="search"] { + -webkit-box-sizing: border-box; + -moz-box-sizing: border-box; + box-sizing: border-box; +} +input[type="radio"], +input[type="checkbox"] { + margin: 4px 0 0; + margin-top: 1px \9; + line-height: normal; +} +input[type="file"] { + display: block; +} +input[type="range"] { + display: block; + width: 100%; +} +select[multiple], +select[size] { + height: auto; +} +input[type="file"]:focus, +input[type="radio"]:focus, +input[type="checkbox"]:focus { + outline: 5px auto -webkit-focus-ring-color; + outline-offset: -2px; +} +output { + display: block; + padding-top: 7px; + font-size: 14px; + line-height: 1.42857143; + color: #555; +} +.form-control { + display: block; + width: 100%; + height: 34px; + padding: 6px 12px; + font-size: 14px; + line-height: 1.42857143; + color: #555; + background-color: #fff; + background-image: none; + border: 1px solid #ccc; + border-radius: 4px; + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075); + box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075); + -webkit-transition: border-color ease-in-out .15s, -webkit-box-shadow ease-in-out .15s; + -o-transition: border-color ease-in-out .15s, box-shadow ease-in-out .15s; + transition: border-color ease-in-out .15s, box-shadow ease-in-out .15s; +} +.form-control:focus { + border-color: #66afe9; + outline: 0; + -webkit-box-shadow: inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, .6); + box-shadow: inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, .6); +} +.form-control::-moz-placeholder { + color: #999; + opacity: 1; +} +.form-control:-ms-input-placeholder { + color: #999; +} +.form-control::-webkit-input-placeholder { + color: #999; +} +.form-control::-ms-expand { + background-color: transparent; + border: 0; +} +.form-control[disabled], +.form-control[readonly], +fieldset[disabled] .form-control { + background-color: #eee; + opacity: 1; +} +.form-control[disabled], +fieldset[disabled] .form-control { + cursor: not-allowed; +} +textarea.form-control { + height: auto; +} +input[type="search"] { + -webkit-appearance: none; +} +@media screen and (-webkit-min-device-pixel-ratio: 0) { + input[type="date"].form-control, + input[type="time"].form-control, + input[type="datetime-local"].form-control, + input[type="month"].form-control { + line-height: 34px; + } + input[type="date"].input-sm, + input[type="time"].input-sm, + input[type="datetime-local"].input-sm, + input[type="month"].input-sm, + .input-group-sm input[type="date"], + .input-group-sm input[type="time"], + .input-group-sm input[type="datetime-local"], + .input-group-sm input[type="month"] { + line-height: 30px; + } + input[type="date"].input-lg, + input[type="time"].input-lg, + input[type="datetime-local"].input-lg, + input[type="month"].input-lg, + .input-group-lg input[type="date"], + .input-group-lg input[type="time"], + .input-group-lg input[type="datetime-local"], + .input-group-lg input[type="month"] { + line-height: 46px; + } +} +.form-group { + margin-bottom: 15px; +} +.radio, +.checkbox { + position: relative; + display: block; + margin-top: 10px; + margin-bottom: 10px; +} +.radio label, +.checkbox label { + min-height: 20px; + padding-left: 20px; + margin-bottom: 0; + font-weight: normal; + cursor: pointer; +} +.radio input[type="radio"], +.radio-inline input[type="radio"], +.checkbox input[type="checkbox"], +.checkbox-inline input[type="checkbox"] { + position: absolute; + margin-top: 4px \9; + margin-left: -20px; +} +.radio + .radio, +.checkbox + .checkbox { + margin-top: -5px; +} +.radio-inline, +.checkbox-inline { + position: relative; + display: inline-block; + padding-left: 20px; + margin-bottom: 0; + font-weight: normal; + vertical-align: middle; + cursor: pointer; +} +.radio-inline + .radio-inline, +.checkbox-inline + .checkbox-inline { + margin-top: 0; + margin-left: 10px; +} +input[type="radio"][disabled], +input[type="checkbox"][disabled], +input[type="radio"].disabled, +input[type="checkbox"].disabled, +fieldset[disabled] input[type="radio"], +fieldset[disabled] input[type="checkbox"] { + cursor: not-allowed; +} +.radio-inline.disabled, +.checkbox-inline.disabled, +fieldset[disabled] .radio-inline, +fieldset[disabled] .checkbox-inline { + cursor: not-allowed; +} +.radio.disabled label, +.checkbox.disabled label, +fieldset[disabled] .radio label, +fieldset[disabled] .checkbox label { + cursor: not-allowed; +} +.form-control-static { + min-height: 34px; + padding-top: 7px; + padding-bottom: 7px; + margin-bottom: 0; +} +.form-control-static.input-lg, +.form-control-static.input-sm { + padding-right: 0; + padding-left: 0; +} +.input-sm { + height: 30px; + padding: 5px 10px; + font-size: 12px; + line-height: 1.5; + border-radius: 3px; +} +select.input-sm { + height: 30px; + line-height: 30px; +} +textarea.input-sm, +select[multiple].input-sm { + height: auto; +} +.form-group-sm .form-control { + height: 30px; + padding: 5px 10px; + font-size: 12px; + line-height: 1.5; + border-radius: 3px; +} +.form-group-sm select.form-control { + height: 30px; + line-height: 30px; +} +.form-group-sm textarea.form-control, +.form-group-sm select[multiple].form-control { + height: auto; +} +.form-group-sm .form-control-static { + height: 30px; + min-height: 32px; + padding: 6px 10px; + font-size: 12px; + line-height: 1.5; +} +.input-lg { + height: 46px; + padding: 10px 16px; + font-size: 18px; + line-height: 1.3333333; + border-radius: 6px; +} +select.input-lg { + height: 46px; + line-height: 46px; +} +textarea.input-lg, +select[multiple].input-lg { + height: auto; +} +.form-group-lg .form-control { + height: 46px; + padding: 10px 16px; + font-size: 18px; + line-height: 1.3333333; + border-radius: 6px; +} +.form-group-lg select.form-control { + height: 46px; + line-height: 46px; +} +.form-group-lg textarea.form-control, +.form-group-lg select[multiple].form-control { + height: auto; +} +.form-group-lg .form-control-static { + height: 46px; + min-height: 38px; + padding: 11px 16px; + font-size: 18px; + line-height: 1.3333333; +} +.has-feedback { + position: relative; +} +.has-feedback .form-control { + padding-right: 42.5px; +} +.form-control-feedback { + position: absolute; + top: 0; + right: 0; + z-index: 2; + display: block; + width: 34px; + height: 34px; + line-height: 34px; + text-align: center; + pointer-events: none; +} +.input-lg + .form-control-feedback, +.input-group-lg + .form-control-feedback, +.form-group-lg .form-control + .form-control-feedback { + width: 46px; + height: 46px; + line-height: 46px; +} +.input-sm + .form-control-feedback, +.input-group-sm + .form-control-feedback, +.form-group-sm .form-control + .form-control-feedback { + width: 30px; + height: 30px; + line-height: 30px; +} +.has-success .help-block, +.has-success .control-label, +.has-success .radio, +.has-success .checkbox, +.has-success .radio-inline, +.has-success .checkbox-inline, +.has-success.radio label, +.has-success.checkbox label, +.has-success.radio-inline label, +.has-success.checkbox-inline label { + color: #3c763d; +} +.has-success .form-control { + border-color: #3c763d; + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075); + box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075); +} +.has-success .form-control:focus { + border-color: #2b542c; + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 6px #67b168; + box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 6px #67b168; +} +.has-success .input-group-addon { + color: #3c763d; + background-color: #dff0d8; + border-color: #3c763d; +} +.has-success .form-control-feedback { + color: #3c763d; +} +.has-warning .help-block, +.has-warning .control-label, +.has-warning .radio, +.has-warning .checkbox, +.has-warning .radio-inline, +.has-warning .checkbox-inline, +.has-warning.radio label, +.has-warning.checkbox label, +.has-warning.radio-inline label, +.has-warning.checkbox-inline label { + color: #8a6d3b; +} +.has-warning .form-control { + border-color: #8a6d3b; + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075); + box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075); +} +.has-warning .form-control:focus { + border-color: #66512c; + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 6px #c0a16b; + box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 6px #c0a16b; +} +.has-warning .input-group-addon { + color: #8a6d3b; + background-color: #fcf8e3; + border-color: #8a6d3b; +} +.has-warning .form-control-feedback { + color: #8a6d3b; +} +.has-error .help-block, +.has-error .control-label, +.has-error .radio, +.has-error .checkbox, +.has-error .radio-inline, +.has-error .checkbox-inline, +.has-error.radio label, +.has-error.checkbox label, +.has-error.radio-inline label, +.has-error.checkbox-inline label { + color: #a94442; +} +.has-error .form-control { + border-color: #a94442; + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075); + box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075); +} +.has-error .form-control:focus { + border-color: #843534; + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 6px #ce8483; + box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 6px #ce8483; +} +.has-error .input-group-addon { + color: #a94442; + background-color: #f2dede; + border-color: #a94442; +} +.has-error .form-control-feedback { + color: #a94442; +} +.has-feedback label ~ .form-control-feedback { + top: 25px; +} +.has-feedback label.sr-only ~ .form-control-feedback { + top: 0; +} +.help-block { + display: block; + margin-top: 5px; + margin-bottom: 10px; + color: #737373; +} +@media (min-width: 768px) { + .form-inline .form-group { + display: inline-block; + margin-bottom: 0; + vertical-align: middle; + } + .form-inline .form-control { + display: inline-block; + width: auto; + vertical-align: middle; + } + .form-inline .form-control-static { + display: inline-block; + } + .form-inline .input-group { + display: inline-table; + vertical-align: middle; + } + .form-inline .input-group .input-group-addon, + .form-inline .input-group .input-group-btn, + .form-inline .input-group .form-control { + width: auto; + } + .form-inline .input-group > .form-control { + width: 100%; + } + .form-inline .control-label { + margin-bottom: 0; + vertical-align: middle; + } + .form-inline .radio, + .form-inline .checkbox { + display: inline-block; + margin-top: 0; + margin-bottom: 0; + vertical-align: middle; + } + .form-inline .radio label, + .form-inline .checkbox label { + padding-left: 0; + } + .form-inline .radio input[type="radio"], + .form-inline .checkbox input[type="checkbox"] { + position: relative; + margin-left: 0; + } + .form-inline .has-feedback .form-control-feedback { + top: 0; + } +} +.form-horizontal .radio, +.form-horizontal .checkbox, +.form-horizontal .radio-inline, +.form-horizontal .checkbox-inline { + padding-top: 7px; + margin-top: 0; + margin-bottom: 0; +} +.form-horizontal .radio, +.form-horizontal .checkbox { + min-height: 27px; +} +.form-horizontal .form-group { + margin-right: -15px; + margin-left: -15px; +} +@media (min-width: 768px) { + .form-horizontal .control-label { + padding-top: 7px; + margin-bottom: 0; + text-align: right; + } +} +.form-horizontal .has-feedback .form-control-feedback { + right: 15px; +} +@media (min-width: 768px) { + .form-horizontal .form-group-lg .control-label { + padding-top: 11px; + font-size: 18px; + } +} +@media (min-width: 768px) { + .form-horizontal .form-group-sm .control-label { + padding-top: 6px; + font-size: 12px; + } +} +.btn { + display: inline-block; + padding: 6px 12px; + margin-bottom: 0; + font-size: 14px; + font-weight: normal; + line-height: 1.42857143; + text-align: center; + white-space: nowrap; + vertical-align: middle; + -ms-touch-action: manipulation; + touch-action: manipulation; + cursor: pointer; + -webkit-user-select: none; + -moz-user-select: none; + -ms-user-select: none; + user-select: none; + background-image: none; + border: 1px solid transparent; + border-radius: 4px; +} +.btn:focus, +.btn:active:focus, +.btn.active:focus, +.btn.focus, +.btn:active.focus, +.btn.active.focus { + outline: 5px auto -webkit-focus-ring-color; + outline-offset: -2px; +} +.btn:hover, +.btn:focus, +.btn.focus { + color: #333; + text-decoration: none; +} +.btn:active, +.btn.active { + background-image: none; + outline: 0; + -webkit-box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125); + box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125); +} +.btn.disabled, +.btn[disabled], +fieldset[disabled] .btn { + cursor: not-allowed; + filter: alpha(opacity=65); + -webkit-box-shadow: none; + box-shadow: none; + opacity: .65; +} +a.btn.disabled, +fieldset[disabled] a.btn { + pointer-events: none; +} +.btn-default { + color: #333; + background-color: #fff; + border-color: #ccc; +} +.btn-default:focus, +.btn-default.focus { + color: #333; + background-color: #e6e6e6; + border-color: #8c8c8c; +} +.btn-default:hover { + color: #333; + background-color: #e6e6e6; + border-color: #adadad; +} +.btn-default:active, +.btn-default.active, +.open > .dropdown-toggle.btn-default { + color: #333; + background-color: #e6e6e6; + border-color: #adadad; +} +.btn-default:active:hover, +.btn-default.active:hover, +.open > .dropdown-toggle.btn-default:hover, +.btn-default:active:focus, +.btn-default.active:focus, +.open > .dropdown-toggle.btn-default:focus, +.btn-default:active.focus, +.btn-default.active.focus, +.open > .dropdown-toggle.btn-default.focus { + color: #333; + background-color: #d4d4d4; + border-color: #8c8c8c; +} +.btn-default:active, +.btn-default.active, +.open > .dropdown-toggle.btn-default { + background-image: none; +} +.btn-default.disabled:hover, +.btn-default[disabled]:hover, +fieldset[disabled] .btn-default:hover, +.btn-default.disabled:focus, +.btn-default[disabled]:focus, +fieldset[disabled] .btn-default:focus, +.btn-default.disabled.focus, +.btn-default[disabled].focus, +fieldset[disabled] .btn-default.focus { + background-color: #fff; + border-color: #ccc; +} +.btn-default .badge { + color: #fff; + background-color: #333; +} +.btn-primary { + color: #fff; + background-color: #337ab7; + border-color: #2e6da4; +} +.btn-primary:focus, +.btn-primary.focus { + color: #fff; + background-color: #286090; + border-color: #122b40; +} +.btn-primary:hover { + color: #fff; + background-color: #286090; + border-color: #204d74; +} +.btn-primary:active, +.btn-primary.active, +.open > .dropdown-toggle.btn-primary { + color: #fff; + background-color: #286090; + border-color: #204d74; +} +.btn-primary:active:hover, +.btn-primary.active:hover, +.open > .dropdown-toggle.btn-primary:hover, +.btn-primary:active:focus, +.btn-primary.active:focus, +.open > .dropdown-toggle.btn-primary:focus, +.btn-primary:active.focus, +.btn-primary.active.focus, +.open > .dropdown-toggle.btn-primary.focus { + color: #fff; + background-color: #204d74; + border-color: #122b40; +} +.btn-primary:active, +.btn-primary.active, +.open > .dropdown-toggle.btn-primary { + background-image: none; +} +.btn-primary.disabled:hover, +.btn-primary[disabled]:hover, +fieldset[disabled] .btn-primary:hover, +.btn-primary.disabled:focus, +.btn-primary[disabled]:focus, +fieldset[disabled] .btn-primary:focus, +.btn-primary.disabled.focus, +.btn-primary[disabled].focus, +fieldset[disabled] .btn-primary.focus { + background-color: #337ab7; + border-color: #2e6da4; +} +.btn-primary .badge { + color: #337ab7; + background-color: #fff; +} +.btn-success { + color: #fff; + background-color: #5cb85c; + border-color: #4cae4c; +} +.btn-success:focus, +.btn-success.focus { + color: #fff; + background-color: #449d44; + border-color: #255625; +} +.btn-success:hover { + color: #fff; + background-color: #449d44; + border-color: #398439; +} +.btn-success:active, +.btn-success.active, +.open > .dropdown-toggle.btn-success { + color: #fff; + background-color: #449d44; + border-color: #398439; +} +.btn-success:active:hover, +.btn-success.active:hover, +.open > .dropdown-toggle.btn-success:hover, +.btn-success:active:focus, +.btn-success.active:focus, +.open > .dropdown-toggle.btn-success:focus, +.btn-success:active.focus, +.btn-success.active.focus, +.open > .dropdown-toggle.btn-success.focus { + color: #fff; + background-color: #398439; + border-color: #255625; +} +.btn-success:active, +.btn-success.active, +.open > .dropdown-toggle.btn-success { + background-image: none; +} +.btn-success.disabled:hover, +.btn-success[disabled]:hover, +fieldset[disabled] .btn-success:hover, +.btn-success.disabled:focus, +.btn-success[disabled]:focus, +fieldset[disabled] .btn-success:focus, +.btn-success.disabled.focus, +.btn-success[disabled].focus, +fieldset[disabled] .btn-success.focus { + background-color: #5cb85c; + border-color: #4cae4c; +} +.btn-success .badge { + color: #5cb85c; + background-color: #fff; +} +.btn-info { + color: #fff; + background-color: #5bc0de; + border-color: #46b8da; +} +.btn-info:focus, +.btn-info.focus { + color: #fff; + background-color: #31b0d5; + border-color: #1b6d85; +} +.btn-info:hover { + color: #fff; + background-color: #31b0d5; + border-color: #269abc; +} +.btn-info:active, +.btn-info.active, +.open > .dropdown-toggle.btn-info { + color: #fff; + background-color: #31b0d5; + border-color: #269abc; +} +.btn-info:active:hover, +.btn-info.active:hover, +.open > .dropdown-toggle.btn-info:hover, +.btn-info:active:focus, +.btn-info.active:focus, +.open > .dropdown-toggle.btn-info:focus, +.btn-info:active.focus, +.btn-info.active.focus, +.open > .dropdown-toggle.btn-info.focus { + color: #fff; + background-color: #269abc; + border-color: #1b6d85; +} +.btn-info:active, +.btn-info.active, +.open > .dropdown-toggle.btn-info { + background-image: none; +} +.btn-info.disabled:hover, +.btn-info[disabled]:hover, +fieldset[disabled] .btn-info:hover, +.btn-info.disabled:focus, +.btn-info[disabled]:focus, +fieldset[disabled] .btn-info:focus, +.btn-info.disabled.focus, +.btn-info[disabled].focus, +fieldset[disabled] .btn-info.focus { + background-color: #5bc0de; + border-color: #46b8da; +} +.btn-info .badge { + color: #5bc0de; + background-color: #fff; +} +.btn-warning { + color: #fff; + background-color: #f0ad4e; + border-color: #eea236; +} +.btn-warning:focus, +.btn-warning.focus { + color: #fff; + background-color: #ec971f; + border-color: #985f0d; +} +.btn-warning:hover { + color: #fff; + background-color: #ec971f; + border-color: #d58512; +} +.btn-warning:active, +.btn-warning.active, +.open > .dropdown-toggle.btn-warning { + color: #fff; + background-color: #ec971f; + border-color: #d58512; +} +.btn-warning:active:hover, +.btn-warning.active:hover, +.open > .dropdown-toggle.btn-warning:hover, +.btn-warning:active:focus, +.btn-warning.active:focus, +.open > .dropdown-toggle.btn-warning:focus, +.btn-warning:active.focus, +.btn-warning.active.focus, +.open > .dropdown-toggle.btn-warning.focus { + color: #fff; + background-color: #d58512; + border-color: #985f0d; +} +.btn-warning:active, +.btn-warning.active, +.open > .dropdown-toggle.btn-warning { + background-image: none; +} +.btn-warning.disabled:hover, +.btn-warning[disabled]:hover, +fieldset[disabled] .btn-warning:hover, +.btn-warning.disabled:focus, +.btn-warning[disabled]:focus, +fieldset[disabled] .btn-warning:focus, +.btn-warning.disabled.focus, +.btn-warning[disabled].focus, +fieldset[disabled] .btn-warning.focus { + background-color: #f0ad4e; + border-color: #eea236; +} +.btn-warning .badge { + color: #f0ad4e; + background-color: #fff; +} +.btn-danger { + color: #fff; + background-color: #d9534f; + border-color: #d43f3a; +} +.btn-danger:focus, +.btn-danger.focus { + color: #fff; + background-color: #c9302c; + border-color: #761c19; +} +.btn-danger:hover { + color: #fff; + background-color: #c9302c; + border-color: #ac2925; +} +.btn-danger:active, +.btn-danger.active, +.open > .dropdown-toggle.btn-danger { + color: #fff; + background-color: #c9302c; + border-color: #ac2925; +} +.btn-danger:active:hover, +.btn-danger.active:hover, +.open > .dropdown-toggle.btn-danger:hover, +.btn-danger:active:focus, +.btn-danger.active:focus, +.open > .dropdown-toggle.btn-danger:focus, +.btn-danger:active.focus, +.btn-danger.active.focus, +.open > .dropdown-toggle.btn-danger.focus { + color: #fff; + background-color: #ac2925; + border-color: #761c19; +} +.btn-danger:active, +.btn-danger.active, +.open > .dropdown-toggle.btn-danger { + background-image: none; +} +.btn-danger.disabled:hover, +.btn-danger[disabled]:hover, +fieldset[disabled] .btn-danger:hover, +.btn-danger.disabled:focus, +.btn-danger[disabled]:focus, +fieldset[disabled] .btn-danger:focus, +.btn-danger.disabled.focus, +.btn-danger[disabled].focus, +fieldset[disabled] .btn-danger.focus { + background-color: #d9534f; + border-color: #d43f3a; +} +.btn-danger .badge { + color: #d9534f; + background-color: #fff; +} +.btn-link { + font-weight: normal; + color: #337ab7; + border-radius: 0; +} +.btn-link, +.btn-link:active, +.btn-link.active, +.btn-link[disabled], +fieldset[disabled] .btn-link { + background-color: transparent; + -webkit-box-shadow: none; + box-shadow: none; +} +.btn-link, +.btn-link:hover, +.btn-link:focus, +.btn-link:active { + border-color: transparent; +} +.btn-link:hover, +.btn-link:focus { + color: #23527c; + text-decoration: underline; + background-color: transparent; +} +.btn-link[disabled]:hover, +fieldset[disabled] .btn-link:hover, +.btn-link[disabled]:focus, +fieldset[disabled] .btn-link:focus { + color: #777; + text-decoration: none; +} +.btn-lg, +.btn-group-lg > .btn { + padding: 10px 16px; + font-size: 18px; + line-height: 1.3333333; + border-radius: 6px; +} +.btn-sm, +.btn-group-sm > .btn { + padding: 5px 10px; + font-size: 12px; + line-height: 1.5; + border-radius: 3px; +} +.btn-xs, +.btn-group-xs > .btn { + padding: 1px 5px; + font-size: 12px; + line-height: 1.5; + border-radius: 3px; +} +.btn-block { + display: block; + width: 100%; +} +.btn-block + .btn-block { + margin-top: 5px; +} +input[type="submit"].btn-block, +input[type="reset"].btn-block, +input[type="button"].btn-block { + width: 100%; +} +.fade { + opacity: 0; + -webkit-transition: opacity .15s linear; + -o-transition: opacity .15s linear; + transition: opacity .15s linear; +} +.fade.in { + opacity: 1; +} +.collapse { + display: none; +} +.collapse.in { + display: block; +} +tr.collapse.in { + display: table-row; +} +tbody.collapse.in { + display: table-row-group; +} +.collapsing { + position: relative; + height: 0; + overflow: hidden; + -webkit-transition-timing-function: ease; + -o-transition-timing-function: ease; + transition-timing-function: ease; + -webkit-transition-duration: .35s; + -o-transition-duration: .35s; + transition-duration: .35s; + -webkit-transition-property: height, visibility; + -o-transition-property: height, visibility; + transition-property: height, visibility; +} +.caret { + display: inline-block; + width: 0; + height: 0; + margin-left: 2px; + vertical-align: middle; + border-top: 4px dashed; + border-top: 4px solid \9; + border-right: 4px solid transparent; + border-left: 4px solid transparent; +} +.dropup, +.dropdown { + position: relative; +} +.dropdown-toggle:focus { + outline: 0; +} +.dropdown-menu { + position: absolute; + top: 100%; + left: 0; + z-index: 1000; + display: none; + float: left; + min-width: 160px; + padding: 5px 0; + margin: 2px 0 0; + font-size: 14px; + text-align: left; + list-style: none; + background-color: #fff; + -webkit-background-clip: padding-box; + background-clip: padding-box; + border: 1px solid #ccc; + border: 1px solid rgba(0, 0, 0, .15); + border-radius: 4px; + -webkit-box-shadow: 0 6px 12px rgba(0, 0, 0, .175); + box-shadow: 0 6px 12px rgba(0, 0, 0, .175); +} +.dropdown-menu.pull-right { + right: 0; + left: auto; +} +.dropdown-menu .divider { + height: 1px; + margin: 9px 0; + overflow: hidden; + background-color: #e5e5e5; +} +.dropdown-menu > li > a { + display: block; + padding: 3px 20px; + clear: both; + font-weight: normal; + line-height: 1.42857143; + color: #333; + white-space: nowrap; +} +.dropdown-menu > li > a:hover, +.dropdown-menu > li > a:focus { + color: #262626; + text-decoration: none; + background-color: #f5f5f5; +} +.dropdown-menu > .active > a, +.dropdown-menu > .active > a:hover, +.dropdown-menu > .active > a:focus { + color: #fff; + text-decoration: none; + background-color: #337ab7; + outline: 0; +} +.dropdown-menu > .disabled > a, +.dropdown-menu > .disabled > a:hover, +.dropdown-menu > .disabled > a:focus { + color: #777; +} +.dropdown-menu > .disabled > a:hover, +.dropdown-menu > .disabled > a:focus { + text-decoration: none; + cursor: not-allowed; + background-color: transparent; + background-image: none; + filter: progid:DXImageTransform.Microsoft.gradient(enabled = false); +} +.open > .dropdown-menu { + display: block; +} +.open > a { + outline: 0; +} +.dropdown-menu-right { + right: 0; + left: auto; +} +.dropdown-menu-left { + right: auto; + left: 0; +} +.dropdown-header { + display: block; + padding: 3px 20px; + font-size: 12px; + line-height: 1.42857143; + color: #777; + white-space: nowrap; +} +.dropdown-backdrop { + position: fixed; + top: 0; + right: 0; + bottom: 0; + left: 0; + z-index: 990; +} +.pull-right > .dropdown-menu { + right: 0; + left: auto; +} +.dropup .caret, +.navbar-fixed-bottom .dropdown .caret { + content: ""; + border-top: 0; + border-bottom: 4px dashed; + border-bottom: 4px solid \9; +} +.dropup .dropdown-menu, +.navbar-fixed-bottom .dropdown .dropdown-menu { + top: auto; + bottom: 100%; + margin-bottom: 2px; +} +@media (min-width: 768px) { + .navbar-right .dropdown-menu { + right: 0; + left: auto; + } + .navbar-right .dropdown-menu-left { + right: auto; + left: 0; + } +} +.btn-group, +.btn-group-vertical { + position: relative; + display: inline-block; + vertical-align: middle; +} +.btn-group > .btn, +.btn-group-vertical > .btn { + position: relative; + float: left; +} +.btn-group > .btn:hover, +.btn-group-vertical > .btn:hover, +.btn-group > .btn:focus, +.btn-group-vertical > .btn:focus, +.btn-group > .btn:active, +.btn-group-vertical > .btn:active, +.btn-group > .btn.active, +.btn-group-vertical > .btn.active { + z-index: 2; +} +.btn-group .btn + .btn, +.btn-group .btn + .btn-group, +.btn-group .btn-group + .btn, +.btn-group .btn-group + .btn-group { + margin-left: -1px; +} +.btn-toolbar { + margin-left: -5px; +} +.btn-toolbar .btn, +.btn-toolbar .btn-group, +.btn-toolbar .input-group { + float: left; +} +.btn-toolbar > .btn, +.btn-toolbar > .btn-group, +.btn-toolbar > .input-group { + margin-left: 5px; +} +.btn-group > .btn:not(:first-child):not(:last-child):not(.dropdown-toggle) { + border-radius: 0; +} +.btn-group > .btn:first-child { + margin-left: 0; +} +.btn-group > .btn:first-child:not(:last-child):not(.dropdown-toggle) { + border-top-right-radius: 0; + border-bottom-right-radius: 0; +} +.btn-group > .btn:last-child:not(:first-child), +.btn-group > .dropdown-toggle:not(:first-child) { + border-top-left-radius: 0; + border-bottom-left-radius: 0; +} +.btn-group > .btn-group { + float: left; +} +.btn-group > .btn-group:not(:first-child):not(:last-child) > .btn { + border-radius: 0; +} +.btn-group > .btn-group:first-child:not(:last-child) > .btn:last-child, +.btn-group > .btn-group:first-child:not(:last-child) > .dropdown-toggle { + border-top-right-radius: 0; + border-bottom-right-radius: 0; +} +.btn-group > .btn-group:last-child:not(:first-child) > .btn:first-child { + border-top-left-radius: 0; + border-bottom-left-radius: 0; +} +.btn-group .dropdown-toggle:active, +.btn-group.open .dropdown-toggle { + outline: 0; +} +.btn-group > .btn + .dropdown-toggle { + padding-right: 8px; + padding-left: 8px; +} +.btn-group > .btn-lg + .dropdown-toggle { + padding-right: 12px; + padding-left: 12px; +} +.btn-group.open .dropdown-toggle { + -webkit-box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125); + box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125); +} +.btn-group.open .dropdown-toggle.btn-link { + -webkit-box-shadow: none; + box-shadow: none; +} +.btn .caret { + margin-left: 0; +} +.btn-lg .caret { + border-width: 5px 5px 0; + border-bottom-width: 0; +} +.dropup .btn-lg .caret { + border-width: 0 5px 5px; +} +.btn-group-vertical > .btn, +.btn-group-vertical > .btn-group, +.btn-group-vertical > .btn-group > .btn { + display: block; + float: none; + width: 100%; + max-width: 100%; +} +.btn-group-vertical > .btn-group > .btn { + float: none; +} +.btn-group-vertical > .btn + .btn, +.btn-group-vertical > .btn + .btn-group, +.btn-group-vertical > .btn-group + .btn, +.btn-group-vertical > .btn-group + .btn-group { + margin-top: -1px; + margin-left: 0; +} +.btn-group-vertical > .btn:not(:first-child):not(:last-child) { + border-radius: 0; +} +.btn-group-vertical > .btn:first-child:not(:last-child) { + border-top-left-radius: 4px; + border-top-right-radius: 4px; + border-bottom-right-radius: 0; + border-bottom-left-radius: 0; +} +.btn-group-vertical > .btn:last-child:not(:first-child) { + border-top-left-radius: 0; + border-top-right-radius: 0; + border-bottom-right-radius: 4px; + border-bottom-left-radius: 4px; +} +.btn-group-vertical > .btn-group:not(:first-child):not(:last-child) > .btn { + border-radius: 0; +} +.btn-group-vertical > .btn-group:first-child:not(:last-child) > .btn:last-child, +.btn-group-vertical > .btn-group:first-child:not(:last-child) > .dropdown-toggle { + border-bottom-right-radius: 0; + border-bottom-left-radius: 0; +} +.btn-group-vertical > .btn-group:last-child:not(:first-child) > .btn:first-child { + border-top-left-radius: 0; + border-top-right-radius: 0; +} +.btn-group-justified { + display: table; + width: 100%; + table-layout: fixed; + border-collapse: separate; +} +.btn-group-justified > .btn, +.btn-group-justified > .btn-group { + display: table-cell; + float: none; + width: 1%; +} +.btn-group-justified > .btn-group .btn { + width: 100%; +} +.btn-group-justified > .btn-group .dropdown-menu { + left: auto; +} +[data-toggle="buttons"] > .btn input[type="radio"], +[data-toggle="buttons"] > .btn-group > .btn input[type="radio"], +[data-toggle="buttons"] > .btn input[type="checkbox"], +[data-toggle="buttons"] > .btn-group > .btn input[type="checkbox"] { + position: absolute; + clip: rect(0, 0, 0, 0); + pointer-events: none; +} +.input-group { + position: relative; + display: table; + border-collapse: separate; +} +.input-group[class*="col-"] { + float: none; + padding-right: 0; + padding-left: 0; +} +.input-group .form-control { + position: relative; + z-index: 2; + float: left; + width: 100%; + margin-bottom: 0; +} +.input-group .form-control:focus { + z-index: 3; +} +.input-group-lg > .form-control, +.input-group-lg > .input-group-addon, +.input-group-lg > .input-group-btn > .btn { + height: 46px; + padding: 10px 16px; + font-size: 18px; + line-height: 1.3333333; + border-radius: 6px; +} +select.input-group-lg > .form-control, +select.input-group-lg > .input-group-addon, +select.input-group-lg > .input-group-btn > .btn { + height: 46px; + line-height: 46px; +} +textarea.input-group-lg > .form-control, +textarea.input-group-lg > .input-group-addon, +textarea.input-group-lg > .input-group-btn > .btn, +select[multiple].input-group-lg > .form-control, +select[multiple].input-group-lg > .input-group-addon, +select[multiple].input-group-lg > .input-group-btn > .btn { + height: auto; +} +.input-group-sm > .form-control, +.input-group-sm > .input-group-addon, +.input-group-sm > .input-group-btn > .btn { + height: 30px; + padding: 5px 10px; + font-size: 12px; + line-height: 1.5; + border-radius: 3px; +} +select.input-group-sm > .form-control, +select.input-group-sm > .input-group-addon, +select.input-group-sm > .input-group-btn > .btn { + height: 30px; + line-height: 30px; +} +textarea.input-group-sm > .form-control, +textarea.input-group-sm > .input-group-addon, +textarea.input-group-sm > .input-group-btn > .btn, +select[multiple].input-group-sm > .form-control, +select[multiple].input-group-sm > .input-group-addon, +select[multiple].input-group-sm > .input-group-btn > .btn { + height: auto; +} +.input-group-addon, +.input-group-btn, +.input-group .form-control { + display: table-cell; +} +.input-group-addon:not(:first-child):not(:last-child), +.input-group-btn:not(:first-child):not(:last-child), +.input-group .form-control:not(:first-child):not(:last-child) { + border-radius: 0; +} +.input-group-addon, +.input-group-btn { + width: 1%; + white-space: nowrap; + vertical-align: middle; +} +.input-group-addon { + padding: 6px 12px; + font-size: 14px; + font-weight: normal; + line-height: 1; + color: #555; + text-align: center; + background-color: #eee; + border: 1px solid #ccc; + border-radius: 4px; +} +.input-group-addon.input-sm { + padding: 5px 10px; + font-size: 12px; + border-radius: 3px; +} +.input-group-addon.input-lg { + padding: 10px 16px; + font-size: 18px; + border-radius: 6px; +} +.input-group-addon input[type="radio"], +.input-group-addon input[type="checkbox"] { + margin-top: 0; +} +.input-group .form-control:first-child, +.input-group-addon:first-child, +.input-group-btn:first-child > .btn, +.input-group-btn:first-child > .btn-group > .btn, +.input-group-btn:first-child > .dropdown-toggle, +.input-group-btn:last-child > .btn:not(:last-child):not(.dropdown-toggle), +.input-group-btn:last-child > .btn-group:not(:last-child) > .btn { + border-top-right-radius: 0; + border-bottom-right-radius: 0; +} +.input-group-addon:first-child { + border-right: 0; +} +.input-group .form-control:last-child, +.input-group-addon:last-child, +.input-group-btn:last-child > .btn, +.input-group-btn:last-child > .btn-group > .btn, +.input-group-btn:last-child > .dropdown-toggle, +.input-group-btn:first-child > .btn:not(:first-child), +.input-group-btn:first-child > .btn-group:not(:first-child) > .btn { + border-top-left-radius: 0; + border-bottom-left-radius: 0; +} +.input-group-addon:last-child { + border-left: 0; +} +.input-group-btn { + position: relative; + font-size: 0; + white-space: nowrap; +} +.input-group-btn > .btn { + position: relative; +} +.input-group-btn > .btn + .btn { + margin-left: -1px; +} +.input-group-btn > .btn:hover, +.input-group-btn > .btn:focus, +.input-group-btn > .btn:active { + z-index: 2; +} +.input-group-btn:first-child > .btn, +.input-group-btn:first-child > .btn-group { + margin-right: -1px; +} +.input-group-btn:last-child > .btn, +.input-group-btn:last-child > .btn-group { + z-index: 2; + margin-left: -1px; +} +.nav { + padding-left: 0; + margin-bottom: 0; + list-style: none; +} +.nav > li { + position: relative; + display: block; +} +.nav > li > a { + position: relative; + display: block; + padding: 10px 15px; +} +.nav > li > a:hover, +.nav > li > a:focus { + text-decoration: none; + background-color: #eee; +} +.nav > li.disabled > a { + color: #777; +} +.nav > li.disabled > a:hover, +.nav > li.disabled > a:focus { + color: #777; + text-decoration: none; + cursor: not-allowed; + background-color: transparent; +} +.nav .open > a, +.nav .open > a:hover, +.nav .open > a:focus { + background-color: #eee; + border-color: #337ab7; +} +.nav .nav-divider { + height: 1px; + margin: 9px 0; + overflow: hidden; + background-color: #e5e5e5; +} +.nav > li > a > img { + max-width: none; +} +.nav-tabs { + border-bottom: 1px solid #ddd; +} +.nav-tabs > li { + float: left; + margin-bottom: -1px; +} +.nav-tabs > li > a { + margin-right: 2px; + line-height: 1.42857143; + border: 1px solid transparent; + border-radius: 4px 4px 0 0; +} +.nav-tabs > li > a:hover { + border-color: #eee #eee #ddd; +} +.nav-tabs > li.active > a, +.nav-tabs > li.active > a:hover, +.nav-tabs > li.active > a:focus { + color: #555; + cursor: default; + background-color: #fff; + border: 1px solid #ddd; + border-bottom-color: transparent; +} +.nav-tabs.nav-justified { + width: 100%; + border-bottom: 0; +} +.nav-tabs.nav-justified > li { + float: none; +} +.nav-tabs.nav-justified > li > a { + margin-bottom: 5px; + text-align: center; +} +.nav-tabs.nav-justified > .dropdown .dropdown-menu { + top: auto; + left: auto; +} +@media (min-width: 768px) { + .nav-tabs.nav-justified > li { + display: table-cell; + width: 1%; + } + .nav-tabs.nav-justified > li > a { + margin-bottom: 0; + } +} +.nav-tabs.nav-justified > li > a { + margin-right: 0; + border-radius: 4px; +} +.nav-tabs.nav-justified > .active > a, +.nav-tabs.nav-justified > .active > a:hover, +.nav-tabs.nav-justified > .active > a:focus { + border: 1px solid #ddd; +} +@media (min-width: 768px) { + .nav-tabs.nav-justified > li > a { + border-bottom: 1px solid #ddd; + border-radius: 4px 4px 0 0; + } + .nav-tabs.nav-justified > .active > a, + .nav-tabs.nav-justified > .active > a:hover, + .nav-tabs.nav-justified > .active > a:focus { + border-bottom-color: #fff; + } +} +.nav-pills > li { + float: left; +} +.nav-pills > li > a { + border-radius: 4px; +} +.nav-pills > li + li { + margin-left: 2px; +} +.nav-pills > li.active > a, +.nav-pills > li.active > a:hover, +.nav-pills > li.active > a:focus { + color: #fff; + background-color: #337ab7; +} +.nav-stacked > li { + float: none; +} +.nav-stacked > li + li { + margin-top: 2px; + margin-left: 0; +} +.nav-justified { + width: 100%; +} +.nav-justified > li { + float: none; +} +.nav-justified > li > a { + margin-bottom: 5px; + text-align: center; +} +.nav-justified > .dropdown .dropdown-menu { + top: auto; + left: auto; +} +@media (min-width: 768px) { + .nav-justified > li { + display: table-cell; + width: 1%; + } + .nav-justified > li > a { + margin-bottom: 0; + } +} +.nav-tabs-justified { + border-bottom: 0; +} +.nav-tabs-justified > li > a { + margin-right: 0; + border-radius: 4px; +} +.nav-tabs-justified > .active > a, +.nav-tabs-justified > .active > a:hover, +.nav-tabs-justified > .active > a:focus { + border: 1px solid #ddd; +} +@media (min-width: 768px) { + .nav-tabs-justified > li > a { + border-bottom: 1px solid #ddd; + border-radius: 4px 4px 0 0; + } + .nav-tabs-justified > .active > a, + .nav-tabs-justified > .active > a:hover, + .nav-tabs-justified > .active > a:focus { + border-bottom-color: #fff; + } +} +.tab-content > .tab-pane { + display: none; +} +.tab-content > .active { + display: block; +} +.nav-tabs .dropdown-menu { + margin-top: -1px; + border-top-left-radius: 0; + border-top-right-radius: 0; +} +.navbar { + position: relative; + min-height: 50px; + margin-bottom: 20px; + border: 1px solid transparent; +} +@media (min-width: 768px) { + .navbar { + border-radius: 4px; + } +} +@media (min-width: 768px) { + .navbar-header { + float: left; + } +} +.navbar-collapse { + padding-right: 15px; + padding-left: 15px; + overflow-x: visible; + -webkit-overflow-scrolling: touch; + border-top: 1px solid transparent; + -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .1); + box-shadow: inset 0 1px 0 rgba(255, 255, 255, .1); +} +.navbar-collapse.in { + overflow-y: auto; +} +@media (min-width: 768px) { + .navbar-collapse { + width: auto; + border-top: 0; + -webkit-box-shadow: none; + box-shadow: none; + } + .navbar-collapse.collapse { + display: block !important; + height: auto !important; + padding-bottom: 0; + overflow: visible !important; + } + .navbar-collapse.in { + overflow-y: visible; + } + .navbar-fixed-top .navbar-collapse, + .navbar-static-top .navbar-collapse, + .navbar-fixed-bottom .navbar-collapse { + padding-right: 0; + padding-left: 0; + } +} +.navbar-fixed-top .navbar-collapse, +.navbar-fixed-bottom .navbar-collapse { + max-height: 340px; +} +@media (max-device-width: 480px) and (orientation: landscape) { + .navbar-fixed-top .navbar-collapse, + .navbar-fixed-bottom .navbar-collapse { + max-height: 200px; + } +} +.container > .navbar-header, +.container-fluid > .navbar-header, +.container > .navbar-collapse, +.container-fluid > .navbar-collapse { + margin-right: -15px; + margin-left: -15px; +} +@media (min-width: 768px) { + .container > .navbar-header, + .container-fluid > .navbar-header, + .container > .navbar-collapse, + .container-fluid > .navbar-collapse { + margin-right: 0; + margin-left: 0; + } +} +.navbar-static-top { + z-index: 1000; + border-width: 0 0 1px; +} +@media (min-width: 768px) { + .navbar-static-top { + border-radius: 0; + } +} +.navbar-fixed-top, +.navbar-fixed-bottom { + position: fixed; + right: 0; + left: 0; + z-index: 1030; +} +@media (min-width: 768px) { + .navbar-fixed-top, + .navbar-fixed-bottom { + border-radius: 0; + } +} +.navbar-fixed-top { + top: 0; + border-width: 0 0 1px; +} +.navbar-fixed-bottom { + bottom: 0; + margin-bottom: 0; + border-width: 1px 0 0; +} +.navbar-brand { + float: left; + height: 50px; + padding: 15px 15px; + font-size: 18px; + line-height: 20px; +} +.navbar-brand:hover, +.navbar-brand:focus { + text-decoration: none; +} +.navbar-brand > img { + display: block; +} +@media (min-width: 768px) { + .navbar > .container .navbar-brand, + .navbar > .container-fluid .navbar-brand { + margin-left: -15px; + } +} +.navbar-toggle { + position: relative; + float: right; + padding: 9px 10px; + margin-top: 8px; + margin-right: 15px; + margin-bottom: 8px; + background-color: transparent; + background-image: none; + border: 1px solid transparent; + border-radius: 4px; +} +.navbar-toggle:focus { + outline: 0; +} +.navbar-toggle .icon-bar { + display: block; + width: 22px; + height: 2px; + border-radius: 1px; +} +.navbar-toggle .icon-bar + .icon-bar { + margin-top: 4px; +} +@media (min-width: 768px) { + .navbar-toggle { + display: none; + } +} +.navbar-nav { + margin: 7.5px -15px; +} +.navbar-nav > li > a { + padding-top: 10px; + padding-bottom: 10px; + line-height: 20px; +} +@media (max-width: 767px) { + .navbar-nav .open .dropdown-menu { + position: static; + float: none; + width: auto; + margin-top: 0; + background-color: transparent; + border: 0; + -webkit-box-shadow: none; + box-shadow: none; + } + .navbar-nav .open .dropdown-menu > li > a, + .navbar-nav .open .dropdown-menu .dropdown-header { + padding: 5px 15px 5px 25px; + } + .navbar-nav .open .dropdown-menu > li > a { + line-height: 20px; + } + .navbar-nav .open .dropdown-menu > li > a:hover, + .navbar-nav .open .dropdown-menu > li > a:focus { + background-image: none; + } +} +@media (min-width: 768px) { + .navbar-nav { + float: left; + margin: 0; + } + .navbar-nav > li { + float: left; + } + .navbar-nav > li > a { + padding-top: 15px; + padding-bottom: 15px; + } +} +.navbar-form { + padding: 10px 15px; + margin-top: 8px; + margin-right: -15px; + margin-bottom: 8px; + margin-left: -15px; + border-top: 1px solid transparent; + border-bottom: 1px solid transparent; + -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .1), 0 1px 0 rgba(255, 255, 255, .1); + box-shadow: inset 0 1px 0 rgba(255, 255, 255, .1), 0 1px 0 rgba(255, 255, 255, .1); +} +@media (min-width: 768px) { + .navbar-form .form-group { + display: inline-block; + margin-bottom: 0; + vertical-align: middle; + } + .navbar-form .form-control { + display: inline-block; + width: auto; + vertical-align: middle; + } + .navbar-form .form-control-static { + display: inline-block; + } + .navbar-form .input-group { + display: inline-table; + vertical-align: middle; + } + .navbar-form .input-group .input-group-addon, + .navbar-form .input-group .input-group-btn, + .navbar-form .input-group .form-control { + width: auto; + } + .navbar-form .input-group > .form-control { + width: 100%; + } + .navbar-form .control-label { + margin-bottom: 0; + vertical-align: middle; + } + .navbar-form .radio, + .navbar-form .checkbox { + display: inline-block; + margin-top: 0; + margin-bottom: 0; + vertical-align: middle; + } + .navbar-form .radio label, + .navbar-form .checkbox label { + padding-left: 0; + } + .navbar-form .radio input[type="radio"], + .navbar-form .checkbox input[type="checkbox"] { + position: relative; + margin-left: 0; + } + .navbar-form .has-feedback .form-control-feedback { + top: 0; + } +} +@media (max-width: 767px) { + .navbar-form .form-group { + margin-bottom: 5px; + } + .navbar-form .form-group:last-child { + margin-bottom: 0; + } +} +@media (min-width: 768px) { + .navbar-form { + width: auto; + padding-top: 0; + padding-bottom: 0; + margin-right: 0; + margin-left: 0; + border: 0; + -webkit-box-shadow: none; + box-shadow: none; + } +} +.navbar-nav > li > .dropdown-menu { + margin-top: 0; + border-top-left-radius: 0; + border-top-right-radius: 0; +} +.navbar-fixed-bottom .navbar-nav > li > .dropdown-menu { + margin-bottom: 0; + border-top-left-radius: 4px; + border-top-right-radius: 4px; + border-bottom-right-radius: 0; + border-bottom-left-radius: 0; +} +.navbar-btn { + margin-top: 8px; + margin-bottom: 8px; +} +.navbar-btn.btn-sm { + margin-top: 10px; + margin-bottom: 10px; +} +.navbar-btn.btn-xs { + margin-top: 14px; + margin-bottom: 14px; +} +.navbar-text { + margin-top: 15px; + margin-bottom: 15px; +} +@media (min-width: 768px) { + .navbar-text { + float: left; + margin-right: 15px; + margin-left: 15px; + } +} +@media (min-width: 768px) { + .navbar-left { + float: left !important; + } + .navbar-right { + float: right !important; + margin-right: -15px; + } + .navbar-right ~ .navbar-right { + margin-right: 0; + } +} +.navbar-default { + background-color: #f8f8f8; + border-color: #e7e7e7; +} +.navbar-default .navbar-brand { + color: #777; +} +.navbar-default .navbar-brand:hover, +.navbar-default .navbar-brand:focus { + color: #5e5e5e; + background-color: transparent; +} +.navbar-default .navbar-text { + color: #777; +} +.navbar-default .navbar-nav > li > a { + color: #777; +} +.navbar-default .navbar-nav > li > a:hover, +.navbar-default .navbar-nav > li > a:focus { + color: #333; + background-color: transparent; +} +.navbar-default .navbar-nav > .active > a, +.navbar-default .navbar-nav > .active > a:hover, +.navbar-default .navbar-nav > .active > a:focus { + color: #555; + background-color: #e7e7e7; +} +.navbar-default .navbar-nav > .disabled > a, +.navbar-default .navbar-nav > .disabled > a:hover, +.navbar-default .navbar-nav > .disabled > a:focus { + color: #ccc; + background-color: transparent; +} +.navbar-default .navbar-toggle { + border-color: #ddd; +} +.navbar-default .navbar-toggle:hover, +.navbar-default .navbar-toggle:focus { + background-color: #ddd; +} +.navbar-default .navbar-toggle .icon-bar { + background-color: #888; +} +.navbar-default .navbar-collapse, +.navbar-default .navbar-form { + border-color: #e7e7e7; +} +.navbar-default .navbar-nav > .open > a, +.navbar-default .navbar-nav > .open > a:hover, +.navbar-default .navbar-nav > .open > a:focus { + color: #555; + background-color: #e7e7e7; +} +@media (max-width: 767px) { + .navbar-default .navbar-nav .open .dropdown-menu > li > a { + color: #777; + } + .navbar-default .navbar-nav .open .dropdown-menu > li > a:hover, + .navbar-default .navbar-nav .open .dropdown-menu > li > a:focus { + color: #333; + background-color: transparent; + } + .navbar-default .navbar-nav .open .dropdown-menu > .active > a, + .navbar-default .navbar-nav .open .dropdown-menu > .active > a:hover, + .navbar-default .navbar-nav .open .dropdown-menu > .active > a:focus { + color: #555; + background-color: #e7e7e7; + } + .navbar-default .navbar-nav .open .dropdown-menu > .disabled > a, + .navbar-default .navbar-nav .open .dropdown-menu > .disabled > a:hover, + .navbar-default .navbar-nav .open .dropdown-menu > .disabled > a:focus { + color: #ccc; + background-color: transparent; + } +} +.navbar-default .navbar-link { + color: #777; +} +.navbar-default .navbar-link:hover { + color: #333; +} +.navbar-default .btn-link { + color: #777; +} +.navbar-default .btn-link:hover, +.navbar-default .btn-link:focus { + color: #333; +} +.navbar-default .btn-link[disabled]:hover, +fieldset[disabled] .navbar-default .btn-link:hover, +.navbar-default .btn-link[disabled]:focus, +fieldset[disabled] .navbar-default .btn-link:focus { + color: #ccc; +} +.navbar-inverse { + background-color: #222; + border-color: #080808; +} +.navbar-inverse .navbar-brand { + color: #9d9d9d; +} +.navbar-inverse .navbar-brand:hover, +.navbar-inverse .navbar-brand:focus { + color: #fff; + background-color: transparent; +} +.navbar-inverse .navbar-text { + color: #9d9d9d; +} +.navbar-inverse .navbar-nav > li > a { + color: #9d9d9d; +} +.navbar-inverse .navbar-nav > li > a:hover, +.navbar-inverse .navbar-nav > li > a:focus { + color: #fff; + background-color: transparent; +} +.navbar-inverse .navbar-nav > .active > a, +.navbar-inverse .navbar-nav > .active > a:hover, +.navbar-inverse .navbar-nav > .active > a:focus { + color: #fff; + background-color: #080808; +} +.navbar-inverse .navbar-nav > .disabled > a, +.navbar-inverse .navbar-nav > .disabled > a:hover, +.navbar-inverse .navbar-nav > .disabled > a:focus { + color: #444; + background-color: transparent; +} +.navbar-inverse .navbar-toggle { + border-color: #333; +} +.navbar-inverse .navbar-toggle:hover, +.navbar-inverse .navbar-toggle:focus { + background-color: #333; +} +.navbar-inverse .navbar-toggle .icon-bar { + background-color: #fff; +} +.navbar-inverse .navbar-collapse, +.navbar-inverse .navbar-form { + border-color: #101010; +} +.navbar-inverse .navbar-nav > .open > a, +.navbar-inverse .navbar-nav > .open > a:hover, +.navbar-inverse .navbar-nav > .open > a:focus { + color: #fff; + background-color: #080808; +} +@media (max-width: 767px) { + .navbar-inverse .navbar-nav .open .dropdown-menu > .dropdown-header { + border-color: #080808; + } + .navbar-inverse .navbar-nav .open .dropdown-menu .divider { + background-color: #080808; + } + .navbar-inverse .navbar-nav .open .dropdown-menu > li > a { + color: #9d9d9d; + } + .navbar-inverse .navbar-nav .open .dropdown-menu > li > a:hover, + .navbar-inverse .navbar-nav .open .dropdown-menu > li > a:focus { + color: #fff; + background-color: transparent; + } + .navbar-inverse .navbar-nav .open .dropdown-menu > .active > a, + .navbar-inverse .navbar-nav .open .dropdown-menu > .active > a:hover, + .navbar-inverse .navbar-nav .open .dropdown-menu > .active > a:focus { + color: #fff; + background-color: #080808; + } + .navbar-inverse .navbar-nav .open .dropdown-menu > .disabled > a, + .navbar-inverse .navbar-nav .open .dropdown-menu > .disabled > a:hover, + .navbar-inverse .navbar-nav .open .dropdown-menu > .disabled > a:focus { + color: #444; + background-color: transparent; + } +} +.navbar-inverse .navbar-link { + color: #9d9d9d; +} +.navbar-inverse .navbar-link:hover { + color: #fff; +} +.navbar-inverse .btn-link { + color: #9d9d9d; +} +.navbar-inverse .btn-link:hover, +.navbar-inverse .btn-link:focus { + color: #fff; +} +.navbar-inverse .btn-link[disabled]:hover, +fieldset[disabled] .navbar-inverse .btn-link:hover, +.navbar-inverse .btn-link[disabled]:focus, +fieldset[disabled] .navbar-inverse .btn-link:focus { + color: #444; +} +.breadcrumb { + padding: 8px 15px; + margin-bottom: 20px; + list-style: none; + background-color: #f5f5f5; + border-radius: 4px; +} +.breadcrumb > li { + display: inline-block; +} +.breadcrumb > li + li:before { + padding: 0 5px; + color: #ccc; + content: "/\00a0"; +} +.breadcrumb > .active { + color: #777; +} +.pagination { + display: inline-block; + padding-left: 0; + margin: 20px 0; + border-radius: 4px; +} +.pagination > li { + display: inline; +} +.pagination > li > a, +.pagination > li > span { + position: relative; + float: left; + padding: 6px 12px; + margin-left: -1px; + line-height: 1.42857143; + color: #337ab7; + text-decoration: none; + background-color: #fff; + border: 1px solid #ddd; +} +.pagination > li:first-child > a, +.pagination > li:first-child > span { + margin-left: 0; + border-top-left-radius: 4px; + border-bottom-left-radius: 4px; +} +.pagination > li:last-child > a, +.pagination > li:last-child > span { + border-top-right-radius: 4px; + border-bottom-right-radius: 4px; +} +.pagination > li > a:hover, +.pagination > li > span:hover, +.pagination > li > a:focus, +.pagination > li > span:focus { + z-index: 2; + color: #23527c; + background-color: #eee; + border-color: #ddd; +} +.pagination > .active > a, +.pagination > .active > span, +.pagination > .active > a:hover, +.pagination > .active > span:hover, +.pagination > .active > a:focus, +.pagination > .active > span:focus { + z-index: 3; + color: #fff; + cursor: default; + background-color: #337ab7; + border-color: #337ab7; +} +.pagination > .disabled > span, +.pagination > .disabled > span:hover, +.pagination > .disabled > span:focus, +.pagination > .disabled > a, +.pagination > .disabled > a:hover, +.pagination > .disabled > a:focus { + color: #777; + cursor: not-allowed; + background-color: #fff; + border-color: #ddd; +} +.pagination-lg > li > a, +.pagination-lg > li > span { + padding: 10px 16px; + font-size: 18px; + line-height: 1.3333333; +} +.pagination-lg > li:first-child > a, +.pagination-lg > li:first-child > span { + border-top-left-radius: 6px; + border-bottom-left-radius: 6px; +} +.pagination-lg > li:last-child > a, +.pagination-lg > li:last-child > span { + border-top-right-radius: 6px; + border-bottom-right-radius: 6px; +} +.pagination-sm > li > a, +.pagination-sm > li > span { + padding: 5px 10px; + font-size: 12px; + line-height: 1.5; +} +.pagination-sm > li:first-child > a, +.pagination-sm > li:first-child > span { + border-top-left-radius: 3px; + border-bottom-left-radius: 3px; +} +.pagination-sm > li:last-child > a, +.pagination-sm > li:last-child > span { + border-top-right-radius: 3px; + border-bottom-right-radius: 3px; +} +.pager { + padding-left: 0; + margin: 20px 0; + text-align: center; + list-style: none; +} +.pager li { + display: inline; +} +.pager li > a, +.pager li > span { + display: inline-block; + padding: 5px 14px; + background-color: #fff; + border: 1px solid #ddd; + border-radius: 15px; +} +.pager li > a:hover, +.pager li > a:focus { + text-decoration: none; + background-color: #eee; +} +.pager .next > a, +.pager .next > span { + float: right; +} +.pager .previous > a, +.pager .previous > span { + float: left; +} +.pager .disabled > a, +.pager .disabled > a:hover, +.pager .disabled > a:focus, +.pager .disabled > span { + color: #777; + cursor: not-allowed; + background-color: #fff; +} +.label { + display: inline; + padding: .2em .6em .3em; + font-size: 75%; + font-weight: bold; + line-height: 1; + color: #fff; + text-align: center; + white-space: nowrap; + vertical-align: baseline; + border-radius: .25em; +} +a.label:hover, +a.label:focus { + color: #fff; + text-decoration: none; + cursor: pointer; +} +.label:empty { + display: none; +} +.btn .label { + position: relative; + top: -1px; +} +.label-default { + background-color: #777; +} +.label-default[href]:hover, +.label-default[href]:focus { + background-color: #5e5e5e; +} +.label-primary { + background-color: #337ab7; +} +.label-primary[href]:hover, +.label-primary[href]:focus { + background-color: #286090; +} +.label-success { + background-color: #5cb85c; +} +.label-success[href]:hover, +.label-success[href]:focus { + background-color: #449d44; +} +.label-info { + background-color: #5bc0de; +} +.label-info[href]:hover, +.label-info[href]:focus { + background-color: #31b0d5; +} +.label-warning { + background-color: #f0ad4e; +} +.label-warning[href]:hover, +.label-warning[href]:focus { + background-color: #ec971f; +} +.label-danger { + background-color: #d9534f; +} +.label-danger[href]:hover, +.label-danger[href]:focus { + background-color: #c9302c; +} +.badge { + display: inline-block; + min-width: 10px; + padding: 3px 7px; + font-size: 12px; + font-weight: bold; + line-height: 1; + color: #fff; + text-align: center; + white-space: nowrap; + vertical-align: middle; + background-color: #777; + border-radius: 10px; +} +.badge:empty { + display: none; +} +.btn .badge { + position: relative; + top: -1px; +} +.btn-xs .badge, +.btn-group-xs > .btn .badge { + top: 0; + padding: 1px 5px; +} +a.badge:hover, +a.badge:focus { + color: #fff; + text-decoration: none; + cursor: pointer; +} +.list-group-item.active > .badge, +.nav-pills > .active > a > .badge { + color: #337ab7; + background-color: #fff; +} +.list-group-item > .badge { + float: right; +} +.list-group-item > .badge + .badge { + margin-right: 5px; +} +.nav-pills > li > a > .badge { + margin-left: 3px; +} +.jumbotron { + padding-top: 30px; + padding-bottom: 30px; + margin-bottom: 30px; + color: inherit; + background-color: #eee; +} +.jumbotron h1, +.jumbotron .h1 { + color: inherit; +} +.jumbotron p { + margin-bottom: 15px; + font-size: 21px; + font-weight: 200; +} +.jumbotron > hr { + border-top-color: #d5d5d5; +} +.container .jumbotron, +.container-fluid .jumbotron { + padding-right: 15px; + padding-left: 15px; + border-radius: 6px; +} +.jumbotron .container { + max-width: 100%; +} +@media screen and (min-width: 768px) { + .jumbotron { + padding-top: 48px; + padding-bottom: 48px; + } + .container .jumbotron, + .container-fluid .jumbotron { + padding-right: 60px; + padding-left: 60px; + } + .jumbotron h1, + .jumbotron .h1 { + font-size: 63px; + } +} +.thumbnail { + display: block; + padding: 4px; + margin-bottom: 20px; + line-height: 1.42857143; + background-color: #fff; + border: 1px solid #ddd; + border-radius: 4px; + -webkit-transition: border .2s ease-in-out; + -o-transition: border .2s ease-in-out; + transition: border .2s ease-in-out; +} +.thumbnail > img, +.thumbnail a > img { + margin-right: auto; + margin-left: auto; +} +a.thumbnail:hover, +a.thumbnail:focus, +a.thumbnail.active { + border-color: #337ab7; +} +.thumbnail .caption { + padding: 9px; + color: #333; +} +.alert { + padding: 15px; + margin-bottom: 20px; + border: 1px solid transparent; + border-radius: 4px; +} +.alert h4 { + margin-top: 0; + color: inherit; +} +.alert .alert-link { + font-weight: bold; +} +.alert > p, +.alert > ul { + margin-bottom: 0; +} +.alert > p + p { + margin-top: 5px; +} +.alert-dismissable, +.alert-dismissible { + padding-right: 35px; +} +.alert-dismissable .close, +.alert-dismissible .close { + position: relative; + top: -2px; + right: -21px; + color: inherit; +} +.alert-success { + color: #3c763d; + background-color: #dff0d8; + border-color: #d6e9c6; +} +.alert-success hr { + border-top-color: #c9e2b3; +} +.alert-success .alert-link { + color: #2b542c; +} +.alert-info { + color: #31708f; + background-color: #d9edf7; + border-color: #bce8f1; +} +.alert-info hr { + border-top-color: #a6e1ec; +} +.alert-info .alert-link { + color: #245269; +} +.alert-warning { + color: #8a6d3b; + background-color: #fcf8e3; + border-color: #faebcc; +} +.alert-warning hr { + border-top-color: #f7e1b5; +} +.alert-warning .alert-link { + color: #66512c; +} +.alert-danger { + color: #a94442; + background-color: #f2dede; + border-color: #ebccd1; +} +.alert-danger hr { + border-top-color: #e4b9c0; +} +.alert-danger .alert-link { + color: #843534; +} +@-webkit-keyframes progress-bar-stripes { + from { + background-position: 40px 0; + } + to { + background-position: 0 0; + } +} +@-o-keyframes progress-bar-stripes { + from { + background-position: 40px 0; + } + to { + background-position: 0 0; + } +} +@keyframes progress-bar-stripes { + from { + background-position: 40px 0; + } + to { + background-position: 0 0; + } +} +.progress { + height: 20px; + margin-bottom: 20px; + overflow: hidden; + background-color: #f5f5f5; + border-radius: 4px; + -webkit-box-shadow: inset 0 1px 2px rgba(0, 0, 0, .1); + box-shadow: inset 0 1px 2px rgba(0, 0, 0, .1); +} +.progress-bar { + float: left; + width: 0; + height: 100%; + font-size: 12px; + line-height: 20px; + color: #fff; + text-align: center; + background-color: #337ab7; + -webkit-box-shadow: inset 0 -1px 0 rgba(0, 0, 0, .15); + box-shadow: inset 0 -1px 0 rgba(0, 0, 0, .15); + -webkit-transition: width .6s ease; + -o-transition: width .6s ease; + transition: width .6s ease; +} +.progress-striped .progress-bar, +.progress-bar-striped { + background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); + background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); + background-image: linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); + -webkit-background-size: 40px 40px; + background-size: 40px 40px; +} +.progress.active .progress-bar, +.progress-bar.active { + -webkit-animation: progress-bar-stripes 2s linear infinite; + -o-animation: progress-bar-stripes 2s linear infinite; + animation: progress-bar-stripes 2s linear infinite; +} +.progress-bar-success { + background-color: #5cb85c; +} +.progress-striped .progress-bar-success { + background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); + background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); + background-image: linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); +} +.progress-bar-info { + background-color: #5bc0de; +} +.progress-striped .progress-bar-info { + background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); + background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); + background-image: linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); +} +.progress-bar-warning { + background-color: #f0ad4e; +} +.progress-striped .progress-bar-warning { + background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); + background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); + background-image: linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); +} +.progress-bar-danger { + background-color: #d9534f; +} +.progress-striped .progress-bar-danger { + background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); + background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); + background-image: linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); +} +.media { + margin-top: 15px; +} +.media:first-child { + margin-top: 0; +} +.media, +.media-body { + overflow: hidden; + zoom: 1; +} +.media-body { + width: 10000px; +} +.media-object { + display: block; +} +.media-object.img-thumbnail { + max-width: none; +} +.media-right, +.media > .pull-right { + padding-left: 10px; +} +.media-left, +.media > .pull-left { + padding-right: 10px; +} +.media-left, +.media-right, +.media-body { + display: table-cell; + vertical-align: top; +} +.media-middle { + vertical-align: middle; +} +.media-bottom { + vertical-align: bottom; +} +.media-heading { + margin-top: 0; + margin-bottom: 5px; +} +.media-list { + padding-left: 0; + list-style: none; +} +.list-group { + padding-left: 0; + margin-bottom: 20px; +} +.list-group-item { + position: relative; + display: block; + padding: 10px 15px; + margin-bottom: -1px; + background-color: #fff; + border: 1px solid #ddd; +} +.list-group-item:first-child { + border-top-left-radius: 4px; + border-top-right-radius: 4px; +} +.list-group-item:last-child { + margin-bottom: 0; + border-bottom-right-radius: 4px; + border-bottom-left-radius: 4px; +} +a.list-group-item, +button.list-group-item { + color: #555; +} +a.list-group-item .list-group-item-heading, +button.list-group-item .list-group-item-heading { + color: #333; +} +a.list-group-item:hover, +button.list-group-item:hover, +a.list-group-item:focus, +button.list-group-item:focus { + color: #555; + text-decoration: none; + background-color: #f5f5f5; +} +button.list-group-item { + width: 100%; + text-align: left; +} +.list-group-item.disabled, +.list-group-item.disabled:hover, +.list-group-item.disabled:focus { + color: #777; + cursor: not-allowed; + background-color: #eee; +} +.list-group-item.disabled .list-group-item-heading, +.list-group-item.disabled:hover .list-group-item-heading, +.list-group-item.disabled:focus .list-group-item-heading { + color: inherit; +} +.list-group-item.disabled .list-group-item-text, +.list-group-item.disabled:hover .list-group-item-text, +.list-group-item.disabled:focus .list-group-item-text { + color: #777; +} +.list-group-item.active, +.list-group-item.active:hover, +.list-group-item.active:focus { + z-index: 2; + color: #fff; + background-color: #337ab7; + border-color: #337ab7; +} +.list-group-item.active .list-group-item-heading, +.list-group-item.active:hover .list-group-item-heading, +.list-group-item.active:focus .list-group-item-heading, +.list-group-item.active .list-group-item-heading > small, +.list-group-item.active:hover .list-group-item-heading > small, +.list-group-item.active:focus .list-group-item-heading > small, +.list-group-item.active .list-group-item-heading > .small, +.list-group-item.active:hover .list-group-item-heading > .small, +.list-group-item.active:focus .list-group-item-heading > .small { + color: inherit; +} +.list-group-item.active .list-group-item-text, +.list-group-item.active:hover .list-group-item-text, +.list-group-item.active:focus .list-group-item-text { + color: #c7ddef; +} +.list-group-item-success { + color: #3c763d; + background-color: #dff0d8; +} +a.list-group-item-success, +button.list-group-item-success { + color: #3c763d; +} +a.list-group-item-success .list-group-item-heading, +button.list-group-item-success .list-group-item-heading { + color: inherit; +} +a.list-group-item-success:hover, +button.list-group-item-success:hover, +a.list-group-item-success:focus, +button.list-group-item-success:focus { + color: #3c763d; + background-color: #d0e9c6; +} +a.list-group-item-success.active, +button.list-group-item-success.active, +a.list-group-item-success.active:hover, +button.list-group-item-success.active:hover, +a.list-group-item-success.active:focus, +button.list-group-item-success.active:focus { + color: #fff; + background-color: #3c763d; + border-color: #3c763d; +} +.list-group-item-info { + color: #31708f; + background-color: #d9edf7; +} +a.list-group-item-info, +button.list-group-item-info { + color: #31708f; +} +a.list-group-item-info .list-group-item-heading, +button.list-group-item-info .list-group-item-heading { + color: inherit; +} +a.list-group-item-info:hover, +button.list-group-item-info:hover, +a.list-group-item-info:focus, +button.list-group-item-info:focus { + color: #31708f; + background-color: #c4e3f3; +} +a.list-group-item-info.active, +button.list-group-item-info.active, +a.list-group-item-info.active:hover, +button.list-group-item-info.active:hover, +a.list-group-item-info.active:focus, +button.list-group-item-info.active:focus { + color: #fff; + background-color: #31708f; + border-color: #31708f; +} +.list-group-item-warning { + color: #8a6d3b; + background-color: #fcf8e3; +} +a.list-group-item-warning, +button.list-group-item-warning { + color: #8a6d3b; +} +a.list-group-item-warning .list-group-item-heading, +button.list-group-item-warning .list-group-item-heading { + color: inherit; +} +a.list-group-item-warning:hover, +button.list-group-item-warning:hover, +a.list-group-item-warning:focus, +button.list-group-item-warning:focus { + color: #8a6d3b; + background-color: #faf2cc; +} +a.list-group-item-warning.active, +button.list-group-item-warning.active, +a.list-group-item-warning.active:hover, +button.list-group-item-warning.active:hover, +a.list-group-item-warning.active:focus, +button.list-group-item-warning.active:focus { + color: #fff; + background-color: #8a6d3b; + border-color: #8a6d3b; +} +.list-group-item-danger { + color: #a94442; + background-color: #f2dede; +} +a.list-group-item-danger, +button.list-group-item-danger { + color: #a94442; +} +a.list-group-item-danger .list-group-item-heading, +button.list-group-item-danger .list-group-item-heading { + color: inherit; +} +a.list-group-item-danger:hover, +button.list-group-item-danger:hover, +a.list-group-item-danger:focus, +button.list-group-item-danger:focus { + color: #a94442; + background-color: #ebcccc; +} +a.list-group-item-danger.active, +button.list-group-item-danger.active, +a.list-group-item-danger.active:hover, +button.list-group-item-danger.active:hover, +a.list-group-item-danger.active:focus, +button.list-group-item-danger.active:focus { + color: #fff; + background-color: #a94442; + border-color: #a94442; +} +.list-group-item-heading { + margin-top: 0; + margin-bottom: 5px; +} +.list-group-item-text { + margin-bottom: 0; + line-height: 1.3; +} +.panel { + margin-bottom: 20px; + background-color: #fff; + border: 1px solid transparent; + border-radius: 4px; + -webkit-box-shadow: 0 1px 1px rgba(0, 0, 0, .05); + box-shadow: 0 1px 1px rgba(0, 0, 0, .05); +} +.panel-body { + padding: 15px; +} +.panel-heading { + padding: 10px 15px; + border-bottom: 1px solid transparent; + border-top-left-radius: 3px; + border-top-right-radius: 3px; +} +.panel-heading > .dropdown .dropdown-toggle { + color: inherit; +} +.panel-title { + margin-top: 0; + margin-bottom: 0; + font-size: 16px; + color: inherit; +} +.panel-title > a, +.panel-title > small, +.panel-title > .small, +.panel-title > small > a, +.panel-title > .small > a { + color: inherit; +} +.panel-footer { + padding: 10px 15px; + background-color: #f5f5f5; + border-top: 1px solid #ddd; + border-bottom-right-radius: 3px; + border-bottom-left-radius: 3px; +} +.panel > .list-group, +.panel > .panel-collapse > .list-group { + margin-bottom: 0; +} +.panel > .list-group .list-group-item, +.panel > .panel-collapse > .list-group .list-group-item { + border-width: 1px 0; + border-radius: 0; +} +.panel > .list-group:first-child .list-group-item:first-child, +.panel > .panel-collapse > .list-group:first-child .list-group-item:first-child { + border-top: 0; + border-top-left-radius: 3px; + border-top-right-radius: 3px; +} +.panel > .list-group:last-child .list-group-item:last-child, +.panel > .panel-collapse > .list-group:last-child .list-group-item:last-child { + border-bottom: 0; + border-bottom-right-radius: 3px; + border-bottom-left-radius: 3px; +} +.panel > .panel-heading + .panel-collapse > .list-group .list-group-item:first-child { + border-top-left-radius: 0; + border-top-right-radius: 0; +} +.panel-heading + .list-group .list-group-item:first-child { + border-top-width: 0; +} +.list-group + .panel-footer { + border-top-width: 0; +} +.panel > .table, +.panel > .table-responsive > .table, +.panel > .panel-collapse > .table { + margin-bottom: 0; +} +.panel > .table caption, +.panel > .table-responsive > .table caption, +.panel > .panel-collapse > .table caption { + padding-right: 15px; + padding-left: 15px; +} +.panel > .table:first-child, +.panel > .table-responsive:first-child > .table:first-child { + border-top-left-radius: 3px; + border-top-right-radius: 3px; +} +.panel > .table:first-child > thead:first-child > tr:first-child, +.panel > .table-responsive:first-child > .table:first-child > thead:first-child > tr:first-child, +.panel > .table:first-child > tbody:first-child > tr:first-child, +.panel > .table-responsive:first-child > .table:first-child > tbody:first-child > tr:first-child { + border-top-left-radius: 3px; + border-top-right-radius: 3px; +} +.panel > .table:first-child > thead:first-child > tr:first-child td:first-child, +.panel > .table-responsive:first-child > .table:first-child > thead:first-child > tr:first-child td:first-child, +.panel > .table:first-child > tbody:first-child > tr:first-child td:first-child, +.panel > .table-responsive:first-child > .table:first-child > tbody:first-child > tr:first-child td:first-child, +.panel > .table:first-child > thead:first-child > tr:first-child th:first-child, +.panel > .table-responsive:first-child > .table:first-child > thead:first-child > tr:first-child th:first-child, +.panel > .table:first-child > tbody:first-child > tr:first-child th:first-child, +.panel > .table-responsive:first-child > .table:first-child > tbody:first-child > tr:first-child th:first-child { + border-top-left-radius: 3px; +} +.panel > .table:first-child > thead:first-child > tr:first-child td:last-child, +.panel > .table-responsive:first-child > .table:first-child > thead:first-child > tr:first-child td:last-child, +.panel > .table:first-child > tbody:first-child > tr:first-child td:last-child, +.panel > .table-responsive:first-child > .table:first-child > tbody:first-child > tr:first-child td:last-child, +.panel > .table:first-child > thead:first-child > tr:first-child th:last-child, +.panel > .table-responsive:first-child > .table:first-child > thead:first-child > tr:first-child th:last-child, +.panel > .table:first-child > tbody:first-child > tr:first-child th:last-child, +.panel > .table-responsive:first-child > .table:first-child > tbody:first-child > tr:first-child th:last-child { + border-top-right-radius: 3px; +} +.panel > .table:last-child, +.panel > .table-responsive:last-child > .table:last-child { + border-bottom-right-radius: 3px; + border-bottom-left-radius: 3px; +} +.panel > .table:last-child > tbody:last-child > tr:last-child, +.panel > .table-responsive:last-child > .table:last-child > tbody:last-child > tr:last-child, +.panel > .table:last-child > tfoot:last-child > tr:last-child, +.panel > .table-responsive:last-child > .table:last-child > tfoot:last-child > tr:last-child { + border-bottom-right-radius: 3px; + border-bottom-left-radius: 3px; +} +.panel > .table:last-child > tbody:last-child > tr:last-child td:first-child, +.panel > .table-responsive:last-child > .table:last-child > tbody:last-child > tr:last-child td:first-child, +.panel > .table:last-child > tfoot:last-child > tr:last-child td:first-child, +.panel > .table-responsive:last-child > .table:last-child > tfoot:last-child > tr:last-child td:first-child, +.panel > .table:last-child > tbody:last-child > tr:last-child th:first-child, +.panel > .table-responsive:last-child > .table:last-child > tbody:last-child > tr:last-child th:first-child, +.panel > .table:last-child > tfoot:last-child > tr:last-child th:first-child, +.panel > .table-responsive:last-child > .table:last-child > tfoot:last-child > tr:last-child th:first-child { + border-bottom-left-radius: 3px; +} +.panel > .table:last-child > tbody:last-child > tr:last-child td:last-child, +.panel > .table-responsive:last-child > .table:last-child > tbody:last-child > tr:last-child td:last-child, +.panel > .table:last-child > tfoot:last-child > tr:last-child td:last-child, +.panel > .table-responsive:last-child > .table:last-child > tfoot:last-child > tr:last-child td:last-child, +.panel > .table:last-child > tbody:last-child > tr:last-child th:last-child, +.panel > .table-responsive:last-child > .table:last-child > tbody:last-child > tr:last-child th:last-child, +.panel > .table:last-child > tfoot:last-child > tr:last-child th:last-child, +.panel > .table-responsive:last-child > .table:last-child > tfoot:last-child > tr:last-child th:last-child { + border-bottom-right-radius: 3px; +} +.panel > .panel-body + .table, +.panel > .panel-body + .table-responsive, +.panel > .table + .panel-body, +.panel > .table-responsive + .panel-body { + border-top: 1px solid #ddd; +} +.panel > .table > tbody:first-child > tr:first-child th, +.panel > .table > tbody:first-child > tr:first-child td { + border-top: 0; +} +.panel > .table-bordered, +.panel > .table-responsive > .table-bordered { + border: 0; +} +.panel > .table-bordered > thead > tr > th:first-child, +.panel > .table-responsive > .table-bordered > thead > tr > th:first-child, +.panel > .table-bordered > tbody > tr > th:first-child, +.panel > .table-responsive > .table-bordered > tbody > tr > th:first-child, +.panel > .table-bordered > tfoot > tr > th:first-child, +.panel > .table-responsive > .table-bordered > tfoot > tr > th:first-child, +.panel > .table-bordered > thead > tr > td:first-child, +.panel > .table-responsive > .table-bordered > thead > tr > td:first-child, +.panel > .table-bordered > tbody > tr > td:first-child, +.panel > .table-responsive > .table-bordered > tbody > tr > td:first-child, +.panel > .table-bordered > tfoot > tr > td:first-child, +.panel > .table-responsive > .table-bordered > tfoot > tr > td:first-child { + border-left: 0; +} +.panel > .table-bordered > thead > tr > th:last-child, +.panel > .table-responsive > .table-bordered > thead > tr > th:last-child, +.panel > .table-bordered > tbody > tr > th:last-child, +.panel > .table-responsive > .table-bordered > tbody > tr > th:last-child, +.panel > .table-bordered > tfoot > tr > th:last-child, +.panel > .table-responsive > .table-bordered > tfoot > tr > th:last-child, +.panel > .table-bordered > thead > tr > td:last-child, +.panel > .table-responsive > .table-bordered > thead > tr > td:last-child, +.panel > .table-bordered > tbody > tr > td:last-child, +.panel > .table-responsive > .table-bordered > tbody > tr > td:last-child, +.panel > .table-bordered > tfoot > tr > td:last-child, +.panel > .table-responsive > .table-bordered > tfoot > tr > td:last-child { + border-right: 0; +} +.panel > .table-bordered > thead > tr:first-child > td, +.panel > .table-responsive > .table-bordered > thead > tr:first-child > td, +.panel > .table-bordered > tbody > tr:first-child > td, +.panel > .table-responsive > .table-bordered > tbody > tr:first-child > td, +.panel > .table-bordered > thead > tr:first-child > th, +.panel > .table-responsive > .table-bordered > thead > tr:first-child > th, +.panel > .table-bordered > tbody > tr:first-child > th, +.panel > .table-responsive > .table-bordered > tbody > tr:first-child > th { + border-bottom: 0; +} +.panel > .table-bordered > tbody > tr:last-child > td, +.panel > .table-responsive > .table-bordered > tbody > tr:last-child > td, +.panel > .table-bordered > tfoot > tr:last-child > td, +.panel > .table-responsive > .table-bordered > tfoot > tr:last-child > td, +.panel > .table-bordered > tbody > tr:last-child > th, +.panel > .table-responsive > .table-bordered > tbody > tr:last-child > th, +.panel > .table-bordered > tfoot > tr:last-child > th, +.panel > .table-responsive > .table-bordered > tfoot > tr:last-child > th { + border-bottom: 0; +} +.panel > .table-responsive { + margin-bottom: 0; + border: 0; +} +.panel-group { + margin-bottom: 20px; +} +.panel-group .panel { + margin-bottom: 0; + border-radius: 4px; +} +.panel-group .panel + .panel { + margin-top: 5px; +} +.panel-group .panel-heading { + border-bottom: 0; +} +.panel-group .panel-heading + .panel-collapse > .panel-body, +.panel-group .panel-heading + .panel-collapse > .list-group { + border-top: 1px solid #ddd; +} +.panel-group .panel-footer { + border-top: 0; +} +.panel-group .panel-footer + .panel-collapse .panel-body { + border-bottom: 1px solid #ddd; +} +.panel-default { + border-color: #ddd; +} +.panel-default > .panel-heading { + color: #333; + background-color: #f5f5f5; + border-color: #ddd; +} +.panel-default > .panel-heading + .panel-collapse > .panel-body { + border-top-color: #ddd; +} +.panel-default > .panel-heading .badge { + color: #f5f5f5; + background-color: #333; +} +.panel-default > .panel-footer + .panel-collapse > .panel-body { + border-bottom-color: #ddd; +} +.panel-primary { + border-color: #337ab7; +} +.panel-primary > .panel-heading { + color: #fff; + background-color: #337ab7; + border-color: #337ab7; +} +.panel-primary > .panel-heading + .panel-collapse > .panel-body { + border-top-color: #337ab7; +} +.panel-primary > .panel-heading .badge { + color: #337ab7; + background-color: #fff; +} +.panel-primary > .panel-footer + .panel-collapse > .panel-body { + border-bottom-color: #337ab7; +} +.panel-success { + border-color: #d6e9c6; +} +.panel-success > .panel-heading { + color: #3c763d; + background-color: #dff0d8; + border-color: #d6e9c6; +} +.panel-success > .panel-heading + .panel-collapse > .panel-body { + border-top-color: #d6e9c6; +} +.panel-success > .panel-heading .badge { + color: #dff0d8; + background-color: #3c763d; +} +.panel-success > .panel-footer + .panel-collapse > .panel-body { + border-bottom-color: #d6e9c6; +} +.panel-info { + border-color: #bce8f1; +} +.panel-info > .panel-heading { + color: #31708f; + background-color: #d9edf7; + border-color: #bce8f1; +} +.panel-info > .panel-heading + .panel-collapse > .panel-body { + border-top-color: #bce8f1; +} +.panel-info > .panel-heading .badge { + color: #d9edf7; + background-color: #31708f; +} +.panel-info > .panel-footer + .panel-collapse > .panel-body { + border-bottom-color: #bce8f1; +} +.panel-warning { + border-color: #faebcc; +} +.panel-warning > .panel-heading { + color: #8a6d3b; + background-color: #fcf8e3; + border-color: #faebcc; +} +.panel-warning > .panel-heading + .panel-collapse > .panel-body { + border-top-color: #faebcc; +} +.panel-warning > .panel-heading .badge { + color: #fcf8e3; + background-color: #8a6d3b; +} +.panel-warning > .panel-footer + .panel-collapse > .panel-body { + border-bottom-color: #faebcc; +} +.panel-danger { + border-color: #ebccd1; +} +.panel-danger > .panel-heading { + color: #a94442; + background-color: #f2dede; + border-color: #ebccd1; +} +.panel-danger > .panel-heading + .panel-collapse > .panel-body { + border-top-color: #ebccd1; +} +.panel-danger > .panel-heading .badge { + color: #f2dede; + background-color: #a94442; +} +.panel-danger > .panel-footer + .panel-collapse > .panel-body { + border-bottom-color: #ebccd1; +} +.embed-responsive { + position: relative; + display: block; + height: 0; + padding: 0; + overflow: hidden; +} +.embed-responsive .embed-responsive-item, +.embed-responsive iframe, +.embed-responsive embed, +.embed-responsive object, +.embed-responsive video { + position: absolute; + top: 0; + bottom: 0; + left: 0; + width: 100%; + height: 100%; + border: 0; +} +.embed-responsive-16by9 { + padding-bottom: 56.25%; +} +.embed-responsive-4by3 { + padding-bottom: 75%; +} +.well { + min-height: 20px; + padding: 19px; + margin-bottom: 20px; + background-color: #f5f5f5; + border: 1px solid #e3e3e3; + border-radius: 4px; + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .05); + box-shadow: inset 0 1px 1px rgba(0, 0, 0, .05); +} +.well blockquote { + border-color: #ddd; + border-color: rgba(0, 0, 0, .15); +} +.well-lg { + padding: 24px; + border-radius: 6px; +} +.well-sm { + padding: 9px; + border-radius: 3px; +} +.close { + float: right; + font-size: 21px; + font-weight: bold; + line-height: 1; + color: #000; + text-shadow: 0 1px 0 #fff; + filter: alpha(opacity=20); + opacity: .2; +} +.close:hover, +.close:focus { + color: #000; + text-decoration: none; + cursor: pointer; + filter: alpha(opacity=50); + opacity: .5; +} +button.close { + -webkit-appearance: none; + padding: 0; + cursor: pointer; + background: transparent; + border: 0; +} +.modal-open { + overflow: hidden; +} +.modal { + position: fixed; + top: 0; + right: 0; + bottom: 0; + left: 0; + z-index: 1050; + display: none; + overflow: hidden; + -webkit-overflow-scrolling: touch; + outline: 0; +} +.modal.fade .modal-dialog { + -webkit-transition: -webkit-transform .3s ease-out; + -o-transition: -o-transform .3s ease-out; + transition: transform .3s ease-out; + -webkit-transform: translate(0, -25%); + -ms-transform: translate(0, -25%); + -o-transform: translate(0, -25%); + transform: translate(0, -25%); +} +.modal.in .modal-dialog { + -webkit-transform: translate(0, 0); + -ms-transform: translate(0, 0); + -o-transform: translate(0, 0); + transform: translate(0, 0); +} +.modal-open .modal { + overflow-x: hidden; + overflow-y: auto; +} +.modal-dialog { + position: relative; + width: auto; + margin: 10px; +} +.modal-content { + position: relative; + background-color: #fff; + -webkit-background-clip: padding-box; + background-clip: padding-box; + border: 1px solid #999; + border: 1px solid rgba(0, 0, 0, .2); + border-radius: 6px; + outline: 0; + -webkit-box-shadow: 0 3px 9px rgba(0, 0, 0, .5); + box-shadow: 0 3px 9px rgba(0, 0, 0, .5); +} +.modal-backdrop { + position: fixed; + top: 0; + right: 0; + bottom: 0; + left: 0; + z-index: 1040; + background-color: #000; +} +.modal-backdrop.fade { + filter: alpha(opacity=0); + opacity: 0; +} +.modal-backdrop.in { + filter: alpha(opacity=50); + opacity: .5; +} +.modal-header { + padding: 15px; + border-bottom: 1px solid #e5e5e5; +} +.modal-header .close { + margin-top: -2px; +} +.modal-title { + margin: 0; + line-height: 1.42857143; +} +.modal-body { + position: relative; + padding: 15px; +} +.modal-footer { + padding: 15px; + text-align: right; + border-top: 1px solid #e5e5e5; +} +.modal-footer .btn + .btn { + margin-bottom: 0; + margin-left: 5px; +} +.modal-footer .btn-group .btn + .btn { + margin-left: -1px; +} +.modal-footer .btn-block + .btn-block { + margin-left: 0; +} +.modal-scrollbar-measure { + position: absolute; + top: -9999px; + width: 50px; + height: 50px; + overflow: scroll; +} +@media (min-width: 768px) { + .modal-dialog { + width: 600px; + margin: 30px auto; + } + .modal-content { + -webkit-box-shadow: 0 5px 15px rgba(0, 0, 0, .5); + box-shadow: 0 5px 15px rgba(0, 0, 0, .5); + } + .modal-sm { + width: 300px; + } +} +@media (min-width: 992px) { + .modal-lg { + width: 900px; + } +} +.tooltip { + position: absolute; + z-index: 1070; + display: block; + font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; + font-size: 12px; + font-style: normal; + font-weight: normal; + line-height: 1.42857143; + text-align: left; + text-align: start; + text-decoration: none; + text-shadow: none; + text-transform: none; + letter-spacing: normal; + word-break: normal; + word-spacing: normal; + word-wrap: normal; + white-space: normal; + filter: alpha(opacity=0); + opacity: 0; + + line-break: auto; +} +.tooltip.in { + filter: alpha(opacity=90); + opacity: .9; +} +.tooltip.top { + padding: 5px 0; + margin-top: -3px; +} +.tooltip.right { + padding: 0 5px; + margin-left: 3px; +} +.tooltip.bottom { + padding: 5px 0; + margin-top: 3px; +} +.tooltip.left { + padding: 0 5px; + margin-left: -3px; +} +.tooltip-inner { + max-width: 200px; + padding: 3px 8px; + color: #fff; + text-align: center; + background-color: #000; + border-radius: 4px; +} +.tooltip-arrow { + position: absolute; + width: 0; + height: 0; + border-color: transparent; + border-style: solid; +} +.tooltip.top .tooltip-arrow { + bottom: 0; + left: 50%; + margin-left: -5px; + border-width: 5px 5px 0; + border-top-color: #000; +} +.tooltip.top-left .tooltip-arrow { + right: 5px; + bottom: 0; + margin-bottom: -5px; + border-width: 5px 5px 0; + border-top-color: #000; +} +.tooltip.top-right .tooltip-arrow { + bottom: 0; + left: 5px; + margin-bottom: -5px; + border-width: 5px 5px 0; + border-top-color: #000; +} +.tooltip.right .tooltip-arrow { + top: 50%; + left: 0; + margin-top: -5px; + border-width: 5px 5px 5px 0; + border-right-color: #000; +} +.tooltip.left .tooltip-arrow { + top: 50%; + right: 0; + margin-top: -5px; + border-width: 5px 0 5px 5px; + border-left-color: #000; +} +.tooltip.bottom .tooltip-arrow { + top: 0; + left: 50%; + margin-left: -5px; + border-width: 0 5px 5px; + border-bottom-color: #000; +} +.tooltip.bottom-left .tooltip-arrow { + top: 0; + right: 5px; + margin-top: -5px; + border-width: 0 5px 5px; + border-bottom-color: #000; +} +.tooltip.bottom-right .tooltip-arrow { + top: 0; + left: 5px; + margin-top: -5px; + border-width: 0 5px 5px; + border-bottom-color: #000; +} +.popover { + position: absolute; + top: 0; + left: 0; + z-index: 1060; + display: none; + max-width: 276px; + padding: 1px; + font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; + font-size: 14px; + font-style: normal; + font-weight: normal; + line-height: 1.42857143; + text-align: left; + text-align: start; + text-decoration: none; + text-shadow: none; + text-transform: none; + letter-spacing: normal; + word-break: normal; + word-spacing: normal; + word-wrap: normal; + white-space: normal; + background-color: #fff; + -webkit-background-clip: padding-box; + background-clip: padding-box; + border: 1px solid #ccc; + border: 1px solid rgba(0, 0, 0, .2); + border-radius: 6px; + -webkit-box-shadow: 0 5px 10px rgba(0, 0, 0, .2); + box-shadow: 0 5px 10px rgba(0, 0, 0, .2); + + line-break: auto; +} +.popover.top { + margin-top: -10px; +} +.popover.right { + margin-left: 10px; +} +.popover.bottom { + margin-top: 10px; +} +.popover.left { + margin-left: -10px; +} +.popover-title { + padding: 8px 14px; + margin: 0; + font-size: 14px; + background-color: #f7f7f7; + border-bottom: 1px solid #ebebeb; + border-radius: 5px 5px 0 0; +} +.popover-content { + padding: 9px 14px; +} +.popover > .arrow, +.popover > .arrow:after { + position: absolute; + display: block; + width: 0; + height: 0; + border-color: transparent; + border-style: solid; +} +.popover > .arrow { + border-width: 11px; +} +.popover > .arrow:after { + content: ""; + border-width: 10px; +} +.popover.top > .arrow { + bottom: -11px; + left: 50%; + margin-left: -11px; + border-top-color: #999; + border-top-color: rgba(0, 0, 0, .25); + border-bottom-width: 0; +} +.popover.top > .arrow:after { + bottom: 1px; + margin-left: -10px; + content: " "; + border-top-color: #fff; + border-bottom-width: 0; +} +.popover.right > .arrow { + top: 50%; + left: -11px; + margin-top: -11px; + border-right-color: #999; + border-right-color: rgba(0, 0, 0, .25); + border-left-width: 0; +} +.popover.right > .arrow:after { + bottom: -10px; + left: 1px; + content: " "; + border-right-color: #fff; + border-left-width: 0; +} +.popover.bottom > .arrow { + top: -11px; + left: 50%; + margin-left: -11px; + border-top-width: 0; + border-bottom-color: #999; + border-bottom-color: rgba(0, 0, 0, .25); +} +.popover.bottom > .arrow:after { + top: 1px; + margin-left: -10px; + content: " "; + border-top-width: 0; + border-bottom-color: #fff; +} +.popover.left > .arrow { + top: 50%; + right: -11px; + margin-top: -11px; + border-right-width: 0; + border-left-color: #999; + border-left-color: rgba(0, 0, 0, .25); +} +.popover.left > .arrow:after { + right: 1px; + bottom: -10px; + content: " "; + border-right-width: 0; + border-left-color: #fff; +} +.carousel { + position: relative; +} +.carousel-inner { + position: relative; + width: 100%; + overflow: hidden; +} +.carousel-inner > .item { + position: relative; + display: none; + -webkit-transition: .6s ease-in-out left; + -o-transition: .6s ease-in-out left; + transition: .6s ease-in-out left; +} +.carousel-inner > .item > img, +.carousel-inner > .item > a > img { + line-height: 1; +} +@media all and (transform-3d), (-webkit-transform-3d) { + .carousel-inner > .item { + -webkit-transition: -webkit-transform .6s ease-in-out; + -o-transition: -o-transform .6s ease-in-out; + transition: transform .6s ease-in-out; + + -webkit-backface-visibility: hidden; + backface-visibility: hidden; + -webkit-perspective: 1000px; + perspective: 1000px; + } + .carousel-inner > .item.next, + .carousel-inner > .item.active.right { + left: 0; + -webkit-transform: translate3d(100%, 0, 0); + transform: translate3d(100%, 0, 0); + } + .carousel-inner > .item.prev, + .carousel-inner > .item.active.left { + left: 0; + -webkit-transform: translate3d(-100%, 0, 0); + transform: translate3d(-100%, 0, 0); + } + .carousel-inner > .item.next.left, + .carousel-inner > .item.prev.right, + .carousel-inner > .item.active { + left: 0; + -webkit-transform: translate3d(0, 0, 0); + transform: translate3d(0, 0, 0); + } +} +.carousel-inner > .active, +.carousel-inner > .next, +.carousel-inner > .prev { + display: block; +} +.carousel-inner > .active { + left: 0; +} +.carousel-inner > .next, +.carousel-inner > .prev { + position: absolute; + top: 0; + width: 100%; +} +.carousel-inner > .next { + left: 100%; +} +.carousel-inner > .prev { + left: -100%; +} +.carousel-inner > .next.left, +.carousel-inner > .prev.right { + left: 0; +} +.carousel-inner > .active.left { + left: -100%; +} +.carousel-inner > .active.right { + left: 100%; +} +.carousel-control { + position: absolute; + top: 0; + bottom: 0; + left: 0; + width: 15%; + font-size: 20px; + color: #fff; + text-align: center; + text-shadow: 0 1px 2px rgba(0, 0, 0, .6); + background-color: rgba(0, 0, 0, 0); + filter: alpha(opacity=50); + opacity: .5; +} +.carousel-control.left { + background-image: -webkit-linear-gradient(left, rgba(0, 0, 0, .5) 0%, rgba(0, 0, 0, .0001) 100%); + background-image: -o-linear-gradient(left, rgba(0, 0, 0, .5) 0%, rgba(0, 0, 0, .0001) 100%); + background-image: -webkit-gradient(linear, left top, right top, from(rgba(0, 0, 0, .5)), to(rgba(0, 0, 0, .0001))); + background-image: linear-gradient(to right, rgba(0, 0, 0, .5) 0%, rgba(0, 0, 0, .0001) 100%); + filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#80000000', endColorstr='#00000000', GradientType=1); + background-repeat: repeat-x; +} +.carousel-control.right { + right: 0; + left: auto; + background-image: -webkit-linear-gradient(left, rgba(0, 0, 0, .0001) 0%, rgba(0, 0, 0, .5) 100%); + background-image: -o-linear-gradient(left, rgba(0, 0, 0, .0001) 0%, rgba(0, 0, 0, .5) 100%); + background-image: -webkit-gradient(linear, left top, right top, from(rgba(0, 0, 0, .0001)), to(rgba(0, 0, 0, .5))); + background-image: linear-gradient(to right, rgba(0, 0, 0, .0001) 0%, rgba(0, 0, 0, .5) 100%); + filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#00000000', endColorstr='#80000000', GradientType=1); + background-repeat: repeat-x; +} +.carousel-control:hover, +.carousel-control:focus { + color: #fff; + text-decoration: none; + filter: alpha(opacity=90); + outline: 0; + opacity: .9; +} +.carousel-control .icon-prev, +.carousel-control .icon-next, +.carousel-control .glyphicon-chevron-left, +.carousel-control .glyphicon-chevron-right { + position: absolute; + top: 50%; + z-index: 5; + display: inline-block; + margin-top: -10px; +} +.carousel-control .icon-prev, +.carousel-control .glyphicon-chevron-left { + left: 50%; + margin-left: -10px; +} +.carousel-control .icon-next, +.carousel-control .glyphicon-chevron-right { + right: 50%; + margin-right: -10px; +} +.carousel-control .icon-prev, +.carousel-control .icon-next { + width: 20px; + height: 20px; + font-family: serif; + line-height: 1; +} +.carousel-control .icon-prev:before { + content: '\2039'; +} +.carousel-control .icon-next:before { + content: '\203a'; +} +.carousel-indicators { + position: absolute; + bottom: 10px; + left: 50%; + z-index: 15; + width: 60%; + padding-left: 0; + margin-left: -30%; + text-align: center; + list-style: none; +} +.carousel-indicators li { + display: inline-block; + width: 10px; + height: 10px; + margin: 1px; + text-indent: -999px; + cursor: pointer; + background-color: #000 \9; + background-color: rgba(0, 0, 0, 0); + border: 1px solid #fff; + border-radius: 10px; +} +.carousel-indicators .active { + width: 12px; + height: 12px; + margin: 0; + background-color: #fff; +} +.carousel-caption { + position: absolute; + right: 15%; + bottom: 20px; + left: 15%; + z-index: 10; + padding-top: 20px; + padding-bottom: 20px; + color: #fff; + text-align: center; + text-shadow: 0 1px 2px rgba(0, 0, 0, .6); +} +.carousel-caption .btn { + text-shadow: none; +} +@media screen and (min-width: 768px) { + .carousel-control .glyphicon-chevron-left, + .carousel-control .glyphicon-chevron-right, + .carousel-control .icon-prev, + .carousel-control .icon-next { + width: 30px; + height: 30px; + margin-top: -10px; + font-size: 30px; + } + .carousel-control .glyphicon-chevron-left, + .carousel-control .icon-prev { + margin-left: -10px; + } + .carousel-control .glyphicon-chevron-right, + .carousel-control .icon-next { + margin-right: -10px; + } + .carousel-caption { + right: 20%; + left: 20%; + padding-bottom: 30px; + } + .carousel-indicators { + bottom: 20px; + } +} +.clearfix:before, +.clearfix:after, +.dl-horizontal dd:before, +.dl-horizontal dd:after, +.container:before, +.container:after, +.container-fluid:before, +.container-fluid:after, +.row:before, +.row:after, +.form-horizontal .form-group:before, +.form-horizontal .form-group:after, +.btn-toolbar:before, +.btn-toolbar:after, +.btn-group-vertical > .btn-group:before, +.btn-group-vertical > .btn-group:after, +.nav:before, +.nav:after, +.navbar:before, +.navbar:after, +.navbar-header:before, +.navbar-header:after, +.navbar-collapse:before, +.navbar-collapse:after, +.pager:before, +.pager:after, +.panel-body:before, +.panel-body:after, +.modal-header:before, +.modal-header:after, +.modal-footer:before, +.modal-footer:after { + display: table; + content: " "; +} +.clearfix:after, +.dl-horizontal dd:after, +.container:after, +.container-fluid:after, +.row:after, +.form-horizontal .form-group:after, +.btn-toolbar:after, +.btn-group-vertical > .btn-group:after, +.nav:after, +.navbar:after, +.navbar-header:after, +.navbar-collapse:after, +.pager:after, +.panel-body:after, +.modal-header:after, +.modal-footer:after { + clear: both; +} +.center-block { + display: block; + margin-right: auto; + margin-left: auto; +} +.pull-right { + float: right !important; +} +.pull-left { + float: left !important; +} +.hide { + display: none !important; +} +.show { + display: block !important; +} +.invisible { + visibility: hidden; +} +.text-hide { + font: 0/0 a; + color: transparent; + text-shadow: none; + background-color: transparent; + border: 0; +} +.hidden { + display: none !important; +} +.affix { + position: fixed; +} +@-ms-viewport { + width: device-width; +} +.visible-xs, +.visible-sm, +.visible-md, +.visible-lg { + display: none !important; +} +.visible-xs-block, +.visible-xs-inline, +.visible-xs-inline-block, +.visible-sm-block, +.visible-sm-inline, +.visible-sm-inline-block, +.visible-md-block, +.visible-md-inline, +.visible-md-inline-block, +.visible-lg-block, +.visible-lg-inline, +.visible-lg-inline-block { + display: none !important; +} +@media (max-width: 767px) { + .visible-xs { + display: block !important; + } + table.visible-xs { + display: table !important; + } + tr.visible-xs { + display: table-row !important; + } + th.visible-xs, + td.visible-xs { + display: table-cell !important; + } +} +@media (max-width: 767px) { + .visible-xs-block { + display: block !important; + } +} +@media (max-width: 767px) { + .visible-xs-inline { + display: inline !important; + } +} +@media (max-width: 767px) { + .visible-xs-inline-block { + display: inline-block !important; + } +} +@media (min-width: 768px) and (max-width: 991px) { + .visible-sm { + display: block !important; + } + table.visible-sm { + display: table !important; + } + tr.visible-sm { + display: table-row !important; + } + th.visible-sm, + td.visible-sm { + display: table-cell !important; + } +} +@media (min-width: 768px) and (max-width: 991px) { + .visible-sm-block { + display: block !important; + } +} +@media (min-width: 768px) and (max-width: 991px) { + .visible-sm-inline { + display: inline !important; + } +} +@media (min-width: 768px) and (max-width: 991px) { + .visible-sm-inline-block { + display: inline-block !important; + } +} +@media (min-width: 992px) and (max-width: 1199px) { + .visible-md { + display: block !important; + } + table.visible-md { + display: table !important; + } + tr.visible-md { + display: table-row !important; + } + th.visible-md, + td.visible-md { + display: table-cell !important; + } +} +@media (min-width: 992px) and (max-width: 1199px) { + .visible-md-block { + display: block !important; + } +} +@media (min-width: 992px) and (max-width: 1199px) { + .visible-md-inline { + display: inline !important; + } +} +@media (min-width: 992px) and (max-width: 1199px) { + .visible-md-inline-block { + display: inline-block !important; + } +} +@media (min-width: 1200px) { + .visible-lg { + display: block !important; + } + table.visible-lg { + display: table !important; + } + tr.visible-lg { + display: table-row !important; + } + th.visible-lg, + td.visible-lg { + display: table-cell !important; + } +} +@media (min-width: 1200px) { + .visible-lg-block { + display: block !important; + } +} +@media (min-width: 1200px) { + .visible-lg-inline { + display: inline !important; + } +} +@media (min-width: 1200px) { + .visible-lg-inline-block { + display: inline-block !important; + } +} +@media (max-width: 767px) { + .hidden-xs { + display: none !important; + } +} +@media (min-width: 768px) and (max-width: 991px) { + .hidden-sm { + display: none !important; + } +} +@media (min-width: 992px) and (max-width: 1199px) { + .hidden-md { + display: none !important; + } +} +@media (min-width: 1200px) { + .hidden-lg { + display: none !important; + } +} +.visible-print { + display: none !important; +} +@media print { + .visible-print { + display: block !important; 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+ */ +/* FONT PATH + * -------------------------- */ +@font-face { + font-family: 'FontAwesome'; + src: url('http://github.com/fonts/fontawesome-webfont.eot?v=4.7.0'); + src: url('http://github.com/fonts/fontawesome-webfont.eot?#iefix&v=4.7.0') format('embedded-opentype'), url('http://github.com/fonts/fontawesome-webfont.woff2?v=4.7.0') format('woff2'), url('http://github.com/fonts/fontawesome-webfont.woff?v=4.7.0') format('woff'), url('http://github.com/fonts/fontawesome-webfont.ttf?v=4.7.0') format('truetype'), url('http://github.com/fonts/fontawesome-webfont.svg?v=4.7.0#fontawesomeregular') format('svg'); + font-weight: normal; + font-style: normal; +} +.fa { + display: inline-block; + font: normal normal normal 14px/1 FontAwesome; + font-size: inherit; + text-rendering: auto; + -webkit-font-smoothing: antialiased; + -moz-osx-font-smoothing: grayscale; +} +/* makes the font 33% larger relative to the icon container */ +.fa-lg { + font-size: 1.33333333em; + line-height: 0.75em; + vertical-align: -15%; +} +.fa-2x { + font-size: 2em; +} +.fa-3x { + font-size: 3em; +} +.fa-4x { + font-size: 4em; +} +.fa-5x { + font-size: 5em; +} +.fa-fw { + width: 1.28571429em; + text-align: center; +} +.fa-ul { + padding-left: 0; + margin-left: 2.14285714em; + list-style-type: none; +} +.fa-ul > li { + position: relative; +} +.fa-li { + position: absolute; + left: -2.14285714em; + width: 2.14285714em; + top: 0.14285714em; + text-align: center; +} +.fa-li.fa-lg { + left: -1.85714286em; +} +.fa-border { + padding: .2em .25em .15em; + border: solid 0.08em #eeeeee; + border-radius: .1em; +} +.fa-pull-left { + float: left; +} +.fa-pull-right { + float: right; +} +.fa.fa-pull-left { + margin-right: .3em; +} +.fa.fa-pull-right { + margin-left: .3em; +} +/* Deprecated as of 4.4.0 */ +.pull-right { + float: right; +} +.pull-left { + float: left; +} +.fa.pull-left { + margin-right: .3em; +} +.fa.pull-right { + margin-left: .3em; +} +.fa-spin { + -webkit-animation: fa-spin 2s infinite linear; + animation: fa-spin 2s infinite linear; +} +.fa-pulse { + -webkit-animation: fa-spin 1s infinite steps(8); + animation: fa-spin 1s infinite steps(8); +} +@-webkit-keyframes fa-spin { + 0% { + -webkit-transform: rotate(0deg); + transform: rotate(0deg); + } + 100% { + -webkit-transform: rotate(359deg); + transform: rotate(359deg); + } +} +@keyframes fa-spin { + 0% { + -webkit-transform: rotate(0deg); + transform: rotate(0deg); + } + 100% { + -webkit-transform: rotate(359deg); + transform: rotate(359deg); + } +} +.fa-rotate-90 { + -ms-filter: "progid:DXImageTransform.Microsoft.BasicImage(rotation=1)"; + -webkit-transform: rotate(90deg); + -ms-transform: rotate(90deg); + transform: rotate(90deg); +} +.fa-rotate-180 { + -ms-filter: "progid:DXImageTransform.Microsoft.BasicImage(rotation=2)"; + -webkit-transform: rotate(180deg); + -ms-transform: rotate(180deg); + transform: rotate(180deg); +} +.fa-rotate-270 { + -ms-filter: "progid:DXImageTransform.Microsoft.BasicImage(rotation=3)"; + -webkit-transform: rotate(270deg); + -ms-transform: rotate(270deg); + transform: rotate(270deg); +} +.fa-flip-horizontal { + -ms-filter: "progid:DXImageTransform.Microsoft.BasicImage(rotation=0, mirror=1)"; + -webkit-transform: scale(-1, 1); + -ms-transform: scale(-1, 1); + transform: scale(-1, 1); +} +.fa-flip-vertical { + -ms-filter: "progid:DXImageTransform.Microsoft.BasicImage(rotation=2, mirror=1)"; + -webkit-transform: scale(1, -1); + -ms-transform: scale(1, -1); + transform: scale(1, -1); +} +:root .fa-rotate-90, +:root .fa-rotate-180, +:root .fa-rotate-270, +:root .fa-flip-horizontal, +:root .fa-flip-vertical { + filter: none; +} +.fa-stack { + position: relative; + display: inline-block; + width: 2em; + height: 2em; + line-height: 2em; + vertical-align: middle; +} +.fa-stack-1x, +.fa-stack-2x { + position: absolute; + left: 0; + width: 100%; + text-align: center; +} +.fa-stack-1x { + line-height: inherit; +} +.fa-stack-2x { + font-size: 2em; +} +.fa-inverse { + color: #ffffff; +} +/* Font Awesome uses the Unicode Private Use Area (PUA) to ensure screen + readers do not read off random characters that represent icons */ +.fa-glass:before { + content: "\f000"; +} +.fa-music:before { + content: "\f001"; +} +.fa-search:before { + content: "\f002"; +} +.fa-envelope-o:before { + content: "\f003"; +} +.fa-heart:before { + content: "\f004"; +} +.fa-star:before { + content: "\f005"; +} +.fa-star-o:before { + content: "\f006"; +} +.fa-user:before { + content: "\f007"; +} +.fa-film:before { + content: "\f008"; +} +.fa-th-large:before { + content: "\f009"; +} +.fa-th:before { + content: "\f00a"; +} +.fa-th-list:before { + content: "\f00b"; +} +.fa-check:before { + content: "\f00c"; +} +.fa-remove:before, +.fa-close:before, +.fa-times:before { + content: "\f00d"; +} +.fa-search-plus:before { + content: "\f00e"; +} +.fa-search-minus:before { + content: "\f010"; +} +.fa-power-off:before { + content: "\f011"; +} +.fa-signal:before { + content: "\f012"; +} +.fa-gear:before, +.fa-cog:before { + content: "\f013"; +} +.fa-trash-o:before { + content: "\f014"; +} +.fa-home:before { + content: "\f015"; +} +.fa-file-o:before { + content: "\f016"; +} +.fa-clock-o:before { + content: "\f017"; +} +.fa-road:before { + content: "\f018"; +} +.fa-download:before { + content: "\f019"; +} +.fa-arrow-circle-o-down:before { + content: "\f01a"; +} +.fa-arrow-circle-o-up:before { + content: "\f01b"; +} +.fa-inbox:before { + content: "\f01c"; +} +.fa-play-circle-o:before { + content: "\f01d"; +} +.fa-rotate-right:before, +.fa-repeat:before { + content: "\f01e"; +} +.fa-refresh:before { + content: "\f021"; +} +.fa-list-alt:before { + content: "\f022"; +} +.fa-lock:before { + content: "\f023"; +} +.fa-flag:before { + content: "\f024"; +} +.fa-headphones:before { + content: "\f025"; +} +.fa-volume-off:before { + content: "\f026"; +} +.fa-volume-down:before { + content: "\f027"; +} +.fa-volume-up:before { + content: "\f028"; +} +.fa-qrcode:before { + content: "\f029"; +} +.fa-barcode:before { + content: "\f02a"; +} +.fa-tag:before { + content: "\f02b"; +} +.fa-tags:before { + content: "\f02c"; +} +.fa-book:before { + content: "\f02d"; +} +.fa-bookmark:before { + content: "\f02e"; +} +.fa-print:before { + content: "\f02f"; +} +.fa-camera:before { + content: "\f030"; +} +.fa-font:before { + content: "\f031"; +} +.fa-bold:before { + content: "\f032"; +} +.fa-italic:before { + content: "\f033"; +} +.fa-text-height:before { + content: "\f034"; +} +.fa-text-width:before { + content: "\f035"; +} +.fa-align-left:before { + content: "\f036"; +} +.fa-align-center:before { + content: "\f037"; +} +.fa-align-right:before { + content: "\f038"; +} +.fa-align-justify:before { + content: "\f039"; +} +.fa-list:before { + content: "\f03a"; +} +.fa-dedent:before, +.fa-outdent:before { + content: "\f03b"; +} +.fa-indent:before { + content: "\f03c"; +} +.fa-video-camera:before { + content: "\f03d"; +} +.fa-photo:before, +.fa-image:before, +.fa-picture-o:before { + content: "\f03e"; +} +.fa-pencil:before { + content: "\f040"; +} +.fa-map-marker:before { + content: "\f041"; +} +.fa-adjust:before { + content: "\f042"; +} +.fa-tint:before { + content: "\f043"; +} +.fa-edit:before, +.fa-pencil-square-o:before { + content: "\f044"; +} +.fa-share-square-o:before { + content: "\f045"; +} +.fa-check-square-o:before { + content: "\f046"; +} +.fa-arrows:before { + content: "\f047"; +} +.fa-step-backward:before { + content: "\f048"; +} +.fa-fast-backward:before { + content: "\f049"; +} +.fa-backward:before { + content: "\f04a"; +} +.fa-play:before { + content: "\f04b"; +} +.fa-pause:before { + content: "\f04c"; +} +.fa-stop:before { + content: "\f04d"; +} +.fa-forward:before { + content: "\f04e"; +} +.fa-fast-forward:before { + content: "\f050"; +} +.fa-step-forward:before { + content: "\f051"; +} +.fa-eject:before { + content: "\f052"; +} +.fa-chevron-left:before { + content: "\f053"; +} +.fa-chevron-right:before { + content: "\f054"; +} +.fa-plus-circle:before { + content: "\f055"; +} +.fa-minus-circle:before { + content: "\f056"; +} +.fa-times-circle:before { + content: "\f057"; +} +.fa-check-circle:before { + content: "\f058"; +} +.fa-question-circle:before { + content: "\f059"; +} +.fa-info-circle:before { + content: "\f05a"; +} +.fa-crosshairs:before { + content: "\f05b"; +} +.fa-times-circle-o:before { + content: "\f05c"; +} +.fa-check-circle-o:before { + content: "\f05d"; +} +.fa-ban:before { + content: "\f05e"; +} +.fa-arrow-left:before { + content: "\f060"; +} +.fa-arrow-right:before { + content: "\f061"; +} +.fa-arrow-up:before { + content: "\f062"; +} +.fa-arrow-down:before { + content: "\f063"; +} +.fa-mail-forward:before, +.fa-share:before { + content: "\f064"; +} +.fa-expand:before { + content: "\f065"; +} +.fa-compress:before { + content: "\f066"; +} +.fa-plus:before { + content: "\f067"; +} +.fa-minus:before { + content: "\f068"; +} +.fa-asterisk:before { + content: "\f069"; +} +.fa-exclamation-circle:before { + content: "\f06a"; +} +.fa-gift:before { + content: "\f06b"; +} +.fa-leaf:before { + content: "\f06c"; +} +.fa-fire:before { + content: "\f06d"; +} +.fa-eye:before { + content: "\f06e"; +} +.fa-eye-slash:before { + content: "\f070"; +} +.fa-warning:before, +.fa-exclamation-triangle:before { + content: "\f071"; +} +.fa-plane:before { + content: "\f072"; +} +.fa-calendar:before { + content: "\f073"; +} +.fa-random:before { + content: "\f074"; +} +.fa-comment:before { + content: "\f075"; +} +.fa-magnet:before { + content: "\f076"; +} +.fa-chevron-up:before { + content: "\f077"; +} +.fa-chevron-down:before { + content: "\f078"; +} +.fa-retweet:before { + content: "\f079"; +} +.fa-shopping-cart:before { + content: "\f07a"; +} +.fa-folder:before { + content: "\f07b"; +} +.fa-folder-open:before { + content: "\f07c"; +} +.fa-arrows-v:before { + content: "\f07d"; +} +.fa-arrows-h:before { + content: "\f07e"; +} +.fa-bar-chart-o:before, +.fa-bar-chart:before { + content: "\f080"; +} +.fa-twitter-square:before { + content: "\f081"; +} +.fa-facebook-square:before { + content: "\f082"; +} +.fa-camera-retro:before { + content: "\f083"; +} +.fa-key:before { + content: "\f084"; +} +.fa-gears:before, +.fa-cogs:before { + content: "\f085"; +} +.fa-comments:before { + content: "\f086"; +} +.fa-thumbs-o-up:before { + content: "\f087"; +} +.fa-thumbs-o-down:before { + content: "\f088"; +} +.fa-star-half:before { + content: "\f089"; +} +.fa-heart-o:before { + content: "\f08a"; +} +.fa-sign-out:before { + content: "\f08b"; +} +.fa-linkedin-square:before { + content: "\f08c"; +} +.fa-thumb-tack:before { + content: "\f08d"; +} +.fa-external-link:before { + content: "\f08e"; +} +.fa-sign-in:before { + content: "\f090"; +} +.fa-trophy:before { + content: "\f091"; +} +.fa-github-square:before { + content: "\f092"; +} +.fa-upload:before { + content: "\f093"; +} +.fa-lemon-o:before { + content: "\f094"; +} +.fa-phone:before { + content: "\f095"; +} +.fa-square-o:before { + content: "\f096"; +} +.fa-bookmark-o:before { + content: "\f097"; +} +.fa-phone-square:before { + content: "\f098"; +} +.fa-twitter:before { + content: "\f099"; +} +.fa-facebook-f:before, +.fa-facebook:before { + content: "\f09a"; +} +.fa-github:before { + content: "\f09b"; +} +.fa-unlock:before { + content: "\f09c"; +} +.fa-credit-card:before { + content: "\f09d"; +} +.fa-feed:before, +.fa-rss:before { + content: "\f09e"; +} +.fa-hdd-o:before { + content: "\f0a0"; +} +.fa-bullhorn:before { + content: "\f0a1"; +} +.fa-bell:before { + content: "\f0f3"; +} +.fa-certificate:before { + content: "\f0a3"; +} +.fa-hand-o-right:before { + content: "\f0a4"; +} +.fa-hand-o-left:before { + content: "\f0a5"; +} +.fa-hand-o-up:before { + content: "\f0a6"; +} +.fa-hand-o-down:before { + content: "\f0a7"; +} +.fa-arrow-circle-left:before { + content: "\f0a8"; +} +.fa-arrow-circle-right:before { + content: "\f0a9"; +} +.fa-arrow-circle-up:before { + content: "\f0aa"; +} +.fa-arrow-circle-down:before { + content: "\f0ab"; +} +.fa-globe:before { + content: "\f0ac"; +} +.fa-wrench:before { + content: "\f0ad"; +} +.fa-tasks:before { + content: "\f0ae"; +} +.fa-filter:before { + content: "\f0b0"; +} +.fa-briefcase:before { + content: "\f0b1"; +} +.fa-arrows-alt:before { + content: "\f0b2"; +} +.fa-group:before, +.fa-users:before { + content: "\f0c0"; +} +.fa-chain:before, +.fa-link:before { + content: "\f0c1"; +} +.fa-cloud:before { + content: "\f0c2"; +} +.fa-flask:before { + content: "\f0c3"; +} +.fa-cut:before, +.fa-scissors:before { + content: "\f0c4"; +} +.fa-copy:before, +.fa-files-o:before { + content: "\f0c5"; +} +.fa-paperclip:before { + content: "\f0c6"; +} +.fa-save:before, +.fa-floppy-o:before { + content: "\f0c7"; +} +.fa-square:before { + content: "\f0c8"; +} +.fa-navicon:before, +.fa-reorder:before, +.fa-bars:before { + content: "\f0c9"; +} +.fa-list-ul:before { + content: "\f0ca"; +} +.fa-list-ol:before { + content: "\f0cb"; +} +.fa-strikethrough:before { + content: "\f0cc"; +} +.fa-underline:before { + content: "\f0cd"; +} +.fa-table:before { + content: "\f0ce"; +} +.fa-magic:before { + content: "\f0d0"; +} +.fa-truck:before { + content: "\f0d1"; +} +.fa-pinterest:before { + content: "\f0d2"; +} +.fa-pinterest-square:before { + content: "\f0d3"; +} +.fa-google-plus-square:before { + content: "\f0d4"; +} +.fa-google-plus:before { + content: "\f0d5"; +} +.fa-money:before { + content: "\f0d6"; +} +.fa-caret-down:before { + content: "\f0d7"; +} +.fa-caret-up:before { + content: "\f0d8"; +} +.fa-caret-left:before { + content: "\f0d9"; +} +.fa-caret-right:before { + content: "\f0da"; +} +.fa-columns:before { + content: "\f0db"; +} +.fa-unsorted:before, +.fa-sort:before { + content: "\f0dc"; +} +.fa-sort-down:before, +.fa-sort-desc:before { + content: "\f0dd"; +} +.fa-sort-up:before, +.fa-sort-asc:before { + content: "\f0de"; +} +.fa-envelope:before { + content: "\f0e0"; +} +.fa-linkedin:before { + content: "\f0e1"; +} +.fa-rotate-left:before, +.fa-undo:before { + content: "\f0e2"; +} +.fa-legal:before, +.fa-gavel:before { + content: "\f0e3"; +} +.fa-dashboard:before, +.fa-tachometer:before { + content: "\f0e4"; +} +.fa-comment-o:before { + content: "\f0e5"; +} +.fa-comments-o:before { + content: "\f0e6"; +} +.fa-flash:before, +.fa-bolt:before { + content: "\f0e7"; +} +.fa-sitemap:before { + content: "\f0e8"; +} +.fa-umbrella:before { + content: "\f0e9"; +} +.fa-paste:before, +.fa-clipboard:before { + content: "\f0ea"; +} +.fa-lightbulb-o:before { + content: "\f0eb"; +} +.fa-exchange:before { + content: "\f0ec"; +} +.fa-cloud-download:before { + content: "\f0ed"; +} +.fa-cloud-upload:before { + content: "\f0ee"; +} +.fa-user-md:before { + content: "\f0f0"; +} +.fa-stethoscope:before { + content: "\f0f1"; +} +.fa-suitcase:before { + content: "\f0f2"; +} +.fa-bell-o:before { + content: "\f0a2"; +} +.fa-coffee:before { + content: "\f0f4"; +} +.fa-cutlery:before { + content: "\f0f5"; +} +.fa-file-text-o:before { + content: "\f0f6"; +} +.fa-building-o:before { + content: "\f0f7"; +} +.fa-hospital-o:before { + content: "\f0f8"; +} +.fa-ambulance:before { + content: "\f0f9"; +} +.fa-medkit:before { + content: "\f0fa"; +} +.fa-fighter-jet:before { + content: "\f0fb"; +} +.fa-beer:before { + content: "\f0fc"; +} +.fa-h-square:before { + content: "\f0fd"; +} +.fa-plus-square:before { + content: "\f0fe"; +} +.fa-angle-double-left:before { + content: "\f100"; +} +.fa-angle-double-right:before { + content: "\f101"; +} +.fa-angle-double-up:before { + content: "\f102"; +} +.fa-angle-double-down:before { + content: "\f103"; +} +.fa-angle-left:before { + content: "\f104"; +} +.fa-angle-right:before { + content: "\f105"; +} +.fa-angle-up:before { + content: "\f106"; +} +.fa-angle-down:before { + content: "\f107"; +} +.fa-desktop:before { + content: "\f108"; +} +.fa-laptop:before { + content: "\f109"; +} +.fa-tablet:before { + content: "\f10a"; +} +.fa-mobile-phone:before, +.fa-mobile:before { + content: "\f10b"; +} +.fa-circle-o:before { + content: "\f10c"; +} +.fa-quote-left:before { + content: "\f10d"; +} +.fa-quote-right:before { + content: "\f10e"; +} +.fa-spinner:before { + content: "\f110"; +} +.fa-circle:before { + content: "\f111"; +} +.fa-mail-reply:before, +.fa-reply:before { + content: "\f112"; +} +.fa-github-alt:before { + content: "\f113"; +} +.fa-folder-o:before { + content: "\f114"; +} +.fa-folder-open-o:before { + content: "\f115"; +} +.fa-smile-o:before { + content: "\f118"; +} +.fa-frown-o:before { + content: "\f119"; +} +.fa-meh-o:before { + content: "\f11a"; +} +.fa-gamepad:before { + content: "\f11b"; +} +.fa-keyboard-o:before { + content: "\f11c"; +} +.fa-flag-o:before { + content: "\f11d"; +} +.fa-flag-checkered:before { + content: "\f11e"; +} +.fa-terminal:before { + content: "\f120"; +} +.fa-code:before { + content: "\f121"; +} +.fa-mail-reply-all:before, +.fa-reply-all:before { + content: "\f122"; +} +.fa-star-half-empty:before, +.fa-star-half-full:before, +.fa-star-half-o:before { + content: "\f123"; +} +.fa-location-arrow:before { + content: "\f124"; +} +.fa-crop:before { + content: "\f125"; +} +.fa-code-fork:before { + content: "\f126"; +} +.fa-unlink:before, +.fa-chain-broken:before { + content: "\f127"; +} +.fa-question:before { + content: "\f128"; +} +.fa-info:before { + content: "\f129"; +} +.fa-exclamation:before { + content: "\f12a"; +} +.fa-superscript:before { + content: "\f12b"; +} +.fa-subscript:before { + content: "\f12c"; +} +.fa-eraser:before { + content: "\f12d"; +} +.fa-puzzle-piece:before { + content: "\f12e"; +} +.fa-microphone:before { + content: "\f130"; +} +.fa-microphone-slash:before { + content: "\f131"; +} +.fa-shield:before { + content: "\f132"; +} +.fa-calendar-o:before { + content: "\f133"; +} +.fa-fire-extinguisher:before { + content: "\f134"; +} +.fa-rocket:before { + content: "\f135"; +} +.fa-maxcdn:before { + content: "\f136"; +} 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content: "\f19c"; +} +.fa-mortar-board:before, +.fa-graduation-cap:before { + content: "\f19d"; +} +.fa-yahoo:before { + content: "\f19e"; +} +.fa-google:before { + content: "\f1a0"; +} +.fa-reddit:before { + content: "\f1a1"; +} +.fa-reddit-square:before { + content: "\f1a2"; +} +.fa-stumbleupon-circle:before { + content: "\f1a3"; +} +.fa-stumbleupon:before { + content: "\f1a4"; +} +.fa-delicious:before { + content: "\f1a5"; +} +.fa-digg:before { + content: "\f1a6"; +} +.fa-pied-piper-pp:before { + content: "\f1a7"; +} +.fa-pied-piper-alt:before { + content: "\f1a8"; +} +.fa-drupal:before { + content: "\f1a9"; +} +.fa-joomla:before { + content: "\f1aa"; +} +.fa-language:before { + content: "\f1ab"; +} +.fa-fax:before { + content: "\f1ac"; +} +.fa-building:before { + content: "\f1ad"; +} +.fa-child:before { + content: "\f1ae"; +} +.fa-paw:before { + content: "\f1b0"; +} +.fa-spoon:before { + content: "\f1b1"; +} +.fa-cube:before { + content: "\f1b2"; +} +.fa-cubes:before { + content: "\f1b3"; +} +.fa-behance:before { + content: "\f1b4"; +} +.fa-behance-square:before { + content: "\f1b5"; +} +.fa-steam:before { + content: "\f1b6"; +} +.fa-steam-square:before { + content: "\f1b7"; +} +.fa-recycle:before { + content: "\f1b8"; +} +.fa-automobile:before, +.fa-car:before { + content: "\f1b9"; +} +.fa-cab:before, +.fa-taxi:before { + content: "\f1ba"; +} +.fa-tree:before { + content: "\f1bb"; +} +.fa-spotify:before { + content: "\f1bc"; +} +.fa-deviantart:before { + content: "\f1bd"; +} +.fa-soundcloud:before { + content: "\f1be"; +} +.fa-database:before { + content: "\f1c0"; +} +.fa-file-pdf-o:before { + content: "\f1c1"; +} +.fa-file-word-o:before { + content: "\f1c2"; +} +.fa-file-excel-o:before { + content: "\f1c3"; +} +.fa-file-powerpoint-o:before { + content: "\f1c4"; +} +.fa-file-photo-o:before, +.fa-file-picture-o:before, +.fa-file-image-o:before { + content: "\f1c5"; +} +.fa-file-zip-o:before, +.fa-file-archive-o:before { + content: "\f1c6"; +} 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content: "\f1d7"; +} +.fa-send:before, +.fa-paper-plane:before { + content: "\f1d8"; +} +.fa-send-o:before, +.fa-paper-plane-o:before { + content: "\f1d9"; +} +.fa-history:before { + content: "\f1da"; +} +.fa-circle-thin:before { + content: "\f1db"; +} +.fa-header:before { + content: "\f1dc"; +} +.fa-paragraph:before { + content: "\f1dd"; +} +.fa-sliders:before { + content: "\f1de"; +} +.fa-share-alt:before { + content: "\f1e0"; +} +.fa-share-alt-square:before { + content: "\f1e1"; +} +.fa-bomb:before { + content: "\f1e2"; +} +.fa-soccer-ball-o:before, +.fa-futbol-o:before { + content: "\f1e3"; +} +.fa-tty:before { + content: "\f1e4"; +} +.fa-binoculars:before { + content: "\f1e5"; +} +.fa-plug:before { + content: "\f1e6"; +} +.fa-slideshare:before { + content: "\f1e7"; +} +.fa-twitch:before { + content: "\f1e8"; +} +.fa-yelp:before { + content: "\f1e9"; +} +.fa-newspaper-o:before { + content: "\f1ea"; +} +.fa-wifi:before { + content: "\f1eb"; +} +.fa-calculator:before { + content: "\f1ec"; +} +.fa-paypal:before { + content: "\f1ed"; +} +.fa-google-wallet:before { + content: "\f1ee"; +} +.fa-cc-visa:before { + content: "\f1f0"; +} +.fa-cc-mastercard:before { + content: "\f1f1"; +} +.fa-cc-discover:before { + content: "\f1f2"; +} +.fa-cc-amex:before { + content: "\f1f3"; +} +.fa-cc-paypal:before { + content: "\f1f4"; +} +.fa-cc-stripe:before { + content: "\f1f5"; +} +.fa-bell-slash:before { + content: "\f1f6"; +} +.fa-bell-slash-o:before { + content: "\f1f7"; +} +.fa-trash:before { + content: "\f1f8"; +} +.fa-copyright:before { + content: "\f1f9"; +} +.fa-at:before { + content: "\f1fa"; +} +.fa-eyedropper:before { + content: "\f1fb"; +} +.fa-paint-brush:before { + content: "\f1fc"; +} +.fa-birthday-cake:before { + content: "\f1fd"; +} +.fa-area-chart:before { + content: "\f1fe"; +} +.fa-pie-chart:before { + content: "\f200"; +} +.fa-line-chart:before { + content: "\f201"; +} +.fa-lastfm:before { + content: "\f202"; +} +.fa-lastfm-square:before { + content: 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+ content: "\f219"; +} +.fa-ship:before { + content: "\f21a"; +} +.fa-user-secret:before { + content: "\f21b"; +} +.fa-motorcycle:before { + content: "\f21c"; +} +.fa-street-view:before { + content: "\f21d"; +} +.fa-heartbeat:before { + content: "\f21e"; +} +.fa-venus:before { + content: "\f221"; +} +.fa-mars:before { + content: "\f222"; +} +.fa-mercury:before { + content: "\f223"; +} +.fa-intersex:before, +.fa-transgender:before { + content: "\f224"; +} +.fa-transgender-alt:before { + content: "\f225"; +} +.fa-venus-double:before { + content: "\f226"; +} +.fa-mars-double:before { + content: "\f227"; +} +.fa-venus-mars:before { + content: "\f228"; +} +.fa-mars-stroke:before { + content: "\f229"; +} +.fa-mars-stroke-v:before { + content: "\f22a"; +} +.fa-mars-stroke-h:before { + content: "\f22b"; +} +.fa-neuter:before { + content: "\f22c"; +} +.fa-genderless:before { + content: "\f22d"; +} +.fa-facebook-official:before { + content: "\f230"; +} +.fa-pinterest-p:before { + content: "\f231"; +} +.fa-whatsapp:before { + content: "\f232"; +} +.fa-server:before { + content: "\f233"; +} +.fa-user-plus:before { + content: "\f234"; +} +.fa-user-times:before { + content: "\f235"; +} +.fa-hotel:before, +.fa-bed:before { + content: "\f236"; +} +.fa-viacoin:before { + content: "\f237"; +} +.fa-train:before { + content: "\f238"; +} +.fa-subway:before { + content: "\f239"; +} +.fa-medium:before { + content: "\f23a"; +} +.fa-yc:before, +.fa-y-combinator:before { + content: "\f23b"; +} +.fa-optin-monster:before { + content: "\f23c"; +} +.fa-opencart:before { + content: "\f23d"; +} +.fa-expeditedssl:before { + content: "\f23e"; +} +.fa-battery-4:before, +.fa-battery:before, +.fa-battery-full:before { + content: "\f240"; +} +.fa-battery-3:before, +.fa-battery-three-quarters:before { + content: "\f241"; +} +.fa-battery-2:before, +.fa-battery-half:before { + content: "\f242"; +} +.fa-battery-1:before, +.fa-battery-quarter:before { + content: "\f243"; +} +.fa-battery-0:before, 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content: "\f256"; +} +.fa-hand-scissors-o:before { + content: "\f257"; +} +.fa-hand-lizard-o:before { + content: "\f258"; +} +.fa-hand-spock-o:before { + content: "\f259"; +} +.fa-hand-pointer-o:before { + content: "\f25a"; +} +.fa-hand-peace-o:before { + content: "\f25b"; +} +.fa-trademark:before { + content: "\f25c"; +} +.fa-registered:before { + content: "\f25d"; +} +.fa-creative-commons:before { + content: "\f25e"; +} +.fa-gg:before { + content: "\f260"; +} +.fa-gg-circle:before { + content: "\f261"; +} +.fa-tripadvisor:before { + content: "\f262"; +} +.fa-odnoklassniki:before { + content: "\f263"; +} +.fa-odnoklassniki-square:before { + content: "\f264"; +} +.fa-get-pocket:before { + content: "\f265"; +} +.fa-wikipedia-w:before { + content: "\f266"; +} +.fa-safari:before { + content: "\f267"; +} +.fa-chrome:before { + content: "\f268"; +} +.fa-firefox:before { + content: "\f269"; +} +.fa-opera:before { + content: "\f26a"; +} +.fa-internet-explorer:before { + content: "\f26b"; +} +.fa-tv:before, +.fa-television:before { + content: "\f26c"; +} +.fa-contao:before { + content: "\f26d"; +} +.fa-500px:before { + content: "\f26e"; +} +.fa-amazon:before { + content: "\f270"; +} +.fa-calendar-plus-o:before { + content: "\f271"; +} +.fa-calendar-minus-o:before { + content: "\f272"; +} +.fa-calendar-times-o:before { + content: "\f273"; +} +.fa-calendar-check-o:before { + content: "\f274"; +} +.fa-industry:before { + content: "\f275"; +} +.fa-map-pin:before { + content: "\f276"; +} +.fa-map-signs:before { + content: "\f277"; +} +.fa-map-o:before { + content: "\f278"; +} +.fa-map:before { + content: "\f279"; +} +.fa-commenting:before { + content: "\f27a"; +} +.fa-commenting-o:before { + content: "\f27b"; +} +.fa-houzz:before { + content: "\f27c"; +} +.fa-vimeo:before { + content: "\f27d"; +} +.fa-black-tie:before { + content: "\f27e"; +} +.fa-fonticons:before { + content: "\f280"; +} +.fa-reddit-alien:before { + content: "\f281"; +} +.fa-edge:before { + content: "\f282"; +} +.fa-credit-card-alt:before { + content: "\f283"; +} +.fa-codiepie:before { + content: "\f284"; +} +.fa-modx:before { + content: "\f285"; +} +.fa-fort-awesome:before { + content: "\f286"; +} +.fa-usb:before { + content: "\f287"; +} +.fa-product-hunt:before { + content: "\f288"; +} +.fa-mixcloud:before { + content: "\f289"; +} +.fa-scribd:before { + content: "\f28a"; +} +.fa-pause-circle:before { + content: "\f28b"; +} +.fa-pause-circle-o:before { + content: "\f28c"; +} +.fa-stop-circle:before { + content: "\f28d"; +} +.fa-stop-circle-o:before { + content: "\f28e"; +} +.fa-shopping-bag:before { + content: "\f290"; +} +.fa-shopping-basket:before { + content: "\f291"; +} +.fa-hashtag:before { + content: "\f292"; +} +.fa-bluetooth:before { + content: "\f293"; +} +.fa-bluetooth-b:before { + content: "\f294"; +} +.fa-percent:before { + content: "\f295"; +} +.fa-gitlab:before { + content: "\f296"; +} +.fa-wpbeginner:before { + content: "\f297"; +} +.fa-wpforms:before { + content: "\f298"; +} +.fa-envira:before { + content: "\f299"; +} +.fa-universal-access:before { + content: "\f29a"; +} +.fa-wheelchair-alt:before { + content: "\f29b"; +} +.fa-question-circle-o:before { + content: "\f29c"; +} +.fa-blind:before { + content: "\f29d"; +} +.fa-audio-description:before { + content: "\f29e"; +} +.fa-volume-control-phone:before { + content: "\f2a0"; +} +.fa-braille:before { + content: "\f2a1"; +} +.fa-assistive-listening-systems:before { + content: "\f2a2"; +} +.fa-asl-interpreting:before, +.fa-american-sign-language-interpreting:before { + content: "\f2a3"; +} +.fa-deafness:before, +.fa-hard-of-hearing:before, +.fa-deaf:before { + content: "\f2a4"; +} +.fa-glide:before { + content: "\f2a5"; +} +.fa-glide-g:before { + content: "\f2a6"; +} +.fa-signing:before, +.fa-sign-language:before { + content: "\f2a7"; +} +.fa-low-vision:before { + content: "\f2a8"; +} +.fa-viadeo:before { + content: "\f2a9"; +} +.fa-viadeo-square:before { + content: "\f2aa"; +} +.fa-snapchat:before { + content: "\f2ab"; +} +.fa-snapchat-ghost:before { + content: "\f2ac"; +} +.fa-snapchat-square:before { + content: "\f2ad"; +} +.fa-pied-piper:before { + content: "\f2ae"; +} +.fa-first-order:before { + content: "\f2b0"; +} +.fa-yoast:before { + content: "\f2b1"; +} +.fa-themeisle:before { + content: "\f2b2"; +} +.fa-google-plus-circle:before, +.fa-google-plus-official:before { + content: "\f2b3"; +} +.fa-fa:before, +.fa-font-awesome:before { + content: "\f2b4"; +} +.fa-handshake-o:before { + content: "\f2b5"; +} +.fa-envelope-open:before { + content: "\f2b6"; +} +.fa-envelope-open-o:before { + content: "\f2b7"; +} +.fa-linode:before { + content: "\f2b8"; +} +.fa-address-book:before { + content: "\f2b9"; +} +.fa-address-book-o:before { + content: "\f2ba"; +} +.fa-vcard:before, +.fa-address-card:before { + content: "\f2bb"; +} +.fa-vcard-o:before, +.fa-address-card-o:before { + content: "\f2bc"; +} +.fa-user-circle:before { + content: "\f2bd"; +} +.fa-user-circle-o:before { + content: "\f2be"; +} +.fa-user-o:before { + content: "\f2c0"; +} +.fa-id-badge:before { + content: "\f2c1"; +} +.fa-drivers-license:before, +.fa-id-card:before { + content: "\f2c2"; +} +.fa-drivers-license-o:before, +.fa-id-card-o:before { + content: "\f2c3"; +} +.fa-quora:before { + content: "\f2c4"; +} +.fa-free-code-camp:before { + content: "\f2c5"; +} +.fa-telegram:before { + content: "\f2c6"; +} +.fa-thermometer-4:before, +.fa-thermometer:before, +.fa-thermometer-full:before { + content: "\f2c7"; +} +.fa-thermometer-3:before, +.fa-thermometer-three-quarters:before { + content: "\f2c8"; +} +.fa-thermometer-2:before, +.fa-thermometer-half:before { + content: "\f2c9"; +} +.fa-thermometer-1:before, +.fa-thermometer-quarter:before { + content: "\f2ca"; +} +.fa-thermometer-0:before, +.fa-thermometer-empty:before { + content: "\f2cb"; +} +.fa-shower:before { + content: "\f2cc"; +} +.fa-bathtub:before, +.fa-s15:before, +.fa-bath:before { + content: "\f2cd"; +} +.fa-podcast:before { + content: "\f2ce"; +} +.fa-window-maximize:before { + content: "\f2d0"; +} +.fa-window-minimize:before { + content: "\f2d1"; +} +.fa-window-restore:before { + content: "\f2d2"; +} +.fa-times-rectangle:before, +.fa-window-close:before { + content: "\f2d3"; +} +.fa-times-rectangle-o:before, +.fa-window-close-o:before { + content: "\f2d4"; +} +.fa-bandcamp:before { + content: "\f2d5"; +} +.fa-grav:before { + content: "\f2d6"; +} +.fa-etsy:before { + content: "\f2d7"; +} +.fa-imdb:before { + content: "\f2d8"; +} +.fa-ravelry:before { + content: "\f2d9"; +} +.fa-eercast:before { + content: "\f2da"; +} +.fa-microchip:before { + content: "\f2db"; +} +.fa-snowflake-o:before { + content: "\f2dc"; +} +.fa-superpowers:before { + content: "\f2dd"; +} +.fa-wpexplorer:before { + content: "\f2de"; +} +.fa-meetup:before { + content: "\f2e0"; +} +.sr-only { + position: absolute; + width: 1px; + height: 1px; + padding: 0; + margin: -1px; + overflow: hidden; + clip: rect(0, 0, 0, 0); + border: 0; +} +.sr-only-focusable:active, +.sr-only-focusable:focus { + position: static; + width: auto; + height: auto; + margin: 0; + overflow: visible; + clip: auto; +} diff --git a/css/font-awesome-4.7.0.min.css b/css/font-awesome-4.7.0.min.css new file mode 100644 index 0000000..540440c --- /dev/null +++ b/css/font-awesome-4.7.0.min.css @@ -0,0 +1,4 @@ +/*! + * Font Awesome 4.7.0 by @davegandy - http://fontawesome.io - @fontawesome + * License - http://fontawesome.io/license (Font: SIL OFL 1.1, CSS: MIT License) + */@font-face{font-family:'FontAwesome';src:url('http://github.com/fonts/fontawesome-webfont.eot?v=4.7.0');src:url('http://github.com/fonts/fontawesome-webfont.eot?#iefix&v=4.7.0') format('embedded-opentype'),url('http://github.com/fonts/fontawesome-webfont.woff2?v=4.7.0') format('woff2'),url('http://github.com/fonts/fontawesome-webfont.woff?v=4.7.0') format('woff'),url('http://github.com/fonts/fontawesome-webfont.ttf?v=4.7.0') 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+ +.hljs-chunk { + color: #aaa; +} diff --git a/css/jupyter-cells.css b/css/jupyter-cells.css new file mode 100644 index 0000000..46def9f --- /dev/null +++ b/css/jupyter-cells.css @@ -0,0 +1,10 @@ +/* Input cells */ +.input code, .input pre { + background-color: #3333aa11; +} + +/* Output cells */ +.output pre { + background-color: #ececec80; + padding: 10px; +} diff --git a/css/pandas-dataframe.css b/css/pandas-dataframe.css new file mode 100644 index 0000000..2c18015 --- /dev/null +++ b/css/pandas-dataframe.css @@ -0,0 +1,36 @@ +/* Pretty Pandas Dataframes */ +/* Supports mkdocs-material color variables */ +.dataframe { + border: 0; + font-size: smaller; +} +.dataframe tr { + border: none; + background: var(--md-code-bg-color, #ffffff); +} +.dataframe tr:nth-child(even) { + background: var(--md-default-bg-color, #f5f5f5); +} +.dataframe tr:hover { + background-color: var(--md-footer-bg-color--dark, #e1f5fe); +} + +.dataframe thead th { + background: var(--md-default-bg-color, #ffffff); + border-bottom: 1px solid #aaa; + font-weight: bold; +} +.dataframe th { + border: none; + padding-left: 10px; + padding-right: 10px; +} + +.dataframe td{ + /* background: #fff; */ + border: none; + text-align: right; + min-width:5em; + padding-left: 10px; + padding-right: 10px; +} diff --git a/datamodel/index.html b/datamodel/index.html new file mode 100644 index 0000000..b586931 --- /dev/null +++ b/datamodel/index.html @@ -0,0 +1,596 @@ + + + + + + + + + + + + + + Data Model - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +

LinkML Map Data Model

+

Datamodel for LinkML schema mappings and transformations.

+

A mapper generates instances of a target data model from +instances of a source data model. This transformation process +is guided by a TransformationSpecification.

+

The specification is independent of any one method for transforming +data. It allows different approaches, including:

+ +

URI: https://w3id.org/linkml/transformer

+

Name: linkml-map

+

Classes

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ClassDescription
AliasedClassalias-class key value pairs for classes
AnyNone
CopyDirectiveInstructs a Schema Mapper in how to map to a target schema. Not used for data transformation.
InverseUsed for back references in mapping to relational model
KeyValNone
SpecificationComponentNone
        ElementDerivationAn abstract grouping for classes that provide a specification of how to derive a target element from a source element.
                ClassDerivationA specification of how to derive a target class from a source class.
                EnumDerivationA specification of how to derive the value of a target enum from a source enum
                PermissibleValueDerivationA specification of how to derive the value of a PV from a source enum
                PrefixDerivationNone
                SlotDerivationA specification of how to derive the value of a target slot from a source slot
        TransformationSpecificationA collection of mappings between source and target classes
StringificationConfigurationNone
UnitConversionConfigurationNone
+

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
SlotDescription
add
aliasname of the class to be aliased
cast_collection_as
class_derivationsInstructions on how to derive a set of classes in the target schema from clas...
class_name
class_namedlocal alias for the class
commentsA list of comments about this component
copy_all
copy_directives
delimiter
derived_fromSource slots that are used to derive this slot
descriptiondescription of the specification component
dictionary_key
element_name
enum_derivationsInstructions on how to derive a set of enums in the target schema
exclude
exclude_all
exprAn expression to be evaluated on the source object to derive the target slot
expression_to_expression_mappingsA mapping table in which the keys and values are expressions
expression_to_value_mappingsA mapping table in which the keys are expressions
hideTrue if this is suppressed
idUnique identifier for this transformation specification
implementsA reference to a specification that this component implements
include
inverse_ofUsed to specify a class-slot tuple that is the inverse of the derived/target ...
is_a
joinsAdditional classes to be joined to derive instances of the target class
key
mirror_source
mixins
nameName of the element in the target schema
over_slots
overridesoverrides source schema slots
permissible_value_derivationsInstructions on how to derive a set of PVs in the target schema
populated_fromName of the class in the source schema
prefixesmaps prefixes to URL expansions
range
reversed
slot_derivationsInstructions on how to derive a set of top level slots in the target schema
slot_name
source_magnitude_slot
source_schemaname of the schema that describes the source (input) objects
source_unit
source_unit_scheme
source_unit_slot
sources
stringification
syntax
target_magnitude_slot
target_schemaname of the schema that describes the target (output) objects
target_unit
target_unit_scheme
target_unit_slot
titlehuman readable title for this transformation specification
type_designator
unit_conversion
value
value_mappingsA mapping table that is applied directly to mappings, in order of precedence
+

Enumerations

+ + + + + + + + + + + + + + + + + +
EnumerationDescription
CollectionType
SerializationSyntaxType
+

Types

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
TypeDescription
BooleanA binary (true or false) value
ClassReference
Curiea compact URI
Datea date (year, month and day) in an idealized calendar
DateOrDatetimeEither a date or a datetime
DatetimeThe combination of a date and time
DecimalA real number with arbitrary precision that conforms to the xsd:decimal speci...
DoubleA real number that conforms to the xsd:double specification
EnumReference
FloatA real number that conforms to the xsd:float specification
IntegerAn integer
JsonpathA string encoding a JSON Path
JsonpointerA string encoding a JSON Pointer
NcnamePrefix part of CURIE
NodeidentifierA URI, CURIE or BNODE that represents a node in a model
ObjectidentifierA URI or CURIE that represents an object in the model
SlotReference
SparqlpathA string encoding a SPARQL Property Path
StringA character string
TimeA time object represents a (local) time of day, independent of any particular...
Uria complete URI
Uriorcuriea URI or a CURIE
+

Subsets

+ + + + + + + + + + + + + +
SubsetDescription
+ +
+ + + + + + + + + +
+
+ + + + + \ No newline at end of file diff --git a/delimiter/index.html b/delimiter/index.html new file mode 100644 index 0000000..79c81cc --- /dev/null +++ b/delimiter/index.html @@ -0,0 +1,148 @@ + + + + + + + + + + + + + + Slot: delimiter - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: delimiter

+

URI: linkmltr:delimiter

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
StringificationConfigurationno
+

Properties

+ +

Examples

+ + + + + + + + + + + + + + + + + +
Value
,
;
+

Identifier and Mapping Information

+

Schema Source

+ +

LinkML Source

+
+ +
name: delimiter
+examples:
+- value: ','
+- value: '|'
+- value: ;
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+alias: delimiter
+owner: StringificationConfiguration
+domain_of:
+- StringificationConfiguration
+range: string
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/derived_from/index.html b/derived_from/index.html new file mode 100644 index 0000000..5686284 --- /dev/null +++ b/derived_from/index.html @@ -0,0 +1,133 @@ + + + + + + + + + + + + + + Slot: derived_from - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: derived_from

+

Source slots that are used to derive this slot. This can be computed from the expr, if the expr is declarative.

+

URI: linkmltr:derived_from

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
SlotDerivationA specification of how to derive the value of a target slot from a source slo...no
+

Properties

+ +

Identifier and Mapping Information

+

Schema Source

+ +

LinkML Source

+
+ +
name: derived_from
+description: Source slots that are used to derive this slot. This can be computed
+  from the expr, if the expr is declarative.
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+multivalued: true
+alias: derived_from
+owner: SlotDerivation
+domain_of:
+- SlotDerivation
+range: SlotReference
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/description/index.html b/description/index.html new file mode 100644 index 0000000..1399aae --- /dev/null +++ b/description/index.html @@ -0,0 +1,161 @@ + + + + + + + + + + + + + + Slot: description - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: description

+

description of the specification component

+

URI: dcterms:description

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
EnumDerivationA specification of how to derive the value of a target enum from a source enu...no
PermissibleValueDerivationA specification of how to derive the value of a PV from a source enumno
ElementDerivationAn abstract grouping for classes that provide a specification of how to deri...no
PrefixDerivationno
SlotDerivationA specification of how to derive the value of a target slot from a source slo...no
ClassDerivationA specification of how to derive a target class from a source classno
SpecificationComponentno
TransformationSpecificationA collection of mappings between source and target classesno
+

Properties

+ +

Identifier and Mapping Information

+

Schema Source

+ +

LinkML Source

+
+ +
name: description
+description: description of the specification component
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+slot_uri: dcterms:description
+alias: description
+owner: SpecificationComponent
+domain_of:
+- SpecificationComponent
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/dictionary_key/index.html b/dictionary_key/index.html new file mode 100644 index 0000000..5e6ca41 --- /dev/null +++ b/dictionary_key/index.html @@ -0,0 +1,124 @@ + + + + + + + + + + + + + + Slot: dictionary_key - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: dictionary_key

+

URI: linkmltr:dictionary_key

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
SlotDerivationA specification of how to derive the value of a target slot from a source slo...no
+

Properties

+ +

Identifier and Mapping Information

+

Schema Source

+ +

LinkML Source

+
+ +
name: dictionary_key
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+alias: dictionary_key
+owner: SlotDerivation
+domain_of:
+- SlotDerivation
+range: string
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/docs/api/compiler.md b/docs/api/compiler.md deleted file mode 100644 index 058a634..0000000 --- a/docs/api/compiler.md +++ /dev/null @@ -1,19 +0,0 @@ -# Compiler Package - -A compiler will compile a Map specification into an alternative representation - -## Compiler (Base Class) - -::: linkml_map.compiler.compiler.Compiler - -## Python Compiler - -::: linkml_map.compiler.python_compiler.PythonCompiler - -## Markdown Compiler - -::: linkml_map.compiler.markdown_compiler.MarkdownCompiler - -### Graphviz Compiler - -::: linkml_map.compiler.graphviz_compiler.GraphvizCompiler \ No newline at end of file diff --git a/docs/api/functions.md b/docs/api/functions.md deleted file mode 100644 index 269d291..0000000 --- a/docs/api/functions.md +++ /dev/null @@ -1,5 +0,0 @@ -# Functions Package - -## Unit Conversion - -::: linkml_map.functions.unit_conversion diff --git a/docs/api/inference.md b/docs/api/inference.md deleted file mode 100644 index 7fb5fc8..0000000 --- a/docs/api/inference.md +++ /dev/null @@ -1,13 +0,0 @@ -# Inference Package - -## Inference Utils - -::: linkml_map.inference.inference - -## Inverter - -::: linkml_map.inference.inverter - -## Schema Mapper - -::: linkml_map.inference.schema_mapper.SchemaMapper \ No newline at end of file diff --git a/docs/api/session.md b/docs/api/session.md deleted file mode 100644 index 332b3f3..0000000 --- a/docs/api/session.md +++ /dev/null @@ -1,4 +0,0 @@ -# Session - -::: linkml_map.session.Session - diff --git a/docs/api/transformer.md b/docs/api/transformer.md deleted file mode 100644 index 7612565..0000000 --- a/docs/api/transformer.md +++ /dev/null @@ -1,10 +0,0 @@ -# Transformer Package - -## Transformer (Base Class) - -::: linkml_map.transformer.transformer.Transformer - -## ObjectTransformer - -::: linkml_map.transformer.object_transformer.ObjectTransformer - diff --git a/docs/examples/MetamodelMapping.ipynb b/docs/examples/MetamodelMapping.ipynb deleted file mode 100644 index ca45138..0000000 --- a/docs/examples/MetamodelMapping.ipynb +++ /dev/null @@ -1,428 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "id": "20a69830e031dd42", - "metadata": { - "collapsed": false, - "jupyter": { - "outputs_hidden": false - } - }, - "source": [ - "# LinkML Metamodel Mappings\n", - "\n", - "The primary use case of LinkML is to map *data* to *data*. However, because the LinkML metamodel is\n", - "expressed as a LinkML schema, it is possible to map to and from the metamodel itself.\n", - "\n", - "__NOTE__ this workflow is not yet fully matured, and is subject to change." - ] - }, - { - "cell_type": "markdown", - "id": "926150383baeb0f1", - "metadata": { - "collapsed": false, - "jupyter": { - "outputs_hidden": false - } - }, - "source": [ - "## Creation of ad-hoc metamodel\n", - "\n", - "Let's assume that we have data represented using models conforming to an ad-hoc metamodel with core constructs: `Schema`, `Table`, and `Column`. We can create a LinkML schema that represents this metamodel as follows:" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "id": "569394bf0a0aa7c4", - "metadata": { - "ExecuteTime": { - "end_time": "2024-04-11T02:15:26.923272Z", - "start_time": "2024-04-11T02:15:26.737620Z" - }, - "collapsed": false, - "jupyter": { - "outputs_hidden": false - } - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "name: test-schema\n", - "id: http://example.org/test-schema\n", - "default_prefix: http://example.org/test-schema/\n", - "classes:\n", - " Schema:\n", - " attributes:\n", - " id:\n", - " description: The name of the schema\n", - " required: true\n", - " tables:\n", - " multivalued: true\n", - " range: Table\n", - " inlined_as_list: true\n", - " tree_root: true\n", - " Table:\n", - " attributes:\n", - " id:\n", - " description: The name of the table\n", - " required: true\n", - " columns:\n", - " multivalued: true\n", - " range: Column\n", - " inlined_as_list: true\n", - " Column:\n", - " attributes:\n", - " id:\n", - " description: The name of the column\n", - " required: true\n", - " primary_key:\n", - " range: boolean\n", - " datatype:\n", - " range: string\n", - "prefixes: {}\n" - ] - } - ], - "source": [ - "import yaml\n", - "from linkml_runtime.linkml_model import SlotDefinition\n", - "from linkml.utils.schema_builder import SchemaBuilder\n", - "\n", - "sb = SchemaBuilder()\n", - "sb.add_class(\"Schema\", \n", - " tree_root=True,\n", - " slots=[\n", - " SlotDefinition(\"id\", required=True, description=\"The name of the schema\"),\n", - " SlotDefinition(\"tables\", range=\"Table\", multivalued=True, inlined_as_list=True),\n", - " ],\n", - " use_attributes=True,\n", - " )\n", - "sb.add_class(\"Table\",\n", - " slots=[\n", - " SlotDefinition(\"id\", required=True, description=\"The name of the table\"),\n", - " SlotDefinition(\"columns\", range=\"Column\", multivalued=True, inlined_as_list=True),\n", - " ],\n", - " use_attributes=True,\n", - " )\n", - "sb.add_class(\"Column\",\n", - " slots=[\n", - " SlotDefinition(\"id\", required=True, description=\"The name of the column\"),\n", - " SlotDefinition(\"primary_key\", range=\"boolean\"),\n", - " SlotDefinition(\"datatype\", range=\"string\"),\n", - " ],\n", - " use_attributes=True,\n", - " )\n", - "\n", - "my_metamodel = sb.as_dict()\n", - "print(yaml.dump(sb.as_dict(), sort_keys=False))" - ] - }, - { - "cell_type": "markdown", - "id": "504e5e995a56d9d", - "metadata": { - "collapsed": false, - "jupyter": { - "outputs_hidden": false - } - }, - "source": [ - "## Example schema conforming to ad-hoc metamodel\n", - "\n", - "Now we'll make an example schema that conforms to this metamodel; this will be a fairly boring schema with a single table `Person` with three columns: `id`, `name`, and `description`:" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "id": "2412c7508be85763", - "metadata": { - "ExecuteTime": { - "end_time": "2024-04-11T02:15:26.927278Z", - "start_time": "2024-04-11T02:15:26.925061Z" - }, - "collapsed": false, - "jupyter": { - "outputs_hidden": false - } - }, - "outputs": [], - "source": [ - "my_schema = {\n", - " \"id\": \"my_schema\",\n", - " \"tables\": [\n", - " {\n", - " \"id\": \"Person\",\n", - " \"columns\": [\n", - " {\n", - " \"id\": \"id\",\n", - " \"primary_key\": True,\n", - " \"datatype\": \"integer\"\n", - " },\n", - " {\n", - " \"id\": \"name\",\n", - " \"datatype\": \"string\"\n", - " },\n", - " {\n", - " \"id\": \"description\",\n", - " \"datatype\": \"string\"\n", - " }\n", - " ]\n", - " },\n", - " ]\n", - "}" - ] - }, - { - "cell_type": "markdown", - "id": "a97465ad75c14ab9", - "metadata": { - "collapsed": false, - "jupyter": { - "outputs_hidden": false - } - }, - "source": [ - "## Mapping to LinkML metamodel\n", - "\n", - "Now we'll create mappings from the ad-hoc metamodel to the LinkML metamodel, where **Table** maps to a LinkML **ClassDefinition**, **Column** maps to a LinkML **SlotDefinition*." - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "id": "781147edebbfeb9c", - "metadata": { - "ExecuteTime": { - "end_time": "2024-04-11T02:15:26.930857Z", - "start_time": "2024-04-11T02:15:26.929165Z" - }, - "collapsed": false, - "jupyter": { - "outputs_hidden": false - } - }, - "outputs": [], - "source": [ - "metamap = {\n", - " \"class_derivations\": {\n", - " \"SchemaDefinition\": {\n", - " \"populated_from\": \"Schema\",\n", - " \"slot_derivations\": {\n", - " \"name\": {\n", - " \"populated_from\": \"id\",\n", - " },\n", - " \"id\": {\n", - " \"expr\": \"'https://example.org/' + id\",\n", - " },\n", - " \"classes\": {\n", - " \"populated_from\": \"tables\",\n", - " \"dictionary_key\": \"name\",\n", - " \"cast_collection_as\": \"MultiValuedDict\",\n", - " },\n", - " }\n", - " },\n", - " \"ClassDefinition\": {\n", - " \"populated_from\": \"Table\",\n", - " \"slot_derivations\": {\n", - " \"name\": {\n", - " \"populated_from\": \"id\",\n", - " },\n", - " \"attributes\": {\n", - " \"populated_from\": \"columns\",\n", - " \"dictionary_key\": \"name\",\n", - " \"cast_collection_as\": \"MultiValuedDict\",\n", - " },\n", - " }\n", - " },\n", - " \"SlotDefinition\": {\n", - " \"populated_from\": \"Column\",\n", - " \"slot_derivations\": {\n", - " \"name\": {\n", - " \"populated_from\": \"id\",\n", - " },\n", - " \"identifier\": {\n", - " \"populated_from\": \"primary_key\",\n", - " },\n", - " \"range\": {\n", - " \"populated_from\": \"datatype\",\n", - " },\n", - " },\n", - " },\n", - " }\n", - "}" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "id": "df33c4db991ce4b3", - "metadata": { - "ExecuteTime": { - "end_time": "2024-04-11T02:15:27.366482Z", - "start_time": "2024-04-11T02:15:26.931843Z" - }, - "collapsed": false, - "jupyter": { - "outputs_hidden": false - } - }, - "outputs": [], - "source": [ - "from linkml_map.session import Session\n", - "\n", - "session = Session()" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "id": "e5edb3e9efa49ed1", - "metadata": { - "ExecuteTime": { - "end_time": "2024-04-11T02:15:27.450810Z", - "start_time": "2024-04-11T02:15:27.369239Z" - }, - "collapsed": false, - "jupyter": { - "outputs_hidden": false - } - }, - "outputs": [], - "source": [ - "session.set_source_schema(my_metamodel)\n", - "session.set_object_transformer(metamap)" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "id": "5fcae9c463c7146b", - "metadata": { - "ExecuteTime": { - "end_time": "2024-04-11T02:15:27.464442Z", - "start_time": "2024-04-11T02:15:27.453655Z" - }, - "collapsed": false, - "jupyter": { - "outputs_hidden": false - } - }, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "WARNING:linkml_map.transformer.object_transformer:Unexpected: my_schema for type Schema\n", - "WARNING:linkml_map.transformer.object_transformer:Unexpected: Person for type Schema\n", - "WARNING:linkml_map.transformer.object_transformer:Unexpected: id for type Schema\n", - "WARNING:linkml_map.transformer.object_transformer:Unexpected: True for type boolean\n", - "WARNING:linkml_map.transformer.object_transformer:Unexpected: integer for type string\n", - "WARNING:linkml_map.transformer.object_transformer:Unexpected: name for type Schema\n", - "WARNING:linkml_map.transformer.object_transformer:Unexpected: string for type string\n", - "WARNING:linkml_map.transformer.object_transformer:Unexpected: description for type Schema\n", - "WARNING:linkml_map.transformer.object_transformer:Unexpected: string for type string\n", - "WARNING:linkml_map.transformer.transformer:Unknown target range SlotDefinition\n", - "WARNING:linkml_map.transformer.transformer:Unknown target range SlotDefinition\n", - "WARNING:linkml_map.transformer.transformer:Unknown target range SlotDefinition\n", - "WARNING:linkml_map.transformer.transformer:Unknown target range SlotDefinition\n", - "WARNING:linkml_map.transformer.transformer:Unknown target range SlotDefinition\n", - "WARNING:linkml_map.transformer.transformer:Unknown target range SlotDefinition\n", - "WARNING:linkml_map.transformer.transformer:Unknown target range SlotDefinition\n", - "WARNING:linkml_map.transformer.transformer:Unknown target range SlotDefinition\n", - "WARNING:linkml_map.transformer.transformer:Unknown target range SlotDefinition\n", - "WARNING:linkml_map.transformer.transformer:Unknown target range ClassDefinition\n", - "WARNING:linkml_map.transformer.transformer:Unknown target range ClassDefinition\n", - "WARNING:linkml_map.transformer.transformer:Unknown target range ClassDefinition\n", - "WARNING:linkml_map.transformer.transformer:Unknown target range ClassDefinition\n", - "WARNING:linkml_map.transformer.transformer:Unknown target range ClassDefinition\n", - "WARNING:linkml_map.transformer.transformer:Unknown target range ClassDefinition\n", - "WARNING:linkml_map.transformer.transformer:Unknown target range ClassDefinition\n" - ] - }, - { - "data": { - "text/plain": [ - "{'name': 'my_schema',\n", - " 'id': 'https://example.org/my_schema',\n", - " 'classes': {'Person': {'attributes': {'id': {'identifier': True,\n", - " 'range': 'integer'},\n", - " 'name': {'identifier': None, 'range': 'string'},\n", - " 'description': {'identifier': None, 'range': 'string'}}}}}" - ] - }, - "execution_count": 6, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "session.transform(my_schema)" - ] - }, - { - "cell_type": "markdown", - "id": "917015b3f12eac2f", - "metadata": { - "collapsed": false, - "jupyter": { - "outputs_hidden": false - } - }, - "source": [ - "## Customizing the LinkML model\n", - "\n", - "A different scenario is where you might want to customize the existing LinkML metamodel, in particular, adding additional\n", - "constraints. For example:\n", - "\n", - "- class and names MUST be alphanumeric with no spaces\n", - "- every element MUST have a definition\n", - "\n", - "**TODO**" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "id": "87c714635c108ea8", - "metadata": { - "ExecuteTime": { - "end_time": "2024-04-11T02:15:27.470074Z", - "start_time": "2024-04-11T02:15:27.466371Z" - }, - "collapsed": false, - "jupyter": { - "outputs_hidden": false - } - }, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.11.0" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/docs/examples/Tutorial-SQLCompiler.ipynb b/docs/examples/Tutorial-SQLCompiler.ipynb deleted file mode 100644 index 06eff30..0000000 --- a/docs/examples/Tutorial-SQLCompiler.ipynb +++ /dev/null @@ -1,379 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "source": [ - "# LinkML-Map tutorial: Compiling to SQL\n", - "\n", - "This tutorial walks through use of the SQL compiler" - ], - "metadata": { - "collapsed": false - }, - "id": "df75d53a3e91e573" - }, - { - "cell_type": "code", - "execution_count": 1, - "outputs": [], - "source": [ - "import yaml" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-05-02T02:30:02.090658Z", - "start_time": "2024-05-02T02:30:02.056825Z" - } - }, - "id": "63a064b31f623bdd" - }, - { - "cell_type": "markdown", - "source": [ - "## Creating an example schema\n", - "\n", - "We will use a LinkML SchemaBuilder object to progressively build up a schema, adding\n", - "additional features as we go.\n", - "\n", - "We'll start with a simple `Person` schema, with a few single valued scalar slots:" - ], - "metadata": { - "collapsed": false - }, - "id": "e2cbd6b8994905f6" - }, - { - "cell_type": "code", - "execution_count": 2, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "name: test-schema\n", - "id: http://example.org/test-schema\n", - "imports:\n", - "- linkml:types\n", - "prefixes:\n", - " linkml: https://w3id.org/linkml/\n", - " test_schema: http://example.org/test-schema/\n", - "default_prefix: test_schema\n", - "default_range: string\n", - "slots:\n", - " family_name:\n", - " range: string\n", - " given_name:\n", - " range: string\n", - " age_in_years:\n", - " range: integer\n", - " height_in_cm:\n", - " range: float\n", - "classes:\n", - " Person:\n", - " slots:\n", - " - family_name\n", - " - given_name\n", - " - age_in_years\n", - " - height_in_cm\n" - ] - } - ], - "source": [ - "from linkml.utils.schema_builder import SchemaBuilder\n", - "from linkml_runtime.linkml_model import SlotDefinition\n", - "\n", - "sb = SchemaBuilder()\n", - "sb.add_class(\"Person\", slots=[SlotDefinition(\"family_name\", range=\"string\"), \n", - " SlotDefinition(\"given_name\", range=\"string\"),\n", - " SlotDefinition(\"age_in_years\", range=\"integer\"),\n", - " SlotDefinition(\"height_in_cm\", range=\"float\"),\n", - " ])\n", - "sb.add_defaults()\n", - "print(yaml.dump(sb.as_dict(), sort_keys=False))" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-05-02T02:30:02.502346Z", - "start_time": "2024-05-02T02:30:02.076600Z" - } - }, - "id": "ef2c60ef7fbcbe20" - }, - { - "cell_type": "markdown", - "source": [ - "## Creating a Transformer Session object\n", - "\n", - "We will use a `Session` object which conveniently wraps a number of different capabilities;\n", - "the first of these capabilities is to map (transform) data objects from one schema to another\n", - "(implicit) schema using a *transformer specification*).\n", - "\n", - "Our initial transformer specification will be a trivial isomorphic one that:\n", - "\n", - "- maps the `Person` class to an `Individual` class\n", - "- passes through `name` fields as-is\n", - "- renames measurement fields (`age_in_years` and `height_in_cm` to `age` and `height`)" - ], - "metadata": { - "collapsed": false - }, - "id": "d4228629dd7e2ef2" - }, - { - "cell_type": "code", - "execution_count": 3, - "outputs": [], - "source": [ - "from linkml_map.session import Session\n", - "\n", - "session = Session()\n", - "session.set_source_schema(sb.as_dict())" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-05-02T02:30:08.124308Z", - "start_time": "2024-05-02T02:30:07.628565Z" - } - }, - "id": "a6257aa9e6ab021e" - }, - { - "cell_type": "code", - "execution_count": 4, - "outputs": [], - "source": [ - "# Transformer specification (in YAML)\n", - "session.set_object_transformer(\"\"\"\n", - "class_derivations:\n", - " Individual:\n", - " populated_from: Person\n", - " slot_derivations:\n", - " family_name:\n", - " populated_from: family_name\n", - " given_name:\n", - " populated_from: given_name\n", - " age:\n", - " populated_from: age_in_years\n", - " height:\n", - " populated_from: height_in_cm\n", - "\"\"\")" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-05-02T02:30:09.067897Z", - "start_time": "2024-05-02T02:30:08.979545Z" - } - }, - "id": "47b95e209790b423" - }, - { - "cell_type": "markdown", - "source": [ - "## Compiling target schema to SQL INSERTs\n", - "\n", - "The LinkML-Map framework can infer the target schema from the mapping.\n", - "We will take the inferred schema and write SQL INSERT statements for it.\n" - ], - "metadata": { - "collapsed": false - }, - "id": "85bf0dfa91d9003" - }, - { - "cell_type": "code", - "execution_count": 11, - "outputs": [], - "source": [ - "from linkml_map.compiler.sql_compiler import SQLCompiler\n", - "\n", - "compiler = SQLCompiler(source_schemaview=session.source_schemaview)" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-05-02T02:34:48.555908Z", - "start_time": "2024-05-02T02:34:48.549282Z" - } - }, - "id": "f1538dfa61775402" - }, - { - "cell_type": "code", - "execution_count": 13, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "CREATE TABLE IF NOT EXISTS Individual (\n", - " family_name TEXT,\n", - " given_name TEXT,\n", - " age INTEGER,\n", - " height REAL\n", - ");\n" - ] - } - ], - "source": [ - "print(compiler.create_target_ddl(session.transformer_specification))" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-05-02T02:35:03.185958Z", - "start_time": "2024-05-02T02:35:03.175807Z" - } - }, - "id": "f5de99c1cd54eae4" - }, - { - "cell_type": "code", - "execution_count": 14, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "CREATE TABLE IF NOT EXISTS Person (\n", - " family_name TEXT,\n", - " given_name TEXT,\n", - " age_in_years INTEGER,\n", - " height_in_cm REAL\n", - ");\n" - ] - } - ], - "source": [ - "print(compiler.create_ddl(session.source_schemaview))" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-05-02T02:35:42.555450Z", - "start_time": "2024-05-02T02:35:42.550999Z" - } - }, - "id": "d776b301cdd1e079" - }, - { - "cell_type": "code", - "execution_count": 15, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "INSERT INTO Individual SELECT \n", - " family_name AS family_name, \n", - " given_name AS given_name, \n", - " age AS age_in_years, \n", - " height AS height_in_cm FROM Individual;\n" - ] - } - ], - "source": [ - "compiled = compiler.compile(session.transformer_specification)\n", - "print(compiled.serialization)" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-05-02T02:35:43.059893Z", - "start_time": "2024-05-02T02:35:43.057856Z" - } - }, - "id": "95b6adb322799f1f" - }, - { - "cell_type": "code", - "execution_count": 17, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "CREATE TABLE IF NOT EXISTS Individual \n", - " family_name AS family_name, \n", - " given_name AS given_name, \n", - " age AS age_in_years, \n", - " height AS height_in_cm); FROM Individual;\n" - ] - } - ], - "source": [ - "compiler.new_table_when_transforming = True\n", - "compiled = compiler.compile(session.transformer_specification)\n", - "print(compiled.serialization)" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-05-02T02:36:33.889820Z", - "start_time": "2024-05-02T02:36:33.873095Z" - } - }, - "id": "c993b563f59d8fe1" - }, - { - "cell_type": "markdown", - "source": [], - "metadata": { - "collapsed": false - }, - "id": "8313d6acb588178e" - }, - { - "cell_type": "code", - "execution_count": 11, - "outputs": [], - "source": [ - "import duckdb" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-03-22T17:13:13.511531Z", - "start_time": "2024-03-22T17:13:10.763461Z" - } - }, - "id": "1c623cdc3c1cfbca" - }, - { - "cell_type": "code", - "execution_count": null, - "outputs": [], - "source": [ - "con = duckdb.connect(database=':memory:')\n" - ], - "metadata": { - "collapsed": false - }, - "id": "564d2bd8387d7c77" - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 2 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython2", - "version": "2.7.6" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/docs/examples/Tutorial.ipynb b/docs/examples/Tutorial.ipynb deleted file mode 100644 index 5a805c7..0000000 --- a/docs/examples/Tutorial.ipynb +++ /dev/null @@ -1,964 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "source": [ - "# LinkML-Map tutorial\n", - "\n", - "This tutorial walks through basic programmatic use of the LinkML-Map framework.\n", - "This is intended for Python developers - note that many of the operations here can also be performed\n", - "at the command line." - ], - "metadata": { - "collapsed": false - }, - "id": "df75d53a3e91e573" - }, - { - "cell_type": "code", - "execution_count": 1, - "outputs": [], - "source": [ - "import yaml" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-04-11T02:31:25.287757Z", - "start_time": "2024-04-11T02:31:25.192334Z" - } - }, - "id": "63a064b31f623bdd" - }, - { - "cell_type": "markdown", - "source": [ - "## Creating an example schema\n", - "\n", - "We will use a LinkML SchemaBuilder object to progressively build up a schema, adding\n", - "additional features as we go.\n", - "\n", - "We'll start with a simple `Person` schema, with a few single valued scalar slots:" - ], - "metadata": { - "collapsed": false - }, - "id": "e2cbd6b8994905f6" - }, - { - "cell_type": "code", - "execution_count": 2, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "name: test-schema\n", - "id: http://example.org/test-schema\n", - "imports:\n", - "- linkml:types\n", - "prefixes:\n", - " linkml: https://w3id.org/linkml/\n", - " test_schema: http://example.org/test-schema/\n", - "default_prefix: test_schema\n", - "default_range: string\n", - "slots:\n", - " family_name:\n", - " range: string\n", - " given_name:\n", - " range: string\n", - " age_in_years:\n", - " range: integer\n", - " height_in_cm:\n", - " range: float\n", - "classes:\n", - " Person:\n", - " slots:\n", - " - family_name\n", - " - given_name\n", - " - age_in_years\n", - " - height_in_cm\n" - ] - } - ], - "source": [ - "from linkml.utils.schema_builder import SchemaBuilder\n", - "from linkml_runtime.linkml_model import SlotDefinition\n", - "\n", - "sb = SchemaBuilder()\n", - "sb.add_class(\"Person\", slots=[SlotDefinition(\"family_name\", range=\"string\"), \n", - " SlotDefinition(\"given_name\", range=\"string\"),\n", - " SlotDefinition(\"age_in_years\", range=\"integer\"),\n", - " SlotDefinition(\"height_in_cm\", range=\"float\"),\n", - " ])\n", - "sb.add_defaults()\n", - "print(yaml.dump(sb.as_dict(), sort_keys=False))" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-04-11T02:31:25.400218Z", - "start_time": "2024-04-11T02:31:25.204882Z" - } - }, - "id": "ef2c60ef7fbcbe20" - }, - { - "cell_type": "markdown", - "source": [ - "## Creating a Transformer Session object\n", - "\n", - "We will use a `Session` object which conveniently wraps a number of different capabilities;\n", - "the first of these capabilities is to map (transform) data objects from one schema to another\n", - "(implicit) schema using a *transformer specification*).\n", - "\n", - "Our initial transformer specification will be a trivial isomorphic one that:\n", - "\n", - "- maps the `Person` class to an `Individual` class\n", - "- passes through `name` fields as-is\n", - "- renames measurement fields (`age_in_years` and `height_in_cm` to `age` and `height`)" - ], - "metadata": { - "collapsed": false - }, - "id": "d4228629dd7e2ef2" - }, - { - "cell_type": "code", - "execution_count": 3, - "outputs": [], - "source": [ - "from linkml_map.session import Session\n", - "\n", - "session = Session()\n", - "session.set_source_schema(sb.as_dict())" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-04-11T02:31:25.845223Z", - "start_time": "2024-04-11T02:31:25.401087Z" - } - }, - "id": "a6257aa9e6ab021e" - }, - { - "cell_type": "code", - "execution_count": 4, - "outputs": [], - "source": [ - "# Transformer specification (in YAML)\n", - "session.set_object_transformer(\"\"\"\n", - "class_derivations:\n", - " Individual:\n", - " populated_from: Person\n", - " slot_derivations:\n", - " family_name:\n", - " populated_from: family_name\n", - " given_name:\n", - " populated_from: given_name\n", - " age:\n", - " populated_from: age_in_years\n", - " height:\n", - " populated_from: height_in_cm\n", - "\"\"\")" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-04-11T02:31:25.931450Z", - "start_time": "2024-04-11T02:31:25.846462Z" - } - }, - "id": "47b95e209790b423" - }, - { - "cell_type": "markdown", - "source": [ - "## Visualizing transformer specifications\n", - "\n", - "We can visualize the transformer specification using graphviz:" - ], - "metadata": { - "collapsed": false - }, - "id": "8313d6acb588178e" - }, - { - "cell_type": "code", - "execution_count": 5, - "outputs": [ - { - "data": { - "image/svg+xml": "\n\n\n\n\n\n\n\n\nsourcePerson\n\nPerson\n\nfamily_name : string\n\ngiven_name : string\n\nage_in_years : integer\n\nheight_in_cm : float\n\n\n\ntargetIndividual\n\nIndividual\n\nfamily_name : string\n\ngiven_name : string\n\nage : integer\n\nheight : float\n\n\n\nsourcePerson:family_name->targetIndividual:family_name\n\n\n\n\n\nsourcePerson:given_name->targetIndividual:given_name\n\n\n\n\n\nsourcePerson:age_in_years->targetIndividual:age\n\n\n\n\n\nsourcePerson:height_in_cm->targetIndividual:height\n\n\n\n\n\n", - "text/plain": "" - }, - "execution_count": 5, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "session.graphviz()" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-04-11T02:31:26.282142Z", - "start_time": "2024-04-11T02:31:25.933036Z" - } - }, - "id": "1c623cdc3c1cfbca" - }, - { - "cell_type": "markdown", - "source": [ - "## Transforming objects\n", - "\n", - "We'll next make a simple `Person` object. Note that for simplicity we are specifying this\n", - "using a Python dictionary. The framework also works with objects instantiating either\n", - "Pydantic or Dataclasses classes (use the `transform_object` method instead of `transform`)." - ], - "metadata": { - "collapsed": false - }, - "id": "a15707b9cd2d3db5" - }, - { - "cell_type": "code", - "execution_count": 6, - "outputs": [ - { - "data": { - "text/plain": "{'family_name': 'Doe', 'given_name': 'Jane', 'age': 42, 'height': 180.0}" - }, - "execution_count": 6, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "obj = {\n", - " \"given_name\": \"Jane\",\n", - " \"family_name\": \"Doe\",\n", - " \"age_in_years\": 42,\n", - " \"height_in_cm\": 180.0,\n", - " }\n", - "session.transform(obj)" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-04-11T02:31:26.287545Z", - "start_time": "2024-04-11T02:31:26.283103Z" - } - }, - "id": "9f4d1fc4ca97f80c" - }, - { - "cell_type": "markdown", - "source": [ - "This does what we expect - it renames the two fields, but leaves all values intact.\n", - "\n", - "Note that because we use using dictionaries here, the renaming of the class has no effect,\n", - "as this is implicit with JSON/dictionaries.\n", - "\n", - "TODO: docs on type designator fields\n", - "\n", - "For command line users, the same thing can be achieved with the `map-data` command." - ], - "metadata": { - "collapsed": false - }, - "id": "b3826284a497d04e" - }, - { - "cell_type": "markdown", - "source": [ - "## Deriving target schemas\n", - "\n", - "LinkML-Transformer is intended as a *declarative* framework, in contrast to writing Python\n", - "transformation code. This allows tools to introspect mappings and perform other kinds of inference.\n", - "An example of this is *deriving the (implicit) target schema*\n", - "\n", - "Here we use the `target_schema` method on the session object to derive the target schema:" - ], - "metadata": { - "collapsed": false - }, - "id": "d6aa71d062e96aa1" - }, - { - "cell_type": "code", - "execution_count": 7, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "name: test-schema-derived\n", - "id: http://example.org/test-schema-derived\n", - "imports:\n", - "- linkml:types\n", - "prefixes:\n", - " linkml:\n", - " prefix_prefix: linkml\n", - " prefix_reference: https://w3id.org/linkml/\n", - " test_schema:\n", - " prefix_prefix: test_schema\n", - " prefix_reference: http://example.org/test-schema/\n", - "default_prefix: http://example.org/test-schema-derived/\n", - "default_range: string\n", - "classes:\n", - " Individual:\n", - " name: Individual\n", - " attributes:\n", - " family_name:\n", - " name: family_name\n", - " domain_of:\n", - " - Person\n", - " range: string\n", - " given_name:\n", - " name: given_name\n", - " domain_of:\n", - " - Person\n", - " range: string\n", - " age:\n", - " name: age\n", - " domain_of:\n", - " - Person\n", - " range: integer\n", - " height:\n", - " name: height\n", - " domain_of:\n", - " - Person\n", - " range: float\n" - ] - } - ], - "source": [ - "from linkml_runtime.dumpers import yaml_dumper\n", - "\n", - "print(yaml_dumper.dumps(session.target_schema))" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-04-11T02:31:26.292850Z", - "start_time": "2024-04-11T02:31:26.285236Z" - } - }, - "id": "687912c18bf6752" - }, - { - "cell_type": "markdown", - "source": [ - "As expected, this is isomorphic to the original (source) schema, with fields and classes renamed." - ], - "metadata": { - "collapsed": false - }, - "id": "2c89abbd8e298981" - }, - { - "cell_type": "markdown", - "source": [ - "## Using Expressions\n", - "\n", - "In addition to renaming fields, we can derive field values via evaluation of function *expressions*.\n", - "\n", - "You are encouraged to follow the subset of Python defined by the LinkML expression language. This provides\n", - "both safety, and declarativity. However, if you need\n", - "to, you can include arbitrary Python code, provided you configure the session to allow this.\n", - "\n", - "We'll keep the original schema, and will provide a new Transformer specification, \n", - "giving an example of both string manipulation functions and arithmetic functions; the latter\n", - "perform unit conversions (later on we will see more flexible and declarative ways to perform unit conversions).\n", - "\n" - ], - "metadata": { - "collapsed": false - }, - "id": "4562b534b6f23910" - }, - { - "cell_type": "code", - "execution_count": 8, - "outputs": [], - "source": [ - "\n", - "session.set_object_transformer(\"\"\"\n", - "class_derivations:\n", - " Individual:\n", - " populated_from: Person\n", - " slot_derivations:\n", - " name:\n", - " expr: \"{given_name} + ' ' + {family_name}\"\n", - " description: Concatenating given and family names\n", - " note this is a bad assumption for names in general,\n", - " this is just for demonstration\n", - " age_in_months:\n", - " expr: age_in_years * 12\n", - " height_in_meters:\n", - " expr: height_in_cm / 100\n", - "\"\"\")\n" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-04-11T02:31:26.333138Z", - "start_time": "2024-04-11T02:31:26.301179Z" - } - }, - "id": "789a7b6535ab410f" - }, - { - "cell_type": "markdown", - "source": [ - "Note that when we visualize this specification, dotted lines are shown indicating a relationship\n", - "between source and target that is different from direct copy:" - ], - "metadata": { - "collapsed": false - }, - "id": "e02eaa2cde3172c8" - }, - { - "cell_type": "code", - "execution_count": 9, - "outputs": [ - { - "data": { - "image/svg+xml": "\n\n\n\n\n\n\n\n\nsourcePerson\n\nPerson\n\nfamily_name : string\n\ngiven_name : string\n\nage_in_years : integer\n\nheight_in_cm : float\n\n\n\ntargetIndividual\n\nIndividual\n\nname : string\n\nage_in_months : string\n\nheight_in_meters : string\n\n\n\nsourcePerson:given_name->targetIndividual:name\n\n\n\n\n\nsourcePerson:family_name->targetIndividual:name\n\n\n\n\n\nsourcePerson:age_in_years->targetIndividual:age_in_months\n\n\n\n\n\nsourcePerson:height_in_cm->targetIndividual:height_in_meters\n\n\n\n\n\n", - "text/plain": "" - }, - "execution_count": 9, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "session.graphviz()" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-04-11T02:31:26.637567Z", - "start_time": "2024-04-11T02:31:26.326951Z" - } - }, - "id": "2a18ccb5d7dc469b" - }, - { - "cell_type": "markdown", - "source": [ - "Now we'll transform the same object as before, and see the results:" - ], - "metadata": { - "collapsed": false - }, - "id": "f7019db8d391ab97" - }, - { - "cell_type": "code", - "execution_count": 10, - "outputs": [ - { - "data": { - "text/plain": "{'name': 'Jane Doe', 'age_in_months': 504, 'height_in_meters': 1.8}" - }, - "execution_count": 10, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "session.transform(obj)" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-04-11T02:31:26.639446Z", - "start_time": "2024-04-11T02:31:26.636456Z" - } - }, - "id": "5e20e98e2b23751f" - }, - { - "cell_type": "markdown", - "source": [ - "As expected, we concatenated the name fields, and converted the age and height fields to different units.\n", - "\n", - "Let's take a look at the derived schema for this new transformation:" - ], - "metadata": { - "collapsed": false - }, - "id": "ad9fd0f70178fd26" - }, - { - "cell_type": "code", - "execution_count": 11, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "name: test-schema-derived\n", - "id: http://example.org/test-schema-derived\n", - "imports:\n", - "- linkml:types\n", - "prefixes:\n", - " linkml:\n", - " prefix_prefix: linkml\n", - " prefix_reference: https://w3id.org/linkml/\n", - " test_schema:\n", - " prefix_prefix: test_schema\n", - " prefix_reference: http://example.org/test-schema/\n", - "default_prefix: http://example.org/test-schema-derived/\n", - "default_range: string\n", - "classes:\n", - " Individual:\n", - " name: Individual\n", - " attributes:\n", - " name:\n", - " name: name\n", - " age_in_months:\n", - " name: age_in_months\n", - " height_in_meters:\n", - " name: height_in_meters\n" - ] - } - ], - "source": [ - "print(yaml_dumper.dumps(session.target_schema))" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-04-11T02:31:26.644551Z", - "start_time": "2024-04-11T02:31:26.642034Z" - } - }, - "id": "7c1f7efef1836364" - }, - { - "cell_type": "markdown", - "source": [ - "Note that at this time, deriving ranges using expressions is not supported, so the two measurement fields\n", - "are erroneously typed as having the `default_range` of `string`. However, in principle, if you use the\n", - "linkml subset of Python it should be possible to infer the range of the derived field, and this may be added\n", - "in future versions. Currently the tool chain is at an early stage of development." - ], - "metadata": { - "collapsed": false - }, - "id": "e87b7f45dc137a68" - }, - { - "cell_type": "markdown", - "source": [ - "## Unit conversions\n", - "\n", - "Next we will look at a different way of doing unit conversions. The LinkML specification allows\n", - "schemas to explicitly declare the units of slots, so let's modify our schema to do this, adding\n", - "a UCUM code for our `height_in_cm` slot:" - ], - "metadata": { - "collapsed": false - }, - "id": "ff3d20924263ec15" - }, - { - "cell_type": "code", - "execution_count": 12, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "name: test-schema\n", - "id: http://example.org/test-schema\n", - "imports:\n", - "- linkml:types\n", - "prefixes:\n", - " linkml: https://w3id.org/linkml/\n", - " test_schema: http://example.org/test-schema/\n", - "default_prefix: test_schema\n", - "default_range: string\n", - "slots:\n", - " family_name:\n", - " range: string\n", - " given_name:\n", - " range: string\n", - " age_in_years:\n", - " range: integer\n", - " height_in_cm:\n", - " range: float\n", - " unit:\n", - " ucum_code: cm\n", - "classes:\n", - " Person:\n", - " slots:\n", - " - family_name\n", - " - given_name\n", - " - age_in_years\n", - " - height_in_cm\n" - ] - } - ], - "source": [ - "from linkml_runtime.linkml_model.units import UnitOfMeasure\n", - "sb.schema.slots['height_in_cm'].unit = UnitOfMeasure(ucum_code='cm')\n", - "session.set_source_schema(sb.as_dict())\n", - "print(yaml.dump(sb.as_dict(), sort_keys=False))" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-04-11T02:31:26.651494Z", - "start_time": "2024-04-11T02:31:26.649509Z" - } - }, - "id": "65a5ce5d97e27f76" - }, - { - "cell_type": "markdown", - "source": [ - "## Adding target_unit to transformer specification\n", - "\n", - "We will create a new transformer specification, focusing on the `height_in_cm` field. We will\n", - "transform this into a `height_in_meters` field, and will use the `target_unit` field to specify\n", - "the target unit." - ], - "metadata": { - "collapsed": false - }, - "id": "c5cf59ec9ac3148e" - }, - { - "cell_type": "code", - "execution_count": 13, - "outputs": [], - "source": [ - "session.set_object_transformer(\"\"\"\n", - "class_derivations:\n", - " Individual:\n", - " populated_from: Person\n", - " slot_derivations:\n", - " name:\n", - " expr: \"{given_name} + ' ' + {family_name}\"\n", - " height_in_meters:\n", - " populated_from: height_in_cm\n", - " unit_conversion:\n", - " target_unit: m\n", - "\"\"\")" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-04-11T02:31:26.697189Z", - "start_time": "2024-04-11T02:31:26.662647Z" - } - }, - "id": "bc99bad97970b1b7" - }, - { - "cell_type": "code", - "execution_count": 14, - "outputs": [ - { - "data": { - "text/plain": "{'name': 'Jane Doe', 'height_in_meters': 1.8}" - }, - "execution_count": 14, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "session.transform(obj)" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-04-11T02:31:26.793669Z", - "start_time": "2024-04-11T02:31:26.682118Z" - } - }, - "id": "831b444d9c47e0ea" - }, - { - "cell_type": "markdown", - "source": [ - "## Units in derived schema\n", - "\n", - "Next we'll look at the derived target schema, and as expected we see that it has inferred\n", - "the target unit for the `height_in_meters` field:" - ], - "metadata": { - "collapsed": false - }, - "id": "6f37087c6dfc30ef" - }, - { - "cell_type": "code", - "execution_count": 15, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "name: test-schema-derived\n", - "id: http://example.org/test-schema-derived\n", - "imports:\n", - "- linkml:types\n", - "prefixes:\n", - " linkml:\n", - " prefix_prefix: linkml\n", - " prefix_reference: https://w3id.org/linkml/\n", - " test_schema:\n", - " prefix_prefix: test_schema\n", - " prefix_reference: http://example.org/test-schema/\n", - "default_prefix: http://example.org/test-schema-derived/\n", - "default_range: string\n", - "classes:\n", - " Individual:\n", - " name: Individual\n", - " attributes:\n", - " name:\n", - " name: name\n", - " height_in_meters:\n", - " name: height_in_meters\n", - " domain_of:\n", - " - Person\n", - " range: float\n", - " unit:\n", - " ucum_code: m\n" - ] - } - ], - "source": [ - "print(yaml_dumper.dumps(session.target_schema))\n" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-04-11T02:31:26.799169Z", - "start_time": "2024-04-11T02:31:26.794539Z" - } - }, - "id": "b589e0e95550962d" - }, - { - "cell_type": "markdown", - "source": [ - "## Tabular serialization" - ], - "metadata": { - "collapsed": false - }, - "id": "8f4c4cb125aade0b" - }, - { - "cell_type": "code", - "execution_count": 16, - "outputs": [], - "source": [ - "slot = sb.add_slot(\"aliases\", multivalued=True, range=\"string\", replace_if_present=True)" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-04-11T02:31:26.800538Z", - "start_time": "2024-04-11T02:31:26.798420Z" - } - }, - "id": "f492b27c0f0fbf88" - }, - { - "cell_type": "code", - "execution_count": 17, - "outputs": [], - "source": [ - "sb.schema.classes['Person'].slots.append(slot.name)" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-04-11T02:31:26.805051Z", - "start_time": "2024-04-11T02:31:26.801378Z" - } - }, - "id": "3ac3f93ab8561300" - }, - { - "cell_type": "code", - "execution_count": 18, - "outputs": [], - "source": [ - "session.set_source_schema(sb.as_dict())" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-04-11T02:31:26.838303Z", - "start_time": "2024-04-11T02:31:26.808019Z" - } - }, - "id": "84262d357323f76e" - }, - { - "cell_type": "code", - "execution_count": 19, - "outputs": [], - "source": [ - "session.set_object_transformer(\"\"\"\n", - "class_derivations:\n", - " Individual:\n", - " populated_from: Person\n", - " slot_derivations:\n", - " family_name:\n", - " populated_from: family_name\n", - " given_name:\n", - " populated_from: given_name\n", - " age:\n", - " populated_from: age_in_years\n", - " height:\n", - " populated_from: height_in_cm\n", - " aliases:\n", - " populated_from: aliases\n", - " stringification:\n", - " delimiter: '|'\n", - "\"\"\") " - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-04-11T02:31:26.874680Z", - "start_time": "2024-04-11T02:31:26.810139Z" - } - }, - "id": "2f282430f48e13c0" - }, - { - "cell_type": "code", - "execution_count": 20, - "outputs": [ - { - "data": { - "text/plain": "{'family_name': 'Doe',\n 'given_name': 'Jane',\n 'age': 42,\n 'height': 180.0,\n 'aliases': 'Jane|Janie|Janey'}" - }, - "execution_count": 20, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "obj = {\n", - " \"given_name\": \"Jane\",\n", - " \"family_name\": \"Doe\",\n", - " \"age_in_years\": 42,\n", - " \"height_in_cm\": 180.0,\n", - " \"aliases\": [\"Jane\", \"Janie\", \"Janey\"]\n", - " }\n", - "flattened = session.transform(obj)\n", - "flattened" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-04-11T02:31:26.885950Z", - "start_time": "2024-04-11T02:31:26.875371Z" - } - }, - "id": "fdd23ae82909770e" - }, - { - "cell_type": "markdown", - "source": [ - "this can easily be serialized to a CSV/TSV" - ], - "metadata": { - "collapsed": false - }, - "id": "c5174dcbf7dd0c43" - }, - { - "cell_type": "markdown", - "source": [ - "## Reverse transform\n", - "\n", - "If a transform does not contain one-way functions,\n", - "it can be *reversed*.\n", - "\n", - "In this case, reversing the transform allows us to map\n", - "from the tabular form back to the richer original representation." - ], - "metadata": { - "collapsed": false - }, - "id": "fae8392b02526408" - }, - { - "cell_type": "code", - "execution_count": 21, - "outputs": [ - { - "data": { - "text/plain": "{'family_name': 'Doe',\n 'given_name': 'Jane',\n 'age_in_years': 42,\n 'height_in_cm': 180.0,\n 'aliases': ['Jane', 'Janie', 'Janey']}" - }, - "execution_count": 21, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "session.reverse_transform(flattened)" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-04-11T02:31:26.917491Z", - "start_time": "2024-04-11T02:31:26.890611Z" - } - }, - "id": "e8c1c3f98081d38" - }, - { - "cell_type": "code", - "execution_count": 21, - "outputs": [], - "source": [], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-04-11T02:31:26.917800Z", - "start_time": "2024-04-11T02:31:26.897056Z" - } - }, - "id": "ee14ace4b1c7d256" - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 2 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython2", - "version": "2.7.6" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/docs/examples/biolink-subsetting.ipynb b/docs/examples/biolink-subsetting.ipynb deleted file mode 100644 index c093617..0000000 --- a/docs/examples/biolink-subsetting.ipynb +++ /dev/null @@ -1,1669 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "id": "bc01d59ced195153", - "metadata": {}, - "source": [ - "# Biolink Model Subsetting\n", - "This notebook demonstrates how to subset the Biolink Model using the Biolink Model schema and a transformation specification in two different ways: first using a transformation specification defined manually in YAML and loaded from the filesystem, and second, using a subset of classes retrieved using SchemaView dynamically." - ] - }, - { - "cell_type": "markdown", - "id": "91b3677392f95575", - "metadata": {}, - "source": [ - "First, we import several LinkML helper packages including SchemaView: https://linkml.io/linkml/developers/schemaview.html \n", - "SchemaView is a LinkML schema introspection tool that provides helpful functions to retrieve model elements by name. It also supports navigating ancestors and descendants of any model element, including classes, slots, types, and permissible values in enumerations. \n" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "id": "e3f86775ef7a9dcc", - "metadata": {}, - "outputs": [], - "source": [ - "from pathlib import Path\n", - "from pytest import fixture\n", - "\n", - "from linkml_runtime.dumpers import yaml_dumper\n", - "from linkml_map.datamodel.transformer_model import TransformationSpecification, ClassDerivation, SlotDerivation, CopyDirective\n", - "from linkml_map.inference.schema_mapper import SchemaMapper\n", - "from linkml_map.session import Session\n", - "from linkml_runtime.utils.schemaview import SchemaView\n", - "from linkml_map.utils.loaders import load_specification\n", - "from linkml_runtime.utils.formatutils import camelcase, underscore\n", - "from pprint import pprint\n", - "\n", - "REPO_ROOT = Path.cwd().parent.parent" - ] - }, - { - "cell_type": "markdown", - "id": "d8d3b8f7bc023dae", - "metadata": {}, - "source": [ - "SchemaView can accept a variety of imports to initialize, including a Path or string representation of a Path or (as we do in this case), a URL of a raw LinkML schema. " - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "id": "8ca1d183bd948863", - "metadata": {}, - "outputs": [], - "source": [ - "schema_url = \"https://raw.githubusercontent.com/biolink/biolink-model/master/biolink-model.yaml/"\n", - "sv = SchemaView(schema_url)\n" - ] - }, - { - "cell_type": "markdown", - "id": "a91dc68f7d162c6f", - "metadata": {}, - "source": [ - "### Creating a Transformation Specification Manually in YAML format.\n", - "In our first example, we develop a \"Transform Specification\" for Biolink Model using Class and Slot Derivations as defined by the linkml-map transformation language. More about that here: https://linkml.io/linkml-map/#TransformationSpecification/" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "id": "b9f39d577790a0dd", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "NamedThing\n", - "Gene\n", - "Disease\n", - "PhenotypicFeature\n", - "Association\n", - "GeneToPhenotypicFeatureAssociation\n", - "\n", - "id\n", - "name\n", - "category\n", - "symbol\n", - "subject\n", - "predicate\n", - "object\n" - ] - } - ], - "source": [ - "transform_file = REPO_ROOT / \"tests/input/examples/biolink/transform/biolink-example-profile.transform.yaml\"\n", - "# Initialize Session and SchemaBuilder\n", - "session = Session()\n", - "\n", - "# Set the source schema in the session\n", - "session.set_source_schema(sv)\n", - "\n", - "tr_spec = load_specification(transform_file)\n", - "mapper = SchemaMapper()\n", - "mapper.source_schemaview = sv\n", - "\n", - "target_schema_obj = mapper.derive_schema(specification=tr_spec,\n", - " target_schema_id=\"biolink-profile\",\n", - " target_schema_name=\"BiolinkProfile\")\n", - "\n", - "\n", - "yaml_dumper.dump(target_schema_obj, \"biolink-profile.yaml\")\n", - "\n", - "transformed_sv = SchemaView(\"biolink-profile.yaml\")\n", - "\n", - "for class_name in transformed_sv.all_classes():\n", - " print(class_name)\n", - "print()\n", - "for slot_name in transformed_sv.all_slots():\n", - " print(slot_name)" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "id": "8ac53bfef2f51db", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Exception: range: label type\n" - ] - } - ], - "source": [ - "!gen-pydantic biolink-profile.yaml" - ] - }, - { - "cell_type": "markdown", - "id": "58dcaf83d20f4dea", - "metadata": {}, - "source": [ - "Note:\n", - "* Still in development is the tracing of provenance between a source schema and a destination schema. Right now there is no provenance. \n", - "* If a class, slot, enum, or type is not included at all in the Derivation, it will not be pushed forward to the destination schema. In development is an option to pull all non-specified components of the source model into the destination model.\n", - "* You can do transformations on a derivation as well, see: https://linkml.io/linkml-map/#examples/Tutorial/#using-expressions\n", - "* You can transform data as well as schemas, but this is currently \"beta\" level development.\n", - "* Custom types are not pulled forward; this is a result of an error at the moment." - ] - }, - { - "cell_type": "markdown", - "id": "48d85f450751e59", - "metadata": {}, - "source": [ - "### Creating a TransformationSpecification using SchemaView and an existing model.\n", - "\n", - "In our second example, we use the Biolink Model directly to derive classes and slots programmatically according to a simple list of \"subset classes\" that we want to extract from the main model in order to produce a subset model according to our specification." - ] - }, - { - "cell_type": "markdown", - "id": "c5a7c5a345c5f87d", - "metadata": {}, - "source": [ - "First, we write a method to extract the classes and slots from Biolink Model using SchemaView" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "id": "87000f75753c5faf", - "metadata": {}, - "outputs": [], - "source": [ - "def get_biolink_class_derivations(sv, subset_classes) -> dict:\n", - " \"\"\"\n", - " Function to get Biolink class definitions\n", - "\n", - " :param sv: SchemaView object\n", - " :param subset_classes: List of classes to subset\n", - " :return: Dictionary of class derivations incl slot derivations\n", - " \"\"\"\n", - " # Example implementation to fetch class definitions\n", - " # This should be replaced with the actual implementation\n", - " class_derivations ={}\n", - " for class_name in subset_classes:\n", - " class_derivation = ClassDerivation(populated_from=class_name,\n", - " name=camelcase(class_name))\n", - " induced_slots = sv.class_induced_slots(class_name)\n", - " for slot in induced_slots:\n", - " slot_derivation = SlotDerivation(populated_from=slot.name, name=underscore(slot.name))\n", - " class_derivation.slot_derivations[underscore(slot.name)] = slot_derivation\n", - " class_derivations[camelcase(class_name)] = class_derivation\n", - " return class_derivations\n" - ] - }, - { - "cell_type": "code", - "execution_count": 14, - "id": "9f1ca647-fda6-493a-aebe-94ee726a7be2", - "metadata": {}, - "outputs": [], - "source": [ - "def get_biolink_class_derivations_direct(sv, subset_classes) -> dict:\n", - " \"\"\"\n", - " Function to get Biolink class definitions\n", - "\n", - " :param sv: SchemaView object\n", - " :param subset_classes: List of classes to subset\n", - " :return: Dictionary of class derivations incl slot derivations\n", - " \"\"\"\n", - " # Example implementation to fetch class definitions\n", - " # This should be replaced with the actual implementation\n", - " class_derivations ={}\n", - " for class_name in subset_classes:\n", - " class_derivation = ClassDerivation(populated_from=class_name,\n", - " name=camelcase(class_name))\n", - " for slot in sv.get_class(class_name).slots:\n", - " slot_derivation = SlotDerivation(populated_from=slot, name=underscore(slot))\n", - " class_derivation.slot_derivations[underscore(slot)] = slot_derivation\n", - " class_derivations[camelcase(class_name)] = class_derivation\n", - " return class_derivations" - ] - }, - { - "cell_type": "code", - "execution_count": 21, - "id": "1193a55025345761", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "class derived: Gene\n", - "class derived: Disease\n", - "class derived: CaseToPhenotypicFeatureAssociation\n", - "class derived: GeneToDiseaseAssociation\n", - "class derived: GeneToPhenotypicFeatureAssociation\n", - "class derived: Case\n", - "class derived: PhenotypicFeature\n", - "slot derived: symbol\n", - "slot derived: xref\n", - "slot derived: has_biological_sequence\n", - "slot derived: id\n", - "slot derived: in_taxon\n", - "slot derived: in_taxon_label\n", - "slot derived: provided_by\n", - "slot derived: full_name\n", - "slot derived: synonym\n", - "slot derived: iri\n", - "slot derived: category\n", - "slot derived: type\n", - "slot derived: name\n", - "slot derived: description\n", - "slot derived: has_attribute\n", - "slot derived: deprecated\n", - "slot derived: subject\n", - "slot derived: predicate\n", - "slot derived: object\n", - "slot derived: sex_qualifier\n", - "slot derived: disease_context_qualifier\n", - "slot derived: subject_specialization_qualifier\n", - "slot derived: object_specialization_qualifier\n", - "slot derived: anatomical_context_qualifier\n", - "slot derived: negated\n", - "slot derived: qualifier\n", - "slot derived: qualifiers\n", - "slot derived: publications\n", - "slot derived: has_evidence\n", - "slot derived: knowledge_source\n", - "slot derived: primary_knowledge_source\n", - "slot derived: aggregator_knowledge_source\n", - "slot derived: knowledge_level\n", - "slot derived: agent_type\n", - "slot derived: timepoint\n", - "slot derived: original_subject\n", - "slot derived: original_predicate\n", - "slot derived: original_object\n", - "slot derived: subject_category\n", - "slot derived: object_category\n", - "slot derived: subject_closure\n", - "slot derived: object_closure\n", - "slot derived: subject_category_closure\n", - "slot derived: object_category_closure\n", - "slot derived: subject_namespace\n", - "slot derived: object_namespace\n", - "slot derived: subject_label_closure\n", - "slot derived: object_label_closure\n", - "slot derived: retrieval_source_ids\n", - "slot derived: p_value\n", - "slot derived: adjusted_p_value\n", - "slot derived: has_supporting_studies\n", - "slot derived: has_count\n", - "slot derived: has_total\n", - "slot derived: has_quotient\n", - "slot derived: has_percentage\n", - "slot derived: subject_aspect_qualifier\n", - "slot derived: subject_direction_qualifier\n", - "slot derived: object_aspect_qualifier\n", - "slot derived: object_direction_qualifier\n", - "slot derived: qualified_predicate\n", - "slot derived: frequency_qualifier\n", - "type copied: string\n", - "type copied: integer\n", - "type copied: boolean\n", - "type copied: float\n", - "type copied: double\n", - "type copied: decimal\n", - "type copied: time\n", - "type copied: date\n", - "type copied: datetime\n", - "type copied: date_or_datetime\n", - "type copied: uriorcurie\n", - "type copied: curie\n", - "type copied: uri\n", - "type copied: ncname\n", - "type copied: objectidentifier\n", - "type copied: nodeidentifier\n", - "type copied: jsonpointer\n", - "type copied: jsonpath\n", - "type copied: sparqlpath\n", - "type copied: chemical formula value\n", - "type copied: iri type\n", - "type copied: label type\n", - "type copied: predicate type\n", - "type copied: narrative text\n", - "type copied: symbol type\n", - "type copied: frequency value\n", - "type copied: percentage frequency value\n", - "type copied: quotient\n", - "type copied: unit\n", - "type copied: time type\n", - "type copied: biological sequence\n" - ] - } - ], - "source": [ - "session = Session()\n", - "\n", - "# Set the source schema in the session\n", - "session.set_source_schema(sv)\n", - "\n", - "subset_classes = [\n", - " \"gene\",\n", - " \"disease\",\n", - " \"case to phenotypic feature association\",\n", - " \"gene to disease association\",\n", - " \"gene to phenotypic feature association\",\n", - " \"case\",\n", - " \"phenotypic feature\",\n", - " ]\n", - "\n", - "class_derivations = get_biolink_class_derivations_direct(sv, subset_classes)\n", - "copy_type_directives = {\n", - " type_name: CopyDirective(element_name=type_name, copy_all=False)\n", - " for type_name, type_def in sv.all_types().items()\n", - "}\n", - "\n", - "ts = TransformationSpecification(class_derivations=class_derivations, copy_directives=copy_type_directives)\n", - "\n", - "mapper = SchemaMapper()\n", - "mapper.source_schemaview = sv\n", - "\n", - "target_schema_obj = mapper.derive_schema(\n", - " specification=ts, target_schema_id=\"biolink-subset\", target_schema_name=\"BiolinkSubset\"\n", - ")\n", - "\n", - "# ugly bit of hacking to demonstrate end-to-end functionality\n", - "target_schema_obj.types = sv.all_types()\n", - "\n", - "yaml_dumper.dump(target_schema_obj, \"biolink-subset.yaml\")\n", - "\n", - "transformed_sv = SchemaView(\"biolink-subset.yaml\")\n", - "\n", - "for class_name in transformed_sv.all_classes():\n", - " print(\"class derived: \", class_name)\n", - "for slot_name in transformed_sv.all_slots():\n", - " print(\"slot derived: \", slot_name)\n", - "for type_name in transformed_sv.all_types():\n", - " print(\"type copied: \", type_name)" - ] - }, - { - "cell_type": "code", - "execution_count": 16, - "id": "f560d74e30c83f1e", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "name: BiolinkSubset\n", - "id: biolink-subset\n", - "imports:\n", - "- linkml:types\n", - "prefixes:\n", - " AGRKB:\n", - " prefix_prefix: AGRKB\n", - " prefix_reference: https://www.alliancegenome.org/\n", - " apollo:\n", - " prefix_prefix: apollo\n", - " prefix_reference: https://github.com/GMOD/Apollo\n", - " AspGD:\n", - " prefix_prefix: AspGD\n", - " prefix_reference: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=\n", - " biolink:\n", - " prefix_prefix: biolink\n", - " prefix_reference: https://w3id.org/biolink/vocab/\n", - " bioschemas:\n", - " prefix_prefix: bioschemas\n", - " prefix_reference: https://bioschemas.org/\n", - " linkml:\n", - " prefix_prefix: linkml\n", - " prefix_reference: https://w3id.org/linkml/\n", - " CAID:\n", - " prefix_prefix: CAID\n", - " prefix_reference: http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=\n", - " CHADO:\n", - " prefix_prefix: CHADO\n", - " prefix_reference: http://gmod.org/wiki/Chado/\n", - " ChemBank:\n", - " prefix_prefix: ChemBank\n", - " prefix_reference: http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=\n", - " CHEMBL.MECHANISM:\n", - " prefix_prefix: CHEMBL.MECHANISM\n", - " prefix_reference: https://www.ebi.ac.uk/chembl/mechanism/inspect/\n", - " CID:\n", - " prefix_prefix: CID\n", - " prefix_reference: http://pubchem.ncbi.nlm.nih.gov/compound/\n", - " CLINVAR:\n", - " prefix_prefix: CLINVAR\n", - " prefix_reference: http://identifiers.org/clinvar\n", - " COAR_RESOURCE:\n", - " prefix_prefix: COAR_RESOURCE\n", - " prefix_reference: http://purl.org/coar/resource_type/\n", - " COG:\n", - " prefix_prefix: COG\n", - " prefix_reference: https://www.ncbi.nlm.nih.gov/research/cog-project/\n", - " ComplexPortal:\n", - " prefix_prefix: ComplexPortal\n", - " prefix_reference: https://www.ebi.ac.uk/complexportal/complex/\n", - " CPT:\n", - " prefix_prefix: CPT\n", - " prefix_reference: https://www.ama-assn.org/practice-management/cpt/\n", - " CTD.CHEMICAL:\n", - " prefix_prefix: CTD.CHEMICAL\n", - " prefix_reference: http://ctdbase.org/detail.go?type=chem&acc=\n", - " CTD.DISEASE:\n", - " prefix_prefix: CTD.DISEASE\n", - " prefix_reference: http://ctdbase.org/detail.go?type=disease&db=MESH&acc=\n", - " CTD.GENE:\n", - " prefix_prefix: CTD.GENE\n", - " prefix_reference: http://ctdbase.org/detail.go?type=gene&acc=\n", - " CTD:\n", - " prefix_prefix: CTD\n", - " prefix_reference: http://ctdbase.org/\n", - " DGIdb:\n", - " prefix_prefix: DGIdb\n", - " prefix_reference: https://www.dgidb.org/interaction_types\n", - " dcat:\n", - " prefix_prefix: dcat\n", - " prefix_reference: http://www.w3.org/ns/dcat#\n", - " dct:\n", - " prefix_prefix: dct\n", - " prefix_reference: http://purl.org/dc/terms/\n", - " dcid:\n", - " prefix_prefix: dcid\n", - " prefix_reference: https://datacommons.org/browser/\n", - " doi:\n", - " prefix_prefix: doi\n", - " prefix_reference: https://doi.org/\n", - " DOID-PROPERTY:\n", - " prefix_prefix: DOID-PROPERTY\n", - " prefix_reference: http://purl.obolibrary.org/obo/doid#\n", - " DrugCentral:\n", - " prefix_prefix: DrugCentral\n", - " prefix_reference: http://drugcentral.org/drugcard/\n", - " ECTO:\n", - " prefix_prefix: ECTO\n", - " prefix_reference: http://purl.obolibrary.org/obo/ECTO_\n", - " EDAM-DATA:\n", - " prefix_prefix: EDAM-DATA\n", - " prefix_reference: http://edamontology.org/data_\n", - " EDAM-FORMAT:\n", - " prefix_prefix: EDAM-FORMAT\n", - " prefix_reference: http://edamontology.org/format_\n", - " EDAM-OPERATION:\n", - " prefix_prefix: EDAM-OPERATION\n", - " prefix_reference: http://edamontology.org/operation_\n", - " EDAM-TOPIC:\n", - " prefix_prefix: EDAM-TOPIC\n", - " prefix_reference: http://edamontology.org/topic_\n", - " EFO:\n", - " prefix_prefix: EFO\n", - " prefix_reference: http://www.ebi.ac.uk/efo/EFO_\n", - " ExO:\n", - " prefix_prefix: ExO\n", - " prefix_reference: http://purl.obolibrary.org/obo/ExO_\n", - " fabio:\n", - " prefix_prefix: fabio\n", - " prefix_reference: http://purl.org/spar/fabio/\n", - " foaf:\n", - " prefix_prefix: foaf\n", - " prefix_reference: http://xmlns.com/foaf/0.1/\n", - " foodb.compound:\n", - " prefix_prefix: foodb.compound\n", - " prefix_reference: http://foodb.ca/compounds/\n", - " foodb.food:\n", - " prefix_prefix: foodb.food\n", - " prefix_reference: http://foodb.ca/foods/\n", - " FYECO:\n", - " prefix_prefix: FYECO\n", - " prefix_reference: https://www.pombase.org/term/\n", - " FYPO:\n", - " prefix_prefix: FYPO\n", - " prefix_reference: http://purl.obolibrary.org/obo/FYPO_\n", - " gff3:\n", - " prefix_prefix: gff3\n", - " prefix_reference: https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#\n", - " GOREL:\n", - " prefix_prefix: GOREL\n", - " prefix_reference: http://purl.obolibrary.org/obo/GOREL_\n", - " GOP:\n", - " prefix_prefix: GOP\n", - " prefix_reference: http://purl.obolibrary.org/obo/go#\n", - " gpi:\n", - " prefix_prefix: gpi\n", - " prefix_reference: https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#\n", - " GSID:\n", - " prefix_prefix: GSID\n", - " prefix_reference: https://scholar.google.com/citations?user=\n", - " GTEx:\n", - " prefix_prefix: GTEx\n", - " prefix_reference: https://www.gtexportal.org/home/gene/\n", - " GTOPDB:\n", - " prefix_prefix: GTOPDB\n", - " prefix_reference: https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=\n", - " gtpo:\n", - " prefix_prefix: gtpo\n", - " prefix_reference: https://rdf.guidetopharmacology.org/ns/gtpo#\n", - " HANCESTRO:\n", - " prefix_prefix: HANCESTRO\n", - " prefix_reference: http://www.ebi.ac.uk/ancestro/ancestro_\n", - " HCPCS:\n", - " prefix_prefix: HCPCS\n", - " prefix_reference: http://purl.bioontology.org/ontology/HCPCS/\n", - " HsapDv:\n", - " prefix_prefix: HsapDv\n", - " prefix_reference: http://purl.obolibrary.org/obo/HsapDv_\n", - " ICD10:\n", - " prefix_prefix: ICD10\n", - " prefix_reference: https://icd.codes/icd9cm/\n", - " ICD9:\n", - " prefix_prefix: ICD9\n", - " prefix_reference: http://translator.ncats.nih.gov/ICD9_\n", - " interpro:\n", - " prefix_prefix: interpro\n", - " prefix_reference: https://www.ebi.ac.uk/interpro/entry/\n", - " INO:\n", - " prefix_prefix: INO\n", - " prefix_reference: http://purl.obolibrary.org/obo/INO_\n", - " isbn:\n", - " prefix_prefix: isbn\n", - " prefix_reference: https://www.isbn-international.org/identifier/\n", - " isni:\n", - " prefix_prefix: isni\n", - " prefix_reference: https://isni.org/isni/\n", - " issn:\n", - " prefix_prefix: issn\n", - " prefix_reference: https://portal.issn.org/resource/ISSN/\n", - " ncats.drug:\n", - " prefix_prefix: ncats.drug\n", - " prefix_reference: https://drugs.ncats.io/drug/\n", - " KEGG.BRITE:\n", - " prefix_prefix: KEGG.BRITE\n", - " prefix_reference: 'https://bioregistry.io/kegg.brite:'\n", - " KEGG:\n", - " prefix_prefix: KEGG\n", - " prefix_reference: http://www.kegg.jp/entry/\n", - " KEGG.GENES:\n", - " prefix_prefix: KEGG.GENES\n", - " prefix_reference: 'https://bioregistry.io/kegg.genes:bsu:'\n", - " KEGG.PATHWAY:\n", - " prefix_prefix: KEGG.PATHWAY\n", - " prefix_reference: 'https://bioregistry.io/kegg.pathway:'\n", - " KEGG.RCLASS:\n", - " prefix_prefix: KEGG.RCLASS\n", - " prefix_reference: 'https://www.genome.jp/dbget-bin/www_bget?rc:'\n", - " LOINC:\n", - " prefix_prefix: LOINC\n", - " prefix_reference: http://loinc.org/rdf/\n", - " MAXO:\n", - " prefix_prefix: MAXO\n", - " prefix_reference: http://purl.obolibrary.org/obo/MAXO_\n", - " medgen:\n", - " prefix_prefix: medgen\n", - " prefix_reference: https://www.ncbi.nlm.nih.gov/medgen/\n", - " metacyc.reaction:\n", - " prefix_prefix: metacyc.reaction\n", - " prefix_reference: 'http://identifiers.org/metacyc.reaction:'\n", - " METANETX.REACTION:\n", - " prefix_prefix: METANETX.REACTION\n", - " prefix_reference: https://www.metanetx.org/equa_info/\n", - " MESH:\n", - " prefix_prefix: MESH\n", - " prefix_reference: http://id.nlm.nih.gov/mesh/\n", - " MI:\n", - " prefix_prefix: MI\n", - " prefix_reference: http://purl.obolibrary.org/obo/MI_\n", - " mirbase:\n", - " prefix_prefix: mirbase\n", - " prefix_reference: http://identifiers.org/mirbase\n", - " mmmp.biomaps:\n", - " prefix_prefix: mmmp.biomaps\n", - " prefix_reference: 'https://bioregistry.io/mmmp.biomaps:'\n", - " MmusDv:\n", - " prefix_prefix: MmusDv\n", - " prefix_reference: http://purl.obolibrary.org/obo/MMUSDV_\n", - " MSigDB:\n", - " prefix_prefix: MSigDB\n", - " prefix_reference: https://www.gsea-msigdb.org/gsea/msigdb/\n", - " NBO-PROPERTY:\n", - " prefix_prefix: NBO-PROPERTY\n", - " prefix_reference: http://purl.obolibrary.org/obo/nbo#\n", - " ncats.bioplanet:\n", - " prefix_prefix: ncats.bioplanet\n", - " prefix_reference: https://tripod.nih.gov/bioplanet/detail.jsp?pid=\n", - " NCBIGene:\n", - " prefix_prefix: NCBIGene\n", - " prefix_reference: http://identifiers.org/ncbigene/\n", - " NCIT-OBO:\n", - " prefix_prefix: NCIT-OBO\n", - " prefix_reference: http://purl.obolibrary.org/obo/ncit#\n", - " NDDF:\n", - " prefix_prefix: NDDF\n", - " prefix_reference: http://purl.bioontology.org/ontology/NDDF/\n", - " NLMID:\n", - " prefix_prefix: NLMID\n", - " prefix_reference: https://www.ncbi.nlm.nih.gov/nlmcatalog/?term=\n", - " OBAN:\n", - " prefix_prefix: OBAN\n", - " prefix_reference: http://purl.org/oban/\n", - " OMIM.PS:\n", - " prefix_prefix: OMIM.PS\n", - " prefix_reference: https://www.omim.org/phenotypicSeries/\n", - " ORCID:\n", - " prefix_prefix: ORCID\n", - " prefix_reference: https://orcid.org/\n", - " orphanet:\n", - " prefix_prefix: orphanet\n", - " prefix_reference: http://www.orpha.net/ORDO/Orphanet_\n", - " os:\n", - " prefix_prefix: os\n", - " prefix_reference: https://github.com/cmungall/owlstar/blob/master/owlstar.ttl\n", - " PANTHER.FAMILY:\n", - " prefix_prefix: PANTHER.FAMILY\n", - " prefix_reference: http://www.pantherdb.org/panther/family.do?clsAccession=\n", - " PathWhiz:\n", - " prefix_prefix: PathWhiz\n", - " prefix_reference: http://smpdb.ca/pathways/#\n", - " pav:\n", - " prefix_prefix: pav\n", - " prefix_reference: http://purl.org/pav/\n", - " PHARMGKB.DRUG:\n", - " prefix_prefix: PHARMGKB.DRUG\n", - " prefix_reference: https://www.pharmgkb.org/chemical/\n", - " PHARMGKB.DISEASE:\n", - " prefix_prefix: PHARMGKB.DISEASE\n", - " prefix_reference: https://www.pharmgkb.org/disease/\n", - " PHARMGKB.GENE:\n", - " prefix_prefix: PHARMGKB.GENE\n", - " prefix_reference: https://www.pharmgkb.org/gene/\n", - " PHARMGKB.PATHWAYS:\n", - " prefix_prefix: PHARMGKB.PATHWAYS\n", - " prefix_reference: https://www.pharmgkb.org/pathway/\n", - " PHARMGKB.VARIANT:\n", - " prefix_prefix: PHARMGKB.VARIANT\n", - " prefix_reference: https://www.pharmgkb.org/variant/\n", - " PHAROS:\n", - " prefix_prefix: PHAROS\n", - " prefix_reference: http://pharos.nih.gov\n", - " PomBase:\n", - " prefix_prefix: PomBase\n", - " prefix_reference: https://www.pombase.org/gene/\n", - " prov:\n", - " prefix_prefix: prov\n", - " prefix_reference: http://www.w3.org/ns/prov#\n", - " qud:\n", - " prefix_prefix: qud\n", - " prefix_reference: http://qudt.org/1.1/schema/qudt#\n", - " REPODB:\n", - " prefix_prefix: REPODB\n", - " prefix_reference: http://apps.chiragjpgroup.org/repoDB/\n", - " ResearchID:\n", - " prefix_prefix: ResearchID\n", - " prefix_reference: https://publons.com/researcher/\n", - " RO:\n", - " prefix_prefix: RO\n", - " prefix_reference: http://purl.obolibrary.org/obo/RO_\n", - " RXNORM:\n", - " prefix_prefix: RXNORM\n", - " prefix_reference: http://purl.bioontology.org/ontology/RXNORM/\n", - " RXCUI:\n", - " prefix_prefix: RXCUI\n", - " prefix_reference: https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=\n", - " schema:\n", - " prefix_prefix: schema\n", - " prefix_reference: http://schema.org/\n", - " ScopusID:\n", - " prefix_prefix: ScopusID\n", - " prefix_reference: https://www.scopus.com/authid/detail.uri?authorId=\n", - " SEED.REACTION:\n", - " prefix_prefix: SEED.REACTION\n", - " prefix_reference: https://modelseed.org/biochem/reactions/\n", - " SEMMEDDB:\n", - " prefix_prefix: SEMMEDDB\n", - " prefix_reference: https://skr3.nlm.nih.gov/SemMedDB\n", - " SIO:\n", - " prefix_prefix: SIO\n", - " prefix_reference: http://semanticscience.org/resource/SIO_\n", - " SNOMEDCT:\n", - " prefix_prefix: SNOMEDCT\n", - " prefix_reference: http://snomed.info/id/\n", - " SPDI:\n", - " prefix_prefix: SPDI\n", - " prefix_reference: https://api.ncbi.nlm.nih.gov/variation/v0/spdi/\n", - " UBERGRAPH:\n", - " prefix_prefix: UBERGRAPH\n", - " prefix_reference: http://translator.renci.org/ubergraph-axioms.ofn#\n", - " UBERON_CORE:\n", - " prefix_prefix: UBERON_CORE\n", - " prefix_reference: http://purl.obolibrary.org/obo/uberon/core#\n", - " UBERON_NONAMESPACE:\n", - " prefix_prefix: UBERON_NONAMESPACE\n", - " prefix_reference: http://purl.obolibrary.org/obo/core#\n", - " STY:\n", - " prefix_prefix: STY\n", - " prefix_reference: http://purl.bioontology.org/ontology/STY/\n", - " UMLSSG:\n", - " prefix_prefix: UMLSSG\n", - " prefix_reference: https://lhncbc.nlm.nih.gov/semanticnetwork/download/sg_archive/SemGroups-v04.txt\n", - " UniProtKB:\n", - " prefix_prefix: UniProtKB\n", - " prefix_reference: http://purl.uniprot.org/uniprot/\n", - " UNIPROT.ISOFORM:\n", - " prefix_prefix: UNIPROT.ISOFORM\n", - " prefix_reference: http://purl.uniprot.org/isoforms/\n", - " VANDF:\n", - " prefix_prefix: VANDF\n", - " prefix_reference: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/\n", - " UO-PROPERTY:\n", - " prefix_prefix: UO-PROPERTY\n", - " prefix_reference: http://purl.obolibrary.org/obo/uo#\n", - " VMC:\n", - " prefix_prefix: VMC\n", - " prefix_reference: https://github.com/ga4gh/vr-spec/\n", - " WBls:\n", - " prefix_prefix: WBls\n", - " prefix_reference: http://purl.obolibrary.org/obo/WBls_\n", - " WBbt:\n", - " prefix_prefix: WBbt\n", - " prefix_reference: http://purl.obolibrary.org/obo/WBbt_\n", - " WBVocab:\n", - " prefix_prefix: WBVocab\n", - " prefix_reference: http://bio2rdf.org/wormbase_vocabulary\n", - " WIKIDATA:\n", - " prefix_prefix: WIKIDATA\n", - " prefix_reference: https://www.wikidata.org/entity/\n", - " WIKIDATA_PROPERTY:\n", - " prefix_prefix: WIKIDATA_PROPERTY\n", - " prefix_reference: https://www.wikidata.org/prop/\n", - " wgs:\n", - " prefix_prefix: wgs\n", - " prefix_reference: http://www.w3.org/2003/01/geo/wgs84_pos\n", - " XPO:\n", - " prefix_prefix: XPO\n", - " prefix_reference: http://purl.obolibrary.org/obo/XPO_\n", - " Xenbase:\n", - " prefix_prefix: Xenbase\n", - " prefix_reference: http://www.xenbase.org/gene/showgene.do?method=display&geneId=\n", - " PMC:\n", - " prefix_prefix: PMC\n", - " prefix_reference: http://europepmc.org/articles/PMC\n", - "default_prefix: biolink-subset/\n", - "default_range: string\n", - "types:\n", - " string:\n", - " name: string\n", - " description: A character string\n", - " notes:\n", - " - In RDF serializations, a slot with range of string is treated as a literal or\n", - " type xsd:string. If you are authoring schemas in LinkML YAML, the type is\n", - " referenced with the lower case \"string\".\n", - " from_schema: https://w3id.org/linkml/types\n", - " exact_mappings:\n", - " - schema:Text\n", - " base: str\n", - " uri: xsd:string\n", - " integer:\n", - " name: integer\n", - " description: An integer\n", - " notes:\n", - " - If you are authoring schemas in LinkML YAML, the type is referenced with the\n", - " lower case \"integer\".\n", - " from_schema: https://w3id.org/linkml/types\n", - " exact_mappings:\n", - " - schema:Integer\n", - " base: int\n", - " uri: xsd:integer\n", - " boolean:\n", - " name: boolean\n", - " description: A binary (true or false) value\n", - " notes:\n", - " - If you are authoring schemas in LinkML YAML, the type is referenced with the\n", - " lower case \"boolean\".\n", - " from_schema: https://w3id.org/linkml/types\n", - " exact_mappings:\n", - " - schema:Boolean\n", - " base: Bool\n", - " uri: xsd:boolean\n", - " repr: bool\n", - " float:\n", - " name: float\n", - " description: A real number that conforms to the xsd:float specification\n", - " notes:\n", - " - If you are authoring schemas in LinkML YAML, the type is referenced with the\n", - " lower case \"float\".\n", - " from_schema: https://w3id.org/linkml/types\n", - " exact_mappings:\n", - " - schema:Float\n", - " base: float\n", - " uri: xsd:float\n", - " double:\n", - " name: double\n", - " description: A real number that conforms to the xsd:double specification\n", - " notes:\n", - " - If you are authoring schemas in LinkML YAML, the type is referenced with the\n", - " lower case \"double\".\n", - " from_schema: https://w3id.org/linkml/types\n", - " close_mappings:\n", - " - schema:Float\n", - " base: float\n", - " uri: xsd:double\n", - " decimal:\n", - " name: decimal\n", - " description: A real number with arbitrary precision that conforms to the xsd:decimal\n", - " specification\n", - " notes:\n", - " - If you are authoring schemas in LinkML YAML, the type is referenced with the\n", - " lower case \"decimal\".\n", - " from_schema: https://w3id.org/linkml/types\n", - " broad_mappings:\n", - " - schema:Number\n", - " base: Decimal\n", - " uri: xsd:decimal\n", - " time:\n", - " name: time\n", - " description: A time object represents a (local) time of day, independent of any\n", - " particular day\n", - " notes:\n", - " - URI is dateTime because OWL reasoners do not work with straight date or time\n", - " - If you are authoring schemas in LinkML YAML, the type is referenced with the\n", - " lower case \"time\".\n", - " from_schema: https://w3id.org/linkml/types\n", - " exact_mappings:\n", - " - schema:Time\n", - " base: XSDTime\n", - " uri: xsd:time\n", - " repr: str\n", - " date:\n", - " name: date\n", - " description: a date (year, month and day) in an idealized calendar\n", - " notes:\n", - " - URI is dateTime because OWL reasoners don't work with straight date or time\n", - " - If you are authoring schemas in LinkML YAML, the type is referenced with the\n", - " lower case \"date\".\n", - " from_schema: https://w3id.org/linkml/types\n", - " exact_mappings:\n", - " - schema:Date\n", - " base: XSDDate\n", - " uri: xsd:date\n", - " repr: str\n", - " datetime:\n", - " name: datetime\n", - " description: The combination of a date and time\n", - " notes:\n", - " - If you are authoring schemas in LinkML YAML, the type is referenced with the\n", - " lower case \"datetime\".\n", - " from_schema: https://w3id.org/linkml/types\n", - " exact_mappings:\n", - " - schema:DateTime\n", - " base: XSDDateTime\n", - " uri: xsd:dateTime\n", - " repr: str\n", - " date_or_datetime:\n", - " name: date_or_datetime\n", - " description: Either a date or a datetime\n", - " notes:\n", - " - If you are authoring schemas in LinkML YAML, the type is referenced with the\n", - " lower case \"date_or_datetime\".\n", - " from_schema: https://w3id.org/linkml/types\n", - " base: str\n", - " uri: linkml:DateOrDatetime\n", - " repr: str\n", - " uriorcurie:\n", - " name: uriorcurie\n", - " description: a URI or a CURIE\n", - " notes:\n", - " - If you are authoring schemas in LinkML YAML, the type is referenced with the\n", - " lower case \"uriorcurie\".\n", - " from_schema: https://w3id.org/linkml/types\n", - " base: URIorCURIE\n", - " uri: xsd:anyURI\n", - " repr: str\n", - " curie:\n", - " name: curie\n", - " conforms_to: https://www.w3.org/TR/curie/\n", - " description: a compact URI\n", - " notes:\n", - " - If you are authoring schemas in LinkML YAML, the type is referenced with the\n", - " lower case \"curie\".\n", - " comments:\n", - " - in RDF serializations this MUST be expanded to a URI\n", - " - in non-RDF serializations MAY be serialized as the compact representation\n", - " from_schema: https://w3id.org/linkml/types\n", - " base: Curie\n", - " uri: xsd:string\n", - " repr: str\n", - " uri:\n", - " name: uri\n", - " conforms_to: https://www.ietf.org/rfc/rfc3987.txt\n", - " description: a complete URI\n", - " notes:\n", - " - If you are authoring schemas in LinkML YAML, the type is referenced with the\n", - " lower case \"uri\".\n", - " comments:\n", - " - in RDF serializations a slot with range of uri is treated as a literal or type\n", - " xsd:anyURI unless it is an identifier or a reference to an identifier, in which\n", - " case it is translated directly to a node\n", - " from_schema: https://w3id.org/linkml/types\n", - " close_mappings:\n", - " - schema:URL\n", - " base: URI\n", - " uri: xsd:anyURI\n", - " repr: str\n", - " ncname:\n", - " name: ncname\n", - " description: Prefix part of CURIE\n", - " notes:\n", - " - If you are authoring schemas in LinkML YAML, the type is referenced with the\n", - " lower case \"ncname\".\n", - " from_schema: https://w3id.org/linkml/types\n", - " base: NCName\n", - " uri: xsd:string\n", - " repr: str\n", - " objectidentifier:\n", - " name: objectidentifier\n", - " description: A URI or CURIE that represents an object in the model.\n", - " notes:\n", - " - If you are authoring schemas in LinkML YAML, the type is referenced with the\n", - " lower case \"objectidentifier\".\n", - " comments:\n", - " - Used for inheritance and type checking\n", - " from_schema: https://w3id.org/linkml/types\n", - " base: ElementIdentifier\n", - " uri: shex:iri\n", - " repr: str\n", - " nodeidentifier:\n", - " name: nodeidentifier\n", - " description: A URI, CURIE or BNODE that represents a node in a model.\n", - " notes:\n", - " - If you are authoring schemas in LinkML YAML, the type is referenced with the\n", - " lower case \"nodeidentifier\".\n", - " from_schema: https://w3id.org/linkml/types\n", - " base: NodeIdentifier\n", - " uri: shex:nonLiteral\n", - " repr: str\n", - " jsonpointer:\n", - " name: jsonpointer\n", - " conforms_to: https://datatracker.ietf.org/doc/html/rfc6901\n", - " description: A string encoding a JSON Pointer. The value of the string MUST conform\n", - " to JSON Point syntax and SHOULD dereference to a valid object within the current\n", - " instance document when encoded in tree form.\n", - " notes:\n", - " - If you are authoring schemas in LinkML YAML, the type is referenced with the\n", - " lower case \"jsonpointer\".\n", - " from_schema: https://w3id.org/linkml/types\n", - " base: str\n", - " uri: xsd:string\n", - " repr: str\n", - " jsonpath:\n", - " name: jsonpath\n", - " conforms_to: https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html\n", - " description: A string encoding a JSON Path. The value of the string MUST conform\n", - " to JSON Point syntax and SHOULD dereference to zero or more valid objects within\n", - " the current instance document when encoded in tree form.\n", - " notes:\n", - " - If you are authoring schemas in LinkML YAML, the type is referenced with the\n", - " lower case \"jsonpath\".\n", - " from_schema: https://w3id.org/linkml/types\n", - " base: str\n", - " uri: xsd:string\n", - " repr: str\n", - " sparqlpath:\n", - " name: sparqlpath\n", - " conforms_to: https://www.w3.org/TR/sparql11-query/#propertypaths\n", - " description: A string encoding a SPARQL Property Path. The value of the string\n", - " MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects\n", - " within the current instance document when encoded as RDF.\n", - " notes:\n", - " - If you are authoring schemas in LinkML YAML, the type is referenced with the\n", - " lower case \"sparqlpath\".\n", - " from_schema: https://w3id.org/linkml/types\n", - " base: str\n", - " uri: xsd:string\n", - " repr: str\n", - " chemical formula value:\n", - " name: chemical formula value\n", - " description: A chemical formula\n", - " notes:\n", - " - Should be implemented as a stronger type\n", - " from_schema: https://w3id.org/biolink/biolink-model\n", - " base: str\n", - " uri: xsd:string\n", - " iri type:\n", - " name: iri type\n", - " description: An IRI\n", - " from_schema: https://w3id.org/biolink/biolink-model\n", - " typeof: uriorcurie\n", - " uri: xsd:string\n", - " label type:\n", - " name: label type\n", - " description: A string that provides a human-readable name for an entity\n", - " from_schema: https://w3id.org/biolink/biolink-model\n", - " typeof: string\n", - " uri: xsd:string\n", - " predicate type:\n", - " name: predicate type\n", - " description: A CURIE from the biolink related_to hierarchy. For example, biolink:related_to,\n", - " biolink:causes, biolink:treats.\n", - " from_schema: https://w3id.org/biolink/biolink-model\n", - " typeof: uriorcurie\n", - " uri: xsd:string\n", - " narrative text:\n", - " name: narrative text\n", - " description: A string that provides a human-readable description of something\n", - " from_schema: https://w3id.org/biolink/biolink-model\n", - " typeof: string\n", - " uri: xsd:string\n", - " symbol type:\n", - " name: symbol type\n", - " from_schema: https://w3id.org/biolink/biolink-model\n", - " typeof: string\n", - " uri: xsd:string\n", - " frequency value:\n", - " name: frequency value\n", - " from_schema: https://w3id.org/biolink/biolink-model\n", - " typeof: string\n", - " uri: UO:0000105\n", - " percentage frequency value:\n", - " name: percentage frequency value\n", - " from_schema: https://w3id.org/biolink/biolink-model\n", - " typeof: double\n", - " uri: UO:0000187\n", - " quotient:\n", - " name: quotient\n", - " from_schema: https://w3id.org/biolink/biolink-model\n", - " aliases:\n", - " - ratio\n", - " typeof: double\n", - " uri: UO:0010006\n", - " unit:\n", - " name: unit\n", - " id_prefixes:\n", - " - UO\n", - " from_schema: https://w3id.org/biolink/biolink-model\n", - " exact_mappings:\n", - " - qud:Unit\n", - " typeof: string\n", - " uri: UO:0000000\n", - " time type:\n", - " name: time type\n", - " from_schema: https://w3id.org/biolink/biolink-model\n", - " typeof: time\n", - " uri: xsd:time\n", - " biological sequence:\n", - " name: biological sequence\n", - " from_schema: https://w3id.org/biolink/biolink-model\n", - " typeof: string\n", - " uri: xsd:string\n", - "classes:\n", - " Gene:\n", - " name: Gene\n", - " id_prefixes:\n", - " - NCBIGene\n", - " - ENSEMBL\n", - " - HGNC\n", - " - MGI\n", - " - ZFIN\n", - " - dictyBase\n", - " - WB\n", - " - WormBase\n", - " - FB\n", - " - RGD\n", - " - SGD\n", - " - PomBase\n", - " - OMIM\n", - " - KEGG.GENES\n", - " - UMLS\n", - " - Xenbase\n", - " - AspGD\n", - " - PHARMGKB.GENE\n", - " description: A region (or regions) that includes all of the sequence elements\n", - " necessary to encode a functional transcript. A gene locus may include regulatory\n", - " regions, transcribed regions and/or other functional sequence regions.\n", - " in_subset:\n", - " - translator_minimal\n", - " - model_organism_database\n", - " exact_mappings:\n", - " - SO:0000704\n", - " - SIO:010035\n", - " - WIKIDATA:Q7187\n", - " - dcid:Gene\n", - " narrow_mappings:\n", - " - bioschemas:gene\n", - " broad_mappings:\n", - " - NCIT:C45822\n", - " attributes:\n", - " symbol:\n", - " name: symbol\n", - " description: Symbol for a particular thing\n", - " exact_mappings:\n", - " - AGRKB:symbol\n", - " - gpi:DB_Object_Symbol\n", - " is_a: node property\n", - " domain: named thing\n", - " domain_of:\n", - " - gene\n", - " xref:\n", - " name: xref\n", - " description: A database cross reference or alternative identifier for a NamedThing\n", - " or edge between two NamedThings. This property should point to a database\n", - " record or webpage that supports the existence of the edge, or gives more\n", - " detail about the edge. This property can be used on a node or edge to provide\n", - " multiple URIs or CURIE cross references.\n", - " in_subset:\n", - " - translator_minimal\n", - " aliases:\n", - " - dbxref\n", - " - Dbxref\n", - " - DbXref\n", - " - record_url\n", - " - source_record_urls\n", - " narrow_mappings:\n", - " - gff3:Dbxref\n", - " - gpi:DB_Xrefs\n", - " domain: named thing\n", - " domain_of:\n", - " - named thing\n", - " - publication\n", - " - retrieval source\n", - " - gene\n", - " - gene product mixin\n", - " range: uriorcurie\n", - " multivalued: true\n", - " Disease:\n", - " name: Disease\n", - " id_prefixes:\n", - " - MONDO\n", - " - DOID\n", - " - OMIM\n", - " - OMIM.PS\n", - " - orphanet\n", - " - EFO\n", - " - UMLS\n", - " - MESH\n", - " - MEDDRA\n", - " - NCIT\n", - " - SNOMEDCT\n", - " - medgen\n", - " - ICD10\n", - " - ICD9\n", - " - KEGG.DISEASE\n", - " - HP\n", - " - MP\n", - " - PHARMGKB.DISEASE\n", - " description: A disorder of structure or function, especially one that produces\n", - " specific signs, phenotypes or symptoms or that affects a specific location and\n", - " is not simply a direct result of physical injury. A disposition to undergo\n", - " pathological processes that exists in an organism because of one or more disorders\n", - " in that organism.\n", - " in_subset:\n", - " - model_organism_database\n", - " - translator_minimal\n", - " aliases:\n", - " - condition\n", - " - disorder\n", - " - medical condition\n", - " exact_mappings:\n", - " - MONDO:0000001\n", - " - DOID:4\n", - " - NCIT:C2991\n", - " - WIKIDATA:Q12136\n", - " - SIO:010299\n", - " - UMLSSG:DISO\n", - " - STY:T047\n", - " - dcid:Disease\n", - " narrow_mappings:\n", - " - STY:T019\n", - " - STY:T020\n", - " - STY:T048\n", - " - STY:T049\n", - " - STY:T191\n", - " - MONDO:0042489\n", - " CaseToPhenotypicFeatureAssociation:\n", - " name: CaseToPhenotypicFeatureAssociation\n", - " description: An association between a case (e.g. individual patient) and a phenotypic\n", - " feature in which the individual has or has had the phenotype.\n", - " defining_slots:\n", - " - subject\n", - " - object\n", - " GeneToDiseaseAssociation:\n", - " name: GeneToDiseaseAssociation\n", - " comments:\n", - " - NCIT:R176 refers to the inverse relationship\n", - " exact_mappings:\n", - " - SIO:000983\n", - " close_mappings:\n", - " - dcid:DiseaseGeneAssociation\n", - " defining_slots:\n", - " - subject\n", - " - object\n", - " GeneToPhenotypicFeatureAssociation:\n", - " name: GeneToPhenotypicFeatureAssociation\n", - " exact_mappings:\n", - " - WBVocab:Gene-Phenotype-Association\n", - " defining_slots:\n", - " - subject\n", - " - object\n", - " Case:\n", - " name: Case\n", - " description: An individual (human) organism that has a patient role in some clinical\n", - " context.\n", - " aliases:\n", - " - patient\n", - " - proband\n", - " PhenotypicFeature:\n", - " name: PhenotypicFeature\n", - " id_prefixes:\n", - " - HP\n", - " - EFO\n", - " - NCIT\n", - " - UMLS\n", - " - MEDDRA\n", - " - MP\n", - " - ZP\n", - " - UPHENO\n", - " - APO\n", - " - FBcv\n", - " - WBPhenotype\n", - " - SNOMEDCT\n", - " - MESH\n", - " - XPO\n", - " - FYPO\n", - " - TO\n", - " description: A combination of entity and quality that makes up a phenotyping statement.\n", - " An observable characteristic of an individual resulting from the interaction\n", - " of its genotype with its molecular and physical environment.\n", - " examples:\n", - " - value: MP:0001262\n", - " description: decreased body weight\n", - " in_subset:\n", - " - model_organism_database\n", - " aliases:\n", - " - sign\n", - " - symptom\n", - " - phenotype\n", - " - trait\n", - " - endophenotype\n", - " exact_mappings:\n", - " - UPHENO:0001001\n", - " - SIO:010056\n", - " - WIKIDATA:Q104053\n", - " - UMLS:C4021819\n", - " - NCIT:C16977\n", - " - SNOMEDCT:8116006\n", - " - MESH:D010641\n", - " narrow_mappings:\n", - " - STY:T184\n", - " - WIKIDATA:Q169872\n", - " - WIKIDATA:Q25203551\n", - " - ZP:00000000\n", - " - FBcv:0001347\n", - " - HP:0000118\n", - " - MP:0000001\n", - " - WBPhenotype:0000886\n", - " - XPO:00000000\n", - " - FYPO:0000001\n", - " - APO:0000017\n", - " - TO:0000387\n", - " - STY:T190\n", - " broad_mappings:\n", - " - BFO:0000019\n", - " - PATO:0000001\n", - "\n" - ] - } - ], - "source": [ - "# print the content of the new schema in LinkML YAML format to view here in the notebook\n", - "yaml_content = yaml_dumper.dumps(target_schema_obj) # Serialize to a string\n", - "print(yaml_content)" - ] - }, - { - "cell_type": "markdown", - "id": "48d65b0bfa68ba6d", - "metadata": {}, - "source": [ - "Notes:\n", - "* notice that if we remove a parent class from this, e.g. remove \"NamedThing\" - the `is_a` path in the descendent classes will be absent. this is to prevent unreachable element errors.\n", - "* notice that helpful defaults are brought in like prefixes, descriptions, aliases, mappings, etc.\n", - " * there will likely be cases where metamodel elements in LinkML are not automatically transferred to the derived schema (as will all our generators, we are working towards feature parity). \n", - "* notice that the transformation automatically makes what were, independent `slot` definitions in Biolink Model into `attributes`. These are more or less functionally equivalent in LinkML, however if you want to specify a slot that can be reused outside of a particular class, it is still best practice to do so with a slot definition rather than an attribute as to not repeat slot definitions." - ] - }, - { - "cell_type": "markdown", - "id": "9addb6853dbd3759", - "metadata": {}, - "source": [ - "### Use derived schema to generate different serializations of the derived model\n", - "\n", - "Now that we have a YAML dump of our derived model, we can use standard LinkML tooling to produce:\n", - "* python dataclasses and pydantic models of our derived schema\n", - "* navigate our derived schema with a SchemaView instance\n", - "* create and deploy automated documentation with the derived schema (see https://github.com/linkml/linkml-project-cookiecutter for more details on using the derived schema in a standard setup)" - ] - }, - { - "cell_type": "code", - "execution_count": 17, - "id": "f8ccc4af61d75af7", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "from __future__ import annotations \n", - "from datetime import (\n", - " datetime,\n", - " date\n", - ")\n", - "from decimal import Decimal \n", - "from enum import Enum \n", - "import re\n", - "import sys\n", - "from typing import (\n", - " Any,\n", - " ClassVar,\n", - " List,\n", - " Literal,\n", - " Dict,\n", - " Optional,\n", - " Union\n", - ")\n", - "from pydantic.version import VERSION as PYDANTIC_VERSION \n", - "if int(PYDANTIC_VERSION[0])>=2:\n", - " from pydantic import (\n", - " BaseModel,\n", - " ConfigDict,\n", - " Field,\n", - " RootModel,\n", - " field_validator\n", - " )\n", - "else:\n", - " from pydantic import (\n", - " BaseModel,\n", - " Field,\n", - " validator\n", - " )\n", - "\n", - "metamodel_version = \"None\"\n", - "version = \"None\"\n", - "\n", - "\n", - "class ConfiguredBaseModel(BaseModel):\n", - " model_config = ConfigDict(\n", - " validate_assignment = True,\n", - " validate_default = True,\n", - " extra = \"forbid\",\n", - " arbitrary_types_allowed = True,\n", - " use_enum_values = True,\n", - " strict = False,\n", - " )\n", - " pass\n", - "\n", - "\n", - "\n", - "\n", - "class LinkMLMeta(RootModel):\n", - " root: Dict[str, Any] = {}\n", - " model_config = ConfigDict(frozen=True)\n", - "\n", - " def __getattr__(self, key:str):\n", - " return getattr(self.root, key)\n", - "\n", - " def __getitem__(self, key:str):\n", - " return self.root[key]\n", - "\n", - " def __setitem__(self, key:str, value):\n", - " self.root[key] = value\n", - "\n", - "\n", - "linkml_meta = LinkMLMeta({'default_prefix': 'biolink-subset/',\n", - " 'id': 'biolink-subset',\n", - " 'name': 'BiolinkSubset'} )\n", - "\n", - "\n", - "class Gene(ConfiguredBaseModel):\n", - " \"\"\"\n", - " A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions.\n", - " \"\"\"\n", - " linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'broad_mappings': ['NCIT:C45822'],\n", - " 'exact_mappings': ['SO:0000704', 'SIO:010035', 'WIKIDATA:Q7187', 'dcid:Gene'],\n", - " 'from_schema': 'biolink-subset',\n", - " 'id_prefixes': ['NCBIGene',\n", - " 'ENSEMBL',\n", - " 'HGNC',\n", - " 'MGI',\n", - " 'ZFIN',\n", - " 'dictyBase',\n", - " 'WB',\n", - " 'WormBase',\n", - " 'FB',\n", - " 'RGD',\n", - " 'SGD',\n", - " 'PomBase',\n", - " 'OMIM',\n", - " 'KEGG.GENES',\n", - " 'UMLS',\n", - " 'Xenbase',\n", - " 'AspGD',\n", - " 'PHARMGKB.GENE'],\n", - " 'in_subset': ['translator_minimal', 'model_organism_database'],\n", - " 'narrow_mappings': ['bioschemas:gene']})\n", - "\n", - " symbol: Optional[str] = Field(None, description=\"\"\"Symbol for a particular thing\"\"\", json_schema_extra = { \"linkml_meta\": {'alias': 'symbol',\n", - " 'domain': 'named thing',\n", - " 'domain_of': ['gene', 'Gene'],\n", - " 'exact_mappings': ['AGRKB:symbol', 'gpi:DB_Object_Symbol'],\n", - " 'is_a': 'node property'} })\n", - " xref: Optional[List[str]] = Field(default_factory=list, description=\"\"\"A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.\"\"\", json_schema_extra = { \"linkml_meta\": {'alias': 'xref',\n", - " 'aliases': ['dbxref', 'Dbxref', 'DbXref', 'record_url', 'source_record_urls'],\n", - " 'domain': 'named thing',\n", - " 'domain_of': ['named thing',\n", - " 'publication',\n", - " 'retrieval source',\n", - " 'gene',\n", - " 'gene product mixin',\n", - " 'Gene'],\n", - " 'in_subset': ['translator_minimal'],\n", - " 'narrow_mappings': ['gff3:Dbxref', 'gpi:DB_Xrefs']} })\n", - "\n", - "\n", - "class Disease(ConfiguredBaseModel):\n", - " \"\"\"\n", - " A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.\n", - " \"\"\"\n", - " linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'aliases': ['condition', 'disorder', 'medical condition'],\n", - " 'exact_mappings': ['MONDO:0000001',\n", - " 'DOID:4',\n", - " 'NCIT:C2991',\n", - " 'WIKIDATA:Q12136',\n", - " 'SIO:010299',\n", - " 'UMLSSG:DISO',\n", - " 'STY:T047',\n", - " 'dcid:Disease'],\n", - " 'from_schema': 'biolink-subset',\n", - " 'id_prefixes': ['MONDO',\n", - " 'DOID',\n", - " 'OMIM',\n", - " 'OMIM.PS',\n", - " 'orphanet',\n", - " 'EFO',\n", - " 'UMLS',\n", - " 'MESH',\n", - " 'MEDDRA',\n", - " 'NCIT',\n", - " 'SNOMEDCT',\n", - " 'medgen',\n", - " 'ICD10',\n", - " 'ICD9',\n", - " 'KEGG.DISEASE',\n", - " 'HP',\n", - " 'MP',\n", - " 'PHARMGKB.DISEASE'],\n", - " 'in_subset': ['model_organism_database', 'translator_minimal'],\n", - " 'narrow_mappings': ['STY:T019',\n", - " 'STY:T020',\n", - " 'STY:T048',\n", - " 'STY:T049',\n", - " 'STY:T191',\n", - " 'MONDO:0042489']})\n", - "\n", - " pass\n", - "\n", - "\n", - "class CaseToPhenotypicFeatureAssociation(ConfiguredBaseModel):\n", - " \"\"\"\n", - " An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype.\n", - " \"\"\"\n", - " linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'defining_slots': ['subject', 'object'], 'from_schema': 'biolink-subset'})\n", - "\n", - " pass\n", - "\n", - "\n", - "class GeneToDiseaseAssociation(ConfiguredBaseModel):\n", - " linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'close_mappings': ['dcid:DiseaseGeneAssociation'],\n", - " 'comments': ['NCIT:R176 refers to the inverse relationship'],\n", - " 'defining_slots': ['subject', 'object'],\n", - " 'exact_mappings': ['SIO:000983'],\n", - " 'from_schema': 'biolink-subset'})\n", - "\n", - " pass\n", - "\n", - "\n", - "class GeneToPhenotypicFeatureAssociation(ConfiguredBaseModel):\n", - " linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'defining_slots': ['subject', 'object'],\n", - " 'exact_mappings': ['WBVocab:Gene-Phenotype-Association'],\n", - " 'from_schema': 'biolink-subset'})\n", - "\n", - " pass\n", - "\n", - "\n", - "class Case(ConfiguredBaseModel):\n", - " \"\"\"\n", - " An individual (human) organism that has a patient role in some clinical context.\n", - " \"\"\"\n", - " linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'aliases': ['patient', 'proband'], 'from_schema': 'biolink-subset'})\n", - "\n", - " pass\n", - "\n", - "\n", - "class PhenotypicFeature(ConfiguredBaseModel):\n", - " \"\"\"\n", - " A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment.\n", - " \"\"\"\n", - " linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'aliases': ['sign', 'symptom', 'phenotype', 'trait', 'endophenotype'],\n", - " 'broad_mappings': ['BFO:0000019', 'PATO:0000001'],\n", - " 'exact_mappings': ['UPHENO:0001001',\n", - " 'SIO:010056',\n", - " 'WIKIDATA:Q104053',\n", - " 'UMLS:C4021819',\n", - " 'NCIT:C16977',\n", - " 'SNOMEDCT:8116006',\n", - " 'MESH:D010641'],\n", - " 'examples': [{'description': 'decreased body weight', 'value': 'MP:0001262'}],\n", - " 'from_schema': 'biolink-subset',\n", - " 'id_prefixes': ['HP',\n", - " 'EFO',\n", - " 'NCIT',\n", - " 'UMLS',\n", - " 'MEDDRA',\n", - " 'MP',\n", - " 'ZP',\n", - " 'UPHENO',\n", - " 'APO',\n", - " 'FBcv',\n", - " 'WBPhenotype',\n", - " 'SNOMEDCT',\n", - " 'MESH',\n", - " 'XPO',\n", - " 'FYPO',\n", - " 'TO'],\n", - " 'in_subset': ['model_organism_database'],\n", - " 'narrow_mappings': ['STY:T184',\n", - " 'WIKIDATA:Q169872',\n", - " 'WIKIDATA:Q25203551',\n", - " 'ZP:00000000',\n", - " 'FBcv:0001347',\n", - " 'HP:0000118',\n", - " 'MP:0000001',\n", - " 'WBPhenotype:0000886',\n", - " 'XPO:00000000',\n", - " 'FYPO:0000001',\n", - " 'APO:0000017',\n", - " 'TO:0000387',\n", - " 'STY:T190']})\n", - "\n", - " pass\n", - "\n", - "\n", - "# Model rebuild\n", - "# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model\n", - "Gene.model_rebuild()\n", - "Disease.model_rebuild()\n", - "CaseToPhenotypicFeatureAssociation.model_rebuild()\n", - "GeneToDiseaseAssociation.model_rebuild()\n", - "GeneToPhenotypicFeatureAssociation.model_rebuild()\n", - "Case.model_rebuild()\n", - "PhenotypicFeature.model_rebuild()\n", - "\n" - ] - } - ], - "source": [ - "!gen-pydantic biolink-subset.yaml" - ] - }, - { - "cell_type": "code", - "execution_count": 20, - "id": "3c811e7ae6de6e3a", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "ValueError: No such slot as \"node property\"\n" - ] - } - ], - "source": [ - "!gen-doc biolink-subset.yaml -d docs" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "f5ef1128-c499-4359-abea-7cff4056d761", - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.11.0" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/docs/examples/denormalizing.ipynb b/docs/examples/denormalizing.ipynb deleted file mode 100644 index aa1d248..0000000 --- a/docs/examples/denormalizing.ipynb +++ /dev/null @@ -1,107 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 3, - "id": "cd2c8429-a0e7-4a95-a7ed-b1fd8a53b89d", - "metadata": {}, - "outputs": [], - "source": [ - "from pathlib import Path\n", - "\n", - "from linkml_runtime.dumpers import yaml_dumper\n", - "from linkml_runtime.utils.schemaview import SchemaView\n", - "\n", - "from linkml_map.inference.schema_mapper import SchemaMapper\n", - "from linkml_map.session import Session\n", - "from linkml_map.utils.loaders import load_specification\n", - "\n", - "REPO_ROOT = Path.cwd().parent.parent" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "id": "121e9e1c-28c2-4fec-bb76-e078836d1f3e", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "MappingSet\n", - "Mapping\n", - "\n", - "mappings\n", - "subject_id\n", - "subject_name\n", - "object_id\n", - "object_name\n", - "predicate_id\n" - ] - } - ], - "source": [ - "input_schema = REPO_ROOT / \"tests/input/examples/flattening/source/normalized.yaml\"\n", - "output_schema = REPO_ROOT / \"tests/input/examples/flattening/target/denormalized.yaml\"\n", - "transformation_specification_file = REPO_ROOT / \"tests/input/examples/flattening/transform/denormalize.transform.yaml\"\n", - "# Initialize Session and SchemaBuilder\n", - "session = Session()\n", - "\n", - "source_schema_view = SchemaView(input_schema)\n", - "target_schema_view = SchemaView(output_schema)\n", - "# Set the source schema in the session\n", - "session.set_source_schema(source_schema_view)\n", - "\n", - "tr_spec = load_specification(transformation_specification_file)\n", - "mapper = SchemaMapper()\n", - "mapper.source_schemaview = source_schema_view\n", - "\n", - "target_schema_obj = mapper.derive_schema(\n", - " specification=tr_spec,\n", - " target_schema_id=\"denormalized-view\",\n", - " target_schema_name=\"DenormalizedView\",\n", - ")\n", - "\n", - "yaml_dumper.dump(target_schema_obj, str(\"denormalized_view.yaml\"))\n", - "\n", - "transformed_sv = SchemaView(\"denormalized_view.yaml\")\n", - "\n", - "for class_name in transformed_sv.all_classes():\n", - " print(class_name)\n", - "print()\n", - "for slot_name in transformed_sv.all_slots():\n", - " print(slot_name)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "bc48f85d-bf7b-44fe-90e1-cd256191c06a", - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.11.0" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/docs/faq.md b/docs/faq.md deleted file mode 100644 index cbccbe0..0000000 --- a/docs/faq.md +++ /dev/null @@ -1,38 +0,0 @@ -# FAQ - -## Why another framework? - -There are a number of excellent frameworks for performing mapping and data transformations. -The LinkML Transformer framework was born out of a need for a framework that: - -- was not inherently tied to: - - a particular serialization format (e.g. RDF, JSON, ...) - - a particular programming language (e.g. Python, Java, ...) - - a particular database system or database language (e.g. PostgreSQL or SQL or SPARQL) - - not tied to a particular kind of transformation (e.g. ORM or Tables to RDF) -- was a natural fit for the LinkML data modeling framework -- was declarative and easy to perform machine reasoning over -- is simple for simple use cases - -In its current state, this framework is less powerful and expressive than many other frameworks -or methodologies for performing transformations. If you need to perform complex data transformations, -you might be better off using an expressive query language like SPARQL or SQL, or even just coding -transformations directly in a programming language or library like Python or Pandas (but note that -even for the coding use case, the LinkML Transformer framework can be useful as a standard way -of *documenting* transformations). - -Currently the main use case for this framework is *mostly isomorphic* transformations, with lightweight -manipulations. These lend themselves well to a declarative framework. Uses cases that are a particularly good fit -involve mapping between data-dictionary like standards, with large numbers of metadata elements, where these -elements can often be mapped one-to-one, or with simple manipulations (e.g. unit conversions). - -The origins lie partly in the SSSOM standard, which is intended as an ultra-simple way of specifying -precise mappings between *entities* (e.g. schema.org Person is the same as DBPedia person). We observed -that many people wanted to extend the language to perform more complex mappings. To address this, we -help a workshop at the Biocuration conference in Padua, Italy in 2022. - -- [Discussion](https://github.com/orgs/linkml/discussions/1829) -- [SSSOM paper](https://academic.oup.com/database/article/doi/10.1093/database/baac035/6591806) -- [SSSOM Update 2023](https://ceur-ws.org/Vol-3591/om2023_STpaper3.pdf) -- [SSSOM Complex Mappings Workshop 2023](https://www.youtube.com/playlist?list=PLqu_J7ADQtKyX55F7RqZtaSS7TwGd3MoR) -- [Mapping Data Structures: Challenges and Approaches](https://doi.org/10.5281/zenodo.10343505) diff --git a/docs/index.md b/docs/index.md deleted file mode 100644 index 8a820ce..0000000 --- a/docs/index.md +++ /dev/null @@ -1,209 +0,0 @@ -# LinkML-Map - -LinkML Map is a framework for specifying and executing mappings between data models. - -Features: - -- YAML-based lightweight syntax -- Python library for executing mappings on data files -- Ability to compile to other frameworks (SQL/DuckDB) -- Derivation of target (implicit) schemas, allowing easy customization of data models (*profiling*) -- Simple YAML dictionaries for simple mappings -- Automatic unit conversion -- Use of subset of Python to specify complex mappings -- Visualizations of mappings -- Mappings are reversible (provided all expressions used are reversible) -- Compatibility with SSSOM - -This documentation are available at: - -- [linkml.io/linkml-map/](https://linkml.io/linkml-map/) - -Status: - -The transformation data model is not yet fully stable, and may be subject to change. -Not all parts of the model are implemented in the reference Python framework. - -## Basic idea - -Given the LinkML schema - -```yaml -id: https://w3id.org/linkml/examples/personinfo -name: personinfo -prefixes: - linkml: https://w3id.org/linkml/ - personinfo: https://w3id.org/linkml/examples/personinfo -imports: - - linkml:types -default_range: string -default_prefix: personinfo - -classes: - Person: - attributes: - id: - given_name: - family_name: - aliases: - multivalued: true - height_in_cm: - range: float - unit: - ucum_code: cm - age_in_years: - range: integer -``` - -and an object that conforms to it, e.g.: - -```yaml -given_name: Jane -family_name: Doe -height_in_cm: 172.0 -age_in_years: 33 -aliases: [Janey, Janie] -``` - -Define a mapping in YAML: - -```yaml -class_derivations: - Individual: - populated_from: Person - slot_derivations: - name: - expr: "{given_name} + ' ' + {family_name}" - description: Concatenating given and family names - note this is a bad assumption for names in general, - this is just for demonstration - height_in_meters: - populated_from: height_in_cm - unit_conversion: - target_unit: m - aliases: - populated_from: aliases - stringification: - delimiter: '|' -``` - -The schema mapping (aka [TransformationSpecification](schema/TransformationSpecification.md)) specifies how to transform the data model. - -The schema mapping is a collection of one or more [ClassDerivation](schema/ClassDerivation.md) objects, -which themselves consist of one or more [SlotDerivation](schema/SlotDerivation.md) objects. - -Transform the data: - -```bash -linkml-map map-data -T tr.yaml -s schema.yaml my-data.yaml -``` - -Giving: - -```yaml -name: Jane Doe -height_in_meters: 1.72 -aliases: Janey|Janie -``` - -## Installation and usage - -Installation and command line usage: - -```bash -pip[x] install linkml-map -cd tests/input/examples/personinfo_basic -linkml-map map-data \ - -T transform/personinfo-to-agent.transform.yaml \ - -s source/personinfo.yaml \ - data/Container-001.yaml \ - -o output/Translated-001.yaml -``` - -The command line has subcommands for: - -- `map-data` - map data from a source schema to a target schema -- `derive-schema` - derive a target schema from a source schema and a mapping -- `invert` - reverses a mapping -- `compile` - compiles a mapping to another framework - - `markdown` - for generating static sites - - `graphviz` - for generating visualizations - - `python` - (partial) - - forthcoming: `r2rml`, ... - -## Details - -This repo contains both: - -- A [data model](schema/) for a data model *transformation language* -- A reference python implementation - -The transformation language is specified in terms of [LinkML](https://linkml.io) schemas. -It is intended to be a *ployglot* transformation language, used for -specifying how to map data models independent of underlying representation -(TSVs, JSON/YAML, RDF, SQL Database, ...). - -Use cases include: - -- ETL and mapping from one data model to another -- Database migrations (one version of a schema to another) -- Creating "profiles" -- Specifying mappings between different serializations of a model (e.g. OO to Relational) -- Mapping between normalized/non-redundant forms and denormalized/query-optimized forms - - -## Data Model - -The data model for transformations mirrors the data model for schemas: - -- A top level [TransformationSpecification](schema/TransformationSpecification.md) class contains: - - Zero or more [ClassDerivation](schema/ClassDerivation.md) objects, specifying how to map to a class, containing - - Zero or more [SlotDerivation](schema/SlotDerivation.md) objects, specifying how to map to a slot - - Zero or more [EnumDerivation](schema/EnumDerivation.md) objects, specifying how to map to an enum - -See the [generated docs](schema/index.md) - -## Conformance Suite - -The Maps conformance suite contains a collection of tests for each feature of the language. - -See: - -* [Compliance Suite](specification/compliance.md) - - -## Running the code - -```bash -linkml-map --help -Usage: linkml-map [OPTIONS] COMMAND [ARGS]... - - CLI for linkml-map. - -Options: - -v, --verbose - -q, --quiet TEXT - --help Show this message and exit. - -Commands: - derive-schema Derive a schema from a source schema and a mapping. - map-data Map data in a source schema using a transformation. -``` - -### map-data - -Transforms (maps) data from a source schema to a target schema. This could range from a simple data dictionary mapping -through to a complex mappings. - -``` -cd tests/input/examples/personinfo_basic -linkml-map map-data -T transform/personinfo-to-agent.transform.yaml -s source/personinfo.yaml data/Container-001.yaml -``` - -### derive-schema - -``` -cd tests/input/examples/personinfo_basic -linkml-map derive-schema -T transform/personinfo-to-agent.transform.yaml source/personinfo.yaml -``` - diff --git a/docs/schema/AliasedClass.md b/docs/schema/AliasedClass.md deleted file mode 100644 index 913f76a..0000000 --- a/docs/schema/AliasedClass.md +++ /dev/null @@ -1,149 +0,0 @@ - - -# Class: AliasedClass - - -_alias-class key value pairs for classes_ - - - - - -URI: [linkmltr:AliasedClass](https://w3id.org/linkml/transformer/AliasedClass) - - - - -```mermaid - classDiagram - class AliasedClass - AliasedClass : alias - - AliasedClass --> None : alias - - AliasedClass : class_named - - AliasedClass --> None : class_named - - -``` - - - - - - - -## Slots - -| Name | Cardinality and Range | Description | Inheritance | -| --- | --- | --- | --- | -| [alias](alias.md) | 0..1
[String](String.md) | name of the class to be aliased | direct | -| [class_named](class_named.md) | 0..1
[String](String.md) | local alias for the class | direct | - - - - - -## Usages - -| used by | used in | type | used | -| --- | --- | --- | --- | -| [ClassDerivation](ClassDerivation.md) | [joins](joins.md) | range | [AliasedClass](AliasedClass.md) | - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - - -## Mappings - -| Mapping Type | Mapped Value | -| --- | --- | -| self | linkmltr:AliasedClass | -| native | linkmltr:AliasedClass | - - - - - -## LinkML Source - - - -### Direct - -
-```yaml -name: AliasedClass -description: alias-class key value pairs for classes -from_schema: https://w3id.org/linkml/transformer -attributes: - alias: - name: alias - description: name of the class to be aliased - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - key: true - domain_of: - - AliasedClass - required: true - class_named: - name: class_named - description: local alias for the class - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - domain_of: - - AliasedClass - -``` -
- -### Induced - -
-```yaml -name: AliasedClass -description: alias-class key value pairs for classes -from_schema: https://w3id.org/linkml/transformer -attributes: - alias: - name: alias - description: name of the class to be aliased - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - key: true - alias: alias - owner: AliasedClass - domain_of: - - AliasedClass - required: true - class_named: - name: class_named - description: local alias for the class - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: class_named - owner: AliasedClass - domain_of: - - AliasedClass - -``` -
\ No newline at end of file diff --git a/docs/schema/Any.md b/docs/schema/Any.md deleted file mode 100644 index bee7827..0000000 --- a/docs/schema/Any.md +++ /dev/null @@ -1,109 +0,0 @@ - - -# Class: Any - - - -URI: [linkml:Any](https://w3id.org/linkml/Any) - - - - - - -```mermaid - classDiagram - class Any - click Any href "../Any" - -``` - - - - - - - -## Slots - -| Name | Cardinality and Range | Description | Inheritance | -| --- | --- | --- | --- | - - - - - -## Usages - -| used by | used in | type | used | -| --- | --- | --- | --- | -| [ElementDerivation](ElementDerivation.md) | [overrides](overrides.md) | range | [Any](Any.md) | -| [ClassDerivation](ClassDerivation.md) | [overrides](overrides.md) | range | [Any](Any.md) | -| [SlotDerivation](SlotDerivation.md) | [overrides](overrides.md) | range | [Any](Any.md) | -| [EnumDerivation](EnumDerivation.md) | [overrides](overrides.md) | range | [Any](Any.md) | -| [PermissibleValueDerivation](PermissibleValueDerivation.md) | [overrides](overrides.md) | range | [Any](Any.md) | -| [PrefixDerivation](PrefixDerivation.md) | [overrides](overrides.md) | range | [Any](Any.md) | -| [KeyVal](KeyVal.md) | [value](value.md) | range | [Any](Any.md) | -| [CopyDirective](CopyDirective.md) | [exclude](exclude.md) | range | [Any](Any.md) | -| [CopyDirective](CopyDirective.md) | [include](include.md) | range | [Any](Any.md) | -| [CopyDirective](CopyDirective.md) | [add](add.md) | range | [Any](Any.md) | - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## Mappings - -| Mapping Type | Mapped Value | -| --- | --- | -| self | linkml:Any | -| native | linkmltr:Any | - - - - - - - -## LinkML Source - - - -### Direct - -
-```yaml -name: Any -from_schema: https://w3id.org/linkml/transformer -class_uri: linkml:Any - -``` -
- -### Induced - -
-```yaml -name: Any -from_schema: https://w3id.org/linkml/transformer -class_uri: linkml:Any - -``` -
\ No newline at end of file diff --git a/docs/schema/Boolean.md b/docs/schema/Boolean.md deleted file mode 100644 index 8518d32..0000000 --- a/docs/schema/Boolean.md +++ /dev/null @@ -1,39 +0,0 @@ -# Type: Boolean - - - - -_A binary (true or false) value_ - - - -URI: [xsd:boolean](http://www.w3.org/2001/XMLSchema#boolean) - -* [base](https://w3id.org/linkml/base): Bool - -* [uri](https://w3id.org/linkml/uri): xsd:boolean - -* [repr](https://w3id.org/linkml/repr): bool - - - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - diff --git a/docs/schema/ClassDerivation.md b/docs/schema/ClassDerivation.md deleted file mode 100644 index ad7f10a..0000000 --- a/docs/schema/ClassDerivation.md +++ /dev/null @@ -1,418 +0,0 @@ - - -# Class: ClassDerivation - - -_A specification of how to derive a target class from a source class._ - - - - - -URI: [linkmltr:ClassDerivation](https://w3id.org/linkml/transformer/ClassDerivation) - - - - -```mermaid - classDiagram - class ClassDerivation - ElementDerivation <|-- ClassDerivation - - ClassDerivation : comments - - ClassDerivation : copy_directives - - ClassDerivation --> CopyDirective : copy_directives - - ClassDerivation : description - - ClassDerivation --> None : description - - ClassDerivation : expression_to_expression_mappings - - ClassDerivation --> KeyVal : expression_to_expression_mappings - - ClassDerivation : expression_to_value_mappings - - ClassDerivation --> KeyVal : expression_to_value_mappings - - ClassDerivation : implements - - ClassDerivation : is_a - - ClassDerivation --> ElementDerivation : is_a - - ClassDerivation : joins - - ClassDerivation --> AliasedClass : joins - - ClassDerivation : mirror_source - - ClassDerivation : mixins - - ClassDerivation --> ElementDerivation : mixins - - ClassDerivation : name - - ClassDerivation --> None : name - - ClassDerivation : overrides - - ClassDerivation --> Any : overrides - - ClassDerivation : populated_from - - ClassDerivation : slot_derivations - - ClassDerivation --> SlotDerivation : slot_derivations - - ClassDerivation : sources - - ClassDerivation : value_mappings - - ClassDerivation --> KeyVal : value_mappings - - -``` - - - - - -## Inheritance -* [SpecificationComponent](SpecificationComponent.md) - * [ElementDerivation](ElementDerivation.md) - * **ClassDerivation** - - - -## Slots - -| Name | Cardinality and Range | Description | Inheritance | -| --- | --- | --- | --- | -| [populated_from](populated_from.md) | 0..1
[ClassReference](ClassReference.md) | Name of the class in the source schema | direct | -| [sources](sources.md) | 0..*
[ClassReference](ClassReference.md) | | direct | -| [joins](joins.md) | 0..*
[AliasedClass](AliasedClass.md) | Additional classes to be joined to derive instances of the target class | direct | -| [slot_derivations](slot_derivations.md) | 0..*
[SlotDerivation](SlotDerivation.md) | | direct | -| [name](name.md) | 1..1
[String](String.md) | Name of the element in the target schema | [ElementDerivation](ElementDerivation.md) | -| [copy_directives](copy_directives.md) | 0..*
[CopyDirective](CopyDirective.md) | | [ElementDerivation](ElementDerivation.md) | -| [overrides](overrides.md) | 0..1
[Any](Any.md) | overrides source schema slots | [ElementDerivation](ElementDerivation.md) | -| [is_a](is_a.md) | 0..1
[ElementDerivation](ElementDerivation.md) | | [ElementDerivation](ElementDerivation.md) | -| [mixins](mixins.md) | 0..*
[ElementDerivation](ElementDerivation.md) | | [ElementDerivation](ElementDerivation.md) | -| [value_mappings](value_mappings.md) | 0..*
[KeyVal](KeyVal.md) | A mapping table that is applied directly to mappings, in order of precedence | [ElementDerivation](ElementDerivation.md) | -| [expression_to_value_mappings](expression_to_value_mappings.md) | 0..*
[KeyVal](KeyVal.md) | A mapping table in which the keys are expressions | [ElementDerivation](ElementDerivation.md) | -| [expression_to_expression_mappings](expression_to_expression_mappings.md) | 0..*
[KeyVal](KeyVal.md) | A mapping table in which the keys and values are expressions | [ElementDerivation](ElementDerivation.md) | -| [mirror_source](mirror_source.md) | 0..1
[Boolean](Boolean.md) | | [ElementDerivation](ElementDerivation.md) | -| [description](description.md) | 0..1
[String](String.md) | description of the specification component | [SpecificationComponent](SpecificationComponent.md) | -| [implements](implements.md) | 0..*
[Uriorcurie](Uriorcurie.md) | A reference to a specification that this component implements | [SpecificationComponent](SpecificationComponent.md) | -| [comments](comments.md) | 0..*
[String](String.md) | A list of comments about this component | [SpecificationComponent](SpecificationComponent.md) | - - - - - -## Usages - -| used by | used in | type | used | -| --- | --- | --- | --- | -| [TransformationSpecification](TransformationSpecification.md) | [class_derivations](class_derivations.md) | range | [ClassDerivation](ClassDerivation.md) | - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - - -## Mappings - -| Mapping Type | Mapped Value | -| --- | --- | -| self | linkmltr:ClassDerivation | -| native | linkmltr:ClassDerivation | - - - - - -## LinkML Source - - - -### Direct - -
-```yaml -name: ClassDerivation -description: A specification of how to derive a target class from a source class. -from_schema: https://w3id.org/linkml/transformer -is_a: ElementDerivation -attributes: - populated_from: - name: populated_from - description: Name of the class in the source schema - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - domain_of: - - ClassDerivation - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - range: ClassReference - sources: - name: sources - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - domain_of: - - ClassDerivation - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - range: ClassReference - joins: - name: joins - description: Additional classes to be joined to derive instances of the target - class - comments: - - not yet implemented - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - domain_of: - - ClassDerivation - range: AliasedClass - inlined: true - slot_derivations: - name: slot_derivations - from_schema: https://w3id.org/linkml/transformer - multivalued: true - domain_of: - - TransformationSpecification - - ClassDerivation - range: SlotDerivation - inlined: true - -``` -
- -### Induced - -
-```yaml -name: ClassDerivation -description: A specification of how to derive a target class from a source class. -from_schema: https://w3id.org/linkml/transformer -is_a: ElementDerivation -attributes: - populated_from: - name: populated_from - description: Name of the class in the source schema - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: populated_from - owner: ClassDerivation - domain_of: - - ClassDerivation - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - range: ClassReference - sources: - name: sources - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: sources - owner: ClassDerivation - domain_of: - - ClassDerivation - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - range: ClassReference - joins: - name: joins - description: Additional classes to be joined to derive instances of the target - class - comments: - - not yet implemented - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: joins - owner: ClassDerivation - domain_of: - - ClassDerivation - range: AliasedClass - inlined: true - slot_derivations: - name: slot_derivations - from_schema: https://w3id.org/linkml/transformer - multivalued: true - alias: slot_derivations - owner: ClassDerivation - domain_of: - - TransformationSpecification - - ClassDerivation - range: SlotDerivation - inlined: true - name: - name: name - description: Name of the element in the target schema - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - key: true - alias: name - owner: ClassDerivation - domain_of: - - ElementDerivation - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - range: string - required: true - copy_directives: - name: copy_directives - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: copy_directives - owner: ClassDerivation - domain_of: - - ElementDerivation - range: CopyDirective - inlined: true - overrides: - name: overrides - description: overrides source schema slots - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: overrides - owner: ClassDerivation - domain_of: - - ElementDerivation - range: Any - is_a: - name: is_a - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: linkml:is_a - alias: is_a - owner: ClassDerivation - domain_of: - - ElementDerivation - range: ElementDerivation - mixins: - name: mixins - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: linkml:mixins - multivalued: true - alias: mixins - owner: ClassDerivation - domain_of: - - ElementDerivation - range: ElementDerivation - inlined: false - value_mappings: - name: value_mappings - description: A mapping table that is applied directly to mappings, in order of - precedence - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: value_mappings - owner: ClassDerivation - domain_of: - - ElementDerivation - range: KeyVal - inlined: true - expression_to_value_mappings: - name: expression_to_value_mappings - description: A mapping table in which the keys are expressions - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: expression_to_value_mappings - owner: ClassDerivation - domain_of: - - ElementDerivation - range: KeyVal - inlined: true - expression_to_expression_mappings: - name: expression_to_expression_mappings - description: A mapping table in which the keys and values are expressions - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: expression_to_expression_mappings - owner: ClassDerivation - domain_of: - - ElementDerivation - range: KeyVal - inlined: true - mirror_source: - name: mirror_source - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: mirror_source - owner: ClassDerivation - domain_of: - - ElementDerivation - range: boolean - description: - name: description - description: description of the specification component - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: dcterms:description - alias: description - owner: ClassDerivation - domain_of: - - SpecificationComponent - range: string - implements: - name: implements - description: A reference to a specification that this component implements. - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: implements - owner: ClassDerivation - domain_of: - - SpecificationComponent - range: uriorcurie - comments: - name: comments - description: A list of comments about this component. Comments are free text, - and may be used to provide additional information about the component, including - instructions for its use. - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: rdfs:comment - multivalued: true - alias: comments - owner: ClassDerivation - domain_of: - - SpecificationComponent - range: string - -``` -
\ No newline at end of file diff --git a/docs/schema/ClassReference.md b/docs/schema/ClassReference.md deleted file mode 100644 index c1ca2fb..0000000 --- a/docs/schema/ClassReference.md +++ /dev/null @@ -1,34 +0,0 @@ -# Type: ClassReference - - - -URI: [xsd:string](http://www.w3.org/2001/XMLSchema#string) - -* [base](https://w3id.org/linkml/base): str - -* [uri](https://w3id.org/linkml/uri): xsd:string - - -* [typeof](https://w3id.org/linkml/typeof): string - - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - diff --git a/docs/schema/CollectionType.md b/docs/schema/CollectionType.md deleted file mode 100644 index 53da9a6..0000000 --- a/docs/schema/CollectionType.md +++ /dev/null @@ -1,64 +0,0 @@ -# Enum: CollectionType - - - -URI: [CollectionType](CollectionType.md) - -## Permissible Values - -| Value | Meaning | Description | -| --- | --- | --- | -| SingleValued | None | | -| MultiValued | None | | -| MultiValuedList | None | | -| MultiValuedDict | None | | - - - - -## Slots - -| Name | Description | -| --- | --- | -| [cast_collection_as](cast_collection_as.md) | | - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: CollectionType -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -permissible_values: - SingleValued: - text: SingleValued - MultiValued: - text: MultiValued - MultiValuedList: - text: MultiValuedList - MultiValuedDict: - text: MultiValuedDict - -``` -
diff --git a/docs/schema/CopyDirective.md b/docs/schema/CopyDirective.md deleted file mode 100644 index 0d5d97e..0000000 --- a/docs/schema/CopyDirective.md +++ /dev/null @@ -1,236 +0,0 @@ - - -# Class: CopyDirective - - -_Instructs a Schema Mapper in how to map to a target schema. Not used for data transformation._ - - - - - -URI: [linkmltr:CopyDirective](https://w3id.org/linkml/transformer/CopyDirective) - - - - -```mermaid - classDiagram - class CopyDirective - CopyDirective : add - - CopyDirective --> Any : add - - CopyDirective : copy_all - - CopyDirective : element_name - - CopyDirective --> None : element_name - - CopyDirective : exclude - - CopyDirective --> Any : exclude - - CopyDirective : exclude_all - - CopyDirective : include - - CopyDirective --> Any : include - - -``` - - - - - - - -## Slots - -| Name | Cardinality and Range | Description | Inheritance | -| --- | --- | --- | --- | -| [element_name](element_name.md) | 0..1
[String](String.md) | | direct | -| [copy_all](copy_all.md) | 0..1
[Boolean](Boolean.md) | | direct | -| [exclude_all](exclude_all.md) | 0..1
[Boolean](Boolean.md) | | direct | -| [exclude](exclude.md) | 0..1
[Any](Any.md) | | direct | -| [include](include.md) | 0..1
[Any](Any.md) | | direct | -| [add](add.md) | 0..1
[Any](Any.md) | | direct | - - - - - -## Usages - -| used by | used in | type | used | -| --- | --- | --- | --- | -| [ElementDerivation](ElementDerivation.md) | [copy_directives](copy_directives.md) | range | [CopyDirective](CopyDirective.md) | -| [ClassDerivation](ClassDerivation.md) | [copy_directives](copy_directives.md) | range | [CopyDirective](CopyDirective.md) | -| [SlotDerivation](SlotDerivation.md) | [copy_directives](copy_directives.md) | range | [CopyDirective](CopyDirective.md) | -| [EnumDerivation](EnumDerivation.md) | [copy_directives](copy_directives.md) | range | [CopyDirective](CopyDirective.md) | -| [PermissibleValueDerivation](PermissibleValueDerivation.md) | [copy_directives](copy_directives.md) | range | [CopyDirective](CopyDirective.md) | -| [PrefixDerivation](PrefixDerivation.md) | [copy_directives](copy_directives.md) | range | [CopyDirective](CopyDirective.md) | - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - - -## Mappings - -| Mapping Type | Mapped Value | -| --- | --- | -| self | linkmltr:CopyDirective | -| native | linkmltr:CopyDirective | - - - - - -## LinkML Source - - - -### Direct - -
-```yaml -name: CopyDirective -description: Instructs a Schema Mapper in how to map to a target schema. Not used - for data transformation. -from_schema: https://w3id.org/linkml/transformer -status: testing -attributes: - element_name: - name: element_name - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - key: true - domain_of: - - CopyDirective - required: true - copy_all: - name: copy_all - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - domain_of: - - CopyDirective - range: boolean - exclude_all: - name: exclude_all - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - domain_of: - - CopyDirective - range: boolean - exclude: - name: exclude - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - domain_of: - - CopyDirective - range: Any - include: - name: include - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - domain_of: - - CopyDirective - range: Any - add: - name: add - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - domain_of: - - CopyDirective - range: Any - -``` -
- -### Induced - -
-```yaml -name: CopyDirective -description: Instructs a Schema Mapper in how to map to a target schema. Not used - for data transformation. -from_schema: https://w3id.org/linkml/transformer -status: testing -attributes: - element_name: - name: element_name - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - key: true - alias: element_name - owner: CopyDirective - domain_of: - - CopyDirective - required: true - copy_all: - name: copy_all - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: copy_all - owner: CopyDirective - domain_of: - - CopyDirective - range: boolean - exclude_all: - name: exclude_all - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: exclude_all - owner: CopyDirective - domain_of: - - CopyDirective - range: boolean - exclude: - name: exclude - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: exclude - owner: CopyDirective - domain_of: - - CopyDirective - range: Any - include: - name: include - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: include - owner: CopyDirective - domain_of: - - CopyDirective - range: Any - add: - name: add - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: add - owner: CopyDirective - domain_of: - - CopyDirective - range: Any - -``` -
\ No newline at end of file diff --git a/docs/schema/Curie.md b/docs/schema/Curie.md deleted file mode 100644 index a99f0ef..0000000 --- a/docs/schema/Curie.md +++ /dev/null @@ -1,44 +0,0 @@ -# Type: Curie - - - - -_a compact URI_ - - - -URI: [xsd:string](http://www.w3.org/2001/XMLSchema#string) - -* [base](https://w3id.org/linkml/base): Curie - -* [uri](https://w3id.org/linkml/uri): xsd:string - -* [repr](https://w3id.org/linkml/repr): str - - - - - - - - -## Comments - -* in RDF serializations this MUST be expanded to a URI -* in non-RDF serializations MAY be serialized as the compact representation - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - diff --git a/docs/schema/Date.md b/docs/schema/Date.md deleted file mode 100644 index 5adf870..0000000 --- a/docs/schema/Date.md +++ /dev/null @@ -1,39 +0,0 @@ -# Type: Date - - - - -_a date (year, month and day) in an idealized calendar_ - - - -URI: [xsd:date](http://www.w3.org/2001/XMLSchema#date) - -* [base](https://w3id.org/linkml/base): XSDDate - -* [uri](https://w3id.org/linkml/uri): xsd:date - -* [repr](https://w3id.org/linkml/repr): str - - - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - diff --git a/docs/schema/DateOrDatetime.md b/docs/schema/DateOrDatetime.md deleted file mode 100644 index 4341277..0000000 --- a/docs/schema/DateOrDatetime.md +++ /dev/null @@ -1,39 +0,0 @@ -# Type: DateOrDatetime - - - - -_Either a date or a datetime_ - - - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -* [base](https://w3id.org/linkml/base): str - -* [uri](https://w3id.org/linkml/uri): linkml:DateOrDatetime - -* [repr](https://w3id.org/linkml/repr): str - - - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - diff --git a/docs/schema/Datetime.md b/docs/schema/Datetime.md deleted file mode 100644 index 3b0dcdf..0000000 --- a/docs/schema/Datetime.md +++ /dev/null @@ -1,39 +0,0 @@ -# Type: Datetime - - - - -_The combination of a date and time_ - - - -URI: [xsd:dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - -* [base](https://w3id.org/linkml/base): XSDDateTime - -* [uri](https://w3id.org/linkml/uri): xsd:dateTime - -* [repr](https://w3id.org/linkml/repr): str - - - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - diff --git a/docs/schema/Decimal.md b/docs/schema/Decimal.md deleted file mode 100644 index 242ae91..0000000 --- a/docs/schema/Decimal.md +++ /dev/null @@ -1,38 +0,0 @@ -# Type: Decimal - - - - -_A real number with arbitrary precision that conforms to the xsd:decimal specification_ - - - -URI: [xsd:decimal](http://www.w3.org/2001/XMLSchema#decimal) - -* [base](https://w3id.org/linkml/base): Decimal - -* [uri](https://w3id.org/linkml/uri): xsd:decimal - - - - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - diff --git a/docs/schema/Double.md b/docs/schema/Double.md deleted file mode 100644 index bdae3d4..0000000 --- a/docs/schema/Double.md +++ /dev/null @@ -1,38 +0,0 @@ -# Type: Double - - - - -_A real number that conforms to the xsd:double specification_ - - - -URI: [xsd:double](http://www.w3.org/2001/XMLSchema#double) - -* [base](https://w3id.org/linkml/base): float - -* [uri](https://w3id.org/linkml/uri): xsd:double - - - - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - diff --git a/docs/schema/ElementDerivation.md b/docs/schema/ElementDerivation.md deleted file mode 100644 index 952b4d4..0000000 --- a/docs/schema/ElementDerivation.md +++ /dev/null @@ -1,419 +0,0 @@ - - -# Class: ElementDerivation - - -_An abstract grouping for classes that provide a specification of how to derive a target element from a source element._ - - - - -* __NOTE__: this is an abstract class and should not be instantiated directly - - -URI: [linkmltr:ElementDerivation](https://w3id.org/linkml/transformer/ElementDerivation) - - - - -```mermaid - classDiagram - class ElementDerivation - SpecificationComponent <|-- ElementDerivation - - - ElementDerivation <|-- ClassDerivation - ElementDerivation <|-- SlotDerivation - ElementDerivation <|-- EnumDerivation - ElementDerivation <|-- PermissibleValueDerivation - ElementDerivation <|-- PrefixDerivation - - - ElementDerivation : comments - - ElementDerivation : copy_directives - - ElementDerivation --> CopyDirective : copy_directives - - ElementDerivation : description - - ElementDerivation --> None : description - - ElementDerivation : expression_to_expression_mappings - - ElementDerivation --> KeyVal : expression_to_expression_mappings - - ElementDerivation : expression_to_value_mappings - - ElementDerivation --> KeyVal : expression_to_value_mappings - - ElementDerivation : implements - - ElementDerivation : is_a - - ElementDerivation --> ElementDerivation : is_a - - ElementDerivation : mirror_source - - ElementDerivation : mixins - - ElementDerivation --> ElementDerivation : mixins - - ElementDerivation : name - - ElementDerivation --> None : name - - ElementDerivation : overrides - - ElementDerivation --> Any : overrides - - ElementDerivation : value_mappings - - ElementDerivation --> KeyVal : value_mappings - - -``` - - - - - -## Inheritance -* [SpecificationComponent](SpecificationComponent.md) - * **ElementDerivation** - * [ClassDerivation](ClassDerivation.md) - * [SlotDerivation](SlotDerivation.md) - * [EnumDerivation](EnumDerivation.md) - * [PermissibleValueDerivation](PermissibleValueDerivation.md) - * [PrefixDerivation](PrefixDerivation.md) - - - -## Slots - -| Name | Cardinality and Range | Description | Inheritance | -| --- | --- | --- | --- | -| [name](name.md) | 0..1
[String](String.md) | Name of the element in the target schema | direct | -| [copy_directives](copy_directives.md) | 0..*
[CopyDirective](CopyDirective.md) | | direct | -| [overrides](overrides.md) | 0..1
[Any](Any.md) | overrides source schema slots | direct | -| [is_a](is_a.md) | 0..1
[ElementDerivation](ElementDerivation.md) | | direct | -| [mixins](mixins.md) | 0..*
[ElementDerivation](ElementDerivation.md) | | direct | -| [value_mappings](value_mappings.md) | 0..*
[KeyVal](KeyVal.md) | A mapping table that is applied directly to mappings, in order of precedence | direct | -| [expression_to_value_mappings](expression_to_value_mappings.md) | 0..*
[KeyVal](KeyVal.md) | A mapping table in which the keys are expressions | direct | -| [expression_to_expression_mappings](expression_to_expression_mappings.md) | 0..*
[KeyVal](KeyVal.md) | A mapping table in which the keys and values are expressions | direct | -| [mirror_source](mirror_source.md) | 0..1
[Boolean](Boolean.md) | | direct | -| [description](description.md) | 0..1
[String](String.md) | description of the specification component | [SpecificationComponent](SpecificationComponent.md) | -| [implements](implements.md) | 0..*
[Uriorcurie](Uriorcurie.md) | A reference to a specification that this component implements | [SpecificationComponent](SpecificationComponent.md) | -| [comments](comments.md) | 0..*
[String](String.md) | A list of comments about this component | [SpecificationComponent](SpecificationComponent.md) | - - - - - -## Usages - -| used by | used in | type | used | -| --- | --- | --- | --- | -| [ElementDerivation](ElementDerivation.md) | [is_a](is_a.md) | range | [ElementDerivation](ElementDerivation.md) | -| [ElementDerivation](ElementDerivation.md) | [mixins](mixins.md) | range | [ElementDerivation](ElementDerivation.md) | -| [ClassDerivation](ClassDerivation.md) | [is_a](is_a.md) | range | [ElementDerivation](ElementDerivation.md) | -| [ClassDerivation](ClassDerivation.md) | [mixins](mixins.md) | range | [ElementDerivation](ElementDerivation.md) | -| [SlotDerivation](SlotDerivation.md) | [is_a](is_a.md) | range | [ElementDerivation](ElementDerivation.md) | -| [SlotDerivation](SlotDerivation.md) | [mixins](mixins.md) | range | [ElementDerivation](ElementDerivation.md) | -| [EnumDerivation](EnumDerivation.md) | [is_a](is_a.md) | range | [ElementDerivation](ElementDerivation.md) | -| [EnumDerivation](EnumDerivation.md) | [mixins](mixins.md) | range | [ElementDerivation](ElementDerivation.md) | -| [PermissibleValueDerivation](PermissibleValueDerivation.md) | [is_a](is_a.md) | range | [ElementDerivation](ElementDerivation.md) | -| [PermissibleValueDerivation](PermissibleValueDerivation.md) | [mixins](mixins.md) | range | [ElementDerivation](ElementDerivation.md) | -| [PrefixDerivation](PrefixDerivation.md) | [is_a](is_a.md) | range | [ElementDerivation](ElementDerivation.md) | -| [PrefixDerivation](PrefixDerivation.md) | [mixins](mixins.md) | range | [ElementDerivation](ElementDerivation.md) | - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - - -## Mappings - -| Mapping Type | Mapped Value | -| --- | --- | -| self | linkmltr:ElementDerivation | -| native | linkmltr:ElementDerivation | - - - - - -## LinkML Source - - - -### Direct - -
-```yaml -name: ElementDerivation -description: An abstract grouping for classes that provide a specification of how - to derive a target element from a source element. -from_schema: https://w3id.org/linkml/transformer -is_a: SpecificationComponent -abstract: true -attributes: - name: - name: name - description: Name of the element in the target schema - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - key: true - domain_of: - - ElementDerivation - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - required: true - copy_directives: - name: copy_directives - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - domain_of: - - ElementDerivation - range: CopyDirective - inlined: true - overrides: - name: overrides - description: overrides source schema slots - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - domain_of: - - ElementDerivation - range: Any - is_a: - name: is_a - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: linkml:is_a - domain_of: - - ElementDerivation - range: ElementDerivation - mixins: - name: mixins - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: linkml:mixins - multivalued: true - domain_of: - - ElementDerivation - range: ElementDerivation - inlined: false - value_mappings: - name: value_mappings - description: A mapping table that is applied directly to mappings, in order of - precedence - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - domain_of: - - ElementDerivation - range: KeyVal - inlined: true - expression_to_value_mappings: - name: expression_to_value_mappings - description: A mapping table in which the keys are expressions - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - domain_of: - - ElementDerivation - range: KeyVal - inlined: true - expression_to_expression_mappings: - name: expression_to_expression_mappings - description: A mapping table in which the keys and values are expressions - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - domain_of: - - ElementDerivation - range: KeyVal - inlined: true - mirror_source: - name: mirror_source - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - domain_of: - - ElementDerivation - range: boolean - -``` -
- -### Induced - -
-```yaml -name: ElementDerivation -description: An abstract grouping for classes that provide a specification of how - to derive a target element from a source element. -from_schema: https://w3id.org/linkml/transformer -is_a: SpecificationComponent -abstract: true -attributes: - name: - name: name - description: Name of the element in the target schema - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - key: true - alias: name - owner: ElementDerivation - domain_of: - - ElementDerivation - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - required: true - copy_directives: - name: copy_directives - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: copy_directives - owner: ElementDerivation - domain_of: - - ElementDerivation - range: CopyDirective - inlined: true - overrides: - name: overrides - description: overrides source schema slots - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: overrides - owner: ElementDerivation - domain_of: - - ElementDerivation - range: Any - is_a: - name: is_a - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: linkml:is_a - alias: is_a - owner: ElementDerivation - domain_of: - - ElementDerivation - range: ElementDerivation - mixins: - name: mixins - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: linkml:mixins - multivalued: true - alias: mixins - owner: ElementDerivation - domain_of: - - ElementDerivation - range: ElementDerivation - inlined: false - value_mappings: - name: value_mappings - description: A mapping table that is applied directly to mappings, in order of - precedence - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: value_mappings - owner: ElementDerivation - domain_of: - - ElementDerivation - range: KeyVal - inlined: true - expression_to_value_mappings: - name: expression_to_value_mappings - description: A mapping table in which the keys are expressions - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: expression_to_value_mappings - owner: ElementDerivation - domain_of: - - ElementDerivation - range: KeyVal - inlined: true - expression_to_expression_mappings: - name: expression_to_expression_mappings - description: A mapping table in which the keys and values are expressions - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: expression_to_expression_mappings - owner: ElementDerivation - domain_of: - - ElementDerivation - range: KeyVal - inlined: true - mirror_source: - name: mirror_source - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: mirror_source - owner: ElementDerivation - domain_of: - - ElementDerivation - range: boolean - description: - name: description - description: description of the specification component - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: dcterms:description - alias: description - owner: ElementDerivation - domain_of: - - SpecificationComponent - range: string - implements: - name: implements - description: A reference to a specification that this component implements. - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: implements - owner: ElementDerivation - domain_of: - - SpecificationComponent - range: uriorcurie - comments: - name: comments - description: A list of comments about this component. Comments are free text, - and may be used to provide additional information about the component, including - instructions for its use. - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: rdfs:comment - multivalued: true - alias: comments - owner: ElementDerivation - domain_of: - - SpecificationComponent - range: string - -``` -
\ No newline at end of file diff --git a/docs/schema/EnumDerivation.md b/docs/schema/EnumDerivation.md deleted file mode 100644 index 86d9015..0000000 --- a/docs/schema/EnumDerivation.md +++ /dev/null @@ -1,442 +0,0 @@ - - -# Class: EnumDerivation - - -_A specification of how to derive the value of a target enum from a source enum_ - - - - - -URI: [linkmltr:EnumDerivation](https://w3id.org/linkml/transformer/EnumDerivation) - - - - -```mermaid - classDiagram - class EnumDerivation - ElementDerivation <|-- EnumDerivation - - EnumDerivation : comments - - EnumDerivation : copy_directives - - EnumDerivation --> CopyDirective : copy_directives - - EnumDerivation : description - - EnumDerivation --> None : description - - EnumDerivation : expr - - EnumDerivation : expression_to_expression_mappings - - EnumDerivation --> KeyVal : expression_to_expression_mappings - - EnumDerivation : expression_to_value_mappings - - EnumDerivation --> KeyVal : expression_to_value_mappings - - EnumDerivation : hide - - EnumDerivation : implements - - EnumDerivation : is_a - - EnumDerivation --> ElementDerivation : is_a - - EnumDerivation : mirror_source - - EnumDerivation : mixins - - EnumDerivation --> ElementDerivation : mixins - - EnumDerivation : name - - EnumDerivation --> None : name - - EnumDerivation : overrides - - EnumDerivation --> Any : overrides - - EnumDerivation : permissible_value_derivations - - EnumDerivation --> PermissibleValueDerivation : permissible_value_derivations - - EnumDerivation : populated_from - - EnumDerivation : sources - - EnumDerivation : value_mappings - - EnumDerivation --> KeyVal : value_mappings - - -``` - - - - - -## Inheritance -* [SpecificationComponent](SpecificationComponent.md) - * [ElementDerivation](ElementDerivation.md) - * **EnumDerivation** - - - -## Slots - -| Name | Cardinality and Range | Description | Inheritance | -| --- | --- | --- | --- | -| [name](name.md) | 0..1
[String](String.md) | Target enum name | direct | -| [populated_from](populated_from.md) | 0..1
[EnumReference](EnumReference.md) | Source enum name | direct | -| [sources](sources.md) | 0..*
[EnumReference](EnumReference.md) | | direct | -| [expr](expr.md) | 0..1
[String](String.md) | An expression to be evaluated on the source object to derive the target slot | direct | -| [hide](hide.md) | 0..1
[Boolean](Boolean.md) | True if this is suppressed | direct | -| [permissible_value_derivations](permissible_value_derivations.md) | 0..*
[PermissibleValueDerivation](PermissibleValueDerivation.md) | Instructions on how to derive a set of PVs in the target schema | direct | -| [copy_directives](copy_directives.md) | 0..*
[CopyDirective](CopyDirective.md) | | [ElementDerivation](ElementDerivation.md) | -| [overrides](overrides.md) | 0..1
[Any](Any.md) | overrides source schema slots | [ElementDerivation](ElementDerivation.md) | -| [is_a](is_a.md) | 0..1
[ElementDerivation](ElementDerivation.md) | | [ElementDerivation](ElementDerivation.md) | -| [mixins](mixins.md) | 0..*
[ElementDerivation](ElementDerivation.md) | | [ElementDerivation](ElementDerivation.md) | -| [value_mappings](value_mappings.md) | 0..*
[KeyVal](KeyVal.md) | A mapping table that is applied directly to mappings, in order of precedence | [ElementDerivation](ElementDerivation.md) | -| [expression_to_value_mappings](expression_to_value_mappings.md) | 0..*
[KeyVal](KeyVal.md) | A mapping table in which the keys are expressions | [ElementDerivation](ElementDerivation.md) | -| [expression_to_expression_mappings](expression_to_expression_mappings.md) | 0..*
[KeyVal](KeyVal.md) | A mapping table in which the keys and values are expressions | [ElementDerivation](ElementDerivation.md) | -| [mirror_source](mirror_source.md) | 0..1
[Boolean](Boolean.md) | | [ElementDerivation](ElementDerivation.md) | -| [description](description.md) | 0..1
[String](String.md) | description of the specification component | [SpecificationComponent](SpecificationComponent.md) | -| [implements](implements.md) | 0..*
[Uriorcurie](Uriorcurie.md) | A reference to a specification that this component implements | [SpecificationComponent](SpecificationComponent.md) | -| [comments](comments.md) | 0..*
[String](String.md) | A list of comments about this component | [SpecificationComponent](SpecificationComponent.md) | - - - - - -## Usages - -| used by | used in | type | used | -| --- | --- | --- | --- | -| [TransformationSpecification](TransformationSpecification.md) | [enum_derivations](enum_derivations.md) | range | [EnumDerivation](EnumDerivation.md) | - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - - -## Mappings - -| Mapping Type | Mapped Value | -| --- | --- | -| self | linkmltr:EnumDerivation | -| native | linkmltr:EnumDerivation | - - - - - -## LinkML Source - - - -### Direct - -
-```yaml -name: EnumDerivation -description: A specification of how to derive the value of a target enum from a source - enum -from_schema: https://w3id.org/linkml/transformer -is_a: ElementDerivation -attributes: - name: - name: name - description: Target enum name - from_schema: https://w3id.org/linkml/transformer - key: true - domain_of: - - ElementDerivation - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - required: true - populated_from: - name: populated_from - description: Source enum name - from_schema: https://w3id.org/linkml/transformer - domain_of: - - ClassDerivation - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - range: EnumReference - sources: - name: sources - from_schema: https://w3id.org/linkml/transformer - multivalued: true - domain_of: - - ClassDerivation - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - range: EnumReference - expr: - name: expr - description: An expression to be evaluated on the source object to derive the - target slot. Should be specified using the LinkML expression language. - from_schema: https://w3id.org/linkml/transformer - domain_of: - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - range: string - hide: - name: hide - description: True if this is suppressed - from_schema: https://w3id.org/linkml/transformer - domain_of: - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - range: boolean - permissible_value_derivations: - name: permissible_value_derivations - description: Instructions on how to derive a set of PVs in the target schema - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - domain_of: - - EnumDerivation - range: PermissibleValueDerivation - inlined: true - -``` -
- -### Induced - -
-```yaml -name: EnumDerivation -description: A specification of how to derive the value of a target enum from a source - enum -from_schema: https://w3id.org/linkml/transformer -is_a: ElementDerivation -attributes: - name: - name: name - description: Target enum name - from_schema: https://w3id.org/linkml/transformer - key: true - alias: name - owner: EnumDerivation - domain_of: - - ElementDerivation - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - required: true - populated_from: - name: populated_from - description: Source enum name - from_schema: https://w3id.org/linkml/transformer - alias: populated_from - owner: EnumDerivation - domain_of: - - ClassDerivation - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - range: EnumReference - sources: - name: sources - from_schema: https://w3id.org/linkml/transformer - multivalued: true - alias: sources - owner: EnumDerivation - domain_of: - - ClassDerivation - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - range: EnumReference - expr: - name: expr - description: An expression to be evaluated on the source object to derive the - target slot. Should be specified using the LinkML expression language. - from_schema: https://w3id.org/linkml/transformer - alias: expr - owner: EnumDerivation - domain_of: - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - range: string - hide: - name: hide - description: True if this is suppressed - from_schema: https://w3id.org/linkml/transformer - alias: hide - owner: EnumDerivation - domain_of: - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - range: boolean - permissible_value_derivations: - name: permissible_value_derivations - description: Instructions on how to derive a set of PVs in the target schema - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: permissible_value_derivations - owner: EnumDerivation - domain_of: - - EnumDerivation - range: PermissibleValueDerivation - inlined: true - copy_directives: - name: copy_directives - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: copy_directives - owner: EnumDerivation - domain_of: - - ElementDerivation - range: CopyDirective - inlined: true - overrides: - name: overrides - description: overrides source schema slots - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: overrides - owner: EnumDerivation - domain_of: - - ElementDerivation - range: Any - is_a: - name: is_a - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: linkml:is_a - alias: is_a - owner: EnumDerivation - domain_of: - - ElementDerivation - range: ElementDerivation - mixins: - name: mixins - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: linkml:mixins - multivalued: true - alias: mixins - owner: EnumDerivation - domain_of: - - ElementDerivation - range: ElementDerivation - inlined: false - value_mappings: - name: value_mappings - description: A mapping table that is applied directly to mappings, in order of - precedence - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: value_mappings - owner: EnumDerivation - domain_of: - - ElementDerivation - range: KeyVal - inlined: true - expression_to_value_mappings: - name: expression_to_value_mappings - description: A mapping table in which the keys are expressions - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: expression_to_value_mappings - owner: EnumDerivation - domain_of: - - ElementDerivation - range: KeyVal - inlined: true - expression_to_expression_mappings: - name: expression_to_expression_mappings - description: A mapping table in which the keys and values are expressions - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: expression_to_expression_mappings - owner: EnumDerivation - domain_of: - - ElementDerivation - range: KeyVal - inlined: true - mirror_source: - name: mirror_source - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: mirror_source - owner: EnumDerivation - domain_of: - - ElementDerivation - range: boolean - description: - name: description - description: description of the specification component - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: dcterms:description - alias: description - owner: EnumDerivation - domain_of: - - SpecificationComponent - range: string - implements: - name: implements - description: A reference to a specification that this component implements. - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: implements - owner: EnumDerivation - domain_of: - - SpecificationComponent - range: uriorcurie - comments: - name: comments - description: A list of comments about this component. Comments are free text, - and may be used to provide additional information about the component, including - instructions for its use. - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: rdfs:comment - multivalued: true - alias: comments - owner: EnumDerivation - domain_of: - - SpecificationComponent - range: string - -``` -
\ No newline at end of file diff --git a/docs/schema/EnumReference.md b/docs/schema/EnumReference.md deleted file mode 100644 index 78acdca..0000000 --- a/docs/schema/EnumReference.md +++ /dev/null @@ -1,34 +0,0 @@ -# Type: EnumReference - - - -URI: [xsd:string](http://www.w3.org/2001/XMLSchema#string) - -* [base](https://w3id.org/linkml/base): str - -* [uri](https://w3id.org/linkml/uri): xsd:string - - -* [typeof](https://w3id.org/linkml/typeof): string - - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - diff --git a/docs/schema/Float.md b/docs/schema/Float.md deleted file mode 100644 index 47af3cb..0000000 --- a/docs/schema/Float.md +++ /dev/null @@ -1,38 +0,0 @@ -# Type: Float - - - - -_A real number that conforms to the xsd:float specification_ - - - -URI: [xsd:float](http://www.w3.org/2001/XMLSchema#float) - -* [base](https://w3id.org/linkml/base): float - -* [uri](https://w3id.org/linkml/uri): xsd:float - - - - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - diff --git a/docs/schema/Integer.md b/docs/schema/Integer.md deleted file mode 100644 index 40483e6..0000000 --- a/docs/schema/Integer.md +++ /dev/null @@ -1,38 +0,0 @@ -# Type: Integer - - - - -_An integer_ - - - -URI: [xsd:integer](http://www.w3.org/2001/XMLSchema#integer) - -* [base](https://w3id.org/linkml/base): int - -* [uri](https://w3id.org/linkml/uri): xsd:integer - - - - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - diff --git a/docs/schema/Inverse.md b/docs/schema/Inverse.md deleted file mode 100644 index 4039b96..0000000 --- a/docs/schema/Inverse.md +++ /dev/null @@ -1,153 +0,0 @@ - - -# Class: Inverse - - -_Used for back references in mapping to relational model_ - - - - - -URI: [linkmltr:Inverse](https://w3id.org/linkml/transformer/Inverse) - - - - -```mermaid - classDiagram - class Inverse - Inverse : class_name - - Inverse --> None : class_name - - Inverse : slot_name - - Inverse --> None : slot_name - - -``` - - - - - - - -## Slots - -| Name | Cardinality and Range | Description | Inheritance | -| --- | --- | --- | --- | -| [slot_name](slot_name.md) | 0..1
[String](String.md) | | direct | -| [class_name](class_name.md) | 0..1
[String](String.md) | | direct | - - - - - -## Usages - -| used by | used in | type | used | -| --- | --- | --- | --- | -| [SlotDerivation](SlotDerivation.md) | [inverse_of](inverse_of.md) | range | [Inverse](Inverse.md) | - - - - -## Aliases - - -* backref -* back_references - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - - -## Mappings - -| Mapping Type | Mapped Value | -| --- | --- | -| self | linkmltr:Inverse | -| native | linkmltr:Inverse | - - - - - -## LinkML Source - - - -### Direct - -
-```yaml -name: Inverse -description: Used for back references in mapping to relational model -from_schema: https://w3id.org/linkml/transformer -aliases: -- backref -- back_references -attributes: - slot_name: - name: slot_name - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - domain_of: - - Inverse - class_name: - name: class_name - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - domain_of: - - Inverse - -``` -
- -### Induced - -
-```yaml -name: Inverse -description: Used for back references in mapping to relational model -from_schema: https://w3id.org/linkml/transformer -aliases: -- backref -- back_references -attributes: - slot_name: - name: slot_name - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: slot_name - owner: Inverse - domain_of: - - Inverse - class_name: - name: class_name - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: class_name - owner: Inverse - domain_of: - - Inverse - -``` -
\ No newline at end of file diff --git a/docs/schema/Jsonpath.md b/docs/schema/Jsonpath.md deleted file mode 100644 index b5c3db6..0000000 --- a/docs/schema/Jsonpath.md +++ /dev/null @@ -1,39 +0,0 @@ -# Type: Jsonpath - - - - -_A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form._ - - - -URI: [xsd:string](http://www.w3.org/2001/XMLSchema#string) - -* [base](https://w3id.org/linkml/base): str - -* [uri](https://w3id.org/linkml/uri): xsd:string - -* [repr](https://w3id.org/linkml/repr): str - - - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - diff --git a/docs/schema/Jsonpointer.md b/docs/schema/Jsonpointer.md deleted file mode 100644 index ac6e805..0000000 --- a/docs/schema/Jsonpointer.md +++ /dev/null @@ -1,39 +0,0 @@ -# Type: Jsonpointer - - - - -_A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form._ - - - -URI: [xsd:string](http://www.w3.org/2001/XMLSchema#string) - -* [base](https://w3id.org/linkml/base): str - -* [uri](https://w3id.org/linkml/uri): xsd:string - -* [repr](https://w3id.org/linkml/repr): str - - - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - diff --git a/docs/schema/KeyVal.md b/docs/schema/KeyVal.md deleted file mode 100644 index b09b2c6..0000000 --- a/docs/schema/KeyVal.md +++ /dev/null @@ -1,158 +0,0 @@ - - -# Class: KeyVal - - - -URI: [linkmltr:KeyVal](https://w3id.org/linkml/transformer/KeyVal) - - - - -```mermaid - classDiagram - class KeyVal - KeyVal : key - - KeyVal --> None : key - - KeyVal : value - - KeyVal --> Any : value - - -``` - - - - - - - -## Slots - -| Name | Cardinality and Range | Description | Inheritance | -| --- | --- | --- | --- | -| [key](key.md) | 0..1
[String](String.md) | | direct | -| [value](value.md) | 0..1
[Any](Any.md) | | direct | - - - - - -## Usages - -| used by | used in | type | used | -| --- | --- | --- | --- | -| [TransformationSpecification](TransformationSpecification.md) | [prefixes](prefixes.md) | range | [KeyVal](KeyVal.md) | -| [ElementDerivation](ElementDerivation.md) | [value_mappings](value_mappings.md) | range | [KeyVal](KeyVal.md) | -| [ElementDerivation](ElementDerivation.md) | [expression_to_value_mappings](expression_to_value_mappings.md) | range | [KeyVal](KeyVal.md) | -| [ElementDerivation](ElementDerivation.md) | [expression_to_expression_mappings](expression_to_expression_mappings.md) | range | [KeyVal](KeyVal.md) | -| [ClassDerivation](ClassDerivation.md) | [value_mappings](value_mappings.md) | range | [KeyVal](KeyVal.md) | -| [ClassDerivation](ClassDerivation.md) | [expression_to_value_mappings](expression_to_value_mappings.md) | range | [KeyVal](KeyVal.md) | -| [ClassDerivation](ClassDerivation.md) | [expression_to_expression_mappings](expression_to_expression_mappings.md) | range | [KeyVal](KeyVal.md) | -| [SlotDerivation](SlotDerivation.md) | [value_mappings](value_mappings.md) | range | [KeyVal](KeyVal.md) | -| [SlotDerivation](SlotDerivation.md) | [expression_to_value_mappings](expression_to_value_mappings.md) | range | [KeyVal](KeyVal.md) | -| [SlotDerivation](SlotDerivation.md) | [expression_to_expression_mappings](expression_to_expression_mappings.md) | range | [KeyVal](KeyVal.md) | -| [EnumDerivation](EnumDerivation.md) | [value_mappings](value_mappings.md) | range | [KeyVal](KeyVal.md) | -| [EnumDerivation](EnumDerivation.md) | [expression_to_value_mappings](expression_to_value_mappings.md) | range | [KeyVal](KeyVal.md) | -| [EnumDerivation](EnumDerivation.md) | [expression_to_expression_mappings](expression_to_expression_mappings.md) | range | [KeyVal](KeyVal.md) | -| [PermissibleValueDerivation](PermissibleValueDerivation.md) | [value_mappings](value_mappings.md) | range | [KeyVal](KeyVal.md) | -| [PermissibleValueDerivation](PermissibleValueDerivation.md) | [expression_to_value_mappings](expression_to_value_mappings.md) | range | [KeyVal](KeyVal.md) | -| [PermissibleValueDerivation](PermissibleValueDerivation.md) | [expression_to_expression_mappings](expression_to_expression_mappings.md) | range | [KeyVal](KeyVal.md) | -| [PrefixDerivation](PrefixDerivation.md) | [value_mappings](value_mappings.md) | range | [KeyVal](KeyVal.md) | -| [PrefixDerivation](PrefixDerivation.md) | [expression_to_value_mappings](expression_to_value_mappings.md) | range | [KeyVal](KeyVal.md) | -| [PrefixDerivation](PrefixDerivation.md) | [expression_to_expression_mappings](expression_to_expression_mappings.md) | range | [KeyVal](KeyVal.md) | - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - - -## Mappings - -| Mapping Type | Mapped Value | -| --- | --- | -| self | linkmltr:KeyVal | -| native | linkmltr:KeyVal | - - - - - -## LinkML Source - - - -### Direct - -
-```yaml -name: KeyVal -from_schema: https://w3id.org/linkml/transformer -attributes: - key: - name: key - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - key: true - domain_of: - - KeyVal - required: true - value: - name: value - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - domain_of: - - KeyVal - range: Any - -``` -
- -### Induced - -
-```yaml -name: KeyVal -from_schema: https://w3id.org/linkml/transformer -attributes: - key: - name: key - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - key: true - alias: key - owner: KeyVal - domain_of: - - KeyVal - required: true - value: - name: value - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: value - owner: KeyVal - domain_of: - - KeyVal - range: Any - -``` -
\ No newline at end of file diff --git a/docs/schema/Ncname.md b/docs/schema/Ncname.md deleted file mode 100644 index 4f46b0f..0000000 --- a/docs/schema/Ncname.md +++ /dev/null @@ -1,39 +0,0 @@ -# Type: Ncname - - - - -_Prefix part of CURIE_ - - - -URI: [xsd:string](http://www.w3.org/2001/XMLSchema#string) - -* [base](https://w3id.org/linkml/base): NCName - -* [uri](https://w3id.org/linkml/uri): xsd:string - -* [repr](https://w3id.org/linkml/repr): str - - - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - diff --git a/docs/schema/Nodeidentifier.md b/docs/schema/Nodeidentifier.md deleted file mode 100644 index ab1e4c9..0000000 --- a/docs/schema/Nodeidentifier.md +++ /dev/null @@ -1,39 +0,0 @@ -# Type: Nodeidentifier - - - - -_A URI, CURIE or BNODE that represents a node in a model._ - - - -URI: [shex:nonLiteral](http://www.w3.org/ns/shex#nonLiteral) - -* [base](https://w3id.org/linkml/base): NodeIdentifier - -* [uri](https://w3id.org/linkml/uri): shex:nonLiteral - -* [repr](https://w3id.org/linkml/repr): str - - - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - diff --git a/docs/schema/Objectidentifier.md b/docs/schema/Objectidentifier.md deleted file mode 100644 index 1c2b304..0000000 --- a/docs/schema/Objectidentifier.md +++ /dev/null @@ -1,43 +0,0 @@ -# Type: Objectidentifier - - - - -_A URI or CURIE that represents an object in the model._ - - - -URI: [shex:iri](http://www.w3.org/ns/shex#iri) - -* [base](https://w3id.org/linkml/base): ElementIdentifier - -* [uri](https://w3id.org/linkml/uri): shex:iri - -* [repr](https://w3id.org/linkml/repr): str - - - - - - - - -## Comments - -* Used for inheritance and type checking - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - diff --git a/docs/schema/PermissibleValueDerivation.md b/docs/schema/PermissibleValueDerivation.md deleted file mode 100644 index 97bb7d2..0000000 --- a/docs/schema/PermissibleValueDerivation.md +++ /dev/null @@ -1,415 +0,0 @@ - - -# Class: PermissibleValueDerivation - - -_A specification of how to derive the value of a PV from a source enum_ - - - - - -URI: [linkmltr:PermissibleValueDerivation](https://w3id.org/linkml/transformer/PermissibleValueDerivation) - - - - -```mermaid - classDiagram - class PermissibleValueDerivation - ElementDerivation <|-- PermissibleValueDerivation - - PermissibleValueDerivation : comments - - PermissibleValueDerivation : copy_directives - - PermissibleValueDerivation --> CopyDirective : copy_directives - - PermissibleValueDerivation : description - - PermissibleValueDerivation --> None : description - - PermissibleValueDerivation : expr - - PermissibleValueDerivation : expression_to_expression_mappings - - PermissibleValueDerivation --> KeyVal : expression_to_expression_mappings - - PermissibleValueDerivation : expression_to_value_mappings - - PermissibleValueDerivation --> KeyVal : expression_to_value_mappings - - PermissibleValueDerivation : hide - - PermissibleValueDerivation : implements - - PermissibleValueDerivation : is_a - - PermissibleValueDerivation --> ElementDerivation : is_a - - PermissibleValueDerivation : mirror_source - - PermissibleValueDerivation : mixins - - PermissibleValueDerivation --> ElementDerivation : mixins - - PermissibleValueDerivation : name - - PermissibleValueDerivation --> None : name - - PermissibleValueDerivation : overrides - - PermissibleValueDerivation --> Any : overrides - - PermissibleValueDerivation : populated_from - - PermissibleValueDerivation : sources - - PermissibleValueDerivation : value_mappings - - PermissibleValueDerivation --> KeyVal : value_mappings - - -``` - - - - - -## Inheritance -* [SpecificationComponent](SpecificationComponent.md) - * [ElementDerivation](ElementDerivation.md) - * **PermissibleValueDerivation** - - - -## Slots - -| Name | Cardinality and Range | Description | Inheritance | -| --- | --- | --- | --- | -| [name](name.md) | 0..1
[String](String.md) | Target permissible value text | direct | -| [expr](expr.md) | 0..1
[String](String.md) | | direct | -| [populated_from](populated_from.md) | 0..1
[String](String.md) | Source permissible value | direct | -| [sources](sources.md) | 0..*
[String](String.md) | | direct | -| [hide](hide.md) | 0..1
[Boolean](Boolean.md) | | direct | -| [copy_directives](copy_directives.md) | 0..*
[CopyDirective](CopyDirective.md) | | [ElementDerivation](ElementDerivation.md) | -| [overrides](overrides.md) | 0..1
[Any](Any.md) | overrides source schema slots | [ElementDerivation](ElementDerivation.md) | -| [is_a](is_a.md) | 0..1
[ElementDerivation](ElementDerivation.md) | | [ElementDerivation](ElementDerivation.md) | -| [mixins](mixins.md) | 0..*
[ElementDerivation](ElementDerivation.md) | | [ElementDerivation](ElementDerivation.md) | -| [value_mappings](value_mappings.md) | 0..*
[KeyVal](KeyVal.md) | A mapping table that is applied directly to mappings, in order of precedence | [ElementDerivation](ElementDerivation.md) | -| [expression_to_value_mappings](expression_to_value_mappings.md) | 0..*
[KeyVal](KeyVal.md) | A mapping table in which the keys are expressions | [ElementDerivation](ElementDerivation.md) | -| [expression_to_expression_mappings](expression_to_expression_mappings.md) | 0..*
[KeyVal](KeyVal.md) | A mapping table in which the keys and values are expressions | [ElementDerivation](ElementDerivation.md) | -| [mirror_source](mirror_source.md) | 0..1
[Boolean](Boolean.md) | | [ElementDerivation](ElementDerivation.md) | -| [description](description.md) | 0..1
[String](String.md) | description of the specification component | [SpecificationComponent](SpecificationComponent.md) | -| [implements](implements.md) | 0..*
[Uriorcurie](Uriorcurie.md) | A reference to a specification that this component implements | [SpecificationComponent](SpecificationComponent.md) | -| [comments](comments.md) | 0..*
[String](String.md) | A list of comments about this component | [SpecificationComponent](SpecificationComponent.md) | - - - - - -## Usages - -| used by | used in | type | used | -| --- | --- | --- | --- | -| [EnumDerivation](EnumDerivation.md) | [permissible_value_derivations](permissible_value_derivations.md) | range | [PermissibleValueDerivation](PermissibleValueDerivation.md) | - - - - - - -## TODOs - -* this is currently under-specified. We will need boolean combinators to express if-then-else - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - - -## Mappings - -| Mapping Type | Mapped Value | -| --- | --- | -| self | linkmltr:PermissibleValueDerivation | -| native | linkmltr:PermissibleValueDerivation | - - - - - -## LinkML Source - - - -### Direct - -
-```yaml -name: PermissibleValueDerivation -description: A specification of how to derive the value of a PV from a source enum -todos: -- this is currently under-specified. We will need boolean combinators to express if-then-else -from_schema: https://w3id.org/linkml/transformer -is_a: ElementDerivation -attributes: - name: - name: name - description: Target permissible value text - from_schema: https://w3id.org/linkml/transformer - key: true - domain_of: - - ElementDerivation - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - required: true - expr: - name: expr - from_schema: https://w3id.org/linkml/transformer - domain_of: - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - range: string - populated_from: - name: populated_from - description: Source permissible value - from_schema: https://w3id.org/linkml/transformer - domain_of: - - ClassDerivation - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - range: string - sources: - name: sources - from_schema: https://w3id.org/linkml/transformer - multivalued: true - domain_of: - - ClassDerivation - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - range: string - hide: - name: hide - from_schema: https://w3id.org/linkml/transformer - domain_of: - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - range: boolean - -``` -
- -### Induced - -
-```yaml -name: PermissibleValueDerivation -description: A specification of how to derive the value of a PV from a source enum -todos: -- this is currently under-specified. We will need boolean combinators to express if-then-else -from_schema: https://w3id.org/linkml/transformer -is_a: ElementDerivation -attributes: - name: - name: name - description: Target permissible value text - from_schema: https://w3id.org/linkml/transformer - key: true - alias: name - owner: PermissibleValueDerivation - domain_of: - - ElementDerivation - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - required: true - expr: - name: expr - from_schema: https://w3id.org/linkml/transformer - alias: expr - owner: PermissibleValueDerivation - domain_of: - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - range: string - populated_from: - name: populated_from - description: Source permissible value - from_schema: https://w3id.org/linkml/transformer - alias: populated_from - owner: PermissibleValueDerivation - domain_of: - - ClassDerivation - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - range: string - sources: - name: sources - from_schema: https://w3id.org/linkml/transformer - multivalued: true - alias: sources - owner: PermissibleValueDerivation - domain_of: - - ClassDerivation - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - range: string - hide: - name: hide - from_schema: https://w3id.org/linkml/transformer - alias: hide - owner: PermissibleValueDerivation - domain_of: - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - range: boolean - copy_directives: - name: copy_directives - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: copy_directives - owner: PermissibleValueDerivation - domain_of: - - ElementDerivation - range: CopyDirective - inlined: true - overrides: - name: overrides - description: overrides source schema slots - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: overrides - owner: PermissibleValueDerivation - domain_of: - - ElementDerivation - range: Any - is_a: - name: is_a - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: linkml:is_a - alias: is_a - owner: PermissibleValueDerivation - domain_of: - - ElementDerivation - range: ElementDerivation - mixins: - name: mixins - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: linkml:mixins - multivalued: true - alias: mixins - owner: PermissibleValueDerivation - domain_of: - - ElementDerivation - range: ElementDerivation - inlined: false - value_mappings: - name: value_mappings - description: A mapping table that is applied directly to mappings, in order of - precedence - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: value_mappings - owner: PermissibleValueDerivation - domain_of: - - ElementDerivation - range: KeyVal - inlined: true - expression_to_value_mappings: - name: expression_to_value_mappings - description: A mapping table in which the keys are expressions - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: expression_to_value_mappings - owner: PermissibleValueDerivation - domain_of: - - ElementDerivation - range: KeyVal - inlined: true - expression_to_expression_mappings: - name: expression_to_expression_mappings - description: A mapping table in which the keys and values are expressions - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: expression_to_expression_mappings - owner: PermissibleValueDerivation - domain_of: - - ElementDerivation - range: KeyVal - inlined: true - mirror_source: - name: mirror_source - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: mirror_source - owner: PermissibleValueDerivation - domain_of: - - ElementDerivation - range: boolean - description: - name: description - description: description of the specification component - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: dcterms:description - alias: description - owner: PermissibleValueDerivation - domain_of: - - SpecificationComponent - range: string - implements: - name: implements - description: A reference to a specification that this component implements. - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: implements - owner: PermissibleValueDerivation - domain_of: - - SpecificationComponent - range: uriorcurie - comments: - name: comments - description: A list of comments about this component. Comments are free text, - and may be used to provide additional information about the component, including - instructions for its use. - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: rdfs:comment - multivalued: true - alias: comments - owner: PermissibleValueDerivation - domain_of: - - SpecificationComponent - range: string - -``` -
\ No newline at end of file diff --git a/docs/schema/PrefixDerivation.md b/docs/schema/PrefixDerivation.md deleted file mode 100644 index 610ef2a..0000000 --- a/docs/schema/PrefixDerivation.md +++ /dev/null @@ -1,291 +0,0 @@ - - -# Class: PrefixDerivation - - - -URI: [linkmltr:PrefixDerivation](https://w3id.org/linkml/transformer/PrefixDerivation) - - - - -```mermaid - classDiagram - class PrefixDerivation - ElementDerivation <|-- PrefixDerivation - - PrefixDerivation : comments - - PrefixDerivation : copy_directives - - PrefixDerivation --> CopyDirective : copy_directives - - PrefixDerivation : description - - PrefixDerivation --> None : description - - PrefixDerivation : expression_to_expression_mappings - - PrefixDerivation --> KeyVal : expression_to_expression_mappings - - PrefixDerivation : expression_to_value_mappings - - PrefixDerivation --> KeyVal : expression_to_value_mappings - - PrefixDerivation : implements - - PrefixDerivation : is_a - - PrefixDerivation --> ElementDerivation : is_a - - PrefixDerivation : mirror_source - - PrefixDerivation : mixins - - PrefixDerivation --> ElementDerivation : mixins - - PrefixDerivation : name - - PrefixDerivation --> None : name - - PrefixDerivation : overrides - - PrefixDerivation --> Any : overrides - - PrefixDerivation : value_mappings - - PrefixDerivation --> KeyVal : value_mappings - - -``` - - - - - -## Inheritance -* [SpecificationComponent](SpecificationComponent.md) - * [ElementDerivation](ElementDerivation.md) - * **PrefixDerivation** - - - -## Slots - -| Name | Cardinality and Range | Description | Inheritance | -| --- | --- | --- | --- | -| [name](name.md) | 1..1
[String](String.md) | Name of the element in the target schema | [ElementDerivation](ElementDerivation.md) | -| [copy_directives](copy_directives.md) | 0..*
[CopyDirective](CopyDirective.md) | | [ElementDerivation](ElementDerivation.md) | -| [overrides](overrides.md) | 0..1
[Any](Any.md) | overrides source schema slots | [ElementDerivation](ElementDerivation.md) | -| [is_a](is_a.md) | 0..1
[ElementDerivation](ElementDerivation.md) | | [ElementDerivation](ElementDerivation.md) | -| [mixins](mixins.md) | 0..*
[ElementDerivation](ElementDerivation.md) | | [ElementDerivation](ElementDerivation.md) | -| [value_mappings](value_mappings.md) | 0..*
[KeyVal](KeyVal.md) | A mapping table that is applied directly to mappings, in order of precedence | [ElementDerivation](ElementDerivation.md) | -| [expression_to_value_mappings](expression_to_value_mappings.md) | 0..*
[KeyVal](KeyVal.md) | A mapping table in which the keys are expressions | [ElementDerivation](ElementDerivation.md) | -| [expression_to_expression_mappings](expression_to_expression_mappings.md) | 0..*
[KeyVal](KeyVal.md) | A mapping table in which the keys and values are expressions | [ElementDerivation](ElementDerivation.md) | -| [mirror_source](mirror_source.md) | 0..1
[Boolean](Boolean.md) | | [ElementDerivation](ElementDerivation.md) | -| [description](description.md) | 0..1
[String](String.md) | description of the specification component | [SpecificationComponent](SpecificationComponent.md) | -| [implements](implements.md) | 0..*
[Uriorcurie](Uriorcurie.md) | A reference to a specification that this component implements | [SpecificationComponent](SpecificationComponent.md) | -| [comments](comments.md) | 0..*
[String](String.md) | A list of comments about this component | [SpecificationComponent](SpecificationComponent.md) | - - - - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - - -## Mappings - -| Mapping Type | Mapped Value | -| --- | --- | -| self | linkmltr:PrefixDerivation | -| native | linkmltr:PrefixDerivation | - - - - - -## LinkML Source - - - -### Direct - -
-```yaml -name: PrefixDerivation -from_schema: https://w3id.org/linkml/transformer -is_a: ElementDerivation - -``` -
- -### Induced - -
-```yaml -name: PrefixDerivation -from_schema: https://w3id.org/linkml/transformer -is_a: ElementDerivation -attributes: - name: - name: name - description: Name of the element in the target schema - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - key: true - alias: name - owner: PrefixDerivation - domain_of: - - ElementDerivation - - SlotDerivation - - EnumDerivation - - PermissibleValueDerivation - range: string - required: true - copy_directives: - name: copy_directives - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: copy_directives - owner: PrefixDerivation - domain_of: - - ElementDerivation - range: CopyDirective - inlined: true - overrides: - name: overrides - description: overrides source schema slots - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: overrides - owner: PrefixDerivation - domain_of: - - ElementDerivation - range: Any - is_a: - name: is_a - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: linkml:is_a - alias: is_a - owner: PrefixDerivation - domain_of: - - ElementDerivation - range: ElementDerivation - mixins: - name: mixins - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: linkml:mixins - multivalued: true - alias: mixins - owner: PrefixDerivation - domain_of: - - ElementDerivation - range: ElementDerivation - inlined: false - value_mappings: - name: value_mappings - description: A mapping table that is applied directly to mappings, in order of - precedence - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: value_mappings - owner: PrefixDerivation - domain_of: - - ElementDerivation - range: KeyVal - inlined: true - expression_to_value_mappings: - name: expression_to_value_mappings - description: A mapping table in which the keys are expressions - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: expression_to_value_mappings - owner: PrefixDerivation - domain_of: - - ElementDerivation - range: KeyVal - inlined: true - expression_to_expression_mappings: - name: expression_to_expression_mappings - description: A mapping table in which the keys and values are expressions - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: expression_to_expression_mappings - owner: PrefixDerivation - domain_of: - - ElementDerivation - range: KeyVal - inlined: true - mirror_source: - name: mirror_source - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: mirror_source - owner: PrefixDerivation - domain_of: - - ElementDerivation - range: boolean - description: - name: description - description: description of the specification component - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: dcterms:description - alias: description - owner: PrefixDerivation - domain_of: - - SpecificationComponent - range: string - implements: - name: implements - description: A reference to a specification that this component implements. - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: implements - owner: PrefixDerivation - domain_of: - - SpecificationComponent - range: uriorcurie - comments: - name: comments - description: A list of comments about this component. Comments are free text, - and may be used to provide additional information about the component, including - instructions for its use. - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: rdfs:comment - multivalued: true - alias: comments - owner: PrefixDerivation - domain_of: - - SpecificationComponent - range: string - -``` -
\ No newline at end of file diff --git a/docs/schema/SerializationSyntaxType.md b/docs/schema/SerializationSyntaxType.md deleted file mode 100644 index 17540d0..0000000 --- a/docs/schema/SerializationSyntaxType.md +++ /dev/null @@ -1,61 +0,0 @@ -# Enum: SerializationSyntaxType - - - -URI: [SerializationSyntaxType](SerializationSyntaxType.md) - -## Permissible Values - -| Value | Meaning | Description | -| --- | --- | --- | -| JSON | None | | -| YAML | None | | -| TURTLE | None | | - - - - -## Slots - -| Name | Description | -| --- | --- | -| [syntax](syntax.md) | | - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: SerializationSyntaxType -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -permissible_values: - JSON: - text: JSON - YAML: - text: YAML - TURTLE: - text: TURTLE - -``` -
diff --git a/docs/schema/SlotReference.md b/docs/schema/SlotReference.md deleted file mode 100644 index 620137d..0000000 --- a/docs/schema/SlotReference.md +++ /dev/null @@ -1,34 +0,0 @@ -# Type: SlotReference - - - -URI: [xsd:string](http://www.w3.org/2001/XMLSchema#string) - -* [base](https://w3id.org/linkml/base): str - -* [uri](https://w3id.org/linkml/uri): xsd:string - - -* [typeof](https://w3id.org/linkml/typeof): string - - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - diff --git a/docs/schema/Sparqlpath.md b/docs/schema/Sparqlpath.md deleted file mode 100644 index f27156c..0000000 --- a/docs/schema/Sparqlpath.md +++ /dev/null @@ -1,39 +0,0 @@ -# Type: Sparqlpath - - - - -_A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF._ - - - -URI: [xsd:string](http://www.w3.org/2001/XMLSchema#string) - -* [base](https://w3id.org/linkml/base): str - -* [uri](https://w3id.org/linkml/uri): xsd:string - -* [repr](https://w3id.org/linkml/repr): str - - - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - diff --git a/docs/schema/SpecificationComponent.md b/docs/schema/SpecificationComponent.md deleted file mode 100644 index 1d02d18..0000000 --- a/docs/schema/SpecificationComponent.md +++ /dev/null @@ -1,176 +0,0 @@ - - -# Class: SpecificationComponent - - -* __NOTE__: this is an abstract class and should not be instantiated directly - - -URI: [linkmltr:SpecificationComponent](https://w3id.org/linkml/transformer/SpecificationComponent) - - - - -```mermaid - classDiagram - class SpecificationComponent - SpecificationComponent <|-- TransformationSpecification - SpecificationComponent <|-- ElementDerivation - - SpecificationComponent : comments - - SpecificationComponent : description - - SpecificationComponent --> None : description - - SpecificationComponent : implements - - -``` - - - - - -## Inheritance -* **SpecificationComponent** - * [TransformationSpecification](TransformationSpecification.md) - * [ElementDerivation](ElementDerivation.md) - - - -## Slots - -| Name | Cardinality and Range | Description | Inheritance | -| --- | --- | --- | --- | -| [description](description.md) | 0..1
[String](String.md) | description of the specification component | direct | -| [implements](implements.md) | 0..*
[Uriorcurie](Uriorcurie.md) | A reference to a specification that this component implements | direct | -| [comments](comments.md) | 0..*
[String](String.md) | A list of comments about this component | direct | - - - - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - - -## Mappings - -| Mapping Type | Mapped Value | -| --- | --- | -| self | linkmltr:SpecificationComponent | -| native | linkmltr:SpecificationComponent | - - - - - -## LinkML Source - - - -### Direct - -
-```yaml -name: SpecificationComponent -from_schema: https://w3id.org/linkml/transformer -abstract: true -attributes: - description: - name: description - description: description of the specification component - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: dcterms:description - domain_of: - - SpecificationComponent - implements: - name: implements - description: A reference to a specification that this component implements. - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - domain_of: - - SpecificationComponent - range: uriorcurie - comments: - name: comments - description: A list of comments about this component. Comments are free text, - and may be used to provide additional information about the component, including - instructions for its use. - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: rdfs:comment - multivalued: true - domain_of: - - SpecificationComponent - range: string - -``` -
- -### Induced - -
-```yaml -name: SpecificationComponent -from_schema: https://w3id.org/linkml/transformer -abstract: true -attributes: - description: - name: description - description: description of the specification component - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: dcterms:description - alias: description - owner: SpecificationComponent - domain_of: - - SpecificationComponent - implements: - name: implements - description: A reference to a specification that this component implements. - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: implements - owner: SpecificationComponent - domain_of: - - SpecificationComponent - range: uriorcurie - comments: - name: comments - description: A list of comments about this component. Comments are free text, - and may be used to provide additional information about the component, including - instructions for its use. - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - slot_uri: rdfs:comment - multivalued: true - alias: comments - owner: SpecificationComponent - domain_of: - - SpecificationComponent - range: string - -``` -
\ No newline at end of file diff --git a/docs/schema/String.md b/docs/schema/String.md deleted file mode 100644 index 82a8a73..0000000 --- a/docs/schema/String.md +++ /dev/null @@ -1,38 +0,0 @@ -# Type: String - - - - -_A character string_ - - - -URI: [xsd:string](http://www.w3.org/2001/XMLSchema#string) - -* [base](https://w3id.org/linkml/base): str - -* [uri](https://w3id.org/linkml/uri): xsd:string - - - - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - diff --git a/docs/schema/StringificationConfiguration.md b/docs/schema/StringificationConfiguration.md deleted file mode 100644 index ef940e0..0000000 --- a/docs/schema/StringificationConfiguration.md +++ /dev/null @@ -1,190 +0,0 @@ - - -# Class: StringificationConfiguration - - - -URI: [linkmltr:StringificationConfiguration](https://w3id.org/linkml/transformer/StringificationConfiguration) - - - - -```mermaid - classDiagram - class StringificationConfiguration - StringificationConfiguration : delimiter - - StringificationConfiguration : over_slots - - StringificationConfiguration : reversed - - StringificationConfiguration : syntax - - StringificationConfiguration --> SerializationSyntaxType : syntax - - -``` - - - - - - - -## Slots - -| Name | Cardinality and Range | Description | Inheritance | -| --- | --- | --- | --- | -| [delimiter](delimiter.md) | 0..1
[String](String.md) | | direct | -| [reversed](reversed.md) | 0..1
[Boolean](Boolean.md) | | direct | -| [over_slots](over_slots.md) | 0..*
[String](String.md) | | direct | -| [syntax](syntax.md) | 0..1
[SerializationSyntaxType](SerializationSyntaxType.md) | | direct | - - - - - -## Usages - -| used by | used in | type | used | -| --- | --- | --- | --- | -| [SlotDerivation](SlotDerivation.md) | [stringification](stringification.md) | range | [StringificationConfiguration](StringificationConfiguration.md) | - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - - -## Mappings - -| Mapping Type | Mapped Value | -| --- | --- | -| self | linkmltr:StringificationConfiguration | -| native | linkmltr:StringificationConfiguration | - - - - - -## LinkML Source - - - -### Direct - -
-```yaml -name: StringificationConfiguration -from_schema: https://w3id.org/linkml/transformer -attributes: - delimiter: - name: delimiter - examples: - - value: ',' - - value: '|' - - value: ; - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - domain_of: - - StringificationConfiguration - range: string - reversed: - name: reversed - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - domain_of: - - StringificationConfiguration - range: boolean - over_slots: - name: over_slots - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - domain_of: - - StringificationConfiguration - range: string - syntax: - name: syntax - examples: - - value: json - - value: yaml - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - domain_of: - - StringificationConfiguration - range: SerializationSyntaxType - -``` -
- -### Induced - -
-```yaml -name: StringificationConfiguration -from_schema: https://w3id.org/linkml/transformer -attributes: - delimiter: - name: delimiter - examples: - - value: ',' - - value: '|' - - value: ; - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: delimiter - owner: StringificationConfiguration - domain_of: - - StringificationConfiguration - range: string - reversed: - name: reversed - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: reversed - owner: StringificationConfiguration - domain_of: - - StringificationConfiguration - range: boolean - over_slots: - name: over_slots - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - multivalued: true - alias: over_slots - owner: StringificationConfiguration - domain_of: - - StringificationConfiguration - range: string - syntax: - name: syntax - examples: - - value: json - - value: yaml - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: syntax - owner: StringificationConfiguration - domain_of: - - StringificationConfiguration - range: SerializationSyntaxType - -``` -
\ No newline at end of file diff --git a/docs/schema/Time.md b/docs/schema/Time.md deleted file mode 100644 index b82a242..0000000 --- a/docs/schema/Time.md +++ /dev/null @@ -1,39 +0,0 @@ -# Type: Time - - - - -_A time object represents a (local) time of day, independent of any particular day_ - - - -URI: [xsd:time](http://www.w3.org/2001/XMLSchema#time) - -* [base](https://w3id.org/linkml/base): XSDTime - -* [uri](https://w3id.org/linkml/uri): xsd:time - -* [repr](https://w3id.org/linkml/repr): str - - - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - diff --git a/docs/schema/UnitConversionConfiguration.md b/docs/schema/UnitConversionConfiguration.md deleted file mode 100644 index a597e0d..0000000 --- a/docs/schema/UnitConversionConfiguration.md +++ /dev/null @@ -1,256 +0,0 @@ - - -# Class: UnitConversionConfiguration - - - -URI: [linkmltr:UnitConversionConfiguration](https://w3id.org/linkml/transformer/UnitConversionConfiguration) - - - - -```mermaid - classDiagram - class UnitConversionConfiguration - UnitConversionConfiguration : source_magnitude_slot - - UnitConversionConfiguration --> None : source_magnitude_slot - - UnitConversionConfiguration : source_unit - - UnitConversionConfiguration --> None : source_unit - - UnitConversionConfiguration : source_unit_scheme - - UnitConversionConfiguration : source_unit_slot - - UnitConversionConfiguration --> None : source_unit_slot - - UnitConversionConfiguration : target_magnitude_slot - - UnitConversionConfiguration --> None : target_magnitude_slot - - UnitConversionConfiguration : target_unit - - UnitConversionConfiguration --> None : target_unit - - UnitConversionConfiguration : target_unit_scheme - - UnitConversionConfiguration : target_unit_slot - - UnitConversionConfiguration --> None : target_unit_slot - - -``` - - - - - - - -## Slots - -| Name | Cardinality and Range | Description | Inheritance | -| --- | --- | --- | --- | -| [target_unit](target_unit.md) | 0..1
[String](String.md) | | direct | -| [target_unit_scheme](target_unit_scheme.md) | 0..1
[String](String.md) | | direct | -| [source_unit](source_unit.md) | 0..1
[String](String.md) | | direct | -| [source_unit_scheme](source_unit_scheme.md) | 0..1
[String](String.md) | | direct | -| [source_unit_slot](source_unit_slot.md) | 0..1
[String](String.md) | | direct | -| [source_magnitude_slot](source_magnitude_slot.md) | 0..1
[String](String.md) | | direct | -| [target_unit_slot](target_unit_slot.md) | 0..1
[String](String.md) | | direct | -| [target_magnitude_slot](target_magnitude_slot.md) | 0..1
[String](String.md) | | direct | - - - - - -## Usages - -| used by | used in | type | used | -| --- | --- | --- | --- | -| [SlotDerivation](SlotDerivation.md) | [unit_conversion](unit_conversion.md) | range | [UnitConversionConfiguration](UnitConversionConfiguration.md) | - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - - -## Mappings - -| Mapping Type | Mapped Value | -| --- | --- | -| self | linkmltr:UnitConversionConfiguration | -| native | linkmltr:UnitConversionConfiguration | - - - - - -## LinkML Source - - - -### Direct - -
-```yaml -name: UnitConversionConfiguration -from_schema: https://w3id.org/linkml/transformer -attributes: - target_unit: - name: target_unit - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - domain_of: - - UnitConversionConfiguration - target_unit_scheme: - name: target_unit_scheme - examples: - - value: ucum - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - domain_of: - - UnitConversionConfiguration - range: string - source_unit: - name: source_unit - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - domain_of: - - UnitConversionConfiguration - source_unit_scheme: - name: source_unit_scheme - examples: - - value: ucum - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - domain_of: - - UnitConversionConfiguration - range: string - source_unit_slot: - name: source_unit_slot - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - domain_of: - - UnitConversionConfiguration - source_magnitude_slot: - name: source_magnitude_slot - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - domain_of: - - UnitConversionConfiguration - target_unit_slot: - name: target_unit_slot - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - domain_of: - - UnitConversionConfiguration - target_magnitude_slot: - name: target_magnitude_slot - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - domain_of: - - UnitConversionConfiguration - -``` -
- -### Induced - -
-```yaml -name: UnitConversionConfiguration -from_schema: https://w3id.org/linkml/transformer -attributes: - target_unit: - name: target_unit - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: target_unit - owner: UnitConversionConfiguration - domain_of: - - UnitConversionConfiguration - target_unit_scheme: - name: target_unit_scheme - examples: - - value: ucum - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: target_unit_scheme - owner: UnitConversionConfiguration - domain_of: - - UnitConversionConfiguration - range: string - source_unit: - name: source_unit - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: source_unit - owner: UnitConversionConfiguration - domain_of: - - UnitConversionConfiguration - source_unit_scheme: - name: source_unit_scheme - examples: - - value: ucum - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: source_unit_scheme - owner: UnitConversionConfiguration - domain_of: - - UnitConversionConfiguration - range: string - source_unit_slot: - name: source_unit_slot - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: source_unit_slot - owner: UnitConversionConfiguration - domain_of: - - UnitConversionConfiguration - source_magnitude_slot: - name: source_magnitude_slot - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: source_magnitude_slot - owner: UnitConversionConfiguration - domain_of: - - UnitConversionConfiguration - target_unit_slot: - name: target_unit_slot - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: target_unit_slot - owner: UnitConversionConfiguration - domain_of: - - UnitConversionConfiguration - target_magnitude_slot: - name: target_magnitude_slot - from_schema: https://w3id.org/linkml/transformer - rank: 1000 - alias: target_magnitude_slot - owner: UnitConversionConfiguration - domain_of: - - UnitConversionConfiguration - -``` -
\ No newline at end of file diff --git a/docs/schema/Uri.md b/docs/schema/Uri.md deleted file mode 100644 index 794c8ae..0000000 --- a/docs/schema/Uri.md +++ /dev/null @@ -1,43 +0,0 @@ -# Type: Uri - - - - -_a complete URI_ - - - -URI: [xsd:anyURI](http://www.w3.org/2001/XMLSchema#anyURI) - -* [base](https://w3id.org/linkml/base): URI - -* [uri](https://w3id.org/linkml/uri): xsd:anyURI - -* [repr](https://w3id.org/linkml/repr): str - - - - - - - - -## Comments - -* in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - diff --git a/docs/schema/Uriorcurie.md b/docs/schema/Uriorcurie.md deleted file mode 100644 index fbcc010..0000000 --- a/docs/schema/Uriorcurie.md +++ /dev/null @@ -1,39 +0,0 @@ -# Type: Uriorcurie - - - - -_a URI or a CURIE_ - - - -URI: [xsd:anyURI](http://www.w3.org/2001/XMLSchema#anyURI) - -* [base](https://w3id.org/linkml/base): URIorCURIE - -* [uri](https://w3id.org/linkml/uri): xsd:anyURI - -* [repr](https://w3id.org/linkml/repr): str - - - - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - diff --git a/docs/schema/about.md b/docs/schema/about.md deleted file mode 100644 index 2269d5d..0000000 --- a/docs/schema/about.md +++ /dev/null @@ -1 +0,0 @@ -# LinkML-Transformer diff --git a/docs/schema/add.md b/docs/schema/add.md deleted file mode 100644 index 36da70f..0000000 --- a/docs/schema/add.md +++ /dev/null @@ -1,65 +0,0 @@ - - -# Slot: add - -URI: [linkmltr:add](https://w3id.org/linkml/transformer/add) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [CopyDirective](CopyDirective.md) | Instructs a Schema Mapper in how to map to a target schema | no | - - - - - - - -## Properties - -* Range: [Any](Any.md) - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: add -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: add -owner: CopyDirective -domain_of: -- CopyDirective -range: Any - -``` -
\ No newline at end of file diff --git a/docs/schema/alias.md b/docs/schema/alias.md deleted file mode 100644 index 9527945..0000000 --- a/docs/schema/alias.md +++ /dev/null @@ -1,74 +0,0 @@ - - -# Slot: alias - - -_name of the class to be aliased_ - - - -URI: [linkmltr:alias](https://w3id.org/linkml/transformer/alias) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [AliasedClass](AliasedClass.md) | alias-class key value pairs for classes | no | - - - - - - - -## Properties - -* Range: NONE - -* Required: True - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: alias -description: name of the class to be aliased -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -key: true -alias: alias -owner: AliasedClass -domain_of: -- AliasedClass -required: true - -``` -
\ No newline at end of file diff --git a/docs/schema/api.md b/docs/schema/api.md deleted file mode 100644 index 79d8007..0000000 --- a/docs/schema/api.md +++ /dev/null @@ -1,9 +0,0 @@ -# Session - -::: linkml_map.session.Session - -# Transformer - - -::: linkml_map.transformer.transformer.Transformer - diff --git a/docs/schema/cast_collection_as.md b/docs/schema/cast_collection_as.md deleted file mode 100644 index 2d1170a..0000000 --- a/docs/schema/cast_collection_as.md +++ /dev/null @@ -1,65 +0,0 @@ - - -# Slot: cast_collection_as - -URI: [linkmltr:cast_collection_as](https://w3id.org/linkml/transformer/cast_collection_as) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slo... | no | - - - - - - - -## Properties - -* Range: [CollectionType](CollectionType.md) - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: cast_collection_as -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: cast_collection_as -owner: SlotDerivation -domain_of: -- SlotDerivation -range: CollectionType - -``` -
\ No newline at end of file diff --git a/docs/schema/class_derivations.md b/docs/schema/class_derivations.md deleted file mode 100644 index 318986e..0000000 --- a/docs/schema/class_derivations.md +++ /dev/null @@ -1,76 +0,0 @@ - - -# Slot: class_derivations - - -_Instructions on how to derive a set of classes in the target schema from classes in the source schema._ - - - -URI: [linkmltr:class_derivations](https://w3id.org/linkml/transformer/class_derivations) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [TransformationSpecification](TransformationSpecification.md) | A collection of mappings between source and target classes | no | - - - - - - - -## Properties - -* Range: [ClassDerivation](ClassDerivation.md) - -* Multivalued: True - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: class_derivations -description: Instructions on how to derive a set of classes in the target schema from - classes in the source schema. -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -multivalued: true -alias: class_derivations -owner: TransformationSpecification -domain_of: -- TransformationSpecification -range: ClassDerivation -inlined: true - -``` -
\ No newline at end of file diff --git a/docs/schema/class_name.md b/docs/schema/class_name.md deleted file mode 100644 index 57b3e2c..0000000 --- a/docs/schema/class_name.md +++ /dev/null @@ -1,64 +0,0 @@ - - -# Slot: class_name - -URI: [linkmltr:class_name](https://w3id.org/linkml/transformer/class_name) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [Inverse](Inverse.md) | Used for back references in mapping to relational model | no | - - - - - - - -## Properties - -* Range: NONE - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: class_name -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: class_name -owner: Inverse -domain_of: -- Inverse - -``` -
\ No newline at end of file diff --git a/docs/schema/class_named.md b/docs/schema/class_named.md deleted file mode 100644 index daa0249..0000000 --- a/docs/schema/class_named.md +++ /dev/null @@ -1,70 +0,0 @@ - - -# Slot: class_named - - -_local alias for the class_ - - - -URI: [linkmltr:class_named](https://w3id.org/linkml/transformer/class_named) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [AliasedClass](AliasedClass.md) | alias-class key value pairs for classes | no | - - - - - - - -## Properties - -* Range: NONE - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: class_named -description: local alias for the class -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: class_named -owner: AliasedClass -domain_of: -- AliasedClass - -``` -
\ No newline at end of file diff --git a/docs/schema/comments.md b/docs/schema/comments.md deleted file mode 100644 index e3e2e1e..0000000 --- a/docs/schema/comments.md +++ /dev/null @@ -1,84 +0,0 @@ - - -# Slot: comments - - -_A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use._ - - - -URI: [rdfs:comment](http://www.w3.org/2000/01/rdf-schema#comment) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [EnumDerivation](EnumDerivation.md) | A specification of how to derive the value of a target enum from a source enu... | no | -| [SpecificationComponent](SpecificationComponent.md) | | no | -| [ClassDerivation](ClassDerivation.md) | A specification of how to derive a target class from a source class | no | -| [PrefixDerivation](PrefixDerivation.md) | | no | -| [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slo... | no | -| [TransformationSpecification](TransformationSpecification.md) | A collection of mappings between source and target classes | no | -| [PermissibleValueDerivation](PermissibleValueDerivation.md) | A specification of how to derive the value of a PV from a source enum | no | -| [ElementDerivation](ElementDerivation.md) | An abstract grouping for classes that provide a specification of how to deri... | no | - - - - - - - -## Properties - -* Range: [String](String.md) - -* Multivalued: True - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: comments -description: A list of comments about this component. Comments are free text, and - may be used to provide additional information about the component, including instructions - for its use. -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -slot_uri: rdfs:comment -multivalued: true -alias: comments -owner: SpecificationComponent -domain_of: -- SpecificationComponent -range: string - -``` -
\ No newline at end of file diff --git a/docs/schema/compiler.md b/docs/schema/compiler.md deleted file mode 100644 index 3e06851..0000000 --- a/docs/schema/compiler.md +++ /dev/null @@ -1,17 +0,0 @@ -# Compiler Package - -A compiler will compile a Map specification into an alternative representation - -## Compiler (Base Class) - -::: linkml_map.compiler.compiler.Compiler - -## Python Compiler - -::: linkml_map.compiler.python_compiler.PythonCompiler - -## Markdown Compiler - -::: linkml_map.compiler.markdown_compiler.MarkdownCompiler - - diff --git a/docs/schema/copy_all.md b/docs/schema/copy_all.md deleted file mode 100644 index 35adf4a..0000000 --- a/docs/schema/copy_all.md +++ /dev/null @@ -1,65 +0,0 @@ - - -# Slot: copy_all - -URI: [linkmltr:copy_all](https://w3id.org/linkml/transformer/copy_all) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [CopyDirective](CopyDirective.md) | Instructs a Schema Mapper in how to map to a target schema | no | - - - - - - - -## Properties - -* Range: [Boolean](Boolean.md) - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: copy_all -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: copy_all -owner: CopyDirective -domain_of: -- CopyDirective -range: boolean - -``` -
\ No newline at end of file diff --git a/docs/schema/copy_directives.md b/docs/schema/copy_directives.md deleted file mode 100644 index 246683d..0000000 --- a/docs/schema/copy_directives.md +++ /dev/null @@ -1,74 +0,0 @@ - - -# Slot: copy_directives - -URI: [linkmltr:copy_directives](https://w3id.org/linkml/transformer/copy_directives) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [EnumDerivation](EnumDerivation.md) | A specification of how to derive the value of a target enum from a source enu... | no | -| [ClassDerivation](ClassDerivation.md) | A specification of how to derive a target class from a source class | no | -| [PrefixDerivation](PrefixDerivation.md) | | no | -| [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slo... | no | -| [PermissibleValueDerivation](PermissibleValueDerivation.md) | A specification of how to derive the value of a PV from a source enum | no | -| [ElementDerivation](ElementDerivation.md) | An abstract grouping for classes that provide a specification of how to deri... | no | - - - - - - - -## Properties - -* Range: [CopyDirective](CopyDirective.md) - -* Multivalued: True - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: copy_directives -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -multivalued: true -alias: copy_directives -owner: ElementDerivation -domain_of: -- ElementDerivation -range: CopyDirective -inlined: true - -``` -
\ No newline at end of file diff --git a/docs/schema/datamodel.md b/docs/schema/datamodel.md deleted file mode 100644 index 66ff1fe..0000000 --- a/docs/schema/datamodel.md +++ /dev/null @@ -1,148 +0,0 @@ -# LinkML Map Data Model - -Datamodel for LinkML schema mappings and transformations. - -A mapper generates instances of a *target* data model from -instances of a *source* data model. This transformation process -is guided by a *TransformationSpecification*. - -The specification is independent of any one method for transforming -data. It allows different approaches, including: - -- direct implementation, transforming python or json objects -- translation of the specification into SQL commands, to operate on relations -- translation of the specification into SPARQL CONSTRUCTs, to operate on triples -- translation into another specification language, such as R2RML - -URI: https://w3id.org/linkml/transformer - -Name: linkml-map - - - -## Classes - -| Class | Description | -| --- | --- | -| [AliasedClass](AliasedClass.md) | alias-class key value pairs for classes | -| [Any](Any.md) | None | -| [CopyDirective](CopyDirective.md) | Instructs a Schema Mapper in how to map to a target schema. Not used for data transformation. | -| [Inverse](Inverse.md) | Used for back references in mapping to relational model | -| [KeyVal](KeyVal.md) | None | -| [SpecificationComponent](SpecificationComponent.md) | None | -|         [ElementDerivation](ElementDerivation.md) | An abstract grouping for classes that provide a specification of how to derive a target element from a source element. | -|                 [ClassDerivation](ClassDerivation.md) | A specification of how to derive a target class from a source class. | -|                 [EnumDerivation](EnumDerivation.md) | A specification of how to derive the value of a target enum from a source enum | -|                 [PermissibleValueDerivation](PermissibleValueDerivation.md) | A specification of how to derive the value of a PV from a source enum | -|                 [PrefixDerivation](PrefixDerivation.md) | None | -|                 [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slot | -|         [TransformationSpecification](TransformationSpecification.md) | A collection of mappings between source and target classes | -| [StringificationConfiguration](StringificationConfiguration.md) | None | -| [UnitConversionConfiguration](UnitConversionConfiguration.md) | None | - - - -## Slots - -| Slot | Description | -| --- | --- | -| [add](add.md) | | -| [alias](alias.md) | name of the class to be aliased | -| [cast_collection_as](cast_collection_as.md) | | -| [class_derivations](class_derivations.md) | Instructions on how to derive a set of classes in the target schema from clas... | -| [class_name](class_name.md) | | -| [class_named](class_named.md) | local alias for the class | -| [comments](comments.md) | A list of comments about this component | -| [copy_all](copy_all.md) | | -| [copy_directives](copy_directives.md) | | -| [delimiter](delimiter.md) | | -| [derived_from](derived_from.md) | Source slots that are used to derive this slot | -| [description](description.md) | description of the specification component | -| [dictionary_key](dictionary_key.md) | | -| [element_name](element_name.md) | | -| [enum_derivations](enum_derivations.md) | Instructions on how to derive a set of enums in the target schema | -| [exclude](exclude.md) | | -| [exclude_all](exclude_all.md) | | -| [expr](expr.md) | An expression to be evaluated on the source object to derive the target slot | -| [expression_to_expression_mappings](expression_to_expression_mappings.md) | A mapping table in which the keys and values are expressions | -| [expression_to_value_mappings](expression_to_value_mappings.md) | A mapping table in which the keys are expressions | -| [hide](hide.md) | True if this is suppressed | -| [id](id.md) | Unique identifier for this transformation specification | -| [implements](implements.md) | A reference to a specification that this component implements | -| [include](include.md) | | -| [inverse_of](inverse_of.md) | Used to specify a class-slot tuple that is the inverse of the derived/target ... | -| [is_a](is_a.md) | | -| [joins](joins.md) | Additional classes to be joined to derive instances of the target class | -| [key](key.md) | | -| [mirror_source](mirror_source.md) | | -| [mixins](mixins.md) | | -| [name](name.md) | Name of the element in the target schema | -| [over_slots](over_slots.md) | | -| [overrides](overrides.md) | overrides source schema slots | -| [permissible_value_derivations](permissible_value_derivations.md) | Instructions on how to derive a set of PVs in the target schema | -| [populated_from](populated_from.md) | Name of the class in the source schema | -| [prefixes](prefixes.md) | maps prefixes to URL expansions | -| [range](range.md) | | -| [reversed](reversed.md) | | -| [slot_derivations](slot_derivations.md) | Instructions on how to derive a set of top level slots in the target schema | -| [slot_name](slot_name.md) | | -| [source_magnitude_slot](source_magnitude_slot.md) | | -| [source_schema](source_schema.md) | name of the schema that describes the source (input) objects | -| [source_unit](source_unit.md) | | -| [source_unit_scheme](source_unit_scheme.md) | | -| [source_unit_slot](source_unit_slot.md) | | -| [sources](sources.md) | | -| [stringification](stringification.md) | | -| [syntax](syntax.md) | | -| [target_magnitude_slot](target_magnitude_slot.md) | | -| [target_schema](target_schema.md) | name of the schema that describes the target (output) objects | -| [target_unit](target_unit.md) | | -| [target_unit_scheme](target_unit_scheme.md) | | -| [target_unit_slot](target_unit_slot.md) | | -| [title](title.md) | human readable title for this transformation specification | -| [type_designator](type_designator.md) | | -| [unit_conversion](unit_conversion.md) | | -| [value](value.md) | | -| [value_mappings](value_mappings.md) | A mapping table that is applied directly to mappings, in order of precedence | - - -## Enumerations - -| Enumeration | Description | -| --- | --- | -| [CollectionType](CollectionType.md) | | -| [SerializationSyntaxType](SerializationSyntaxType.md) | | - - -## Types - -| Type | Description | -| --- | --- | -| [Boolean](Boolean.md) | A binary (true or false) value | -| [ClassReference](ClassReference.md) | | -| [Curie](Curie.md) | a compact URI | -| [Date](Date.md) | a date (year, month and day) in an idealized calendar | -| [DateOrDatetime](DateOrDatetime.md) | Either a date or a datetime | -| [Datetime](Datetime.md) | The combination of a date and time | -| [Decimal](Decimal.md) | A real number with arbitrary precision that conforms to the xsd:decimal speci... | -| [Double](Double.md) | A real number that conforms to the xsd:double specification | -| [EnumReference](EnumReference.md) | | -| [Float](Float.md) | A real number that conforms to the xsd:float specification | -| [Integer](Integer.md) | An integer | -| [Jsonpath](Jsonpath.md) | A string encoding a JSON Path | -| [Jsonpointer](Jsonpointer.md) | A string encoding a JSON Pointer | -| [Ncname](Ncname.md) | Prefix part of CURIE | -| [Nodeidentifier](Nodeidentifier.md) | A URI, CURIE or BNODE that represents a node in a model | -| [Objectidentifier](Objectidentifier.md) | A URI or CURIE that represents an object in the model | -| [SlotReference](SlotReference.md) | | -| [Sparqlpath](Sparqlpath.md) | A string encoding a SPARQL Property Path | -| [String](String.md) | A character string | -| [Time](Time.md) | A time object represents a (local) time of day, independent of any particular... | -| [Uri](Uri.md) | a complete URI | -| [Uriorcurie](Uriorcurie.md) | a URI or a CURIE | - - -## Subsets - -| Subset | Description | -| --- | --- | diff --git a/docs/schema/delimiter.md b/docs/schema/delimiter.md deleted file mode 100644 index dbf0b2a..0000000 --- a/docs/schema/delimiter.md +++ /dev/null @@ -1,78 +0,0 @@ - - -# Slot: delimiter - -URI: [linkmltr:delimiter](https://w3id.org/linkml/transformer/delimiter) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [StringificationConfiguration](StringificationConfiguration.md) | | no | - - - - - - - -## Properties - -* Range: [String](String.md) - - - - - - -## Examples - -| Value | -| --- | -| , | -| | | -| ; | - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: delimiter -examples: -- value: ',' -- value: '|' -- value: ; -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: delimiter -owner: StringificationConfiguration -domain_of: -- StringificationConfiguration -range: string - -``` -
\ No newline at end of file diff --git a/docs/schema/derived_from.md b/docs/schema/derived_from.md deleted file mode 100644 index aae7646..0000000 --- a/docs/schema/derived_from.md +++ /dev/null @@ -1,75 +0,0 @@ - - -# Slot: derived_from - - -_Source slots that are used to derive this slot. This can be computed from the expr, if the expr is declarative._ - - - -URI: [linkmltr:derived_from](https://w3id.org/linkml/transformer/derived_from) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slo... | no | - - - - - - - -## Properties - -* Range: [SlotReference](SlotReference.md) - -* Multivalued: True - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: derived_from -description: Source slots that are used to derive this slot. This can be computed - from the expr, if the expr is declarative. -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -multivalued: true -alias: derived_from -owner: SlotDerivation -domain_of: -- SlotDerivation -range: SlotReference - -``` -
\ No newline at end of file diff --git a/docs/schema/description.md b/docs/schema/description.md deleted file mode 100644 index a3af74c..0000000 --- a/docs/schema/description.md +++ /dev/null @@ -1,78 +0,0 @@ - - -# Slot: description - - -_description of the specification component_ - - - -URI: [dcterms:description](http://purl.org/dc/terms/description) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [EnumDerivation](EnumDerivation.md) | A specification of how to derive the value of a target enum from a source enu... | no | -| [SpecificationComponent](SpecificationComponent.md) | | no | -| [ClassDerivation](ClassDerivation.md) | A specification of how to derive a target class from a source class | no | -| [PrefixDerivation](PrefixDerivation.md) | | no | -| [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slo... | no | -| [TransformationSpecification](TransformationSpecification.md) | A collection of mappings between source and target classes | no | -| [PermissibleValueDerivation](PermissibleValueDerivation.md) | A specification of how to derive the value of a PV from a source enum | no | -| [ElementDerivation](ElementDerivation.md) | An abstract grouping for classes that provide a specification of how to deri... | no | - - - - - - - -## Properties - -* Range: NONE - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: description -description: description of the specification component -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -slot_uri: dcterms:description -alias: description -owner: SpecificationComponent -domain_of: -- SpecificationComponent - -``` -
\ No newline at end of file diff --git a/docs/schema/dictionary_key.md b/docs/schema/dictionary_key.md deleted file mode 100644 index 9ad45d6..0000000 --- a/docs/schema/dictionary_key.md +++ /dev/null @@ -1,65 +0,0 @@ - - -# Slot: dictionary_key - -URI: [linkmltr:dictionary_key](https://w3id.org/linkml/transformer/dictionary_key) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slo... | no | - - - - - - - -## Properties - -* Range: [String](String.md) - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: dictionary_key -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: dictionary_key -owner: SlotDerivation -domain_of: -- SlotDerivation -range: string - -``` -
\ No newline at end of file diff --git a/docs/schema/element_name.md b/docs/schema/element_name.md deleted file mode 100644 index 98fe14c..0000000 --- a/docs/schema/element_name.md +++ /dev/null @@ -1,68 +0,0 @@ - - -# Slot: element_name - -URI: [linkmltr:element_name](https://w3id.org/linkml/transformer/element_name) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [CopyDirective](CopyDirective.md) | Instructs a Schema Mapper in how to map to a target schema | no | - - - - - - - -## Properties - -* Range: NONE - -* Required: True - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: element_name -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -key: true -alias: element_name -owner: CopyDirective -domain_of: -- CopyDirective -required: true - -``` -
\ No newline at end of file diff --git a/docs/schema/enum_derivations.md b/docs/schema/enum_derivations.md deleted file mode 100644 index 460bc24..0000000 --- a/docs/schema/enum_derivations.md +++ /dev/null @@ -1,75 +0,0 @@ - - -# Slot: enum_derivations - - -_Instructions on how to derive a set of enums in the target schema_ - - - -URI: [linkmltr:enum_derivations](https://w3id.org/linkml/transformer/enum_derivations) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [TransformationSpecification](TransformationSpecification.md) | A collection of mappings between source and target classes | no | - - - - - - - -## Properties - -* Range: [EnumDerivation](EnumDerivation.md) - -* Multivalued: True - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: enum_derivations -description: Instructions on how to derive a set of enums in the target schema -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -multivalued: true -alias: enum_derivations -owner: TransformationSpecification -domain_of: -- TransformationSpecification -range: EnumDerivation -inlined: true - -``` -
\ No newline at end of file diff --git a/docs/schema/exclude.md b/docs/schema/exclude.md deleted file mode 100644 index 231779a..0000000 --- a/docs/schema/exclude.md +++ /dev/null @@ -1,65 +0,0 @@ - - -# Slot: exclude - -URI: [linkmltr:exclude](https://w3id.org/linkml/transformer/exclude) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [CopyDirective](CopyDirective.md) | Instructs a Schema Mapper in how to map to a target schema | no | - - - - - - - -## Properties - -* Range: [Any](Any.md) - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: exclude -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: exclude -owner: CopyDirective -domain_of: -- CopyDirective -range: Any - -``` -
\ No newline at end of file diff --git a/docs/schema/exclude_all.md b/docs/schema/exclude_all.md deleted file mode 100644 index 880028c..0000000 --- a/docs/schema/exclude_all.md +++ /dev/null @@ -1,65 +0,0 @@ - - -# Slot: exclude_all - -URI: [linkmltr:exclude_all](https://w3id.org/linkml/transformer/exclude_all) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [CopyDirective](CopyDirective.md) | Instructs a Schema Mapper in how to map to a target schema | no | - - - - - - - -## Properties - -* Range: [Boolean](Boolean.md) - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: exclude_all -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: exclude_all -owner: CopyDirective -domain_of: -- CopyDirective -range: boolean - -``` -
\ No newline at end of file diff --git a/docs/schema/expr.md b/docs/schema/expr.md deleted file mode 100644 index 3990f1c..0000000 --- a/docs/schema/expr.md +++ /dev/null @@ -1,58 +0,0 @@ - - -# Slot: expr - -URI: [linkmltr:expr](https://w3id.org/linkml/transformer/expr) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slo... | no | -| [EnumDerivation](EnumDerivation.md) | A specification of how to derive the value of a target enum from a source enu... | no | -| [PermissibleValueDerivation](PermissibleValueDerivation.md) | A specification of how to derive the value of a PV from a source enum | no | - - - - - - - -## Properties - -* Range: NONE - - - - - -## Identifier and Mapping Information - - - - - - - - -## LinkML Source - -
-```yaml -name: expr -alias: expr -domain_of: -- SlotDerivation -- EnumDerivation -- PermissibleValueDerivation - -``` -
\ No newline at end of file diff --git a/docs/schema/expression_to_expression_mappings.md b/docs/schema/expression_to_expression_mappings.md deleted file mode 100644 index ae40067..0000000 --- a/docs/schema/expression_to_expression_mappings.md +++ /dev/null @@ -1,80 +0,0 @@ - - -# Slot: expression_to_expression_mappings - - -_A mapping table in which the keys and values are expressions_ - - - -URI: [linkmltr:expression_to_expression_mappings](https://w3id.org/linkml/transformer/expression_to_expression_mappings) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [EnumDerivation](EnumDerivation.md) | A specification of how to derive the value of a target enum from a source enu... | no | -| [ClassDerivation](ClassDerivation.md) | A specification of how to derive a target class from a source class | no | -| [PrefixDerivation](PrefixDerivation.md) | | no | -| [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slo... | no | -| [PermissibleValueDerivation](PermissibleValueDerivation.md) | A specification of how to derive the value of a PV from a source enum | no | -| [ElementDerivation](ElementDerivation.md) | An abstract grouping for classes that provide a specification of how to deri... | no | - - - - - - - -## Properties - -* Range: [KeyVal](KeyVal.md) - -* Multivalued: True - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: expression_to_expression_mappings -description: A mapping table in which the keys and values are expressions -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -multivalued: true -alias: expression_to_expression_mappings -owner: ElementDerivation -domain_of: -- ElementDerivation -range: KeyVal -inlined: true - -``` -
\ No newline at end of file diff --git a/docs/schema/expression_to_value_mappings.md b/docs/schema/expression_to_value_mappings.md deleted file mode 100644 index b1b27d3..0000000 --- a/docs/schema/expression_to_value_mappings.md +++ /dev/null @@ -1,80 +0,0 @@ - - -# Slot: expression_to_value_mappings - - -_A mapping table in which the keys are expressions_ - - - -URI: [linkmltr:expression_to_value_mappings](https://w3id.org/linkml/transformer/expression_to_value_mappings) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [EnumDerivation](EnumDerivation.md) | A specification of how to derive the value of a target enum from a source enu... | no | -| [ClassDerivation](ClassDerivation.md) | A specification of how to derive a target class from a source class | no | -| [PrefixDerivation](PrefixDerivation.md) | | no | -| [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slo... | no | -| [PermissibleValueDerivation](PermissibleValueDerivation.md) | A specification of how to derive the value of a PV from a source enum | no | -| [ElementDerivation](ElementDerivation.md) | An abstract grouping for classes that provide a specification of how to deri... | no | - - - - - - - -## Properties - -* Range: [KeyVal](KeyVal.md) - -* Multivalued: True - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: expression_to_value_mappings -description: A mapping table in which the keys are expressions -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -multivalued: true -alias: expression_to_value_mappings -owner: ElementDerivation -domain_of: -- ElementDerivation -range: KeyVal -inlined: true - -``` -
\ No newline at end of file diff --git a/docs/schema/faq.md b/docs/schema/faq.md deleted file mode 100644 index cbccbe0..0000000 --- a/docs/schema/faq.md +++ /dev/null @@ -1,38 +0,0 @@ -# FAQ - -## Why another framework? - -There are a number of excellent frameworks for performing mapping and data transformations. -The LinkML Transformer framework was born out of a need for a framework that: - -- was not inherently tied to: - - a particular serialization format (e.g. RDF, JSON, ...) - - a particular programming language (e.g. Python, Java, ...) - - a particular database system or database language (e.g. PostgreSQL or SQL or SPARQL) - - not tied to a particular kind of transformation (e.g. ORM or Tables to RDF) -- was a natural fit for the LinkML data modeling framework -- was declarative and easy to perform machine reasoning over -- is simple for simple use cases - -In its current state, this framework is less powerful and expressive than many other frameworks -or methodologies for performing transformations. If you need to perform complex data transformations, -you might be better off using an expressive query language like SPARQL or SQL, or even just coding -transformations directly in a programming language or library like Python or Pandas (but note that -even for the coding use case, the LinkML Transformer framework can be useful as a standard way -of *documenting* transformations). - -Currently the main use case for this framework is *mostly isomorphic* transformations, with lightweight -manipulations. These lend themselves well to a declarative framework. Uses cases that are a particularly good fit -involve mapping between data-dictionary like standards, with large numbers of metadata elements, where these -elements can often be mapped one-to-one, or with simple manipulations (e.g. unit conversions). - -The origins lie partly in the SSSOM standard, which is intended as an ultra-simple way of specifying -precise mappings between *entities* (e.g. schema.org Person is the same as DBPedia person). We observed -that many people wanted to extend the language to perform more complex mappings. To address this, we -help a workshop at the Biocuration conference in Padua, Italy in 2022. - -- [Discussion](https://github.com/orgs/linkml/discussions/1829) -- [SSSOM paper](https://academic.oup.com/database/article/doi/10.1093/database/baac035/6591806) -- [SSSOM Update 2023](https://ceur-ws.org/Vol-3591/om2023_STpaper3.pdf) -- [SSSOM Complex Mappings Workshop 2023](https://www.youtube.com/playlist?list=PLqu_J7ADQtKyX55F7RqZtaSS7TwGd3MoR) -- [Mapping Data Structures: Challenges and Approaches](https://doi.org/10.5281/zenodo.10343505) diff --git a/docs/schema/functions.md b/docs/schema/functions.md deleted file mode 100644 index 269d291..0000000 --- a/docs/schema/functions.md +++ /dev/null @@ -1,5 +0,0 @@ -# Functions Package - -## Unit Conversion - -::: linkml_map.functions.unit_conversion diff --git a/docs/schema/hide.md b/docs/schema/hide.md deleted file mode 100644 index 7ecb62b..0000000 --- a/docs/schema/hide.md +++ /dev/null @@ -1,58 +0,0 @@ - - -# Slot: hide - -URI: [linkmltr:hide](https://w3id.org/linkml/transformer/hide) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slo... | no | -| [EnumDerivation](EnumDerivation.md) | A specification of how to derive the value of a target enum from a source enu... | no | -| [PermissibleValueDerivation](PermissibleValueDerivation.md) | A specification of how to derive the value of a PV from a source enum | no | - - - - - - - -## Properties - -* Range: NONE - - - - - -## Identifier and Mapping Information - - - - - - - - -## LinkML Source - -
-```yaml -name: hide -alias: hide -domain_of: -- SlotDerivation -- EnumDerivation -- PermissibleValueDerivation - -``` -
\ No newline at end of file diff --git a/docs/schema/id.md b/docs/schema/id.md deleted file mode 100644 index bd15b16..0000000 --- a/docs/schema/id.md +++ /dev/null @@ -1,71 +0,0 @@ - - -# Slot: id - - -_Unique identifier for this transformation specification_ - - - -URI: [schema:identifier](http://schema.org/identifier) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [TransformationSpecification](TransformationSpecification.md) | A collection of mappings between source and target classes | no | - - - - - - - -## Properties - -* Range: NONE - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: id -description: Unique identifier for this transformation specification -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -slot_uri: schema:identifier -alias: id -owner: TransformationSpecification -domain_of: -- TransformationSpecification - -``` -
\ No newline at end of file diff --git a/docs/schema/implements.md b/docs/schema/implements.md deleted file mode 100644 index e229f0f..0000000 --- a/docs/schema/implements.md +++ /dev/null @@ -1,81 +0,0 @@ - - -# Slot: implements - - -_A reference to a specification that this component implements._ - - - -URI: [linkmltr:implements](https://w3id.org/linkml/transformer/implements) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [EnumDerivation](EnumDerivation.md) | A specification of how to derive the value of a target enum from a source enu... | no | -| [SpecificationComponent](SpecificationComponent.md) | | no | -| [ClassDerivation](ClassDerivation.md) | A specification of how to derive a target class from a source class | no | -| [PrefixDerivation](PrefixDerivation.md) | | no | -| [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slo... | no | -| [TransformationSpecification](TransformationSpecification.md) | A collection of mappings between source and target classes | no | -| [PermissibleValueDerivation](PermissibleValueDerivation.md) | A specification of how to derive the value of a PV from a source enum | no | -| [ElementDerivation](ElementDerivation.md) | An abstract grouping for classes that provide a specification of how to deri... | no | - - - - - - - -## Properties - -* Range: [Uriorcurie](Uriorcurie.md) - -* Multivalued: True - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: implements -description: A reference to a specification that this component implements. -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -multivalued: true -alias: implements -owner: SpecificationComponent -domain_of: -- SpecificationComponent -range: uriorcurie - -``` -
\ No newline at end of file diff --git a/docs/schema/include.md b/docs/schema/include.md deleted file mode 100644 index 488115c..0000000 --- a/docs/schema/include.md +++ /dev/null @@ -1,65 +0,0 @@ - - -# Slot: include - -URI: [linkmltr:include](https://w3id.org/linkml/transformer/include) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [CopyDirective](CopyDirective.md) | Instructs a Schema Mapper in how to map to a target schema | no | - - - - - - - -## Properties - -* Range: [Any](Any.md) - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: include -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: include -owner: CopyDirective -domain_of: -- CopyDirective -range: Any - -``` -
\ No newline at end of file diff --git a/docs/schema/index.md b/docs/schema/index.md deleted file mode 100644 index 66ff1fe..0000000 --- a/docs/schema/index.md +++ /dev/null @@ -1,148 +0,0 @@ -# LinkML Map Data Model - -Datamodel for LinkML schema mappings and transformations. - -A mapper generates instances of a *target* data model from -instances of a *source* data model. This transformation process -is guided by a *TransformationSpecification*. - -The specification is independent of any one method for transforming -data. It allows different approaches, including: - -- direct implementation, transforming python or json objects -- translation of the specification into SQL commands, to operate on relations -- translation of the specification into SPARQL CONSTRUCTs, to operate on triples -- translation into another specification language, such as R2RML - -URI: https://w3id.org/linkml/transformer - -Name: linkml-map - - - -## Classes - -| Class | Description | -| --- | --- | -| [AliasedClass](AliasedClass.md) | alias-class key value pairs for classes | -| [Any](Any.md) | None | -| [CopyDirective](CopyDirective.md) | Instructs a Schema Mapper in how to map to a target schema. Not used for data transformation. | -| [Inverse](Inverse.md) | Used for back references in mapping to relational model | -| [KeyVal](KeyVal.md) | None | -| [SpecificationComponent](SpecificationComponent.md) | None | -|         [ElementDerivation](ElementDerivation.md) | An abstract grouping for classes that provide a specification of how to derive a target element from a source element. | -|                 [ClassDerivation](ClassDerivation.md) | A specification of how to derive a target class from a source class. | -|                 [EnumDerivation](EnumDerivation.md) | A specification of how to derive the value of a target enum from a source enum | -|                 [PermissibleValueDerivation](PermissibleValueDerivation.md) | A specification of how to derive the value of a PV from a source enum | -|                 [PrefixDerivation](PrefixDerivation.md) | None | -|                 [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slot | -|         [TransformationSpecification](TransformationSpecification.md) | A collection of mappings between source and target classes | -| [StringificationConfiguration](StringificationConfiguration.md) | None | -| [UnitConversionConfiguration](UnitConversionConfiguration.md) | None | - - - -## Slots - -| Slot | Description | -| --- | --- | -| [add](add.md) | | -| [alias](alias.md) | name of the class to be aliased | -| [cast_collection_as](cast_collection_as.md) | | -| [class_derivations](class_derivations.md) | Instructions on how to derive a set of classes in the target schema from clas... | -| [class_name](class_name.md) | | -| [class_named](class_named.md) | local alias for the class | -| [comments](comments.md) | A list of comments about this component | -| [copy_all](copy_all.md) | | -| [copy_directives](copy_directives.md) | | -| [delimiter](delimiter.md) | | -| [derived_from](derived_from.md) | Source slots that are used to derive this slot | -| [description](description.md) | description of the specification component | -| [dictionary_key](dictionary_key.md) | | -| [element_name](element_name.md) | | -| [enum_derivations](enum_derivations.md) | Instructions on how to derive a set of enums in the target schema | -| [exclude](exclude.md) | | -| [exclude_all](exclude_all.md) | | -| [expr](expr.md) | An expression to be evaluated on the source object to derive the target slot | -| [expression_to_expression_mappings](expression_to_expression_mappings.md) | A mapping table in which the keys and values are expressions | -| [expression_to_value_mappings](expression_to_value_mappings.md) | A mapping table in which the keys are expressions | -| [hide](hide.md) | True if this is suppressed | -| [id](id.md) | Unique identifier for this transformation specification | -| [implements](implements.md) | A reference to a specification that this component implements | -| [include](include.md) | | -| [inverse_of](inverse_of.md) | Used to specify a class-slot tuple that is the inverse of the derived/target ... | -| [is_a](is_a.md) | | -| [joins](joins.md) | Additional classes to be joined to derive instances of the target class | -| [key](key.md) | | -| [mirror_source](mirror_source.md) | | -| [mixins](mixins.md) | | -| [name](name.md) | Name of the element in the target schema | -| [over_slots](over_slots.md) | | -| [overrides](overrides.md) | overrides source schema slots | -| [permissible_value_derivations](permissible_value_derivations.md) | Instructions on how to derive a set of PVs in the target schema | -| [populated_from](populated_from.md) | Name of the class in the source schema | -| [prefixes](prefixes.md) | maps prefixes to URL expansions | -| [range](range.md) | | -| [reversed](reversed.md) | | -| [slot_derivations](slot_derivations.md) | Instructions on how to derive a set of top level slots in the target schema | -| [slot_name](slot_name.md) | | -| [source_magnitude_slot](source_magnitude_slot.md) | | -| [source_schema](source_schema.md) | name of the schema that describes the source (input) objects | -| [source_unit](source_unit.md) | | -| [source_unit_scheme](source_unit_scheme.md) | | -| [source_unit_slot](source_unit_slot.md) | | -| [sources](sources.md) | | -| [stringification](stringification.md) | | -| [syntax](syntax.md) | | -| [target_magnitude_slot](target_magnitude_slot.md) | | -| [target_schema](target_schema.md) | name of the schema that describes the target (output) objects | -| [target_unit](target_unit.md) | | -| [target_unit_scheme](target_unit_scheme.md) | | -| [target_unit_slot](target_unit_slot.md) | | -| [title](title.md) | human readable title for this transformation specification | -| [type_designator](type_designator.md) | | -| [unit_conversion](unit_conversion.md) | | -| [value](value.md) | | -| [value_mappings](value_mappings.md) | A mapping table that is applied directly to mappings, in order of precedence | - - -## Enumerations - -| Enumeration | Description | -| --- | --- | -| [CollectionType](CollectionType.md) | | -| [SerializationSyntaxType](SerializationSyntaxType.md) | | - - -## Types - -| Type | Description | -| --- | --- | -| [Boolean](Boolean.md) | A binary (true or false) value | -| [ClassReference](ClassReference.md) | | -| [Curie](Curie.md) | a compact URI | -| [Date](Date.md) | a date (year, month and day) in an idealized calendar | -| [DateOrDatetime](DateOrDatetime.md) | Either a date or a datetime | -| [Datetime](Datetime.md) | The combination of a date and time | -| [Decimal](Decimal.md) | A real number with arbitrary precision that conforms to the xsd:decimal speci... | -| [Double](Double.md) | A real number that conforms to the xsd:double specification | -| [EnumReference](EnumReference.md) | | -| [Float](Float.md) | A real number that conforms to the xsd:float specification | -| [Integer](Integer.md) | An integer | -| [Jsonpath](Jsonpath.md) | A string encoding a JSON Path | -| [Jsonpointer](Jsonpointer.md) | A string encoding a JSON Pointer | -| [Ncname](Ncname.md) | Prefix part of CURIE | -| [Nodeidentifier](Nodeidentifier.md) | A URI, CURIE or BNODE that represents a node in a model | -| [Objectidentifier](Objectidentifier.md) | A URI or CURIE that represents an object in the model | -| [SlotReference](SlotReference.md) | | -| [Sparqlpath](Sparqlpath.md) | A string encoding a SPARQL Property Path | -| [String](String.md) | A character string | -| [Time](Time.md) | A time object represents a (local) time of day, independent of any particular... | -| [Uri](Uri.md) | a complete URI | -| [Uriorcurie](Uriorcurie.md) | a URI or a CURIE | - - -## Subsets - -| Subset | Description | -| --- | --- | diff --git a/docs/schema/inverse_of.md b/docs/schema/inverse_of.md deleted file mode 100644 index 4a17626..0000000 --- a/docs/schema/inverse_of.md +++ /dev/null @@ -1,74 +0,0 @@ - - -# Slot: inverse_of - - -_Used to specify a class-slot tuple that is the inverse of the derived/target slot. This is used primarily for mapping to relational databases or formalisms that do not allow multiple values. The class representing the repeated element has a foreign key slot inserted in that 'back references' the original multivalued slot._ - - - -URI: [linkmltr:inverse_of](https://w3id.org/linkml/transformer/inverse_of) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slo... | no | - - - - - - - -## Properties - -* Range: [Inverse](Inverse.md) - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: inverse_of -description: Used to specify a class-slot tuple that is the inverse of the derived/target - slot. This is used primarily for mapping to relational databases or formalisms that - do not allow multiple values. The class representing the repeated element has a - foreign key slot inserted in that 'back references' the original multivalued slot. -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: inverse_of -owner: SlotDerivation -domain_of: -- SlotDerivation -range: Inverse - -``` -
\ No newline at end of file diff --git a/docs/schema/is_a.md b/docs/schema/is_a.md deleted file mode 100644 index d60aa32..0000000 --- a/docs/schema/is_a.md +++ /dev/null @@ -1,71 +0,0 @@ - - -# Slot: is_a - -URI: [linkml:is_a](https://w3id.org/linkml/is_a) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [EnumDerivation](EnumDerivation.md) | A specification of how to derive the value of a target enum from a source enu... | no | -| [ClassDerivation](ClassDerivation.md) | A specification of how to derive a target class from a source class | no | -| [PrefixDerivation](PrefixDerivation.md) | | no | -| [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slo... | no | -| [PermissibleValueDerivation](PermissibleValueDerivation.md) | A specification of how to derive the value of a PV from a source enum | no | -| [ElementDerivation](ElementDerivation.md) | An abstract grouping for classes that provide a specification of how to deri... | no | - - - - - - - -## Properties - -* Range: [ElementDerivation](ElementDerivation.md) - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: is_a -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -slot_uri: linkml:is_a -alias: is_a -owner: ElementDerivation -domain_of: -- ElementDerivation -range: ElementDerivation - -``` -
\ No newline at end of file diff --git a/docs/schema/joins.md b/docs/schema/joins.md deleted file mode 100644 index 3af1fc4..0000000 --- a/docs/schema/joins.md +++ /dev/null @@ -1,81 +0,0 @@ - - -# Slot: joins - - -_Additional classes to be joined to derive instances of the target class_ - - - -URI: [linkmltr:joins](https://w3id.org/linkml/transformer/joins) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [ClassDerivation](ClassDerivation.md) | A specification of how to derive a target class from a source class | no | - - - - - - - -## Properties - -* Range: [AliasedClass](AliasedClass.md) - -* Multivalued: True - - - - - -## Comments - -* not yet implemented - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: joins -description: Additional classes to be joined to derive instances of the target class -comments: -- not yet implemented -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -multivalued: true -alias: joins -owner: ClassDerivation -domain_of: -- ClassDerivation -range: AliasedClass -inlined: true - -``` -
\ No newline at end of file diff --git a/docs/schema/key.md b/docs/schema/key.md deleted file mode 100644 index cf77dcb..0000000 --- a/docs/schema/key.md +++ /dev/null @@ -1,68 +0,0 @@ - - -# Slot: key - -URI: [linkmltr:key](https://w3id.org/linkml/transformer/key) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [KeyVal](KeyVal.md) | | no | - - - - - - - -## Properties - -* Range: NONE - -* Required: True - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: key -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -key: true -alias: key -owner: KeyVal -domain_of: -- KeyVal -required: true - -``` -
\ No newline at end of file diff --git a/docs/schema/mirror_source.md b/docs/schema/mirror_source.md deleted file mode 100644 index 0303ec4..0000000 --- a/docs/schema/mirror_source.md +++ /dev/null @@ -1,70 +0,0 @@ - - -# Slot: mirror_source - -URI: [linkmltr:mirror_source](https://w3id.org/linkml/transformer/mirror_source) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [EnumDerivation](EnumDerivation.md) | A specification of how to derive the value of a target enum from a source enu... | no | -| [ClassDerivation](ClassDerivation.md) | A specification of how to derive a target class from a source class | no | -| [PrefixDerivation](PrefixDerivation.md) | | no | -| [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slo... | no | -| [PermissibleValueDerivation](PermissibleValueDerivation.md) | A specification of how to derive the value of a PV from a source enum | no | -| [ElementDerivation](ElementDerivation.md) | An abstract grouping for classes that provide a specification of how to deri... | no | - - - - - - - -## Properties - -* Range: [Boolean](Boolean.md) - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: mirror_source -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: mirror_source -owner: ElementDerivation -domain_of: -- ElementDerivation -range: boolean - -``` -
\ No newline at end of file diff --git a/docs/schema/mixins.md b/docs/schema/mixins.md deleted file mode 100644 index c455d1e..0000000 --- a/docs/schema/mixins.md +++ /dev/null @@ -1,75 +0,0 @@ - - -# Slot: mixins - -URI: [linkml:mixins](https://w3id.org/linkml/mixins) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [EnumDerivation](EnumDerivation.md) | A specification of how to derive the value of a target enum from a source enu... | no | -| [ClassDerivation](ClassDerivation.md) | A specification of how to derive a target class from a source class | no | -| [PrefixDerivation](PrefixDerivation.md) | | no | -| [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slo... | no | -| [PermissibleValueDerivation](PermissibleValueDerivation.md) | A specification of how to derive the value of a PV from a source enum | no | -| [ElementDerivation](ElementDerivation.md) | An abstract grouping for classes that provide a specification of how to deri... | no | - - - - - - - -## Properties - -* Range: [ElementDerivation](ElementDerivation.md) - -* Multivalued: True - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: mixins -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -slot_uri: linkml:mixins -multivalued: true -alias: mixins -owner: ElementDerivation -domain_of: -- ElementDerivation -range: ElementDerivation -inlined: false - -``` -
\ No newline at end of file diff --git a/docs/schema/name.md b/docs/schema/name.md deleted file mode 100644 index 450b8df..0000000 --- a/docs/schema/name.md +++ /dev/null @@ -1,62 +0,0 @@ - - -# Slot: name - -URI: [linkmltr:name](https://w3id.org/linkml/transformer/name) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [EnumDerivation](EnumDerivation.md) | A specification of how to derive the value of a target enum from a source enu... | no | -| [ClassDerivation](ClassDerivation.md) | A specification of how to derive a target class from a source class | no | -| [PrefixDerivation](PrefixDerivation.md) | | no | -| [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slo... | no | -| [PermissibleValueDerivation](PermissibleValueDerivation.md) | A specification of how to derive the value of a PV from a source enum | no | -| [ElementDerivation](ElementDerivation.md) | An abstract grouping for classes that provide a specification of how to deri... | no | - - - - - - - -## Properties - -* Range: NONE - - - - - -## Identifier and Mapping Information - - - - - - - - -## LinkML Source - -
-```yaml -name: name -alias: name -domain_of: -- ElementDerivation -- SlotDerivation -- EnumDerivation -- PermissibleValueDerivation - -``` -
\ No newline at end of file diff --git a/docs/schema/over_slots.md b/docs/schema/over_slots.md deleted file mode 100644 index cbbdc33..0000000 --- a/docs/schema/over_slots.md +++ /dev/null @@ -1,68 +0,0 @@ - - -# Slot: over_slots - -URI: [linkmltr:over_slots](https://w3id.org/linkml/transformer/over_slots) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [StringificationConfiguration](StringificationConfiguration.md) | | no | - - - - - - - -## Properties - -* Range: [String](String.md) - -* Multivalued: True - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: over_slots -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -multivalued: true -alias: over_slots -owner: StringificationConfiguration -domain_of: -- StringificationConfiguration -range: string - -``` -
\ No newline at end of file diff --git a/docs/schema/overrides.md b/docs/schema/overrides.md deleted file mode 100644 index 5eb2c42..0000000 --- a/docs/schema/overrides.md +++ /dev/null @@ -1,76 +0,0 @@ - - -# Slot: overrides - - -_overrides source schema slots_ - - - -URI: [linkmltr:overrides](https://w3id.org/linkml/transformer/overrides) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [EnumDerivation](EnumDerivation.md) | A specification of how to derive the value of a target enum from a source enu... | no | -| [ClassDerivation](ClassDerivation.md) | A specification of how to derive a target class from a source class | no | -| [PrefixDerivation](PrefixDerivation.md) | | no | -| [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slo... | no | -| [PermissibleValueDerivation](PermissibleValueDerivation.md) | A specification of how to derive the value of a PV from a source enum | no | -| [ElementDerivation](ElementDerivation.md) | An abstract grouping for classes that provide a specification of how to deri... | no | - - - - - - - -## Properties - -* Range: [Any](Any.md) - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: overrides -description: overrides source schema slots -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: overrides -owner: ElementDerivation -domain_of: -- ElementDerivation -range: Any - -``` -
\ No newline at end of file diff --git a/docs/schema/overview.md b/docs/schema/overview.md deleted file mode 100644 index 9f5ae88..0000000 --- a/docs/schema/overview.md +++ /dev/null @@ -1,1002 +0,0 @@ -# Mapping Between LinkML Schemas - -# Draft -2022-06-24 - -# Problem: map data from one schema to another - -* Problem: Map d1 → d2 - * Assumption d1 and d2 conform to two separate schemas\, s1→ s2 -* Sub\-problems: - * Ingest/Import: my data warehouse conforms to s2 \(e\.g\. Monarch ingest\) - * Export: make my data ingest friendly - * Migrations: s1 and s2 are different versions of the same schema -* Not in scope: in\-schema syntactic or structural transforms - * JSON to YAML\, JSON to TSV\, JSON to SQL\, JSON to RDF\, ORM\, … - * In LinkML this is already largely solved -* The actual problem space is highly varied - * S1 and S2 may be trivially isomorphic - * S1 and S2 may differ in complex or nuanced ways - -# There are many existing approaches - -* Generic frameworks\, driven by declarative specification in Domain Specific Language \(DSL\) -* JSON\-based - * Google whistle - * _[jsonpath\-lift](https://www.npmjs.com/package/jsonpath-lifter)_ -* XSLT -* Semweb - * YARRML\, R2RML -* Many many more… -* Bespoke transforms: non\-declarative -* Implement in python/awk/etc\. -* Hybrid: bespoke with some declarative mappings in ad\-hoc format -* E\.g\. NMDC ingest framework - -# Traps with declarative mapping - -* Declarative is great\, until it’s not -* Anti\-patterns: - * Insufficient expressivity to carry out real world tasks - * Bolting on features to mapping DSL until it’s a fully\-featured Turing\-complete language - * Optimization/scalability at mercy of framework - * Messy layering between DSL and host language - * It can be useful to leverage host language features \(e\.g arbitrary python function\) - * But this can get confusing: - * NFNF: Neither fish nor fowl - * Limits optimizations \(forces iterative host language calls\) - -# YARRRML - -![](img/Mapping%20Between%20LinkML%20Schemas0.png) - - _[https://rml\.io/yarrrml/](https://rml.io/yarrrml/)_ - -# YARRRML notes - -* Has a playground\, which is great -* Mixes two concerns: - * 1\. Isomorphic structural mapping between JSON/TSVs and RDF \(already covered by JSON\-LD\) - * 2\. Mapping - * This isn’t necessarily bad \- it’s quite practical\, but a little unsatisfying IMO - -# jsonpath-lifter - -![](img/Mapping%20Between%20LinkML%20Schemas1.png) - -![](img/Mapping%20Between%20LinkML%20Schemas2.png) - -![](img/Mapping%20Between%20LinkML%20Schemas3.png) - -![](img/Mapping%20Between%20LinkML%20Schemas4.png) - -![](img/Mapping%20Between%20LinkML%20Schemas5.png) - -![](img/Mapping%20Between%20LinkML%20Schemas6.png) - -![](img/Mapping%20Between%20LinkML%20Schemas7.png) - -Was proposed for CCDH CRDC\-node mappings - -Doesn’t seem widely used - -Is there a big advantage over simply writing javascript functions? - -# Koza (previously: bioweave) - -![](img/Mapping%20Between%20LinkML%20Schemas8.png) - -![](img/Mapping%20Between%20LinkML%20Schemas9.png) - -# ETL frameworks - -* There are many many ETL frameworks - * E\.g\. WebKarma -* Inherently mixing of concerns - * Here we are concerned with the “T” part -* Do existing frameworks separate out the T as a modular composable component? - * I’m not sure - -# Do we need Yet Another Mapping Framework? - -* LinkML philosophy: -* Embrace\, extend\, _parasitize_ -* Develop lightweight ways to map - * Map mappings to existing mapping frameworks - * This actually makes sense even if it sounds kind of meta… - -# Level 0 Mapping: Isomorphic, same URIs - -classes: - -Person: - -class\_uri: __sdo:Person__ - -attributes: - -family\_name: - -slot\_uri: __sdo:familyName__ - -address: - -slot\_uri: __sdo:address__ - -classes: - -Agent: - -class\_uri: __sdo:Person__ - -attributes: - -surname: - -slot\_uri: __sdo:familyName__ - -home\_address: - -slot\_uri: __sdo:address__ - -family\_name: Wu - -address: 1 my street\, Oakville - -surname: Wu - -home\_address: 1 my street\, Oakville - -# Level 0: handled by standard linkml convert to/from RDF - -classes: - -Person: - -class\_uri: __sdo:Person__ - -attributes: - -family\_name: - -slot\_uri: __sdo:familyName__ - -address: - -slot\_uri: __sdo:address__ - -classes: - -Agent: - -class\_uri: __sdo:Person__ - -attributes: - -surname: - -slot\_uri: __sdo:familyName__ - -home\_address: - -slot\_uri: __sdo:address__ - -_data2 \(yaml/json\)_ - -_d_ _ata1 \(yaml/json\)_ - -family\_name: Wu - -address: 1 my street\, Oakville - -surname: Wu - -home\_address: 1 my street\, Oakville - -_d_ _ata1\.ttl == data2\.ttl_ - -\[sdo:familyName “Wu” ; - -sdo:address “1 my street\, Oakville” - -\] - -# Level 0: Enums TODO: add example here. Basically this works the same way - -# Level 0: HOWTO - -Compose two commands: - -linkml\-convert \-s schema1\.yaml data1\.yaml \-o data1\.ttl - -linkml\-convert \-s schema2\.yaml data1\.ttl \-o data2\.yaml - -That’s it\! - -TODO: - -Write a wrapper \(linkml\-map\-data?\) that does this in one command - -# Level 0: other considerations - -* Going via RDF in theory eliminates inlining differences - * E\.g\. s1 inlines address objects\, s2 uses references \(inlined: false\) and includes a separate index slot for addresses -* Current status: - * Currently when going from s1 to s2\, no index slots are generated - * This could be done as part of the general rdflib framework - -# Lessons learned so far: annotate your schema with URIs! - -* Annotating schemas with URIs is _optional_ with LinkML - * But your future self and data users will thank you for careful schema annotation\! -* Hints: - * Schema\-automator can provide suggestions for your element and enum URIs - * Sometimes plain semweb URIs \(e\.g\. schema\.org\) can be easier for interoperation than overly granular OBO ones - * E\.g modeling Personhood as a _role_ vs straightforward schema:Person - -# Level 1 Mapping: Isomorphic, different URIs - -name: example\-semweb\-schema - -classes: - -Person: - -class\_uri: __sdo:Person__ - -attributes: - -family\_name: - -slot\_uri: __sdo:familyName__ - -address: - -slot\_uri: __sdo:address__ - -name: example\-OBO\-schema - -classes: - -Person: - -class\_uri: __NCBITaxon:9606__ \#\# Homo sapiens - -attributes: - -surname: - -slot\_uri: __IAO:0000590__ \#\# written name - -home\_address: - -slot\_uri: __IAO:0000422__ \#\# postal address - -family\_name: Wu - -address: 1 my street\, Oakville - -surname: Wu - -home\_address: 1 my street\, Oakville - -# Level 1 Mapping: mediated by URI mapping - -name: example\-semweb\-schema - -classes: - -Person: - -class\_uri: __sdo:Person__ - -attributes: - -family\_name: - -slot\_uri: __sdo:familyName__ - -address: - -slot\_uri: __sdo:address__ - -name: example\-OBO\-schema - -classes: - -Person: - -class\_uri: __NCBITaxon:9606__ \#\# Homo sapiens - -attributes: - -surname: - -slot\_uri: __IAO:0000590__ \#\# written name - -home\_address: - -slot\_uri: __IAO:0000422__ \#\# postal address - -| subject_id | object_id | -| :-: | :-: | -| sdo:Person | NCBITaxon:9606 | -| sdo:familyName | IAO:nnnn | -| sdo:address | IAO:0000422 | - -family\_name: Wu - -address: 1 my street\, Oakville - -surname: Wu - -home\_address: 1 my street\, Oakville - -\[sdo:familyName “Wu” - -sdo:address “1 my street\, Oakville” - -\] - -\[sdo:familyName “Wu” - -sdo:address “1 my street\, Oakville” - -\] - -# Level 1: HOWTO - -* Compose three commands: -* linkml\-convert \-s schema1\.yaml data1\.yaml \-o data1\.ttl -* sssom\-map\-iris \-i data1\.ttl \-m schema1\-to\-schema2\.sssom\.tsv \-o data2\.ttl -* linkml\-convert \-s schema2\.yaml data2\.ttl \-o data2\.yaml -* That’s it\! -* TODO: -* sssom\-map\-iris does not yet exist \(?\)\, but should be trivial -* Fold into wrapper CLI tool -* Nuances: -* Schemas have nuanced differences: not everything with be skos:exact -* We can distinguish 3 flavors of level 1 mapping: - * Precise\, bidirectional: follow exact only - * Valid\, unidirectional: follow exact \+ broad - * Loose: any mapping - -# Level 1 variant: mappings in schema - -name: example\-semweb\-schema - -classes: - -Person: - -class\_uri: __sdo:Person__ - -__ __ exact\_mappings: \[“NCBITaxon:9606”\] - -attributes: - -family\_name: - -slot\_uri: __sdo:familyName__ - -__ exact\_mappings: \[“IAO:nnnn”\]__ - -address: - -slot\_uri: __sdo:address__ - -__ exact\_mappings: \[“IAO:0000422”\]__ - -name: example\-OBO\-schema - -classes: - -Person: - -class\_uri: __NCBITaxon:9606__ \#\# Homo sapiens - -attributes: - -surname: - -slot\_uri: __IAO:0000590__ \#\# written name - -home\_address: - -slot\_uri: __IAO:0000422__ \#\# postal address - -family\_name: Wu - -address: 1 my street\, Oakville - -surname: Wu - -home\_address: 1 my street\, Oakville - -\[sdo:familyName “Wu” - -sdo:address “1 my street\, Oakville” - -\] - -\[sdo:familyName “Wu” - -sdo:address “1 my street\, Oakville” - -\] - -# Advantages of RDF as an intermediate - -* Use of IRIs -* Separation of concerns - * Structural differences \(e\.g\. inlining\) are already handled by linkml convert - * Allows us to focus on semantic mappings - -# Lessons learned so far: think about mappings - -![](img/Mapping%20Between%20LinkML%20Schemas10.png) - -![](img/Mapping%20Between%20LinkML%20Schemas11.png) - -_[https://linkml\.io/linkml/faq/modeling\.html\#when\-is\-it\-important\-to\-have\-mappings](https://linkml.io/linkml/faq/modeling.html#when-is-it-important-to-have-mappings)_ - -_[https://github\.com/alliance\-genome/agr\_curation\_schema/blob/main/model/schema/agent\.yaml](https://github.com/alliance-genome/agr_curation_schema/blob/main/model/schema/agent.yaml)_ - -# More complex mappings: level 2 and above - -* TODO: define levels 2 and above -* Examples of kinds of features: - * merging/splitting fields; e\.g\. full\_name = first \+ “ “ \+ last - * Unit conversion or baked\-in units to explicit units - * Normalization/denormalization \(aka flattening\) - * Complex logic - * If conditions A\, B\, C and not D are met then copy field F from X to Y - -# LinkML Rule and Inference Framework - -* Current use case is __intra\-schema__ inference - * Easy to invoke on command line - * Needs more docs\! -* Could form basis of __inter\-schema__ DSL -* Examples - * Schemas differ in units - * Schemas differ in categorical vs quantitative - -![](img/Mapping%20Between%20LinkML%20Schemas12.png) - -Current use case is __intra\-schema__ inference - -Could form basis of __inter\-schema__ DSL - -![](img/Mapping%20Between%20LinkML%20Schemas13.png) - -# Datalog - -Datalog could serve as the powerful basis of an expressive declarative transformation language - -![](img/Mapping%20Between%20LinkML%20Schemas14.png) - -_[https://linkml\.io/linkml\-datalog](https://linkml.io/linkml-datalog)_ - -# Approach for level 2+ - -* Do we even want a generic mapping framework in LinkML here? -* This is a good “ __parasitization__ hook” - * Do complex stuff using an existing framework - * TBD: derive or semi\-derive mapping specification? -* This is also a code bespoke procedural code hook - * Do the generic stuff with linkml\-convert and isomorphic IRI mapping - * Do more complex stuff in code - -# General approach for level 2+; same to same - -name: example\-semweb\-schema - -classes: - -Person: - -class\_uri: __sdo:Person__ - -attributes: - -family\_name: - -slot\_uri: __sdo:familyName__ - -address: - -slot\_uri: __sdo:address__ - -name: example\-OBO\-schema - -classes: - -Person: - -class\_uri: __NCBITaxon:9606__ \#\# Homo sapiens - -attributes: - -surname: - -slot\_uri: __IAO:0000590__ \#\# written name - -home\_address: - -slot\_uri: __IAO:0000422__ \#\# postal address - -family\_name: Wu - -address: 1 my street\, Oakville - -surname: Wu - -home\_address: 1 my street\, Oakville - -JSON _OR_ XML _OR_ YAML _OR_ RDF _OR_ SQL - -__JSON __ _OR_ __ XML __ _OR_ __ YAML __ _OR_ __ RDF __ _OR_ __ SQL__ - -__\(matches the one on the left\)__ - -__Existing __ __mapping__ __ framework \(X to X\)__ - -# Example of same-to-same: jsonpath-lifter - -name: example\-semweb\-schema - -classes: - -Person: - -class\_uri: __sdo:Person__ - -attributes: - -family\_name: - -slot\_uri: __sdo:familyName__ - -address: - -slot\_uri: __sdo:address__ - -name: example\-OBO\-schema - -classes: - -Person: - -class\_uri: __NCBITaxon:9606__ \#\# Homo sapiens - -attributes: - -surname: - -slot\_uri: __IAO:0000590__ \#\# written name - -home\_address: - -slot\_uri: __IAO:0000422__ \#\# postal address - -family\_name: Wu - -address: 1 my street\, Oakville - -surname: Wu - -home\_address: 1 my street\, Oakville - -__Jsonpath\-lifter \(JSON to JSON\)__ - -# Example of same-to-same: awk - -# Example of same-to-same: SQL - -INSERT INTO Agent AS SELECT - -Person\.last\_name AS Agent\.surname\, - -CONCAT\(Person\.full\_name\, “ “\, Person\.first\) AS Agent\.full\_name\, - -… - -CONSTRUCT \{ - -\[ - -a schema:Person ; - -my:fullName STRCAT\(\.\.\.\) - -\] - -\} - -WHERE \{ - -?person a schema:Person ; - -schema:firstName ; - -schema:lastName ; - -… - -\} - -__SPARQL CONSTRUCT__ - -__RDF__ __ Engine or Triplestore__ - -# Example of same-to-same: Python (LinkML objects) - -def convert\(p: Person\) \-> Agent: - -return Agent\(p\.id\, - -full\_name=f”\{\.\.\} \{\.\.\}”\, - -… - -__Conversion script__ - -# General approach for level 2+; heteromorphic - -name: example\-semweb\-schema - -classes: - -Person: - -class\_uri: __sdo:Person__ - -attributes: - -family\_name: - -slot\_uri: __sdo:familyName__ - -address: - -slot\_uri: __sdo:address__ - -name: example\-OBO\-schema - -classes: - -Person: - -class\_uri: __NCBITaxon:9606__ \#\# Homo sapiens - -attributes: - -surname: - -slot\_uri: __IAO:0000590__ \#\# written name - -home\_address: - -slot\_uri: __IAO:0000422__ \#\# postal address - -family\_name: Wu - -address: 1 my street\, Oakville - -surname: Wu - -home\_address: 1 my street\, Oakville - -_L_ _inkml\-convert_ - -_OPTIONAL_ - -_L_ _inkml\-convert_ - -_OPTIONAL_ - -JSON _OR_ XML _OR_ YAML _OR_ RDF _OR_ SQL - -__JSON __ _OR_ __ XML __ _OR_ __ YAML __ _OR_ __ RDF __ _OR_ __ SQL__ - -__\(__ _different_ __ from the one on the left\)__ - -__Existing mapping framework \(X to Y\)__ - -# Example: YARRRML - -name: example\-semweb\-schema - -classes: - -Person: - -class\_uri: __sdo:Person__ - -attributes: - -family\_name: - -slot\_uri: __sdo:familyName__ - -address: - -slot\_uri: __sdo:address__ - -name: example\-OBO\-schema - -classes: - -Person: - -class\_uri: __NCBITaxon:9606__ \#\# Homo sapiens - -attributes: - -surname: - -slot\_uri: __IAO:0000590__ \#\# written name - -home\_address: - -slot\_uri: __IAO:0000422__ \#\# postal address - -![](img/Mapping%20Between%20LinkML%20Schemas15.png) - -family\_name: Wu - -address: 1 my street\, Oakville - -surname: Wu - -home\_address: 1 my street\, Oakville - -__YARRRML \(JSON/YAML to RDF\)__ - -# Example: YARRRML, native mappings - -name: example\-semweb\-schema - -classes: - -Person: - -class\_uri: __sdo:Person__ - -attributes: - -family\_name: - -slot\_uri: __sdo:familyName__ - -address: - -slot\_uri: __sdo:address__ - -name: example\-OBO\-schema - -classes: - -Person: - -class\_uri: __NCBITaxon:9606__ \#\# Homo sapiens - -attributes: - -surname: - -slot\_uri: __IAO:0000590__ \#\# written name - -home\_address: - -slot\_uri: __IAO:0000422__ \#\# postal address - -family\_name: Wu - -address: 1 my street\, Oakville - -surname: Wu - -home\_address: 1 my street\, Oakville - -__mapping\.yarrrml\.yml__ - -# Example: YARRRML, compiled mappings - -name: example\-semweb\-schema - -classes: - -Person: - -class\_uri: __sdo:Person__ - -attributes: - -family\_name: - -slot\_uri: __sdo:familyName__ - -address: - -slot\_uri: __sdo:address__ - -Mappings __:__ - -__ … \< TO BE DEFINED LINKML MAPPING SPEC >__ - -name: example\-OBO\-schema - -classes: - -Person: - -class\_uri: __NCBITaxon:9606__ \#\# Homo sapiens - -attributes: - -surname: - -slot\_uri: __IAO:0000590__ \#\# written name - -home\_address: - -slot\_uri: __IAO:0000422__ \#\# postal address - -family\_name: Wu - -address: 1 my street\, Oakville - -surname: Wu - -home\_address: 1 my street\, Oakville - -__mapping\.yarrrml\.yml__ - -# Hyperparasitism is good - -name: example\-semweb\-schema - -classes: - -Person: - -class\_uri: __sdo:Person__ - -attributes: - -family\_name: - -slot\_uri: __sdo:familyName__ - -address: - -slot\_uri: __sdo:address__ - -Mappings __:__ - -__ … \< TO BE DEFINED LINKML MAPPING SPEC >__ - -name: example\-OBO\-schema - -classes: - -Person: - -class\_uri: __NCBITaxon:9606__ \#\# Homo sapiens - -attributes: - -surname: - -slot\_uri: __IAO:0000590__ \#\# written name - -home\_address: - -slot\_uri: __IAO:0000422__ \#\# postal address - -__mapping\.yarrrml\.yml__ - -family\_name: Wu - -address: 1 my street\, Oakville - -surname: Wu - -home\_address: 1 my street\, Oakville - -# Alternative: Direct translation language - -* Desiderata -* Ability to compile to scalable frameworks - * E\.g\. compile to SQL -* Simple for simple tasks -* Layer on existing expression language - * Provides path to safe subset of host language \(Python\) - * Can be easily implemented in other languages - -![](img/Mapping%20Between%20LinkML%20Schemas16.png) - -![](img/Mapping%20Between%20LinkML%20Schemas17.png) - -# Normalized to Denormalized (modeling SSSOM) - -SQL INSERT \(or CREATE VIEW\) - -![](img/Mapping%20Between%20LinkML%20Schemas18.png) - -SQL FROM Clause - -\(implicit INNER JOIN/WHERE\) - -SQL SELECT … AS clause - -# Relationship to profiles TODO - -Profiles/IGs can be seen as a sub\-case of schema mapping - -# Current progress - -_[https://github\.com/linkml/linkml/issues/533](https://github.com/linkml/linkml/issues/533)_ map to YARRRML - -Vincent Vemonet has started on linkml\->rml - -_[https://github\.com/vemonet/linkml/blob/add\-gen\-rml/linkml/generators/rmlgen\.py](https://github.com/vemonet/linkml/blob/add-gen-rml/linkml/generators/rmlgen.py)_ - -# Relationship to Koza - -# Koza ingests often require multiple files - -![](img/Mapping%20Between%20LinkML%20Schemas19.png) - -![](img/Mapping%20Between%20LinkML%20Schemas20.png) - -# See Also - -Revisiting BioWeave \(Kent Shefchek\, 2020?\) - -_[https://docs\.google\.com/presentation/d/1DYiWXoz3iHM2PvMFD0hRpJ544tnHawg00PBwNuESo44/edit\#slide=id\.gb33d7ddd1b\_0\_93](https://docs.google.com/presentation/d/1DYiWXoz3iHM2PvMFD0hRpJ544tnHawg00PBwNuESo44/edit#slide=id.gb33d7ddd1b_0_93)_ - -# Automating mapping - -* Should we pursue approaches to automate mapping? - * Some of the functionality is already in schema\-automator\. E\.g\. auto\-annotating schema elements using ontologies -* Isomorphic schema mapping discovery analogous to ontology mapping - * Can a boomer type approach help? - * E\.g\. given multiple loose mappings with alternative interpretations\, which ones give coherent results -* Other approaches - * Inductive Logic Programming: transformations as logic programs - * Genetic programming: transformations as lambda functions - * Deep Learning: e\.g\. Language Models for translation -* There is already a rich literature spanning decades here to be parasitized… - -# Summary: just tell me what to do today - -* For isomorphic mappings: - * Stay within LinkML/SSSOM - * No need for custom code\, it all works -* For complex mappings: - * It depends\! - * Do the structural mapping with linkml\-convert - * Implement the complex logic as you see fit\, depending on multiple factors\. Any of the following may be valid - * Koza - * Awk - * SPARQL CONSTRUCTS or SELECTS - * Custom python - * YARRRML - * SQL INSERTs - * XSLT - * Jsonpath\-lifter - * …\. - -# Roadmap - -* 2022: Continue to gather use cases\, experiment -* 2023: If funding permits - * Extend metamodel to include complex mapping - * Implement EITHER - * Parasitizing converters - * Direct mapping framework - * TBD: Is this Koza2? - diff --git a/docs/schema/permissible_value_derivations.md b/docs/schema/permissible_value_derivations.md deleted file mode 100644 index e470ae8..0000000 --- a/docs/schema/permissible_value_derivations.md +++ /dev/null @@ -1,75 +0,0 @@ - - -# Slot: permissible_value_derivations - - -_Instructions on how to derive a set of PVs in the target schema_ - - - -URI: [linkmltr:permissible_value_derivations](https://w3id.org/linkml/transformer/permissible_value_derivations) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [EnumDerivation](EnumDerivation.md) | A specification of how to derive the value of a target enum from a source enu... | no | - - - - - - - -## Properties - -* Range: [PermissibleValueDerivation](PermissibleValueDerivation.md) - -* Multivalued: True - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: permissible_value_derivations -description: Instructions on how to derive a set of PVs in the target schema -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -multivalued: true -alias: permissible_value_derivations -owner: EnumDerivation -domain_of: -- EnumDerivation -range: PermissibleValueDerivation -inlined: true - -``` -
\ No newline at end of file diff --git a/docs/schema/populated_from.md b/docs/schema/populated_from.md deleted file mode 100644 index 9d3aada..0000000 --- a/docs/schema/populated_from.md +++ /dev/null @@ -1,60 +0,0 @@ - - -# Slot: populated_from - -URI: [linkmltr:populated_from](https://w3id.org/linkml/transformer/populated_from) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slo... | no | -| [ClassDerivation](ClassDerivation.md) | A specification of how to derive a target class from a source class | no | -| [EnumDerivation](EnumDerivation.md) | A specification of how to derive the value of a target enum from a source enu... | no | -| [PermissibleValueDerivation](PermissibleValueDerivation.md) | A specification of how to derive the value of a PV from a source enum | no | - - - - - - - -## Properties - -* Range: NONE - - - - - -## Identifier and Mapping Information - - - - - - - - -## LinkML Source - -
-```yaml -name: populated_from -alias: populated_from -domain_of: -- ClassDerivation -- SlotDerivation -- EnumDerivation -- PermissibleValueDerivation - -``` -
\ No newline at end of file diff --git a/docs/schema/prefixes.md b/docs/schema/prefixes.md deleted file mode 100644 index 309676e..0000000 --- a/docs/schema/prefixes.md +++ /dev/null @@ -1,76 +0,0 @@ - - -# Slot: prefixes - - -_maps prefixes to URL expansions_ - - - -URI: [sh:declare](http://www.w3.org/ns/shacl#declare) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [TransformationSpecification](TransformationSpecification.md) | A collection of mappings between source and target classes | no | - - - - - - - -## Properties - -* Range: [KeyVal](KeyVal.md) - -* Multivalued: True - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: prefixes -description: maps prefixes to URL expansions -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -slot_uri: sh:declare -multivalued: true -alias: prefixes -owner: TransformationSpecification -domain_of: -- TransformationSpecification -range: KeyVal -inlined: true - -``` -
\ No newline at end of file diff --git a/docs/schema/range.md b/docs/schema/range.md deleted file mode 100644 index e28aa8e..0000000 --- a/docs/schema/range.md +++ /dev/null @@ -1,66 +0,0 @@ - - -# Slot: range - -URI: [linkml:range](https://w3id.org/linkml/range) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slo... | no | - - - - - - - -## Properties - -* Range: [String](String.md) - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: range -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -slot_uri: linkml:range -alias: range -owner: SlotDerivation -domain_of: -- SlotDerivation -range: string - -``` -
\ No newline at end of file diff --git a/docs/schema/reversed.md b/docs/schema/reversed.md deleted file mode 100644 index b5bc137..0000000 --- a/docs/schema/reversed.md +++ /dev/null @@ -1,65 +0,0 @@ - - -# Slot: reversed - -URI: [linkmltr:reversed](https://w3id.org/linkml/transformer/reversed) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [StringificationConfiguration](StringificationConfiguration.md) | | no | - - - - - - - -## Properties - -* Range: [Boolean](Boolean.md) - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: reversed -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: reversed -owner: StringificationConfiguration -domain_of: -- StringificationConfiguration -range: boolean - -``` -
\ No newline at end of file diff --git a/docs/schema/same_as.md b/docs/schema/same_as.md deleted file mode 100644 index d9c3d08..0000000 --- a/docs/schema/same_as.md +++ /dev/null @@ -1,32 +0,0 @@ -# Slot: same_as -_Name of the class in the source schema_ - - -URI: [https://w3id.org/linkml/transformer/same_as](https://w3id.org/linkml/transformer/same_as) - - - - - - -## Properties - - * Range: [xsd:string](xsd:string) - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - diff --git a/docs/schema/session.md b/docs/schema/session.md deleted file mode 100644 index 332b3f3..0000000 --- a/docs/schema/session.md +++ /dev/null @@ -1,4 +0,0 @@ -# Session - -::: linkml_map.session.Session - diff --git a/docs/schema/slot_derivations.md b/docs/schema/slot_derivations.md deleted file mode 100644 index 81ac4b6..0000000 --- a/docs/schema/slot_derivations.md +++ /dev/null @@ -1,56 +0,0 @@ - - -# Slot: slot_derivations - -URI: [linkmltr:slot_derivations](https://w3id.org/linkml/transformer/slot_derivations) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [ClassDerivation](ClassDerivation.md) | A specification of how to derive a target class from a source class | no | -| [TransformationSpecification](TransformationSpecification.md) | A collection of mappings between source and target classes | no | - - - - - - - -## Properties - -* Range: NONE - - - - - -## Identifier and Mapping Information - - - - - - - - -## LinkML Source - -
-```yaml -name: slot_derivations -alias: slot_derivations -domain_of: -- TransformationSpecification -- ClassDerivation - -``` -
\ No newline at end of file diff --git a/docs/schema/slot_name.md b/docs/schema/slot_name.md deleted file mode 100644 index 4b9b99b..0000000 --- a/docs/schema/slot_name.md +++ /dev/null @@ -1,64 +0,0 @@ - - -# Slot: slot_name - -URI: [linkmltr:slot_name](https://w3id.org/linkml/transformer/slot_name) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [Inverse](Inverse.md) | Used for back references in mapping to relational model | no | - - - - - - - -## Properties - -* Range: NONE - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: slot_name -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: slot_name -owner: Inverse -domain_of: -- Inverse - -``` -
\ No newline at end of file diff --git a/docs/schema/source_magnitude_slot.md b/docs/schema/source_magnitude_slot.md deleted file mode 100644 index 14b60c0..0000000 --- a/docs/schema/source_magnitude_slot.md +++ /dev/null @@ -1,64 +0,0 @@ - - -# Slot: source_magnitude_slot - -URI: [linkmltr:source_magnitude_slot](https://w3id.org/linkml/transformer/source_magnitude_slot) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [UnitConversionConfiguration](UnitConversionConfiguration.md) | | no | - - - - - - - -## Properties - -* Range: NONE - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: source_magnitude_slot -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: source_magnitude_slot -owner: UnitConversionConfiguration -domain_of: -- UnitConversionConfiguration - -``` -
\ No newline at end of file diff --git a/docs/schema/source_schema.md b/docs/schema/source_schema.md deleted file mode 100644 index 0c68a78..0000000 --- a/docs/schema/source_schema.md +++ /dev/null @@ -1,70 +0,0 @@ - - -# Slot: source_schema - - -_name of the schema that describes the source (input) objects_ - - - -URI: [linkmltr:source_schema](https://w3id.org/linkml/transformer/source_schema) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [TransformationSpecification](TransformationSpecification.md) | A collection of mappings between source and target classes | no | - - - - - - - -## Properties - -* Range: NONE - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: source_schema -description: name of the schema that describes the source (input) objects -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: source_schema -owner: TransformationSpecification -domain_of: -- TransformationSpecification - -``` -
\ No newline at end of file diff --git a/docs/schema/source_unit.md b/docs/schema/source_unit.md deleted file mode 100644 index 7e54fdc..0000000 --- a/docs/schema/source_unit.md +++ /dev/null @@ -1,64 +0,0 @@ - - -# Slot: source_unit - -URI: [linkmltr:source_unit](https://w3id.org/linkml/transformer/source_unit) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [UnitConversionConfiguration](UnitConversionConfiguration.md) | | no | - - - - - - - -## Properties - -* Range: NONE - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: source_unit -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: source_unit -owner: UnitConversionConfiguration -domain_of: -- UnitConversionConfiguration - -``` -
\ No newline at end of file diff --git a/docs/schema/source_unit_scheme.md b/docs/schema/source_unit_scheme.md deleted file mode 100644 index 01f2ab7..0000000 --- a/docs/schema/source_unit_scheme.md +++ /dev/null @@ -1,74 +0,0 @@ - - -# Slot: source_unit_scheme - -URI: [linkmltr:source_unit_scheme](https://w3id.org/linkml/transformer/source_unit_scheme) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [UnitConversionConfiguration](UnitConversionConfiguration.md) | | no | - - - - - - - -## Properties - -* Range: [String](String.md) - - - - - - -## Examples - -| Value | -| --- | -| ucum | - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: source_unit_scheme -examples: -- value: ucum -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: source_unit_scheme -owner: UnitConversionConfiguration -domain_of: -- UnitConversionConfiguration -range: string - -``` -
\ No newline at end of file diff --git a/docs/schema/source_unit_slot.md b/docs/schema/source_unit_slot.md deleted file mode 100644 index 815dfff..0000000 --- a/docs/schema/source_unit_slot.md +++ /dev/null @@ -1,64 +0,0 @@ - - -# Slot: source_unit_slot - -URI: [linkmltr:source_unit_slot](https://w3id.org/linkml/transformer/source_unit_slot) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [UnitConversionConfiguration](UnitConversionConfiguration.md) | | no | - - - - - - - -## Properties - -* Range: NONE - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: source_unit_slot -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: source_unit_slot -owner: UnitConversionConfiguration -domain_of: -- UnitConversionConfiguration - -``` -
\ No newline at end of file diff --git a/docs/schema/sources.md b/docs/schema/sources.md deleted file mode 100644 index 9e8e7c8..0000000 --- a/docs/schema/sources.md +++ /dev/null @@ -1,60 +0,0 @@ - - -# Slot: sources - -URI: [linkmltr:sources](https://w3id.org/linkml/transformer/sources) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slo... | no | -| [ClassDerivation](ClassDerivation.md) | A specification of how to derive a target class from a source class | no | -| [EnumDerivation](EnumDerivation.md) | A specification of how to derive the value of a target enum from a source enu... | no | -| [PermissibleValueDerivation](PermissibleValueDerivation.md) | A specification of how to derive the value of a PV from a source enum | no | - - - - - - - -## Properties - -* Range: NONE - - - - - -## Identifier and Mapping Information - - - - - - - - -## LinkML Source - -
-```yaml -name: sources -alias: sources -domain_of: -- ClassDerivation -- SlotDerivation -- EnumDerivation -- PermissibleValueDerivation - -``` -
\ No newline at end of file diff --git a/docs/schema/stringification.md b/docs/schema/stringification.md deleted file mode 100644 index 2f9bab9..0000000 --- a/docs/schema/stringification.md +++ /dev/null @@ -1,65 +0,0 @@ - - -# Slot: stringification - -URI: [linkmltr:stringification](https://w3id.org/linkml/transformer/stringification) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slo... | no | - - - - - - - -## Properties - -* Range: [StringificationConfiguration](StringificationConfiguration.md) - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: stringification -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: stringification -owner: SlotDerivation -domain_of: -- SlotDerivation -range: StringificationConfiguration - -``` -
\ No newline at end of file diff --git a/docs/schema/syntax.md b/docs/schema/syntax.md deleted file mode 100644 index 263bdb1..0000000 --- a/docs/schema/syntax.md +++ /dev/null @@ -1,76 +0,0 @@ - - -# Slot: syntax - -URI: [linkmltr:syntax](https://w3id.org/linkml/transformer/syntax) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [StringificationConfiguration](StringificationConfiguration.md) | | no | - - - - - - - -## Properties - -* Range: [SerializationSyntaxType](SerializationSyntaxType.md) - - - - - - -## Examples - -| Value | -| --- | -| json | -| yaml | - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: syntax -examples: -- value: json -- value: yaml -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: syntax -owner: StringificationConfiguration -domain_of: -- StringificationConfiguration -range: SerializationSyntaxType - -``` -
\ No newline at end of file diff --git a/docs/schema/target_magnitude_slot.md b/docs/schema/target_magnitude_slot.md deleted file mode 100644 index 1aa58b6..0000000 --- a/docs/schema/target_magnitude_slot.md +++ /dev/null @@ -1,64 +0,0 @@ - - -# Slot: target_magnitude_slot - -URI: [linkmltr:target_magnitude_slot](https://w3id.org/linkml/transformer/target_magnitude_slot) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [UnitConversionConfiguration](UnitConversionConfiguration.md) | | no | - - - - - - - -## Properties - -* Range: NONE - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: target_magnitude_slot -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: target_magnitude_slot -owner: UnitConversionConfiguration -domain_of: -- UnitConversionConfiguration - -``` -
\ No newline at end of file diff --git a/docs/schema/target_schema.md b/docs/schema/target_schema.md deleted file mode 100644 index ab06533..0000000 --- a/docs/schema/target_schema.md +++ /dev/null @@ -1,70 +0,0 @@ - - -# Slot: target_schema - - -_name of the schema that describes the target (output) objects_ - - - -URI: [linkmltr:target_schema](https://w3id.org/linkml/transformer/target_schema) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [TransformationSpecification](TransformationSpecification.md) | A collection of mappings between source and target classes | no | - - - - - - - -## Properties - -* Range: NONE - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: target_schema -description: name of the schema that describes the target (output) objects -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: target_schema -owner: TransformationSpecification -domain_of: -- TransformationSpecification - -``` -
\ No newline at end of file diff --git a/docs/schema/target_unit.md b/docs/schema/target_unit.md deleted file mode 100644 index 631ab38..0000000 --- a/docs/schema/target_unit.md +++ /dev/null @@ -1,64 +0,0 @@ - - -# Slot: target_unit - -URI: [linkmltr:target_unit](https://w3id.org/linkml/transformer/target_unit) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [UnitConversionConfiguration](UnitConversionConfiguration.md) | | no | - - - - - - - -## Properties - -* Range: NONE - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: target_unit -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: target_unit -owner: UnitConversionConfiguration -domain_of: -- UnitConversionConfiguration - -``` -
\ No newline at end of file diff --git a/docs/schema/target_unit_scheme.md b/docs/schema/target_unit_scheme.md deleted file mode 100644 index 5447d31..0000000 --- a/docs/schema/target_unit_scheme.md +++ /dev/null @@ -1,74 +0,0 @@ - - -# Slot: target_unit_scheme - -URI: [linkmltr:target_unit_scheme](https://w3id.org/linkml/transformer/target_unit_scheme) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [UnitConversionConfiguration](UnitConversionConfiguration.md) | | no | - - - - - - - -## Properties - -* Range: [String](String.md) - - - - - - -## Examples - -| Value | -| --- | -| ucum | - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: target_unit_scheme -examples: -- value: ucum -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: target_unit_scheme -owner: UnitConversionConfiguration -domain_of: -- UnitConversionConfiguration -range: string - -``` -
\ No newline at end of file diff --git a/docs/schema/target_unit_slot.md b/docs/schema/target_unit_slot.md deleted file mode 100644 index 16a5030..0000000 --- a/docs/schema/target_unit_slot.md +++ /dev/null @@ -1,64 +0,0 @@ - - -# Slot: target_unit_slot - -URI: [linkmltr:target_unit_slot](https://w3id.org/linkml/transformer/target_unit_slot) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [UnitConversionConfiguration](UnitConversionConfiguration.md) | | no | - - - - - - - -## Properties - -* Range: NONE - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: target_unit_slot -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: target_unit_slot -owner: UnitConversionConfiguration -domain_of: -- UnitConversionConfiguration - -``` -
\ No newline at end of file diff --git a/docs/schema/title.md b/docs/schema/title.md deleted file mode 100644 index 3543db3..0000000 --- a/docs/schema/title.md +++ /dev/null @@ -1,71 +0,0 @@ - - -# Slot: title - - -_human readable title for this transformation specification_ - - - -URI: [dcterms:title](http://purl.org/dc/terms/title) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [TransformationSpecification](TransformationSpecification.md) | A collection of mappings between source and target classes | no | - - - - - - - -## Properties - -* Range: NONE - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: title -description: human readable title for this transformation specification -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -slot_uri: dcterms:title -alias: title -owner: TransformationSpecification -domain_of: -- TransformationSpecification - -``` -
\ No newline at end of file diff --git a/docs/schema/transformer.md b/docs/schema/transformer.md deleted file mode 100644 index 7612565..0000000 --- a/docs/schema/transformer.md +++ /dev/null @@ -1,10 +0,0 @@ -# Transformer Package - -## Transformer (Base Class) - -::: linkml_map.transformer.transformer.Transformer - -## ObjectTransformer - -::: linkml_map.transformer.object_transformer.ObjectTransformer - diff --git a/docs/schema/type_designator.md b/docs/schema/type_designator.md deleted file mode 100644 index 5794c49..0000000 --- a/docs/schema/type_designator.md +++ /dev/null @@ -1,65 +0,0 @@ - - -# Slot: type_designator - -URI: [linkmltr:type_designator](https://w3id.org/linkml/transformer/type_designator) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slo... | no | - - - - - - - -## Properties - -* Range: [Boolean](Boolean.md) - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: type_designator -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: type_designator -owner: SlotDerivation -domain_of: -- SlotDerivation -range: boolean - -``` -
\ No newline at end of file diff --git a/docs/schema/types.md b/docs/schema/types.md deleted file mode 100644 index 557e79b..0000000 --- a/docs/schema/types.md +++ /dev/null @@ -1,6 +0,0 @@ -# types - -Shared type definitions for the core LinkML mode and metamodel - -URI: https://w3id.org/linkml/types - diff --git a/docs/schema/unit.md b/docs/schema/unit.md deleted file mode 100644 index 0afad10..0000000 --- a/docs/schema/unit.md +++ /dev/null @@ -1,62 +0,0 @@ -# Slot: unit - -URI: [linkmltr:unit](https://w3id.org/linkml/transformer/unit) - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -[SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slo... | no | - - - - - - - -## Properties - -* Range: [String](String.md) - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: unit -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: unit -owner: SlotDerivation -domain_of: -- SlotDerivation -range: string - -``` -
\ No newline at end of file diff --git a/docs/schema/unit_conversion.md b/docs/schema/unit_conversion.md deleted file mode 100644 index 74dc286..0000000 --- a/docs/schema/unit_conversion.md +++ /dev/null @@ -1,65 +0,0 @@ - - -# Slot: unit_conversion - -URI: [linkmltr:unit_conversion](https://w3id.org/linkml/transformer/unit_conversion) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slo... | no | - - - - - - - -## Properties - -* Range: [UnitConversionConfiguration](UnitConversionConfiguration.md) - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: unit_conversion -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: unit_conversion -owner: SlotDerivation -domain_of: -- SlotDerivation -range: UnitConversionConfiguration - -``` -
\ No newline at end of file diff --git a/docs/schema/value.md b/docs/schema/value.md deleted file mode 100644 index b281cf4..0000000 --- a/docs/schema/value.md +++ /dev/null @@ -1,65 +0,0 @@ - - -# Slot: value - -URI: [linkmltr:value](https://w3id.org/linkml/transformer/value) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [KeyVal](KeyVal.md) | | no | - - - - - - - -## Properties - -* Range: [Any](Any.md) - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: value -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -alias: value -owner: KeyVal -domain_of: -- KeyVal -range: Any - -``` -
\ No newline at end of file diff --git a/docs/schema/value_mappings.md b/docs/schema/value_mappings.md deleted file mode 100644 index 3501dc4..0000000 --- a/docs/schema/value_mappings.md +++ /dev/null @@ -1,80 +0,0 @@ - - -# Slot: value_mappings - - -_A mapping table that is applied directly to mappings, in order of precedence_ - - - -URI: [linkmltr:value_mappings](https://w3id.org/linkml/transformer/value_mappings) - - - - - - - - - -## Applicable Classes - -| Name | Description | Modifies Slot | -| --- | --- | --- | -| [EnumDerivation](EnumDerivation.md) | A specification of how to derive the value of a target enum from a source enu... | no | -| [ClassDerivation](ClassDerivation.md) | A specification of how to derive a target class from a source class | no | -| [PrefixDerivation](PrefixDerivation.md) | | no | -| [SlotDerivation](SlotDerivation.md) | A specification of how to derive the value of a target slot from a source slo... | no | -| [PermissibleValueDerivation](PermissibleValueDerivation.md) | A specification of how to derive the value of a PV from a source enum | no | -| [ElementDerivation](ElementDerivation.md) | An abstract grouping for classes that provide a specification of how to deri... | no | - - - - - - - -## Properties - -* Range: [KeyVal](KeyVal.md) - -* Multivalued: True - - - - - -## Identifier and Mapping Information - - - - - - - -### Schema Source - - -* from schema: https://w3id.org/linkml/transformer - - - - -## LinkML Source - -
-```yaml -name: value_mappings -description: A mapping table that is applied directly to mappings, in order of precedence -from_schema: https://w3id.org/linkml/transformer -rank: 1000 -multivalued: true -alias: value_mappings -owner: ElementDerivation -domain_of: -- ElementDerivation -range: KeyVal -inlined: true - -``` -
\ No newline at end of file diff --git a/element_name/index.html b/element_name/index.html new file mode 100644 index 0000000..0b4627e --- /dev/null +++ b/element_name/index.html @@ -0,0 +1,130 @@ + + + + + + + + + + + + + + Slot: element_name - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: element_name

+

URI: linkmltr:element_name

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
CopyDirectiveInstructs a Schema Mapper in how to map to a target schemano
+

Properties

+
    +
  • +

    Range: NONE

    +
  • +
  • +

    Required: True

    +
  • +
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/linkml/transformer
  • +
+

LinkML Source

+
+ +
name: element_name
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+key: true
+alias: element_name
+owner: CopyDirective
+domain_of:
+- CopyDirective
+required: true
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/enum_derivations/index.html b/enum_derivations/index.html new file mode 100644 index 0000000..313cd2e --- /dev/null +++ b/enum_derivations/index.html @@ -0,0 +1,133 @@ + + + + + + + + + + + + + + Slot: enum_derivations - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: enum_derivations

+

Instructions on how to derive a set of enums in the target schema

+

URI: linkmltr:enum_derivations

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
TransformationSpecificationA collection of mappings between source and target classesno
+

Properties

+ +

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/linkml/transformer
  • +
+

LinkML Source

+
+ +
name: enum_derivations
+description: Instructions on how to derive a set of enums in the target schema
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+multivalued: true
+alias: enum_derivations
+owner: TransformationSpecification
+domain_of:
+- TransformationSpecification
+range: EnumDerivation
+inlined: true
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/examples/Tutorial/index.html b/examples/Tutorial/index.html new file mode 100644 index 0000000..cddbef7 --- /dev/null +++ b/examples/Tutorial/index.html @@ -0,0 +1,1123 @@ + + + + + + + + + + + + + + Tutorial - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + +
+
+
+

LinkML-Map tutorial

+

This tutorial walks through basic programmatic use of the LinkML-Map framework. +This is intended for Python developers - note that many of the operations here can also be performed +at the command line.

+
+
+
+
+
+ + +
import yaml
+
+ + +
+
+
+
+
+

Creating an example schema

+

We will use a LinkML SchemaBuilder object to progressively build up a schema, adding +additional features as we go.

+

We'll start with a simple Person schema, with a few single valued scalar slots:

+
+
+
+
+
+ + +
from linkml.utils.schema_builder import SchemaBuilder
+from linkml_runtime.linkml_model import SlotDefinition
+
+sb = SchemaBuilder()
+sb.add_class("Person", slots=[SlotDefinition("family_name", range="string"), 
+                              SlotDefinition("given_name", range="string"),
+                              SlotDefinition("age_in_years", range="integer"),
+                              SlotDefinition("height_in_cm", range="float"),
+                              ])
+sb.add_defaults()
+print(yaml.dump(sb.as_dict(), sort_keys=False))
+
+ + +
+
+
+
+
+
+name: test-schema
+id: http://example.org/test-schema
+imports:
+- linkml:types
+prefixes:
+  linkml: https://w3id.org/linkml/
+  test_schema: http://example.org/test-schema/
+default_prefix: test_schema
+default_range: string
+slots:
+  family_name:
+    range: string
+  given_name:
+    range: string
+  age_in_years:
+    range: integer
+  height_in_cm:
+    range: float
+classes:
+  Person:
+    slots:
+    - family_name
+    - given_name
+    - age_in_years
+    - height_in_cm
+
+
+
+
+
+
+
+
+
+
+

Creating a Transformer Session object

+

We will use a Session object which conveniently wraps a number of different capabilities; +the first of these capabilities is to map (transform) data objects from one schema to another +(implicit) schema using a transformer specification).

+

Our initial transformer specification will be a trivial isomorphic one that:

+
    +
  • maps the Person class to an Individual class
  • +
  • passes through name fields as-is
  • +
  • renames measurement fields (age_in_years and height_in_cm to age and height)
  • +
+
+
+
+
+
+ + +
from linkml_map.session import Session
+
+session = Session()
+session.set_source_schema(sb.as_dict())
+
+ + +
+
+
+
+ + +
# Transformer specification (in YAML)
+session.set_object_transformer("""
+class_derivations:
+  Individual:
+    populated_from: Person
+    slot_derivations:
+      family_name:
+        populated_from: family_name
+      given_name:
+        populated_from: given_name
+      age:
+        populated_from: age_in_years
+      height:
+        populated_from: height_in_cm
+""")
+
+ + +
+
+
+
+
+

Visualizing transformer specifications

+

We can visualize the transformer specification using graphviz:

+
+
+
+
+
+ + +
session.graphviz()
+
+ + +
+
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + +sourcePerson + +Person + +family_name : string + +given_name : string + +age_in_years : integer + +height_in_cm : float + + + + + + +targetIndividual + +Individual + +family_name : string + +given_name : string + +age : integer + +height : float + + + + + + +sourcePerson:family_name->targetIndividual:family_name + + + + + + + + +sourcePerson:given_name->targetIndividual:given_name + + + + + + + + +sourcePerson:age_in_years->targetIndividual:age + + + + + + + + +sourcePerson:height_in_cm->targetIndividual:height + + + + + +
+
+
+
+
+
+
+
+

Transforming objects

+

We'll next make a simple Person object. Note that for simplicity we are specifying this +using a Python dictionary. The framework also works with objects instantiating either +Pydantic or Dataclasses classes (use the transform_object method instead of transform).

+
+
+
+
+
+ + +
obj = {
+        "given_name": "Jane",
+        "family_name": "Doe",
+        "age_in_years": 42,
+        "height_in_cm": 180.0,
+    }
+session.transform(obj)
+
+ + +
+
+
+
+
+
+{'family_name': 'Doe', 'given_name': 'Jane', 'age': 42, 'height': 180.0}
+
+
+
+
+
+
+
+
+
+

This does what we expect - it renames the two fields, but leaves all values intact.

+

Note that because we use using dictionaries here, the renaming of the class has no effect, +as this is implicit with JSON/dictionaries.

+

TODO: docs on type designator fields

+

For command line users, the same thing can be achieved with the map-data command.

+
+
+
+
+
+
+

Deriving target schemas

+

LinkML-Transformer is intended as a declarative framework, in contrast to writing Python +transformation code. This allows tools to introspect mappings and perform other kinds of inference. +An example of this is deriving the (implicit) target schema

+

Here we use the target_schema method on the session object to derive the target schema:

+
+
+
+
+
+ + +
from linkml_runtime.dumpers import yaml_dumper
+
+print(yaml_dumper.dumps(session.target_schema))
+
+ + +
+
+
+
+
+
+name: test-schema-derived
+id: http://example.org/test-schema-derived
+imports:
+- linkml:types
+prefixes:
+  linkml:
+    prefix_prefix: linkml
+    prefix_reference: https://w3id.org/linkml/
+  test_schema:
+    prefix_prefix: test_schema
+    prefix_reference: http://example.org/test-schema/
+default_prefix: http://example.org/test-schema-derived/
+default_range: string
+classes:
+  Individual:
+    name: Individual
+    attributes:
+      family_name:
+        name: family_name
+        domain_of:
+        - Person
+        range: string
+      given_name:
+        name: given_name
+        domain_of:
+        - Person
+        range: string
+      age:
+        name: age
+        domain_of:
+        - Person
+        range: integer
+      height:
+        name: height
+        domain_of:
+        - Person
+        range: float
+
+
+
+
+
+
+
+
+
+
+

As expected, this is isomorphic to the original (source) schema, with fields and classes renamed.

+
+
+
+
+
+
+

Using Expressions

+

In addition to renaming fields, we can derive field values via evaluation of function expressions.

+

You are encouraged to follow the subset of Python defined by the LinkML expression language. This provides +both safety, and declarativity. However, if you need +to, you can include arbitrary Python code, provided you configure the session to allow this.

+

We'll keep the original schema, and will provide a new Transformer specification, +giving an example of both string manipulation functions and arithmetic functions; the latter +perform unit conversions (later on we will see more flexible and declarative ways to perform unit conversions).

+
+
+
+
+
+ + +

+session.set_object_transformer("""
+class_derivations:
+  Individual:
+    populated_from: Person
+    slot_derivations:
+      name:
+        expr: "{given_name} + ' ' + {family_name}"
+        description: Concatenating given and family names
+          note this is a bad assumption for names in general,
+          this is just for demonstration
+      age_in_months:
+        expr: age_in_years * 12
+      height_in_meters:
+        expr: height_in_cm / 100
+""")
+
+
+ + +
+
+
+
+
+

Note that when we visualize this specification, dotted lines are shown indicating a relationship +between source and target that is different from direct copy:

+
+
+
+
+
+ + +
session.graphviz()
+
+ + +
+
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + +sourcePerson + +Person + +family_name : string + +given_name : string + +age_in_years : integer + +height_in_cm : float + + + + + + +targetIndividual + +Individual + +name : string + +age_in_months : string + +height_in_meters : string + + + + + + +sourcePerson:given_name->targetIndividual:name + + + + + + + + +sourcePerson:family_name->targetIndividual:name + + + + + + + + +sourcePerson:age_in_years->targetIndividual:age_in_months + + + + + + + + +sourcePerson:height_in_cm->targetIndividual:height_in_meters + + + + + +
+
+
+
+
+
+
+
+

Now we'll transform the same object as before, and see the results:

+
+
+
+
+
+ + +
session.transform(obj)
+
+ + +
+
+
+
+
+
+{'name': 'Jane Doe', 'age_in_months': 504, 'height_in_meters': 1.8}
+
+
+
+
+
+
+
+
+
+

As expected, we concatenated the name fields, and converted the age and height fields to different units.

+

Let's take a look at the derived schema for this new transformation:

+
+
+
+
+
+ + +
print(yaml_dumper.dumps(session.target_schema))
+
+ + +
+
+
+
+
+
+name: test-schema-derived
+id: http://example.org/test-schema-derived
+imports:
+- linkml:types
+prefixes:
+  linkml:
+    prefix_prefix: linkml
+    prefix_reference: https://w3id.org/linkml/
+  test_schema:
+    prefix_prefix: test_schema
+    prefix_reference: http://example.org/test-schema/
+default_prefix: http://example.org/test-schema-derived/
+default_range: string
+classes:
+  Individual:
+    name: Individual
+    attributes:
+      name:
+        name: name
+      age_in_months:
+        name: age_in_months
+      height_in_meters:
+        name: height_in_meters
+
+
+
+
+
+
+
+
+
+
+

Note that at this time, deriving ranges using expressions is not supported, so the two measurement fields +are erroneously typed as having the default_range of string. However, in principle, if you use the +linkml subset of Python it should be possible to infer the range of the derived field, and this may be added +in future versions. Currently the tool chain is at an early stage of development.

+
+
+
+
+
+
+

Unit conversions

+

Next we will look at a different way of doing unit conversions. The LinkML specification allows +schemas to explicitly declare the units of slots, so let's modify our schema to do this, adding +a UCUM code for our height_in_cm slot:

+
+
+
+
+
+ + +
from linkml_runtime.linkml_model.units import UnitOfMeasure
+sb.schema.slots['height_in_cm'].unit = UnitOfMeasure(ucum_code='cm')
+session.set_source_schema(sb.as_dict())
+print(yaml.dump(sb.as_dict(), sort_keys=False))
+
+ + +
+
+
+
+
+
+name: test-schema
+id: http://example.org/test-schema
+imports:
+- linkml:types
+prefixes:
+  linkml: https://w3id.org/linkml/
+  test_schema: http://example.org/test-schema/
+default_prefix: test_schema
+default_range: string
+slots:
+  family_name:
+    range: string
+  given_name:
+    range: string
+  age_in_years:
+    range: integer
+  height_in_cm:
+    range: float
+    unit:
+      ucum_code: cm
+classes:
+  Person:
+    slots:
+    - family_name
+    - given_name
+    - age_in_years
+    - height_in_cm
+
+
+
+
+
+
+
+
+
+
+

Adding target_unit to transformer specification

+

We will create a new transformer specification, focusing on the height_in_cm field. We will +transform this into a height_in_meters field, and will use the target_unit field to specify +the target unit.

+
+
+
+
+
+ + +
session.set_object_transformer("""
+class_derivations:
+  Individual:
+    populated_from: Person
+    slot_derivations:
+      name:
+        expr: "{given_name} + ' ' + {family_name}"
+      height_in_meters:
+        populated_from: height_in_cm
+        unit_conversion:
+          target_unit: m
+""")
+
+ + +
+
+
+
+ + +
session.transform(obj)
+
+ + +
+
+
+
+
+
+{'name': 'Jane Doe', 'height_in_meters': 1.8}
+
+
+
+
+
+
+
+
+
+

Units in derived schema

+

Next we'll look at the derived target schema, and as expected we see that it has inferred +the target unit for the height_in_meters field:

+
+
+
+
+
+ + +
print(yaml_dumper.dumps(session.target_schema))
+
+
+ + +
+
+
+
+
+
+name: test-schema-derived
+id: http://example.org/test-schema-derived
+imports:
+- linkml:types
+prefixes:
+  linkml:
+    prefix_prefix: linkml
+    prefix_reference: https://w3id.org/linkml/
+  test_schema:
+    prefix_prefix: test_schema
+    prefix_reference: http://example.org/test-schema/
+default_prefix: http://example.org/test-schema-derived/
+default_range: string
+classes:
+  Individual:
+    name: Individual
+    attributes:
+      name:
+        name: name
+      height_in_meters:
+        name: height_in_meters
+        domain_of:
+        - Person
+        range: float
+        unit:
+          ucum_code: m
+
+
+
+
+
+
+
+
+
+
+

Tabular serialization

+
+
+
+
+
+ + +
slot = sb.add_slot("aliases", multivalued=True, range="string", replace_if_present=True)
+
+ + +
+
+
+
+ + +
sb.schema.classes['Person'].slots.append(slot.name)
+
+ + +
+
+
+
+ + +
session.set_source_schema(sb.as_dict())
+
+ + +
+
+
+
+ + +
session.set_object_transformer("""
+class_derivations:
+  Individual:
+    populated_from: Person
+    slot_derivations:
+      family_name:
+        populated_from: family_name
+      given_name:
+        populated_from: given_name
+      age:
+        populated_from: age_in_years
+      height:
+        populated_from: height_in_cm
+      aliases:
+        populated_from: aliases
+        stringification:
+          delimiter: '|'
+""")    
+
+ + +
+
+
+
+ + +
obj = {
+        "given_name": "Jane",
+        "family_name": "Doe",
+        "age_in_years": 42,
+        "height_in_cm": 180.0,
+        "aliases": ["Jane", "Janie", "Janey"]
+    }
+flattened = session.transform(obj)
+flattened
+
+ + +
+
+
+
+
+
+{'family_name': 'Doe',
+ 'given_name': 'Jane',
+ 'age': 42,
+ 'height': 180.0,
+ 'aliases': 'Jane|Janie|Janey'}
+
+
+
+
+
+
+
+
+
+

this can easily be serialized to a CSV/TSV

+
+
+
+
+
+
+

Reverse transform

+

If a transform does not contain one-way functions, +it can be reversed.

+

In this case, reversing the transform allows us to map +from the tabular form back to the richer original representation.

+
+
+
+
+
+ + +
session.reverse_transform(flattened)
+
+ + +
+
+
+
+
+
+{'family_name': 'Doe',
+ 'given_name': 'Jane',
+ 'age_in_years': 42,
+ 'height_in_cm': 180.0,
+ 'aliases': ['Jane', 'Janie', 'Janey']}
+
+
+
+
+
+
+
+
+ + +

+
+ + +
+
+ +
+ + + + + + + + + +
+
+ + + + + \ No newline at end of file diff --git a/exclude/index.html b/exclude/index.html new file mode 100644 index 0000000..92d28c5 --- /dev/null +++ b/exclude/index.html @@ -0,0 +1,124 @@ + + + + + + + + + + + + + + Slot: exclude - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: exclude

+

URI: linkmltr:exclude

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
CopyDirectiveInstructs a Schema Mapper in how to map to a target schemano
+

Properties

+ +

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/linkml/transformer
  • +
+

LinkML Source

+
+ +
name: exclude
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+alias: exclude
+owner: CopyDirective
+domain_of:
+- CopyDirective
+range: Any
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/exclude_all/index.html b/exclude_all/index.html new file mode 100644 index 0000000..b2c61d5 --- /dev/null +++ b/exclude_all/index.html @@ -0,0 +1,124 @@ + + + + + + + + + + + + + + Slot: exclude_all - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: exclude_all

+

URI: linkmltr:exclude_all

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
CopyDirectiveInstructs a Schema Mapper in how to map to a target schemano
+

Properties

+ +

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/linkml/transformer
  • +
+

LinkML Source

+
+ +
name: exclude_all
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+alias: exclude_all
+owner: CopyDirective
+domain_of:
+- CopyDirective
+range: boolean
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/expr/index.html b/expr/index.html new file mode 100644 index 0000000..991eb04 --- /dev/null +++ b/expr/index.html @@ -0,0 +1,128 @@ + + + + + + + + + + + + + + Slot: expr - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: expr

+

URI: linkmltr:expr

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
EnumDerivationA specification of how to derive the value of a target enum from a source enu...no
PermissibleValueDerivationA specification of how to derive the value of a PV from a source enumno
SlotDerivationA specification of how to derive the value of a target slot from a source slo...no
+

Properties

+
    +
  • Range: NONE
  • +
+

Identifier and Mapping Information

+

LinkML Source

+
+ +
name: expr
+alias: expr
+domain_of:
+- SlotDerivation
+- EnumDerivation
+- PermissibleValueDerivation
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/expression_to_expression_mappings/index.html b/expression_to_expression_mappings/index.html new file mode 100644 index 0000000..9bb03d4 --- /dev/null +++ b/expression_to_expression_mappings/index.html @@ -0,0 +1,158 @@ + + + + + + + + + + + + + + Slot: expression_to_expression_mappings - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: expression_to_expression_mappings

+

A mapping table in which the keys and values are expressions

+

URI: linkmltr:expression_to_expression_mappings

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
EnumDerivationA specification of how to derive the value of a target enum from a source enu...no
ElementDerivationAn abstract grouping for classes that provide a specification of how to deri...no
PrefixDerivationno
SlotDerivationA specification of how to derive the value of a target slot from a source slo...no
ClassDerivationA specification of how to derive a target class from a source classno
PermissibleValueDerivationA specification of how to derive the value of a PV from a source enumno
+

Properties

+
    +
  • +

    Range: KeyVal

    +
  • +
  • +

    Multivalued: True

    +
  • +
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/linkml/transformer
  • +
+

LinkML Source

+
+ +
name: expression_to_expression_mappings
+description: A mapping table in which the keys and values are expressions
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+multivalued: true
+alias: expression_to_expression_mappings
+owner: ElementDerivation
+domain_of:
+- ElementDerivation
+range: KeyVal
+inlined: true
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/expression_to_value_mappings/index.html b/expression_to_value_mappings/index.html new file mode 100644 index 0000000..2cbcb9d --- /dev/null +++ b/expression_to_value_mappings/index.html @@ -0,0 +1,158 @@ + + + + + + + + + + + + + + Slot: expression_to_value_mappings - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: expression_to_value_mappings

+

A mapping table in which the keys are expressions

+

URI: linkmltr:expression_to_value_mappings

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
EnumDerivationA specification of how to derive the value of a target enum from a source enu...no
ElementDerivationAn abstract grouping for classes that provide a specification of how to deri...no
PrefixDerivationno
SlotDerivationA specification of how to derive the value of a target slot from a source slo...no
ClassDerivationA specification of how to derive a target class from a source classno
PermissibleValueDerivationA specification of how to derive the value of a PV from a source enumno
+

Properties

+
    +
  • +

    Range: KeyVal

    +
  • +
  • +

    Multivalued: True

    +
  • +
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/linkml/transformer
  • +
+

LinkML Source

+
+ +
name: expression_to_value_mappings
+description: A mapping table in which the keys are expressions
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+multivalued: true
+alias: expression_to_value_mappings
+owner: ElementDerivation
+domain_of:
+- ElementDerivation
+range: KeyVal
+inlined: true
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/faq/index.html b/faq/index.html new file mode 100644 index 0000000..3a5eae2 --- /dev/null +++ b/faq/index.html @@ -0,0 +1,147 @@ + + + + + + + + + + + + + + FAQ - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +

FAQ

+

Why another framework?

+

There are a number of excellent frameworks for performing mapping and data transformations. +The LinkML Transformer framework was born out of a need for a framework that:

+
    +
  • was not inherently tied to:
      +
    • a particular serialization format (e.g. RDF, JSON, ...)
    • +
    • a particular programming language (e.g. Python, Java, ...)
    • +
    • a particular database system or database language (e.g. PostgreSQL or SQL or SPARQL)
    • +
    • not tied to a particular kind of transformation (e.g. ORM or Tables to RDF)
    • +
    +
  • +
  • was a natural fit for the LinkML data modeling framework
  • +
  • was declarative and easy to perform machine reasoning over
  • +
  • is simple for simple use cases
  • +
+

In its current state, this framework is less powerful and expressive than many other frameworks +or methodologies for performing transformations. If you need to perform complex data transformations, +you might be better off using an expressive query language like SPARQL or SQL, or even just coding +transformations directly in a programming language or library like Python or Pandas (but note that +even for the coding use case, the LinkML Transformer framework can be useful as a standard way +of documenting transformations).

+

Currently the main use case for this framework is mostly isomorphic transformations, with lightweight +manipulations. These lend themselves well to a declarative framework. Uses cases that are a particularly good fit +involve mapping between data-dictionary like standards, with large numbers of metadata elements, where these +elements can often be mapped one-to-one, or with simple manipulations (e.g. unit conversions).

+

The origins lie partly in the SSSOM standard, which is intended as an ultra-simple way of specifying +precise mappings between entities (e.g. schema.org Person is the same as DBPedia person). We observed +that many people wanted to extend the language to perform more complex mappings. To address this, we +help a workshop at the Biocuration conference in Padua, Italy in 2022.

+ + +
+ + + + + + + + + +
+
+ + + + + \ No newline at end of file diff --git a/fonts/fontawesome-webfont.eot b/fonts/fontawesome-webfont.eot new file mode 100644 index 0000000..e9f60ca Binary files /dev/null and b/fonts/fontawesome-webfont.eot differ diff --git a/fonts/fontawesome-webfont.svg b/fonts/fontawesome-webfont.svg new file mode 100644 index 0000000..855c845 --- /dev/null +++ b/fonts/fontawesome-webfont.svg @@ -0,0 +1,2671 @@ + + + + +Created by FontForge 20120731 at Mon Oct 24 17:37:40 2016 + By ,,, +Copyright Dave Gandy 2016. All rights reserved. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/fonts/fontawesome-webfont.ttf b/fonts/fontawesome-webfont.ttf new file mode 100644 index 0000000..35acda2 Binary files /dev/null and b/fonts/fontawesome-webfont.ttf differ diff --git a/fonts/fontawesome-webfont.woff b/fonts/fontawesome-webfont.woff new file mode 100644 index 0000000..400014a Binary files /dev/null and b/fonts/fontawesome-webfont.woff differ diff --git a/fonts/fontawesome-webfont.woff2 b/fonts/fontawesome-webfont.woff2 new file mode 100644 index 0000000..4d13fc6 Binary files /dev/null and b/fonts/fontawesome-webfont.woff2 differ diff --git a/fonts/glyphicons-halflings-regular.eot b/fonts/glyphicons-halflings-regular.eot new file mode 100644 index 0000000..b93a495 Binary files /dev/null and b/fonts/glyphicons-halflings-regular.eot differ diff --git a/fonts/glyphicons-halflings-regular.svg b/fonts/glyphicons-halflings-regular.svg new file mode 100644 index 0000000..94fb549 --- /dev/null +++ b/fonts/glyphicons-halflings-regular.svg @@ -0,0 +1,288 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/fonts/glyphicons-halflings-regular.ttf b/fonts/glyphicons-halflings-regular.ttf new file mode 100644 index 0000000..1413fc6 Binary files /dev/null and b/fonts/glyphicons-halflings-regular.ttf differ diff --git a/fonts/glyphicons-halflings-regular.woff b/fonts/glyphicons-halflings-regular.woff new file mode 100644 index 0000000..9e61285 Binary files /dev/null and b/fonts/glyphicons-halflings-regular.woff differ diff --git a/fonts/glyphicons-halflings-regular.woff2 b/fonts/glyphicons-halflings-regular.woff2 new file mode 100644 index 0000000..64539b5 Binary files /dev/null and b/fonts/glyphicons-halflings-regular.woff2 differ diff --git a/hide/index.html b/hide/index.html new file mode 100644 index 0000000..b7539b2 --- /dev/null +++ b/hide/index.html @@ -0,0 +1,128 @@ + + + + + + + + + + + + + + Slot: hide - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: hide

+

URI: linkmltr:hide

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
EnumDerivationA specification of how to derive the value of a target enum from a source enu...no
PermissibleValueDerivationA specification of how to derive the value of a PV from a source enumno
SlotDerivationA specification of how to derive the value of a target slot from a source slo...no
+

Properties

+
    +
  • Range: NONE
  • +
+

Identifier and Mapping Information

+

LinkML Source

+
+ +
name: hide
+alias: hide
+domain_of:
+- SlotDerivation
+- EnumDerivation
+- PermissibleValueDerivation
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/id/index.html b/id/index.html new file mode 100644 index 0000000..62f3fe4 --- /dev/null +++ b/id/index.html @@ -0,0 +1,126 @@ + + + + + + + + + + + + + + Slot: id - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: id

+

Unique identifier for this transformation specification

+

URI: schema:identifier

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
TransformationSpecificationA collection of mappings between source and target classesno
+

Properties

+
    +
  • Range: NONE
  • +
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/linkml/transformer
  • +
+

LinkML Source

+
+ +
name: id
+description: Unique identifier for this transformation specification
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+slot_uri: schema:identifier
+alias: id
+owner: TransformationSpecification
+domain_of:
+- TransformationSpecification
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/img/favicon.ico b/img/favicon.ico new file mode 100644 index 0000000..e85006a Binary files /dev/null and b/img/favicon.ico differ diff --git a/implements/index.html b/implements/index.html new file mode 100644 index 0000000..0b2ac90 --- /dev/null +++ b/implements/index.html @@ -0,0 +1,167 @@ + + + + + + + + + + + + + + Slot: implements - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: implements

+

A reference to a specification that this component implements.

+

URI: linkmltr:implements

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
EnumDerivationA specification of how to derive the value of a target enum from a source enu...no
PermissibleValueDerivationA specification of how to derive the value of a PV from a source enumno
ElementDerivationAn abstract grouping for classes that provide a specification of how to deri...no
PrefixDerivationno
SlotDerivationA specification of how to derive the value of a target slot from a source slo...no
ClassDerivationA specification of how to derive a target class from a source classno
SpecificationComponentno
TransformationSpecificationA collection of mappings between source and target classesno
+

Properties

+ +

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/linkml/transformer
  • +
+

LinkML Source

+
+ +
name: implements
+description: A reference to a specification that this component implements.
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+multivalued: true
+alias: implements
+owner: SpecificationComponent
+domain_of:
+- SpecificationComponent
+range: uriorcurie
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/include/index.html b/include/index.html new file mode 100644 index 0000000..d17f36e --- /dev/null +++ b/include/index.html @@ -0,0 +1,124 @@ + + + + + + + + + + + + + + Slot: include - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: include

+

URI: linkmltr:include

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
CopyDirectiveInstructs a Schema Mapper in how to map to a target schemano
+

Properties

+ +

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/linkml/transformer
  • +
+

LinkML Source

+
+ +
name: include
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+alias: include
+owner: CopyDirective
+domain_of:
+- CopyDirective
+range: Any
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/index.html b/index.html new file mode 100644 index 0000000..f6dc7ed --- /dev/null +++ b/index.html @@ -0,0 +1,356 @@ + + + + + + + + + + + + + + LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +
+ +
+
+ +
+ + + + + + + + + + + + +

LinkML-Map

+

LinkML Map is a framework for specifying and executing mappings between data models.

+

Features:

+
    +
  • YAML-based lightweight syntax
  • +
  • Python library for executing mappings on data files
  • +
  • Ability to compile to other frameworks (SQL/DuckDB)
  • +
  • Derivation of target (implicit) schemas, allowing easy customization of data models (profiling)
  • +
  • Simple YAML dictionaries for simple mappings
  • +
  • Automatic unit conversion
  • +
  • Use of subset of Python to specify complex mappings
  • +
  • Visualizations of mappings
  • +
  • Mappings are reversible (provided all expressions used are reversible)
  • +
  • Compatibility with SSSOM
  • +
+

This documentation are available at:

+ +

Status:

+

The transformation data model is not yet fully stable, and may be subject to change. +Not all parts of the model are implemented in the reference Python framework.

+

Basic idea

+

Given an object that conforms to a LinkML schema,e.g.:

+
given_name: Jane
+family_name: Doe
+height_in_cm: 172.0
+age_in_years: 33
+aliases: [Janey, Janie]
+
+

Define a mapping in YAML:

+
class_derivations:
+  Individual:
+    populated_from: Person
+    slot_derivations:
+      name:
+        expr: "{given_name} + ' ' + {family_name}"
+        description: Concatenating given and family names
+          note this is a bad assumption for names in general,
+          this is just for demonstration
+      height_in_meters:
+        populated_from: height_in_cm
+        unit_conversion:
+          target_unit: m
+      aliases:
+        populated_from: aliases
+        stringification:
+          delimiter: '|'
+
+

The schema mapping (aka TransformationSpecification) specifies how to transform the data model.

+

The schema mapping is a collection of one or more ClassDerivation objects, +which themselves consist of one or more SlotDerivation objects.

+

Transform the data:

+
linkml-tr map-data -T tr.yaml -s schema.yaml my-data.yaml
+
+

Giving:

+
name: Jane Doe
+height_in_meters: 1.72
+aliases: Janey|Janie
+
+

Installation and usage

+

Installation and command line usage:

+
pip[x] install linkml-map
+cd tests/input/examples/personinfo_basic
+linkml-tr map-data \
+  -T transform/personinfo-to-agent.transform.yaml \
+  -s source/personinfo.yaml \
+   data/Container-001.yaml \
+   -o output/Translated-001.yaml
+
+

The command line has subcommands for:

+
    +
  • map-data - map data from a source schema to a target schema
  • +
  • derive-schema - derive a target schema from a source schema and a mapping
  • +
  • invert - reverses a mapping
  • +
  • compile - compiles a mapping to another framework
      +
    • markdown - for generating static sites
    • +
    • graphviz - for generating visualizations
    • +
    • python - (partial)
    • +
    • forthcoming: r2rml, ...
    • +
    +
  • +
+

Details

+

This repo contains both:

+
    +
  • A data model for a data model transformation language
  • +
  • A reference python implementation
  • +
+

The transformation language is specified in terms of LinkML schemas. +It is intended to be a ployglot transformation language, used for +specifying how to map data models independent of underlying representation +(TSVs, JSON/YAML, RDF, SQL Database, ...).

+

Use cases include:

+
    +
  • ETL and mapping from one data model to another
  • +
  • Database migrations (one version of a schema to another)
  • +
  • Creating "profiles"
  • +
  • Specifying mappings between different serializations of a model (e.g. OO to Relational)
  • +
  • Mapping between normalized/non-redundant forms and denormalized/query-optimized forms
  • +
+

Data Model

+

The data model for transformations mirrors the data model for schemas:

+ +

See the generated docs

+

Conformance Suite

+

The Maps conformance suite contains a collection of tests for each feature of the language.

+

See:

+ +

Running the code

+
linkml-tr --help
+Usage: linkml-tr [OPTIONS] COMMAND [ARGS]...
+
+  CLI for linkml-map.
+
+Options:
+  -v, --verbose
+  -q, --quiet TEXT
+  --help            Show this message and exit.
+
+Commands:
+  derive-schema  Derive a schema from a source schema and a mapping.
+  map-data       Map data in a source schema using a transformation.
+
+

map-data

+

Transforms (maps) data from a source schema to a target schema. This could range from a simple data dictionary mapping +through to a complex mappings.

+
cd tests/input/examples/personinfo_basic
+linkml-tr map-data -T transform/personinfo-to-agent.transform.yaml -s source/personinfo.yaml  data/Container-001.yaml
+
+

derive-schema

+
cd tests/input/examples/personinfo_basic
+linkml-tr derive-schema -T transform/personinfo-to-agent.transform.yaml source/personinfo.yaml
+
+ +
+ + + + + + + + + +
+
+ + + + + + \ No newline at end of file diff --git a/inverse_of/index.html b/inverse_of/index.html new file mode 100644 index 0000000..a6f9090 --- /dev/null +++ b/inverse_of/index.html @@ -0,0 +1,129 @@ + + + + + + + + + + + + + + Slot: inverse_of - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: inverse_of

+

Used to specify a class-slot tuple that is the inverse of the derived/target slot. This is used primarily for mapping to relational databases or formalisms that do not allow multiple values. The class representing the repeated element has a foreign key slot inserted in that 'back references' the original multivalued slot.

+

URI: linkmltr:inverse_of

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
SlotDerivationA specification of how to derive the value of a target slot from a source slo...no
+

Properties

+ +

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/linkml/transformer
  • +
+

LinkML Source

+
+ +
name: inverse_of
+description: Used to specify a class-slot tuple that is the inverse of the derived/target
+  slot. This is used primarily for mapping to relational databases or formalisms that
+  do not allow multiple values. The class representing the repeated element has a
+  foreign key slot inserted in that 'back references' the original multivalued slot.
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+alias: inverse_of
+owner: SlotDerivation
+domain_of:
+- SlotDerivation
+range: Inverse
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/is_a/index.html b/is_a/index.html new file mode 100644 index 0000000..2496213 --- /dev/null +++ b/is_a/index.html @@ -0,0 +1,150 @@ + + + + + + + + + + + + + + Slot: is_a - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: is_a

+

URI: linkml:is_a

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
EnumDerivationA specification of how to derive the value of a target enum from a source enu...no
ElementDerivationAn abstract grouping for classes that provide a specification of how to deri...no
PrefixDerivationno
SlotDerivationA specification of how to derive the value of a target slot from a source slo...no
ClassDerivationA specification of how to derive a target class from a source classno
PermissibleValueDerivationA specification of how to derive the value of a PV from a source enumno
+

Properties

+ +

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/linkml/transformer
  • +
+

LinkML Source

+
+ +
name: is_a
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+slot_uri: linkml:is_a
+alias: is_a
+owner: ElementDerivation
+domain_of:
+- ElementDerivation
+range: ElementDerivation
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/joins/index.html b/joins/index.html new file mode 100644 index 0000000..fab0ae7 --- /dev/null +++ b/joins/index.html @@ -0,0 +1,140 @@ + + + + + + + + + + + + + + Slot: joins - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +

Slot: joins

+

Additional classes to be joined to derive instances of the target class

+

URI: linkmltr:joins

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
ClassDerivationA specification of how to derive a target class from a source classno
+

Properties

+ +

Comments

+
    +
  • not yet implemented
  • +
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/linkml/transformer
  • +
+

LinkML Source

+
+ +
name: joins
+description: Additional classes to be joined to derive instances of the target class
+comments:
+- not yet implemented
+from_schema: https://w3id.org/linkml/transformer
+rank: 1000
+multivalued: true
+alias: joins
+owner: ClassDerivation
+domain_of:
+- ClassDerivation
+range: AliasedClass
+inlined: true
+
+
+ +
+ +
+ + +
+
+ + + + + \ No newline at end of file diff --git a/js/base.js b/js/base.js new file mode 100644 index 0000000..51d5b5e --- /dev/null +++ b/js/base.js @@ -0,0 +1,568 @@ +/* global window, document, $, hljs, elasticlunr, base_url, is_top_frame */ +/* exported getParam, onIframeLoad */ +"use strict"; + +// The full page consists of a main window with navigation and table of contents, and an inner +// iframe containing the current article. Which article is shown is determined by the main +// window's #hash portion of the URL. In fact, we use the simple rule: main window's URL of +// "rootUrl#relPath" corresponds to iframe's URL of "rootUrl/relPath". +// +// The main frame and the contents of the index page actually live in a single generated html +// file: the outer frame hides one half, and the inner hides the other. TODO: this should be +// possible to greatly simplify after mkdocs-1.0 release. + +var mainWindow = is_top_frame ? window : (window.parent !== window ? window.parent : null); +var iframeWindow = null; +var rootUrl = qualifyUrl(base_url); +var searchIndex = null; +var showPageToc = true; +var MutationObserver = window.MutationObserver || window.WebKitMutationObserver; + +var Keys = { + ENTER: 13, + ESCAPE: 27, + UP: 38, + DOWN: 40, +}; + +function startsWith(str, prefix) { return str.lastIndexOf(prefix, 0) === 0; } +function endsWith(str, suffix) { return str.indexOf(suffix, str.length - suffix.length) !== -1; } + +/** + * Returns whether to use small-screen mode. Note that the same size is used in css @media block. + */ +function isSmallScreen() { + return window.matchMedia("(max-width: 600px)").matches; +} + +/** + * Given a relative URL, returns the absolute one, relying on the browser to convert it. + */ +function qualifyUrl(url) { + var a = document.createElement('a'); + a.href = url; + return a.href; +} + +/** + * Turns an absolute path to relative, stripping out rootUrl + separator. + */ +function getRelPath(separator, absUrl) { + var prefix = rootUrl + (endsWith(rootUrl, separator) ? '' : separator); + return startsWith(absUrl, prefix) ? absUrl.slice(prefix.length) : null; +} + +/** + * Turns a relative path to absolute, adding a prefix of rootUrl + separator. + */ +function getAbsUrl(separator, relPath) { + var sep = endsWith(rootUrl, separator) ? '' : separator; + return relPath === null ? null : rootUrl + sep + relPath; +} + +/** + * Redirects the iframe to reflect the path represented by the main window's current URL. + * (In our design, nothing should change iframe's src except via updateIframe(), or back/forward + * history is likely to get messed up.) + */ +function updateIframe(enableForwardNav) { + // Grey out the "forward" button if we don't expect 'forward' to work. + $('#hist-fwd').toggleClass('greybtn', !enableForwardNav); + + var targetRelPath = getRelPath('#', mainWindow.location.href) || ''; + var targetIframeUrl = getAbsUrl('/', targetRelPath); + var loc = iframeWindow.location; + var currentIframeUrl = _safeGetLocationHref(loc); + + console.log("updateIframe: %s -> %s (%s)", currentIframeUrl, targetIframeUrl, + currentIframeUrl === targetIframeUrl ? "same" : "replacing"); + + if (currentIframeUrl !== targetIframeUrl) { + loc.replace(targetIframeUrl); + onIframeBeforeLoad(targetIframeUrl); + } + document.body.scrollTop = 0; +} + +/** + * Returns location.href, catching exception that's triggered if the iframe is on a different domain. + */ +function _safeGetLocationHref(location) { + try { + return location.href; + } catch (e) { + return null; + } +} + +/** + * Returns the value of the given parameter in the URL's query portion. + */ +function getParam(key) { + var params = window.location.search.substring(1).split('&'); + for (var i = 0; i < params.length; i++) { + var param = params[i].split('='); + if (param[0] === key) { + return decodeURIComponent(param[1].replace(/\+/g, '%20')); + } + } +} + +/** + * Update the state of the button toggling table-of-contents. TOC has different behavior + * depending on screen size, so the button's behavior depends on that too. + */ +function updateTocButtonState() { + var shown; + if (isSmallScreen()) { + shown = $('.wm-toc-pane').hasClass('wm-toc-dropdown'); + } else { + shown = !$('#main-content').hasClass('wm-toc-hidden'); + } + $('#wm-toc-button').toggleClass('active', shown); +} + +/** + * Update the height of the iframe container. On small screens, we adjust it to fit the iframe + * contents, so that the page scrolls as a whole rather than inside the iframe. + */ +function updateContentHeight() { + if (isSmallScreen()) { + $('.wm-content-pane').height(iframeWindow.document.body.offsetHeight + 20); + $('.wm-article').attr('scrolling', 'no'); + } else { + $('.wm-content-pane').height(''); + $('.wm-article').attr('scrolling', 'auto'); + } +} + +/** + * When TOC is a dropdown (on small screens), close it. + */ +function closeTempItems() { + $('.wm-toc-dropdown').removeClass('wm-toc-dropdown'); + $('#mkdocs-search-query').closest('.wm-top-tool').removeClass('wm-top-tool-expanded'); + updateTocButtonState(); +} + +/** + * Visit the given URL. This changes the hash of the top page to reflect the new URL's relative + * path, and points the iframe to the new URL. + */ +function visitUrl(url, event) { + var relPath = getRelPath('/', url); + if (relPath !== null) { + event.preventDefault(); + var newUrl = getAbsUrl('#', relPath); + if (newUrl !== mainWindow.location.href) { + mainWindow.history.pushState(null, '', newUrl); + updateIframe(false); + } + closeTempItems(); + iframeWindow.focus(); + } +} + +/** + * Adjusts link to point to a top page, converting URL from "base/path" to "base#path". It also + * sets a data-adjusted attribute on the link, to skip adjustments on future clicks. + */ +function adjustLink(linkEl) { + if (!linkEl.hasAttribute('data-wm-adjusted')) { + linkEl.setAttribute('data-wm-adjusted', 'done'); + var relPath = getRelPath('/', linkEl.href); + if (relPath !== null) { + var newUrl = getAbsUrl('#', relPath); + linkEl.href = newUrl; + } + } +} + +/** + * Given a URL, strips query and fragment, returning just the path. + */ +function cleanUrlPath(relUrl) { + return relUrl.replace(/[#?].*/, ''); +} + +/** + * Initialize the main window. + */ +function initMainWindow() { + // wm-toc-button either opens the table of contents in the side-pane, or (on smaller screens) + // shows the side-pane as a drop-down. + $('#wm-toc-button').on('click', function(e) { + if (isSmallScreen()) { + $('.wm-toc-pane').toggleClass('wm-toc-dropdown'); + $('#wm-main-content').removeClass('wm-toc-hidden'); + } else { + $('#main-content').toggleClass('wm-toc-hidden'); + closeTempItems(); + } + updateTocButtonState(); + }); + + // Update the state of the wm-toc-button + updateTocButtonState(); + $(window).on('resize', function() { + updateTocButtonState(); + updateContentHeight(); + }); + + // Connect up the Back and Forward buttons (if present). + $('#hist-back').on('click', function(e) { window.history.back(); }); + $('#hist-fwd').on('click', function(e) { window.history.forward(); }); + + // When the side-pane is a dropdown, hide it on click-away. + $(window).on('blur', closeTempItems); + + // When we click on an opener in the table of contents, open it. + $('.wm-toc-pane').on('click', '.wm-toc-opener', function(e) { + $(this).toggleClass('wm-toc-open'); + $(this).next('.wm-toc-li-nested').collapse('toggle'); + }); + $('.wm-toc-pane').on('click', '.wm-page-toc-opener', function(e) { + // Ignore clicks while transitioning. + if ($(this).next('.wm-page-toc').hasClass('collapsing')) { return; } + showPageToc = !showPageToc; + $(this).toggleClass('wm-page-toc-open', showPageToc); + $(this).next('.wm-page-toc').collapse(showPageToc ? 'show' : 'hide'); + }); + + // Once the article loads in the side-pane, close the dropdown. + $('.wm-article').on('load', function() { + document.title = iframeWindow.document.title; + updateContentHeight(); + + // We want to update content height whenever the height of the iframe's content changes. + // Using MutationObserver seems to be the best way to do that. + var observer = new MutationObserver(updateContentHeight); + observer.observe(iframeWindow.document.body, { + attributes: true, + childList: true, + characterData: true, + subtree: true + }); + + iframeWindow.focus(); + }); + + // Initialize search functionality. + initSearch(); + + // Load the iframe now, and whenever we navigate the top frame. + setTimeout(function() { updateIframe(false); }, 0); + // For our usage, 'popstate' or 'hashchange' would work, but only 'hashchange' work on IE. + $(window).on('hashchange', function() { updateIframe(true); }); +} + +function onIframeBeforeLoad(url) { + $('.wm-current').removeClass('wm-current'); + closeTempItems(); + + var tocLi = getTocLi(url); + tocLi.addClass('wm-current'); + tocLi.parents('.wm-toc-li-nested') + // It's better to open parent items immediately without a transition. + .removeClass('collapsing').addClass('collapse in').height('') + .prev('.wm-toc-opener').addClass('wm-toc-open'); +} + +function getTocLi(url) { + var relPath = getAbsUrl('#', getRelPath('/', cleanUrlPath(url))); + var selector = '.wm-article-link[href="' + relPath + '"]'; + return $(selector).closest('.wm-toc-li'); +} + +var _deferIframeLoad = false; + +// Sometimes iframe is loaded before main window's ready callback. In this case, we defer +// onIframeLoad call until the main window has initialized. +function ensureIframeLoaded() { + if (_deferIframeLoad) { + onIframeLoad(); + } +} + +function onIframeLoad() { + if (!iframeWindow) { _deferIframeLoad = true; return; } + var url = iframeWindow.location.href; + onIframeBeforeLoad(url); + + if (iframeWindow.pageToc) { + var relPath = getAbsUrl('#', getRelPath('/', cleanUrlPath(url))); + renderPageToc(getTocLi(url), relPath, iframeWindow.pageToc); + } + iframeWindow.focus(); +} + +/** + * Hides a bootstrap collapsible element, and removes it from DOM once hidden. + */ +function collapseAndRemove(collapsibleElem) { + if (!collapsibleElem.hasClass('in')) { + // If the element is already hidden, just remove it immediately. + collapsibleElem.remove(); + } else { + collapsibleElem.on('hidden.bs.collapse', function() { + collapsibleElem.remove(); + }) + .collapse('hide'); + } +} + +function renderPageToc(parentElem, pageUrl, pageToc) { + var ul = $('
    '); + function addItem(tocItem) { + ul.append($('
  • ') + .append($('') + .attr('href', pageUrl + tocItem.url) + .attr('data-wm-adjusted', 'done') + .text(tocItem.title))); + if (tocItem.children) { + tocItem.children.forEach(addItem); + } + } + pageToc.forEach(addItem); + + $('.wm-page-toc-opener').removeClass('wm-page-toc-opener wm-page-toc-open'); + collapseAndRemove($('.wm-page-toc')); + + parentElem.addClass('wm-page-toc-opener').toggleClass('wm-page-toc-open', showPageToc); + $('
  • ').append(ul).insertAfter(parentElem) + .collapse(showPageToc ? 'show' : 'hide'); +} + + +if (!mainWindow) { + // This is a page that ought to be in an iframe. Redirect to load the top page instead. + var topUrl = getAbsUrl('#', getRelPath('/', window.location.href)); + if (topUrl) { + window.location.href = topUrl; + } + +} else { + // Adjust all links to point to the top page with the right hash fragment. + $(document).ready(function() { + $('a').each(function() { adjustLink(this); }); + }); + + // For any dynamically-created links, adjust them on click. + $(document).on('click', 'a:not([data-wm-adjusted])', function(e) { adjustLink(this); }); +} + +if (is_top_frame) { + // Main window. + $(document).ready(function() { + iframeWindow = $('.wm-article')[0].contentWindow; + initMainWindow(); + ensureIframeLoaded(); + }); + +} else { + // Article contents. + iframeWindow = window; + if (mainWindow) { + mainWindow.onIframeLoad(); + } + + // Other initialization of iframe contents. + hljs.initHighlightingOnLoad(); + $(document).ready(function() { + $('table').addClass('table table-striped table-hover table-bordered table-condensed'); + }); +} + + +var searchIndexReady = false; + +/** + * Initialize search functionality. + */ +function initSearch() { + // Create elasticlunr index. + searchIndex = elasticlunr(function() { + this.setRef('location'); + this.addField('title'); + this.addField('text'); + }); + + var searchBox = $('#mkdocs-search-query'); + var searchResults = $('#mkdocs-search-results'); + + // Fetch the prebuilt index data, and add to the index. + $.getJSON(base_url + '/search/search_index.json') + .done(function(data) { + data.docs.forEach(function(doc) { + searchIndex.addDoc(doc); + }); + searchIndexReady = true; + $(document).trigger('searchIndexReady'); + }); + + function showSearchResults(optShow) { + var show = (optShow === false ? false : Boolean(searchBox.val())); + if (show) { + doSearch({ + resultsElem: searchResults, + query: searchBox.val(), + snippetLen: 100, + limit: 10 + }); + } + searchResults.parent().toggleClass('open', show); + return show; + } + + searchBox.on('click', function(e) { + if (!searchResults.parent().hasClass('open')) { + if (showSearchResults()) { + e.stopPropagation(); + } + } + }); + + // Search automatically and show results on keyup event. + searchBox.on('keyup', function(e) { + var show = (e.which !== Keys.ESCAPE && e.which !== Keys.ENTER); + showSearchResults(show); + }); + + // Open the search box (and run the search) on up/down arrow keys. + searchBox.on('keydown', function(e) { + if (e.which === Keys.UP || e.which === Keys.DOWN) { + if (showSearchResults()) { + e.stopPropagation(); + e.preventDefault(); + setTimeout(function() { + searchResults.find('a').eq(e.which === Keys.UP ? -1 : 0).focus(); + }, 0); + } + } + }); + + searchResults.on('keydown', function(e) { + if (e.which === Keys.UP || e.which === Keys.DOWN) { + if (searchResults.find('a').eq(e.which === Keys.UP ? 0 : -1)[0] === e.target) { + searchBox.focus(); + e.stopPropagation(); + e.preventDefault(); + } + } + }); + + $(searchResults).on('click', '.search-all', function(e) { + e.stopPropagation(); + e.preventDefault(); + $('#wm-search-form').trigger('submit'); + }); + + // Redirect to the search page on Enter or button-click (form submit). + $('#wm-search-form').on('submit', function(e) { + var url = this.action + '?' + $(this).serialize(); + visitUrl(url, e); + searchResults.parent().removeClass('open'); + }); + + $('#wm-search-show,#wm-search-go').on('click', function(e) { + if (isSmallScreen()) { + e.preventDefault(); + var el = $('#mkdocs-search-query').closest('.wm-top-tool'); + el.toggleClass('wm-top-tool-expanded'); + if (el.hasClass('wm-top-tool-expanded')) { + setTimeout(function() { + $('#mkdocs-search-query').focus(); + showSearchResults(); + }, 0); + $('#mkdocs-search-query').focus(); + } + } + }); +} + +function escapeRegex(s) { + return s.replace(/[-\/\\^$*+?.()|[\]{}]/g, '\\$&'); +} + +/** + * This helps construct useful snippets to show in search results, and highlight matches. + */ +function SnippetBuilder(query) { + var termsPattern = elasticlunr.tokenizer(query).map(escapeRegex).join("|"); + this._termsRegex = termsPattern ? new RegExp(termsPattern, "gi") : null; +} + +SnippetBuilder.prototype.getSnippet = function(text, len) { + if (!this._termsRegex) { + return text.slice(0, len); + } + + // Find a position that includes something we searched for. + var pos = text.search(this._termsRegex); + if (pos < 0) { pos = 0; } + + // Find a period before that position (a good starting point). + var start = text.lastIndexOf('.', pos) + 1; + if (pos - start > 30) { + // If too long to previous period, give it 30 characters, and find a space before that. + start = text.lastIndexOf(' ', pos - 30) + 1; + } + var rawSnippet = text.slice(start, start + len); + return rawSnippet.replace(this._termsRegex, '$&'); +}; + +/** + * Search the elasticlunr index for the given query, and populate the dropdown with results. + */ +function doSearch(options) { + var resultsElem = options.resultsElem; + resultsElem.empty(); + + // If the index isn't ready, wait for it, and search again when ready. + if (!searchIndexReady) { + resultsElem.append($('
  • SEARCHING...
  • ')); + $(document).one('searchIndexReady', function() { doSearch(options); }); + return; + } + + var query = options.query; + var snippetLen = options.snippetLen; + var limit = options.limit; + + if (query === '') { return; } + + var results = searchIndex.search(query, { + fields: { title: {boost: 10}, text: { boost: 1 } }, + expand: true, + bool: "AND" + }); + + var snippetBuilder = new SnippetBuilder(query); + if (results.length > 0){ + var len = Math.min(results.length, limit || Infinity); + for (var i = 0; i < len; i++) { + var doc = searchIndex.documentStore.getDoc(results[i].ref); + var snippet = snippetBuilder.getSnippet(doc.text, snippetLen); + resultsElem.append( + $('
  • ').append($('').attr('href', pathJoin(base_url, doc.location)) + .append($('
    ').text(doc.title)) + .append($('
    ').html(snippet))) + ); + } + resultsElem.find('a').each(function() { adjustLink(this); }); + if (limit) { + resultsElem.append($('
  • ')); + resultsElem.append($( + '
  • ' + + '
    SEE ALL RESULTS
  • ')); + } + } else { + resultsElem.append($('
  • NO RESULTS FOUND
  • ')); + } +} + +function pathJoin(prefix, suffix) { + var nPrefix = endsWith(prefix, "/") ? prefix.slice(0, -1) : prefix; + var nSuffix = startsWith(suffix, "/") ? suffix.slice(1) : suffix; + return nPrefix + "/" + nSuffix; +} diff --git a/js/bootstrap-3.3.7.js b/js/bootstrap-3.3.7.js new file mode 100644 index 0000000..8a2e99a --- /dev/null +++ b/js/bootstrap-3.3.7.js @@ -0,0 +1,2377 @@ +/*! + * Bootstrap v3.3.7 (http://getbootstrap.com) + * Copyright 2011-2016 Twitter, Inc. + * Licensed under the MIT license + */ + +if (typeof jQuery === 'undefined') { + throw new Error('Bootstrap\'s JavaScript requires jQuery') +} + ++function ($) { + 'use strict'; + var version = $.fn.jquery.split(' ')[0].split('.') + if ((version[0] < 2 && version[1] < 9) || (version[0] == 1 && version[1] == 9 && version[2] < 1) || (version[0] > 3)) { + throw new Error('Bootstrap\'s JavaScript requires jQuery version 1.9.1 or higher, but lower than version 4') + } +}(jQuery); + +/* ======================================================================== + * Bootstrap: transition.js v3.3.7 + * http://getbootstrap.com/javascript/#transitions + * ======================================================================== + * Copyright 2011-2016 Twitter, Inc. + * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE) + * ======================================================================== */ + + ++function ($) { + 'use strict'; + + // CSS TRANSITION SUPPORT (Shoutout: http://www.modernizr.com/) + // ============================================================ + + function transitionEnd() { + var el = document.createElement('bootstrap') + + var transEndEventNames = { + WebkitTransition : 'webkitTransitionEnd', + MozTransition : 'transitionend', + OTransition : 'oTransitionEnd otransitionend', + transition : 'transitionend' + } + + for (var name in transEndEventNames) { + if (el.style[name] !== undefined) { + return { end: transEndEventNames[name] } + } + } + + return false // explicit for ie8 ( ._.) + } + + // http://blog.alexmaccaw.com/css-transitions + $.fn.emulateTransitionEnd = function (duration) { + var called = false + var $el = this + $(this).one('bsTransitionEnd', function () { called = true }) + var callback = function () { if (!called) $($el).trigger($.support.transition.end) } + setTimeout(callback, duration) + return this + } + + $(function () { + $.support.transition = transitionEnd() + + if (!$.support.transition) return + + $.event.special.bsTransitionEnd = { + bindType: $.support.transition.end, + delegateType: $.support.transition.end, + handle: function (e) { + if ($(e.target).is(this)) return e.handleObj.handler.apply(this, arguments) + } + } + }) + +}(jQuery); + +/* ======================================================================== + * Bootstrap: alert.js v3.3.7 + * http://getbootstrap.com/javascript/#alerts + * ======================================================================== + * Copyright 2011-2016 Twitter, Inc. + * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE) + * ======================================================================== */ + + ++function ($) { + 'use strict'; + + // ALERT CLASS DEFINITION + // ====================== + + var dismiss = '[data-dismiss="alert"]' + var Alert = function (el) { + $(el).on('click', dismiss, this.close) + } + + Alert.VERSION = '3.3.7' + + Alert.TRANSITION_DURATION = 150 + + Alert.prototype.close = function (e) { + var $this = $(this) + var selector = $this.attr('data-target') + + if (!selector) { + selector = $this.attr('href') + selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') // strip for ie7 + } + + var $parent = $(selector === '#' ? [] : selector) + + if (e) e.preventDefault() + + if (!$parent.length) { + $parent = $this.closest('.alert') + } + + $parent.trigger(e = $.Event('close.bs.alert')) + + if (e.isDefaultPrevented()) return + + $parent.removeClass('in') + + function removeElement() { + // detach from parent, fire event then clean up data + $parent.detach().trigger('closed.bs.alert').remove() + } + + $.support.transition && $parent.hasClass('fade') ? + $parent + .one('bsTransitionEnd', removeElement) + .emulateTransitionEnd(Alert.TRANSITION_DURATION) : + removeElement() + } + + + // ALERT PLUGIN DEFINITION + // ======================= + + function Plugin(option) { + return this.each(function () { + var $this = $(this) + var data = $this.data('bs.alert') + + if (!data) $this.data('bs.alert', (data = new Alert(this))) + if (typeof option == 'string') data[option].call($this) + }) + } + + var old = $.fn.alert + + $.fn.alert = Plugin + $.fn.alert.Constructor = Alert + + + // ALERT NO CONFLICT + // ================= + + $.fn.alert.noConflict = function () { + $.fn.alert = old + return this + } + + + // ALERT DATA-API + // ============== + + $(document).on('click.bs.alert.data-api', dismiss, Alert.prototype.close) + +}(jQuery); + +/* ======================================================================== + * Bootstrap: button.js v3.3.7 + * http://getbootstrap.com/javascript/#buttons + * ======================================================================== + * Copyright 2011-2016 Twitter, Inc. + * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE) + * ======================================================================== */ + + ++function ($) { + 'use strict'; + + // BUTTON PUBLIC CLASS DEFINITION + // ============================== + + var Button = function (element, options) { + this.$element = $(element) + this.options = $.extend({}, Button.DEFAULTS, options) + this.isLoading = false + } + + Button.VERSION = '3.3.7' + + Button.DEFAULTS = { + loadingText: 'loading...' + } + + Button.prototype.setState = function (state) { + var d = 'disabled' + var $el = this.$element + var val = $el.is('input') ? 'val' : 'html' + var data = $el.data() + + state += 'Text' + + if (data.resetText == null) $el.data('resetText', $el[val]()) + + // push to event loop to allow forms to submit + setTimeout($.proxy(function () { + $el[val](data[state] == null ? this.options[state] : data[state]) + + if (state == 'loadingText') { + this.isLoading = true + $el.addClass(d).attr(d, d).prop(d, true) + } else if (this.isLoading) { + this.isLoading = false + $el.removeClass(d).removeAttr(d).prop(d, false) + } + }, this), 0) + } + + Button.prototype.toggle = function () { + var changed = true + var $parent = this.$element.closest('[data-toggle="buttons"]') + + if ($parent.length) { + var $input = this.$element.find('input') + if ($input.prop('type') == 'radio') { + if ($input.prop('checked')) changed = false + $parent.find('.active').removeClass('active') + this.$element.addClass('active') + } else if ($input.prop('type') == 'checkbox') { + if (($input.prop('checked')) !== this.$element.hasClass('active')) changed = false + this.$element.toggleClass('active') + } + $input.prop('checked', this.$element.hasClass('active')) + if (changed) $input.trigger('change') + } else { + this.$element.attr('aria-pressed', !this.$element.hasClass('active')) + this.$element.toggleClass('active') + } + } + + + // BUTTON PLUGIN DEFINITION + // ======================== + + function Plugin(option) { + return this.each(function () { + var $this = $(this) + var data = $this.data('bs.button') + var options = typeof option == 'object' && option + + if (!data) $this.data('bs.button', (data = new Button(this, options))) + + if (option == 'toggle') data.toggle() + else if (option) data.setState(option) + }) + } + + var old = $.fn.button + + $.fn.button = Plugin + $.fn.button.Constructor = Button + + + // BUTTON NO CONFLICT + // ================== + + $.fn.button.noConflict = function () { + $.fn.button = old + return this + } + + + // BUTTON DATA-API + // =============== + + $(document) + .on('click.bs.button.data-api', '[data-toggle^="button"]', function (e) { + var $btn = $(e.target).closest('.btn') + Plugin.call($btn, 'toggle') + if (!($(e.target).is('input[type="radio"], input[type="checkbox"]'))) { + // Prevent double click on radios, and the double selections (so cancellation) on checkboxes + e.preventDefault() + // The target component still receive the focus + if ($btn.is('input,button')) $btn.trigger('focus') + else $btn.find('input:visible,button:visible').first().trigger('focus') + } + }) + .on('focus.bs.button.data-api blur.bs.button.data-api', '[data-toggle^="button"]', function (e) { + $(e.target).closest('.btn').toggleClass('focus', /^focus(in)?$/.test(e.type)) + }) + +}(jQuery); + +/* ======================================================================== + * Bootstrap: carousel.js v3.3.7 + * http://getbootstrap.com/javascript/#carousel + * ======================================================================== + * Copyright 2011-2016 Twitter, Inc. + * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE) + * ======================================================================== */ + + ++function ($) { + 'use strict'; + + // CAROUSEL CLASS DEFINITION + // ========================= + + var Carousel = function (element, options) { + this.$element = $(element) + this.$indicators = this.$element.find('.carousel-indicators') + this.options = options + this.paused = null + this.sliding = null + this.interval = null + this.$active = null + this.$items = null + + this.options.keyboard && this.$element.on('keydown.bs.carousel', $.proxy(this.keydown, this)) + + this.options.pause == 'hover' && !('ontouchstart' in document.documentElement) && this.$element + .on('mouseenter.bs.carousel', $.proxy(this.pause, this)) + .on('mouseleave.bs.carousel', $.proxy(this.cycle, this)) + } + + Carousel.VERSION = '3.3.7' + + Carousel.TRANSITION_DURATION = 600 + + Carousel.DEFAULTS = { + interval: 5000, + pause: 'hover', + wrap: true, + keyboard: true + } + + Carousel.prototype.keydown = function (e) { + if (/input|textarea/i.test(e.target.tagName)) return + switch (e.which) { + case 37: this.prev(); break + case 39: this.next(); break + default: return + } + + e.preventDefault() + } + + Carousel.prototype.cycle = function (e) { + e || (this.paused = false) + + this.interval && clearInterval(this.interval) + + this.options.interval + && !this.paused + && (this.interval = setInterval($.proxy(this.next, this), this.options.interval)) + + return this + } + + Carousel.prototype.getItemIndex = function (item) { + this.$items = item.parent().children('.item') + return this.$items.index(item || this.$active) + } + + Carousel.prototype.getItemForDirection = function (direction, active) { + var activeIndex = this.getItemIndex(active) + var willWrap = (direction == 'prev' && activeIndex === 0) + || (direction == 'next' && activeIndex == (this.$items.length - 1)) + if (willWrap && !this.options.wrap) return active + var delta = direction == 'prev' ? -1 : 1 + var itemIndex = (activeIndex + delta) % this.$items.length + return this.$items.eq(itemIndex) + } + + Carousel.prototype.to = function (pos) { + var that = this + var activeIndex = this.getItemIndex(this.$active = this.$element.find('.item.active')) + + if (pos > (this.$items.length - 1) || pos < 0) return + + if (this.sliding) return this.$element.one('slid.bs.carousel', function () { that.to(pos) }) // yes, "slid" + if (activeIndex == pos) return this.pause().cycle() + + return this.slide(pos > activeIndex ? 'next' : 'prev', this.$items.eq(pos)) + } + + Carousel.prototype.pause = function (e) { + e || (this.paused = true) + + if (this.$element.find('.next, .prev').length && $.support.transition) { + this.$element.trigger($.support.transition.end) + this.cycle(true) + } + + this.interval = clearInterval(this.interval) + + return this + } + + Carousel.prototype.next = function () { + if (this.sliding) return + return this.slide('next') + } + + Carousel.prototype.prev = function () { + if (this.sliding) return + return this.slide('prev') + } + + Carousel.prototype.slide = function (type, next) { + var $active = this.$element.find('.item.active') + var $next = next || this.getItemForDirection(type, $active) + var isCycling = this.interval + var direction = type == 'next' ? 'left' : 'right' + var that = this + + if ($next.hasClass('active')) return (this.sliding = false) + + var relatedTarget = $next[0] + var slideEvent = $.Event('slide.bs.carousel', { + relatedTarget: relatedTarget, + direction: direction + }) + this.$element.trigger(slideEvent) + if (slideEvent.isDefaultPrevented()) return + + this.sliding = true + + isCycling && this.pause() + + if (this.$indicators.length) { + this.$indicators.find('.active').removeClass('active') + var $nextIndicator = $(this.$indicators.children()[this.getItemIndex($next)]) + $nextIndicator && $nextIndicator.addClass('active') + } + + var slidEvent = $.Event('slid.bs.carousel', { relatedTarget: relatedTarget, direction: direction }) // yes, "slid" + if ($.support.transition && this.$element.hasClass('slide')) { + $next.addClass(type) + $next[0].offsetWidth // force reflow + $active.addClass(direction) + $next.addClass(direction) + $active + .one('bsTransitionEnd', function () { + $next.removeClass([type, direction].join(' ')).addClass('active') + $active.removeClass(['active', direction].join(' ')) + that.sliding = false + setTimeout(function () { + that.$element.trigger(slidEvent) + }, 0) + }) + .emulateTransitionEnd(Carousel.TRANSITION_DURATION) + } else { + $active.removeClass('active') + $next.addClass('active') + this.sliding = false + this.$element.trigger(slidEvent) + } + + isCycling && this.cycle() + + return this + } + + + // CAROUSEL PLUGIN DEFINITION + // ========================== + + function Plugin(option) { + return this.each(function () { + var $this = $(this) + var data = $this.data('bs.carousel') + var options = $.extend({}, Carousel.DEFAULTS, $this.data(), typeof option == 'object' && option) + var action = typeof option == 'string' ? option : options.slide + + if (!data) $this.data('bs.carousel', (data = new Carousel(this, options))) + if (typeof option == 'number') data.to(option) + else if (action) data[action]() + else if (options.interval) data.pause().cycle() + }) + } + + var old = $.fn.carousel + + $.fn.carousel = Plugin + $.fn.carousel.Constructor = Carousel + + + // CAROUSEL NO CONFLICT + // ==================== + + $.fn.carousel.noConflict = function () { + $.fn.carousel = old + return this + } + + + // CAROUSEL DATA-API + // ================= + + var clickHandler = function (e) { + var href + var $this = $(this) + var $target = $($this.attr('data-target') || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) // strip for ie7 + if (!$target.hasClass('carousel')) return + var options = $.extend({}, $target.data(), $this.data()) + var slideIndex = $this.attr('data-slide-to') + if (slideIndex) options.interval = false + + Plugin.call($target, options) + + if (slideIndex) { + $target.data('bs.carousel').to(slideIndex) + } + + e.preventDefault() + } + + $(document) + .on('click.bs.carousel.data-api', '[data-slide]', clickHandler) + .on('click.bs.carousel.data-api', '[data-slide-to]', clickHandler) + + $(window).on('load', function () { + $('[data-ride="carousel"]').each(function () { + var $carousel = $(this) + Plugin.call($carousel, $carousel.data()) + }) + }) + +}(jQuery); + +/* ======================================================================== + * Bootstrap: collapse.js v3.3.7 + * http://getbootstrap.com/javascript/#collapse + * ======================================================================== + * Copyright 2011-2016 Twitter, Inc. + * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE) + * ======================================================================== */ + +/* jshint latedef: false */ + ++function ($) { + 'use strict'; + + // COLLAPSE PUBLIC CLASS DEFINITION + // ================================ + + var Collapse = function (element, options) { + this.$element = $(element) + this.options = $.extend({}, Collapse.DEFAULTS, options) + this.$trigger = $('[data-toggle="collapse"][href="#' + element.id + '"],' + + '[data-toggle="collapse"][data-target="#' + element.id + '"]') + this.transitioning = null + + if (this.options.parent) { + this.$parent = this.getParent() + } else { + this.addAriaAndCollapsedClass(this.$element, this.$trigger) + } + + if (this.options.toggle) this.toggle() + } + + Collapse.VERSION = '3.3.7' + + Collapse.TRANSITION_DURATION = 350 + + Collapse.DEFAULTS = { + toggle: true + } + + Collapse.prototype.dimension = function () { + var hasWidth = this.$element.hasClass('width') + return hasWidth ? 'width' : 'height' + } + + Collapse.prototype.show = function () { + if (this.transitioning || this.$element.hasClass('in')) return + + var activesData + var actives = this.$parent && this.$parent.children('.panel').children('.in, .collapsing') + + if (actives && actives.length) { + activesData = actives.data('bs.collapse') + if (activesData && activesData.transitioning) return + } + + var startEvent = $.Event('show.bs.collapse') + this.$element.trigger(startEvent) + if (startEvent.isDefaultPrevented()) return + + if (actives && actives.length) { + Plugin.call(actives, 'hide') + activesData || actives.data('bs.collapse', null) + } + + var dimension = this.dimension() + + this.$element + .removeClass('collapse') + .addClass('collapsing')[dimension](0) + .attr('aria-expanded', true) + + this.$trigger + .removeClass('collapsed') + .attr('aria-expanded', true) + + this.transitioning = 1 + + var complete = function () { + this.$element + .removeClass('collapsing') + .addClass('collapse in')[dimension]('') + this.transitioning = 0 + this.$element + .trigger('shown.bs.collapse') + } + + if (!$.support.transition) return complete.call(this) + + var scrollSize = $.camelCase(['scroll', dimension].join('-')) + + this.$element + .one('bsTransitionEnd', $.proxy(complete, this)) + .emulateTransitionEnd(Collapse.TRANSITION_DURATION)[dimension](this.$element[0][scrollSize]) + } + + Collapse.prototype.hide = function () { + if (this.transitioning || !this.$element.hasClass('in')) return + + var startEvent = $.Event('hide.bs.collapse') + this.$element.trigger(startEvent) + if (startEvent.isDefaultPrevented()) return + + var dimension = this.dimension() + + this.$element[dimension](this.$element[dimension]())[0].offsetHeight + + this.$element + .addClass('collapsing') + .removeClass('collapse in') + .attr('aria-expanded', false) + + this.$trigger + .addClass('collapsed') + .attr('aria-expanded', false) + + this.transitioning = 1 + + var complete = function () { + this.transitioning = 0 + this.$element + .removeClass('collapsing') + .addClass('collapse') + .trigger('hidden.bs.collapse') + } + + if (!$.support.transition) return complete.call(this) + + this.$element + [dimension](0) + .one('bsTransitionEnd', $.proxy(complete, this)) + .emulateTransitionEnd(Collapse.TRANSITION_DURATION) + } + + Collapse.prototype.toggle = function () { + this[this.$element.hasClass('in') ? 'hide' : 'show']() + } + + Collapse.prototype.getParent = function () { + return $(this.options.parent) + .find('[data-toggle="collapse"][data-parent="' + this.options.parent + '"]') + .each($.proxy(function (i, element) { + var $element = $(element) + this.addAriaAndCollapsedClass(getTargetFromTrigger($element), $element) + }, this)) + .end() + } + + Collapse.prototype.addAriaAndCollapsedClass = function ($element, $trigger) { + var isOpen = $element.hasClass('in') + + $element.attr('aria-expanded', isOpen) + $trigger + .toggleClass('collapsed', !isOpen) + .attr('aria-expanded', isOpen) + } + + function getTargetFromTrigger($trigger) { + var href + var target = $trigger.attr('data-target') + || (href = $trigger.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '') // strip for ie7 + + return $(target) + } + + + // COLLAPSE PLUGIN DEFINITION + // ========================== + + function Plugin(option) { + return this.each(function () { + var $this = $(this) + var data = $this.data('bs.collapse') + var options = $.extend({}, Collapse.DEFAULTS, $this.data(), typeof option == 'object' && option) + + if (!data && options.toggle && /show|hide/.test(option)) options.toggle = false + if (!data) $this.data('bs.collapse', (data = new Collapse(this, options))) + if (typeof option == 'string') data[option]() + }) + } + + var old = $.fn.collapse + + $.fn.collapse = Plugin + $.fn.collapse.Constructor = Collapse + + + // COLLAPSE NO CONFLICT + // ==================== + + $.fn.collapse.noConflict = function () { + $.fn.collapse = old + return this + } + + + // COLLAPSE DATA-API + // ================= + + $(document).on('click.bs.collapse.data-api', '[data-toggle="collapse"]', function (e) { + var $this = $(this) + + if (!$this.attr('data-target')) e.preventDefault() + + var $target = getTargetFromTrigger($this) + var data = $target.data('bs.collapse') + var option = data ? 'toggle' : $this.data() + + Plugin.call($target, option) + }) + +}(jQuery); + +/* ======================================================================== + * Bootstrap: dropdown.js v3.3.7 + * http://getbootstrap.com/javascript/#dropdowns + * ======================================================================== + * Copyright 2011-2016 Twitter, Inc. + * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE) + * ======================================================================== */ + + ++function ($) { + 'use strict'; + + // DROPDOWN CLASS DEFINITION + // ========================= + + var backdrop = '.dropdown-backdrop' + var toggle = '[data-toggle="dropdown"]' + var Dropdown = function (element) { + $(element).on('click.bs.dropdown', this.toggle) + } + + Dropdown.VERSION = '3.3.7' + + function getParent($this) { + var selector = $this.attr('data-target') + + if (!selector) { + selector = $this.attr('href') + selector = selector && /#[A-Za-z]/.test(selector) && selector.replace(/.*(?=#[^\s]*$)/, '') // strip for ie7 + } + + var $parent = selector && $(selector) + + return $parent && $parent.length ? $parent : $this.parent() + } + + function clearMenus(e) { + if (e && e.which === 3) return + $(backdrop).remove() + $(toggle).each(function () { + var $this = $(this) + var $parent = getParent($this) + var relatedTarget = { relatedTarget: this } + + if (!$parent.hasClass('open')) return + + if (e && e.type == 'click' && /input|textarea/i.test(e.target.tagName) && $.contains($parent[0], e.target)) return + + $parent.trigger(e = $.Event('hide.bs.dropdown', relatedTarget)) + + if (e.isDefaultPrevented()) return + + $this.attr('aria-expanded', 'false') + $parent.removeClass('open').trigger($.Event('hidden.bs.dropdown', relatedTarget)) + }) + } + + Dropdown.prototype.toggle = function (e) { + var $this = $(this) + + if ($this.is('.disabled, :disabled')) return + + var $parent = getParent($this) + var isActive = $parent.hasClass('open') + + clearMenus() + + if (!isActive) { + if ('ontouchstart' in document.documentElement && !$parent.closest('.navbar-nav').length) { + // if mobile we use a backdrop because click events don't delegate + $(document.createElement('div')) + .addClass('dropdown-backdrop') + .insertAfter($(this)) + .on('click', clearMenus) + } + + var relatedTarget = { relatedTarget: this } + $parent.trigger(e = $.Event('show.bs.dropdown', relatedTarget)) + + if (e.isDefaultPrevented()) return + + $this + .trigger('focus') + .attr('aria-expanded', 'true') + + $parent + .toggleClass('open') + .trigger($.Event('shown.bs.dropdown', relatedTarget)) + } + + return false + } + + Dropdown.prototype.keydown = function (e) { + if (!/(38|40|27|32)/.test(e.which) || /input|textarea/i.test(e.target.tagName)) return + + var $this = $(this) + + e.preventDefault() + e.stopPropagation() + + if ($this.is('.disabled, :disabled')) return + + var $parent = getParent($this) + var isActive = $parent.hasClass('open') + + if (!isActive && e.which != 27 || isActive && e.which == 27) { + if (e.which == 27) $parent.find(toggle).trigger('focus') + return $this.trigger('click') + } + + var desc = ' li:not(.disabled):visible a' + var $items = $parent.find('.dropdown-menu' + desc) + + if (!$items.length) return + + var index = $items.index(e.target) + + if (e.which == 38 && index > 0) index-- // up + if (e.which == 40 && index < $items.length - 1) index++ // down + if (!~index) index = 0 + + $items.eq(index).trigger('focus') + } + + + // DROPDOWN PLUGIN DEFINITION + // ========================== + + function Plugin(option) { + return this.each(function () { + var $this = $(this) + var data = $this.data('bs.dropdown') + + if (!data) $this.data('bs.dropdown', (data = new Dropdown(this))) + if (typeof option == 'string') data[option].call($this) + }) + } + + var old = $.fn.dropdown + + $.fn.dropdown = Plugin + $.fn.dropdown.Constructor = Dropdown + + + // DROPDOWN NO CONFLICT + // ==================== + + $.fn.dropdown.noConflict = function () { + $.fn.dropdown = old + return this + } + + + // APPLY TO STANDARD DROPDOWN ELEMENTS + // =================================== + + $(document) + .on('click.bs.dropdown.data-api', clearMenus) + .on('click.bs.dropdown.data-api', '.dropdown form', function (e) { e.stopPropagation() }) + .on('click.bs.dropdown.data-api', toggle, Dropdown.prototype.toggle) + .on('keydown.bs.dropdown.data-api', toggle, Dropdown.prototype.keydown) + .on('keydown.bs.dropdown.data-api', '.dropdown-menu', Dropdown.prototype.keydown) + +}(jQuery); + +/* ======================================================================== + * Bootstrap: modal.js v3.3.7 + * http://getbootstrap.com/javascript/#modals + * ======================================================================== + * Copyright 2011-2016 Twitter, Inc. + * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE) + * ======================================================================== */ + + ++function ($) { + 'use strict'; + + // MODAL CLASS DEFINITION + // ====================== + + var Modal = function (element, options) { + this.options = options + this.$body = $(document.body) + this.$element = $(element) + this.$dialog = this.$element.find('.modal-dialog') + this.$backdrop = null + this.isShown = null + this.originalBodyPad = null + this.scrollbarWidth = 0 + this.ignoreBackdropClick = false + + if (this.options.remote) { + this.$element + .find('.modal-content') + .load(this.options.remote, $.proxy(function () { + this.$element.trigger('loaded.bs.modal') + }, this)) + } + } + + Modal.VERSION = '3.3.7' + + Modal.TRANSITION_DURATION = 300 + Modal.BACKDROP_TRANSITION_DURATION = 150 + + Modal.DEFAULTS = { + backdrop: true, + keyboard: true, + show: true + } + + Modal.prototype.toggle = function (_relatedTarget) { + return this.isShown ? this.hide() : this.show(_relatedTarget) + } + + Modal.prototype.show = function (_relatedTarget) { + var that = this + var e = $.Event('show.bs.modal', { relatedTarget: _relatedTarget }) + + this.$element.trigger(e) + + if (this.isShown || e.isDefaultPrevented()) return + + this.isShown = true + + this.checkScrollbar() + this.setScrollbar() + this.$body.addClass('modal-open') + + this.escape() + this.resize() + + this.$element.on('click.dismiss.bs.modal', '[data-dismiss="modal"]', $.proxy(this.hide, this)) + + this.$dialog.on('mousedown.dismiss.bs.modal', function () { + that.$element.one('mouseup.dismiss.bs.modal', function (e) { + if ($(e.target).is(that.$element)) that.ignoreBackdropClick = true + }) + }) + + this.backdrop(function () { + var transition = $.support.transition && that.$element.hasClass('fade') + + if (!that.$element.parent().length) { + that.$element.appendTo(that.$body) // don't move modals dom position + } + + that.$element + .show() + .scrollTop(0) + + that.adjustDialog() + + if (transition) { + that.$element[0].offsetWidth // force reflow + } + + that.$element.addClass('in') + + that.enforceFocus() + + var e = $.Event('shown.bs.modal', { relatedTarget: _relatedTarget }) + + transition ? + that.$dialog // wait for modal to slide in + .one('bsTransitionEnd', function () { + that.$element.trigger('focus').trigger(e) + }) + .emulateTransitionEnd(Modal.TRANSITION_DURATION) : + that.$element.trigger('focus').trigger(e) + }) + } + + Modal.prototype.hide = function (e) { + if (e) e.preventDefault() + + e = $.Event('hide.bs.modal') + + this.$element.trigger(e) + + if (!this.isShown || e.isDefaultPrevented()) return + + this.isShown = false + + this.escape() + this.resize() + + $(document).off('focusin.bs.modal') + + this.$element + .removeClass('in') + .off('click.dismiss.bs.modal') + .off('mouseup.dismiss.bs.modal') + + this.$dialog.off('mousedown.dismiss.bs.modal') + + $.support.transition && this.$element.hasClass('fade') ? + this.$element + .one('bsTransitionEnd', $.proxy(this.hideModal, this)) + .emulateTransitionEnd(Modal.TRANSITION_DURATION) : + this.hideModal() + } + + Modal.prototype.enforceFocus = function () { + $(document) + .off('focusin.bs.modal') // guard against infinite focus loop + .on('focusin.bs.modal', $.proxy(function (e) { + if (document !== e.target && + this.$element[0] !== e.target && + !this.$element.has(e.target).length) { + this.$element.trigger('focus') + } + }, this)) + } + + Modal.prototype.escape = function () { + if (this.isShown && this.options.keyboard) { + this.$element.on('keydown.dismiss.bs.modal', $.proxy(function (e) { + e.which == 27 && this.hide() + }, this)) + } else if (!this.isShown) { + this.$element.off('keydown.dismiss.bs.modal') + } + } + + Modal.prototype.resize = function () { + if (this.isShown) { + $(window).on('resize.bs.modal', $.proxy(this.handleUpdate, this)) + } else { + $(window).off('resize.bs.modal') + } + } + + Modal.prototype.hideModal = function () { + var that = this + this.$element.hide() + this.backdrop(function () { + that.$body.removeClass('modal-open') + that.resetAdjustments() + that.resetScrollbar() + that.$element.trigger('hidden.bs.modal') + }) + } + + Modal.prototype.removeBackdrop = function () { + this.$backdrop && this.$backdrop.remove() + this.$backdrop = null + } + + Modal.prototype.backdrop = function (callback) { + var that = this + var animate = this.$element.hasClass('fade') ? 'fade' : '' + + if (this.isShown && this.options.backdrop) { + var doAnimate = $.support.transition && animate + + this.$backdrop = $(document.createElement('div')) + .addClass('modal-backdrop ' + animate) + .appendTo(this.$body) + + this.$element.on('click.dismiss.bs.modal', $.proxy(function (e) { + if (this.ignoreBackdropClick) { + this.ignoreBackdropClick = false + return + } + if (e.target !== e.currentTarget) return + this.options.backdrop == 'static' + ? this.$element[0].focus() + : this.hide() + }, this)) + + if (doAnimate) this.$backdrop[0].offsetWidth // force reflow + + this.$backdrop.addClass('in') + + if (!callback) return + + doAnimate ? + this.$backdrop + .one('bsTransitionEnd', callback) + .emulateTransitionEnd(Modal.BACKDROP_TRANSITION_DURATION) : + callback() + + } else if (!this.isShown && this.$backdrop) { + this.$backdrop.removeClass('in') + + var callbackRemove = function () { + that.removeBackdrop() + callback && callback() + } + $.support.transition && this.$element.hasClass('fade') ? + this.$backdrop + .one('bsTransitionEnd', callbackRemove) + .emulateTransitionEnd(Modal.BACKDROP_TRANSITION_DURATION) : + callbackRemove() + + } else if (callback) { + callback() + } + } + + // these following methods are used to handle overflowing modals + + Modal.prototype.handleUpdate = function () { + this.adjustDialog() + } + + Modal.prototype.adjustDialog = function () { + var modalIsOverflowing = this.$element[0].scrollHeight > document.documentElement.clientHeight + + this.$element.css({ + paddingLeft: !this.bodyIsOverflowing && modalIsOverflowing ? this.scrollbarWidth : '', + paddingRight: this.bodyIsOverflowing && !modalIsOverflowing ? this.scrollbarWidth : '' + }) + } + + Modal.prototype.resetAdjustments = function () { + this.$element.css({ + paddingLeft: '', + paddingRight: '' + }) + } + + Modal.prototype.checkScrollbar = function () { + var fullWindowWidth = window.innerWidth + if (!fullWindowWidth) { // workaround for missing window.innerWidth in IE8 + var documentElementRect = document.documentElement.getBoundingClientRect() + fullWindowWidth = documentElementRect.right - Math.abs(documentElementRect.left) + } + this.bodyIsOverflowing = document.body.clientWidth < fullWindowWidth + this.scrollbarWidth = this.measureScrollbar() + } + + Modal.prototype.setScrollbar = function () { + var bodyPad = parseInt((this.$body.css('padding-right') || 0), 10) + this.originalBodyPad = document.body.style.paddingRight || '' + if (this.bodyIsOverflowing) this.$body.css('padding-right', bodyPad + this.scrollbarWidth) + } + + Modal.prototype.resetScrollbar = function () { + this.$body.css('padding-right', this.originalBodyPad) + } + + Modal.prototype.measureScrollbar = function () { // thx walsh + var scrollDiv = document.createElement('div') + scrollDiv.className = 'modal-scrollbar-measure' + this.$body.append(scrollDiv) + var scrollbarWidth = scrollDiv.offsetWidth - scrollDiv.clientWidth + this.$body[0].removeChild(scrollDiv) + return scrollbarWidth + } + + + // MODAL PLUGIN DEFINITION + // ======================= + + function Plugin(option, _relatedTarget) { + return this.each(function () { + var $this = $(this) + var data = $this.data('bs.modal') + var options = $.extend({}, Modal.DEFAULTS, $this.data(), typeof option == 'object' && option) + + if (!data) $this.data('bs.modal', (data = new Modal(this, options))) + if (typeof option == 'string') data[option](_relatedTarget) + else if (options.show) data.show(_relatedTarget) + }) + } + + var old = $.fn.modal + + $.fn.modal = Plugin + $.fn.modal.Constructor = Modal + + + // MODAL NO CONFLICT + // ================= + + $.fn.modal.noConflict = function () { + $.fn.modal = old + return this + } + + + // MODAL DATA-API + // ============== + + $(document).on('click.bs.modal.data-api', '[data-toggle="modal"]', function (e) { + var $this = $(this) + var href = $this.attr('href') + var $target = $($this.attr('data-target') || (href && href.replace(/.*(?=#[^\s]+$)/, ''))) // strip for ie7 + var option = $target.data('bs.modal') ? 'toggle' : $.extend({ remote: !/#/.test(href) && href }, $target.data(), $this.data()) + + if ($this.is('a')) e.preventDefault() + + $target.one('show.bs.modal', function (showEvent) { + if (showEvent.isDefaultPrevented()) return // only register focus restorer if modal will actually get shown + $target.one('hidden.bs.modal', function () { + $this.is(':visible') && $this.trigger('focus') + }) + }) + Plugin.call($target, option, this) + }) + +}(jQuery); + +/* ======================================================================== + * Bootstrap: tooltip.js v3.3.7 + * http://getbootstrap.com/javascript/#tooltip + * Inspired by the original jQuery.tipsy by Jason Frame + * ======================================================================== + * Copyright 2011-2016 Twitter, Inc. + * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE) + * ======================================================================== */ + + ++function ($) { + 'use strict'; + + // TOOLTIP PUBLIC CLASS DEFINITION + // =============================== + + var Tooltip = function (element, options) { + this.type = null + this.options = null + this.enabled = null + this.timeout = null + this.hoverState = null + this.$element = null + this.inState = null + + this.init('tooltip', element, options) + } + + Tooltip.VERSION = '3.3.7' + + Tooltip.TRANSITION_DURATION = 150 + + Tooltip.DEFAULTS = { + animation: true, + placement: 'top', + selector: false, + template: '', + trigger: 'hover focus', + title: '', + delay: 0, + html: false, + container: false, + viewport: { + selector: 'body', + padding: 0 + } + } + + Tooltip.prototype.init = function (type, element, options) { + this.enabled = true + this.type = type + this.$element = $(element) + this.options = this.getOptions(options) + this.$viewport = this.options.viewport && $($.isFunction(this.options.viewport) ? this.options.viewport.call(this, this.$element) : (this.options.viewport.selector || this.options.viewport)) + this.inState = { click: false, hover: false, focus: false } + + if (this.$element[0] instanceof document.constructor && !this.options.selector) { + throw new Error('`selector` option must be specified when initializing ' + this.type + ' on the window.document object!') + } + + var triggers = this.options.trigger.split(' ') + + for (var i = triggers.length; i--;) { + var trigger = triggers[i] + + if (trigger == 'click') { + this.$element.on('click.' + this.type, this.options.selector, $.proxy(this.toggle, this)) + } else if (trigger != 'manual') { + var eventIn = trigger == 'hover' ? 'mouseenter' : 'focusin' + var eventOut = trigger == 'hover' ? 'mouseleave' : 'focusout' + + this.$element.on(eventIn + '.' + this.type, this.options.selector, $.proxy(this.enter, this)) + this.$element.on(eventOut + '.' + this.type, this.options.selector, $.proxy(this.leave, this)) + } + } + + this.options.selector ? + (this._options = $.extend({}, this.options, { trigger: 'manual', selector: '' })) : + this.fixTitle() + } + + Tooltip.prototype.getDefaults = function () { + return Tooltip.DEFAULTS + } + + Tooltip.prototype.getOptions = function (options) { + options = $.extend({}, this.getDefaults(), this.$element.data(), options) + + if (options.delay && typeof options.delay == 'number') { + options.delay = { + show: options.delay, + hide: options.delay + } + } + + return options + } + + Tooltip.prototype.getDelegateOptions = function () { + var options = {} + var defaults = this.getDefaults() + + this._options && $.each(this._options, function (key, value) { + if (defaults[key] != value) options[key] = value + }) + + return options + } + + Tooltip.prototype.enter = function (obj) { + var self = obj instanceof this.constructor ? + obj : $(obj.currentTarget).data('bs.' + this.type) + + if (!self) { + self = new this.constructor(obj.currentTarget, this.getDelegateOptions()) + $(obj.currentTarget).data('bs.' + this.type, self) + } + + if (obj instanceof $.Event) { + self.inState[obj.type == 'focusin' ? 'focus' : 'hover'] = true + } + + if (self.tip().hasClass('in') || self.hoverState == 'in') { + self.hoverState = 'in' + return + } + + clearTimeout(self.timeout) + + self.hoverState = 'in' + + if (!self.options.delay || !self.options.delay.show) return self.show() + + self.timeout = setTimeout(function () { + if (self.hoverState == 'in') self.show() + }, self.options.delay.show) + } + + Tooltip.prototype.isInStateTrue = function () { + for (var key in this.inState) { + if (this.inState[key]) return true + } + + return false + } + + Tooltip.prototype.leave = function (obj) { + var self = obj instanceof this.constructor ? + obj : $(obj.currentTarget).data('bs.' + this.type) + + if (!self) { + self = new this.constructor(obj.currentTarget, this.getDelegateOptions()) + $(obj.currentTarget).data('bs.' + this.type, self) + } + + if (obj instanceof $.Event) { + self.inState[obj.type == 'focusout' ? 'focus' : 'hover'] = false + } + + if (self.isInStateTrue()) return + + clearTimeout(self.timeout) + + self.hoverState = 'out' + + if (!self.options.delay || !self.options.delay.hide) return self.hide() + + self.timeout = setTimeout(function () { + if (self.hoverState == 'out') self.hide() + }, self.options.delay.hide) + } + + Tooltip.prototype.show = function () { + var e = $.Event('show.bs.' + this.type) + + if (this.hasContent() && this.enabled) { + this.$element.trigger(e) + + var inDom = $.contains(this.$element[0].ownerDocument.documentElement, this.$element[0]) + if (e.isDefaultPrevented() || !inDom) return + var that = this + + var $tip = this.tip() + + var tipId = this.getUID(this.type) + + this.setContent() + $tip.attr('id', tipId) + this.$element.attr('aria-describedby', tipId) + + if (this.options.animation) $tip.addClass('fade') + + var placement = typeof this.options.placement == 'function' ? + this.options.placement.call(this, $tip[0], this.$element[0]) : + this.options.placement + + var autoToken = /\s?auto?\s?/i + var autoPlace = autoToken.test(placement) + if (autoPlace) placement = placement.replace(autoToken, '') || 'top' + + $tip + .detach() + .css({ top: 0, left: 0, display: 'block' }) + .addClass(placement) + .data('bs.' + this.type, this) + + this.options.container ? $tip.appendTo(this.options.container) : $tip.insertAfter(this.$element) + this.$element.trigger('inserted.bs.' + this.type) + + var pos = this.getPosition() + var actualWidth = $tip[0].offsetWidth + var actualHeight = $tip[0].offsetHeight + + if (autoPlace) { + var orgPlacement = placement + var viewportDim = this.getPosition(this.$viewport) + + placement = placement == 'bottom' && pos.bottom + actualHeight > viewportDim.bottom ? 'top' : + placement == 'top' && pos.top - actualHeight < viewportDim.top ? 'bottom' : + placement == 'right' && pos.right + actualWidth > viewportDim.width ? 'left' : + placement == 'left' && pos.left - actualWidth < viewportDim.left ? 'right' : + placement + + $tip + .removeClass(orgPlacement) + .addClass(placement) + } + + var calculatedOffset = this.getCalculatedOffset(placement, pos, actualWidth, actualHeight) + + this.applyPlacement(calculatedOffset, placement) + + var complete = function () { + var prevHoverState = that.hoverState + that.$element.trigger('shown.bs.' + that.type) + that.hoverState = null + + if (prevHoverState == 'out') that.leave(that) + } + + $.support.transition && this.$tip.hasClass('fade') ? + $tip + .one('bsTransitionEnd', complete) + .emulateTransitionEnd(Tooltip.TRANSITION_DURATION) : + complete() + } + } + + Tooltip.prototype.applyPlacement = function (offset, placement) { + var $tip = this.tip() + var width = $tip[0].offsetWidth + var height = $tip[0].offsetHeight + + // manually read margins because getBoundingClientRect includes difference + var marginTop = parseInt($tip.css('margin-top'), 10) + var marginLeft = parseInt($tip.css('margin-left'), 10) + + // we must check for NaN for ie 8/9 + if (isNaN(marginTop)) marginTop = 0 + if (isNaN(marginLeft)) marginLeft = 0 + + offset.top += marginTop + offset.left += marginLeft + + // $.fn.offset doesn't round pixel values + // so we use setOffset directly with our own function B-0 + $.offset.setOffset($tip[0], $.extend({ + using: function (props) { + $tip.css({ + top: Math.round(props.top), + left: Math.round(props.left) + }) + } + }, offset), 0) + + $tip.addClass('in') + + // check to see if placing tip in new offset caused the tip to resize itself + var actualWidth = $tip[0].offsetWidth + var actualHeight = $tip[0].offsetHeight + + if (placement == 'top' && actualHeight != height) { + offset.top = offset.top + height - actualHeight + } + + var delta = this.getViewportAdjustedDelta(placement, offset, actualWidth, actualHeight) + + if (delta.left) offset.left += delta.left + else offset.top += delta.top + + var isVertical = /top|bottom/.test(placement) + var arrowDelta = isVertical ? delta.left * 2 - width + actualWidth : delta.top * 2 - height + actualHeight + var arrowOffsetPosition = isVertical ? 'offsetWidth' : 'offsetHeight' + + $tip.offset(offset) + this.replaceArrow(arrowDelta, $tip[0][arrowOffsetPosition], isVertical) + } + + Tooltip.prototype.replaceArrow = function (delta, dimension, isVertical) { + this.arrow() + .css(isVertical ? 'left' : 'top', 50 * (1 - delta / dimension) + '%') + .css(isVertical ? 'top' : 'left', '') + } + + Tooltip.prototype.setContent = function () { + var $tip = this.tip() + var title = this.getTitle() + + $tip.find('.tooltip-inner')[this.options.html ? 'html' : 'text'](title) + $tip.removeClass('fade in top bottom left right') + } + + Tooltip.prototype.hide = function (callback) { + var that = this + var $tip = $(this.$tip) + var e = $.Event('hide.bs.' + this.type) + + function complete() { + if (that.hoverState != 'in') $tip.detach() + if (that.$element) { // TODO: Check whether guarding this code with this `if` is really necessary. + that.$element + .removeAttr('aria-describedby') + .trigger('hidden.bs.' + that.type) + } + callback && callback() + } + + this.$element.trigger(e) + + if (e.isDefaultPrevented()) return + + $tip.removeClass('in') + + $.support.transition && $tip.hasClass('fade') ? + $tip + .one('bsTransitionEnd', complete) + .emulateTransitionEnd(Tooltip.TRANSITION_DURATION) : + complete() + + this.hoverState = null + + return this + } + + Tooltip.prototype.fixTitle = function () { + var $e = this.$element + if ($e.attr('title') || typeof $e.attr('data-original-title') != 'string') { + $e.attr('data-original-title', $e.attr('title') || '').attr('title', '') + } + } + + Tooltip.prototype.hasContent = function () { + return this.getTitle() + } + + Tooltip.prototype.getPosition = function ($element) { + $element = $element || this.$element + + var el = $element[0] + var isBody = el.tagName == 'BODY' + + var elRect = el.getBoundingClientRect() + if (elRect.width == null) { + // width and height are missing in IE8, so compute them manually; see https://github.com/twbs/bootstrap/issues/14093 + elRect = $.extend({}, elRect, { width: elRect.right - elRect.left, height: elRect.bottom - elRect.top }) + } + var isSvg = window.SVGElement && el instanceof window.SVGElement + // Avoid using $.offset() on SVGs since it gives incorrect results in jQuery 3. + // See https://github.com/twbs/bootstrap/issues/20280 + var elOffset = isBody ? { top: 0, left: 0 } : (isSvg ? null : $element.offset()) + var scroll = { scroll: isBody ? document.documentElement.scrollTop || document.body.scrollTop : $element.scrollTop() } + var outerDims = isBody ? { width: $(window).width(), height: $(window).height() } : null + + return $.extend({}, elRect, scroll, outerDims, elOffset) + } + + Tooltip.prototype.getCalculatedOffset = function (placement, pos, actualWidth, actualHeight) { + return placement == 'bottom' ? { top: pos.top + pos.height, left: pos.left + pos.width / 2 - actualWidth / 2 } : + placement == 'top' ? { top: pos.top - actualHeight, left: pos.left + pos.width / 2 - actualWidth / 2 } : + placement == 'left' ? { top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left - actualWidth } : + /* placement == 'right' */ { top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left + pos.width } + + } + + Tooltip.prototype.getViewportAdjustedDelta = function (placement, pos, actualWidth, actualHeight) { + var delta = { top: 0, left: 0 } + if (!this.$viewport) return delta + + var viewportPadding = this.options.viewport && this.options.viewport.padding || 0 + var viewportDimensions = this.getPosition(this.$viewport) + + if (/right|left/.test(placement)) { + var topEdgeOffset = pos.top - viewportPadding - viewportDimensions.scroll + var bottomEdgeOffset = pos.top + viewportPadding - viewportDimensions.scroll + actualHeight + if (topEdgeOffset < viewportDimensions.top) { // top overflow + delta.top = viewportDimensions.top - topEdgeOffset + } else if (bottomEdgeOffset > viewportDimensions.top + viewportDimensions.height) { // bottom overflow + delta.top = viewportDimensions.top + viewportDimensions.height - bottomEdgeOffset + } + } else { + var leftEdgeOffset = pos.left - viewportPadding + var rightEdgeOffset = pos.left + viewportPadding + actualWidth + if (leftEdgeOffset < viewportDimensions.left) { // left overflow + delta.left = viewportDimensions.left - leftEdgeOffset + } else if (rightEdgeOffset > viewportDimensions.right) { // right overflow + delta.left = viewportDimensions.left + viewportDimensions.width - rightEdgeOffset + } + } + + return delta + } + + Tooltip.prototype.getTitle = function () { + var title + var $e = this.$element + var o = this.options + + title = $e.attr('data-original-title') + || (typeof o.title == 'function' ? o.title.call($e[0]) : o.title) + + return title + } + + Tooltip.prototype.getUID = function (prefix) { + do prefix += ~~(Math.random() * 1000000) + while (document.getElementById(prefix)) + return prefix + } + + Tooltip.prototype.tip = function () { + if (!this.$tip) { + this.$tip = $(this.options.template) + if (this.$tip.length != 1) { + throw new Error(this.type + ' `template` option must consist of exactly 1 top-level element!') + } + } + return this.$tip + } + + Tooltip.prototype.arrow = function () { + return (this.$arrow = this.$arrow || this.tip().find('.tooltip-arrow')) + } + + Tooltip.prototype.enable = function () { + this.enabled = true + } + + Tooltip.prototype.disable = function () { + this.enabled = false + } + + Tooltip.prototype.toggleEnabled = function () { + this.enabled = !this.enabled + } + + Tooltip.prototype.toggle = function (e) { + var self = this + if (e) { + self = $(e.currentTarget).data('bs.' + this.type) + if (!self) { + self = new this.constructor(e.currentTarget, this.getDelegateOptions()) + $(e.currentTarget).data('bs.' + this.type, self) + } + } + + if (e) { + self.inState.click = !self.inState.click + if (self.isInStateTrue()) self.enter(self) + else self.leave(self) + } else { + self.tip().hasClass('in') ? self.leave(self) : self.enter(self) + } + } + + Tooltip.prototype.destroy = function () { + var that = this + clearTimeout(this.timeout) + this.hide(function () { + that.$element.off('.' + that.type).removeData('bs.' + that.type) + if (that.$tip) { + that.$tip.detach() + } + that.$tip = null + that.$arrow = null + that.$viewport = null + that.$element = null + }) + } + + + // TOOLTIP PLUGIN DEFINITION + // ========================= + + function Plugin(option) { + return this.each(function () { + var $this = $(this) + var data = $this.data('bs.tooltip') + var options = typeof option == 'object' && option + + if (!data && /destroy|hide/.test(option)) return + if (!data) $this.data('bs.tooltip', (data = new Tooltip(this, options))) + if (typeof option == 'string') data[option]() + }) + } + + var old = $.fn.tooltip + + $.fn.tooltip = Plugin + $.fn.tooltip.Constructor = Tooltip + + + // TOOLTIP NO CONFLICT + // =================== + + $.fn.tooltip.noConflict = function () { + $.fn.tooltip = old + return this + } + +}(jQuery); + +/* ======================================================================== + * Bootstrap: popover.js v3.3.7 + * http://getbootstrap.com/javascript/#popovers + * ======================================================================== + * Copyright 2011-2016 Twitter, Inc. + * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE) + * ======================================================================== */ + + ++function ($) { + 'use strict'; + + // POPOVER PUBLIC CLASS DEFINITION + // =============================== + + var Popover = function (element, options) { + this.init('popover', element, options) + } + + if (!$.fn.tooltip) throw new Error('Popover requires tooltip.js') + + Popover.VERSION = '3.3.7' + + Popover.DEFAULTS = $.extend({}, $.fn.tooltip.Constructor.DEFAULTS, { + placement: 'right', + trigger: 'click', + content: '', + template: '' + }) + + + // NOTE: POPOVER EXTENDS tooltip.js + // ================================ + + Popover.prototype = $.extend({}, $.fn.tooltip.Constructor.prototype) + + Popover.prototype.constructor = Popover + + Popover.prototype.getDefaults = function () { + return Popover.DEFAULTS + } + + Popover.prototype.setContent = function () { + var $tip = this.tip() + var title = this.getTitle() + var content = this.getContent() + + $tip.find('.popover-title')[this.options.html ? 'html' : 'text'](title) + $tip.find('.popover-content').children().detach().end()[ // we use append for html objects to maintain js events + this.options.html ? (typeof content == 'string' ? 'html' : 'append') : 'text' + ](content) + + $tip.removeClass('fade top bottom left right in') + + // IE8 doesn't accept hiding via the `:empty` pseudo selector, we have to do + // this manually by checking the contents. + if (!$tip.find('.popover-title').html()) $tip.find('.popover-title').hide() + } + + Popover.prototype.hasContent = function () { + return this.getTitle() || this.getContent() + } + + Popover.prototype.getContent = function () { + var $e = this.$element + var o = this.options + + return $e.attr('data-content') + || (typeof o.content == 'function' ? + o.content.call($e[0]) : + o.content) + } + + Popover.prototype.arrow = function () { + return (this.$arrow = this.$arrow || this.tip().find('.arrow')) + } + + + // POPOVER PLUGIN DEFINITION + // ========================= + + function Plugin(option) { + return this.each(function () { + var $this = $(this) + var data = $this.data('bs.popover') + var options = typeof option == 'object' && option + + if (!data && /destroy|hide/.test(option)) return + if (!data) $this.data('bs.popover', (data = new Popover(this, options))) + if (typeof option == 'string') data[option]() + }) + } + + var old = $.fn.popover + + $.fn.popover = Plugin + $.fn.popover.Constructor = Popover + + + // POPOVER NO CONFLICT + // =================== + + $.fn.popover.noConflict = function () { + $.fn.popover = old + return this + } + +}(jQuery); + +/* ======================================================================== + * Bootstrap: scrollspy.js v3.3.7 + * http://getbootstrap.com/javascript/#scrollspy + * ======================================================================== + * Copyright 2011-2016 Twitter, Inc. + * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE) + * ======================================================================== */ + + ++function ($) { + 'use strict'; + + // SCROLLSPY CLASS DEFINITION + // ========================== + + function ScrollSpy(element, options) { + this.$body = $(document.body) + this.$scrollElement = $(element).is(document.body) ? $(window) : $(element) + this.options = $.extend({}, ScrollSpy.DEFAULTS, options) + this.selector = (this.options.target || '') + ' .nav li > a' + this.offsets = [] + this.targets = [] + this.activeTarget = null + this.scrollHeight = 0 + + this.$scrollElement.on('scroll.bs.scrollspy', $.proxy(this.process, this)) + this.refresh() + this.process() + } + + ScrollSpy.VERSION = '3.3.7' + + ScrollSpy.DEFAULTS = { + offset: 10 + } + + ScrollSpy.prototype.getScrollHeight = function () { + return this.$scrollElement[0].scrollHeight || Math.max(this.$body[0].scrollHeight, document.documentElement.scrollHeight) + } + + ScrollSpy.prototype.refresh = function () { + var that = this + var offsetMethod = 'offset' + var offsetBase = 0 + + this.offsets = [] + this.targets = [] + this.scrollHeight = this.getScrollHeight() + + if (!$.isWindow(this.$scrollElement[0])) { + offsetMethod = 'position' + offsetBase = this.$scrollElement.scrollTop() + } + + this.$body + .find(this.selector) + .map(function () { + var $el = $(this) + var href = $el.data('target') || $el.attr('href') + var $href = /^#./.test(href) && $(href) + + return ($href + && $href.length + && $href.is(':visible') + && [[$href[offsetMethod]().top + offsetBase, href]]) || null + }) + .sort(function (a, b) { return a[0] - b[0] }) + .each(function () { + that.offsets.push(this[0]) + that.targets.push(this[1]) + }) + } + + ScrollSpy.prototype.process = function () { + var scrollTop = this.$scrollElement.scrollTop() + this.options.offset + var scrollHeight = this.getScrollHeight() + var maxScroll = this.options.offset + scrollHeight - this.$scrollElement.height() + var offsets = this.offsets + var targets = this.targets + var activeTarget = this.activeTarget + var i + + if (this.scrollHeight != scrollHeight) { + this.refresh() + } + + if (scrollTop >= maxScroll) { + return activeTarget != (i = targets[targets.length - 1]) && this.activate(i) + } + + if (activeTarget && scrollTop < offsets[0]) { + this.activeTarget = null + return this.clear() + } + + for (i = offsets.length; i--;) { + activeTarget != targets[i] + && scrollTop >= offsets[i] + && (offsets[i + 1] === undefined || scrollTop < offsets[i + 1]) + && this.activate(targets[i]) + } + } + + ScrollSpy.prototype.activate = function (target) { + this.activeTarget = target + + this.clear() + + var selector = this.selector + + '[data-target="' + target + '"],' + + this.selector + '[href="' + target + '"]' + + var active = $(selector) + .parents('li') + .addClass('active') + + if (active.parent('.dropdown-menu').length) { + active = active + .closest('li.dropdown') + .addClass('active') + } + + active.trigger('activate.bs.scrollspy') + } + + ScrollSpy.prototype.clear = function () { + $(this.selector) + .parentsUntil(this.options.target, '.active') + .removeClass('active') + } + + + // SCROLLSPY PLUGIN DEFINITION + // =========================== + + function Plugin(option) { + return this.each(function () { + var $this = $(this) + var data = $this.data('bs.scrollspy') + var options = typeof option == 'object' && option + + if (!data) $this.data('bs.scrollspy', (data = new ScrollSpy(this, options))) + if (typeof option == 'string') data[option]() + }) + } + + var old = $.fn.scrollspy + + $.fn.scrollspy = Plugin + $.fn.scrollspy.Constructor = ScrollSpy + + + // SCROLLSPY NO CONFLICT + // ===================== + + $.fn.scrollspy.noConflict = function () { + $.fn.scrollspy = old + return this + } + + + // SCROLLSPY DATA-API + // ================== + + $(window).on('load.bs.scrollspy.data-api', function () { + $('[data-spy="scroll"]').each(function () { + var $spy = $(this) + Plugin.call($spy, $spy.data()) + }) + }) + +}(jQuery); + +/* ======================================================================== + * Bootstrap: tab.js v3.3.7 + * http://getbootstrap.com/javascript/#tabs + * ======================================================================== + * Copyright 2011-2016 Twitter, Inc. + * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE) + * ======================================================================== */ + + ++function ($) { + 'use strict'; + + // TAB CLASS DEFINITION + // ==================== + + var Tab = function (element) { + // jscs:disable requireDollarBeforejQueryAssignment + this.element = $(element) + // jscs:enable requireDollarBeforejQueryAssignment + } + + Tab.VERSION = '3.3.7' + + Tab.TRANSITION_DURATION = 150 + + Tab.prototype.show = function () { + var $this = this.element + var $ul = $this.closest('ul:not(.dropdown-menu)') + var selector = $this.data('target') + + if (!selector) { + selector = $this.attr('href') + selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') // strip for ie7 + } + + if ($this.parent('li').hasClass('active')) return + + var $previous = $ul.find('.active:last a') + var hideEvent = $.Event('hide.bs.tab', { + relatedTarget: $this[0] + }) + var showEvent = $.Event('show.bs.tab', { + relatedTarget: $previous[0] + }) + + $previous.trigger(hideEvent) + $this.trigger(showEvent) + + if (showEvent.isDefaultPrevented() || hideEvent.isDefaultPrevented()) return + + var $target = $(selector) + + this.activate($this.closest('li'), $ul) + this.activate($target, $target.parent(), function () { + $previous.trigger({ + type: 'hidden.bs.tab', + relatedTarget: $this[0] + }) + $this.trigger({ + type: 'shown.bs.tab', + relatedTarget: $previous[0] + }) + }) + } + + Tab.prototype.activate = function (element, container, callback) { + var $active = container.find('> .active') + var transition = callback + && $.support.transition + && ($active.length && $active.hasClass('fade') || !!container.find('> .fade').length) + + function next() { + $active + .removeClass('active') + .find('> .dropdown-menu > .active') + .removeClass('active') + .end() + .find('[data-toggle="tab"]') + .attr('aria-expanded', false) + + element + .addClass('active') + .find('[data-toggle="tab"]') + .attr('aria-expanded', true) + + if (transition) { + element[0].offsetWidth // reflow for transition + element.addClass('in') + } else { + element.removeClass('fade') + } + + if (element.parent('.dropdown-menu').length) { + element + .closest('li.dropdown') + .addClass('active') + .end() + .find('[data-toggle="tab"]') + .attr('aria-expanded', true) + } + + callback && callback() + } + + $active.length && transition ? + $active + .one('bsTransitionEnd', next) + .emulateTransitionEnd(Tab.TRANSITION_DURATION) : + next() + + $active.removeClass('in') + } + + + // TAB PLUGIN DEFINITION + // ===================== + + function Plugin(option) { + return this.each(function () { + var $this = $(this) + var data = $this.data('bs.tab') + + if (!data) $this.data('bs.tab', (data = new Tab(this))) + if (typeof option == 'string') data[option]() + }) + } + + var old = $.fn.tab + + $.fn.tab = Plugin + $.fn.tab.Constructor = Tab + + + // TAB NO CONFLICT + // =============== + + $.fn.tab.noConflict = function () { + $.fn.tab = old + return this + } + + + // TAB DATA-API + // ============ + + var clickHandler = function (e) { + e.preventDefault() + Plugin.call($(this), 'show') + } + + $(document) + .on('click.bs.tab.data-api', '[data-toggle="tab"]', clickHandler) + .on('click.bs.tab.data-api', '[data-toggle="pill"]', clickHandler) + +}(jQuery); + +/* ======================================================================== + * Bootstrap: affix.js v3.3.7 + * http://getbootstrap.com/javascript/#affix + * ======================================================================== + * Copyright 2011-2016 Twitter, Inc. + * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE) + * ======================================================================== */ + + ++function ($) { + 'use strict'; + + // AFFIX CLASS DEFINITION + // ====================== + + var Affix = function (element, options) { + this.options = $.extend({}, Affix.DEFAULTS, options) + + this.$target = $(this.options.target) + .on('scroll.bs.affix.data-api', $.proxy(this.checkPosition, this)) + .on('click.bs.affix.data-api', $.proxy(this.checkPositionWithEventLoop, this)) + + this.$element = $(element) + this.affixed = null + this.unpin = null + this.pinnedOffset = null + + this.checkPosition() + } + + Affix.VERSION = '3.3.7' + + Affix.RESET = 'affix affix-top affix-bottom' + + Affix.DEFAULTS = { + offset: 0, + target: window + } + + Affix.prototype.getState = function (scrollHeight, height, offsetTop, offsetBottom) { + var scrollTop = this.$target.scrollTop() + var position = this.$element.offset() + var targetHeight = this.$target.height() + + if (offsetTop != null && this.affixed == 'top') return scrollTop < offsetTop ? 'top' : false + + if (this.affixed == 'bottom') { + if (offsetTop != null) return (scrollTop + this.unpin <= position.top) ? false : 'bottom' + return (scrollTop + targetHeight <= scrollHeight - offsetBottom) ? false : 'bottom' + } + + var initializing = this.affixed == null + var colliderTop = initializing ? scrollTop : position.top + var colliderHeight = initializing ? targetHeight : height + + if (offsetTop != null && scrollTop <= offsetTop) return 'top' + if (offsetBottom != null && (colliderTop + colliderHeight >= scrollHeight - offsetBottom)) return 'bottom' + + return false + } + + Affix.prototype.getPinnedOffset = function () { + if (this.pinnedOffset) return this.pinnedOffset + this.$element.removeClass(Affix.RESET).addClass('affix') + var scrollTop = this.$target.scrollTop() + var position = this.$element.offset() + return (this.pinnedOffset = position.top - scrollTop) + } + + Affix.prototype.checkPositionWithEventLoop = function () { + setTimeout($.proxy(this.checkPosition, this), 1) + } + + Affix.prototype.checkPosition = function () { + if (!this.$element.is(':visible')) return + + var height = this.$element.height() + var offset = this.options.offset + var offsetTop = offset.top + var offsetBottom = offset.bottom + var scrollHeight = Math.max($(document).height(), $(document.body).height()) + + if (typeof offset != 'object') offsetBottom = offsetTop = offset + if (typeof offsetTop == 'function') offsetTop = offset.top(this.$element) + if (typeof offsetBottom == 'function') offsetBottom = offset.bottom(this.$element) + + var affix = this.getState(scrollHeight, height, offsetTop, offsetBottom) + + if (this.affixed != affix) { + if (this.unpin != null) this.$element.css('top', '') + + var affixType = 'affix' + (affix ? '-' + affix : '') + var e = $.Event(affixType + '.bs.affix') + + this.$element.trigger(e) + + if (e.isDefaultPrevented()) return + + this.affixed = affix + this.unpin = affix == 'bottom' ? this.getPinnedOffset() : null + + this.$element + .removeClass(Affix.RESET) + .addClass(affixType) + .trigger(affixType.replace('affix', 'affixed') + '.bs.affix') + } + + if (affix == 'bottom') { + this.$element.offset({ + top: scrollHeight - height - offsetBottom + }) + } + } + + + // AFFIX PLUGIN DEFINITION + // ======================= + + function Plugin(option) { + return this.each(function () { + var $this = $(this) + var data = $this.data('bs.affix') + var options = typeof option == 'object' && option + + if (!data) $this.data('bs.affix', (data = new Affix(this, options))) + if (typeof option == 'string') data[option]() + }) + } + + var old = $.fn.affix + + $.fn.affix = Plugin + $.fn.affix.Constructor = Affix + + + // AFFIX NO CONFLICT + // ================= + + $.fn.affix.noConflict = function () { + $.fn.affix = old + return this + } + + + // AFFIX DATA-API + // ============== + + $(window).on('load', function () { + $('[data-spy="affix"]').each(function () { + var $spy = $(this) + var data = $spy.data() + + data.offset = data.offset || {} + + if (data.offsetBottom != null) data.offset.bottom = data.offsetBottom + if (data.offsetTop != null) data.offset.top = data.offsetTop + + Plugin.call($spy, data) + }) + }) + +}(jQuery); diff --git a/js/bootstrap-3.3.7.min.js b/js/bootstrap-3.3.7.min.js new file mode 100644 index 0000000..9bcd2fc --- /dev/null +++ b/js/bootstrap-3.3.7.min.js @@ -0,0 +1,7 @@ +/*! + * Bootstrap v3.3.7 (http://getbootstrap.com) + * Copyright 2011-2016 Twitter, Inc. + * Licensed under the MIT license + */ +if("undefined"==typeof jQuery)throw new Error("Bootstrap's JavaScript requires jQuery");+function(a){"use strict";var b=a.fn.jquery.split(" ")[0].split(".");if(b[0]<2&&b[1]<9||1==b[0]&&9==b[1]&&b[2]<1||b[0]>3)throw new Error("Bootstrap's JavaScript 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When using this convenience function a new index will be created with the + * following functions already in the pipeline: + * + * 1. elasticlunr.trimmer - trim non-word character + * 2. elasticlunr.StopWordFilter - filters out any stop words before they enter the + * index + * 3. elasticlunr.stemmer - stems the tokens before entering the index. + * + * + * Example: + * + * var idx = elasticlunr(function () { + * this.addField('id'); + * this.addField('title'); + * this.addField('body'); + * + * //this.setRef('id'); // default ref is 'id' + * + * this.pipeline.add(function () { + * // some custom pipeline function + * }); + * }); + * + * idx.addDoc({ + * id: 1, + * title: 'Oracle released database 12g', + * body: 'Yestaday, Oracle has released their latest database, named 12g, more robust. this product will increase Oracle profit.' + * }); + * + * idx.addDoc({ + * id: 2, + * title: 'Oracle released annual profit report', + * body: 'Yestaday, Oracle has released their annual profit report of 2015, total profit is 12.5 Billion.' + * }); + * + * # simple search + * idx.search('oracle database'); + * + * # search with query-time boosting + * idx.search('oracle database', {fields: {title: {boost: 2}, body: {boost: 1}}}); + * + * @param {Function} config A function that will be called with the new instance + * of the elasticlunr.Index as both its context and first parameter. It can be used to + * customize the instance of new elasticlunr.Index. + * @namespace + * @module + * @return {elasticlunr.Index} + * + */ +var elasticlunr = function (config) { + var idx = new elasticlunr.Index; + + idx.pipeline.add( + elasticlunr.trimmer, + elasticlunr.stopWordFilter, + elasticlunr.stemmer + ); + + if (config) config.call(idx, idx); + + return idx; +}; + +elasticlunr.version = "0.9.5"; + +// only used this to make elasticlunr.js compatible with lunr-languages +// this is a trick to define a global alias of elasticlunr +lunr = elasticlunr; + +/*! + * elasticlunr.utils + * Copyright (C) 2016 Oliver Nightingale + * Copyright (C) 2016 Wei Song + */ + +/** + * A namespace containing utils for the rest of the elasticlunr library + */ +elasticlunr.utils = {}; + +/** + * Print a warning message to the console. + * + * @param {String} message The message to be printed. + * @memberOf Utils + */ +elasticlunr.utils.warn = (function (global) { + return function (message) { + if (global.console && console.warn) { + console.warn(message); + } + }; +})(this); + +/** + * Convert an object to string. + * + * In the case of `null` and `undefined` the function returns + * an empty string, in all other cases the result of calling + * `toString` on the passed object is returned. + * + * @param {object} obj The object to convert to a string. + * @return {String} string representation of the passed object. + * @memberOf Utils + */ +elasticlunr.utils.toString = function (obj) { + if (obj === void 0 || obj === null) { + return ""; + } + + return obj.toString(); +}; +/*! + * elasticlunr.EventEmitter + * Copyright (C) 2016 Oliver Nightingale + * Copyright (C) 2016 Wei Song + */ + +/** + * elasticlunr.EventEmitter is an event emitter for elasticlunr. + * It manages adding and removing event handlers and triggering events and their handlers. + * + * Each event could has multiple corresponding functions, + * these functions will be called as the sequence that they are added into the event. + * + * @constructor + */ +elasticlunr.EventEmitter = function () { + this.events = {}; +}; + +/** + * Binds a handler function to a specific event(s). + * + * Can bind a single function to many different events in one call. + * + * @param {String} [eventName] The name(s) of events to bind this function to. + * @param {Function} fn The function to call when an event is fired. + * @memberOf EventEmitter + */ +elasticlunr.EventEmitter.prototype.addListener = function () { + var args = Array.prototype.slice.call(arguments), + fn = args.pop(), + names = args; + + if (typeof fn !== "function") throw new TypeError ("last argument must be a function"); + + names.forEach(function (name) { + if (!this.hasHandler(name)) this.events[name] = []; + this.events[name].push(fn); + }, this); +}; + +/** + * Removes a handler function from a specific event. + * + * @param {String} eventName The name of the event to remove this function from. + * @param {Function} fn The function to remove from an event. + * @memberOf EventEmitter + */ +elasticlunr.EventEmitter.prototype.removeListener = function (name, fn) { + if (!this.hasHandler(name)) return; + + var fnIndex = this.events[name].indexOf(fn); + if (fnIndex === -1) return; + + this.events[name].splice(fnIndex, 1); + + if (this.events[name].length == 0) delete this.events[name]; +}; + +/** + * Call all functions that bounded to the given event. + * + * Additional data can be passed to the event handler as arguments to `emit` + * after the event name. + * + * @param {String} eventName The name of the event to emit. + * @memberOf EventEmitter + */ +elasticlunr.EventEmitter.prototype.emit = function (name) { + if (!this.hasHandler(name)) return; + + var args = Array.prototype.slice.call(arguments, 1); + + this.events[name].forEach(function (fn) { + fn.apply(undefined, args); + }, this); +}; + +/** + * Checks whether a handler has ever been stored against an event. + * + * @param {String} eventName The name of the event to check. + * @private + * @memberOf EventEmitter + */ +elasticlunr.EventEmitter.prototype.hasHandler = function (name) { + return name in this.events; +}; +/*! + * elasticlunr.tokenizer + * Copyright (C) 2016 Oliver Nightingale + * Copyright (C) 2016 Wei Song + */ + +/** + * A function for splitting a string into tokens. + * Currently English is supported as default. + * Uses `elasticlunr.tokenizer.seperator` to split strings, you could change + * the value of this property to set how you want strings are split into tokens. + * IMPORTANT: use elasticlunr.tokenizer.seperator carefully, if you are not familiar with + * text process, then you'd better not change it. + * + * @module + * @param {String} str The string that you want to tokenize. + * @see elasticlunr.tokenizer.seperator + * @return {Array} + */ +elasticlunr.tokenizer = function (str) { + if (!arguments.length || str === null || str === undefined) return []; + if (Array.isArray(str)) { + var arr = str.filter(function(token) { + if (token === null || token === undefined) { + return false; + } + + return true; + }); + + arr = arr.map(function (t) { + return elasticlunr.utils.toString(t).toLowerCase(); + }); + + var out = []; + arr.forEach(function(item) { + var tokens = item.split(elasticlunr.tokenizer.seperator); + out = out.concat(tokens); + }, this); + + return out; + } + + return str.toString().trim().toLowerCase().split(elasticlunr.tokenizer.seperator); +}; + +/** + * Default string seperator. + */ +elasticlunr.tokenizer.defaultSeperator = /[\s\-]+/; + +/** + * The sperator used to split a string into tokens. Override this property to change the behaviour of + * `elasticlunr.tokenizer` behaviour when tokenizing strings. By default this splits on whitespace and hyphens. + * + * @static + * @see elasticlunr.tokenizer + */ +elasticlunr.tokenizer.seperator = elasticlunr.tokenizer.defaultSeperator; + +/** + * Set up customized string seperator + * + * @param {Object} sep The customized seperator that you want to use to tokenize a string. + */ +elasticlunr.tokenizer.setSeperator = function(sep) { + if (sep !== null && sep !== undefined && typeof(sep) === 'object') { + elasticlunr.tokenizer.seperator = sep; + } +} + +/** + * Reset string seperator + * + */ +elasticlunr.tokenizer.resetSeperator = function() { + elasticlunr.tokenizer.seperator = elasticlunr.tokenizer.defaultSeperator; +} + +/** + * Get string seperator + * + */ +elasticlunr.tokenizer.getSeperator = function() { + return elasticlunr.tokenizer.seperator; +} +/*! + * elasticlunr.Pipeline + * Copyright (C) 2016 Oliver Nightingale + * Copyright (C) 2016 Wei Song + */ + +/** + * elasticlunr.Pipelines maintain an ordered list of functions to be applied to + * both documents tokens and query tokens. + * + * An instance of elasticlunr.Index will contain a pipeline + * with a trimmer, a stop word filter, an English stemmer. Extra + * functions can be added before or after either of these functions or these + * default functions can be removed. + * + * When run the pipeline, it will call each function in turn. + * + * The output of the functions in the pipeline will be passed to the next function + * in the pipeline. To exclude a token from entering the index the function + * should return undefined, the rest of the pipeline will not be called with + * this token. + * + * For serialisation of pipelines to work, all functions used in an instance of + * a pipeline should be registered with elasticlunr.Pipeline. Registered functions can + * then be loaded. If trying to load a serialised pipeline that uses functions + * that are not registered an error will be thrown. + * + * If not planning on serialising the pipeline then registering pipeline functions + * is not necessary. + * + * @constructor + */ +elasticlunr.Pipeline = function () { + this._queue = []; +}; + +elasticlunr.Pipeline.registeredFunctions = {}; + +/** + * Register a function in the pipeline. + * + * Functions that are used in the pipeline should be registered if the pipeline + * needs to be serialised, or a serialised pipeline needs to be loaded. + * + * Registering a function does not add it to a pipeline, functions must still be + * added to instances of the pipeline for them to be used when running a pipeline. + * + * @param {Function} fn The function to register. + * @param {String} label The label to register this function with + * @memberOf Pipeline + */ +elasticlunr.Pipeline.registerFunction = function (fn, label) { + if (label in elasticlunr.Pipeline.registeredFunctions) { + elasticlunr.utils.warn('Overwriting existing registered function: ' + label); + } + + fn.label = label; + elasticlunr.Pipeline.registeredFunctions[label] = fn; +}; + +/** + * Get a registered function in the pipeline. + * + * @param {String} label The label of registered function. + * @return {Function} + * @memberOf Pipeline + */ +elasticlunr.Pipeline.getRegisteredFunction = function (label) { + if ((label in elasticlunr.Pipeline.registeredFunctions) !== true) { + return null; + } + + return elasticlunr.Pipeline.registeredFunctions[label]; +}; + +/** + * Warns if the function is not registered as a Pipeline function. + * + * @param {Function} fn The function to check for. + * @private + * @memberOf Pipeline + */ +elasticlunr.Pipeline.warnIfFunctionNotRegistered = function (fn) { + var isRegistered = fn.label && (fn.label in this.registeredFunctions); + + if (!isRegistered) { + elasticlunr.utils.warn('Function is not registered with pipeline. This may cause problems when serialising the index.\n', fn); + } +}; + +/** + * Loads a previously serialised pipeline. + * + * All functions to be loaded must already be registered with elasticlunr.Pipeline. + * If any function from the serialised data has not been registered then an + * error will be thrown. + * + * @param {Object} serialised The serialised pipeline to load. + * @return {elasticlunr.Pipeline} + * @memberOf Pipeline + */ +elasticlunr.Pipeline.load = function (serialised) { + var pipeline = new elasticlunr.Pipeline; + + serialised.forEach(function (fnName) { + var fn = elasticlunr.Pipeline.getRegisteredFunction(fnName); + + if (fn) { + pipeline.add(fn); + } else { + throw new Error('Cannot load un-registered function: ' + fnName); + } + }); + + return pipeline; +}; + +/** + * Adds new functions to the end of the pipeline. + * + * Logs a warning if the function has not been registered. + * + * @param {Function} functions Any number of functions to add to the pipeline. + * @memberOf Pipeline + */ +elasticlunr.Pipeline.prototype.add = function () { + var fns = Array.prototype.slice.call(arguments); + + fns.forEach(function (fn) { + elasticlunr.Pipeline.warnIfFunctionNotRegistered(fn); + this._queue.push(fn); + }, this); +}; + +/** + * Adds a single function after a function that already exists in the + * pipeline. + * + * Logs a warning if the function has not been registered. + * If existingFn is not found, throw an Exception. + * + * @param {Function} existingFn A function that already exists in the pipeline. + * @param {Function} newFn The new function to add to the pipeline. + * @memberOf Pipeline + */ +elasticlunr.Pipeline.prototype.after = function (existingFn, newFn) { + elasticlunr.Pipeline.warnIfFunctionNotRegistered(newFn); + + var pos = this._queue.indexOf(existingFn); + if (pos === -1) { + throw new Error('Cannot find existingFn'); + } + + this._queue.splice(pos + 1, 0, newFn); +}; + +/** + * Adds a single function before a function that already exists in the + * pipeline. + * + * Logs a warning if the function has not been registered. + * If existingFn is not found, throw an Exception. + * + * @param {Function} existingFn A function that already exists in the pipeline. + * @param {Function} newFn The new function to add to the pipeline. + * @memberOf Pipeline + */ +elasticlunr.Pipeline.prototype.before = function (existingFn, newFn) { + elasticlunr.Pipeline.warnIfFunctionNotRegistered(newFn); + + var pos = this._queue.indexOf(existingFn); + if (pos === -1) { + throw new Error('Cannot find existingFn'); + } + + this._queue.splice(pos, 0, newFn); +}; + +/** + * Removes a function from the pipeline. + * + * @param {Function} fn The function to remove from the pipeline. + * @memberOf Pipeline + */ +elasticlunr.Pipeline.prototype.remove = function (fn) { + var pos = this._queue.indexOf(fn); + if (pos === -1) { + return; + } + + this._queue.splice(pos, 1); +}; + +/** + * Runs the current list of functions that registered in the pipeline against the + * input tokens. + * + * @param {Array} tokens The tokens to run through the pipeline. + * @return {Array} + * @memberOf Pipeline + */ +elasticlunr.Pipeline.prototype.run = function (tokens) { + var out = [], + tokenLength = tokens.length, + pipelineLength = this._queue.length; + + for (var i = 0; i < tokenLength; i++) { + var token = tokens[i]; + + for (var j = 0; j < pipelineLength; j++) { + token = this._queue[j](token, i, tokens); + if (token === void 0 || token === null) break; + }; + + if (token !== void 0 && token !== null) out.push(token); + }; + + return out; +}; + +/** + * Resets the pipeline by removing any existing processors. + * + * @memberOf Pipeline + */ +elasticlunr.Pipeline.prototype.reset = function () { + this._queue = []; +}; + + /** + * Get the pipeline if user want to check the pipeline. + * + * @memberOf Pipeline + */ + elasticlunr.Pipeline.prototype.get = function () { + return this._queue; + }; + +/** + * Returns a representation of the pipeline ready for serialisation. + * Only serialize pipeline function's name. Not storing function, so when + * loading the archived JSON index file, corresponding pipeline function is + * added by registered function of elasticlunr.Pipeline.registeredFunctions + * + * Logs a warning if the function has not been registered. + * + * @return {Array} + * @memberOf Pipeline + */ +elasticlunr.Pipeline.prototype.toJSON = function () { + return this._queue.map(function (fn) { + elasticlunr.Pipeline.warnIfFunctionNotRegistered(fn); + return fn.label; + }); +}; +/*! + * elasticlunr.Index + * Copyright (C) 2016 Oliver Nightingale + * Copyright (C) 2016 Wei Song + */ + +/** + * elasticlunr.Index is object that manages a search index. It contains the indexes + * and stores all the tokens and document lookups. It also provides the main + * user facing API for the library. + * + * @constructor + */ +elasticlunr.Index = function () { + this._fields = []; + this._ref = 'id'; + this.pipeline = new elasticlunr.Pipeline; + this.documentStore = new elasticlunr.DocumentStore; + this.index = {}; + this.eventEmitter = new elasticlunr.EventEmitter; + this._idfCache = {}; + + this.on('add', 'remove', 'update', (function () { + this._idfCache = {}; + }).bind(this)); +}; + +/** + * Bind a handler to events being emitted by the index. + * + * The handler can be bound to many events at the same time. + * + * @param {String} [eventName] The name(s) of events to bind the function to. + * @param {Function} fn The serialised set to load. + * @memberOf Index + */ +elasticlunr.Index.prototype.on = function () { + var args = Array.prototype.slice.call(arguments); + return this.eventEmitter.addListener.apply(this.eventEmitter, args); +}; + +/** + * Removes a handler from an event being emitted by the index. + * + * @param {String} eventName The name of events to remove the function from. + * @param {Function} fn The serialised set to load. + * @memberOf Index + */ +elasticlunr.Index.prototype.off = function (name, fn) { + return this.eventEmitter.removeListener(name, fn); +}; + +/** + * Loads a previously serialised index. + * + * Issues a warning if the index being imported was serialised + * by a different version of elasticlunr. + * + * @param {Object} serialisedData The serialised set to load. + * @return {elasticlunr.Index} + * @memberOf Index + */ +elasticlunr.Index.load = function (serialisedData) { + if (serialisedData.version !== elasticlunr.version) { + elasticlunr.utils.warn('version mismatch: current ' + + elasticlunr.version + ' importing ' + serialisedData.version); + } + + var idx = new this; + + idx._fields = serialisedData.fields; + idx._ref = serialisedData.ref; + idx.documentStore = elasticlunr.DocumentStore.load(serialisedData.documentStore); + idx.pipeline = elasticlunr.Pipeline.load(serialisedData.pipeline); + idx.index = {}; + for (var field in serialisedData.index) { + idx.index[field] = elasticlunr.InvertedIndex.load(serialisedData.index[field]); + } + + return idx; +}; + +/** + * Adds a field to the list of fields that will be searchable within documents in the index. + * + * Remember that inner index is build based on field, which means each field has one inverted index. + * + * Fields should be added before any documents are added to the index, fields + * that are added after documents are added to the index will only apply to new + * documents added to the index. + * + * @param {String} fieldName The name of the field within the document that should be indexed + * @return {elasticlunr.Index} + * @memberOf Index + */ +elasticlunr.Index.prototype.addField = function (fieldName) { + this._fields.push(fieldName); + this.index[fieldName] = new elasticlunr.InvertedIndex; + return this; +}; + +/** + * Sets the property used to uniquely identify documents added to the index, + * by default this property is 'id'. + * + * This should only be changed before adding documents to the index, changing + * the ref property without resetting the index can lead to unexpected results. + * + * @param {String} refName The property to use to uniquely identify the + * documents in the index. + * @param {Boolean} emitEvent Whether to emit add events, defaults to true + * @return {elasticlunr.Index} + * @memberOf Index + */ +elasticlunr.Index.prototype.setRef = function (refName) { + this._ref = refName; + return this; +}; + +/** + * + * Set if the JSON format original documents are save into elasticlunr.DocumentStore + * + * Defaultly save all the original JSON documents. + * + * @param {Boolean} save Whether to save the original JSON documents. + * @return {elasticlunr.Index} + * @memberOf Index + */ +elasticlunr.Index.prototype.saveDocument = function (save) { + this.documentStore = new elasticlunr.DocumentStore(save); + return this; +}; + +/** + * Add a JSON format document to the index. + * + * This is the way new documents enter the index, this function will run the + * fields from the document through the index's pipeline and then add it to + * the index, it will then show up in search results. + * + * An 'add' event is emitted with the document that has been added and the index + * the document has been added to. This event can be silenced by passing false + * as the second argument to add. + * + * @param {Object} doc The JSON format document to add to the index. + * @param {Boolean} emitEvent Whether or not to emit events, default true. + * @memberOf Index + */ +elasticlunr.Index.prototype.addDoc = function (doc, emitEvent) { + if (!doc) return; + var emitEvent = emitEvent === undefined ? true : emitEvent; + + var docRef = doc[this._ref]; + + this.documentStore.addDoc(docRef, doc); + this._fields.forEach(function (field) { + var fieldTokens = this.pipeline.run(elasticlunr.tokenizer(doc[field])); + this.documentStore.addFieldLength(docRef, field, fieldTokens.length); + + var tokenCount = {}; + fieldTokens.forEach(function (token) { + if (token in tokenCount) tokenCount[token] += 1; + else tokenCount[token] = 1; + }, this); + + for (var token in tokenCount) { + var termFrequency = tokenCount[token]; + termFrequency = Math.sqrt(termFrequency); + this.index[field].addToken(token, { ref: docRef, tf: termFrequency }); + } + }, this); + + if (emitEvent) this.eventEmitter.emit('add', doc, this); +}; + +/** + * Removes a document from the index by doc ref. + * + * To make sure documents no longer show up in search results they can be + * removed from the index using this method. + * + * A 'remove' event is emitted with the document that has been removed and the index + * the document has been removed from. This event can be silenced by passing false + * as the second argument to remove. + * + * If user setting DocumentStore not storing the documents, then remove doc by docRef is not allowed. + * + * @param {String|Integer} docRef The document ref to remove from the index. + * @param {Boolean} emitEvent Whether to emit remove events, defaults to true + * @memberOf Index + */ +elasticlunr.Index.prototype.removeDocByRef = function (docRef, emitEvent) { + if (!docRef) return; + if (this.documentStore.isDocStored() === false) { + return; + } + + if (!this.documentStore.hasDoc(docRef)) return; + var doc = this.documentStore.getDoc(docRef); + this.removeDoc(doc, false); +}; + +/** + * Removes a document from the index. + * This remove operation could work even the original doc is not store in the DocumentStore. + * + * To make sure documents no longer show up in search results they can be + * removed from the index using this method. + * + * A 'remove' event is emitted with the document that has been removed and the index + * the document has been removed from. This event can be silenced by passing false + * as the second argument to remove. + * + * + * @param {Object} doc The document ref to remove from the index. + * @param {Boolean} emitEvent Whether to emit remove events, defaults to true + * @memberOf Index + */ +elasticlunr.Index.prototype.removeDoc = function (doc, emitEvent) { + if (!doc) return; + + var emitEvent = emitEvent === undefined ? true : emitEvent; + + var docRef = doc[this._ref]; + if (!this.documentStore.hasDoc(docRef)) return; + + this.documentStore.removeDoc(docRef); + + this._fields.forEach(function (field) { + var fieldTokens = this.pipeline.run(elasticlunr.tokenizer(doc[field])); + fieldTokens.forEach(function (token) { + this.index[field].removeToken(token, docRef); + }, this); + }, this); + + if (emitEvent) this.eventEmitter.emit('remove', doc, this); +}; + +/** + * Updates a document in the index. + * + * When a document contained within the index gets updated, fields changed, + * added or removed, to make sure it correctly matched against search queries, + * it should be updated in the index. + * + * This method is just a wrapper around `remove` and `add` + * + * An 'update' event is emitted with the document that has been updated and the index. + * This event can be silenced by passing false as the second argument to update. Only + * an update event will be fired, the 'add' and 'remove' events of the underlying calls + * are silenced. + * + * @param {Object} doc The document to update in the index. + * @param {Boolean} emitEvent Whether to emit update events, defaults to true + * @see Index.prototype.remove + * @see Index.prototype.add + * @memberOf Index + */ +elasticlunr.Index.prototype.updateDoc = function (doc, emitEvent) { + var emitEvent = emitEvent === undefined ? true : emitEvent; + + this.removeDocByRef(doc[this._ref], false); + this.addDoc(doc, false); + + if (emitEvent) this.eventEmitter.emit('update', doc, this); +}; + +/** + * Calculates the inverse document frequency for a token within the index of a field. + * + * @param {String} token The token to calculate the idf of. + * @param {String} field The field to compute idf. + * @see Index.prototype.idf + * @private + * @memberOf Index + */ +elasticlunr.Index.prototype.idf = function (term, field) { + var cacheKey = "@" + field + '/' + term; + if (Object.prototype.hasOwnProperty.call(this._idfCache, cacheKey)) return this._idfCache[cacheKey]; + + var df = this.index[field].getDocFreq(term); + var idf = 1 + Math.log(this.documentStore.length / (df + 1)); + this._idfCache[cacheKey] = idf; + + return idf; +}; + +/** + * get fields of current index instance + * + * @return {Array} + */ +elasticlunr.Index.prototype.getFields = function () { + return this._fields.slice(); +}; + +/** + * Searches the index using the passed query. + * Queries should be a string, multiple words are allowed. + * + * If config is null, will search all fields defaultly, and lead to OR based query. + * If config is specified, will search specified with query time boosting. + * + * All query tokens are passed through the same pipeline that document tokens + * are passed through, so any language processing involved will be run on every + * query term. + * + * Each query term is expanded, so that the term 'he' might be expanded to + * 'hello' and 'help' if those terms were already included in the index. + * + * Matching documents are returned as an array of objects, each object contains + * the matching document ref, as set for this index, and the similarity score + * for this document against the query. + * + * @param {String} query The query to search the index with. + * @param {JSON} userConfig The user query config, JSON format. + * @return {Object} + * @see Index.prototype.idf + * @see Index.prototype.documentVector + * @memberOf Index + */ +elasticlunr.Index.prototype.search = function (query, userConfig) { + if (!query) return []; + + var configStr = null; + if (userConfig != null) { + configStr = JSON.stringify(userConfig); + } + + var config = new elasticlunr.Configuration(configStr, this.getFields()).get(); + + var queryTokens = this.pipeline.run(elasticlunr.tokenizer(query)); + + var queryResults = {}; + + for (var field in config) { + var fieldSearchResults = this.fieldSearch(queryTokens, field, config); + var fieldBoost = config[field].boost; + + for (var docRef in fieldSearchResults) { + fieldSearchResults[docRef] = fieldSearchResults[docRef] * fieldBoost; + } + + for (var docRef in fieldSearchResults) { + if (docRef in queryResults) { + queryResults[docRef] += fieldSearchResults[docRef]; + } else { + queryResults[docRef] = fieldSearchResults[docRef]; + } + } + } + + var results = []; + for (var docRef in queryResults) { + results.push({ref: docRef, score: queryResults[docRef]}); + } + + results.sort(function (a, b) { return b.score - a.score; }); + return results; +}; + +/** + * search queryTokens in specified field. + * + * @param {Array} queryTokens The query tokens to query in this field. + * @param {String} field Field to query in. + * @param {elasticlunr.Configuration} config The user query config, JSON format. + * @return {Object} + */ +elasticlunr.Index.prototype.fieldSearch = function (queryTokens, fieldName, config) { + var booleanType = config[fieldName].bool; + var expand = config[fieldName].expand; + var boost = config[fieldName].boost; + var scores = null; + var docTokens = {}; + + // Do nothing if the boost is 0 + if (boost === 0) { + return; + } + + queryTokens.forEach(function (token) { + var tokens = [token]; + if (expand == true) { + tokens = this.index[fieldName].expandToken(token); + } + // Consider every query token in turn. If expanded, each query token + // corresponds to a set of tokens, which is all tokens in the + // index matching the pattern queryToken* . + // For the set of tokens corresponding to a query token, find and score + // all matching documents. Store those scores in queryTokenScores, + // keyed by docRef. + // Then, depending on the value of booleanType, combine the scores + // for this query token with previous scores. If booleanType is OR, + // then merge the scores by summing into the accumulated total, adding + // new document scores are required (effectively a union operator). + // If booleanType is AND, accumulate scores only if the document + // has previously been scored by another query token (an intersection + // operation0. + // Furthermore, since when booleanType is AND, additional + // query tokens can't add new documents to the result set, use the + // current document set to limit the processing of each new query + // token for efficiency (i.e., incremental intersection). + + var queryTokenScores = {}; + tokens.forEach(function (key) { + var docs = this.index[fieldName].getDocs(key); + var idf = this.idf(key, fieldName); + + if (scores && booleanType == 'AND') { + // special case, we can rule out documents that have been + // already been filtered out because they weren't scored + // by previous query token passes. + var filteredDocs = {}; + for (var docRef in scores) { + if (docRef in docs) { + filteredDocs[docRef] = docs[docRef]; + } + } + docs = filteredDocs; + } + // only record appeared token for retrieved documents for the + // original token, not for expaned token. + // beause for doing coordNorm for a retrieved document, coordNorm only care how many + // query token appear in that document. + // so expanded token should not be added into docTokens, if added, this will pollute the + // coordNorm + if (key == token) { + this.fieldSearchStats(docTokens, key, docs); + } + + for (var docRef in docs) { + var tf = this.index[fieldName].getTermFrequency(key, docRef); + var fieldLength = this.documentStore.getFieldLength(docRef, fieldName); + var fieldLengthNorm = 1; + if (fieldLength != 0) { + fieldLengthNorm = 1 / Math.sqrt(fieldLength); + } + + var penality = 1; + if (key != token) { + // currently I'm not sure if this penality is enough, + // need to do verification + penality = (1 - (key.length - token.length) / key.length) * 0.15; + } + + var score = tf * idf * fieldLengthNorm * penality; + + if (docRef in queryTokenScores) { + queryTokenScores[docRef] += score; + } else { + queryTokenScores[docRef] = score; + } + } + }, this); + + scores = this.mergeScores(scores, queryTokenScores, booleanType); + }, this); + + scores = this.coordNorm(scores, docTokens, queryTokens.length); + return scores; +}; + +/** + * Merge the scores from one set of tokens into an accumulated score table. + * Exact operation depends on the op parameter. If op is 'AND', then only the + * intersection of the two score lists is retained. Otherwise, the union of + * the two score lists is returned. For internal use only. + * + * @param {Object} bool accumulated scores. Should be null on first call. + * @param {String} scores new scores to merge into accumScores. + * @param {Object} op merge operation (should be 'AND' or 'OR'). + * + */ + +elasticlunr.Index.prototype.mergeScores = function (accumScores, scores, op) { + if (!accumScores) { + return scores; + } + if (op == 'AND') { + var intersection = {}; + for (var docRef in scores) { + if (docRef in accumScores) { + intersection[docRef] = accumScores[docRef] + scores[docRef]; + } + } + return intersection; + } else { + for (var docRef in scores) { + if (docRef in accumScores) { + accumScores[docRef] += scores[docRef]; + } else { + accumScores[docRef] = scores[docRef]; + } + } + return accumScores; + } +}; + + +/** + * Record the occuring query token of retrieved doc specified by doc field. + * Only for inner user. + * + * @param {Object} docTokens a data structure stores which token appears in the retrieved doc. + * @param {String} token query token + * @param {Object} docs the retrieved documents of the query token + * + */ +elasticlunr.Index.prototype.fieldSearchStats = function (docTokens, token, docs) { + for (var doc in docs) { + if (doc in docTokens) { + docTokens[doc].push(token); + } else { + docTokens[doc] = [token]; + } + } +}; + +/** + * coord norm the score of a doc. + * if a doc contain more query tokens, then the score will larger than the doc + * contains less query tokens. + * + * only for inner use. + * + * @param {Object} results first results + * @param {Object} docs field search results of a token + * @param {Integer} n query token number + * @return {Object} + */ +elasticlunr.Index.prototype.coordNorm = function (scores, docTokens, n) { + for (var doc in scores) { + if (!(doc in docTokens)) continue; + var tokens = docTokens[doc].length; + scores[doc] = scores[doc] * tokens / n; + } + + return scores; +}; + +/** + * Returns a representation of the index ready for serialisation. + * + * @return {Object} + * @memberOf Index + */ +elasticlunr.Index.prototype.toJSON = function () { + var indexJson = {}; + this._fields.forEach(function (field) { + indexJson[field] = this.index[field].toJSON(); + }, this); + + return { + version: elasticlunr.version, + fields: this._fields, + ref: this._ref, + documentStore: this.documentStore.toJSON(), + index: indexJson, + pipeline: this.pipeline.toJSON() + }; +}; + +/** + * Applies a plugin to the current index. + * + * A plugin is a function that is called with the index as its context. + * Plugins can be used to customise or extend the behaviour the index + * in some way. A plugin is just a function, that encapsulated the custom + * behaviour that should be applied to the index. + * + * The plugin function will be called with the index as its argument, additional + * arguments can also be passed when calling use. The function will be called + * with the index as its context. + * + * Example: + * + * var myPlugin = function (idx, arg1, arg2) { + * // `this` is the index to be extended + * // apply any extensions etc here. + * } + * + * var idx = elasticlunr(function () { + * this.use(myPlugin, 'arg1', 'arg2') + * }) + * + * @param {Function} plugin The plugin to apply. + * @memberOf Index + */ +elasticlunr.Index.prototype.use = function (plugin) { + var args = Array.prototype.slice.call(arguments, 1); + args.unshift(this); + plugin.apply(this, args); +}; +/*! + * elasticlunr.DocumentStore + * Copyright (C) 2016 Wei Song + */ + +/** + * elasticlunr.DocumentStore is a simple key-value document store used for storing sets of tokens for + * documents stored in index. + * + * elasticlunr.DocumentStore store original JSON format documents that you could build search snippet by this original JSON document. + * + * user could choose whether original JSON format document should be store, if no configuration then document will be stored defaultly. + * If user care more about the index size, user could select not store JSON documents, then this will has some defects, such as user + * could not use JSON document to generate snippets of search results. + * + * @param {Boolean} save If the original JSON document should be stored. + * @constructor + * @module + */ +elasticlunr.DocumentStore = function (save) { + if (save === null || save === undefined) { + this._save = true; + } else { + this._save = save; + } + + this.docs = {}; + this.docInfo = {}; + this.length = 0; +}; + +/** + * Loads a previously serialised document store + * + * @param {Object} serialisedData The serialised document store to load. + * @return {elasticlunr.DocumentStore} + */ +elasticlunr.DocumentStore.load = function (serialisedData) { + var store = new this; + + store.length = serialisedData.length; + store.docs = serialisedData.docs; + store.docInfo = serialisedData.docInfo; + store._save = serialisedData.save; + + return store; +}; + +/** + * check if current instance store the original doc + * + * @return {Boolean} + */ +elasticlunr.DocumentStore.prototype.isDocStored = function () { + return this._save; +}; + +/** + * Stores the given doc in the document store against the given id. + * If docRef already exist, then update doc. + * + * Document is store by original JSON format, then you could use original document to generate search snippets. + * + * @param {Integer|String} docRef The key used to store the JSON format doc. + * @param {Object} doc The JSON format doc. + */ +elasticlunr.DocumentStore.prototype.addDoc = function (docRef, doc) { + if (!this.hasDoc(docRef)) this.length++; + + if (this._save === true) { + this.docs[docRef] = clone(doc); + } else { + this.docs[docRef] = null; + } +}; + +/** + * Retrieves the JSON doc from the document store for a given key. + * + * If docRef not found, return null. + * If user set not storing the documents, return null. + * + * @param {Integer|String} docRef The key to lookup and retrieve from the document store. + * @return {Object} + * @memberOf DocumentStore + */ +elasticlunr.DocumentStore.prototype.getDoc = function (docRef) { + if (this.hasDoc(docRef) === false) return null; + return this.docs[docRef]; +}; + +/** + * Checks whether the document store contains a key (docRef). + * + * @param {Integer|String} docRef The id to look up in the document store. + * @return {Boolean} + * @memberOf DocumentStore + */ +elasticlunr.DocumentStore.prototype.hasDoc = function (docRef) { + return docRef in this.docs; +}; + +/** + * Removes the value for a key in the document store. + * + * @param {Integer|String} docRef The id to remove from the document store. + * @memberOf DocumentStore + */ +elasticlunr.DocumentStore.prototype.removeDoc = function (docRef) { + if (!this.hasDoc(docRef)) return; + + delete this.docs[docRef]; + delete this.docInfo[docRef]; + this.length--; +}; + +/** + * Add field length of a document's field tokens from pipeline results. + * The field length of a document is used to do field length normalization even without the original JSON document stored. + * + * @param {Integer|String} docRef document's id or reference + * @param {String} fieldName field name + * @param {Integer} length field length + */ +elasticlunr.DocumentStore.prototype.addFieldLength = function (docRef, fieldName, length) { + if (docRef === null || docRef === undefined) return; + if (this.hasDoc(docRef) == false) return; + + if (!this.docInfo[docRef]) this.docInfo[docRef] = {}; + this.docInfo[docRef][fieldName] = length; +}; + +/** + * Update field length of a document's field tokens from pipeline results. + * The field length of a document is used to do field length normalization even without the original JSON document stored. + * + * @param {Integer|String} docRef document's id or reference + * @param {String} fieldName field name + * @param {Integer} length field length + */ +elasticlunr.DocumentStore.prototype.updateFieldLength = function (docRef, fieldName, length) { + if (docRef === null || docRef === undefined) return; + if (this.hasDoc(docRef) == false) return; + + this.addFieldLength(docRef, fieldName, length); +}; + +/** + * get field length of a document by docRef + * + * @param {Integer|String} docRef document id or reference + * @param {String} fieldName field name + * @return {Integer} field length + */ +elasticlunr.DocumentStore.prototype.getFieldLength = function (docRef, fieldName) { + if (docRef === null || docRef === undefined) return 0; + + if (!(docRef in this.docs)) return 0; + if (!(fieldName in this.docInfo[docRef])) return 0; + return this.docInfo[docRef][fieldName]; +}; + +/** + * Returns a JSON representation of the document store used for serialisation. + * + * @return {Object} JSON format + * @memberOf DocumentStore + */ +elasticlunr.DocumentStore.prototype.toJSON = function () { + return { + docs: this.docs, + docInfo: this.docInfo, + length: this.length, + save: this._save + }; +}; + +/** + * Cloning object + * + * @param {Object} object in JSON format + * @return {Object} copied object + */ +function clone(obj) { + if (null === obj || "object" !== typeof obj) return obj; + + var copy = obj.constructor(); + + for (var attr in obj) { + if (obj.hasOwnProperty(attr)) copy[attr] = obj[attr]; + } + + return copy; +} +/*! + * elasticlunr.stemmer + * Copyright (C) 2016 Oliver Nightingale + * Copyright (C) 2016 Wei Song + * Includes code from - http://tartarus.org/~martin/PorterStemmer/js.txt + */ + +/** + * elasticlunr.stemmer is an english language stemmer, this is a JavaScript + * implementation of the PorterStemmer taken from http://tartarus.org/~martin + * + * @module + * @param {String} str The string to stem + * @return {String} + * @see elasticlunr.Pipeline + */ +elasticlunr.stemmer = (function(){ + var step2list = { + "ational" : "ate", + "tional" : "tion", + "enci" : "ence", + "anci" : "ance", + "izer" : "ize", + "bli" : "ble", + "alli" : "al", + "entli" : "ent", + "eli" : "e", + "ousli" : "ous", + "ization" : "ize", + "ation" : "ate", + "ator" : "ate", + "alism" : "al", + "iveness" : "ive", + "fulness" : "ful", + "ousness" : "ous", + "aliti" : "al", + "iviti" : "ive", + "biliti" : "ble", + "logi" : "log" + }, + + step3list = { + "icate" : "ic", + "ative" : "", + "alize" : "al", + "iciti" : "ic", + "ical" : "ic", + "ful" : "", + "ness" : "" + }, + + c = "[^aeiou]", // consonant + v = "[aeiouy]", // vowel + C = c + "[^aeiouy]*", // consonant sequence + V = v + "[aeiou]*", // vowel sequence + + mgr0 = "^(" + C + ")?" + V + C, // [C]VC... is m>0 + meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$", // [C]VC[V] is m=1 + mgr1 = "^(" + C + ")?" + V + C + V + C, // [C]VCVC... is m>1 + s_v = "^(" + C + ")?" + v; // vowel in stem + + var re_mgr0 = new RegExp(mgr0); + var re_mgr1 = new RegExp(mgr1); + var re_meq1 = new RegExp(meq1); + var re_s_v = new RegExp(s_v); + + var re_1a = /^(.+?)(ss|i)es$/; + var re2_1a = /^(.+?)([^s])s$/; + var re_1b = /^(.+?)eed$/; + var re2_1b = /^(.+?)(ed|ing)$/; + var re_1b_2 = /.$/; + var re2_1b_2 = /(at|bl|iz)$/; + var re3_1b_2 = new RegExp("([^aeiouylsz])\\1$"); + var re4_1b_2 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + + var re_1c = /^(.+?[^aeiou])y$/; + var re_2 = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + + var re_3 = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + + var re_4 = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + var re2_4 = /^(.+?)(s|t)(ion)$/; + + var re_5 = /^(.+?)e$/; + var re_5_1 = /ll$/; + var re3_5 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + + var porterStemmer = function porterStemmer(w) { + var stem, + suffix, + firstch, + re, + re2, + re3, + re4; + + if (w.length < 3) { return w; } + + firstch = w.substr(0,1); + if (firstch == "y") { + w = firstch.toUpperCase() + w.substr(1); + } + + // Step 1a + re = re_1a + re2 = re2_1a; + + if (re.test(w)) { w = w.replace(re,"$1$2"); } + else if (re2.test(w)) { w = w.replace(re2,"$1$2"); } + + // Step 1b + re = re_1b; + re2 = re2_1b; + if (re.test(w)) { + var fp = re.exec(w); + re = re_mgr0; + if (re.test(fp[1])) { + re = re_1b_2; + w = w.replace(re,""); + } + } else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = re_s_v; + if (re2.test(stem)) { + w = stem; + re2 = re2_1b_2; + re3 = re3_1b_2; + re4 = re4_1b_2; + if (re2.test(w)) { w = w + "e"; } + else if (re3.test(w)) { re = re_1b_2; w = w.replace(re,""); } + else if (re4.test(w)) { w = w + "e"; } + } + } + + // Step 1c - replace suffix y or Y by i if preceded by a non-vowel which is not the first letter of the word (so cry -> cri, by -> by, say -> say) + re = re_1c; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + w = stem + "i"; + } + + // Step 2 + re = re_2; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = re_mgr0; + if (re.test(stem)) { + w = stem + step2list[suffix]; + } + } + + // Step 3 + re = re_3; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = re_mgr0; + if (re.test(stem)) { + w = stem + step3list[suffix]; + } + } + + // Step 4 + re = re_4; + re2 = re2_4; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = re_mgr1; + if (re.test(stem)) { + w = stem; + } + } else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = re_mgr1; + if (re2.test(stem)) { + w = stem; + } + } + + // Step 5 + re = re_5; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = re_mgr1; + re2 = re_meq1; + re3 = re3_5; + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) { + w = stem; + } + } + + re = re_5_1; + re2 = re_mgr1; + if (re.test(w) && re2.test(w)) { + re = re_1b_2; + w = w.replace(re,""); + } + + // and turn initial Y back to y + + if (firstch == "y") { + w = firstch.toLowerCase() + w.substr(1); + } + + return w; + }; + + return porterStemmer; +})(); + +elasticlunr.Pipeline.registerFunction(elasticlunr.stemmer, 'stemmer'); +/*! + * elasticlunr.stopWordFilter + * Copyright (C) 2016 Oliver Nightingale + * Copyright (C) 2016 Wei Song + */ + +/** + * elasticlunr.stopWordFilter is an English language stop words filter, any words + * contained in the stop word list will not be passed through the filter. + * + * This is intended to be used in the Pipeline. If the token does not pass the + * filter then undefined will be returned. + * Currently this StopwordFilter using dictionary to do O(1) time complexity stop word filtering. + * + * @module + * @param {String} token The token to pass through the filter + * @return {String} + * @see elasticlunr.Pipeline + */ +elasticlunr.stopWordFilter = function (token) { + if (token && elasticlunr.stopWordFilter.stopWords[token] !== true) { + return token; + } +}; + +/** + * Remove predefined stop words + * if user want to use customized stop words, user could use this function to delete + * all predefined stopwords. + * + * @return {null} + */ +elasticlunr.clearStopWords = function () { + elasticlunr.stopWordFilter.stopWords = {}; +}; + +/** + * Add customized stop words + * user could use this function to add customized stop words + * + * @params {Array} words customized stop words + * @return {null} + */ +elasticlunr.addStopWords = function (words) { + if (words == null || Array.isArray(words) === false) return; + + words.forEach(function (word) { + elasticlunr.stopWordFilter.stopWords[word] = true; + }, this); +}; + +/** + * Reset to default stop words + * user could use this function to restore default stop words + * + * @return {null} + */ +elasticlunr.resetStopWords = function () { + elasticlunr.stopWordFilter.stopWords = elasticlunr.defaultStopWords; +}; + +elasticlunr.defaultStopWords = { + "": true, + "a": true, + "able": true, + "about": true, + "across": true, + "after": true, + "all": true, + "almost": true, + "also": true, + "am": true, + "among": true, + "an": true, + "and": true, + "any": true, + "are": true, + "as": true, + "at": true, + "be": true, + "because": true, + "been": true, + "but": true, + "by": true, + "can": true, + "cannot": true, + "could": true, + "dear": true, + "did": true, + "do": true, + "does": true, + "either": true, + "else": true, + "ever": true, + "every": true, + "for": true, + "from": true, + "get": true, + "got": true, + "had": true, + "has": true, + "have": true, + "he": true, + "her": true, + "hers": true, + "him": true, + "his": true, + "how": true, + "however": true, + "i": true, + "if": true, + "in": true, + "into": true, + "is": true, + "it": true, + "its": true, + "just": true, + "least": true, + "let": true, + "like": true, + "likely": true, + "may": true, + "me": true, + "might": true, + "most": true, + "must": true, + "my": true, + "neither": true, + "no": true, + "nor": true, + "not": true, + "of": true, + "off": true, + "often": true, + "on": true, + "only": true, + "or": true, + "other": true, + "our": true, + "own": true, + "rather": true, + "said": true, + "say": true, + "says": true, + "she": true, + "should": true, + "since": true, + "so": true, + "some": true, + "than": true, + "that": true, + "the": true, + "their": true, + "them": true, + "then": true, + "there": true, + "these": true, + "they": true, + "this": true, + "tis": true, + "to": true, + "too": true, + "twas": true, + "us": true, + "wants": true, + "was": true, + "we": true, + "were": true, + "what": true, + "when": true, + "where": true, + "which": true, + "while": true, + "who": true, + "whom": true, + "why": true, + "will": true, + "with": true, + "would": true, + "yet": true, + "you": true, + "your": true +}; + +elasticlunr.stopWordFilter.stopWords = elasticlunr.defaultStopWords; + +elasticlunr.Pipeline.registerFunction(elasticlunr.stopWordFilter, 'stopWordFilter'); +/*! + * elasticlunr.trimmer + * Copyright (C) 2016 Oliver Nightingale + * Copyright (C) 2016 Wei Song + */ + +/** + * elasticlunr.trimmer is a pipeline function for trimming non word + * characters from the begining and end of tokens before they + * enter the index. + * + * This implementation may not work correctly for non latin + * characters and should either be removed or adapted for use + * with languages with non-latin characters. + * + * @module + * @param {String} token The token to pass through the filter + * @return {String} + * @see elasticlunr.Pipeline + */ +elasticlunr.trimmer = function (token) { + if (token === null || token === undefined) { + throw new Error('token should not be undefined'); + } + + return token + .replace(/^\W+/, '') + .replace(/\W+$/, ''); +}; + +elasticlunr.Pipeline.registerFunction(elasticlunr.trimmer, 'trimmer'); +/*! + * elasticlunr.InvertedIndex + * Copyright (C) 2016 Wei Song + * Includes code from - http://tartarus.org/~martin/PorterStemmer/js.txt + */ + +/** + * elasticlunr.InvertedIndex is used for efficiently storing and + * lookup of documents that contain a given token. + * + * @constructor + */ +elasticlunr.InvertedIndex = function () { + this.root = { docs: {}, df: 0 }; +}; + +/** + * Loads a previously serialised inverted index. + * + * @param {Object} serialisedData The serialised inverted index to load. + * @return {elasticlunr.InvertedIndex} + */ +elasticlunr.InvertedIndex.load = function (serialisedData) { + var idx = new this; + idx.root = serialisedData.root; + + return idx; +}; + +/** + * Adds a {token: tokenInfo} pair to the inverted index. + * If the token already exist, then update the tokenInfo. + * + * tokenInfo format: { ref: 1, tf: 2} + * tokenInfor should contains the document's ref and the tf(token frequency) of that token in + * the document. + * + * By default this function starts at the root of the current inverted index, however + * it can start at any node of the inverted index if required. + * + * @param {String} token + * @param {Object} tokenInfo format: { ref: 1, tf: 2} + * @param {Object} root An optional node at which to start looking for the + * correct place to enter the doc, by default the root of this elasticlunr.InvertedIndex + * is used. + * @memberOf InvertedIndex + */ +elasticlunr.InvertedIndex.prototype.addToken = function (token, tokenInfo, root) { + var root = root || this.root, + idx = 0; + + while (idx <= token.length - 1) { + var key = token[idx]; + + if (!(key in root)) root[key] = {docs: {}, df: 0}; + idx += 1; + root = root[key]; + } + + var docRef = tokenInfo.ref; + if (!root.docs[docRef]) { + // if this doc not exist, then add this doc + root.docs[docRef] = {tf: tokenInfo.tf}; + root.df += 1; + } else { + // if this doc already exist, then update tokenInfo + root.docs[docRef] = {tf: tokenInfo.tf}; + } +}; + +/** + * Checks whether a token is in this elasticlunr.InvertedIndex. + * + * + * @param {String} token The token to be checked + * @return {Boolean} + * @memberOf InvertedIndex + */ +elasticlunr.InvertedIndex.prototype.hasToken = function (token) { + if (!token) return false; + + var node = this.root; + + for (var i = 0; i < token.length; i++) { + if (!node[token[i]]) return false; + node = node[token[i]]; + } + + return true; +}; + +/** + * Retrieve a node from the inverted index for a given token. + * If token not found in this InvertedIndex, return null. + * + * + * @param {String} token The token to get the node for. + * @return {Object} + * @see InvertedIndex.prototype.get + * @memberOf InvertedIndex + */ +elasticlunr.InvertedIndex.prototype.getNode = function (token) { + if (!token) return null; + + var node = this.root; + + for (var i = 0; i < token.length; i++) { + if (!node[token[i]]) return null; + node = node[token[i]]; + } + + return node; +}; + +/** + * Retrieve the documents of a given token. + * If token not found, return {}. + * + * + * @param {String} token The token to get the documents for. + * @return {Object} + * @memberOf InvertedIndex + */ +elasticlunr.InvertedIndex.prototype.getDocs = function (token) { + var node = this.getNode(token); + if (node == null) { + return {}; + } + + return node.docs; +}; + +/** + * Retrieve term frequency of given token in given docRef. + * If token or docRef not found, return 0. + * + * + * @param {String} token The token to get the documents for. + * @param {String|Integer} docRef + * @return {Integer} + * @memberOf InvertedIndex + */ +elasticlunr.InvertedIndex.prototype.getTermFrequency = function (token, docRef) { + var node = this.getNode(token); + + if (node == null) { + return 0; + } + + if (!(docRef in node.docs)) { + return 0; + } + + return node.docs[docRef].tf; +}; + +/** + * Retrieve the document frequency of given token. + * If token not found, return 0. + * + * + * @param {String} token The token to get the documents for. + * @return {Object} + * @memberOf InvertedIndex + */ +elasticlunr.InvertedIndex.prototype.getDocFreq = function (token) { + var node = this.getNode(token); + + if (node == null) { + return 0; + } + + return node.df; +}; + +/** + * Remove the document identified by document's ref from the token in the inverted index. + * + * + * @param {String} token Remove the document from which token. + * @param {String} ref The ref of the document to remove from given token. + * @memberOf InvertedIndex + */ +elasticlunr.InvertedIndex.prototype.removeToken = function (token, ref) { + if (!token) return; + var node = this.getNode(token); + + if (node == null) return; + + if (ref in node.docs) { + delete node.docs[ref]; + node.df -= 1; + } +}; + +/** + * Find all the possible suffixes of given token using tokens currently in the inverted index. + * If token not found, return empty Array. + * + * @param {String} token The token to expand. + * @return {Array} + * @memberOf InvertedIndex + */ +elasticlunr.InvertedIndex.prototype.expandToken = function (token, memo, root) { + if (token == null || token == '') return []; + var memo = memo || []; + + if (root == void 0) { + root = this.getNode(token); + if (root == null) return memo; + } + + if (root.df > 0) memo.push(token); + + for (var key in root) { + if (key === 'docs') continue; + if (key === 'df') continue; + this.expandToken(token + key, memo, root[key]); + } + + return memo; +}; + +/** + * Returns a representation of the inverted index ready for serialisation. + * + * @return {Object} + * @memberOf InvertedIndex + */ +elasticlunr.InvertedIndex.prototype.toJSON = function () { + return { + root: this.root + }; +}; + +/*! + * elasticlunr.Configuration + * Copyright (C) 2016 Wei Song + */ + + /** + * elasticlunr.Configuration is used to analyze the user search configuration. + * + * By elasticlunr.Configuration user could set query-time boosting, boolean model in each field. + * + * Currently configuration supports: + * 1. query-time boosting, user could set how to boost each field. + * 2. boolean model chosing, user could choose which boolean model to use for each field. + * 3. token expandation, user could set token expand to True to improve Recall. Default is False. + * + * Query time boosting must be configured by field category, "boolean" model could be configured + * by both field category or globally as the following example. Field configuration for "boolean" + * will overwrite global configuration. + * Token expand could be configured both by field category or golbally. Local field configuration will + * overwrite global configuration. + * + * configuration example: + * { + * fields:{ + * title: {boost: 2}, + * body: {boost: 1} + * }, + * bool: "OR" + * } + * + * "bool" field configuation overwrite global configuation example: + * { + * fields:{ + * title: {boost: 2, bool: "AND"}, + * body: {boost: 1} + * }, + * bool: "OR" + * } + * + * "expand" example: + * { + * fields:{ + * title: {boost: 2, bool: "AND"}, + * body: {boost: 1} + * }, + * bool: "OR", + * expand: true + * } + * + * "expand" example for field category: + * { + * fields:{ + * title: {boost: 2, bool: "AND", expand: true}, + * body: {boost: 1} + * }, + * bool: "OR" + * } + * + * setting the boost to 0 ignores the field (this will only search the title): + * { + * fields:{ + * title: {boost: 1}, + * body: {boost: 0} + * } + * } + * + * then, user could search with configuration to do query-time boosting. + * idx.search('oracle database', {fields: {title: {boost: 2}, body: {boost: 1}}}); + * + * + * @constructor + * + * @param {String} config user configuration + * @param {Array} fields fields of index instance + * @module + */ +elasticlunr.Configuration = function (config, fields) { + var config = config || ''; + + if (fields == undefined || fields == null) { + throw new Error('fields should not be null'); + } + + this.config = {}; + + var userConfig; + try { + userConfig = JSON.parse(config); + this.buildUserConfig(userConfig, fields); + } catch (error) { + elasticlunr.utils.warn('user configuration parse failed, will use default configuration'); + this.buildDefaultConfig(fields); + } +}; + +/** + * Build default search configuration. + * + * @param {Array} fields fields of index instance + */ +elasticlunr.Configuration.prototype.buildDefaultConfig = function (fields) { + this.reset(); + fields.forEach(function (field) { + this.config[field] = { + boost: 1, + bool: "OR", + expand: false + }; + }, this); +}; + +/** + * Build user configuration. + * + * @param {JSON} config User JSON configuratoin + * @param {Array} fields fields of index instance + */ +elasticlunr.Configuration.prototype.buildUserConfig = function (config, fields) { + var global_bool = "OR"; + var global_expand = false; + + this.reset(); + if ('bool' in config) { + global_bool = config['bool'] || global_bool; + } + + if ('expand' in config) { + global_expand = config['expand'] || global_expand; + } + + if ('fields' in config) { + for (var field in config['fields']) { + if (fields.indexOf(field) > -1) { + var field_config = config['fields'][field]; + var field_expand = global_expand; + if (field_config.expand != undefined) { + field_expand = field_config.expand; + } + + this.config[field] = { + boost: (field_config.boost || field_config.boost === 0) ? field_config.boost : 1, + bool: field_config.bool || global_bool, + expand: field_expand + }; + } else { + elasticlunr.utils.warn('field name in user configuration not found in index instance fields'); + } + } + } else { + this.addAllFields2UserConfig(global_bool, global_expand, fields); + } +}; + +/** + * Add all fields to user search configuration. + * + * @param {String} bool Boolean model + * @param {String} expand Expand model + * @param {Array} fields fields of index instance + */ +elasticlunr.Configuration.prototype.addAllFields2UserConfig = function (bool, expand, fields) { + fields.forEach(function (field) { + this.config[field] = { + boost: 1, + bool: bool, + expand: expand + }; + }, this); +}; + +/** + * get current user configuration + */ +elasticlunr.Configuration.prototype.get = function () { + return this.config; +}; + +/** + * reset user search configuration. + */ +elasticlunr.Configuration.prototype.reset = function () { + this.config = {}; +}; +/** + * sorted_set.js is added only to make elasticlunr.js compatible with lunr-languages. + * if elasticlunr.js support different languages by default, this will make elasticlunr.js + * much bigger that not good for browser usage. + * + */ + + +/*! + * lunr.SortedSet + * Copyright (C) 2016 Oliver Nightingale + */ + +/** + * lunr.SortedSets are used to maintain an array of uniq values in a sorted + * order. + * + * @constructor + */ +lunr.SortedSet = function () { + this.length = 0 + this.elements = [] +} + +/** + * Loads a previously serialised sorted set. + * + * @param {Array} serialisedData The serialised set to load. + * @returns {lunr.SortedSet} + * @memberOf SortedSet + */ +lunr.SortedSet.load = function (serialisedData) { + var set = new this + + set.elements = serialisedData + set.length = serialisedData.length + + return set +} + +/** + * Inserts new items into the set in the correct position to maintain the + * order. + * + * @param {Object} The objects to add to this set. + * @memberOf SortedSet + */ +lunr.SortedSet.prototype.add = function () { + var i, element + + for (i = 0; i < arguments.length; i++) { + element = arguments[i] + if (~this.indexOf(element)) continue + this.elements.splice(this.locationFor(element), 0, element) + } + + this.length = this.elements.length +} + +/** + * Converts this sorted set into an array. + * + * @returns {Array} + * @memberOf SortedSet + */ +lunr.SortedSet.prototype.toArray = function () { + return this.elements.slice() +} + +/** + * Creates a new array with the results of calling a provided function on every + * element in this sorted set. + * + * Delegates to Array.prototype.map and has the same signature. + * + * @param {Function} fn The function that is called on each element of the + * set. + * @param {Object} ctx An optional object that can be used as the context + * for the function fn. + * @returns {Array} + * @memberOf SortedSet + */ +lunr.SortedSet.prototype.map = function (fn, ctx) { + return this.elements.map(fn, ctx) +} + +/** + * Executes a provided function once per sorted set element. + * + * Delegates to Array.prototype.forEach and has the same signature. + * + * @param {Function} fn The function that is called on each element of the + * set. + * @param {Object} ctx An optional object that can be used as the context + * @memberOf SortedSet + * for the function fn. + */ +lunr.SortedSet.prototype.forEach = function (fn, ctx) { + return this.elements.forEach(fn, ctx) +} + +/** + * Returns the index at which a given element can be found in the + * sorted set, or -1 if it is not present. + * + * @param {Object} elem The object to locate in the sorted set. + * @returns {Number} + * @memberOf SortedSet + */ +lunr.SortedSet.prototype.indexOf = function (elem) { + var start = 0, + end = this.elements.length, + sectionLength = end - start, + pivot = start + Math.floor(sectionLength / 2), + pivotElem = this.elements[pivot] + + while (sectionLength > 1) { + if (pivotElem === elem) return pivot + + if (pivotElem < elem) start = pivot + if (pivotElem > elem) end = pivot + + sectionLength = end - start + pivot = start + Math.floor(sectionLength / 2) + pivotElem = this.elements[pivot] + } + + if (pivotElem === elem) return pivot + + return -1 +} + +/** + * Returns the position within the sorted set that an element should be + * inserted at to maintain the current order of the set. + * + * This function assumes that the element to search for does not already exist + * in the sorted set. + * + * @param {Object} elem The elem to find the position for in the set + * @returns {Number} + * @memberOf SortedSet + */ +lunr.SortedSet.prototype.locationFor = function (elem) { + var start = 0, + end = this.elements.length, + sectionLength = end - start, + pivot = start + Math.floor(sectionLength / 2), + pivotElem = this.elements[pivot] + + while (sectionLength > 1) { + if (pivotElem < elem) start = pivot + if (pivotElem > elem) end = pivot + + sectionLength = end - start + pivot = start + Math.floor(sectionLength / 2) + pivotElem = this.elements[pivot] + } + + if (pivotElem > elem) return pivot + if (pivotElem < elem) return pivot + 1 +} + +/** + * Creates a new lunr.SortedSet that contains the elements in the intersection + * of this set and the passed set. + * + * @param {lunr.SortedSet} otherSet The set to intersect with this set. + * @returns {lunr.SortedSet} + * @memberOf SortedSet + */ +lunr.SortedSet.prototype.intersect = function (otherSet) { + var intersectSet = new lunr.SortedSet, + i = 0, j = 0, + a_len = this.length, b_len = otherSet.length, + a = this.elements, b = otherSet.elements + + while (true) { + if (i > a_len - 1 || j > b_len - 1) break + + if (a[i] === b[j]) { + intersectSet.add(a[i]) + i++, j++ + continue + } + + if (a[i] < b[j]) { + i++ + continue + } + + if (a[i] > b[j]) { + j++ + continue + } + }; + + return intersectSet +} + +/** + * Makes a copy of this set + * + * @returns {lunr.SortedSet} + * @memberOf SortedSet + */ +lunr.SortedSet.prototype.clone = function () { + var clone = new lunr.SortedSet + + clone.elements = this.toArray() + clone.length = clone.elements.length + + return clone +} + +/** + * Creates a new lunr.SortedSet that contains the elements in the union + * of this set and the passed set. + * + * @param {lunr.SortedSet} otherSet The set to union with this set. + * @returns {lunr.SortedSet} + * @memberOf SortedSet + */ +lunr.SortedSet.prototype.union = function (otherSet) { + var longSet, shortSet, unionSet + + if (this.length >= otherSet.length) { + longSet = this, shortSet = otherSet + } else { + longSet = otherSet, shortSet = this + } + + unionSet = longSet.clone() + + for(var i = 0, shortSetElements = shortSet.toArray(); i < shortSetElements.length; i++){ + unionSet.add(shortSetElements[i]) + } + + return unionSet +} + +/** + * Returns a representation of the sorted set ready for serialisation. + * + * @returns {Array} + * @memberOf SortedSet + */ +lunr.SortedSet.prototype.toJSON = function () { + return this.toArray() +} + /** + * export the module via AMD, CommonJS or as a browser global + * Export code from https://github.com/umdjs/umd/blob/master/returnExports.js + */ + ;(function (root, factory) { + if (typeof define === 'function' && define.amd) { + // AMD. Register as an anonymous module. + define(factory) + } else if (typeof exports === 'object') { + /** + * Node. Does not work with strict CommonJS, but + * only CommonJS-like enviroments that support module.exports, + * like Node. + */ + module.exports = factory() + } else { + // Browser globals (root is window) + root.elasticlunr = factory() + } + }(this, function () { + /** + * Just return a value to define the module export. + * This example returns an object, but the module + * can return a function as the exported value. + */ + return elasticlunr + })) +})(); diff --git a/js/elasticlunr.min.js b/js/elasticlunr.min.js new file mode 100644 index 0000000..32cb1bc --- /dev/null +++ b/js/elasticlunr.min.js @@ -0,0 +1,10 @@ +/** + * elasticlunr - http://weixsong.github.io + * Lightweight full-text search engine in Javascript for browser search and offline search. - 0.9.5 + * + * Copyright (C) 2016 Oliver Nightingale + * Copyright (C) 2016 Wei Song + * MIT Licensed + * @license + */ +!function(){function e(e){if(null===e||"object"!=typeof e)return e;var t=e.constructor();for(var n in e)e.hasOwnProperty(n)&&(t[n]=e[n]);return t}var t=function(e){var n=new t.Index;return n.pipeline.add(t.trimmer,t.stopWordFilter,t.stemmer),e&&e.call(n,n),n};t.version="0.9.5",lunr=t,t.utils={},t.utils.warn=function(e){return function(t){e.console&&console.warn&&console.warn(t)}}(this),t.utils.toString=function(e){return void 0===e||null===e?"":e.toString()},t.EventEmitter=function(){this.events={}},t.EventEmitter.prototype.addListener=function(){var e=Array.prototype.slice.call(arguments),t=e.pop(),n=e;if("function"!=typeof t)throw new TypeError("last argument must be a function");n.forEach(function(e){this.hasHandler(e)||(this.events[e]=[]),this.events[e].push(t)},this)},t.EventEmitter.prototype.removeListener=function(e,t){if(this.hasHandler(e)){var n=this.events[e].indexOf(t);-1!==n&&(this.events[e].splice(n,1),0==this.events[e].length&&delete this.events[e])}},t.EventEmitter.prototype.emit=function(e){if(this.hasHandler(e)){var t=Array.prototype.slice.call(arguments,1);this.events[e].forEach(function(e){e.apply(void 0,t)},this)}},t.EventEmitter.prototype.hasHandler=function(e){return e in this.events},t.tokenizer=function(e){if(!arguments.length||null===e||void 0===e)return[];if(Array.isArray(e)){var n=e.filter(function(e){return null===e||void 0===e?!1:!0});n=n.map(function(e){return t.utils.toString(e).toLowerCase()});var i=[];return n.forEach(function(e){var n=e.split(t.tokenizer.seperator);i=i.concat(n)},this),i}return e.toString().trim().toLowerCase().split(t.tokenizer.seperator)},t.tokenizer.defaultSeperator=/[\s\-]+/,t.tokenizer.seperator=t.tokenizer.defaultSeperator,t.tokenizer.setSeperator=function(e){null!==e&&void 0!==e&&"object"==typeof e&&(t.tokenizer.seperator=e)},t.tokenizer.resetSeperator=function(){t.tokenizer.seperator=t.tokenizer.defaultSeperator},t.tokenizer.getSeperator=function(){return t.tokenizer.seperator},t.Pipeline=function(){this._queue=[]},t.Pipeline.registeredFunctions={},t.Pipeline.registerFunction=function(e,n){n in t.Pipeline.registeredFunctions&&t.utils.warn("Overwriting existing registered function: "+n),e.label=n,t.Pipeline.registeredFunctions[n]=e},t.Pipeline.getRegisteredFunction=function(e){return e in t.Pipeline.registeredFunctions!=!0?null:t.Pipeline.registeredFunctions[e]},t.Pipeline.warnIfFunctionNotRegistered=function(e){var n=e.label&&e.label in this.registeredFunctions;n||t.utils.warn("Function is not registered with pipeline. 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ConjugateTranspose Conjunction Connect ConnectedComponents ConnectedGraphQ ConnesWindow ConoverTest ConsoleMessage ConsoleMessagePacket ConsolePrint Constant ConstantArray Constants ConstrainedMax ConstrainedMin ContentPadding ContentsBoundingBox ContentSelectable ContentSize Context ContextMenu Contexts ContextToFilename ContextToFileName Continuation Continue ContinuedFraction ContinuedFractionK ContinuousAction ContinuousMarkovProcess ContinuousTimeModelQ ContinuousWaveletData ContinuousWaveletTransform ContourDetect ContourGraphics ContourIntegral ContourLabels ContourLines ContourPlot ContourPlot3D Contours ContourShading ContourSmoothing ContourStyle ContraharmonicMean Control ControlActive ControlAlignment ControllabilityGramian ControllabilityMatrix ControllableDecomposition ControllableModelQ ControllerDuration ControllerInformation ControllerInformationData ControllerLinking ControllerManipulate ControllerMethod ControllerPath ControllerState ControlPlacement ControlsRendering ControlType Convergents ConversionOptions ConversionRules ConvertToBitmapPacket ConvertToPostScript ConvertToPostScriptPacket Convolve ConwayGroupCo1 ConwayGroupCo2 ConwayGroupCo3 CoordinateChartData CoordinatesToolOptions CoordinateTransform CoordinateTransformData CoprimeQ Coproduct CopulaDistribution Copyable CopyDirectory CopyFile CopyTag CopyToClipboard CornerFilter CornerNeighbors Correlation CorrelationDistance CorrelationFunction CorrelationTest Cos Cosh CoshIntegral CosineDistance CosineWindow CosIntegral Cot Coth Count CounterAssignments CounterBox CounterBoxOptions CounterClockwiseContourIntegral CounterEvaluator CounterFunction CounterIncrements CounterStyle CounterStyleMenuListing CountRoots CountryData Covariance CovarianceEstimatorFunction CovarianceFunction CoxianDistribution CoxIngersollRossProcess CoxModel CoxModelFit CramerVonMisesTest CreateArchive CreateDialog CreateDirectory CreateDocument CreateIntermediateDirectories CreatePalette CreatePalettePacket CreateScheduledTask CreateTemporary CreateWindow CriticalityFailureImportance CriticalitySuccessImportance CriticalSection Cross CrossingDetect CrossMatrix Csc Csch CubeRoot Cubics Cuboid CuboidBox Cumulant CumulantGeneratingFunction Cup CupCap Curl CurlyDoubleQuote CurlyQuote CurrentImage CurrentlySpeakingPacket CurrentValue CurvatureFlowFilter CurveClosed Cyan CycleGraph CycleIndexPolynomial Cycles CyclicGroup Cyclotomic Cylinder CylinderBox CylindricalDecomposition D DagumDistribution DamerauLevenshteinDistance DampingFactor Darker Dashed Dashing DataCompression DataDistribution DataRange DataReversed Date DateDelimiters DateDifference DateFunction DateList DateListLogPlot DateListPlot DatePattern DatePlus DateRange DateString DateTicksFormat DaubechiesWavelet DavisDistribution DawsonF DayCount DayCountConvention DayMatchQ DayName DayPlus DayRange DayRound DeBruijnGraph Debug DebugTag Decimal DeclareKnownSymbols DeclarePackage Decompose Decrement DedekindEta Default DefaultAxesStyle DefaultBaseStyle DefaultBoxStyle DefaultButton DefaultColor DefaultControlPlacement DefaultDuplicateCellStyle DefaultDuration DefaultElement DefaultFaceGridsStyle DefaultFieldHintStyle DefaultFont DefaultFontProperties DefaultFormatType DefaultFormatTypeForStyle DefaultFrameStyle DefaultFrameTicksStyle DefaultGridLinesStyle DefaultInlineFormatType DefaultInputFormatType DefaultLabelStyle DefaultMenuStyle DefaultNaturalLanguage DefaultNewCellStyle DefaultNewInlineCellStyle DefaultNotebook DefaultOptions DefaultOutputFormatType DefaultStyle DefaultStyleDefinitions DefaultTextFormatType DefaultTextInlineFormatType DefaultTicksStyle DefaultTooltipStyle DefaultValues Defer DefineExternal DefineInputStreamMethod DefineOutputStreamMethod Definition Degree DegreeCentrality DegreeGraphDistribution DegreeLexicographic DegreeReverseLexicographic Deinitialization Del Deletable Delete DeleteBorderComponents DeleteCases DeleteContents DeleteDirectory DeleteDuplicates DeleteFile DeleteSmallComponents DeleteWithContents DeletionWarning Delimiter DelimiterFlashTime DelimiterMatching Delimiters Denominator DensityGraphics DensityHistogram DensityPlot DependentVariables Deploy Deployed Depth DepthFirstScan Derivative DerivativeFilter DescriptorStateSpace DesignMatrix Det DGaussianWavelet DiacriticalPositioning Diagonal DiagonalMatrix Dialog DialogIndent DialogInput DialogLevel DialogNotebook DialogProlog DialogReturn DialogSymbols Diamond DiamondMatrix DiceDissimilarity DictionaryLookup DifferenceDelta DifferenceOrder DifferenceRoot DifferenceRootReduce Differences DifferentialD DifferentialRoot DifferentialRootReduce DifferentiatorFilter DigitBlock DigitBlockMinimum DigitCharacter DigitCount DigitQ DihedralGroup Dilation Dimensions DiracComb DiracDelta DirectedEdge DirectedEdges DirectedGraph DirectedGraphQ DirectedInfinity Direction Directive Directory DirectoryName DirectoryQ DirectoryStack DirichletCharacter DirichletConvolve DirichletDistribution DirichletL DirichletTransform DirichletWindow DisableConsolePrintPacket DiscreteChirpZTransform DiscreteConvolve DiscreteDelta DiscreteHadamardTransform DiscreteIndicator DiscreteLQEstimatorGains DiscreteLQRegulatorGains DiscreteLyapunovSolve DiscreteMarkovProcess DiscretePlot DiscretePlot3D DiscreteRatio DiscreteRiccatiSolve DiscreteShift DiscreteTimeModelQ DiscreteUniformDistribution DiscreteVariables DiscreteWaveletData DiscreteWaveletPacketTransform DiscreteWaveletTransform Discriminant Disjunction Disk DiskBox DiskMatrix Dispatch DispersionEstimatorFunction Display DisplayAllSteps DisplayEndPacket DisplayFlushImagePacket DisplayForm DisplayFunction DisplayPacket DisplayRules DisplaySetSizePacket DisplayString DisplayTemporary DisplayWith DisplayWithRef DisplayWithVariable DistanceFunction DistanceTransform Distribute Distributed DistributedContexts DistributeDefinitions DistributionChart DistributionDomain DistributionFitTest DistributionParameterAssumptions DistributionParameterQ Dithering Div Divergence Divide DivideBy Dividers Divisible Divisors DivisorSigma DivisorSum DMSList DMSString Do DockedCells DocumentNotebook DominantColors DOSTextFormat Dot DotDashed DotEqual Dotted DoubleBracketingBar DoubleContourIntegral DoubleDownArrow DoubleLeftArrow DoubleLeftRightArrow DoubleLeftTee DoubleLongLeftArrow DoubleLongLeftRightArrow DoubleLongRightArrow DoubleRightArrow DoubleRightTee DoubleUpArrow DoubleUpDownArrow DoubleVerticalBar DoublyInfinite Down DownArrow DownArrowBar DownArrowUpArrow DownLeftRightVector DownLeftTeeVector DownLeftVector DownLeftVectorBar DownRightTeeVector DownRightVector DownRightVectorBar Downsample DownTee DownTeeArrow DownValues DragAndDrop DrawEdges DrawFrontFaces DrawHighlighted Drop DSolve Dt DualLinearProgramming DualSystemsModel DumpGet DumpSave DuplicateFreeQ Dynamic DynamicBox DynamicBoxOptions DynamicEvaluationTimeout DynamicLocation DynamicModule DynamicModuleBox DynamicModuleBoxOptions DynamicModuleParent DynamicModuleValues DynamicName DynamicNamespace DynamicReference DynamicSetting DynamicUpdating DynamicWrapper DynamicWrapperBox DynamicWrapperBoxOptions E EccentricityCentrality EdgeAdd EdgeBetweennessCentrality EdgeCapacity EdgeCapForm EdgeColor EdgeConnectivity EdgeCost EdgeCount EdgeCoverQ EdgeDashing EdgeDelete EdgeDetect EdgeForm EdgeIndex EdgeJoinForm EdgeLabeling EdgeLabels EdgeLabelStyle EdgeList EdgeOpacity EdgeQ EdgeRenderingFunction EdgeRules EdgeShapeFunction EdgeStyle EdgeThickness EdgeWeight Editable EditButtonSettings EditCellTagsSettings EditDistance EffectiveInterest Eigensystem Eigenvalues EigenvectorCentrality Eigenvectors Element ElementData Eliminate EliminationOrder EllipticE EllipticExp EllipticExpPrime EllipticF EllipticFilterModel EllipticK EllipticLog EllipticNomeQ EllipticPi EllipticReducedHalfPeriods EllipticTheta EllipticThetaPrime EmitSound EmphasizeSyntaxErrors EmpiricalDistribution Empty EmptyGraphQ EnableConsolePrintPacket Enabled Encode End EndAdd EndDialogPacket EndFrontEndInteractionPacket EndOfFile EndOfLine EndOfString EndPackage EngineeringForm Enter EnterExpressionPacket EnterTextPacket Entropy EntropyFilter Environment Epilog Equal EqualColumns EqualRows EqualTilde EquatedTo Equilibrium EquirippleFilterKernel Equivalent Erf Erfc Erfi ErlangB ErlangC ErlangDistribution Erosion ErrorBox ErrorBoxOptions ErrorNorm ErrorPacket ErrorsDialogSettings EstimatedDistribution EstimatedProcess EstimatorGains EstimatorRegulator EuclideanDistance EulerE EulerGamma EulerianGraphQ EulerPhi Evaluatable Evaluate Evaluated EvaluatePacket EvaluationCell EvaluationCompletionAction EvaluationElements EvaluationMode EvaluationMonitor EvaluationNotebook EvaluationObject EvaluationOrder Evaluator EvaluatorNames EvenQ EventData EventEvaluator EventHandler EventHandlerTag EventLabels ExactBlackmanWindow ExactNumberQ ExactRootIsolation ExampleData Except ExcludedForms ExcludePods Exclusions ExclusionsStyle Exists Exit ExitDialog Exp Expand ExpandAll ExpandDenominator ExpandFileName ExpandNumerator Expectation ExpectationE ExpectedValue ExpGammaDistribution ExpIntegralE ExpIntegralEi Exponent ExponentFunction ExponentialDistribution ExponentialFamily ExponentialGeneratingFunction ExponentialMovingAverage ExponentialPowerDistribution ExponentPosition ExponentStep Export ExportAutoReplacements ExportPacket ExportString Expression ExpressionCell ExpressionPacket ExpToTrig ExtendedGCD Extension ExtentElementFunction ExtentMarkers ExtentSize ExternalCall ExternalDataCharacterEncoding Extract ExtractArchive ExtremeValueDistribution FaceForm FaceGrids FaceGridsStyle Factor FactorComplete Factorial Factorial2 FactorialMoment FactorialMomentGeneratingFunction FactorialPower FactorInteger FactorList FactorSquareFree FactorSquareFreeList FactorTerms FactorTermsList Fail FailureDistribution False FARIMAProcess FEDisableConsolePrintPacket FeedbackSector FeedbackSectorStyle FeedbackType FEEnableConsolePrintPacket Fibonacci FieldHint FieldHintStyle FieldMasked FieldSize File FileBaseName FileByteCount FileDate FileExistsQ FileExtension FileFormat FileHash FileInformation FileName FileNameDepth FileNameDialogSettings FileNameDrop FileNameJoin FileNames FileNameSetter FileNameSplit FileNameTake FilePrint FileType FilledCurve FilledCurveBox Filling FillingStyle FillingTransform FilterRules FinancialBond FinancialData FinancialDerivative FinancialIndicator Find FindArgMax FindArgMin FindClique FindClusters FindCurvePath FindDistributionParameters FindDivisions FindEdgeCover FindEdgeCut FindEulerianCycle FindFaces FindFile FindFit FindGeneratingFunction FindGeoLocation FindGeometricTransform FindGraphCommunities FindGraphIsomorphism FindGraphPartition FindHamiltonianCycle FindIndependentEdgeSet FindIndependentVertexSet FindInstance FindIntegerNullVector FindKClan FindKClique FindKClub FindKPlex FindLibrary FindLinearRecurrence FindList FindMaximum FindMaximumFlow FindMaxValue FindMinimum FindMinimumCostFlow FindMinimumCut FindMinValue FindPermutation FindPostmanTour FindProcessParameters FindRoot FindSequenceFunction FindSettings FindShortestPath FindShortestTour FindThreshold FindVertexCover FindVertexCut Fine FinishDynamic FiniteAbelianGroupCount FiniteGroupCount FiniteGroupData First FirstPassageTimeDistribution FischerGroupFi22 FischerGroupFi23 FischerGroupFi24Prime FisherHypergeometricDistribution FisherRatioTest FisherZDistribution Fit FitAll FittedModel FixedPoint FixedPointList FlashSelection Flat Flatten FlattenAt FlatTopWindow FlipView Floor FlushPrintOutputPacket Fold FoldList Font FontColor FontFamily FontForm FontName FontOpacity FontPostScriptName FontProperties FontReencoding FontSize FontSlant FontSubstitutions FontTracking FontVariations FontWeight For ForAll Format FormatRules FormatType FormatTypeAutoConvert FormatValues FormBox FormBoxOptions FortranForm Forward ForwardBackward Fourier FourierCoefficient FourierCosCoefficient FourierCosSeries FourierCosTransform FourierDCT FourierDCTFilter FourierDCTMatrix FourierDST FourierDSTMatrix FourierMatrix FourierParameters FourierSequenceTransform FourierSeries FourierSinCoefficient FourierSinSeries FourierSinTransform FourierTransform FourierTrigSeries FractionalBrownianMotionProcess FractionalPart FractionBox FractionBoxOptions FractionLine Frame FrameBox FrameBoxOptions Framed FrameInset FrameLabel Frameless FrameMargins FrameStyle FrameTicks FrameTicksStyle FRatioDistribution FrechetDistribution FreeQ FrequencySamplingFilterKernel FresnelC FresnelS Friday FrobeniusNumber FrobeniusSolve FromCharacterCode FromCoefficientRules FromContinuedFraction FromDate FromDigits FromDMS Front FrontEndDynamicExpression FrontEndEventActions FrontEndExecute FrontEndObject FrontEndResource FrontEndResourceString FrontEndStackSize FrontEndToken FrontEndTokenExecute FrontEndValueCache FrontEndVersion FrontFaceColor FrontFaceOpacity Full FullAxes FullDefinition FullForm FullGraphics FullOptions FullSimplify Function FunctionExpand FunctionInterpolation FunctionSpace FussellVeselyImportance GaborFilter GaborMatrix GaborWavelet GainMargins GainPhaseMargins Gamma GammaDistribution GammaRegularized GapPenalty Gather GatherBy GaugeFaceElementFunction GaugeFaceStyle GaugeFrameElementFunction GaugeFrameSize GaugeFrameStyle GaugeLabels GaugeMarkers GaugeStyle GaussianFilter GaussianIntegers GaussianMatrix GaussianWindow GCD GegenbauerC General GeneralizedLinearModelFit GenerateConditions GeneratedCell GeneratedParameters GeneratingFunction Generic GenericCylindricalDecomposition GenomeData GenomeLookup GeodesicClosing GeodesicDilation GeodesicErosion GeodesicOpening GeoDestination GeodesyData GeoDirection GeoDistance GeoGridPosition GeometricBrownianMotionProcess GeometricDistribution GeometricMean GeometricMeanFilter GeometricTransformation GeometricTransformation3DBox GeometricTransformation3DBoxOptions GeometricTransformationBox GeometricTransformationBoxOptions GeoPosition GeoPositionENU GeoPositionXYZ GeoProjectionData GestureHandler GestureHandlerTag Get GetBoundingBoxSizePacket GetContext GetEnvironment GetFileName GetFrontEndOptionsDataPacket GetLinebreakInformationPacket GetMenusPacket GetPageBreakInformationPacket Glaisher GlobalClusteringCoefficient GlobalPreferences GlobalSession Glow GoldenRatio GompertzMakehamDistribution GoodmanKruskalGamma GoodmanKruskalGammaTest Goto Grad Gradient GradientFilter GradientOrientationFilter Graph GraphAssortativity GraphCenter GraphComplement GraphData GraphDensity GraphDiameter GraphDifference GraphDisjointUnion GraphDistance GraphDistanceMatrix GraphElementData GraphEmbedding GraphHighlight GraphHighlightStyle GraphHub Graphics Graphics3D Graphics3DBox Graphics3DBoxOptions GraphicsArray GraphicsBaseline GraphicsBox GraphicsBoxOptions GraphicsColor GraphicsColumn GraphicsComplex GraphicsComplex3DBox GraphicsComplex3DBoxOptions GraphicsComplexBox GraphicsComplexBoxOptions GraphicsContents GraphicsData GraphicsGrid GraphicsGridBox GraphicsGroup GraphicsGroup3DBox GraphicsGroup3DBoxOptions GraphicsGroupBox GraphicsGroupBoxOptions GraphicsGrouping GraphicsHighlightColor GraphicsRow GraphicsSpacing GraphicsStyle GraphIntersection GraphLayout GraphLinkEfficiency GraphPeriphery GraphPlot GraphPlot3D GraphPower GraphPropertyDistribution GraphQ GraphRadius GraphReciprocity GraphRoot GraphStyle GraphUnion Gray GrayLevel GreatCircleDistance Greater GreaterEqual GreaterEqualLess GreaterFullEqual GreaterGreater GreaterLess GreaterSlantEqual GreaterTilde Green Grid GridBaseline GridBox GridBoxAlignment GridBoxBackground GridBoxDividers GridBoxFrame GridBoxItemSize GridBoxItemStyle GridBoxOptions GridBoxSpacings GridCreationSettings GridDefaultElement GridElementStyleOptions GridFrame GridFrameMargins GridGraph GridLines GridLinesStyle GroebnerBasis GroupActionBase GroupCentralizer GroupElementFromWord GroupElementPosition GroupElementQ GroupElements GroupElementToWord GroupGenerators GroupMultiplicationTable GroupOrbits GroupOrder GroupPageBreakWithin GroupSetwiseStabilizer GroupStabilizer GroupStabilizerChain Gudermannian GumbelDistribution HaarWavelet HadamardMatrix HalfNormalDistribution HamiltonianGraphQ HammingDistance HammingWindow HankelH1 HankelH2 HankelMatrix HannPoissonWindow HannWindow HaradaNortonGroupHN HararyGraph HarmonicMean HarmonicMeanFilter HarmonicNumber Hash HashTable Haversine HazardFunction Head HeadCompose Heads HeavisideLambda HeavisidePi HeavisideTheta HeldGroupHe HeldPart HelpBrowserLookup HelpBrowserNotebook HelpBrowserSettings HermiteDecomposition HermiteH HermitianMatrixQ HessenbergDecomposition Hessian HexadecimalCharacter Hexahedron HexahedronBox HexahedronBoxOptions HiddenSurface HighlightGraph HighlightImage HighpassFilter HigmanSimsGroupHS HilbertFilter HilbertMatrix Histogram Histogram3D HistogramDistribution HistogramList HistogramTransform HistogramTransformInterpolation HitMissTransform HITSCentrality HodgeDual HoeffdingD HoeffdingDTest Hold HoldAll HoldAllComplete HoldComplete HoldFirst HoldForm HoldPattern HoldRest HolidayCalendar HomeDirectory HomePage Horizontal HorizontalForm HorizontalGauge HorizontalScrollPosition HornerForm HotellingTSquareDistribution HoytDistribution HTMLSave Hue HumpDownHump HumpEqual HurwitzLerchPhi HurwitzZeta HyperbolicDistribution HypercubeGraph HyperexponentialDistribution Hyperfactorial Hypergeometric0F1 Hypergeometric0F1Regularized Hypergeometric1F1 Hypergeometric1F1Regularized Hypergeometric2F1 Hypergeometric2F1Regularized HypergeometricDistribution HypergeometricPFQ HypergeometricPFQRegularized HypergeometricU Hyperlink HyperlinkCreationSettings Hyphenation HyphenationOptions HypoexponentialDistribution HypothesisTestData I Identity IdentityMatrix If IgnoreCase Im Image Image3D Image3DSlices ImageAccumulate ImageAdd ImageAdjust ImageAlign ImageApply ImageAspectRatio ImageAssemble ImageCache ImageCacheValid ImageCapture ImageChannels ImageClip ImageColorSpace ImageCompose ImageConvolve ImageCooccurrence ImageCorners ImageCorrelate ImageCorrespondingPoints ImageCrop ImageData ImageDataPacket ImageDeconvolve ImageDemosaic ImageDifference ImageDimensions ImageDistance ImageEffect ImageFeatureTrack ImageFileApply ImageFileFilter ImageFileScan ImageFilter ImageForestingComponents ImageForwardTransformation ImageHistogram ImageKeypoints ImageLevels ImageLines ImageMargins ImageMarkers ImageMeasurements ImageMultiply ImageOffset ImagePad ImagePadding ImagePartition ImagePeriodogram ImagePerspectiveTransformation ImageQ ImageRangeCache ImageReflect ImageRegion ImageResize ImageResolution ImageRotate ImageRotated ImageScaled ImageScan ImageSize ImageSizeAction ImageSizeCache ImageSizeMultipliers ImageSizeRaw ImageSubtract ImageTake ImageTransformation ImageTrim ImageType ImageValue ImageValuePositions Implies Import ImportAutoReplacements ImportString ImprovementImportance In IncidenceGraph IncidenceList IncidenceMatrix IncludeConstantBasis IncludeFileExtension IncludePods IncludeSingularTerm Increment Indent IndentingNewlineSpacings IndentMaxFraction IndependenceTest IndependentEdgeSetQ IndependentUnit IndependentVertexSetQ Indeterminate IndexCreationOptions Indexed IndexGraph IndexTag Inequality InexactNumberQ InexactNumbers Infinity Infix Information Inherited InheritScope Initialization InitializationCell InitializationCellEvaluation InitializationCellWarning InlineCounterAssignments InlineCounterIncrements InlineRules Inner Inpaint Input InputAliases InputAssumptions InputAutoReplacements InputField InputFieldBox InputFieldBoxOptions InputForm InputGrouping InputNamePacket InputNotebook InputPacket InputSettings InputStream InputString InputStringPacket InputToBoxFormPacket Insert InsertionPointObject InsertResults Inset Inset3DBox Inset3DBoxOptions InsetBox InsetBoxOptions Install InstallService InString Integer IntegerDigits IntegerExponent IntegerLength IntegerPart IntegerPartitions IntegerQ Integers IntegerString Integral Integrate Interactive InteractiveTradingChart Interlaced Interleaving InternallyBalancedDecomposition InterpolatingFunction InterpolatingPolynomial Interpolation InterpolationOrder InterpolationPoints InterpolationPrecision Interpretation InterpretationBox InterpretationBoxOptions InterpretationFunction InterpretTemplate InterquartileRange Interrupt InterruptSettings Intersection Interval IntervalIntersection IntervalMemberQ IntervalUnion Inverse InverseBetaRegularized InverseCDF InverseChiSquareDistribution InverseContinuousWaveletTransform InverseDistanceTransform InverseEllipticNomeQ InverseErf InverseErfc InverseFourier InverseFourierCosTransform InverseFourierSequenceTransform InverseFourierSinTransform InverseFourierTransform InverseFunction InverseFunctions InverseGammaDistribution InverseGammaRegularized InverseGaussianDistribution InverseGudermannian InverseHaversine InverseJacobiCD InverseJacobiCN InverseJacobiCS InverseJacobiDC InverseJacobiDN InverseJacobiDS InverseJacobiNC InverseJacobiND InverseJacobiNS InverseJacobiSC InverseJacobiSD InverseJacobiSN InverseLaplaceTransform InversePermutation InverseRadon InverseSeries InverseSurvivalFunction InverseWaveletTransform InverseWeierstrassP InverseZTransform Invisible InvisibleApplication InvisibleTimes IrreduciblePolynomialQ IsolatingInterval IsomorphicGraphQ IsotopeData Italic Item ItemBox ItemBoxOptions ItemSize ItemStyle ItoProcess JaccardDissimilarity JacobiAmplitude Jacobian JacobiCD JacobiCN JacobiCS JacobiDC JacobiDN JacobiDS JacobiNC JacobiND JacobiNS JacobiP JacobiSC JacobiSD JacobiSN JacobiSymbol JacobiZeta JankoGroupJ1 JankoGroupJ2 JankoGroupJ3 JankoGroupJ4 JarqueBeraALMTest JohnsonDistribution Join Joined JoinedCurve JoinedCurveBox JoinForm JordanDecomposition JordanModelDecomposition K KagiChart KaiserBesselWindow KaiserWindow KalmanEstimator KalmanFilter KarhunenLoeveDecomposition KaryTree KatzCentrality KCoreComponents KDistribution KelvinBei KelvinBer KelvinKei KelvinKer KendallTau KendallTauTest KernelExecute KernelMixtureDistribution KernelObject Kernels Ket Khinchin KirchhoffGraph KirchhoffMatrix KleinInvariantJ KnightTourGraph KnotData KnownUnitQ KolmogorovSmirnovTest KroneckerDelta KroneckerModelDecomposition KroneckerProduct KroneckerSymbol KuiperTest KumaraswamyDistribution Kurtosis KuwaharaFilter Label Labeled LabeledSlider LabelingFunction LabelStyle LaguerreL LambdaComponents LambertW LanczosWindow LandauDistribution Language LanguageCategory LaplaceDistribution LaplaceTransform Laplacian LaplacianFilter LaplacianGaussianFilter Large Larger Last Latitude LatitudeLongitude LatticeData LatticeReduce Launch LaunchKernels LayeredGraphPlot LayerSizeFunction LayoutInformation LCM LeafCount LeapYearQ LeastSquares LeastSquaresFilterKernel Left LeftArrow LeftArrowBar LeftArrowRightArrow LeftDownTeeVector LeftDownVector LeftDownVectorBar LeftRightArrow LeftRightVector LeftTee LeftTeeArrow LeftTeeVector LeftTriangle LeftTriangleBar LeftTriangleEqual LeftUpDownVector LeftUpTeeVector LeftUpVector LeftUpVectorBar LeftVector LeftVectorBar LegendAppearance Legended LegendFunction LegendLabel LegendLayout LegendMargins LegendMarkers LegendMarkerSize LegendreP LegendreQ LegendreType Length LengthWhile LerchPhi Less LessEqual LessEqualGreater LessFullEqual LessGreater LessLess LessSlantEqual LessTilde LetterCharacter LetterQ Level LeveneTest LeviCivitaTensor LevyDistribution Lexicographic LibraryFunction LibraryFunctionError LibraryFunctionInformation LibraryFunctionLoad LibraryFunctionUnload LibraryLoad LibraryUnload LicenseID LiftingFilterData LiftingWaveletTransform LightBlue LightBrown LightCyan Lighter LightGray LightGreen Lighting LightingAngle LightMagenta LightOrange LightPink LightPurple LightRed LightSources LightYellow Likelihood Limit LimitsPositioning LimitsPositioningTokens LindleyDistribution Line Line3DBox LinearFilter LinearFractionalTransform LinearModelFit LinearOffsetFunction LinearProgramming LinearRecurrence LinearSolve LinearSolveFunction LineBox LineBreak LinebreakAdjustments LineBreakChart LineBreakWithin LineColor LineForm LineGraph LineIndent LineIndentMaxFraction LineIntegralConvolutionPlot LineIntegralConvolutionScale LineLegend LineOpacity LineSpacing LineWrapParts LinkActivate LinkClose LinkConnect LinkConnectedQ LinkCreate LinkError LinkFlush LinkFunction LinkHost LinkInterrupt LinkLaunch LinkMode LinkObject LinkOpen LinkOptions LinkPatterns LinkProtocol LinkRead LinkReadHeld LinkReadyQ Links LinkWrite LinkWriteHeld LiouvilleLambda List Listable ListAnimate ListContourPlot ListContourPlot3D ListConvolve ListCorrelate ListCurvePathPlot ListDeconvolve ListDensityPlot Listen ListFourierSequenceTransform ListInterpolation ListLineIntegralConvolutionPlot ListLinePlot ListLogLinearPlot ListLogLogPlot ListLogPlot ListPicker ListPickerBox ListPickerBoxBackground ListPickerBoxOptions ListPlay ListPlot ListPlot3D ListPointPlot3D ListPolarPlot ListQ ListStreamDensityPlot ListStreamPlot ListSurfacePlot3D ListVectorDensityPlot ListVectorPlot ListVectorPlot3D ListZTransform Literal LiteralSearch LocalClusteringCoefficient LocalizeVariables LocationEquivalenceTest LocationTest Locator LocatorAutoCreate LocatorBox LocatorBoxOptions LocatorCentering LocatorPane LocatorPaneBox LocatorPaneBoxOptions LocatorRegion Locked Log Log10 Log2 LogBarnesG LogGamma LogGammaDistribution LogicalExpand LogIntegral LogisticDistribution LogitModelFit LogLikelihood LogLinearPlot LogLogisticDistribution LogLogPlot LogMultinormalDistribution LogNormalDistribution LogPlot LogRankTest LogSeriesDistribution LongEqual Longest LongestAscendingSequence LongestCommonSequence LongestCommonSequencePositions LongestCommonSubsequence LongestCommonSubsequencePositions LongestMatch LongForm Longitude LongLeftArrow LongLeftRightArrow LongRightArrow Loopback LoopFreeGraphQ LowerCaseQ LowerLeftArrow LowerRightArrow LowerTriangularize LowpassFilter LQEstimatorGains LQGRegulator LQOutputRegulatorGains LQRegulatorGains LUBackSubstitution LucasL LuccioSamiComponents LUDecomposition LyapunovSolve LyonsGroupLy MachineID MachineName MachineNumberQ MachinePrecision MacintoshSystemPageSetup Magenta Magnification Magnify MainSolve MaintainDynamicCaches Majority MakeBoxes MakeExpression MakeRules MangoldtLambda ManhattanDistance Manipulate Manipulator MannWhitneyTest MantissaExponent Manual Map MapAll MapAt MapIndexed MAProcess MapThread MarcumQ MardiaCombinedTest MardiaKurtosisTest MardiaSkewnessTest MarginalDistribution MarkovProcessProperties Masking MatchingDissimilarity MatchLocalNameQ MatchLocalNames MatchQ Material MathematicaNotation MathieuC MathieuCharacteristicA MathieuCharacteristicB MathieuCharacteristicExponent MathieuCPrime MathieuGroupM11 MathieuGroupM12 MathieuGroupM22 MathieuGroupM23 MathieuGroupM24 MathieuS MathieuSPrime MathMLForm MathMLText Matrices MatrixExp MatrixForm MatrixFunction MatrixLog MatrixPlot MatrixPower MatrixQ MatrixRank Max MaxBend MaxDetect MaxExtraBandwidths MaxExtraConditions MaxFeatures MaxFilter Maximize MaxIterations MaxMemoryUsed MaxMixtureKernels MaxPlotPoints MaxPoints MaxRecursion MaxStableDistribution MaxStepFraction MaxSteps MaxStepSize MaxValue MaxwellDistribution McLaughlinGroupMcL Mean MeanClusteringCoefficient MeanDegreeConnectivity MeanDeviation MeanFilter MeanGraphDistance MeanNeighborDegree MeanShift MeanShiftFilter Median MedianDeviation MedianFilter Medium MeijerG MeixnerDistribution MemberQ MemoryConstrained MemoryInUse Menu MenuAppearance MenuCommandKey MenuEvaluator MenuItem MenuPacket MenuSortingValue MenuStyle MenuView MergeDifferences Mesh MeshFunctions MeshRange MeshShading MeshStyle Message MessageDialog MessageList MessageName MessageOptions MessagePacket Messages MessagesNotebook MetaCharacters MetaInformation Method MethodOptions MexicanHatWavelet MeyerWavelet Min MinDetect MinFilter MinimalPolynomial MinimalStateSpaceModel Minimize Minors MinRecursion MinSize MinStableDistribution Minus MinusPlus MinValue Missing MissingDataMethod MittagLefflerE MixedRadix MixedRadixQuantity MixtureDistribution Mod Modal Mode Modular ModularLambda Module Modulus MoebiusMu Moment Momentary MomentConvert MomentEvaluate MomentGeneratingFunction Monday Monitor MonomialList MonomialOrder MonsterGroupM MorletWavelet MorphologicalBinarize MorphologicalBranchPoints MorphologicalComponents MorphologicalEulerNumber MorphologicalGraph MorphologicalPerimeter MorphologicalTransform Most MouseAnnotation MouseAppearance MouseAppearanceTag MouseButtons Mouseover MousePointerNote MousePosition MovingAverage MovingMedian MoyalDistribution MultiedgeStyle MultilaunchWarning MultiLetterItalics MultiLetterStyle MultilineFunction Multinomial MultinomialDistribution MultinormalDistribution MultiplicativeOrder Multiplicity Multiselection MultivariateHypergeometricDistribution MultivariatePoissonDistribution MultivariateTDistribution N NakagamiDistribution NameQ Names NamespaceBox Nand NArgMax NArgMin NBernoulliB NCache NDSolve NDSolveValue Nearest NearestFunction NeedCurrentFrontEndPackagePacket NeedCurrentFrontEndSymbolsPacket NeedlemanWunschSimilarity Needs Negative NegativeBinomialDistribution NegativeMultinomialDistribution NeighborhoodGraph Nest NestedGreaterGreater NestedLessLess NestedScriptRules NestList NestWhile NestWhileList NevilleThetaC NevilleThetaD NevilleThetaN NevilleThetaS NewPrimitiveStyle NExpectation Next NextPrime NHoldAll NHoldFirst NHoldRest NicholsGridLines NicholsPlot NIntegrate NMaximize NMaxValue NMinimize NMinValue NominalVariables NonAssociative NoncentralBetaDistribution NoncentralChiSquareDistribution NoncentralFRatioDistribution NoncentralStudentTDistribution NonCommutativeMultiply NonConstants None NonlinearModelFit NonlocalMeansFilter NonNegative NonPositive Nor NorlundB Norm Normal NormalDistribution NormalGrouping Normalize NormalizedSquaredEuclideanDistance NormalsFunction NormFunction Not NotCongruent NotCupCap NotDoubleVerticalBar Notebook NotebookApply NotebookAutoSave NotebookClose NotebookConvertSettings NotebookCreate NotebookCreateReturnObject NotebookDefault NotebookDelete NotebookDirectory NotebookDynamicExpression NotebookEvaluate NotebookEventActions NotebookFileName NotebookFind NotebookFindReturnObject NotebookGet NotebookGetLayoutInformationPacket NotebookGetMisspellingsPacket NotebookInformation NotebookInterfaceObject NotebookLocate NotebookObject NotebookOpen NotebookOpenReturnObject NotebookPath NotebookPrint NotebookPut NotebookPutReturnObject NotebookRead NotebookResetGeneratedCells Notebooks NotebookSave NotebookSaveAs NotebookSelection NotebookSetupLayoutInformationPacket NotebooksMenu NotebookWrite NotElement NotEqualTilde NotExists NotGreater NotGreaterEqual NotGreaterFullEqual NotGreaterGreater NotGreaterLess NotGreaterSlantEqual NotGreaterTilde NotHumpDownHump NotHumpEqual NotLeftTriangle NotLeftTriangleBar NotLeftTriangleEqual NotLess NotLessEqual NotLessFullEqual NotLessGreater NotLessLess NotLessSlantEqual NotLessTilde NotNestedGreaterGreater NotNestedLessLess NotPrecedes NotPrecedesEqual NotPrecedesSlantEqual NotPrecedesTilde NotReverseElement NotRightTriangle NotRightTriangleBar NotRightTriangleEqual NotSquareSubset NotSquareSubsetEqual NotSquareSuperset NotSquareSupersetEqual NotSubset NotSubsetEqual NotSucceeds NotSucceedsEqual NotSucceedsSlantEqual NotSucceedsTilde NotSuperset NotSupersetEqual NotTilde NotTildeEqual NotTildeFullEqual NotTildeTilde NotVerticalBar NProbability NProduct NProductFactors NRoots NSolve NSum NSumTerms Null NullRecords NullSpace NullWords Number NumberFieldClassNumber NumberFieldDiscriminant NumberFieldFundamentalUnits NumberFieldIntegralBasis NumberFieldNormRepresentatives NumberFieldRegulator NumberFieldRootsOfUnity NumberFieldSignature NumberForm NumberFormat NumberMarks NumberMultiplier NumberPadding NumberPoint NumberQ NumberSeparator NumberSigns NumberString Numerator NumericFunction NumericQ NuttallWindow NValues NyquistGridLines NyquistPlot O ObservabilityGramian ObservabilityMatrix ObservableDecomposition ObservableModelQ OddQ Off Offset OLEData On ONanGroupON OneIdentity Opacity Open OpenAppend Opener OpenerBox OpenerBoxOptions OpenerView OpenFunctionInspectorPacket Opening OpenRead OpenSpecialOptions OpenTemporary OpenWrite Operate OperatingSystem OptimumFlowData Optional OptionInspectorSettings OptionQ Options OptionsPacket OptionsPattern OptionValue OptionValueBox OptionValueBoxOptions Or Orange Order OrderDistribution OrderedQ Ordering Orderless OrnsteinUhlenbeckProcess Orthogonalize Out Outer OutputAutoOverwrite OutputControllabilityMatrix OutputControllableModelQ OutputForm OutputFormData OutputGrouping OutputMathEditExpression OutputNamePacket OutputResponse OutputSizeLimit OutputStream Over OverBar OverDot Overflow OverHat Overlaps Overlay OverlayBox OverlayBoxOptions Overscript OverscriptBox OverscriptBoxOptions OverTilde OverVector OwenT OwnValues PackingMethod PaddedForm Padding PadeApproximant PadLeft PadRight PageBreakAbove PageBreakBelow PageBreakWithin PageFooterLines PageFooters PageHeaderLines PageHeaders PageHeight PageRankCentrality PageWidth PairedBarChart PairedHistogram PairedSmoothHistogram PairedTTest PairedZTest PaletteNotebook PalettePath Pane PaneBox PaneBoxOptions Panel PanelBox PanelBoxOptions Paneled PaneSelector PaneSelectorBox PaneSelectorBoxOptions PaperWidth ParabolicCylinderD ParagraphIndent ParagraphSpacing ParallelArray ParallelCombine ParallelDo ParallelEvaluate Parallelization Parallelize ParallelMap ParallelNeeds ParallelProduct ParallelSubmit ParallelSum ParallelTable ParallelTry Parameter ParameterEstimator ParameterMixtureDistribution ParameterVariables ParametricFunction ParametricNDSolve ParametricNDSolveValue ParametricPlot ParametricPlot3D ParentConnect ParentDirectory ParentForm Parenthesize ParentList ParetoDistribution Part PartialCorrelationFunction PartialD ParticleData Partition PartitionsP PartitionsQ ParzenWindow PascalDistribution PassEventsDown PassEventsUp Paste PasteBoxFormInlineCells PasteButton Path PathGraph PathGraphQ Pattern PatternSequence PatternTest PauliMatrix PaulWavelet Pause PausedTime PDF PearsonChiSquareTest PearsonCorrelationTest PearsonDistribution PerformanceGoal PeriodicInterpolation Periodogram PeriodogramArray PermutationCycles PermutationCyclesQ PermutationGroup PermutationLength PermutationList PermutationListQ PermutationMax PermutationMin PermutationOrder PermutationPower PermutationProduct PermutationReplace Permutations PermutationSupport Permute PeronaMalikFilter Perpendicular PERTDistribution PetersenGraph PhaseMargins Pi Pick PIDData PIDDerivativeFilter PIDFeedforward PIDTune Piecewise PiecewiseExpand PieChart PieChart3D PillaiTrace PillaiTraceTest Pink Pivoting PixelConstrained PixelValue PixelValuePositions Placed Placeholder PlaceholderReplace Plain PlanarGraphQ Play PlayRange Plot Plot3D Plot3Matrix PlotDivision PlotJoined PlotLabel PlotLayout PlotLegends PlotMarkers PlotPoints PlotRange PlotRangeClipping PlotRangePadding PlotRegion PlotStyle Plus PlusMinus Pochhammer PodStates PodWidth Point Point3DBox PointBox PointFigureChart PointForm PointLegend PointSize PoissonConsulDistribution PoissonDistribution PoissonProcess PoissonWindow PolarAxes PolarAxesOrigin PolarGridLines PolarPlot PolarTicks PoleZeroMarkers PolyaAeppliDistribution PolyGamma Polygon Polygon3DBox Polygon3DBoxOptions PolygonBox PolygonBoxOptions PolygonHoleScale PolygonIntersections PolygonScale PolyhedronData PolyLog PolynomialExtendedGCD PolynomialForm PolynomialGCD PolynomialLCM PolynomialMod PolynomialQ PolynomialQuotient PolynomialQuotientRemainder PolynomialReduce PolynomialRemainder Polynomials PopupMenu PopupMenuBox PopupMenuBoxOptions PopupView PopupWindow Position Positive PositiveDefiniteMatrixQ PossibleZeroQ Postfix PostScript Power PowerDistribution PowerExpand PowerMod PowerModList PowerSpectralDensity PowersRepresentations PowerSymmetricPolynomial Precedence PrecedenceForm Precedes PrecedesEqual PrecedesSlantEqual PrecedesTilde Precision PrecisionGoal PreDecrement PredictionRoot PreemptProtect PreferencesPath Prefix PreIncrement Prepend PrependTo PreserveImageOptions Previous PriceGraphDistribution PrimaryPlaceholder Prime PrimeNu PrimeOmega PrimePi PrimePowerQ PrimeQ Primes PrimeZetaP PrimitiveRoot PrincipalComponents PrincipalValue Print PrintAction PrintForm PrintingCopies PrintingOptions PrintingPageRange PrintingStartingPageNumber PrintingStyleEnvironment PrintPrecision PrintTemporary Prism PrismBox PrismBoxOptions PrivateCellOptions PrivateEvaluationOptions PrivateFontOptions PrivateFrontEndOptions PrivateNotebookOptions PrivatePaths Probability ProbabilityDistribution ProbabilityPlot ProbabilityPr ProbabilityScalePlot ProbitModelFit ProcessEstimator ProcessParameterAssumptions ProcessParameterQ ProcessStateDomain ProcessTimeDomain Product ProductDistribution ProductLog ProgressIndicator ProgressIndicatorBox 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RogersTanimotoDissimilarity Root RootApproximant RootIntervals RootLocusPlot RootMeanSquare RootOfUnityQ RootReduce Roots RootSum Rotate RotateLabel RotateLeft RotateRight RotationAction RotationBox RotationBoxOptions RotationMatrix RotationTransform Round RoundImplies RoundingRadius Row RowAlignments RowBackgrounds RowBox RowHeights RowLines RowMinHeight RowReduce RowsEqual RowSpacings RSolve RudvalisGroupRu Rule RuleCondition RuleDelayed RuleForm RulerUnits Run RunScheduledTask RunThrough RuntimeAttributes RuntimeOptions RussellRaoDissimilarity SameQ SameTest SampleDepth SampledSoundFunction SampledSoundList SampleRate SamplingPeriod SARIMAProcess SARMAProcess SatisfiabilityCount SatisfiabilityInstances SatisfiableQ Saturday Save Saveable SaveAutoDelete SaveDefinitions SawtoothWave Scale Scaled ScaleDivisions ScaledMousePosition ScaleOrigin ScalePadding ScaleRanges ScaleRangeStyle ScalingFunctions ScalingMatrix ScalingTransform Scan ScheduledTaskActiveQ ScheduledTaskData 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But as of jQuery 3.0 (2016), strict mode should be common +// enough that all such attempts are guarded in a try block. +"use strict"; + +var arr = []; + +var document = window.document; + +var getProto = Object.getPrototypeOf; + +var slice = arr.slice; + +var concat = arr.concat; + +var push = arr.push; + +var indexOf = arr.indexOf; + +var class2type = {}; + +var toString = class2type.toString; + +var hasOwn = class2type.hasOwnProperty; + +var fnToString = hasOwn.toString; + +var ObjectFunctionString = fnToString.call( Object ); + +var support = {}; + + + + function DOMEval( code, doc ) { + doc = doc || document; + + var script = doc.createElement( "script" ); + + script.text = code; + doc.head.appendChild( script ).parentNode.removeChild( script ); + } +/* global Symbol */ +// Defining this global in .eslintrc.json would create a danger of using the global +// unguarded in another place, it seems safer to define global only for this module + + + +var + version = "3.2.1", + + // Define a local copy of jQuery + jQuery = function( selector, context ) { + + // The jQuery object is actually just the init constructor 'enhanced' + // Need init if jQuery is called (just allow error to be thrown if not included) + return new jQuery.fn.init( selector, context ); + }, + + // Support: Android <=4.0 only + // Make sure we trim BOM and NBSP + rtrim = /^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g, + + // Matches dashed string for camelizing + rmsPrefix = /^-ms-/, + rdashAlpha = /-([a-z])/g, + + // Used by jQuery.camelCase as callback to replace() + fcamelCase = function( all, letter ) { + return letter.toUpperCase(); + }; + +jQuery.fn = jQuery.prototype = { + + // The current version of jQuery being used + jquery: version, + + constructor: jQuery, + + // The default length of a jQuery object is 0 + length: 0, + + toArray: function() { + return slice.call( this ); + }, + + // Get the Nth element in the matched element set OR + // Get the whole matched element set as a clean array + get: function( num ) { + + // Return all the elements in a clean array + if ( num == null ) { + return slice.call( this ); + } + + // Return just the one element from the set + return num < 0 ? this[ num + this.length ] : this[ num ]; + }, + + // Take an array of elements and push it onto the stack + // (returning the new matched element set) + pushStack: function( elems ) { + + // Build a new jQuery matched element set + var ret = jQuery.merge( this.constructor(), elems ); + + // Add the old object onto the stack (as a reference) + ret.prevObject = this; + + // Return the newly-formed element set + return ret; + }, + + // Execute a callback for every element in the matched set. + each: function( callback ) { + return jQuery.each( this, callback ); + }, + + map: function( callback ) { + return this.pushStack( jQuery.map( this, function( elem, i ) { + return callback.call( elem, i, elem ); + } ) ); + }, + + slice: function() { + return this.pushStack( slice.apply( this, arguments ) ); + }, + + first: function() { + return this.eq( 0 ); + }, + + last: function() { + return this.eq( -1 ); + }, + + eq: function( i ) { + var len = this.length, + j = +i + ( i < 0 ? len : 0 ); + return this.pushStack( j >= 0 && j < len ? [ this[ j ] ] : [] ); + }, + + end: function() { + return this.prevObject || this.constructor(); + }, + + // For internal use only. + // Behaves like an Array's method, not like a jQuery method. + push: push, + sort: arr.sort, + splice: arr.splice +}; + +jQuery.extend = jQuery.fn.extend = function() { + var options, name, src, copy, copyIsArray, clone, + target = arguments[ 0 ] || {}, + i = 1, + length = arguments.length, + deep = false; + + // Handle a deep copy situation + if ( typeof target === "boolean" ) { + deep = target; + + // Skip the boolean and the target + target = arguments[ i ] || {}; + i++; + } + + // Handle case when target is a string or something (possible in deep copy) + if ( typeof target !== "object" && !jQuery.isFunction( target ) ) { + target = {}; + } + + // Extend jQuery itself if only one argument is passed + if ( i === length ) { + target = this; + i--; + } + + for ( ; i < length; i++ ) { + + // Only deal with non-null/undefined values + if ( ( options = arguments[ i ] ) != null ) { + + // Extend the base object + for ( name in options ) { + src = target[ name ]; + copy = options[ name ]; + + // Prevent never-ending loop + if ( target === copy ) { + continue; + } + + // Recurse if we're merging plain objects or arrays + if ( deep && copy && ( jQuery.isPlainObject( copy ) || + ( copyIsArray = Array.isArray( copy ) ) ) ) { + + if ( copyIsArray ) { + copyIsArray = false; + clone = src && Array.isArray( src ) ? src : []; + + } else { + clone = src && jQuery.isPlainObject( src ) ? src : {}; + } + + // Never move original objects, clone them + target[ name ] = jQuery.extend( deep, clone, copy ); + + // Don't bring in undefined values + } else if ( copy !== undefined ) { + target[ name ] = copy; + } + } + } + } + + // Return the modified object + return target; +}; + +jQuery.extend( { + + // Unique for each copy of jQuery on the page + expando: "jQuery" + ( version + Math.random() ).replace( /\D/g, "" ), + + // Assume jQuery is ready without the ready module + isReady: true, + + error: function( msg ) { + throw new Error( msg ); + }, + + noop: function() {}, + + isFunction: function( obj ) { + return jQuery.type( obj ) === "function"; + }, + + isWindow: function( obj ) { + return obj != null && obj === obj.window; + }, + + isNumeric: function( obj ) { + + // As of jQuery 3.0, isNumeric is limited to + // strings and numbers (primitives or objects) + // that can be coerced to finite numbers (gh-2662) + var type = jQuery.type( obj ); + return ( type === "number" || type === "string" ) && + + // parseFloat NaNs numeric-cast false positives ("") + // ...but misinterprets leading-number strings, particularly hex literals ("0x...") + // subtraction forces infinities to NaN + !isNaN( obj - parseFloat( obj ) ); + }, + + isPlainObject: function( obj ) { + var proto, Ctor; + + // Detect obvious negatives + // Use toString instead of jQuery.type to catch host objects + if ( !obj || toString.call( obj ) !== "[object Object]" ) { + return false; + } + + proto = getProto( obj ); + + // Objects with no prototype (e.g., `Object.create( null )`) are plain + if ( !proto ) { + return true; + } + + // Objects with prototype are plain iff they were constructed by a global Object function + Ctor = hasOwn.call( proto, "constructor" ) && proto.constructor; + return typeof Ctor === "function" && fnToString.call( Ctor ) === ObjectFunctionString; + }, + + isEmptyObject: function( obj ) { + + /* eslint-disable no-unused-vars */ + // See https://github.com/eslint/eslint/issues/6125 + var name; + + for ( name in obj ) { + return false; + } + return true; + }, + + type: function( obj ) { + if ( obj == null ) { + return obj + ""; + } + + // Support: Android <=2.3 only (functionish RegExp) + return typeof obj === "object" || typeof obj === "function" ? + class2type[ toString.call( obj ) ] || "object" : + typeof obj; + }, + + // Evaluates a script in a global context + globalEval: function( code ) { + DOMEval( code ); + }, + + // Convert dashed to camelCase; used by the css and data modules + // Support: IE <=9 - 11, Edge 12 - 13 + // Microsoft forgot to hump their vendor prefix (#9572) + camelCase: function( string ) { + return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase ); + }, + + each: function( obj, callback ) { + var length, i = 0; + + if ( isArrayLike( obj ) ) { + length = obj.length; + for ( ; i < length; i++ ) { + if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) { + break; + } + } + } else { + for ( i in obj ) { + if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) { + break; + } + } + } + + return obj; + }, + + // Support: Android <=4.0 only + trim: function( text ) { + return text == null ? + "" : + ( text + "" ).replace( rtrim, "" ); + }, + + // results is for internal usage only + makeArray: function( arr, results ) { + var ret = results || []; + + if ( arr != null ) { + if ( isArrayLike( Object( arr ) ) ) { + jQuery.merge( ret, + typeof arr === "string" ? + [ arr ] : arr + ); + } else { + push.call( ret, arr ); + } + } + + return ret; + }, + + inArray: function( elem, arr, i ) { + return arr == null ? -1 : indexOf.call( arr, elem, i ); + }, + + // Support: Android <=4.0 only, PhantomJS 1 only + // push.apply(_, arraylike) throws on ancient WebKit + merge: function( first, second ) { + var len = +second.length, + j = 0, + i = first.length; + + for ( ; j < len; j++ ) { + first[ i++ ] = second[ j ]; + } + + first.length = i; + + return first; + }, + + grep: function( elems, callback, invert ) { + var callbackInverse, + matches = [], + i = 0, + length = elems.length, + callbackExpect = !invert; + + // Go through the array, only saving the items + // that pass the validator function + for ( ; i < length; i++ ) { + callbackInverse = !callback( elems[ i ], i ); + if ( callbackInverse !== callbackExpect ) { + matches.push( elems[ i ] ); + } + } + + return matches; + }, + + // arg is for internal usage only + map: function( elems, callback, arg ) { + var length, value, + i = 0, + ret = []; + + // Go through the array, translating each of the items to their new values + if ( isArrayLike( elems ) ) { + length = elems.length; + for ( ; i < length; i++ ) { + value = callback( elems[ i ], i, arg ); + + if ( value != null ) { + ret.push( value ); + } + } + + // Go through every key on the object, + } else { + for ( i in elems ) { + value = callback( elems[ i ], i, arg ); + + if ( value != null ) { + ret.push( value ); + } + } + } + + // Flatten any nested arrays + return concat.apply( [], ret ); + }, + + // A global GUID counter for objects + guid: 1, + + // Bind a function to a context, optionally partially applying any + // arguments. + proxy: function( fn, context ) { + var tmp, args, proxy; + + if ( typeof context === "string" ) { + tmp = fn[ context ]; + context = fn; + fn = tmp; + } + + // Quick check to determine if target is callable, in the spec + // this throws a TypeError, but we will just return undefined. + if ( !jQuery.isFunction( fn ) ) { + return undefined; + } + + // Simulated bind + args = slice.call( arguments, 2 ); + proxy = function() { + return fn.apply( context || this, args.concat( slice.call( arguments ) ) ); + }; + + // Set the guid of unique handler to the same of original handler, so it can be removed + proxy.guid = fn.guid = fn.guid || jQuery.guid++; + + return proxy; + }, + + now: Date.now, + + // jQuery.support is not used in Core but other projects attach their + // properties to it so it needs to exist. + support: support +} ); + +if ( typeof Symbol === "function" ) { + jQuery.fn[ Symbol.iterator ] = arr[ Symbol.iterator ]; +} + +// Populate the class2type map +jQuery.each( "Boolean Number String Function Array Date RegExp Object Error Symbol".split( " " ), +function( i, name ) { + class2type[ "[object " + name + "]" ] = name.toLowerCase(); +} ); + +function isArrayLike( obj ) { + + // Support: real iOS 8.2 only (not reproducible in simulator) + // `in` check used to prevent JIT error (gh-2145) + // hasOwn isn't used here due to false negatives + // regarding Nodelist length in IE + var length = !!obj && "length" in obj && obj.length, + type = jQuery.type( obj ); + + if ( type === "function" || jQuery.isWindow( obj ) ) { + return false; + } + + return type === "array" || length === 0 || + typeof length === "number" && length > 0 && ( length - 1 ) in obj; +} +var Sizzle = +/*! + * Sizzle CSS Selector Engine v2.3.3 + * https://sizzlejs.com/ + * + * Copyright jQuery Foundation and other contributors + * Released under the MIT license + * http://jquery.org/license + * + * Date: 2016-08-08 + */ +(function( window ) { + +var i, + support, + Expr, + getText, + isXML, + tokenize, + compile, + select, + outermostContext, + sortInput, + hasDuplicate, + + // Local document vars + setDocument, + document, + docElem, + documentIsHTML, + rbuggyQSA, + rbuggyMatches, + matches, + contains, + + // Instance-specific data + expando = "sizzle" + 1 * new Date(), + preferredDoc = window.document, + dirruns = 0, + done = 0, + classCache = createCache(), + tokenCache = createCache(), + compilerCache = createCache(), + sortOrder = function( a, b ) { + if ( a === b ) { + hasDuplicate = true; + } + return 0; + }, + + // Instance methods + hasOwn = ({}).hasOwnProperty, + arr = [], + pop = arr.pop, + push_native = arr.push, + push = arr.push, + slice = arr.slice, + // Use a stripped-down indexOf as it's faster than native + // https://jsperf.com/thor-indexof-vs-for/5 + indexOf = function( list, elem ) { + var i = 0, + len = list.length; + for ( ; i < len; i++ ) { + if ( list[i] === elem ) { + return i; + } + } + return -1; + }, + + booleans = "checked|selected|async|autofocus|autoplay|controls|defer|disabled|hidden|ismap|loop|multiple|open|readonly|required|scoped", + + // Regular expressions + + // http://www.w3.org/TR/css3-selectors/#whitespace + whitespace = "[\\x20\\t\\r\\n\\f]", + + // http://www.w3.org/TR/CSS21/syndata.html#value-def-identifier + identifier = "(?:\\\\.|[\\w-]|[^\0-\\xa0])+", + + // Attribute selectors: http://www.w3.org/TR/selectors/#attribute-selectors + attributes = "\\[" + whitespace + "*(" + identifier + ")(?:" + whitespace + + // Operator (capture 2) + "*([*^$|!~]?=)" + whitespace + + // "Attribute values must be CSS identifiers [capture 5] or strings [capture 3 or capture 4]" + "*(?:'((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\"|(" + identifier + "))|)" + whitespace + + "*\\]", + + pseudos = ":(" + identifier + ")(?:\\((" + + // To reduce the number of selectors needing tokenize in the preFilter, prefer arguments: + // 1. quoted (capture 3; capture 4 or capture 5) + "('((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\")|" + + // 2. simple (capture 6) + "((?:\\\\.|[^\\\\()[\\]]|" + attributes + ")*)|" + + // 3. anything else (capture 2) + ".*" + + ")\\)|)", + + // Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter + rwhitespace = new RegExp( whitespace + "+", "g" ), + rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + whitespace + "+$", "g" ), + + rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ), + rcombinators = new RegExp( "^" + whitespace + "*([>+~]|" + whitespace + ")" + whitespace + "*" ), + + rattributeQuotes = new RegExp( "=" + whitespace + "*([^\\]'\"]*?)" + whitespace + "*\\]", "g" ), + + rpseudo = new RegExp( pseudos ), + ridentifier = new RegExp( "^" + identifier + "$" ), + + matchExpr = { + "ID": new RegExp( "^#(" + identifier + ")" ), + "CLASS": new RegExp( "^\\.(" + identifier + ")" ), + "TAG": new RegExp( "^(" + identifier + "|[*])" ), + "ATTR": new RegExp( "^" + attributes ), + "PSEUDO": new RegExp( "^" + pseudos ), + "CHILD": new RegExp( "^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\(" + whitespace + + "*(even|odd|(([+-]|)(\\d*)n|)" + whitespace + "*(?:([+-]|)" + whitespace + + "*(\\d+)|))" + whitespace + "*\\)|)", "i" ), + "bool": new RegExp( "^(?:" + booleans + ")$", "i" ), + // For use in libraries implementing .is() + // We use this for POS matching in `select` + "needsContext": new RegExp( "^" + whitespace + "*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\(" + + whitespace + "*((?:-\\d)?\\d*)" + whitespace + "*\\)|)(?=[^-]|$)", "i" ) + }, + + rinputs = /^(?:input|select|textarea|button)$/i, + rheader = /^h\d$/i, + + rnative = /^[^{]+\{\s*\[native \w/, + + // Easily-parseable/retrievable ID or TAG or CLASS selectors + rquickExpr = /^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/, + + rsibling = /[+~]/, + + // CSS escapes + // http://www.w3.org/TR/CSS21/syndata.html#escaped-characters + runescape = new RegExp( "\\\\([\\da-f]{1,6}" + whitespace + "?|(" + whitespace + ")|.)", "ig" ), + funescape = function( _, escaped, escapedWhitespace ) { + var high = "0x" + escaped - 0x10000; + // NaN means non-codepoint + // Support: Firefox<24 + // Workaround erroneous numeric interpretation of +"0x" + return high !== high || escapedWhitespace ? + escaped : + high < 0 ? + // BMP codepoint + String.fromCharCode( high + 0x10000 ) : + // Supplemental Plane codepoint (surrogate pair) + String.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 ); + }, + + // CSS string/identifier serialization + // https://drafts.csswg.org/cssom/#common-serializing-idioms + rcssescape = /([\0-\x1f\x7f]|^-?\d)|^-$|[^\0-\x1f\x7f-\uFFFF\w-]/g, + fcssescape = function( ch, asCodePoint ) { + if ( asCodePoint ) { + + // U+0000 NULL becomes U+FFFD REPLACEMENT CHARACTER + if ( ch === "\0" ) { + return "\uFFFD"; + } + + // Control characters and (dependent upon position) numbers get escaped as code points + return ch.slice( 0, -1 ) + "\\" + ch.charCodeAt( ch.length - 1 ).toString( 16 ) + " "; + } + + // Other potentially-special ASCII characters get backslash-escaped + return "\\" + ch; + }, + + // Used for iframes + // See setDocument() + // Removing the function wrapper causes a "Permission Denied" + // error in IE + unloadHandler = function() { + setDocument(); + }, + + disabledAncestor = addCombinator( + function( elem ) { + return elem.disabled === true && ("form" in elem || "label" in elem); + }, + { dir: "parentNode", next: "legend" } + ); + +// Optimize for push.apply( _, NodeList ) +try { + push.apply( + (arr = slice.call( preferredDoc.childNodes )), + preferredDoc.childNodes + ); + // Support: Android<4.0 + // Detect silently failing push.apply + arr[ preferredDoc.childNodes.length ].nodeType; +} catch ( e ) { + push = { apply: arr.length ? + + // Leverage slice if possible + function( target, els ) { + push_native.apply( target, slice.call(els) ); + } : + + // Support: IE<9 + // Otherwise append directly + function( target, els ) { + var j = target.length, + i = 0; + // Can't trust NodeList.length + while ( (target[j++] = els[i++]) ) {} + target.length = j - 1; + } + }; +} + +function Sizzle( selector, context, results, seed ) { + var m, i, elem, nid, match, groups, newSelector, + newContext = context && context.ownerDocument, + + // nodeType defaults to 9, since context defaults to document + nodeType = context ? context.nodeType : 9; + + results = results || []; + + // Return early from calls with invalid selector or context + if ( typeof selector !== "string" || !selector || + nodeType !== 1 && nodeType !== 9 && nodeType !== 11 ) { + + return results; + } + + // Try to shortcut find operations (as opposed to filters) in HTML documents + if ( !seed ) { + + if ( ( context ? context.ownerDocument || context : preferredDoc ) !== document ) { + setDocument( context ); + } + context = context || document; + + if ( documentIsHTML ) { + + // If the selector is sufficiently simple, try using a "get*By*" DOM method + // (excepting DocumentFragment context, where the methods don't exist) + if ( nodeType !== 11 && (match = rquickExpr.exec( selector )) ) { + + // ID selector + if ( (m = match[1]) ) { + + // Document context + if ( nodeType === 9 ) { + if ( (elem = context.getElementById( m )) ) { + + // Support: IE, Opera, Webkit + // TODO: identify versions + // getElementById can match elements by name instead of ID + if ( elem.id === m ) { + results.push( elem ); + return results; + } + } else { + return results; + } + + // Element context + } else { + + // Support: IE, Opera, Webkit + // TODO: identify versions + // getElementById can match elements by name instead of ID + if ( newContext && (elem = newContext.getElementById( m )) && + contains( context, elem ) && + elem.id === m ) { + + results.push( elem ); + return results; + } + } + + // Type selector + } else if ( match[2] ) { + push.apply( results, context.getElementsByTagName( selector ) ); + return results; + + // Class selector + } else if ( (m = match[3]) && support.getElementsByClassName && + context.getElementsByClassName ) { + + push.apply( results, context.getElementsByClassName( m ) ); + return results; + } + } + + // Take advantage of querySelectorAll + if ( support.qsa && + !compilerCache[ selector + " " ] && + (!rbuggyQSA || !rbuggyQSA.test( selector )) ) { + + if ( nodeType !== 1 ) { + newContext = context; + newSelector = selector; + + // qSA looks outside Element context, which is not what we want + // Thanks to Andrew Dupont for this workaround technique + // Support: IE <=8 + // Exclude object elements + } else if ( context.nodeName.toLowerCase() !== "object" ) { + + // Capture the context ID, setting it first if necessary + if ( (nid = context.getAttribute( "id" )) ) { + nid = nid.replace( rcssescape, fcssescape ); + } else { + context.setAttribute( "id", (nid = expando) ); + } + + // Prefix every selector in the list + groups = tokenize( selector ); + i = groups.length; + while ( i-- ) { + groups[i] = "#" + nid + " " + toSelector( groups[i] ); + } + newSelector = groups.join( "," ); + + // Expand context for sibling selectors + newContext = rsibling.test( selector ) && testContext( context.parentNode ) || + context; + } + + if ( newSelector ) { + try { + push.apply( results, + newContext.querySelectorAll( newSelector ) + ); + return results; + } catch ( qsaError ) { + } finally { + if ( nid === expando ) { + context.removeAttribute( "id" ); + } + } + } + } + } + } + + // All others + return select( selector.replace( rtrim, "$1" ), context, results, seed ); +} + +/** + * Create key-value caches of limited size + * @returns {function(string, object)} Returns the Object data after storing it on itself with + * property name the (space-suffixed) string and (if the cache is larger than Expr.cacheLength) + * deleting the oldest entry + */ +function createCache() { + var keys = []; + + function cache( key, value ) { + // Use (key + " ") to avoid collision with native prototype properties (see Issue #157) + if ( keys.push( key + " " ) > Expr.cacheLength ) { + // Only keep the most recent entries + delete cache[ keys.shift() ]; + } + return (cache[ key + " " ] = value); + } + return cache; +} + +/** + * Mark a function for special use by Sizzle + * @param {Function} fn The function to mark + */ +function markFunction( fn ) { + fn[ expando ] = true; + return fn; +} + +/** + * Support testing using an element + * @param {Function} fn Passed the created element and returns a boolean result + */ +function assert( fn ) { + var el = document.createElement("fieldset"); + + try { + return !!fn( el ); + } catch (e) { + return false; + } finally { + // Remove from its parent by default + if ( el.parentNode ) { + el.parentNode.removeChild( el ); + } + // release memory in IE + el = null; + } +} + +/** + * Adds the same handler for all of the specified attrs + * @param {String} attrs Pipe-separated list of attributes + * @param {Function} handler The method that will be applied + */ +function addHandle( attrs, handler ) { + var arr = attrs.split("|"), + i = arr.length; + + while ( i-- ) { + Expr.attrHandle[ arr[i] ] = handler; + } +} + +/** + * Checks document order of two siblings + * @param {Element} a + * @param {Element} b + * @returns {Number} Returns less than 0 if a precedes b, greater than 0 if a follows b + */ +function siblingCheck( a, b ) { + var cur = b && a, + diff = cur && a.nodeType === 1 && b.nodeType === 1 && + a.sourceIndex - b.sourceIndex; + + // Use IE sourceIndex if available on both nodes + if ( diff ) { + return diff; + } + + // Check if b follows a + if ( cur ) { + while ( (cur = cur.nextSibling) ) { + if ( cur === b ) { + return -1; + } + } + } + + return a ? 1 : -1; +} + +/** + * Returns a function to use in pseudos for input types + * @param {String} type + */ +function createInputPseudo( type ) { + return function( elem ) { + var name = elem.nodeName.toLowerCase(); + return name === "input" && elem.type === type; + }; +} + +/** + * Returns a function to use in pseudos for buttons + * @param {String} type + */ +function createButtonPseudo( type ) { + return function( elem ) { + var name = elem.nodeName.toLowerCase(); + return (name === "input" || name === "button") && elem.type === type; + }; +} + +/** + * Returns a function to use in pseudos for :enabled/:disabled + * @param {Boolean} disabled true for :disabled; false for :enabled + */ +function createDisabledPseudo( disabled ) { + + // Known :disabled false positives: fieldset[disabled] > legend:nth-of-type(n+2) :can-disable + return function( elem ) { + + // Only certain elements can match :enabled or :disabled + // https://html.spec.whatwg.org/multipage/scripting.html#selector-enabled + // https://html.spec.whatwg.org/multipage/scripting.html#selector-disabled + if ( "form" in elem ) { + + // Check for inherited disabledness on relevant non-disabled elements: + // * listed form-associated elements in a disabled fieldset + // https://html.spec.whatwg.org/multipage/forms.html#category-listed + // https://html.spec.whatwg.org/multipage/forms.html#concept-fe-disabled + // * option elements in a disabled optgroup + // https://html.spec.whatwg.org/multipage/forms.html#concept-option-disabled + // All such elements have a "form" property. + if ( elem.parentNode && elem.disabled === false ) { + + // Option elements defer to a parent optgroup if present + if ( "label" in elem ) { + if ( "label" in elem.parentNode ) { + return elem.parentNode.disabled === disabled; + } else { + return elem.disabled === disabled; + } + } + + // Support: IE 6 - 11 + // Use the isDisabled shortcut property to check for disabled fieldset ancestors + return elem.isDisabled === disabled || + + // Where there is no isDisabled, check manually + /* jshint -W018 */ + elem.isDisabled !== !disabled && + disabledAncestor( elem ) === disabled; + } + + return elem.disabled === disabled; + + // Try to winnow out elements that can't be disabled before trusting the disabled property. + // Some victims get caught in our net (label, legend, menu, track), but it shouldn't + // even exist on them, let alone have a boolean value. + } else if ( "label" in elem ) { + return elem.disabled === disabled; + } + + // Remaining elements are neither :enabled nor :disabled + return false; + }; +} + +/** + * Returns a function to use in pseudos for positionals + * @param {Function} fn + */ +function createPositionalPseudo( fn ) { + return markFunction(function( argument ) { + argument = +argument; + return markFunction(function( seed, matches ) { + var j, + matchIndexes = fn( [], seed.length, argument ), + i = matchIndexes.length; + + // Match elements found at the specified indexes + while ( i-- ) { + if ( seed[ (j = matchIndexes[i]) ] ) { + seed[j] = !(matches[j] = seed[j]); + } + } + }); + }); +} + +/** + * Checks a node for validity as a Sizzle context + * @param {Element|Object=} context + * @returns {Element|Object|Boolean} The input node if acceptable, otherwise a falsy value + */ +function testContext( context ) { + return context && typeof context.getElementsByTagName !== "undefined" && context; +} + +// Expose support vars for convenience +support = Sizzle.support = {}; + +/** + * Detects XML nodes + * @param {Element|Object} elem An element or a document + * @returns {Boolean} True iff elem is a non-HTML XML node + */ +isXML = Sizzle.isXML = function( elem ) { + // documentElement is verified for cases where it doesn't yet exist + // (such as loading iframes in IE - #4833) + var documentElement = elem && (elem.ownerDocument || elem).documentElement; + return documentElement ? documentElement.nodeName !== "HTML" : false; +}; + +/** + * Sets document-related variables once based on the current document + * @param {Element|Object} [doc] An element or document object to use to set the document + * @returns {Object} Returns the current document + */ +setDocument = Sizzle.setDocument = function( node ) { + var hasCompare, subWindow, + doc = node ? node.ownerDocument || node : preferredDoc; + + // Return early if doc is invalid or already selected + if ( doc === document || doc.nodeType !== 9 || !doc.documentElement ) { + return document; + } + + // Update global variables + document = doc; + docElem = document.documentElement; + documentIsHTML = !isXML( document ); + + // Support: IE 9-11, Edge + // Accessing iframe documents after unload throws "permission denied" errors (jQuery #13936) + if ( preferredDoc !== document && + (subWindow = document.defaultView) && subWindow.top !== subWindow ) { + + // Support: IE 11, Edge + if ( subWindow.addEventListener ) { + subWindow.addEventListener( "unload", unloadHandler, false ); + + // Support: IE 9 - 10 only + } else if ( subWindow.attachEvent ) { + subWindow.attachEvent( "onunload", unloadHandler ); + } + } + + /* Attributes + ---------------------------------------------------------------------- */ + + // Support: IE<8 + // Verify that getAttribute really returns attributes and not properties + // (excepting IE8 booleans) + support.attributes = assert(function( el ) { + el.className = "i"; + return !el.getAttribute("className"); + }); + + /* getElement(s)By* + ---------------------------------------------------------------------- */ + + // Check if getElementsByTagName("*") returns only elements + support.getElementsByTagName = assert(function( el ) { + el.appendChild( document.createComment("") ); + return !el.getElementsByTagName("*").length; + }); + + // Support: IE<9 + support.getElementsByClassName = rnative.test( document.getElementsByClassName ); + + // Support: IE<10 + // Check if getElementById returns elements by name + // The broken getElementById methods don't pick up programmatically-set names, + // so use a roundabout getElementsByName test + support.getById = assert(function( el ) { + docElem.appendChild( el ).id = expando; + return !document.getElementsByName || !document.getElementsByName( expando ).length; + }); + + // ID filter and find + if ( support.getById ) { + Expr.filter["ID"] = function( id ) { + var attrId = id.replace( runescape, funescape ); + return function( elem ) { + return elem.getAttribute("id") === attrId; + }; + }; + Expr.find["ID"] = function( id, context ) { + if ( typeof context.getElementById !== "undefined" && documentIsHTML ) { + var elem = context.getElementById( id ); + return elem ? [ elem ] : []; + } + }; + } else { + Expr.filter["ID"] = function( id ) { + var attrId = id.replace( runescape, funescape ); + return function( elem ) { + var node = typeof elem.getAttributeNode !== "undefined" && + elem.getAttributeNode("id"); + return node && node.value === attrId; + }; + }; + + // Support: IE 6 - 7 only + // getElementById is not reliable as a find shortcut + Expr.find["ID"] = function( id, context ) { + if ( typeof context.getElementById !== "undefined" && documentIsHTML ) { + var node, i, elems, + elem = context.getElementById( id ); + + if ( elem ) { + + // Verify the id attribute + node = elem.getAttributeNode("id"); + if ( node && node.value === id ) { + return [ elem ]; + } + + // Fall back on getElementsByName + elems = context.getElementsByName( id ); + i = 0; + while ( (elem = elems[i++]) ) { + node = elem.getAttributeNode("id"); + if ( node && node.value === id ) { + return [ elem ]; + } + } + } + + return []; + } + }; + } + + // Tag + Expr.find["TAG"] = support.getElementsByTagName ? + function( tag, context ) { + if ( typeof context.getElementsByTagName !== "undefined" ) { + return context.getElementsByTagName( tag ); + + // DocumentFragment nodes don't have gEBTN + } else if ( support.qsa ) { + return context.querySelectorAll( tag ); + } + } : + + function( tag, context ) { + var elem, + tmp = [], + i = 0, + // By happy coincidence, a (broken) gEBTN appears on DocumentFragment nodes too + results = context.getElementsByTagName( tag ); + + // Filter out possible comments + if ( tag === "*" ) { + while ( (elem = results[i++]) ) { + if ( elem.nodeType === 1 ) { + tmp.push( elem ); + } + } + + return tmp; + } + return results; + }; + + // Class + Expr.find["CLASS"] = support.getElementsByClassName && function( className, context ) { + if ( typeof context.getElementsByClassName !== "undefined" && documentIsHTML ) { + return context.getElementsByClassName( className ); + } + }; + + /* QSA/matchesSelector + ---------------------------------------------------------------------- */ + + // QSA and matchesSelector support + + // matchesSelector(:active) reports false when true (IE9/Opera 11.5) + rbuggyMatches = []; + + // qSa(:focus) reports false when true (Chrome 21) + // We allow this because of a bug in IE8/9 that throws an error + // whenever `document.activeElement` is accessed on an iframe + // So, we allow :focus to pass through QSA all the time to avoid the IE error + // See https://bugs.jquery.com/ticket/13378 + rbuggyQSA = []; + + if ( (support.qsa = rnative.test( document.querySelectorAll )) ) { + // Build QSA regex + // Regex strategy adopted from Diego Perini + assert(function( el ) { + // Select is set to empty string on purpose + // This is to test IE's treatment of not explicitly + // setting a boolean content attribute, + // since its presence should be enough + // https://bugs.jquery.com/ticket/12359 + docElem.appendChild( el ).innerHTML = "" + + ""; + + // Support: IE8, Opera 11-12.16 + // Nothing should be selected when empty strings follow ^= or $= or *= + // The test attribute must be unknown in Opera but "safe" for WinRT + // https://msdn.microsoft.com/en-us/library/ie/hh465388.aspx#attribute_section + if ( el.querySelectorAll("[msallowcapture^='']").length ) { + rbuggyQSA.push( "[*^$]=" + whitespace + "*(?:''|\"\")" ); + } + + // Support: IE8 + // Boolean attributes and "value" are not treated correctly + if ( !el.querySelectorAll("[selected]").length ) { + rbuggyQSA.push( "\\[" + whitespace + "*(?:value|" + booleans + ")" ); + } + + // Support: Chrome<29, Android<4.4, Safari<7.0+, iOS<7.0+, PhantomJS<1.9.8+ + if ( !el.querySelectorAll( "[id~=" + expando + "-]" ).length ) { + rbuggyQSA.push("~="); + } + + // Webkit/Opera - :checked should return selected option elements + // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked + // IE8 throws error here and will not see later tests + if ( !el.querySelectorAll(":checked").length ) { + rbuggyQSA.push(":checked"); + } + + // Support: Safari 8+, iOS 8+ + // https://bugs.webkit.org/show_bug.cgi?id=136851 + // In-page `selector#id sibling-combinator selector` fails + if ( !el.querySelectorAll( "a#" + expando + "+*" ).length ) { + rbuggyQSA.push(".#.+[+~]"); + } + }); + + assert(function( el ) { + el.innerHTML = "" + + ""; + + // Support: Windows 8 Native Apps + // The type and name attributes are restricted during .innerHTML assignment + var input = document.createElement("input"); + input.setAttribute( "type", "hidden" ); + el.appendChild( input ).setAttribute( "name", "D" ); + + // Support: IE8 + // Enforce case-sensitivity of name attribute + if ( el.querySelectorAll("[name=d]").length ) { + rbuggyQSA.push( "name" + whitespace + "*[*^$|!~]?=" ); + } + + // FF 3.5 - :enabled/:disabled and hidden elements (hidden elements are still enabled) + // IE8 throws error here and will not see later tests + if ( el.querySelectorAll(":enabled").length !== 2 ) { + rbuggyQSA.push( ":enabled", ":disabled" ); + } + + // Support: IE9-11+ + // IE's :disabled selector does not pick up the children of disabled fieldsets + docElem.appendChild( el ).disabled = true; + if ( el.querySelectorAll(":disabled").length !== 2 ) { + rbuggyQSA.push( ":enabled", ":disabled" ); + } + + // Opera 10-11 does not throw on post-comma invalid pseudos + el.querySelectorAll("*,:x"); + rbuggyQSA.push(",.*:"); + }); + } + + if ( (support.matchesSelector = rnative.test( (matches = docElem.matches || + docElem.webkitMatchesSelector || + docElem.mozMatchesSelector || + docElem.oMatchesSelector || + docElem.msMatchesSelector) )) ) { + + assert(function( el ) { + // Check to see if it's possible to do matchesSelector + // on a disconnected node (IE 9) + support.disconnectedMatch = matches.call( el, "*" ); + + // This should fail with an exception + // Gecko does not error, returns false instead + matches.call( el, "[s!='']:x" ); + rbuggyMatches.push( "!=", pseudos ); + }); + } + + rbuggyQSA = rbuggyQSA.length && new RegExp( rbuggyQSA.join("|") ); + rbuggyMatches = rbuggyMatches.length && new RegExp( rbuggyMatches.join("|") ); + + /* Contains + ---------------------------------------------------------------------- */ + hasCompare = rnative.test( docElem.compareDocumentPosition ); + + // Element contains another + // Purposefully self-exclusive + // As in, an element does not contain itself + contains = hasCompare || rnative.test( docElem.contains ) ? + function( a, b ) { + var adown = a.nodeType === 9 ? a.documentElement : a, + bup = b && b.parentNode; + return a === bup || !!( bup && bup.nodeType === 1 && ( + adown.contains ? + adown.contains( bup ) : + a.compareDocumentPosition && a.compareDocumentPosition( bup ) & 16 + )); + } : + function( a, b ) { + if ( b ) { + while ( (b = b.parentNode) ) { + if ( b === a ) { + return true; + } + } + } + return false; + }; + + /* Sorting + ---------------------------------------------------------------------- */ + + // Document order sorting + sortOrder = hasCompare ? + function( a, b ) { + + // Flag for duplicate removal + if ( a === b ) { + hasDuplicate = true; + return 0; + } + + // Sort on method existence if only one input has compareDocumentPosition + var compare = !a.compareDocumentPosition - !b.compareDocumentPosition; + if ( compare ) { + return compare; + } + + // Calculate position if both inputs belong to the same document + compare = ( a.ownerDocument || a ) === ( b.ownerDocument || b ) ? + a.compareDocumentPosition( b ) : + + // Otherwise we know they are disconnected + 1; + + // Disconnected nodes + if ( compare & 1 || + (!support.sortDetached && b.compareDocumentPosition( a ) === compare) ) { + + // Choose the first element that is related to our preferred document + if ( a === document || a.ownerDocument === preferredDoc && contains(preferredDoc, a) ) { + return -1; + } + if ( b === document || b.ownerDocument === preferredDoc && contains(preferredDoc, b) ) { + return 1; + } + + // Maintain original order + return sortInput ? + ( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) : + 0; + } + + return compare & 4 ? -1 : 1; + } : + function( a, b ) { + // Exit early if the nodes are identical + if ( a === b ) { + hasDuplicate = true; + return 0; + } + + var cur, + i = 0, + aup = a.parentNode, + bup = b.parentNode, + ap = [ a ], + bp = [ b ]; + + // Parentless nodes are either documents or disconnected + if ( !aup || !bup ) { + return a === document ? -1 : + b === document ? 1 : + aup ? -1 : + bup ? 1 : + sortInput ? + ( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) : + 0; + + // If the nodes are siblings, we can do a quick check + } else if ( aup === bup ) { + return siblingCheck( a, b ); + } + + // Otherwise we need full lists of their ancestors for comparison + cur = a; + while ( (cur = cur.parentNode) ) { + ap.unshift( cur ); + } + cur = b; + while ( (cur = cur.parentNode) ) { + bp.unshift( cur ); + } + + // Walk down the tree looking for a discrepancy + while ( ap[i] === bp[i] ) { + i++; + } + + return i ? + // Do a sibling check if the nodes have a common ancestor + siblingCheck( ap[i], bp[i] ) : + + // Otherwise nodes in our document sort first + ap[i] === preferredDoc ? -1 : + bp[i] === preferredDoc ? 1 : + 0; + }; + + return document; +}; + +Sizzle.matches = function( expr, elements ) { + return Sizzle( expr, null, null, elements ); +}; + +Sizzle.matchesSelector = function( elem, expr ) { + // Set document vars if needed + if ( ( elem.ownerDocument || elem ) !== document ) { + setDocument( elem ); + } + + // Make sure that attribute selectors are quoted + expr = expr.replace( rattributeQuotes, "='$1']" ); + + if ( support.matchesSelector && documentIsHTML && + !compilerCache[ expr + " " ] && + ( !rbuggyMatches || !rbuggyMatches.test( expr ) ) && + ( !rbuggyQSA || !rbuggyQSA.test( expr ) ) ) { + + try { + var ret = matches.call( elem, expr ); + + // IE 9's matchesSelector returns false on disconnected nodes + if ( ret || support.disconnectedMatch || + // As well, disconnected nodes are said to be in a document + // fragment in IE 9 + elem.document && elem.document.nodeType !== 11 ) { + return ret; + } + } catch (e) {} + } + + return Sizzle( expr, document, null, [ elem ] ).length > 0; +}; + +Sizzle.contains = function( context, elem ) { + // Set document vars if needed + if ( ( context.ownerDocument || context ) !== document ) { + setDocument( context ); + } + return contains( context, elem ); +}; + +Sizzle.attr = function( elem, name ) { + // Set document vars if needed + if ( ( elem.ownerDocument || elem ) !== document ) { + setDocument( elem ); + } + + var fn = Expr.attrHandle[ name.toLowerCase() ], + // Don't get fooled by Object.prototype properties (jQuery #13807) + val = fn && hasOwn.call( Expr.attrHandle, name.toLowerCase() ) ? + fn( elem, name, !documentIsHTML ) : + undefined; + + return val !== undefined ? + val : + support.attributes || !documentIsHTML ? + elem.getAttribute( name ) : + (val = elem.getAttributeNode(name)) && val.specified ? + val.value : + null; +}; + +Sizzle.escape = function( sel ) { + return (sel + "").replace( rcssescape, fcssescape ); +}; + +Sizzle.error = function( msg ) { + throw new Error( "Syntax error, unrecognized expression: " + msg ); +}; + +/** + * Document sorting and removing duplicates + * @param {ArrayLike} results + */ +Sizzle.uniqueSort = function( results ) { + var elem, + duplicates = [], + j = 0, + i = 0; + + // Unless we *know* we can detect duplicates, assume their presence + hasDuplicate = !support.detectDuplicates; + sortInput = !support.sortStable && results.slice( 0 ); + results.sort( sortOrder ); + + if ( hasDuplicate ) { + while ( (elem = results[i++]) ) { + if ( elem === results[ i ] ) { + j = duplicates.push( i ); + } + } + while ( j-- ) { + results.splice( duplicates[ j ], 1 ); + } + } + + // Clear input after sorting to release objects + // See https://github.com/jquery/sizzle/pull/225 + sortInput = null; + + return results; +}; + +/** + * Utility function for retrieving the text value of an array of DOM nodes + * @param {Array|Element} elem + */ +getText = Sizzle.getText = function( elem ) { + var node, + ret = "", + i = 0, + nodeType = elem.nodeType; + + if ( !nodeType ) { + // If no nodeType, this is expected to be an array + while ( (node = elem[i++]) ) { + // Do not traverse comment nodes + ret += getText( node ); + } + } else if ( nodeType === 1 || nodeType === 9 || nodeType === 11 ) { + // Use textContent for elements + // innerText usage removed for consistency of new lines (jQuery #11153) + if ( typeof elem.textContent === "string" ) { + return elem.textContent; + } else { + // Traverse its children + for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) { + ret += getText( elem ); + } + } + } else if ( nodeType === 3 || nodeType === 4 ) { + return elem.nodeValue; + } + // Do not include comment or processing instruction nodes + + return ret; +}; + +Expr = Sizzle.selectors = { + + // Can be adjusted by the user + cacheLength: 50, + + createPseudo: markFunction, + + match: matchExpr, + + attrHandle: {}, + + find: {}, + + relative: { + ">": { dir: "parentNode", first: true }, + " ": { dir: "parentNode" }, + "+": { dir: "previousSibling", first: true }, + "~": { dir: "previousSibling" } + }, + + preFilter: { + "ATTR": function( match ) { + match[1] = match[1].replace( runescape, funescape ); + + // Move the given value to match[3] whether quoted or unquoted + match[3] = ( match[3] || match[4] || match[5] || "" ).replace( runescape, funescape ); + + if ( match[2] === "~=" ) { + match[3] = " " + match[3] + " "; + } + + return match.slice( 0, 4 ); + }, + + "CHILD": function( match ) { + /* matches from matchExpr["CHILD"] + 1 type (only|nth|...) + 2 what (child|of-type) + 3 argument (even|odd|\d*|\d*n([+-]\d+)?|...) + 4 xn-component of xn+y argument ([+-]?\d*n|) + 5 sign of xn-component + 6 x of xn-component + 7 sign of y-component + 8 y of y-component + */ + match[1] = match[1].toLowerCase(); + + if ( match[1].slice( 0, 3 ) === "nth" ) { + // nth-* requires argument + if ( !match[3] ) { + Sizzle.error( match[0] ); + } + + // numeric x and y parameters for Expr.filter.CHILD + // remember that false/true cast respectively to 0/1 + match[4] = +( match[4] ? match[5] + (match[6] || 1) : 2 * ( match[3] === "even" || match[3] === "odd" ) ); + match[5] = +( ( match[7] + match[8] ) || match[3] === "odd" ); + + // other types prohibit arguments + } else if ( match[3] ) { + Sizzle.error( match[0] ); + } + + return match; + }, + + "PSEUDO": function( match ) { + var excess, + unquoted = !match[6] && match[2]; + + if ( matchExpr["CHILD"].test( match[0] ) ) { + return null; + } + + // Accept quoted arguments as-is + if ( match[3] ) { + match[2] = match[4] || match[5] || ""; + + // Strip excess characters from unquoted arguments + } else if ( unquoted && rpseudo.test( unquoted ) && + // Get excess from tokenize (recursively) + (excess = tokenize( unquoted, true )) && + // advance to the next closing parenthesis + (excess = unquoted.indexOf( ")", unquoted.length - excess ) - unquoted.length) ) { + + // excess is a negative index + match[0] = match[0].slice( 0, excess ); + match[2] = unquoted.slice( 0, excess ); + } + + // Return only captures needed by the pseudo filter method (type and argument) + return match.slice( 0, 3 ); + } + }, + + filter: { + + "TAG": function( nodeNameSelector ) { + var nodeName = nodeNameSelector.replace( runescape, funescape ).toLowerCase(); + return nodeNameSelector === "*" ? + function() { return true; } : + function( elem ) { + return elem.nodeName && elem.nodeName.toLowerCase() === nodeName; + }; + }, + + "CLASS": function( className ) { + var pattern = classCache[ className + " " ]; + + return pattern || + (pattern = new RegExp( "(^|" + whitespace + ")" + className + "(" + whitespace + "|$)" )) && + classCache( className, function( elem ) { + return pattern.test( typeof elem.className === "string" && elem.className || typeof elem.getAttribute !== "undefined" && elem.getAttribute("class") || "" ); + }); + }, + + "ATTR": function( name, operator, check ) { + return function( elem ) { + var result = Sizzle.attr( elem, name ); + + if ( result == null ) { + return operator === "!="; + } + if ( !operator ) { + return true; + } + + result += ""; + + return operator === "=" ? result === check : + operator === "!=" ? result !== check : + operator === "^=" ? check && result.indexOf( check ) === 0 : + operator === "*=" ? check && result.indexOf( check ) > -1 : + operator === "$=" ? check && result.slice( -check.length ) === check : + operator === "~=" ? ( " " + result.replace( rwhitespace, " " ) + " " ).indexOf( check ) > -1 : + operator === "|=" ? result === check || result.slice( 0, check.length + 1 ) === check + "-" : + false; + }; + }, + + "CHILD": function( type, what, argument, first, last ) { + var simple = type.slice( 0, 3 ) !== "nth", + forward = type.slice( -4 ) !== "last", + ofType = what === "of-type"; + + return first === 1 && last === 0 ? + + // Shortcut for :nth-*(n) + function( elem ) { + return !!elem.parentNode; + } : + + function( elem, context, xml ) { + var cache, uniqueCache, outerCache, node, nodeIndex, start, + dir = simple !== forward ? "nextSibling" : "previousSibling", + parent = elem.parentNode, + name = ofType && elem.nodeName.toLowerCase(), + useCache = !xml && !ofType, + diff = false; + + if ( parent ) { + + // :(first|last|only)-(child|of-type) + if ( simple ) { + while ( dir ) { + node = elem; + while ( (node = node[ dir ]) ) { + if ( ofType ? + node.nodeName.toLowerCase() === name : + node.nodeType === 1 ) { + + return false; + } + } + // Reverse direction for :only-* (if we haven't yet done so) + start = dir = type === "only" && !start && "nextSibling"; + } + return true; + } + + start = [ forward ? parent.firstChild : parent.lastChild ]; + + // non-xml :nth-child(...) stores cache data on `parent` + if ( forward && useCache ) { + + // Seek `elem` from a previously-cached index + + // ...in a gzip-friendly way + node = parent; + outerCache = node[ expando ] || (node[ expando ] = {}); + + // Support: IE <9 only + // Defend against cloned attroperties (jQuery gh-1709) + uniqueCache = outerCache[ node.uniqueID ] || + (outerCache[ node.uniqueID ] = {}); + + cache = uniqueCache[ type ] || []; + nodeIndex = cache[ 0 ] === dirruns && cache[ 1 ]; + diff = nodeIndex && cache[ 2 ]; + node = nodeIndex && parent.childNodes[ nodeIndex ]; + + while ( (node = ++nodeIndex && node && node[ dir ] || + + // Fallback to seeking `elem` from the start + (diff = nodeIndex = 0) || start.pop()) ) { + + // When found, cache indexes on `parent` and break + if ( node.nodeType === 1 && ++diff && node === elem ) { + uniqueCache[ type ] = [ dirruns, nodeIndex, diff ]; + break; + } + } + + } else { + // Use previously-cached element index if available + if ( useCache ) { + // ...in a gzip-friendly way + node = elem; + outerCache = node[ expando ] || (node[ expando ] = {}); + + // Support: IE <9 only + // Defend against cloned attroperties (jQuery gh-1709) + uniqueCache = outerCache[ node.uniqueID ] || + (outerCache[ node.uniqueID ] = {}); + + cache = uniqueCache[ type ] || []; + nodeIndex = cache[ 0 ] === dirruns && cache[ 1 ]; + diff = nodeIndex; + } + + // xml :nth-child(...) + // or :nth-last-child(...) or :nth(-last)?-of-type(...) + if ( diff === false ) { + // Use the same loop as above to seek `elem` from the start + while ( (node = ++nodeIndex && node && node[ dir ] || + (diff = nodeIndex = 0) || start.pop()) ) { + + if ( ( ofType ? + node.nodeName.toLowerCase() === name : + node.nodeType === 1 ) && + ++diff ) { + + // Cache the index of each encountered element + if ( useCache ) { + outerCache = node[ expando ] || (node[ expando ] = {}); + + // Support: IE <9 only + // Defend against cloned attroperties (jQuery gh-1709) + uniqueCache = outerCache[ node.uniqueID ] || + (outerCache[ node.uniqueID ] = {}); + + uniqueCache[ type ] = [ dirruns, diff ]; + } + + if ( node === elem ) { + break; + } + } + } + } + } + + // Incorporate the offset, then check against cycle size + diff -= last; + return diff === first || ( diff % first === 0 && diff / first >= 0 ); + } + }; + }, + + "PSEUDO": function( pseudo, argument ) { + // pseudo-class names are case-insensitive + // http://www.w3.org/TR/selectors/#pseudo-classes + // Prioritize by case sensitivity in case custom pseudos are added with uppercase letters + // Remember that setFilters inherits from pseudos + var args, + fn = Expr.pseudos[ pseudo ] || Expr.setFilters[ pseudo.toLowerCase() ] || + Sizzle.error( "unsupported pseudo: " + pseudo ); + + // The user may use createPseudo to indicate that + // arguments are needed to create the filter function + // just as Sizzle does + if ( fn[ expando ] ) { + return fn( argument ); + } + + // But maintain support for old signatures + if ( fn.length > 1 ) { + args = [ pseudo, pseudo, "", argument ]; + return Expr.setFilters.hasOwnProperty( pseudo.toLowerCase() ) ? + markFunction(function( seed, matches ) { + var idx, + matched = fn( seed, argument ), + i = matched.length; + while ( i-- ) { + idx = indexOf( seed, matched[i] ); + seed[ idx ] = !( matches[ idx ] = matched[i] ); + } + }) : + function( elem ) { + return fn( elem, 0, args ); + }; + } + + return fn; + } + }, + + pseudos: { + // Potentially complex pseudos + "not": markFunction(function( selector ) { + // Trim the selector passed to compile + // to avoid treating leading and trailing + // spaces as combinators + var input = [], + results = [], + matcher = compile( selector.replace( rtrim, "$1" ) ); + + return matcher[ expando ] ? + markFunction(function( seed, matches, context, xml ) { + var elem, + unmatched = matcher( seed, null, xml, [] ), + i = seed.length; + + // Match elements unmatched by `matcher` + while ( i-- ) { + if ( (elem = unmatched[i]) ) { + seed[i] = !(matches[i] = elem); + } + } + }) : + function( elem, context, xml ) { + input[0] = elem; + matcher( input, null, xml, results ); + // Don't keep the element (issue #299) + input[0] = null; + return !results.pop(); + }; + }), + + "has": markFunction(function( selector ) { + return function( elem ) { + return Sizzle( selector, elem ).length > 0; + }; + }), + + "contains": markFunction(function( text ) { + text = text.replace( runescape, funescape ); + return function( elem ) { + return ( elem.textContent || elem.innerText || getText( elem ) ).indexOf( text ) > -1; + }; + }), + + // "Whether an element is represented by a :lang() selector + // is based solely on the element's language value + // being equal to the identifier C, + // or beginning with the identifier C immediately followed by "-". + // The matching of C against the element's language value is performed case-insensitively. + // The identifier C does not have to be a valid language name." + // http://www.w3.org/TR/selectors/#lang-pseudo + "lang": markFunction( function( lang ) { + // lang value must be a valid identifier + if ( !ridentifier.test(lang || "") ) { + Sizzle.error( "unsupported lang: " + lang ); + } + lang = lang.replace( runescape, funescape ).toLowerCase(); + return function( elem ) { + var elemLang; + do { + if ( (elemLang = documentIsHTML ? + elem.lang : + elem.getAttribute("xml:lang") || elem.getAttribute("lang")) ) { + + elemLang = elemLang.toLowerCase(); + return elemLang === lang || elemLang.indexOf( lang + "-" ) === 0; + } + } while ( (elem = elem.parentNode) && elem.nodeType === 1 ); + return false; + }; + }), + + // Miscellaneous + "target": function( elem ) { + var hash = window.location && window.location.hash; + return hash && hash.slice( 1 ) === elem.id; + }, + + "root": function( elem ) { + return elem === docElem; + }, + + "focus": function( elem ) { + return elem === document.activeElement && (!document.hasFocus || document.hasFocus()) && !!(elem.type || elem.href || ~elem.tabIndex); + }, + + // Boolean properties + "enabled": createDisabledPseudo( false ), + "disabled": createDisabledPseudo( true ), + + "checked": function( elem ) { + // In CSS3, :checked should return both checked and selected elements + // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked + var nodeName = elem.nodeName.toLowerCase(); + return (nodeName === "input" && !!elem.checked) || (nodeName === "option" && !!elem.selected); + }, + + "selected": function( elem ) { + // Accessing this property makes selected-by-default + // options in Safari work properly + if ( elem.parentNode ) { + elem.parentNode.selectedIndex; + } + + return elem.selected === true; + }, + + // Contents + "empty": function( elem ) { + // http://www.w3.org/TR/selectors/#empty-pseudo + // :empty is negated by element (1) or content nodes (text: 3; cdata: 4; entity ref: 5), + // but not by others (comment: 8; processing instruction: 7; etc.) + // nodeType < 6 works because attributes (2) do not appear as children + for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) { + if ( elem.nodeType < 6 ) { + return false; + } + } + return true; + }, + + "parent": function( elem ) { + return !Expr.pseudos["empty"]( elem ); + }, + + // Element/input types + "header": function( elem ) { + return rheader.test( elem.nodeName ); + }, + + "input": function( elem ) { + return rinputs.test( elem.nodeName ); + }, + + "button": function( elem ) { + var name = elem.nodeName.toLowerCase(); + return name === "input" && elem.type === "button" || name === "button"; + }, + + "text": function( elem ) { + var attr; + return elem.nodeName.toLowerCase() === "input" && + elem.type === "text" && + + // Support: IE<8 + // New HTML5 attribute values (e.g., "search") appear with elem.type === "text" + ( (attr = elem.getAttribute("type")) == null || attr.toLowerCase() === "text" ); + }, + + // Position-in-collection + "first": createPositionalPseudo(function() { + return [ 0 ]; + }), + + "last": createPositionalPseudo(function( matchIndexes, length ) { + return [ length - 1 ]; + }), + + "eq": createPositionalPseudo(function( matchIndexes, length, argument ) { + return [ argument < 0 ? argument + length : argument ]; + }), + + "even": createPositionalPseudo(function( matchIndexes, length ) { + var i = 0; + for ( ; i < length; i += 2 ) { + matchIndexes.push( i ); + } + return matchIndexes; + }), + + "odd": createPositionalPseudo(function( matchIndexes, length ) { + var i = 1; + for ( ; i < length; i += 2 ) { + matchIndexes.push( i ); + } + return matchIndexes; + }), + + "lt": createPositionalPseudo(function( matchIndexes, length, argument ) { + var i = argument < 0 ? argument + length : argument; + for ( ; --i >= 0; ) { + matchIndexes.push( i ); + } + return matchIndexes; + }), + + "gt": createPositionalPseudo(function( matchIndexes, length, argument ) { + var i = argument < 0 ? argument + length : argument; + for ( ; ++i < length; ) { + matchIndexes.push( i ); + } + return matchIndexes; + }) + } +}; + +Expr.pseudos["nth"] = Expr.pseudos["eq"]; + +// Add button/input type pseudos +for ( i in { radio: true, checkbox: true, file: true, password: true, image: true } ) { + Expr.pseudos[ i ] = createInputPseudo( i ); +} +for ( i in { submit: true, reset: true } ) { + Expr.pseudos[ i ] = createButtonPseudo( i ); +} + +// Easy API for creating new setFilters +function setFilters() {} +setFilters.prototype = Expr.filters = Expr.pseudos; +Expr.setFilters = new setFilters(); + +tokenize = Sizzle.tokenize = function( selector, parseOnly ) { + var matched, match, tokens, type, + soFar, groups, preFilters, + cached = tokenCache[ selector + " " ]; + + if ( cached ) { + return parseOnly ? 0 : cached.slice( 0 ); + } + + soFar = selector; + groups = []; + preFilters = Expr.preFilter; + + while ( soFar ) { + + // Comma and first run + if ( !matched || (match = rcomma.exec( soFar )) ) { + if ( match ) { + // Don't consume trailing commas as valid + soFar = soFar.slice( match[0].length ) || soFar; + } + groups.push( (tokens = []) ); + } + + matched = false; + + // Combinators + if ( (match = rcombinators.exec( soFar )) ) { + matched = match.shift(); + tokens.push({ + value: matched, + // Cast descendant combinators to space + type: match[0].replace( rtrim, " " ) + }); + soFar = soFar.slice( matched.length ); + } + + // Filters + for ( type in Expr.filter ) { + if ( (match = matchExpr[ type ].exec( soFar )) && (!preFilters[ type ] || + (match = preFilters[ type ]( match ))) ) { + matched = match.shift(); + tokens.push({ + value: matched, + type: type, + matches: match + }); + soFar = soFar.slice( matched.length ); + } + } + + if ( !matched ) { + break; + } + } + + // Return the length of the invalid excess + // if we're just parsing + // Otherwise, throw an error or return tokens + return parseOnly ? + soFar.length : + soFar ? + Sizzle.error( selector ) : + // Cache the tokens + tokenCache( selector, groups ).slice( 0 ); +}; + +function toSelector( tokens ) { + var i = 0, + len = tokens.length, + selector = ""; + for ( ; i < len; i++ ) { + selector += tokens[i].value; + } + return selector; +} + +function addCombinator( matcher, combinator, base ) { + var dir = combinator.dir, + skip = combinator.next, + key = skip || dir, + checkNonElements = base && key === "parentNode", + doneName = done++; + + return combinator.first ? + // Check against closest ancestor/preceding element + function( elem, context, xml ) { + while ( (elem = elem[ dir ]) ) { + if ( elem.nodeType === 1 || checkNonElements ) { + return matcher( elem, context, xml ); + } + } + return false; + } : + + // Check against all ancestor/preceding elements + function( elem, context, xml ) { + var oldCache, uniqueCache, outerCache, + newCache = [ dirruns, doneName ]; + + // We can't set arbitrary data on XML nodes, so they don't benefit from combinator caching + if ( xml ) { + while ( (elem = elem[ dir ]) ) { + if ( elem.nodeType === 1 || checkNonElements ) { + if ( matcher( elem, context, xml ) ) { + return true; + } + } + } + } else { + while ( (elem = elem[ dir ]) ) { + if ( elem.nodeType === 1 || checkNonElements ) { + outerCache = elem[ expando ] || (elem[ expando ] = {}); + + // Support: IE <9 only + // Defend against cloned attroperties (jQuery gh-1709) + uniqueCache = outerCache[ elem.uniqueID ] || (outerCache[ elem.uniqueID ] = {}); + + if ( skip && skip === elem.nodeName.toLowerCase() ) { + elem = elem[ dir ] || elem; + } else if ( (oldCache = uniqueCache[ key ]) && + oldCache[ 0 ] === dirruns && oldCache[ 1 ] === doneName ) { + + // Assign to newCache so results back-propagate to previous elements + return (newCache[ 2 ] = oldCache[ 2 ]); + } else { + // Reuse newcache so results back-propagate to previous elements + uniqueCache[ key ] = newCache; + + // A match means we're done; a fail means we have to keep checking + if ( (newCache[ 2 ] = matcher( elem, context, xml )) ) { + return true; + } + } + } + } + } + return false; + }; +} + +function elementMatcher( matchers ) { + return matchers.length > 1 ? + function( elem, context, xml ) { + var i = matchers.length; + while ( i-- ) { + if ( !matchers[i]( elem, context, xml ) ) { + return false; + } + } + return true; + } : + matchers[0]; +} + +function multipleContexts( selector, contexts, results ) { + var i = 0, + len = contexts.length; + for ( ; i < len; i++ ) { + Sizzle( selector, contexts[i], results ); + } + return results; +} + +function condense( unmatched, map, filter, context, xml ) { + var elem, + newUnmatched = [], + i = 0, + len = unmatched.length, + mapped = map != null; + + for ( ; i < len; i++ ) { + if ( (elem = unmatched[i]) ) { + if ( !filter || filter( elem, context, xml ) ) { + newUnmatched.push( elem ); + if ( mapped ) { + map.push( i ); + } + } + } + } + + return newUnmatched; +} + +function setMatcher( preFilter, selector, matcher, postFilter, postFinder, postSelector ) { + if ( postFilter && !postFilter[ expando ] ) { + postFilter = setMatcher( postFilter ); + } + if ( postFinder && !postFinder[ expando ] ) { + postFinder = setMatcher( postFinder, postSelector ); + } + return markFunction(function( seed, results, context, xml ) { + var temp, i, elem, + preMap = [], + postMap = [], + preexisting = results.length, + + // Get initial elements from seed or context + elems = seed || multipleContexts( selector || "*", context.nodeType ? [ context ] : context, [] ), + + // Prefilter to get matcher input, preserving a map for seed-results synchronization + matcherIn = preFilter && ( seed || !selector ) ? + condense( elems, preMap, preFilter, context, xml ) : + elems, + + matcherOut = matcher ? + // If we have a postFinder, or filtered seed, or non-seed postFilter or preexisting results, + postFinder || ( seed ? preFilter : preexisting || postFilter ) ? + + // ...intermediate processing is necessary + [] : + + // ...otherwise use results directly + results : + matcherIn; + + // Find primary matches + if ( matcher ) { + matcher( matcherIn, matcherOut, context, xml ); + } + + // Apply postFilter + if ( postFilter ) { + temp = condense( matcherOut, postMap ); + postFilter( temp, [], context, xml ); + + // Un-match failing elements by moving them back to matcherIn + i = temp.length; + while ( i-- ) { + if ( (elem = temp[i]) ) { + matcherOut[ postMap[i] ] = !(matcherIn[ postMap[i] ] = elem); + } + } + } + + if ( seed ) { + if ( postFinder || preFilter ) { + if ( postFinder ) { + // Get the final matcherOut by condensing this intermediate into postFinder contexts + temp = []; + i = matcherOut.length; + while ( i-- ) { + if ( (elem = matcherOut[i]) ) { + // Restore matcherIn since elem is not yet a final match + temp.push( (matcherIn[i] = elem) ); + } + } + postFinder( null, (matcherOut = []), temp, xml ); + } + + // Move matched elements from seed to results to keep them synchronized + i = matcherOut.length; + while ( i-- ) { + if ( (elem = matcherOut[i]) && + (temp = postFinder ? indexOf( seed, elem ) : preMap[i]) > -1 ) { + + seed[temp] = !(results[temp] = elem); + } + } + } + + // Add elements to results, through postFinder if defined + } else { + matcherOut = condense( + matcherOut === results ? + matcherOut.splice( preexisting, matcherOut.length ) : + matcherOut + ); + if ( postFinder ) { + postFinder( null, results, matcherOut, xml ); + } else { + push.apply( results, matcherOut ); + } + } + }); +} + +function matcherFromTokens( tokens ) { + var checkContext, matcher, j, + len = tokens.length, + leadingRelative = Expr.relative[ tokens[0].type ], + implicitRelative = leadingRelative || Expr.relative[" "], + i = leadingRelative ? 1 : 0, + + // The foundational matcher ensures that elements are reachable from top-level context(s) + matchContext = addCombinator( function( elem ) { + return elem === checkContext; + }, implicitRelative, true ), + matchAnyContext = addCombinator( function( elem ) { + return indexOf( checkContext, elem ) > -1; + }, implicitRelative, true ), + matchers = [ function( elem, context, xml ) { + var ret = ( !leadingRelative && ( xml || context !== outermostContext ) ) || ( + (checkContext = context).nodeType ? + matchContext( elem, context, xml ) : + matchAnyContext( elem, context, xml ) ); + // Avoid hanging onto element (issue #299) + checkContext = null; + return ret; + } ]; + + for ( ; i < len; i++ ) { + if ( (matcher = Expr.relative[ tokens[i].type ]) ) { + matchers = [ addCombinator(elementMatcher( matchers ), matcher) ]; + } else { + matcher = Expr.filter[ tokens[i].type ].apply( null, tokens[i].matches ); + + // Return special upon seeing a positional matcher + if ( matcher[ expando ] ) { + // Find the next relative operator (if any) for proper handling + j = ++i; + for ( ; j < len; j++ ) { + if ( Expr.relative[ tokens[j].type ] ) { + break; + } + } + return setMatcher( + i > 1 && elementMatcher( matchers ), + i > 1 && toSelector( + // If the preceding token was a descendant combinator, insert an implicit any-element `*` + tokens.slice( 0, i - 1 ).concat({ value: tokens[ i - 2 ].type === " " ? "*" : "" }) + ).replace( rtrim, "$1" ), + matcher, + i < j && matcherFromTokens( tokens.slice( i, j ) ), + j < len && matcherFromTokens( (tokens = tokens.slice( j )) ), + j < len && toSelector( tokens ) + ); + } + matchers.push( matcher ); + } + } + + return elementMatcher( matchers ); +} + +function matcherFromGroupMatchers( elementMatchers, setMatchers ) { + var bySet = setMatchers.length > 0, + byElement = elementMatchers.length > 0, + superMatcher = function( seed, context, xml, results, outermost ) { + var elem, j, matcher, + matchedCount = 0, + i = "0", + unmatched = seed && [], + setMatched = [], + contextBackup = outermostContext, + // We must always have either seed elements or outermost context + elems = seed || byElement && Expr.find["TAG"]( "*", outermost ), + // Use integer dirruns iff this is the outermost matcher + dirrunsUnique = (dirruns += contextBackup == null ? 1 : Math.random() || 0.1), + len = elems.length; + + if ( outermost ) { + outermostContext = context === document || context || outermost; + } + + // Add elements passing elementMatchers directly to results + // Support: IE<9, Safari + // Tolerate NodeList properties (IE: "length"; Safari: ) matching elements by id + for ( ; i !== len && (elem = elems[i]) != null; i++ ) { + if ( byElement && elem ) { + j = 0; + if ( !context && elem.ownerDocument !== document ) { + setDocument( elem ); + xml = !documentIsHTML; + } + while ( (matcher = elementMatchers[j++]) ) { + if ( matcher( elem, context || document, xml) ) { + results.push( elem ); + break; + } + } + if ( outermost ) { + dirruns = dirrunsUnique; + } + } + + // Track unmatched elements for set filters + if ( bySet ) { + // They will have gone through all possible matchers + if ( (elem = !matcher && elem) ) { + matchedCount--; + } + + // Lengthen the array for every element, matched or not + if ( seed ) { + unmatched.push( elem ); + } + } + } + + // `i` is now the count of elements visited above, and adding it to `matchedCount` + // makes the latter nonnegative. + matchedCount += i; + + // Apply set filters to unmatched elements + // NOTE: This can be skipped if there are no unmatched elements (i.e., `matchedCount` + // equals `i`), unless we didn't visit _any_ elements in the above loop because we have + // no element matchers and no seed. + // Incrementing an initially-string "0" `i` allows `i` to remain a string only in that + // case, which will result in a "00" `matchedCount` that differs from `i` but is also + // numerically zero. + if ( bySet && i !== matchedCount ) { + j = 0; + while ( (matcher = setMatchers[j++]) ) { + matcher( unmatched, setMatched, context, xml ); + } + + if ( seed ) { + // Reintegrate element matches to eliminate the need for sorting + if ( matchedCount > 0 ) { + while ( i-- ) { + if ( !(unmatched[i] || setMatched[i]) ) { + setMatched[i] = pop.call( results ); + } + } + } + + // Discard index placeholder values to get only actual matches + setMatched = condense( setMatched ); + } + + // Add matches to results + push.apply( results, setMatched ); + + // Seedless set matches succeeding multiple successful matchers stipulate sorting + if ( outermost && !seed && setMatched.length > 0 && + ( matchedCount + setMatchers.length ) > 1 ) { + + Sizzle.uniqueSort( results ); + } + } + + // Override manipulation of globals by nested matchers + if ( outermost ) { + dirruns = dirrunsUnique; + outermostContext = contextBackup; + } + + return unmatched; + }; + + return bySet ? + markFunction( superMatcher ) : + superMatcher; +} + +compile = Sizzle.compile = function( selector, match /* Internal Use Only */ ) { + var i, + setMatchers = [], + elementMatchers = [], + cached = compilerCache[ selector + " " ]; + + if ( !cached ) { + // Generate a function of recursive functions that can be used to check each element + if ( !match ) { + match = tokenize( selector ); + } + i = match.length; + while ( i-- ) { + cached = matcherFromTokens( match[i] ); + if ( cached[ expando ] ) { + setMatchers.push( cached ); + } else { + elementMatchers.push( cached ); + } + } + + // Cache the compiled function + cached = compilerCache( selector, matcherFromGroupMatchers( elementMatchers, setMatchers ) ); + + // Save selector and tokenization + cached.selector = selector; + } + return cached; +}; + +/** + * A low-level selection function that works with Sizzle's compiled + * selector functions + * @param {String|Function} selector A selector or a pre-compiled + * selector function built with Sizzle.compile + * @param {Element} context + * @param {Array} [results] + * @param {Array} [seed] A set of elements to match against + */ +select = Sizzle.select = function( selector, context, results, seed ) { + var i, tokens, token, type, find, + compiled = typeof selector === "function" && selector, + match = !seed && tokenize( (selector = compiled.selector || selector) ); + + results = results || []; + + // Try to minimize operations if there is only one selector in the list and no seed + // (the latter of which guarantees us context) + if ( match.length === 1 ) { + + // Reduce context if the leading compound selector is an ID + tokens = match[0] = match[0].slice( 0 ); + if ( tokens.length > 2 && (token = tokens[0]).type === "ID" && + context.nodeType === 9 && documentIsHTML && Expr.relative[ tokens[1].type ] ) { + + context = ( Expr.find["ID"]( token.matches[0].replace(runescape, funescape), context ) || [] )[0]; + if ( !context ) { + return results; + + // Precompiled matchers will still verify ancestry, so step up a level + } else if ( compiled ) { + context = context.parentNode; + } + + selector = selector.slice( tokens.shift().value.length ); + } + + // Fetch a seed set for right-to-left matching + i = matchExpr["needsContext"].test( selector ) ? 0 : tokens.length; + while ( i-- ) { + token = tokens[i]; + + // Abort if we hit a combinator + if ( Expr.relative[ (type = token.type) ] ) { + break; + } + if ( (find = Expr.find[ type ]) ) { + // Search, expanding context for leading sibling combinators + if ( (seed = find( + token.matches[0].replace( runescape, funescape ), + rsibling.test( tokens[0].type ) && testContext( context.parentNode ) || context + )) ) { + + // If seed is empty or no tokens remain, we can return early + tokens.splice( i, 1 ); + selector = seed.length && toSelector( tokens ); + if ( !selector ) { + push.apply( results, seed ); + return results; + } + + break; + } + } + } + } + + // Compile and execute a filtering function if one is not provided + // Provide `match` to avoid retokenization if we modified the selector above + ( compiled || compile( selector, match ) )( + seed, + context, + !documentIsHTML, + results, + !context || rsibling.test( selector ) && testContext( context.parentNode ) || context + ); + return results; +}; + +// One-time assignments + +// Sort stability +support.sortStable = expando.split("").sort( sortOrder ).join("") === expando; + +// Support: Chrome 14-35+ +// Always assume duplicates if they aren't passed to the comparison function +support.detectDuplicates = !!hasDuplicate; + +// Initialize against the default document +setDocument(); + +// Support: Webkit<537.32 - Safari 6.0.3/Chrome 25 (fixed in Chrome 27) +// Detached nodes confoundingly follow *each other* +support.sortDetached = assert(function( el ) { + // Should return 1, but returns 4 (following) + return el.compareDocumentPosition( document.createElement("fieldset") ) & 1; +}); + +// Support: IE<8 +// Prevent attribute/property "interpolation" +// https://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx +if ( !assert(function( el ) { + el.innerHTML = ""; + return el.firstChild.getAttribute("href") === "#" ; +}) ) { + addHandle( "type|href|height|width", function( elem, name, isXML ) { + if ( !isXML ) { + return elem.getAttribute( name, name.toLowerCase() === "type" ? 1 : 2 ); + } + }); +} + +// Support: IE<9 +// Use defaultValue in place of getAttribute("value") +if ( !support.attributes || !assert(function( el ) { + el.innerHTML = ""; + el.firstChild.setAttribute( "value", "" ); + return el.firstChild.getAttribute( "value" ) === ""; +}) ) { + addHandle( "value", function( elem, name, isXML ) { + if ( !isXML && elem.nodeName.toLowerCase() === "input" ) { + return elem.defaultValue; + } + }); +} + +// Support: IE<9 +// Use getAttributeNode to fetch booleans when getAttribute lies +if ( !assert(function( el ) { + return el.getAttribute("disabled") == null; +}) ) { + addHandle( booleans, function( elem, name, isXML ) { + var val; + if ( !isXML ) { + return elem[ name ] === true ? name.toLowerCase() : + (val = elem.getAttributeNode( name )) && val.specified ? + val.value : + null; + } + }); +} + +return Sizzle; + +})( window ); + + + +jQuery.find = Sizzle; +jQuery.expr = Sizzle.selectors; + +// Deprecated +jQuery.expr[ ":" ] = jQuery.expr.pseudos; +jQuery.uniqueSort = jQuery.unique = Sizzle.uniqueSort; +jQuery.text = Sizzle.getText; +jQuery.isXMLDoc = Sizzle.isXML; +jQuery.contains = Sizzle.contains; +jQuery.escapeSelector = Sizzle.escape; + + + + +var dir = function( elem, dir, until ) { + var matched = [], + truncate = until !== undefined; + + while ( ( elem = elem[ dir ] ) && elem.nodeType !== 9 ) { + if ( elem.nodeType === 1 ) { + if ( truncate && jQuery( elem ).is( until ) ) { + break; + } + matched.push( elem ); + } + } + return matched; +}; + + +var siblings = function( n, elem ) { + var matched = []; + + for ( ; n; n = n.nextSibling ) { + if ( n.nodeType === 1 && n !== elem ) { + matched.push( n ); + } + } + + return matched; +}; + + +var rneedsContext = jQuery.expr.match.needsContext; + + + +function nodeName( elem, name ) { + + return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase(); + +}; +var rsingleTag = ( /^<([a-z][^\/\0>:\x20\t\r\n\f]*)[\x20\t\r\n\f]*\/?>(?:<\/\1>|)$/i ); + + + +var risSimple = /^.[^:#\[\.,]*$/; + +// Implement the identical functionality for filter and not +function winnow( elements, qualifier, not ) { + if ( jQuery.isFunction( qualifier ) ) { + return jQuery.grep( elements, function( elem, i ) { + return !!qualifier.call( elem, i, elem ) !== not; + } ); + } + + // Single element + if ( qualifier.nodeType ) { + return jQuery.grep( elements, function( elem ) { + return ( elem === qualifier ) !== not; + } ); + } + + // Arraylike of elements (jQuery, arguments, Array) + if ( typeof qualifier !== "string" ) { + return jQuery.grep( elements, function( elem ) { + return ( indexOf.call( qualifier, elem ) > -1 ) !== not; + } ); + } + + // Simple selector that can be filtered directly, removing non-Elements + if ( risSimple.test( qualifier ) ) { + return jQuery.filter( qualifier, elements, not ); + } + + // Complex selector, compare the two sets, removing non-Elements + qualifier = jQuery.filter( qualifier, elements ); + return jQuery.grep( elements, function( elem ) { + return ( indexOf.call( qualifier, elem ) > -1 ) !== not && elem.nodeType === 1; + } ); +} + +jQuery.filter = function( expr, elems, not ) { + var elem = elems[ 0 ]; + + if ( not ) { + expr = ":not(" + expr + ")"; + } + + if ( elems.length === 1 && elem.nodeType === 1 ) { + return jQuery.find.matchesSelector( elem, expr ) ? [ elem ] : []; + } + + return jQuery.find.matches( expr, jQuery.grep( elems, function( elem ) { + return elem.nodeType === 1; + } ) ); +}; + +jQuery.fn.extend( { + find: function( selector ) { + var i, ret, + len = this.length, + self = this; + + if ( typeof selector !== "string" ) { + return this.pushStack( jQuery( selector ).filter( function() { + for ( i = 0; i < len; i++ ) { + if ( jQuery.contains( self[ i ], this ) ) { + return true; + } + } + } ) ); + } + + ret = this.pushStack( [] ); + + for ( i = 0; i < len; i++ ) { + jQuery.find( selector, self[ i ], ret ); + } + + return len > 1 ? jQuery.uniqueSort( ret ) : ret; + }, + filter: function( selector ) { + return this.pushStack( winnow( this, selector || [], false ) ); + }, + not: function( selector ) { + return this.pushStack( winnow( this, selector || [], true ) ); + }, + is: function( selector ) { + return !!winnow( + this, + + // If this is a positional/relative selector, check membership in the returned set + // so $("p:first").is("p:last") won't return true for a doc with two "p". + typeof selector === "string" && rneedsContext.test( selector ) ? + jQuery( selector ) : + selector || [], + false + ).length; + } +} ); + + +// Initialize a jQuery object + + +// A central reference to the root jQuery(document) +var rootjQuery, + + // A simple way to check for HTML strings + // Prioritize #id over to avoid XSS via location.hash (#9521) + // Strict HTML recognition (#11290: must start with <) + // Shortcut simple #id case for speed + rquickExpr = /^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]+))$/, + + init = jQuery.fn.init = function( selector, context, root ) { + var match, elem; + + // HANDLE: $(""), $(null), $(undefined), $(false) + if ( !selector ) { + return this; + } + + // Method init() accepts an alternate rootjQuery + // so migrate can support jQuery.sub (gh-2101) + root = root || rootjQuery; + + // Handle HTML strings + if ( typeof selector === "string" ) { + if ( selector[ 0 ] === "<" && + selector[ selector.length - 1 ] === ">" && + selector.length >= 3 ) { + + // Assume that strings that start and end with <> are HTML and skip the regex check + match = [ null, selector, null ]; + + } else { + match = rquickExpr.exec( selector ); + } + + // Match html or make sure no context is specified for #id + if ( match && ( match[ 1 ] || !context ) ) { + + // HANDLE: $(html) -> $(array) + if ( match[ 1 ] ) { + context = context instanceof jQuery ? context[ 0 ] : context; + + // Option to run scripts is true for back-compat + // Intentionally let the error be thrown if parseHTML is not present + jQuery.merge( this, jQuery.parseHTML( + match[ 1 ], + context && context.nodeType ? context.ownerDocument || context : document, + true + ) ); + + // HANDLE: $(html, props) + if ( rsingleTag.test( match[ 1 ] ) && jQuery.isPlainObject( context ) ) { + for ( match in context ) { + + // Properties of context are called as methods if possible + if ( jQuery.isFunction( this[ match ] ) ) { + this[ match ]( context[ match ] ); + + // ...and otherwise set as attributes + } else { + this.attr( match, context[ match ] ); + } + } + } + + return this; + + // HANDLE: $(#id) + } else { + elem = document.getElementById( match[ 2 ] ); + + if ( elem ) { + + // Inject the element directly into the jQuery object + this[ 0 ] = elem; + this.length = 1; + } + return this; + } + + // HANDLE: $(expr, $(...)) + } else if ( !context || context.jquery ) { + return ( context || root ).find( selector ); + + // HANDLE: $(expr, context) + // (which is just equivalent to: $(context).find(expr) + } else { + return this.constructor( context ).find( selector ); + } + + // HANDLE: $(DOMElement) + } else if ( selector.nodeType ) { + this[ 0 ] = selector; + this.length = 1; + return this; + + // HANDLE: $(function) + // Shortcut for document ready + } else if ( jQuery.isFunction( selector ) ) { + return root.ready !== undefined ? + root.ready( selector ) : + + // Execute immediately if ready is not present + selector( jQuery ); + } + + return jQuery.makeArray( selector, this ); + }; + +// Give the init function the jQuery prototype for later instantiation +init.prototype = jQuery.fn; + +// Initialize central reference +rootjQuery = jQuery( document ); + + +var rparentsprev = /^(?:parents|prev(?:Until|All))/, + + // Methods guaranteed to produce a unique set when starting from a unique set + guaranteedUnique = { + children: true, + contents: true, + next: true, + prev: true + }; + +jQuery.fn.extend( { + has: function( target ) { + var targets = jQuery( target, this ), + l = targets.length; + + return this.filter( function() { + var i = 0; + for ( ; i < l; i++ ) { + if ( jQuery.contains( this, targets[ i ] ) ) { + return true; + } + } + } ); + }, + + closest: function( selectors, context ) { + var cur, + i = 0, + l = this.length, + matched = [], + targets = typeof selectors !== "string" && jQuery( selectors ); + + // Positional selectors never match, since there's no _selection_ context + if ( !rneedsContext.test( selectors ) ) { + for ( ; i < l; i++ ) { + for ( cur = this[ i ]; cur && cur !== context; cur = cur.parentNode ) { + + // Always skip document fragments + if ( cur.nodeType < 11 && ( targets ? + targets.index( cur ) > -1 : + + // Don't pass non-elements to Sizzle + cur.nodeType === 1 && + jQuery.find.matchesSelector( cur, selectors ) ) ) { + + matched.push( cur ); + break; + } + } + } + } + + return this.pushStack( matched.length > 1 ? jQuery.uniqueSort( matched ) : matched ); + }, + + // Determine the position of an element within the set + index: function( elem ) { + + // No argument, return index in parent + if ( !elem ) { + return ( this[ 0 ] && this[ 0 ].parentNode ) ? this.first().prevAll().length : -1; + } + + // Index in selector + if ( typeof elem === "string" ) { + return indexOf.call( jQuery( elem ), this[ 0 ] ); + } + + // Locate the position of the desired element + return indexOf.call( this, + + // If it receives a jQuery object, the first element is used + elem.jquery ? elem[ 0 ] : elem + ); + }, + + add: function( selector, context ) { + return this.pushStack( + jQuery.uniqueSort( + jQuery.merge( this.get(), jQuery( selector, context ) ) + ) + ); + }, + + addBack: function( selector ) { + return this.add( selector == null ? + this.prevObject : this.prevObject.filter( selector ) + ); + } +} ); + +function sibling( cur, dir ) { + while ( ( cur = cur[ dir ] ) && cur.nodeType !== 1 ) {} + return cur; +} + +jQuery.each( { + parent: function( elem ) { + var parent = elem.parentNode; + return parent && parent.nodeType !== 11 ? parent : null; + }, + parents: function( elem ) { + return dir( elem, "parentNode" ); + }, + parentsUntil: function( elem, i, until ) { + return dir( elem, "parentNode", until ); + }, + next: function( elem ) { + return sibling( elem, "nextSibling" ); + }, + prev: function( elem ) { + return sibling( elem, "previousSibling" ); + }, + nextAll: function( elem ) { + return dir( elem, "nextSibling" ); + }, + prevAll: function( elem ) { + return dir( elem, "previousSibling" ); + }, + nextUntil: function( elem, i, until ) { + return dir( elem, "nextSibling", until ); + }, + prevUntil: function( elem, i, until ) { + return dir( elem, "previousSibling", until ); + }, + siblings: function( elem ) { + return siblings( ( elem.parentNode || {} ).firstChild, elem ); + }, + children: function( elem ) { + return siblings( elem.firstChild ); + }, + contents: function( elem ) { + if ( nodeName( elem, "iframe" ) ) { + return elem.contentDocument; + } + + // Support: IE 9 - 11 only, iOS 7 only, Android Browser <=4.3 only + // Treat the template element as a regular one in browsers that + // don't support it. + if ( nodeName( elem, "template" ) ) { + elem = elem.content || elem; + } + + return jQuery.merge( [], elem.childNodes ); + } +}, function( name, fn ) { + jQuery.fn[ name ] = function( until, selector ) { + var matched = jQuery.map( this, fn, until ); + + if ( name.slice( -5 ) !== "Until" ) { + selector = until; + } + + if ( selector && typeof selector === "string" ) { + matched = jQuery.filter( selector, matched ); + } + + if ( this.length > 1 ) { + + // Remove duplicates + if ( !guaranteedUnique[ name ] ) { + jQuery.uniqueSort( matched ); + } + + // Reverse order for parents* and prev-derivatives + if ( rparentsprev.test( name ) ) { + matched.reverse(); + } + } + + return this.pushStack( matched ); + }; +} ); +var rnothtmlwhite = ( /[^\x20\t\r\n\f]+/g ); + + + +// Convert String-formatted options into Object-formatted ones +function createOptions( options ) { + var object = {}; + jQuery.each( options.match( rnothtmlwhite ) || [], function( _, flag ) { + object[ flag ] = true; + } ); + return object; +} + +/* + * Create a callback list using the following parameters: + * + * options: an optional list of space-separated options that will change how + * the callback list behaves or a more traditional option object + * + * By default a callback list will act like an event callback list and can be + * "fired" multiple times. + * + * Possible options: + * + * once: will ensure the callback list can only be fired once (like a Deferred) + * + * memory: will keep track of previous values and will call any callback added + * after the list has been fired right away with the latest "memorized" + * values (like a Deferred) + * + * unique: will ensure a callback can only be added once (no duplicate in the list) + * + * stopOnFalse: interrupt callings when a callback returns false + * + */ +jQuery.Callbacks = function( options ) { + + // Convert options from String-formatted to Object-formatted if needed + // (we check in cache first) + options = typeof options === "string" ? + createOptions( options ) : + jQuery.extend( {}, options ); + + var // Flag to know if list is currently firing + firing, + + // Last fire value for non-forgettable lists + memory, + + // Flag to know if list was already fired + fired, + + // Flag to prevent firing + locked, + + // Actual callback list + list = [], + + // Queue of execution data for repeatable lists + queue = [], + + // Index of currently firing callback (modified by add/remove as needed) + firingIndex = -1, + + // Fire callbacks + fire = function() { + + // Enforce single-firing + locked = locked || options.once; + + // Execute callbacks for all pending executions, + // respecting firingIndex overrides and runtime changes + fired = firing = true; + for ( ; queue.length; firingIndex = -1 ) { + memory = queue.shift(); + while ( ++firingIndex < list.length ) { + + // Run callback and check for early termination + if ( list[ firingIndex ].apply( memory[ 0 ], memory[ 1 ] ) === false && + options.stopOnFalse ) { + + // Jump to end and forget the data so .add doesn't re-fire + firingIndex = list.length; + memory = false; + } + } + } + + // Forget the data if we're done with it + if ( !options.memory ) { + memory = false; + } + + firing = false; + + // Clean up if we're done firing for good + if ( locked ) { + + // Keep an empty list if we have data for future add calls + if ( memory ) { + list = []; + + // Otherwise, this object is spent + } else { + list = ""; + } + } + }, + + // Actual Callbacks object + self = { + + // Add a callback or a collection of callbacks to the list + add: function() { + if ( list ) { + + // If we have memory from a past run, we should fire after adding + if ( memory && !firing ) { + firingIndex = list.length - 1; + queue.push( memory ); + } + + ( function add( args ) { + jQuery.each( args, function( _, arg ) { + if ( jQuery.isFunction( arg ) ) { + if ( !options.unique || !self.has( arg ) ) { + list.push( arg ); + } + } else if ( arg && arg.length && jQuery.type( arg ) !== "string" ) { + + // Inspect recursively + add( arg ); + } + } ); + } )( arguments ); + + if ( memory && !firing ) { + fire(); + } + } + return this; + }, + + // Remove a callback from the list + remove: function() { + jQuery.each( arguments, function( _, arg ) { + var index; + while ( ( index = jQuery.inArray( arg, list, index ) ) > -1 ) { + list.splice( index, 1 ); + + // Handle firing indexes + if ( index <= firingIndex ) { + firingIndex--; + } + } + } ); + return this; + }, + + // Check if a given callback is in the list. + // If no argument is given, return whether or not list has callbacks attached. + has: function( fn ) { + return fn ? + jQuery.inArray( fn, list ) > -1 : + list.length > 0; + }, + + // Remove all callbacks from the list + empty: function() { + if ( list ) { + list = []; + } + return this; + }, + + // Disable .fire and .add + // Abort any current/pending executions + // Clear all callbacks and values + disable: function() { + locked = queue = []; + list = memory = ""; + return this; + }, + disabled: function() { + return !list; + }, + + // Disable .fire + // Also disable .add unless we have memory (since it would have no effect) + // Abort any pending executions + lock: function() { + locked = queue = []; + if ( !memory && !firing ) { + list = memory = ""; + } + return this; + }, + locked: function() { + return !!locked; + }, + + // Call all callbacks with the given context and arguments + fireWith: function( context, args ) { + if ( !locked ) { + args = args || []; + args = [ context, args.slice ? args.slice() : args ]; + queue.push( args ); + if ( !firing ) { + fire(); + } + } + return this; + }, + + // Call all the callbacks with the given arguments + fire: function() { + self.fireWith( this, arguments ); + return this; + }, + + // To know if the callbacks have already been called at least once + fired: function() { + return !!fired; + } + }; + + return self; +}; + + +function Identity( v ) { + return v; +} +function Thrower( ex ) { + throw ex; +} + +function adoptValue( value, resolve, reject, noValue ) { + var method; + + try { + + // Check for promise aspect first to privilege synchronous behavior + if ( value && jQuery.isFunction( ( method = value.promise ) ) ) { + method.call( value ).done( resolve ).fail( reject ); + + // Other thenables + } else if ( value && jQuery.isFunction( ( method = value.then ) ) ) { + method.call( value, resolve, reject ); + + // Other non-thenables + } else { + + // Control `resolve` arguments by letting Array#slice cast boolean `noValue` to integer: + // * false: [ value ].slice( 0 ) => resolve( value ) + // * true: [ value ].slice( 1 ) => resolve() + resolve.apply( undefined, [ value ].slice( noValue ) ); + } + + // For Promises/A+, convert exceptions into rejections + // Since jQuery.when doesn't unwrap thenables, we can skip the extra checks appearing in + // Deferred#then to conditionally suppress rejection. + } catch ( value ) { + + // Support: Android 4.0 only + // Strict mode functions invoked without .call/.apply get global-object context + reject.apply( undefined, [ value ] ); + } +} + +jQuery.extend( { + + Deferred: function( func ) { + var tuples = [ + + // action, add listener, callbacks, + // ... .then handlers, argument index, [final state] + [ "notify", "progress", jQuery.Callbacks( "memory" ), + jQuery.Callbacks( "memory" ), 2 ], + [ "resolve", "done", jQuery.Callbacks( "once memory" ), + jQuery.Callbacks( "once memory" ), 0, "resolved" ], + [ "reject", "fail", jQuery.Callbacks( "once memory" ), + jQuery.Callbacks( "once memory" ), 1, "rejected" ] + ], + state = "pending", + promise = { + state: function() { + return state; + }, + always: function() { + deferred.done( arguments ).fail( arguments ); + return this; + }, + "catch": function( fn ) { + return promise.then( null, fn ); + }, + + // Keep pipe for back-compat + pipe: function( /* fnDone, fnFail, fnProgress */ ) { + var fns = arguments; + + return jQuery.Deferred( function( newDefer ) { + jQuery.each( tuples, function( i, tuple ) { + + // Map tuples (progress, done, fail) to arguments (done, fail, progress) + var fn = jQuery.isFunction( fns[ tuple[ 4 ] ] ) && fns[ tuple[ 4 ] ]; + + // deferred.progress(function() { bind to newDefer or newDefer.notify }) + // deferred.done(function() { bind to newDefer or newDefer.resolve }) + // deferred.fail(function() { bind to newDefer or newDefer.reject }) + deferred[ tuple[ 1 ] ]( function() { + var returned = fn && fn.apply( this, arguments ); + if ( returned && jQuery.isFunction( returned.promise ) ) { + returned.promise() + .progress( newDefer.notify ) + .done( newDefer.resolve ) + .fail( newDefer.reject ); + } else { + newDefer[ tuple[ 0 ] + "With" ]( + this, + fn ? [ returned ] : arguments + ); + } + } ); + } ); + fns = null; + } ).promise(); + }, + then: function( onFulfilled, onRejected, onProgress ) { + var maxDepth = 0; + function resolve( depth, deferred, handler, special ) { + return function() { + var that = this, + args = arguments, + mightThrow = function() { + var returned, then; + + // Support: Promises/A+ section 2.3.3.3.3 + // https://promisesaplus.com/#point-59 + // Ignore double-resolution attempts + if ( depth < maxDepth ) { + return; + } + + returned = handler.apply( that, args ); + + // Support: Promises/A+ section 2.3.1 + // https://promisesaplus.com/#point-48 + if ( returned === deferred.promise() ) { + throw new TypeError( "Thenable self-resolution" ); + } + + // Support: Promises/A+ sections 2.3.3.1, 3.5 + // https://promisesaplus.com/#point-54 + // https://promisesaplus.com/#point-75 + // Retrieve `then` only once + then = returned && + + // Support: Promises/A+ section 2.3.4 + // https://promisesaplus.com/#point-64 + // Only check objects and functions for thenability + ( typeof returned === "object" || + typeof returned === "function" ) && + returned.then; + + // Handle a returned thenable + if ( jQuery.isFunction( then ) ) { + + // Special processors (notify) just wait for resolution + if ( special ) { + then.call( + returned, + resolve( maxDepth, deferred, Identity, special ), + resolve( maxDepth, deferred, Thrower, special ) + ); + + // Normal processors (resolve) also hook into progress + } else { + + // ...and disregard older resolution values + maxDepth++; + + then.call( + returned, + resolve( maxDepth, deferred, Identity, special ), + resolve( maxDepth, deferred, Thrower, special ), + resolve( maxDepth, deferred, Identity, + deferred.notifyWith ) + ); + } + + // Handle all other returned values + } else { + + // Only substitute handlers pass on context + // and multiple values (non-spec behavior) + if ( handler !== Identity ) { + that = undefined; + args = [ returned ]; + } + + // Process the value(s) + // Default process is resolve + ( special || deferred.resolveWith )( that, args ); + } + }, + + // Only normal processors (resolve) catch and reject exceptions + process = special ? + mightThrow : + function() { + try { + mightThrow(); + } catch ( e ) { + + if ( jQuery.Deferred.exceptionHook ) { + jQuery.Deferred.exceptionHook( e, + process.stackTrace ); + } + + // Support: Promises/A+ section 2.3.3.3.4.1 + // https://promisesaplus.com/#point-61 + // Ignore post-resolution exceptions + if ( depth + 1 >= maxDepth ) { + + // Only substitute handlers pass on context + // and multiple values (non-spec behavior) + if ( handler !== Thrower ) { + that = undefined; + args = [ e ]; + } + + deferred.rejectWith( that, args ); + } + } + }; + + // Support: Promises/A+ section 2.3.3.3.1 + // https://promisesaplus.com/#point-57 + // Re-resolve promises immediately to dodge false rejection from + // subsequent errors + if ( depth ) { + process(); + } else { + + // Call an optional hook to record the stack, in case of exception + // since it's otherwise lost when execution goes async + if ( jQuery.Deferred.getStackHook ) { + process.stackTrace = jQuery.Deferred.getStackHook(); + } + window.setTimeout( process ); + } + }; + } + + return jQuery.Deferred( function( newDefer ) { + + // progress_handlers.add( ... ) + tuples[ 0 ][ 3 ].add( + resolve( + 0, + newDefer, + jQuery.isFunction( onProgress ) ? + onProgress : + Identity, + newDefer.notifyWith + ) + ); + + // fulfilled_handlers.add( ... ) + tuples[ 1 ][ 3 ].add( + resolve( + 0, + newDefer, + jQuery.isFunction( onFulfilled ) ? + onFulfilled : + Identity + ) + ); + + // rejected_handlers.add( ... ) + tuples[ 2 ][ 3 ].add( + resolve( + 0, + newDefer, + jQuery.isFunction( onRejected ) ? + onRejected : + Thrower + ) + ); + } ).promise(); + }, + + // Get a promise for this deferred + // If obj is provided, the promise aspect is added to the object + promise: function( obj ) { + return obj != null ? jQuery.extend( obj, promise ) : promise; + } + }, + deferred = {}; + + // Add list-specific methods + jQuery.each( tuples, function( i, tuple ) { + var list = tuple[ 2 ], + stateString = tuple[ 5 ]; + + // promise.progress = list.add + // promise.done = list.add + // promise.fail = list.add + promise[ tuple[ 1 ] ] = list.add; + + // Handle state + if ( stateString ) { + list.add( + function() { + + // state = "resolved" (i.e., fulfilled) + // state = "rejected" + state = stateString; + }, + + // rejected_callbacks.disable + // fulfilled_callbacks.disable + tuples[ 3 - i ][ 2 ].disable, + + // progress_callbacks.lock + tuples[ 0 ][ 2 ].lock + ); + } + + // progress_handlers.fire + // fulfilled_handlers.fire + // rejected_handlers.fire + list.add( tuple[ 3 ].fire ); + + // deferred.notify = function() { deferred.notifyWith(...) } + // deferred.resolve = function() { deferred.resolveWith(...) } + // deferred.reject = function() { deferred.rejectWith(...) } + deferred[ tuple[ 0 ] ] = function() { + deferred[ tuple[ 0 ] + "With" ]( this === deferred ? undefined : this, arguments ); + return this; + }; + + // deferred.notifyWith = list.fireWith + // deferred.resolveWith = list.fireWith + // deferred.rejectWith = list.fireWith + deferred[ tuple[ 0 ] + "With" ] = list.fireWith; + } ); + + // Make the deferred a promise + promise.promise( deferred ); + + // Call given func if any + if ( func ) { + func.call( deferred, deferred ); + } + + // All done! + return deferred; + }, + + // Deferred helper + when: function( singleValue ) { + var + + // count of uncompleted subordinates + remaining = arguments.length, + + // count of unprocessed arguments + i = remaining, + + // subordinate fulfillment data + resolveContexts = Array( i ), + resolveValues = slice.call( arguments ), + + // the master Deferred + master = jQuery.Deferred(), + + // subordinate callback factory + updateFunc = function( i ) { + return function( value ) { + resolveContexts[ i ] = this; + resolveValues[ i ] = arguments.length > 1 ? slice.call( arguments ) : value; + if ( !( --remaining ) ) { + master.resolveWith( resolveContexts, resolveValues ); + } + }; + }; + + // Single- and empty arguments are adopted like Promise.resolve + if ( remaining <= 1 ) { + adoptValue( singleValue, master.done( updateFunc( i ) ).resolve, master.reject, + !remaining ); + + // Use .then() to unwrap secondary thenables (cf. gh-3000) + if ( master.state() === "pending" || + jQuery.isFunction( resolveValues[ i ] && resolveValues[ i ].then ) ) { + + return master.then(); + } + } + + // Multiple arguments are aggregated like Promise.all array elements + while ( i-- ) { + adoptValue( resolveValues[ i ], updateFunc( i ), master.reject ); + } + + return master.promise(); + } +} ); + + +// These usually indicate a programmer mistake during development, +// warn about them ASAP rather than swallowing them by default. +var rerrorNames = /^(Eval|Internal|Range|Reference|Syntax|Type|URI)Error$/; + +jQuery.Deferred.exceptionHook = function( error, stack ) { + + // Support: IE 8 - 9 only + // Console exists when dev tools are open, which can happen at any time + if ( window.console && window.console.warn && error && rerrorNames.test( error.name ) ) { + window.console.warn( "jQuery.Deferred exception: " + error.message, error.stack, stack ); + } +}; + + + + +jQuery.readyException = function( error ) { + window.setTimeout( function() { + throw error; + } ); +}; + + + + +// The deferred used on DOM ready +var readyList = jQuery.Deferred(); + +jQuery.fn.ready = function( fn ) { + + readyList + .then( fn ) + + // Wrap jQuery.readyException in a function so that the lookup + // happens at the time of error handling instead of callback + // registration. + .catch( function( error ) { + jQuery.readyException( error ); + } ); + + return this; +}; + +jQuery.extend( { + + // Is the DOM ready to be used? Set to true once it occurs. + isReady: false, + + // A counter to track how many items to wait for before + // the ready event fires. See #6781 + readyWait: 1, + + // Handle when the DOM is ready + ready: function( wait ) { + + // Abort if there are pending holds or we're already ready + if ( wait === true ? --jQuery.readyWait : jQuery.isReady ) { + return; + } + + // Remember that the DOM is ready + jQuery.isReady = true; + + // If a normal DOM Ready event fired, decrement, and wait if need be + if ( wait !== true && --jQuery.readyWait > 0 ) { + return; + } + + // If there are functions bound, to execute + readyList.resolveWith( document, [ jQuery ] ); + } +} ); + +jQuery.ready.then = readyList.then; + +// The ready event handler and self cleanup method +function completed() { + document.removeEventListener( "DOMContentLoaded", completed ); + window.removeEventListener( "load", completed ); + jQuery.ready(); +} + +// Catch cases where $(document).ready() is called +// after the browser event has already occurred. +// Support: IE <=9 - 10 only +// Older IE sometimes signals "interactive" too soon +if ( document.readyState === "complete" || + ( document.readyState !== "loading" && !document.documentElement.doScroll ) ) { + + // Handle it asynchronously to allow scripts the opportunity to delay ready + window.setTimeout( jQuery.ready ); + +} else { + + // Use the handy event callback + document.addEventListener( "DOMContentLoaded", completed ); + + // A fallback to window.onload, that will always work + window.addEventListener( "load", completed ); +} + + + + +// Multifunctional method to get and set values of a collection +// The value/s can optionally be executed if it's a function +var access = function( elems, fn, key, value, chainable, emptyGet, raw ) { + var i = 0, + len = elems.length, + bulk = key == null; + + // Sets many values + if ( jQuery.type( key ) === "object" ) { + chainable = true; + for ( i in key ) { + access( elems, fn, i, key[ i ], true, emptyGet, raw ); + } + + // Sets one value + } else if ( value !== undefined ) { + chainable = true; + + if ( !jQuery.isFunction( value ) ) { + raw = true; + } + + if ( bulk ) { + + // Bulk operations run against the entire set + if ( raw ) { + fn.call( elems, value ); + fn = null; + + // ...except when executing function values + } else { + bulk = fn; + fn = function( elem, key, value ) { + return bulk.call( jQuery( elem ), value ); + }; + } + } + + if ( fn ) { + for ( ; i < len; i++ ) { + fn( + elems[ i ], key, raw ? + value : + value.call( elems[ i ], i, fn( elems[ i ], key ) ) + ); + } + } + } + + if ( chainable ) { + return elems; + } + + // Gets + if ( bulk ) { + return fn.call( elems ); + } + + return len ? fn( elems[ 0 ], key ) : emptyGet; +}; +var acceptData = function( owner ) { + + // Accepts only: + // - Node + // - Node.ELEMENT_NODE + // - Node.DOCUMENT_NODE + // - Object + // - Any + return owner.nodeType === 1 || owner.nodeType === 9 || !( +owner.nodeType ); +}; + + + + +function Data() { + this.expando = jQuery.expando + Data.uid++; +} + +Data.uid = 1; + +Data.prototype = { + + cache: function( owner ) { + + // Check if the owner object already has a cache + var value = owner[ this.expando ]; + + // If not, create one + if ( !value ) { + value = {}; + + // We can accept data for non-element nodes in modern browsers, + // but we should not, see #8335. + // Always return an empty object. + if ( acceptData( owner ) ) { + + // If it is a node unlikely to be stringify-ed or looped over + // use plain assignment + if ( owner.nodeType ) { + owner[ this.expando ] = value; + + // Otherwise secure it in a non-enumerable property + // configurable must be true to allow the property to be + // deleted when data is removed + } else { + Object.defineProperty( owner, this.expando, { + value: value, + configurable: true + } ); + } + } + } + + return value; + }, + set: function( owner, data, value ) { + var prop, + cache = this.cache( owner ); + + // Handle: [ owner, key, value ] args + // Always use camelCase key (gh-2257) + if ( typeof data === "string" ) { + cache[ jQuery.camelCase( data ) ] = value; + + // Handle: [ owner, { properties } ] args + } else { + + // Copy the properties one-by-one to the cache object + for ( prop in data ) { + cache[ jQuery.camelCase( prop ) ] = data[ prop ]; + } + } + return cache; + }, + get: function( owner, key ) { + return key === undefined ? + this.cache( owner ) : + + // Always use camelCase key (gh-2257) + owner[ this.expando ] && owner[ this.expando ][ jQuery.camelCase( key ) ]; + }, + access: function( owner, key, value ) { + + // In cases where either: + // + // 1. No key was specified + // 2. A string key was specified, but no value provided + // + // Take the "read" path and allow the get method to determine + // which value to return, respectively either: + // + // 1. The entire cache object + // 2. The data stored at the key + // + if ( key === undefined || + ( ( key && typeof key === "string" ) && value === undefined ) ) { + + return this.get( owner, key ); + } + + // When the key is not a string, or both a key and value + // are specified, set or extend (existing objects) with either: + // + // 1. An object of properties + // 2. A key and value + // + this.set( owner, key, value ); + + // Since the "set" path can have two possible entry points + // return the expected data based on which path was taken[*] + return value !== undefined ? value : key; + }, + remove: function( owner, key ) { + var i, + cache = owner[ this.expando ]; + + if ( cache === undefined ) { + return; + } + + if ( key !== undefined ) { + + // Support array or space separated string of keys + if ( Array.isArray( key ) ) { + + // If key is an array of keys... + // We always set camelCase keys, so remove that. + key = key.map( jQuery.camelCase ); + } else { + key = jQuery.camelCase( key ); + + // If a key with the spaces exists, use it. + // Otherwise, create an array by matching non-whitespace + key = key in cache ? + [ key ] : + ( key.match( rnothtmlwhite ) || [] ); + } + + i = key.length; + + while ( i-- ) { + delete cache[ key[ i ] ]; + } + } + + // Remove the expando if there's no more data + if ( key === undefined || jQuery.isEmptyObject( cache ) ) { + + // Support: Chrome <=35 - 45 + // Webkit & Blink performance suffers when deleting properties + // from DOM nodes, so set to undefined instead + // https://bugs.chromium.org/p/chromium/issues/detail?id=378607 (bug restricted) + if ( owner.nodeType ) { + owner[ this.expando ] = undefined; + } else { + delete owner[ this.expando ]; + } + } + }, + hasData: function( owner ) { + var cache = owner[ this.expando ]; + return cache !== undefined && !jQuery.isEmptyObject( cache ); + } +}; +var dataPriv = new Data(); + +var dataUser = new Data(); + + + +// Implementation Summary +// +// 1. Enforce API surface and semantic compatibility with 1.9.x branch +// 2. Improve the module's maintainability by reducing the storage +// paths to a single mechanism. +// 3. Use the same single mechanism to support "private" and "user" data. +// 4. _Never_ expose "private" data to user code (TODO: Drop _data, _removeData) +// 5. Avoid exposing implementation details on user objects (eg. expando properties) +// 6. Provide a clear path for implementation upgrade to WeakMap in 2014 + +var rbrace = /^(?:\{[\w\W]*\}|\[[\w\W]*\])$/, + rmultiDash = /[A-Z]/g; + +function getData( data ) { + if ( data === "true" ) { + return true; + } + + if ( data === "false" ) { + return false; + } + + if ( data === "null" ) { + return null; + } + + // Only convert to a number if it doesn't change the string + if ( data === +data + "" ) { + return +data; + } + + if ( rbrace.test( data ) ) { + return JSON.parse( data ); + } + + return data; +} + +function dataAttr( elem, key, data ) { + var name; + + // If nothing was found internally, try to fetch any + // data from the HTML5 data-* attribute + if ( data === undefined && elem.nodeType === 1 ) { + name = "data-" + key.replace( rmultiDash, "-$&" ).toLowerCase(); + data = elem.getAttribute( name ); + + if ( typeof data === "string" ) { + try { + data = getData( data ); + } catch ( e ) {} + + // Make sure we set the data so it isn't changed later + dataUser.set( elem, key, data ); + } else { + data = undefined; + } + } + return data; +} + +jQuery.extend( { + hasData: function( elem ) { + return dataUser.hasData( elem ) || dataPriv.hasData( elem ); + }, + + data: function( elem, name, data ) { + return dataUser.access( elem, name, data ); + }, + + removeData: function( elem, name ) { + dataUser.remove( elem, name ); + }, + + // TODO: Now that all calls to _data and _removeData have been replaced + // with direct calls to dataPriv methods, these can be deprecated. + _data: function( elem, name, data ) { + return dataPriv.access( elem, name, data ); + }, + + _removeData: function( elem, name ) { + dataPriv.remove( elem, name ); + } +} ); + +jQuery.fn.extend( { + data: function( key, value ) { + var i, name, data, + elem = this[ 0 ], + attrs = elem && elem.attributes; + + // Gets all values + if ( key === undefined ) { + if ( this.length ) { + data = dataUser.get( elem ); + + if ( elem.nodeType === 1 && !dataPriv.get( elem, "hasDataAttrs" ) ) { + i = attrs.length; + while ( i-- ) { + + // Support: IE 11 only + // The attrs elements can be null (#14894) + if ( attrs[ i ] ) { + name = attrs[ i ].name; + if ( name.indexOf( "data-" ) === 0 ) { + name = jQuery.camelCase( name.slice( 5 ) ); + dataAttr( elem, name, data[ name ] ); + } + } + } + dataPriv.set( elem, "hasDataAttrs", true ); + } + } + + return data; + } + + // Sets multiple values + if ( typeof key === "object" ) { + return this.each( function() { + dataUser.set( this, key ); + } ); + } + + return access( this, function( value ) { + var data; + + // The calling jQuery object (element matches) is not empty + // (and therefore has an element appears at this[ 0 ]) and the + // `value` parameter was not undefined. An empty jQuery object + // will result in `undefined` for elem = this[ 0 ] which will + // throw an exception if an attempt to read a data cache is made. + if ( elem && value === undefined ) { + + // Attempt to get data from the cache + // The key will always be camelCased in Data + data = dataUser.get( elem, key ); + if ( data !== undefined ) { + return data; + } + + // Attempt to "discover" the data in + // HTML5 custom data-* attrs + data = dataAttr( elem, key ); + if ( data !== undefined ) { + return data; + } + + // We tried really hard, but the data doesn't exist. + return; + } + + // Set the data... + this.each( function() { + + // We always store the camelCased key + dataUser.set( this, key, value ); + } ); + }, null, value, arguments.length > 1, null, true ); + }, + + removeData: function( key ) { + return this.each( function() { + dataUser.remove( this, key ); + } ); + } +} ); + + +jQuery.extend( { + queue: function( elem, type, data ) { + var queue; + + if ( elem ) { + type = ( type || "fx" ) + "queue"; + queue = dataPriv.get( elem, type ); + + // Speed up dequeue by getting out quickly if this is just a lookup + if ( data ) { + if ( !queue || Array.isArray( data ) ) { + queue = dataPriv.access( elem, type, jQuery.makeArray( data ) ); + } else { + queue.push( data ); + } + } + return queue || []; + } + }, + + dequeue: function( elem, type ) { + type = type || "fx"; + + var queue = jQuery.queue( elem, type ), + startLength = queue.length, + fn = queue.shift(), + hooks = jQuery._queueHooks( elem, type ), + next = function() { + jQuery.dequeue( elem, type ); + }; + + // If the fx queue is dequeued, always remove the progress sentinel + if ( fn === "inprogress" ) { + fn = queue.shift(); + startLength--; + } + + if ( fn ) { + + // Add a progress sentinel to prevent the fx queue from being + // automatically dequeued + if ( type === "fx" ) { + queue.unshift( "inprogress" ); + } + + // Clear up the last queue stop function + delete hooks.stop; + fn.call( elem, next, hooks ); + } + + if ( !startLength && hooks ) { + hooks.empty.fire(); + } + }, + + // Not public - generate a queueHooks object, or return the current one + _queueHooks: function( elem, type ) { + var key = type + "queueHooks"; + return dataPriv.get( elem, key ) || dataPriv.access( elem, key, { + empty: jQuery.Callbacks( "once memory" ).add( function() { + dataPriv.remove( elem, [ type + "queue", key ] ); + } ) + } ); + } +} ); + +jQuery.fn.extend( { + queue: function( type, data ) { + var setter = 2; + + if ( typeof type !== "string" ) { + data = type; + type = "fx"; + setter--; + } + + if ( arguments.length < setter ) { + return jQuery.queue( this[ 0 ], type ); + } + + return data === undefined ? + this : + this.each( function() { + var queue = jQuery.queue( this, type, data ); + + // Ensure a hooks for this queue + jQuery._queueHooks( this, type ); + + if ( type === "fx" && queue[ 0 ] !== "inprogress" ) { + jQuery.dequeue( this, type ); + } + } ); + }, + dequeue: function( type ) { + return this.each( function() { + jQuery.dequeue( this, type ); + } ); + }, + clearQueue: function( type ) { + return this.queue( type || "fx", [] ); + }, + + // Get a promise resolved when queues of a certain type + // are emptied (fx is the type by default) + promise: function( type, obj ) { + var tmp, + count = 1, + defer = jQuery.Deferred(), + elements = this, + i = this.length, + resolve = function() { + if ( !( --count ) ) { + defer.resolveWith( elements, [ elements ] ); + } + }; + + if ( typeof type !== "string" ) { + obj = type; + type = undefined; + } + type = type || "fx"; + + while ( i-- ) { + tmp = dataPriv.get( elements[ i ], type + "queueHooks" ); + if ( tmp && tmp.empty ) { + count++; + tmp.empty.add( resolve ); + } + } + resolve(); + return defer.promise( obj ); + } +} ); +var pnum = ( /[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/ ).source; + +var rcssNum = new RegExp( "^(?:([+-])=|)(" + pnum + ")([a-z%]*)$", "i" ); + + +var cssExpand = [ "Top", "Right", "Bottom", "Left" ]; + +var isHiddenWithinTree = function( elem, el ) { + + // isHiddenWithinTree might be called from jQuery#filter function; + // in that case, element will be second argument + elem = el || elem; + + // Inline style trumps all + return elem.style.display === "none" || + elem.style.display === "" && + + // Otherwise, check computed style + // Support: Firefox <=43 - 45 + // Disconnected elements can have computed display: none, so first confirm that elem is + // in the document. + jQuery.contains( elem.ownerDocument, elem ) && + + jQuery.css( elem, "display" ) === "none"; + }; + +var swap = function( elem, options, callback, args ) { + var ret, name, + old = {}; + + // Remember the old values, and insert the new ones + for ( name in options ) { + old[ name ] = elem.style[ name ]; + elem.style[ name ] = options[ name ]; + } + + ret = callback.apply( elem, args || [] ); + + // Revert the old values + for ( name in options ) { + elem.style[ name ] = old[ name ]; + } + + return ret; +}; + + + + +function adjustCSS( elem, prop, valueParts, tween ) { + var adjusted, + scale = 1, + maxIterations = 20, + currentValue = tween ? + function() { + return tween.cur(); + } : + function() { + return jQuery.css( elem, prop, "" ); + }, + initial = currentValue(), + unit = valueParts && valueParts[ 3 ] || ( jQuery.cssNumber[ prop ] ? "" : "px" ), + + // Starting value computation is required for potential unit mismatches + initialInUnit = ( jQuery.cssNumber[ prop ] || unit !== "px" && +initial ) && + rcssNum.exec( jQuery.css( elem, prop ) ); + + if ( initialInUnit && initialInUnit[ 3 ] !== unit ) { + + // Trust units reported by jQuery.css + unit = unit || initialInUnit[ 3 ]; + + // Make sure we update the tween properties later on + valueParts = valueParts || []; + + // Iteratively approximate from a nonzero starting point + initialInUnit = +initial || 1; + + do { + + // If previous iteration zeroed out, double until we get *something*. + // Use string for doubling so we don't accidentally see scale as unchanged below + scale = scale || ".5"; + + // Adjust and apply + initialInUnit = initialInUnit / scale; + jQuery.style( elem, prop, initialInUnit + unit ); + + // Update scale, tolerating zero or NaN from tween.cur() + // Break the loop if scale is unchanged or perfect, or if we've just had enough. + } while ( + scale !== ( scale = currentValue() / initial ) && scale !== 1 && --maxIterations + ); + } + + if ( valueParts ) { + initialInUnit = +initialInUnit || +initial || 0; + + // Apply relative offset (+=/-=) if specified + adjusted = valueParts[ 1 ] ? + initialInUnit + ( valueParts[ 1 ] + 1 ) * valueParts[ 2 ] : + +valueParts[ 2 ]; + if ( tween ) { + tween.unit = unit; + tween.start = initialInUnit; + tween.end = adjusted; + } + } + return adjusted; +} + + +var defaultDisplayMap = {}; + +function getDefaultDisplay( elem ) { + var temp, + doc = elem.ownerDocument, + nodeName = elem.nodeName, + display = defaultDisplayMap[ nodeName ]; + + if ( display ) { + return display; + } + + temp = doc.body.appendChild( doc.createElement( nodeName ) ); + display = jQuery.css( temp, "display" ); + + temp.parentNode.removeChild( temp ); + + if ( display === "none" ) { + display = "block"; + } + defaultDisplayMap[ nodeName ] = display; + + return display; +} + +function showHide( elements, show ) { + var display, elem, + values = [], + index = 0, + length = elements.length; + + // Determine new display value for elements that need to change + for ( ; index < length; index++ ) { + elem = elements[ index ]; + if ( !elem.style ) { + continue; + } + + display = elem.style.display; + if ( show ) { + + // Since we force visibility upon cascade-hidden elements, an immediate (and slow) + // check is required in this first loop unless we have a nonempty display value (either + // inline or about-to-be-restored) + if ( display === "none" ) { + values[ index ] = dataPriv.get( elem, "display" ) || null; + if ( !values[ index ] ) { + elem.style.display = ""; + } + } + if ( elem.style.display === "" && isHiddenWithinTree( elem ) ) { + values[ index ] = getDefaultDisplay( elem ); + } + } else { + if ( display !== "none" ) { + values[ index ] = "none"; + + // Remember what we're overwriting + dataPriv.set( elem, "display", display ); + } + } + } + + // Set the display of the elements in a second loop to avoid constant reflow + for ( index = 0; index < length; index++ ) { + if ( values[ index ] != null ) { + elements[ index ].style.display = values[ index ]; + } + } + + return elements; +} + +jQuery.fn.extend( { + show: function() { + return showHide( this, true ); + }, + hide: function() { + return showHide( this ); + }, + toggle: function( state ) { + if ( typeof state === "boolean" ) { + return state ? this.show() : this.hide(); + } + + return this.each( function() { + if ( isHiddenWithinTree( this ) ) { + jQuery( this ).show(); + } else { + jQuery( this ).hide(); + } + } ); + } +} ); +var rcheckableType = ( /^(?:checkbox|radio)$/i ); + +var rtagName = ( /<([a-z][^\/\0>\x20\t\r\n\f]+)/i ); + +var rscriptType = ( /^$|\/(?:java|ecma)script/i ); + + + +// We have to close these tags to support XHTML (#13200) +var wrapMap = { + + // Support: IE <=9 only + option: [ 1, "" ], + + // XHTML parsers do not magically insert elements in the + // same way that tag soup parsers do. So we cannot shorten + // this by omitting or other required elements. + thead: [ 1, "", "
    " ], + col: [ 2, "", "
    " ], + tr: [ 2, "", "
    " ], + td: [ 3, "", "
    " ], + + _default: [ 0, "", "" ] +}; + +// Support: IE <=9 only +wrapMap.optgroup = wrapMap.option; + +wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead; +wrapMap.th = wrapMap.td; + + +function getAll( context, tag ) { + + // Support: IE <=9 - 11 only + // Use typeof to avoid zero-argument method invocation on host objects (#15151) + var ret; + + if ( typeof context.getElementsByTagName !== "undefined" ) { + ret = context.getElementsByTagName( tag || "*" ); + + } else if ( typeof context.querySelectorAll !== "undefined" ) { + ret = context.querySelectorAll( tag || "*" ); + + } else { + ret = []; + } + + if ( tag === undefined || tag && nodeName( context, tag ) ) { + return jQuery.merge( [ context ], ret ); + } + + return ret; +} + + +// Mark scripts as having already been evaluated +function setGlobalEval( elems, refElements ) { + var i = 0, + l = elems.length; + + for ( ; i < l; i++ ) { + dataPriv.set( + elems[ i ], + "globalEval", + !refElements || dataPriv.get( refElements[ i ], "globalEval" ) + ); + } +} + + +var rhtml = /<|&#?\w+;/; + +function buildFragment( elems, context, scripts, selection, ignored ) { + var elem, tmp, tag, wrap, contains, j, + fragment = context.createDocumentFragment(), + nodes = [], + i = 0, + l = elems.length; + + for ( ; i < l; i++ ) { + elem = elems[ i ]; + + if ( elem || elem === 0 ) { + + // Add nodes directly + if ( jQuery.type( elem ) === "object" ) { + + // Support: Android <=4.0 only, PhantomJS 1 only + // push.apply(_, arraylike) throws on ancient WebKit + jQuery.merge( nodes, elem.nodeType ? [ elem ] : elem ); + + // Convert non-html into a text node + } else if ( !rhtml.test( elem ) ) { + nodes.push( context.createTextNode( elem ) ); + + // Convert html into DOM nodes + } else { + tmp = tmp || fragment.appendChild( context.createElement( "div" ) ); + + // Deserialize a standard representation + tag = ( rtagName.exec( elem ) || [ "", "" ] )[ 1 ].toLowerCase(); + wrap = wrapMap[ tag ] || wrapMap._default; + tmp.innerHTML = wrap[ 1 ] + jQuery.htmlPrefilter( elem ) + wrap[ 2 ]; + + // Descend through wrappers to the right content + j = wrap[ 0 ]; + while ( j-- ) { + tmp = tmp.lastChild; + } + + // Support: Android <=4.0 only, PhantomJS 1 only + // push.apply(_, arraylike) throws on ancient WebKit + jQuery.merge( nodes, tmp.childNodes ); + + // Remember the top-level container + tmp = fragment.firstChild; + + // Ensure the created nodes are orphaned (#12392) + tmp.textContent = ""; + } + } + } + + // Remove wrapper from fragment + fragment.textContent = ""; + + i = 0; + while ( ( elem = nodes[ i++ ] ) ) { + + // Skip elements already in the context collection (trac-4087) + if ( selection && jQuery.inArray( elem, selection ) > -1 ) { + if ( ignored ) { + ignored.push( elem ); + } + continue; + } + + contains = jQuery.contains( elem.ownerDocument, elem ); + + // Append to fragment + tmp = getAll( fragment.appendChild( elem ), "script" ); + + // Preserve script evaluation history + if ( contains ) { + setGlobalEval( tmp ); + } + + // Capture executables + if ( scripts ) { + j = 0; + while ( ( elem = tmp[ j++ ] ) ) { + if ( rscriptType.test( elem.type || "" ) ) { + scripts.push( elem ); + } + } + } + } + + return fragment; +} + + +( function() { + var fragment = document.createDocumentFragment(), + div = fragment.appendChild( document.createElement( "div" ) ), + input = document.createElement( "input" ); + + // Support: Android 4.0 - 4.3 only + // Check state lost if the name is set (#11217) + // Support: Windows Web Apps (WWA) + // `name` and `type` must use .setAttribute for WWA (#14901) + input.setAttribute( "type", "radio" ); + input.setAttribute( "checked", "checked" ); + input.setAttribute( "name", "t" ); + + div.appendChild( input ); + + // Support: Android <=4.1 only + // Older WebKit doesn't clone checked state correctly in fragments + support.checkClone = div.cloneNode( true ).cloneNode( true ).lastChild.checked; + + // Support: IE <=11 only + // Make sure textarea (and checkbox) defaultValue is properly cloned + div.innerHTML = ""; + support.noCloneChecked = !!div.cloneNode( true ).lastChild.defaultValue; +} )(); +var documentElement = document.documentElement; + + + +var + rkeyEvent = /^key/, + rmouseEvent = /^(?:mouse|pointer|contextmenu|drag|drop)|click/, + rtypenamespace = /^([^.]*)(?:\.(.+)|)/; + +function returnTrue() { + return true; +} + +function returnFalse() { + return false; +} + +// Support: IE <=9 only +// See #13393 for more info +function safeActiveElement() { + try { + return document.activeElement; + } catch ( err ) { } +} + +function on( elem, types, selector, data, fn, one ) { + var origFn, type; + + // Types can be a map of types/handlers + if ( typeof types === "object" ) { + + // ( types-Object, selector, data ) + if ( typeof selector !== "string" ) { + + // ( types-Object, data ) + data = data || selector; + selector = undefined; + } + for ( type in types ) { + on( elem, type, selector, data, types[ type ], one ); + } + return elem; + } + + if ( data == null && fn == null ) { + + // ( types, fn ) + fn = selector; + data = selector = undefined; + } else if ( fn == null ) { + if ( typeof selector === "string" ) { + + // ( types, selector, fn ) + fn = data; + data = undefined; + } else { + + // ( types, data, fn ) + fn = data; + data = selector; + selector = undefined; + } + } + if ( fn === false ) { + fn = returnFalse; + } else if ( !fn ) { + return elem; + } + + if ( one === 1 ) { + origFn = fn; + fn = function( event ) { + + // Can use an empty set, since event contains the info + jQuery().off( event ); + return origFn.apply( this, arguments ); + }; + + // Use same guid so caller can remove using origFn + fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ ); + } + return elem.each( function() { + jQuery.event.add( this, types, fn, data, selector ); + } ); +} + +/* + * Helper functions for managing events -- not part of the public interface. + * Props to Dean Edwards' addEvent library for many of the ideas. + */ +jQuery.event = { + + global: {}, + + add: function( elem, types, handler, data, selector ) { + + var handleObjIn, eventHandle, tmp, + events, t, handleObj, + special, handlers, type, namespaces, origType, + elemData = dataPriv.get( elem ); + + // Don't attach events to noData or text/comment nodes (but allow plain objects) + if ( !elemData ) { + return; + } + + // Caller can pass in an object of custom data in lieu of the handler + if ( handler.handler ) { + handleObjIn = handler; + handler = handleObjIn.handler; + selector = handleObjIn.selector; + } + + // Ensure that invalid selectors throw exceptions at attach time + // Evaluate against documentElement in case elem is a non-element node (e.g., document) + if ( selector ) { + jQuery.find.matchesSelector( documentElement, selector ); + } + + // Make sure that the handler has a unique ID, used to find/remove it later + if ( !handler.guid ) { + handler.guid = jQuery.guid++; + } + + // Init the element's event structure and main handler, if this is the first + if ( !( events = elemData.events ) ) { + events = elemData.events = {}; + } + if ( !( eventHandle = elemData.handle ) ) { + eventHandle = elemData.handle = function( e ) { + + // Discard the second event of a jQuery.event.trigger() and + // when an event is called after a page has unloaded + return typeof jQuery !== "undefined" && jQuery.event.triggered !== e.type ? + jQuery.event.dispatch.apply( elem, arguments ) : undefined; + }; + } + + // Handle multiple events separated by a space + types = ( types || "" ).match( rnothtmlwhite ) || [ "" ]; + t = types.length; + while ( t-- ) { + tmp = rtypenamespace.exec( types[ t ] ) || []; + type = origType = tmp[ 1 ]; + namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort(); + + // There *must* be a type, no attaching namespace-only handlers + if ( !type ) { + continue; + } + + // If event changes its type, use the special event handlers for the changed type + special = jQuery.event.special[ type ] || {}; + + // If selector defined, determine special event api type, otherwise given type + type = ( selector ? special.delegateType : special.bindType ) || type; + + // Update special based on newly reset type + special = jQuery.event.special[ type ] || {}; + + // handleObj is passed to all event handlers + handleObj = jQuery.extend( { + type: type, + origType: origType, + data: data, + handler: handler, + guid: handler.guid, + selector: selector, + needsContext: selector && jQuery.expr.match.needsContext.test( selector ), + namespace: namespaces.join( "." ) + }, handleObjIn ); + + // Init the event handler queue if we're the first + if ( !( handlers = events[ type ] ) ) { + handlers = events[ type ] = []; + handlers.delegateCount = 0; + + // Only use addEventListener if the special events handler returns false + if ( !special.setup || + special.setup.call( elem, data, namespaces, eventHandle ) === false ) { + + if ( elem.addEventListener ) { + elem.addEventListener( type, eventHandle ); + } + } + } + + if ( special.add ) { + special.add.call( elem, handleObj ); + + if ( !handleObj.handler.guid ) { + handleObj.handler.guid = handler.guid; + } + } + + // Add to the element's handler list, delegates in front + if ( selector ) { + handlers.splice( handlers.delegateCount++, 0, handleObj ); + } else { + handlers.push( handleObj ); + } + + // Keep track of which events have ever been used, for event optimization + jQuery.event.global[ type ] = true; + } + + }, + + // Detach an event or set of events from an element + remove: function( elem, types, handler, selector, mappedTypes ) { + + var j, origCount, tmp, + events, t, handleObj, + special, handlers, type, namespaces, origType, + elemData = dataPriv.hasData( elem ) && dataPriv.get( elem ); + + if ( !elemData || !( events = elemData.events ) ) { + return; + } + + // Once for each type.namespace in types; type may be omitted + types = ( types || "" ).match( rnothtmlwhite ) || [ "" ]; + t = types.length; + while ( t-- ) { + tmp = rtypenamespace.exec( types[ t ] ) || []; + type = origType = tmp[ 1 ]; + namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort(); + + // Unbind all events (on this namespace, if provided) for the element + if ( !type ) { + for ( type in events ) { + jQuery.event.remove( elem, type + types[ t ], handler, selector, true ); + } + continue; + } + + special = jQuery.event.special[ type ] || {}; + type = ( selector ? special.delegateType : special.bindType ) || type; + handlers = events[ type ] || []; + tmp = tmp[ 2 ] && + new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" ); + + // Remove matching events + origCount = j = handlers.length; + while ( j-- ) { + handleObj = handlers[ j ]; + + if ( ( mappedTypes || origType === handleObj.origType ) && + ( !handler || handler.guid === handleObj.guid ) && + ( !tmp || tmp.test( handleObj.namespace ) ) && + ( !selector || selector === handleObj.selector || + selector === "**" && handleObj.selector ) ) { + handlers.splice( j, 1 ); + + if ( handleObj.selector ) { + handlers.delegateCount--; + } + if ( special.remove ) { + special.remove.call( elem, handleObj ); + } + } + } + + // Remove generic event handler if we removed something and no more handlers exist + // (avoids potential for endless recursion during removal of special event handlers) + if ( origCount && !handlers.length ) { + if ( !special.teardown || + special.teardown.call( elem, namespaces, elemData.handle ) === false ) { + + jQuery.removeEvent( elem, type, elemData.handle ); + } + + delete events[ type ]; + } + } + + // Remove data and the expando if it's no longer used + if ( jQuery.isEmptyObject( events ) ) { + dataPriv.remove( elem, "handle events" ); + } + }, + + dispatch: function( nativeEvent ) { + + // Make a writable jQuery.Event from the native event object + var event = jQuery.event.fix( nativeEvent ); + + var i, j, ret, matched, handleObj, handlerQueue, + args = new Array( arguments.length ), + handlers = ( dataPriv.get( this, "events" ) || {} )[ event.type ] || [], + special = jQuery.event.special[ event.type ] || {}; + + // Use the fix-ed jQuery.Event rather than the (read-only) native event + args[ 0 ] = event; + + for ( i = 1; i < arguments.length; i++ ) { + args[ i ] = arguments[ i ]; + } + + event.delegateTarget = this; + + // Call the preDispatch hook for the mapped type, and let it bail if desired + if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) { + return; + } + + // Determine handlers + handlerQueue = jQuery.event.handlers.call( this, event, handlers ); + + // Run delegates first; they may want to stop propagation beneath us + i = 0; + while ( ( matched = handlerQueue[ i++ ] ) && !event.isPropagationStopped() ) { + event.currentTarget = matched.elem; + + j = 0; + while ( ( handleObj = matched.handlers[ j++ ] ) && + !event.isImmediatePropagationStopped() ) { + + // Triggered event must either 1) have no namespace, or 2) have namespace(s) + // a subset or equal to those in the bound event (both can have no namespace). + if ( !event.rnamespace || event.rnamespace.test( handleObj.namespace ) ) { + + event.handleObj = handleObj; + event.data = handleObj.data; + + ret = ( ( jQuery.event.special[ handleObj.origType ] || {} ).handle || + handleObj.handler ).apply( matched.elem, args ); + + if ( ret !== undefined ) { + if ( ( event.result = ret ) === false ) { + event.preventDefault(); + event.stopPropagation(); + } + } + } + } + } + + // Call the postDispatch hook for the mapped type + if ( special.postDispatch ) { + special.postDispatch.call( this, event ); + } + + return event.result; + }, + + handlers: function( event, handlers ) { + var i, handleObj, sel, matchedHandlers, matchedSelectors, + handlerQueue = [], + delegateCount = handlers.delegateCount, + cur = event.target; + + // Find delegate handlers + if ( delegateCount && + + // Support: IE <=9 + // Black-hole SVG instance trees (trac-13180) + cur.nodeType && + + // Support: Firefox <=42 + // Suppress spec-violating clicks indicating a non-primary pointer button (trac-3861) + // https://www.w3.org/TR/DOM-Level-3-Events/#event-type-click + // Support: IE 11 only + // ...but not arrow key "clicks" of radio inputs, which can have `button` -1 (gh-2343) + !( event.type === "click" && event.button >= 1 ) ) { + + for ( ; cur !== this; cur = cur.parentNode || this ) { + + // Don't check non-elements (#13208) + // Don't process clicks on disabled elements (#6911, #8165, #11382, #11764) + if ( cur.nodeType === 1 && !( event.type === "click" && cur.disabled === true ) ) { + matchedHandlers = []; + matchedSelectors = {}; + for ( i = 0; i < delegateCount; i++ ) { + handleObj = handlers[ i ]; + + // Don't conflict with Object.prototype properties (#13203) + sel = handleObj.selector + " "; + + if ( matchedSelectors[ sel ] === undefined ) { + matchedSelectors[ sel ] = handleObj.needsContext ? + jQuery( sel, this ).index( cur ) > -1 : + jQuery.find( sel, this, null, [ cur ] ).length; + } + if ( matchedSelectors[ sel ] ) { + matchedHandlers.push( handleObj ); + } + } + if ( matchedHandlers.length ) { + handlerQueue.push( { elem: cur, handlers: matchedHandlers } ); + } + } + } + } + + // Add the remaining (directly-bound) handlers + cur = this; + if ( delegateCount < handlers.length ) { + handlerQueue.push( { elem: cur, handlers: handlers.slice( delegateCount ) } ); + } + + return handlerQueue; + }, + + addProp: function( name, hook ) { + Object.defineProperty( jQuery.Event.prototype, name, { + enumerable: true, + configurable: true, + + get: jQuery.isFunction( hook ) ? + function() { + if ( this.originalEvent ) { + return hook( this.originalEvent ); + } + } : + function() { + if ( this.originalEvent ) { + return this.originalEvent[ name ]; + } + }, + + set: function( value ) { + Object.defineProperty( this, name, { + enumerable: true, + configurable: true, + writable: true, + value: value + } ); + } + } ); + }, + + fix: function( originalEvent ) { + return originalEvent[ jQuery.expando ] ? + originalEvent : + new jQuery.Event( originalEvent ); + }, + + special: { + load: { + + // Prevent triggered image.load events from bubbling to window.load + noBubble: true + }, + focus: { + + // Fire native event if possible so blur/focus sequence is correct + trigger: function() { + if ( this !== safeActiveElement() && this.focus ) { + this.focus(); + return false; + } + }, + delegateType: "focusin" + }, + blur: { + trigger: function() { + if ( this === safeActiveElement() && this.blur ) { + this.blur(); + return false; + } + }, + delegateType: "focusout" + }, + click: { + + // For checkbox, fire native event so checked state will be right + trigger: function() { + if ( this.type === "checkbox" && this.click && nodeName( this, "input" ) ) { + this.click(); + return false; + } + }, + + // For cross-browser consistency, don't fire native .click() on links + _default: function( event ) { + return nodeName( event.target, "a" ); + } + }, + + beforeunload: { + postDispatch: function( event ) { + + // Support: Firefox 20+ + // Firefox doesn't alert if the returnValue field is not set. + if ( event.result !== undefined && event.originalEvent ) { + event.originalEvent.returnValue = event.result; + } + } + } + } +}; + +jQuery.removeEvent = function( elem, type, handle ) { + + // This "if" is needed for plain objects + if ( elem.removeEventListener ) { + elem.removeEventListener( type, handle ); + } +}; + +jQuery.Event = function( src, props ) { + + // Allow instantiation without the 'new' keyword + if ( !( this instanceof jQuery.Event ) ) { + return new jQuery.Event( src, props ); + } + + // Event object + if ( src && src.type ) { + this.originalEvent = src; + this.type = src.type; + + // Events bubbling up the document may have been marked as prevented + // by a handler lower down the tree; reflect the correct value. + this.isDefaultPrevented = src.defaultPrevented || + src.defaultPrevented === undefined && + + // Support: Android <=2.3 only + src.returnValue === false ? + returnTrue : + returnFalse; + + // Create target properties + // Support: Safari <=6 - 7 only + // Target should not be a text node (#504, #13143) + this.target = ( src.target && src.target.nodeType === 3 ) ? + src.target.parentNode : + src.target; + + this.currentTarget = src.currentTarget; + this.relatedTarget = src.relatedTarget; + + // Event type + } else { + this.type = src; + } + + // Put explicitly provided properties onto the event object + if ( props ) { + jQuery.extend( this, props ); + } + + // Create a timestamp if incoming event doesn't have one + this.timeStamp = src && src.timeStamp || jQuery.now(); + + // Mark it as fixed + this[ jQuery.expando ] = true; +}; + +// jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding +// https://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html +jQuery.Event.prototype = { + constructor: jQuery.Event, + isDefaultPrevented: returnFalse, + isPropagationStopped: returnFalse, + isImmediatePropagationStopped: returnFalse, + isSimulated: false, + + preventDefault: function() { + var e = this.originalEvent; + + this.isDefaultPrevented = returnTrue; + + if ( e && !this.isSimulated ) { + e.preventDefault(); + } + }, + stopPropagation: function() { + var e = this.originalEvent; + + this.isPropagationStopped = returnTrue; + + if ( e && !this.isSimulated ) { + e.stopPropagation(); + } + }, + stopImmediatePropagation: function() { + var e = this.originalEvent; + + this.isImmediatePropagationStopped = returnTrue; + + if ( e && !this.isSimulated ) { + e.stopImmediatePropagation(); + } + + this.stopPropagation(); + } +}; + +// Includes all common event props including KeyEvent and MouseEvent specific props +jQuery.each( { + altKey: true, + bubbles: true, + cancelable: true, + changedTouches: true, + ctrlKey: true, + detail: true, + eventPhase: true, + metaKey: true, + pageX: true, + pageY: true, + shiftKey: true, + view: true, + "char": true, + charCode: true, + key: true, + keyCode: true, + button: true, + buttons: true, + clientX: true, + clientY: true, + offsetX: true, + offsetY: true, + pointerId: true, + pointerType: true, + screenX: true, + screenY: true, + targetTouches: true, + toElement: true, + touches: true, + + which: function( event ) { + var button = event.button; + + // Add which for key events + if ( event.which == null && rkeyEvent.test( event.type ) ) { + return event.charCode != null ? event.charCode : event.keyCode; + } + + // Add which for click: 1 === left; 2 === middle; 3 === right + if ( !event.which && button !== undefined && rmouseEvent.test( event.type ) ) { + if ( button & 1 ) { + return 1; + } + + if ( button & 2 ) { + return 3; + } + + if ( button & 4 ) { + return 2; + } + + return 0; + } + + return event.which; + } +}, jQuery.event.addProp ); + +// Create mouseenter/leave events using mouseover/out and event-time checks +// so that event delegation works in jQuery. +// Do the same for pointerenter/pointerleave and pointerover/pointerout +// +// Support: Safari 7 only +// Safari sends mouseenter too often; see: +// https://bugs.chromium.org/p/chromium/issues/detail?id=470258 +// for the description of the bug (it existed in older Chrome versions as well). +jQuery.each( { + mouseenter: "mouseover", + mouseleave: "mouseout", + pointerenter: "pointerover", + pointerleave: "pointerout" +}, function( orig, fix ) { + jQuery.event.special[ orig ] = { + delegateType: fix, + bindType: fix, + + handle: function( event ) { + var ret, + target = this, + related = event.relatedTarget, + handleObj = event.handleObj; + + // For mouseenter/leave call the handler if related is outside the target. + // NB: No relatedTarget if the mouse left/entered the browser window + if ( !related || ( related !== target && !jQuery.contains( target, related ) ) ) { + event.type = handleObj.origType; + ret = handleObj.handler.apply( this, arguments ); + event.type = fix; + } + return ret; + } + }; +} ); + +jQuery.fn.extend( { + + on: function( types, selector, data, fn ) { + return on( this, types, selector, data, fn ); + }, + one: function( types, selector, data, fn ) { + return on( this, types, selector, data, fn, 1 ); + }, + off: function( types, selector, fn ) { + var handleObj, type; + if ( types && types.preventDefault && types.handleObj ) { + + // ( event ) dispatched jQuery.Event + handleObj = types.handleObj; + jQuery( types.delegateTarget ).off( + handleObj.namespace ? + handleObj.origType + "." + handleObj.namespace : + handleObj.origType, + handleObj.selector, + handleObj.handler + ); + return this; + } + if ( typeof types === "object" ) { + + // ( types-object [, selector] ) + for ( type in types ) { + this.off( type, selector, types[ type ] ); + } + return this; + } + if ( selector === false || typeof selector === "function" ) { + + // ( types [, fn] ) + fn = selector; + selector = undefined; + } + if ( fn === false ) { + fn = returnFalse; + } + return this.each( function() { + jQuery.event.remove( this, types, fn, selector ); + } ); + } +} ); + + +var + + /* eslint-disable max-len */ + + // See https://github.com/eslint/eslint/issues/3229 + rxhtmlTag = /<(?!area|br|col|embed|hr|img|input|link|meta|param)(([a-z][^\/\0>\x20\t\r\n\f]*)[^>]*)\/>/gi, + + /* eslint-enable */ + + // Support: IE <=10 - 11, Edge 12 - 13 + // In IE/Edge using regex groups here causes severe slowdowns. + // See https://connect.microsoft.com/IE/feedback/details/1736512/ + rnoInnerhtml = /\s*$/g; + +// Prefer a tbody over its parent table for containing new rows +function manipulationTarget( elem, content ) { + if ( nodeName( elem, "table" ) && + nodeName( content.nodeType !== 11 ? content : content.firstChild, "tr" ) ) { + + return jQuery( ">tbody", elem )[ 0 ] || elem; + } + + return elem; +} + +// Replace/restore the type attribute of script elements for safe DOM manipulation +function disableScript( elem ) { + elem.type = ( elem.getAttribute( "type" ) !== null ) + "/" + elem.type; + return elem; +} +function restoreScript( elem ) { + var match = rscriptTypeMasked.exec( elem.type ); + + if ( match ) { + elem.type = match[ 1 ]; + } else { + elem.removeAttribute( "type" ); + } + + return elem; +} + +function cloneCopyEvent( src, dest ) { + var i, l, type, pdataOld, pdataCur, udataOld, udataCur, events; + + if ( dest.nodeType !== 1 ) { + return; + } + + // 1. Copy private data: events, handlers, etc. + if ( dataPriv.hasData( src ) ) { + pdataOld = dataPriv.access( src ); + pdataCur = dataPriv.set( dest, pdataOld ); + events = pdataOld.events; + + if ( events ) { + delete pdataCur.handle; + pdataCur.events = {}; + + for ( type in events ) { + for ( i = 0, l = events[ type ].length; i < l; i++ ) { + jQuery.event.add( dest, type, events[ type ][ i ] ); + } + } + } + } + + // 2. Copy user data + if ( dataUser.hasData( src ) ) { + udataOld = dataUser.access( src ); + udataCur = jQuery.extend( {}, udataOld ); + + dataUser.set( dest, udataCur ); + } +} + +// Fix IE bugs, see support tests +function fixInput( src, dest ) { + var nodeName = dest.nodeName.toLowerCase(); + + // Fails to persist the checked state of a cloned checkbox or radio button. + if ( nodeName === "input" && rcheckableType.test( src.type ) ) { + dest.checked = src.checked; + + // Fails to return the selected option to the default selected state when cloning options + } else if ( nodeName === "input" || nodeName === "textarea" ) { + dest.defaultValue = src.defaultValue; + } +} + +function domManip( collection, args, callback, ignored ) { + + // Flatten any nested arrays + args = concat.apply( [], args ); + + var fragment, first, scripts, hasScripts, node, doc, + i = 0, + l = collection.length, + iNoClone = l - 1, + value = args[ 0 ], + isFunction = jQuery.isFunction( value ); + + // We can't cloneNode fragments that contain checked, in WebKit + if ( isFunction || + ( l > 1 && typeof value === "string" && + !support.checkClone && rchecked.test( value ) ) ) { + return collection.each( function( index ) { + var self = collection.eq( index ); + if ( isFunction ) { + args[ 0 ] = value.call( this, index, self.html() ); + } + domManip( self, args, callback, ignored ); + } ); + } + + if ( l ) { + fragment = buildFragment( args, collection[ 0 ].ownerDocument, false, collection, ignored ); + first = fragment.firstChild; + + if ( fragment.childNodes.length === 1 ) { + fragment = first; + } + + // Require either new content or an interest in ignored elements to invoke the callback + if ( first || ignored ) { + scripts = jQuery.map( getAll( fragment, "script" ), disableScript ); + hasScripts = scripts.length; + + // Use the original fragment for the last item + // instead of the first because it can end up + // being emptied incorrectly in certain situations (#8070). + for ( ; i < l; i++ ) { + node = fragment; + + if ( i !== iNoClone ) { + node = jQuery.clone( node, true, true ); + + // Keep references to cloned scripts for later restoration + if ( hasScripts ) { + + // Support: Android <=4.0 only, PhantomJS 1 only + // push.apply(_, arraylike) throws on ancient WebKit + jQuery.merge( scripts, getAll( node, "script" ) ); + } + } + + callback.call( collection[ i ], node, i ); + } + + if ( hasScripts ) { + doc = scripts[ scripts.length - 1 ].ownerDocument; + + // Reenable scripts + jQuery.map( scripts, restoreScript ); + + // Evaluate executable scripts on first document insertion + for ( i = 0; i < hasScripts; i++ ) { + node = scripts[ i ]; + if ( rscriptType.test( node.type || "" ) && + !dataPriv.access( node, "globalEval" ) && + jQuery.contains( doc, node ) ) { + + if ( node.src ) { + + // Optional AJAX dependency, but won't run scripts if not present + if ( jQuery._evalUrl ) { + jQuery._evalUrl( node.src ); + } + } else { + DOMEval( node.textContent.replace( rcleanScript, "" ), doc ); + } + } + } + } + } + } + + return collection; +} + +function remove( elem, selector, keepData ) { + var node, + nodes = selector ? jQuery.filter( selector, elem ) : elem, + i = 0; + + for ( ; ( node = nodes[ i ] ) != null; i++ ) { + if ( !keepData && node.nodeType === 1 ) { + jQuery.cleanData( getAll( node ) ); + } + + if ( node.parentNode ) { + if ( keepData && jQuery.contains( node.ownerDocument, node ) ) { + setGlobalEval( getAll( node, "script" ) ); + } + node.parentNode.removeChild( node ); + } + } + + return elem; +} + +jQuery.extend( { + htmlPrefilter: function( html ) { + return html.replace( rxhtmlTag, "<$1>" ); + }, + + clone: function( elem, dataAndEvents, deepDataAndEvents ) { + var i, l, srcElements, destElements, + clone = elem.cloneNode( true ), + inPage = jQuery.contains( elem.ownerDocument, elem ); + + // Fix IE cloning issues + if ( !support.noCloneChecked && ( elem.nodeType === 1 || elem.nodeType === 11 ) && + !jQuery.isXMLDoc( elem ) ) { + + // We eschew Sizzle here for performance reasons: https://jsperf.com/getall-vs-sizzle/2 + destElements = getAll( clone ); + srcElements = getAll( elem ); + + for ( i = 0, l = srcElements.length; i < l; i++ ) { + fixInput( srcElements[ i ], destElements[ i ] ); + } + } + + // Copy the events from the original to the clone + if ( dataAndEvents ) { + if ( deepDataAndEvents ) { + srcElements = srcElements || getAll( elem ); + destElements = destElements || getAll( clone ); + + for ( i = 0, l = srcElements.length; i < l; i++ ) { + cloneCopyEvent( srcElements[ i ], destElements[ i ] ); + } + } else { + cloneCopyEvent( elem, clone ); + } + } + + // Preserve script evaluation history + destElements = getAll( clone, "script" ); + if ( destElements.length > 0 ) { + setGlobalEval( destElements, !inPage && getAll( elem, "script" ) ); + } + + // Return the cloned set + return clone; + }, + + cleanData: function( elems ) { + var data, elem, type, + special = jQuery.event.special, + i = 0; + + for ( ; ( elem = elems[ i ] ) !== undefined; i++ ) { + if ( acceptData( elem ) ) { + if ( ( data = elem[ dataPriv.expando ] ) ) { + if ( data.events ) { + for ( type in data.events ) { + if ( special[ type ] ) { + jQuery.event.remove( elem, type ); + + // This is a shortcut to avoid jQuery.event.remove's overhead + } else { + jQuery.removeEvent( elem, type, data.handle ); + } + } + } + + // Support: Chrome <=35 - 45+ + // Assign undefined instead of using delete, see Data#remove + elem[ dataPriv.expando ] = undefined; + } + if ( elem[ dataUser.expando ] ) { + + // Support: Chrome <=35 - 45+ + // Assign undefined instead of using delete, see Data#remove + elem[ dataUser.expando ] = undefined; + } + } + } + } +} ); + +jQuery.fn.extend( { + detach: function( selector ) { + return remove( this, selector, true ); + }, + + remove: function( selector ) { + return remove( this, selector ); + }, + + text: function( value ) { + return access( this, function( value ) { + return value === undefined ? + jQuery.text( this ) : + this.empty().each( function() { + if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { + this.textContent = value; + } + } ); + }, null, value, arguments.length ); + }, + + append: function() { + return domManip( this, arguments, function( elem ) { + if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { + var target = manipulationTarget( this, elem ); + target.appendChild( elem ); + } + } ); + }, + + prepend: function() { + return domManip( this, arguments, function( elem ) { + if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { + var target = manipulationTarget( this, elem ); + target.insertBefore( elem, target.firstChild ); + } + } ); + }, + + before: function() { + return domManip( this, arguments, function( elem ) { + if ( this.parentNode ) { + this.parentNode.insertBefore( elem, this ); + } + } ); + }, + + after: function() { + return domManip( this, arguments, function( elem ) { + if ( this.parentNode ) { + this.parentNode.insertBefore( elem, this.nextSibling ); + } + } ); + }, + + empty: function() { + var elem, + i = 0; + + for ( ; ( elem = this[ i ] ) != null; i++ ) { + if ( elem.nodeType === 1 ) { + + // Prevent memory leaks + jQuery.cleanData( getAll( elem, false ) ); + + // Remove any remaining nodes + elem.textContent = ""; + } + } + + return this; + }, + + clone: function( dataAndEvents, deepDataAndEvents ) { + dataAndEvents = dataAndEvents == null ? false : dataAndEvents; + deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents; + + return this.map( function() { + return jQuery.clone( this, dataAndEvents, deepDataAndEvents ); + } ); + }, + + html: function( value ) { + return access( this, function( value ) { + var elem = this[ 0 ] || {}, + i = 0, + l = this.length; + + if ( value === undefined && elem.nodeType === 1 ) { + return elem.innerHTML; + } + + // See if we can take a shortcut and just use innerHTML + if ( typeof value === "string" && !rnoInnerhtml.test( value ) && + !wrapMap[ ( rtagName.exec( value ) || [ "", "" ] )[ 1 ].toLowerCase() ] ) { + + value = jQuery.htmlPrefilter( value ); + + try { + for ( ; i < l; i++ ) { + elem = this[ i ] || {}; + + // Remove element nodes and prevent memory leaks + if ( elem.nodeType === 1 ) { + jQuery.cleanData( getAll( elem, false ) ); + elem.innerHTML = value; + } + } + + elem = 0; + + // If using innerHTML throws an exception, use the fallback method + } catch ( e ) {} + } + + if ( elem ) { + this.empty().append( value ); + } + }, null, value, arguments.length ); + }, + + replaceWith: function() { + var ignored = []; + + // Make the changes, replacing each non-ignored context element with the new content + return domManip( this, arguments, function( elem ) { + var parent = this.parentNode; + + if ( jQuery.inArray( this, ignored ) < 0 ) { + jQuery.cleanData( getAll( this ) ); + if ( parent ) { + parent.replaceChild( elem, this ); + } + } + + // Force callback invocation + }, ignored ); + } +} ); + +jQuery.each( { + appendTo: "append", + prependTo: "prepend", + insertBefore: "before", + insertAfter: "after", + replaceAll: "replaceWith" +}, function( name, original ) { + jQuery.fn[ name ] = function( selector ) { + var elems, + ret = [], + insert = jQuery( selector ), + last = insert.length - 1, + i = 0; + + for ( ; i <= last; i++ ) { + elems = i === last ? this : this.clone( true ); + jQuery( insert[ i ] )[ original ]( elems ); + + // Support: Android <=4.0 only, PhantomJS 1 only + // .get() because push.apply(_, arraylike) throws on ancient WebKit + push.apply( ret, elems.get() ); + } + + return this.pushStack( ret ); + }; +} ); +var rmargin = ( /^margin/ ); + +var rnumnonpx = new RegExp( "^(" + pnum + ")(?!px)[a-z%]+$", "i" ); + +var getStyles = function( elem ) { + + // Support: IE <=11 only, Firefox <=30 (#15098, #14150) + // IE throws on elements created in popups + // FF meanwhile throws on frame elements through "defaultView.getComputedStyle" + var view = elem.ownerDocument.defaultView; + + if ( !view || !view.opener ) { + view = window; + } + + return view.getComputedStyle( elem ); + }; + + + +( function() { + + // Executing both pixelPosition & boxSizingReliable tests require only one layout + // so they're executed at the same time to save the second computation. + function computeStyleTests() { + + // This is a singleton, we need to execute it only once + if ( !div ) { + return; + } + + div.style.cssText = + "box-sizing:border-box;" + + "position:relative;display:block;" + + "margin:auto;border:1px;padding:1px;" + + "top:1%;width:50%"; + div.innerHTML = ""; + documentElement.appendChild( container ); + + var divStyle = window.getComputedStyle( div ); + pixelPositionVal = divStyle.top !== "1%"; + + // Support: Android 4.0 - 4.3 only, Firefox <=3 - 44 + reliableMarginLeftVal = divStyle.marginLeft === "2px"; + boxSizingReliableVal = divStyle.width === "4px"; + + // Support: Android 4.0 - 4.3 only + // Some styles come back with percentage values, even though they shouldn't + div.style.marginRight = "50%"; + pixelMarginRightVal = divStyle.marginRight === "4px"; + + documentElement.removeChild( container ); + + // Nullify the div so it wouldn't be stored in the memory and + // it will also be a sign that checks already performed + div = null; + } + + var pixelPositionVal, boxSizingReliableVal, pixelMarginRightVal, reliableMarginLeftVal, + container = document.createElement( "div" ), + div = document.createElement( "div" ); + + // Finish early in limited (non-browser) environments + if ( !div.style ) { + return; + } + + // Support: IE <=9 - 11 only + // Style of cloned element affects source element cloned (#8908) + div.style.backgroundClip = "content-box"; + div.cloneNode( true ).style.backgroundClip = ""; + support.clearCloneStyle = div.style.backgroundClip === "content-box"; + + container.style.cssText = "border:0;width:8px;height:0;top:0;left:-9999px;" + + "padding:0;margin-top:1px;position:absolute"; + container.appendChild( div ); + + jQuery.extend( support, { + pixelPosition: function() { + computeStyleTests(); + return pixelPositionVal; + }, + boxSizingReliable: function() { + computeStyleTests(); + return boxSizingReliableVal; + }, + pixelMarginRight: function() { + computeStyleTests(); + return pixelMarginRightVal; + }, + reliableMarginLeft: function() { + computeStyleTests(); + return reliableMarginLeftVal; + } + } ); +} )(); + + +function curCSS( elem, name, computed ) { + var width, minWidth, maxWidth, ret, + + // Support: Firefox 51+ + // Retrieving style before computed somehow + // fixes an issue with getting wrong values + // on detached elements + style = elem.style; + + computed = computed || getStyles( elem ); + + // getPropertyValue is needed for: + // .css('filter') (IE 9 only, #12537) + // .css('--customProperty) (#3144) + if ( computed ) { + ret = computed.getPropertyValue( name ) || computed[ name ]; + + if ( ret === "" && !jQuery.contains( elem.ownerDocument, elem ) ) { + ret = jQuery.style( elem, name ); + } + + // A tribute to the "awesome hack by Dean Edwards" + // Android Browser returns percentage for some values, + // but width seems to be reliably pixels. + // This is against the CSSOM draft spec: + // https://drafts.csswg.org/cssom/#resolved-values + if ( !support.pixelMarginRight() && rnumnonpx.test( ret ) && rmargin.test( name ) ) { + + // Remember the original values + width = style.width; + minWidth = style.minWidth; + maxWidth = style.maxWidth; + + // Put in the new values to get a computed value out + style.minWidth = style.maxWidth = style.width = ret; + ret = computed.width; + + // Revert the changed values + style.width = width; + style.minWidth = minWidth; + style.maxWidth = maxWidth; + } + } + + return ret !== undefined ? + + // Support: IE <=9 - 11 only + // IE returns zIndex value as an integer. + ret + "" : + ret; +} + + +function addGetHookIf( conditionFn, hookFn ) { + + // Define the hook, we'll check on the first run if it's really needed. + return { + get: function() { + if ( conditionFn() ) { + + // Hook not needed (or it's not possible to use it due + // to missing dependency), remove it. + delete this.get; + return; + } + + // Hook needed; redefine it so that the support test is not executed again. + return ( this.get = hookFn ).apply( this, arguments ); + } + }; +} + + +var + + // Swappable if display is none or starts with table + // except "table", "table-cell", or "table-caption" + // See here for display values: https://developer.mozilla.org/en-US/docs/CSS/display + rdisplayswap = /^(none|table(?!-c[ea]).+)/, + rcustomProp = /^--/, + cssShow = { position: "absolute", visibility: "hidden", display: "block" }, + cssNormalTransform = { + letterSpacing: "0", + fontWeight: "400" + }, + + cssPrefixes = [ "Webkit", "Moz", "ms" ], + emptyStyle = document.createElement( "div" ).style; + +// Return a css property mapped to a potentially vendor prefixed property +function vendorPropName( name ) { + + // Shortcut for names that are not vendor prefixed + if ( name in emptyStyle ) { + return name; + } + + // Check for vendor prefixed names + var capName = name[ 0 ].toUpperCase() + name.slice( 1 ), + i = cssPrefixes.length; + + while ( i-- ) { + name = cssPrefixes[ i ] + capName; + if ( name in emptyStyle ) { + return name; + } + } +} + +// Return a property mapped along what jQuery.cssProps suggests or to +// a vendor prefixed property. +function finalPropName( name ) { + var ret = jQuery.cssProps[ name ]; + if ( !ret ) { + ret = jQuery.cssProps[ name ] = vendorPropName( name ) || name; + } + return ret; +} + +function setPositiveNumber( elem, value, subtract ) { + + // Any relative (+/-) values have already been + // normalized at this point + var matches = rcssNum.exec( value ); + return matches ? + + // Guard against undefined "subtract", e.g., when used as in cssHooks + Math.max( 0, matches[ 2 ] - ( subtract || 0 ) ) + ( matches[ 3 ] || "px" ) : + value; +} + +function augmentWidthOrHeight( elem, name, extra, isBorderBox, styles ) { + var i, + val = 0; + + // If we already have the right measurement, avoid augmentation + if ( extra === ( isBorderBox ? "border" : "content" ) ) { + i = 4; + + // Otherwise initialize for horizontal or vertical properties + } else { + i = name === "width" ? 1 : 0; + } + + for ( ; i < 4; i += 2 ) { + + // Both box models exclude margin, so add it if we want it + if ( extra === "margin" ) { + val += jQuery.css( elem, extra + cssExpand[ i ], true, styles ); + } + + if ( isBorderBox ) { + + // border-box includes padding, so remove it if we want content + if ( extra === "content" ) { + val -= jQuery.css( elem, "padding" + cssExpand[ i ], true, styles ); + } + + // At this point, extra isn't border nor margin, so remove border + if ( extra !== "margin" ) { + val -= jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles ); + } + } else { + + // At this point, extra isn't content, so add padding + val += jQuery.css( elem, "padding" + cssExpand[ i ], true, styles ); + + // At this point, extra isn't content nor padding, so add border + if ( extra !== "padding" ) { + val += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles ); + } + } + } + + return val; +} + +function getWidthOrHeight( elem, name, extra ) { + + // Start with computed style + var valueIsBorderBox, + styles = getStyles( elem ), + val = curCSS( elem, name, styles ), + isBorderBox = jQuery.css( elem, "boxSizing", false, styles ) === "border-box"; + + // Computed unit is not pixels. Stop here and return. + if ( rnumnonpx.test( val ) ) { + return val; + } + + // Check for style in case a browser which returns unreliable values + // for getComputedStyle silently falls back to the reliable elem.style + valueIsBorderBox = isBorderBox && + ( support.boxSizingReliable() || val === elem.style[ name ] ); + + // Fall back to offsetWidth/Height when value is "auto" + // This happens for inline elements with no explicit setting (gh-3571) + if ( val === "auto" ) { + val = elem[ "offset" + name[ 0 ].toUpperCase() + name.slice( 1 ) ]; + } + + // Normalize "", auto, and prepare for extra + val = parseFloat( val ) || 0; + + // Use the active box-sizing model to add/subtract irrelevant styles + return ( val + + augmentWidthOrHeight( + elem, + name, + extra || ( isBorderBox ? "border" : "content" ), + valueIsBorderBox, + styles + ) + ) + "px"; +} + +jQuery.extend( { + + // Add in style property hooks for overriding the default + // behavior of getting and setting a style property + cssHooks: { + opacity: { + get: function( elem, computed ) { + if ( computed ) { + + // We should always get a number back from opacity + var ret = curCSS( elem, "opacity" ); + return ret === "" ? "1" : ret; + } + } + } + }, + + // Don't automatically add "px" to these possibly-unitless properties + cssNumber: { + "animationIterationCount": true, + "columnCount": true, + "fillOpacity": true, + "flexGrow": true, + "flexShrink": true, + "fontWeight": true, + "lineHeight": true, + "opacity": true, + "order": true, + "orphans": true, + "widows": true, + "zIndex": true, + "zoom": true + }, + + // Add in properties whose names you wish to fix before + // setting or getting the value + cssProps: { + "float": "cssFloat" + }, + + // Get and set the style property on a DOM Node + style: function( elem, name, value, extra ) { + + // Don't set styles on text and comment nodes + if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 || !elem.style ) { + return; + } + + // Make sure that we're working with the right name + var ret, type, hooks, + origName = jQuery.camelCase( name ), + isCustomProp = rcustomProp.test( name ), + style = elem.style; + + // Make sure that we're working with the right name. We don't + // want to query the value if it is a CSS custom property + // since they are user-defined. + if ( !isCustomProp ) { + name = finalPropName( origName ); + } + + // Gets hook for the prefixed version, then unprefixed version + hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ]; + + // Check if we're setting a value + if ( value !== undefined ) { + type = typeof value; + + // Convert "+=" or "-=" to relative numbers (#7345) + if ( type === "string" && ( ret = rcssNum.exec( value ) ) && ret[ 1 ] ) { + value = adjustCSS( elem, name, ret ); + + // Fixes bug #9237 + type = "number"; + } + + // Make sure that null and NaN values aren't set (#7116) + if ( value == null || value !== value ) { + return; + } + + // If a number was passed in, add the unit (except for certain CSS properties) + if ( type === "number" ) { + value += ret && ret[ 3 ] || ( jQuery.cssNumber[ origName ] ? "" : "px" ); + } + + // background-* props affect original clone's values + if ( !support.clearCloneStyle && value === "" && name.indexOf( "background" ) === 0 ) { + style[ name ] = "inherit"; + } + + // If a hook was provided, use that value, otherwise just set the specified value + if ( !hooks || !( "set" in hooks ) || + ( value = hooks.set( elem, value, extra ) ) !== undefined ) { + + if ( isCustomProp ) { + style.setProperty( name, value ); + } else { + style[ name ] = value; + } + } + + } else { + + // If a hook was provided get the non-computed value from there + if ( hooks && "get" in hooks && + ( ret = hooks.get( elem, false, extra ) ) !== undefined ) { + + return ret; + } + + // Otherwise just get the value from the style object + return style[ name ]; + } + }, + + css: function( elem, name, extra, styles ) { + var val, num, hooks, + origName = jQuery.camelCase( name ), + isCustomProp = rcustomProp.test( name ); + + // Make sure that we're working with the right name. We don't + // want to modify the value if it is a CSS custom property + // since they are user-defined. + if ( !isCustomProp ) { + name = finalPropName( origName ); + } + + // Try prefixed name followed by the unprefixed name + hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ]; + + // If a hook was provided get the computed value from there + if ( hooks && "get" in hooks ) { + val = hooks.get( elem, true, extra ); + } + + // Otherwise, if a way to get the computed value exists, use that + if ( val === undefined ) { + val = curCSS( elem, name, styles ); + } + + // Convert "normal" to computed value + if ( val === "normal" && name in cssNormalTransform ) { + val = cssNormalTransform[ name ]; + } + + // Make numeric if forced or a qualifier was provided and val looks numeric + if ( extra === "" || extra ) { + num = parseFloat( val ); + return extra === true || isFinite( num ) ? num || 0 : val; + } + + return val; + } +} ); + +jQuery.each( [ "height", "width" ], function( i, name ) { + jQuery.cssHooks[ name ] = { + get: function( elem, computed, extra ) { + if ( computed ) { + + // Certain elements can have dimension info if we invisibly show them + // but it must have a current display style that would benefit + return rdisplayswap.test( jQuery.css( elem, "display" ) ) && + + // Support: Safari 8+ + // Table columns in Safari have non-zero offsetWidth & zero + // getBoundingClientRect().width unless display is changed. + // Support: IE <=11 only + // Running getBoundingClientRect on a disconnected node + // in IE throws an error. + ( !elem.getClientRects().length || !elem.getBoundingClientRect().width ) ? + swap( elem, cssShow, function() { + return getWidthOrHeight( elem, name, extra ); + } ) : + getWidthOrHeight( elem, name, extra ); + } + }, + + set: function( elem, value, extra ) { + var matches, + styles = extra && getStyles( elem ), + subtract = extra && augmentWidthOrHeight( + elem, + name, + extra, + jQuery.css( elem, "boxSizing", false, styles ) === "border-box", + styles + ); + + // Convert to pixels if value adjustment is needed + if ( subtract && ( matches = rcssNum.exec( value ) ) && + ( matches[ 3 ] || "px" ) !== "px" ) { + + elem.style[ name ] = value; + value = jQuery.css( elem, name ); + } + + return setPositiveNumber( elem, value, subtract ); + } + }; +} ); + +jQuery.cssHooks.marginLeft = addGetHookIf( support.reliableMarginLeft, + function( elem, computed ) { + if ( computed ) { + return ( parseFloat( curCSS( elem, "marginLeft" ) ) || + elem.getBoundingClientRect().left - + swap( elem, { marginLeft: 0 }, function() { + return elem.getBoundingClientRect().left; + } ) + ) + "px"; + } + } +); + +// These hooks are used by animate to expand properties +jQuery.each( { + margin: "", + padding: "", + border: "Width" +}, function( prefix, suffix ) { + jQuery.cssHooks[ prefix + suffix ] = { + expand: function( value ) { + var i = 0, + expanded = {}, + + // Assumes a single number if not a string + parts = typeof value === "string" ? value.split( " " ) : [ value ]; + + for ( ; i < 4; i++ ) { + expanded[ prefix + cssExpand[ i ] + suffix ] = + parts[ i ] || parts[ i - 2 ] || parts[ 0 ]; + } + + return expanded; + } + }; + + if ( !rmargin.test( prefix ) ) { + jQuery.cssHooks[ prefix + suffix ].set = setPositiveNumber; + } +} ); + +jQuery.fn.extend( { + css: function( name, value ) { + return access( this, function( elem, name, value ) { + var styles, len, + map = {}, + i = 0; + + if ( Array.isArray( name ) ) { + styles = getStyles( elem ); + len = name.length; + + for ( ; i < len; i++ ) { + map[ name[ i ] ] = jQuery.css( elem, name[ i ], false, styles ); + } + + return map; + } + + return value !== undefined ? + jQuery.style( elem, name, value ) : + jQuery.css( elem, name ); + }, name, value, arguments.length > 1 ); + } +} ); + + +function Tween( elem, options, prop, end, easing ) { + return new Tween.prototype.init( elem, options, prop, end, easing ); +} +jQuery.Tween = Tween; + +Tween.prototype = { + constructor: Tween, + init: function( elem, options, prop, end, easing, unit ) { + this.elem = elem; + this.prop = prop; + this.easing = easing || jQuery.easing._default; + this.options = options; + this.start = this.now = this.cur(); + this.end = end; + this.unit = unit || ( jQuery.cssNumber[ prop ] ? "" : "px" ); + }, + cur: function() { + var hooks = Tween.propHooks[ this.prop ]; + + return hooks && hooks.get ? + hooks.get( this ) : + Tween.propHooks._default.get( this ); + }, + run: function( percent ) { + var eased, + hooks = Tween.propHooks[ this.prop ]; + + if ( this.options.duration ) { + this.pos = eased = jQuery.easing[ this.easing ]( + percent, this.options.duration * percent, 0, 1, this.options.duration + ); + } else { + this.pos = eased = percent; + } + this.now = ( this.end - this.start ) * eased + this.start; + + if ( this.options.step ) { + this.options.step.call( this.elem, this.now, this ); + } + + if ( hooks && hooks.set ) { + hooks.set( this ); + } else { + Tween.propHooks._default.set( this ); + } + return this; + } +}; + +Tween.prototype.init.prototype = Tween.prototype; + +Tween.propHooks = { + _default: { + get: function( tween ) { + var result; + + // Use a property on the element directly when it is not a DOM element, + // or when there is no matching style property that exists. + if ( tween.elem.nodeType !== 1 || + tween.elem[ tween.prop ] != null && tween.elem.style[ tween.prop ] == null ) { + return tween.elem[ tween.prop ]; + } + + // Passing an empty string as a 3rd parameter to .css will automatically + // attempt a parseFloat and fallback to a string if the parse fails. + // Simple values such as "10px" are parsed to Float; + // complex values such as "rotate(1rad)" are returned as-is. + result = jQuery.css( tween.elem, tween.prop, "" ); + + // Empty strings, null, undefined and "auto" are converted to 0. + return !result || result === "auto" ? 0 : result; + }, + set: function( tween ) { + + // Use step hook for back compat. + // Use cssHook if its there. + // Use .style if available and use plain properties where available. + if ( jQuery.fx.step[ tween.prop ] ) { + jQuery.fx.step[ tween.prop ]( tween ); + } else if ( tween.elem.nodeType === 1 && + ( tween.elem.style[ jQuery.cssProps[ tween.prop ] ] != null || + jQuery.cssHooks[ tween.prop ] ) ) { + jQuery.style( tween.elem, tween.prop, tween.now + tween.unit ); + } else { + tween.elem[ tween.prop ] = tween.now; + } + } + } +}; + +// Support: IE <=9 only +// Panic based approach to setting things on disconnected nodes +Tween.propHooks.scrollTop = Tween.propHooks.scrollLeft = { + set: function( tween ) { + if ( tween.elem.nodeType && tween.elem.parentNode ) { + tween.elem[ tween.prop ] = tween.now; + } + } +}; + +jQuery.easing = { + linear: function( p ) { + return p; + }, + swing: function( p ) { + return 0.5 - Math.cos( p * Math.PI ) / 2; + }, + _default: "swing" +}; + +jQuery.fx = Tween.prototype.init; + +// Back compat <1.8 extension point +jQuery.fx.step = {}; + + + + +var + fxNow, inProgress, + rfxtypes = /^(?:toggle|show|hide)$/, + rrun = /queueHooks$/; + +function schedule() { + if ( inProgress ) { + if ( document.hidden === false && window.requestAnimationFrame ) { + window.requestAnimationFrame( schedule ); + } else { + window.setTimeout( schedule, jQuery.fx.interval ); + } + + jQuery.fx.tick(); + } +} + +// Animations created synchronously will run synchronously +function createFxNow() { + window.setTimeout( function() { + fxNow = undefined; + } ); + return ( fxNow = jQuery.now() ); +} + +// Generate parameters to create a standard animation +function genFx( type, includeWidth ) { + var which, + i = 0, + attrs = { height: type }; + + // If we include width, step value is 1 to do all cssExpand values, + // otherwise step value is 2 to skip over Left and Right + includeWidth = includeWidth ? 1 : 0; + for ( ; i < 4; i += 2 - includeWidth ) { + which = cssExpand[ i ]; + attrs[ "margin" + which ] = attrs[ "padding" + which ] = type; + } + + if ( includeWidth ) { + attrs.opacity = attrs.width = type; + } + + return attrs; +} + +function createTween( value, prop, animation ) { + var tween, + collection = ( Animation.tweeners[ prop ] || [] ).concat( Animation.tweeners[ "*" ] ), + index = 0, + length = collection.length; + for ( ; index < length; index++ ) { + if ( ( tween = collection[ index ].call( animation, prop, value ) ) ) { + + // We're done with this property + return tween; + } + } +} + +function defaultPrefilter( elem, props, opts ) { + var prop, value, toggle, hooks, oldfire, propTween, restoreDisplay, display, + isBox = "width" in props || "height" in props, + anim = this, + orig = {}, + style = elem.style, + hidden = elem.nodeType && isHiddenWithinTree( elem ), + dataShow = dataPriv.get( elem, "fxshow" ); + + // Queue-skipping animations hijack the fx hooks + if ( !opts.queue ) { + hooks = jQuery._queueHooks( elem, "fx" ); + if ( hooks.unqueued == null ) { + hooks.unqueued = 0; + oldfire = hooks.empty.fire; + hooks.empty.fire = function() { + if ( !hooks.unqueued ) { + oldfire(); + } + }; + } + hooks.unqueued++; + + anim.always( function() { + + // Ensure the complete handler is called before this completes + anim.always( function() { + hooks.unqueued--; + if ( !jQuery.queue( elem, "fx" ).length ) { + hooks.empty.fire(); + } + } ); + } ); + } + + // Detect show/hide animations + for ( prop in props ) { + value = props[ prop ]; + if ( rfxtypes.test( value ) ) { + delete props[ prop ]; + toggle = toggle || value === "toggle"; + if ( value === ( hidden ? "hide" : "show" ) ) { + + // Pretend to be hidden if this is a "show" and + // there is still data from a stopped show/hide + if ( value === "show" && dataShow && dataShow[ prop ] !== undefined ) { + hidden = true; + + // Ignore all other no-op show/hide data + } else { + continue; + } + } + orig[ prop ] = dataShow && dataShow[ prop ] || jQuery.style( elem, prop ); + } + } + + // Bail out if this is a no-op like .hide().hide() + propTween = !jQuery.isEmptyObject( props ); + if ( !propTween && jQuery.isEmptyObject( orig ) ) { + return; + } + + // Restrict "overflow" and "display" styles during box animations + if ( isBox && elem.nodeType === 1 ) { + + // Support: IE <=9 - 11, Edge 12 - 13 + // Record all 3 overflow attributes because IE does not infer the shorthand + // from identically-valued overflowX and overflowY + opts.overflow = [ style.overflow, style.overflowX, style.overflowY ]; + + // Identify a display type, preferring old show/hide data over the CSS cascade + restoreDisplay = dataShow && dataShow.display; + if ( restoreDisplay == null ) { + restoreDisplay = dataPriv.get( elem, "display" ); + } + display = jQuery.css( elem, "display" ); + if ( display === "none" ) { + if ( restoreDisplay ) { + display = restoreDisplay; + } else { + + // Get nonempty value(s) by temporarily forcing visibility + showHide( [ elem ], true ); + restoreDisplay = elem.style.display || restoreDisplay; + display = jQuery.css( elem, "display" ); + showHide( [ elem ] ); + } + } + + // Animate inline elements as inline-block + if ( display === "inline" || display === "inline-block" && restoreDisplay != null ) { + if ( jQuery.css( elem, "float" ) === "none" ) { + + // Restore the original display value at the end of pure show/hide animations + if ( !propTween ) { + anim.done( function() { + style.display = restoreDisplay; + } ); + if ( restoreDisplay == null ) { + display = style.display; + restoreDisplay = display === "none" ? "" : display; + } + } + style.display = "inline-block"; + } + } + } + + if ( opts.overflow ) { + style.overflow = "hidden"; + anim.always( function() { + style.overflow = opts.overflow[ 0 ]; + style.overflowX = opts.overflow[ 1 ]; + style.overflowY = opts.overflow[ 2 ]; + } ); + } + + // Implement show/hide animations + propTween = false; + for ( prop in orig ) { + + // General show/hide setup for this element animation + if ( !propTween ) { + if ( dataShow ) { + if ( "hidden" in dataShow ) { + hidden = dataShow.hidden; + } + } else { + dataShow = dataPriv.access( elem, "fxshow", { display: restoreDisplay } ); + } + + // Store hidden/visible for toggle so `.stop().toggle()` "reverses" + if ( toggle ) { + dataShow.hidden = !hidden; + } + + // Show elements before animating them + if ( hidden ) { + showHide( [ elem ], true ); + } + + /* eslint-disable no-loop-func */ + + anim.done( function() { + + /* eslint-enable no-loop-func */ + + // The final step of a "hide" animation is actually hiding the element + if ( !hidden ) { + showHide( [ elem ] ); + } + dataPriv.remove( elem, "fxshow" ); + for ( prop in orig ) { + jQuery.style( elem, prop, orig[ prop ] ); + } + } ); + } + + // Per-property setup + propTween = createTween( hidden ? dataShow[ prop ] : 0, prop, anim ); + if ( !( prop in dataShow ) ) { + dataShow[ prop ] = propTween.start; + if ( hidden ) { + propTween.end = propTween.start; + propTween.start = 0; + } + } + } +} + +function propFilter( props, specialEasing ) { + var index, name, easing, value, hooks; + + // camelCase, specialEasing and expand cssHook pass + for ( index in props ) { + name = jQuery.camelCase( index ); + easing = specialEasing[ name ]; + value = props[ index ]; + if ( Array.isArray( value ) ) { + easing = value[ 1 ]; + value = props[ index ] = value[ 0 ]; + } + + if ( index !== name ) { + props[ name ] = value; + delete props[ index ]; + } + + hooks = jQuery.cssHooks[ name ]; + if ( hooks && "expand" in hooks ) { + value = hooks.expand( value ); + delete props[ name ]; + + // Not quite $.extend, this won't overwrite existing keys. + // Reusing 'index' because we have the correct "name" + for ( index in value ) { + if ( !( index in props ) ) { + props[ index ] = value[ index ]; + specialEasing[ index ] = easing; + } + } + } else { + specialEasing[ name ] = easing; + } + } +} + +function Animation( elem, properties, options ) { + var result, + stopped, + index = 0, + length = Animation.prefilters.length, + deferred = jQuery.Deferred().always( function() { + + // Don't match elem in the :animated selector + delete tick.elem; + } ), + tick = function() { + if ( stopped ) { + return false; + } + var currentTime = fxNow || createFxNow(), + remaining = Math.max( 0, animation.startTime + animation.duration - currentTime ), + + // Support: Android 2.3 only + // Archaic crash bug won't allow us to use `1 - ( 0.5 || 0 )` (#12497) + temp = remaining / animation.duration || 0, + percent = 1 - temp, + index = 0, + length = animation.tweens.length; + + for ( ; index < length; index++ ) { + animation.tweens[ index ].run( percent ); + } + + deferred.notifyWith( elem, [ animation, percent, remaining ] ); + + // If there's more to do, yield + if ( percent < 1 && length ) { + return remaining; + } + + // If this was an empty animation, synthesize a final progress notification + if ( !length ) { + deferred.notifyWith( elem, [ animation, 1, 0 ] ); + } + + // Resolve the animation and report its conclusion + deferred.resolveWith( elem, [ animation ] ); + return false; + }, + animation = deferred.promise( { + elem: elem, + props: jQuery.extend( {}, properties ), + opts: jQuery.extend( true, { + specialEasing: {}, + easing: jQuery.easing._default + }, options ), + originalProperties: properties, + originalOptions: options, + startTime: fxNow || createFxNow(), + duration: options.duration, + tweens: [], + createTween: function( prop, end ) { + var tween = jQuery.Tween( elem, animation.opts, prop, end, + animation.opts.specialEasing[ prop ] || animation.opts.easing ); + animation.tweens.push( tween ); + return tween; + }, + stop: function( gotoEnd ) { + var index = 0, + + // If we are going to the end, we want to run all the tweens + // otherwise we skip this part + length = gotoEnd ? animation.tweens.length : 0; + if ( stopped ) { + return this; + } + stopped = true; + for ( ; index < length; index++ ) { + animation.tweens[ index ].run( 1 ); + } + + // Resolve when we played the last frame; otherwise, reject + if ( gotoEnd ) { + deferred.notifyWith( elem, [ animation, 1, 0 ] ); + deferred.resolveWith( elem, [ animation, gotoEnd ] ); + } else { + deferred.rejectWith( elem, [ animation, gotoEnd ] ); + } + return this; + } + } ), + props = animation.props; + + propFilter( props, animation.opts.specialEasing ); + + for ( ; index < length; index++ ) { + result = Animation.prefilters[ index ].call( animation, elem, props, animation.opts ); + if ( result ) { + if ( jQuery.isFunction( result.stop ) ) { + jQuery._queueHooks( animation.elem, animation.opts.queue ).stop = + jQuery.proxy( result.stop, result ); + } + return result; + } + } + + jQuery.map( props, createTween, animation ); + + if ( jQuery.isFunction( animation.opts.start ) ) { + animation.opts.start.call( elem, animation ); + } + + // Attach callbacks from options + animation + .progress( animation.opts.progress ) + .done( animation.opts.done, animation.opts.complete ) + .fail( animation.opts.fail ) + .always( animation.opts.always ); + + jQuery.fx.timer( + jQuery.extend( tick, { + elem: elem, + anim: animation, + queue: animation.opts.queue + } ) + ); + + return animation; +} + +jQuery.Animation = jQuery.extend( Animation, { + + tweeners: { + "*": [ function( prop, value ) { + var tween = this.createTween( prop, value ); + adjustCSS( tween.elem, prop, rcssNum.exec( value ), tween ); + return tween; + } ] + }, + + tweener: function( props, callback ) { + if ( jQuery.isFunction( props ) ) { + callback = props; + props = [ "*" ]; + } else { + props = props.match( rnothtmlwhite ); + } + + var prop, + index = 0, + length = props.length; + + for ( ; index < length; index++ ) { + prop = props[ index ]; + Animation.tweeners[ prop ] = Animation.tweeners[ prop ] || []; + Animation.tweeners[ prop ].unshift( callback ); + } + }, + + prefilters: [ defaultPrefilter ], + + prefilter: function( callback, prepend ) { + if ( prepend ) { + Animation.prefilters.unshift( callback ); + } else { + Animation.prefilters.push( callback ); + } + } +} ); + +jQuery.speed = function( speed, easing, fn ) { + var opt = speed && typeof speed === "object" ? jQuery.extend( {}, speed ) : { + complete: fn || !fn && easing || + jQuery.isFunction( speed ) && speed, + duration: speed, + easing: fn && easing || easing && !jQuery.isFunction( easing ) && easing + }; + + // Go to the end state if fx are off + if ( jQuery.fx.off ) { + opt.duration = 0; + + } else { + if ( typeof opt.duration !== "number" ) { + if ( opt.duration in jQuery.fx.speeds ) { + opt.duration = jQuery.fx.speeds[ opt.duration ]; + + } else { + opt.duration = jQuery.fx.speeds._default; + } + } + } + + // Normalize opt.queue - true/undefined/null -> "fx" + if ( opt.queue == null || opt.queue === true ) { + opt.queue = "fx"; + } + + // Queueing + opt.old = opt.complete; + + opt.complete = function() { + if ( jQuery.isFunction( opt.old ) ) { + opt.old.call( this ); + } + + if ( opt.queue ) { + jQuery.dequeue( this, opt.queue ); + } + }; + + return opt; +}; + +jQuery.fn.extend( { + fadeTo: function( speed, to, easing, callback ) { + + // Show any hidden elements after setting opacity to 0 + return this.filter( isHiddenWithinTree ).css( "opacity", 0 ).show() + + // Animate to the value specified + .end().animate( { opacity: to }, speed, easing, callback ); + }, + animate: function( prop, speed, easing, callback ) { + var empty = jQuery.isEmptyObject( prop ), + optall = jQuery.speed( speed, easing, callback ), + doAnimation = function() { + + // Operate on a copy of prop so per-property easing won't be lost + var anim = Animation( this, jQuery.extend( {}, prop ), optall ); + + // Empty animations, or finishing resolves immediately + if ( empty || dataPriv.get( this, "finish" ) ) { + anim.stop( true ); + } + }; + doAnimation.finish = doAnimation; + + return empty || optall.queue === false ? + this.each( doAnimation ) : + this.queue( optall.queue, doAnimation ); + }, + stop: function( type, clearQueue, gotoEnd ) { + var stopQueue = function( hooks ) { + var stop = hooks.stop; + delete hooks.stop; + stop( gotoEnd ); + }; + + if ( typeof type !== "string" ) { + gotoEnd = clearQueue; + clearQueue = type; + type = undefined; + } + if ( clearQueue && type !== false ) { + this.queue( type || "fx", [] ); + } + + return this.each( function() { + var dequeue = true, + index = type != null && type + "queueHooks", + timers = jQuery.timers, + data = dataPriv.get( this ); + + if ( index ) { + if ( data[ index ] && data[ index ].stop ) { + stopQueue( data[ index ] ); + } + } else { + for ( index in data ) { + if ( data[ index ] && data[ index ].stop && rrun.test( index ) ) { + stopQueue( data[ index ] ); + } + } + } + + for ( index = timers.length; index--; ) { + if ( timers[ index ].elem === this && + ( type == null || timers[ index ].queue === type ) ) { + + timers[ index ].anim.stop( gotoEnd ); + dequeue = false; + timers.splice( index, 1 ); + } + } + + // Start the next in the queue if the last step wasn't forced. + // Timers currently will call their complete callbacks, which + // will dequeue but only if they were gotoEnd. + if ( dequeue || !gotoEnd ) { + jQuery.dequeue( this, type ); + } + } ); + }, + finish: function( type ) { + if ( type !== false ) { + type = type || "fx"; + } + return this.each( function() { + var index, + data = dataPriv.get( this ), + queue = data[ type + "queue" ], + hooks = data[ type + "queueHooks" ], + timers = jQuery.timers, + length = queue ? queue.length : 0; + + // Enable finishing flag on private data + data.finish = true; + + // Empty the queue first + jQuery.queue( this, type, [] ); + + if ( hooks && hooks.stop ) { + hooks.stop.call( this, true ); + } + + // Look for any active animations, and finish them + for ( index = timers.length; index--; ) { + if ( timers[ index ].elem === this && timers[ index ].queue === type ) { + timers[ index ].anim.stop( true ); + timers.splice( index, 1 ); + } + } + + // Look for any animations in the old queue and finish them + for ( index = 0; index < length; index++ ) { + if ( queue[ index ] && queue[ index ].finish ) { + queue[ index ].finish.call( this ); + } + } + + // Turn off finishing flag + delete data.finish; + } ); + } +} ); + +jQuery.each( [ "toggle", "show", "hide" ], function( i, name ) { + var cssFn = jQuery.fn[ name ]; + jQuery.fn[ name ] = function( speed, easing, callback ) { + return speed == null || typeof speed === "boolean" ? + cssFn.apply( this, arguments ) : + this.animate( genFx( name, true ), speed, easing, callback ); + }; +} ); + +// Generate shortcuts for custom animations +jQuery.each( { + slideDown: genFx( "show" ), + slideUp: genFx( "hide" ), + slideToggle: genFx( "toggle" ), + fadeIn: { opacity: "show" }, + fadeOut: { opacity: "hide" }, + fadeToggle: { opacity: "toggle" } +}, function( name, props ) { + jQuery.fn[ name ] = function( speed, easing, callback ) { + return this.animate( props, speed, easing, callback ); + }; +} ); + +jQuery.timers = []; +jQuery.fx.tick = function() { + var timer, + i = 0, + timers = jQuery.timers; + + fxNow = jQuery.now(); + + for ( ; i < timers.length; i++ ) { + timer = timers[ i ]; + + // Run the timer and safely remove it when done (allowing for external removal) + if ( !timer() && timers[ i ] === timer ) { + timers.splice( i--, 1 ); + } + } + + if ( !timers.length ) { + jQuery.fx.stop(); + } + fxNow = undefined; +}; + +jQuery.fx.timer = function( timer ) { + jQuery.timers.push( timer ); + jQuery.fx.start(); +}; + +jQuery.fx.interval = 13; +jQuery.fx.start = function() { + if ( inProgress ) { + return; + } + + inProgress = true; + schedule(); +}; + +jQuery.fx.stop = function() { + inProgress = null; +}; + +jQuery.fx.speeds = { + slow: 600, + fast: 200, + + // Default speed + _default: 400 +}; + + +// Based off of the plugin by Clint Helfers, with permission. +// https://web.archive.org/web/20100324014747/http://blindsignals.com/index.php/2009/07/jquery-delay/ +jQuery.fn.delay = function( time, type ) { + time = jQuery.fx ? jQuery.fx.speeds[ time ] || time : time; + type = type || "fx"; + + return this.queue( type, function( next, hooks ) { + var timeout = window.setTimeout( next, time ); + hooks.stop = function() { + window.clearTimeout( timeout ); + }; + } ); +}; + + +( function() { + var input = document.createElement( "input" ), + select = document.createElement( "select" ), + opt = select.appendChild( document.createElement( "option" ) ); + + input.type = "checkbox"; + + // Support: Android <=4.3 only + // Default value for a checkbox should be "on" + support.checkOn = input.value !== ""; + + // Support: IE <=11 only + // Must access selectedIndex to make default options select + support.optSelected = opt.selected; + + // Support: IE <=11 only + // An input loses its value after becoming a radio + input = document.createElement( "input" ); + input.value = "t"; + input.type = "radio"; + support.radioValue = input.value === "t"; +} )(); + + +var boolHook, + attrHandle = jQuery.expr.attrHandle; + +jQuery.fn.extend( { + attr: function( name, value ) { + return access( this, jQuery.attr, name, value, arguments.length > 1 ); + }, + + removeAttr: function( name ) { + return this.each( function() { + jQuery.removeAttr( this, name ); + } ); + } +} ); + +jQuery.extend( { + attr: function( elem, name, value ) { + var ret, hooks, + nType = elem.nodeType; + + // Don't get/set attributes on text, comment and attribute nodes + if ( nType === 3 || nType === 8 || nType === 2 ) { + return; + } + + // Fallback to prop when attributes are not supported + if ( typeof elem.getAttribute === "undefined" ) { + return jQuery.prop( elem, name, value ); + } + + // Attribute hooks are determined by the lowercase version + // Grab necessary hook if one is defined + if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) { + hooks = jQuery.attrHooks[ name.toLowerCase() ] || + ( jQuery.expr.match.bool.test( name ) ? boolHook : undefined ); + } + + if ( value !== undefined ) { + if ( value === null ) { + jQuery.removeAttr( elem, name ); + return; + } + + if ( hooks && "set" in hooks && + ( ret = hooks.set( elem, value, name ) ) !== undefined ) { + return ret; + } + + elem.setAttribute( name, value + "" ); + return value; + } + + if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) { + return ret; + } + + ret = jQuery.find.attr( elem, name ); + + // Non-existent attributes return null, we normalize to undefined + return ret == null ? undefined : ret; + }, + + attrHooks: { + type: { + set: function( elem, value ) { + if ( !support.radioValue && value === "radio" && + nodeName( elem, "input" ) ) { + var val = elem.value; + elem.setAttribute( "type", value ); + if ( val ) { + elem.value = val; + } + return value; + } + } + } + }, + + removeAttr: function( elem, value ) { + var name, + i = 0, + + // Attribute names can contain non-HTML whitespace characters + // https://html.spec.whatwg.org/multipage/syntax.html#attributes-2 + attrNames = value && value.match( rnothtmlwhite ); + + if ( attrNames && elem.nodeType === 1 ) { + while ( ( name = attrNames[ i++ ] ) ) { + elem.removeAttribute( name ); + } + } + } +} ); + +// Hooks for boolean attributes +boolHook = { + set: function( elem, value, name ) { + if ( value === false ) { + + // Remove boolean attributes when set to false + jQuery.removeAttr( elem, name ); + } else { + elem.setAttribute( name, name ); + } + return name; + } +}; + +jQuery.each( jQuery.expr.match.bool.source.match( /\w+/g ), function( i, name ) { + var getter = attrHandle[ name ] || jQuery.find.attr; + + attrHandle[ name ] = function( elem, name, isXML ) { + var ret, handle, + lowercaseName = name.toLowerCase(); + + if ( !isXML ) { + + // Avoid an infinite loop by temporarily removing this function from the getter + handle = attrHandle[ lowercaseName ]; + attrHandle[ lowercaseName ] = ret; + ret = getter( elem, name, isXML ) != null ? + lowercaseName : + null; + attrHandle[ lowercaseName ] = handle; + } + return ret; + }; +} ); + + + + +var rfocusable = /^(?:input|select|textarea|button)$/i, + rclickable = /^(?:a|area)$/i; + +jQuery.fn.extend( { + prop: function( name, value ) { + return access( this, jQuery.prop, name, value, arguments.length > 1 ); + }, + + removeProp: function( name ) { + return this.each( function() { + delete this[ jQuery.propFix[ name ] || name ]; + } ); + } +} ); + +jQuery.extend( { + prop: function( elem, name, value ) { + var ret, hooks, + nType = elem.nodeType; + + // Don't get/set properties on text, comment and attribute nodes + if ( nType === 3 || nType === 8 || nType === 2 ) { + return; + } + + if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) { + + // Fix name and attach hooks + name = jQuery.propFix[ name ] || name; + hooks = jQuery.propHooks[ name ]; + } + + if ( value !== undefined ) { + if ( hooks && "set" in hooks && + ( ret = hooks.set( elem, value, name ) ) !== undefined ) { + return ret; + } + + return ( elem[ name ] = value ); + } + + if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) { + return ret; + } + + return elem[ name ]; + }, + + propHooks: { + tabIndex: { + get: function( elem ) { + + // Support: IE <=9 - 11 only + // elem.tabIndex doesn't always return the + // correct value when it hasn't been explicitly set + // https://web.archive.org/web/20141116233347/http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/ + // Use proper attribute retrieval(#12072) + var tabindex = jQuery.find.attr( elem, "tabindex" ); + + if ( tabindex ) { + return parseInt( tabindex, 10 ); + } + + if ( + rfocusable.test( elem.nodeName ) || + rclickable.test( elem.nodeName ) && + elem.href + ) { + return 0; + } + + return -1; + } + } + }, + + propFix: { + "for": "htmlFor", + "class": "className" + } +} ); + +// Support: IE <=11 only +// Accessing the selectedIndex property +// forces the browser to respect setting selected +// on the option +// The getter ensures a default option is selected +// when in an optgroup +// eslint rule "no-unused-expressions" is disabled for this code +// since it considers such accessions noop +if ( !support.optSelected ) { + jQuery.propHooks.selected = { + get: function( elem ) { + + /* eslint no-unused-expressions: "off" */ + + var parent = elem.parentNode; + if ( parent && parent.parentNode ) { + parent.parentNode.selectedIndex; + } + return null; + }, + set: function( elem ) { + + /* eslint no-unused-expressions: "off" */ + + var parent = elem.parentNode; + if ( parent ) { + parent.selectedIndex; + + if ( parent.parentNode ) { + parent.parentNode.selectedIndex; + } + } + } + }; +} + +jQuery.each( [ + "tabIndex", + "readOnly", + "maxLength", + "cellSpacing", + "cellPadding", + "rowSpan", + "colSpan", + "useMap", + "frameBorder", + "contentEditable" +], function() { + jQuery.propFix[ this.toLowerCase() ] = this; +} ); + + + + + // Strip and collapse whitespace according to HTML spec + // https://html.spec.whatwg.org/multipage/infrastructure.html#strip-and-collapse-whitespace + function stripAndCollapse( value ) { + var tokens = value.match( rnothtmlwhite ) || []; + return tokens.join( " " ); + } + + +function getClass( elem ) { + return elem.getAttribute && elem.getAttribute( "class" ) || ""; +} + +jQuery.fn.extend( { + addClass: function( value ) { + var classes, elem, cur, curValue, clazz, j, finalValue, + i = 0; + + if ( jQuery.isFunction( value ) ) { + return this.each( function( j ) { + jQuery( this ).addClass( value.call( this, j, getClass( this ) ) ); + } ); + } + + if ( typeof value === "string" && value ) { + classes = value.match( rnothtmlwhite ) || []; + + while ( ( elem = this[ i++ ] ) ) { + curValue = getClass( elem ); + cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " ); + + if ( cur ) { + j = 0; + while ( ( clazz = classes[ j++ ] ) ) { + if ( cur.indexOf( " " + clazz + " " ) < 0 ) { + cur += clazz + " "; + } + } + + // Only assign if different to avoid unneeded rendering. + finalValue = stripAndCollapse( cur ); + if ( curValue !== finalValue ) { + elem.setAttribute( "class", finalValue ); + } + } + } + } + + return this; + }, + + removeClass: function( value ) { + var classes, elem, cur, curValue, clazz, j, finalValue, + i = 0; + + if ( jQuery.isFunction( value ) ) { + return this.each( function( j ) { + jQuery( this ).removeClass( value.call( this, j, getClass( this ) ) ); + } ); + } + + if ( !arguments.length ) { + return this.attr( "class", "" ); + } + + if ( typeof value === "string" && value ) { + classes = value.match( rnothtmlwhite ) || []; + + while ( ( elem = this[ i++ ] ) ) { + curValue = getClass( elem ); + + // This expression is here for better compressibility (see addClass) + cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " ); + + if ( cur ) { + j = 0; + while ( ( clazz = classes[ j++ ] ) ) { + + // Remove *all* instances + while ( cur.indexOf( " " + clazz + " " ) > -1 ) { + cur = cur.replace( " " + clazz + " ", " " ); + } + } + + // Only assign if different to avoid unneeded rendering. + finalValue = stripAndCollapse( cur ); + if ( curValue !== finalValue ) { + elem.setAttribute( "class", finalValue ); + } + } + } + } + + return this; + }, + + toggleClass: function( value, stateVal ) { + var type = typeof value; + + if ( typeof stateVal === "boolean" && type === "string" ) { + return stateVal ? this.addClass( value ) : this.removeClass( value ); + } + + if ( jQuery.isFunction( value ) ) { + return this.each( function( i ) { + jQuery( this ).toggleClass( + value.call( this, i, getClass( this ), stateVal ), + stateVal + ); + } ); + } + + return this.each( function() { + var className, i, self, classNames; + + if ( type === "string" ) { + + // Toggle individual class names + i = 0; + self = jQuery( this ); + classNames = value.match( rnothtmlwhite ) || []; + + while ( ( className = classNames[ i++ ] ) ) { + + // Check each className given, space separated list + if ( self.hasClass( className ) ) { + self.removeClass( className ); + } else { + self.addClass( className ); + } + } + + // Toggle whole class name + } else if ( value === undefined || type === "boolean" ) { + className = getClass( this ); + if ( className ) { + + // Store className if set + dataPriv.set( this, "__className__", className ); + } + + // If the element has a class name or if we're passed `false`, + // then remove the whole classname (if there was one, the above saved it). + // Otherwise bring back whatever was previously saved (if anything), + // falling back to the empty string if nothing was stored. + if ( this.setAttribute ) { + this.setAttribute( "class", + className || value === false ? + "" : + dataPriv.get( this, "__className__" ) || "" + ); + } + } + } ); + }, + + hasClass: function( selector ) { + var className, elem, + i = 0; + + className = " " + selector + " "; + while ( ( elem = this[ i++ ] ) ) { + if ( elem.nodeType === 1 && + ( " " + stripAndCollapse( getClass( elem ) ) + " " ).indexOf( className ) > -1 ) { + return true; + } + } + + return false; + } +} ); + + + + +var rreturn = /\r/g; + +jQuery.fn.extend( { + val: function( value ) { + var hooks, ret, isFunction, + elem = this[ 0 ]; + + if ( !arguments.length ) { + if ( elem ) { + hooks = jQuery.valHooks[ elem.type ] || + jQuery.valHooks[ elem.nodeName.toLowerCase() ]; + + if ( hooks && + "get" in hooks && + ( ret = hooks.get( elem, "value" ) ) !== undefined + ) { + return ret; + } + + ret = elem.value; + + // Handle most common string cases + if ( typeof ret === "string" ) { + return ret.replace( rreturn, "" ); + } + + // Handle cases where value is null/undef or number + return ret == null ? "" : ret; + } + + return; + } + + isFunction = jQuery.isFunction( value ); + + return this.each( function( i ) { + var val; + + if ( this.nodeType !== 1 ) { + return; + } + + if ( isFunction ) { + val = value.call( this, i, jQuery( this ).val() ); + } else { + val = value; + } + + // Treat null/undefined as ""; convert numbers to string + if ( val == null ) { + val = ""; + + } else if ( typeof val === "number" ) { + val += ""; + + } else if ( Array.isArray( val ) ) { + val = jQuery.map( val, function( value ) { + return value == null ? "" : value + ""; + } ); + } + + hooks = jQuery.valHooks[ this.type ] || jQuery.valHooks[ this.nodeName.toLowerCase() ]; + + // If set returns undefined, fall back to normal setting + if ( !hooks || !( "set" in hooks ) || hooks.set( this, val, "value" ) === undefined ) { + this.value = val; + } + } ); + } +} ); + +jQuery.extend( { + valHooks: { + option: { + get: function( elem ) { + + var val = jQuery.find.attr( elem, "value" ); + return val != null ? + val : + + // Support: IE <=10 - 11 only + // option.text throws exceptions (#14686, #14858) + // Strip and collapse whitespace + // https://html.spec.whatwg.org/#strip-and-collapse-whitespace + stripAndCollapse( jQuery.text( elem ) ); + } + }, + select: { + get: function( elem ) { + var value, option, i, + options = elem.options, + index = elem.selectedIndex, + one = elem.type === "select-one", + values = one ? null : [], + max = one ? index + 1 : options.length; + + if ( index < 0 ) { + i = max; + + } else { + i = one ? index : 0; + } + + // Loop through all the selected options + for ( ; i < max; i++ ) { + option = options[ i ]; + + // Support: IE <=9 only + // IE8-9 doesn't update selected after form reset (#2551) + if ( ( option.selected || i === index ) && + + // Don't return options that are disabled or in a disabled optgroup + !option.disabled && + ( !option.parentNode.disabled || + !nodeName( option.parentNode, "optgroup" ) ) ) { + + // Get the specific value for the option + value = jQuery( option ).val(); + + // We don't need an array for one selects + if ( one ) { + return value; + } + + // Multi-Selects return an array + values.push( value ); + } + } + + return values; + }, + + set: function( elem, value ) { + var optionSet, option, + options = elem.options, + values = jQuery.makeArray( value ), + i = options.length; + + while ( i-- ) { + option = options[ i ]; + + /* eslint-disable no-cond-assign */ + + if ( option.selected = + jQuery.inArray( jQuery.valHooks.option.get( option ), values ) > -1 + ) { + optionSet = true; + } + + /* eslint-enable no-cond-assign */ + } + + // Force browsers to behave consistently when non-matching value is set + if ( !optionSet ) { + elem.selectedIndex = -1; + } + return values; + } + } + } +} ); + +// Radios and checkboxes getter/setter +jQuery.each( [ "radio", "checkbox" ], function() { + jQuery.valHooks[ this ] = { + set: function( elem, value ) { + if ( Array.isArray( value ) ) { + return ( elem.checked = jQuery.inArray( jQuery( elem ).val(), value ) > -1 ); + } + } + }; + if ( !support.checkOn ) { + jQuery.valHooks[ this ].get = function( elem ) { + return elem.getAttribute( "value" ) === null ? "on" : elem.value; + }; + } +} ); + + + + +// Return jQuery for attributes-only inclusion + + +var rfocusMorph = /^(?:focusinfocus|focusoutblur)$/; + +jQuery.extend( jQuery.event, { + + trigger: function( event, data, elem, onlyHandlers ) { + + var i, cur, tmp, bubbleType, ontype, handle, special, + eventPath = [ elem || document ], + type = hasOwn.call( event, "type" ) ? event.type : event, + namespaces = hasOwn.call( event, "namespace" ) ? event.namespace.split( "." ) : []; + + cur = tmp = elem = elem || document; + + // Don't do events on text and comment nodes + if ( elem.nodeType === 3 || elem.nodeType === 8 ) { + return; + } + + // focus/blur morphs to focusin/out; ensure we're not firing them right now + if ( rfocusMorph.test( type + jQuery.event.triggered ) ) { + return; + } + + if ( type.indexOf( "." ) > -1 ) { + + // Namespaced trigger; create a regexp to match event type in handle() + namespaces = type.split( "." ); + type = namespaces.shift(); + namespaces.sort(); + } + ontype = type.indexOf( ":" ) < 0 && "on" + type; + + // Caller can pass in a jQuery.Event object, Object, or just an event type string + event = event[ jQuery.expando ] ? + event : + new jQuery.Event( type, typeof event === "object" && event ); + + // Trigger bitmask: & 1 for native handlers; & 2 for jQuery (always true) + event.isTrigger = onlyHandlers ? 2 : 3; + event.namespace = namespaces.join( "." ); + event.rnamespace = event.namespace ? + new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" ) : + null; + + // Clean up the event in case it is being reused + event.result = undefined; + if ( !event.target ) { + event.target = elem; + } + + // Clone any incoming data and prepend the event, creating the handler arg list + data = data == null ? + [ event ] : + jQuery.makeArray( data, [ event ] ); + + // Allow special events to draw outside the lines + special = jQuery.event.special[ type ] || {}; + if ( !onlyHandlers && special.trigger && special.trigger.apply( elem, data ) === false ) { + return; + } + + // Determine event propagation path in advance, per W3C events spec (#9951) + // Bubble up to document, then to window; watch for a global ownerDocument var (#9724) + if ( !onlyHandlers && !special.noBubble && !jQuery.isWindow( elem ) ) { + + bubbleType = special.delegateType || type; + if ( !rfocusMorph.test( bubbleType + type ) ) { + cur = cur.parentNode; + } + for ( ; cur; cur = cur.parentNode ) { + eventPath.push( cur ); + tmp = cur; + } + + // Only add window if we got to document (e.g., not plain obj or detached DOM) + if ( tmp === ( elem.ownerDocument || document ) ) { + eventPath.push( tmp.defaultView || tmp.parentWindow || window ); + } + } + + // Fire handlers on the event path + i = 0; + while ( ( cur = eventPath[ i++ ] ) && !event.isPropagationStopped() ) { + + event.type = i > 1 ? + bubbleType : + special.bindType || type; + + // jQuery handler + handle = ( dataPriv.get( cur, "events" ) || {} )[ event.type ] && + dataPriv.get( cur, "handle" ); + if ( handle ) { + handle.apply( cur, data ); + } + + // Native handler + handle = ontype && cur[ ontype ]; + if ( handle && handle.apply && acceptData( cur ) ) { + event.result = handle.apply( cur, data ); + if ( event.result === false ) { + event.preventDefault(); + } + } + } + event.type = type; + + // If nobody prevented the default action, do it now + if ( !onlyHandlers && !event.isDefaultPrevented() ) { + + if ( ( !special._default || + special._default.apply( eventPath.pop(), data ) === false ) && + acceptData( elem ) ) { + + // Call a native DOM method on the target with the same name as the event. + // Don't do default actions on window, that's where global variables be (#6170) + if ( ontype && jQuery.isFunction( elem[ type ] ) && !jQuery.isWindow( elem ) ) { + + // Don't re-trigger an onFOO event when we call its FOO() method + tmp = elem[ ontype ]; + + if ( tmp ) { + elem[ ontype ] = null; + } + + // Prevent re-triggering of the same event, since we already bubbled it above + jQuery.event.triggered = type; + elem[ type ](); + jQuery.event.triggered = undefined; + + if ( tmp ) { + elem[ ontype ] = tmp; + } + } + } + } + + return event.result; + }, + + // Piggyback on a donor event to simulate a different one + // Used only for `focus(in | out)` events + simulate: function( type, elem, event ) { + var e = jQuery.extend( + new jQuery.Event(), + event, + { + type: type, + isSimulated: true + } + ); + + jQuery.event.trigger( e, null, elem ); + } + +} ); + +jQuery.fn.extend( { + + trigger: function( type, data ) { + return this.each( function() { + jQuery.event.trigger( type, data, this ); + } ); + }, + triggerHandler: function( type, data ) { + var elem = this[ 0 ]; + if ( elem ) { + return jQuery.event.trigger( type, data, elem, true ); + } + } +} ); + + +jQuery.each( ( "blur focus focusin focusout resize scroll click dblclick " + + "mousedown mouseup mousemove mouseover mouseout mouseenter mouseleave " + + "change select submit keydown keypress keyup contextmenu" ).split( " " ), + function( i, name ) { + + // Handle event binding + jQuery.fn[ name ] = function( data, fn ) { + return arguments.length > 0 ? + this.on( name, null, data, fn ) : + this.trigger( name ); + }; +} ); + +jQuery.fn.extend( { + hover: function( fnOver, fnOut ) { + return this.mouseenter( fnOver ).mouseleave( fnOut || fnOver ); + } +} ); + + + + +support.focusin = "onfocusin" in window; + + +// Support: Firefox <=44 +// Firefox doesn't have focus(in | out) events +// Related ticket - https://bugzilla.mozilla.org/show_bug.cgi?id=687787 +// +// Support: Chrome <=48 - 49, Safari <=9.0 - 9.1 +// focus(in | out) events fire after focus & blur events, +// which is spec violation - http://www.w3.org/TR/DOM-Level-3-Events/#events-focusevent-event-order +// Related ticket - https://bugs.chromium.org/p/chromium/issues/detail?id=449857 +if ( !support.focusin ) { + jQuery.each( { focus: "focusin", blur: "focusout" }, function( orig, fix ) { + + // Attach a single capturing handler on the document while someone wants focusin/focusout + var handler = function( event ) { + jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ) ); + }; + + jQuery.event.special[ fix ] = { + setup: function() { + var doc = this.ownerDocument || this, + attaches = dataPriv.access( doc, fix ); + + if ( !attaches ) { + doc.addEventListener( orig, handler, true ); + } + dataPriv.access( doc, fix, ( attaches || 0 ) + 1 ); + }, + teardown: function() { + var doc = this.ownerDocument || this, + attaches = dataPriv.access( doc, fix ) - 1; + + if ( !attaches ) { + doc.removeEventListener( orig, handler, true ); + dataPriv.remove( doc, fix ); + + } else { + dataPriv.access( doc, fix, attaches ); + } + } + }; + } ); +} +var location = window.location; + +var nonce = jQuery.now(); + +var rquery = ( /\?/ ); + + + +// Cross-browser xml parsing +jQuery.parseXML = function( data ) { + var xml; + if ( !data || typeof data !== "string" ) { + return null; + } + + // Support: IE 9 - 11 only + // IE throws on parseFromString with invalid input. + try { + xml = ( new window.DOMParser() ).parseFromString( data, "text/xml" ); + } catch ( e ) { + xml = undefined; + } + + if ( !xml || xml.getElementsByTagName( "parsererror" ).length ) { + jQuery.error( "Invalid XML: " + data ); + } + return xml; +}; + + +var + rbracket = /\[\]$/, + rCRLF = /\r?\n/g, + rsubmitterTypes = /^(?:submit|button|image|reset|file)$/i, + rsubmittable = /^(?:input|select|textarea|keygen)/i; + +function buildParams( prefix, obj, traditional, add ) { + var name; + + if ( Array.isArray( obj ) ) { + + // Serialize array item. + jQuery.each( obj, function( i, v ) { + if ( traditional || rbracket.test( prefix ) ) { + + // Treat each array item as a scalar. + add( prefix, v ); + + } else { + + // Item is non-scalar (array or object), encode its numeric index. + buildParams( + prefix + "[" + ( typeof v === "object" && v != null ? i : "" ) + "]", + v, + traditional, + add + ); + } + } ); + + } else if ( !traditional && jQuery.type( obj ) === "object" ) { + + // Serialize object item. + for ( name in obj ) { + buildParams( prefix + "[" + name + "]", obj[ name ], traditional, add ); + } + + } else { + + // Serialize scalar item. + add( prefix, obj ); + } +} + +// Serialize an array of form elements or a set of +// key/values into a query string +jQuery.param = function( a, traditional ) { + var prefix, + s = [], + add = function( key, valueOrFunction ) { + + // If value is a function, invoke it and use its return value + var value = jQuery.isFunction( valueOrFunction ) ? + valueOrFunction() : + valueOrFunction; + + s[ s.length ] = encodeURIComponent( key ) + "=" + + encodeURIComponent( value == null ? "" : value ); + }; + + // If an array was passed in, assume that it is an array of form elements. + if ( Array.isArray( a ) || ( a.jquery && !jQuery.isPlainObject( a ) ) ) { + + // Serialize the form elements + jQuery.each( a, function() { + add( this.name, this.value ); + } ); + + } else { + + // If traditional, encode the "old" way (the way 1.3.2 or older + // did it), otherwise encode params recursively. + for ( prefix in a ) { + buildParams( prefix, a[ prefix ], traditional, add ); + } + } + + // Return the resulting serialization + return s.join( "&" ); +}; + +jQuery.fn.extend( { + serialize: function() { + return jQuery.param( this.serializeArray() ); + }, + serializeArray: function() { + return this.map( function() { + + // Can add propHook for "elements" to filter or add form elements + var elements = jQuery.prop( this, "elements" ); + return elements ? jQuery.makeArray( elements ) : this; + } ) + .filter( function() { + var type = this.type; + + // Use .is( ":disabled" ) so that fieldset[disabled] works + return this.name && !jQuery( this ).is( ":disabled" ) && + rsubmittable.test( this.nodeName ) && !rsubmitterTypes.test( type ) && + ( this.checked || !rcheckableType.test( type ) ); + } ) + .map( function( i, elem ) { + var val = jQuery( this ).val(); + + if ( val == null ) { + return null; + } + + if ( Array.isArray( val ) ) { + return jQuery.map( val, function( val ) { + return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) }; + } ); + } + + return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) }; + } ).get(); + } +} ); + + +var + r20 = /%20/g, + rhash = /#.*$/, + rantiCache = /([?&])_=[^&]*/, + rheaders = /^(.*?):[ \t]*([^\r\n]*)$/mg, + + // #7653, #8125, #8152: local protocol detection + rlocalProtocol = /^(?:about|app|app-storage|.+-extension|file|res|widget):$/, + rnoContent = /^(?:GET|HEAD)$/, + rprotocol = /^\/\//, + + /* Prefilters + * 1) They are useful to introduce custom dataTypes (see ajax/jsonp.js for an example) + * 2) These are called: + * - BEFORE asking for a transport + * - AFTER param serialization (s.data is a string if s.processData is true) + * 3) key is the dataType + * 4) the catchall symbol "*" can be used + * 5) execution will start with transport dataType and THEN continue down to "*" if needed + */ + prefilters = {}, + + /* Transports bindings + * 1) key is the dataType + * 2) the catchall symbol "*" can be used + * 3) selection will start with transport dataType and THEN go to "*" if needed + */ + transports = {}, + + // Avoid comment-prolog char sequence (#10098); must appease lint and evade compression + allTypes = "*/".concat( "*" ), + + // Anchor tag for parsing the document origin + originAnchor = document.createElement( "a" ); + originAnchor.href = location.href; + +// Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport +function addToPrefiltersOrTransports( structure ) { + + // dataTypeExpression is optional and defaults to "*" + return function( dataTypeExpression, func ) { + + if ( typeof dataTypeExpression !== "string" ) { + func = dataTypeExpression; + dataTypeExpression = "*"; + } + + var dataType, + i = 0, + dataTypes = dataTypeExpression.toLowerCase().match( rnothtmlwhite ) || []; + + if ( jQuery.isFunction( func ) ) { + + // For each dataType in the dataTypeExpression + while ( ( dataType = dataTypes[ i++ ] ) ) { + + // Prepend if requested + if ( dataType[ 0 ] === "+" ) { + dataType = dataType.slice( 1 ) || "*"; + ( structure[ dataType ] = structure[ dataType ] || [] ).unshift( func ); + + // Otherwise append + } else { + ( structure[ dataType ] = structure[ dataType ] || [] ).push( func ); + } + } + } + }; +} + +// Base inspection function for prefilters and transports +function inspectPrefiltersOrTransports( structure, options, originalOptions, jqXHR ) { + + var inspected = {}, + seekingTransport = ( structure === transports ); + + function inspect( dataType ) { + var selected; + inspected[ dataType ] = true; + jQuery.each( structure[ dataType ] || [], function( _, prefilterOrFactory ) { + var dataTypeOrTransport = prefilterOrFactory( options, originalOptions, jqXHR ); + if ( typeof dataTypeOrTransport === "string" && + !seekingTransport && !inspected[ dataTypeOrTransport ] ) { + + options.dataTypes.unshift( dataTypeOrTransport ); + inspect( dataTypeOrTransport ); + return false; + } else if ( seekingTransport ) { + return !( selected = dataTypeOrTransport ); + } + } ); + return selected; + } + + return inspect( options.dataTypes[ 0 ] ) || !inspected[ "*" ] && inspect( "*" ); +} + +// A special extend for ajax options +// that takes "flat" options (not to be deep extended) +// Fixes #9887 +function ajaxExtend( target, src ) { + var key, deep, + flatOptions = jQuery.ajaxSettings.flatOptions || {}; + + for ( key in src ) { + if ( src[ key ] !== undefined ) { + ( flatOptions[ key ] ? target : ( deep || ( deep = {} ) ) )[ key ] = src[ key ]; + } + } + if ( deep ) { + jQuery.extend( true, target, deep ); + } + + return target; +} + +/* Handles responses to an ajax request: + * - finds the right dataType (mediates between content-type and expected dataType) + * - returns the corresponding response + */ +function ajaxHandleResponses( s, jqXHR, responses ) { + + var ct, type, finalDataType, firstDataType, + contents = s.contents, + dataTypes = s.dataTypes; + + // Remove auto dataType and get content-type in the process + while ( dataTypes[ 0 ] === "*" ) { + dataTypes.shift(); + if ( ct === undefined ) { + ct = s.mimeType || jqXHR.getResponseHeader( "Content-Type" ); + } + } + + // Check if we're dealing with a known content-type + if ( ct ) { + for ( type in contents ) { + if ( contents[ type ] && contents[ type ].test( ct ) ) { + dataTypes.unshift( type ); + break; + } + } + } + + // Check to see if we have a response for the expected dataType + if ( dataTypes[ 0 ] in responses ) { + finalDataType = dataTypes[ 0 ]; + } else { + + // Try convertible dataTypes + for ( type in responses ) { + if ( !dataTypes[ 0 ] || s.converters[ type + " " + dataTypes[ 0 ] ] ) { + finalDataType = type; + break; + } + if ( !firstDataType ) { + firstDataType = type; + } + } + + // Or just use first one + finalDataType = finalDataType || firstDataType; + } + + // If we found a dataType + // We add the dataType to the list if needed + // and return the corresponding response + if ( finalDataType ) { + if ( finalDataType !== dataTypes[ 0 ] ) { + dataTypes.unshift( finalDataType ); + } + return responses[ finalDataType ]; + } +} + +/* Chain conversions given the request and the original response + * Also sets the responseXXX fields on the jqXHR instance + */ +function ajaxConvert( s, response, jqXHR, isSuccess ) { + var conv2, current, conv, tmp, prev, + converters = {}, + + // Work with a copy of dataTypes in case we need to modify it for conversion + dataTypes = s.dataTypes.slice(); + + // Create converters map with lowercased keys + if ( dataTypes[ 1 ] ) { + for ( conv in s.converters ) { + converters[ conv.toLowerCase() ] = s.converters[ conv ]; + } + } + + current = dataTypes.shift(); + + // Convert to each sequential dataType + while ( current ) { + + if ( s.responseFields[ current ] ) { + jqXHR[ s.responseFields[ current ] ] = response; + } + + // Apply the dataFilter if provided + if ( !prev && isSuccess && s.dataFilter ) { + response = s.dataFilter( response, s.dataType ); + } + + prev = current; + current = dataTypes.shift(); + + if ( current ) { + + // There's only work to do if current dataType is non-auto + if ( current === "*" ) { + + current = prev; + + // Convert response if prev dataType is non-auto and differs from current + } else if ( prev !== "*" && prev !== current ) { + + // Seek a direct converter + conv = converters[ prev + " " + current ] || converters[ "* " + current ]; + + // If none found, seek a pair + if ( !conv ) { + for ( conv2 in converters ) { + + // If conv2 outputs current + tmp = conv2.split( " " ); + if ( tmp[ 1 ] === current ) { + + // If prev can be converted to accepted input + conv = converters[ prev + " " + tmp[ 0 ] ] || + converters[ "* " + tmp[ 0 ] ]; + if ( conv ) { + + // Condense equivalence converters + if ( conv === true ) { + conv = converters[ conv2 ]; + + // Otherwise, insert the intermediate dataType + } else if ( converters[ conv2 ] !== true ) { + current = tmp[ 0 ]; + dataTypes.unshift( tmp[ 1 ] ); + } + break; + } + } + } + } + + // Apply converter (if not an equivalence) + if ( conv !== true ) { + + // Unless errors are allowed to bubble, catch and return them + if ( conv && s.throws ) { + response = conv( response ); + } else { + try { + response = conv( response ); + } catch ( e ) { + return { + state: "parsererror", + error: conv ? e : "No conversion from " + prev + " to " + current + }; + } + } + } + } + } + } + + return { state: "success", data: response }; +} + +jQuery.extend( { + + // Counter for holding the number of active queries + active: 0, + + // Last-Modified header cache for next request + lastModified: {}, + etag: {}, + + ajaxSettings: { + url: location.href, + type: "GET", + isLocal: rlocalProtocol.test( location.protocol ), + global: true, + processData: true, + async: true, + contentType: "application/x-www-form-urlencoded; charset=UTF-8", + + /* + timeout: 0, + data: null, + dataType: null, + username: null, + password: null, + cache: null, + throws: false, + traditional: false, + headers: {}, + */ + + accepts: { + "*": allTypes, + text: "text/plain", + html: "text/html", + xml: "application/xml, text/xml", + json: "application/json, text/javascript" + }, + + contents: { + xml: /\bxml\b/, + html: /\bhtml/, + json: /\bjson\b/ + }, + + responseFields: { + xml: "responseXML", + text: "responseText", + json: "responseJSON" + }, + + // Data converters + // Keys separate source (or catchall "*") and destination types with a single space + converters: { + + // Convert anything to text + "* text": String, + + // Text to html (true = no transformation) + "text html": true, + + // Evaluate text as a json expression + "text json": JSON.parse, + + // Parse text as xml + "text xml": jQuery.parseXML + }, + + // For options that shouldn't be deep extended: + // you can add your own custom options here if + // and when you create one that shouldn't be + // deep extended (see ajaxExtend) + flatOptions: { + url: true, + context: true + } + }, + + // Creates a full fledged settings object into target + // with both ajaxSettings and settings fields. + // If target is omitted, writes into ajaxSettings. + ajaxSetup: function( target, settings ) { + return settings ? + + // Building a settings object + ajaxExtend( ajaxExtend( target, jQuery.ajaxSettings ), settings ) : + + // Extending ajaxSettings + ajaxExtend( jQuery.ajaxSettings, target ); + }, + + ajaxPrefilter: addToPrefiltersOrTransports( prefilters ), + ajaxTransport: addToPrefiltersOrTransports( transports ), + + // Main method + ajax: function( url, options ) { + + // If url is an object, simulate pre-1.5 signature + if ( typeof url === "object" ) { + options = url; + url = undefined; + } + + // Force options to be an object + options = options || {}; + + var transport, + + // URL without anti-cache param + cacheURL, + + // Response headers + responseHeadersString, + responseHeaders, + + // timeout handle + timeoutTimer, + + // Url cleanup var + urlAnchor, + + // Request state (becomes false upon send and true upon completion) + completed, + + // To know if global events are to be dispatched + fireGlobals, + + // Loop variable + i, + + // uncached part of the url + uncached, + + // Create the final options object + s = jQuery.ajaxSetup( {}, options ), + + // Callbacks context + callbackContext = s.context || s, + + // Context for global events is callbackContext if it is a DOM node or jQuery collection + globalEventContext = s.context && + ( callbackContext.nodeType || callbackContext.jquery ) ? + jQuery( callbackContext ) : + jQuery.event, + + // Deferreds + deferred = jQuery.Deferred(), + completeDeferred = jQuery.Callbacks( "once memory" ), + + // Status-dependent callbacks + statusCode = s.statusCode || {}, + + // Headers (they are sent all at once) + requestHeaders = {}, + requestHeadersNames = {}, + + // Default abort message + strAbort = "canceled", + + // Fake xhr + jqXHR = { + readyState: 0, + + // Builds headers hashtable if needed + getResponseHeader: function( key ) { + var match; + if ( completed ) { + if ( !responseHeaders ) { + responseHeaders = {}; + while ( ( match = rheaders.exec( responseHeadersString ) ) ) { + responseHeaders[ match[ 1 ].toLowerCase() ] = match[ 2 ]; + } + } + match = responseHeaders[ key.toLowerCase() ]; + } + return match == null ? null : match; + }, + + // Raw string + getAllResponseHeaders: function() { + return completed ? responseHeadersString : null; + }, + + // Caches the header + setRequestHeader: function( name, value ) { + if ( completed == null ) { + name = requestHeadersNames[ name.toLowerCase() ] = + requestHeadersNames[ name.toLowerCase() ] || name; + requestHeaders[ name ] = value; + } + return this; + }, + + // Overrides response content-type header + overrideMimeType: function( type ) { + if ( completed == null ) { + s.mimeType = type; + } + return this; + }, + + // Status-dependent callbacks + statusCode: function( map ) { + var code; + if ( map ) { + if ( completed ) { + + // Execute the appropriate callbacks + jqXHR.always( map[ jqXHR.status ] ); + } else { + + // Lazy-add the new callbacks in a way that preserves old ones + for ( code in map ) { + statusCode[ code ] = [ statusCode[ code ], map[ code ] ]; + } + } + } + return this; + }, + + // Cancel the request + abort: function( statusText ) { + var finalText = statusText || strAbort; + if ( transport ) { + transport.abort( finalText ); + } + done( 0, finalText ); + return this; + } + }; + + // Attach deferreds + deferred.promise( jqXHR ); + + // Add protocol if not provided (prefilters might expect it) + // Handle falsy url in the settings object (#10093: consistency with old signature) + // We also use the url parameter if available + s.url = ( ( url || s.url || location.href ) + "" ) + .replace( rprotocol, location.protocol + "//" ); + + // Alias method option to type as per ticket #12004 + s.type = options.method || options.type || s.method || s.type; + + // Extract dataTypes list + s.dataTypes = ( s.dataType || "*" ).toLowerCase().match( rnothtmlwhite ) || [ "" ]; + + // A cross-domain request is in order when the origin doesn't match the current origin. + if ( s.crossDomain == null ) { + urlAnchor = document.createElement( "a" ); + + // Support: IE <=8 - 11, Edge 12 - 13 + // IE throws exception on accessing the href property if url is malformed, + // e.g. http://example.com:80x/ + try { + urlAnchor.href = s.url; + + // Support: IE <=8 - 11 only + // Anchor's host property isn't correctly set when s.url is relative + urlAnchor.href = urlAnchor.href; + s.crossDomain = originAnchor.protocol + "//" + originAnchor.host !== + urlAnchor.protocol + "//" + urlAnchor.host; + } catch ( e ) { + + // If there is an error parsing the URL, assume it is crossDomain, + // it can be rejected by the transport if it is invalid + s.crossDomain = true; + } + } + + // Convert data if not already a string + if ( s.data && s.processData && typeof s.data !== "string" ) { + s.data = jQuery.param( s.data, s.traditional ); + } + + // Apply prefilters + inspectPrefiltersOrTransports( prefilters, s, options, jqXHR ); + + // If request was aborted inside a prefilter, stop there + if ( completed ) { + return jqXHR; + } + + // We can fire global events as of now if asked to + // Don't fire events if jQuery.event is undefined in an AMD-usage scenario (#15118) + fireGlobals = jQuery.event && s.global; + + // Watch for a new set of requests + if ( fireGlobals && jQuery.active++ === 0 ) { + jQuery.event.trigger( "ajaxStart" ); + } + + // Uppercase the type + s.type = s.type.toUpperCase(); + + // Determine if request has content + s.hasContent = !rnoContent.test( s.type ); + + // Save the URL in case we're toying with the If-Modified-Since + // and/or If-None-Match header later on + // Remove hash to simplify url manipulation + cacheURL = s.url.replace( rhash, "" ); + + // More options handling for requests with no content + if ( !s.hasContent ) { + + // Remember the hash so we can put it back + uncached = s.url.slice( cacheURL.length ); + + // If data is available, append data to url + if ( s.data ) { + cacheURL += ( rquery.test( cacheURL ) ? "&" : "?" ) + s.data; + + // #9682: remove data so that it's not used in an eventual retry + delete s.data; + } + + // Add or update anti-cache param if needed + if ( s.cache === false ) { + cacheURL = cacheURL.replace( rantiCache, "$1" ); + uncached = ( rquery.test( cacheURL ) ? "&" : "?" ) + "_=" + ( nonce++ ) + uncached; + } + + // Put hash and anti-cache on the URL that will be requested (gh-1732) + s.url = cacheURL + uncached; + + // Change '%20' to '+' if this is encoded form body content (gh-2658) + } else if ( s.data && s.processData && + ( s.contentType || "" ).indexOf( "application/x-www-form-urlencoded" ) === 0 ) { + s.data = s.data.replace( r20, "+" ); + } + + // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode. + if ( s.ifModified ) { + if ( jQuery.lastModified[ cacheURL ] ) { + jqXHR.setRequestHeader( "If-Modified-Since", jQuery.lastModified[ cacheURL ] ); + } + if ( jQuery.etag[ cacheURL ] ) { + jqXHR.setRequestHeader( "If-None-Match", jQuery.etag[ cacheURL ] ); + } + } + + // Set the correct header, if data is being sent + if ( s.data && s.hasContent && s.contentType !== false || options.contentType ) { + jqXHR.setRequestHeader( "Content-Type", s.contentType ); + } + + // Set the Accepts header for the server, depending on the dataType + jqXHR.setRequestHeader( + "Accept", + s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[ 0 ] ] ? + s.accepts[ s.dataTypes[ 0 ] ] + + ( s.dataTypes[ 0 ] !== "*" ? ", " + allTypes + "; q=0.01" : "" ) : + s.accepts[ "*" ] + ); + + // Check for headers option + for ( i in s.headers ) { + jqXHR.setRequestHeader( i, s.headers[ i ] ); + } + + // Allow custom headers/mimetypes and early abort + if ( s.beforeSend && + ( s.beforeSend.call( callbackContext, jqXHR, s ) === false || completed ) ) { + + // Abort if not done already and return + return jqXHR.abort(); + } + + // Aborting is no longer a cancellation + strAbort = "abort"; + + // Install callbacks on deferreds + completeDeferred.add( s.complete ); + jqXHR.done( s.success ); + jqXHR.fail( s.error ); + + // Get transport + transport = inspectPrefiltersOrTransports( transports, s, options, jqXHR ); + + // If no transport, we auto-abort + if ( !transport ) { + done( -1, "No Transport" ); + } else { + jqXHR.readyState = 1; + + // Send global event + if ( fireGlobals ) { + globalEventContext.trigger( "ajaxSend", [ jqXHR, s ] ); + } + + // If request was aborted inside ajaxSend, stop there + if ( completed ) { + return jqXHR; + } + + // Timeout + if ( s.async && s.timeout > 0 ) { + timeoutTimer = window.setTimeout( function() { + jqXHR.abort( "timeout" ); + }, s.timeout ); + } + + try { + completed = false; + transport.send( requestHeaders, done ); + } catch ( e ) { + + // Rethrow post-completion exceptions + if ( completed ) { + throw e; + } + + // Propagate others as results + done( -1, e ); + } + } + + // Callback for when everything is done + function done( status, nativeStatusText, responses, headers ) { + var isSuccess, success, error, response, modified, + statusText = nativeStatusText; + + // Ignore repeat invocations + if ( completed ) { + return; + } + + completed = true; + + // Clear timeout if it exists + if ( timeoutTimer ) { + window.clearTimeout( timeoutTimer ); + } + + // Dereference transport for early garbage collection + // (no matter how long the jqXHR object will be used) + transport = undefined; + + // Cache response headers + responseHeadersString = headers || ""; + + // Set readyState + jqXHR.readyState = status > 0 ? 4 : 0; + + // Determine if successful + isSuccess = status >= 200 && status < 300 || status === 304; + + // Get response data + if ( responses ) { + response = ajaxHandleResponses( s, jqXHR, responses ); + } + + // Convert no matter what (that way responseXXX fields are always set) + response = ajaxConvert( s, response, jqXHR, isSuccess ); + + // If successful, handle type chaining + if ( isSuccess ) { + + // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode. + if ( s.ifModified ) { + modified = jqXHR.getResponseHeader( "Last-Modified" ); + if ( modified ) { + jQuery.lastModified[ cacheURL ] = modified; + } + modified = jqXHR.getResponseHeader( "etag" ); + if ( modified ) { + jQuery.etag[ cacheURL ] = modified; + } + } + + // if no content + if ( status === 204 || s.type === "HEAD" ) { + statusText = "nocontent"; + + // if not modified + } else if ( status === 304 ) { + statusText = "notmodified"; + + // If we have data, let's convert it + } else { + statusText = response.state; + success = response.data; + error = response.error; + isSuccess = !error; + } + } else { + + // Extract error from statusText and normalize for non-aborts + error = statusText; + if ( status || !statusText ) { + statusText = "error"; + if ( status < 0 ) { + status = 0; + } + } + } + + // Set data for the fake xhr object + jqXHR.status = status; + jqXHR.statusText = ( nativeStatusText || statusText ) + ""; + + // Success/Error + if ( isSuccess ) { + deferred.resolveWith( callbackContext, [ success, statusText, jqXHR ] ); + } else { + deferred.rejectWith( callbackContext, [ jqXHR, statusText, error ] ); + } + + // Status-dependent callbacks + jqXHR.statusCode( statusCode ); + statusCode = undefined; + + if ( fireGlobals ) { + globalEventContext.trigger( isSuccess ? "ajaxSuccess" : "ajaxError", + [ jqXHR, s, isSuccess ? success : error ] ); + } + + // Complete + completeDeferred.fireWith( callbackContext, [ jqXHR, statusText ] ); + + if ( fireGlobals ) { + globalEventContext.trigger( "ajaxComplete", [ jqXHR, s ] ); + + // Handle the global AJAX counter + if ( !( --jQuery.active ) ) { + jQuery.event.trigger( "ajaxStop" ); + } + } + } + + return jqXHR; + }, + + getJSON: function( url, data, callback ) { + return jQuery.get( url, data, callback, "json" ); + }, + + getScript: function( url, callback ) { + return jQuery.get( url, undefined, callback, "script" ); + } +} ); + +jQuery.each( [ "get", "post" ], function( i, method ) { + jQuery[ method ] = function( url, data, callback, type ) { + + // Shift arguments if data argument was omitted + if ( jQuery.isFunction( data ) ) { + type = type || callback; + callback = data; + data = undefined; + } + + // The url can be an options object (which then must have .url) + return jQuery.ajax( jQuery.extend( { + url: url, + type: method, + dataType: type, + data: data, + success: callback + }, jQuery.isPlainObject( url ) && url ) ); + }; +} ); + + +jQuery._evalUrl = function( url ) { + return jQuery.ajax( { + url: url, + + // Make this explicit, since user can override this through ajaxSetup (#11264) + type: "GET", + dataType: "script", + cache: true, + async: false, + global: false, + "throws": true + } ); +}; + + +jQuery.fn.extend( { + wrapAll: function( html ) { + var wrap; + + if ( this[ 0 ] ) { + if ( jQuery.isFunction( html ) ) { + html = html.call( this[ 0 ] ); + } + + // The elements to wrap the target around + wrap = jQuery( html, this[ 0 ].ownerDocument ).eq( 0 ).clone( true ); + + if ( this[ 0 ].parentNode ) { + wrap.insertBefore( this[ 0 ] ); + } + + wrap.map( function() { + var elem = this; + + while ( elem.firstElementChild ) { + elem = elem.firstElementChild; + } + + return elem; + } ).append( this ); + } + + return this; + }, + + wrapInner: function( html ) { + if ( jQuery.isFunction( html ) ) { + return this.each( function( i ) { + jQuery( this ).wrapInner( html.call( this, i ) ); + } ); + } + + return this.each( function() { + var self = jQuery( this ), + contents = self.contents(); + + if ( contents.length ) { + contents.wrapAll( html ); + + } else { + self.append( html ); + } + } ); + }, + + wrap: function( html ) { + var isFunction = jQuery.isFunction( html ); + + return this.each( function( i ) { + jQuery( this ).wrapAll( isFunction ? html.call( this, i ) : html ); + } ); + }, + + unwrap: function( selector ) { + this.parent( selector ).not( "body" ).each( function() { + jQuery( this ).replaceWith( this.childNodes ); + } ); + return this; + } +} ); + + +jQuery.expr.pseudos.hidden = function( elem ) { + return !jQuery.expr.pseudos.visible( elem ); +}; +jQuery.expr.pseudos.visible = function( elem ) { + return !!( elem.offsetWidth || elem.offsetHeight || elem.getClientRects().length ); +}; + + + + +jQuery.ajaxSettings.xhr = function() { + try { + return new window.XMLHttpRequest(); + } catch ( e ) {} +}; + +var xhrSuccessStatus = { + + // File protocol always yields status code 0, assume 200 + 0: 200, + + // Support: IE <=9 only + // #1450: sometimes IE returns 1223 when it should be 204 + 1223: 204 + }, + xhrSupported = jQuery.ajaxSettings.xhr(); + +support.cors = !!xhrSupported && ( "withCredentials" in xhrSupported ); +support.ajax = xhrSupported = !!xhrSupported; + +jQuery.ajaxTransport( function( options ) { + var callback, errorCallback; + + // Cross domain only allowed if supported through XMLHttpRequest + if ( support.cors || xhrSupported && !options.crossDomain ) { + return { + send: function( headers, complete ) { + var i, + xhr = options.xhr(); + + xhr.open( + options.type, + options.url, + options.async, + options.username, + options.password + ); + + // Apply custom fields if provided + if ( options.xhrFields ) { + for ( i in options.xhrFields ) { + xhr[ i ] = options.xhrFields[ i ]; + } + } + + // Override mime type if needed + if ( options.mimeType && xhr.overrideMimeType ) { + xhr.overrideMimeType( options.mimeType ); + } + + // X-Requested-With header + // For cross-domain requests, seeing as conditions for a preflight are + // akin to a jigsaw puzzle, we simply never set it to be sure. + // (it can always be set on a per-request basis or even using ajaxSetup) + // For same-domain requests, won't change header if already provided. + if ( !options.crossDomain && !headers[ "X-Requested-With" ] ) { + headers[ "X-Requested-With" ] = "XMLHttpRequest"; + } + + // Set headers + for ( i in headers ) { + xhr.setRequestHeader( i, headers[ i ] ); + } + + // Callback + callback = function( type ) { + return function() { + if ( callback ) { + callback = errorCallback = xhr.onload = + xhr.onerror = xhr.onabort = xhr.onreadystatechange = null; + + if ( type === "abort" ) { + xhr.abort(); + } else if ( type === "error" ) { + + // Support: IE <=9 only + // On a manual native abort, IE9 throws + // errors on any property access that is not readyState + if ( typeof xhr.status !== "number" ) { + complete( 0, "error" ); + } else { + complete( + + // File: protocol always yields status 0; see #8605, #14207 + xhr.status, + xhr.statusText + ); + } + } else { + complete( + xhrSuccessStatus[ xhr.status ] || xhr.status, + xhr.statusText, + + // Support: IE <=9 only + // IE9 has no XHR2 but throws on binary (trac-11426) + // For XHR2 non-text, let the caller handle it (gh-2498) + ( xhr.responseType || "text" ) !== "text" || + typeof xhr.responseText !== "string" ? + { binary: xhr.response } : + { text: xhr.responseText }, + xhr.getAllResponseHeaders() + ); + } + } + }; + }; + + // Listen to events + xhr.onload = callback(); + errorCallback = xhr.onerror = callback( "error" ); + + // Support: IE 9 only + // Use onreadystatechange to replace onabort + // to handle uncaught aborts + if ( xhr.onabort !== undefined ) { + xhr.onabort = errorCallback; + } else { + xhr.onreadystatechange = function() { + + // Check readyState before timeout as it changes + if ( xhr.readyState === 4 ) { + + // Allow onerror to be called first, + // but that will not handle a native abort + // Also, save errorCallback to a variable + // as xhr.onerror cannot be accessed + window.setTimeout( function() { + if ( callback ) { + errorCallback(); + } + } ); + } + }; + } + + // Create the abort callback + callback = callback( "abort" ); + + try { + + // Do send the request (this may raise an exception) + xhr.send( options.hasContent && options.data || null ); + } catch ( e ) { + + // #14683: Only rethrow if this hasn't been notified as an error yet + if ( callback ) { + throw e; + } + } + }, + + abort: function() { + if ( callback ) { + callback(); + } + } + }; + } +} ); + + + + +// Prevent auto-execution of scripts when no explicit dataType was provided (See gh-2432) +jQuery.ajaxPrefilter( function( s ) { + if ( s.crossDomain ) { + s.contents.script = false; + } +} ); + +// Install script dataType +jQuery.ajaxSetup( { + accepts: { + script: "text/javascript, application/javascript, " + + "application/ecmascript, application/x-ecmascript" + }, + contents: { + script: /\b(?:java|ecma)script\b/ + }, + converters: { + "text script": function( text ) { + jQuery.globalEval( text ); + return text; + } + } +} ); + +// Handle cache's special case and crossDomain +jQuery.ajaxPrefilter( "script", function( s ) { + if ( s.cache === undefined ) { + s.cache = false; + } + if ( s.crossDomain ) { + s.type = "GET"; + } +} ); + +// Bind script tag hack transport +jQuery.ajaxTransport( "script", function( s ) { + + // This transport only deals with cross domain requests + if ( s.crossDomain ) { + var script, callback; + return { + send: function( _, complete ) { + script = jQuery( " + + + + + + + + + + + + + +
    + + + + + +

    Slot: key

    +

    URI: linkmltr:key

    + + +

    Applicable Classes

    + + + + + + + + + + + + + + + +
    NameDescriptionModifies Slot
    KeyValno
    +

    Properties

    +
      +
    • +

      Range: NONE

      +
    • +
    • +

      Required: True

      +
    • +
    +

    Identifier and Mapping Information

    +

    Schema Source

    +
      +
    • from schema: https://w3id.org/linkml/transformer
    • +
    +

    LinkML Source

    +
    + +
    name: key
    +from_schema: https://w3id.org/linkml/transformer
    +rank: 1000
    +key: true
    +alias: key
    +owner: KeyVal
    +domain_of:
    +- KeyVal
    +required: true
    +
    +
    + +
    + +
    + + +
    +
    + + + + + \ No newline at end of file diff --git a/linkml-map/index.html b/linkml-map/index.html new file mode 100644 index 0000000..f28256b --- /dev/null +++ b/linkml-map/index.html @@ -0,0 +1,89 @@ + + + + + + + + + + + + + + linkml-map - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + +

    linkml-map

    +

    Datamodel for LinkML schema mappings and transformations.

    +

    A mapper generates instances of a target data model from +instances of a source data model. This transformation process +is guided by a TransformationSpecification.

    +

    The specification is independent of any one method for transforming +data. It allows different approaches, including:

    +
      +
    • direct implementation, transforming python or json objects
    • +
    • translation of the specification into SQL commands, to operate on relations
    • +
    • translation of the specification into SPARQL CONSTRUCTs, to operate on triples
    • +
    • translation into another specification language, such as R2RML
    • +
    +

    URI: https://w3id.org/linkml/transformer

    + +
    + + +
    +
    + + + + + \ No newline at end of file diff --git a/mirror_source/index.html b/mirror_source/index.html new file mode 100644 index 0000000..f889065 --- /dev/null +++ b/mirror_source/index.html @@ -0,0 +1,149 @@ + + + + + + + + + + + + + + Slot: mirror_source - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + +

    Slot: mirror_source

    +

    URI: linkmltr:mirror_source

    + + +

    Applicable Classes

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    NameDescriptionModifies Slot
    EnumDerivationA specification of how to derive the value of a target enum from a source enu...no
    ElementDerivationAn abstract grouping for classes that provide a specification of how to deri...no
    PrefixDerivationno
    SlotDerivationA specification of how to derive the value of a target slot from a source slo...no
    ClassDerivationA specification of how to derive a target class from a source classno
    PermissibleValueDerivationA specification of how to derive the value of a PV from a source enumno
    +

    Properties

    + +

    Identifier and Mapping Information

    +

    Schema Source

    +
      +
    • from schema: https://w3id.org/linkml/transformer
    • +
    +

    LinkML Source

    +
    + +
    name: mirror_source
    +from_schema: https://w3id.org/linkml/transformer
    +rank: 1000
    +alias: mirror_source
    +owner: ElementDerivation
    +domain_of:
    +- ElementDerivation
    +range: boolean
    +
    +
    + +
    + +
    + + +
    +
    + + + + + \ No newline at end of file diff --git a/mixins/index.html b/mixins/index.html new file mode 100644 index 0000000..2bbba17 --- /dev/null +++ b/mixins/index.html @@ -0,0 +1,157 @@ + + + + + + + + + + + + + + Slot: mixins - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + +

    Slot: mixins

    +

    URI: linkml:mixins

    + + +

    Applicable Classes

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    NameDescriptionModifies Slot
    EnumDerivationA specification of how to derive the value of a target enum from a source enu...no
    ElementDerivationAn abstract grouping for classes that provide a specification of how to deri...no
    PrefixDerivationno
    SlotDerivationA specification of how to derive the value of a target slot from a source slo...no
    ClassDerivationA specification of how to derive a target class from a source classno
    PermissibleValueDerivationA specification of how to derive the value of a PV from a source enumno
    +

    Properties

    + +

    Identifier and Mapping Information

    +

    Schema Source

    +
      +
    • from schema: https://w3id.org/linkml/transformer
    • +
    +

    LinkML Source

    +
    + +
    name: mixins
    +from_schema: https://w3id.org/linkml/transformer
    +rank: 1000
    +slot_uri: linkml:mixins
    +multivalued: true
    +alias: mixins
    +owner: ElementDerivation
    +domain_of:
    +- ElementDerivation
    +range: ElementDerivation
    +inlined: false
    +
    +
    + +
    + +
    + + +
    +
    + + + + + \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml deleted file mode 100644 index b5bb05b..0000000 --- a/mkdocs.yml +++ /dev/null @@ -1,44 +0,0 @@ -site_name: "LinkML-Map" -theme: -# name: material - name: windmill - features: - - content.tabs.link -plugins: - - search - - mermaid2 - - mkdocstrings: - handlers: - python: - options: - show_source: true - show_root_toc_entry: false - show_category_heading: false - toc_depth: 1 - - autorefs - - mknotebooks: - execute: false -markdown_extensions: -- admonition -- codehilite -- pymdownx.superfences -nav: - - Index: index.md - - Examples: - Tutorial: examples/Tutorial.ipynb - Compilation to SQL: examples/Tutorial-SQLCompiler.ipynb - Metamodel Mapping: examples/MetamodelMapping.ipynb - - Specification: - Data Model: schema/datamodel.md - Compliance Suite: specification/compliance.md - - API: - - Session: api/session.md - - Transformer: api/transformer.md - - Compiler: api/compiler.md - # - Importer: api/importer.md - - Inference: api/inference.md - - Functions: api/functions.md - # - Subsetter: api/subsetter.md - - FAQ: faq.md -site_url: https://linkml.github.io/linkml-map/ -repo_url: https://github.com/linkml/linkml-map/ diff --git a/name/index.html b/name/index.html new file mode 100644 index 0000000..0a687cf --- /dev/null +++ b/name/index.html @@ -0,0 +1,144 @@ + + + + + + + + + + + + + + Slot: name - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + +

    Slot: name

    +

    URI: linkmltr:name

    + + +

    Applicable Classes

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    NameDescriptionModifies Slot
    EnumDerivationA specification of how to derive the value of a target enum from a source enu...no
    ElementDerivationAn abstract grouping for classes that provide a specification of how to deri...no
    PrefixDerivationno
    SlotDerivationA specification of how to derive the value of a target slot from a source slo...no
    ClassDerivationA specification of how to derive a target class from a source classno
    PermissibleValueDerivationA specification of how to derive the value of a PV from a source enumno
    +

    Properties

    +
      +
    • Range: NONE
    • +
    +

    Identifier and Mapping Information

    +

    LinkML Source

    +
    + +
    name: name
    +alias: name
    +domain_of:
    +- ElementDerivation
    +- SlotDerivation
    +- EnumDerivation
    +- PermissibleValueDerivation
    +
    +
    + +
    + +
    + + +
    +
    + + + + + \ No newline at end of file diff --git a/over_slots/index.html b/over_slots/index.html new file mode 100644 index 0000000..054eceb --- /dev/null +++ b/over_slots/index.html @@ -0,0 +1,130 @@ + + + + + + + + + + + + + + Slot: over_slots - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + +

    Slot: over_slots

    +

    URI: linkmltr:over_slots

    + + +

    Applicable Classes

    + + + + + + + + + + + + + + + +
    NameDescriptionModifies Slot
    StringificationConfigurationno
    +

    Properties

    +
      +
    • +

      Range: String

      +
    • +
    • +

      Multivalued: True

      +
    • +
    +

    Identifier and Mapping Information

    +

    Schema Source

    +
      +
    • from schema: https://w3id.org/linkml/transformer
    • +
    +

    LinkML Source

    +
    + +
    name: over_slots
    +from_schema: https://w3id.org/linkml/transformer
    +rank: 1000
    +multivalued: true
    +alias: over_slots
    +owner: StringificationConfiguration
    +domain_of:
    +- StringificationConfiguration
    +range: string
    +
    +
    + +
    + +
    + + +
    +
    + + + + + \ No newline at end of file diff --git a/overrides/index.html b/overrides/index.html new file mode 100644 index 0000000..822938d --- /dev/null +++ b/overrides/index.html @@ -0,0 +1,151 @@ + + + + + + + + + + + + + + Slot: overrides - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + +

    Slot: overrides

    +

    overrides source schema slots

    +

    URI: linkmltr:overrides

    + + +

    Applicable Classes

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    NameDescriptionModifies Slot
    EnumDerivationA specification of how to derive the value of a target enum from a source enu...no
    ElementDerivationAn abstract grouping for classes that provide a specification of how to deri...no
    PrefixDerivationno
    SlotDerivationA specification of how to derive the value of a target slot from a source slo...no
    ClassDerivationA specification of how to derive a target class from a source classno
    PermissibleValueDerivationA specification of how to derive the value of a PV from a source enumno
    +

    Properties

    + +

    Identifier and Mapping Information

    +

    Schema Source

    +
      +
    • from schema: https://w3id.org/linkml/transformer
    • +
    +

    LinkML Source

    +
    + +
    name: overrides
    +description: overrides source schema slots
    +from_schema: https://w3id.org/linkml/transformer
    +rank: 1000
    +alias: overrides
    +owner: ElementDerivation
    +domain_of:
    +- ElementDerivation
    +range: Any
    +
    +
    + +
    + +
    + + +
    +
    + + + + + \ No newline at end of file diff --git a/permissible_value_derivations/index.html b/permissible_value_derivations/index.html new file mode 100644 index 0000000..08b179c --- /dev/null +++ b/permissible_value_derivations/index.html @@ -0,0 +1,133 @@ + + + + + + + + + + + + + + Slot: permissible_value_derivations - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + +

    Slot: permissible_value_derivations

    +

    Instructions on how to derive a set of PVs in the target schema

    +

    URI: linkmltr:permissible_value_derivations

    + + +

    Applicable Classes

    + + + + + + + + + + + + + + + +
    NameDescriptionModifies Slot
    EnumDerivationA specification of how to derive the value of a target enum from a source enu...no
    +

    Properties

    + +

    Identifier and Mapping Information

    +

    Schema Source

    +
      +
    • from schema: https://w3id.org/linkml/transformer
    • +
    +

    LinkML Source

    +
    + +
    name: permissible_value_derivations
    +description: Instructions on how to derive a set of PVs in the target schema
    +from_schema: https://w3id.org/linkml/transformer
    +rank: 1000
    +multivalued: true
    +alias: permissible_value_derivations
    +owner: EnumDerivation
    +domain_of:
    +- EnumDerivation
    +range: PermissibleValueDerivation
    +inlined: true
    +
    +
    + +
    + +
    + + +
    +
    + + + + + \ No newline at end of file diff --git a/populated_from/index.html b/populated_from/index.html new file mode 100644 index 0000000..f017914 --- /dev/null +++ b/populated_from/index.html @@ -0,0 +1,134 @@ + + + + + + + + + + + + + + Slot: populated_from - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + +

    Slot: populated_from

    +

    URI: linkmltr:populated_from

    + + +

    Applicable Classes

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    NameDescriptionModifies Slot
    EnumDerivationA specification of how to derive the value of a target enum from a source enu...no
    PermissibleValueDerivationA specification of how to derive the value of a PV from a source enumno
    SlotDerivationA specification of how to derive the value of a target slot from a source slo...no
    ClassDerivationA specification of how to derive a target class from a source classno
    +

    Properties

    +
      +
    • Range: NONE
    • +
    +

    Identifier and Mapping Information

    +

    LinkML Source

    +
    + +
    name: populated_from
    +alias: populated_from
    +domain_of:
    +- ClassDerivation
    +- SlotDerivation
    +- EnumDerivation
    +- PermissibleValueDerivation
    +
    +
    + +
    + +
    + + +
    +
    + + + + + \ No newline at end of file diff --git a/prefixes/index.html b/prefixes/index.html new file mode 100644 index 0000000..084d737 --- /dev/null +++ b/prefixes/index.html @@ -0,0 +1,134 @@ + + + + + + + + + + + + + + Slot: prefixes - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + +

    Slot: prefixes

    +

    maps prefixes to URL expansions

    +

    URI: sh:declare

    + + +

    Applicable Classes

    + + + + + + + + + + + + + + + +
    NameDescriptionModifies Slot
    TransformationSpecificationA collection of mappings between source and target classesno
    +

    Properties

    +
      +
    • +

      Range: KeyVal

      +
    • +
    • +

      Multivalued: True

      +
    • +
    +

    Identifier and Mapping Information

    +

    Schema Source

    +
      +
    • from schema: https://w3id.org/linkml/transformer
    • +
    +

    LinkML Source

    +
    + +
    name: prefixes
    +description: maps prefixes to URL expansions
    +from_schema: https://w3id.org/linkml/transformer
    +rank: 1000
    +slot_uri: sh:declare
    +multivalued: true
    +alias: prefixes
    +owner: TransformationSpecification
    +domain_of:
    +- TransformationSpecification
    +range: KeyVal
    +inlined: true
    +
    +
    + +
    + +
    + + +
    +
    + + + + + \ No newline at end of file diff --git a/project.Makefile b/project.Makefile deleted file mode 100644 index 9953614..0000000 --- a/project.Makefile +++ /dev/null @@ -1,15 +0,0 @@ -tests/model/%.py: tests/input/%.yaml - $(RUN) gen-python $< > $@.tmp && mv $@.tmp $@ - -specification: src/docs/specification/compliance.md - -docs/specification/compliance.md: tests/test_compliance/test_compliance_suite.py - mkdir -p docs/specification - $(RUN) pytest $< -s -q --tb no --disable-warnings > $@.tmp && perl -pne 's@^\.#@#@' $@.tmp > $@.tmp.md && pandoc -f gfm --toc --toc-depth=2 -s $@.tmp.md -o $@ && rm $@.tmp && rm $@.tmp.md - -%-doctest: % - $(RUN) python -m doctest --option ELLIPSIS --option NORMALIZE_WHITESPACE $< - -doctest: - $(RUN) python -m doctest --option ELLIPSIS --option NORMALIZE_WHITESPACE src/linkml_map/*.py src/linkml_map/*/*.py - diff --git a/pyproject.toml b/pyproject.toml deleted file mode 100644 index 8aa384c..0000000 --- a/pyproject.toml +++ /dev/null @@ -1,183 +0,0 @@ -[project] -name = "linkml-map" -description = "a framework for specifying and executing mappings between data models" -readme = "README.md" -authors = [ - {name = "cmungall", email = "cjm@berkeleybop.org"}, -] -requires-python = "<=3.13,>=3.9" -dynamic = [ "version" ] - -dependencies = [ - "asteval<1,>=0", - "click<9,>=8", - "curies", - "deepdiff>=8.6.1", - "duckdb<1,>=0", - "graphviz<1.0.0,>=0.20.3", - "jinja2<4,>=3", - "lark<2,>=1", - "linkml-runtime>=1.9.1", - "pint<1,>=0", - "pydantic>=2.11.3", - "pyyaml", - "ucumvert<1,>=0", -] - -[dependency-groups] -dev = [ - "deepdiff>=8.6.1", - "deptry<1.0.0,>=0.23.0", - "jupyter<2.0.0,>=1.1.1", - "linkml>=1.8.7", - "mkdocs-mermaid2-plugin<1.0.0,>=0.6.0", - "mkdocs-windmill", - "mkdocstrings[crystal,python]", - "mknotebooks<1.0.0,>=0.8.0", - "pytest>=8.3.5", - "ruff>=0.11.5", - "tox>=4.25.0", -] - -[project.scripts] -linkml-map = "linkml_map.cli.cli:main" - -[tool.deptry] -known_first_party = ["linkml_map"] -extend_exclude = ["docs"] - -# See https://hatch.pypa.io/latest/config/build/#file-selection for how to -# explicitly include files other than default into the build distributions. -[build-system] -requires = ["hatchling", "uv-dynamic-versioning"] -build-backend = "hatchling.build" - -[tool.hatch.version] -source = "uv-dynamic-versioning" - -# Ref.: https://github.com/ninoseki/uv-dynamic-versioning/ -[tool.uv-dynamic-versioning] -vcs = "git" -style = "pep440" -fallback-version = "0.0.0" - - -# Ref: https://github.com/codespell-project/codespell#using-a-config-file -[tool.codespell] -skip = '.git,*.pdf,*.svg,go.sum,*.lock' -check-hidden = true -ignore-regex = '(^\s*"image/\S+": ".*|\b(KEGG.BRITE|mor.nlm.nih.gov)\b)' -ignore-words-list = 'infarction,amination,assertIn,brite,ehr,mor,brite,nin,mirgate' - -[tool.ruff] -line-length = 100 -target-version = "py312" - -[tool.ruff.format] -exclude = [ - "docs/", - "src/linkml_map/datamodel", - "tests/input" -] - -[tool.ruff.lint] -exclude = [ - "docs/", - "src/linkml_map/datamodel", - "tests/input" -] - -select = [ - # core - "F", # Pyflakes - "E", # pycodestyle errors - "W", # pycodestyle warnings - "C90", # mccabe + - "I", # isort - "N", # pep8-naming - "D", # pydocstyle - "UP", # pyupgrade - # extensions - "YTT", # flake8-2020 - "ANN", # flake8-annotations - "ASYNC", # flake8-async - "S", # flake8-bandit - "BLE", # flake8-blind-except - "FBT", # flake8-boolean-trap - "B", # flake8-bugbear - "A", # flake8-builtins - # "COM", # flake8-commas - # "CPY", # flake8-copyright - "C4", # flake8-comprehensions - "DTZ", # flake8-datetimez - "T10", # flake8-debugger - # "DJ", # flake8-django - "EM", # flake8-errmsg - "EXE", # flake8-executable - "FA", # flake8-future-annotations - "ISC", # flake8-implicit-str-concat - "ICN", # flake8-import-conventions - "G", # flake8-logging-format - "INP", # flake8-no-pep420 - "PIE", # flake8-pie - "T20", # flake8-print - "PYI", # flake8-pyi - "PT", # flake8-pytest-style - "Q", # flake8-quotes - "RSE", # flake8-raise - "RET", # flake8-return - "SLF", # flake8-self - "SLOT", # flake8-slots - "SIM", # flake8-simplify - "TID", # flake8-tidy-imports - "TCH", # flake8-type-checking - "INT", # flake8-gettext - "ARG", # flake8-unused-arguments - # "PTH", # flake8-use-pathlib - # "TD", # flake8-todos - # "FIX", # flake8-fixme - "ERA", # eradicate - "PD", # pandas-vet - "PGH", # pygrep-hooks - "PL", # Pylint - "TRY", # tryceratops - "FLY", # flynt - "NPY", # NumPy-specific rules - "AIR", # Airflow - "PERF", # Perflint - "FURB", # refurb - "LOG", # flake8-logging - "RUF", # Ruff-specific rules -] - -ignore = [ - # UP007: non-pep604-annotation-union - fix when 3.9 is dropped - "UP007", - # D200: unnecessary-multiline-docstring - "D200", - # D203: one-blank-line-before-class (conflicts with D211) - "D203", - # D212: multi-line-summary-first-line (conflicts with D213) - "D212", - # E203: whitespace before ',', ';', or ':' - "E203", - # E501: line length (specified elsewhere) - "E501", - # ISC001: conflicts with Ruff's formatter - "ISC001", - # C901: complex-structure - needs code change - "C901", - # E731: lambda-assignment - needs code change - "E731", - # B024: abstract-base-class-without-abstract-method - "B024", - # T201: print - "T201" -] - -[tool.ruff.lint.per-file-ignores] -"tests/**/*.py" = ["S101"] # use of assert - -[tool.ruff.lint.mccabe] -# Flag errors (`C901`) whenever the complexity level exceeds 15. -max-complexity = 15 diff --git a/range/index.html b/range/index.html new file mode 100644 index 0000000..fa8f3cc --- /dev/null +++ b/range/index.html @@ -0,0 +1,125 @@ + + + + + + + + + + + + + + Slot: range - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + +

    Slot: range

    +

    URI: linkml:range

    + + +

    Applicable Classes

    + + + + + + + + + + + + + + + +
    NameDescriptionModifies Slot
    SlotDerivationA specification of how to derive the value of a target slot from a source slo...no
    +

    Properties

    + +

    Identifier and Mapping Information

    +

    Schema Source

    +
      +
    • from schema: https://w3id.org/linkml/transformer
    • +
    +

    LinkML Source

    +
    + +
    name: range
    +from_schema: https://w3id.org/linkml/transformer
    +rank: 1000
    +slot_uri: linkml:range
    +alias: range
    +owner: SlotDerivation
    +domain_of:
    +- SlotDerivation
    +range: string
    +
    +
    + +
    + +
    + + +
    +
    + + + + + \ No newline at end of file diff --git a/reversed/index.html b/reversed/index.html new file mode 100644 index 0000000..0ec4943 --- /dev/null +++ b/reversed/index.html @@ -0,0 +1,124 @@ + + + + + + + + + + + + + + Slot: reversed - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + +

    Slot: reversed

    +

    URI: linkmltr:reversed

    + + +

    Applicable Classes

    + + + + + + + + + + + + + + + +
    NameDescriptionModifies Slot
    StringificationConfigurationno
    +

    Properties

    + +

    Identifier and Mapping Information

    +

    Schema Source

    +
      +
    • from schema: https://w3id.org/linkml/transformer
    • +
    +

    LinkML Source

    +
    + +
    name: reversed
    +from_schema: https://w3id.org/linkml/transformer
    +rank: 1000
    +alias: reversed
    +owner: StringificationConfiguration
    +domain_of:
    +- StringificationConfiguration
    +range: boolean
    +
    +
    + +
    + +
    + + +
    +
    + + + + + \ No newline at end of file diff --git a/search.html b/search.html new file mode 100644 index 0000000..eba5e40 --- /dev/null +++ b/search.html @@ -0,0 +1,84 @@ + + + + + + + + + + + + + + LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + +

    Search Results

    + +
      + Searching... +
    + + + + +
    + + +
    +
    + + + + + \ No newline at end of file diff --git a/search/search_index.json b/search/search_index.json new file mode 100644 index 0000000..702ff84 --- /dev/null +++ b/search/search_index.json @@ -0,0 +1 @@ +{"config":{"indexing":"full","lang":["en"],"min_search_length":3,"prebuild_index":false,"separator":"[\\s\\-]+"},"docs":[{"location":"","text":"LinkML-Map LinkML Map is a framework for specifying and executing mappings between data models. Features: YAML-based lightweight syntax Python library for executing mappings on data files Ability to compile to other frameworks (SQL/DuckDB) Derivation of target (implicit) schemas, allowing easy customization of data models ( profiling ) Simple YAML dictionaries for simple mappings Automatic unit conversion Use of subset of Python to specify complex mappings Visualizations of mappings Mappings are reversible (provided all expressions used are reversible) Compatibility with SSSOM This documentation are available at: linkml.io/linkml-map/ Status: The transformation data model is not yet fully stable, and may be subject to change. Not all parts of the model are implemented in the reference Python framework. Basic idea Given an object that conforms to a LinkML schema,e.g.: given_name: Jane family_name: Doe height_in_cm: 172.0 age_in_years: 33 aliases: [Janey, Janie] Define a mapping in YAML: class_derivations: Individual: populated_from: Person slot_derivations: name: expr: \"{given_name} + ' ' + {family_name}\" description: Concatenating given and family names note this is a bad assumption for names in general, this is just for demonstration height_in_meters: populated_from: height_in_cm unit_conversion: target_unit: m aliases: populated_from: aliases stringification: delimiter: '|' The schema mapping (aka TransformationSpecification ) specifies how to transform the data model. The schema mapping is a collection of one or more ClassDerivation objects, which themselves consist of one or more SlotDerivation objects. Transform the data: linkml-tr map-data -T tr.yaml -s schema.yaml my-data.yaml Giving: name: Jane Doe height_in_meters: 1.72 aliases: Janey|Janie Installation and usage Installation and command line usage: pip[x] install linkml-map cd tests/input/examples/personinfo_basic linkml-tr map-data \\ -T transform/personinfo-to-agent.transform.yaml \\ -s source/personinfo.yaml \\ data/Container-001.yaml \\ -o output/Translated-001.yaml The command line has subcommands for: map-data - map data from a source schema to a target schema derive-schema - derive a target schema from a source schema and a mapping invert - reverses a mapping compile - compiles a mapping to another framework markdown - for generating static sites graphviz - for generating visualizations python - (partial) forthcoming: r2rml , ... Details This repo contains both: A data model for a data model transformation language A reference python implementation The transformation language is specified in terms of LinkML schemas. It is intended to be a ployglot transformation language, used for specifying how to map data models independent of underlying representation (TSVs, JSON/YAML, RDF, SQL Database, ...). Use cases include: ETL and mapping from one data model to another Database migrations (one version of a schema to another) Creating \"profiles\" Specifying mappings between different serializations of a model (e.g. OO to Relational) Mapping between normalized/non-redundant forms and denormalized/query-optimized forms Data Model The data model for transformations mirrors the data model for schemas: A top level TransformationSpecification class contains: Zero or more ClassDerivation objects, specifying how to map to a class, containing Zero or more SlotDerivation objects, specifying how to map to a slot Zero or more EnumDerivation objects, specifying how to map to an enum See the generated docs Conformance Suite The Maps conformance suite contains a collection of tests for each feature of the language. See: Compliance Suite Running the code linkml-tr --help Usage: linkml-tr [OPTIONS] COMMAND [ARGS]... CLI for linkml-map. Options: -v, --verbose -q, --quiet TEXT --help Show this message and exit. Commands: derive-schema Derive a schema from a source schema and a mapping. map-data Map data in a source schema using a transformation. map-data Transforms (maps) data from a source schema to a target schema. This could range from a simple data dictionary mapping through to a complex mappings. cd tests/input/examples/personinfo_basic linkml-tr map-data -T transform/personinfo-to-agent.transform.yaml -s source/personinfo.yaml data/Container-001.yaml derive-schema cd tests/input/examples/personinfo_basic linkml-tr derive-schema -T transform/personinfo-to-agent.transform.yaml source/personinfo.yaml","title":"Index"},{"location":"#linkml-map","text":"LinkML Map is a framework for specifying and executing mappings between data models. Features: YAML-based lightweight syntax Python library for executing mappings on data files Ability to compile to other frameworks (SQL/DuckDB) Derivation of target (implicit) schemas, allowing easy customization of data models ( profiling ) Simple YAML dictionaries for simple mappings Automatic unit conversion Use of subset of Python to specify complex mappings Visualizations of mappings Mappings are reversible (provided all expressions used are reversible) Compatibility with SSSOM This documentation are available at: linkml.io/linkml-map/ Status: The transformation data model is not yet fully stable, and may be subject to change. Not all parts of the model are implemented in the reference Python framework.","title":"LinkML-Map"},{"location":"#basic-idea","text":"Given an object that conforms to a LinkML schema,e.g.: given_name: Jane family_name: Doe height_in_cm: 172.0 age_in_years: 33 aliases: [Janey, Janie] Define a mapping in YAML: class_derivations: Individual: populated_from: Person slot_derivations: name: expr: \"{given_name} + ' ' + {family_name}\" description: Concatenating given and family names note this is a bad assumption for names in general, this is just for demonstration height_in_meters: populated_from: height_in_cm unit_conversion: target_unit: m aliases: populated_from: aliases stringification: delimiter: '|' The schema mapping (aka TransformationSpecification ) specifies how to transform the data model. The schema mapping is a collection of one or more ClassDerivation objects, which themselves consist of one or more SlotDerivation objects. Transform the data: linkml-tr map-data -T tr.yaml -s schema.yaml my-data.yaml Giving: name: Jane Doe height_in_meters: 1.72 aliases: Janey|Janie","title":"Basic idea"},{"location":"#installation-and-usage","text":"Installation and command line usage: pip[x] install linkml-map cd tests/input/examples/personinfo_basic linkml-tr map-data \\ -T transform/personinfo-to-agent.transform.yaml \\ -s source/personinfo.yaml \\ data/Container-001.yaml \\ -o output/Translated-001.yaml The command line has subcommands for: map-data - map data from a source schema to a target schema derive-schema - derive a target schema from a source schema and a mapping invert - reverses a mapping compile - compiles a mapping to another framework markdown - for generating static sites graphviz - for generating visualizations python - (partial) forthcoming: r2rml , ...","title":"Installation and usage"},{"location":"#details","text":"This repo contains both: A data model for a data model transformation language A reference python implementation The transformation language is specified in terms of LinkML schemas. It is intended to be a ployglot transformation language, used for specifying how to map data models independent of underlying representation (TSVs, JSON/YAML, RDF, SQL Database, ...). Use cases include: ETL and mapping from one data model to another Database migrations (one version of a schema to another) Creating \"profiles\" Specifying mappings between different serializations of a model (e.g. OO to Relational) Mapping between normalized/non-redundant forms and denormalized/query-optimized forms","title":"Details"},{"location":"#data-model","text":"The data model for transformations mirrors the data model for schemas: A top level TransformationSpecification class contains: Zero or more ClassDerivation objects, specifying how to map to a class, containing Zero or more SlotDerivation objects, specifying how to map to a slot Zero or more EnumDerivation objects, specifying how to map to an enum See the generated docs","title":"Data Model"},{"location":"#conformance-suite","text":"The Maps conformance suite contains a collection of tests for each feature of the language. See: Compliance Suite","title":"Conformance Suite"},{"location":"#running-the-code","text":"linkml-tr --help Usage: linkml-tr [OPTIONS] COMMAND [ARGS]... CLI for linkml-map. Options: -v, --verbose -q, --quiet TEXT --help Show this message and exit. Commands: derive-schema Derive a schema from a source schema and a mapping. map-data Map data in a source schema using a transformation.","title":"Running the code"},{"location":"#map-data","text":"Transforms (maps) data from a source schema to a target schema. This could range from a simple data dictionary mapping through to a complex mappings. cd tests/input/examples/personinfo_basic linkml-tr map-data -T transform/personinfo-to-agent.transform.yaml -s source/personinfo.yaml data/Container-001.yaml","title":"map-data"},{"location":"#derive-schema","text":"cd tests/input/examples/personinfo_basic linkml-tr derive-schema -T transform/personinfo-to-agent.transform.yaml source/personinfo.yaml","title":"derive-schema"},{"location":"AliasedClass/","text":"Class: AliasedClass alias-class key value pairs for classes URI: linkmltr:AliasedClass classDiagram class AliasedClass AliasedClass : alias AliasedClass --> None : alias AliasedClass : class_named AliasedClass --> None : class_named Slots Name Cardinality and Range Description Inheritance alias 0..1 String name of the class to be aliased direct class_named 0..1 String local alias for the class direct Usages used by used in type used ClassDerivation joins range AliasedClass Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer Mappings Mapping Type Mapped Value self linkmltr:AliasedClass native linkmltr:AliasedClass LinkML Source Direct name: AliasedClass description: alias-class key value pairs for classes from_schema: https://w3id.org/linkml/transformer attributes: alias: name: alias description: name of the class to be aliased from_schema: https://w3id.org/linkml/transformer rank: 1000 key: true domain_of: - AliasedClass required: true class_named: name: class_named description: local alias for the class from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - AliasedClass Induced name: AliasedClass description: alias-class key value pairs for classes from_schema: https://w3id.org/linkml/transformer attributes: alias: name: alias description: name of the class to be aliased from_schema: https://w3id.org/linkml/transformer rank: 1000 key: true alias: alias owner: AliasedClass domain_of: - AliasedClass required: true class_named: name: class_named description: local alias for the class from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: class_named owner: AliasedClass domain_of: - AliasedClass","title":"Class: AliasedClass"},{"location":"AliasedClass/#class-aliasedclass","text":"alias-class key value pairs for classes URI: linkmltr:AliasedClass classDiagram class AliasedClass AliasedClass : alias AliasedClass --> None : alias AliasedClass : class_named AliasedClass --> None : class_named","title":"Class: AliasedClass"},{"location":"AliasedClass/#slots","text":"Name Cardinality and Range Description Inheritance alias 0..1 String name of the class to be aliased direct class_named 0..1 String local alias for the class direct","title":"Slots"},{"location":"AliasedClass/#usages","text":"used by used in type used ClassDerivation joins range AliasedClass","title":"Usages"},{"location":"AliasedClass/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"AliasedClass/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"AliasedClass/#mappings","text":"Mapping Type Mapped Value self linkmltr:AliasedClass native linkmltr:AliasedClass","title":"Mappings"},{"location":"AliasedClass/#linkml-source","text":"","title":"LinkML Source"},{"location":"AliasedClass/#direct","text":"name: AliasedClass description: alias-class key value pairs for classes from_schema: https://w3id.org/linkml/transformer attributes: alias: name: alias description: name of the class to be aliased from_schema: https://w3id.org/linkml/transformer rank: 1000 key: true domain_of: - AliasedClass required: true class_named: name: class_named description: local alias for the class from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - AliasedClass","title":"Direct"},{"location":"AliasedClass/#induced","text":"name: AliasedClass description: alias-class key value pairs for classes from_schema: https://w3id.org/linkml/transformer attributes: alias: name: alias description: name of the class to be aliased from_schema: https://w3id.org/linkml/transformer rank: 1000 key: true alias: alias owner: AliasedClass domain_of: - AliasedClass required: true class_named: name: class_named description: local alias for the class from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: class_named owner: AliasedClass domain_of: - AliasedClass","title":"Induced"},{"location":"Any/","text":"Class: Any URI: linkml:Any classDiagram class Any Slots Name Cardinality and Range Description Inheritance Usages used by used in type used ElementDerivation overrides range Any ClassDerivation overrides range Any SlotDerivation overrides range Any EnumDerivation overrides range Any PermissibleValueDerivation overrides range Any PrefixDerivation overrides range Any KeyVal value range Any CopyDirective exclude range Any CopyDirective include range Any CopyDirective add range Any Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer Mappings Mapping Type Mapped Value self linkml:Any native linkmltr:Any LinkML Source Direct name: Any from_schema: https://w3id.org/linkml/transformer class_uri: linkml:Any Induced name: Any from_schema: https://w3id.org/linkml/transformer class_uri: linkml:Any","title":"Class: Any"},{"location":"Any/#class-any","text":"URI: linkml:Any classDiagram class Any","title":"Class: Any"},{"location":"Any/#slots","text":"Name Cardinality and Range Description Inheritance","title":"Slots"},{"location":"Any/#usages","text":"used by used in type used ElementDerivation overrides range Any ClassDerivation overrides range Any SlotDerivation overrides range Any EnumDerivation overrides range Any PermissibleValueDerivation overrides range Any PrefixDerivation overrides range Any KeyVal value range Any CopyDirective exclude range Any CopyDirective include range Any CopyDirective add range Any","title":"Usages"},{"location":"Any/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Any/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"Any/#mappings","text":"Mapping Type Mapped Value self linkml:Any native linkmltr:Any","title":"Mappings"},{"location":"Any/#linkml-source","text":"","title":"LinkML Source"},{"location":"Any/#direct","text":"name: Any from_schema: https://w3id.org/linkml/transformer class_uri: linkml:Any","title":"Direct"},{"location":"Any/#induced","text":"name: Any from_schema: https://w3id.org/linkml/transformer class_uri: linkml:Any","title":"Induced"},{"location":"Boolean/","text":"Type: Boolean A binary (true or false) value URI: xsd:boolean base : Bool uri : xsd:boolean repr : bool Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer","title":"Type: Boolean"},{"location":"Boolean/#type-boolean","text":"A binary (true or false) value URI: xsd:boolean base : Bool uri : xsd:boolean repr : bool","title":"Type: Boolean"},{"location":"Boolean/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Boolean/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"ClassDerivation/","text":"Class: ClassDerivation A specification of how to derive a target class from a source class. URI: linkmltr:ClassDerivation classDiagram class ClassDerivation ElementDerivation <|-- ClassDerivation ClassDerivation : comments ClassDerivation : copy_directives ClassDerivation --> CopyDirective : copy_directives ClassDerivation : description ClassDerivation --> None : description ClassDerivation : expression_to_expression_mappings ClassDerivation --> KeyVal : expression_to_expression_mappings ClassDerivation : expression_to_value_mappings ClassDerivation --> KeyVal : expression_to_value_mappings ClassDerivation : implements ClassDerivation : is_a ClassDerivation --> ElementDerivation : is_a ClassDerivation : joins ClassDerivation --> AliasedClass : joins ClassDerivation : mirror_source ClassDerivation : mixins ClassDerivation --> ElementDerivation : mixins ClassDerivation : name ClassDerivation --> None : name ClassDerivation : overrides ClassDerivation --> Any : overrides ClassDerivation : populated_from ClassDerivation : slot_derivations ClassDerivation --> SlotDerivation : slot_derivations ClassDerivation : sources ClassDerivation : value_mappings ClassDerivation --> KeyVal : value_mappings Inheritance SpecificationComponent ElementDerivation ClassDerivation Slots Name Cardinality and Range Description Inheritance populated_from 0..1 ClassReference Name of the class in the source schema direct sources 0..* ClassReference direct joins 0..* AliasedClass Additional classes to be joined to derive instances of the target class direct slot_derivations 0..* SlotDerivation direct name 1..1 String Name of the element in the target schema ElementDerivation copy_directives 0..* CopyDirective ElementDerivation overrides 0..1 Any overrides source schema slots ElementDerivation is_a 0..1 ElementDerivation ElementDerivation mixins 0..* ElementDerivation ElementDerivation value_mappings 0..* KeyVal A mapping table that is applied directly to mappings, in order of precedence ElementDerivation expression_to_value_mappings 0..* KeyVal A mapping table in which the keys are expressions ElementDerivation expression_to_expression_mappings 0..* KeyVal A mapping table in which the keys and values are expressions ElementDerivation mirror_source 0..1 Boolean ElementDerivation description 0..1 String description of the specification component SpecificationComponent implements 0..* Uriorcurie A reference to a specification that this component implements SpecificationComponent comments 0..* String A list of comments about this component SpecificationComponent Usages used by used in type used TransformationSpecification class_derivations range ClassDerivation Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer Mappings Mapping Type Mapped Value self linkmltr:ClassDerivation native linkmltr:ClassDerivation LinkML Source Direct name: ClassDerivation description: A specification of how to derive a target class from a source class. from_schema: https://w3id.org/linkml/transformer is_a: ElementDerivation attributes: populated_from: name: populated_from description: Name of the class in the source schema from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: ClassReference sources: name: sources from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: ClassReference joins: name: joins description: Additional classes to be joined to derive instances of the target class comments: - not yet implemented from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - ClassDerivation range: AliasedClass inlined: true slot_derivations: name: slot_derivations from_schema: https://w3id.org/linkml/transformer multivalued: true domain_of: - TransformationSpecification - ClassDerivation range: SlotDerivation inlined: true Induced name: ClassDerivation description: A specification of how to derive a target class from a source class. from_schema: https://w3id.org/linkml/transformer is_a: ElementDerivation attributes: populated_from: name: populated_from description: Name of the class in the source schema from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: populated_from owner: ClassDerivation domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: ClassReference sources: name: sources from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: sources owner: ClassDerivation domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: ClassReference joins: name: joins description: Additional classes to be joined to derive instances of the target class comments: - not yet implemented from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: joins owner: ClassDerivation domain_of: - ClassDerivation range: AliasedClass inlined: true slot_derivations: name: slot_derivations from_schema: https://w3id.org/linkml/transformer multivalued: true alias: slot_derivations owner: ClassDerivation domain_of: - TransformationSpecification - ClassDerivation range: SlotDerivation inlined: true name: name: name description: Name of the element in the target schema from_schema: https://w3id.org/linkml/transformer rank: 1000 key: true alias: name owner: ClassDerivation domain_of: - ElementDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: string required: true copy_directives: name: copy_directives from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: copy_directives owner: ClassDerivation domain_of: - ElementDerivation range: CopyDirective inlined: true overrides: name: overrides description: overrides source schema slots from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: overrides owner: ClassDerivation domain_of: - ElementDerivation range: Any is_a: name: is_a from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:is_a alias: is_a owner: ClassDerivation domain_of: - ElementDerivation range: ElementDerivation mixins: name: mixins from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:mixins multivalued: true alias: mixins owner: ClassDerivation domain_of: - ElementDerivation range: ElementDerivation inlined: false value_mappings: name: value_mappings description: A mapping table that is applied directly to mappings, in order of precedence from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: value_mappings owner: ClassDerivation domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_value_mappings: name: expression_to_value_mappings description: A mapping table in which the keys are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_value_mappings owner: ClassDerivation domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_expression_mappings: name: expression_to_expression_mappings description: A mapping table in which the keys and values are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_expression_mappings owner: ClassDerivation domain_of: - ElementDerivation range: KeyVal inlined: true mirror_source: name: mirror_source from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: mirror_source owner: ClassDerivation domain_of: - ElementDerivation range: boolean description: name: description description: description of the specification component from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: dcterms:description alias: description owner: ClassDerivation domain_of: - SpecificationComponent range: string implements: name: implements description: A reference to a specification that this component implements. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: implements owner: ClassDerivation domain_of: - SpecificationComponent range: uriorcurie comments: name: comments description: A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use. from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: rdfs:comment multivalued: true alias: comments owner: ClassDerivation domain_of: - SpecificationComponent range: string","title":"Class: ClassDerivation"},{"location":"ClassDerivation/#class-classderivation","text":"A specification of how to derive a target class from a source class. URI: linkmltr:ClassDerivation classDiagram class ClassDerivation ElementDerivation <|-- ClassDerivation ClassDerivation : comments ClassDerivation : copy_directives ClassDerivation --> CopyDirective : copy_directives ClassDerivation : description ClassDerivation --> None : description ClassDerivation : expression_to_expression_mappings ClassDerivation --> KeyVal : expression_to_expression_mappings ClassDerivation : expression_to_value_mappings ClassDerivation --> KeyVal : expression_to_value_mappings ClassDerivation : implements ClassDerivation : is_a ClassDerivation --> ElementDerivation : is_a ClassDerivation : joins ClassDerivation --> AliasedClass : joins ClassDerivation : mirror_source ClassDerivation : mixins ClassDerivation --> ElementDerivation : mixins ClassDerivation : name ClassDerivation --> None : name ClassDerivation : overrides ClassDerivation --> Any : overrides ClassDerivation : populated_from ClassDerivation : slot_derivations ClassDerivation --> SlotDerivation : slot_derivations ClassDerivation : sources ClassDerivation : value_mappings ClassDerivation --> KeyVal : value_mappings","title":"Class: ClassDerivation"},{"location":"ClassDerivation/#inheritance","text":"SpecificationComponent ElementDerivation ClassDerivation","title":"Inheritance"},{"location":"ClassDerivation/#slots","text":"Name Cardinality and Range Description Inheritance populated_from 0..1 ClassReference Name of the class in the source schema direct sources 0..* ClassReference direct joins 0..* AliasedClass Additional classes to be joined to derive instances of the target class direct slot_derivations 0..* SlotDerivation direct name 1..1 String Name of the element in the target schema ElementDerivation copy_directives 0..* CopyDirective ElementDerivation overrides 0..1 Any overrides source schema slots ElementDerivation is_a 0..1 ElementDerivation ElementDerivation mixins 0..* ElementDerivation ElementDerivation value_mappings 0..* KeyVal A mapping table that is applied directly to mappings, in order of precedence ElementDerivation expression_to_value_mappings 0..* KeyVal A mapping table in which the keys are expressions ElementDerivation expression_to_expression_mappings 0..* KeyVal A mapping table in which the keys and values are expressions ElementDerivation mirror_source 0..1 Boolean ElementDerivation description 0..1 String description of the specification component SpecificationComponent implements 0..* Uriorcurie A reference to a specification that this component implements SpecificationComponent comments 0..* String A list of comments about this component SpecificationComponent","title":"Slots"},{"location":"ClassDerivation/#usages","text":"used by used in type used TransformationSpecification class_derivations range ClassDerivation","title":"Usages"},{"location":"ClassDerivation/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ClassDerivation/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"ClassDerivation/#mappings","text":"Mapping Type Mapped Value self linkmltr:ClassDerivation native linkmltr:ClassDerivation","title":"Mappings"},{"location":"ClassDerivation/#linkml-source","text":"","title":"LinkML Source"},{"location":"ClassDerivation/#direct","text":"name: ClassDerivation description: A specification of how to derive a target class from a source class. from_schema: https://w3id.org/linkml/transformer is_a: ElementDerivation attributes: populated_from: name: populated_from description: Name of the class in the source schema from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: ClassReference sources: name: sources from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: ClassReference joins: name: joins description: Additional classes to be joined to derive instances of the target class comments: - not yet implemented from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - ClassDerivation range: AliasedClass inlined: true slot_derivations: name: slot_derivations from_schema: https://w3id.org/linkml/transformer multivalued: true domain_of: - TransformationSpecification - ClassDerivation range: SlotDerivation inlined: true","title":"Direct"},{"location":"ClassDerivation/#induced","text":"name: ClassDerivation description: A specification of how to derive a target class from a source class. from_schema: https://w3id.org/linkml/transformer is_a: ElementDerivation attributes: populated_from: name: populated_from description: Name of the class in the source schema from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: populated_from owner: ClassDerivation domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: ClassReference sources: name: sources from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: sources owner: ClassDerivation domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: ClassReference joins: name: joins description: Additional classes to be joined to derive instances of the target class comments: - not yet implemented from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: joins owner: ClassDerivation domain_of: - ClassDerivation range: AliasedClass inlined: true slot_derivations: name: slot_derivations from_schema: https://w3id.org/linkml/transformer multivalued: true alias: slot_derivations owner: ClassDerivation domain_of: - TransformationSpecification - ClassDerivation range: SlotDerivation inlined: true name: name: name description: Name of the element in the target schema from_schema: https://w3id.org/linkml/transformer rank: 1000 key: true alias: name owner: ClassDerivation domain_of: - ElementDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: string required: true copy_directives: name: copy_directives from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: copy_directives owner: ClassDerivation domain_of: - ElementDerivation range: CopyDirective inlined: true overrides: name: overrides description: overrides source schema slots from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: overrides owner: ClassDerivation domain_of: - ElementDerivation range: Any is_a: name: is_a from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:is_a alias: is_a owner: ClassDerivation domain_of: - ElementDerivation range: ElementDerivation mixins: name: mixins from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:mixins multivalued: true alias: mixins owner: ClassDerivation domain_of: - ElementDerivation range: ElementDerivation inlined: false value_mappings: name: value_mappings description: A mapping table that is applied directly to mappings, in order of precedence from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: value_mappings owner: ClassDerivation domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_value_mappings: name: expression_to_value_mappings description: A mapping table in which the keys are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_value_mappings owner: ClassDerivation domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_expression_mappings: name: expression_to_expression_mappings description: A mapping table in which the keys and values are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_expression_mappings owner: ClassDerivation domain_of: - ElementDerivation range: KeyVal inlined: true mirror_source: name: mirror_source from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: mirror_source owner: ClassDerivation domain_of: - ElementDerivation range: boolean description: name: description description: description of the specification component from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: dcterms:description alias: description owner: ClassDerivation domain_of: - SpecificationComponent range: string implements: name: implements description: A reference to a specification that this component implements. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: implements owner: ClassDerivation domain_of: - SpecificationComponent range: uriorcurie comments: name: comments description: A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use. from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: rdfs:comment multivalued: true alias: comments owner: ClassDerivation domain_of: - SpecificationComponent range: string","title":"Induced"},{"location":"ClassReference/","text":"Type: ClassReference URI: xsd:string base : str uri : xsd:string typeof : string Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer","title":"Type: ClassReference"},{"location":"ClassReference/#type-classreference","text":"URI: xsd:string base : str uri : xsd:string typeof : string","title":"Type: ClassReference"},{"location":"ClassReference/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ClassReference/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"CollectionType/","text":"Enum: CollectionType URI: CollectionType Permissible Values Value Meaning Description SingleValued None MultiValued None MultiValuedList None MultiValuedDict None Slots Name Description cast_collection_as Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer LinkML Source name: CollectionType from_schema: https://w3id.org/linkml/transformer rank: 1000 permissible_values: SingleValued: text: SingleValued MultiValued: text: MultiValued MultiValuedList: text: MultiValuedList MultiValuedDict: text: MultiValuedDict","title":"Enum: CollectionType"},{"location":"CollectionType/#enum-collectiontype","text":"URI: CollectionType","title":"Enum: CollectionType"},{"location":"CollectionType/#permissible-values","text":"Value Meaning Description SingleValued None MultiValued None MultiValuedList None MultiValuedDict None","title":"Permissible Values"},{"location":"CollectionType/#slots","text":"Name Description cast_collection_as","title":"Slots"},{"location":"CollectionType/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"CollectionType/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"CollectionType/#linkml-source","text":"name: CollectionType from_schema: https://w3id.org/linkml/transformer rank: 1000 permissible_values: SingleValued: text: SingleValued MultiValued: text: MultiValued MultiValuedList: text: MultiValuedList MultiValuedDict: text: MultiValuedDict","title":"LinkML Source"},{"location":"CopyDirective/","text":"Class: CopyDirective Instructs a Schema Mapper in how to map to a target schema. Not used for data transformation. URI: linkmltr:CopyDirective classDiagram class CopyDirective CopyDirective : add CopyDirective --> Any : add CopyDirective : copy_all CopyDirective : element_name CopyDirective --> None : element_name CopyDirective : exclude CopyDirective --> Any : exclude CopyDirective : exclude_all CopyDirective : include CopyDirective --> Any : include Slots Name Cardinality and Range Description Inheritance element_name 0..1 String direct copy_all 0..1 Boolean direct exclude_all 0..1 Boolean direct exclude 0..1 Any direct include 0..1 Any direct add 0..1 Any direct Usages used by used in type used ElementDerivation copy_directives range CopyDirective ClassDerivation copy_directives range CopyDirective SlotDerivation copy_directives range CopyDirective EnumDerivation copy_directives range CopyDirective PermissibleValueDerivation copy_directives range CopyDirective PrefixDerivation copy_directives range CopyDirective Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer Mappings Mapping Type Mapped Value self linkmltr:CopyDirective native linkmltr:CopyDirective LinkML Source Direct name: CopyDirective description: Instructs a Schema Mapper in how to map to a target schema. Not used for data transformation. from_schema: https://w3id.org/linkml/transformer status: testing attributes: element_name: name: element_name from_schema: https://w3id.org/linkml/transformer rank: 1000 key: true domain_of: - CopyDirective required: true copy_all: name: copy_all from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - CopyDirective range: boolean exclude_all: name: exclude_all from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - CopyDirective range: boolean exclude: name: exclude from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - CopyDirective range: Any include: name: include from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - CopyDirective range: Any add: name: add from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - CopyDirective range: Any Induced name: CopyDirective description: Instructs a Schema Mapper in how to map to a target schema. Not used for data transformation. from_schema: https://w3id.org/linkml/transformer status: testing attributes: element_name: name: element_name from_schema: https://w3id.org/linkml/transformer rank: 1000 key: true alias: element_name owner: CopyDirective domain_of: - CopyDirective required: true copy_all: name: copy_all from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: copy_all owner: CopyDirective domain_of: - CopyDirective range: boolean exclude_all: name: exclude_all from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: exclude_all owner: CopyDirective domain_of: - CopyDirective range: boolean exclude: name: exclude from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: exclude owner: CopyDirective domain_of: - CopyDirective range: Any include: name: include from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: include owner: CopyDirective domain_of: - CopyDirective range: Any add: name: add from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: add owner: CopyDirective domain_of: - CopyDirective range: Any","title":"Class: CopyDirective"},{"location":"CopyDirective/#class-copydirective","text":"Instructs a Schema Mapper in how to map to a target schema. Not used for data transformation. URI: linkmltr:CopyDirective classDiagram class CopyDirective CopyDirective : add CopyDirective --> Any : add CopyDirective : copy_all CopyDirective : element_name CopyDirective --> None : element_name CopyDirective : exclude CopyDirective --> Any : exclude CopyDirective : exclude_all CopyDirective : include CopyDirective --> Any : include","title":"Class: CopyDirective"},{"location":"CopyDirective/#slots","text":"Name Cardinality and Range Description Inheritance element_name 0..1 String direct copy_all 0..1 Boolean direct exclude_all 0..1 Boolean direct exclude 0..1 Any direct include 0..1 Any direct add 0..1 Any direct","title":"Slots"},{"location":"CopyDirective/#usages","text":"used by used in type used ElementDerivation copy_directives range CopyDirective ClassDerivation copy_directives range CopyDirective SlotDerivation copy_directives range CopyDirective EnumDerivation copy_directives range CopyDirective PermissibleValueDerivation copy_directives range CopyDirective PrefixDerivation copy_directives range CopyDirective","title":"Usages"},{"location":"CopyDirective/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"CopyDirective/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"CopyDirective/#mappings","text":"Mapping Type Mapped Value self linkmltr:CopyDirective native linkmltr:CopyDirective","title":"Mappings"},{"location":"CopyDirective/#linkml-source","text":"","title":"LinkML Source"},{"location":"CopyDirective/#direct","text":"name: CopyDirective description: Instructs a Schema Mapper in how to map to a target schema. Not used for data transformation. from_schema: https://w3id.org/linkml/transformer status: testing attributes: element_name: name: element_name from_schema: https://w3id.org/linkml/transformer rank: 1000 key: true domain_of: - CopyDirective required: true copy_all: name: copy_all from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - CopyDirective range: boolean exclude_all: name: exclude_all from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - CopyDirective range: boolean exclude: name: exclude from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - CopyDirective range: Any include: name: include from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - CopyDirective range: Any add: name: add from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - CopyDirective range: Any","title":"Direct"},{"location":"CopyDirective/#induced","text":"name: CopyDirective description: Instructs a Schema Mapper in how to map to a target schema. Not used for data transformation. from_schema: https://w3id.org/linkml/transformer status: testing attributes: element_name: name: element_name from_schema: https://w3id.org/linkml/transformer rank: 1000 key: true alias: element_name owner: CopyDirective domain_of: - CopyDirective required: true copy_all: name: copy_all from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: copy_all owner: CopyDirective domain_of: - CopyDirective range: boolean exclude_all: name: exclude_all from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: exclude_all owner: CopyDirective domain_of: - CopyDirective range: boolean exclude: name: exclude from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: exclude owner: CopyDirective domain_of: - CopyDirective range: Any include: name: include from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: include owner: CopyDirective domain_of: - CopyDirective range: Any add: name: add from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: add owner: CopyDirective domain_of: - CopyDirective range: Any","title":"Induced"},{"location":"Curie/","text":"Type: Curie a compact URI URI: xsd:string base : Curie uri : xsd:string repr : str Comments in RDF serializations this MUST be expanded to a URI in non-RDF serializations MAY be serialized as the compact representation Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer","title":"Type: Curie"},{"location":"Curie/#type-curie","text":"a compact URI URI: xsd:string base : Curie uri : xsd:string repr : str","title":"Type: Curie"},{"location":"Curie/#comments","text":"in RDF serializations this MUST be expanded to a URI in non-RDF serializations MAY be serialized as the compact representation","title":"Comments"},{"location":"Curie/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Curie/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"Date/","text":"Type: Date a date (year, month and day) in an idealized calendar URI: xsd:date base : XSDDate uri : xsd:date repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer","title":"Type: Date"},{"location":"Date/#type-date","text":"a date (year, month and day) in an idealized calendar URI: xsd:date base : XSDDate uri : xsd:date repr : str","title":"Type: Date"},{"location":"Date/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Date/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"DateOrDatetime/","text":"Type: DateOrDatetime Either a date or a datetime URI: linkml:DateOrDatetime base : str uri : linkml:DateOrDatetime repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer","title":"Type: DateOrDatetime"},{"location":"DateOrDatetime/#type-dateordatetime","text":"Either a date or a datetime URI: linkml:DateOrDatetime base : str uri : linkml:DateOrDatetime repr : str","title":"Type: DateOrDatetime"},{"location":"DateOrDatetime/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"DateOrDatetime/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"Datetime/","text":"Type: Datetime The combination of a date and time URI: xsd:dateTime base : XSDDateTime uri : xsd:dateTime repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer","title":"Type: Datetime"},{"location":"Datetime/#type-datetime","text":"The combination of a date and time URI: xsd:dateTime base : XSDDateTime uri : xsd:dateTime repr : str","title":"Type: Datetime"},{"location":"Datetime/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Datetime/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"Decimal/","text":"Type: Decimal A real number with arbitrary precision that conforms to the xsd:decimal specification URI: xsd:decimal base : Decimal uri : xsd:decimal Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer","title":"Type: Decimal"},{"location":"Decimal/#type-decimal","text":"A real number with arbitrary precision that conforms to the xsd:decimal specification URI: xsd:decimal base : Decimal uri : xsd:decimal","title":"Type: Decimal"},{"location":"Decimal/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Decimal/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"Double/","text":"Type: Double A real number that conforms to the xsd:double specification URI: xsd:double base : float uri : xsd:double Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer","title":"Type: Double"},{"location":"Double/#type-double","text":"A real number that conforms to the xsd:double specification URI: xsd:double base : float uri : xsd:double","title":"Type: Double"},{"location":"Double/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Double/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"ElementDerivation/","text":"Class: ElementDerivation An abstract grouping for classes that provide a specification of how to derive a target element from a source element. NOTE : this is an abstract class and should not be instantiated directly URI: linkmltr:ElementDerivation classDiagram class ElementDerivation SpecificationComponent <|-- ElementDerivation ElementDerivation <|-- ClassDerivation ElementDerivation <|-- SlotDerivation ElementDerivation <|-- EnumDerivation ElementDerivation <|-- PermissibleValueDerivation ElementDerivation <|-- PrefixDerivation ElementDerivation : comments ElementDerivation : copy_directives ElementDerivation --> CopyDirective : copy_directives ElementDerivation : description ElementDerivation --> None : description ElementDerivation : expression_to_expression_mappings ElementDerivation --> KeyVal : expression_to_expression_mappings ElementDerivation : expression_to_value_mappings ElementDerivation --> KeyVal : expression_to_value_mappings ElementDerivation : implements ElementDerivation : is_a ElementDerivation --> ElementDerivation : is_a ElementDerivation : mirror_source ElementDerivation : mixins ElementDerivation --> ElementDerivation : mixins ElementDerivation : name ElementDerivation --> None : name ElementDerivation : overrides ElementDerivation --> Any : overrides ElementDerivation : value_mappings ElementDerivation --> KeyVal : value_mappings Inheritance SpecificationComponent ElementDerivation ClassDerivation SlotDerivation EnumDerivation PermissibleValueDerivation PrefixDerivation Slots Name Cardinality and Range Description Inheritance name 0..1 String Name of the element in the target schema direct copy_directives 0..* CopyDirective direct overrides 0..1 Any overrides source schema slots direct is_a 0..1 ElementDerivation direct mixins 0..* ElementDerivation direct value_mappings 0..* KeyVal A mapping table that is applied directly to mappings, in order of precedence direct expression_to_value_mappings 0..* KeyVal A mapping table in which the keys are expressions direct expression_to_expression_mappings 0..* KeyVal A mapping table in which the keys and values are expressions direct mirror_source 0..1 Boolean direct description 0..1 String description of the specification component SpecificationComponent implements 0..* Uriorcurie A reference to a specification that this component implements SpecificationComponent comments 0..* String A list of comments about this component SpecificationComponent Usages used by used in type used ElementDerivation is_a range ElementDerivation ElementDerivation mixins range ElementDerivation ClassDerivation is_a range ElementDerivation ClassDerivation mixins range ElementDerivation SlotDerivation is_a range ElementDerivation SlotDerivation mixins range ElementDerivation EnumDerivation is_a range ElementDerivation EnumDerivation mixins range ElementDerivation PermissibleValueDerivation is_a range ElementDerivation PermissibleValueDerivation mixins range ElementDerivation PrefixDerivation is_a range ElementDerivation PrefixDerivation mixins range ElementDerivation Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer Mappings Mapping Type Mapped Value self linkmltr:ElementDerivation native linkmltr:ElementDerivation LinkML Source Direct name: ElementDerivation description: An abstract grouping for classes that provide a specification of how to derive a target element from a source element. from_schema: https://w3id.org/linkml/transformer is_a: SpecificationComponent abstract: true attributes: name: name: name description: Name of the element in the target schema from_schema: https://w3id.org/linkml/transformer rank: 1000 key: true domain_of: - ElementDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation required: true copy_directives: name: copy_directives from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - ElementDerivation range: CopyDirective inlined: true overrides: name: overrides description: overrides source schema slots from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - ElementDerivation range: Any is_a: name: is_a from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:is_a domain_of: - ElementDerivation range: ElementDerivation mixins: name: mixins from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:mixins multivalued: true domain_of: - ElementDerivation range: ElementDerivation inlined: false value_mappings: name: value_mappings description: A mapping table that is applied directly to mappings, in order of precedence from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_value_mappings: name: expression_to_value_mappings description: A mapping table in which the keys are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_expression_mappings: name: expression_to_expression_mappings description: A mapping table in which the keys and values are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - ElementDerivation range: KeyVal inlined: true mirror_source: name: mirror_source from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - ElementDerivation range: boolean Induced name: ElementDerivation description: An abstract grouping for classes that provide a specification of how to derive a target element from a source element. from_schema: https://w3id.org/linkml/transformer is_a: SpecificationComponent abstract: true attributes: name: name: name description: Name of the element in the target schema from_schema: https://w3id.org/linkml/transformer rank: 1000 key: true alias: name owner: ElementDerivation domain_of: - ElementDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation required: true copy_directives: name: copy_directives from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: copy_directives owner: ElementDerivation domain_of: - ElementDerivation range: CopyDirective inlined: true overrides: name: overrides description: overrides source schema slots from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: overrides owner: ElementDerivation domain_of: - ElementDerivation range: Any is_a: name: is_a from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:is_a alias: is_a owner: ElementDerivation domain_of: - ElementDerivation range: ElementDerivation mixins: name: mixins from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:mixins multivalued: true alias: mixins owner: ElementDerivation domain_of: - ElementDerivation range: ElementDerivation inlined: false value_mappings: name: value_mappings description: A mapping table that is applied directly to mappings, in order of precedence from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: value_mappings owner: ElementDerivation domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_value_mappings: name: expression_to_value_mappings description: A mapping table in which the keys are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_value_mappings owner: ElementDerivation domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_expression_mappings: name: expression_to_expression_mappings description: A mapping table in which the keys and values are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_expression_mappings owner: ElementDerivation domain_of: - ElementDerivation range: KeyVal inlined: true mirror_source: name: mirror_source from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: mirror_source owner: ElementDerivation domain_of: - ElementDerivation range: boolean description: name: description description: description of the specification component from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: dcterms:description alias: description owner: ElementDerivation domain_of: - SpecificationComponent range: string implements: name: implements description: A reference to a specification that this component implements. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: implements owner: ElementDerivation domain_of: - SpecificationComponent range: uriorcurie comments: name: comments description: A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use. from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: rdfs:comment multivalued: true alias: comments owner: ElementDerivation domain_of: - SpecificationComponent range: string","title":"Class: ElementDerivation"},{"location":"ElementDerivation/#class-elementderivation","text":"An abstract grouping for classes that provide a specification of how to derive a target element from a source element. NOTE : this is an abstract class and should not be instantiated directly URI: linkmltr:ElementDerivation classDiagram class ElementDerivation SpecificationComponent <|-- ElementDerivation ElementDerivation <|-- ClassDerivation ElementDerivation <|-- SlotDerivation ElementDerivation <|-- EnumDerivation ElementDerivation <|-- PermissibleValueDerivation ElementDerivation <|-- PrefixDerivation ElementDerivation : comments ElementDerivation : copy_directives ElementDerivation --> CopyDirective : copy_directives ElementDerivation : description ElementDerivation --> None : description ElementDerivation : expression_to_expression_mappings ElementDerivation --> KeyVal : expression_to_expression_mappings ElementDerivation : expression_to_value_mappings ElementDerivation --> KeyVal : expression_to_value_mappings ElementDerivation : implements ElementDerivation : is_a ElementDerivation --> ElementDerivation : is_a ElementDerivation : mirror_source ElementDerivation : mixins ElementDerivation --> ElementDerivation : mixins ElementDerivation : name ElementDerivation --> None : name ElementDerivation : overrides ElementDerivation --> Any : overrides ElementDerivation : value_mappings ElementDerivation --> KeyVal : value_mappings","title":"Class: ElementDerivation"},{"location":"ElementDerivation/#inheritance","text":"SpecificationComponent ElementDerivation ClassDerivation SlotDerivation EnumDerivation PermissibleValueDerivation PrefixDerivation","title":"Inheritance"},{"location":"ElementDerivation/#slots","text":"Name Cardinality and Range Description Inheritance name 0..1 String Name of the element in the target schema direct copy_directives 0..* CopyDirective direct overrides 0..1 Any overrides source schema slots direct is_a 0..1 ElementDerivation direct mixins 0..* ElementDerivation direct value_mappings 0..* KeyVal A mapping table that is applied directly to mappings, in order of precedence direct expression_to_value_mappings 0..* KeyVal A mapping table in which the keys are expressions direct expression_to_expression_mappings 0..* KeyVal A mapping table in which the keys and values are expressions direct mirror_source 0..1 Boolean direct description 0..1 String description of the specification component SpecificationComponent implements 0..* Uriorcurie A reference to a specification that this component implements SpecificationComponent comments 0..* String A list of comments about this component SpecificationComponent","title":"Slots"},{"location":"ElementDerivation/#usages","text":"used by used in type used ElementDerivation is_a range ElementDerivation ElementDerivation mixins range ElementDerivation ClassDerivation is_a range ElementDerivation ClassDerivation mixins range ElementDerivation SlotDerivation is_a range ElementDerivation SlotDerivation mixins range ElementDerivation EnumDerivation is_a range ElementDerivation EnumDerivation mixins range ElementDerivation PermissibleValueDerivation is_a range ElementDerivation PermissibleValueDerivation mixins range ElementDerivation PrefixDerivation is_a range ElementDerivation PrefixDerivation mixins range ElementDerivation","title":"Usages"},{"location":"ElementDerivation/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ElementDerivation/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"ElementDerivation/#mappings","text":"Mapping Type Mapped Value self linkmltr:ElementDerivation native linkmltr:ElementDerivation","title":"Mappings"},{"location":"ElementDerivation/#linkml-source","text":"","title":"LinkML Source"},{"location":"ElementDerivation/#direct","text":"name: ElementDerivation description: An abstract grouping for classes that provide a specification of how to derive a target element from a source element. from_schema: https://w3id.org/linkml/transformer is_a: SpecificationComponent abstract: true attributes: name: name: name description: Name of the element in the target schema from_schema: https://w3id.org/linkml/transformer rank: 1000 key: true domain_of: - ElementDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation required: true copy_directives: name: copy_directives from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - ElementDerivation range: CopyDirective inlined: true overrides: name: overrides description: overrides source schema slots from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - ElementDerivation range: Any is_a: name: is_a from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:is_a domain_of: - ElementDerivation range: ElementDerivation mixins: name: mixins from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:mixins multivalued: true domain_of: - ElementDerivation range: ElementDerivation inlined: false value_mappings: name: value_mappings description: A mapping table that is applied directly to mappings, in order of precedence from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_value_mappings: name: expression_to_value_mappings description: A mapping table in which the keys are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_expression_mappings: name: expression_to_expression_mappings description: A mapping table in which the keys and values are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - ElementDerivation range: KeyVal inlined: true mirror_source: name: mirror_source from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - ElementDerivation range: boolean","title":"Direct"},{"location":"ElementDerivation/#induced","text":"name: ElementDerivation description: An abstract grouping for classes that provide a specification of how to derive a target element from a source element. from_schema: https://w3id.org/linkml/transformer is_a: SpecificationComponent abstract: true attributes: name: name: name description: Name of the element in the target schema from_schema: https://w3id.org/linkml/transformer rank: 1000 key: true alias: name owner: ElementDerivation domain_of: - ElementDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation required: true copy_directives: name: copy_directives from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: copy_directives owner: ElementDerivation domain_of: - ElementDerivation range: CopyDirective inlined: true overrides: name: overrides description: overrides source schema slots from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: overrides owner: ElementDerivation domain_of: - ElementDerivation range: Any is_a: name: is_a from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:is_a alias: is_a owner: ElementDerivation domain_of: - ElementDerivation range: ElementDerivation mixins: name: mixins from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:mixins multivalued: true alias: mixins owner: ElementDerivation domain_of: - ElementDerivation range: ElementDerivation inlined: false value_mappings: name: value_mappings description: A mapping table that is applied directly to mappings, in order of precedence from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: value_mappings owner: ElementDerivation domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_value_mappings: name: expression_to_value_mappings description: A mapping table in which the keys are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_value_mappings owner: ElementDerivation domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_expression_mappings: name: expression_to_expression_mappings description: A mapping table in which the keys and values are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_expression_mappings owner: ElementDerivation domain_of: - ElementDerivation range: KeyVal inlined: true mirror_source: name: mirror_source from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: mirror_source owner: ElementDerivation domain_of: - ElementDerivation range: boolean description: name: description description: description of the specification component from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: dcterms:description alias: description owner: ElementDerivation domain_of: - SpecificationComponent range: string implements: name: implements description: A reference to a specification that this component implements. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: implements owner: ElementDerivation domain_of: - SpecificationComponent range: uriorcurie comments: name: comments description: A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use. from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: rdfs:comment multivalued: true alias: comments owner: ElementDerivation domain_of: - SpecificationComponent range: string","title":"Induced"},{"location":"EnumDerivation/","text":"Class: EnumDerivation A specification of how to derive the value of a target enum from a source enum URI: linkmltr:EnumDerivation classDiagram class EnumDerivation ElementDerivation <|-- EnumDerivation EnumDerivation : comments EnumDerivation : copy_directives EnumDerivation --> CopyDirective : copy_directives EnumDerivation : description EnumDerivation --> None : description EnumDerivation : expr EnumDerivation : expression_to_expression_mappings EnumDerivation --> KeyVal : expression_to_expression_mappings EnumDerivation : expression_to_value_mappings EnumDerivation --> KeyVal : expression_to_value_mappings EnumDerivation : hide EnumDerivation : implements EnumDerivation : is_a EnumDerivation --> ElementDerivation : is_a EnumDerivation : mirror_source EnumDerivation : mixins EnumDerivation --> ElementDerivation : mixins EnumDerivation : name EnumDerivation --> None : name EnumDerivation : overrides EnumDerivation --> Any : overrides EnumDerivation : permissible_value_derivations EnumDerivation --> PermissibleValueDerivation : permissible_value_derivations EnumDerivation : populated_from EnumDerivation : sources EnumDerivation : value_mappings EnumDerivation --> KeyVal : value_mappings Inheritance SpecificationComponent ElementDerivation EnumDerivation Slots Name Cardinality and Range Description Inheritance name 0..1 String Target enum name direct populated_from 0..1 EnumReference Source enum name direct sources 0..* EnumReference direct expr 0..1 String An expression to be evaluated on the source object to derive the target slot direct hide 0..1 Boolean True if this is suppressed direct permissible_value_derivations 0..* PermissibleValueDerivation Instructions on how to derive a set of PVs in the target schema direct copy_directives 0..* CopyDirective ElementDerivation overrides 0..1 Any overrides source schema slots ElementDerivation is_a 0..1 ElementDerivation ElementDerivation mixins 0..* ElementDerivation ElementDerivation value_mappings 0..* KeyVal A mapping table that is applied directly to mappings, in order of precedence ElementDerivation expression_to_value_mappings 0..* KeyVal A mapping table in which the keys are expressions ElementDerivation expression_to_expression_mappings 0..* KeyVal A mapping table in which the keys and values are expressions ElementDerivation mirror_source 0..1 Boolean ElementDerivation description 0..1 String description of the specification component SpecificationComponent implements 0..* Uriorcurie A reference to a specification that this component implements SpecificationComponent comments 0..* String A list of comments about this component SpecificationComponent Usages used by used in type used TransformationSpecification enum_derivations range EnumDerivation Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer Mappings Mapping Type Mapped Value self linkmltr:EnumDerivation native linkmltr:EnumDerivation LinkML Source Direct name: EnumDerivation description: A specification of how to derive the value of a target enum from a source enum from_schema: https://w3id.org/linkml/transformer is_a: ElementDerivation attributes: name: name: name description: Target enum name from_schema: https://w3id.org/linkml/transformer key: true domain_of: - ElementDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation required: true populated_from: name: populated_from description: Source enum name from_schema: https://w3id.org/linkml/transformer domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: EnumReference sources: name: sources from_schema: https://w3id.org/linkml/transformer multivalued: true domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: EnumReference expr: name: expr description: An expression to be evaluated on the source object to derive the target slot. Should be specified using the LinkML expression language. from_schema: https://w3id.org/linkml/transformer domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: string hide: name: hide description: True if this is suppressed from_schema: https://w3id.org/linkml/transformer domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: boolean permissible_value_derivations: name: permissible_value_derivations description: Instructions on how to derive a set of PVs in the target schema from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - EnumDerivation range: PermissibleValueDerivation inlined: true Induced name: EnumDerivation description: A specification of how to derive the value of a target enum from a source enum from_schema: https://w3id.org/linkml/transformer is_a: ElementDerivation attributes: name: name: name description: Target enum name from_schema: https://w3id.org/linkml/transformer key: true alias: name owner: EnumDerivation domain_of: - ElementDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation required: true populated_from: name: populated_from description: Source enum name from_schema: https://w3id.org/linkml/transformer alias: populated_from owner: EnumDerivation domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: EnumReference sources: name: sources from_schema: https://w3id.org/linkml/transformer multivalued: true alias: sources owner: EnumDerivation domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: EnumReference expr: name: expr description: An expression to be evaluated on the source object to derive the target slot. Should be specified using the LinkML expression language. from_schema: https://w3id.org/linkml/transformer alias: expr owner: EnumDerivation domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: string hide: name: hide description: True if this is suppressed from_schema: https://w3id.org/linkml/transformer alias: hide owner: EnumDerivation domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: boolean permissible_value_derivations: name: permissible_value_derivations description: Instructions on how to derive a set of PVs in the target schema from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: permissible_value_derivations owner: EnumDerivation domain_of: - EnumDerivation range: PermissibleValueDerivation inlined: true copy_directives: name: copy_directives from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: copy_directives owner: EnumDerivation domain_of: - ElementDerivation range: CopyDirective inlined: true overrides: name: overrides description: overrides source schema slots from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: overrides owner: EnumDerivation domain_of: - ElementDerivation range: Any is_a: name: is_a from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:is_a alias: is_a owner: EnumDerivation domain_of: - ElementDerivation range: ElementDerivation mixins: name: mixins from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:mixins multivalued: true alias: mixins owner: EnumDerivation domain_of: - ElementDerivation range: ElementDerivation inlined: false value_mappings: name: value_mappings description: A mapping table that is applied directly to mappings, in order of precedence from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: value_mappings owner: EnumDerivation domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_value_mappings: name: expression_to_value_mappings description: A mapping table in which the keys are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_value_mappings owner: EnumDerivation domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_expression_mappings: name: expression_to_expression_mappings description: A mapping table in which the keys and values are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_expression_mappings owner: EnumDerivation domain_of: - ElementDerivation range: KeyVal inlined: true mirror_source: name: mirror_source from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: mirror_source owner: EnumDerivation domain_of: - ElementDerivation range: boolean description: name: description description: description of the specification component from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: dcterms:description alias: description owner: EnumDerivation domain_of: - SpecificationComponent range: string implements: name: implements description: A reference to a specification that this component implements. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: implements owner: EnumDerivation domain_of: - SpecificationComponent range: uriorcurie comments: name: comments description: A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use. from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: rdfs:comment multivalued: true alias: comments owner: EnumDerivation domain_of: - SpecificationComponent range: string","title":"Class: EnumDerivation"},{"location":"EnumDerivation/#class-enumderivation","text":"A specification of how to derive the value of a target enum from a source enum URI: linkmltr:EnumDerivation classDiagram class EnumDerivation ElementDerivation <|-- EnumDerivation EnumDerivation : comments EnumDerivation : copy_directives EnumDerivation --> CopyDirective : copy_directives EnumDerivation : description EnumDerivation --> None : description EnumDerivation : expr EnumDerivation : expression_to_expression_mappings EnumDerivation --> KeyVal : expression_to_expression_mappings EnumDerivation : expression_to_value_mappings EnumDerivation --> KeyVal : expression_to_value_mappings EnumDerivation : hide EnumDerivation : implements EnumDerivation : is_a EnumDerivation --> ElementDerivation : is_a EnumDerivation : mirror_source EnumDerivation : mixins EnumDerivation --> ElementDerivation : mixins EnumDerivation : name EnumDerivation --> None : name EnumDerivation : overrides EnumDerivation --> Any : overrides EnumDerivation : permissible_value_derivations EnumDerivation --> PermissibleValueDerivation : permissible_value_derivations EnumDerivation : populated_from EnumDerivation : sources EnumDerivation : value_mappings EnumDerivation --> KeyVal : value_mappings","title":"Class: EnumDerivation"},{"location":"EnumDerivation/#inheritance","text":"SpecificationComponent ElementDerivation EnumDerivation","title":"Inheritance"},{"location":"EnumDerivation/#slots","text":"Name Cardinality and Range Description Inheritance name 0..1 String Target enum name direct populated_from 0..1 EnumReference Source enum name direct sources 0..* EnumReference direct expr 0..1 String An expression to be evaluated on the source object to derive the target slot direct hide 0..1 Boolean True if this is suppressed direct permissible_value_derivations 0..* PermissibleValueDerivation Instructions on how to derive a set of PVs in the target schema direct copy_directives 0..* CopyDirective ElementDerivation overrides 0..1 Any overrides source schema slots ElementDerivation is_a 0..1 ElementDerivation ElementDerivation mixins 0..* ElementDerivation ElementDerivation value_mappings 0..* KeyVal A mapping table that is applied directly to mappings, in order of precedence ElementDerivation expression_to_value_mappings 0..* KeyVal A mapping table in which the keys are expressions ElementDerivation expression_to_expression_mappings 0..* KeyVal A mapping table in which the keys and values are expressions ElementDerivation mirror_source 0..1 Boolean ElementDerivation description 0..1 String description of the specification component SpecificationComponent implements 0..* Uriorcurie A reference to a specification that this component implements SpecificationComponent comments 0..* String A list of comments about this component SpecificationComponent","title":"Slots"},{"location":"EnumDerivation/#usages","text":"used by used in type used TransformationSpecification enum_derivations range EnumDerivation","title":"Usages"},{"location":"EnumDerivation/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"EnumDerivation/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"EnumDerivation/#mappings","text":"Mapping Type Mapped Value self linkmltr:EnumDerivation native linkmltr:EnumDerivation","title":"Mappings"},{"location":"EnumDerivation/#linkml-source","text":"","title":"LinkML Source"},{"location":"EnumDerivation/#direct","text":"name: EnumDerivation description: A specification of how to derive the value of a target enum from a source enum from_schema: https://w3id.org/linkml/transformer is_a: ElementDerivation attributes: name: name: name description: Target enum name from_schema: https://w3id.org/linkml/transformer key: true domain_of: - ElementDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation required: true populated_from: name: populated_from description: Source enum name from_schema: https://w3id.org/linkml/transformer domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: EnumReference sources: name: sources from_schema: https://w3id.org/linkml/transformer multivalued: true domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: EnumReference expr: name: expr description: An expression to be evaluated on the source object to derive the target slot. Should be specified using the LinkML expression language. from_schema: https://w3id.org/linkml/transformer domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: string hide: name: hide description: True if this is suppressed from_schema: https://w3id.org/linkml/transformer domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: boolean permissible_value_derivations: name: permissible_value_derivations description: Instructions on how to derive a set of PVs in the target schema from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - EnumDerivation range: PermissibleValueDerivation inlined: true","title":"Direct"},{"location":"EnumDerivation/#induced","text":"name: EnumDerivation description: A specification of how to derive the value of a target enum from a source enum from_schema: https://w3id.org/linkml/transformer is_a: ElementDerivation attributes: name: name: name description: Target enum name from_schema: https://w3id.org/linkml/transformer key: true alias: name owner: EnumDerivation domain_of: - ElementDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation required: true populated_from: name: populated_from description: Source enum name from_schema: https://w3id.org/linkml/transformer alias: populated_from owner: EnumDerivation domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: EnumReference sources: name: sources from_schema: https://w3id.org/linkml/transformer multivalued: true alias: sources owner: EnumDerivation domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: EnumReference expr: name: expr description: An expression to be evaluated on the source object to derive the target slot. Should be specified using the LinkML expression language. from_schema: https://w3id.org/linkml/transformer alias: expr owner: EnumDerivation domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: string hide: name: hide description: True if this is suppressed from_schema: https://w3id.org/linkml/transformer alias: hide owner: EnumDerivation domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: boolean permissible_value_derivations: name: permissible_value_derivations description: Instructions on how to derive a set of PVs in the target schema from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: permissible_value_derivations owner: EnumDerivation domain_of: - EnumDerivation range: PermissibleValueDerivation inlined: true copy_directives: name: copy_directives from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: copy_directives owner: EnumDerivation domain_of: - ElementDerivation range: CopyDirective inlined: true overrides: name: overrides description: overrides source schema slots from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: overrides owner: EnumDerivation domain_of: - ElementDerivation range: Any is_a: name: is_a from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:is_a alias: is_a owner: EnumDerivation domain_of: - ElementDerivation range: ElementDerivation mixins: name: mixins from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:mixins multivalued: true alias: mixins owner: EnumDerivation domain_of: - ElementDerivation range: ElementDerivation inlined: false value_mappings: name: value_mappings description: A mapping table that is applied directly to mappings, in order of precedence from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: value_mappings owner: EnumDerivation domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_value_mappings: name: expression_to_value_mappings description: A mapping table in which the keys are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_value_mappings owner: EnumDerivation domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_expression_mappings: name: expression_to_expression_mappings description: A mapping table in which the keys and values are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_expression_mappings owner: EnumDerivation domain_of: - ElementDerivation range: KeyVal inlined: true mirror_source: name: mirror_source from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: mirror_source owner: EnumDerivation domain_of: - ElementDerivation range: boolean description: name: description description: description of the specification component from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: dcterms:description alias: description owner: EnumDerivation domain_of: - SpecificationComponent range: string implements: name: implements description: A reference to a specification that this component implements. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: implements owner: EnumDerivation domain_of: - SpecificationComponent range: uriorcurie comments: name: comments description: A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use. from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: rdfs:comment multivalued: true alias: comments owner: EnumDerivation domain_of: - SpecificationComponent range: string","title":"Induced"},{"location":"EnumReference/","text":"Type: EnumReference URI: xsd:string base : str uri : xsd:string typeof : string Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer","title":"Type: EnumReference"},{"location":"EnumReference/#type-enumreference","text":"URI: xsd:string base : str uri : xsd:string typeof : string","title":"Type: EnumReference"},{"location":"EnumReference/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"EnumReference/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"Float/","text":"Type: Float A real number that conforms to the xsd:float specification URI: xsd:float base : float uri : xsd:float Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer","title":"Type: Float"},{"location":"Float/#type-float","text":"A real number that conforms to the xsd:float specification URI: xsd:float base : float uri : xsd:float","title":"Type: Float"},{"location":"Float/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Float/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"Integer/","text":"Type: Integer An integer URI: xsd:integer base : int uri : xsd:integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer","title":"Type: Integer"},{"location":"Integer/#type-integer","text":"An integer URI: xsd:integer base : int uri : xsd:integer","title":"Type: Integer"},{"location":"Integer/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Integer/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"Inverse/","text":"Class: Inverse Used for back references in mapping to relational model URI: linkmltr:Inverse classDiagram class Inverse Inverse : class_name Inverse --> None : class_name Inverse : slot_name Inverse --> None : slot_name Slots Name Cardinality and Range Description Inheritance slot_name 0..1 String direct class_name 0..1 String direct Usages used by used in type used SlotDerivation inverse_of range Inverse Aliases backref back_references Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer Mappings Mapping Type Mapped Value self linkmltr:Inverse native linkmltr:Inverse LinkML Source Direct name: Inverse description: Used for back references in mapping to relational model from_schema: https://w3id.org/linkml/transformer aliases: - backref - back_references attributes: slot_name: name: slot_name from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - Inverse class_name: name: class_name from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - Inverse Induced name: Inverse description: Used for back references in mapping to relational model from_schema: https://w3id.org/linkml/transformer aliases: - backref - back_references attributes: slot_name: name: slot_name from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: slot_name owner: Inverse domain_of: - Inverse class_name: name: class_name from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: class_name owner: Inverse domain_of: - Inverse","title":"Class: Inverse"},{"location":"Inverse/#class-inverse","text":"Used for back references in mapping to relational model URI: linkmltr:Inverse classDiagram class Inverse Inverse : class_name Inverse --> None : class_name Inverse : slot_name Inverse --> None : slot_name","title":"Class: Inverse"},{"location":"Inverse/#slots","text":"Name Cardinality and Range Description Inheritance slot_name 0..1 String direct class_name 0..1 String direct","title":"Slots"},{"location":"Inverse/#usages","text":"used by used in type used SlotDerivation inverse_of range Inverse","title":"Usages"},{"location":"Inverse/#aliases","text":"backref back_references","title":"Aliases"},{"location":"Inverse/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Inverse/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"Inverse/#mappings","text":"Mapping Type Mapped Value self linkmltr:Inverse native linkmltr:Inverse","title":"Mappings"},{"location":"Inverse/#linkml-source","text":"","title":"LinkML Source"},{"location":"Inverse/#direct","text":"name: Inverse description: Used for back references in mapping to relational model from_schema: https://w3id.org/linkml/transformer aliases: - backref - back_references attributes: slot_name: name: slot_name from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - Inverse class_name: name: class_name from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - Inverse","title":"Direct"},{"location":"Inverse/#induced","text":"name: Inverse description: Used for back references in mapping to relational model from_schema: https://w3id.org/linkml/transformer aliases: - backref - back_references attributes: slot_name: name: slot_name from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: slot_name owner: Inverse domain_of: - Inverse class_name: name: class_name from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: class_name owner: Inverse domain_of: - Inverse","title":"Induced"},{"location":"Jsonpath/","text":"Type: Jsonpath A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. URI: xsd:string base : str uri : xsd:string repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer","title":"Type: Jsonpath"},{"location":"Jsonpath/#type-jsonpath","text":"A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. URI: xsd:string base : str uri : xsd:string repr : str","title":"Type: Jsonpath"},{"location":"Jsonpath/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Jsonpath/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"Jsonpointer/","text":"Type: Jsonpointer A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. URI: xsd:string base : str uri : xsd:string repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer","title":"Type: Jsonpointer"},{"location":"Jsonpointer/#type-jsonpointer","text":"A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. 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KeyVal required: true value: name: value from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - KeyVal range: Any Induced name: KeyVal from_schema: https://w3id.org/linkml/transformer attributes: key: name: key from_schema: https://w3id.org/linkml/transformer rank: 1000 key: true alias: key owner: KeyVal domain_of: - KeyVal required: true value: name: value from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: value owner: KeyVal domain_of: - KeyVal range: Any","title":"Class: KeyVal"},{"location":"KeyVal/#class-keyval","text":"URI: linkmltr:KeyVal classDiagram class KeyVal KeyVal : key KeyVal --> None : key KeyVal : value KeyVal --> Any : value","title":"Class: KeyVal"},{"location":"KeyVal/#slots","text":"Name Cardinality and Range Description Inheritance key 0..1 String direct value 0..1 Any direct","title":"Slots"},{"location":"KeyVal/#usages","text":"used by used in type used TransformationSpecification prefixes range KeyVal ElementDerivation value_mappings range KeyVal ElementDerivation expression_to_value_mappings range KeyVal ElementDerivation expression_to_expression_mappings range KeyVal ClassDerivation value_mappings range KeyVal ClassDerivation expression_to_value_mappings range KeyVal ClassDerivation expression_to_expression_mappings range KeyVal SlotDerivation value_mappings range KeyVal SlotDerivation expression_to_value_mappings range KeyVal SlotDerivation expression_to_expression_mappings range KeyVal EnumDerivation value_mappings range KeyVal EnumDerivation expression_to_value_mappings range KeyVal EnumDerivation expression_to_expression_mappings range KeyVal PermissibleValueDerivation value_mappings range KeyVal PermissibleValueDerivation expression_to_value_mappings range KeyVal PermissibleValueDerivation expression_to_expression_mappings range KeyVal PrefixDerivation value_mappings range KeyVal PrefixDerivation expression_to_value_mappings range KeyVal PrefixDerivation expression_to_expression_mappings range KeyVal","title":"Usages"},{"location":"KeyVal/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"KeyVal/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"KeyVal/#mappings","text":"Mapping Type Mapped Value self linkmltr:KeyVal native linkmltr:KeyVal","title":"Mappings"},{"location":"KeyVal/#linkml-source","text":"","title":"LinkML Source"},{"location":"KeyVal/#direct","text":"name: KeyVal from_schema: https://w3id.org/linkml/transformer attributes: key: name: key from_schema: https://w3id.org/linkml/transformer rank: 1000 key: true domain_of: - KeyVal required: true value: name: value from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - KeyVal range: Any","title":"Direct"},{"location":"KeyVal/#induced","text":"name: KeyVal from_schema: https://w3id.org/linkml/transformer attributes: key: name: key from_schema: https://w3id.org/linkml/transformer rank: 1000 key: true alias: key owner: KeyVal domain_of: - KeyVal required: true value: name: value from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: value owner: KeyVal domain_of: - KeyVal range: Any","title":"Induced"},{"location":"Ncname/","text":"Type: Ncname Prefix part of CURIE URI: xsd:string base : NCName uri : xsd:string repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer","title":"Type: Ncname"},{"location":"Ncname/#type-ncname","text":"Prefix part of CURIE URI: xsd:string base : NCName uri : xsd:string repr : str","title":"Type: Ncname"},{"location":"Ncname/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Ncname/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"Nodeidentifier/","text":"Type: Nodeidentifier A URI, CURIE or BNODE that represents a node in a model. 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URI: shex:iri base : ElementIdentifier uri : shex:iri repr : str","title":"Type: Objectidentifier"},{"location":"Objectidentifier/#comments","text":"Used for inheritance and type checking","title":"Comments"},{"location":"Objectidentifier/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Objectidentifier/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"PermissibleValueDerivation/","text":"Class: PermissibleValueDerivation A specification of how to derive the value of a PV from a source enum URI: linkmltr:PermissibleValueDerivation classDiagram class PermissibleValueDerivation ElementDerivation <|-- PermissibleValueDerivation PermissibleValueDerivation : comments PermissibleValueDerivation : copy_directives PermissibleValueDerivation --> CopyDirective : copy_directives PermissibleValueDerivation : description PermissibleValueDerivation --> None : description PermissibleValueDerivation : expr PermissibleValueDerivation : expression_to_expression_mappings PermissibleValueDerivation --> KeyVal : expression_to_expression_mappings PermissibleValueDerivation : expression_to_value_mappings PermissibleValueDerivation --> KeyVal : expression_to_value_mappings PermissibleValueDerivation : hide PermissibleValueDerivation : implements PermissibleValueDerivation : is_a PermissibleValueDerivation --> ElementDerivation : is_a PermissibleValueDerivation : mirror_source PermissibleValueDerivation : mixins PermissibleValueDerivation --> ElementDerivation : mixins PermissibleValueDerivation : name PermissibleValueDerivation --> None : name PermissibleValueDerivation : overrides PermissibleValueDerivation --> Any : overrides PermissibleValueDerivation : populated_from PermissibleValueDerivation : sources PermissibleValueDerivation : value_mappings PermissibleValueDerivation --> KeyVal : value_mappings Inheritance SpecificationComponent ElementDerivation PermissibleValueDerivation Slots Name Cardinality and Range Description Inheritance name 0..1 String Target permissible value text direct expr 0..1 String direct populated_from 0..1 String Source permissible value direct sources 0..* String direct hide 0..1 Boolean direct copy_directives 0..* CopyDirective ElementDerivation overrides 0..1 Any overrides source schema slots ElementDerivation is_a 0..1 ElementDerivation ElementDerivation mixins 0..* ElementDerivation ElementDerivation value_mappings 0..* KeyVal A mapping table that is applied directly to mappings, in order of precedence ElementDerivation expression_to_value_mappings 0..* KeyVal A mapping table in which the keys are expressions ElementDerivation expression_to_expression_mappings 0..* KeyVal A mapping table in which the keys and values are expressions ElementDerivation mirror_source 0..1 Boolean ElementDerivation description 0..1 String description of the specification component SpecificationComponent implements 0..* Uriorcurie A reference to a specification that this component implements SpecificationComponent comments 0..* String A list of comments about this component SpecificationComponent Usages used by used in type used EnumDerivation permissible_value_derivations range PermissibleValueDerivation TODOs this is currently under-specified. We will need boolean combinators to express if-then-else Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer Mappings Mapping Type Mapped Value self linkmltr:PermissibleValueDerivation native linkmltr:PermissibleValueDerivation LinkML Source Direct name: PermissibleValueDerivation description: A specification of how to derive the value of a PV from a source enum todos: - this is currently under-specified. We will need boolean combinators to express if-then-else from_schema: https://w3id.org/linkml/transformer is_a: ElementDerivation attributes: name: name: name description: Target permissible value text from_schema: https://w3id.org/linkml/transformer key: true domain_of: - ElementDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation required: true expr: name: expr from_schema: https://w3id.org/linkml/transformer domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: string populated_from: name: populated_from description: Source permissible value from_schema: https://w3id.org/linkml/transformer domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: string sources: name: sources from_schema: https://w3id.org/linkml/transformer multivalued: true domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: string hide: name: hide from_schema: https://w3id.org/linkml/transformer domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: boolean Induced name: PermissibleValueDerivation description: A specification of how to derive the value of a PV from a source enum todos: - this is currently under-specified. We will need boolean combinators to express if-then-else from_schema: https://w3id.org/linkml/transformer is_a: ElementDerivation attributes: name: name: name description: Target permissible value text from_schema: https://w3id.org/linkml/transformer key: true alias: name owner: PermissibleValueDerivation domain_of: - ElementDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation required: true expr: name: expr from_schema: https://w3id.org/linkml/transformer alias: expr owner: PermissibleValueDerivation domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: string populated_from: name: populated_from description: Source permissible value from_schema: https://w3id.org/linkml/transformer alias: populated_from owner: PermissibleValueDerivation domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: string sources: name: sources from_schema: https://w3id.org/linkml/transformer multivalued: true alias: sources owner: PermissibleValueDerivation domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: string hide: name: hide from_schema: https://w3id.org/linkml/transformer alias: hide owner: PermissibleValueDerivation domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: boolean copy_directives: name: copy_directives from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: copy_directives owner: PermissibleValueDerivation domain_of: - ElementDerivation range: CopyDirective inlined: true overrides: name: overrides description: overrides source schema slots from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: overrides owner: PermissibleValueDerivation domain_of: - ElementDerivation range: Any is_a: name: is_a from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:is_a alias: is_a owner: PermissibleValueDerivation domain_of: - ElementDerivation range: ElementDerivation mixins: name: mixins from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:mixins multivalued: true alias: mixins owner: PermissibleValueDerivation domain_of: - ElementDerivation range: ElementDerivation inlined: false value_mappings: name: value_mappings description: A mapping table that is applied directly to mappings, in order of precedence from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: value_mappings owner: PermissibleValueDerivation domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_value_mappings: name: expression_to_value_mappings description: A mapping table in which the keys are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_value_mappings owner: PermissibleValueDerivation domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_expression_mappings: name: expression_to_expression_mappings description: A mapping table in which the keys and values are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_expression_mappings owner: PermissibleValueDerivation domain_of: - ElementDerivation range: KeyVal inlined: true mirror_source: name: mirror_source from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: mirror_source owner: PermissibleValueDerivation domain_of: - ElementDerivation range: boolean description: name: description description: description of the specification component from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: dcterms:description alias: description owner: PermissibleValueDerivation domain_of: - SpecificationComponent range: string implements: name: implements description: A reference to a specification that this component implements. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: implements owner: PermissibleValueDerivation domain_of: - SpecificationComponent range: uriorcurie comments: name: comments description: A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use. from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: rdfs:comment multivalued: true alias: comments owner: PermissibleValueDerivation domain_of: - SpecificationComponent range: string","title":"Class: PermissibleValueDerivation"},{"location":"PermissibleValueDerivation/#class-permissiblevaluederivation","text":"A specification of how to derive the value of a PV from a source enum URI: linkmltr:PermissibleValueDerivation classDiagram class PermissibleValueDerivation ElementDerivation <|-- PermissibleValueDerivation PermissibleValueDerivation : comments PermissibleValueDerivation : copy_directives PermissibleValueDerivation --> CopyDirective : copy_directives PermissibleValueDerivation : description PermissibleValueDerivation --> None : description PermissibleValueDerivation : expr PermissibleValueDerivation : expression_to_expression_mappings PermissibleValueDerivation --> KeyVal : expression_to_expression_mappings PermissibleValueDerivation : expression_to_value_mappings PermissibleValueDerivation --> KeyVal : expression_to_value_mappings PermissibleValueDerivation : hide PermissibleValueDerivation : implements PermissibleValueDerivation : is_a PermissibleValueDerivation --> ElementDerivation : is_a PermissibleValueDerivation : mirror_source PermissibleValueDerivation : mixins PermissibleValueDerivation --> ElementDerivation : mixins PermissibleValueDerivation : name PermissibleValueDerivation --> None : name PermissibleValueDerivation : overrides PermissibleValueDerivation --> Any : overrides PermissibleValueDerivation : populated_from PermissibleValueDerivation : sources PermissibleValueDerivation : value_mappings PermissibleValueDerivation --> KeyVal : value_mappings","title":"Class: PermissibleValueDerivation"},{"location":"PermissibleValueDerivation/#inheritance","text":"SpecificationComponent ElementDerivation PermissibleValueDerivation","title":"Inheritance"},{"location":"PermissibleValueDerivation/#slots","text":"Name Cardinality and Range Description Inheritance name 0..1 String Target permissible value text direct expr 0..1 String direct populated_from 0..1 String Source permissible value direct sources 0..* String direct hide 0..1 Boolean direct copy_directives 0..* CopyDirective ElementDerivation overrides 0..1 Any overrides source schema slots ElementDerivation is_a 0..1 ElementDerivation ElementDerivation mixins 0..* ElementDerivation ElementDerivation value_mappings 0..* KeyVal A mapping table that is applied directly to mappings, in order of precedence ElementDerivation expression_to_value_mappings 0..* KeyVal A mapping table in which the keys are expressions ElementDerivation expression_to_expression_mappings 0..* KeyVal A mapping table in which the keys and values are expressions ElementDerivation mirror_source 0..1 Boolean ElementDerivation description 0..1 String description of the specification component SpecificationComponent implements 0..* Uriorcurie A reference to a specification that this component implements SpecificationComponent comments 0..* String A list of comments about this component SpecificationComponent","title":"Slots"},{"location":"PermissibleValueDerivation/#usages","text":"used by used in type used EnumDerivation permissible_value_derivations range PermissibleValueDerivation","title":"Usages"},{"location":"PermissibleValueDerivation/#todos","text":"this is currently under-specified. We will need boolean combinators to express if-then-else","title":"TODOs"},{"location":"PermissibleValueDerivation/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"PermissibleValueDerivation/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"PermissibleValueDerivation/#mappings","text":"Mapping Type Mapped Value self linkmltr:PermissibleValueDerivation native linkmltr:PermissibleValueDerivation","title":"Mappings"},{"location":"PermissibleValueDerivation/#linkml-source","text":"","title":"LinkML Source"},{"location":"PermissibleValueDerivation/#direct","text":"name: PermissibleValueDerivation description: A specification of how to derive the value of a PV from a source enum todos: - this is currently under-specified. We will need boolean combinators to express if-then-else from_schema: https://w3id.org/linkml/transformer is_a: ElementDerivation attributes: name: name: name description: Target permissible value text from_schema: https://w3id.org/linkml/transformer key: true domain_of: - ElementDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation required: true expr: name: expr from_schema: https://w3id.org/linkml/transformer domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: string populated_from: name: populated_from description: Source permissible value from_schema: https://w3id.org/linkml/transformer domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: string sources: name: sources from_schema: https://w3id.org/linkml/transformer multivalued: true domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: string hide: name: hide from_schema: https://w3id.org/linkml/transformer domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: boolean","title":"Direct"},{"location":"PermissibleValueDerivation/#induced","text":"name: PermissibleValueDerivation description: A specification of how to derive the value of a PV from a source enum todos: - this is currently under-specified. We will need boolean combinators to express if-then-else from_schema: https://w3id.org/linkml/transformer is_a: ElementDerivation attributes: name: name: name description: Target permissible value text from_schema: https://w3id.org/linkml/transformer key: true alias: name owner: PermissibleValueDerivation domain_of: - ElementDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation required: true expr: name: expr from_schema: https://w3id.org/linkml/transformer alias: expr owner: PermissibleValueDerivation domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: string populated_from: name: populated_from description: Source permissible value from_schema: https://w3id.org/linkml/transformer alias: populated_from owner: PermissibleValueDerivation domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: string sources: name: sources from_schema: https://w3id.org/linkml/transformer multivalued: true alias: sources owner: PermissibleValueDerivation domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: string hide: name: hide from_schema: https://w3id.org/linkml/transformer alias: hide owner: PermissibleValueDerivation domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: boolean copy_directives: name: copy_directives from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: copy_directives owner: PermissibleValueDerivation domain_of: - ElementDerivation range: CopyDirective inlined: true overrides: name: overrides description: overrides source schema slots from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: overrides owner: PermissibleValueDerivation domain_of: - ElementDerivation range: Any is_a: name: is_a from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:is_a alias: is_a owner: PermissibleValueDerivation domain_of: - ElementDerivation range: ElementDerivation mixins: name: mixins from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:mixins multivalued: true alias: mixins owner: PermissibleValueDerivation domain_of: - ElementDerivation range: ElementDerivation inlined: false value_mappings: name: value_mappings description: A mapping table that is applied directly to mappings, in order of precedence from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: value_mappings owner: PermissibleValueDerivation domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_value_mappings: name: expression_to_value_mappings description: A mapping table in which the keys are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_value_mappings owner: PermissibleValueDerivation domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_expression_mappings: name: expression_to_expression_mappings description: A mapping table in which the keys and values are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_expression_mappings owner: PermissibleValueDerivation domain_of: - ElementDerivation range: KeyVal inlined: true mirror_source: name: mirror_source from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: mirror_source owner: PermissibleValueDerivation domain_of: - ElementDerivation range: boolean description: name: description description: description of the specification component from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: dcterms:description alias: description owner: PermissibleValueDerivation domain_of: - SpecificationComponent range: string implements: name: implements description: A reference to a specification that this component implements. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: implements owner: PermissibleValueDerivation domain_of: - SpecificationComponent range: uriorcurie comments: name: comments description: A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use. from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: rdfs:comment multivalued: true alias: comments owner: PermissibleValueDerivation domain_of: - SpecificationComponent range: string","title":"Induced"},{"location":"PrefixDerivation/","text":"Class: PrefixDerivation URI: linkmltr:PrefixDerivation classDiagram class PrefixDerivation ElementDerivation <|-- PrefixDerivation PrefixDerivation : comments PrefixDerivation : copy_directives PrefixDerivation --> CopyDirective : copy_directives PrefixDerivation : description PrefixDerivation --> None : description PrefixDerivation : expression_to_expression_mappings PrefixDerivation --> KeyVal : expression_to_expression_mappings PrefixDerivation : expression_to_value_mappings PrefixDerivation --> KeyVal : expression_to_value_mappings PrefixDerivation : implements PrefixDerivation : is_a PrefixDerivation --> ElementDerivation : is_a PrefixDerivation : mirror_source PrefixDerivation : mixins PrefixDerivation --> ElementDerivation : mixins PrefixDerivation : name PrefixDerivation --> None : name PrefixDerivation : overrides PrefixDerivation --> Any : overrides PrefixDerivation : value_mappings PrefixDerivation --> KeyVal : value_mappings Inheritance SpecificationComponent ElementDerivation PrefixDerivation Slots Name Cardinality and Range Description Inheritance name 1..1 String Name of the element in the target schema ElementDerivation copy_directives 0..* CopyDirective ElementDerivation overrides 0..1 Any overrides source schema slots ElementDerivation is_a 0..1 ElementDerivation ElementDerivation mixins 0..* ElementDerivation ElementDerivation value_mappings 0..* KeyVal A mapping table that is applied directly to mappings, in order of precedence ElementDerivation expression_to_value_mappings 0..* KeyVal A mapping table in which the keys are expressions ElementDerivation expression_to_expression_mappings 0..* KeyVal A mapping table in which the keys and values are expressions ElementDerivation mirror_source 0..1 Boolean ElementDerivation description 0..1 String description of the specification component SpecificationComponent implements 0..* Uriorcurie A reference to a specification that this component implements SpecificationComponent comments 0..* String A list of comments about this component SpecificationComponent Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer Mappings Mapping Type Mapped Value self linkmltr:PrefixDerivation native linkmltr:PrefixDerivation LinkML Source Direct name: PrefixDerivation from_schema: https://w3id.org/linkml/transformer is_a: ElementDerivation Induced name: PrefixDerivation from_schema: https://w3id.org/linkml/transformer is_a: ElementDerivation attributes: name: name: name description: Name of the element in the target schema from_schema: https://w3id.org/linkml/transformer rank: 1000 key: true alias: name owner: PrefixDerivation domain_of: - ElementDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: string required: true copy_directives: name: copy_directives from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: copy_directives owner: PrefixDerivation domain_of: - ElementDerivation range: CopyDirective inlined: true overrides: name: overrides description: overrides source schema slots from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: overrides owner: PrefixDerivation domain_of: - ElementDerivation range: Any is_a: name: is_a from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:is_a alias: is_a owner: PrefixDerivation domain_of: - ElementDerivation range: ElementDerivation mixins: name: mixins from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:mixins multivalued: true alias: mixins owner: PrefixDerivation domain_of: - ElementDerivation range: ElementDerivation inlined: false value_mappings: name: value_mappings description: A mapping table that is applied directly to mappings, in order of precedence from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: value_mappings owner: PrefixDerivation domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_value_mappings: name: expression_to_value_mappings description: A mapping table in which the keys are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_value_mappings owner: PrefixDerivation domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_expression_mappings: name: expression_to_expression_mappings description: A mapping table in which the keys and values are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_expression_mappings owner: PrefixDerivation domain_of: - ElementDerivation range: KeyVal inlined: true mirror_source: name: mirror_source from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: mirror_source owner: PrefixDerivation domain_of: - ElementDerivation range: boolean description: name: description description: description of the specification component from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: dcterms:description alias: description owner: PrefixDerivation domain_of: - SpecificationComponent range: string implements: name: implements description: A reference to a specification that this component implements. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: implements owner: PrefixDerivation domain_of: - SpecificationComponent range: uriorcurie comments: name: comments description: A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use. from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: rdfs:comment multivalued: true alias: comments owner: PrefixDerivation domain_of: - SpecificationComponent range: string","title":"Class: PrefixDerivation"},{"location":"PrefixDerivation/#class-prefixderivation","text":"URI: linkmltr:PrefixDerivation classDiagram class PrefixDerivation ElementDerivation <|-- PrefixDerivation PrefixDerivation : comments PrefixDerivation : copy_directives PrefixDerivation --> CopyDirective : copy_directives PrefixDerivation : description PrefixDerivation --> None : description PrefixDerivation : expression_to_expression_mappings PrefixDerivation --> KeyVal : expression_to_expression_mappings PrefixDerivation : expression_to_value_mappings PrefixDerivation --> KeyVal : expression_to_value_mappings PrefixDerivation : implements PrefixDerivation : is_a PrefixDerivation --> ElementDerivation : is_a PrefixDerivation : mirror_source PrefixDerivation : mixins PrefixDerivation --> ElementDerivation : mixins PrefixDerivation : name PrefixDerivation --> None : name PrefixDerivation : overrides PrefixDerivation --> Any : overrides PrefixDerivation : value_mappings PrefixDerivation --> KeyVal : value_mappings","title":"Class: PrefixDerivation"},{"location":"PrefixDerivation/#inheritance","text":"SpecificationComponent ElementDerivation PrefixDerivation","title":"Inheritance"},{"location":"PrefixDerivation/#slots","text":"Name Cardinality and Range Description Inheritance name 1..1 String Name of the element in the target schema ElementDerivation copy_directives 0..* CopyDirective ElementDerivation overrides 0..1 Any overrides source schema slots ElementDerivation is_a 0..1 ElementDerivation ElementDerivation mixins 0..* ElementDerivation ElementDerivation value_mappings 0..* KeyVal A mapping table that is applied directly to mappings, in order of precedence ElementDerivation expression_to_value_mappings 0..* KeyVal A mapping table in which the keys are expressions ElementDerivation expression_to_expression_mappings 0..* KeyVal A mapping table in which the keys and values are expressions ElementDerivation mirror_source 0..1 Boolean ElementDerivation description 0..1 String description of the specification component SpecificationComponent implements 0..* Uriorcurie A reference to a specification that this component implements SpecificationComponent comments 0..* String A list of comments about this component SpecificationComponent","title":"Slots"},{"location":"PrefixDerivation/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"PrefixDerivation/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"PrefixDerivation/#mappings","text":"Mapping Type Mapped Value self linkmltr:PrefixDerivation native linkmltr:PrefixDerivation","title":"Mappings"},{"location":"PrefixDerivation/#linkml-source","text":"","title":"LinkML Source"},{"location":"PrefixDerivation/#direct","text":"name: PrefixDerivation from_schema: https://w3id.org/linkml/transformer is_a: ElementDerivation","title":"Direct"},{"location":"PrefixDerivation/#induced","text":"name: PrefixDerivation from_schema: https://w3id.org/linkml/transformer is_a: ElementDerivation attributes: name: name: name description: Name of the element in the target schema from_schema: https://w3id.org/linkml/transformer rank: 1000 key: true alias: name owner: PrefixDerivation domain_of: - ElementDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: string required: true copy_directives: name: copy_directives from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: copy_directives owner: PrefixDerivation domain_of: - ElementDerivation range: CopyDirective inlined: true overrides: name: overrides description: overrides source schema slots from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: overrides owner: PrefixDerivation domain_of: - ElementDerivation range: Any is_a: name: is_a from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:is_a alias: is_a owner: PrefixDerivation domain_of: - ElementDerivation range: ElementDerivation mixins: name: mixins from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:mixins multivalued: true alias: mixins owner: PrefixDerivation domain_of: - ElementDerivation range: ElementDerivation inlined: false value_mappings: name: value_mappings description: A mapping table that is applied directly to mappings, in order of precedence from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: value_mappings owner: PrefixDerivation domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_value_mappings: name: expression_to_value_mappings description: A mapping table in which the keys are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_value_mappings owner: PrefixDerivation domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_expression_mappings: name: expression_to_expression_mappings description: A mapping table in which the keys and values are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_expression_mappings owner: PrefixDerivation domain_of: - ElementDerivation range: KeyVal inlined: true mirror_source: name: mirror_source from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: mirror_source owner: PrefixDerivation domain_of: - ElementDerivation range: boolean description: name: description description: description of the specification component from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: dcterms:description alias: description owner: PrefixDerivation domain_of: - SpecificationComponent range: string implements: name: implements description: A reference to a specification that this component implements. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: implements owner: PrefixDerivation domain_of: - SpecificationComponent range: uriorcurie comments: name: comments description: A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use. from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: rdfs:comment multivalued: true alias: comments owner: PrefixDerivation domain_of: - SpecificationComponent range: string","title":"Induced"},{"location":"SerializationSyntaxType/","text":"Enum: SerializationSyntaxType URI: SerializationSyntaxType Permissible Values Value Meaning Description JSON None YAML None TURTLE None Slots Name Description syntax Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer LinkML Source name: SerializationSyntaxType from_schema: https://w3id.org/linkml/transformer rank: 1000 permissible_values: JSON: text: JSON YAML: text: YAML TURTLE: text: TURTLE","title":"Enum: SerializationSyntaxType"},{"location":"SerializationSyntaxType/#enum-serializationsyntaxtype","text":"URI: SerializationSyntaxType","title":"Enum: SerializationSyntaxType"},{"location":"SerializationSyntaxType/#permissible-values","text":"Value Meaning Description JSON None YAML None TURTLE None","title":"Permissible Values"},{"location":"SerializationSyntaxType/#slots","text":"Name Description syntax","title":"Slots"},{"location":"SerializationSyntaxType/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SerializationSyntaxType/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"SerializationSyntaxType/#linkml-source","text":"name: SerializationSyntaxType from_schema: https://w3id.org/linkml/transformer rank: 1000 permissible_values: JSON: text: JSON YAML: text: YAML TURTLE: text: TURTLE","title":"LinkML Source"},{"location":"SlotDerivation/","text":"Class: SlotDerivation A specification of how to derive the value of a target slot from a source slot URI: linkmltr:SlotDerivation classDiagram class SlotDerivation ElementDerivation <|-- SlotDerivation SlotDerivation : cast_collection_as SlotDerivation --> CollectionType : cast_collection_as SlotDerivation : comments SlotDerivation : copy_directives SlotDerivation --> CopyDirective : copy_directives SlotDerivation : derived_from SlotDerivation : description SlotDerivation --> None : description SlotDerivation : dictionary_key SlotDerivation : expr SlotDerivation : expression_to_expression_mappings SlotDerivation --> KeyVal : expression_to_expression_mappings SlotDerivation : expression_to_value_mappings SlotDerivation --> KeyVal : expression_to_value_mappings SlotDerivation : hide SlotDerivation : implements SlotDerivation : inverse_of SlotDerivation --> Inverse : inverse_of SlotDerivation : is_a SlotDerivation --> ElementDerivation : is_a SlotDerivation : mirror_source SlotDerivation : mixins SlotDerivation --> ElementDerivation : mixins SlotDerivation : name SlotDerivation --> None : name SlotDerivation : overrides SlotDerivation --> Any : overrides SlotDerivation : populated_from SlotDerivation : range SlotDerivation : sources SlotDerivation : stringification SlotDerivation --> StringificationConfiguration : stringification SlotDerivation : type_designator SlotDerivation : unit_conversion SlotDerivation --> UnitConversionConfiguration : unit_conversion SlotDerivation : value_mappings SlotDerivation --> KeyVal : value_mappings Inheritance SpecificationComponent ElementDerivation SlotDerivation Slots Name Cardinality and Range Description Inheritance name 0..1 String Target slot name direct populated_from 0..1 SlotReference Source slot name direct sources 0..* SlotReference direct derived_from 0..* SlotReference Source slots that are used to derive this slot direct expr 0..1 String An expression to be evaluated on the source object to derive the target slot direct range 0..1 String direct unit_conversion 0..1 UnitConversionConfiguration direct inverse_of 0..1 Inverse Used to specify a class-slot tuple that is the inverse of the derived/target ... direct hide 0..1 Boolean True if this is suppressed direct type_designator 0..1 Boolean direct cast_collection_as 0..1 CollectionType direct dictionary_key 0..1 String direct stringification 0..1 StringificationConfiguration direct copy_directives 0..* CopyDirective ElementDerivation overrides 0..1 Any overrides source schema slots ElementDerivation is_a 0..1 ElementDerivation ElementDerivation mixins 0..* ElementDerivation ElementDerivation value_mappings 0..* KeyVal A mapping table that is applied directly to mappings, in order of precedence ElementDerivation expression_to_value_mappings 0..* KeyVal A mapping table in which the keys are expressions ElementDerivation expression_to_expression_mappings 0..* KeyVal A mapping table in which the keys and values are expressions ElementDerivation mirror_source 0..1 Boolean ElementDerivation description 0..1 String description of the specification component SpecificationComponent implements 0..* Uriorcurie A reference to a specification that this component implements SpecificationComponent comments 0..* String A list of comments about this component SpecificationComponent Usages used by used in type used TransformationSpecification slot_derivations range SlotDerivation ClassDerivation slot_derivations range SlotDerivation Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer Mappings Mapping Type Mapped Value self linkmltr:SlotDerivation native linkmltr:SlotDerivation LinkML Source Direct name: SlotDerivation description: A specification of how to derive the value of a target slot from a source slot from_schema: https://w3id.org/linkml/transformer is_a: ElementDerivation attributes: name: name: name description: Target slot name from_schema: https://w3id.org/linkml/transformer key: true domain_of: - ElementDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation required: true populated_from: name: populated_from description: Source slot name from_schema: https://w3id.org/linkml/transformer domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: SlotReference sources: name: sources from_schema: https://w3id.org/linkml/transformer multivalued: true domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: SlotReference derived_from: name: derived_from description: Source slots that are used to derive this slot. This can be computed from the expr, if the expr is declarative. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - SlotDerivation range: SlotReference expr: name: expr description: An expression to be evaluated on the source object to derive the target slot. Should be specified using the LinkML expression language. from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: string range: name: range from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:range domain_of: - SlotDerivation range: string unit_conversion: name: unit_conversion from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - SlotDerivation range: UnitConversionConfiguration inverse_of: name: inverse_of description: Used to specify a class-slot tuple that is the inverse of the derived/target slot. This is used primarily for mapping to relational databases or formalisms that do not allow multiple values. The class representing the repeated element has a foreign key slot inserted in that 'back references' the original multivalued slot. from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - SlotDerivation range: Inverse hide: name: hide description: True if this is suppressed from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: boolean type_designator: name: type_designator from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - SlotDerivation range: boolean cast_collection_as: name: cast_collection_as from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - SlotDerivation range: CollectionType dictionary_key: name: dictionary_key from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - SlotDerivation range: string stringification: name: stringification from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - SlotDerivation range: StringificationConfiguration Induced name: SlotDerivation description: A specification of how to derive the value of a target slot from a source slot from_schema: https://w3id.org/linkml/transformer is_a: ElementDerivation attributes: name: name: name description: Target slot name from_schema: https://w3id.org/linkml/transformer key: true alias: name owner: SlotDerivation domain_of: - ElementDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation required: true populated_from: name: populated_from description: Source slot name from_schema: https://w3id.org/linkml/transformer alias: populated_from owner: SlotDerivation domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: SlotReference sources: name: sources from_schema: https://w3id.org/linkml/transformer multivalued: true alias: sources owner: SlotDerivation domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: SlotReference derived_from: name: derived_from description: Source slots that are used to derive this slot. This can be computed from the expr, if the expr is declarative. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: derived_from owner: SlotDerivation domain_of: - SlotDerivation range: SlotReference expr: name: expr description: An expression to be evaluated on the source object to derive the target slot. Should be specified using the LinkML expression language. from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: expr owner: SlotDerivation domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: string range: name: range from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:range alias: range owner: SlotDerivation domain_of: - SlotDerivation range: string unit_conversion: name: unit_conversion from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: unit_conversion owner: SlotDerivation domain_of: - SlotDerivation range: UnitConversionConfiguration inverse_of: name: inverse_of description: Used to specify a class-slot tuple that is the inverse of the derived/target slot. This is used primarily for mapping to relational databases or formalisms that do not allow multiple values. The class representing the repeated element has a foreign key slot inserted in that 'back references' the original multivalued slot. from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: inverse_of owner: SlotDerivation domain_of: - SlotDerivation range: Inverse hide: name: hide description: True if this is suppressed from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: hide owner: SlotDerivation domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: boolean type_designator: name: type_designator from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: type_designator owner: SlotDerivation domain_of: - SlotDerivation range: boolean cast_collection_as: name: cast_collection_as from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: cast_collection_as owner: SlotDerivation domain_of: - SlotDerivation range: CollectionType dictionary_key: name: dictionary_key from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: dictionary_key owner: SlotDerivation domain_of: - SlotDerivation range: string stringification: name: stringification from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: stringification owner: SlotDerivation domain_of: - SlotDerivation range: StringificationConfiguration copy_directives: name: copy_directives from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: copy_directives owner: SlotDerivation domain_of: - ElementDerivation range: CopyDirective inlined: true overrides: name: overrides description: overrides source schema slots from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: overrides owner: SlotDerivation domain_of: - ElementDerivation range: Any is_a: name: is_a from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:is_a alias: is_a owner: SlotDerivation domain_of: - ElementDerivation range: ElementDerivation mixins: name: mixins from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:mixins multivalued: true alias: mixins owner: SlotDerivation domain_of: - ElementDerivation range: ElementDerivation inlined: false value_mappings: name: value_mappings description: A mapping table that is applied directly to mappings, in order of precedence from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: value_mappings owner: SlotDerivation domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_value_mappings: name: expression_to_value_mappings description: A mapping table in which the keys are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_value_mappings owner: SlotDerivation domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_expression_mappings: name: expression_to_expression_mappings description: A mapping table in which the keys and values are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_expression_mappings owner: SlotDerivation domain_of: - ElementDerivation range: KeyVal inlined: true mirror_source: name: mirror_source from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: mirror_source owner: SlotDerivation domain_of: - ElementDerivation range: boolean description: name: description description: description of the specification component from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: dcterms:description alias: description owner: SlotDerivation domain_of: - SpecificationComponent range: string implements: name: implements description: A reference to a specification that this component implements. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: implements owner: SlotDerivation domain_of: - SpecificationComponent range: uriorcurie comments: name: comments description: A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use. from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: rdfs:comment multivalued: true alias: comments owner: SlotDerivation domain_of: - SpecificationComponent range: string","title":"Class: SlotDerivation"},{"location":"SlotDerivation/#class-slotderivation","text":"A specification of how to derive the value of a target slot from a source slot URI: linkmltr:SlotDerivation classDiagram class SlotDerivation ElementDerivation <|-- SlotDerivation SlotDerivation : cast_collection_as SlotDerivation --> CollectionType : cast_collection_as SlotDerivation : comments SlotDerivation : copy_directives SlotDerivation --> CopyDirective : copy_directives SlotDerivation : derived_from SlotDerivation : description SlotDerivation --> None : description SlotDerivation : dictionary_key SlotDerivation : expr SlotDerivation : expression_to_expression_mappings SlotDerivation --> KeyVal : expression_to_expression_mappings SlotDerivation : expression_to_value_mappings SlotDerivation --> KeyVal : expression_to_value_mappings SlotDerivation : hide SlotDerivation : implements SlotDerivation : inverse_of SlotDerivation --> Inverse : inverse_of SlotDerivation : is_a SlotDerivation --> ElementDerivation : is_a SlotDerivation : mirror_source SlotDerivation : mixins SlotDerivation --> ElementDerivation : mixins SlotDerivation : name SlotDerivation --> None : name SlotDerivation : overrides SlotDerivation --> Any : overrides SlotDerivation : populated_from SlotDerivation : range SlotDerivation : sources SlotDerivation : stringification SlotDerivation --> StringificationConfiguration : stringification SlotDerivation : type_designator SlotDerivation : unit_conversion SlotDerivation --> UnitConversionConfiguration : unit_conversion SlotDerivation : value_mappings SlotDerivation --> KeyVal : value_mappings","title":"Class: SlotDerivation"},{"location":"SlotDerivation/#inheritance","text":"SpecificationComponent ElementDerivation SlotDerivation","title":"Inheritance"},{"location":"SlotDerivation/#slots","text":"Name Cardinality and Range Description Inheritance name 0..1 String Target slot name direct populated_from 0..1 SlotReference Source slot name direct sources 0..* SlotReference direct derived_from 0..* SlotReference Source slots that are used to derive this slot direct expr 0..1 String An expression to be evaluated on the source object to derive the target slot direct range 0..1 String direct unit_conversion 0..1 UnitConversionConfiguration direct inverse_of 0..1 Inverse Used to specify a class-slot tuple that is the inverse of the derived/target ... direct hide 0..1 Boolean True if this is suppressed direct type_designator 0..1 Boolean direct cast_collection_as 0..1 CollectionType direct dictionary_key 0..1 String direct stringification 0..1 StringificationConfiguration direct copy_directives 0..* CopyDirective ElementDerivation overrides 0..1 Any overrides source schema slots ElementDerivation is_a 0..1 ElementDerivation ElementDerivation mixins 0..* ElementDerivation ElementDerivation value_mappings 0..* KeyVal A mapping table that is applied directly to mappings, in order of precedence ElementDerivation expression_to_value_mappings 0..* KeyVal A mapping table in which the keys are expressions ElementDerivation expression_to_expression_mappings 0..* KeyVal A mapping table in which the keys and values are expressions ElementDerivation mirror_source 0..1 Boolean ElementDerivation description 0..1 String description of the specification component SpecificationComponent implements 0..* Uriorcurie A reference to a specification that this component implements SpecificationComponent comments 0..* String A list of comments about this component SpecificationComponent","title":"Slots"},{"location":"SlotDerivation/#usages","text":"used by used in type used TransformationSpecification slot_derivations range SlotDerivation ClassDerivation slot_derivations range SlotDerivation","title":"Usages"},{"location":"SlotDerivation/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SlotDerivation/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"SlotDerivation/#mappings","text":"Mapping Type Mapped Value self linkmltr:SlotDerivation native linkmltr:SlotDerivation","title":"Mappings"},{"location":"SlotDerivation/#linkml-source","text":"","title":"LinkML Source"},{"location":"SlotDerivation/#direct","text":"name: SlotDerivation description: A specification of how to derive the value of a target slot from a source slot from_schema: https://w3id.org/linkml/transformer is_a: ElementDerivation attributes: name: name: name description: Target slot name from_schema: https://w3id.org/linkml/transformer key: true domain_of: - ElementDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation required: true populated_from: name: populated_from description: Source slot name from_schema: https://w3id.org/linkml/transformer domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: SlotReference sources: name: sources from_schema: https://w3id.org/linkml/transformer multivalued: true domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: SlotReference derived_from: name: derived_from description: Source slots that are used to derive this slot. This can be computed from the expr, if the expr is declarative. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - SlotDerivation range: SlotReference expr: name: expr description: An expression to be evaluated on the source object to derive the target slot. Should be specified using the LinkML expression language. from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: string range: name: range from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:range domain_of: - SlotDerivation range: string unit_conversion: name: unit_conversion from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - SlotDerivation range: UnitConversionConfiguration inverse_of: name: inverse_of description: Used to specify a class-slot tuple that is the inverse of the derived/target slot. This is used primarily for mapping to relational databases or formalisms that do not allow multiple values. The class representing the repeated element has a foreign key slot inserted in that 'back references' the original multivalued slot. from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - SlotDerivation range: Inverse hide: name: hide description: True if this is suppressed from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: boolean type_designator: name: type_designator from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - SlotDerivation range: boolean cast_collection_as: name: cast_collection_as from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - SlotDerivation range: CollectionType dictionary_key: name: dictionary_key from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - SlotDerivation range: string stringification: name: stringification from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - SlotDerivation range: StringificationConfiguration","title":"Direct"},{"location":"SlotDerivation/#induced","text":"name: SlotDerivation description: A specification of how to derive the value of a target slot from a source slot from_schema: https://w3id.org/linkml/transformer is_a: ElementDerivation attributes: name: name: name description: Target slot name from_schema: https://w3id.org/linkml/transformer key: true alias: name owner: SlotDerivation domain_of: - ElementDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation required: true populated_from: name: populated_from description: Source slot name from_schema: https://w3id.org/linkml/transformer alias: populated_from owner: SlotDerivation domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: SlotReference sources: name: sources from_schema: https://w3id.org/linkml/transformer multivalued: true alias: sources owner: SlotDerivation domain_of: - ClassDerivation - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: SlotReference derived_from: name: derived_from description: Source slots that are used to derive this slot. This can be computed from the expr, if the expr is declarative. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: derived_from owner: SlotDerivation domain_of: - SlotDerivation range: SlotReference expr: name: expr description: An expression to be evaluated on the source object to derive the target slot. Should be specified using the LinkML expression language. from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: expr owner: SlotDerivation domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: string range: name: range from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:range alias: range owner: SlotDerivation domain_of: - SlotDerivation range: string unit_conversion: name: unit_conversion from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: unit_conversion owner: SlotDerivation domain_of: - SlotDerivation range: UnitConversionConfiguration inverse_of: name: inverse_of description: Used to specify a class-slot tuple that is the inverse of the derived/target slot. This is used primarily for mapping to relational databases or formalisms that do not allow multiple values. The class representing the repeated element has a foreign key slot inserted in that 'back references' the original multivalued slot. from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: inverse_of owner: SlotDerivation domain_of: - SlotDerivation range: Inverse hide: name: hide description: True if this is suppressed from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: hide owner: SlotDerivation domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation range: boolean type_designator: name: type_designator from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: type_designator owner: SlotDerivation domain_of: - SlotDerivation range: boolean cast_collection_as: name: cast_collection_as from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: cast_collection_as owner: SlotDerivation domain_of: - SlotDerivation range: CollectionType dictionary_key: name: dictionary_key from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: dictionary_key owner: SlotDerivation domain_of: - SlotDerivation range: string stringification: name: stringification from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: stringification owner: SlotDerivation domain_of: - SlotDerivation range: StringificationConfiguration copy_directives: name: copy_directives from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: copy_directives owner: SlotDerivation domain_of: - ElementDerivation range: CopyDirective inlined: true overrides: name: overrides description: overrides source schema slots from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: overrides owner: SlotDerivation domain_of: - ElementDerivation range: Any is_a: name: is_a from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:is_a alias: is_a owner: SlotDerivation domain_of: - ElementDerivation range: ElementDerivation mixins: name: mixins from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:mixins multivalued: true alias: mixins owner: SlotDerivation domain_of: - ElementDerivation range: ElementDerivation inlined: false value_mappings: name: value_mappings description: A mapping table that is applied directly to mappings, in order of precedence from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: value_mappings owner: SlotDerivation domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_value_mappings: name: expression_to_value_mappings description: A mapping table in which the keys are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_value_mappings owner: SlotDerivation domain_of: - ElementDerivation range: KeyVal inlined: true expression_to_expression_mappings: name: expression_to_expression_mappings description: A mapping table in which the keys and values are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_expression_mappings owner: SlotDerivation domain_of: - ElementDerivation range: KeyVal inlined: true mirror_source: name: mirror_source from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: mirror_source owner: SlotDerivation domain_of: - ElementDerivation range: boolean description: name: description description: description of the specification component from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: dcterms:description alias: description owner: SlotDerivation domain_of: - SpecificationComponent range: string implements: name: implements description: A reference to a specification that this component implements. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: implements owner: SlotDerivation domain_of: - SpecificationComponent range: uriorcurie comments: name: comments description: A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use. from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: rdfs:comment multivalued: true alias: comments owner: SlotDerivation domain_of: - SpecificationComponent range: string","title":"Induced"},{"location":"SlotReference/","text":"Type: SlotReference URI: xsd:string base : str uri : xsd:string typeof : string Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer","title":"Type: SlotReference"},{"location":"SlotReference/#type-slotreference","text":"URI: xsd:string base : str uri : xsd:string typeof : string","title":"Type: SlotReference"},{"location":"SlotReference/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SlotReference/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"Sparqlpath/","text":"Type: Sparqlpath A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. URI: xsd:string base : str uri : xsd:string repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer","title":"Type: Sparqlpath"},{"location":"Sparqlpath/#type-sparqlpath","text":"A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. URI: xsd:string base : str uri : xsd:string repr : str","title":"Type: Sparqlpath"},{"location":"Sparqlpath/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Sparqlpath/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"SpecificationComponent/","text":"Class: SpecificationComponent NOTE : this is an abstract class and should not be instantiated directly URI: linkmltr:SpecificationComponent classDiagram class SpecificationComponent SpecificationComponent <|-- TransformationSpecification SpecificationComponent <|-- ElementDerivation SpecificationComponent : comments SpecificationComponent : description SpecificationComponent --> None : description SpecificationComponent : implements Inheritance SpecificationComponent TransformationSpecification ElementDerivation Slots Name Cardinality and Range Description Inheritance description 0..1 String description of the specification component direct implements 0..* Uriorcurie A reference to a specification that this component implements direct comments 0..* String A list of comments about this component direct Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer Mappings Mapping Type Mapped Value self linkmltr:SpecificationComponent native linkmltr:SpecificationComponent LinkML Source Direct name: SpecificationComponent from_schema: https://w3id.org/linkml/transformer abstract: true attributes: description: name: description description: description of the specification component from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: dcterms:description domain_of: - SpecificationComponent implements: name: implements description: A reference to a specification that this component implements. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - SpecificationComponent range: uriorcurie comments: name: comments description: A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use. from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: rdfs:comment multivalued: true domain_of: - SpecificationComponent range: string Induced name: SpecificationComponent from_schema: https://w3id.org/linkml/transformer abstract: true attributes: description: name: description description: description of the specification component from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: dcterms:description alias: description owner: SpecificationComponent domain_of: - SpecificationComponent implements: name: implements description: A reference to a specification that this component implements. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: implements owner: SpecificationComponent domain_of: - SpecificationComponent range: uriorcurie comments: name: comments description: A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use. from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: rdfs:comment multivalued: true alias: comments owner: SpecificationComponent domain_of: - SpecificationComponent range: string","title":"Class: SpecificationComponent"},{"location":"SpecificationComponent/#class-specificationcomponent","text":"NOTE : this is an abstract class and should not be instantiated directly URI: linkmltr:SpecificationComponent classDiagram class SpecificationComponent SpecificationComponent <|-- TransformationSpecification SpecificationComponent <|-- ElementDerivation SpecificationComponent : comments SpecificationComponent : description SpecificationComponent --> None : description SpecificationComponent : implements","title":"Class: SpecificationComponent"},{"location":"SpecificationComponent/#inheritance","text":"SpecificationComponent TransformationSpecification ElementDerivation","title":"Inheritance"},{"location":"SpecificationComponent/#slots","text":"Name Cardinality and Range Description Inheritance description 0..1 String description of the specification component direct implements 0..* Uriorcurie A reference to a specification that this component implements direct comments 0..* String A list of comments about this component direct","title":"Slots"},{"location":"SpecificationComponent/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecificationComponent/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"SpecificationComponent/#mappings","text":"Mapping Type Mapped Value self linkmltr:SpecificationComponent native linkmltr:SpecificationComponent","title":"Mappings"},{"location":"SpecificationComponent/#linkml-source","text":"","title":"LinkML Source"},{"location":"SpecificationComponent/#direct","text":"name: SpecificationComponent from_schema: https://w3id.org/linkml/transformer abstract: true attributes: description: name: description description: description of the specification component from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: dcterms:description domain_of: - SpecificationComponent implements: name: implements description: A reference to a specification that this component implements. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - SpecificationComponent range: uriorcurie comments: name: comments description: A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use. from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: rdfs:comment multivalued: true domain_of: - SpecificationComponent range: string","title":"Direct"},{"location":"SpecificationComponent/#induced","text":"name: SpecificationComponent from_schema: https://w3id.org/linkml/transformer abstract: true attributes: description: name: description description: description of the specification component from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: dcterms:description alias: description owner: SpecificationComponent domain_of: - SpecificationComponent implements: name: implements description: A reference to a specification that this component implements. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: implements owner: SpecificationComponent domain_of: - SpecificationComponent range: uriorcurie comments: name: comments description: A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use. from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: rdfs:comment multivalued: true alias: comments owner: SpecificationComponent domain_of: - SpecificationComponent range: string","title":"Induced"},{"location":"String/","text":"Type: String A character string URI: xsd:string base : str uri : xsd:string Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer","title":"Type: String"},{"location":"String/#type-string","text":"A character string URI: xsd:string base : str uri : xsd:string","title":"Type: String"},{"location":"String/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"String/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"StringificationConfiguration/","text":"Class: StringificationConfiguration URI: linkmltr:StringificationConfiguration classDiagram class StringificationConfiguration StringificationConfiguration : delimiter StringificationConfiguration : over_slots StringificationConfiguration : reversed StringificationConfiguration : syntax StringificationConfiguration --> SerializationSyntaxType : syntax Slots Name Cardinality and Range Description Inheritance delimiter 0..1 String direct reversed 0..1 Boolean direct over_slots 0..* String direct syntax 0..1 SerializationSyntaxType direct Usages used by used in type used SlotDerivation stringification range StringificationConfiguration Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer Mappings Mapping Type Mapped Value self linkmltr:StringificationConfiguration native linkmltr:StringificationConfiguration LinkML Source Direct name: StringificationConfiguration from_schema: https://w3id.org/linkml/transformer attributes: delimiter: name: delimiter examples: - value: ',' - value: '|' - value: ; from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - StringificationConfiguration range: string reversed: name: reversed from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - StringificationConfiguration range: boolean over_slots: name: over_slots from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - StringificationConfiguration range: string syntax: name: syntax examples: - value: json - value: yaml from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - StringificationConfiguration range: SerializationSyntaxType Induced name: StringificationConfiguration from_schema: https://w3id.org/linkml/transformer attributes: delimiter: name: delimiter examples: - value: ',' - value: '|' - value: ; from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: delimiter owner: StringificationConfiguration domain_of: - StringificationConfiguration range: string reversed: name: reversed from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: reversed owner: StringificationConfiguration domain_of: - StringificationConfiguration range: boolean over_slots: name: over_slots from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: over_slots owner: StringificationConfiguration domain_of: - StringificationConfiguration range: string syntax: name: syntax examples: - value: json - value: yaml from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: syntax owner: StringificationConfiguration domain_of: - StringificationConfiguration range: SerializationSyntaxType","title":"Class: StringificationConfiguration"},{"location":"StringificationConfiguration/#class-stringificationconfiguration","text":"URI: linkmltr:StringificationConfiguration classDiagram class StringificationConfiguration StringificationConfiguration : delimiter StringificationConfiguration : over_slots StringificationConfiguration : reversed StringificationConfiguration : syntax StringificationConfiguration --> SerializationSyntaxType : syntax","title":"Class: StringificationConfiguration"},{"location":"StringificationConfiguration/#slots","text":"Name Cardinality and Range Description Inheritance delimiter 0..1 String direct reversed 0..1 Boolean direct over_slots 0..* String direct syntax 0..1 SerializationSyntaxType direct","title":"Slots"},{"location":"StringificationConfiguration/#usages","text":"used by used in type used SlotDerivation stringification range StringificationConfiguration","title":"Usages"},{"location":"StringificationConfiguration/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"StringificationConfiguration/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"StringificationConfiguration/#mappings","text":"Mapping Type Mapped Value self linkmltr:StringificationConfiguration native linkmltr:StringificationConfiguration","title":"Mappings"},{"location":"StringificationConfiguration/#linkml-source","text":"","title":"LinkML Source"},{"location":"StringificationConfiguration/#direct","text":"name: StringificationConfiguration from_schema: https://w3id.org/linkml/transformer attributes: delimiter: name: delimiter examples: - value: ',' - value: '|' - value: ; from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - StringificationConfiguration range: string reversed: name: reversed from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - StringificationConfiguration range: boolean over_slots: name: over_slots from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - StringificationConfiguration range: string syntax: name: syntax examples: - value: json - value: yaml from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - StringificationConfiguration range: SerializationSyntaxType","title":"Direct"},{"location":"StringificationConfiguration/#induced","text":"name: StringificationConfiguration from_schema: https://w3id.org/linkml/transformer attributes: delimiter: name: delimiter examples: - value: ',' - value: '|' - value: ; from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: delimiter owner: StringificationConfiguration domain_of: - StringificationConfiguration range: string reversed: name: reversed from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: reversed owner: StringificationConfiguration domain_of: - StringificationConfiguration range: boolean over_slots: name: over_slots from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: over_slots owner: StringificationConfiguration domain_of: - StringificationConfiguration range: string syntax: name: syntax examples: - value: json - value: yaml from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: syntax owner: StringificationConfiguration domain_of: - StringificationConfiguration range: SerializationSyntaxType","title":"Induced"},{"location":"Time/","text":"Type: Time A time object represents a (local) time of day, independent of any particular day URI: xsd:time base : XSDTime uri : xsd:time repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer","title":"Type: Time"},{"location":"Time/#type-time","text":"A time object represents a (local) time of day, independent of any particular day URI: xsd:time base : XSDTime uri : xsd:time repr : str","title":"Type: Time"},{"location":"Time/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Time/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"TransformationSpecification/","text":"Class: TransformationSpecification A collection of mappings between source and target classes URI: linkmltr:TransformationSpecification classDiagram class TransformationSpecification SpecificationComponent <|-- TransformationSpecification TransformationSpecification : class_derivations TransformationSpecification --> ClassDerivation : class_derivations TransformationSpecification : comments TransformationSpecification : description TransformationSpecification --> None : description TransformationSpecification : enum_derivations TransformationSpecification --> EnumDerivation : enum_derivations TransformationSpecification : id TransformationSpecification --> None : id TransformationSpecification : implements TransformationSpecification : prefixes TransformationSpecification --> KeyVal : prefixes TransformationSpecification : slot_derivations TransformationSpecification --> SlotDerivation : slot_derivations TransformationSpecification : source_schema TransformationSpecification --> None : source_schema TransformationSpecification : target_schema TransformationSpecification --> None : target_schema TransformationSpecification : title TransformationSpecification --> None : title Inheritance SpecificationComponent TransformationSpecification Slots Name Cardinality and Range Description Inheritance id 0..1 String Unique identifier for this transformation specification direct title 0..1 String human readable title for this transformation specification direct prefixes 0..* KeyVal maps prefixes to URL expansions direct source_schema 0..1 String name of the schema that describes the source (input) objects direct target_schema 0..1 String name of the schema that describes the target (output) objects direct class_derivations 0..* ClassDerivation Instructions on how to derive a set of classes in the target schema from clas... direct enum_derivations 0..* EnumDerivation Instructions on how to derive a set of enums in the target schema direct slot_derivations 0..* SlotDerivation Instructions on how to derive a set of top level slots in the target schema direct description 0..1 String description of the specification component SpecificationComponent implements 0..* Uriorcurie A reference to a specification that this component implements SpecificationComponent comments 0..* String A list of comments about this component SpecificationComponent Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer Mappings Mapping Type Mapped Value self linkmltr:TransformationSpecification native linkmltr:TransformationSpecification LinkML Source Direct name: TransformationSpecification description: A collection of mappings between source and target classes from_schema: https://w3id.org/linkml/transformer is_a: SpecificationComponent attributes: id: name: id description: Unique identifier for this transformation specification from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: schema:identifier domain_of: - TransformationSpecification title: name: title description: human readable title for this transformation specification from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: dcterms:title domain_of: - TransformationSpecification prefixes: name: prefixes description: maps prefixes to URL expansions from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: sh:declare multivalued: true domain_of: - TransformationSpecification range: KeyVal inlined: true source_schema: name: source_schema description: name of the schema that describes the source (input) objects from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - TransformationSpecification target_schema: name: target_schema description: name of the schema that describes the target (output) objects from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - TransformationSpecification class_derivations: name: class_derivations description: Instructions on how to derive a set of classes in the target schema from classes in the source schema. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - TransformationSpecification range: ClassDerivation inlined: true enum_derivations: name: enum_derivations description: Instructions on how to derive a set of enums in the target schema from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - TransformationSpecification range: EnumDerivation inlined: true slot_derivations: name: slot_derivations description: Instructions on how to derive a set of top level slots in the target schema from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - TransformationSpecification - ClassDerivation range: SlotDerivation inlined: true tree_root: true Induced name: TransformationSpecification description: A collection of mappings between source and target classes from_schema: https://w3id.org/linkml/transformer is_a: SpecificationComponent attributes: id: name: id description: Unique identifier for this transformation specification from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: schema:identifier alias: id owner: TransformationSpecification domain_of: - TransformationSpecification title: name: title description: human readable title for this transformation specification from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: dcterms:title alias: title owner: TransformationSpecification domain_of: - TransformationSpecification prefixes: name: prefixes description: maps prefixes to URL expansions from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: sh:declare multivalued: true alias: prefixes owner: TransformationSpecification domain_of: - TransformationSpecification range: KeyVal inlined: true source_schema: name: source_schema description: name of the schema that describes the source (input) objects from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: source_schema owner: TransformationSpecification domain_of: - TransformationSpecification target_schema: name: target_schema description: name of the schema that describes the target (output) objects from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: target_schema owner: TransformationSpecification domain_of: - TransformationSpecification class_derivations: name: class_derivations description: Instructions on how to derive a set of classes in the target schema from classes in the source schema. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: class_derivations owner: TransformationSpecification domain_of: - TransformationSpecification range: ClassDerivation inlined: true enum_derivations: name: enum_derivations description: Instructions on how to derive a set of enums in the target schema from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: enum_derivations owner: TransformationSpecification domain_of: - TransformationSpecification range: EnumDerivation inlined: true slot_derivations: name: slot_derivations description: Instructions on how to derive a set of top level slots in the target schema from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: slot_derivations owner: TransformationSpecification domain_of: - TransformationSpecification - ClassDerivation range: SlotDerivation inlined: true description: name: description description: description of the specification component from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: dcterms:description alias: description owner: TransformationSpecification domain_of: - SpecificationComponent range: string implements: name: implements description: A reference to a specification that this component implements. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: implements owner: TransformationSpecification domain_of: - SpecificationComponent range: uriorcurie comments: name: comments description: A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use. from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: rdfs:comment multivalued: true alias: comments owner: TransformationSpecification domain_of: - SpecificationComponent range: string tree_root: true","title":"Class: TransformationSpecification"},{"location":"TransformationSpecification/#class-transformationspecification","text":"A collection of mappings between source and target classes URI: linkmltr:TransformationSpecification classDiagram class TransformationSpecification SpecificationComponent <|-- TransformationSpecification TransformationSpecification : class_derivations TransformationSpecification --> ClassDerivation : class_derivations TransformationSpecification : comments TransformationSpecification : description TransformationSpecification --> None : description TransformationSpecification : enum_derivations TransformationSpecification --> EnumDerivation : enum_derivations TransformationSpecification : id TransformationSpecification --> None : id TransformationSpecification : implements TransformationSpecification : prefixes TransformationSpecification --> KeyVal : prefixes TransformationSpecification : slot_derivations TransformationSpecification --> SlotDerivation : slot_derivations TransformationSpecification : source_schema TransformationSpecification --> None : source_schema TransformationSpecification : target_schema TransformationSpecification --> None : target_schema TransformationSpecification : title TransformationSpecification --> None : title","title":"Class: TransformationSpecification"},{"location":"TransformationSpecification/#inheritance","text":"SpecificationComponent TransformationSpecification","title":"Inheritance"},{"location":"TransformationSpecification/#slots","text":"Name Cardinality and Range Description Inheritance id 0..1 String Unique identifier for this transformation specification direct title 0..1 String human readable title for this transformation specification direct prefixes 0..* KeyVal maps prefixes to URL expansions direct source_schema 0..1 String name of the schema that describes the source (input) objects direct target_schema 0..1 String name of the schema that describes the target (output) objects direct class_derivations 0..* ClassDerivation Instructions on how to derive a set of classes in the target schema from clas... direct enum_derivations 0..* EnumDerivation Instructions on how to derive a set of enums in the target schema direct slot_derivations 0..* SlotDerivation Instructions on how to derive a set of top level slots in the target schema direct description 0..1 String description of the specification component SpecificationComponent implements 0..* Uriorcurie A reference to a specification that this component implements SpecificationComponent comments 0..* String A list of comments about this component SpecificationComponent","title":"Slots"},{"location":"TransformationSpecification/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"TransformationSpecification/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"TransformationSpecification/#mappings","text":"Mapping Type Mapped Value self linkmltr:TransformationSpecification native linkmltr:TransformationSpecification","title":"Mappings"},{"location":"TransformationSpecification/#linkml-source","text":"","title":"LinkML Source"},{"location":"TransformationSpecification/#direct","text":"name: TransformationSpecification description: A collection of mappings between source and target classes from_schema: https://w3id.org/linkml/transformer is_a: SpecificationComponent attributes: id: name: id description: Unique identifier for this transformation specification from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: schema:identifier domain_of: - TransformationSpecification title: name: title description: human readable title for this transformation specification from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: dcterms:title domain_of: - TransformationSpecification prefixes: name: prefixes description: maps prefixes to URL expansions from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: sh:declare multivalued: true domain_of: - TransformationSpecification range: KeyVal inlined: true source_schema: name: source_schema description: name of the schema that describes the source (input) objects from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - TransformationSpecification target_schema: name: target_schema description: name of the schema that describes the target (output) objects from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - TransformationSpecification class_derivations: name: class_derivations description: Instructions on how to derive a set of classes in the target schema from classes in the source schema. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - TransformationSpecification range: ClassDerivation inlined: true enum_derivations: name: enum_derivations description: Instructions on how to derive a set of enums in the target schema from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - TransformationSpecification range: EnumDerivation inlined: true slot_derivations: name: slot_derivations description: Instructions on how to derive a set of top level slots in the target schema from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true domain_of: - TransformationSpecification - ClassDerivation range: SlotDerivation inlined: true tree_root: true","title":"Direct"},{"location":"TransformationSpecification/#induced","text":"name: TransformationSpecification description: A collection of mappings between source and target classes from_schema: https://w3id.org/linkml/transformer is_a: SpecificationComponent attributes: id: name: id description: Unique identifier for this transformation specification from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: schema:identifier alias: id owner: TransformationSpecification domain_of: - TransformationSpecification title: name: title description: human readable title for this transformation specification from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: dcterms:title alias: title owner: TransformationSpecification domain_of: - TransformationSpecification prefixes: name: prefixes description: maps prefixes to URL expansions from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: sh:declare multivalued: true alias: prefixes owner: TransformationSpecification domain_of: - TransformationSpecification range: KeyVal inlined: true source_schema: name: source_schema description: name of the schema that describes the source (input) objects from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: source_schema owner: TransformationSpecification domain_of: - TransformationSpecification target_schema: name: target_schema description: name of the schema that describes the target (output) objects from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: target_schema owner: TransformationSpecification domain_of: - TransformationSpecification class_derivations: name: class_derivations description: Instructions on how to derive a set of classes in the target schema from classes in the source schema. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: class_derivations owner: TransformationSpecification domain_of: - TransformationSpecification range: ClassDerivation inlined: true enum_derivations: name: enum_derivations description: Instructions on how to derive a set of enums in the target schema from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: enum_derivations owner: TransformationSpecification domain_of: - TransformationSpecification range: EnumDerivation inlined: true slot_derivations: name: slot_derivations description: Instructions on how to derive a set of top level slots in the target schema from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: slot_derivations owner: TransformationSpecification domain_of: - TransformationSpecification - ClassDerivation range: SlotDerivation inlined: true description: name: description description: description of the specification component from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: dcterms:description alias: description owner: TransformationSpecification domain_of: - SpecificationComponent range: string implements: name: implements description: A reference to a specification that this component implements. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: implements owner: TransformationSpecification domain_of: - SpecificationComponent range: uriorcurie comments: name: comments description: A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use. from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: rdfs:comment multivalued: true alias: comments owner: TransformationSpecification domain_of: - SpecificationComponent range: string tree_root: true","title":"Induced"},{"location":"UnitConversionConfiguration/","text":"Class: UnitConversionConfiguration URI: linkmltr:UnitConversionConfiguration classDiagram class UnitConversionConfiguration UnitConversionConfiguration : source_magnitude_slot UnitConversionConfiguration --> None : source_magnitude_slot UnitConversionConfiguration : source_unit UnitConversionConfiguration --> None : source_unit UnitConversionConfiguration : source_unit_scheme UnitConversionConfiguration : source_unit_slot UnitConversionConfiguration --> None : source_unit_slot UnitConversionConfiguration : target_magnitude_slot UnitConversionConfiguration --> None : target_magnitude_slot UnitConversionConfiguration : target_unit UnitConversionConfiguration --> None : target_unit UnitConversionConfiguration : target_unit_scheme UnitConversionConfiguration : target_unit_slot UnitConversionConfiguration --> None : target_unit_slot Slots Name Cardinality and Range Description Inheritance target_unit 0..1 String direct target_unit_scheme 0..1 String direct source_unit 0..1 String direct source_unit_scheme 0..1 String direct source_unit_slot 0..1 String direct source_magnitude_slot 0..1 String direct target_unit_slot 0..1 String direct target_magnitude_slot 0..1 String direct Usages used by used in type used SlotDerivation unit_conversion range UnitConversionConfiguration Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer Mappings Mapping Type Mapped Value self linkmltr:UnitConversionConfiguration native linkmltr:UnitConversionConfiguration LinkML Source Direct name: UnitConversionConfiguration from_schema: https://w3id.org/linkml/transformer attributes: target_unit: name: target_unit from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - UnitConversionConfiguration target_unit_scheme: name: target_unit_scheme examples: - value: ucum from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - UnitConversionConfiguration range: string source_unit: name: source_unit from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - UnitConversionConfiguration source_unit_scheme: name: source_unit_scheme examples: - value: ucum from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - UnitConversionConfiguration range: string source_unit_slot: name: source_unit_slot from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - UnitConversionConfiguration source_magnitude_slot: name: source_magnitude_slot from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - UnitConversionConfiguration target_unit_slot: name: target_unit_slot from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - UnitConversionConfiguration target_magnitude_slot: name: target_magnitude_slot from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - UnitConversionConfiguration Induced name: UnitConversionConfiguration from_schema: https://w3id.org/linkml/transformer attributes: target_unit: name: target_unit from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: target_unit owner: UnitConversionConfiguration domain_of: - UnitConversionConfiguration target_unit_scheme: name: target_unit_scheme examples: - value: ucum from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: target_unit_scheme owner: UnitConversionConfiguration domain_of: - UnitConversionConfiguration range: string source_unit: name: source_unit from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: source_unit owner: UnitConversionConfiguration domain_of: - UnitConversionConfiguration source_unit_scheme: name: source_unit_scheme examples: - value: ucum from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: source_unit_scheme owner: UnitConversionConfiguration domain_of: - UnitConversionConfiguration range: string source_unit_slot: name: source_unit_slot from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: source_unit_slot owner: UnitConversionConfiguration domain_of: - UnitConversionConfiguration source_magnitude_slot: name: source_magnitude_slot from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: source_magnitude_slot owner: UnitConversionConfiguration domain_of: - UnitConversionConfiguration target_unit_slot: name: target_unit_slot from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: target_unit_slot owner: UnitConversionConfiguration domain_of: - UnitConversionConfiguration target_magnitude_slot: name: target_magnitude_slot from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: target_magnitude_slot owner: UnitConversionConfiguration domain_of: - UnitConversionConfiguration","title":"Class: UnitConversionConfiguration"},{"location":"UnitConversionConfiguration/#class-unitconversionconfiguration","text":"URI: linkmltr:UnitConversionConfiguration classDiagram class UnitConversionConfiguration UnitConversionConfiguration : source_magnitude_slot UnitConversionConfiguration --> None : source_magnitude_slot UnitConversionConfiguration : source_unit UnitConversionConfiguration --> None : source_unit UnitConversionConfiguration : source_unit_scheme UnitConversionConfiguration : source_unit_slot UnitConversionConfiguration --> None : source_unit_slot UnitConversionConfiguration : target_magnitude_slot UnitConversionConfiguration --> None : target_magnitude_slot UnitConversionConfiguration : target_unit UnitConversionConfiguration --> None : target_unit UnitConversionConfiguration : target_unit_scheme UnitConversionConfiguration : target_unit_slot UnitConversionConfiguration --> None : target_unit_slot","title":"Class: UnitConversionConfiguration"},{"location":"UnitConversionConfiguration/#slots","text":"Name Cardinality and Range Description Inheritance target_unit 0..1 String direct target_unit_scheme 0..1 String direct source_unit 0..1 String direct source_unit_scheme 0..1 String direct source_unit_slot 0..1 String direct source_magnitude_slot 0..1 String direct target_unit_slot 0..1 String direct target_magnitude_slot 0..1 String direct","title":"Slots"},{"location":"UnitConversionConfiguration/#usages","text":"used by used in type used SlotDerivation unit_conversion range UnitConversionConfiguration","title":"Usages"},{"location":"UnitConversionConfiguration/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"UnitConversionConfiguration/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"UnitConversionConfiguration/#mappings","text":"Mapping Type Mapped Value self linkmltr:UnitConversionConfiguration native linkmltr:UnitConversionConfiguration","title":"Mappings"},{"location":"UnitConversionConfiguration/#linkml-source","text":"","title":"LinkML Source"},{"location":"UnitConversionConfiguration/#direct","text":"name: UnitConversionConfiguration from_schema: https://w3id.org/linkml/transformer attributes: target_unit: name: target_unit from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - UnitConversionConfiguration target_unit_scheme: name: target_unit_scheme examples: - value: ucum from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - UnitConversionConfiguration range: string source_unit: name: source_unit from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - UnitConversionConfiguration source_unit_scheme: name: source_unit_scheme examples: - value: ucum from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - UnitConversionConfiguration range: string source_unit_slot: name: source_unit_slot from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - UnitConversionConfiguration source_magnitude_slot: name: source_magnitude_slot from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - UnitConversionConfiguration target_unit_slot: name: target_unit_slot from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - UnitConversionConfiguration target_magnitude_slot: name: target_magnitude_slot from_schema: https://w3id.org/linkml/transformer rank: 1000 domain_of: - UnitConversionConfiguration","title":"Direct"},{"location":"UnitConversionConfiguration/#induced","text":"name: UnitConversionConfiguration from_schema: https://w3id.org/linkml/transformer attributes: target_unit: name: target_unit from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: target_unit owner: UnitConversionConfiguration domain_of: - UnitConversionConfiguration target_unit_scheme: name: target_unit_scheme examples: - value: ucum from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: target_unit_scheme owner: UnitConversionConfiguration domain_of: - UnitConversionConfiguration range: string source_unit: name: source_unit from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: source_unit owner: UnitConversionConfiguration domain_of: - UnitConversionConfiguration source_unit_scheme: name: source_unit_scheme examples: - value: ucum from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: source_unit_scheme owner: UnitConversionConfiguration domain_of: - UnitConversionConfiguration range: string source_unit_slot: name: source_unit_slot from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: source_unit_slot owner: UnitConversionConfiguration domain_of: - UnitConversionConfiguration source_magnitude_slot: name: source_magnitude_slot from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: source_magnitude_slot owner: UnitConversionConfiguration domain_of: - UnitConversionConfiguration target_unit_slot: name: target_unit_slot from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: target_unit_slot owner: UnitConversionConfiguration domain_of: - UnitConversionConfiguration target_magnitude_slot: name: target_magnitude_slot from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: target_magnitude_slot owner: UnitConversionConfiguration domain_of: - UnitConversionConfiguration","title":"Induced"},{"location":"Uri/","text":"Type: Uri a complete URI URI: xsd:anyURI base : URI uri : xsd:anyURI repr : str Comments in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer","title":"Type: Uri"},{"location":"Uri/#type-uri","text":"a complete URI URI: xsd:anyURI base : URI uri : xsd:anyURI repr : str","title":"Type: Uri"},{"location":"Uri/#comments","text":"in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node","title":"Comments"},{"location":"Uri/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Uri/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"Uriorcurie/","text":"Type: Uriorcurie a URI or a CURIE URI: xsd:anyURI base : URIorCURIE uri : xsd:anyURI repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer","title":"Type: Uriorcurie"},{"location":"Uriorcurie/#type-uriorcurie","text":"a URI or a CURIE URI: xsd:anyURI base : URIorCURIE uri : xsd:anyURI repr : str","title":"Type: Uriorcurie"},{"location":"Uriorcurie/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Uriorcurie/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"add/","text":"Slot: add URI: linkmltr:add Applicable Classes Name Description Modifies Slot CopyDirective Instructs a Schema Mapper in how to map to a target schema no Properties Range: Any Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer LinkML Source name: add from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: add owner: CopyDirective domain_of: - CopyDirective range: Any","title":"Slot: add"},{"location":"add/#slot-add","text":"URI: linkmltr:add","title":"Slot: add"},{"location":"add/#applicable-classes","text":"Name Description Modifies Slot CopyDirective Instructs a Schema Mapper in how to map to a target schema no","title":"Applicable Classes"},{"location":"add/#properties","text":"Range: Any","title":"Properties"},{"location":"add/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"add/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"add/#linkml-source","text":"name: add from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: add owner: CopyDirective domain_of: - CopyDirective range: Any","title":"LinkML Source"},{"location":"alias/","text":"Slot: alias name of the class to be aliased URI: linkmltr:alias Applicable Classes Name Description Modifies Slot AliasedClass alias-class key value pairs for classes no Properties Range: NONE Required: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer LinkML Source name: alias description: name of the class to be aliased from_schema: https://w3id.org/linkml/transformer rank: 1000 key: true alias: alias owner: AliasedClass domain_of: - AliasedClass required: true","title":"Slot: alias"},{"location":"alias/#slot-alias","text":"name of the class to be aliased URI: linkmltr:alias","title":"Slot: alias"},{"location":"alias/#applicable-classes","text":"Name Description Modifies Slot AliasedClass alias-class key value pairs for classes no","title":"Applicable Classes"},{"location":"alias/#properties","text":"Range: NONE Required: True","title":"Properties"},{"location":"alias/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"alias/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"alias/#linkml-source","text":"name: alias description: name of the class to be aliased from_schema: https://w3id.org/linkml/transformer rank: 1000 key: true alias: alias owner: AliasedClass domain_of: - AliasedClass required: true","title":"LinkML Source"},{"location":"cast_collection_as/","text":"Slot: cast_collection_as URI: linkmltr:cast_collection_as Applicable Classes Name Description Modifies Slot SlotDerivation A specification of how to derive the value of a target slot from a source slo... no Properties Range: CollectionType Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer LinkML Source name: cast_collection_as from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: cast_collection_as owner: SlotDerivation domain_of: - SlotDerivation range: CollectionType","title":"Slot: cast_collection_as"},{"location":"cast_collection_as/#slot-cast_collection_as","text":"URI: linkmltr:cast_collection_as","title":"Slot: cast_collection_as"},{"location":"cast_collection_as/#applicable-classes","text":"Name Description Modifies Slot SlotDerivation A specification of how to derive the value of a target slot from a source slo... no","title":"Applicable Classes"},{"location":"cast_collection_as/#properties","text":"Range: CollectionType","title":"Properties"},{"location":"cast_collection_as/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"cast_collection_as/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"cast_collection_as/#linkml-source","text":"name: cast_collection_as from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: cast_collection_as owner: SlotDerivation domain_of: - SlotDerivation range: CollectionType","title":"LinkML Source"},{"location":"class_derivations/","text":"Slot: class_derivations Instructions on how to derive a set of classes in the target schema from classes in the source schema. URI: linkmltr:class_derivations Applicable Classes Name Description Modifies Slot TransformationSpecification A collection of mappings between source and target classes no Properties Range: ClassDerivation Multivalued: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer LinkML Source name: class_derivations description: Instructions on how to derive a set of classes in the target schema from classes in the source schema. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: class_derivations owner: TransformationSpecification domain_of: - TransformationSpecification range: ClassDerivation inlined: true","title":"Slot: class_derivations"},{"location":"class_derivations/#slot-class_derivations","text":"Instructions on how to derive a set of classes in the target schema from classes in the source schema. URI: linkmltr:class_derivations","title":"Slot: class_derivations"},{"location":"class_derivations/#applicable-classes","text":"Name Description Modifies Slot TransformationSpecification A collection of mappings between source and target classes no","title":"Applicable Classes"},{"location":"class_derivations/#properties","text":"Range: ClassDerivation Multivalued: True","title":"Properties"},{"location":"class_derivations/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"class_derivations/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"class_derivations/#linkml-source","text":"name: class_derivations description: Instructions on how to derive a set of classes in the target schema from classes in the source schema. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: class_derivations owner: TransformationSpecification domain_of: - TransformationSpecification range: ClassDerivation inlined: true","title":"LinkML Source"},{"location":"class_name/","text":"Slot: class_name URI: linkmltr:class_name Applicable Classes Name Description Modifies Slot Inverse Used for back references in mapping to relational model no Properties Range: NONE Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer LinkML Source name: class_name from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: class_name owner: Inverse domain_of: - Inverse","title":"Slot: class_name"},{"location":"class_name/#slot-class_name","text":"URI: linkmltr:class_name","title":"Slot: class_name"},{"location":"class_name/#applicable-classes","text":"Name Description Modifies Slot Inverse Used for back references in mapping to relational model no","title":"Applicable Classes"},{"location":"class_name/#properties","text":"Range: NONE","title":"Properties"},{"location":"class_name/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"class_name/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"class_name/#linkml-source","text":"name: class_name from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: class_name owner: Inverse domain_of: - Inverse","title":"LinkML Source"},{"location":"class_named/","text":"Slot: class_named local alias for the class URI: linkmltr:class_named Applicable Classes Name Description Modifies Slot AliasedClass alias-class key value pairs for classes no Properties Range: NONE Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer LinkML Source name: class_named description: local alias for the class from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: class_named owner: AliasedClass domain_of: - AliasedClass","title":"Slot: class_named"},{"location":"class_named/#slot-class_named","text":"local alias for the class URI: linkmltr:class_named","title":"Slot: class_named"},{"location":"class_named/#applicable-classes","text":"Name Description Modifies Slot AliasedClass alias-class key value pairs for classes no","title":"Applicable Classes"},{"location":"class_named/#properties","text":"Range: NONE","title":"Properties"},{"location":"class_named/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"class_named/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"class_named/#linkml-source","text":"name: class_named description: local alias for the class from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: class_named owner: AliasedClass domain_of: - AliasedClass","title":"LinkML Source"},{"location":"comments/","text":"Slot: comments A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use. 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CopyDirective range: boolean","title":"LinkML Source"},{"location":"expr/","text":"Slot: expr URI: linkmltr:expr Applicable Classes Name Description Modifies Slot EnumDerivation A specification of how to derive the value of a target enum from a source enu... no PermissibleValueDerivation A specification of how to derive the value of a PV from a source enum no SlotDerivation A specification of how to derive the value of a target slot from a source slo... no Properties Range: NONE Identifier and Mapping Information LinkML Source name: expr alias: expr domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation","title":"Slot: expr"},{"location":"expr/#slot-expr","text":"URI: linkmltr:expr","title":"Slot: expr"},{"location":"expr/#applicable-classes","text":"Name Description Modifies Slot EnumDerivation A specification of how to derive the value of a target enum from a source enu... no PermissibleValueDerivation A specification of how to derive the value of a PV from a source enum no SlotDerivation A specification of how to derive the value of a target slot from a source slo... no","title":"Applicable Classes"},{"location":"expr/#properties","text":"Range: NONE","title":"Properties"},{"location":"expr/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"expr/#linkml-source","text":"name: expr alias: expr domain_of: - 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ElementDerivation range: KeyVal inlined: true","title":"Slot: expression_to_expression_mappings"},{"location":"expression_to_expression_mappings/#slot-expression_to_expression_mappings","text":"A mapping table in which the keys and values are expressions URI: linkmltr:expression_to_expression_mappings","title":"Slot: expression_to_expression_mappings"},{"location":"expression_to_expression_mappings/#applicable-classes","text":"Name Description Modifies Slot EnumDerivation A specification of how to derive the value of a target enum from a source enu... no ElementDerivation An abstract grouping for classes that provide a specification of how to deri... no PrefixDerivation no SlotDerivation A specification of how to derive the value of a target slot from a source slo... no ClassDerivation A specification of how to derive a target class from a source class no PermissibleValueDerivation A specification of how to derive the value of a PV from a source enum no","title":"Applicable Classes"},{"location":"expression_to_expression_mappings/#properties","text":"Range: KeyVal Multivalued: True","title":"Properties"},{"location":"expression_to_expression_mappings/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"expression_to_expression_mappings/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"expression_to_expression_mappings/#linkml-source","text":"name: expression_to_expression_mappings description: A mapping table in which the keys and values are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_expression_mappings owner: ElementDerivation domain_of: - ElementDerivation range: KeyVal inlined: true","title":"LinkML Source"},{"location":"expression_to_value_mappings/","text":"Slot: expression_to_value_mappings A mapping table in which the keys are expressions URI: linkmltr:expression_to_value_mappings Applicable Classes Name Description Modifies Slot EnumDerivation A specification of how to derive the value of a target enum from a source enu... no ElementDerivation An abstract grouping for classes that provide a specification of how to deri... no PrefixDerivation no SlotDerivation A specification of how to derive the value of a target slot from a source slo... no ClassDerivation A specification of how to derive a target class from a source class no PermissibleValueDerivation A specification of how to derive the value of a PV from a source enum no Properties Range: KeyVal Multivalued: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer LinkML Source name: expression_to_value_mappings description: A mapping table in which the keys are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_value_mappings owner: ElementDerivation domain_of: - ElementDerivation range: KeyVal inlined: true","title":"Slot: expression_to_value_mappings"},{"location":"expression_to_value_mappings/#slot-expression_to_value_mappings","text":"A mapping table in which the keys are expressions URI: linkmltr:expression_to_value_mappings","title":"Slot: expression_to_value_mappings"},{"location":"expression_to_value_mappings/#applicable-classes","text":"Name Description Modifies Slot EnumDerivation A specification of how to derive the value of a target enum from a source enu... no ElementDerivation An abstract grouping for classes that provide a specification of how to deri... no PrefixDerivation no SlotDerivation A specification of how to derive the value of a target slot from a source slo... no ClassDerivation A specification of how to derive a target class from a source class no PermissibleValueDerivation A specification of how to derive the value of a PV from a source enum no","title":"Applicable Classes"},{"location":"expression_to_value_mappings/#properties","text":"Range: KeyVal Multivalued: True","title":"Properties"},{"location":"expression_to_value_mappings/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"expression_to_value_mappings/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"expression_to_value_mappings/#linkml-source","text":"name: expression_to_value_mappings description: A mapping table in which the keys are expressions from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: expression_to_value_mappings owner: ElementDerivation domain_of: - ElementDerivation range: KeyVal inlined: true","title":"LinkML Source"},{"location":"faq/","text":"FAQ Why another framework? There are a number of excellent frameworks for performing mapping and data transformations. The LinkML Transformer framework was born out of a need for a framework that: was not inherently tied to: a particular serialization format (e.g. RDF, JSON, ...) a particular programming language (e.g. Python, Java, ...) a particular database system or database language (e.g. PostgreSQL or SQL or SPARQL) not tied to a particular kind of transformation (e.g. ORM or Tables to RDF) was a natural fit for the LinkML data modeling framework was declarative and easy to perform machine reasoning over is simple for simple use cases In its current state, this framework is less powerful and expressive than many other frameworks or methodologies for performing transformations. If you need to perform complex data transformations, you might be better off using an expressive query language like SPARQL or SQL, or even just coding transformations directly in a programming language or library like Python or Pandas (but note that even for the coding use case, the LinkML Transformer framework can be useful as a standard way of documenting transformations). Currently the main use case for this framework is mostly isomorphic transformations, with lightweight manipulations. These lend themselves well to a declarative framework. Uses cases that are a particularly good fit involve mapping between data-dictionary like standards, with large numbers of metadata elements, where these elements can often be mapped one-to-one, or with simple manipulations (e.g. unit conversions). The origins lie partly in the SSSOM standard, which is intended as an ultra-simple way of specifying precise mappings between entities (e.g. schema.org Person is the same as DBPedia person). We observed that many people wanted to extend the language to perform more complex mappings. To address this, we help a workshop at the Biocuration conference in Padua, Italy in 2022. Discussion SSSOM paper SSSOM Update 2023 SSSOM Complex Mappings Workshop 2023 Mapping Data Structures: Challenges and Approaches","title":"FAQ"},{"location":"faq/#faq","text":"","title":"FAQ"},{"location":"faq/#why-another-framework","text":"There are a number of excellent frameworks for performing mapping and data transformations. The LinkML Transformer framework was born out of a need for a framework that: was not inherently tied to: a particular serialization format (e.g. RDF, JSON, ...) a particular programming language (e.g. Python, Java, ...) a particular database system or database language (e.g. PostgreSQL or SQL or SPARQL) not tied to a particular kind of transformation (e.g. ORM or Tables to RDF) was a natural fit for the LinkML data modeling framework was declarative and easy to perform machine reasoning over is simple for simple use cases In its current state, this framework is less powerful and expressive than many other frameworks or methodologies for performing transformations. If you need to perform complex data transformations, you might be better off using an expressive query language like SPARQL or SQL, or even just coding transformations directly in a programming language or library like Python or Pandas (but note that even for the coding use case, the LinkML Transformer framework can be useful as a standard way of documenting transformations). Currently the main use case for this framework is mostly isomorphic transformations, with lightweight manipulations. These lend themselves well to a declarative framework. Uses cases that are a particularly good fit involve mapping between data-dictionary like standards, with large numbers of metadata elements, where these elements can often be mapped one-to-one, or with simple manipulations (e.g. unit conversions). The origins lie partly in the SSSOM standard, which is intended as an ultra-simple way of specifying precise mappings between entities (e.g. schema.org Person is the same as DBPedia person). We observed that many people wanted to extend the language to perform more complex mappings. To address this, we help a workshop at the Biocuration conference in Padua, Italy in 2022. Discussion SSSOM paper SSSOM Update 2023 SSSOM Complex Mappings Workshop 2023 Mapping Data Structures: Challenges and Approaches","title":"Why another framework?"},{"location":"hide/","text":"Slot: hide URI: linkmltr:hide Applicable Classes Name Description Modifies Slot EnumDerivation A specification of how to derive the value of a target enum from a source enu... no PermissibleValueDerivation A specification of how to derive the value of a PV from a source enum no SlotDerivation A specification of how to derive the value of a target slot from a source slo... no Properties Range: NONE Identifier and Mapping Information LinkML Source name: hide alias: hide domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation","title":"Slot: hide"},{"location":"hide/#slot-hide","text":"URI: linkmltr:hide","title":"Slot: hide"},{"location":"hide/#applicable-classes","text":"Name Description Modifies Slot EnumDerivation A specification of how to derive the value of a target enum from a source enu... no PermissibleValueDerivation A specification of how to derive the value of a PV from a source enum no SlotDerivation A specification of how to derive the value of a target slot from a source slo... no","title":"Applicable Classes"},{"location":"hide/#properties","text":"Range: NONE","title":"Properties"},{"location":"hide/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"hide/#linkml-source","text":"name: hide alias: hide domain_of: - SlotDerivation - EnumDerivation - PermissibleValueDerivation","title":"LinkML Source"},{"location":"id/","text":"Slot: id Unique identifier for this transformation specification URI: schema:identifier Applicable Classes Name Description Modifies Slot TransformationSpecification A collection of mappings between source and target classes no Properties Range: NONE Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer LinkML Source name: id description: Unique identifier for this transformation specification from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: schema:identifier alias: id owner: TransformationSpecification domain_of: - TransformationSpecification","title":"Slot: id"},{"location":"id/#slot-id","text":"Unique identifier for this transformation specification URI: schema:identifier","title":"Slot: id"},{"location":"id/#applicable-classes","text":"Name Description Modifies Slot TransformationSpecification A collection of mappings between source and target classes no","title":"Applicable Classes"},{"location":"id/#properties","text":"Range: NONE","title":"Properties"},{"location":"id/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"id/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"id/#linkml-source","text":"name: id description: Unique identifier for this transformation specification from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: schema:identifier alias: id owner: TransformationSpecification domain_of: - TransformationSpecification","title":"LinkML Source"},{"location":"implements/","text":"Slot: implements A reference to a specification that this component implements. URI: linkmltr:implements Applicable Classes Name Description Modifies Slot EnumDerivation A specification of how to derive the value of a target enum from a source enu... no PermissibleValueDerivation A specification of how to derive the value of a PV from a source enum no ElementDerivation An abstract grouping for classes that provide a specification of how to deri... no PrefixDerivation no SlotDerivation A specification of how to derive the value of a target slot from a source slo... no ClassDerivation A specification of how to derive a target class from a source class no SpecificationComponent no TransformationSpecification A collection of mappings between source and target classes no Properties Range: Uriorcurie Multivalued: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer LinkML Source name: implements description: A reference to a specification that this component implements. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: implements owner: SpecificationComponent domain_of: - SpecificationComponent range: uriorcurie","title":"Slot: implements"},{"location":"implements/#slot-implements","text":"A reference to a specification that this component implements. URI: linkmltr:implements","title":"Slot: implements"},{"location":"implements/#applicable-classes","text":"Name Description Modifies Slot EnumDerivation A specification of how to derive the value of a target enum from a source enu... no PermissibleValueDerivation A specification of how to derive the value of a PV from a source enum no ElementDerivation An abstract grouping for classes that provide a specification of how to deri... no PrefixDerivation no SlotDerivation A specification of how to derive the value of a target slot from a source slo... no ClassDerivation A specification of how to derive a target class from a source class no SpecificationComponent no TransformationSpecification A collection of mappings between source and target classes no","title":"Applicable Classes"},{"location":"implements/#properties","text":"Range: Uriorcurie Multivalued: True","title":"Properties"},{"location":"implements/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"implements/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"implements/#linkml-source","text":"name: implements description: A reference to a specification that this component implements. from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: implements owner: SpecificationComponent domain_of: - SpecificationComponent range: uriorcurie","title":"LinkML Source"},{"location":"include/","text":"Slot: include URI: linkmltr:include Applicable Classes Name Description Modifies Slot CopyDirective Instructs a Schema Mapper in how to map to a target schema no Properties Range: Any Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer LinkML Source name: include from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: include owner: CopyDirective domain_of: - CopyDirective range: Any","title":"Slot: include"},{"location":"include/#slot-include","text":"URI: linkmltr:include","title":"Slot: include"},{"location":"include/#applicable-classes","text":"Name Description Modifies Slot CopyDirective Instructs a Schema Mapper in how to map to a target schema no","title":"Applicable Classes"},{"location":"include/#properties","text":"Range: Any","title":"Properties"},{"location":"include/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"include/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"include/#linkml-source","text":"name: include from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: include owner: CopyDirective domain_of: - CopyDirective range: Any","title":"LinkML Source"},{"location":"inverse_of/","text":"Slot: inverse_of Used to specify a class-slot tuple that is the inverse of the derived/target slot. This is used primarily for mapping to relational databases or formalisms that do not allow multiple values. The class representing the repeated element has a foreign key slot inserted in that 'back references' the original multivalued slot. URI: linkmltr:inverse_of Applicable Classes Name Description Modifies Slot SlotDerivation A specification of how to derive the value of a target slot from a source slo... no Properties Range: Inverse Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer LinkML Source name: inverse_of description: Used to specify a class-slot tuple that is the inverse of the derived/target slot. This is used primarily for mapping to relational databases or formalisms that do not allow multiple values. The class representing the repeated element has a foreign key slot inserted in that 'back references' the original multivalued slot. from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: inverse_of owner: SlotDerivation domain_of: - SlotDerivation range: Inverse","title":"Slot: inverse_of"},{"location":"inverse_of/#slot-inverse_of","text":"Used to specify a class-slot tuple that is the inverse of the derived/target slot. This is used primarily for mapping to relational databases or formalisms that do not allow multiple values. The class representing the repeated element has a foreign key slot inserted in that 'back references' the original multivalued slot. URI: linkmltr:inverse_of","title":"Slot: inverse_of"},{"location":"inverse_of/#applicable-classes","text":"Name Description Modifies Slot SlotDerivation A specification of how to derive the value of a target slot from a source slo... no","title":"Applicable Classes"},{"location":"inverse_of/#properties","text":"Range: Inverse","title":"Properties"},{"location":"inverse_of/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"inverse_of/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"inverse_of/#linkml-source","text":"name: inverse_of description: Used to specify a class-slot tuple that is the inverse of the derived/target slot. This is used primarily for mapping to relational databases or formalisms that do not allow multiple values. The class representing the repeated element has a foreign key slot inserted in that 'back references' the original multivalued slot. from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: inverse_of owner: SlotDerivation domain_of: - SlotDerivation range: Inverse","title":"LinkML Source"},{"location":"is_a/","text":"Slot: is_a URI: linkml:is_a Applicable Classes Name Description Modifies Slot EnumDerivation A specification of how to derive the value of a target enum from a source enu... no ElementDerivation An abstract grouping for classes that provide a specification of how to deri... no PrefixDerivation no SlotDerivation A specification of how to derive the value of a target slot from a source slo... no ClassDerivation A specification of how to derive a target class from a source class no PermissibleValueDerivation A specification of how to derive the value of a PV from a source enum no Properties Range: ElementDerivation Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer LinkML Source name: is_a from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:is_a alias: is_a owner: ElementDerivation domain_of: - ElementDerivation range: ElementDerivation","title":"Slot: is_a"},{"location":"is_a/#slot-is_a","text":"URI: linkml:is_a","title":"Slot: is_a"},{"location":"is_a/#applicable-classes","text":"Name Description Modifies Slot EnumDerivation A specification of how to derive the value of a target enum from a source enu... no ElementDerivation An abstract grouping for classes that provide a specification of how to deri... no PrefixDerivation no SlotDerivation A specification of how to derive the value of a target slot from a source slo... no ClassDerivation A specification of how to derive a target class from a source class no PermissibleValueDerivation A specification of how to derive the value of a PV from a source enum no","title":"Applicable Classes"},{"location":"is_a/#properties","text":"Range: ElementDerivation","title":"Properties"},{"location":"is_a/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"is_a/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"is_a/#linkml-source","text":"name: is_a from_schema: https://w3id.org/linkml/transformer rank: 1000 slot_uri: linkml:is_a alias: is_a owner: ElementDerivation domain_of: - ElementDerivation range: ElementDerivation","title":"LinkML Source"},{"location":"joins/","text":"Slot: joins Additional classes to be joined to derive instances of the target class URI: linkmltr:joins Applicable Classes Name Description Modifies Slot ClassDerivation A specification of how to derive a target class from a source class no Properties Range: AliasedClass Multivalued: True Comments not yet implemented Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer LinkML Source name: joins description: Additional classes to be joined to derive instances of the target class comments: - not yet implemented from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: joins owner: ClassDerivation domain_of: - ClassDerivation range: AliasedClass inlined: true","title":"Slot: joins"},{"location":"joins/#slot-joins","text":"Additional classes to be joined to derive instances of the target class URI: linkmltr:joins","title":"Slot: joins"},{"location":"joins/#applicable-classes","text":"Name Description Modifies Slot ClassDerivation A specification of how to derive a target class from a source class no","title":"Applicable Classes"},{"location":"joins/#properties","text":"Range: AliasedClass Multivalued: True","title":"Properties"},{"location":"joins/#comments","text":"not yet implemented","title":"Comments"},{"location":"joins/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"joins/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"joins/#linkml-source","text":"name: joins description: Additional classes to be joined to derive instances of the target class comments: - not yet implemented from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: joins owner: ClassDerivation domain_of: - ClassDerivation range: AliasedClass inlined: true","title":"LinkML Source"},{"location":"key/","text":"Slot: key URI: linkmltr:key Applicable Classes Name Description Modifies Slot KeyVal no Properties Range: NONE Required: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer LinkML Source name: key from_schema: https://w3id.org/linkml/transformer rank: 1000 key: true alias: key owner: KeyVal domain_of: - KeyVal required: true","title":"Slot: key"},{"location":"key/#slot-key","text":"URI: linkmltr:key","title":"Slot: key"},{"location":"key/#applicable-classes","text":"Name Description Modifies Slot KeyVal no","title":"Applicable Classes"},{"location":"key/#properties","text":"Range: NONE Required: True","title":"Properties"},{"location":"key/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"key/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"key/#linkml-source","text":"name: key from_schema: https://w3id.org/linkml/transformer rank: 1000 key: true alias: key owner: KeyVal domain_of: - KeyVal required: true","title":"LinkML Source"},{"location":"linkml-map/","text":"linkml-map Datamodel for LinkML schema mappings and transformations. A mapper generates instances of a target data model from instances of a source data model. This transformation process is guided by a TransformationSpecification . The specification is independent of any one method for transforming data. It allows different approaches, including: direct implementation, transforming python or json objects translation of the specification into SQL commands, to operate on relations translation of the specification into SPARQL CONSTRUCTs, to operate on triples translation into another specification language, such as R2RML URI: https://w3id.org/linkml/transformer","title":"linkml-map"},{"location":"linkml-map/#linkml-map","text":"Datamodel for LinkML schema mappings and transformations. A mapper generates instances of a target data model from instances of a source data model. This transformation process is guided by a TransformationSpecification . The specification is independent of any one method for transforming data. It allows different approaches, including: direct implementation, transforming python or json objects translation of the specification into SQL commands, to operate on relations translation of the specification into SPARQL CONSTRUCTs, to operate on triples translation into another specification language, such as R2RML URI: https://w3id.org/linkml/transformer","title":"linkml-map"},{"location":"mirror_source/","text":"Slot: mirror_source URI: linkmltr:mirror_source Applicable Classes Name Description Modifies Slot EnumDerivation A specification of how to derive the value of a target enum from a source enu... no ElementDerivation An abstract grouping for classes that provide a specification of how to deri... no PrefixDerivation no SlotDerivation A specification of how to derive the value of a target slot from a source slo... no ClassDerivation A specification of how to derive a target class from a source class no PermissibleValueDerivation A specification of how to derive the value of a PV from a source enum no Properties Range: Boolean Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer LinkML Source name: mirror_source from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: mirror_source owner: ElementDerivation domain_of: - ElementDerivation range: boolean","title":"Slot: mirror_source"},{"location":"mirror_source/#slot-mirror_source","text":"URI: linkmltr:mirror_source","title":"Slot: mirror_source"},{"location":"mirror_source/#applicable-classes","text":"Name Description Modifies Slot EnumDerivation A specification of how to derive the value of a target enum from a source enu... no ElementDerivation An abstract grouping for classes that provide a specification of how to deri... no PrefixDerivation no SlotDerivation A specification of how to derive the value of a target slot from a source slo... no ClassDerivation A specification of how to derive a target class from a source class no PermissibleValueDerivation A specification of how to derive the value of a PV from a source enum no","title":"Applicable Classes"},{"location":"mirror_source/#properties","text":"Range: Boolean","title":"Properties"},{"location":"mirror_source/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"mirror_source/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"mirror_source/#linkml-source","text":"name: mirror_source from_schema: https://w3id.org/linkml/transformer rank: 1000 alias: mirror_source owner: ElementDerivation domain_of: - 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KeyVal range: Any","title":"LinkML Source"},{"location":"value_mappings/","text":"Slot: value_mappings A mapping table that is applied directly to mappings, in order of precedence URI: linkmltr:value_mappings Applicable Classes Name Description Modifies Slot EnumDerivation A specification of how to derive the value of a target enum from a source enu... no ElementDerivation An abstract grouping for classes that provide a specification of how to deri... no PrefixDerivation no SlotDerivation A specification of how to derive the value of a target slot from a source slo... no ClassDerivation A specification of how to derive a target class from a source class no PermissibleValueDerivation A specification of how to derive the value of a PV from a source enum no Properties Range: KeyVal Multivalued: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/linkml/transformer LinkML Source name: value_mappings description: A mapping table that is applied directly to mappings, in order of precedence from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: value_mappings owner: ElementDerivation domain_of: - ElementDerivation range: KeyVal inlined: true","title":"Slot: value_mappings"},{"location":"value_mappings/#slot-value_mappings","text":"A mapping table that is applied directly to mappings, in order of precedence URI: linkmltr:value_mappings","title":"Slot: value_mappings"},{"location":"value_mappings/#applicable-classes","text":"Name Description Modifies Slot EnumDerivation A specification of how to derive the value of a target enum from a source enu... no ElementDerivation An abstract grouping for classes that provide a specification of how to deri... no PrefixDerivation no SlotDerivation A specification of how to derive the value of a target slot from a source slo... no ClassDerivation A specification of how to derive a target class from a source class no PermissibleValueDerivation A specification of how to derive the value of a PV from a source enum no","title":"Applicable Classes"},{"location":"value_mappings/#properties","text":"Range: KeyVal Multivalued: True","title":"Properties"},{"location":"value_mappings/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"value_mappings/#schema-source","text":"from schema: https://w3id.org/linkml/transformer","title":"Schema Source"},{"location":"value_mappings/#linkml-source","text":"name: value_mappings description: A mapping table that is applied directly to mappings, in order of precedence from_schema: https://w3id.org/linkml/transformer rank: 1000 multivalued: true alias: value_mappings owner: ElementDerivation domain_of: - ElementDerivation range: KeyVal inlined: true","title":"LinkML Source"},{"location":"examples/Tutorial/","text":"(function() { function addWidgetsRenderer() { var requireJsScript = document.createElement('script'); requireJsScript.src = 'https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js'; var mimeElement = document.querySelector('script[type=\"application/vnd.jupyter.widget-view+json\"]'); var jupyterWidgetsScript = document.createElement('script'); var widgetRendererSrc = 'https://unpkg.com/@jupyter-widgets/html-manager@*/dist/embed-amd.js'; var widgetState; // Fallback for older version: try { widgetState = mimeElement && JSON.parse(mimeElement.innerHTML); if (widgetState && (widgetState.version_major < 2 || !widgetState.version_major)) { widgetRendererSrc = 'jupyter-js-widgets@*/dist/embed.js'; } } catch(e) {} jupyterWidgetsScript.src = widgetRendererSrc; document.body.appendChild(requireJsScript); document.body.appendChild(jupyterWidgetsScript); } document.addEventListener('DOMContentLoaded', addWidgetsRenderer); }()); LinkML-Map tutorial This tutorial walks through basic programmatic use of the LinkML-Map framework. This is intended for Python developers - note that many of the operations here can also be performed at the command line. import yaml Creating an example schema We will use a LinkML SchemaBuilder object to progressively build up a schema, adding additional features as we go. We'll start with a simple Person schema, with a few single valued scalar slots: from linkml.utils.schema_builder import SchemaBuilder from linkml_runtime.linkml_model import SlotDefinition sb = SchemaBuilder() sb.add_class(\"Person\", slots=[SlotDefinition(\"family_name\", range=\"string\"), SlotDefinition(\"given_name\", range=\"string\"), SlotDefinition(\"age_in_years\", range=\"integer\"), SlotDefinition(\"height_in_cm\", range=\"float\"), ]) sb.add_defaults() print(yaml.dump(sb.as_dict(), sort_keys=False)) name: test-schema id: http://example.org/test-schema imports: - linkml:types prefixes: linkml: https://w3id.org/linkml/ test_schema: http://example.org/test-schema/ default_prefix: test_schema default_range: string slots: family_name: range: string given_name: range: string age_in_years: range: integer height_in_cm: range: float classes: Person: slots: - family_name - given_name - age_in_years - height_in_cm Creating a Transformer Session object We will use a Session object which conveniently wraps a number of different capabilities; the first of these capabilities is to map (transform) data objects from one schema to another (implicit) schema using a transformer specification ). Our initial transformer specification will be a trivial isomorphic one that: maps the Person class to an Individual class passes through name fields as-is renames measurement fields ( age_in_years and height_in_cm to age and height ) from linkml_map.session import Session session = Session() session.set_source_schema(sb.as_dict()) # Transformer specification (in YAML) session.set_object_transformer(\"\"\" class_derivations: Individual: populated_from: Person slot_derivations: family_name: populated_from: family_name given_name: populated_from: given_name age: populated_from: age_in_years height: populated_from: height_in_cm \"\"\") Visualizing transformer specifications We can visualize the transformer specification using graphviz: session.graphviz() sourcePerson Person family_name : string given_name : string age_in_years : integer height_in_cm : float targetIndividual Individual family_name : string given_name : string age : integer height : float sourcePerson:family_name->targetIndividual:family_name sourcePerson:given_name->targetIndividual:given_name sourcePerson:age_in_years->targetIndividual:age sourcePerson:height_in_cm->targetIndividual:height Transforming objects We'll next make a simple Person object. Note that for simplicity we are specifying this using a Python dictionary. The framework also works with objects instantiating either Pydantic or Dataclasses classes (use the transform_object method instead of transform ). obj = { \"given_name\": \"Jane\", \"family_name\": \"Doe\", \"age_in_years\": 42, \"height_in_cm\": 180.0, } session.transform(obj) {'family_name': 'Doe', 'given_name': 'Jane', 'age': 42, 'height': 180.0} This does what we expect - it renames the two fields, but leaves all values intact. Note that because we use using dictionaries here, the renaming of the class has no effect, as this is implicit with JSON/dictionaries. TODO: docs on type designator fields For command line users, the same thing can be achieved with the map-data command. Deriving target schemas LinkML-Transformer is intended as a declarative framework, in contrast to writing Python transformation code. This allows tools to introspect mappings and perform other kinds of inference. An example of this is deriving the (implicit) target schema Here we use the target_schema method on the session object to derive the target schema: from linkml_runtime.dumpers import yaml_dumper print(yaml_dumper.dumps(session.target_schema)) name: test-schema-derived id: http://example.org/test-schema-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test_schema: prefix_prefix: test_schema prefix_reference: http://example.org/test-schema/ default_prefix: http://example.org/test-schema-derived/ default_range: string classes: Individual: name: Individual attributes: family_name: name: family_name domain_of: - Person range: string given_name: name: given_name domain_of: - Person range: string age: name: age domain_of: - Person range: integer height: name: height domain_of: - Person range: float As expected, this is isomorphic to the original (source) schema, with fields and classes renamed. Using Expressions In addition to renaming fields, we can derive field values via evaluation of function expressions . You are encouraged to follow the subset of Python defined by the LinkML expression language. This provides both safety, and declarativity. However, if you need to, you can include arbitrary Python code, provided you configure the session to allow this. We'll keep the original schema, and will provide a new Transformer specification, giving an example of both string manipulation functions and arithmetic functions; the latter perform unit conversions (later on we will see more flexible and declarative ways to perform unit conversions). session.set_object_transformer(\"\"\" class_derivations: Individual: populated_from: Person slot_derivations: name: expr: \"{given_name} + ' ' + {family_name}\" description: Concatenating given and family names note this is a bad assumption for names in general, this is just for demonstration age_in_months: expr: age_in_years * 12 height_in_meters: expr: height_in_cm / 100 \"\"\") Note that when we visualize this specification, dotted lines are shown indicating a relationship between source and target that is different from direct copy: session.graphviz() sourcePerson Person family_name : string given_name : string age_in_years : integer height_in_cm : float targetIndividual Individual name : string age_in_months : string height_in_meters : string sourcePerson:given_name->targetIndividual:name sourcePerson:family_name->targetIndividual:name sourcePerson:age_in_years->targetIndividual:age_in_months sourcePerson:height_in_cm->targetIndividual:height_in_meters Now we'll transform the same object as before, and see the results: session.transform(obj) {'name': 'Jane Doe', 'age_in_months': 504, 'height_in_meters': 1.8} As expected, we concatenated the name fields, and converted the age and height fields to different units. Let's take a look at the derived schema for this new transformation: print(yaml_dumper.dumps(session.target_schema)) name: test-schema-derived id: http://example.org/test-schema-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test_schema: prefix_prefix: test_schema prefix_reference: http://example.org/test-schema/ default_prefix: http://example.org/test-schema-derived/ default_range: string classes: Individual: name: Individual attributes: name: name: name age_in_months: name: age_in_months height_in_meters: name: height_in_meters Note that at this time, deriving ranges using expressions is not supported, so the two measurement fields are erroneously typed as having the default_range of string . However, in principle, if you use the linkml subset of Python it should be possible to infer the range of the derived field, and this may be added in future versions. Currently the tool chain is at an early stage of development. Unit conversions Next we will look at a different way of doing unit conversions. The LinkML specification allows schemas to explicitly declare the units of slots, so let's modify our schema to do this, adding a UCUM code for our height_in_cm slot: from linkml_runtime.linkml_model.units import UnitOfMeasure sb.schema.slots['height_in_cm'].unit = UnitOfMeasure(ucum_code='cm') session.set_source_schema(sb.as_dict()) print(yaml.dump(sb.as_dict(), sort_keys=False)) name: test-schema id: http://example.org/test-schema imports: - linkml:types prefixes: linkml: https://w3id.org/linkml/ test_schema: http://example.org/test-schema/ default_prefix: test_schema default_range: string slots: family_name: range: string given_name: range: string age_in_years: range: integer height_in_cm: range: float unit: ucum_code: cm classes: Person: slots: - family_name - given_name - age_in_years - height_in_cm Adding target_unit to transformer specification We will create a new transformer specification, focusing on the height_in_cm field. We will transform this into a height_in_meters field, and will use the target_unit field to specify the target unit. session.set_object_transformer(\"\"\" class_derivations: Individual: populated_from: Person slot_derivations: name: expr: \"{given_name} + ' ' + {family_name}\" height_in_meters: populated_from: height_in_cm unit_conversion: target_unit: m \"\"\") session.transform(obj) {'name': 'Jane Doe', 'height_in_meters': 1.8} Units in derived schema Next we'll look at the derived target schema, and as expected we see that it has inferred the target unit for the height_in_meters field: print(yaml_dumper.dumps(session.target_schema)) name: test-schema-derived id: http://example.org/test-schema-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test_schema: prefix_prefix: test_schema prefix_reference: http://example.org/test-schema/ default_prefix: http://example.org/test-schema-derived/ default_range: string classes: Individual: name: Individual attributes: name: name: name height_in_meters: name: height_in_meters domain_of: - Person range: float unit: ucum_code: m Tabular serialization slot = sb.add_slot(\"aliases\", multivalued=True, range=\"string\", replace_if_present=True) sb.schema.classes['Person'].slots.append(slot.name) session.set_source_schema(sb.as_dict()) session.set_object_transformer(\"\"\" class_derivations: Individual: populated_from: Person slot_derivations: family_name: populated_from: family_name given_name: populated_from: given_name age: populated_from: age_in_years height: populated_from: height_in_cm aliases: populated_from: aliases stringification: delimiter: '|' \"\"\") obj = { \"given_name\": \"Jane\", \"family_name\": \"Doe\", \"age_in_years\": 42, \"height_in_cm\": 180.0, \"aliases\": [\"Jane\", \"Janie\", \"Janey\"] } flattened = session.transform(obj) flattened {'family_name': 'Doe', 'given_name': 'Jane', 'age': 42, 'height': 180.0, 'aliases': 'Jane|Janie|Janey'} this can easily be serialized to a CSV/TSV Reverse transform If a transform does not contain one-way functions, it can be reversed . In this case, reversing the transform allows us to map from the tabular form back to the richer original representation. session.reverse_transform(flattened) {'family_name': 'Doe', 'given_name': 'Jane', 'age_in_years': 42, 'height_in_cm': 180.0, 'aliases': ['Jane', 'Janie', 'Janey']}","title":"Tutorial"},{"location":"examples/Tutorial/#linkml-map-tutorial","text":"This tutorial walks through basic programmatic use of the LinkML-Map framework. This is intended for Python developers - note that many of the operations here can also be performed at the command line. import yaml","title":"LinkML-Map tutorial"},{"location":"examples/Tutorial/#creating-an-example-schema","text":"We will use a LinkML SchemaBuilder object to progressively build up a schema, adding additional features as we go. We'll start with a simple Person schema, with a few single valued scalar slots: from linkml.utils.schema_builder import SchemaBuilder from linkml_runtime.linkml_model import SlotDefinition sb = SchemaBuilder() sb.add_class(\"Person\", slots=[SlotDefinition(\"family_name\", range=\"string\"), SlotDefinition(\"given_name\", range=\"string\"), SlotDefinition(\"age_in_years\", range=\"integer\"), SlotDefinition(\"height_in_cm\", range=\"float\"), ]) sb.add_defaults() print(yaml.dump(sb.as_dict(), sort_keys=False)) name: test-schema id: http://example.org/test-schema imports: - linkml:types prefixes: linkml: https://w3id.org/linkml/ test_schema: http://example.org/test-schema/ default_prefix: test_schema default_range: string slots: family_name: range: string given_name: range: string age_in_years: range: integer height_in_cm: range: float classes: Person: slots: - family_name - given_name - age_in_years - height_in_cm","title":"Creating an example schema"},{"location":"examples/Tutorial/#creating-a-transformer-session-object","text":"We will use a Session object which conveniently wraps a number of different capabilities; the first of these capabilities is to map (transform) data objects from one schema to another (implicit) schema using a transformer specification ). Our initial transformer specification will be a trivial isomorphic one that: maps the Person class to an Individual class passes through name fields as-is renames measurement fields ( age_in_years and height_in_cm to age and height ) from linkml_map.session import Session session = Session() session.set_source_schema(sb.as_dict()) # Transformer specification (in YAML) session.set_object_transformer(\"\"\" class_derivations: Individual: populated_from: Person slot_derivations: family_name: populated_from: family_name given_name: populated_from: given_name age: populated_from: age_in_years height: populated_from: height_in_cm \"\"\")","title":"Creating a Transformer Session object"},{"location":"examples/Tutorial/#visualizing-transformer-specifications","text":"We can visualize the transformer specification using graphviz: session.graphviz() sourcePerson Person family_name : string given_name : string age_in_years : integer height_in_cm : float targetIndividual Individual family_name : string given_name : string age : integer height : float sourcePerson:family_name->targetIndividual:family_name sourcePerson:given_name->targetIndividual:given_name sourcePerson:age_in_years->targetIndividual:age sourcePerson:height_in_cm->targetIndividual:height","title":"Visualizing transformer specifications"},{"location":"examples/Tutorial/#transforming-objects","text":"We'll next make a simple Person object. Note that for simplicity we are specifying this using a Python dictionary. The framework also works with objects instantiating either Pydantic or Dataclasses classes (use the transform_object method instead of transform ). obj = { \"given_name\": \"Jane\", \"family_name\": \"Doe\", \"age_in_years\": 42, \"height_in_cm\": 180.0, } session.transform(obj) {'family_name': 'Doe', 'given_name': 'Jane', 'age': 42, 'height': 180.0} This does what we expect - it renames the two fields, but leaves all values intact. Note that because we use using dictionaries here, the renaming of the class has no effect, as this is implicit with JSON/dictionaries. TODO: docs on type designator fields For command line users, the same thing can be achieved with the map-data command.","title":"Transforming objects"},{"location":"examples/Tutorial/#deriving-target-schemas","text":"LinkML-Transformer is intended as a declarative framework, in contrast to writing Python transformation code. This allows tools to introspect mappings and perform other kinds of inference. An example of this is deriving the (implicit) target schema Here we use the target_schema method on the session object to derive the target schema: from linkml_runtime.dumpers import yaml_dumper print(yaml_dumper.dumps(session.target_schema)) name: test-schema-derived id: http://example.org/test-schema-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test_schema: prefix_prefix: test_schema prefix_reference: http://example.org/test-schema/ default_prefix: http://example.org/test-schema-derived/ default_range: string classes: Individual: name: Individual attributes: family_name: name: family_name domain_of: - Person range: string given_name: name: given_name domain_of: - Person range: string age: name: age domain_of: - Person range: integer height: name: height domain_of: - Person range: float As expected, this is isomorphic to the original (source) schema, with fields and classes renamed.","title":"Deriving target schemas"},{"location":"examples/Tutorial/#using-expressions","text":"In addition to renaming fields, we can derive field values via evaluation of function expressions . You are encouraged to follow the subset of Python defined by the LinkML expression language. This provides both safety, and declarativity. However, if you need to, you can include arbitrary Python code, provided you configure the session to allow this. We'll keep the original schema, and will provide a new Transformer specification, giving an example of both string manipulation functions and arithmetic functions; the latter perform unit conversions (later on we will see more flexible and declarative ways to perform unit conversions). session.set_object_transformer(\"\"\" class_derivations: Individual: populated_from: Person slot_derivations: name: expr: \"{given_name} + ' ' + {family_name}\" description: Concatenating given and family names note this is a bad assumption for names in general, this is just for demonstration age_in_months: expr: age_in_years * 12 height_in_meters: expr: height_in_cm / 100 \"\"\") Note that when we visualize this specification, dotted lines are shown indicating a relationship between source and target that is different from direct copy: session.graphviz() sourcePerson Person family_name : string given_name : string age_in_years : integer height_in_cm : float targetIndividual Individual name : string age_in_months : string height_in_meters : string sourcePerson:given_name->targetIndividual:name sourcePerson:family_name->targetIndividual:name sourcePerson:age_in_years->targetIndividual:age_in_months sourcePerson:height_in_cm->targetIndividual:height_in_meters Now we'll transform the same object as before, and see the results: session.transform(obj) {'name': 'Jane Doe', 'age_in_months': 504, 'height_in_meters': 1.8} As expected, we concatenated the name fields, and converted the age and height fields to different units. Let's take a look at the derived schema for this new transformation: print(yaml_dumper.dumps(session.target_schema)) name: test-schema-derived id: http://example.org/test-schema-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test_schema: prefix_prefix: test_schema prefix_reference: http://example.org/test-schema/ default_prefix: http://example.org/test-schema-derived/ default_range: string classes: Individual: name: Individual attributes: name: name: name age_in_months: name: age_in_months height_in_meters: name: height_in_meters Note that at this time, deriving ranges using expressions is not supported, so the two measurement fields are erroneously typed as having the default_range of string . However, in principle, if you use the linkml subset of Python it should be possible to infer the range of the derived field, and this may be added in future versions. Currently the tool chain is at an early stage of development.","title":"Using Expressions"},{"location":"examples/Tutorial/#unit-conversions","text":"Next we will look at a different way of doing unit conversions. The LinkML specification allows schemas to explicitly declare the units of slots, so let's modify our schema to do this, adding a UCUM code for our height_in_cm slot: from linkml_runtime.linkml_model.units import UnitOfMeasure sb.schema.slots['height_in_cm'].unit = UnitOfMeasure(ucum_code='cm') session.set_source_schema(sb.as_dict()) print(yaml.dump(sb.as_dict(), sort_keys=False)) name: test-schema id: http://example.org/test-schema imports: - linkml:types prefixes: linkml: https://w3id.org/linkml/ test_schema: http://example.org/test-schema/ default_prefix: test_schema default_range: string slots: family_name: range: string given_name: range: string age_in_years: range: integer height_in_cm: range: float unit: ucum_code: cm classes: Person: slots: - family_name - given_name - age_in_years - height_in_cm","title":"Unit conversions"},{"location":"examples/Tutorial/#adding-target_unit-to-transformer-specification","text":"We will create a new transformer specification, focusing on the height_in_cm field. We will transform this into a height_in_meters field, and will use the target_unit field to specify the target unit. session.set_object_transformer(\"\"\" class_derivations: Individual: populated_from: Person slot_derivations: name: expr: \"{given_name} + ' ' + {family_name}\" height_in_meters: populated_from: height_in_cm unit_conversion: target_unit: m \"\"\") session.transform(obj) {'name': 'Jane Doe', 'height_in_meters': 1.8}","title":"Adding target_unit to transformer specification"},{"location":"examples/Tutorial/#units-in-derived-schema","text":"Next we'll look at the derived target schema, and as expected we see that it has inferred the target unit for the height_in_meters field: print(yaml_dumper.dumps(session.target_schema)) name: test-schema-derived id: http://example.org/test-schema-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test_schema: prefix_prefix: test_schema prefix_reference: http://example.org/test-schema/ default_prefix: http://example.org/test-schema-derived/ default_range: string classes: Individual: name: Individual attributes: name: name: name height_in_meters: name: height_in_meters domain_of: - Person range: float unit: ucum_code: m","title":"Units in derived schema"},{"location":"examples/Tutorial/#tabular-serialization","text":"slot = sb.add_slot(\"aliases\", multivalued=True, range=\"string\", replace_if_present=True) sb.schema.classes['Person'].slots.append(slot.name) session.set_source_schema(sb.as_dict()) session.set_object_transformer(\"\"\" class_derivations: Individual: populated_from: Person slot_derivations: family_name: populated_from: family_name given_name: populated_from: given_name age: populated_from: age_in_years height: populated_from: height_in_cm aliases: populated_from: aliases stringification: delimiter: '|' \"\"\") obj = { \"given_name\": \"Jane\", \"family_name\": \"Doe\", \"age_in_years\": 42, \"height_in_cm\": 180.0, \"aliases\": [\"Jane\", \"Janie\", \"Janey\"] } flattened = session.transform(obj) flattened {'family_name': 'Doe', 'given_name': 'Jane', 'age': 42, 'height': 180.0, 'aliases': 'Jane|Janie|Janey'} this can easily be serialized to a CSV/TSV","title":"Tabular serialization"},{"location":"examples/Tutorial/#reverse-transform","text":"If a transform does not contain one-way functions, it can be reversed . In this case, reversing the transform allows us to map from the tabular form back to the richer original representation. session.reverse_transform(flattened) {'family_name': 'Doe', 'given_name': 'Jane', 'age_in_years': 42, 'height_in_cm': 180.0, 'aliases': ['Jane', 'Janie', 'Janey']}","title":"Reverse transform"},{"location":"specification/compliance/","text":"LinkML-Map Compliance Suite Feature Set: test_map_types Feature Set: test_map_collections Feature Set: test_expr Feature Set: test_simple_unit_conversion Feature Set: test_complex_unit_conversion Feature Set: test_stringify Feature Set: test_isomorphic Feature Set: test_join Feature Set: test_map_enum Feature Set: test_inheritance LinkML-Map Compliance Suite This is the output from running the full compliance test suite. It is organized into Feature Sets that test a particular feature or group of features, and combinations of different schemas, input objects, and transformation specifications. This is intended to exhaustively test all combinations of features, and provide informative output. Each test is designed to demonstrate: data mapping (transformation) derived schemas inversion (reverse transformation) (in some cases) compilation to other frameworks (coming soon) Feature Set: test_map_types Test mapping between basic data types. This test uses an ultra-minimal schema with a single class and a single attribute, the transformation specification maps that attribute onto itself, with a different type, demonstrating type coercion. Some cases will be trivially isomorphic (where source_datatype == target_datatype ), but these are executed anyway. source_datatype : linkml datatype of source object target_datatype : linkml datatype of target object source_value : value of source object target_value : expected value of slot in target object invertible : True if the transformation is invertible Combo: test_map_types[string-string-foo-foo-True] Mapping string => string Isomorphic mapping: input should equal output Source Schema : name: types description: Minimal single-attribute schema for testing datatype mapping id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: string Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 range: string Object Transformation : Source Object: s1: foo Target Object: s1: foo Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: string Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 range: string Combo: test_map_types[integer-integer-5-5-True] Mapping integer => integer Isomorphic mapping: input should equal output Source Schema : name: types description: Minimal single-attribute schema for testing datatype mapping id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: integer Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 range: integer Object Transformation : Source Object: s1: 5 Target Object: s1: 5 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: integer Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 range: integer Combo: test_map_types[string-integer-5-5-True] Mapping string => integer Should coerce datatype Source Schema : name: types description: Minimal single-attribute schema for testing datatype mapping id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: string Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 range: integer Object Transformation : Source Object: s1: '5' Target Object: s1: 5 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: integer Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 range: string Combo: test_map_types[integer-float-5-5.0-True] {#combo-test_map_typesinteger-float-5-50-true} Mapping integer => float Should coerce datatype Source Schema : name: types description: Minimal single-attribute schema for testing datatype mapping id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: integer Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 range: float Object Transformation : Source Object: s1: 5 Target Object: s1: 5.0 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 range: integer Combo: test_map_types[float-integer-5.0-5-True] {#combo-test_map_typesfloat-integer-50-5-true} Mapping float => integer Should coerce datatype Source Schema : name: types description: Minimal single-attribute schema for testing datatype mapping id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 range: integer Object Transformation : Source Object: s1: 5.0 Target Object: s1: 5 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: integer Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 range: float Combo: test_map_types[float-integer-5.2-5-False] {#combo-test_map_typesfloat-integer-52-5-false} Mapping float => integer Should coerce datatype Source Schema : name: types description: Minimal single-attribute schema for testing datatype mapping id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 range: integer Object Transformation : Source Object: s1: 5.2 Target Object: s1: 5 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: integer Combo: test_map_types[integer-boolean-5-True-False] Mapping integer => boolean Should coerce datatype Source Schema : name: types description: Minimal single-attribute schema for testing datatype mapping id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: integer Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 range: boolean Object Transformation : Source Object: s1: 5 Target Object: s1: true Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: boolean Combo: test_map_types[integer-boolean-0-False-False] Mapping integer => boolean Should coerce datatype Source Schema : name: types description: Minimal single-attribute schema for testing datatype mapping id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: integer Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 range: boolean Object Transformation : Source Object: s1: 0 Target Object: s1: false Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: boolean Feature Set: test_map_collections Test mapping between collection data types (lists and dicts). This makes use of the cast_collection_as construct source_datatype : target_datatype : source_value : target_value : invertible : Combo: test_map_collections[string-string-source_value0-target_value0-True] Mapping string => string Isomorphic mapping: input should equal output Source Schema : name: types description: Mapping between collection types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: ds: name: ds multivalued: true range: D inlined: true inlined_as_list: true tree_root: true D: name: D attributes: id: name: id identifier: true s1: name: s1 range: string Transformer Specification : class_derivations: C: name: C slot_derivations: ds: name: ds populated_from: ds cast_collection_as: MultiValuedDict dictionary_key: id D: name: D slot_derivations: id: name: id populated_from: id s1: name: s1 populated_from: s1 range: string Object Transformation : Source Object: ds: - id: X s1: foo - id: Y s1: bar Target Object: ds: X: s1: foo Y: s1: bar Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: ds: name: ds multivalued: true domain_of: - C range: D inlined: true inlined_as_list: false tree_root: true D: name: D attributes: id: name: id identifier: true domain_of: - D required: true s1: name: s1 domain_of: - D range: string Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: ds: name: ds populated_from: ds cast_collection_as: MultiValuedList D: name: D populated_from: D slot_derivations: id: name: id populated_from: id s1: name: s1 populated_from: s1 range: string Combo: test_map_collections[string-string-source_value1-target_value1-True] Mapping string => string Isomorphic mapping: input should equal output Source Schema : name: types description: Mapping between collection types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: ds: name: ds multivalued: true range: D inlined: true inlined_as_list: false tree_root: true D: name: D attributes: id: name: id identifier: true s1: name: s1 range: string Transformer Specification : class_derivations: C: name: C slot_derivations: ds: name: ds populated_from: ds cast_collection_as: MultiValuedList D: name: D slot_derivations: id: name: id populated_from: id s1: name: s1 populated_from: s1 range: string Object Transformation : Source Object: ds: X: s1: foo Y: s1: bar Target Object: ds: - id: X s1: foo - id: Y s1: bar Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: ds: name: ds multivalued: true domain_of: - C range: D inlined: true inlined_as_list: true tree_root: true D: name: D attributes: id: name: id identifier: true domain_of: - D required: true s1: name: s1 domain_of: - D range: string Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: ds: name: ds populated_from: ds cast_collection_as: MultiValuedDict dictionary_key: id D: name: D populated_from: D slot_derivations: id: name: id populated_from: id s1: name: s1 populated_from: s1 range: string Feature Set: test_expr Test transformation using pythonic expressions. This test uses a simple source schema with two slots ( s1 and s2 ). These are combined using a pythonic expression, to populate the only slot in the target schema (called derived ). The values of s1 and s2 can be numbers or strings. If the expression wraps a slot in {...} then the presence of a None forces the entire expression to be None Limitations: At this time, the framework cannot generate a complete derived schema or inversion for expressions. This will be fixed in future. expr : pythonic expression source_object : source object target_value : expected value of slot in target object Combo: test_expr[s1 + s2-source_object0-11] {#combo-test_exprs1--s2-source_object0-11} Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: integer s2: name: s2 range: integer tree_root: true Transformer Specification : class_derivations: C: name: C populated_from: C slot_derivations: derived: name: derived expr: s1 + s2 Object Transformation : Source Object: s1: 5 s2: 6 Target Object: derived: 11 Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C attributes: derived: name: derived tree_root: true Combo: test_expr[{s1} + {s2}-source_object1-11] {#combo-test_exprs1--s2-source_object1-11} Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: integer s2: name: s2 range: integer tree_root: true Transformer Specification : class_derivations: C: name: C populated_from: C slot_derivations: derived: name: derived expr: '{s1} + {s2}' Object Transformation : Source Object: s1: 5 s2: 6 Target Object: derived: 11 Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C attributes: derived: name: derived tree_root: true Combo: test_expr[{s1} + {s2}-source_object2-None] {#combo-test_exprs1--s2-source_object2-none} Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: integer tree_root: true Transformer Specification : class_derivations: C: name: C populated_from: C slot_derivations: derived: name: derived expr: '{s1} + {s2}' Object Transformation : Source Object: s1: 5 Target Object: {} Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C attributes: derived: name: derived tree_root: true Combo: test_expr[s1 + s2.s3-source_object3-11] {#combo-test_exprs1--s2s3-source_object3-11} Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: integer s2: name: s2 range: D tree_root: true D: name: D attributes: s3: name: s3 range: integer Transformer Specification : class_derivations: C: name: C populated_from: C slot_derivations: derived: name: derived expr: s1 + s2.s3 Object Transformation : Source Object: s1: 5 s2: s3: 6 Target Object: derived: 11 Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C attributes: derived: name: derived tree_root: true Combo: test_expr[s1 + s2.s3.s4-source_object4-11] {#combo-test_exprs1--s2s3s4-source_object4-11} Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: integer s2: name: s2 range: D tree_root: true D: name: D attributes: s4: name: s4 range: integer s3: name: s3 range: D Transformer Specification : class_derivations: C: name: C populated_from: C slot_derivations: derived: name: derived expr: s1 + s2.s3.s4 Object Transformation : Source Object: s1: 5 s2: s3: s4: 6 Target Object: derived: 11 Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C attributes: derived: name: derived tree_root: true Combo: test_expr[s1 + s2-source_object5-ab] {#combo-test_exprs1--s2-source_object5-ab} Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: string s2: name: s2 range: string tree_root: true Transformer Specification : class_derivations: C: name: C populated_from: C slot_derivations: derived: name: derived expr: s1 + s2 Object Transformation : Source Object: s1: a s2: b Target Object: derived: ab Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C attributes: derived: name: derived tree_root: true Combo: test_expr[s1 + s2-source_object6-target_value6] {#combo-test_exprs1--s2-source_object6-target_value6} Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 multivalued: true range: string s2: name: s2 multivalued: true range: string tree_root: true Transformer Specification : class_derivations: C: name: C populated_from: C slot_derivations: derived: name: derived expr: s1 + s2 Object Transformation : Source Object: s1: - a s2: - b Target Object: derived: - a - b Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C attributes: derived: name: derived tree_root: true Combo: test_expr[len(s1)-source_object7-1] Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 multivalued: true range: string tree_root: true Transformer Specification : class_derivations: C: name: C populated_from: C slot_derivations: derived: name: derived expr: len(s1) Object Transformation : Source Object: s1: - a Target Object: derived: 1 Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C attributes: derived: name: derived tree_root: true Combo: test_expr[s1 \\< s2-source_object8-True] {#combo-test_exprs1--s2-source_object8-true} Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: integer s2: name: s2 range: integer tree_root: true Transformer Specification : class_derivations: C: name: C populated_from: C slot_derivations: derived: name: derived expr: s1 < s2 Object Transformation : Source Object: s1: 5 s2: 6 Target Object: derived: true Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C attributes: derived: name: derived tree_root: true Feature Set: test_simple_unit_conversion Test unit conversion. This test uses a simple source schema with a single class and a single attribute, where the attribute is described using the units metaslot. The recommended way to describe unit slots in LinkML is with UCUM, but a number of other schemes can be used. We explicitly test for some known cases where UCUM uses non-standard units (e.g. Cel, mo), as well as UCUM-specific syntax (e.g. m.s-1 ) and extensions (e.g. using annotations like {Cre} ). Developers note: to run this test, the units extension should be installed: poetry install -E units This installs the pint framework. source_slot : name of slot in source schema target_slot : name of slot in target schema source_unit : unit of source slot target_unit : unit of target slot source_value : magnitude of source slot (to be converted) target_value : expected magnitude of target slot (output of conversion) err : Combo: test_simple_unit_conversion[s1-s1-m-cm-ucum_code-1.0-100.0-None-None] {#combo-test_simple_unit_conversions1-s1-m-cm-ucum_code-10-1000-none-none} Unit Conversion: 1.0 m => 100.0 cm [with s1] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float unit: ucum_code: m Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: cm Object Transformation : Source Object: s1: 1.0 Target Object: s1: 100.0 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float unit: ucum_code: cm Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: m target_unit_scheme: ucum_code source_unit: cm Combo: test_simple_unit_conversion[s1-s1-m-cm-symbol-1.0-100.0-None-None] {#combo-test_simple_unit_conversions1-s1-m-cm-symbol-10-1000-none-none} Unit Conversion: 1.0 m => 100.0 cm [with s1] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float unit: symbol: m Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: cm Object Transformation : Source Object: s1: 1.0 Target Object: s1: 100.0 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float unit: ucum_code: cm Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: m target_unit_scheme: symbol source_unit: cm Combo: test_simple_unit_conversion[s1-s1-m-m-ucum_code-1.0-1.0-None-None] {#combo-test_simple_unit_conversions1-s1-m-m-ucum_code-10-10-none-none} Unit Conversion: 1.0 m => 1.0 m [with s1] Isomorphic mapping: input should equal output Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float unit: ucum_code: m Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: m Object Transformation : Source Object: s1: 1.0 Target Object: s1: 1.0 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float unit: ucum_code: m Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: m target_unit_scheme: ucum_code source_unit: m Combo: test_simple_unit_conversion[s1-s1-a-mo-ucum_code-10.0-120.0-None-None] {#combo-test_simple_unit_conversions1-s1-a-mo-ucum_code-100-1200-none-none} Unit Conversion: 10.0 a => 120.0 mo [with s1] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float unit: ucum_code: a Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: mo Object Transformation : Source Object: s1: 10.0 Target Object: s1: 120.0 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float unit: ucum_code: mo Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: a target_unit_scheme: ucum_code source_unit: mo Combo: test_simple_unit_conversion[s1-s1-a-mo-symbol-10.0-None-UndefinedUnitError-None] {#combo-test_simple_unit_conversions1-s1-a-mo-symbol-100-none-undefineduniterror-none} Unit Conversion: 10.0 a => None mo [with s1] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float unit: symbol: a Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: mo Object Transformation : Expected Error : UndefinedUnitError Source Object: s1: 10.0 Target Object: null ... Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float unit: ucum_code: mo Combo: test_simple_unit_conversion[s1-s1-m-ml-ucum_code-1.0-None-DimensionalityError-None] {#combo-test_simple_unit_conversions1-s1-m-ml-ucum_code-10-none-dimensionalityerror-none} Unit Conversion: 1.0 m => None ml [with s1] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float unit: ucum_code: m Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: ml Object Transformation : Expected Error : DimensionalityError Source Object: s1: 1.0 Target Object: null ... Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float unit: ucum_code: ml Combo: test_simple_unit_conversion[s1-s1-m-pinknoodles-ucum_code-1.0-None-UndefinedUnitError-None] {#combo-test_simple_unit_conversions1-s1-m-pinknoodles-ucum_code-10-none-undefineduniterror-none} Unit Conversion: 1.0 m => None pinknoodles [with s1] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float unit: ucum_code: m Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: pinknoodles Object Transformation : Expected Error : UndefinedUnitError Source Object: s1: 1.0 Target Object: null ... Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float unit: ucum_code: pinknoodles Combo: test_simple_unit_conversion[s1-s1-ml-m-ucum_code-1.0-None-DimensionalityError-None] {#combo-test_simple_unit_conversions1-s1-ml-m-ucum_code-10-none-dimensionalityerror-none} Unit Conversion: 1.0 ml => None m [with s1] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float unit: ucum_code: ml Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: m Object Transformation : Expected Error : DimensionalityError Source Object: s1: 1.0 Target Object: null ... Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float unit: ucum_code: m Combo: test_simple_unit_conversion[s1-s1-pinknoodles-m-ucum_code-1.0-None-UndefinedUnitError-None] {#combo-test_simple_unit_conversions1-s1-pinknoodles-m-ucum_code-10-none-undefineduniterror-none} Unit Conversion: 1.0 pinknoodles => None m [with s1] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float unit: ucum_code: pinknoodles Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: m Object Transformation : Expected Error : UndefinedUnitError Source Object: s1: 1.0 Target Object: null ... Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float unit: ucum_code: m Combo: test_simple_unit_conversion[s1-s1-m/s-cm/s-ucum_code-1.0-100.0-None-None] {#combo-test_simple_unit_conversions1-s1-ms-cms-ucum_code-10-1000-none-none} Unit Conversion: 1.0 m/s => 100.0 cm/s [with s1] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float unit: ucum_code: m/s Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: cm/s Object Transformation : Source Object: s1: 1.0 Target Object: s1: 100.0 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float unit: ucum_code: cm/s Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: m/s target_unit_scheme: ucum_code source_unit: cm/s Combo: test_simple_unit_conversion[s1-s1-m.s-1-cm.s-1-ucum_code-1.0-100.0-None-None] {#combo-test_simple_unit_conversions1-s1-ms-1-cms-1-ucum_code-10-1000-none-none} Unit Conversion: 1.0 m.s-1 => 100.0 cm.s-1 [with s1] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float unit: ucum_code: m.s-1 Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: cm.s-1 Object Transformation : Source Object: s1: 1.0 Target Object: s1: 100.0 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float unit: ucum_code: cm.s-1 Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: m.s-1 target_unit_scheme: ucum_code source_unit: cm.s-1 Combo: test_simple_unit_conversion[s1-s1-g.m2-1-kg.m2-1-ucum_code-1.0-0.001-None-https://github.com/dalito/ucumvert/issues/8] {#combo-test_simple_unit_conversions1-s1-gm2-1-kgm2-1-ucum_code-10-0001-none-httpsgithubcomdalitoucumvertissues8} s### Combo: test_simple_unit_conversion[height_in_m-height_in_cm-m-cm-ucum_code-1.0-100.0-None-None] Unit Conversion: 1.0 m => 100.0 cm [with height_in_m] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: height_in_m: name: height_in_m range: float unit: ucum_code: m Transformer Specification : class_derivations: C: name: C slot_derivations: height_in_cm: name: height_in_cm populated_from: height_in_m unit_conversion: target_unit: cm Object Transformation : Source Object: height_in_m: 1.0 Target Object: height_in_cm: 100.0 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: height_in_cm: name: height_in_cm domain_of: - C range: float unit: ucum_code: cm Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: height_in_m: name: height_in_m populated_from: height_in_cm unit_conversion: target_unit: m target_unit_scheme: ucum_code source_unit: cm Combo: test_simple_unit_conversion[s1-s1-m[H2O]{35Cel}-m[H2O]{35Cel}-ucum_code-1.0-1.0-None-None] {#combo-test_simple_unit_conversions1-s1-mh2o35cel-mh2o35cel-ucum_code-10-10-none-none} Unit Conversion: 1.0 m[H2O]{35Cel} => 1.0 m[H2O]{35Cel} [with s1] Isomorphic mapping: input should equal output Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float unit: ucum_code: m[H2O]{35Cel} Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: m[H2O]{35Cel} Object Transformation : Source Object: s1: 1.0 Target Object: s1: 1.0 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float unit: ucum_code: m[H2O]{35Cel} Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: m[H2O]{35Cel} target_unit_scheme: ucum_code source_unit: m[H2O]{35Cel} Feature Set: test_complex_unit_conversion Test unit conversion, from complex object to simple scalar. source_unit : target_unit : source_value : target_value : roundtrip_object : err : Combo: test_complex_unit_conversion[m-cm-1.0-100.0-roundtrip_object0-None] {#combo-test_complex_unit_conversionm-cm-10-1000-roundtrip_object0-none} Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: Q: name: Q attributes: magnitude: name: magnitude range: float unit: name: unit range: string C: name: C attributes: q: name: q range: Q tree_root: true Transformer Specification : class_derivations: D: name: D populated_from: C slot_derivations: q_in_cm: name: q_in_cm populated_from: q unit_conversion: target_unit: cm source_unit_slot: unit source_magnitude_slot: magnitude Object Transformation : Source Object: q: magnitude: 1.0 unit: m Target Object: q_in_cm: 100.0 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: D: name: D attributes: q_in_cm: name: q_in_cm domain_of: - C range: Q unit: ucum_code: cm tree_root: true Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: D slot_derivations: q: name: q populated_from: q_in_cm unit_conversion: source_unit: cm target_unit_slot: unit target_magnitude_slot: magnitude Combo: test_complex_unit_conversion[cm-cm-100.0-100.0-roundtrip_object1-None] {#combo-test_complex_unit_conversioncm-cm-1000-1000-roundtrip_object1-none} Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: Q: name: Q attributes: magnitude: name: magnitude range: float unit: name: unit range: string C: name: C attributes: q: name: q range: Q tree_root: true Transformer Specification : class_derivations: D: name: D populated_from: C slot_derivations: q_in_cm: name: q_in_cm populated_from: q unit_conversion: target_unit: cm source_unit_slot: unit source_magnitude_slot: magnitude Object Transformation : Source Object: q: magnitude: 100.0 unit: cm Target Object: q_in_cm: 100.0 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: D: name: D attributes: q_in_cm: name: q_in_cm domain_of: - C range: Q unit: ucum_code: cm tree_root: true Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: D slot_derivations: q: name: q populated_from: q_in_cm unit_conversion: source_unit: cm target_unit_slot: unit target_magnitude_slot: magnitude Combo: test_complex_unit_conversion[cm-ml-100.0-None-None-DimensionalityError] {#combo-test_complex_unit_conversioncm-ml-1000-none-none-dimensionalityerror} Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: Q: name: Q attributes: magnitude: name: magnitude range: float unit: name: unit range: string C: name: C attributes: q: name: q range: Q tree_root: true Transformer Specification : class_derivations: D: name: D populated_from: C slot_derivations: q_in_ml: name: q_in_ml populated_from: q unit_conversion: target_unit: ml source_unit_slot: unit source_magnitude_slot: magnitude Object Transformation : Expected Error : DimensionalityError Source Object: q: magnitude: 100.0 unit: cm Target Object: null ... Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: D: name: D attributes: q_in_ml: name: q_in_ml domain_of: - C range: Q unit: ucum_code: ml tree_root: true Combo: test_complex_unit_conversion[cm-pinknoodles-100.0-None-None-UndefinedUnitError] {#combo-test_complex_unit_conversioncm-pinknoodles-1000-none-none-undefineduniterror} Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: Q: name: Q attributes: magnitude: name: magnitude range: float unit: name: unit range: string C: name: C attributes: q: name: q range: Q tree_root: true Transformer Specification : class_derivations: D: name: D populated_from: C slot_derivations: q_in_pinknoodles: name: q_in_pinknoodles populated_from: q unit_conversion: target_unit: pinknoodles source_unit_slot: unit source_magnitude_slot: magnitude Object Transformation : Expected Error : UndefinedUnitError Source Object: q: magnitude: 100.0 unit: cm Target Object: null ... Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: D: name: D attributes: q_in_pinknoodles: name: q_in_pinknoodles domain_of: - C range: Q unit: ucum_code: pinknoodles tree_root: true Feature Set: test_stringify Test compaction of multivalued slots into a string. Stringification is primarily intended for mapping from complex nested formats to simple tabular TSV formats, where some of the following methodologies can be used: flattening lists using an (internal) delimiter flattening lists or more complex objects using JSON or YAML syntax : SerializationSyntaxType delimiter : delimiter to use in stringification source_value : source value (a list) target_value : expected value of slot in target object (a string) Combo: test_stringify[None-,-source_value0-a,b] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 multivalued: true range: string Transformer Specification : class_derivations: D: name: D populated_from: C slot_derivations: s1_verbatim: name: s1_verbatim populated_from: s1 stringification: delimiter: ',' Object Transformation : Source Object: s1: - a - b Target Object: s1_verbatim: a,b Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: D: name: D attributes: s1_verbatim: name: s1_verbatim multivalued: false domain_of: - C range: string Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: D slot_derivations: s1: name: s1 populated_from: s1_verbatim stringification: delimiter: ',' reversed: true Compiled Specification (SQLCompiler) : INSERT INTO D SELECT s1_verbatim AS STRING_AGG(s1, \\',\\') FROM D; Combo: test_stringify[None-|-source_value1-a|b] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 multivalued: true range: string Transformer Specification : class_derivations: D: name: D populated_from: C slot_derivations: s1_verbatim: name: s1_verbatim populated_from: s1 stringification: delimiter: '|' Object Transformation : Source Object: s1: - a - b Target Object: s1_verbatim: a|b Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: D: name: D attributes: s1_verbatim: name: s1_verbatim multivalued: false domain_of: - C range: string Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: D slot_derivations: s1: name: s1 populated_from: s1_verbatim stringification: delimiter: '|' reversed: true Compiled Specification (SQLCompiler) : INSERT INTO D SELECT s1_verbatim AS STRING_AGG(s1, \\'|\\') FROM D; Combo: test_stringify[None-|-source_value2-a] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 multivalued: true range: string Transformer Specification : class_derivations: D: name: D populated_from: C slot_derivations: s1_verbatim: name: s1_verbatim populated_from: s1 stringification: delimiter: '|' Object Transformation : Source Object: s1: - a Target Object: s1_verbatim: a Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: D: name: D attributes: s1_verbatim: name: s1_verbatim multivalued: false domain_of: - C range: string Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: D slot_derivations: s1: name: s1 populated_from: s1_verbatim stringification: delimiter: '|' reversed: true Compiled Specification (SQLCompiler) : INSERT INTO D SELECT s1_verbatim AS STRING_AGG(s1, \\'|\\') FROM D; Combo: test_stringify[None-|-source_value3-] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 multivalued: true range: string Transformer Specification : class_derivations: D: name: D populated_from: C slot_derivations: s1_verbatim: name: s1_verbatim populated_from: s1 stringification: delimiter: '|' Object Transformation : Source Object: {} Target Object: s1_verbatim: '' Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: D: name: D attributes: s1_verbatim: name: s1_verbatim multivalued: false domain_of: - C range: string Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: D slot_derivations: s1: name: s1 populated_from: s1_verbatim stringification: delimiter: '|' reversed: true Compiled Specification (SQLCompiler) : INSERT INTO D SELECT s1_verbatim AS STRING_AGG(s1, \\'|\\') FROM D; Combo: test_stringify[JSON-None-source_value4-[\\\"a\\\", \\\"b\\\"]] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 multivalued: true range: string Transformer Specification : class_derivations: D: name: D populated_from: C slot_derivations: s1_verbatim: name: s1_verbatim populated_from: s1 stringification: syntax: JSON Object Transformation : Source Object: s1: - a - b Target Object: s1_verbatim: '[\"a\", \"b\"]' Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: D: name: D attributes: s1_verbatim: name: s1_verbatim multivalued: false domain_of: - C range: string Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: D slot_derivations: s1: name: s1 populated_from: s1_verbatim stringification: reversed: true syntax: JSON Compiled Specification (SQLCompiler) : INSERT INTO D SELECT s1_verbatim AS CAST(s1 AS TEXT) FROM D; Combo: test_stringify[JSON-None-source_value5-[]] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 multivalued: true range: string Transformer Specification : class_derivations: D: name: D populated_from: C slot_derivations: s1_verbatim: name: s1_verbatim populated_from: s1 stringification: syntax: JSON Object Transformation : Source Object: {} Target Object: s1_verbatim: '[]' Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: D: name: D attributes: s1_verbatim: name: s1_verbatim multivalued: false domain_of: - C range: string Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: D slot_derivations: s1: name: s1 populated_from: s1_verbatim stringification: reversed: true syntax: JSON Compiled Specification (SQLCompiler) : INSERT INTO D SELECT s1_verbatim AS CAST(s1 AS TEXT) FROM D; Combo: test_stringify[YAML-None-source_value6-[a, b]] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 multivalued: true range: string Transformer Specification : class_derivations: D: name: D populated_from: C slot_derivations: s1_verbatim: name: s1_verbatim populated_from: s1 stringification: syntax: YAML Object Transformation : Source Object: s1: - a - b Target Object: s1_verbatim: '[a, b]' Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: D: name: D attributes: s1_verbatim: name: s1_verbatim multivalued: false domain_of: - C range: string Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: D slot_derivations: s1: name: s1 populated_from: s1_verbatim stringification: reversed: true syntax: YAML Compiled Specification (SQLCompiler) : INSERT INTO D SELECT s1_verbatim AS s1 FROM D; Feature Set: test_isomorphic Test mapping a schema to an identical schema (i.e copy). This also tests for the ability to recursively descend a nested structure. source_object : use_expr : supply_source_schema : TODO: always True for now Combo: test_isomorphic[True-True-source_object0] Source Schema : name: isomorphic id: isomorphic imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: Container: name: Container attributes: c_list: name: c_list multivalued: true range: C d: name: d range: D tree_root: true C: name: C attributes: s1: name: s1 range: string s2: name: s2 range: string D: name: D attributes: s3: name: s3 range: string Transformer Specification : class_derivations: Container: name: Container populated_from: Container slot_derivations: c_list: name: c_list populated_from: c_list range: C d: name: d populated_from: d range: D C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 s2: name: s2 populated_from: s2 D: name: D populated_from: D slot_derivations: s3: name: s3 expr: s3 Object Transformation : Source Object: c_list: - s1: a s2: b - s1: c s2: d d: s3: e Target Object: c_list: - s1: a s2: b - s1: c s2: d d: s3: e Target Schema (Derived) : name: isomorphic-derived id: isomorphic-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: isomorphic-derived/ classes: Container: name: Container attributes: c_list: name: c_list multivalued: true domain_of: - Container range: C d: name: d domain_of: - Container range: D tree_root: true C: name: C attributes: s1: name: s1 domain_of: - C range: string s2: name: s2 domain_of: - C range: string D: name: D attributes: s3: name: s3 domain_of: - D range: string Inverted Transformation Specification (Derived): class_derivations: Container: name: Container populated_from: Container slot_derivations: c_list: name: c_list populated_from: c_list range: C d: name: d populated_from: d range: D C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 s2: name: s2 populated_from: s2 D: name: D populated_from: D slot_derivations: s3: name: s3 populated_from: s3 Combo: test_isomorphic[True-False-source_object0] Source Schema : name: isomorphic id: isomorphic imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: Container: name: Container attributes: c_list: name: c_list multivalued: true range: C d: name: d range: D tree_root: true C: name: C attributes: s1: name: s1 range: string s2: name: s2 range: string D: name: D attributes: s3: name: s3 range: string Transformer Specification : class_derivations: Container: name: Container populated_from: Container slot_derivations: c_list: name: c_list populated_from: c_list range: C d: name: d populated_from: d range: D C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 s2: name: s2 populated_from: s2 D: name: D populated_from: D slot_derivations: s3: name: s3 populated_from: s3 Object Transformation : Source Object: c_list: - s1: a s2: b - s1: c s2: d d: s3: e Target Object: c_list: - s1: a s2: b - s1: c s2: d d: s3: e Target Schema (Derived) : name: isomorphic-derived id: isomorphic-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: isomorphic-derived/ classes: Container: name: Container attributes: c_list: name: c_list multivalued: true domain_of: - Container range: C d: name: d domain_of: - Container range: D tree_root: true C: name: C attributes: s1: name: s1 domain_of: - C range: string s2: name: s2 domain_of: - C range: string D: name: D attributes: s3: name: s3 domain_of: - D range: string Inverted Transformation Specification (Derived): class_derivations: Container: name: Container populated_from: Container slot_derivations: c_list: name: c_list populated_from: c_list range: C d: name: d populated_from: d range: D C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 s2: name: s2 populated_from: s2 D: name: D populated_from: D slot_derivations: s3: name: s3 populated_from: s3 Feature Set: test_join Test joining two objects into a single object, aka denormalization. source_object : normalized source object target_object : denormalized target object inlined : True if the source objects are inlined Combo: test_join[source_object0-target_object0-True] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: R: name: R attributes: s1: name: s1 range: E inlined: true s2: name: s2 range: E inlined: true tree_root: true E: name: E attributes: id: name: id identifier: true range: string name: name: name range: string Transformer Specification : class_derivations: R: name: R populated_from: R slot_derivations: s1_id: name: s1_id expr: s1.id s1_name: name: s1_name expr: s1.name s2_id: name: s2_id expr: s2.id s2_name: name: s2_name expr: s2.name Object Transformation : Source Object: s1: id: x1 name: foo s2: id: x2 name: bar Target Object: s1_id: x1 s1_name: foo s2_id: x2 s2_name: bar Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: R: name: R attributes: s1_id: name: s1_id s1_name: name: s1_name s2_id: name: s2_id s2_name: name: s2_name tree_root: true Combo: test_join[source_object0-target_object0-False] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: R: name: R attributes: s1: name: s1 range: E inlined: false s2: name: s2 range: E inlined: false tree_root: false E: name: E attributes: id: name: id identifier: true range: string name: name: name range: string Container: name: Container attributes: r_list: name: r_list multivalued: true range: R e_list: name: e_list multivalued: true range: E inlined_as_list: true tree_root: true Transformer Specification : class_derivations: R: name: R populated_from: R slot_derivations: s1_id: name: s1_id expr: s1.id s1_name: name: s1_name expr: s1.name s2_id: name: s2_id expr: s2.id s2_name: name: s2_name expr: s2.name Container: name: Container populated_from: Container slot_derivations: r_list: name: r_list populated_from: r_list Object Transformation : Source Object: r_list: - s1: x1 s2: x2 e_list: - id: x1 name: foo - id: x2 name: bar Target Object: r_list: - s1_id: x1 s1_name: foo s2_id: x2 s2_name: bar Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: R: name: R attributes: s1_id: name: s1_id s1_name: name: s1_name s2_id: name: s2_id s2_name: name: s2_name tree_root: false Container: name: Container attributes: r_list: name: r_list multivalued: true domain_of: - Container range: R tree_root: true Feature Set: test_map_enum Test mapping between enum values. Currently this only supports simple dictionary-style mapping between permissible values, akin to SSSOM, but in future additional expressivity will be supported, including: mapping ranges to categorical values boolean/branching logic source_value : mapping : target_value : Combo: test_map_enum[A-mapping0-B-False] Source Schema : name: enums id: enums imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test enums: E: name: E permissible_values: A: text: A B: text: B C: text: C classes: C: name: C attributes: s1: name: s1 range: E Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 enum_derivations: E: name: E mirror_source: false populated_from: E permissible_value_derivations: B: name: B populated_from: A Object Transformation : Source Object: s1: A Target Object: s1: B Target Schema (Derived) : name: enums-derived id: enums-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: enums-derived/ enums: E: name: E permissible_values: A: text: A B: text: B C: text: C classes: C: name: C attributes: s1: name: s1 domain_of: - C range: E Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 enum_derivations: E: name: E populated_from: E permissible_value_derivations: A: name: A populated_from: B Combo: test_map_enum[Z-mapping1-None-False] Source Schema : name: enums id: enums imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test enums: E: name: E permissible_values: A: text: A B: text: B C: text: C classes: C: name: C attributes: s1: name: s1 range: E Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 enum_derivations: E: name: E mirror_source: false populated_from: E permissible_value_derivations: B: name: B populated_from: A Object Transformation : Source Object: s1: Z Target Object: {} Target Schema (Derived) : name: enums-derived id: enums-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: enums-derived/ enums: E: name: E permissible_values: A: text: A B: text: B C: text: C classes: C: name: C attributes: s1: name: s1 domain_of: - C range: E Combo: test_map_enum[C-mapping2-C-True] Source Schema : name: enums id: enums imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test enums: E: name: E permissible_values: A: text: A B: text: B C: text: C classes: C: name: C attributes: s1: name: s1 range: E Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 enum_derivations: E: name: E mirror_source: true populated_from: E permissible_value_derivations: B: name: B populated_from: A s### Combo: test_map_enum[A-mapping3-B-False] Source Schema : name: enums id: enums imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test enums: E: name: E permissible_values: A: text: A B: text: B C: text: C classes: C: name: C attributes: s1: name: s1 range: E Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 enum_derivations: E: name: E mirror_source: false populated_from: E permissible_value_derivations: B: name: B sources: - A - C Object Transformation : Source Object: s1: A Target Object: s1: B Target Schema (Derived) : name: enums-derived id: enums-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: enums-derived/ enums: E: name: E permissible_values: A: text: A B: text: B C: text: C classes: C: name: C attributes: s1: name: s1 domain_of: - C range: E Combo: test_map_enum[C-mapping4-B-False] Source Schema : name: enums id: enums imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test enums: E: name: E permissible_values: A: text: A B: text: B C: text: C classes: C: name: C attributes: s1: name: s1 range: E Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 enum_derivations: E: name: E mirror_source: false populated_from: E permissible_value_derivations: B: name: B sources: - A - C Object Transformation : Source Object: s1: C Target Object: s1: B Target Schema (Derived) : name: enums-derived id: enums-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: enums-derived/ enums: E: name: E permissible_values: A: text: A B: text: B C: text: C classes: C: name: C attributes: s1: name: s1 domain_of: - C range: E Feature Set: test_inheritance Test inheritance. Transformation specifications can utilize inheritance, in the same way that LinkML schemas can. is_a : use is_as instead of mixins in test schema flatten : roll down inherited slots Combo: test_inheritance[False-True] Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C is_a: D attributes: s1: name: s1 range: integer tree_root: true D: name: D attributes: s2: name: s2 range: integer Transformer Specification : class_derivations: C: name: C is_a: D populated_from: C slot_derivations: s1: name: s1 expr: s1 + 1 D: name: D populated_from: D slot_derivations: s2: name: s2 expr: s2 + 1 Object Transformation : Source Object: s1: 1 s2: 2 Target Object: s1: 2 s2: 3 Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C is_a: D attributes: s1: name: s1 domain_of: - C range: integer tree_root: true D: name: D attributes: s2: name: s2 domain_of: - D range: integer Combo: test_inheritance[False-False] Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C mixins: - D attributes: s1: name: s1 range: integer tree_root: true D: name: D attributes: s2: name: s2 range: integer Transformer Specification : class_derivations: C: name: C mixins: - D populated_from: C slot_derivations: s1: name: s1 expr: s1 + 1 D: name: D populated_from: D slot_derivations: s2: name: s2 expr: s2 + 1 Object Transformation : Source Object: s1: 1 s2: 2 Target Object: s1: 2 s2: 3 Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C mixins: - D attributes: s1: name: s1 domain_of: - C range: integer tree_root: true D: name: D attributes: s2: name: s2 domain_of: - D range: integer Combo: test_inheritance[True-True] Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C is_a: D attributes: s1: name: s1 range: integer tree_root: true D: name: D attributes: s2: name: s2 range: integer Transformer Specification : class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 expr: s1 + 1 s2: name: s2 expr: s2 + 1 Object Transformation : Source Object: s1: 1 s2: 2 Target Object: s1: 2 s2: 3 Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: integer s2: name: s2 domain_of: - D range: integer tree_root: true Combo: test_inheritance[True-False] Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C mixins: - D attributes: s1: name: s1 range: integer tree_root: true D: name: D attributes: s2: name: s2 range: integer Transformer Specification : class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 expr: s1 + 1 s2: name: s2 expr: s2 + 1 Object Transformation : Source Object: s1: 1 s2: 2 Target Object: s1: 2 s2: 3 Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: integer s2: name: s2 domain_of: - D range: integer tree_root: true . 55 passed, 2 skipped, 83 warnings in 3.98s","title":"Compliance Suite"},{"location":"specification/compliance/#linkml-map-compliance-suite","text":"This is the output from running the full compliance test suite. It is organized into Feature Sets that test a particular feature or group of features, and combinations of different schemas, input objects, and transformation specifications. This is intended to exhaustively test all combinations of features, and provide informative output. Each test is designed to demonstrate: data mapping (transformation) derived schemas inversion (reverse transformation) (in some cases) compilation to other frameworks (coming soon)","title":"LinkML-Map Compliance Suite"},{"location":"specification/compliance/#feature-set-test_map_types","text":"Test mapping between basic data types. This test uses an ultra-minimal schema with a single class and a single attribute, the transformation specification maps that attribute onto itself, with a different type, demonstrating type coercion. Some cases will be trivially isomorphic (where source_datatype == target_datatype ), but these are executed anyway. source_datatype : linkml datatype of source object target_datatype : linkml datatype of target object source_value : value of source object target_value : expected value of slot in target object invertible : True if the transformation is invertible","title":"Feature Set: test_map_types"},{"location":"specification/compliance/#combo-test_map_typesstring-string-foo-foo-true","text":"Mapping string => string Isomorphic mapping: input should equal output Source Schema : name: types description: Minimal single-attribute schema for testing datatype mapping id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: string Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 range: string Object Transformation : Source Object: s1: foo Target Object: s1: foo Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: string Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 range: string","title":"Combo: test_map_types[string-string-foo-foo-True]"},{"location":"specification/compliance/#combo-test_map_typesinteger-integer-5-5-true","text":"Mapping integer => integer Isomorphic mapping: input should equal output Source Schema : name: types description: Minimal single-attribute schema for testing datatype mapping id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: integer Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 range: integer Object Transformation : Source Object: s1: 5 Target Object: s1: 5 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: integer Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 range: integer","title":"Combo: test_map_types[integer-integer-5-5-True]"},{"location":"specification/compliance/#combo-test_map_typesstring-integer-5-5-true","text":"Mapping string => integer Should coerce datatype Source Schema : name: types description: Minimal single-attribute schema for testing datatype mapping id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: string Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 range: integer Object Transformation : Source Object: s1: '5' Target Object: s1: 5 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: integer Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 range: string","title":"Combo: test_map_types[string-integer-5-5-True]"},{"location":"specification/compliance/#combo-test_map_typesinteger-float-5-50-true-combo-test_map_typesinteger-float-5-50-true","text":"Mapping integer => float Should coerce datatype Source Schema : name: types description: Minimal single-attribute schema for testing datatype mapping id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: integer Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 range: float Object Transformation : Source Object: s1: 5 Target Object: s1: 5.0 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 range: integer","title":"Combo: test_map_types[integer-float-5-5.0-True] {#combo-test_map_typesinteger-float-5-50-true}"},{"location":"specification/compliance/#combo-test_map_typesfloat-integer-50-5-true-combo-test_map_typesfloat-integer-50-5-true","text":"Mapping float => integer Should coerce datatype Source Schema : name: types description: Minimal single-attribute schema for testing datatype mapping id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 range: integer Object Transformation : Source Object: s1: 5.0 Target Object: s1: 5 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: integer Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 range: float","title":"Combo: test_map_types[float-integer-5.0-5-True] {#combo-test_map_typesfloat-integer-50-5-true}"},{"location":"specification/compliance/#combo-test_map_typesfloat-integer-52-5-false-combo-test_map_typesfloat-integer-52-5-false","text":"Mapping float => integer Should coerce datatype Source Schema : name: types description: Minimal single-attribute schema for testing datatype mapping id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 range: integer Object Transformation : Source Object: s1: 5.2 Target Object: s1: 5 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: integer","title":"Combo: test_map_types[float-integer-5.2-5-False] {#combo-test_map_typesfloat-integer-52-5-false}"},{"location":"specification/compliance/#combo-test_map_typesinteger-boolean-5-true-false","text":"Mapping integer => boolean Should coerce datatype Source Schema : name: types description: Minimal single-attribute schema for testing datatype mapping id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: integer Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 range: boolean Object Transformation : Source Object: s1: 5 Target Object: s1: true Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: boolean","title":"Combo: test_map_types[integer-boolean-5-True-False]"},{"location":"specification/compliance/#combo-test_map_typesinteger-boolean-0-false-false","text":"Mapping integer => boolean Should coerce datatype Source Schema : name: types description: Minimal single-attribute schema for testing datatype mapping id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: integer Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 range: boolean Object Transformation : Source Object: s1: 0 Target Object: s1: false Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: boolean","title":"Combo: test_map_types[integer-boolean-0-False-False]"},{"location":"specification/compliance/#feature-set-test_map_collections","text":"Test mapping between collection data types (lists and dicts). This makes use of the cast_collection_as construct source_datatype : target_datatype : source_value : target_value : invertible :","title":"Feature Set: test_map_collections"},{"location":"specification/compliance/#combo-test_map_collectionsstring-string-source_value0-target_value0-true","text":"Mapping string => string Isomorphic mapping: input should equal output Source Schema : name: types description: Mapping between collection types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: ds: name: ds multivalued: true range: D inlined: true inlined_as_list: true tree_root: true D: name: D attributes: id: name: id identifier: true s1: name: s1 range: string Transformer Specification : class_derivations: C: name: C slot_derivations: ds: name: ds populated_from: ds cast_collection_as: MultiValuedDict dictionary_key: id D: name: D slot_derivations: id: name: id populated_from: id s1: name: s1 populated_from: s1 range: string Object Transformation : Source Object: ds: - id: X s1: foo - id: Y s1: bar Target Object: ds: X: s1: foo Y: s1: bar Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: ds: name: ds multivalued: true domain_of: - C range: D inlined: true inlined_as_list: false tree_root: true D: name: D attributes: id: name: id identifier: true domain_of: - D required: true s1: name: s1 domain_of: - D range: string Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: ds: name: ds populated_from: ds cast_collection_as: MultiValuedList D: name: D populated_from: D slot_derivations: id: name: id populated_from: id s1: name: s1 populated_from: s1 range: string","title":"Combo: test_map_collections[string-string-source_value0-target_value0-True]"},{"location":"specification/compliance/#combo-test_map_collectionsstring-string-source_value1-target_value1-true","text":"Mapping string => string Isomorphic mapping: input should equal output Source Schema : name: types description: Mapping between collection types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: ds: name: ds multivalued: true range: D inlined: true inlined_as_list: false tree_root: true D: name: D attributes: id: name: id identifier: true s1: name: s1 range: string Transformer Specification : class_derivations: C: name: C slot_derivations: ds: name: ds populated_from: ds cast_collection_as: MultiValuedList D: name: D slot_derivations: id: name: id populated_from: id s1: name: s1 populated_from: s1 range: string Object Transformation : Source Object: ds: X: s1: foo Y: s1: bar Target Object: ds: - id: X s1: foo - id: Y s1: bar Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: ds: name: ds multivalued: true domain_of: - C range: D inlined: true inlined_as_list: true tree_root: true D: name: D attributes: id: name: id identifier: true domain_of: - D required: true s1: name: s1 domain_of: - D range: string Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: ds: name: ds populated_from: ds cast_collection_as: MultiValuedDict dictionary_key: id D: name: D populated_from: D slot_derivations: id: name: id populated_from: id s1: name: s1 populated_from: s1 range: string","title":"Combo: test_map_collections[string-string-source_value1-target_value1-True]"},{"location":"specification/compliance/#feature-set-test_expr","text":"Test transformation using pythonic expressions. This test uses a simple source schema with two slots ( s1 and s2 ). These are combined using a pythonic expression, to populate the only slot in the target schema (called derived ). The values of s1 and s2 can be numbers or strings. If the expression wraps a slot in {...} then the presence of a None forces the entire expression to be None Limitations: At this time, the framework cannot generate a complete derived schema or inversion for expressions. This will be fixed in future. expr : pythonic expression source_object : source object target_value : expected value of slot in target object","title":"Feature Set: test_expr"},{"location":"specification/compliance/#combo-test_exprs1-s2-source_object0-11-combo-test_exprs1-s2-source_object0-11","text":"Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: integer s2: name: s2 range: integer tree_root: true Transformer Specification : class_derivations: C: name: C populated_from: C slot_derivations: derived: name: derived expr: s1 + s2 Object Transformation : Source Object: s1: 5 s2: 6 Target Object: derived: 11 Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C attributes: derived: name: derived tree_root: true","title":"Combo: test_expr[s1 + s2-source_object0-11] {#combo-test_exprs1--s2-source_object0-11}"},{"location":"specification/compliance/#combo-test_exprs1-s2-source_object1-11-combo-test_exprs1-s2-source_object1-11","text":"Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: integer s2: name: s2 range: integer tree_root: true Transformer Specification : class_derivations: C: name: C populated_from: C slot_derivations: derived: name: derived expr: '{s1} + {s2}' Object Transformation : Source Object: s1: 5 s2: 6 Target Object: derived: 11 Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C attributes: derived: name: derived tree_root: true","title":"Combo: test_expr[{s1} + {s2}-source_object1-11] {#combo-test_exprs1--s2-source_object1-11}"},{"location":"specification/compliance/#combo-test_exprs1-s2-source_object2-none-combo-test_exprs1-s2-source_object2-none","text":"Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: integer tree_root: true Transformer Specification : class_derivations: C: name: C populated_from: C slot_derivations: derived: name: derived expr: '{s1} + {s2}' Object Transformation : Source Object: s1: 5 Target Object: {} Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C attributes: derived: name: derived tree_root: true","title":"Combo: test_expr[{s1} + {s2}-source_object2-None] {#combo-test_exprs1--s2-source_object2-none}"},{"location":"specification/compliance/#combo-test_exprs1-s2s3-source_object3-11-combo-test_exprs1-s2s3-source_object3-11","text":"Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: integer s2: name: s2 range: D tree_root: true D: name: D attributes: s3: name: s3 range: integer Transformer Specification : class_derivations: C: name: C populated_from: C slot_derivations: derived: name: derived expr: s1 + s2.s3 Object Transformation : Source Object: s1: 5 s2: s3: 6 Target Object: derived: 11 Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C attributes: derived: name: derived tree_root: true","title":"Combo: test_expr[s1 + s2.s3-source_object3-11] {#combo-test_exprs1--s2s3-source_object3-11}"},{"location":"specification/compliance/#combo-test_exprs1-s2s3s4-source_object4-11-combo-test_exprs1-s2s3s4-source_object4-11","text":"Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: integer s2: name: s2 range: D tree_root: true D: name: D attributes: s4: name: s4 range: integer s3: name: s3 range: D Transformer Specification : class_derivations: C: name: C populated_from: C slot_derivations: derived: name: derived expr: s1 + s2.s3.s4 Object Transformation : Source Object: s1: 5 s2: s3: s4: 6 Target Object: derived: 11 Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C attributes: derived: name: derived tree_root: true","title":"Combo: test_expr[s1 + s2.s3.s4-source_object4-11] {#combo-test_exprs1--s2s3s4-source_object4-11}"},{"location":"specification/compliance/#combo-test_exprs1-s2-source_object5-ab-combo-test_exprs1-s2-source_object5-ab","text":"Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: string s2: name: s2 range: string tree_root: true Transformer Specification : class_derivations: C: name: C populated_from: C slot_derivations: derived: name: derived expr: s1 + s2 Object Transformation : Source Object: s1: a s2: b Target Object: derived: ab Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C attributes: derived: name: derived tree_root: true","title":"Combo: test_expr[s1 + s2-source_object5-ab] {#combo-test_exprs1--s2-source_object5-ab}"},{"location":"specification/compliance/#combo-test_exprs1-s2-source_object6-target_value6-combo-test_exprs1-s2-source_object6-target_value6","text":"Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 multivalued: true range: string s2: name: s2 multivalued: true range: string tree_root: true Transformer Specification : class_derivations: C: name: C populated_from: C slot_derivations: derived: name: derived expr: s1 + s2 Object Transformation : Source Object: s1: - a s2: - b Target Object: derived: - a - b Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C attributes: derived: name: derived tree_root: true","title":"Combo: test_expr[s1 + s2-source_object6-target_value6] {#combo-test_exprs1--s2-source_object6-target_value6}"},{"location":"specification/compliance/#combo-test_exprlens1-source_object7-1","text":"Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 multivalued: true range: string tree_root: true Transformer Specification : class_derivations: C: name: C populated_from: C slot_derivations: derived: name: derived expr: len(s1) Object Transformation : Source Object: s1: - a Target Object: derived: 1 Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C attributes: derived: name: derived tree_root: true","title":"Combo: test_expr[len(s1)-source_object7-1]"},{"location":"specification/compliance/#combo-test_exprs1-s2-source_object8-true-combo-test_exprs1-s2-source_object8-true","text":"Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: integer s2: name: s2 range: integer tree_root: true Transformer Specification : class_derivations: C: name: C populated_from: C slot_derivations: derived: name: derived expr: s1 < s2 Object Transformation : Source Object: s1: 5 s2: 6 Target Object: derived: true Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C attributes: derived: name: derived tree_root: true","title":"Combo: test_expr[s1 \\< s2-source_object8-True] {#combo-test_exprs1--s2-source_object8-true}"},{"location":"specification/compliance/#feature-set-test_simple_unit_conversion","text":"Test unit conversion. This test uses a simple source schema with a single class and a single attribute, where the attribute is described using the units metaslot. The recommended way to describe unit slots in LinkML is with UCUM, but a number of other schemes can be used. We explicitly test for some known cases where UCUM uses non-standard units (e.g. Cel, mo), as well as UCUM-specific syntax (e.g. m.s-1 ) and extensions (e.g. using annotations like {Cre} ). Developers note: to run this test, the units extension should be installed: poetry install -E units This installs the pint framework. source_slot : name of slot in source schema target_slot : name of slot in target schema source_unit : unit of source slot target_unit : unit of target slot source_value : magnitude of source slot (to be converted) target_value : expected magnitude of target slot (output of conversion) err :","title":"Feature Set: test_simple_unit_conversion"},{"location":"specification/compliance/#combo-test_simple_unit_conversions1-s1-m-cm-ucum_code-10-1000-none-none-combo-test_simple_unit_conversions1-s1-m-cm-ucum_code-10-1000-none-none","text":"Unit Conversion: 1.0 m => 100.0 cm [with s1] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float unit: ucum_code: m Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: cm Object Transformation : Source Object: s1: 1.0 Target Object: s1: 100.0 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float unit: ucum_code: cm Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: m target_unit_scheme: ucum_code source_unit: cm","title":"Combo: test_simple_unit_conversion[s1-s1-m-cm-ucum_code-1.0-100.0-None-None] {#combo-test_simple_unit_conversions1-s1-m-cm-ucum_code-10-1000-none-none}"},{"location":"specification/compliance/#combo-test_simple_unit_conversions1-s1-m-cm-symbol-10-1000-none-none-combo-test_simple_unit_conversions1-s1-m-cm-symbol-10-1000-none-none","text":"Unit Conversion: 1.0 m => 100.0 cm [with s1] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float unit: symbol: m Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: cm Object Transformation : Source Object: s1: 1.0 Target Object: s1: 100.0 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float unit: ucum_code: cm Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: m target_unit_scheme: symbol source_unit: cm","title":"Combo: test_simple_unit_conversion[s1-s1-m-cm-symbol-1.0-100.0-None-None] {#combo-test_simple_unit_conversions1-s1-m-cm-symbol-10-1000-none-none}"},{"location":"specification/compliance/#combo-test_simple_unit_conversions1-s1-m-m-ucum_code-10-10-none-none-combo-test_simple_unit_conversions1-s1-m-m-ucum_code-10-10-none-none","text":"Unit Conversion: 1.0 m => 1.0 m [with s1] Isomorphic mapping: input should equal output Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float unit: ucum_code: m Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: m Object Transformation : Source Object: s1: 1.0 Target Object: s1: 1.0 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float unit: ucum_code: m Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: m target_unit_scheme: ucum_code source_unit: m","title":"Combo: test_simple_unit_conversion[s1-s1-m-m-ucum_code-1.0-1.0-None-None] {#combo-test_simple_unit_conversions1-s1-m-m-ucum_code-10-10-none-none}"},{"location":"specification/compliance/#combo-test_simple_unit_conversions1-s1-a-mo-ucum_code-100-1200-none-none-combo-test_simple_unit_conversions1-s1-a-mo-ucum_code-100-1200-none-none","text":"Unit Conversion: 10.0 a => 120.0 mo [with s1] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float unit: ucum_code: a Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: mo Object Transformation : Source Object: s1: 10.0 Target Object: s1: 120.0 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float unit: ucum_code: mo Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: a target_unit_scheme: ucum_code source_unit: mo","title":"Combo: test_simple_unit_conversion[s1-s1-a-mo-ucum_code-10.0-120.0-None-None] {#combo-test_simple_unit_conversions1-s1-a-mo-ucum_code-100-1200-none-none}"},{"location":"specification/compliance/#combo-test_simple_unit_conversions1-s1-a-mo-symbol-100-none-undefineduniterror-none-combo-test_simple_unit_conversions1-s1-a-mo-symbol-100-none-undefineduniterror-none","text":"Unit Conversion: 10.0 a => None mo [with s1] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float unit: symbol: a Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: mo Object Transformation : Expected Error : UndefinedUnitError Source Object: s1: 10.0 Target Object: null ... Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float unit: ucum_code: mo","title":"Combo: test_simple_unit_conversion[s1-s1-a-mo-symbol-10.0-None-UndefinedUnitError-None] {#combo-test_simple_unit_conversions1-s1-a-mo-symbol-100-none-undefineduniterror-none}"},{"location":"specification/compliance/#combo-test_simple_unit_conversions1-s1-m-ml-ucum_code-10-none-dimensionalityerror-none-combo-test_simple_unit_conversions1-s1-m-ml-ucum_code-10-none-dimensionalityerror-none","text":"Unit Conversion: 1.0 m => None ml [with s1] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float unit: ucum_code: m Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: ml Object Transformation : Expected Error : DimensionalityError Source Object: s1: 1.0 Target Object: null ... Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float unit: ucum_code: ml","title":"Combo: test_simple_unit_conversion[s1-s1-m-ml-ucum_code-1.0-None-DimensionalityError-None] {#combo-test_simple_unit_conversions1-s1-m-ml-ucum_code-10-none-dimensionalityerror-none}"},{"location":"specification/compliance/#combo-test_simple_unit_conversions1-s1-m-pinknoodles-ucum_code-10-none-undefineduniterror-none-combo-test_simple_unit_conversions1-s1-m-pinknoodles-ucum_code-10-none-undefineduniterror-none","text":"Unit Conversion: 1.0 m => None pinknoodles [with s1] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float unit: ucum_code: m Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: pinknoodles Object Transformation : Expected Error : UndefinedUnitError Source Object: s1: 1.0 Target Object: null ... Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float unit: ucum_code: pinknoodles","title":"Combo: test_simple_unit_conversion[s1-s1-m-pinknoodles-ucum_code-1.0-None-UndefinedUnitError-None] {#combo-test_simple_unit_conversions1-s1-m-pinknoodles-ucum_code-10-none-undefineduniterror-none}"},{"location":"specification/compliance/#combo-test_simple_unit_conversions1-s1-ml-m-ucum_code-10-none-dimensionalityerror-none-combo-test_simple_unit_conversions1-s1-ml-m-ucum_code-10-none-dimensionalityerror-none","text":"Unit Conversion: 1.0 ml => None m [with s1] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float unit: ucum_code: ml Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: m Object Transformation : Expected Error : DimensionalityError Source Object: s1: 1.0 Target Object: null ... Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float unit: ucum_code: m","title":"Combo: test_simple_unit_conversion[s1-s1-ml-m-ucum_code-1.0-None-DimensionalityError-None] {#combo-test_simple_unit_conversions1-s1-ml-m-ucum_code-10-none-dimensionalityerror-none}"},{"location":"specification/compliance/#combo-test_simple_unit_conversions1-s1-pinknoodles-m-ucum_code-10-none-undefineduniterror-none-combo-test_simple_unit_conversions1-s1-pinknoodles-m-ucum_code-10-none-undefineduniterror-none","text":"Unit Conversion: 1.0 pinknoodles => None m [with s1] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float unit: ucum_code: pinknoodles Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: m Object Transformation : Expected Error : UndefinedUnitError Source Object: s1: 1.0 Target Object: null ... Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float unit: ucum_code: m","title":"Combo: test_simple_unit_conversion[s1-s1-pinknoodles-m-ucum_code-1.0-None-UndefinedUnitError-None] {#combo-test_simple_unit_conversions1-s1-pinknoodles-m-ucum_code-10-none-undefineduniterror-none}"},{"location":"specification/compliance/#combo-test_simple_unit_conversions1-s1-ms-cms-ucum_code-10-1000-none-none-combo-test_simple_unit_conversions1-s1-ms-cms-ucum_code-10-1000-none-none","text":"Unit Conversion: 1.0 m/s => 100.0 cm/s [with s1] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float unit: ucum_code: m/s Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: cm/s Object Transformation : Source Object: s1: 1.0 Target Object: s1: 100.0 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float unit: ucum_code: cm/s Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: m/s target_unit_scheme: ucum_code source_unit: cm/s","title":"Combo: test_simple_unit_conversion[s1-s1-m/s-cm/s-ucum_code-1.0-100.0-None-None] {#combo-test_simple_unit_conversions1-s1-ms-cms-ucum_code-10-1000-none-none}"},{"location":"specification/compliance/#combo-test_simple_unit_conversions1-s1-ms-1-cms-1-ucum_code-10-1000-none-none-combo-test_simple_unit_conversions1-s1-ms-1-cms-1-ucum_code-10-1000-none-none","text":"Unit Conversion: 1.0 m.s-1 => 100.0 cm.s-1 [with s1] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float unit: ucum_code: m.s-1 Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: cm.s-1 Object Transformation : Source Object: s1: 1.0 Target Object: s1: 100.0 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float unit: ucum_code: cm.s-1 Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: m.s-1 target_unit_scheme: ucum_code source_unit: cm.s-1","title":"Combo: test_simple_unit_conversion[s1-s1-m.s-1-cm.s-1-ucum_code-1.0-100.0-None-None] {#combo-test_simple_unit_conversions1-s1-ms-1-cms-1-ucum_code-10-1000-none-none}"},{"location":"specification/compliance/#combo-test_simple_unit_conversions1-s1-gm2-1-kgm2-1-ucum_code-10-0001-none-httpsgithubcomdalitoucumvertissues8-combo-test_simple_unit_conversions1-s1-gm2-1-kgm2-1-ucum_code-10-0001-none-httpsgithubcomdalitoucumvertissues8","text":"s### Combo: test_simple_unit_conversion[height_in_m-height_in_cm-m-cm-ucum_code-1.0-100.0-None-None] Unit Conversion: 1.0 m => 100.0 cm [with height_in_m] Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: height_in_m: name: height_in_m range: float unit: ucum_code: m Transformer Specification : class_derivations: C: name: C slot_derivations: height_in_cm: name: height_in_cm populated_from: height_in_m unit_conversion: target_unit: cm Object Transformation : Source Object: height_in_m: 1.0 Target Object: height_in_cm: 100.0 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: height_in_cm: name: height_in_cm domain_of: - C range: float unit: ucum_code: cm Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: height_in_m: name: height_in_m populated_from: height_in_cm unit_conversion: target_unit: m target_unit_scheme: ucum_code source_unit: cm","title":"Combo: test_simple_unit_conversion[s1-s1-g.m2-1-kg.m2-1-ucum_code-1.0-0.001-None-https://github.com/dalito/ucumvert/issues/8] {#combo-test_simple_unit_conversions1-s1-gm2-1-kgm2-1-ucum_code-10-0001-none-httpsgithubcomdalitoucumvertissues8}"},{"location":"specification/compliance/#combo-test_simple_unit_conversions1-s1-mh2o35cel-mh2o35cel-ucum_code-10-10-none-none-combo-test_simple_unit_conversions1-s1-mh2o35cel-mh2o35cel-ucum_code-10-10-none-none","text":"Unit Conversion: 1.0 m[H2O]{35Cel} => 1.0 m[H2O]{35Cel} [with s1] Isomorphic mapping: input should equal output Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 range: float unit: ucum_code: m[H2O]{35Cel} Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: m[H2O]{35Cel} Object Transformation : Source Object: s1: 1.0 Target Object: s1: 1.0 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: float unit: ucum_code: m[H2O]{35Cel} Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 unit_conversion: target_unit: m[H2O]{35Cel} target_unit_scheme: ucum_code source_unit: m[H2O]{35Cel}","title":"Combo: test_simple_unit_conversion[s1-s1-m[H2O]{35Cel}-m[H2O]{35Cel}-ucum_code-1.0-1.0-None-None] {#combo-test_simple_unit_conversions1-s1-mh2o35cel-mh2o35cel-ucum_code-10-10-none-none}"},{"location":"specification/compliance/#feature-set-test_complex_unit_conversion","text":"Test unit conversion, from complex object to simple scalar. source_unit : target_unit : source_value : target_value : roundtrip_object : err :","title":"Feature Set: test_complex_unit_conversion"},{"location":"specification/compliance/#combo-test_complex_unit_conversionm-cm-10-1000-roundtrip_object0-none-combo-test_complex_unit_conversionm-cm-10-1000-roundtrip_object0-none","text":"Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: Q: name: Q attributes: magnitude: name: magnitude range: float unit: name: unit range: string C: name: C attributes: q: name: q range: Q tree_root: true Transformer Specification : class_derivations: D: name: D populated_from: C slot_derivations: q_in_cm: name: q_in_cm populated_from: q unit_conversion: target_unit: cm source_unit_slot: unit source_magnitude_slot: magnitude Object Transformation : Source Object: q: magnitude: 1.0 unit: m Target Object: q_in_cm: 100.0 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: D: name: D attributes: q_in_cm: name: q_in_cm domain_of: - C range: Q unit: ucum_code: cm tree_root: true Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: D slot_derivations: q: name: q populated_from: q_in_cm unit_conversion: source_unit: cm target_unit_slot: unit target_magnitude_slot: magnitude","title":"Combo: test_complex_unit_conversion[m-cm-1.0-100.0-roundtrip_object0-None] {#combo-test_complex_unit_conversionm-cm-10-1000-roundtrip_object0-none}"},{"location":"specification/compliance/#combo-test_complex_unit_conversioncm-cm-1000-1000-roundtrip_object1-none-combo-test_complex_unit_conversioncm-cm-1000-1000-roundtrip_object1-none","text":"Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: Q: name: Q attributes: magnitude: name: magnitude range: float unit: name: unit range: string C: name: C attributes: q: name: q range: Q tree_root: true Transformer Specification : class_derivations: D: name: D populated_from: C slot_derivations: q_in_cm: name: q_in_cm populated_from: q unit_conversion: target_unit: cm source_unit_slot: unit source_magnitude_slot: magnitude Object Transformation : Source Object: q: magnitude: 100.0 unit: cm Target Object: q_in_cm: 100.0 Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: D: name: D attributes: q_in_cm: name: q_in_cm domain_of: - C range: Q unit: ucum_code: cm tree_root: true Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: D slot_derivations: q: name: q populated_from: q_in_cm unit_conversion: source_unit: cm target_unit_slot: unit target_magnitude_slot: magnitude","title":"Combo: test_complex_unit_conversion[cm-cm-100.0-100.0-roundtrip_object1-None] {#combo-test_complex_unit_conversioncm-cm-1000-1000-roundtrip_object1-none}"},{"location":"specification/compliance/#combo-test_complex_unit_conversioncm-ml-1000-none-none-dimensionalityerror-combo-test_complex_unit_conversioncm-ml-1000-none-none-dimensionalityerror","text":"Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: Q: name: Q attributes: magnitude: name: magnitude range: float unit: name: unit range: string C: name: C attributes: q: name: q range: Q tree_root: true Transformer Specification : class_derivations: D: name: D populated_from: C slot_derivations: q_in_ml: name: q_in_ml populated_from: q unit_conversion: target_unit: ml source_unit_slot: unit source_magnitude_slot: magnitude Object Transformation : Expected Error : DimensionalityError Source Object: q: magnitude: 100.0 unit: cm Target Object: null ... Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: D: name: D attributes: q_in_ml: name: q_in_ml domain_of: - C range: Q unit: ucum_code: ml tree_root: true","title":"Combo: test_complex_unit_conversion[cm-ml-100.0-None-None-DimensionalityError] {#combo-test_complex_unit_conversioncm-ml-1000-none-none-dimensionalityerror}"},{"location":"specification/compliance/#combo-test_complex_unit_conversioncm-pinknoodles-1000-none-none-undefineduniterror-combo-test_complex_unit_conversioncm-pinknoodles-1000-none-none-undefineduniterror","text":"Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: Q: name: Q attributes: magnitude: name: magnitude range: float unit: name: unit range: string C: name: C attributes: q: name: q range: Q tree_root: true Transformer Specification : class_derivations: D: name: D populated_from: C slot_derivations: q_in_pinknoodles: name: q_in_pinknoodles populated_from: q unit_conversion: target_unit: pinknoodles source_unit_slot: unit source_magnitude_slot: magnitude Object Transformation : Expected Error : UndefinedUnitError Source Object: q: magnitude: 100.0 unit: cm Target Object: null ... Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: D: name: D attributes: q_in_pinknoodles: name: q_in_pinknoodles domain_of: - C range: Q unit: ucum_code: pinknoodles tree_root: true","title":"Combo: test_complex_unit_conversion[cm-pinknoodles-100.0-None-None-UndefinedUnitError] {#combo-test_complex_unit_conversioncm-pinknoodles-1000-none-none-undefineduniterror}"},{"location":"specification/compliance/#feature-set-test_stringify","text":"Test compaction of multivalued slots into a string. Stringification is primarily intended for mapping from complex nested formats to simple tabular TSV formats, where some of the following methodologies can be used: flattening lists using an (internal) delimiter flattening lists or more complex objects using JSON or YAML syntax : SerializationSyntaxType delimiter : delimiter to use in stringification source_value : source value (a list) target_value : expected value of slot in target object (a string)","title":"Feature Set: test_stringify"},{"location":"specification/compliance/#combo-test_stringifynone-source_value0-ab","text":"Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 multivalued: true range: string Transformer Specification : class_derivations: D: name: D populated_from: C slot_derivations: s1_verbatim: name: s1_verbatim populated_from: s1 stringification: delimiter: ',' Object Transformation : Source Object: s1: - a - b Target Object: s1_verbatim: a,b Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: D: name: D attributes: s1_verbatim: name: s1_verbatim multivalued: false domain_of: - C range: string Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: D slot_derivations: s1: name: s1 populated_from: s1_verbatim stringification: delimiter: ',' reversed: true Compiled Specification (SQLCompiler) : INSERT INTO D SELECT s1_verbatim AS STRING_AGG(s1, \\',\\') FROM D;","title":"Combo: test_stringify[None-,-source_value0-a,b]"},{"location":"specification/compliance/#combo-test_stringifynone-source_value1-ab","text":"Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 multivalued: true range: string Transformer Specification : class_derivations: D: name: D populated_from: C slot_derivations: s1_verbatim: name: s1_verbatim populated_from: s1 stringification: delimiter: '|' Object Transformation : Source Object: s1: - a - b Target Object: s1_verbatim: a|b Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: D: name: D attributes: s1_verbatim: name: s1_verbatim multivalued: false domain_of: - C range: string Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: D slot_derivations: s1: name: s1 populated_from: s1_verbatim stringification: delimiter: '|' reversed: true Compiled Specification (SQLCompiler) : INSERT INTO D SELECT s1_verbatim AS STRING_AGG(s1, \\'|\\') FROM D;","title":"Combo: test_stringify[None-|-source_value1-a|b]"},{"location":"specification/compliance/#combo-test_stringifynone-source_value2-a","text":"Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 multivalued: true range: string Transformer Specification : class_derivations: D: name: D populated_from: C slot_derivations: s1_verbatim: name: s1_verbatim populated_from: s1 stringification: delimiter: '|' Object Transformation : Source Object: s1: - a Target Object: s1_verbatim: a Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: D: name: D attributes: s1_verbatim: name: s1_verbatim multivalued: false domain_of: - C range: string Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: D slot_derivations: s1: name: s1 populated_from: s1_verbatim stringification: delimiter: '|' reversed: true Compiled Specification (SQLCompiler) : INSERT INTO D SELECT s1_verbatim AS STRING_AGG(s1, \\'|\\') FROM D;","title":"Combo: test_stringify[None-|-source_value2-a]"},{"location":"specification/compliance/#combo-test_stringifynone-source_value3-","text":"Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 multivalued: true range: string Transformer Specification : class_derivations: D: name: D populated_from: C slot_derivations: s1_verbatim: name: s1_verbatim populated_from: s1 stringification: delimiter: '|' Object Transformation : Source Object: {} Target Object: s1_verbatim: '' Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: D: name: D attributes: s1_verbatim: name: s1_verbatim multivalued: false domain_of: - C range: string Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: D slot_derivations: s1: name: s1 populated_from: s1_verbatim stringification: delimiter: '|' reversed: true Compiled Specification (SQLCompiler) : INSERT INTO D SELECT s1_verbatim AS STRING_AGG(s1, \\'|\\') FROM D;","title":"Combo: test_stringify[None-|-source_value3-]"},{"location":"specification/compliance/#combo-test_stringifyjson-none-source_value4-a-b","text":"Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 multivalued: true range: string Transformer Specification : class_derivations: D: name: D populated_from: C slot_derivations: s1_verbatim: name: s1_verbatim populated_from: s1 stringification: syntax: JSON Object Transformation : Source Object: s1: - a - b Target Object: s1_verbatim: '[\"a\", \"b\"]' Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: D: name: D attributes: s1_verbatim: name: s1_verbatim multivalued: false domain_of: - C range: string Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: D slot_derivations: s1: name: s1 populated_from: s1_verbatim stringification: reversed: true syntax: JSON Compiled Specification (SQLCompiler) : INSERT INTO D SELECT s1_verbatim AS CAST(s1 AS TEXT) FROM D;","title":"Combo: test_stringify[JSON-None-source_value4-[\\\"a\\\", \\\"b\\\"]]"},{"location":"specification/compliance/#combo-test_stringifyjson-none-source_value5-","text":"Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 multivalued: true range: string Transformer Specification : class_derivations: D: name: D populated_from: C slot_derivations: s1_verbatim: name: s1_verbatim populated_from: s1 stringification: syntax: JSON Object Transformation : Source Object: {} Target Object: s1_verbatim: '[]' Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: D: name: D attributes: s1_verbatim: name: s1_verbatim multivalued: false domain_of: - C range: string Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: D slot_derivations: s1: name: s1 populated_from: s1_verbatim stringification: reversed: true syntax: JSON Compiled Specification (SQLCompiler) : INSERT INTO D SELECT s1_verbatim AS CAST(s1 AS TEXT) FROM D;","title":"Combo: test_stringify[JSON-None-source_value5-[]]"},{"location":"specification/compliance/#combo-test_stringifyyaml-none-source_value6-a-b","text":"Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C attributes: s1: name: s1 multivalued: true range: string Transformer Specification : class_derivations: D: name: D populated_from: C slot_derivations: s1_verbatim: name: s1_verbatim populated_from: s1 stringification: syntax: YAML Object Transformation : Source Object: s1: - a - b Target Object: s1_verbatim: '[a, b]' Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: D: name: D attributes: s1_verbatim: name: s1_verbatim multivalued: false domain_of: - C range: string Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: D slot_derivations: s1: name: s1 populated_from: s1_verbatim stringification: reversed: true syntax: YAML Compiled Specification (SQLCompiler) : INSERT INTO D SELECT s1_verbatim AS s1 FROM D;","title":"Combo: test_stringify[YAML-None-source_value6-[a, b]]"},{"location":"specification/compliance/#feature-set-test_isomorphic","text":"Test mapping a schema to an identical schema (i.e copy). This also tests for the ability to recursively descend a nested structure. source_object : use_expr : supply_source_schema : TODO: always True for now","title":"Feature Set: test_isomorphic"},{"location":"specification/compliance/#combo-test_isomorphictrue-true-source_object0","text":"Source Schema : name: isomorphic id: isomorphic imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: Container: name: Container attributes: c_list: name: c_list multivalued: true range: C d: name: d range: D tree_root: true C: name: C attributes: s1: name: s1 range: string s2: name: s2 range: string D: name: D attributes: s3: name: s3 range: string Transformer Specification : class_derivations: Container: name: Container populated_from: Container slot_derivations: c_list: name: c_list populated_from: c_list range: C d: name: d populated_from: d range: D C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 s2: name: s2 populated_from: s2 D: name: D populated_from: D slot_derivations: s3: name: s3 expr: s3 Object Transformation : Source Object: c_list: - s1: a s2: b - s1: c s2: d d: s3: e Target Object: c_list: - s1: a s2: b - s1: c s2: d d: s3: e Target Schema (Derived) : name: isomorphic-derived id: isomorphic-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: isomorphic-derived/ classes: Container: name: Container attributes: c_list: name: c_list multivalued: true domain_of: - Container range: C d: name: d domain_of: - Container range: D tree_root: true C: name: C attributes: s1: name: s1 domain_of: - C range: string s2: name: s2 domain_of: - C range: string D: name: D attributes: s3: name: s3 domain_of: - D range: string Inverted Transformation Specification (Derived): class_derivations: Container: name: Container populated_from: Container slot_derivations: c_list: name: c_list populated_from: c_list range: C d: name: d populated_from: d range: D C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 s2: name: s2 populated_from: s2 D: name: D populated_from: D slot_derivations: s3: name: s3 populated_from: s3","title":"Combo: test_isomorphic[True-True-source_object0]"},{"location":"specification/compliance/#combo-test_isomorphictrue-false-source_object0","text":"Source Schema : name: isomorphic id: isomorphic imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: Container: name: Container attributes: c_list: name: c_list multivalued: true range: C d: name: d range: D tree_root: true C: name: C attributes: s1: name: s1 range: string s2: name: s2 range: string D: name: D attributes: s3: name: s3 range: string Transformer Specification : class_derivations: Container: name: Container populated_from: Container slot_derivations: c_list: name: c_list populated_from: c_list range: C d: name: d populated_from: d range: D C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 s2: name: s2 populated_from: s2 D: name: D populated_from: D slot_derivations: s3: name: s3 populated_from: s3 Object Transformation : Source Object: c_list: - s1: a s2: b - s1: c s2: d d: s3: e Target Object: c_list: - s1: a s2: b - s1: c s2: d d: s3: e Target Schema (Derived) : name: isomorphic-derived id: isomorphic-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: isomorphic-derived/ classes: Container: name: Container attributes: c_list: name: c_list multivalued: true domain_of: - Container range: C d: name: d domain_of: - Container range: D tree_root: true C: name: C attributes: s1: name: s1 domain_of: - C range: string s2: name: s2 domain_of: - C range: string D: name: D attributes: s3: name: s3 domain_of: - D range: string Inverted Transformation Specification (Derived): class_derivations: Container: name: Container populated_from: Container slot_derivations: c_list: name: c_list populated_from: c_list range: C d: name: d populated_from: d range: D C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 s2: name: s2 populated_from: s2 D: name: D populated_from: D slot_derivations: s3: name: s3 populated_from: s3","title":"Combo: test_isomorphic[True-False-source_object0]"},{"location":"specification/compliance/#feature-set-test_join","text":"Test joining two objects into a single object, aka denormalization. source_object : normalized source object target_object : denormalized target object inlined : True if the source objects are inlined","title":"Feature Set: test_join"},{"location":"specification/compliance/#combo-test_joinsource_object0-target_object0-true","text":"Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: R: name: R attributes: s1: name: s1 range: E inlined: true s2: name: s2 range: E inlined: true tree_root: true E: name: E attributes: id: name: id identifier: true range: string name: name: name range: string Transformer Specification : class_derivations: R: name: R populated_from: R slot_derivations: s1_id: name: s1_id expr: s1.id s1_name: name: s1_name expr: s1.name s2_id: name: s2_id expr: s2.id s2_name: name: s2_name expr: s2.name Object Transformation : Source Object: s1: id: x1 name: foo s2: id: x2 name: bar Target Object: s1_id: x1 s1_name: foo s2_id: x2 s2_name: bar Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: R: name: R attributes: s1_id: name: s1_id s1_name: name: s1_name s2_id: name: s2_id s2_name: name: s2_name tree_root: true","title":"Combo: test_join[source_object0-target_object0-True]"},{"location":"specification/compliance/#combo-test_joinsource_object0-target_object0-false","text":"Source Schema : name: types id: types imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: R: name: R attributes: s1: name: s1 range: E inlined: false s2: name: s2 range: E inlined: false tree_root: false E: name: E attributes: id: name: id identifier: true range: string name: name: name range: string Container: name: Container attributes: r_list: name: r_list multivalued: true range: R e_list: name: e_list multivalued: true range: E inlined_as_list: true tree_root: true Transformer Specification : class_derivations: R: name: R populated_from: R slot_derivations: s1_id: name: s1_id expr: s1.id s1_name: name: s1_name expr: s1.name s2_id: name: s2_id expr: s2.id s2_name: name: s2_name expr: s2.name Container: name: Container populated_from: Container slot_derivations: r_list: name: r_list populated_from: r_list Object Transformation : Source Object: r_list: - s1: x1 s2: x2 e_list: - id: x1 name: foo - id: x2 name: bar Target Object: r_list: - s1_id: x1 s1_name: foo s2_id: x2 s2_name: bar Target Schema (Derived) : name: types-derived id: types-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: types-derived/ classes: R: name: R attributes: s1_id: name: s1_id s1_name: name: s1_name s2_id: name: s2_id s2_name: name: s2_name tree_root: false Container: name: Container attributes: r_list: name: r_list multivalued: true domain_of: - Container range: R tree_root: true","title":"Combo: test_join[source_object0-target_object0-False]"},{"location":"specification/compliance/#feature-set-test_map_enum","text":"Test mapping between enum values. Currently this only supports simple dictionary-style mapping between permissible values, akin to SSSOM, but in future additional expressivity will be supported, including: mapping ranges to categorical values boolean/branching logic source_value : mapping : target_value :","title":"Feature Set: test_map_enum"},{"location":"specification/compliance/#combo-test_map_enuma-mapping0-b-false","text":"Source Schema : name: enums id: enums imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test enums: E: name: E permissible_values: A: text: A B: text: B C: text: C classes: C: name: C attributes: s1: name: s1 range: E Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 enum_derivations: E: name: E mirror_source: false populated_from: E permissible_value_derivations: B: name: B populated_from: A Object Transformation : Source Object: s1: A Target Object: s1: B Target Schema (Derived) : name: enums-derived id: enums-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: enums-derived/ enums: E: name: E permissible_values: A: text: A B: text: B C: text: C classes: C: name: C attributes: s1: name: s1 domain_of: - C range: E Inverted Transformation Specification (Derived): class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 populated_from: s1 enum_derivations: E: name: E populated_from: E permissible_value_derivations: A: name: A populated_from: B","title":"Combo: test_map_enum[A-mapping0-B-False]"},{"location":"specification/compliance/#combo-test_map_enumz-mapping1-none-false","text":"Source Schema : name: enums id: enums imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test enums: E: name: E permissible_values: A: text: A B: text: B C: text: C classes: C: name: C attributes: s1: name: s1 range: E Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 enum_derivations: E: name: E mirror_source: false populated_from: E permissible_value_derivations: B: name: B populated_from: A Object Transformation : Source Object: s1: Z Target Object: {} Target Schema (Derived) : name: enums-derived id: enums-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: enums-derived/ enums: E: name: E permissible_values: A: text: A B: text: B C: text: C classes: C: name: C attributes: s1: name: s1 domain_of: - C range: E","title":"Combo: test_map_enum[Z-mapping1-None-False]"},{"location":"specification/compliance/#combo-test_map_enumc-mapping2-c-true","text":"Source Schema : name: enums id: enums imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test enums: E: name: E permissible_values: A: text: A B: text: B C: text: C classes: C: name: C attributes: s1: name: s1 range: E Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 enum_derivations: E: name: E mirror_source: true populated_from: E permissible_value_derivations: B: name: B populated_from: A s### Combo: test_map_enum[A-mapping3-B-False] Source Schema : name: enums id: enums imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test enums: E: name: E permissible_values: A: text: A B: text: B C: text: C classes: C: name: C attributes: s1: name: s1 range: E Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 enum_derivations: E: name: E mirror_source: false populated_from: E permissible_value_derivations: B: name: B sources: - A - C Object Transformation : Source Object: s1: A Target Object: s1: B Target Schema (Derived) : name: enums-derived id: enums-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: enums-derived/ enums: E: name: E permissible_values: A: text: A B: text: B C: text: C classes: C: name: C attributes: s1: name: s1 domain_of: - C range: E","title":"Combo: test_map_enum[C-mapping2-C-True]"},{"location":"specification/compliance/#combo-test_map_enumc-mapping4-b-false","text":"Source Schema : name: enums id: enums imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test enums: E: name: E permissible_values: A: text: A B: text: B C: text: C classes: C: name: C attributes: s1: name: s1 range: E Transformer Specification : class_derivations: C: name: C slot_derivations: s1: name: s1 populated_from: s1 enum_derivations: E: name: E mirror_source: false populated_from: E permissible_value_derivations: B: name: B sources: - A - C Object Transformation : Source Object: s1: C Target Object: s1: B Target Schema (Derived) : name: enums-derived id: enums-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: enums-derived/ enums: E: name: E permissible_values: A: text: A B: text: B C: text: C classes: C: name: C attributes: s1: name: s1 domain_of: - C range: E","title":"Combo: test_map_enum[C-mapping4-B-False]"},{"location":"specification/compliance/#feature-set-test_inheritance","text":"Test inheritance. Transformation specifications can utilize inheritance, in the same way that LinkML schemas can. is_a : use is_as instead of mixins in test schema flatten : roll down inherited slots","title":"Feature Set: test_inheritance"},{"location":"specification/compliance/#combo-test_inheritancefalse-true","text":"Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C is_a: D attributes: s1: name: s1 range: integer tree_root: true D: name: D attributes: s2: name: s2 range: integer Transformer Specification : class_derivations: C: name: C is_a: D populated_from: C slot_derivations: s1: name: s1 expr: s1 + 1 D: name: D populated_from: D slot_derivations: s2: name: s2 expr: s2 + 1 Object Transformation : Source Object: s1: 1 s2: 2 Target Object: s1: 2 s2: 3 Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C is_a: D attributes: s1: name: s1 domain_of: - C range: integer tree_root: true D: name: D attributes: s2: name: s2 domain_of: - D range: integer","title":"Combo: test_inheritance[False-True]"},{"location":"specification/compliance/#combo-test_inheritancefalse-false","text":"Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C mixins: - D attributes: s1: name: s1 range: integer tree_root: true D: name: D attributes: s2: name: s2 range: integer Transformer Specification : class_derivations: C: name: C mixins: - D populated_from: C slot_derivations: s1: name: s1 expr: s1 + 1 D: name: D populated_from: D slot_derivations: s2: name: s2 expr: s2 + 1 Object Transformation : Source Object: s1: 1 s2: 2 Target Object: s1: 2 s2: 3 Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C mixins: - D attributes: s1: name: s1 domain_of: - C range: integer tree_root: true D: name: D attributes: s2: name: s2 domain_of: - D range: integer","title":"Combo: test_inheritance[False-False]"},{"location":"specification/compliance/#combo-test_inheritancetrue-true","text":"Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C is_a: D attributes: s1: name: s1 range: integer tree_root: true D: name: D attributes: s2: name: s2 range: integer Transformer Specification : class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 expr: s1 + 1 s2: name: s2 expr: s2 + 1 Object Transformation : Source Object: s1: 1 s2: 2 Target Object: s1: 2 s2: 3 Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: integer s2: name: s2 domain_of: - D range: integer tree_root: true","title":"Combo: test_inheritance[True-True]"},{"location":"specification/compliance/#combo-test_inheritancetrue-false","text":"Source Schema : name: expr id: expr imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: test classes: C: name: C mixins: - D attributes: s1: name: s1 range: integer tree_root: true D: name: D attributes: s2: name: s2 range: integer Transformer Specification : class_derivations: C: name: C populated_from: C slot_derivations: s1: name: s1 expr: s1 + 1 s2: name: s2 expr: s2 + 1 Object Transformation : Source Object: s1: 1 s2: 2 Target Object: s1: 2 s2: 3 Target Schema (Derived) : name: expr-derived id: expr-derived imports: - linkml:types prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ test: prefix_prefix: test prefix_reference: http://example.org/test/ default_prefix: expr-derived/ classes: C: name: C attributes: s1: name: s1 domain_of: - C range: integer s2: name: s2 domain_of: - D range: integer tree_root: true . 55 passed, 2 skipped, 83 warnings in 3.98s","title":"Combo: test_inheritance[True-False]"}]} \ No newline at end of file diff --git a/sitemap.xml b/sitemap.xml new file mode 100644 index 0000000..2a854a3 --- /dev/null +++ b/sitemap.xml @@ -0,0 +1,518 @@ + + + + https://linkml.github.io/linkml-map/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/AliasedClass/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/Any/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/Boolean/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/ClassDerivation/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/ClassReference/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/CollectionType/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/CopyDirective/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/Curie/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/Date/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/DateOrDatetime/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/Datetime/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/Decimal/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/Double/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/ElementDerivation/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/EnumDerivation/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/EnumReference/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/Float/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/Integer/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/Inverse/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/Jsonpath/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/Jsonpointer/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/KeyVal/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/Ncname/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/Nodeidentifier/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/Objectidentifier/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/PermissibleValueDerivation/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/PrefixDerivation/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/SerializationSyntaxType/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/SlotDerivation/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/SlotReference/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/Sparqlpath/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/SpecificationComponent/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/String/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/StringificationConfiguration/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/Time/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/TransformationSpecification/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/UnitConversionConfiguration/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/Uri/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/Uriorcurie/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/add/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/alias/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/cast_collection_as/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/class_derivations/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/class_name/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/class_named/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/comments/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/copy_all/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/copy_directives/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/datamodel/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/delimiter/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/derived_from/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/description/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/dictionary_key/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/element_name/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/enum_derivations/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/exclude/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/exclude_all/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/expr/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/expression_to_expression_mappings/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/expression_to_value_mappings/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/faq/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/hide/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/id/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/implements/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/include/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/inverse_of/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/is_a/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/joins/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/key/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/linkml-map/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/mirror_source/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/mixins/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/name/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/over_slots/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/overrides/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/permissible_value_derivations/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/populated_from/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/prefixes/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/range/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/reversed/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/slot_derivations/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/slot_name/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/source_magnitude_slot/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/source_schema/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/source_unit/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/source_unit_scheme/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/source_unit_slot/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/sources/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/stringification/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/syntax/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/target_magnitude_slot/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/target_schema/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/target_unit/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/target_unit_scheme/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/target_unit_slot/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/title/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/type_designator/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/unit_conversion/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/value/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/value_mappings/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/examples/Tutorial/ + 2024-04-12 + daily + + + https://linkml.github.io/linkml-map/specification/compliance/ + 2024-04-12 + daily + + \ No newline at end of file diff --git a/sitemap.xml.gz b/sitemap.xml.gz new file mode 100644 index 0000000..a01224f Binary files /dev/null and b/sitemap.xml.gz differ diff --git a/slot_derivations/index.html b/slot_derivations/index.html new file mode 100644 index 0000000..e87e6c2 --- /dev/null +++ b/slot_derivations/index.html @@ -0,0 +1,122 @@ + + + + + + + + + + + + + + Slot: slot_derivations - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + +

    Slot: slot_derivations

    +

    URI: linkmltr:slot_derivations

    + + +

    Applicable Classes

    + + + + + + + + + + + + + + + + + + + + +
    NameDescriptionModifies Slot
    TransformationSpecificationA collection of mappings between source and target classesno
    ClassDerivationA specification of how to derive a target class from a source classno
    +

    Properties

    +
      +
    • Range: NONE
    • +
    +

    Identifier and Mapping Information

    +

    LinkML Source

    +
    + +
    name: slot_derivations
    +alias: slot_derivations
    +domain_of:
    +- TransformationSpecification
    +- ClassDerivation
    +
    +
    + +
    + +
    + + +
    +
    + + + + + \ No newline at end of file diff --git a/slot_name/index.html b/slot_name/index.html new file mode 100644 index 0000000..6de6e2f --- /dev/null +++ b/slot_name/index.html @@ -0,0 +1,123 @@ + + + + + + + + + + + + + + Slot: slot_name - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + +

    Slot: slot_name

    +

    URI: linkmltr:slot_name

    + + +

    Applicable Classes

    + + + + + + + + + + + + + + + +
    NameDescriptionModifies Slot
    InverseUsed for back references in mapping to relational modelno
    +

    Properties

    +
      +
    • Range: NONE
    • +
    +

    Identifier and Mapping Information

    +

    Schema Source

    +
      +
    • from schema: https://w3id.org/linkml/transformer
    • +
    +

    LinkML Source

    +
    + +
    name: slot_name
    +from_schema: https://w3id.org/linkml/transformer
    +rank: 1000
    +alias: slot_name
    +owner: Inverse
    +domain_of:
    +- Inverse
    +
    +
    + +
    + +
    + + +
    +
    + + + + + \ No newline at end of file diff --git a/source_magnitude_slot/index.html b/source_magnitude_slot/index.html new file mode 100644 index 0000000..c8f5242 --- /dev/null +++ b/source_magnitude_slot/index.html @@ -0,0 +1,123 @@ + + + + + + + + + + + + + + Slot: source_magnitude_slot - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + +

    Slot: source_magnitude_slot

    +

    URI: linkmltr:source_magnitude_slot

    + + +

    Applicable Classes

    + + + + + + + + + + + + + + + +
    NameDescriptionModifies Slot
    UnitConversionConfigurationno
    +

    Properties

    +
      +
    • Range: NONE
    • +
    +

    Identifier and Mapping Information

    +

    Schema Source

    +
      +
    • from schema: https://w3id.org/linkml/transformer
    • +
    +

    LinkML Source

    +
    + +
    name: source_magnitude_slot
    +from_schema: https://w3id.org/linkml/transformer
    +rank: 1000
    +alias: source_magnitude_slot
    +owner: UnitConversionConfiguration
    +domain_of:
    +- UnitConversionConfiguration
    +
    +
    + +
    + +
    + + +
    +
    + + + + + \ No newline at end of file diff --git a/source_schema/index.html b/source_schema/index.html new file mode 100644 index 0000000..a71f6cb --- /dev/null +++ b/source_schema/index.html @@ -0,0 +1,125 @@ + + + + + + + + + + + + + + Slot: source_schema - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + +

    Slot: source_schema

    +

    name of the schema that describes the source (input) objects

    +

    URI: linkmltr:source_schema

    + + +

    Applicable Classes

    + + + + + + + + + + + + + + + +
    NameDescriptionModifies Slot
    TransformationSpecificationA collection of mappings between source and target classesno
    +

    Properties

    +
      +
    • Range: NONE
    • +
    +

    Identifier and Mapping Information

    +

    Schema Source

    +
      +
    • from schema: https://w3id.org/linkml/transformer
    • +
    +

    LinkML Source

    +
    + +
    name: source_schema
    +description: name of the schema that describes the source (input) objects
    +from_schema: https://w3id.org/linkml/transformer
    +rank: 1000
    +alias: source_schema
    +owner: TransformationSpecification
    +domain_of:
    +- TransformationSpecification
    +
    +
    + +
    + +
    + + +
    +
    + + + + + \ No newline at end of file diff --git a/source_unit/index.html b/source_unit/index.html new file mode 100644 index 0000000..460a892 --- /dev/null +++ b/source_unit/index.html @@ -0,0 +1,123 @@ + + + + + + + + + + + + + + Slot: source_unit - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + +

    Slot: source_unit

    +

    URI: linkmltr:source_unit

    + + +

    Applicable Classes

    + + + + + + + + + + + + + + + +
    NameDescriptionModifies Slot
    UnitConversionConfigurationno
    +

    Properties

    +
      +
    • Range: NONE
    • +
    +

    Identifier and Mapping Information

    +

    Schema Source

    +
      +
    • from schema: https://w3id.org/linkml/transformer
    • +
    +

    LinkML Source

    +
    + +
    name: source_unit
    +from_schema: https://w3id.org/linkml/transformer
    +rank: 1000
    +alias: source_unit
    +owner: UnitConversionConfiguration
    +domain_of:
    +- UnitConversionConfiguration
    +
    +
    + +
    + +
    + + +
    +
    + + + + + \ No newline at end of file diff --git a/source_unit_scheme/index.html b/source_unit_scheme/index.html new file mode 100644 index 0000000..777e872 --- /dev/null +++ b/source_unit_scheme/index.html @@ -0,0 +1,140 @@ + + + + + + + + + + + + + + Slot: source_unit_scheme - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + +

    Slot: source_unit_scheme

    +

    URI: linkmltr:source_unit_scheme

    + + +

    Applicable Classes

    + + + + + + + + + + + + + + + +
    NameDescriptionModifies Slot
    UnitConversionConfigurationno
    +

    Properties

    + +

    Examples

    + + + + + + + + + + + +
    Value
    ucum
    +

    Identifier and Mapping Information

    +

    Schema Source

    +
      +
    • from schema: https://w3id.org/linkml/transformer
    • +
    +

    LinkML Source

    +
    + +
    name: source_unit_scheme
    +examples:
    +- value: ucum
    +from_schema: https://w3id.org/linkml/transformer
    +rank: 1000
    +alias: source_unit_scheme
    +owner: UnitConversionConfiguration
    +domain_of:
    +- UnitConversionConfiguration
    +range: string
    +
    +
    + +
    + +
    + + +
    +
    + + + + + \ No newline at end of file diff --git a/source_unit_slot/index.html b/source_unit_slot/index.html new file mode 100644 index 0000000..27df9b5 --- /dev/null +++ b/source_unit_slot/index.html @@ -0,0 +1,123 @@ + + + + + + + + + + + + + + Slot: source_unit_slot - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + +

    Slot: source_unit_slot

    +

    URI: linkmltr:source_unit_slot

    + + +

    Applicable Classes

    + + + + + + + + + + + + + + + +
    NameDescriptionModifies Slot
    UnitConversionConfigurationno
    +

    Properties

    +
      +
    • Range: NONE
    • +
    +

    Identifier and Mapping Information

    +

    Schema Source

    +
      +
    • from schema: https://w3id.org/linkml/transformer
    • +
    +

    LinkML Source

    +
    + +
    name: source_unit_slot
    +from_schema: https://w3id.org/linkml/transformer
    +rank: 1000
    +alias: source_unit_slot
    +owner: UnitConversionConfiguration
    +domain_of:
    +- UnitConversionConfiguration
    +
    +
    + +
    + +
    + + +
    +
    + + + + + \ No newline at end of file diff --git a/sources/index.html b/sources/index.html new file mode 100644 index 0000000..4334c61 --- /dev/null +++ b/sources/index.html @@ -0,0 +1,134 @@ + + + + + + + + + + + + + + Slot: sources - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + +

    Slot: sources

    +

    URI: linkmltr:sources

    + + +

    Applicable Classes

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    NameDescriptionModifies Slot
    EnumDerivationA specification of how to derive the value of a target enum from a source enu...no
    PermissibleValueDerivationA specification of how to derive the value of a PV from a source enumno
    SlotDerivationA specification of how to derive the value of a target slot from a source slo...no
    ClassDerivationA specification of how to derive a target class from a source classno
    +

    Properties

    +
      +
    • Range: NONE
    • +
    +

    Identifier and Mapping Information

    +

    LinkML Source

    +
    + +
    name: sources
    +alias: sources
    +domain_of:
    +- ClassDerivation
    +- SlotDerivation
    +- EnumDerivation
    +- PermissibleValueDerivation
    +
    +
    + +
    + +
    + + +
    +
    + + + + + \ No newline at end of file diff --git a/docs/specification/compliance.md b/specification/compliance/index.html similarity index 52% rename from docs/specification/compliance.md rename to specification/compliance/index.html index 0702dd2..82c07a8 100644 --- a/docs/specification/compliance.md +++ b/specification/compliance/index.html @@ -1,69 +1,149 @@ -- [LinkML-Map Compliance Suite](#linkml-map-compliance-suite) - - [Feature Set: test\_map\_types](#feature-set-test_map_types) - - [Feature Set: - test\_map\_collections](#feature-set-test_map_collections) - - [Feature Set: test\_expr](#feature-set-test_expr) - - [Feature Set: - test\_simple\_unit\_conversion](#feature-set-test_simple_unit_conversion) - - [Feature Set: - test\_complex\_unit\_conversion](#feature-set-test_complex_unit_conversion) - - [Feature Set: test\_stringify](#feature-set-test_stringify) - - [Feature Set: test\_isomorphic](#feature-set-test_isomorphic) - - [Feature Set: test\_join](#feature-set-test_join) - - [Feature Set: test\_map\_enum](#feature-set-test_map_enum) - - [Feature Set: test\_inheritance](#feature-set-test_inheritance) - -LinkML-Map Compliance Suite -=========================== - -This is the output from running the full compliance test suite. - -``` {.yaml} -Time_executed: 2024-07-03 -Package: /Users/cjm/repos/linkml-map/tests/test_compliance/test_compliance_suite.py -``` - -It is organized into **Feature Sets** that test a particular feature or -group of features, and **combinations** of different schemas, input + + + + + + + + + + + + + + Compliance Suite - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + + +

    LinkML-Map Compliance Suite

    +

    This is the output from running the full compliance test suite.

    +

    It is organized into Feature Sets that test a particular feature or +group of features, and combinations of different schemas, input objects, and transformation specifications. This is intended to exhaustively test all combinations of features, and provide informative -output. - -Each test is designed to demonstrate: - -- data mapping (transformation) -- derived schemas -- inversion (reverse transformation) (in some cases) -- compilation to other frameworks (coming soon) - -Feature Set: test\_map\_types ------------------------------ - -Test mapping between basic data types. - -This test uses an ultra-minimal schema with a single class and a single +output.

    +

    Each test is designed to demonstrate:

    +
      +
    • data mapping (transformation)
    • +
    • derived schemas
    • +
    • inversion (reverse transformation) (in some cases)
    • +
    • compilation to other frameworks (coming soon)
    • +
    +

    Feature Set: test_map_types

    +

    Test mapping between basic data types.

    +

    This test uses an ultra-minimal schema with a single class and a single attribute, the transformation specification maps that attribute onto -itself, with a different type, demonstrating type coercion. - -Some cases will be trivially isomorphic (where `source_datatype` == -`target_datatype`), but these are executed anyway. - -- **source\_datatype**: linkml datatype of source object -- **target\_datatype**: linkml datatype of target object -- **source\_value**: value of source object -- **target\_value**: expected value of slot in target object -- **invertible**: True if the transformation is invertible - -### Combo: test\_map\_types\[string-string-foo-foo-True\] - -Mapping `string` =\> `string` - -Isomorphic mapping: input should equal output - -**Source Schema**: - -``` {.yaml} -name: types +itself, with a different type, demonstrating type coercion.

    +

    Some cases will be trivially isomorphic (where source_datatype == +target_datatype), but these are executed anyway.

    +
      +
    • source_datatype: linkml datatype of source object
    • +
    • target_datatype: linkml datatype of target object
    • +
    • source_value: value of source object
    • +
    • target_value: expected value of slot in target object
    • +
    • invertible: True if the transformation is invertible
    • +
    +

    Combo: test_map_types[string-string-foo-foo-True]

    +

    Mapping string => string

    +

    Isomorphic mapping: input should equal output

    +

    Source Schema:

    +
    name: types
     description: Minimal single-attribute schema for testing datatype mapping
     id: types
     imports:
    @@ -84,12 +164,9 @@
             name: s1
             range: string
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -98,28 +175,22 @@
             populated_from: s1
             range: string
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: foo
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1: foo
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: foo
    +
    +
    +
      +
    • Target Object:
    • +
    +
    s1: foo
    +
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -141,12 +212,9 @@
             - C
             range: string
     
    -```
    -
    -**Inverted Transformation Specification** (Derived):
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -156,18 +224,12 @@
             populated_from: s1
             range: string
     
    -```
    -
    -### Combo: test\_map\_types\[integer-integer-5-5-True\]
    -
    -Mapping `integer` =\> `integer`
    -
    -Isomorphic mapping: input should equal output
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Combo: test_map_types[integer-integer-5-5-True]

    +

    Mapping integer => integer

    +

    Isomorphic mapping: input should equal output

    +

    Source Schema:

    +
    name: types
     description: Minimal single-attribute schema for testing datatype mapping
     id: types
     imports:
    @@ -188,12 +250,9 @@
             name: s1
             range: integer
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -202,28 +261,22 @@
             populated_from: s1
             range: integer
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 5
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1: 5
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: 5
    +
    +
    +
      +
    • Target Object:
    • +
    +
    s1: 5
    +
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -245,12 +298,9 @@
             - C
             range: integer
     
    -```
    -
    -**Inverted Transformation Specification** (Derived):
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -260,18 +310,12 @@
             populated_from: s1
             range: integer
     
    -```
    -
    -### Combo: test\_map\_types\[string-integer-5-5-True\]
    -
    -Mapping `string` =\> `integer`
    -
    -Should coerce datatype
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Combo: test_map_types[string-integer-5-5-True]

    +

    Mapping string => integer

    +

    Should coerce datatype

    +

    Source Schema:

    +
    name: types
     description: Minimal single-attribute schema for testing datatype mapping
     id: types
     imports:
    @@ -292,12 +336,9 @@
             name: s1
             range: string
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -306,28 +347,22 @@
             populated_from: s1
             range: integer
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: '5'
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1: 5
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: '5'
    +
    +
    +
      +
    • Target Object:
    • +
    +
    s1: 5
    +
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -349,12 +384,9 @@
             - C
             range: integer
     
    -```
    -
    -**Inverted Transformation Specification** (Derived):
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -364,18 +396,12 @@
             populated_from: s1
             range: string
     
    -```
    -
    -### Combo: test\_map\_types\[integer-float-5-5.0-True\] {#combo-test_map_typesinteger-float-5-50-true}
    -
    -Mapping `integer` =\> `float`
    -
    -Should coerce datatype
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Combo: test_map_types[integer-float-5-5.0-True] {#combo-test_map_typesinteger-float-5-50-true}

    +

    Mapping integer => float

    +

    Should coerce datatype

    +

    Source Schema:

    +
    name: types
     description: Minimal single-attribute schema for testing datatype mapping
     id: types
     imports:
    @@ -396,12 +422,9 @@
             name: s1
             range: integer
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -410,28 +433,22 @@
             populated_from: s1
             range: float
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 5
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1: 5.0
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: 5
    +
    +
    +
      +
    • Target Object:
    • +
    +
    s1: 5.0
    +
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -453,12 +470,9 @@
             - C
             range: float
     
    -```
    -
    -**Inverted Transformation Specification** (Derived):
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -468,18 +482,12 @@
             populated_from: s1
             range: integer
     
    -```
    -
    -### Combo: test\_map\_types\[float-integer-5.0-5-True\] {#combo-test_map_typesfloat-integer-50-5-true}
    -
    -Mapping `float` =\> `integer`
    -
    -Should coerce datatype
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Combo: test_map_types[float-integer-5.0-5-True] {#combo-test_map_typesfloat-integer-50-5-true}

    +

    Mapping float => integer

    +

    Should coerce datatype

    +

    Source Schema:

    +
    name: types
     description: Minimal single-attribute schema for testing datatype mapping
     id: types
     imports:
    @@ -500,12 +508,9 @@
             name: s1
             range: float
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -514,28 +519,22 @@
             populated_from: s1
             range: integer
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 5.0
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1: 5
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: 5.0
    +
    +
    +
      +
    • Target Object:
    • +
    +
    s1: 5
    +
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -557,12 +556,9 @@
             - C
             range: integer
     
    -```
    -
    -**Inverted Transformation Specification** (Derived):
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -572,18 +568,12 @@
             populated_from: s1
             range: float
     
    -```
    -
    -### Combo: test\_map\_types\[float-integer-5.2-5-False\] {#combo-test_map_typesfloat-integer-52-5-false}
    -
    -Mapping `float` =\> `integer`
    -
    -Should coerce datatype
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Combo: test_map_types[float-integer-5.2-5-False] {#combo-test_map_typesfloat-integer-52-5-false}

    +

    Mapping float => integer

    +

    Should coerce datatype

    +

    Source Schema:

    +
    name: types
     description: Minimal single-attribute schema for testing datatype mapping
     id: types
     imports:
    @@ -604,12 +594,9 @@
             name: s1
             range: float
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -618,28 +605,22 @@
             populated_from: s1
             range: integer
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 5.2
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1: 5
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: 5.2
    +
    +
    +
      +
    • Target Object:
    • +
    +
    s1: 5
    +
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -661,18 +642,12 @@
             - C
             range: integer
     
    -```
    -
    -### Combo: test\_map\_types\[integer-boolean-5-True-False\]
    -
    -Mapping `integer` =\> `boolean`
    -
    -Should coerce datatype
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Combo: test_map_types[integer-boolean-5-True-False]

    +

    Mapping integer => boolean

    +

    Should coerce datatype

    +

    Source Schema:

    +
    name: types
     description: Minimal single-attribute schema for testing datatype mapping
     id: types
     imports:
    @@ -693,12 +668,9 @@
             name: s1
             range: integer
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -707,28 +679,22 @@
             populated_from: s1
             range: boolean
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 5
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1: true
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: 5
    +
    +
    +
      +
    • Target Object:
    • +
    +
    s1: true
    +
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -750,18 +716,12 @@
             - C
             range: boolean
     
    -```
    -
    -### Combo: test\_map\_types\[integer-boolean-0-False-False\]
    -
    -Mapping `integer` =\> `boolean`
    -
    -Should coerce datatype
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Combo: test_map_types[integer-boolean-0-False-False]

    +

    Mapping integer => boolean

    +

    Should coerce datatype

    +

    Source Schema:

    +
    name: types
     description: Minimal single-attribute schema for testing datatype mapping
     id: types
     imports:
    @@ -782,12 +742,9 @@
             name: s1
             range: integer
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -796,28 +753,22 @@
             populated_from: s1
             range: boolean
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 0
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1: false
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: 0
    +
    +
    +
      +
    • Target Object:
    • +
    +
    s1: false
    +
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -839,31 +790,22 @@
             - C
             range: boolean
     
    -```
    -
    -Feature Set: test\_map\_collections
    ------------------------------------
    -
    -Test mapping between collection data types (lists and dicts).
    -
    -This makes use of the `cast_collection_as` construct
    -
    --   **source\_datatype**: linkml datatype of source object
    --   **target\_datatype**: linkml datatype of target object
    --   **source\_value**: value of source object
    --   **target\_value**: expected value of slot in target object
    --   **invertible**: True if the transformation is invertible
    -
    -### Combo: test\_map\_collections\[string-string-source\_value0-target\_value0-True\]
    -
    -Mapping `string` =\> `string`
    -
    -Isomorphic mapping: **input must equal output**
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Feature Set: test_map_collections

    +

    Test mapping between collection data types (lists and dicts).

    +

    This makes use of the cast_collection_as construct

    +
      +
    • source_datatype:
    • +
    • target_datatype:
    • +
    • source_value:
    • +
    • target_value:
    • +
    • invertible:
    • +
    +

    Combo: test_map_collections[string-string-source_value0-target_value0-True]

    +

    Mapping string => string

    +

    Isomorphic mapping: input should equal output

    +

    Source Schema:

    +
    name: types
     description: Mapping between collection types
     id: types
     imports:
    @@ -882,8 +824,8 @@
         attributes:
           ds:
             name: ds
    -        range: D
             multivalued: true
    +        range: D
             inlined: true
             inlined_as_list: true
         tree_root: true
    @@ -897,12 +839,9 @@
             name: s1
             range: string
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -922,36 +861,30 @@
             populated_from: s1
             range: string
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -ds:
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    ds:
     - id: X
       s1: foo
     - id: Y
       s1: bar
     
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -ds:
    +
    +
      +
    • Target Object:
    • +
    +
    ds:
       X:
         s1: foo
       Y:
         s1: bar
     
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -969,10 +902,10 @@
         attributes:
           ds:
             name: ds
    +        multivalued: true
             domain_of:
             - C
             range: D
    -        multivalued: true
             inlined: true
             inlined_as_list: false
         tree_root: true
    @@ -991,12 +924,9 @@
             - D
             range: string
     
    -```
    -
    -**Inverted Transformation Specification** (Derived):
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -1017,18 +947,12 @@
             populated_from: s1
             range: string
     
    -```
    -
    -### Combo: test\_map\_collections\[string-string-source\_value1-target\_value1-True\]
    -
    -Mapping `string` =\> `string`
    -
    -Isomorphic mapping: **input must equal output**
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Combo: test_map_collections[string-string-source_value1-target_value1-True]

    +

    Mapping string => string

    +

    Isomorphic mapping: input should equal output

    +

    Source Schema:

    +
    name: types
     description: Mapping between collection types
     id: types
     imports:
    @@ -1047,8 +971,8 @@
         attributes:
           ds:
             name: ds
    -        range: D
             multivalued: true
    +        range: D
             inlined: true
             inlined_as_list: false
         tree_root: true
    @@ -1062,12 +986,9 @@
             name: s1
             range: string
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -1086,36 +1007,30 @@
             populated_from: s1
             range: string
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -ds:
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    ds:
       X:
         s1: foo
       Y:
         s1: bar
     
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -ds:
    +
    +
      +
    • Target Object:
    • +
    +
    ds:
     - id: X
       s1: foo
     - id: Y
       s1: bar
     
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -1133,10 +1048,10 @@
         attributes:
           ds:
             name: ds
    +        multivalued: true
             domain_of:
             - C
             range: D
    -        multivalued: true
             inlined: true
             inlined_as_list: true
         tree_root: true
    @@ -1155,12 +1070,9 @@
             - D
             range: string
     
    -```
    -
    -**Inverted Transformation Specification** (Derived):
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -1182,41 +1094,26 @@
             populated_from: s1
             range: string
     
    -```
    -
    -Feature Set: test\_expr
    ------------------------
    -
    -Test transformation using pythonic expressions.
    -
    -This test uses a simple source schema with two slots (`s1` and `s2`).
    +
    +

    Feature Set: test_expr

    +

    Test transformation using pythonic expressions.

    +

    This test uses a simple source schema with two slots (s1 and s2). These are combined using a pythonic expression, to populate the only -slot in the target schema (called `derived`). - -The values of `s1` and `s2` can be numbers or strings. - -If the expression wraps a slot in `{...}` then the presence of a None -forces the entire expression to be `None` - -Limitations: At this time, the framework cannot generate a complete +slot in the target schema (called derived).

    +

    The values of s1 and s2 can be numbers or strings.

    +

    If the expression wraps a slot in {...} then the presence of a None +forces the entire expression to be None

    +

    Limitations: At this time, the framework cannot generate a complete derived schema or inversion for expressions. This will be fixed in -future. - -- See also: [LinkML - Expressions](https://linkml.io/linkml/schemas/expression-language.html) - - - -- **expr**: pythonic expression -- **source\_object**: source object -- **target\_value**: expected value of slot in target object - -### Combo: test\_expr\[s1 + s2-source\_object0-11\] {#combo-test_exprs1--s2-source_object0-11} - -**Source Schema**: - -``` {.yaml} -name: expr +future.

    +
      +
    • expr: pythonic expression
    • +
    • source_object: source object
    • +
    • target_value: expected value of slot in target object
    • +
    +

    Combo: test_expr[s1 + s2-source_object0-11] {#combo-test_exprs1--s2-source_object0-11}

    +

    Source Schema:

    +
    name: expr
     id: expr
     imports:
     - linkml:types
    @@ -1240,12 +1137,9 @@
             range: integer
         tree_root: true
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -1254,29 +1148,23 @@
             name: derived
             expr: s1 + s2
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 5
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: 5
     s2: 6
     
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -derived: 11
    -
    -```
    -
    -**Target Schema (Derived)**:
    +
    +
      +
    • Target Object:
    • +
    +
    derived: 11
     
    -``` {.yaml}
    -name: expr-derived
    +
    +

    Target Schema (Derived):

    +
    name: expr-derived
     id: expr-derived
     imports:
     - linkml:types
    @@ -1296,14 +1184,10 @@
             name: derived
         tree_root: true
     
    -```
    -
    -### Combo: test\_expr\[{s1} + {s2}-source\_object1-11\] {#combo-test_exprs1--s2-source_object1-11}
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: expr
    +
    +

    Combo: test_expr[{s1} + {s2}-source_object1-11] {#combo-test_exprs1--s2-source_object1-11}

    +

    Source Schema:

    +
    name: expr
     id: expr
     imports:
     - linkml:types
    @@ -1327,12 +1211,9 @@
             range: integer
         tree_root: true
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -1341,29 +1222,23 @@
             name: derived
             expr: '{s1} + {s2}'
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 5
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: 5
     s2: 6
     
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -derived: 11
    +
    +
      +
    • Target Object:
    • +
    +
    derived: 11
     
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: expr-derived
    +
    +

    Target Schema (Derived):

    +
    name: expr-derived
     id: expr-derived
     imports:
     - linkml:types
    @@ -1383,14 +1258,10 @@
             name: derived
         tree_root: true
     
    -```
    -
    -### Combo: test\_expr\[{s1} + {s2}-source\_object2-None\] {#combo-test_exprs1--s2-source_object2-none}
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: expr
    +
    +

    Combo: test_expr[{s1} + {s2}-source_object2-None] {#combo-test_exprs1--s2-source_object2-none}

    +

    Source Schema:

    +
    name: expr
     id: expr
     imports:
     - linkml:types
    @@ -1411,12 +1282,9 @@
             range: integer
         tree_root: true
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -1425,28 +1293,22 @@
             name: derived
             expr: '{s1} + {s2}'
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 5
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -{}
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: expr-derived
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: 5
    +
    +
    +
      +
    • Target Object:
    • +
    +
    {}
    +
    +
    +

    Target Schema (Derived):

    +
    name: expr-derived
     id: expr-derived
     imports:
     - linkml:types
    @@ -1466,14 +1328,10 @@
             name: derived
         tree_root: true
     
    -```
    -
    -### Combo: test\_expr\[s1 + s2.s3-source\_object3-11\] {#combo-test_exprs1--s2s3-source_object3-11}
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: expr
    +
    +

    Combo: test_expr[s1 + s2.s3-source_object3-11] {#combo-test_exprs1--s2s3-source_object3-11}

    +

    Source Schema:

    +
    name: expr
     id: expr
     imports:
     - linkml:types
    @@ -1503,12 +1361,9 @@
             name: s3
             range: integer
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -1517,30 +1372,24 @@
             name: derived
             expr: s1 + s2.s3
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 5
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: 5
     s2:
       s3: 6
     
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -derived: 11
    -
    -```
    +
    +
      +
    • Target Object:
    • +
    +
    derived: 11
     
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: expr-derived
    +
    +

    Target Schema (Derived):

    +
    name: expr-derived
     id: expr-derived
     imports:
     - linkml:types
    @@ -1560,14 +1409,10 @@
             name: derived
         tree_root: true
     
    -```
    -
    -### Combo: test\_expr\[s1 + s2.s3.s4-source\_object4-11\] {#combo-test_exprs1--s2s3s4-source_object4-11}
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: expr
    +
    +

    Combo: test_expr[s1 + s2.s3.s4-source_object4-11] {#combo-test_exprs1--s2s3s4-source_object4-11}

    +

    Source Schema:

    +
    name: expr
     id: expr
     imports:
     - linkml:types
    @@ -1600,12 +1445,9 @@
             name: s3
             range: D
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -1614,31 +1456,25 @@
             name: derived
             expr: s1 + s2.s3.s4
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 5
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: 5
     s2:
       s3:
         s4: 6
     
    -```
    -
    --   Target Object:
    +
    +
      +
    • Target Object:
    • +
    +
    derived: 11
     
    -``` {.yaml}
    -derived: 11
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: expr-derived
    +
    +

    Target Schema (Derived):

    +
    name: expr-derived
     id: expr-derived
     imports:
     - linkml:types
    @@ -1658,14 +1494,10 @@
             name: derived
         tree_root: true
     
    -```
    -
    -### Combo: test\_expr\[s1 + s2-source\_object5-ab\] {#combo-test_exprs1--s2-source_object5-ab}
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: expr
    +
    +

    Combo: test_expr[s1 + s2-source_object5-ab] {#combo-test_exprs1--s2-source_object5-ab}

    +

    Source Schema:

    +
    name: expr
     id: expr
     imports:
     - linkml:types
    @@ -1689,12 +1521,9 @@
             range: string
         tree_root: true
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -1703,29 +1532,23 @@
             name: derived
             expr: s1 + s2
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: a
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: a
     s2: b
     
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -derived: ab
    +
    +
      +
    • Target Object:
    • +
    +
    derived: ab
     
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: expr-derived
    +
    +

    Target Schema (Derived):

    +
    name: expr-derived
     id: expr-derived
     imports:
     - linkml:types
    @@ -1745,14 +1568,10 @@
             name: derived
         tree_root: true
     
    -```
    -
    -### Combo: test\_expr\[s1 + s2-source\_object6-target\_value6\] {#combo-test_exprs1--s2-source_object6-target_value6}
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: expr
    +
    +

    Combo: test_expr[s1 + s2-source_object6-target_value6] {#combo-test_exprs1--s2-source_object6-target_value6}

    +

    Source Schema:

    +
    name: expr
     id: expr
     imports:
     - linkml:types
    @@ -1770,20 +1589,17 @@
         attributes:
           s1:
             name: s1
    -        range: string
             multivalued: true
    +        range: string
           s2:
             name: s2
    -        range: string
             multivalued: true
    +        range: string
         tree_root: true
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -1792,33 +1608,27 @@
             name: derived
             expr: s1 + s2
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1:
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1:
     - a
     s2:
     - b
     
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -derived:
    +
    +
      +
    • Target Object:
    • +
    +
    derived:
     - a
     - b
     
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: expr-derived
    +
    +

    Target Schema (Derived):

    +
    name: expr-derived
     id: expr-derived
     imports:
     - linkml:types
    @@ -1838,14 +1648,10 @@
             name: derived
         tree_root: true
     
    -```
    -
    -### Combo: test\_expr\[len(s1)-source\_object7-1\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: expr
    +
    +

    Combo: test_expr[len(s1)-source_object7-1]

    +

    Source Schema:

    +
    name: expr
     id: expr
     imports:
     - linkml:types
    @@ -1863,16 +1669,13 @@
         attributes:
           s1:
             name: s1
    -        range: string
             multivalued: true
    +        range: string
         tree_root: true
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -1881,29 +1684,23 @@
             name: derived
             expr: len(s1)
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1:
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1:
     - a
     
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -derived: 1
    -
    -```
    +
    +
      +
    • Target Object:
    • +
    +
    derived: 1
     
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: expr-derived
    +
    +

    Target Schema (Derived):

    +
    name: expr-derived
     id: expr-derived
     imports:
     - linkml:types
    @@ -1923,14 +1720,10 @@
             name: derived
         tree_root: true
     
    -```
    -
    -### Combo: test\_expr\[s1 \< s2-source\_object8-True\] {#combo-test_exprs1--s2-source_object8-true}
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: expr
    +
    +

    Combo: test_expr[s1 \< s2-source_object8-True] {#combo-test_exprs1--s2-source_object8-true}

    +

    Source Schema:

    +
    name: expr
     id: expr
     imports:
     - linkml:types
    @@ -1954,43 +1747,34 @@
             range: integer
         tree_root: true
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         populated_from: C
         slot_derivations:
           derived:
             name: derived
    -        expr: s1 < s2
    -
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 5
    +        expr: s1 < s2
    +
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: 5
     s2: 6
     
    -```
    +
    +
      +
    • Target Object:
    • +
    +
    derived: true
     
    --   Target Object:
    -
    -``` {.yaml}
    -derived: true
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: expr-derived
    +
    +

    Target Schema (Derived):

    +
    name: expr-derived
     id: expr-derived
     imports:
     - linkml:types
    @@ -2010,40 +1794,35 @@
             name: derived
         tree_root: true
     
    -```
    -
    -Feature Set: test\_simple\_unit\_conversion
    --------------------------------------------
    -
    -Test unit conversion.
    -
    -This test uses a simple source schema with a single class and a single
    +
    +

    Feature Set: test_simple_unit_conversion

    +

    Test unit conversion.

    +

    This test uses a simple source schema with a single class and a single attribute, where the attribute is described using the -[units](https://w3id.org/linkml/units) metaslot. - -The recommended way to describe unit slots in LinkML is with UCUM, but a +units metaslot.

    +

    The recommended way to describe unit slots in LinkML is with UCUM, but a number of other schemes can be used. We explicitly test for some known cases where UCUM uses non-standard units (e.g. Cel, mo), as well as -UCUM-specific syntax (e.g. `m.s-1`) and extensions (e.g. using -annotations like `{Cre}`). - -- **source\_slot**: name of slot in source schema -- **target\_slot**: name of slot in target schema -- **source\_unit**: unit of source slot -- **target\_unit**: unit of target slot -- **source\_value**: magnitude of source slot (to be converted) -- **target\_value**: expected magnitude of target slot (output of - conversion) -- **err**: - -### Combo: test\_simple\_unit\_conversion\[s1-s1-m-cm-ucum\_code-1.0-100.0-None-None\] {#combo-test_simple_unit_conversions1-s1-m-cm-ucum_code-10-1000-none-none} - -Unit Conversion: `1.0` `m` =\> `100.0` `cm` \[with s1\] - -**Source Schema**: - -``` {.yaml} -name: types +UCUM-specific syntax (e.g. m.s-1) and extensions (e.g. using +annotations like {Cre}).

    +

    Developers note: to run this test, the units extension should be +installed:

    +

    poetry install -E units

    +

    This installs the pint framework.

    +
      +
    • source_slot: name of slot in source schema
    • +
    • target_slot: name of slot in target schema
    • +
    • source_unit: unit of source slot
    • +
    • target_unit: unit of target slot
    • +
    • source_value: magnitude of source slot (to be converted)
    • +
    • target_value: expected magnitude of target slot (output of + conversion)
    • +
    • err:
    • +
    +

    Combo: test_simple_unit_conversion[s1-s1-m-cm-ucum_code-1.0-100.0-None-None] {#combo-test_simple_unit_conversions1-s1-m-cm-ucum_code-10-1000-none-none}

    +

    Unit Conversion: 1.0 m => 100.0 cm [with s1]

    +

    Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -2065,12 +1844,9 @@
             unit:
               ucum_code: m
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -2080,28 +1856,22 @@
             unit_conversion:
               target_unit: cm
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 1.0
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1: 100.0
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: 1.0
    +
    +
    +
      +
    • Target Object:
    • +
    +
    s1: 100.0
    +
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -2125,12 +1895,9 @@
             unit:
               ucum_code: cm
     
    -```
    -
    -**Inverted Transformation Specification** (Derived):
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -2143,16 +1910,11 @@
               target_unit_scheme: ucum_code
               source_unit: cm
     
    -```
    -
    -### Combo: test\_simple\_unit\_conversion\[s1-s1-m-cm-symbol-1.0-100.0-None-None\] {#combo-test_simple_unit_conversions1-s1-m-cm-symbol-10-1000-none-none}
    -
    -Unit Conversion: `1.0` `m` =\> `100.0` `cm` \[with s1\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Combo: test_simple_unit_conversion[s1-s1-m-cm-symbol-1.0-100.0-None-None] {#combo-test_simple_unit_conversions1-s1-m-cm-symbol-10-1000-none-none}

    +

    Unit Conversion: 1.0 m => 100.0 cm [with s1]

    +

    Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -2174,12 +1936,9 @@
             unit:
               symbol: m
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -2189,28 +1948,22 @@
             unit_conversion:
               target_unit: cm
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 1.0
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1: 100.0
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: 1.0
    +
    +
    +
      +
    • Target Object:
    • +
    +
    s1: 100.0
    +
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -2234,12 +1987,9 @@
             unit:
               ucum_code: cm
     
    -```
    -
    -**Inverted Transformation Specification** (Derived):
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -2252,16 +2002,11 @@
               target_unit_scheme: symbol
               source_unit: cm
     
    -```
    -
    -### Combo: test\_simple\_unit\_conversion\[s1-s1-m-m-ucum\_code-1.0-1.0-None-None\] {#combo-test_simple_unit_conversions1-s1-m-m-ucum_code-10-10-none-none}
    -
    -Unit Conversion: `1.0` `m` =\> `1.0` `m` \[with s1\]
    -
    -Isomorphic mapping: **input must equal output** **Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Combo: test_simple_unit_conversion[s1-s1-m-m-ucum_code-1.0-1.0-None-None] {#combo-test_simple_unit_conversions1-s1-m-m-ucum_code-10-10-none-none}

    +

    Unit Conversion: 1.0 m => 1.0 m [with s1]

    +

    Isomorphic mapping: input should equal output Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -2283,12 +2028,9 @@
             unit:
               ucum_code: m
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -2298,28 +2040,22 @@
             unit_conversion:
               target_unit: m
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 1.0
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1: 1.0
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: 1.0
    +
    +
    +
      +
    • Target Object:
    • +
    +
    s1: 1.0
    +
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -2343,12 +2079,9 @@
             unit:
               ucum_code: m
     
    -```
    -
    -**Inverted Transformation Specification** (Derived):
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -2361,16 +2094,11 @@
               target_unit_scheme: ucum_code
               source_unit: m
     
    -```
    -
    -### Combo: test\_simple\_unit\_conversion\[s1-s1-a-mo-ucum\_code-10.0-120.0-None-None\] {#combo-test_simple_unit_conversions1-s1-a-mo-ucum_code-100-1200-none-none}
    -
    -Unit Conversion: `10.0` `a` =\> `120.0` `mo` \[with s1\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Combo: test_simple_unit_conversion[s1-s1-a-mo-ucum_code-10.0-120.0-None-None] {#combo-test_simple_unit_conversions1-s1-a-mo-ucum_code-100-1200-none-none}

    +

    Unit Conversion: 10.0 a => 120.0 mo [with s1]

    +

    Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -2392,12 +2120,9 @@
             unit:
               ucum_code: a
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -2407,28 +2132,22 @@
             unit_conversion:
               target_unit: mo
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 10.0
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1: 120.0
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: 10.0
    +
    +
    +
      +
    • Target Object:
    • +
    +
    s1: 120.0
    +
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -2452,12 +2171,9 @@
             unit:
               ucum_code: mo
     
    -```
    -
    -**Inverted Transformation Specification** (Derived):
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -2470,16 +2186,11 @@
               target_unit_scheme: ucum_code
               source_unit: mo
     
    -```
    -
    -### Combo: test\_simple\_unit\_conversion\[s1-s1-a-mo-symbol-10.0-None-UndefinedUnitError-None\] {#combo-test_simple_unit_conversions1-s1-a-mo-symbol-100-none-undefineduniterror-none}
    -
    -Unit Conversion: `10.0` `a` =\> `None` `mo` \[with s1\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Combo: test_simple_unit_conversion[s1-s1-a-mo-symbol-10.0-None-UndefinedUnitError-None] {#combo-test_simple_unit_conversions1-s1-a-mo-symbol-100-none-undefineduniterror-none}

    +

    Unit Conversion: 10.0 a => None mo [with s1]

    +

    Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -2501,12 +2212,9 @@
             unit:
               symbol: a
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -2516,31 +2224,24 @@
             unit_conversion:
               target_unit: mo
     
    -```
    -
    -**Object Transformation**:
    -
    -**Expected Error**: UndefinedUnitError
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 10.0
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -null
    +
    +

    Object Transformation:

    +

    Expected Error: UndefinedUnitError

    +
      +
    • Source Object:
    • +
    +
    s1: 10.0
    +
    +
    +
      +
    • Target Object:
    • +
    +
    null
     ...
     
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -2564,16 +2265,11 @@
             unit:
               ucum_code: mo
     
    -```
    -
    -### Combo: test\_simple\_unit\_conversion\[s1-s1-m-ml-ucum\_code-1.0-None-DimensionalityError-None\] {#combo-test_simple_unit_conversions1-s1-m-ml-ucum_code-10-none-dimensionalityerror-none}
    -
    -Unit Conversion: `1.0` `m` =\> `None` `ml` \[with s1\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Combo: test_simple_unit_conversion[s1-s1-m-ml-ucum_code-1.0-None-DimensionalityError-None] {#combo-test_simple_unit_conversions1-s1-m-ml-ucum_code-10-none-dimensionalityerror-none}

    +

    Unit Conversion: 1.0 m => None ml [with s1]

    +

    Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -2595,12 +2291,9 @@
             unit:
               ucum_code: m
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -2610,31 +2303,24 @@
             unit_conversion:
               target_unit: ml
     
    -```
    -
    -**Object Transformation**:
    -
    -**Expected Error**: DimensionalityError
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 1.0
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -null
    +
    +

    Object Transformation:

    +

    Expected Error: DimensionalityError

    +
      +
    • Source Object:
    • +
    +
    s1: 1.0
    +
    +
    +
      +
    • Target Object:
    • +
    +
    null
     ...
     
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -2658,16 +2344,11 @@
             unit:
               ucum_code: ml
     
    -```
    -
    -### Combo: test\_simple\_unit\_conversion\[s1-s1-m-pinknoodles-ucum\_code-1.0-None-UndefinedUnitError-None\] {#combo-test_simple_unit_conversions1-s1-m-pinknoodles-ucum_code-10-none-undefineduniterror-none}
    -
    -Unit Conversion: `1.0` `m` =\> `None` `pinknoodles` \[with s1\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Combo: test_simple_unit_conversion[s1-s1-m-pinknoodles-ucum_code-1.0-None-UndefinedUnitError-None] {#combo-test_simple_unit_conversions1-s1-m-pinknoodles-ucum_code-10-none-undefineduniterror-none}

    +

    Unit Conversion: 1.0 m => None pinknoodles [with s1]

    +

    Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -2689,12 +2370,9 @@
             unit:
               ucum_code: m
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -2702,33 +2380,26 @@
             name: s1
             populated_from: s1
             unit_conversion:
    -          target_unit: pinknoodles
    -
    -```
    -
    -**Object Transformation**:
    -
    -**Expected Error**: UndefinedUnitError
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 1.0
    -
    -```
    -
    --   Target Object:
    +          target_unit: pinknoodles
     
    -``` {.yaml}
    -null
    +
    +

    Object Transformation:

    +

    Expected Error: UndefinedUnitError

    +
      +
    • Source Object:
    • +
    +
    s1: 1.0
    +
    +
    +
      +
    • Target Object:
    • +
    +
    null
     ...
     
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -2752,16 +2423,11 @@
             unit:
               ucum_code: pinknoodles
     
    -```
    -
    -### Combo: test\_simple\_unit\_conversion\[s1-s1-ml-m-ucum\_code-1.0-None-DimensionalityError-None\] {#combo-test_simple_unit_conversions1-s1-ml-m-ucum_code-10-none-dimensionalityerror-none}
    -
    -Unit Conversion: `1.0` `ml` =\> `None` `m` \[with s1\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Combo: test_simple_unit_conversion[s1-s1-ml-m-ucum_code-1.0-None-DimensionalityError-None] {#combo-test_simple_unit_conversions1-s1-ml-m-ucum_code-10-none-dimensionalityerror-none}

    +

    Unit Conversion: 1.0 ml => None m [with s1]

    +

    Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -2783,12 +2449,9 @@
             unit:
               ucum_code: ml
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -2798,31 +2461,24 @@
             unit_conversion:
               target_unit: m
     
    -```
    -
    -**Object Transformation**:
    -
    -**Expected Error**: DimensionalityError
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 1.0
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -null
    +
    +

    Object Transformation:

    +

    Expected Error: DimensionalityError

    +
      +
    • Source Object:
    • +
    +
    s1: 1.0
    +
    +
    +
      +
    • Target Object:
    • +
    +
    null
     ...
     
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -2846,16 +2502,11 @@
             unit:
               ucum_code: m
     
    -```
    -
    -### Combo: test\_simple\_unit\_conversion\[s1-s1-pinknoodles-m-ucum\_code-1.0-None-UndefinedUnitError-None\] {#combo-test_simple_unit_conversions1-s1-pinknoodles-m-ucum_code-10-none-undefineduniterror-none}
    -
    -Unit Conversion: `1.0` `pinknoodles` =\> `None` `m` \[with s1\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Combo: test_simple_unit_conversion[s1-s1-pinknoodles-m-ucum_code-1.0-None-UndefinedUnitError-None] {#combo-test_simple_unit_conversions1-s1-pinknoodles-m-ucum_code-10-none-undefineduniterror-none}

    +

    Unit Conversion: 1.0 pinknoodles => None m [with s1]

    +

    Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -2877,12 +2528,9 @@
             unit:
               ucum_code: pinknoodles
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -2892,31 +2540,24 @@
             unit_conversion:
               target_unit: m
     
    -```
    -
    -**Object Transformation**:
    -
    -**Expected Error**: UndefinedUnitError
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 1.0
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -null
    +
    +

    Object Transformation:

    +

    Expected Error: UndefinedUnitError

    +
      +
    • Source Object:
    • +
    +
    s1: 1.0
    +
    +
    +
      +
    • Target Object:
    • +
    +
    null
     ...
     
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -2940,16 +2581,11 @@
             unit:
               ucum_code: m
     
    -```
    -
    -### Combo: test\_simple\_unit\_conversion\[s1-s1-m/s-cm/s-ucum\_code-1.0-100.0-None-None\] {#combo-test_simple_unit_conversions1-s1-ms-cms-ucum_code-10-1000-none-none}
    -
    -Unit Conversion: `1.0` `m/s` =\> `100.0` `cm/s` \[with s1\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Combo: test_simple_unit_conversion[s1-s1-m/s-cm/s-ucum_code-1.0-100.0-None-None] {#combo-test_simple_unit_conversions1-s1-ms-cms-ucum_code-10-1000-none-none}

    +

    Unit Conversion: 1.0 m/s => 100.0 cm/s [with s1]

    +

    Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -2971,12 +2607,9 @@
             unit:
               ucum_code: m/s
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -2986,28 +2619,22 @@
             unit_conversion:
               target_unit: cm/s
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 1.0
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1: 100.0
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: 1.0
    +
    +
    +
      +
    • Target Object:
    • +
    +
    s1: 100.0
    +
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -3031,12 +2658,9 @@
             unit:
               ucum_code: cm/s
     
    -```
    -
    -**Inverted Transformation Specification** (Derived):
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -3049,16 +2673,11 @@
               target_unit_scheme: ucum_code
               source_unit: cm/s
     
    -```
    -
    -### Combo: test\_simple\_unit\_conversion\[s1-s1-m.s-1-cm.s-1-ucum\_code-1.0-100.0-None-None\] {#combo-test_simple_unit_conversions1-s1-ms-1-cms-1-ucum_code-10-1000-none-none}
    -
    -Unit Conversion: `1.0` `m.s-1` =\> `100.0` `cm.s-1` \[with s1\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Combo: test_simple_unit_conversion[s1-s1-m.s-1-cm.s-1-ucum_code-1.0-100.0-None-None] {#combo-test_simple_unit_conversions1-s1-ms-1-cms-1-ucum_code-10-1000-none-none}

    +

    Unit Conversion: 1.0 m.s-1 => 100.0 cm.s-1 [with s1]

    +

    Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -3080,12 +2699,9 @@
             unit:
               ucum_code: m.s-1
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -3095,28 +2711,22 @@
             unit_conversion:
               target_unit: cm.s-1
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 1.0
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1: 100.0
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: 1.0
    +
    +
    +
      +
    • Target Object:
    • +
    +
    s1: 100.0
    +
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -3140,12 +2750,9 @@
             unit:
               ucum_code: cm.s-1
     
    -```
    -
    -**Inverted Transformation Specification** (Derived):
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -3158,19 +2765,13 @@
               target_unit_scheme: ucum_code
               source_unit: cm.s-1
     
    -```
    -
    -### Combo: test\_simple\_unit\_conversion\[s1-s1-g.m2-1-kg.m2-1-ucum\_code-1.0-0.001-None-https://github.com/dalito/ucumvert/issues/8\] {#combo-test_simple_unit_conversions1-s1-gm2-1-kgm2-1-ucum_code-10-0001-none-httpsgithubcomdalitoucumvertissues8}
    -
    -s\#\#\# Combo:
    -test\_simple\_unit\_conversion\[height\_in\_m-height\_in\_cm-m-cm-ucum\_code-1.0-100.0-None-None\]
    -
    -Unit Conversion: `1.0` `m` =\> `100.0` `cm` \[with height\_in\_m\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Combo: test_simple_unit_conversion[s1-s1-g.m2-1-kg.m2-1-ucum_code-1.0-0.001-None-https://github.com/dalito/ucumvert/issues/8] {#combo-test_simple_unit_conversions1-s1-gm2-1-kgm2-1-ucum_code-10-0001-none-httpsgithubcomdalitoucumvertissues8}

    +

    s### Combo: +test_simple_unit_conversion[height_in_m-height_in_cm-m-cm-ucum_code-1.0-100.0-None-None]

    +

    Unit Conversion: 1.0 m => 100.0 cm [with height_in_m]

    +

    Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -3192,12 +2793,9 @@
             unit:
               ucum_code: m
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -3207,28 +2805,22 @@
             unit_conversion:
               target_unit: cm
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -height_in_m: 1.0
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -height_in_cm: 100.0
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    height_in_m: 1.0
    +
    +
    +
      +
    • Target Object:
    • +
    +
    height_in_cm: 100.0
    +
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -3252,12 +2844,9 @@
             unit:
               ucum_code: cm
     
    -```
    -
    -**Inverted Transformation Specification** (Derived):
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -3270,17 +2859,11 @@
               target_unit_scheme: ucum_code
               source_unit: cm
     
    -```
    -
    -### Combo: test\_simple\_unit\_conversion\[s1-s1-m\[H2O\]{35Cel}-m\[H2O\]{35Cel}-ucum\_code-1.0-1.0-None-None\] {#combo-test_simple_unit_conversions1-s1-mh2o35cel-mh2o35cel-ucum_code-10-10-none-none}
    -
    -Unit Conversion: `1.0` `m[H2O]{35Cel}` =\> `1.0` `m[H2O]{35Cel}` \[with
    -s1\]
    -
    -Isomorphic mapping: **input must equal output** **Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Combo: test_simple_unit_conversion[s1-s1-m[H2O]{35Cel}-m[H2O]{35Cel}-ucum_code-1.0-1.0-None-None] {#combo-test_simple_unit_conversions1-s1-mh2o35cel-mh2o35cel-ucum_code-10-10-none-none}

    +

    Unit Conversion: 1.0 m[H2O]{35Cel} => 1.0 m[H2O]{35Cel} [with s1]

    +

    Isomorphic mapping: input should equal output Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -3302,12 +2885,9 @@
             unit:
               ucum_code: m[H2O]{35Cel}
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -3317,28 +2897,22 @@
             unit_conversion:
               target_unit: m[H2O]{35Cel}
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 1.0
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1: 1.0
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: 1.0
    +
    +
    +
      +
    • Target Object:
    • +
    +
    s1: 1.0
    +
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -3362,12 +2936,9 @@
             unit:
               ucum_code: m[H2O]{35Cel}
     
    -```
    -
    -**Inverted Transformation Specification** (Derived):
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -3380,33 +2951,20 @@
               target_unit_scheme: ucum_code
               source_unit: m[H2O]{35Cel}
     
    -```
    -
    -Feature Set: test\_complex\_unit\_conversion
    ---------------------------------------------
    -
    -Test unit conversion, from complex object to simple scalar.
    -
    -An example complex object would be an object with separate attributes
    -for representing magnitude (value) and unit.
    -
    -For example `magnitude: 1.0, unit: "m"`
    -
    --   **source\_unit**: unit of source slot
    --   **target\_unit**: unit of target slot
    --   **source\_value**: magnitude of source slot (to be converted)
    --   **target\_value**: expected magnitude of target slot (output of
    -    conversion)
    --   **roundtrip\_object**: expected value of passing target object back
    -    through inverted transformation
    --   **err**: True if expected to raise an Error
    -
    -### Combo: test\_complex\_unit\_conversion\[m-cm-1.0-100.0-roundtrip\_object0-None\] {#combo-test_complex_unit_conversionm-cm-10-1000-roundtrip_object0-none}
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Feature Set: test_complex_unit_conversion

    +

    Test unit conversion, from complex object to simple scalar.

    +
      +
    • source_unit:
    • +
    • target_unit:
    • +
    • source_value:
    • +
    • target_value:
    • +
    • roundtrip_object:
    • +
    • err:
    • +
    +

    Combo: test_complex_unit_conversion[m-cm-1.0-100.0-roundtrip_object0-None] {#combo-test_complex_unit_conversionm-cm-10-1000-roundtrip_object0-none}

    +

    Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -3436,12 +2994,9 @@
             range: Q
         tree_root: true
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       D:
         name: D
         populated_from: C
    @@ -3454,30 +3009,24 @@
               source_unit_slot: unit
               source_magnitude_slot: magnitude
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -q:
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    q:
       magnitude: 1.0
       unit: m
     
    -```
    -
    --   Target Object:
    +
    +
      +
    • Target Object:
    • +
    +
    q_in_cm: 100.0
     
    -``` {.yaml}
    -q_in_cm: 100.0
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -3502,12 +3051,9 @@
               ucum_code: cm
         tree_root: true
     
    -```
    -
    -**Inverted Transformation Specification** (Derived):
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       C:
         name: C
         populated_from: D
    @@ -3520,14 +3066,10 @@
               target_unit_slot: unit
               target_magnitude_slot: magnitude
     
    -```
    -
    -### Combo: test\_complex\_unit\_conversion\[cm-cm-100.0-100.0-roundtrip\_object1-None\] {#combo-test_complex_unit_conversioncm-cm-1000-1000-roundtrip_object1-none}
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Combo: test_complex_unit_conversion[cm-cm-100.0-100.0-roundtrip_object1-None] {#combo-test_complex_unit_conversioncm-cm-1000-1000-roundtrip_object1-none}

    +

    Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -3557,12 +3099,9 @@
             range: Q
         tree_root: true
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       D:
         name: D
         populated_from: C
    @@ -3575,30 +3114,24 @@
               source_unit_slot: unit
               source_magnitude_slot: magnitude
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -q:
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    q:
       magnitude: 100.0
       unit: cm
     
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -q_in_cm: 100.0
    -
    -```
    +
    +
      +
    • Target Object:
    • +
    +
    q_in_cm: 100.0
     
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -3623,12 +3156,9 @@
               ucum_code: cm
         tree_root: true
     
    -```
    -
    -**Inverted Transformation Specification** (Derived):
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       C:
         name: C
         populated_from: D
    @@ -3641,14 +3171,10 @@
               target_unit_slot: unit
               target_magnitude_slot: magnitude
     
    -```
    -
    -### Combo: test\_complex\_unit\_conversion\[cm-ml-100.0-None-None-DimensionalityError\] {#combo-test_complex_unit_conversioncm-ml-1000-none-none-dimensionalityerror}
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Combo: test_complex_unit_conversion[cm-ml-100.0-None-None-DimensionalityError] {#combo-test_complex_unit_conversioncm-ml-1000-none-none-dimensionalityerror}

    +

    Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -3678,12 +3204,9 @@
             range: Q
         tree_root: true
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       D:
         name: D
         populated_from: C
    @@ -3696,33 +3219,26 @@
               source_unit_slot: unit
               source_magnitude_slot: magnitude
     
    -```
    -
    -**Object Transformation**:
    -
    -**Expected Error**: DimensionalityError
    -
    --   Source Object:
    -
    -``` {.yaml}
    -q:
    +
    +

    Object Transformation:

    +

    Expected Error: DimensionalityError

    +
      +
    • Source Object:
    • +
    +
    q:
       magnitude: 100.0
       unit: cm
     
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -null
    +
    +
      +
    • Target Object:
    • +
    +
    null
     ...
     
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -3747,14 +3263,10 @@
               ucum_code: ml
         tree_root: true
     
    -```
    -
    -### Combo: test\_complex\_unit\_conversion\[cm-pinknoodles-100.0-None-None-UndefinedUnitError\] {#combo-test_complex_unit_conversioncm-pinknoodles-1000-none-none-undefineduniterror}
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Combo: test_complex_unit_conversion[cm-pinknoodles-100.0-None-None-UndefinedUnitError] {#combo-test_complex_unit_conversioncm-pinknoodles-1000-none-none-undefineduniterror}

    +

    Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -3784,12 +3296,9 @@
             range: Q
         tree_root: true
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       D:
         name: D
         populated_from: C
    @@ -3802,33 +3311,26 @@
               source_unit_slot: unit
               source_magnitude_slot: magnitude
     
    -```
    -
    -**Object Transformation**:
    -
    -**Expected Error**: UndefinedUnitError
    -
    --   Source Object:
    -
    -``` {.yaml}
    -q:
    +
    +

    Object Transformation:

    +

    Expected Error: UndefinedUnitError

    +
      +
    • Source Object:
    • +
    +
    q:
       magnitude: 100.0
       unit: cm
     
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -null
    +
    +
      +
    • Target Object:
    • +
    +
    null
     ...
     
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -3853,37 +3355,28 @@
               ucum_code: pinknoodles
         tree_root: true
     
    -```
    -
    -Feature Set: test\_stringify
    -----------------------------
    -
    -Test compaction of multivalued slots into a string.
    -
    -Stringification is primarily intended for mapping from complex nested
    +
    +

    Feature Set: test_stringify

    +

    Test compaction of multivalued slots into a string.

    +

    Stringification is primarily intended for mapping from complex nested formats to simple tabular TSV formats, where some of the following -methodologies can be used: - -- flattening lists using an (internal) delimiter -- flattening lists or more complex objects using JSON or YAML - -For example, `["a", "b"]` =\> `"a,b"` - -As a convention we use `s1_verbatim` as a slot/attribute name for the -stringified form. - -- **syntax**: SerializationSyntaxType -- **delimiter**: delimiter to use in stringification -- **source\_value**: source value (a list) -- **target\_value**: expected value of slot in target object (a - string) - -### Combo: test\_stringify\[None-,-source\_value0-a,b\] - -**Source Schema**: +methodologies can be used:

    +
      +
    • flattening lists using an (internal) delimiter
    • +
    • flattening lists or more complex objects using JSON or YAML
    • +
    + -``` {.yaml} -name: types +
      +
    • syntax: SerializationSyntaxType
    • +
    • delimiter: delimiter to use in stringification
    • +
    • source_value: source value (a list)
    • +
    • target_value: expected value of slot in target object (a + string)
    • +
    +

    Combo: test_stringify[None-,-source_value0-a,b]

    +

    Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -3901,15 +3394,12 @@
         attributes:
           s1:
             name: s1
    -        range: string
             multivalued: true
    +        range: string
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       D:
         name: D
         populated_from: C
    @@ -3920,30 +3410,24 @@
             stringification:
               delimiter: ','
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1:
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1:
     - a
     - b
     
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1_verbatim: a,b
    +
    +
      +
    • Target Object:
    • +
    +
    s1_verbatim: a,b
     
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -3961,17 +3445,14 @@
         attributes:
           s1_verbatim:
             name: s1_verbatim
    +        multivalued: false
             domain_of:
             - C
             range: string
    -        multivalued: false
     
    -```
    -
    -**Inverted Transformation Specification** (Derived):
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       C:
         name: C
         populated_from: D
    @@ -3983,18 +3464,12 @@
               delimiter: ','
               reversed: true
     
    -```
    -
    -**Compiled Specification (SQLCompiler)**:
    -
    -INSERT INTO D SELECT s1\_verbatim AS STRING\_AGG(s1, \',\') FROM D;
    -
    -### Combo: test\_stringify\[None-\|-source\_value1-a\|b\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Compiled Specification (SQLCompiler):

    +

    INSERT INTO D SELECT s1_verbatim AS STRING_AGG(s1, \',\') FROM D;

    +

    Combo: test_stringify[None-|-source_value1-a|b]

    +

    Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -4012,15 +3487,12 @@
         attributes:
           s1:
             name: s1
    -        range: string
             multivalued: true
    +        range: string
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       D:
         name: D
         populated_from: C
    @@ -4031,30 +3503,24 @@
             stringification:
               delimiter: '|'
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1:
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1:
     - a
     - b
     
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1_verbatim: a|b
    +
    +
      +
    • Target Object:
    • +
    +
    s1_verbatim: a|b
     
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -4072,17 +3538,14 @@
         attributes:
           s1_verbatim:
             name: s1_verbatim
    +        multivalued: false
             domain_of:
             - C
             range: string
    -        multivalued: false
     
    -```
    -
    -**Inverted Transformation Specification** (Derived):
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       C:
         name: C
         populated_from: D
    @@ -4094,18 +3557,12 @@
               delimiter: '|'
               reversed: true
     
    -```
    -
    -**Compiled Specification (SQLCompiler)**:
    -
    -INSERT INTO D SELECT s1\_verbatim AS STRING\_AGG(s1, \'\|\') FROM D;
    -
    -### Combo: test\_stringify\[None-\|-source\_value2-a\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Compiled Specification (SQLCompiler):

    +

    INSERT INTO D SELECT s1_verbatim AS STRING_AGG(s1, \'|\') FROM D;

    +

    Combo: test_stringify[None-|-source_value2-a]

    +

    Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -4123,15 +3580,12 @@
         attributes:
           s1:
             name: s1
    -        range: string
             multivalued: true
    +        range: string
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       D:
         name: D
         populated_from: C
    @@ -4142,29 +3596,23 @@
             stringification:
               delimiter: '|'
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1:
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1:
     - a
     
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1_verbatim: a
    +
    +
      +
    • Target Object:
    • +
    +
    s1_verbatim: a
     
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -4182,17 +3630,14 @@
         attributes:
           s1_verbatim:
             name: s1_verbatim
    +        multivalued: false
             domain_of:
             - C
             range: string
    -        multivalued: false
     
    -```
    -
    -**Inverted Transformation Specification** (Derived):
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       C:
         name: C
         populated_from: D
    @@ -4204,18 +3649,12 @@
               delimiter: '|'
               reversed: true
     
    -```
    -
    -**Compiled Specification (SQLCompiler)**:
    -
    -INSERT INTO D SELECT s1\_verbatim AS STRING\_AGG(s1, \'\|\') FROM D;
    -
    -### Combo: test\_stringify\[None-\|-source\_value3-\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Compiled Specification (SQLCompiler):

    +

    INSERT INTO D SELECT s1_verbatim AS STRING_AGG(s1, \'|\') FROM D;

    +

    Combo: test_stringify[None-|-source_value3-]

    +

    Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -4233,15 +3672,12 @@
         attributes:
           s1:
             name: s1
    -        range: string
             multivalued: true
    +        range: string
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       D:
         name: D
         populated_from: C
    @@ -4252,28 +3688,22 @@
             stringification:
               delimiter: '|'
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -{}
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1_verbatim: ''
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    {}
    +
    +
    +
      +
    • Target Object:
    • +
    +
    s1_verbatim: ''
    +
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -4291,17 +3721,14 @@
         attributes:
           s1_verbatim:
             name: s1_verbatim
    +        multivalued: false
             domain_of:
             - C
             range: string
    -        multivalued: false
    -
    -```
    -
    -**Inverted Transformation Specification** (Derived):
     
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       C:
         name: C
         populated_from: D
    @@ -4309,22 +3736,16 @@
           s1:
             name: s1
             populated_from: s1_verbatim
    -        stringification:
    -          delimiter: '|'
    -          reversed: true
    -
    -```
    -
    -**Compiled Specification (SQLCompiler)**:
    -
    -INSERT INTO D SELECT s1\_verbatim AS STRING\_AGG(s1, \'\|\') FROM D;
    -
    -### Combo: test\_stringify\[JSON-None-source\_value4-\[\"a\", \"b\"\]\]
    -
    -**Source Schema**:
    +        stringification:
    +          delimiter: '|'
    +          reversed: true
     
    -``` {.yaml}
    -name: types
    +
    +

    Compiled Specification (SQLCompiler):

    +

    INSERT INTO D SELECT s1_verbatim AS STRING_AGG(s1, \'|\') FROM D;

    +

    Combo: test_stringify[JSON-None-source_value4-[\"a\", \"b\"]]

    +

    Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -4342,15 +3763,12 @@
         attributes:
           s1:
             name: s1
    -        range: string
             multivalued: true
    +        range: string
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       D:
         name: D
         populated_from: C
    @@ -4361,30 +3779,24 @@
             stringification:
               syntax: JSON
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1:
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1:
     - a
     - b
     
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1_verbatim: '["a", "b"]'
    +
    +
      +
    • Target Object:
    • +
    +
    s1_verbatim: '["a", "b"]'
     
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -4402,17 +3814,14 @@
         attributes:
           s1_verbatim:
             name: s1_verbatim
    +        multivalued: false
             domain_of:
             - C
             range: string
    -        multivalued: false
     
    -```
    -
    -**Inverted Transformation Specification** (Derived):
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       C:
         name: C
         populated_from: D
    @@ -4424,18 +3833,12 @@
               reversed: true
               syntax: JSON
     
    -```
    -
    -**Compiled Specification (SQLCompiler)**:
    -
    -INSERT INTO D SELECT s1\_verbatim AS CAST(s1 AS TEXT) FROM D;
    -
    -### Combo: test\_stringify\[JSON-None-source\_value5-\[\]\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Compiled Specification (SQLCompiler):

    +

    INSERT INTO D SELECT s1_verbatim AS CAST(s1 AS TEXT) FROM D;

    +

    Combo: test_stringify[JSON-None-source_value5-[]]

    +

    Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -4453,15 +3856,12 @@
         attributes:
           s1:
             name: s1
    -        range: string
             multivalued: true
    +        range: string
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       D:
         name: D
         populated_from: C
    @@ -4472,28 +3872,22 @@
             stringification:
               syntax: JSON
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -{}
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1_verbatim: '[]'
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    {}
    +
    +
    +
      +
    • Target Object:
    • +
    +
    s1_verbatim: '[]'
    +
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -4511,17 +3905,14 @@
         attributes:
           s1_verbatim:
             name: s1_verbatim
    +        multivalued: false
             domain_of:
             - C
             range: string
    -        multivalued: false
    -
    -```
    -
    -**Inverted Transformation Specification** (Derived):
     
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       C:
         name: C
         populated_from: D
    @@ -4533,18 +3924,12 @@
               reversed: true
               syntax: JSON
     
    -```
    -
    -**Compiled Specification (SQLCompiler)**:
    -
    -INSERT INTO D SELECT s1\_verbatim AS CAST(s1 AS TEXT) FROM D;
    -
    -### Combo: test\_stringify\[YAML-None-source\_value6-\[a, b\]\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Compiled Specification (SQLCompiler):

    +

    INSERT INTO D SELECT s1_verbatim AS CAST(s1 AS TEXT) FROM D;

    +

    Combo: test_stringify[YAML-None-source_value6-[a, b]]

    +

    Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -4562,15 +3947,12 @@
         attributes:
           s1:
             name: s1
    -        range: string
             multivalued: true
    +        range: string
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       D:
         name: D
         populated_from: C
    @@ -4581,30 +3963,24 @@
             stringification:
               syntax: YAML
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1:
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1:
     - a
     - b
     
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1_verbatim: '[a, b]'
    -
    -```
    -
    -**Target Schema (Derived)**:
    +
    +
      +
    • Target Object:
    • +
    +
    s1_verbatim: '[a, b]'
     
    -``` {.yaml}
    -name: types-derived
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -4622,17 +3998,14 @@
         attributes:
           s1_verbatim:
             name: s1_verbatim
    +        multivalued: false
             domain_of:
             - C
             range: string
    -        multivalued: false
    -
    -```
    -
    -**Inverted Transformation Specification** (Derived):
     
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       C:
         name: C
         populated_from: D
    @@ -4644,30 +4017,21 @@
               reversed: true
               syntax: YAML
     
    -```
    -
    -**Compiled Specification (SQLCompiler)**:
    -
    -INSERT INTO D SELECT s1\_verbatim AS s1 FROM D;
    -
    -Feature Set: test\_isomorphic
    ------------------------------
    -
    -Test mapping a schema to an identical schema (i.e copy).
    -
    -This also tests for the ability to recursively descend a nested
    -structure.
    -
    --   **source\_object**:
    --   **use\_expr**:
    --   **supply\_source\_schema**: TODO: always True for now
    -
    -### Combo: test\_isomorphic\[True-True-source\_object0\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: isomorphic
    +
    +

    Compiled Specification (SQLCompiler):

    +

    INSERT INTO D SELECT s1_verbatim AS s1 FROM D;

    +

    Feature Set: test_isomorphic

    +

    Test mapping a schema to an identical schema (i.e copy).

    +

    This also tests for the ability to recursively descend a nested +structure.

    +
      +
    • source_object:
    • +
    • use_expr:
    • +
    • supply_source_schema: TODO: always True for now
    • +
    +

    Combo: test_isomorphic[True-True-source_object0]

    +

    Source Schema:

    +
    name: isomorphic
     id: isomorphic
     imports:
     - linkml:types
    @@ -4685,8 +4049,8 @@
         attributes:
           c_list:
             name: c_list
    -        range: C
             multivalued: true
    +        range: C
           d:
             name: d
             range: D
    @@ -4707,12 +4071,9 @@
             name: s3
             range: string
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       Container:
         name: Container
         populated_from: Container
    @@ -4743,14 +4104,12 @@
             name: s3
             expr: s3
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -c_list:
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    c_list:
     - s1: a
       s2: b
     - s1: c
    @@ -4758,12 +4117,11 @@
     d:
       s3: e
     
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -c_list:
    +
    +
      +
    • Target Object:
    • +
    +
    c_list:
     - s1: a
       s2: b
     - s1: c
    @@ -4771,12 +4129,9 @@
     d:
       s3: e
     
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: isomorphic-derived
    +
    +

    Target Schema (Derived):

    +
    name: isomorphic-derived
     id: isomorphic-derived
     imports:
     - linkml:types
    @@ -4794,10 +4149,10 @@
         attributes:
           c_list:
             name: c_list
    +        multivalued: true
             domain_of:
             - Container
             range: C
    -        multivalued: true
           d:
             name: d
             domain_of:
    @@ -4826,12 +4181,9 @@
             - D
             range: string
     
    -```
    -
    -**Inverted Transformation Specification** (Derived):
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       Container:
         name: Container
         populated_from: Container
    @@ -4862,14 +4214,10 @@
             name: s3
             populated_from: s3
     
    -```
    -
    -### Combo: test\_isomorphic\[True-False-source\_object0\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: isomorphic
    +
    +

    Combo: test_isomorphic[True-False-source_object0]

    +

    Source Schema:

    +
    name: isomorphic
     id: isomorphic
     imports:
     - linkml:types
    @@ -4887,8 +4235,8 @@
         attributes:
           c_list:
             name: c_list
    -        range: C
             multivalued: true
    +        range: C
           d:
             name: d
             range: D
    @@ -4909,12 +4257,9 @@
             name: s3
             range: string
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       Container:
         name: Container
         populated_from: Container
    @@ -4945,14 +4290,12 @@
             name: s3
             populated_from: s3
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -c_list:
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    c_list:
     - s1: a
       s2: b
     - s1: c
    @@ -4960,12 +4303,11 @@
     d:
       s3: e
     
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -c_list:
    +
    +
      +
    • Target Object:
    • +
    +
    c_list:
     - s1: a
       s2: b
     - s1: c
    @@ -4973,12 +4315,9 @@
     d:
       s3: e
     
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: isomorphic-derived
    +
    +

    Target Schema (Derived):

    +
    name: isomorphic-derived
     id: isomorphic-derived
     imports:
     - linkml:types
    @@ -4996,10 +4335,10 @@
         attributes:
           c_list:
             name: c_list
    +        multivalued: true
             domain_of:
             - Container
             range: C
    -        multivalued: true
           d:
             name: d
             domain_of:
    @@ -5028,12 +4367,9 @@
             - D
             range: string
     
    -```
    -
    -**Inverted Transformation Specification** (Derived):
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       Container:
         name: Container
         populated_from: Container
    @@ -5064,23 +4400,17 @@
             name: s3
             populated_from: s3
     
    -```
    -
    -Feature Set: test\_join
    ------------------------
    -
    -Test joining two objects into a single object, aka denormalization.
    -
    --   **source\_object**: normalized source object
    --   **target\_object**: denormalized target object
    --   **inlined**: True if the source objects are inlined
    -
    -### Combo: test\_join\[source\_object0-target\_object0-True\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Feature Set: test_join

    +

    Test joining two objects into a single object, aka denormalization.

    +
      +
    • source_object: normalized source object
    • +
    • target_object: denormalized target object
    • +
    • inlined: True if the source objects are inlined
    • +
    +

    Combo: test_join[source_object0-target_object0-True]

    +

    Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -5116,12 +4446,9 @@
             name: name
             range: string
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       R:
         name: R
         populated_from: R
    @@ -5139,36 +4466,30 @@
             name: s2_name
             expr: s2.name
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1:
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1:
       id: x1
       name: foo
     s2:
       id: x2
       name: bar
     
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1_id: x1
    +
    +
      +
    • Target Object:
    • +
    +
    s1_id: x1
     s1_name: foo
     s2_id: x2
     s2_name: bar
     
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -5194,14 +4515,10 @@
             name: s2_name
         tree_root: true
     
    -```
    -
    -### Combo: test\_join\[source\_object0-target\_object0-False\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: types
    +
    +

    Combo: test_join[source_object0-target_object0-False]

    +

    Source Schema:

    +
    name: types
     id: types
     imports:
     - linkml:types
    @@ -5241,21 +4558,18 @@
         attributes:
           r_list:
             name: r_list
    -        range: R
             multivalued: true
    +        range: R
           e_list:
             name: e_list
    -        range: E
             multivalued: true
    +        range: E
             inlined_as_list: true
         tree_root: true
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       R:
         name: R
         populated_from: R
    @@ -5280,14 +4594,12 @@
             name: r_list
             populated_from: r_list
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -r_list:
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    r_list:
     - s1: x1
       s2: x2
     e_list:
    @@ -5296,23 +4608,19 @@
     - id: x2
       name: bar
     
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -r_list:
    +
    +
      +
    • Target Object:
    • +
    +
    r_list:
     - s1_id: x1
       s1_name: foo
       s2_id: x2
       s2_name: bar
     
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: types-derived
    +
    +

    Target Schema (Derived):

    +
    name: types-derived
     id: types-derived
     imports:
     - linkml:types
    @@ -5342,38 +4650,32 @@
         attributes:
           r_list:
             name: r_list
    +        multivalued: true
             domain_of:
             - Container
             range: R
    -        multivalued: true
         tree_root: true
     
    -```
    -
    -Feature Set: test\_map\_enum
    -----------------------------
    -
    -Test mapping between enum values.
    -
    -Currently this only supports simple dictionary-style mapping between
    +
    +

    Feature Set: test_map_enum

    +

    Test mapping between enum values.

    +

    Currently this only supports simple dictionary-style mapping between permissible values, akin to SSSOM, but in future additional expressivity -will be supported, including: - -- mapping ranges to categorical values -- boolean/branching logic - +will be supported, including:

    +
      +
    • mapping ranges to categorical values
    • +
    • boolean/branching logic
    • +
    -- **source\_value**: source enum permissible value to be mapped -- **mapping**: mapping from source to target enum permissible values -- **target\_value**: expected target enum permissible value - -### Combo: test\_map\_enum\[A-mapping0-B-False\] - -**Source Schema**: - -``` {.yaml} -name: enums +
      +
    • source_value:
    • +
    • mapping:
    • +
    • target_value:
    • +
    +

    Combo: test_map_enum[A-mapping0-B-False]

    +

    Source Schema:

    +
    name: enums
     id: enums
     imports:
     - linkml:types
    @@ -5403,12 +4705,9 @@
             name: s1
             range: E
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -5425,28 +4724,22 @@
             name: B
             populated_from: A
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: A
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1: B
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: enums-derived
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: A
    +
    +
    +
      +
    • Target Object:
    • +
    +
    s1: B
    +
    +
    +

    Target Schema (Derived):

    +
    name: enums-derived
     id: enums-derived
     imports:
     - linkml:types
    @@ -5478,12 +4771,9 @@
             - C
             range: E
     
    -```
    -
    -**Inverted Transformation Specification** (Derived):
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Inverted Transformation Specification (Derived):

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -5500,14 +4790,10 @@
             name: A
             populated_from: B
     
    -```
    -
    -### Combo: test\_map\_enum\[Z-mapping1-None-False\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: enums
    +
    +

    Combo: test_map_enum[Z-mapping1-None-False]

    +

    Source Schema:

    +
    name: enums
     id: enums
     imports:
     - linkml:types
    @@ -5537,12 +4823,9 @@
             name: s1
             range: E
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -5559,28 +4842,22 @@
             name: B
             populated_from: A
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: Z
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -{}
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: enums-derived
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: Z
    +
    +
    +
      +
    • Target Object:
    • +
    +
    {}
    +
    +
    +

    Target Schema (Derived):

    +
    name: enums-derived
     id: enums-derived
     imports:
     - linkml:types
    @@ -5612,14 +4889,10 @@
             - C
             range: E
     
    -```
    -
    -### Combo: test\_map\_enum\[C-mapping2-C-True\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: enums
    +
    +

    Combo: test_map_enum[C-mapping2-C-True]

    +

    Source Schema:

    +
    name: enums
     id: enums
     imports:
     - linkml:types
    @@ -5649,12 +4922,9 @@
             name: s1
             range: E
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -5671,14 +4941,10 @@
             name: B
             populated_from: A
     
    -```
    -
    -s\#\#\# Combo: test\_map\_enum\[A-mapping3-B-False\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: enums
    +
    +

    s### Combo: test_map_enum[A-mapping3-B-False]

    +

    Source Schema:

    +
    name: enums
     id: enums
     imports:
     - linkml:types
    @@ -5708,12 +4974,9 @@
             name: s1
             range: E
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -5732,28 +4995,22 @@
             - A
             - C
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: A
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1: B
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: enums-derived
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: A
    +
    +
    +
      +
    • Target Object:
    • +
    +
    s1: B
    +
    +
    +

    Target Schema (Derived):

    +
    name: enums-derived
     id: enums-derived
     imports:
     - linkml:types
    @@ -5785,14 +5042,10 @@
             - C
             range: E
     
    -```
    -
    -### Combo: test\_map\_enum\[C-mapping4-B-False\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: enums
    +
    +

    Combo: test_map_enum[C-mapping4-B-False]

    +

    Source Schema:

    +
    name: enums
     id: enums
     imports:
     - linkml:types
    @@ -5822,12 +5075,9 @@
             name: s1
             range: E
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         slot_derivations:
    @@ -5846,28 +5096,22 @@
             - A
             - C
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: C
    -
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1: B
    -
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: enums-derived
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: C
    +
    +
    +
      +
    • Target Object:
    • +
    +
    s1: B
    +
    +
    +

    Target Schema (Derived):

    +
    name: enums-derived
     id: enums-derived
     imports:
     - linkml:types
    @@ -5899,25 +5143,18 @@
             - C
             range: E
     
    -```
    -
    -Feature Set: test\_inheritance
    -------------------------------
    -
    -Test inheritance.
    -
    -Transformation specifications can utilize inheritance, in the same way
    -that LinkML schemas can.
    -
    --   **is\_a**: use is\_as instead of mixins in test schema
    --   **flatten**: roll down inherited slots
    -
    -### Combo: test\_inheritance\[False-True\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: expr
    +
    +

    Feature Set: test_inheritance

    +

    Test inheritance.

    +

    Transformation specifications can utilize inheritance, in the same way +that LinkML schemas can.

    +
      +
    • is_a: use is_as instead of mixins in test schema
    • +
    • flatten: roll down inherited slots
    • +
    +

    Combo: test_inheritance[False-True]

    +

    Source Schema:

    +
    name: expr
     id: expr
     imports:
     - linkml:types
    @@ -5945,12 +5182,9 @@
             name: s2
             range: integer
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         is_a: D
    @@ -5967,30 +5201,24 @@
             name: s2
             expr: s2 + 1
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 1
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: 1
     s2: 2
     
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1: 2
    +
    +
      +
    • Target Object:
    • +
    +
    s1: 2
     s2: 3
     
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: expr-derived
    +
    +

    Target Schema (Derived):

    +
    name: expr-derived
     id: expr-derived
     imports:
     - linkml:types
    @@ -6022,14 +5250,10 @@
             - D
             range: integer
     
    -```
    -
    -### Combo: test\_inheritance\[False-False\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: expr
    +
    +

    Combo: test_inheritance[False-False]

    +

    Source Schema:

    +
    name: expr
     id: expr
     imports:
     - linkml:types
    @@ -6058,12 +5282,9 @@
             name: s2
             range: integer
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         mixins:
    @@ -6081,30 +5302,24 @@
             name: s2
             expr: s2 + 1
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 1
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: 1
     s2: 2
     
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1: 2
    +
    +
      +
    • Target Object:
    • +
    +
    s1: 2
     s2: 3
     
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: expr-derived
    +
    +

    Target Schema (Derived):

    +
    name: expr-derived
     id: expr-derived
     imports:
     - linkml:types
    @@ -6137,14 +5352,10 @@
             - D
             range: integer
     
    -```
    -
    -### Combo: test\_inheritance\[True-True\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: expr
    +
    +

    Combo: test_inheritance[True-True]

    +

    Source Schema:

    +
    name: expr
     id: expr
     imports:
     - linkml:types
    @@ -6172,12 +5383,9 @@
             name: s2
             range: integer
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -6189,30 +5397,24 @@
             name: s2
             expr: s2 + 1
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 1
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: 1
     s2: 2
     
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1: 2
    +
    +
      +
    • Target Object:
    • +
    +
    s1: 2
     s2: 3
     
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: expr-derived
    +
    +

    Target Schema (Derived):

    +
    name: expr-derived
     id: expr-derived
     imports:
     - linkml:types
    @@ -6240,14 +5442,10 @@
             range: integer
         tree_root: true
     
    -```
    -
    -### Combo: test\_inheritance\[True-False\]
    -
    -**Source Schema**:
    -
    -``` {.yaml}
    -name: expr
    +
    +

    Combo: test_inheritance[True-False]

    +

    Source Schema:

    +
    name: expr
     id: expr
     imports:
     - linkml:types
    @@ -6276,12 +5474,9 @@
             name: s2
             range: integer
     
    -```
    -
    -**Transformer Specification**:
    -
    -``` {.yaml}
    -class_derivations:
    +
    +

    Transformer Specification:

    +
    class_derivations:
       C:
         name: C
         populated_from: C
    @@ -6293,30 +5488,24 @@
             name: s2
             expr: s2 + 1
     
    -```
    -
    -**Object Transformation**:
    -
    --   Source Object:
    -
    -``` {.yaml}
    -s1: 1
    +
    +

    Object Transformation:

    +
      +
    • Source Object:
    • +
    +
    s1: 1
     s2: 2
     
    -```
    -
    --   Target Object:
    -
    -``` {.yaml}
    -s1: 2
    +
    +
      +
    • Target Object:
    • +
    +
    s1: 2
     s2: 3
     
    -```
    -
    -**Target Schema (Derived)**:
    -
    -``` {.yaml}
    -name: expr-derived
    +
    +

    Target Schema (Derived):

    +
    name: expr-derived
     id: expr-derived
     imports:
     - linkml:types
    @@ -6344,6 +5533,49 @@
             range: integer
         tree_root: true
     
    -```
    -
    -. 55 passed, 2 skipped, 83 warnings in 4.60s
    +
    +

    . 55 passed, 2 skipped, 83 warnings in 3.98s

    + +
    + + + + + + + + + +
    +
    + + + + + \ No newline at end of file diff --git a/src/linkml_map/__init__.py b/src/linkml_map/__init__.py deleted file mode 100644 index e2f2ce0..0000000 --- a/src/linkml_map/__init__.py +++ /dev/null @@ -1,6 +0,0 @@ -from linkml_map.transformer.object_transformer import ObjectTransformer - -__all__ = [ - "ObjectTransformer", - "Session", -] diff --git a/src/linkml_map/cli/cli.py b/src/linkml_map/cli/cli.py deleted file mode 100644 index 6676713..0000000 --- a/src/linkml_map/cli/cli.py +++ /dev/null @@ -1,228 +0,0 @@ -"""Command line interface for linkml-map.""" - -import logging -import sys - -import click - -__all__ = [ - "main", -] - -from typing import Any, Optional, Union - -import yaml -from linkml_runtime import SchemaView -from linkml_runtime.dumpers import yaml_dumper - -from linkml_map.compiler.markdown_compiler import MarkdownCompiler -from linkml_map.compiler.python_compiler import PythonCompiler -from linkml_map.inference.inverter import TransformationSpecificationInverter -from linkml_map.inference.schema_mapper import SchemaMapper -from linkml_map.transformer.object_transformer import ObjectTransformer - -# CLI options -output_option = click.option("-o", "--output", help="Output file.") -schema_option = click.option("-s", "--schema", help="Path to source schema.") -transformer_specification_option = click.option( - "-T", "--transformer-specification", help="Path to transformer specification." -) - -logger = logging.getLogger(__name__) - - -@click.group() -@click.option("-v", "--verbose", count=True) -@click.option("-q", "--quiet") -# @click.version_option(__version__) -def main(verbose: int, quiet: bool) -> None: - """CLI for linkml-map.""" - logger = logging.getLogger() - if verbose >= 2: - logger.setLevel(level=logging.DEBUG) - elif verbose == 1: - logger.setLevel(level=logging.INFO) - else: - logger.setLevel(level=logging.WARNING) - if quiet: - logger.setLevel(level=logging.ERROR) - logger.info(f"Logger {logger.name} set to level {logger.level}") - - -@main.command() -@output_option -@transformer_specification_option -@schema_option -@click.option("--source-type") -@click.option( - "--unrestricted-eval/--no-unrestricted-eval", - default=False, - show_default=True, - help="Allow unrestricted eval of python expressions.", -) -@click.argument("input_data") -def map_data( - input_data: str, - schema: str, - source_type: Optional[str], - transformer_specification: str, - output: Optional[str], - **kwargs: dict[str, Any], -) -> None: - """ - Map data from a source schema to a target schema using a transformation specification. - - Example: - linkml-map map-data -T X-to-Y-tr.yaml -s X.yaml X-data.yaml - - """ - logger.info( - f"Transforming {input_data} conforming to {schema} using {transformer_specification}" - ) - tr = ObjectTransformer(**kwargs) - tr.source_schemaview = SchemaView(schema) - tr.load_transformer_specification(transformer_specification) - with open(input_data) as file: - input_obj = yaml.safe_load(file) - tr.index(input_obj, source_type) - tr_obj = tr.map_object(input_obj, source_type) - dump_output(tr_obj, "yaml", output) - - -@main.command() -@output_option -@transformer_specification_option -@schema_option -@click.option("--target", default="python", show_default=True, help="Target representation.") -def compile( - schema: str, - transformer_specification: str, - target: str, - output: Optional[str], - **kwargs: Optional[dict[str, Any]], -) -> None: - """ - Compiles a schema to another representation. - - Example: - linkml-map compile -T X-to-Y-tr.yaml -s X.yaml - - """ - logger.info(f"Compiling {transformer_specification} with {schema}") - sv = SchemaView(schema) - compiler_args = {"source_schemaview": sv} - if target == "python": - compiler = PythonCompiler(**compiler_args) - elif target == "markdown": - compiler = MarkdownCompiler(**compiler_args) - else: - msg = f"Compiler {target} not implemented" - raise NotImplementedError(msg) - tr = ObjectTransformer() - tr.source_schemaview = sv - tr.load_transformer_specification(transformer_specification) - result = compiler.compile(tr.specification) - # dump as-is, no encoding - dump_output(result.serialization, None, output) - - -@main.command() -@output_option -@transformer_specification_option -@click.argument("schema") -def derive_schema( - schema: str, - transformer_specification: str, - output: Optional[str], - **kwargs: Optional[dict[str, Any]], -) -> None: - """ - Derive a schema from a source schema and a transformation specification. - - This can be thought of as "copying" the source to a target, using the transformation - specification as a "patch" - - Notes: - the implementation is currently incomplete; the derived schema may not be valid - linkml, e.g. there may be "dangling" references. - - Example: - linkml-map derive-schema -T transform/personinfo-to-agent.transform.yaml source/personinfo.yaml - - """ - logger.info(f"Transforming {schema} using {transformer_specification}") - tr = ObjectTransformer() - tr.load_transformer_specification(transformer_specification) - mapper = SchemaMapper(transformer=tr) - mapper.source_schemaview = SchemaView(schema) - target_schema = mapper.derive_schema() - dump_output(target_schema, "yaml", output) - - -@main.command() -@output_option -@transformer_specification_option -@click.option("--strict/--no-strict", default=True, show_default=True, help="Strict mode.") -@click.argument("schema") -def invert( - schema: str, - transformer_specification: str, - output: Optional[str], - **kwargs: Optional[dict[str, Any]], -) -> None: - """ - Invert a transformation specification. - - Example: - linkml-map invert -T transform/personinfo-to-agent.transform.yaml source/personinfo.yaml - - """ - logger.info(f"Inverting {transformer_specification} using {schema} as source") - tr = ObjectTransformer() - tr.load_transformer_specification(transformer_specification) - inverter = TransformationSpecificationInverter( - source_schemaview=SchemaView(schema), - **kwargs, - ) - inverted_spec = inverter.invert(tr.specification) - dump_output(inverted_spec, "yaml", output) - - -def dump_output( - output_data: Union[dict[str, Any], list[Any], str], - output_format: Optional[str] = None, - file_path: Optional[str] = None, -) -> None: - """ - Dump output as YAML to a file or stdout. - - :param output_data: data to dump - :type output_data: dict[str, Any] | list[Any] | str - :param output_format: format for dumped data, defaults to None - :type output_format: Optional[str], optional - :param file_path: path to an output file, defaults to None - :type file_path: Optional[str], optional - """ - if output_data is None: - # this should already have been caught... - msg = "No output to be printed" - raise ValueError(msg) - - text_dump = output_data - if output_format == "yaml": - text_dump = yaml_dumper.dumps(output_data) - elif output_format: - # some other defined output format - msg = f"Output format {output_format} is not supported" - raise NotImplementedError(msg) - - if not file_path: - sys.stdout.write(text_dump) - return - - with open(file_path, "w", encoding="utf-8") as fh: - fh.write(text_dump) - - -if __name__ == "__main__": - main() diff --git a/src/linkml_map/compiler/__init__.py b/src/linkml_map/compiler/__init__.py deleted file mode 100644 index 1445353..0000000 --- a/src/linkml_map/compiler/__init__.py +++ /dev/null @@ -1 +0,0 @@ -"""Compiles schemas into other transformation frameworks.""" diff --git a/src/linkml_map/compiler/awk_compiler.py b/src/linkml_map/compiler/awk_compiler.py deleted file mode 100644 index f68aedb..0000000 --- a/src/linkml_map/compiler/awk_compiler.py +++ /dev/null @@ -1,13 +0,0 @@ -from linkml_map.compiler.compiler import CompiledSpecification, Compiler -from linkml_map.datamodel.transformer_model import TransformationSpecification - - -class AWKCompiler(Compiler): - """ - Compiles a Transformation Specification to an Awk script. - - Note: this is only expected to work for flat schemas. - """ - - def compile(self, specification: TransformationSpecification) -> CompiledSpecification: - raise NotImplementedError diff --git a/src/linkml_map/compiler/compiler.py b/src/linkml_map/compiler/compiler.py deleted file mode 100644 index 60b5499..0000000 --- a/src/linkml_map/compiler/compiler.py +++ /dev/null @@ -1,89 +0,0 @@ -""" -Compilers are responsible for compiling a transformation specification into an alternative representation. - -This is the opposite of an importer. - -For example: - -- LinkML-Transformer Specifications to R2RML -- LinkML-Transformer Specifications to awk scripts -- LinkML-Transformer Specifications to SQL -- LinkML-Transformer Specifications to Python (OO) -- LinkML-Transformer Specifications to Pandas -- LinkML-Transformer Specifications to Hamilton -""" - -from abc import ABC -from collections.abc import Iterator -from dataclasses import dataclass, field -from types import ModuleType -from typing import Optional - -from linkml_runtime import SchemaView -from linkml_runtime.dumpers import yaml_dumper -from linkml_runtime.utils.compile_python import compile_python - -from linkml_map.datamodel.transformer_model import TransformationSpecification -from linkml_map.inference.schema_mapper import SchemaMapper - - -@dataclass -class CompiledSpecification: - serialization: str = field(default="") - - _module: Optional[ModuleType] = None - - @property - def module(self) -> ModuleType: - if not self._module: - self._module = compile_python(self.serialization) - return self._module - - -@dataclass -class Compiler(ABC): - """ - Base class for all compilers. - - A compiler will compile a transformation specification into - an alternative representation. - - An example compiler would be a R2RML compiler. - - Note: Compilers and Importers will in general be implemented by providing - mapping specifications - """ - - source_schemaview: SchemaView = None - """A view over the schema describing the source.""" - - source_python_module: str = None - """The python module containing the source classes.""" - - target_python_module: str = None - """The python module containing the target classes.""" - - def compile(self, specification: TransformationSpecification) -> CompiledSpecification: - """ - Transform source object into an instance of the target class. - - :param specification: - :return: - """ - s = self._compile_header(specification) - for chunk in self._compile_iterator(specification): - s += chunk - return CompiledSpecification(serialization=s) - - def _compile_header(self, specification: TransformationSpecification) -> str: - return "" - - def _compile_iterator(self, specification: TransformationSpecification) -> Iterator[str]: - raise NotImplementedError - - def derived_target_schemaview(self, specification: TransformationSpecification) -> SchemaView: - """ - Return a view over the target schema, including any derived classes. - """ - mapper = SchemaMapper(source_schemaview=self.source_schemaview) - return SchemaView(yaml_dumper.dumps(mapper.derive_schema(specification))) diff --git a/src/linkml_map/compiler/graphviz_compiler.py b/src/linkml_map/compiler/graphviz_compiler.py deleted file mode 100644 index 846abdd..0000000 --- a/src/linkml_map/compiler/graphviz_compiler.py +++ /dev/null @@ -1,110 +0,0 @@ -import re -from dataclasses import dataclass -from typing import Optional - -from graphviz import Digraph -from linkml_runtime import SchemaView -from pydantic import BaseModel - -from linkml_map.compiler.compiler import CompiledSpecification, Compiler -from linkml_map.datamodel.transformer_model import TransformationSpecification - - -class Record(BaseModel): - """ - A simplified representation of a class, UML-style. - """ - - name: str - source: str - fields: list[tuple[str, str]] = [] - - @property - def id(self) -> str: - return f"{self.source}{self.name}" - - def __str__(self) -> str: - return ( - f"""< - - - """ - + "".join( - [ - f'' - for f in self.fields - ] - ) - + """ -
    {self.name}
    {f[0]} : {f[1]}
    >""" - ) - - -@dataclass -class GraphvizObject(CompiledSpecification): - digraph: Digraph = None - - def render(self, file_path: str, format="png", view=False) -> None: - """ - Render a graphviz graph to a file. - - :param file_path: - :return: - """ - self.digraph.render(file_path, format=format, view=view) - - -class GraphvizCompiler(Compiler): - """ - Compile a Transformation Specification to GraphViz. - """ - - def compile( - self, specification: TransformationSpecification, elements: Optional[list[str]] = None - ) -> GraphvizObject: - dg = Digraph(comment="UML Class Diagram", format="png") - dg.attr(rankdir="LR") # Set graph direction from left to right - target_schemaview = self.derived_target_schemaview(specification) - source_schemaview = self.source_schemaview - - records = [] - records += self.add_records(source_schemaview, "source") - records += self.add_records(target_schemaview, "target") - - for record in records: - dg.node(record.id, str(record), shape="plaintext") - - # Define the class nodes with fields in UML format using HTML-like labels - # for precise control over the stacking of the fields - for target_cn, cd in specification.class_derivations.items(): - source_cn = cd.populated_from - if source_cn is None: - source_cn = cd.name - if elements is not None and target_cn not in elements: - continue - source_record = Record(name=source_cn, source="source") - target_record = Record(name=target_cn, source="target") - for sd in cd.slot_derivations.values(): - target_slot = sd.name - target_id = f"{target_record.id}:{target_slot}" - source_slot = sd.populated_from - if source_slot: - source_id = f"{source_record.id}:{source_slot}" - dg.edge(source_id, target_id) - elif sd.expr: - # TODO: do this in a less hacky way - tokens = re.findall(r"\w+", sd.expr) - for token in tokens: - if token not in source_schemaview.all_slots(): - continue - dg.edge(f"{source_record.id}:{token}", target_id, style="dashed") - return GraphvizObject(digraph=dg, serialization=dg.source) - - def add_records(self, schemaview: SchemaView, source: str) -> list[Record]: - records = [] - for cn in schemaview.all_classes(): - record = Record(name=cn, source=source) - for induced_slot in schemaview.class_induced_slots(cn): - record.fields.append((induced_slot.name, induced_slot.range)) - records.append(record) - return records diff --git a/src/linkml_map/compiler/j2_based_compiler.py b/src/linkml_map/compiler/j2_based_compiler.py deleted file mode 100644 index cda3e68..0000000 --- a/src/linkml_map/compiler/j2_based_compiler.py +++ /dev/null @@ -1,38 +0,0 @@ -from dataclasses import dataclass - -from jinja2 import Environment, FileSystemLoader - -from linkml_map.compiler.compiler import CompiledSpecification, Compiler -from linkml_map.compiler.templates import TEMPLATE_DIR -from linkml_map.datamodel.transformer_model import TransformationSpecification - - -@dataclass -class J2BasedCompiler(Compiler): - """ - Compiles a Transformation Specification using a Jinja2 template. - """ - - template_dir: str = None - """The directory containing the Jinja2 template.""" - - template_name: str = None - """The name of the Jinja2 template.""" - - def compile(self, specification: TransformationSpecification) -> CompiledSpecification: - template_dir = self.template_dir - if not template_dir: - template_dir = TEMPLATE_DIR - if not template_dir: - msg = "template_dir must be set" - raise ValueError(msg) - loader = FileSystemLoader(template_dir) - env = Environment(loader=loader, autoescape=True) - if not self.template_name: - msg = "template_name must be set" - raise ValueError(msg) - template = env.get_template(self.template_name) - rendered = template.render( - spec=specification, - ) - return CompiledSpecification(serialization=rendered) diff --git a/src/linkml_map/compiler/markdown_compiler.py b/src/linkml_map/compiler/markdown_compiler.py deleted file mode 100644 index 552d835..0000000 --- a/src/linkml_map/compiler/markdown_compiler.py +++ /dev/null @@ -1,12 +0,0 @@ -from dataclasses import dataclass - -from linkml_map.compiler.j2_based_compiler import J2BasedCompiler - - -@dataclass -class MarkdownCompiler(J2BasedCompiler): - """ - Compiles a Transformation Specification to Markdown. - """ - - template_name: str = "markdown.j2" diff --git a/src/linkml_map/compiler/python_compiler.py b/src/linkml_map/compiler/python_compiler.py deleted file mode 100644 index cf14d86..0000000 --- a/src/linkml_map/compiler/python_compiler.py +++ /dev/null @@ -1,110 +0,0 @@ -from collections.abc import Iterator -from copy import deepcopy -from dataclasses import dataclass - -from jinja2 import Template - -from linkml_map.compiler.compiler import Compiler -from linkml_map.datamodel.transformer_model import ( - ClassDerivation, - TransformationSpecification, -) -from linkml_map.inference.inference import induce_missing_values - -CD_TEMPLATE = """ -{% macro gen_slot_derivation_value(sd, var) -%} -{%- if sd.range -%} -derive_{{ sd.range }}({{ var }}) -{%- else -%} -{%- if var is not none -%} -{{ var }} -{%- else -%} -None -{%- endif -%} -{%- endif -%} -{%- endmacro %} -{% macro gen_slot_derivation(sd, force_singlevalued=False) -%} -{%- if not force_singlevalued and sd.populated_from and induced_slots[sd.populated_from].multivalued -%} - [ {{ gen_slot_derivation_value(sd, "x") }} for x in {{ gen_slot_derivation(sd, force_singlevalued=True) }} ] -{%- else -%} - {%- if sd.populated_from -%} - source_object.{{ sd.populated_from }} - {%- elif sd.expr -%} - {%- if '\n' in sd.expr -%} - gen_{{ sd.name }}(source_object) - {%- elif '{' in sd.expr and '}' in sd.expr -%} - {{ sd.expr|replace('{', '')|replace('}', '') }} - {%- else -%} - {{ sd.expr }} - {%- endif -%} - {%- else -%} - None - {%- endif -%} -{%- endif -%} -{%- endmacro %} -{% macro gen_slot_derivation_defs(sd) -%} -{% if sd.expr and '\n' in sd.expr %} - - def gen_{{ sd.name }}(src): - target = None - {%- for line in sd.expr.split('\n') %} - {{ line }} - {%- endfor -%} - return target -{% endif %} -{%- endmacro %} -def derive_{{ cd.name }}( - source_object: {{ source_module }}.{{ cd.populated_from }} - ) -> {{ target_module }}.{{ cd.name }}: - # assign slots -{%- for slot in source_slots %} - {{ slot.name }} = source_object.{{ slot.name }} -{%- endfor %} -{%- for sd in cd.slot_derivations.values() -%} - {{ gen_slot_derivation_defs(sd) }} -{%- endfor %} - - return tgt.{{ cd.name }}( - {%- for sd in cd.slot_derivations.values() %} - {{ sd.name }}={{ gen_slot_derivation(sd) }}, - {%- endfor %} - ) -""" - - -@dataclass -class PythonCompiler(Compiler): - """ - Compiles a Transformation Specification to Python code. - """ - - def _compile_header(self, specification: TransformationSpecification) -> str: - s = "" - if self.source_python_module: - s += f"import {self.source_python_module} as src\n" - if self.target_python_module: - s += f"import {self.target_python_module} as tgt\n" - s += "\nNULL = None\n\n" - return s - - def _compile_iterator(self, specification: TransformationSpecification) -> Iterator[str]: - specification = deepcopy(specification) - induce_missing_values(specification, self.source_schemaview) - for cd in specification.class_derivations.values(): - yield from self._compiled_class_derivations_iter(cd) - - def _compiled_class_derivations_iter(self, cd: ClassDerivation) -> Iterator[str]: - sv = self.source_schemaview - populated_from = cd.populated_from if cd.populated_from else cd.name - if populated_from not in sv.all_classes(): - return - induced_slots = {s.name: s for s in sv.class_induced_slots(populated_from)} - t = Template(CD_TEMPLATE) - yield t.render( - cd=cd, - source_module="src", - target_module="tgt", - induced_slots=induced_slots, - schemaview=sv, - source_slots=sv.class_induced_slots(populated_from), - ) diff --git a/src/linkml_map/compiler/r2rml_compiler.py b/src/linkml_map/compiler/r2rml_compiler.py deleted file mode 100644 index 0669d8f..0000000 --- a/src/linkml_map/compiler/r2rml_compiler.py +++ /dev/null @@ -1,12 +0,0 @@ -from linkml_map.compiler.compiler import CompiledSpecification, Compiler -from linkml_map.datamodel.transformer_model import TransformationSpecification - - -class R2RMLCompiler(Compiler): - """ - Compiles a Transformation Specification to R2RML. - - """ - - def compile(self, specification: TransformationSpecification) -> CompiledSpecification: - raise NotImplementedError diff --git a/src/linkml_map/compiler/sparql_compiler.py b/src/linkml_map/compiler/sparql_compiler.py deleted file mode 100644 index 3ec78df..0000000 --- a/src/linkml_map/compiler/sparql_compiler.py +++ /dev/null @@ -1,12 +0,0 @@ -from linkml_map.compiler.compiler import CompiledSpecification, Compiler -from linkml_map.datamodel.transformer_model import TransformationSpecification - - -class SPARQLCompiler(Compiler): - """ - Compiles a Transformation Specification to SPARQL Construct. - - """ - - def compile(self, specification: TransformationSpecification) -> CompiledSpecification: - raise NotImplementedError diff --git a/src/linkml_map/compiler/sql_compiler.py b/src/linkml_map/compiler/sql_compiler.py deleted file mode 100644 index 2562f0f..0000000 --- a/src/linkml_map/compiler/sql_compiler.py +++ /dev/null @@ -1,139 +0,0 @@ -from linkml_runtime import SchemaView -from linkml_runtime.linkml_model import SlotDefinition - -from linkml_map.compiler.compiler import CompiledSpecification, Compiler -from linkml_map.datamodel.transformer_model import ( - ClassDerivation, - SerializationSyntaxType, - TransformationSpecification, -) - -LINKML_TO_SQL_TYPE_MAP = { - "string": "TEXT", - "integer": "INTEGER", - "boolean": "BOOLEAN", - "float": "REAL", - "decimal": "REAL", - "datetime": "TIMESTAMP", - "date": "DATE", - "time": "TIME", - "uri": "TEXT", - "any": "TEXT", -} - - -class SQLCompiler(Compiler): - """ - Compiles a Transformation Specification to SQL CREATE TABLE or VIEW statements. - - Note: this is currently highly geared towards DuckDB. - """ - - add_if_not_exists: bool = True - new_table_when_transforming: bool = False - - def compile(self, specification: TransformationSpecification) -> CompiledSpecification: - compiled = CompiledSpecification() - for cd in specification.class_derivations.values(): - self.compile_class(compiled, cd, specification) - return compiled - - def compile_class( - self, - compiled: CompiledSpecification, - cd: ClassDerivation, - specification: TransformationSpecification, - ) -> None: - """ - Compile a class derivation to SQL. - - :param compiled: (modified in place) - :param cd: - :param specification: - :return: - """ - stmt = "" - if self.new_table_when_transforming: - stmt += "CREATE TABLE " - if self.add_if_not_exists: - stmt += "IF NOT EXISTS " - stmt += f"{cd.name} \n" - else: - stmt += f"INSERT INTO {cd.name} SELECT \n" - col_trs = [] - for sd in cd.slot_derivations.values(): - col_trs.append(self.compile_slot_derivation(sd)) - if not col_trs: - return - stmt += ", \n".join(col_trs) - stmt += f" FROM {cd.name}" - compiled.serialization += f"{stmt};\n" - - def compile_slot_derivation(self, sd) -> str: - expr = sd.populated_from - if expr is None: - expr = sd.name - if sd.stringification: - syntax = sd.stringification.syntax - delimiter = sd.stringification.delimiter - if sd.stringification.reversed: - pass - # duckdb specific? - elif syntax == SerializationSyntaxType.JSON: - expr = f"CAST({expr} AS TEXT)" - elif delimiter: - expr = f"STRING_AGG({expr}, '{delimiter}')" - return f" {sd.name} AS {expr}" - - def create_ddl(self, schemaview: SchemaView) -> str: - """ - Create DDL for the entire schema. - - Note core LinkML has a SQL DDL generator, but this is primarily for pure relational models. - - DuckDB allows complex datatypes. - - TODO: move to LinkML core - :param schemaview: - :return: - """ - ddl = [] - for c in schemaview.all_classes().values(): - if c.mixin or c.abstract: - continue - col_strs = [] - for s in schemaview.class_induced_slots(c.name): - col_strs.append(f" {s.name} {self.sql_type(s, schemaview)}") - if not col_strs: - continue - ddl.append(f"CREATE TABLE IF NOT EXISTS {c.name} (") - ddl.append(",\n".join(col_strs)) - ddl.append(");") - return "\n".join(ddl) - - def create_target_ddl(self, specification: TransformationSpecification) -> str: - target_sv = self.derived_target_schemaview(specification) - return self.create_ddl(target_sv) - - def sql_type(self, slot: SlotDefinition, schemaview: SchemaView) -> str: - """ - Map LinkML types to DuckDB SQL types. - - :param slot: - :param schemaview: - :return: - """ - typ = "TEXT" - if slot.range: - if slot.range in LINKML_TO_SQL_TYPE_MAP: - typ = LINKML_TO_SQL_TYPE_MAP.get(slot.range, typ) - elif slot.range in schemaview.all_classes(): - if slot.inlined: - typ = "TEXT" - else: - # TODO: consider structs - typ = "JSON" - - if slot.multivalued: - typ = f"{typ}[]" - return typ diff --git a/src/linkml_map/compiler/sssom_compiler.py b/src/linkml_map/compiler/sssom_compiler.py deleted file mode 100644 index 6bed9f2..0000000 --- a/src/linkml_map/compiler/sssom_compiler.py +++ /dev/null @@ -1,13 +0,0 @@ -from linkml_map.compiler.compiler import CompiledSpecification, Compiler -from linkml_map.datamodel.transformer_model import TransformationSpecification - - -class SSSOMCompiler(Compiler): - """ - Compiles a Transformation Specification to SSSOM. - - Note: SSSOM has less expressivity so this is expected to be highly lossy - """ - - def compile(self, specification: TransformationSpecification) -> CompiledSpecification: - raise NotImplementedError diff --git a/src/linkml_map/compiler/templates/__init__.py b/src/linkml_map/compiler/templates/__init__.py deleted file mode 100644 index b7107f3..0000000 --- a/src/linkml_map/compiler/templates/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -from pathlib import Path - -TEMPLATE_DIR = Path(__file__).parent diff --git a/src/linkml_map/compiler/templates/markdown.j2 b/src/linkml_map/compiler/templates/markdown.j2 deleted file mode 100644 index 90e2f6b..0000000 --- a/src/linkml_map/compiler/templates/markdown.j2 +++ /dev/null @@ -1,25 +0,0 @@ -# {{ spec.title }} - -## Class Mappings -{% for cd in spec.class_derivations.values() %} - -### {{ cd.name }} `<-` {{ cd.populated_from }} - -| Target | Target Range | Source | Source Range | Info | -| ------ | ------ | ---- | ---- | ---- | - {%- for sd in cd.slot_derivations.values() %} -| {{ sd.name }} | | {{ sd.range }} | {% if sd.expr is not none %} [expression] {% else %} {{ sd.populated_from }} {% endif %} | . | . | - {%- endfor -%} -{% endfor %} - -## Enum Mappings - -{% for ed in spec.enum_derivations.values() %} -### Target enum {{ ed.name }} - -| Target | Source | Info | -| ------ | ------ | ---- | - {%- for pvd in ed.permissible_value_derivations.values() %} -| {{ pvd.name }} | {{ pvd.populated_from }} | . | - {%- endfor -%} -{% endfor %} diff --git a/src/linkml_map/compiler/tr/__init__.py b/src/linkml_map/compiler/tr/__init__.py deleted file mode 100644 index 2754620..0000000 --- a/src/linkml_map/compiler/tr/__init__.py +++ /dev/null @@ -1,4 +0,0 @@ -from pathlib import Path - -COMPILER_TRANSFORMATIONS_DIR = Path(__file__).parent -TR_TO_MAPPING_TABLES = COMPILER_TRANSFORMATIONS_DIR / "transformer_to_mapping_tables.tr.yaml" diff --git a/src/linkml_map/compiler/tr/transformer_to_mapping_tables.tr.yaml b/src/linkml_map/compiler/tr/transformer_to_mapping_tables.tr.yaml deleted file mode 100644 index 7d135f5..0000000 --- a/src/linkml_map/compiler/tr/transformer_to_mapping_tables.tr.yaml +++ /dev/null @@ -1,29 +0,0 @@ -description: >- - Maps between the full transformation spec data model and simple tables. TODO - -class_derivations: - MappingSet: - populated_from: TransformationSpecification - slot_derivations: - id: - populated_from: id - title: - populated_from: title - class_mappings: - populated_from: class_derivations - ClassMapping: - populated_from: ClassDerivation - slot_derivations: - subject_id: - populated_from: populated_from - object_id: - populated_from: name - slot_mappings: - populated_from: slot_derivations - SlotMapping: - populated_from: SlotDerivation - slot_derivations: - subject_id: - populated_from: populated_from - object_id: - populated_from: name \ No newline at end of file diff --git a/src/linkml_map/datamodel/__init__.py b/src/linkml_map/datamodel/__init__.py deleted file mode 100644 index 68b3fed..0000000 --- a/src/linkml_map/datamodel/__init__.py +++ /dev/null @@ -1,4 +0,0 @@ -from pathlib import Path - -SCHEMA_DIR = Path(__file__).parent -TR_SCHEMA = SCHEMA_DIR / "transformer_model.yaml" diff --git a/src/linkml_map/datamodel/sssom.map.yaml b/src/linkml_map/datamodel/sssom.map.yaml deleted file mode 100644 index 0531876..0000000 --- a/src/linkml_map/datamodel/sssom.map.yaml +++ /dev/null @@ -1,8 +0,0 @@ -class_derivations: - Mapping: - any_of: - - populated_from: ClassDerivation - slot_derivations: - .. - - populated_from: SlotDerivation - diff --git a/src/linkml_map/datamodel/transformer_model.py b/src/linkml_map/datamodel/transformer_model.py deleted file mode 100644 index e0adc17..0000000 --- a/src/linkml_map/datamodel/transformer_model.py +++ /dev/null @@ -1,657 +0,0 @@ -from __future__ import annotations - -import re -import sys -from datetime import ( - date, - datetime, - time -) -from decimal import Decimal -from enum import Enum -from typing import ( - Any, - ClassVar, - Dict, - List, - Literal, - Optional, - Union -) - -from pydantic import ( - BaseModel, - ConfigDict, - Field, - RootModel, - field_validator -) - - -metamodel_version = "None" -version = "None" - - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment = True, - validate_default = True, - extra = "forbid", - arbitrary_types_allowed = True, - use_enum_values = True, - strict = False, - ) - pass - - - - -class LinkMLMeta(RootModel): - root: Dict[str, Any] = {} - model_config = ConfigDict(frozen=True) - - def __getattr__(self, key:str): - return getattr(self.root, key) - - def __getitem__(self, key:str): - return self.root[key] - - def __setitem__(self, key:str, value): - self.root[key] = value - - def __contains__(self, key:str) -> bool: - return key in self.root - - -linkml_meta = LinkMLMeta({'default_prefix': 'linkmlmap', - 'description': 'Datamodel for LinkML schema mappings and transformations.\n' - '\n' - 'A mapper generates instances of a *target* data model from\n' - 'instances of a *source* data model. This transformation ' - 'process\n' - 'is guided by a *TransformationSpecification*.\n' - '\n' - 'The specification is independent of any one method for ' - 'transforming\n' - 'data. It allows different approaches, including:\n' - '\n' - '- direct implementation, transforming python or json objects\n' - '- translation of the specification into SQL commands, to ' - 'operate on relations\n' - '- translation of the specification into SPARQL CONSTRUCTs, to ' - 'operate on triples\n' - '- translation into another specification language, such as ' - 'R2RML', - 'id': 'https://w3id.org/linkml/transformer', - 'imports': ['linkml:types'], - 'name': 'linkml-map', - 'prefixes': {'STATO': {'prefix_prefix': 'STATO', - 'prefix_reference': 'http://purl.obolibrary.org/obo/STATO_'}, - 'dcterms': {'prefix_prefix': 'dcterms', - 'prefix_reference': 'http://purl.org/dc/terms/'}, - 'linkml': {'prefix_prefix': 'linkml', - 'prefix_reference': 'https://w3id.org/linkml/'}, - 'linkmlmap': {'prefix_prefix': 'linkmlmap', - 'prefix_reference': 'https://w3id.org/linkml/transformer/'}, - 'rdfs': {'prefix_prefix': 'rdfs', - 'prefix_reference': 'http://www.w3.org/2000/01/rdf-schema#'}, - 'schema': {'prefix_prefix': 'schema', - 'prefix_reference': 'http://schema.org/'}, - 'sh': {'prefix_prefix': 'sh', - 'prefix_reference': 'http://www.w3.org/ns/shacl#'}}, - 'source_file': 'src/linkml_map/datamodel/transformer_model.yaml', - 'title': 'LinkML Map Data Model', - 'types': {'ClassReference': {'from_schema': 'https://w3id.org/linkml/transformer', - 'name': 'ClassReference', - 'typeof': 'string'}, - 'EnumReference': {'from_schema': 'https://w3id.org/linkml/transformer', - 'name': 'EnumReference', - 'typeof': 'string'}, - 'SlotReference': {'from_schema': 'https://w3id.org/linkml/transformer', - 'name': 'SlotReference', - 'typeof': 'string'}}} ) - -class CollectionType(str, Enum): - SingleValued = "SingleValued" - MultiValued = "MultiValued" - MultiValuedList = "MultiValuedList" - MultiValuedDict = "MultiValuedDict" - - -class SerializationSyntaxType(str, Enum): - JSON = "JSON" - YAML = "YAML" - TURTLE = "TURTLE" - - -class AggregationType(str, Enum): - SUM = "SUM" - AVERAGE = "AVERAGE" - COUNT = "COUNT" - MIN = "MIN" - MAX = "MAX" - STD_DEV = "STD_DEV" - VARIANCE = "VARIANCE" - MEDIAN = "MEDIAN" - MODE = "MODE" - CUSTOM = "CUSTOM" - SET = "SET" - LIST = "LIST" - ARRAY = "ARRAY" - - -class InvalidValueHandlingStrategy(str, Enum): - IGNORE = "IGNORE" - TREAT_AS_ZERO = "TREAT_AS_ZERO" - ERROR_OUT = "ERROR_OUT" - - -class PivotDirectionType(str, Enum): - MELT = "MELT" - UNMELT = "UNMELT" - - - -class SpecificationComponent(ConfiguredBaseModel): - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, 'from_schema': 'https://w3id.org/linkml/transformer'}) - - description: Optional[str] = Field(default=None, description="""description of the specification component""", json_schema_extra = { "linkml_meta": {'alias': 'description', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'dcterms:description'} }) - implements: Optional[List[str]] = Field(default_factory=list, description="""A reference to a specification that this component implements.""", json_schema_extra = { "linkml_meta": {'alias': 'implements', 'domain_of': ['SpecificationComponent']} }) - comments: Optional[List[str]] = Field(default_factory=list, description="""A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use.""", json_schema_extra = { "linkml_meta": {'alias': 'comments', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'rdfs:comment'} }) - - -class TransformationSpecification(SpecificationComponent): - """ - A collection of mappings between source and target classes - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer', 'tree_root': True}) - - id: Optional[str] = Field(default=None, description="""Unique identifier for this transformation specification""", json_schema_extra = { "linkml_meta": {'alias': 'id', - 'domain_of': ['TransformationSpecification'], - 'slot_uri': 'schema:identifier'} }) - title: Optional[str] = Field(default=None, description="""human readable title for this transformation specification""", json_schema_extra = { "linkml_meta": {'alias': 'title', - 'domain_of': ['TransformationSpecification'], - 'slot_uri': 'dcterms:title'} }) - prefixes: Optional[Dict[str, KeyVal]] = Field(default_factory=dict, description="""maps prefixes to URL expansions""", json_schema_extra = { "linkml_meta": {'alias': 'prefixes', - 'domain_of': ['TransformationSpecification'], - 'slot_uri': 'sh:declare'} }) - copy_directives: Optional[Dict[str, CopyDirective]] = Field(default_factory=dict, json_schema_extra = { "linkml_meta": {'alias': 'copy_directives', - 'domain_of': ['TransformationSpecification', 'ElementDerivation']} }) - source_schema: Optional[str] = Field(default=None, description="""name of the schema that describes the source (input) objects""", json_schema_extra = { "linkml_meta": {'alias': 'source_schema', 'domain_of': ['TransformationSpecification']} }) - target_schema: Optional[str] = Field(default=None, description="""name of the schema that describes the target (output) objects""", json_schema_extra = { "linkml_meta": {'alias': 'target_schema', 'domain_of': ['TransformationSpecification']} }) - class_derivations: Optional[Dict[str, ClassDerivation]] = Field(default_factory=dict, description="""Instructions on how to derive a set of classes in the target schema from classes in the source schema.""", json_schema_extra = { "linkml_meta": {'alias': 'class_derivations', - 'domain_of': ['TransformationSpecification', 'ObjectDerivation']} }) - enum_derivations: Optional[Dict[str, EnumDerivation]] = Field(default_factory=dict, description="""Instructions on how to derive a set of enums in the target schema""", json_schema_extra = { "linkml_meta": {'alias': 'enum_derivations', 'domain_of': ['TransformationSpecification']} }) - slot_derivations: Optional[Dict[str, SlotDerivation]] = Field(default_factory=dict, description="""Instructions on how to derive a set of top level slots in the target schema""", json_schema_extra = { "linkml_meta": {'alias': 'slot_derivations', - 'domain_of': ['TransformationSpecification', 'ClassDerivation']} }) - description: Optional[str] = Field(default=None, description="""description of the specification component""", json_schema_extra = { "linkml_meta": {'alias': 'description', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'dcterms:description'} }) - implements: Optional[List[str]] = Field(default_factory=list, description="""A reference to a specification that this component implements.""", json_schema_extra = { "linkml_meta": {'alias': 'implements', 'domain_of': ['SpecificationComponent']} }) - comments: Optional[List[str]] = Field(default_factory=list, description="""A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use.""", json_schema_extra = { "linkml_meta": {'alias': 'comments', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'rdfs:comment'} }) - - -class ElementDerivation(SpecificationComponent): - """ - An abstract grouping for classes that provide a specification of how to derive a target element from a source element. - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, 'from_schema': 'https://w3id.org/linkml/transformer'}) - - name: str = Field(default=..., description="""Name of the element in the target schema""", json_schema_extra = { "linkml_meta": {'alias': 'name', - 'domain_of': ['ElementDerivation', - 'ObjectDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - copy_directives: Optional[Dict[str, CopyDirective]] = Field(default_factory=dict, json_schema_extra = { "linkml_meta": {'alias': 'copy_directives', - 'domain_of': ['TransformationSpecification', 'ElementDerivation']} }) - overrides: Optional[Any] = Field(default=None, description="""overrides source schema slots""", json_schema_extra = { "linkml_meta": {'alias': 'overrides', 'domain_of': ['ElementDerivation']} }) - is_a: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'is_a', 'domain_of': ['ElementDerivation'], 'slot_uri': 'linkml:is_a'} }) - mixins: Optional[List[str]] = Field(default_factory=list, json_schema_extra = { "linkml_meta": {'alias': 'mixins', - 'domain_of': ['ElementDerivation'], - 'slot_uri': 'linkml:mixins'} }) - value_mappings: Optional[Dict[str, KeyVal]] = Field(default_factory=dict, description="""A mapping table that is applied directly to mappings, in order of precedence""", json_schema_extra = { "linkml_meta": {'alias': 'value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_value_mappings: Optional[Dict[str, KeyVal]] = Field(default_factory=dict, description="""A mapping table in which the keys are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_expression_mappings: Optional[Dict[str, KeyVal]] = Field(default_factory=dict, description="""A mapping table in which the keys and values are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_expression_mappings', - 'domain_of': ['ElementDerivation']} }) - mirror_source: Optional[bool] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'mirror_source', 'domain_of': ['ElementDerivation']} }) - description: Optional[str] = Field(default=None, description="""description of the specification component""", json_schema_extra = { "linkml_meta": {'alias': 'description', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'dcterms:description'} }) - implements: Optional[List[str]] = Field(default_factory=list, description="""A reference to a specification that this component implements.""", json_schema_extra = { "linkml_meta": {'alias': 'implements', 'domain_of': ['SpecificationComponent']} }) - comments: Optional[List[str]] = Field(default_factory=list, description="""A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use.""", json_schema_extra = { "linkml_meta": {'alias': 'comments', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'rdfs:comment'} }) - - -class ClassDerivation(ElementDerivation): - """ - A specification of how to derive a target class from a source class. - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer'}) - - populated_from: Optional[str] = Field(default=None, description="""Name of the class in the source schema""", json_schema_extra = { "linkml_meta": {'alias': 'populated_from', - 'domain_of': ['ClassDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - sources: Optional[List[str]] = Field(default_factory=list, json_schema_extra = { "linkml_meta": {'alias': 'sources', - 'domain_of': ['ClassDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - joins: Optional[Dict[str, AliasedClass]] = Field(default_factory=dict, description="""Additional classes to be joined to derive instances of the target class""", json_schema_extra = { "linkml_meta": {'alias': 'joins', - 'comments': ['not yet implemented'], - 'domain_of': ['ClassDerivation']} }) - slot_derivations: Optional[Dict[str, SlotDerivation]] = Field(default_factory=dict, json_schema_extra = { "linkml_meta": {'alias': 'slot_derivations', - 'domain_of': ['TransformationSpecification', 'ClassDerivation']} }) - target_definition: Optional[Any] = Field(default=None, description="""LinkML class definition object for this slot.""", json_schema_extra = { "linkml_meta": {'alias': 'target_definition', - 'comments': ['currently defined as Any to avoid coupling with metamodel'], - 'domain_of': ['ClassDerivation', 'SlotDerivation']} }) - name: str = Field(default=..., description="""Name of the element in the target schema""", json_schema_extra = { "linkml_meta": {'alias': 'name', - 'domain_of': ['ElementDerivation', - 'ObjectDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - copy_directives: Optional[Dict[str, CopyDirective]] = Field(default_factory=dict, json_schema_extra = { "linkml_meta": {'alias': 'copy_directives', - 'domain_of': ['TransformationSpecification', 'ElementDerivation']} }) - overrides: Optional[Any] = Field(default=None, description="""overrides source schema slots""", json_schema_extra = { "linkml_meta": {'alias': 'overrides', 'domain_of': ['ElementDerivation']} }) - is_a: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'is_a', 'domain_of': ['ElementDerivation'], 'slot_uri': 'linkml:is_a'} }) - mixins: Optional[List[str]] = Field(default_factory=list, json_schema_extra = { "linkml_meta": {'alias': 'mixins', - 'domain_of': ['ElementDerivation'], - 'slot_uri': 'linkml:mixins'} }) - value_mappings: Optional[Dict[str, KeyVal]] = Field(default_factory=dict, description="""A mapping table that is applied directly to mappings, in order of precedence""", json_schema_extra = { "linkml_meta": {'alias': 'value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_value_mappings: Optional[Dict[str, KeyVal]] = Field(default_factory=dict, description="""A mapping table in which the keys are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_expression_mappings: Optional[Dict[str, KeyVal]] = Field(default_factory=dict, description="""A mapping table in which the keys and values are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_expression_mappings', - 'domain_of': ['ElementDerivation']} }) - mirror_source: Optional[bool] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'mirror_source', 'domain_of': ['ElementDerivation']} }) - description: Optional[str] = Field(default=None, description="""description of the specification component""", json_schema_extra = { "linkml_meta": {'alias': 'description', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'dcterms:description'} }) - implements: Optional[List[str]] = Field(default_factory=list, description="""A reference to a specification that this component implements.""", json_schema_extra = { "linkml_meta": {'alias': 'implements', 'domain_of': ['SpecificationComponent']} }) - comments: Optional[List[str]] = Field(default_factory=list, description="""A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use.""", json_schema_extra = { "linkml_meta": {'alias': 'comments', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'rdfs:comment'} }) - - -class ObjectDerivation(ElementDerivation): - """ - Temporary placeholder for object_derivations - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer'}) - - name: Optional[str] = Field(default=None, description="""Name of the element in the target schema""", json_schema_extra = { "linkml_meta": {'alias': 'name', - 'domain_of': ['ElementDerivation', - 'ObjectDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - class_derivations: Optional[Dict[str, ClassDerivation]] = Field(default_factory=dict, json_schema_extra = { "linkml_meta": {'alias': 'class_derivations', - 'domain_of': ['TransformationSpecification', 'ObjectDerivation']} }) - copy_directives: Optional[Dict[str, CopyDirective]] = Field(default_factory=dict, json_schema_extra = { "linkml_meta": {'alias': 'copy_directives', - 'domain_of': ['TransformationSpecification', 'ElementDerivation']} }) - overrides: Optional[Any] = Field(default=None, description="""overrides source schema slots""", json_schema_extra = { "linkml_meta": {'alias': 'overrides', 'domain_of': ['ElementDerivation']} }) - is_a: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'is_a', 'domain_of': ['ElementDerivation'], 'slot_uri': 'linkml:is_a'} }) - mixins: Optional[List[str]] = Field(default_factory=list, json_schema_extra = { "linkml_meta": {'alias': 'mixins', - 'domain_of': ['ElementDerivation'], - 'slot_uri': 'linkml:mixins'} }) - value_mappings: Optional[Dict[str, KeyVal]] = Field(default_factory=dict, description="""A mapping table that is applied directly to mappings, in order of precedence""", json_schema_extra = { "linkml_meta": {'alias': 'value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_value_mappings: Optional[Dict[str, KeyVal]] = Field(default_factory=dict, description="""A mapping table in which the keys are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_expression_mappings: Optional[Dict[str, KeyVal]] = Field(default_factory=dict, description="""A mapping table in which the keys and values are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_expression_mappings', - 'domain_of': ['ElementDerivation']} }) - mirror_source: Optional[bool] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'mirror_source', 'domain_of': ['ElementDerivation']} }) - description: Optional[str] = Field(default=None, description="""description of the specification component""", json_schema_extra = { "linkml_meta": {'alias': 'description', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'dcterms:description'} }) - implements: Optional[List[str]] = Field(default_factory=list, description="""A reference to a specification that this component implements.""", json_schema_extra = { "linkml_meta": {'alias': 'implements', 'domain_of': ['SpecificationComponent']} }) - comments: Optional[List[str]] = Field(default_factory=list, description="""A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use.""", json_schema_extra = { "linkml_meta": {'alias': 'comments', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'rdfs:comment'} }) - - -class AliasedClass(ConfiguredBaseModel): - """ - alias-class key value pairs for classes - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer'}) - - alias: str = Field(default=..., description="""name of the class to be aliased""", json_schema_extra = { "linkml_meta": {'alias': 'alias', 'domain_of': ['AliasedClass']} }) - class_named: Optional[str] = Field(default=None, description="""local alias for the class""", json_schema_extra = { "linkml_meta": {'alias': 'class_named', 'domain_of': ['AliasedClass']} }) - - -class SlotDerivation(ElementDerivation): - """ - A specification of how to derive the value of a target slot from a source slot - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer'}) - - name: str = Field(default=..., description="""Target slot name""", json_schema_extra = { "linkml_meta": {'alias': 'name', - 'domain_of': ['ElementDerivation', - 'ObjectDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - populated_from: Optional[str] = Field(default=None, description="""Source slot name""", json_schema_extra = { "linkml_meta": {'alias': 'populated_from', - 'domain_of': ['ClassDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - sources: Optional[List[str]] = Field(default_factory=list, json_schema_extra = { "linkml_meta": {'alias': 'sources', - 'domain_of': ['ClassDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - object_derivations: Optional[List[ObjectDerivation]] = Field(default_factory=list, description="""One or more object derivations used to construct the slot value(s), which must be instances of a class.""", json_schema_extra = { "linkml_meta": {'alias': 'object_derivations', 'domain_of': ['SlotDerivation']} }) - derived_from: Optional[List[str]] = Field(default_factory=list, description="""Source slots that are used to derive this slot. This can be computed from the expr, if the expr is declarative.""", json_schema_extra = { "linkml_meta": {'alias': 'derived_from', 'domain_of': ['SlotDerivation']} }) - expr: Optional[str] = Field(default=None, description="""An expression to be evaluated on the source object to derive the target slot. Should be specified using the LinkML expression language.""", json_schema_extra = { "linkml_meta": {'alias': 'expr', - 'domain_of': ['SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - value: Optional[Any] = Field(default=None, description="""A constant value to assign to the target slot.""", json_schema_extra = { "linkml_meta": {'alias': 'value', 'domain_of': ['SlotDerivation', 'KeyVal']} }) - range: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'range', 'domain_of': ['SlotDerivation'], 'slot_uri': 'linkml:range'} }) - unit_conversion: Optional[UnitConversionConfiguration] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'unit_conversion', 'domain_of': ['SlotDerivation']} }) - inverse_of: Optional[Inverse] = Field(default=None, description="""Used to specify a class-slot tuple that is the inverse of the derived/target slot. This is used primarily for mapping to relational databases or formalisms that do not allow multiple values. The class representing the repeated element has a foreign key slot inserted in that 'back references' the original multivalued slot.""", json_schema_extra = { "linkml_meta": {'alias': 'inverse_of', 'domain_of': ['SlotDerivation']} }) - hide: Optional[bool] = Field(default=None, description="""True if this is suppressed""", json_schema_extra = { "linkml_meta": {'alias': 'hide', - 'domain_of': ['SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - type_designator: Optional[bool] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'type_designator', 'domain_of': ['SlotDerivation']} }) - target_definition: Optional[Any] = Field(default=None, description="""LinkML definition object for this slot.""", json_schema_extra = { "linkml_meta": {'alias': 'target_definition', - 'comments': ['currently defined as Any to avoid coupling with metamodel'], - 'domain_of': ['ClassDerivation', 'SlotDerivation']} }) - cast_collection_as: Optional[CollectionType] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'cast_collection_as', 'domain_of': ['SlotDerivation']} }) - dictionary_key: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'dictionary_key', 'domain_of': ['SlotDerivation']} }) - stringification: Optional[StringificationConfiguration] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'stringification', 'domain_of': ['SlotDerivation']} }) - aggregation_operation: Optional[AggregationOperation] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'aggregation_operation', 'domain_of': ['SlotDerivation']} }) - copy_directives: Optional[Dict[str, CopyDirective]] = Field(default_factory=dict, json_schema_extra = { "linkml_meta": {'alias': 'copy_directives', - 'domain_of': ['TransformationSpecification', 'ElementDerivation']} }) - overrides: Optional[Any] = Field(default=None, description="""overrides source schema slots""", json_schema_extra = { "linkml_meta": {'alias': 'overrides', 'domain_of': ['ElementDerivation']} }) - is_a: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'is_a', 'domain_of': ['ElementDerivation'], 'slot_uri': 'linkml:is_a'} }) - mixins: Optional[List[str]] = Field(default_factory=list, json_schema_extra = { "linkml_meta": {'alias': 'mixins', - 'domain_of': ['ElementDerivation'], - 'slot_uri': 'linkml:mixins'} }) - value_mappings: Optional[Dict[str, KeyVal]] = Field(default_factory=dict, description="""A mapping table that is applied directly to mappings, in order of precedence""", json_schema_extra = { "linkml_meta": {'alias': 'value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_value_mappings: Optional[Dict[str, KeyVal]] = Field(default_factory=dict, description="""A mapping table in which the keys are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_expression_mappings: Optional[Dict[str, KeyVal]] = Field(default_factory=dict, description="""A mapping table in which the keys and values are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_expression_mappings', - 'domain_of': ['ElementDerivation']} }) - mirror_source: Optional[bool] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'mirror_source', 'domain_of': ['ElementDerivation']} }) - description: Optional[str] = Field(default=None, description="""description of the specification component""", json_schema_extra = { "linkml_meta": {'alias': 'description', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'dcterms:description'} }) - implements: Optional[List[str]] = Field(default_factory=list, description="""A reference to a specification that this component implements.""", json_schema_extra = { "linkml_meta": {'alias': 'implements', 'domain_of': ['SpecificationComponent']} }) - comments: Optional[List[str]] = Field(default_factory=list, description="""A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use.""", json_schema_extra = { "linkml_meta": {'alias': 'comments', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'rdfs:comment'} }) - - -class EnumDerivation(ElementDerivation): - """ - A specification of how to derive the value of a target enum from a source enum - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer'}) - - name: str = Field(default=..., description="""Target enum name""", json_schema_extra = { "linkml_meta": {'alias': 'name', - 'domain_of': ['ElementDerivation', - 'ObjectDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - populated_from: Optional[str] = Field(default=None, description="""Source enum name""", json_schema_extra = { "linkml_meta": {'alias': 'populated_from', - 'domain_of': ['ClassDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - sources: Optional[List[str]] = Field(default_factory=list, json_schema_extra = { "linkml_meta": {'alias': 'sources', - 'domain_of': ['ClassDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - expr: Optional[str] = Field(default=None, description="""An expression to be evaluated on the source object to derive the target slot. Should be specified using the LinkML expression language.""", json_schema_extra = { "linkml_meta": {'alias': 'expr', - 'domain_of': ['SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - hide: Optional[bool] = Field(default=None, description="""True if this is suppressed""", json_schema_extra = { "linkml_meta": {'alias': 'hide', - 'domain_of': ['SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - permissible_value_derivations: Optional[Dict[str, PermissibleValueDerivation]] = Field(default_factory=dict, description="""Instructions on how to derive a set of PVs in the target schema""", json_schema_extra = { "linkml_meta": {'alias': 'permissible_value_derivations', 'domain_of': ['EnumDerivation']} }) - copy_directives: Optional[Dict[str, CopyDirective]] = Field(default_factory=dict, json_schema_extra = { "linkml_meta": {'alias': 'copy_directives', - 'domain_of': ['TransformationSpecification', 'ElementDerivation']} }) - overrides: Optional[Any] = Field(default=None, description="""overrides source schema slots""", json_schema_extra = { "linkml_meta": {'alias': 'overrides', 'domain_of': ['ElementDerivation']} }) - is_a: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'is_a', 'domain_of': ['ElementDerivation'], 'slot_uri': 'linkml:is_a'} }) - mixins: Optional[List[str]] = Field(default_factory=list, json_schema_extra = { "linkml_meta": {'alias': 'mixins', - 'domain_of': ['ElementDerivation'], - 'slot_uri': 'linkml:mixins'} }) - value_mappings: Optional[Dict[str, KeyVal]] = Field(default_factory=dict, description="""A mapping table that is applied directly to mappings, in order of precedence""", json_schema_extra = { "linkml_meta": {'alias': 'value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_value_mappings: Optional[Dict[str, KeyVal]] = Field(default_factory=dict, description="""A mapping table in which the keys are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_expression_mappings: Optional[Dict[str, KeyVal]] = Field(default_factory=dict, description="""A mapping table in which the keys and values are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_expression_mappings', - 'domain_of': ['ElementDerivation']} }) - mirror_source: Optional[bool] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'mirror_source', 'domain_of': ['ElementDerivation']} }) - description: Optional[str] = Field(default=None, description="""description of the specification component""", json_schema_extra = { "linkml_meta": {'alias': 'description', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'dcterms:description'} }) - implements: Optional[List[str]] = Field(default_factory=list, description="""A reference to a specification that this component implements.""", json_schema_extra = { "linkml_meta": {'alias': 'implements', 'domain_of': ['SpecificationComponent']} }) - comments: Optional[List[str]] = Field(default_factory=list, description="""A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use.""", json_schema_extra = { "linkml_meta": {'alias': 'comments', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'rdfs:comment'} }) - - -class PermissibleValueDerivation(ElementDerivation): - """ - A specification of how to derive the value of a PV from a source enum - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer', - 'todos': ['this is currently under-specified. We will need boolean ' - 'combinators to express if-then-else']}) - - name: str = Field(default=..., description="""Target permissible value text""", json_schema_extra = { "linkml_meta": {'alias': 'name', - 'domain_of': ['ElementDerivation', - 'ObjectDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - expr: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'expr', - 'domain_of': ['SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - populated_from: Optional[str] = Field(default=None, description="""Source permissible value""", json_schema_extra = { "linkml_meta": {'alias': 'populated_from', - 'domain_of': ['ClassDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - sources: Optional[List[str]] = Field(default_factory=list, json_schema_extra = { "linkml_meta": {'alias': 'sources', - 'domain_of': ['ClassDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - hide: Optional[bool] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'hide', - 'domain_of': ['SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - copy_directives: Optional[Dict[str, CopyDirective]] = Field(default_factory=dict, json_schema_extra = { "linkml_meta": {'alias': 'copy_directives', - 'domain_of': ['TransformationSpecification', 'ElementDerivation']} }) - overrides: Optional[Any] = Field(default=None, description="""overrides source schema slots""", json_schema_extra = { "linkml_meta": {'alias': 'overrides', 'domain_of': ['ElementDerivation']} }) - is_a: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'is_a', 'domain_of': ['ElementDerivation'], 'slot_uri': 'linkml:is_a'} }) - mixins: Optional[List[str]] = Field(default_factory=list, json_schema_extra = { "linkml_meta": {'alias': 'mixins', - 'domain_of': ['ElementDerivation'], - 'slot_uri': 'linkml:mixins'} }) - value_mappings: Optional[Dict[str, KeyVal]] = Field(default_factory=dict, description="""A mapping table that is applied directly to mappings, in order of precedence""", json_schema_extra = { "linkml_meta": {'alias': 'value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_value_mappings: Optional[Dict[str, KeyVal]] = Field(default_factory=dict, description="""A mapping table in which the keys are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_expression_mappings: Optional[Dict[str, KeyVal]] = Field(default_factory=dict, description="""A mapping table in which the keys and values are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_expression_mappings', - 'domain_of': ['ElementDerivation']} }) - mirror_source: Optional[bool] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'mirror_source', 'domain_of': ['ElementDerivation']} }) - description: Optional[str] = Field(default=None, description="""description of the specification component""", json_schema_extra = { "linkml_meta": {'alias': 'description', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'dcterms:description'} }) - implements: Optional[List[str]] = Field(default_factory=list, description="""A reference to a specification that this component implements.""", json_schema_extra = { "linkml_meta": {'alias': 'implements', 'domain_of': ['SpecificationComponent']} }) - comments: Optional[List[str]] = Field(default_factory=list, description="""A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use.""", json_schema_extra = { "linkml_meta": {'alias': 'comments', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'rdfs:comment'} }) - - -class PrefixDerivation(ElementDerivation): - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer'}) - - name: str = Field(default=..., description="""Name of the element in the target schema""", json_schema_extra = { "linkml_meta": {'alias': 'name', - 'domain_of': ['ElementDerivation', - 'ObjectDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - copy_directives: Optional[Dict[str, CopyDirective]] = Field(default_factory=dict, json_schema_extra = { "linkml_meta": {'alias': 'copy_directives', - 'domain_of': ['TransformationSpecification', 'ElementDerivation']} }) - overrides: Optional[Any] = Field(default=None, description="""overrides source schema slots""", json_schema_extra = { "linkml_meta": {'alias': 'overrides', 'domain_of': ['ElementDerivation']} }) - is_a: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'is_a', 'domain_of': ['ElementDerivation'], 'slot_uri': 'linkml:is_a'} }) - mixins: Optional[List[str]] = Field(default_factory=list, json_schema_extra = { "linkml_meta": {'alias': 'mixins', - 'domain_of': ['ElementDerivation'], - 'slot_uri': 'linkml:mixins'} }) - value_mappings: Optional[Dict[str, KeyVal]] = Field(default_factory=dict, description="""A mapping table that is applied directly to mappings, in order of precedence""", json_schema_extra = { "linkml_meta": {'alias': 'value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_value_mappings: Optional[Dict[str, KeyVal]] = Field(default_factory=dict, description="""A mapping table in which the keys are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_expression_mappings: Optional[Dict[str, KeyVal]] = Field(default_factory=dict, description="""A mapping table in which the keys and values are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_expression_mappings', - 'domain_of': ['ElementDerivation']} }) - mirror_source: Optional[bool] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'mirror_source', 'domain_of': ['ElementDerivation']} }) - description: Optional[str] = Field(default=None, description="""description of the specification component""", json_schema_extra = { "linkml_meta": {'alias': 'description', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'dcterms:description'} }) - implements: Optional[List[str]] = Field(default_factory=list, description="""A reference to a specification that this component implements.""", json_schema_extra = { "linkml_meta": {'alias': 'implements', 'domain_of': ['SpecificationComponent']} }) - comments: Optional[List[str]] = Field(default_factory=list, description="""A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use.""", json_schema_extra = { "linkml_meta": {'alias': 'comments', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'rdfs:comment'} }) - - -class UnitConversionConfiguration(ConfiguredBaseModel): - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer'}) - - target_unit: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'target_unit', 'domain_of': ['UnitConversionConfiguration']} }) - target_unit_scheme: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'target_unit_scheme', - 'domain_of': ['UnitConversionConfiguration'], - 'examples': [{'value': 'ucum'}]} }) - source_unit: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'source_unit', 'domain_of': ['UnitConversionConfiguration']} }) - source_unit_scheme: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'source_unit_scheme', - 'domain_of': ['UnitConversionConfiguration'], - 'examples': [{'value': 'ucum'}]} }) - source_unit_slot: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'source_unit_slot', 'domain_of': ['UnitConversionConfiguration']} }) - source_magnitude_slot: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'source_magnitude_slot', 'domain_of': ['UnitConversionConfiguration']} }) - target_unit_slot: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'target_unit_slot', 'domain_of': ['UnitConversionConfiguration']} }) - target_magnitude_slot: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'target_magnitude_slot', 'domain_of': ['UnitConversionConfiguration']} }) - - -class StringificationConfiguration(ConfiguredBaseModel): - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer'}) - - delimiter: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'delimiter', - 'domain_of': ['StringificationConfiguration'], - 'examples': [{'value': ','}, {'value': '|'}, {'value': ';'}]} }) - reversed: Optional[bool] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'reversed', 'domain_of': ['StringificationConfiguration']} }) - over_slots: Optional[List[str]] = Field(default_factory=list, json_schema_extra = { "linkml_meta": {'alias': 'over_slots', 'domain_of': ['StringificationConfiguration']} }) - syntax: Optional[SerializationSyntaxType] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'syntax', - 'domain_of': ['StringificationConfiguration'], - 'examples': [{'value': 'json'}, {'value': 'yaml'}]} }) - - -class Inverse(ConfiguredBaseModel): - """ - Used for back references in mapping to relational model - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'aliases': ['backref', 'back_references'], - 'from_schema': 'https://w3id.org/linkml/transformer'}) - - slot_name: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'slot_name', 'domain_of': ['Inverse']} }) - class_name: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'class_name', 'domain_of': ['Inverse']} }) - - -class TransformationOperation(ConfiguredBaseModel): - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, 'from_schema': 'https://w3id.org/linkml/transformer'}) - - pass - - -class AggregationOperation(TransformationOperation): - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer'}) - - operator: AggregationType = Field(default=..., json_schema_extra = { "linkml_meta": {'alias': 'operator', 'domain_of': ['AggregationOperation']} }) - null_handling: Optional[InvalidValueHandlingStrategy] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'null_handling', - 'domain_of': ['AggregationOperation', 'GroupingOperation']} }) - invalid_value_handling: Optional[InvalidValueHandlingStrategy] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'invalid_value_handling', 'domain_of': ['AggregationOperation']} }) - - -class GroupingOperation(TransformationOperation): - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer'}) - - null_handling: Optional[InvalidValueHandlingStrategy] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'null_handling', - 'domain_of': ['AggregationOperation', 'GroupingOperation']} }) - - -class PivotOperation(TransformationOperation): - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'aliases': ['melt/unmelt', 'reification/dereification'], - 'from_schema': 'https://w3id.org/linkml/transformer'}) - - direction: PivotDirectionType = Field(default=..., json_schema_extra = { "linkml_meta": {'alias': 'direction', 'domain_of': ['PivotOperation']} }) - variable_slot: Optional[str] = Field(default="variable", description="""Slot to use for the variable column in the melted/long representation. In EAV this is the name of the 'A' variable""", json_schema_extra = { "linkml_meta": {'alias': 'variable_slot', - 'aliases': ['var_name'], - 'domain_of': ['PivotOperation'], - 'ifabsent': 'string(variable)'} }) - value_slot: Optional[str] = Field(default="value", description="""Slot to use for the value column in the melted/long representation. In EAV this is the name of the 'V' variable""", json_schema_extra = { "linkml_meta": {'alias': 'value_slot', - 'aliases': ['value_name'], - 'domain_of': ['PivotOperation'], - 'ifabsent': 'string(value)'} }) - unmelt_to_class: Optional[str] = Field(default=None, description="""In an unmelt operation, attributes (which are values in the long/melted/EAV representation) must conform to valid attributes in this class""", json_schema_extra = { "linkml_meta": {'alias': 'unmelt_to_class', 'domain_of': ['PivotOperation']} }) - unmelt_to_slots: Optional[List[str]] = Field(default_factory=list, json_schema_extra = { "linkml_meta": {'alias': 'unmelt_to_slots', 'domain_of': ['PivotOperation']} }) - - -class KeyVal(ConfiguredBaseModel): - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer'}) - - key: str = Field(default=..., json_schema_extra = { "linkml_meta": {'alias': 'key', 'domain_of': ['KeyVal']} }) - value: Optional[Any] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'value', 'domain_of': ['SlotDerivation', 'KeyVal']} }) - - -class CopyDirective(ConfiguredBaseModel): - """ - Instructs a Schema Mapper in how to map to a target schema. Not used for data transformation. - This is the process to process a directive: 1. If `copy_all`, add all sub-elements to the list of sub-elements to be copied. 2. If `exclude`, remove the specified sub-elements from the above list. 3. If `exclude_all`, clean-up the above list. Effectively making previous steps useless. 4. If `include`, add the specified sub-elements from the list result of previous steps. - Implementations might decide to somehow report (error, warning,...) meaningless combinations (like specifying `copy_all` and `exclude_all`). - Validation on the correctness of the resulting derived schema might be done optionally by the implementation. For example, removing a slot but keeping a class that requires it would invalidate the derived-schema. It is always possible to validate the schema with the LinkML linter after derivation. - What are the considered sub-elements depends on the calls of Element to be transformed. For example, for a class they are `slots` and `attributes`. - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer', 'status': 'testing'}) - - element_name: str = Field(default=..., json_schema_extra = { "linkml_meta": {'alias': 'element_name', 'domain_of': ['CopyDirective']} }) - copy_all: Optional[bool] = Field(default=None, description="""Copy all sub-elements of the Element being derived.""", json_schema_extra = { "linkml_meta": {'alias': 'copy_all', 'domain_of': ['CopyDirective']} }) - exclude_all: Optional[bool] = Field(default=None, description="""Do not copy any of the sub-elements of the Element being derived.""", json_schema_extra = { "linkml_meta": {'alias': 'exclude_all', 'domain_of': ['CopyDirective']} }) - exclude: Optional[Any] = Field(default=None, description="""Remove certain sub-elements from the list of sub-elements to be copied. -As of now there it is under-specified, how to specify the sub-elements to exclude. One possible implementation would be a list where all element types can be mixed, since there might not be name conflicts across element types.""", json_schema_extra = { "linkml_meta": {'alias': 'exclude', 'domain_of': ['CopyDirective']} }) - include: Optional[Any] = Field(default=None, description="""Add certain sub-elements to the list of sub-elements to be copied. -As of now there it is under-specified, how to specify the sub-elements to include. One possible implementation would be a list where all element types can be mixed, since there might not be name conflicts across element types.""", json_schema_extra = { "linkml_meta": {'alias': 'include', 'domain_of': ['CopyDirective']} }) - add: Optional[Any] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'add', 'domain_of': ['CopyDirective']} }) - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -SpecificationComponent.model_rebuild() -TransformationSpecification.model_rebuild() -ElementDerivation.model_rebuild() -ClassDerivation.model_rebuild() -ObjectDerivation.model_rebuild() -AliasedClass.model_rebuild() -SlotDerivation.model_rebuild() -EnumDerivation.model_rebuild() -PermissibleValueDerivation.model_rebuild() -PrefixDerivation.model_rebuild() -UnitConversionConfiguration.model_rebuild() -StringificationConfiguration.model_rebuild() -Inverse.model_rebuild() -TransformationOperation.model_rebuild() -AggregationOperation.model_rebuild() -GroupingOperation.model_rebuild() -PivotOperation.model_rebuild() -KeyVal.model_rebuild() -CopyDirective.model_rebuild() - diff --git a/src/linkml_map/datamodel/transformer_model.yaml b/src/linkml_map/datamodel/transformer_model.yaml deleted file mode 100644 index e2acb12..0000000 --- a/src/linkml_map/datamodel/transformer_model.yaml +++ /dev/null @@ -1,533 +0,0 @@ -id: https://w3id.org/linkml/transformer -name: linkml-map -title: LinkML Map Data Model -description: |- - Datamodel for LinkML schema mappings and transformations. - - A mapper generates instances of a *target* data model from - instances of a *source* data model. This transformation process - is guided by a *TransformationSpecification*. - - The specification is independent of any one method for transforming - data. It allows different approaches, including: - - - direct implementation, transforming python or json objects - - translation of the specification into SQL commands, to operate on relations - - translation of the specification into SPARQL CONSTRUCTs, to operate on triples - - translation into another specification language, such as R2RML -prefixes: - linkml: https://w3id.org/linkml/ - linkmlmap: https://w3id.org/linkml/transformer/ - dcterms: http://purl.org/dc/terms/ - schema: http://schema.org/ - rdfs: http://www.w3.org/2000/01/rdf-schema# - sh: http://www.w3.org/ns/shacl# - STATO: http://purl.obolibrary.org/obo/STATO_ -default_prefix: linkmlmap - -imports: - - linkml:types - -types: - - ClassReference: - typeof: string - - SlotReference: - typeof: string - - EnumReference: - typeof: string - -classes: - - Any: - class_uri: linkml:Any - - SpecificationComponent: - abstract: true - attributes: - description: - description: description of the specification component - slot_uri: dcterms:description - implements: - description: A reference to a specification that this component implements. - multivalued: true - range: uriorcurie - comments: - description: >- - A list of comments about this component. Comments are free text, and may be - used to provide additional information about the component, including - instructions for its use. - multivalued: true - range: string - slot_uri: rdfs:comment - - TransformationSpecification: - is_a: SpecificationComponent - description: A collection of mappings between source and target classes - tree_root: true - attributes: - id: - # identifier: true - description: Unique identifier for this transformation specification - slot_uri: schema:identifier - title: - description: human readable title for this transformation specification - slot_uri: dcterms:title - prefixes: - description: maps prefixes to URL expansions - range: KeyVal - multivalued: true - inlined: true - slot_uri: sh:declare - copy_directives: - range: CopyDirective - multivalued: true - inlined: true - source_schema: - description: name of the schema that describes the source (input) objects - target_schema: - description: name of the schema that describes the target (output) objects - class_derivations: - description: >- - Instructions on how to derive a set of classes in the target schema - from classes in the source schema. - range: ClassDerivation - multivalued: true - inlined: true - enum_derivations: - description: >- - Instructions on how to derive a set of enums in the target schema - range: EnumDerivation - multivalued: true - inlined: true - slot_derivations: - description: >- - Instructions on how to derive a set of top level slots in the target schema - range: SlotDerivation - multivalued: true - inlined: true - - ElementDerivation: - is_a: SpecificationComponent - abstract: true - description: >- - An abstract grouping for classes that provide a specification of how to - derive a target element from a source element. - attributes: - name: - key: true - description: Name of the element in the target schema - copy_directives: - range: CopyDirective - multivalued: true - inlined: true - overrides: - description: overrides source schema slots - range: Any - #multivalued: true - #inlined: true - is_a: - range: ElementDerivation - slot_uri: linkml:is_a - mixins: - range: ElementDerivation - multivalued: true - inlined: false - slot_uri: linkml:mixins - value_mappings: - range: KeyVal - multivalued: true - inlined: true - description: >- - A mapping table that is applied directly to mappings, in order of precedence - expression_to_value_mappings: - range: KeyVal - multivalued: true - inlined: true - description: >- - A mapping table in which the keys are expressions - expression_to_expression_mappings: - range: KeyVal - multivalued: true - inlined: true - description: >- - A mapping table in which the keys and values are expressions - mirror_source: - range: boolean - - - ClassDerivation: - is_a: ElementDerivation - description: >- - A specification of how to derive a target class from a source class. - attributes: - #name: - # key: true - # description: Name of the class in the target schema - populated_from: - range: ClassReference - description: Name of the class in the source schema - sources: - range: ClassReference - multivalued: true - joins: - range: AliasedClass - multivalued: true - inlined: true - description: Additional classes to be joined to derive instances of the target class - comments: - - not yet implemented - slot_derivations: - range: SlotDerivation - multivalued: true - inlined: true - target_definition: - range: Any - description: >- - LinkML class definition object for this slot. - comments: - - currently defined as Any to avoid coupling with metamodel - - ObjectDerivation: - is_a: ElementDerivation - description: Temporary placeholder for object_derivations - attributes: - name: - description: Name of the element in the target schema - required: false - class_derivations: - range: ClassDerivation - multivalued: true - inlined: true - - AliasedClass: - description: alias-class key value pairs for classes - attributes: - alias: - key: true - description: name of the class to be aliased - class_named: - description: local alias for the class - - SlotDerivation: - is_a: ElementDerivation - description: A specification of how to derive the value of a target slot from a source slot - attributes: - name: - key: true - description: Target slot name - populated_from: - range: SlotReference - description: Source slot name - sources: - range: SlotReference - multivalued: true - object_derivations: - description: >- - One or more object derivations used to construct the slot value(s), - which must be instances of a class. - range: ObjectDerivation - multivalued: true - inlined: true - inlined_as_list: true - derived_from: - range: SlotReference - multivalued: true - description: Source slots that are used to derive this slot. This can be computed from the expr, - if the expr is declarative. - expr: - range: string - description: >- - An expression to be evaluated on the source object to derive the target slot. - Should be specified using the LinkML expression language. - value: - range: Any - description: >- - A constant value to assign to the target slot. - range: - slot_uri: linkml:range - range: string - unit_conversion: - range: UnitConversionConfiguration - inverse_of: - range: Inverse - description: >- - Used to specify a class-slot tuple that is the inverse of the derived/target slot. - This is used primarily for mapping to relational databases or formalisms that do - not allow multiple values. The class representing the repeated element has a foreign - key slot inserted in that 'back references' the original multivalued slot. - hide: - range: boolean - description: True if this is suppressed - type_designator: - range: boolean - target_definition: - range: Any - description: >- - LinkML definition object for this slot. - comments: - - currently defined as Any to avoid coupling with metamodel - cast_collection_as: - range: CollectionType - dictionary_key: - range: string - stringification: - range: StringificationConfiguration - aggregation_operation: - range: AggregationOperation - - EnumDerivation: - is_a: ElementDerivation - description: A specification of how to derive the value of a target enum from a source enum - attributes: - name: - key: true - description: Target enum name - populated_from: - range: EnumReference - description: Source enum name - sources: - range: EnumReference - multivalued: true - expr: - range: string - description: >- - An expression to be evaluated on the source object to derive the target slot. - Should be specified using the LinkML expression language. - hide: - range: boolean - description: True if this is suppressed - permissible_value_derivations: - description: Instructions on how to derive a set of PVs in the target schema - range: PermissibleValueDerivation - multivalued: true - inlined: true - - PermissibleValueDerivation: - is_a: ElementDerivation - description: A specification of how to derive the value of a PV from a source enum - todos: - - this is currently under-specified. We will need boolean combinators to express if-then-else - attributes: - name: - key: true - description: Target permissible value text - expr: - range: string - populated_from: - range: string - description: Source permissible value - sources: - range: string - multivalued: true - hide: - range: boolean - - PrefixDerivation: - is_a: ElementDerivation - - UnitConversionConfiguration: - attributes: - target_unit: - target_unit_scheme: - range: string - examples: - - value: ucum - source_unit: - source_unit_scheme: - range: string - examples: - - value: ucum - source_unit_slot: - source_magnitude_slot: - target_unit_slot: - target_magnitude_slot: - - StringificationConfiguration: - attributes: - delimiter: - range: string - examples: - - value: ',' - - value: '|' - - value: ';' - reversed: - range: boolean - over_slots: - range: string - multivalued: true - syntax: - range: SerializationSyntaxType - examples: - - value: 'json' - - value: 'yaml' - - Inverse: - description: Used for back references in mapping to relational model - aliases: - - backref - - back_references - attributes: - slot_name: - class_name: - - TransformationOperation: - abstract: true - - AggregationOperation: - is_a: TransformationOperation - attributes: - operator: - range: AggregationType - required: true - null_handling: - range: InvalidValueHandlingStrategy - invalid_value_handling: - range: InvalidValueHandlingStrategy - - GroupingOperation: - is_a: TransformationOperation - attributes: - null_handling: - range: InvalidValueHandlingStrategy - - PivotOperation: - aliases: - - melt/unmelt - - reification/dereification - is_a: TransformationOperation - attributes: - direction: - range: PivotDirectionType - required: true - variable_slot: - aliases: - - var_name - range: SlotReference - ifabsent: string(variable) - description: Slot to use for the variable column in the melted/long representation. - In EAV this is the name of the 'A' variable - value_slot: - aliases: - - value_name - range: SlotReference - ifabsent: string(value) - description: Slot to use for the value column in the melted/long representation. - In EAV this is the name of the 'V' variable - unmelt_to_class: - description: In an unmelt operation, attributes (which are values in the long/melted/EAV - representation) must conform to valid attributes in this class - range: ClassReference - unmelt_to_slots: - range: SlotReference - multivalued: true - - KeyVal: - attributes: - key: - key: true - value: - range: Any - - CopyDirective: - description: >- - Instructs a Schema Mapper in how to map to a target schema. Not used for data transformation. - - This is the process to process a directive: - 1. If `copy_all`, add all sub-elements to the list of sub-elements to be copied. - 2. If `exclude`, remove the specified sub-elements from the above list. - 3. If `exclude_all`, clean-up the above list. Effectively making previous steps useless. - 4. If `include`, add the specified sub-elements from the list result of previous steps. - - Implementations might decide to somehow report (error, warning,...) meaningless combinations (like specifying `copy_all` and `exclude_all`). - - Validation on the correctness of the resulting derived schema might be done optionally by the implementation. - For example, removing a slot but keeping a class that requires it would invalidate the derived-schema. - It is always possible to validate the schema with the LinkML linter after derivation. - - What are the considered sub-elements depends on the calls of Element to be transformed. - For example, for a class they are `slots` and `attributes`. - status: testing - attributes: - element_name: - key: true - copy_all: - range: boolean - description: Copy all sub-elements of the Element being derived. - exclude_all: - range: boolean - description: Do not copy any of the sub-elements of the Element being derived. - exclude: - range: Any - description: >- - Remove certain sub-elements from the list of sub-elements to be copied. - - As of now there it is under-specified, how to specify the sub-elements to exclude. - One possible implementation would be a list where all element types can be mixed, since there might not be name conflicts across element types. - include: - range: Any - description: >- - Add certain sub-elements to the list of sub-elements to be copied. - - As of now there it is under-specified, how to specify the sub-elements to include. - One possible implementation would be a list where all element types can be mixed, since there might not be name conflicts across element types. - add: - range: Any - -enums: - CollectionType: - permissible_values: - SingleValued: - MultiValued: - MultiValuedList: - MultiValuedDict: - SerializationSyntaxType: - permissible_values: - JSON: - YAML: - TURTLE: - AggregationType: - permissible_values: - SUM: - AVERAGE: - aliases: - - mean - - avg - exact_mappings: - - STATO:0000230 - COUNT: - exact_mappings: - - STATO:0000047 - MIN: - MAX: - STD_DEV: - exact_mappings: - - STATO:0000237 - VARIANCE: - MEDIAN: - exact_mappings: - - STATO:0000674 - MODE: - exact_mappings: - - STATO:0000033 - CUSTOM: - SET: - LIST: - ARRAY: - InvalidValueHandlingStrategy: - permissible_values: - IGNORE: - TREAT_AS_ZERO: - ERROR_OUT: - PivotDirectionType: - permissible_values: - MELT: - aliases: - - unpivot - - wide to long - UNMELT: - aliases: - - pivot - - long to wide diff --git a/src/linkml_map/datamodel/transformer_model_new.py b/src/linkml_map/datamodel/transformer_model_new.py deleted file mode 100644 index 3410b69..0000000 --- a/src/linkml_map/datamodel/transformer_model_new.py +++ /dev/null @@ -1,649 +0,0 @@ -from __future__ import annotations - -import re -import sys -from datetime import ( - date, - datetime, - time -) -from decimal import Decimal -from enum import Enum -from typing import ( - Any, - ClassVar, - Dict, - List, - Literal, - Optional, - Union -) - -from pydantic import ( - BaseModel, - ConfigDict, - Field, - RootModel, - field_validator -) - - -metamodel_version = "None" -version = "None" - - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment = True, - validate_default = True, - extra = "forbid", - arbitrary_types_allowed = True, - use_enum_values = True, - strict = False, - ) - pass - - - - -class LinkMLMeta(RootModel): - root: Dict[str, Any] = {} - model_config = ConfigDict(frozen=True) - - def __getattr__(self, key:str): - return getattr(self.root, key) - - def __getitem__(self, key:str): - return self.root[key] - - def __setitem__(self, key:str, value): - self.root[key] = value - - def __contains__(self, key:str) -> bool: - return key in self.root - - -linkml_meta = LinkMLMeta({'default_prefix': 'linkmlmap', - 'description': 'Datamodel for LinkML schema mappings and transformations.\n' - '\n' - 'A mapper generates instances of a *target* data model from\n' - 'instances of a *source* data model. This transformation ' - 'process\n' - 'is guided by a *TransformationSpecification*.\n' - '\n' - 'The specification is independent of any one method for ' - 'transforming\n' - 'data. It allows different approaches, including:\n' - '\n' - '- direct implementation, transforming python or json objects\n' - '- translation of the specification into SQL commands, to ' - 'operate on relations\n' - '- translation of the specification into SPARQL CONSTRUCTs, to ' - 'operate on triples\n' - '- translation into another specification language, such as ' - 'R2RML', - 'id': 'https://w3id.org/linkml/transformer', - 'imports': ['linkml:types'], - 'name': 'linkml-map', - 'prefixes': {'STATO': {'prefix_prefix': 'STATO', - 'prefix_reference': 'http://purl.obolibrary.org/obo/STATO_'}, - 'dcterms': {'prefix_prefix': 'dcterms', - 'prefix_reference': 'http://purl.org/dc/terms/'}, - 'linkml': {'prefix_prefix': 'linkml', - 'prefix_reference': 'https://w3id.org/linkml/'}, - 'linkmlmap': {'prefix_prefix': 'linkmlmap', - 'prefix_reference': 'https://w3id.org/linkml/transformer/'}, - 'rdfs': {'prefix_prefix': 'rdfs', - 'prefix_reference': 'http://www.w3.org/2000/01/rdf-schema#'}, - 'schema': {'prefix_prefix': 'schema', - 'prefix_reference': 'http://schema.org/'}, - 'sh': {'prefix_prefix': 'sh', - 'prefix_reference': 'http://www.w3.org/ns/shacl#'}}, - 'source_file': 'src/linkml_map/datamodel/transformer_model.yaml', - 'title': 'LinkML Map Data Model', - 'types': {'ClassReference': {'from_schema': 'https://w3id.org/linkml/transformer', - 'name': 'ClassReference', - 'typeof': 'string'}, - 'EnumReference': {'from_schema': 'https://w3id.org/linkml/transformer', - 'name': 'EnumReference', - 'typeof': 'string'}, - 'SlotReference': {'from_schema': 'https://w3id.org/linkml/transformer', - 'name': 'SlotReference', - 'typeof': 'string'}}} ) - -class CollectionType(str, Enum): - SingleValued = "SingleValued" - MultiValued = "MultiValued" - MultiValuedList = "MultiValuedList" - MultiValuedDict = "MultiValuedDict" - - -class SerializationSyntaxType(str, Enum): - JSON = "JSON" - YAML = "YAML" - TURTLE = "TURTLE" - - -class AggregationType(str, Enum): - SUM = "SUM" - AVERAGE = "AVERAGE" - COUNT = "COUNT" - MIN = "MIN" - MAX = "MAX" - STD_DEV = "STD_DEV" - VARIANCE = "VARIANCE" - MEDIAN = "MEDIAN" - MODE = "MODE" - CUSTOM = "CUSTOM" - SET = "SET" - LIST = "LIST" - ARRAY = "ARRAY" - - -class InvalidValueHandlingStrategy(str, Enum): - IGNORE = "IGNORE" - TREAT_AS_ZERO = "TREAT_AS_ZERO" - ERROR_OUT = "ERROR_OUT" - - -class PivotDirectionType(str, Enum): - MELT = "MELT" - UNMELT = "UNMELT" - - - -class SpecificationComponent(ConfiguredBaseModel): - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, 'from_schema': 'https://w3id.org/linkml/transformer'}) - - description: Optional[str] = Field(default=None, description="""description of the specification component""", json_schema_extra = { "linkml_meta": {'alias': 'description', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'dcterms:description'} }) - implements: Optional[List[str]] = Field(default=None, description="""A reference to a specification that this component implements.""", json_schema_extra = { "linkml_meta": {'alias': 'implements', 'domain_of': ['SpecificationComponent']} }) - comments: Optional[List[str]] = Field(default=None, description="""A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use.""", json_schema_extra = { "linkml_meta": {'alias': 'comments', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'rdfs:comment'} }) - - -class TransformationSpecification(SpecificationComponent): - """ - A collection of mappings between source and target classes - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer', 'tree_root': True}) - - id: Optional[str] = Field(default=None, description="""Unique identifier for this transformation specification""", json_schema_extra = { "linkml_meta": {'alias': 'id', - 'domain_of': ['TransformationSpecification'], - 'slot_uri': 'schema:identifier'} }) - title: Optional[str] = Field(default=None, description="""human readable title for this transformation specification""", json_schema_extra = { "linkml_meta": {'alias': 'title', - 'domain_of': ['TransformationSpecification'], - 'slot_uri': 'dcterms:title'} }) - prefixes: Optional[Dict[str, KeyVal]] = Field(default=None, description="""maps prefixes to URL expansions""", json_schema_extra = { "linkml_meta": {'alias': 'prefixes', - 'domain_of': ['TransformationSpecification'], - 'slot_uri': 'sh:declare'} }) - copy_directives: Optional[Dict[str, CopyDirective]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'copy_directives', - 'domain_of': ['TransformationSpecification', 'ElementDerivation']} }) - source_schema: Optional[str] = Field(default=None, description="""name of the schema that describes the source (input) objects""", json_schema_extra = { "linkml_meta": {'alias': 'source_schema', 'domain_of': ['TransformationSpecification']} }) - target_schema: Optional[str] = Field(default=None, description="""name of the schema that describes the target (output) objects""", json_schema_extra = { "linkml_meta": {'alias': 'target_schema', 'domain_of': ['TransformationSpecification']} }) - class_derivations: Optional[Dict[str, ClassDerivation]] = Field(default=None, description="""Instructions on how to derive a set of classes in the target schema from classes in the source schema.""", json_schema_extra = { "linkml_meta": {'alias': 'class_derivations', - 'domain_of': ['TransformationSpecification', 'ObjectDerivation']} }) - enum_derivations: Optional[Dict[str, EnumDerivation]] = Field(default=None, description="""Instructions on how to derive a set of enums in the target schema""", json_schema_extra = { "linkml_meta": {'alias': 'enum_derivations', 'domain_of': ['TransformationSpecification']} }) - slot_derivations: Optional[Dict[str, SlotDerivation]] = Field(default=None, description="""Instructions on how to derive a set of top level slots in the target schema""", json_schema_extra = { "linkml_meta": {'alias': 'slot_derivations', - 'domain_of': ['TransformationSpecification', 'ClassDerivation']} }) - description: Optional[str] = Field(default=None, description="""description of the specification component""", json_schema_extra = { "linkml_meta": {'alias': 'description', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'dcterms:description'} }) - implements: Optional[List[str]] = Field(default=None, description="""A reference to a specification that this component implements.""", json_schema_extra = { "linkml_meta": {'alias': 'implements', 'domain_of': ['SpecificationComponent']} }) - comments: Optional[List[str]] = Field(default=None, description="""A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use.""", json_schema_extra = { "linkml_meta": {'alias': 'comments', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'rdfs:comment'} }) - - -class ElementDerivation(SpecificationComponent): - """ - An abstract grouping for classes that provide a specification of how to derive a target element from a source element. - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, 'from_schema': 'https://w3id.org/linkml/transformer'}) - - name: str = Field(default=..., description="""Name of the element in the target schema""", json_schema_extra = { "linkml_meta": {'alias': 'name', - 'domain_of': ['ElementDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - copy_directives: Optional[Dict[str, CopyDirective]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'copy_directives', - 'domain_of': ['TransformationSpecification', 'ElementDerivation']} }) - overrides: Optional[Any] = Field(default=None, description="""overrides source schema slots""", json_schema_extra = { "linkml_meta": {'alias': 'overrides', 'domain_of': ['ElementDerivation']} }) - is_a: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'is_a', 'domain_of': ['ElementDerivation'], 'slot_uri': 'linkml:is_a'} }) - mixins: Optional[List[str]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'mixins', - 'domain_of': ['ElementDerivation'], - 'slot_uri': 'linkml:mixins'} }) - value_mappings: Optional[Dict[str, KeyVal]] = Field(default=None, description="""A mapping table that is applied directly to mappings, in order of precedence""", json_schema_extra = { "linkml_meta": {'alias': 'value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_value_mappings: Optional[Dict[str, KeyVal]] = Field(default=None, description="""A mapping table in which the keys are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_expression_mappings: Optional[Dict[str, KeyVal]] = Field(default=None, description="""A mapping table in which the keys and values are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_expression_mappings', - 'domain_of': ['ElementDerivation']} }) - mirror_source: Optional[bool] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'mirror_source', 'domain_of': ['ElementDerivation']} }) - description: Optional[str] = Field(default=None, description="""description of the specification component""", json_schema_extra = { "linkml_meta": {'alias': 'description', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'dcterms:description'} }) - implements: Optional[List[str]] = Field(default=None, description="""A reference to a specification that this component implements.""", json_schema_extra = { "linkml_meta": {'alias': 'implements', 'domain_of': ['SpecificationComponent']} }) - comments: Optional[List[str]] = Field(default=None, description="""A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use.""", json_schema_extra = { "linkml_meta": {'alias': 'comments', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'rdfs:comment'} }) - - -class ClassDerivation(ElementDerivation): - """ - A specification of how to derive a target class from a source class. - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer'}) - - populated_from: Optional[str] = Field(default=None, description="""Name of the class in the source schema""", json_schema_extra = { "linkml_meta": {'alias': 'populated_from', - 'domain_of': ['ClassDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - sources: Optional[List[str]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'sources', - 'domain_of': ['ClassDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - joins: Optional[Dict[str, AliasedClass]] = Field(default=None, description="""Additional classes to be joined to derive instances of the target class""", json_schema_extra = { "linkml_meta": {'alias': 'joins', - 'comments': ['not yet implemented'], - 'domain_of': ['ClassDerivation']} }) - slot_derivations: Optional[Dict[str, SlotDerivation]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'slot_derivations', - 'domain_of': ['TransformationSpecification', 'ClassDerivation']} }) - target_definition: Optional[Any] = Field(default=None, description="""LinkML class definition object for this slot.""", json_schema_extra = { "linkml_meta": {'alias': 'target_definition', - 'comments': ['currently defined as Any to avoid coupling with metamodel'], - 'domain_of': ['ClassDerivation', 'SlotDerivation']} }) - name: str = Field(default=..., description="""Name of the element in the target schema""", json_schema_extra = { "linkml_meta": {'alias': 'name', - 'domain_of': ['ElementDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - copy_directives: Optional[Dict[str, CopyDirective]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'copy_directives', - 'domain_of': ['TransformationSpecification', 'ElementDerivation']} }) - overrides: Optional[Any] = Field(default=None, description="""overrides source schema slots""", json_schema_extra = { "linkml_meta": {'alias': 'overrides', 'domain_of': ['ElementDerivation']} }) - is_a: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'is_a', 'domain_of': ['ElementDerivation'], 'slot_uri': 'linkml:is_a'} }) - mixins: Optional[List[str]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'mixins', - 'domain_of': ['ElementDerivation'], - 'slot_uri': 'linkml:mixins'} }) - value_mappings: Optional[Dict[str, KeyVal]] = Field(default=None, description="""A mapping table that is applied directly to mappings, in order of precedence""", json_schema_extra = { "linkml_meta": {'alias': 'value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_value_mappings: Optional[Dict[str, KeyVal]] = Field(default=None, description="""A mapping table in which the keys are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_expression_mappings: Optional[Dict[str, KeyVal]] = Field(default=None, description="""A mapping table in which the keys and values are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_expression_mappings', - 'domain_of': ['ElementDerivation']} }) - mirror_source: Optional[bool] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'mirror_source', 'domain_of': ['ElementDerivation']} }) - description: Optional[str] = Field(default=None, description="""description of the specification component""", json_schema_extra = { "linkml_meta": {'alias': 'description', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'dcterms:description'} }) - implements: Optional[List[str]] = Field(default=None, description="""A reference to a specification that this component implements.""", json_schema_extra = { "linkml_meta": {'alias': 'implements', 'domain_of': ['SpecificationComponent']} }) - comments: Optional[List[str]] = Field(default=None, description="""A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use.""", json_schema_extra = { "linkml_meta": {'alias': 'comments', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'rdfs:comment'} }) - - -class ObjectDerivation(ElementDerivation): - """ - Temporary placeholder for object_derivations - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer'}) - - class_derivations: Optional[List[str]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'class_derivations', - 'domain_of': ['TransformationSpecification', 'ObjectDerivation']} }) - name: str = Field(default=..., description="""Name of the element in the target schema""", json_schema_extra = { "linkml_meta": {'alias': 'name', - 'domain_of': ['ElementDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - copy_directives: Optional[Dict[str, CopyDirective]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'copy_directives', - 'domain_of': ['TransformationSpecification', 'ElementDerivation']} }) - overrides: Optional[Any] = Field(default=None, description="""overrides source schema slots""", json_schema_extra = { "linkml_meta": {'alias': 'overrides', 'domain_of': ['ElementDerivation']} }) - is_a: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'is_a', 'domain_of': ['ElementDerivation'], 'slot_uri': 'linkml:is_a'} }) - mixins: Optional[List[str]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'mixins', - 'domain_of': ['ElementDerivation'], - 'slot_uri': 'linkml:mixins'} }) - value_mappings: Optional[Dict[str, KeyVal]] = Field(default=None, description="""A mapping table that is applied directly to mappings, in order of precedence""", json_schema_extra = { "linkml_meta": {'alias': 'value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_value_mappings: Optional[Dict[str, KeyVal]] = Field(default=None, description="""A mapping table in which the keys are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_expression_mappings: Optional[Dict[str, KeyVal]] = Field(default=None, description="""A mapping table in which the keys and values are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_expression_mappings', - 'domain_of': ['ElementDerivation']} }) - mirror_source: Optional[bool] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'mirror_source', 'domain_of': ['ElementDerivation']} }) - description: Optional[str] = Field(default=None, description="""description of the specification component""", json_schema_extra = { "linkml_meta": {'alias': 'description', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'dcterms:description'} }) - implements: Optional[List[str]] = Field(default=None, description="""A reference to a specification that this component implements.""", json_schema_extra = { "linkml_meta": {'alias': 'implements', 'domain_of': ['SpecificationComponent']} }) - comments: Optional[List[str]] = Field(default=None, description="""A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use.""", json_schema_extra = { "linkml_meta": {'alias': 'comments', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'rdfs:comment'} }) - - -class AliasedClass(ConfiguredBaseModel): - """ - alias-class key value pairs for classes - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer'}) - - alias: str = Field(default=..., description="""name of the class to be aliased""", json_schema_extra = { "linkml_meta": {'alias': 'alias', 'domain_of': ['AliasedClass']} }) - class_named: Optional[str] = Field(default=None, description="""local alias for the class""", json_schema_extra = { "linkml_meta": {'alias': 'class_named', 'domain_of': ['AliasedClass']} }) - - -class SlotDerivation(ElementDerivation): - """ - A specification of how to derive the value of a target slot from a source slot - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer'}) - - name: str = Field(default=..., description="""Target slot name""", json_schema_extra = { "linkml_meta": {'alias': 'name', - 'domain_of': ['ElementDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - populated_from: Optional[str] = Field(default=None, description="""Source slot name""", json_schema_extra = { "linkml_meta": {'alias': 'populated_from', - 'domain_of': ['ClassDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - sources: Optional[List[str]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'sources', - 'domain_of': ['ClassDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - object_derivations: Optional[List[str]] = Field(default=None, description="""One or more object derivations used to construct the slot value(s), which must be instances of a class.""", json_schema_extra = { "linkml_meta": {'alias': 'object_derivations', 'domain_of': ['SlotDerivation']} }) - derived_from: Optional[List[str]] = Field(default=None, description="""Source slots that are used to derive this slot. This can be computed from the expr, if the expr is declarative.""", json_schema_extra = { "linkml_meta": {'alias': 'derived_from', 'domain_of': ['SlotDerivation']} }) - expr: Optional[str] = Field(default=None, description="""An expression to be evaluated on the source object to derive the target slot. Should be specified using the LinkML expression language.""", json_schema_extra = { "linkml_meta": {'alias': 'expr', - 'domain_of': ['SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - range: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'range', 'domain_of': ['SlotDerivation'], 'slot_uri': 'linkml:range'} }) - unit_conversion: Optional[UnitConversionConfiguration] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'unit_conversion', 'domain_of': ['SlotDerivation']} }) - inverse_of: Optional[Inverse] = Field(default=None, description="""Used to specify a class-slot tuple that is the inverse of the derived/target slot. This is used primarily for mapping to relational databases or formalisms that do not allow multiple values. The class representing the repeated element has a foreign key slot inserted in that 'back references' the original multivalued slot.""", json_schema_extra = { "linkml_meta": {'alias': 'inverse_of', 'domain_of': ['SlotDerivation']} }) - hide: Optional[bool] = Field(default=None, description="""True if this is suppressed""", json_schema_extra = { "linkml_meta": {'alias': 'hide', - 'domain_of': ['SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - type_designator: Optional[bool] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'type_designator', 'domain_of': ['SlotDerivation']} }) - target_definition: Optional[Any] = Field(default=None, description="""LinkML definition object for this slot.""", json_schema_extra = { "linkml_meta": {'alias': 'target_definition', - 'comments': ['currently defined as Any to avoid coupling with metamodel'], - 'domain_of': ['ClassDerivation', 'SlotDerivation']} }) - cast_collection_as: Optional[CollectionType] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'cast_collection_as', 'domain_of': ['SlotDerivation']} }) - dictionary_key: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'dictionary_key', 'domain_of': ['SlotDerivation']} }) - stringification: Optional[StringificationConfiguration] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'stringification', 'domain_of': ['SlotDerivation']} }) - aggregation_operation: Optional[AggregationOperation] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'aggregation_operation', 'domain_of': ['SlotDerivation']} }) - copy_directives: Optional[Dict[str, CopyDirective]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'copy_directives', - 'domain_of': ['TransformationSpecification', 'ElementDerivation']} }) - overrides: Optional[Any] = Field(default=None, description="""overrides source schema slots""", json_schema_extra = { "linkml_meta": {'alias': 'overrides', 'domain_of': ['ElementDerivation']} }) - is_a: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'is_a', 'domain_of': ['ElementDerivation'], 'slot_uri': 'linkml:is_a'} }) - mixins: Optional[List[str]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'mixins', - 'domain_of': ['ElementDerivation'], - 'slot_uri': 'linkml:mixins'} }) - value_mappings: Optional[Dict[str, KeyVal]] = Field(default=None, description="""A mapping table that is applied directly to mappings, in order of precedence""", json_schema_extra = { "linkml_meta": {'alias': 'value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_value_mappings: Optional[Dict[str, KeyVal]] = Field(default=None, description="""A mapping table in which the keys are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_expression_mappings: Optional[Dict[str, KeyVal]] = Field(default=None, description="""A mapping table in which the keys and values are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_expression_mappings', - 'domain_of': ['ElementDerivation']} }) - mirror_source: Optional[bool] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'mirror_source', 'domain_of': ['ElementDerivation']} }) - description: Optional[str] = Field(default=None, description="""description of the specification component""", json_schema_extra = { "linkml_meta": {'alias': 'description', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'dcterms:description'} }) - implements: Optional[List[str]] = Field(default=None, description="""A reference to a specification that this component implements.""", json_schema_extra = { "linkml_meta": {'alias': 'implements', 'domain_of': ['SpecificationComponent']} }) - comments: Optional[List[str]] = Field(default=None, description="""A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use.""", json_schema_extra = { "linkml_meta": {'alias': 'comments', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'rdfs:comment'} }) - - -class EnumDerivation(ElementDerivation): - """ - A specification of how to derive the value of a target enum from a source enum - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer'}) - - name: str = Field(default=..., description="""Target enum name""", json_schema_extra = { "linkml_meta": {'alias': 'name', - 'domain_of': ['ElementDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - populated_from: Optional[str] = Field(default=None, description="""Source enum name""", json_schema_extra = { "linkml_meta": {'alias': 'populated_from', - 'domain_of': ['ClassDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - sources: Optional[List[str]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'sources', - 'domain_of': ['ClassDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - expr: Optional[str] = Field(default=None, description="""An expression to be evaluated on the source object to derive the target slot. Should be specified using the LinkML expression language.""", json_schema_extra = { "linkml_meta": {'alias': 'expr', - 'domain_of': ['SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - hide: Optional[bool] = Field(default=None, description="""True if this is suppressed""", json_schema_extra = { "linkml_meta": {'alias': 'hide', - 'domain_of': ['SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - permissible_value_derivations: Optional[Dict[str, PermissibleValueDerivation]] = Field(default=None, description="""Instructions on how to derive a set of PVs in the target schema""", json_schema_extra = { "linkml_meta": {'alias': 'permissible_value_derivations', 'domain_of': ['EnumDerivation']} }) - copy_directives: Optional[Dict[str, CopyDirective]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'copy_directives', - 'domain_of': ['TransformationSpecification', 'ElementDerivation']} }) - overrides: Optional[Any] = Field(default=None, description="""overrides source schema slots""", json_schema_extra = { "linkml_meta": {'alias': 'overrides', 'domain_of': ['ElementDerivation']} }) - is_a: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'is_a', 'domain_of': ['ElementDerivation'], 'slot_uri': 'linkml:is_a'} }) - mixins: Optional[List[str]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'mixins', - 'domain_of': ['ElementDerivation'], - 'slot_uri': 'linkml:mixins'} }) - value_mappings: Optional[Dict[str, KeyVal]] = Field(default=None, description="""A mapping table that is applied directly to mappings, in order of precedence""", json_schema_extra = { "linkml_meta": {'alias': 'value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_value_mappings: Optional[Dict[str, KeyVal]] = Field(default=None, description="""A mapping table in which the keys are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_expression_mappings: Optional[Dict[str, KeyVal]] = Field(default=None, description="""A mapping table in which the keys and values are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_expression_mappings', - 'domain_of': ['ElementDerivation']} }) - mirror_source: Optional[bool] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'mirror_source', 'domain_of': ['ElementDerivation']} }) - description: Optional[str] = Field(default=None, description="""description of the specification component""", json_schema_extra = { "linkml_meta": {'alias': 'description', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'dcterms:description'} }) - implements: Optional[List[str]] = Field(default=None, description="""A reference to a specification that this component implements.""", json_schema_extra = { "linkml_meta": {'alias': 'implements', 'domain_of': ['SpecificationComponent']} }) - comments: Optional[List[str]] = Field(default=None, description="""A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use.""", json_schema_extra = { "linkml_meta": {'alias': 'comments', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'rdfs:comment'} }) - - -class PermissibleValueDerivation(ElementDerivation): - """ - A specification of how to derive the value of a PV from a source enum - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer', - 'todos': ['this is currently under-specified. We will need boolean ' - 'combinators to express if-then-else']}) - - name: str = Field(default=..., description="""Target permissible value text""", json_schema_extra = { "linkml_meta": {'alias': 'name', - 'domain_of': ['ElementDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - expr: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'expr', - 'domain_of': ['SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - populated_from: Optional[str] = Field(default=None, description="""Source permissible value""", json_schema_extra = { "linkml_meta": {'alias': 'populated_from', - 'domain_of': ['ClassDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - sources: Optional[List[str]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'sources', - 'domain_of': ['ClassDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - hide: Optional[bool] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'hide', - 'domain_of': ['SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - copy_directives: Optional[Dict[str, CopyDirective]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'copy_directives', - 'domain_of': ['TransformationSpecification', 'ElementDerivation']} }) - overrides: Optional[Any] = Field(default=None, description="""overrides source schema slots""", json_schema_extra = { "linkml_meta": {'alias': 'overrides', 'domain_of': ['ElementDerivation']} }) - is_a: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'is_a', 'domain_of': ['ElementDerivation'], 'slot_uri': 'linkml:is_a'} }) - mixins: Optional[List[str]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'mixins', - 'domain_of': ['ElementDerivation'], - 'slot_uri': 'linkml:mixins'} }) - value_mappings: Optional[Dict[str, KeyVal]] = Field(default=None, description="""A mapping table that is applied directly to mappings, in order of precedence""", json_schema_extra = { "linkml_meta": {'alias': 'value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_value_mappings: Optional[Dict[str, KeyVal]] = Field(default=None, description="""A mapping table in which the keys are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_expression_mappings: Optional[Dict[str, KeyVal]] = Field(default=None, description="""A mapping table in which the keys and values are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_expression_mappings', - 'domain_of': ['ElementDerivation']} }) - mirror_source: Optional[bool] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'mirror_source', 'domain_of': ['ElementDerivation']} }) - description: Optional[str] = Field(default=None, description="""description of the specification component""", json_schema_extra = { "linkml_meta": {'alias': 'description', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'dcterms:description'} }) - implements: Optional[List[str]] = Field(default=None, description="""A reference to a specification that this component implements.""", json_schema_extra = { "linkml_meta": {'alias': 'implements', 'domain_of': ['SpecificationComponent']} }) - comments: Optional[List[str]] = Field(default=None, description="""A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use.""", json_schema_extra = { "linkml_meta": {'alias': 'comments', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'rdfs:comment'} }) - - -class PrefixDerivation(ElementDerivation): - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer'}) - - name: str = Field(default=..., description="""Name of the element in the target schema""", json_schema_extra = { "linkml_meta": {'alias': 'name', - 'domain_of': ['ElementDerivation', - 'SlotDerivation', - 'EnumDerivation', - 'PermissibleValueDerivation']} }) - copy_directives: Optional[Dict[str, CopyDirective]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'copy_directives', - 'domain_of': ['TransformationSpecification', 'ElementDerivation']} }) - overrides: Optional[Any] = Field(default=None, description="""overrides source schema slots""", json_schema_extra = { "linkml_meta": {'alias': 'overrides', 'domain_of': ['ElementDerivation']} }) - is_a: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'is_a', 'domain_of': ['ElementDerivation'], 'slot_uri': 'linkml:is_a'} }) - mixins: Optional[List[str]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'mixins', - 'domain_of': ['ElementDerivation'], - 'slot_uri': 'linkml:mixins'} }) - value_mappings: Optional[Dict[str, KeyVal]] = Field(default=None, description="""A mapping table that is applied directly to mappings, in order of precedence""", json_schema_extra = { "linkml_meta": {'alias': 'value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_value_mappings: Optional[Dict[str, KeyVal]] = Field(default=None, description="""A mapping table in which the keys are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_value_mappings', 'domain_of': ['ElementDerivation']} }) - expression_to_expression_mappings: Optional[Dict[str, KeyVal]] = Field(default=None, description="""A mapping table in which the keys and values are expressions""", json_schema_extra = { "linkml_meta": {'alias': 'expression_to_expression_mappings', - 'domain_of': ['ElementDerivation']} }) - mirror_source: Optional[bool] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'mirror_source', 'domain_of': ['ElementDerivation']} }) - description: Optional[str] = Field(default=None, description="""description of the specification component""", json_schema_extra = { "linkml_meta": {'alias': 'description', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'dcterms:description'} }) - implements: Optional[List[str]] = Field(default=None, description="""A reference to a specification that this component implements.""", json_schema_extra = { "linkml_meta": {'alias': 'implements', 'domain_of': ['SpecificationComponent']} }) - comments: Optional[List[str]] = Field(default=None, description="""A list of comments about this component. Comments are free text, and may be used to provide additional information about the component, including instructions for its use.""", json_schema_extra = { "linkml_meta": {'alias': 'comments', - 'domain_of': ['SpecificationComponent'], - 'slot_uri': 'rdfs:comment'} }) - - -class UnitConversionConfiguration(ConfiguredBaseModel): - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer'}) - - target_unit: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'target_unit', 'domain_of': ['UnitConversionConfiguration']} }) - target_unit_scheme: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'target_unit_scheme', - 'domain_of': ['UnitConversionConfiguration'], - 'examples': [{'value': 'ucum'}]} }) - source_unit: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'source_unit', 'domain_of': ['UnitConversionConfiguration']} }) - source_unit_scheme: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'source_unit_scheme', - 'domain_of': ['UnitConversionConfiguration'], - 'examples': [{'value': 'ucum'}]} }) - source_unit_slot: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'source_unit_slot', 'domain_of': ['UnitConversionConfiguration']} }) - source_magnitude_slot: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'source_magnitude_slot', 'domain_of': ['UnitConversionConfiguration']} }) - target_unit_slot: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'target_unit_slot', 'domain_of': ['UnitConversionConfiguration']} }) - target_magnitude_slot: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'target_magnitude_slot', 'domain_of': ['UnitConversionConfiguration']} }) - - -class StringificationConfiguration(ConfiguredBaseModel): - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer'}) - - delimiter: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'delimiter', - 'domain_of': ['StringificationConfiguration'], - 'examples': [{'value': ','}, {'value': '|'}, {'value': ';'}]} }) - reversed: Optional[bool] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'reversed', 'domain_of': ['StringificationConfiguration']} }) - over_slots: Optional[List[str]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'over_slots', 'domain_of': ['StringificationConfiguration']} }) - syntax: Optional[SerializationSyntaxType] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'syntax', - 'domain_of': ['StringificationConfiguration'], - 'examples': [{'value': 'json'}, {'value': 'yaml'}]} }) - - -class Inverse(ConfiguredBaseModel): - """ - Used for back references in mapping to relational model - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'aliases': ['backref', 'back_references'], - 'from_schema': 'https://w3id.org/linkml/transformer'}) - - slot_name: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'slot_name', 'domain_of': ['Inverse']} }) - class_name: Optional[str] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'class_name', 'domain_of': ['Inverse']} }) - - -class TransformationOperation(ConfiguredBaseModel): - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, 'from_schema': 'https://w3id.org/linkml/transformer'}) - - pass - - -class AggregationOperation(TransformationOperation): - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer'}) - - operator: AggregationType = Field(default=..., json_schema_extra = { "linkml_meta": {'alias': 'operator', 'domain_of': ['AggregationOperation']} }) - null_handling: Optional[InvalidValueHandlingStrategy] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'null_handling', - 'domain_of': ['AggregationOperation', 'GroupingOperation']} }) - invalid_value_handling: Optional[InvalidValueHandlingStrategy] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'invalid_value_handling', 'domain_of': ['AggregationOperation']} }) - - -class GroupingOperation(TransformationOperation): - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer'}) - - null_handling: Optional[InvalidValueHandlingStrategy] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'null_handling', - 'domain_of': ['AggregationOperation', 'GroupingOperation']} }) - - -class PivotOperation(TransformationOperation): - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'aliases': ['melt/unmelt', 'reification/dereification'], - 'from_schema': 'https://w3id.org/linkml/transformer'}) - - direction: PivotDirectionType = Field(default=..., json_schema_extra = { "linkml_meta": {'alias': 'direction', 'domain_of': ['PivotOperation']} }) - variable_slot: Optional[str] = Field(default="variable", description="""Slot to use for the variable column in the melted/long representation. In EAV this is the name of the 'A' variable""", json_schema_extra = { "linkml_meta": {'alias': 'variable_slot', - 'aliases': ['var_name'], - 'domain_of': ['PivotOperation'], - 'ifabsent': 'string(variable)'} }) - value_slot: Optional[str] = Field(default="value", description="""Slot to use for the value column in the melted/long representation. In EAV this is the name of the 'V' variable""", json_schema_extra = { "linkml_meta": {'alias': 'value_slot', - 'aliases': ['value_name'], - 'domain_of': ['PivotOperation'], - 'ifabsent': 'string(value)'} }) - unmelt_to_class: Optional[str] = Field(default=None, description="""In an unmelt operation, attributes (which are values in the long/melted/EAV representation) must conform to valid attributes in this class""", json_schema_extra = { "linkml_meta": {'alias': 'unmelt_to_class', 'domain_of': ['PivotOperation']} }) - unmelt_to_slots: Optional[List[str]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'unmelt_to_slots', 'domain_of': ['PivotOperation']} }) - - -class KeyVal(ConfiguredBaseModel): - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer'}) - - key: str = Field(default=..., json_schema_extra = { "linkml_meta": {'alias': 'key', 'domain_of': ['KeyVal']} }) - value: Optional[Any] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'value', 'domain_of': ['KeyVal']} }) - - -class CopyDirective(ConfiguredBaseModel): - """ - Instructs a Schema Mapper in how to map to a target schema. Not used for data transformation. - This is the process to process a directive: 1. If `copy_all`, add all sub-elements to the list of sub-elements to be copied. 2. If `exclude`, remove the specified sub-elements from the above list. 3. If `exclude_all`, clean-up the above list. Effectively making previous steps useless. 4. If `include`, add the specified sub-elements from the list result of previous steps. - Implementations might decide to somehow report (error, warning,...) meaningless combinations (like specifying `copy_all` and `exclude_all`). - Validation on the correctness of the resulting derived schema might be done optionally by the implementation. For example, removing a slot but keeping a class that requires it would invalidate the derived-schema. It is always possible to validate the schema with the LinkML linter after derivation. - What are the considered sub-elements depends on the calls of Element to be transformed. For example, for a class they are `slots` and `attributes`. - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/transformer', 'status': 'testing'}) - - element_name: str = Field(default=..., json_schema_extra = { "linkml_meta": {'alias': 'element_name', 'domain_of': ['CopyDirective']} }) - copy_all: Optional[bool] = Field(default=None, description="""Copy all sub-elements of the Element being derived.""", json_schema_extra = { "linkml_meta": {'alias': 'copy_all', 'domain_of': ['CopyDirective']} }) - exclude_all: Optional[bool] = Field(default=None, description="""Do not copy any of the sub-elements of the Element being derived.""", json_schema_extra = { "linkml_meta": {'alias': 'exclude_all', 'domain_of': ['CopyDirective']} }) - exclude: Optional[Any] = Field(default=None, description="""Remove certain sub-elements from the list of sub-elements to be copied. -As of now there it is under-specified, how to specify the sub-elements to exclude. One possible implementation would be a list where all element types can be mixed, since there might not be name conflicts across element types.""", json_schema_extra = { "linkml_meta": {'alias': 'exclude', 'domain_of': ['CopyDirective']} }) - include: Optional[Any] = Field(default=None, description="""Add certain sub-elements to the list of sub-elements to be copied. -As of now there it is under-specified, how to specify the sub-elements to include. One possible implementation would be a list where all element types can be mixed, since there might not be name conflicts across element types.""", json_schema_extra = { "linkml_meta": {'alias': 'include', 'domain_of': ['CopyDirective']} }) - add: Optional[Any] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'add', 'domain_of': ['CopyDirective']} }) - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -SpecificationComponent.model_rebuild() -TransformationSpecification.model_rebuild() -ElementDerivation.model_rebuild() -ClassDerivation.model_rebuild() -ObjectDerivation.model_rebuild() -AliasedClass.model_rebuild() -SlotDerivation.model_rebuild() -EnumDerivation.model_rebuild() -PermissibleValueDerivation.model_rebuild() -PrefixDerivation.model_rebuild() -UnitConversionConfiguration.model_rebuild() -StringificationConfiguration.model_rebuild() -Inverse.model_rebuild() -TransformationOperation.model_rebuild() -AggregationOperation.model_rebuild() -GroupingOperation.model_rebuild() -PivotOperation.model_rebuild() -KeyVal.model_rebuild() -CopyDirective.model_rebuild() - diff --git a/src/linkml_map/functions/__init__.py b/src/linkml_map/functions/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/src/linkml_map/functions/unit_conversion.py b/src/linkml_map/functions/unit_conversion.py deleted file mode 100644 index bb966a2..0000000 --- a/src/linkml_map/functions/unit_conversion.py +++ /dev/null @@ -1,164 +0,0 @@ -""" -Basic unit conversion functions. - -Currently only native pint units or UCUM units are supported. - -For UCUM, the ucumvert library is used to convert UCUM units to pint units, -see ``_. -""" - -from enum import Enum -from functools import lru_cache -from typing import Any, Optional, Union - -import lark -import pint -from ucumvert import PintUcumRegistry - - -class UnitSystem(str, Enum): - """Enumeration of supported unit systems.""" - - UCUM = "ucum" - IEC61360 = "iec61360" - SI = "SI" - - -REGISTRIES = { - UnitSystem.UCUM: PintUcumRegistry(), -} - - -class UndefinedUnitError(Exception): - """ - Raised when a unit is not defined. - - Note: equivalent to the pint error, but the - pint dependency is optional - """ - - -class QuantitySyntaxError(Exception): - """ - Raised when a quantity cannot be parsed. - """ - - -class DimensionalityError(Exception): - """ - Raised when a unit conversion cannot be performed. - - Note: equivalent to the pint error, but the - pint dependency is optional - """ - - -def convert_units( - magnitude: float, from_unit: str, to_unit: str, system: Optional[UnitSystem] = None -) -> Any: - """ - Convert a quantity between units. - - >>> convert_units(1, "m", "cm") - 100.0 - >>> convert_units(1, "m", "cm", system=UnitSystem.UCUM) - 100.0 - >>> convert_units(1, "m", "cm", system=UnitSystem.SI) - 100.0 - >>> convert_units(1.0, "hectare", "m^2", system=UnitSystem.SI) - 10000.0 - >>> convert_units(1.0, "hectare", "m ** 2", system=UnitSystem.SI) - 10000.0 - >>> convert_units(1.0, "hectare", "m ** 2", system=None) - 10000.0 - >>> convert_units(1.0, "km2", "m2", system=UnitSystem.UCUM) - 1000000.0 - - :param magnitude: - :param from_unit: - :param to_unit: - :return: converted magnitude - """ - ureg: pint.UnitRegistry = get_unit_registry(system) - from_unit = normalize_unit(from_unit, system) - to_unit = normalize_unit(to_unit, system) - try: - from_unit_q = ureg.parse_units(from_unit) - except lark.exceptions.UnexpectedCharacters as err: - msg = f"Cannot parse unit: {from_unit}" - raise UndefinedUnitError(msg) from err - except pint.errors.UndefinedUnitError as err: - msg = f"Unknown source unit: {from_unit}" - raise UndefinedUnitError(msg) from err - quantity = magnitude * from_unit_q - try: - return quantity.to(to_unit).magnitude - except pint.errors.UndefinedUnitError as err: - msg = f"Unknown target unit: {from_unit}" - raise UndefinedUnitError(msg) from err - except pint.errors.DimensionalityError as err: - msg = f"Cannot convert from {from_unit} to {to_unit}" - raise DimensionalityError(msg) from err - - -@lru_cache -def get_unit_registry( - system: Optional[UnitSystem] = None, -) -> Union[pint.UnitRegistry, PintUcumRegistry]: - """ - Get a unit registry. - - >>> ureg = get_unit_registry(UnitSystem.UCUM) - >>> ureg.from_ucum("m/s2.kg") - - >>> str(_) - '1.0 kilogram * meter / second ** 2' - >>> ureg.from_ucum("m[H2O]{35Cel}") # UCUM code with annotation - - >>> _.to("mbar") - - >>> ureg("degC") # a standard pint unit - - >>> ureg.from_ucum("g/m2") - - >>> _.to(ureg.from_ucum("kg/m2")) - - >>> ureg.from_ucum("nmol/mmol{Cre}") - - >>> sireg = get_unit_registry(UnitSystem.SI) - >>> sireg("degC") - - >>> sireg("ha") - - - :param system: currently only supported values are None or UnitSystem.UCUM - :return: - """ - import pint - - ureg = pint.UnitRegistry() - if not system: - return ureg - if system in REGISTRIES: - return REGISTRIES[system] - if system.value in dir(ureg.sys): - ureg.default_system = system.value - return ureg - msg = f"Unknown unit system: {system}" - raise NotImplementedError(msg) - - -def normalize_unit(unit: str, system: Optional[UnitSystem] = None) -> str: - """Normalize the unit to UnitSystem.UCUM, if possible.""" - if system is None or system != UnitSystem.UCUM: - return unit - - # this is UnitSystem.UCUM - try: - return str(get_unit_registry(system).from_ucum(unit)) - except pint.errors.UndefinedUnitError as err: - msg = f"Unknown unit: {unit}" - raise UndefinedUnitError(msg) from err - except lark.exceptions.UnexpectedCharacters as err: - msg = f"Cannot parse unit: {unit}" - raise UndefinedUnitError(msg) from err diff --git a/src/linkml_map/importer/__init__.py b/src/linkml_map/importer/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/src/linkml_map/importer/importer.py b/src/linkml_map/importer/importer.py deleted file mode 100644 index b3427b5..0000000 --- a/src/linkml_map/importer/importer.py +++ /dev/null @@ -1,35 +0,0 @@ -""" -Importers are responsible for translating an external mapping specification into the LinkML transformation model. - -For example: - - - SSSOM to LinkML-Transformer Specifications - - YARRRML to LinkML-Transformer Specifications -""" - -from abc import ABC, abstractmethod -from dataclasses import dataclass -from typing import Any - -from linkml_map.datamodel.transformer_model import TransformationSpecification - - -@dataclass -class Importer(ABC): - """ - Base class for all importers. - - A compiler will translate an external mapping spec into the LinkML transformation model. - - An example importer would be sssom. - """ - - @abstractmethod - def import_specification(self, input: Any) -> TransformationSpecification: - """ - Import into a specification. - - :param specification: - :return: - """ - raise NotImplementedError diff --git a/src/linkml_map/inference/__init__.py b/src/linkml_map/inference/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/src/linkml_map/inference/inference.py b/src/linkml_map/inference/inference.py deleted file mode 100644 index f269fce..0000000 --- a/src/linkml_map/inference/inference.py +++ /dev/null @@ -1,45 +0,0 @@ -"""Infer missing values in a specification.""" - -from linkml_runtime import SchemaView - -from linkml_map.datamodel.transformer_model import TransformationSpecification - - -def induce_missing_values( - specification: TransformationSpecification, source_schemaview: SchemaView -) -> None: - """ - Infer missing values in a specification. - - Currently only uses copy directives. - - :param specification: - :param source_schemaview: - :return: - """ - for cd in specification.class_derivations.values(): - if not cd.populated_from: - cd.populated_from = cd.name - for cd in specification.class_derivations.values(): - for sd in cd.slot_derivations.values(): - if sd.object_derivations: - #skip inference for object derivations, inferencese come from class derivation later - #TODO: we may need to do the inference for the internal class slots - continue - # for null mappings, assume that the slot is copied from the same slot in the source - # TODO: decide if this is the desired behavior - if sd.populated_from is None and sd.expr is None: - sd.populated_from = sd.name - if sd.range is None and sd.value is not None: - sd.range = "string" - if not sd.range and sd.populated_from: - # auto-populate range field - if cd.populated_from not in source_schemaview.all_classes(): - continue - source_induced_slot = source_schemaview.induced_slot( - sd.populated_from, cd.populated_from - ) - source_induced_slot_range = source_induced_slot.range - for range_cd in specification.class_derivations.values(): - if range_cd.populated_from == source_induced_slot_range: - sd.range = range_cd.name diff --git a/src/linkml_map/inference/inverter.py b/src/linkml_map/inference/inverter.py deleted file mode 100644 index e256ee7..0000000 --- a/src/linkml_map/inference/inverter.py +++ /dev/null @@ -1,182 +0,0 @@ -"""Invert a transformation specification.""" - -import logging -import re -from copy import copy -from dataclasses import dataclass, field -from typing import Optional - -from linkml_runtime import SchemaView - -from linkml_map.datamodel.transformer_model import ( - ClassDerivation, - CollectionType, - EnumDerivation, - PermissibleValueDerivation, - SlotDerivation, - TransformationSpecification, - UnitConversionConfiguration, -) - -logger = logging.getLogger(__name__) - - -class NonInvertibleSpecificationError(ValueError): - """Error thrown when a specification is not invertible.""" - - -@dataclass -class TransformationSpecificationInverter: - """ - Invert a transformation specification. - """ - - source_schemaview: SchemaView = None - """The source schema for the forward transformation. - Note this becomes the target schema for the generated inverse transformation, - because the goal of the inverted transformation is to map back to the original source.""" - - target_schemaview: SchemaView = None - """The target schema for the forward transformation. - Note this becomes the source schema for the generated inverse transformation.""" - - strict: bool = field(default=True) - - def invert(self, spec: TransformationSpecification) -> TransformationSpecification: - """ - Invert a transformation specification. - - :param spec: - :return: - """ - logger.info("Inverting specification") - inverted_spec = TransformationSpecification() - for cd in spec.class_derivations.values(): - inverted_cd = self.invert_class_derivation(cd, spec) - inverted_spec.class_derivations[inverted_cd.name] = inverted_cd - for ed in spec.enum_derivations.values(): - inverted_ed = self.invert_enum_derivation(ed, spec) - inverted_spec.enum_derivations[inverted_ed.name] = inverted_ed - return inverted_spec - - def invert_class_derivation( - self, cd: ClassDerivation, spec: TransformationSpecification - ) -> ClassDerivation: - """ - Invert a class derivation. - - :param cd: - :param spec: - :return: - """ - inverted_cd = ClassDerivation( - name=cd.populated_from if cd.populated_from else cd.name, populated_from=cd.name - ) - for sd in cd.slot_derivations.values(): - inverted_sd = self.invert_slot_derivation(sd, cd, spec) - if inverted_sd: - inverted_cd.slot_derivations[inverted_sd.name] = inverted_sd - elif self.strict: - msg = f"Cannot invert slot derivation: {sd.name}" - raise NonInvertibleSpecificationError(msg) - return inverted_cd - - def invert_enum_derivation( - self, ed: EnumDerivation, spec: TransformationSpecification - ) -> EnumDerivation: - """ - Invert an enum derivation. - - :param ed: - :param spec: - :return: - """ - inverted_ed = EnumDerivation( - name=ed.populated_from if ed.populated_from else ed.name, populated_from=ed.name - ) - if inverted_ed.expr: - msg = "TODO: invert enum derivation with expression" - raise NonInvertibleSpecificationError(msg) - for pv_deriv in ed.permissible_value_derivations.values(): - inverted_pv_deriv = PermissibleValueDerivation( - name=pv_deriv.populated_from if pv_deriv.populated_from else pv_deriv.name, - populated_from=pv_deriv.name, - ) - inverted_ed.permissible_value_derivations[inverted_pv_deriv.name] = inverted_pv_deriv - return inverted_ed - - def invert_slot_derivation( - self, sd: SlotDerivation, cd: ClassDerivation, spec: TransformationSpecification - ) -> Optional[SlotDerivation]: - """ - Invert a slot derivation. - - :param sd: - :param cd: - :param spec: - :return: - """ - populated_from = sd.populated_from - if sd.expr: - if re.match(r"^\w+$", sd.expr): - populated_from = sd.expr - else: - if not self.strict: - return None - # TODO: add logic for reversible expressions - msg = f"Cannot invert expression {sd.expr} in slot derivation: {sd.name}" - raise NonInvertibleSpecificationError(msg) - - if not populated_from: - # use defaults. TODO: decide on semantics of defaults - populated_from = sd.name - inverted_sd = SlotDerivation(name=populated_from, populated_from=sd.name) - source_cls_name = cd.populated_from - if ( - source_cls_name is None or source_cls_name in self.source_schemaview.all_classes() - ) and sd.populated_from: - source_slot = self.source_schemaview.induced_slot(sd.populated_from, source_cls_name) - else: - source_slot = None - if sd.range: - inverted_sd.range = source_slot.range - if source_slot.range in self.source_schemaview.all_classes(): - id_slot = self.source_schemaview.get_identifier_slot( - source_slot.range, use_key=True - ) - if id_slot: - inverted_sd.dictionary_key = id_slot.name - if source_slot and source_slot.multivalued: - if source_slot.inlined_as_list: - inverted_sd.cast_collection_as = CollectionType.MultiValuedList - elif source_slot.inlined and source_slot.range in self.source_schemaview.all_classes(): - id_slot = self.source_schemaview.get_identifier_slot( - source_slot.range, use_key=True - ) - if id_slot: - inverted_sd.cast_collection_as = CollectionType.MultiValuedDict - inverted_sd.dictionary_key = id_slot.name - if sd.unit_conversion: - source_slot = self.source_schemaview.induced_slot(sd.populated_from, source_cls_name) - target_unit = None - target_unit_scheme = None - if source_slot.unit is not None: - for p in ["ucum_code", "symbol"]: - target_unit = getattr(source_slot.unit, p, None) - if target_unit is not None: - target_unit_scheme = p - break - inverted_uc = UnitConversionConfiguration( - target_unit=target_unit, target_unit_scheme=target_unit_scheme - ) - if sd.unit_conversion.source_unit_slot: - inverted_uc.target_unit_slot = sd.unit_conversion.source_unit_slot - if sd.unit_conversion.source_magnitude_slot: - inverted_uc.target_magnitude_slot = sd.unit_conversion.source_magnitude_slot - if sd.unit_conversion.target_unit: - inverted_uc.source_unit = sd.unit_conversion.target_unit - inverted_sd.unit_conversion = inverted_uc - if sd.stringification: - inverted_sd.stringification = copy(sd.stringification) - inverted_sd.stringification.reversed = not inverted_sd.stringification.reversed - return inverted_sd diff --git a/src/linkml_map/inference/schema_mapper.py b/src/linkml_map/inference/schema_mapper.py deleted file mode 100644 index eddddb9..0000000 --- a/src/linkml_map/inference/schema_mapper.py +++ /dev/null @@ -1,369 +0,0 @@ -""" -A SchemaMapper translates a source schema and transformation specification into a target schema. - -AKA profiling -""" - -import logging -from collections import defaultdict -from copy import copy -from dataclasses import dataclass, field -from typing import Any, Optional - -from linkml_runtime import SchemaView -from linkml_runtime.dumpers import json_dumper -from linkml_runtime.linkml_model import ( - ClassDefinition, - ClassDefinitionName, - Element, - EnumDefinition, - PermissibleValue, - SchemaDefinition, - SlotDefinition, -) -from linkml_runtime.linkml_model.units import UnitOfMeasure - -from linkml_map.datamodel.transformer_model import ( - ClassDerivation, - CollectionType, - CopyDirective, - EnumDerivation, - TransformationSpecification, -) -from linkml_map.transformer.transformer import Transformer - -logger = logging.getLogger(__name__) - - -@dataclass -class SchemaMapper: - """ - Translates a source schema and transformation specification into a target schema. - """ - - source_schemaview: SchemaView = None - - transformer: Transformer = None - - source_to_target_class_mappings: dict[str, list[str]] = field( - default_factory=lambda: defaultdict(list) - ) - - slot_info: dict[tuple[str, str], Any] = field(default_factory=dict) - - def _copy_dict( - self, - copy_directive: CopyDirective, - src_elements, - tgt_elements, - ) -> None: - if copy_directive.copy_all: - for element in src_elements: - tgt_elements[element] = src_elements[element] - if copy_directive.exclude: - for element in src_elements: - if element in copy_directive.exclude: - del tgt_elements[element] - if copy_directive.exclude_all: - elements_to_delete = list(tgt_elements) - for element in elements_to_delete: - del tgt_elements[element] - if copy_directive.include: - for element in copy_directive.include: - if element in src_elements: - tgt_elements[element] = src_elements[element] - - def _copy_list( - self, - copy_directive: CopyDirective, - src_elements, - tgt_elements, - ) -> None: - if copy_directive.copy_all: - for element in src_elements: - tgt_elements.append(element) - if copy_directive.exclude: - for element in src_elements: - if copy_directive.exclude: - tgt_elements.remove(element) - if copy_directive.exclude_all: - for element in tgt_elements: - tgt_elements.remove(element) - if copy_directive.include: - for element in copy_directive.include: - if element in src_elements: - tgt_elements.append(element) - - def _copy_schema( - self, - copy_directives: list[CopyDirective], - source: SchemaDefinition, - target: SchemaDefinition, - ) -> SchemaDefinition: - if type(copy_directives) is dict: - copy_directives_list = copy_directives.values() - else: - copy_directives_list = copy_directives - - for copy_directive in copy_directives_list: - for element_type in ["classes", "slots", "enums", "types"]: - if not hasattr(source, element_type): - continue - src_elements = getattr(source, element_type) - tgt_elements = getattr(target, element_type) - self._copy_dict(copy_directive, src_elements, tgt_elements) - return target - - def _copy_class( - self, - copy_directives: list[CopyDirective], - source: ClassDefinition, - target: ClassDefinition, - ) -> ClassDefinition: - if type(copy_directives) is dict: - copy_directives_list = copy_directives.values() - else: - copy_directives_list = copy_directives - - for copy_directive in copy_directives_list: - if hasattr(source, "attributes"): - # copy attributes (which is a dict) - src_elements = source.attributes - tgt_elements = target.attributes - self._copy_dict(copy_directive, src_elements, tgt_elements) - if hasattr(source, "slots"): - # copy slots (which is a list) - src_elements = source.slots - tgt_elements = target.slots - self._copy_list(copy_directive, src_elements, tgt_elements) - return target - - def derive_schema( - self, - specification: Optional[TransformationSpecification] = None, - target_schema_id: Optional[str] = None, - target_schema_name: Optional[str] = None, - suffix="-derived", - ) -> SchemaDefinition: - """ - Use a transformation specification to generate a target/profile schema from a source schema. - - :param specification: - :return: - """ - if specification is None: - specification = self.transformer.specification - source_schemaview = self.source_schemaview - source_schema = source_schemaview.schema - if target_schema_id is None: - target_schema_id = source_schema.id + suffix - if target_schema_name is None: - target_schema_name = source_schema.name + suffix - target_schema = SchemaDefinition(id=target_schema_id, name=target_schema_name) - if hasattr(specification, "copy_directives"): - target_schema = self._copy_schema( - specification.copy_directives, - source_schema, - target_schema, - ) - for im in source_schema.imports: - target_schema.imports.append(im) - for prefix in source_schema.prefixes.values(): - target_schema.prefixes[prefix.prefix_prefix] = prefix - for class_derivation in specification.class_derivations.values(): - class_definition = self._derive_class(class_derivation) - target_schema.classes[class_definition.name] = class_definition - for enum_derivation in specification.enum_derivations.values(): - enum_definition = self._derive_enum(enum_derivation) - target_schema.enums[enum_definition.name] = enum_definition - target_schema.default_range = source_schema.default_range - for cd in target_schema.classes.values(): - self._rewire_class(cd) - for (cn, sn), info in self.slot_info.items(): - cd = target_schema.classes[cn] - sd = cd.attributes[sn] - for k, v in info.items(): - setattr(sd, k, v) - return target_schema - - def _derive_class(self, class_derivation: ClassDerivation) -> ClassDefinition: - """ - Derive a class from a class derivation. - """ - populated_from = class_derivation.populated_from - if not populated_from: - populated_from = class_derivation.name - logger.info(f"Populating {class_derivation.name} from {populated_from}") - source_class = self.source_schemaview.get_class(populated_from) - if source_class is None: - logger.warning(f"No such class {populated_from}") - target_class = ClassDefinition(name=class_derivation.name) - else: - target_class = copy(source_class) - target_class.from_schema = None - target_class.name = class_derivation.name - target_class.slots = [] - target_class.attributes = {} - target_class.slot_usage = {} - if hasattr(class_derivation, "copy_directives"): - target_class = self._copy_class( - class_derivation.copy_directives, - source_class, - target_class, - ) - for slot_derivation in class_derivation.slot_derivations.values(): - slot_definition = self._derive_slot(slot_derivation) - target_class.attributes[slot_definition.name] = slot_definition - if class_derivation.is_a: - target_class.is_a = class_derivation.is_a - if class_derivation.mixins: - target_class.mixins = class_derivation.mixins - if class_derivation.target_definition: - spec_defn = ClassDefinition( - name=target_class.name, **class_derivation.target_definition - ) - for k, v in vars(spec_defn).items(): - curr_v = getattr(target_class, k, None) - if curr_v is None or curr_v in ([], {}): - setattr(target_class, k, v) - self.source_to_target_class_mappings[populated_from].append(target_class.name) - if class_derivation.overrides: - curr = json_dumper.to_dict(target_class) - for k, v in class_derivation.overrides.items(): - curr[k] = v - target_class = ClassDefinition(**curr) - return target_class - - def _derive_enum(self, enum_derivation: EnumDerivation) -> EnumDefinition: - """ - Derive an enum from an enum derivation. - - :param enum_derivation: - :return: - """ - populated_from = enum_derivation.populated_from - if not populated_from: - populated_from = enum_derivation.name - source_enum = self.source_schemaview.get_enum(populated_from) - if source_enum is None: - logger.warning(f"No such enum {populated_from}") - target_enum = ClassDefinition(name=enum_derivation.name) - else: - target_enum = copy(source_enum) - target_enum.from_schema = None - target_enum.name = enum_derivation.name - target_enum.slots = [] - target_enum.attributes = {} - target_enum.slot_usage = {} - for pv_derivation in enum_derivation.permissible_value_derivations.values(): - if pv_derivation.populated_from: - pv = PermissibleValue(text=pv_derivation.populated_from) - target_enum.permissible_values[pv.text] = pv - elif pv_derivation.sources: - for source in pv_derivation.sources: - pv = PermissibleValue(text=source) - target_enum.permissible_values[pv.text] = pv - else: - msg = f"Missing populated_from or sources for {pv_derivation}" - raise ValueError(msg) - if enum_derivation.mirror_source: - for pv in source_enum.permissible_values.values(): - if pv.text not in target_enum.permissible_values: - target_enum.permissible_values[pv.text] = copy(pv) - self.source_to_target_class_mappings[populated_from].append(target_enum.name) - return target_enum - - def _derive_slot(self, slot_derivation) -> SlotDefinition: - """ - Derive a slot from a slot derivation. - """ - populated_from = slot_derivation.populated_from - if not populated_from: - populated_from = slot_derivation.name - source_slot = self.source_schemaview.get_slot(populated_from) - if source_slot is None: - target_slot = SlotDefinition(name=slot_derivation.name) - else: - target_slot = copy(source_slot) - target_slot.from_schema = None - target_slot.owner = None - target_slot.name = slot_derivation.name - if slot_derivation.range: - target_slot.range = slot_derivation.range - if slot_derivation.target_definition: - spec_defn = SlotDefinition(name=target_slot.name, **slot_derivation.target_definition) - for k, v in vars(spec_defn).items(): - setattr(target_slot, k, v) - if slot_derivation.unit_conversion: - target_slot.unit = UnitOfMeasure(ucum_code=slot_derivation.unit_conversion.target_unit) - if slot_derivation.stringification: - if slot_derivation.stringification.reversed: - target_slot.multivalued = True - else: - target_slot.multivalued = False - if slot_derivation.dictionary_key: - target_slot.inlined = True - target_slot.inlined_as_list = False - self.slot_info[(target_slot.range, slot_derivation.dictionary_key)] = { - "identifier": True - } - if slot_derivation.cast_collection_as: - if slot_derivation.cast_collection_as == CollectionType.MultiValued: - target_slot.inlined = True - elif slot_derivation.cast_collection_as == CollectionType.MultiValuedList: - target_slot.inlined_as_list = True - elif slot_derivation.cast_collection_as == CollectionType.MultiValuedDict: - target_slot.inlined = True - target_slot.inlined_as_list = False - if slot_derivation.overrides: - curr = json_dumper.to_dict(target_slot) - for k, v in slot_derivation.overrides.items(): - curr[k] = v - target_slot = SlotDefinition(**curr) - return target_slot - - def _rewire_class(self, class_definition: ClassDefinition) -> None: - if class_definition.is_a: - class_definition.is_a = self._rewire_parent(class_definition, class_definition.is_a) - mixins = [self._rewire_parent(class_definition, m) for m in class_definition.mixins] - class_definition.mixins = [m for m in mixins if m is not None] - - def _rewire_parent( - self, class_definition: ClassDefinition, parent: ClassDefinitionName - ) -> Optional[str]: - if parent in self.source_to_target_class_mappings: - new_parents = self.source_to_target_class_mappings[parent] - if len(new_parents) > 1: - msg = f"Cannot rewire to non-isomorphic mappings {parent} => {new_parents}" - raise ValueError(msg) - if len(new_parents) == 1: - return new_parents[0] - parent_cls = self.source_schemaview.get_class(parent) - if parent_cls.is_a: - return self._rewire_parent(class_definition, parent_cls.is_a) - return None - - def copy_attributes( - self, - target_element: Element, - source_element: Element, - copy_directive: CopyDirective, - ) -> None: - """ - Copy attributes from source to target according to a directive. - - :param target_element: - :param source_element: - :param copy_directive: - :return: - """ - for k, v in vars(source_element).items(): - included = False - if copy_directive.include_all: - included = True - if k in copy_directive.include: - included = True - if k in copy_directive.exclude: - included = False - if included: - setattr(target_element, k, v) diff --git a/src/linkml_map/session.py b/src/linkml_map/session.py deleted file mode 100644 index 65a6c48..0000000 --- a/src/linkml_map/session.py +++ /dev/null @@ -1,170 +0,0 @@ -import logging -from dataclasses import dataclass -from pathlib import Path -from typing import Any, Optional, Union - -import yaml -from linkml_runtime import SchemaView -from linkml_runtime.dumpers import yaml_dumper -from linkml_runtime.linkml_model import SchemaDefinition -from linkml_runtime.processing.referencevalidator import ReferenceValidator -from linkml_runtime.utils.introspection import package_schemaview - -from linkml_map import ObjectTransformer -from linkml_map.datamodel.transformer_model import TransformationSpecification -from linkml_map.inference.inverter import TransformationSpecificationInverter -from linkml_map.inference.schema_mapper import SchemaMapper -from linkml_map.transformer.transformer import Transformer - -logger = logging.getLogger(__name__) - - -@dataclass -class Session: - """ - A wrapper object for a transformer session. - - Todo: - - rename to Manager? - - consolidate configuration - - include source and target database - - - current spec, src_sv, tgt_sv all live in both this class and transformer - - """ - - transformer_specification: Optional[TransformationSpecification] = None - source_schemaview: Optional[SchemaView] = None - transformer: Optional[Transformer] = None - object_transformer: Optional[ObjectTransformer] = None - schema_mapper: Optional[SchemaMapper] = None - _target_schema: Optional[SchemaDefinition] = None - _target_schemaview: Optional[SchemaView] = None - - def set_transformer_specification( - self, specification: Optional[Union[TransformationSpecification, dict, str, Path]] = None - ) -> None: - if isinstance(specification, Path): - specification = str(specification) - if isinstance(specification, TransformationSpecification): - self.transformer_specification = specification - elif isinstance(specification, dict): - # TODO: centralize this code - normalizer = ReferenceValidator( - package_schemaview("linkml_map.datamodel.transformer_model") - ) - normalizer.expand_all = True - specification = normalizer.normalize(specification) - self.transformer_specification = TransformationSpecification(**specification) - elif isinstance(specification, str): - if "\n" in specification: - obj = yaml.safe_load(specification) - else: - obj = yaml.safe_load(open(specification)) - self.set_transformer_specification(obj) - - def set_source_schema( - self, schema: Union[str, Path, dict, SchemaView, SchemaDefinition] - ) -> None: - """ - Set the schema from a path or SchemaView object. - """ - if isinstance(schema, str): - sv = SchemaView(schema) - elif isinstance(schema, Path): - sv = SchemaView(str(schema)) - elif isinstance(schema, dict): - sv = SchemaView(yaml_dumper.dumps(schema)) - elif isinstance(schema, SchemaView): - sv = schema - elif isinstance(schema, SchemaDefinition): - sv = SchemaView(schema) - else: - msg = f"Unsupported schema type: {type(schema)}" - raise ValueError(msg) - self.source_schemaview = sv - self._target_schema = None - - def set_transformer( - self, - transformer: Optional[Union[Transformer, type[Transformer]]], - **kwargs, - ) -> None: - if isinstance(transformer, type): - transformer = transformer() - transformer.specification = self.transformer_specification - self.transformer = transformer - - def set_object_transformer( - self, - transformer: Optional[ - Union[ObjectTransformer, TransformationSpecification, dict, str, Path] - ] = None, - ) -> None: - if transformer is None: - if self.object_transformer is not None: - logger.info("No change") - return - logger.warning("No transformer specified") - return - if transformer is not None: - if isinstance(transformer, ObjectTransformer): - self.object_transformer = transformer - else: - self.set_transformer_specification(transformer) - self.object_transformer = ObjectTransformer() - self.object_transformer.specification = self.transformer_specification - self._target_schema = None - - @property - def target_schema(self) -> SchemaDefinition: - if self._target_schema is None: - if not self.schema_mapper: - self.schema_mapper = SchemaMapper(source_schemaview=self.source_schemaview) - self._target_schema = self.schema_mapper.derive_schema(self.transformer_specification) - return self._target_schema - - @property - def target_schemaview(self) -> SchemaView: - if self._target_schemaview is None: - # TODO: simplify - self._target_schemaview = SchemaView(yaml_dumper.dumps(self.target_schema)) - return self._target_schemaview - - def transform(self, obj: dict, **kwargs) -> dict: - if self.object_transformer is None: - msg = "No transformer specified" - raise ValueError(msg) - if not self.object_transformer.source_schemaview: - self.object_transformer.source_schemaview = self.source_schemaview - return self.object_transformer.map_object(obj, **kwargs) - - def reverse_transform(self, obj: dict, **kwargs) -> dict: - inv_spec = self.invert() - reverse_transformer = ObjectTransformer() - reverse_transformer.specification = inv_spec - reverse_transformer.source_schemaview = SchemaView(yaml_dumper.dumps(self.target_schema)) - return reverse_transformer.map_object(obj, **kwargs) - - def invert(self, in_place=False) -> TransformationSpecification: - """ - Invert the transformer specification. - """ - inverter = TransformationSpecificationInverter( - source_schemaview=self.source_schemaview, - target_schemaview=SchemaView(yaml_dumper.dumps(self.target_schema)), - ) - inv_spec = inverter.invert(self.transformer_specification) - if in_place: - raise NotImplementedError - return inv_spec - - def graphviz(self, **kwargs) -> Any: - """ - Return a graphviz representation of the schema. - """ - from linkml_map.compiler.graphviz_compiler import GraphvizCompiler - - gc = GraphvizCompiler(source_schemaview=self.source_schemaview) - compiled = gc.compile(self.transformer_specification) - return compiled.digraph diff --git a/src/linkml_map/transformer/__init__.py b/src/linkml_map/transformer/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/src/linkml_map/transformer/duckdb_transformer.py b/src/linkml_map/transformer/duckdb_transformer.py deleted file mode 100644 index 0d0aaf9..0000000 --- a/src/linkml_map/transformer/duckdb_transformer.py +++ /dev/null @@ -1,76 +0,0 @@ -"""A Transformer that works on DuckDB data.""" - -import logging -from dataclasses import dataclass -from typing import Any, Optional, Union - -from duckdb import DuckDBPyConnection - -from linkml_map.compiler.sql_compiler import SQLCompiler -from linkml_map.transformer.transformer import OBJECT_TYPE, Transformer - -DICT_OBJ = dict[str, Any] -DATABASE = Union[str, DuckDBPyConnection] - - -logger = logging.getLogger(__name__) - - -@dataclass -class DuckDBTransformer(Transformer): - """ - A Transformer that works on DuckDB data. - """ - - def map_object( - self, - source_obj: OBJECT_TYPE, - source_type: Optional[str] = None, - target_type: Optional[str] = None, - **kwargs: Optional[dict[str, Any]], - ) -> OBJECT_TYPE: - """ - Transform a source object into a target object. - - :param source_obj: source data structure - :param source_type: source_obj instantiates this (may be class, type, or enum) - :param target_type: target_obj instantiates this (may be class, type, or enum) - :return: transformed data, either as type target_type or a dictionary - """ - msg = "DuckDBTransformer.transform" - raise NotImplementedError(msg) - - def map_database( - self, - source_database: DATABASE, - target_database: Optional[DATABASE] = None, - **kwargs: Optional[dict[str, Any]], - ) -> OBJECT_TYPE: - """ - Transform source resource. - - :param source_database: - :param target_database: - :param kwargs: - :return: - """ - import duckdb - - if target_database is None: - target_database = source_database - - def _connect(db: DATABASE) -> DuckDBPyConnection: - if isinstance(db, str): - return duckdb.connect(db) - return db - - source_connection = _connect(source_database) - target_connection = _connect(target_database) - sql_compiler = SQLCompiler() - source_connection.sql(sql_compiler.create_ddl(self.source_schemaview)) - target_connection.sql(sql_compiler.create_ddl(self.target_schemaview)) - if not self.specification: - msg = "No specification provided." - raise ValueError(msg) - compiled = sql_compiler.compile(self.specification) - source_connection.execute(compiled.serialization) diff --git a/src/linkml_map/transformer/object_transformer.py b/src/linkml_map/transformer/object_transformer.py deleted file mode 100644 index 3a08bd1..0000000 --- a/src/linkml_map/transformer/object_transformer.py +++ /dev/null @@ -1,530 +0,0 @@ -"""A Transformer that works on in-memory dict objects.""" - -import json -import logging -from collections.abc import Iterator, Mapping -from dataclasses import dataclass -from typing import Any, Optional, Union - -import yaml -from asteval import Interpreter -from linkml_runtime import SchemaView -from linkml_runtime.index.object_index import ObjectIndex -from linkml_runtime.utils.yamlutils import YAMLRoot -from pydantic import BaseModel - -from linkml_map.datamodel.transformer_model import ( - ClassDerivation, - CollectionType, - SerializationSyntaxType, - SlotDerivation, -) -from linkml_map.functions.unit_conversion import UnitSystem, convert_units -from linkml_map.transformer.transformer import OBJECT_TYPE, Transformer -from linkml_map.utils.dynamic_object import DynObj, dynamic_object -from linkml_map.utils.eval_utils import eval_expr, eval_expr_with_mapping - -DICT_OBJ = dict[str, Any] - - -logger = logging.getLogger(__name__) - - -class Bindings(Mapping): - """ - Efficiently access source object attributes. - """ - - def __init__( # noqa: PLR0913 - self, - object_transformer: "ObjectTransformer", - source_obj: OBJECT_TYPE, - source_obj_typed: OBJECT_TYPE, - source_type: str, - sv: SchemaView, - bindings: dict, - ) -> None: - self.object_transformer: ObjectTransformer = object_transformer - self.source_obj: OBJECT_TYPE = source_obj - self.source_obj_typed: OBJECT_TYPE = source_obj_typed - self.source_type: str = source_type - self.sv: SchemaView = sv - self.bindings: dict = {} - if bindings: - self.bindings.update(bindings) - - def get_ctxt_obj_and_dict(self, source_obj: OBJECT_TYPE = None) -> tuple[DynObj, OBJECT_TYPE]: - """ - Transform a source object into a typed context object and dictionary, and cache results. - - :param source_obj: Source data. Should be a subset of source_obj provided in the constructor. - If None the full source_obj from constructor is used. - :return: Tuple of typed context object and context dictionary. The object is the dictionary - with keys converted to member variables. - """ - if source_obj is None: - source_obj = self.source_obj - - if self.object_transformer.object_index: - if not self.source_obj_typed: - source_obj_dyn = dynamic_object(source_obj, self.sv, self.source_type) - else: - source_obj_dyn = self.source_obj_typed - # Clear cache: Cache doesn't work since the cache key is the same when source_obj has only a subset - # of its keys. eg. {"age": self.source_obj["age"]} and {"name": self.source_obj["name"]} - # (with optionally the identifier key included) will have the same cache key, and so `bless` will - # incorrectly return the same cached values. - self.object_transformer.object_index.clear_proxy_object_cache() - - ctxt_obj = self.object_transformer.object_index.bless(source_obj_dyn) - ctxt_dict = { - k: getattr(ctxt_obj, k) for k in ctxt_obj._attributes() if not k.startswith("_") - } - else: - do = dynamic_object(source_obj, self.sv, self.source_type) - ctxt_obj = do - ctxt_dict = vars(do) - - self.bindings.update(ctxt_dict) - - return ctxt_obj, ctxt_dict - - def _all_keys(self) -> list[Any]: - keys = list(self.source_obj.keys()) + list(self.bindings.keys()) - # Remove duplicate keys (ie. found in both source_obj and bindings), and retain original order - return list(dict.fromkeys(keys).keys()) - - def __len__(self) -> int: - return len(self._all_keys()) - - def __iter__(self) -> Iterator: - return iter(self._all_keys()) - - def __getitem__(self, name: Any) -> Any: - if name not in self.bindings: - _ = self.get_ctxt_obj_and_dict({name: self.source_obj[name]}) - - return self.bindings.get(name) - - def __setitem__(self, name: Any, value: Any) -> None: - del name, value - msg = f"__setitem__ not allowed on class {self.__class__.__name__}" - raise RuntimeError(msg) - - -@dataclass -class ObjectTransformer(Transformer): - """ - A Transformer that works on in-memory dict objects. - - This works recursively - """ - - object_index: ObjectIndex = None - - def index(self, source_obj: Any, target: Optional[str] = None) -> None: - """ - Create an index over a container object. - - :param source_obj: source data structure to be indexed - :param target: class to convert source object into - """ - if isinstance(source_obj, dict): - if target is None: - [target] = [ - c.name for c in self.source_schemaview.all_classes().values() if c.tree_root - ] - if target is None: - msg = f"target must be passed if source_obj is dict: {source_obj}" - raise ValueError(msg) - source_obj_typed = dynamic_object(source_obj, self.source_schemaview, target) - self.object_index = ObjectIndex(source_obj_typed, schemaview=self.source_schemaview) - else: - self.object_index = ObjectIndex(source_obj, schemaview=self.source_schemaview) - - def map_object( - self, - source_obj: OBJECT_TYPE, - source_type: Optional[str] = None, - target_type: Optional[str] = None, - class_derivation: Optional[ClassDerivation] = None, - ) -> Union[DICT_OBJ, Any]: - """ - Transform a source object into a target object. - - :param source_obj: source data structure - :param source_type: source_obj instantiates this (may be class, type, or enum) - :param target_type: target_obj instantiates this (may be class, type, or enum) - :return: transformed data, either as type target_type or a dictionary - """ - sv = self.source_schemaview - if source_type is None and sv is None: - # TODO: use smarter method - source_type = next(iter(self.specification.class_derivations.values())).name - if source_type is None and sv is not None: - source_types = [c.name for c in sv.all_classes().values() if c.tree_root] - if len(source_types) == 1: - source_type = source_types[0] - elif len(source_types) > 1: - msg = "No source type specified and multiple root classes found" - raise ValueError(msg) - elif len(source_types) == 0: - if len(sv.all_classes()) == 1: - source_type = next(iter(sv.all_classes().keys())) - else: - msg = "No source type specified and no root classes found" - raise ValueError(msg) - - if source_type in sv.all_types(): - if target_type: - if target_type == "string": - return str(source_obj) - if target_type == "integer": - return int(source_obj) - if target_type in {"float", "double"}: - return float(source_obj) - if target_type == "uri": - return self.expand_curie(source_obj) - if target_type == "curie": - return self.compress_uri(source_obj) - return source_obj - if source_type in sv.all_enums(): - # TODO: enum derivations - return self.transform_enum(source_obj, source_type, source_obj) - source_obj_typed = None - if isinstance(source_obj, (BaseModel, YAMLRoot)): - # ensure dict - source_obj_typed = source_obj - source_obj = vars(source_obj) - if not isinstance(source_obj, dict): - logger.warning(f"Unexpected: {source_obj} for type {source_type}") - return source_obj - class_deriv = class_derivation or self._get_class_derivation(source_type) - tgt_attrs = {} - bindings = None - # map each slot assignment in source_obj, if there is a slot_derivation - for slot_derivation in class_deriv.slot_derivations.values(): - v = None - source_class_slot = None - if slot_derivation.value is not None: - v = slot_derivation.value - if slot_derivation.range is None: - slot_derivation.range = "string" - elif slot_derivation.unit_conversion: - v = self._perform_unit_conversion(slot_derivation, source_obj, sv, source_type) - elif slot_derivation.expr: - if bindings is None: - bindings = Bindings( - self, - source_obj=source_obj, - source_obj_typed=source_obj_typed, - source_type=source_type, - sv=sv, - bindings={"NULL": None}, - ) - - try: - v = eval_expr_with_mapping(slot_derivation.expr, bindings) - except Exception as err: - if not self.unrestricted_eval: - msg = f"Expression not in safe subset: {slot_derivation.expr}" - raise RuntimeError(msg) from err - ctxt_obj, _ = bindings.get_ctxt_obj_and_dict() - aeval = Interpreter(usersyms={"src": ctxt_obj, "target": None}) - aeval(slot_derivation.expr) - v = aeval.symtable["target"] - elif slot_derivation.populated_from: - v = source_obj.get(slot_derivation.populated_from, None) - if slot_derivation.value_mappings and v is not None: - mapped = slot_derivation.value_mappings.get(str(v), None) - v = mapped.value if mapped is not None else None - source_class_slot = sv.induced_slot(slot_derivation.populated_from, source_type) - logger.debug( - f"Pop slot {slot_derivation.name} => {v} using {slot_derivation.populated_from} // {source_obj}" - ) - elif slot_derivation.sources: - vmap = {s: source_obj.get(s, None) for s in slot_derivation.sources} - vmap = {k: v for k, v in vmap.items() if v is not None} - if len(vmap.keys()) > 1: - msg = f"Multiple sources for {slot_derivation.name}: {vmap}" - raise ValueError(msg) - if len(vmap.keys()) == 1: - v = next(iter(vmap.values())) - source_class_slot_name = next(iter(vmap.keys())) - source_class_slot = sv.induced_slot(source_class_slot_name, source_type) - else: - v = None - source_class_slot = None - - logger.debug( - f"Pop slot {slot_derivation.name} => {v} using {slot_derivation.populated_from} // {source_obj}" - ) - elif slot_derivation.object_derivations: - # We'll collect all derived objects here - derived_objs = [] - - for obj_derivation in slot_derivation.object_derivations: - for target_cls, cls_derivation in obj_derivation.class_derivations.items(): - # Determine the correct source object to use - source_sub_obj = source_obj # You may refine this if needed - - # Recursively map the sub-object - nested_result = self.map_object( - source_sub_obj, - source_type=cls_derivation.populated_from, - target_type=target_cls, - class_derivation=cls_derivation, - ) - derived_objs.append(nested_result) - - # If the slot is multivalued, we assign the whole list - # Otherwise, just assign the first (for now; error/warning later if >1) - target_class_slot = self.target_schemaview.induced_slot(slot_derivation.name, target_type) - if target_class_slot.multivalued: - v = derived_objs - else: - v = derived_objs[0] if derived_objs else None - else: - source_class_slot = sv.induced_slot(slot_derivation.name, source_type) - v = source_obj.get(slot_derivation.name, None) - if source_class_slot and v is not None: - # slot is mapped and there is a value in the assignment - target_range = slot_derivation.range - source_class_slot_range = source_class_slot.range - if source_class_slot.multivalued: - if isinstance(v, list): - v = [self.map_object(v1, source_class_slot_range, target_range) for v1 in v] - elif isinstance(v, dict): - v = { - k1: self.map_object(v1, source_class_slot_range, target_range) - for k1, v1 in v.items() - } - else: - v = [self.map_object(v, source_class_slot_range, target_range)] - else: - v = self.map_object(v, source_class_slot_range, target_range) - if ( - self._is_coerce_to_multivalued(slot_derivation, class_deriv) - and v is not None - and not isinstance(v, list) - ): - v = self._singlevalued_to_multivalued(v, slot_derivation) - if self._is_coerce_to_singlevalued(slot_derivation, class_deriv) and isinstance( - v, list - ): - v = self._multivalued_to_singlevalued(v, slot_derivation) - v = self._coerce_datatype(v, target_range) - if slot_derivation.dictionary_key and isinstance(v, list): - # List to CompactDict - v = {v1[slot_derivation.dictionary_key]: v1 for v1 in v} - for v1 in v.values(): - del v1[slot_derivation.dictionary_key] - elif ( - slot_derivation.cast_collection_as - and slot_derivation.cast_collection_as == CollectionType.MultiValuedList - and isinstance(v, dict) - ): - # CompactDict to List - src_rng = source_class_slot.range - src_rng_id_slot = self.source_schemaview.get_identifier_slot( - src_rng, use_key=True - ) - if src_rng_id_slot: - v = [{**v1, src_rng_id_slot.name: k} for k, v1 in v.items()] - else: - v = list(v.values()) - tgt_attrs[str(slot_derivation.name)] = v - return tgt_attrs - - def _perform_unit_conversion( - self, - slot_derivation: SlotDerivation, - source_obj: Any, - sv: SchemaView, - source_type: str, - ) -> Union[float, dict, None]: - uc = slot_derivation.unit_conversion - curr_v = source_obj.get(slot_derivation.populated_from, None) - if curr_v is None: - logger.debug(f"No value found for slot '{slot_derivation.populated_from}'; skipping conversion") - return None - - # Get the slot from schema - slot = sv.induced_slot(slot_derivation.populated_from, source_type) - schema_unit = None - from_unit = None - system = UnitSystem.UCUM - - # --- Step 1: Get unit from schema --- - if slot.unit: - if slot.unit.ucum_code: - schema_unit = slot.unit.ucum_code - elif slot.unit.iec61360code: - schema_unit = slot.unit.iec61360code - system = UnitSystem.IEC61360 - elif slot.unit.symbol: - schema_unit = slot.unit.symbol - system = None - elif slot.unit.abbreviation: - schema_unit = slot.unit.abbreviation - system = None - elif slot.unit.descriptive_name: - schema_unit = slot.unit.descriptive_name - system = None - else: - raise NotImplementedError( - f"Cannot determine unit system for slot '{slot.name}' — all unit fields are None") - - # --- Step 2: Get unit from transformer spec --- - spec_unit = uc.source_unit if uc.source_unit else None - - # --- Step 3: Validate unit source --- - if schema_unit and spec_unit: - if schema_unit != spec_unit: - raise ValueError( - f"Mismatch in source units for slot '{slot_derivation.populated_from}': " - f"schema unit '{schema_unit}' vs. transformation spec '{spec_unit}'" - ) - from_unit = schema_unit - elif schema_unit: - from_unit = schema_unit - elif spec_unit: - from_unit = spec_unit - else: - # Handle structured unit slot case: don't raise here if source_unit_slot is set, - # defer unit extraction to Step 4 - if uc.source_unit_slot: - from_unit = None - else: - raise ValueError( - f"No source unit provided in schema or transformation spec for slot '{slot_derivation.populated_from}'" - ) - - # --- Step 4: Determine magnitude and possibly from_unit --- - if uc.source_unit_slot: - # Structured input, e.g., {"value": 120, "unit": "cm"} - from_unit_val = curr_v.get(uc.source_unit_slot) - if from_unit_val: - if from_unit and from_unit_val != from_unit: - raise ValueError( - f"Value unit '{from_unit_val}' does not match expected '{from_unit}' for slot '{slot_derivation.populated_from}'" - ) - from_unit = from_unit_val - else: - raise ValueError( - f"Missing unit in structured value for slot '{slot_derivation.populated_from}': {curr_v}") - - magnitude = curr_v.get(uc.source_magnitude_slot) - if magnitude is None: - raise ValueError( - f"Missing magnitude in structured value for slot '{slot_derivation.populated_from}': {curr_v}") - else: - magnitude = curr_v - - # --- Step 5: Convert --- - to_unit = uc.target_unit or from_unit - if from_unit == to_unit: - result = magnitude - else: - result = convert_units(magnitude, from_unit=from_unit, to_unit=to_unit, system=system) - - # --- Step 6: Structure result if needed --- - if uc.target_magnitude_slot: - return {uc.target_magnitude_slot: result, uc.target_unit_slot: to_unit} - return result - - def _multivalued_to_singlevalued(self, vs: list[Any], slot_derivation: SlotDerivation) -> Any: - if slot_derivation.stringification: - stringification = slot_derivation.stringification - delimiter = stringification.delimiter - if delimiter: - return delimiter.join(vs) - if stringification.syntax: - if stringification.syntax == SerializationSyntaxType.JSON: - return json.dumps(vs) - if stringification.syntax == SerializationSyntaxType.YAML: - return yaml.dump(vs, default_flow_style=True).strip() - msg = f"Unknown syntax: {stringification.syntax}" - raise ValueError(msg) - msg = f"Cannot convert multivalued to single valued: {vs}; no delimiter" - raise ValueError(msg) - if len(vs) > 1: - msg = f"Cannot coerce multiple values {vs}" - raise ValueError(msg) - if len(vs) == 0: - return None - return vs[0] - - def _singlevalued_to_multivalued(self, v: Any, slot_derivation: SlotDerivation) -> list[Any]: - stringification = slot_derivation.stringification - if stringification: - delimiter = stringification.delimiter - if delimiter: - vs = v.split(slot_derivation.stringification.delimiter) - if vs == [""]: - vs = [] - elif stringification.syntax: - syntax = stringification.syntax - if syntax == SerializationSyntaxType.JSON: - vs = json.loads(v) - elif syntax == SerializationSyntaxType.YAML: - vs = yaml.safe_load(v) - else: - msg = f"Unknown syntax: {syntax}" - raise ValueError(msg) - else: - msg = f"Cannot convert single valued to multivalued: {v}; no delimiter" - raise ValueError(msg) - return vs - return [v] - - def transform_object( - self, - source_obj: Union[YAMLRoot, BaseModel], - target_class: Optional[Union[type[YAMLRoot], type[BaseModel]]] = None, - ) -> Union[YAMLRoot, BaseModel]: - """ - Transform an object into an object of class target_class. - - :param source_obj: source object - :type source_obj: Union[YAMLRoot, BaseModel] - :param target_class: class to transform the object into, defaults to None - :type target_class: Optional[Union[Type[YAMLRoot], Type[BaseModel]]], optional - :return: transformed object of class target_class - :rtype: Union[YAMLRoot, BaseModel] - """ - if not target_class: - msg = "No target_class specified for transform_object" - raise ValueError(msg) - - source_type = type(source_obj) - source_type_name = source_type.__name__ - # if isinstance(source_obj, YAMLRoot): - # source_obj_dict = json_dumper.to_dict(source_obj) - # elif isinstance(source_obj, BaseModel): - # source_obj_dict = source_obj.dict() - # else: - # raise ValueError(f"Do not know how to handle type: {typ}") - tr_obj_dict = self.map_object(source_obj, source_type_name) - return target_class(**tr_obj_dict) - - def transform_enum(self, source_value: str, enum_name: str, source_obj: Any) -> Optional[str]: - enum_deriv = self._get_enum_derivation(enum_name) - if enum_deriv.expr: - try: - if enum_deriv.expr: - v = eval_expr(enum_deriv.expr, **source_obj, NULL=None) - except Exception: - aeval = Interpreter(usersyms={"src": source_obj, "target": None}) - aeval(enum_deriv.expr) - v = aeval.symtable["target"] - if v is not None: - return v - for pv_deriv in enum_deriv.permissible_value_derivations.values(): - if source_value == pv_deriv.populated_from: - return pv_deriv.name - if source_value in pv_deriv.sources: - return pv_deriv.name - if enum_deriv.mirror_source: - return str(source_value) - return None diff --git a/src/linkml_map/transformer/transformer.py b/src/linkml_map/transformer/transformer.py deleted file mode 100644 index 14ff730..0000000 --- a/src/linkml_map/transformer/transformer.py +++ /dev/null @@ -1,290 +0,0 @@ -""" -Transformers (aka data mappers) are used to transform objects from one class to another using a transformation specification. -""" - -import logging -from abc import ABC -from copy import deepcopy -from dataclasses import dataclass, field -from pathlib import Path -from typing import Any, Optional, Union - -import yaml -from curies import Converter -from linkml_runtime import SchemaView -from linkml_runtime.processing.referencevalidator import ReferenceValidator -from linkml_runtime.utils.introspection import package_schemaview -from linkml_runtime.utils.yamlutils import YAMLRoot -from pydantic import BaseModel - -from linkml_map.datamodel.transformer_model import ( - ClassDerivation, - CollectionType, - EnumDerivation, - SlotDerivation, - TransformationSpecification, -) -from linkml_map.inference.inference import induce_missing_values - -logger = logging.getLogger(__name__) - - -OBJECT_TYPE = Union[dict[str, Any], BaseModel, YAMLRoot] -"""An object can be a plain python dict, a pydantic object, or a linkml YAMLRoot""" - - -@dataclass -class Transformer(ABC): - """ - Base class for all transformers. - - A transformer will generate an instance of a target class from - an instance of a source class, making use of a specification. - - This is an abstract class. Different implementations will - subclass this - """ - - specification: TransformationSpecification = None - """A specification of how to generate target objects from source objects.""" - - source_schemaview: SchemaView = None - """A view over the schema describing the input/source object.""" - - _derived_specification: TransformationSpecification = None - """A specification with inferred missing values.""" - - target_schemaview: Optional[SchemaView] = None - """A view over the schema describing the output/target object.""" - - unrestricted_eval: bool = field(default=False) - """Set to True to allow arbitrary evals as part of transformation.""" - - _curie_converter: Converter = None - - def map_object( - self, obj: OBJECT_TYPE, source_type: Optional[str] = None, **kwargs: dict[str, Any] - ) -> OBJECT_TYPE: - """ - Transform source object into an instance of the target class. - - :param obj: - :param source_type: - :return: - """ - raise NotImplementedError - - def map_database( - self, source_database: Any, target_database: Optional[Any] = None, **kwargs: dict[str, Any] - ) -> OBJECT_TYPE: - """ - Transform source resource. - - :param source_database: - :param target_database: - :param kwargs: - :return: - """ - raise NotImplementedError - - def load_source_schema(self, path: Union[str, Path, dict]) -> None: - """ - Set source_schemaview from a schema path. - - :param path: - """ - if isinstance(path, Path): - path = str(path) - self.source_schemaview = SchemaView(path) - - def load_transformer_specification(self, path: Union[str, Path]) -> None: - """ - Set specification from a schema path. - - :param path: - :return: - """ - with open(path) as f: - obj = yaml.safe_load(f) - # necessary to expand first - normalizer = ReferenceValidator( - package_schemaview("linkml_map.datamodel.transformer_model") - ) - normalizer.expand_all = True - obj = normalizer.normalize(obj) - self.specification = TransformationSpecification(**obj) - - def normalize_transform_spec( - self, - obj: dict[str, Any], - normalizer: ReferenceValidator - ) -> dict: - """ - Recursively normalize class_derivations and their nested object_derivations. - """ - obj = normalizer.normalize(obj) - - class_derivations = obj.get("class_derivations", {}) - for class_name, class_spec in class_derivations.items(): - slot_derivations = class_spec.get("slot_derivations", {}) - for slot, slot_spec in slot_derivations.items(): - # Check for nested object_derivations - object_derivations = slot_spec.get("object_derivations", []) - for i, od in enumerate(object_derivations): - # Recursively normalize each nested class_derivation block - od_normalized = self.normalize_transform_spec(od, normalizer) - object_derivations[i] = od_normalized - return obj - - def create_transformer_specification(self, obj: dict[str, Any]) -> None: - """ - Create specification from a dict. - - TODO: this will no longer be necessary when pydantic supports inlined as dict - - :param path: - :return: - """ - normalizer = ReferenceValidator( - package_schemaview("linkml_map.datamodel.transformer_model") - ) - normalizer.expand_all = True - obj = self.normalize_transform_spec(obj, normalizer) - self.specification = TransformationSpecification(**obj) - - @property - def derived_specification(self) -> Optional[TransformationSpecification]: - if self._derived_specification is None: - if self.specification is None: - return None - self._derived_specification = deepcopy(self.specification) - induce_missing_values(self._derived_specification, self.source_schemaview) - return self._derived_specification - - def _get_class_derivation(self, target_class_name: str) -> ClassDerivation: - spec = self.derived_specification - matching_tgt_class_derivs = [ - deriv - for deriv in spec.class_derivations.values() - if deriv.populated_from == target_class_name - or (not deriv.populated_from and target_class_name == deriv.name) - ] - logger.debug(f"Target class derivations={matching_tgt_class_derivs}") - if len(matching_tgt_class_derivs) != 1: - msg = f"Could not find class derivation for {target_class_name} (results={len(matching_tgt_class_derivs)})" - raise ValueError(msg) - cd = matching_tgt_class_derivs[0] - ancmap = self._class_derivation_ancestors(cd) - if ancmap: - cd = deepcopy(cd) - for ancestor in ancmap.values(): - for k, v in ancestor.__dict__.items(): - if v is not None and v != []: - curr_v = getattr(cd, k, None) - if isinstance(curr_v, list): - curr_v.extend(v) - elif isinstance(curr_v, dict): - curr_v.update({**v, **curr_v}) - elif curr_v is None: - setattr(cd, k, v) - return cd - - def _class_derivation_ancestors(self, cd: ClassDerivation) -> dict[str, ClassDerivation]: - """ - Return a map of all class derivations that are ancestors of the given class derivation. - - :param cd: - :return: - """ - spec = self.specification - ancestors = {} - parents = cd.mixins + ([cd.is_a] if cd.is_a else []) - for parent in parents: - ancestors[parent] = spec.class_derivations[parent] - ancestors.update(self._class_derivation_ancestors(spec.class_derivations[parent])) - return ancestors - - def _get_enum_derivation(self, target_enum_name: str) -> EnumDerivation: - spec = self.derived_specification - matching_tgt_enum_derivs = [ - deriv - for deriv in spec.enum_derivations.values() - if deriv.populated_from == target_enum_name - or (not deriv.populated_from and target_enum_name == deriv.name) - ] - logger.debug(f"Target enum derivations={matching_tgt_enum_derivs}") - if len(matching_tgt_enum_derivs) != 1: - msg = f"Could not find what to derive from a source {target_enum_name}" - raise ValueError(msg) - return matching_tgt_enum_derivs[0] - - def _is_coerce_to_multivalued( - self, slot_derivation: SlotDerivation, class_derivation: ClassDerivation - ) -> bool: - cast_as = slot_derivation.cast_collection_as - if cast_as and cast_as in [ - CollectionType.MultiValued, - CollectionType.MultiValuedDict, - CollectionType.MultiValuedDict, - ]: - return True - if slot_derivation.stringification and slot_derivation.stringification.reversed: - return True - sv = self.target_schemaview - if sv: - slot = sv.induced_slot(slot_derivation.name, class_derivation.name) - if slot.multivalued: - return True - return False - - def _is_coerce_to_singlevalued( - self, slot_derivation: SlotDerivation, class_derivation: ClassDerivation - ) -> bool: - cast_as = slot_derivation.cast_collection_as - if cast_as and cast_as == CollectionType(CollectionType.SingleValued): - return True - if slot_derivation.stringification and not slot_derivation.stringification.reversed: - return True - sv = self.target_schemaview - if sv: - slot = sv.induced_slot(slot_derivation.name, class_derivation.name) - if not slot.multivalued: - return True - return False - - def _coerce_datatype(self, v: Any, target_range: Optional[str]) -> Any: - if target_range is None: - return v - if isinstance(v, list): - return [self._coerce_datatype(v1, target_range) for v1 in v] - if isinstance(v, dict): - return {k: self._coerce_datatype(v1, target_range) for k, v1 in v.items()} - cmap = { - "integer": int, - "float": float, - "string": str, - "boolean": bool, - } - cls = cmap.get(target_range) - if not cls: - logger.warning(f"Unknown target range {target_range}") - return v - if isinstance(v, cls): - return v - return cls(v) - - @property - def curie_converter(self) -> Converter: - if not self._curie_converter: - self._curie_converter = Converter([]) - for prefix in self.source_schemaview.schema.prefixes.values(): - self._curie_converter.add_prefix(prefix.prefix_prefix, prefix.prefix_reference) - for prefix in self.specification.prefixes.values(): - self._curie_converter.add_prefix(prefix.key, prefix.value) - return self._curie_converter - - def expand_curie(self, curie: str) -> str: - return self.curie_converter.expand(curie) - - def compress_uri(self, uri: str) -> str: - return self.curie_converter.compress(uri) diff --git a/src/linkml_map/utils/__init__.py b/src/linkml_map/utils/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/src/linkml_map/utils/dynamic_object.py b/src/linkml_map/utils/dynamic_object.py deleted file mode 100644 index f6752a3..0000000 --- a/src/linkml_map/utils/dynamic_object.py +++ /dev/null @@ -1,51 +0,0 @@ -"""Generate an object from a dict.""" - -from typing import Any - -from linkml_runtime import SchemaView - - -class DynObj: - def __init__(self, **kwargs) -> None: - for k, v in kwargs.items(): - setattr(self, k, v) - - def __str__(self) -> str: - return str(vars(self)) - - def __getattr__(self, p: str) -> Any: - return vars(self).get(p, None) - - -def dynamic_object(obj: dict, sv: SchemaView, target: str): - """ - Generate a dynamic object from a dict. - - :param obj: - :param sv: - :param target: - :return: - """ - if target in sv.all_enums(): - return obj - if target in sv.all_types(): - return obj - if not isinstance(obj, dict): - return obj - attrs = {} - for k, v in obj.items(): - slot = sv.induced_slot(k, target) - rng = slot.range - if slot.multivalued: - if isinstance(v, list): - v = [dynamic_object(x, sv, rng) for x in v] - if isinstance(v, dict): - v = {xk: dynamic_object(x, sv, rng) for xk, x in v.items()} - id_slot = sv.get_identifier_slot(slot.range) - for k1, v1 in v.items(): - setattr(v1, id_slot.name, k1) - else: - v = dynamic_object(v, sv, rng) - attrs[k] = v - cls = type(target, (DynObj,), {}) - return cls(**attrs) diff --git a/src/linkml_map/utils/eval_utils.py b/src/linkml_map/utils/eval_utils.py deleted file mode 100644 index 7305958..0000000 --- a/src/linkml_map/utils/eval_utils.py +++ /dev/null @@ -1,222 +0,0 @@ -""" -meta-circular interpreter for evaluating python expressions. - - - See ``_ - -TODO: move to core -""" - -import ast -import operator as op -from collections.abc import Mapping - -# supported operators -from typing import Any - -operators = { - ast.Add: op.add, - ast.Sub: op.sub, - ast.Mult: op.mul, - ast.Div: op.truediv, - ast.Pow: op.pow, - ast.BitXor: op.xor, - ast.USub: op.neg, -} -compare_operators = {ast.Eq: op.eq, ast.Lt: op.lt, ast.LtE: op.le, ast.Gt: op.gt, ast.GtE: op.ge} - - -def eval_conditional(*conds: list[tuple[bool, Any]]) -> Any: - """ - Evaluate a conditional. - - >>> x = 10 - >>> eval_conditional((x < 25, 'low'), (x > 25, 'high'), (True, 'low')) - 'low' - - :param conds: conditionals to be evaluated - :return: Any - """ - for is_true, val in conds: - if is_true: - return val - return None - - -funcs = { - "max": (True, max), - "min": (True, min), - "len": (True, len), - "str": (False, str), - "strlen": (False, len), - "case": (False, eval_conditional), -} - - -class UnsetValueError(Exception): - pass - - -def eval_expr_with_mapping(expr: str, mapping: Mapping) -> Any: - """ - Evaluate a given expression, with restricted syntax. - - This function is equivalent to eval_expr where **kwargs has been switched to a Mapping (eg. a dictionary). - See eval_expr for details. - """ - if expr == "None": - # TODO: do this as part of parsing - return None - try: - return eval_(ast.parse(expr, mode="eval").body, mapping) - except UnsetValueError: - return None - - -def eval_expr(expr: str, **kwargs) -> Any: - """ - Evaluate a given expression, with restricted syntax. - - >>> eval_expr('2^6') - 4 - >>> eval_expr('2**6') - 64 - >>> eval_expr('1 + 2*3**(4^5) / (6 + -7)') - -5.0 - - Variables: - - variables can be passed - - >>> eval_expr('{x} + {y}', x=1, y=2) - 3 - - Nulls: - - - If a variable is enclosed in {}s then entire expression will eval to None if variable is unset - - >>> print(eval_expr('{x} + {y}', x=None, y=2)) - None - - - Functions: - - - only a small set of functions are currently supported. All SPARQL functions will be supported in future - - >>> eval_expr('strlen("a" + "bc")') - 3 - - Paths: - - - Expressions such as `person.name` can be used on objects to lookup by attribute/slot - - Paths can be chained, e.g. `person.address.street` - - Operations on lists are distributed, e.g `container.persons.name` will return a list of names - - Similarly `strlen(container.persons.name)` will return a list whose members are the lengths of all names - - :param expr: expression to evaluate - """ - return eval_expr_with_mapping(expr, kwargs) - - -def eval_(node, bindings=None): - if isinstance(node, ast.Num): - return node.n - if isinstance(node, ast.Str): - if "s" in vars(node): - return node.s - return node.value - if isinstance(node, ast.Constant): - return node.value - if isinstance(node, ast.NameConstant): - # can be removed when python 3.7 is no longer supported - return node.value - if isinstance(node, ast.Name): - if not bindings: - bindings = {} - return bindings.get(node.id) - if isinstance(node, ast.Subscript): - if isinstance(node.slice, ast.Index): - # required for python 3.7 - k = eval_(node.slice.value, bindings) - else: - k = eval_(node.slice, bindings) - v = eval_(node.value, bindings) - return v[k] - if isinstance(node, ast.Attribute): - # e.g. for person.name, this returns the val of person - v = eval_(node.value, bindings) - - # lookup attribute, potentially distributing the results over collections - def _get(obj: Any, k: str, recurse=True) -> Any: - if isinstance(obj, dict): - # dicts are treated as collections; distribute results - if recurse: - return [_get(e, k, False) for e in obj.values()] - return obj.get(k) - if isinstance(obj, list): - # attributes are distributed over lists - return [_get(e, k, False) for e in obj] - if obj is None: - return None - return getattr(obj, k) - - return _get(v, node.attr) - if isinstance(node, ast.List): - return [eval_(x, bindings) for x in node.elts] - if isinstance(node, ast.Set): - # sets are not part of the language; we use {x} as notation for x - if len(node.elts) != 1: - msg = "The {} must enclose a single variable" - raise ValueError(msg) - e = node.elts[0] - if not isinstance(e, ast.Name): - msg = "The {} must enclose a variable" - raise ValueError(msg) - v = eval_(e, bindings) - if v is None: - msg = f"{e} is not set" - raise UnsetValueError(msg) - return v - if isinstance(node, ast.Tuple): - return tuple([eval_(x, bindings) for x in node.elts]) - if isinstance(node, ast.Dict): - return { - eval_(k, bindings): eval_(v, bindings) - for k, v in zip(node.keys, node.values, strict=False) - } - if isinstance(node, ast.Compare): # - if len(node.ops) != 1: - msg = f"Must be exactly one op in {node}" - raise ValueError(msg) - if type(node.ops[0]) not in compare_operators: - msg = f"Not implemented: {node.ops[0]} in {node}" - raise NotImplementedError(msg) - py_op = compare_operators[type(node.ops[0])] - if len(node.comparators) != 1: - msg = f"Must be exactly one comparator in {node}" - raise ValueError(msg) - right = node.comparators[0] - return py_op(eval_(node.left, bindings), eval_(right, bindings)) - if isinstance(node, ast.BinOp): # - return operators[type(node.op)](eval_(node.left, bindings), eval_(node.right, bindings)) - if isinstance(node, ast.UnaryOp): # e.g., -1 - return operators[type(node.op)](eval_(node.operand, bindings)) - # elif isinstance(node, ast.Match): - # # implementing this would restrict python version to 3.10 - # # https://stackoverflow.com/questions/60208/replacements-for-switch-statement-in-python - # raise NotImplementedError(f'Not supported') - if isinstance(node, ast.IfExp): - if eval_(node.test, bindings): - return eval_(node.body, bindings) - return eval_(node.orelse, bindings) - if isinstance(node, ast.Call): - if isinstance(node.func, ast.Name): - fn = node.func.id - if fn in funcs: - takes_list, func = funcs[fn] - args = [eval_(x, bindings) for x in node.args] - if isinstance(args[0], list) and not takes_list: - return [func(*[x] + args[1:]) for x in args[0]] - return func(*args) - msg = f"Call {node.func} not implemented. node = {node}" - raise NotImplementedError(msg) - raise TypeError(node) diff --git a/src/linkml_map/utils/loaders.py b/src/linkml_map/utils/loaders.py deleted file mode 100644 index 2d89439..0000000 --- a/src/linkml_map/utils/loaders.py +++ /dev/null @@ -1,22 +0,0 @@ -from pathlib import Path -from typing import Union - -import yaml -from linkml_runtime.processing.referencevalidator import ReferenceValidator -from linkml_runtime.utils.introspection import package_schemaview - -from linkml_map.datamodel.transformer_model import TransformationSpecification - - -def load_specification(path: Union[Path, str]) -> TransformationSpecification: - if isinstance(path, Path): - path = str(path) - with open(path) as f: - obj = yaml.safe_load(f) - # necessary to expand first - normalizer = ReferenceValidator( - package_schemaview("linkml_map.datamodel.transformer_model") - ) - normalizer.expand_all = True - obj = normalizer.normalize(obj) - return TransformationSpecification(**obj) diff --git a/src/linkml_map/utils/multi_file_transformer.py b/src/linkml_map/utils/multi_file_transformer.py deleted file mode 100644 index 6f76007..0000000 --- a/src/linkml_map/utils/multi_file_transformer.py +++ /dev/null @@ -1,215 +0,0 @@ -"""Iterate through all examples in a folder testing them for validity.""" - -import glob -import logging -import os -import re -from collections.abc import Mapping -from dataclasses import dataclass, field -from pathlib import Path -from typing import Optional, Union - -import yaml -from linkml_runtime import SchemaView -from linkml_runtime.dumpers import yaml_dumper -from pydantic import BaseModel - -from linkml_map.inference.schema_mapper import SchemaMapper -from linkml_map.transformer.object_transformer import ObjectTransformer - - -class Step(BaseModel): - source_data: str - target_data: Optional[str] = None - source_class: str = None - target_class: str = None - - -class Transformation(BaseModel): - description: Optional[str] = None - source_schema: str = None - target_schema: str = None - transformation_specification: str = None - steps: list[Step] = None - - -class Instructions(BaseModel): - description: Optional[str] = None - transformations: list[Transformation] = [] - - -@dataclass -class MultiFileTransformer: - """ - Processes a collection of inputs in one folder. - - Assumes folder structures: - - - {package} - - source/{source_schema}.yaml :: the schema to transform from - - transform/{transform_spec}.transform.yaml :: mapping spec - - data/{SourceClassName}-{LocalId}.yaml :: data to transform - - target/{SourceClassName}-{LocalId}.yaml :: expected output data - """ - - source_schema_directory_base: str = field(default_factory=lambda: "source") - transform_specification_directory_base: str = field(default_factory=lambda: "transform") - source_data_directory_base: str = field(default_factory=lambda: "data") - target_schema_directory_base: str = field(default_factory=lambda: "target") - target_data_directory_base: str = field(default_factory=lambda: "output") - - input_formats: Optional[list[str]] = field(default_factory=lambda: ["yaml"]) - """Expected formats for input data""" - - output_formats: Optional[list[str]] = field(default_factory=lambda: ["yaml"]) - - prefix_map: Optional[Mapping[str, str]] = None - """Custom prefix map, for emitting RDF/turtle.""" - - def process_directory(self, root_directory: Union[str, Path], **kwargs): - """ - Process all transformations in a directory. - - :param root_directory: - :return: - """ - instructions = self.infer_instructions(root_directory) - return self.process_instructions(instructions, root_directory, **kwargs) - - def infer_instructions(self, root_directory: Union[str, Path]) -> Instructions: - """ - Infer instructions from either explicit yaml or directory layout. - """ - if isinstance(root_directory, str): - root_directory = Path(root_directory) - if not root_directory.exists(): - msg = f"No such directory {root_directory}" - raise ValueError(msg) - instructions_file = root_directory / "instructions.yaml" - if instructions_file.exists(): - with open(instructions_file) as file: - return Instructions(**yaml.safe_load(file)) - source_schema_directory = root_directory / self.source_schema_directory_base - if not source_schema_directory.exists(): - msg = f"Expected {source_schema_directory}" - raise ValueError(msg) - transform_specification_directory = ( - root_directory / self.transform_specification_directory_base - ) - if not transform_specification_directory.exists(): - msg = f"Expected {transform_specification_directory}" - raise ValueError(msg) - target_schema_directory = root_directory / self.target_schema_directory_base - input_schemas = glob.glob(os.path.join(str(source_schema_directory), "*.yaml")) - if not input_schemas: - msg = f"Expected schemas in {source_schema_directory}" - raise ValueError(msg) - transform_files = glob.glob( - os.path.join(str(transform_specification_directory), "*.transform.yaml") - ) - instructions = Instructions(description="auto-inducted") - for input_schema in input_schemas: - for transform_file in transform_files: - tr = Transformation( - source_schema=input_schema, - transformation_specification=transform_file, - steps=[], - ) - target_schema_base = None - if len(input_schemas) != 1: - # resolve which schema the transform applies to - matches = re.match(r"^(\w+)-to-(\w+)\.", transform_file) - if not matches: - msg = f"Ambiguous: {transform_file}" - raise ValueError(msg) - src, target_schema_base = matches.group(1, 2) - if src not in input_schema: - continue - instructions.transformations.append(tr) - data_files = glob.glob( - os.path.join(str(root_directory / self.source_data_directory_base), "*.yaml") - ) - for data_file in data_files: - if target_schema_base and target_schema_base not in data_file: - continue - target_data = str(Path(self.target_data_directory_base) / Path(data_file).name) - target_data = target_data.replace(".yaml", ".transformed.yaml") - step = Step(source_data=data_file, target_data=target_data) - step.source_class = Path(data_file).stem.split("-")[-2] - tr.steps.append(step) - target_schemas = glob.glob(os.path.join(str(target_schema_directory), "*.yaml")) - if len(target_schemas) > 1: - target_schemas = [s for s in target_schemas if target_schema_base in s] - if len(target_schemas) != 1: - msg = f"Could not determine target schema from: {target_schemas}" - raise ValueError(msg) - if target_schemas: - tr.target_schema = target_schemas[0] - else: - tr.target_schema = str(Path(target_schema_directory) / "target.yaml") - if not tr.steps: - msg = f"Could not infer steps from {data_files}" - raise ValueError(msg) - if not tr.transformation_specification: - msg = f"No spec {tr}" - raise ValueError(msg) - return instructions - - def process_instructions( - self, - instructions: Instructions, - root_directory: Optional[Union[str, Path]], - output_directory=None, - test_mode=False, - ) -> None: - """ - Process a set of instructions to transform one or more files. - - :param instructions: - :param root_directory: - :param output_directory: - :param test_mode: - :return: - """ - if isinstance(root_directory, str): - root_directory = Path(root_directory) - if isinstance(output_directory, str): - root_directory = Path(output_directory) - if not output_directory: - output_directory = root_directory - logging.info(f"Processing: {instructions.description}") - for tr in instructions.transformations: - source_schema_path = str(root_directory / tr.source_schema) - sv = SchemaView(source_schema_path) - transformer = ObjectTransformer(unrestricted_eval=True) - transformer.load_source_schema(source_schema_path) - tr_path = str(root_directory / tr.transformation_specification) - transformer.load_transformer_specification(tr_path) - if tr.target_schema: - target_schema_path = root_directory / tr.target_schema - mapper = SchemaMapper() - mapper.source_schemaview = sv - target_schema_obj = mapper.derive_schema(transformer.specification) - if not target_schema_path.exists(): - target_schema_path.parent.mkdir(exist_ok=True, parents=True) - yaml_dumper.dump(target_schema_obj, str(target_schema_path)) - for step in tr.steps: - input_obj = yaml.safe_load(open(str(root_directory / step.source_data))) - transformer.index(input_obj, step.source_class) - target_obj = transformer.map_object(input_obj, source_type=step.source_class) - if step.target_data: - out_path = output_directory / step.target_data - out_path.parent.mkdir(parents=True, exist_ok=True) - if out_path.exists(): - line1 = open(str(out_path)).readline() - overwrite = "OVERWRITE" in line1 - with open(str(out_path)) as f: - compare_obj = yaml.safe_load(f) - if compare_obj != target_obj: - if test_mode and not overwrite: - msg = f"Output different than expected: {compare_obj}" - raise ValueError(msg) - logging.warning(f"Different: {compare_obj}") - with open(str(out_path), "w", encoding="utf-8") as f: - yaml_str = yaml.dump(target_obj, sort_keys=False) - f.write(yaml_str) diff --git a/stringification/index.html b/stringification/index.html new file mode 100644 index 0000000..ec7ccf9 --- /dev/null +++ b/stringification/index.html @@ -0,0 +1,124 @@ + + + + + + + + + + + + + + Slot: stringification - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + +

    Slot: stringification

    +

    URI: linkmltr:stringification

    + + +

    Applicable Classes

    + + + + + + + + + + + + + + + +
    NameDescriptionModifies Slot
    SlotDerivationA specification of how to derive the value of a target slot from a source slo...no
    +

    Properties

    + +

    Identifier and Mapping Information

    +

    Schema Source

    +
      +
    • from schema: https://w3id.org/linkml/transformer
    • +
    +

    LinkML Source

    +
    + +
    name: stringification
    +from_schema: https://w3id.org/linkml/transformer
    +rank: 1000
    +alias: stringification
    +owner: SlotDerivation
    +domain_of:
    +- SlotDerivation
    +range: StringificationConfiguration
    +
    +
    + +
    + +
    + + +
    +
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    + + + + + +

    Slot: target_magnitude_slot

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    UnitConversionConfigurationno
    +

    Properties

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    NameDescriptionModifies Slot
    UnitConversionConfigurationno
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    Examples

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    + + + + + +

    Slot: target_unit_slot

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    Applicable Classes

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    UnitConversionConfigurationno
    +

    Properties

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    + + + + + \ No newline at end of file diff --git a/templates/pydantic/attribute.py.jinja b/templates/pydantic/attribute.py.jinja deleted file mode 100644 index 62237fb..0000000 --- a/templates/pydantic/attribute.py.jinja +++ /dev/null @@ -1,18 +0,0 @@ -{{name}}: {{ range }} = Field({%- if field == 'None' and multivalued %}default_factory={{ "dict" if (inlined_as_dict or "Dict[" in range) else "list" }}{% elif field == 'None' %}default=None{% else %}default={{ field }}{% endif %} -{%- if title != None %}, title="{{title}}"{% endif -%} -{%- if description %}, description="""{{description}}"""{% endif -%} -{%- if equals_number != None %} - , le={{equals_number}}, ge={{equals_number}} -{%- else -%} - {%- if minimum_value != None %}, ge={{minimum_value}}{% endif -%} - {%- if maximum_value != None %}, le={{maximum_value}}{% endif -%} -{%- endif -%} -{%- if multivalued and exact_cardinality != None -%} - , min_length={{exact_cardinality}}, max_length={{exact_cardinality}} -{%- elif multivalued -%} - {%- if minimum_cardinality != None %}, min_length={{minimum_cardinality}}{% endif -%} - {%- if maximum_cardinality != None %}, max_length={{maximum_cardinality}}{% endif -%} -{%- endif -%} -{%- if meta -%} - , json_schema_extra = { "linkml_meta": {{ meta | pprint | indent(width=8) }} } -{%- endif -%}) \ No newline at end of file diff --git a/tests/__init__.py b/tests/__init__.py deleted file mode 100644 index 364cdf9..0000000 --- a/tests/__init__.py +++ /dev/null @@ -1,55 +0,0 @@ -import os -from pathlib import Path - -SRC = "source" -TGT = "target" -TR = "transform" -DATA = "data" -INPUT = "input" -OUTPUT = "output" - -ROOT = os.path.abspath(os.path.dirname(__file__)) -INPUT_DIR = Path(ROOT) / INPUT -OUTPUT_DIR = Path(ROOT) / OUTPUT -EXAMPLE_DIR = Path(INPUT_DIR) / "examples" - -PERSONINFO_BASIC_EXAMPLE_DIR = Path(EXAMPLE_DIR) / "personinfo_basic" -PERSONINFO_SRC_SCHEMA = PERSONINFO_BASIC_EXAMPLE_DIR / SRC / "personinfo.yaml" -PERSONINFO_TGT_SCHEMA = PERSONINFO_BASIC_EXAMPLE_DIR / TGT / "agent.yaml" -PERSONINFO_TR = PERSONINFO_BASIC_EXAMPLE_DIR / TR / "personinfo-to-agent.transform.yaml" -PERSONINFO_DATA = PERSONINFO_BASIC_EXAMPLE_DIR / DATA / "Person-001.yaml" -PERSONINFO_CONTAINER_DATA = PERSONINFO_BASIC_EXAMPLE_DIR / DATA / "Container-001.yaml" -PERSONINFO_TGT_DATA = PERSONINFO_BASIC_EXAMPLE_DIR / OUTPUT / "Person-001.transformed.yaml" -PERSONINFO_CONTAINER_TGT_DATA = ( - PERSONINFO_BASIC_EXAMPLE_DIR / OUTPUT / "Container-001.transformed.yaml" -) -PERSONINFO_TR_COMPILED_MD = PERSONINFO_BASIC_EXAMPLE_DIR / OUTPUT / "personinfo_compiled.md" -PERSONINFO_TR_COMPILED_PY = PERSONINFO_BASIC_EXAMPLE_DIR / OUTPUT / "personinfo_compiled.py" -PERSONINFO_DERIVED = PERSONINFO_BASIC_EXAMPLE_DIR / OUTPUT / "personinfo_derived.yaml" - - -FLATTENING_BASIC_EXAMPLE_DIR = Path(EXAMPLE_DIR) / "flattening" -FLATTENING_SRC_SCHEMA = FLATTENING_BASIC_EXAMPLE_DIR / SRC / "normalized.yaml" -FLATTENING_TGT_SCHEMA = FLATTENING_BASIC_EXAMPLE_DIR / TGT / "denormalized.yaml" -FLATTENING_TR = FLATTENING_BASIC_EXAMPLE_DIR / TR / "denormalize.transform.yaml" -FLATTENING_DATA = FLATTENING_BASIC_EXAMPLE_DIR / DATA / "MappingSet-001.yaml" - -BIOLINK_BASIC_EXAMPLE_DIR = Path(EXAMPLE_DIR) / "biolink" -BIOLINK_SRC_SCHEMA = BIOLINK_BASIC_EXAMPLE_DIR / SRC / "biolink.yaml" -BIOLINK_TGT_SCHEMA = BIOLINK_BASIC_EXAMPLE_DIR / TGT / "monarch.yaml" -BIOLINK_TR = BIOLINK_BASIC_EXAMPLE_DIR / TR / "biolink-example-profile.transform.yaml" -BIOLINK_DATA = BIOLINK_BASIC_EXAMPLE_DIR / DATA / "Association-001.yaml" - - -# TODO: migrate these to example dir -SCHEMA1 = str(PERSONINFO_SRC_SCHEMA) -SCHEMA2 = str(PERSONINFO_TGT_SCHEMA) -SPECIFICATION = str(PERSONINFO_TR) - -NORM_SCHEMA = str(FLATTENING_SRC_SCHEMA) -DENORM_SCHEMA = str(FLATTENING_TGT_SCHEMA) -DENORM_SPECIFICATION = str(FLATTENING_TR) - - -def output_path(fn: str) -> str: - return str(Path(OUTPUT_DIR) / fn) diff --git a/tests/conftest.py b/tests/conftest.py deleted file mode 100644 index a90c51f..0000000 --- a/tests/conftest.py +++ /dev/null @@ -1,54 +0,0 @@ -from linkml_runtime import SchemaView -from pathlib import Path -import pytest -from tests.scaffold import (SOURCE_SCHEMA, TARGET_SCHEMA, TRANSFORM_SPEC, INPUT_DATA, EXPECTED_DATA) -from typing import Callable -import yaml - -def yaml_load(file_path: Path) -> dict: - return yaml.safe_load(file_path.read_text()) - -class StrictDict(dict): - """A dict that disallows overwriting with a different value.""" - - def __setitem__(self, key, value): - """Set an item, disallowing overwrites with different values.""" - if key in self and self[key] != value: - raise ValueError( - f"Duplicate assignment to expected key '{key}': " - f"existing={self[key]!r}, new={value!r}" - ) - super().__setitem__(key, value) - - def update(self, *args, **kwargs): - """Update the dictionary, disallowing overwrites with different values.""" - other = dict(*args, **kwargs) - for key, value in other.items(): - self[key] = value - -@pytest.fixture -def scaffold(): - """Fresh scaffold per test.""" - return { - "source_schema": SchemaView(SOURCE_SCHEMA), - "target_schema": SchemaView(TARGET_SCHEMA), - "transform_spec": yaml_load(TRANSFORM_SPEC), - "input_data": yaml_load(INPUT_DATA), - "expected": StrictDict(yaml_load(EXPECTED_DATA)), - } - -# Global registry to collect setup functions for unit parameterization and integration scaffolds. -# They are *not* tests, so pytest cannot discover them automatically. -TEST_SETUP_FUNCTIONS = [] - -def add_to_test_setup(func: Callable) -> Callable: - """Decorator to register a setup function for test scaffold.""" - TEST_SETUP_FUNCTIONS.append(func) - return func - -@pytest.fixture -def integration_scaffold(scaffold): - """Return a scaffold with all registered integration setup functions applied.""" - for setup_func in TEST_SETUP_FUNCTIONS: - setup_func(scaffold) - return scaffold diff --git a/tests/input/__init__.py b/tests/input/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/tests/input/attic/denormalize-mapping.yaml b/tests/input/attic/denormalize-mapping.yaml deleted file mode 100644 index 60e5918..0000000 --- a/tests/input/attic/denormalize-mapping.yaml +++ /dev/null @@ -1,36 +0,0 @@ -id: denormalize-mapping -title: denormalize mappings -prefixes: - foo: foo -source_schema: s1 -target_schema: s2 -class_derivations: - MappingSet: - populated_from: MappingSet - slot_derivations: - mappings: - populated_from: mappings - - Mapping: - populated_from: Mapping - #joins: - # subject: Entity - # object: Entity - slot_derivations: -# id: ## implicitly mapping.id -# creator: -# license: - subject_id: - expr: subject.id - subject_name: - expr: subject.name - object_id: - expr: object.id - object_name: - expr: object.name - predicate_id: - ## implicitly: mapping.predicate - populated_from: predicate - #predicate_name: - # expr: "predicate.name" - diff --git a/tests/input/attic/mapping_denorm.yaml b/tests/input/attic/mapping_denorm.yaml deleted file mode 100644 index eeb1db7..0000000 --- a/tests/input/attic/mapping_denorm.yaml +++ /dev/null @@ -1,53 +0,0 @@ -id: https://w3id.org/linkml/examples/mappings-norm -name: mappings_norm -description: |- - Normalized Mappings -license: https://creativecommons.org/publicdomain/zero/1.0/ -default_curi_maps: - - semweb_context -imports: - - linkml:types -prefixes: - mappings: https://w3id.org/linkml/examples/mappings-norm/ - linkml: https://w3id.org/linkml/ -default_prefix: mappings -default_range: string - -emit_prefixes: - - rdf - - rdfs - - xsd - - skos - -classes: - - MappingSet: - tree_root: true - attributes: - mappings: - range: Mapping - multivalued: true - inlined: true - - Mapping: - slots: - - subject_id - - subject_name - - object_id - - object_name - - predicate_id - - predicate_name - -slots: - id: - identifier: true - slot_uri: schema:identifier - name: - slot_uri: rdfs:label - predicate: - subject_id: - subject_name: - object_id: - object_name: - predicate_id: - predicate_name: diff --git a/tests/input/attic/mapping_norm.yaml b/tests/input/attic/mapping_norm.yaml deleted file mode 100644 index 3d0abda..0000000 --- a/tests/input/attic/mapping_norm.yaml +++ /dev/null @@ -1,56 +0,0 @@ -id: https://w3id.org/linkml/examples/mappings-norm -name: mappings_norm -description: |- - Normalized Mappings -license: https://creativecommons.org/publicdomain/zero/1.0/ -default_curi_maps: - - semweb_context -imports: - - linkml:types -prefixes: - mappings: https://w3id.org/linkml/examples/mappings-norm/ - linkml: https://w3id.org/linkml/ -default_prefix: mappings -default_range: string - -emit_prefixes: - - rdf - - rdfs - - xsd - - skos - -classes: - - MappingSet: - tree_root: true - attributes: - mappings: - range: Mapping - multivalued: true - inlined: true - entities: - range: Entity - multivalued: true - inlined: true - - Mapping: - slots: - - subject - - object - - predicate - Entity: - slots: - - id - - name - -slots: - id: - identifier: true - slot_uri: schema:identifier - name: - slot_uri: rdfs:label - predicate: - subject: - range: Entity - object: - range: Entity \ No newline at end of file diff --git a/tests/input/attic/mappingset-norm-example-01.yaml b/tests/input/attic/mappingset-norm-example-01.yaml deleted file mode 100644 index 02f1240..0000000 --- a/tests/input/attic/mappingset-norm-example-01.yaml +++ /dev/null @@ -1,9 +0,0 @@ -mappings: - - subject: X:1 - object: Y:1 - predicate: P:1 -entities: - "X:1": - name: x1 - "Y:1": - name: y1 \ No newline at end of file diff --git a/tests/input/attic/personinfo-s1-example-data-01.yaml b/tests/input/attic/personinfo-s1-example-data-01.yaml deleted file mode 100644 index f606c36..0000000 --- a/tests/input/attic/personinfo-s1-example-data-01.yaml +++ /dev/null @@ -1,11 +0,0 @@ -id: P:001 -name: fred bloggs -primary_email: fred.bloggs@example.com -age_in_years: 33 -gender: nonbinary man -has_familial_relationships: - - type: SIBLING_OF - related_to: P:002 -current_address: - street: 1 oak street - city: oaktown \ No newline at end of file diff --git a/tests/input/attic/personinfo_s1.yaml b/tests/input/attic/personinfo_s1.yaml deleted file mode 100644 index 79cc8a7..0000000 --- a/tests/input/attic/personinfo_s1.yaml +++ /dev/null @@ -1,279 +0,0 @@ -id: https://w3id.org/linkml/examples/personinfo -name: personinfo -description: |- - Information about people, based on [schema.org](http://schema.org) -license: https://creativecommons.org/publicdomain/zero/1.0/ -default_curi_maps: - - semweb_context -imports: - - linkml:types -prefixes: - personinfo: https://w3id.org/linkml/examples/personinfo/ - linkml: https://w3id.org/linkml/ - schema: http://schema.org/ - rdfs: http://www.w3.org/2000/01/rdf-schema# - prov: http://www.w3.org/ns/prov# - GSSO: http://purl.obolibrary.org/obo/GSSO_ - famrel: https://example.org/FamilialRelations# - # DATA PREFIXES - P: http://example.org/P/ - ROR: http://example.org/ror/ - CODE: http://example.org/code/ - GEO: http://example.org/geoloc/ -default_prefix: personinfo -default_range: string - -emit_prefixes: - - rdf - - rdfs - - xsd - - skos - -classes: - - NamedThing: - description: >- - A generic grouping for any identifiable entity - slots: - - id - - name - - description - - image - close_mappings: - - schema:Thing - - Person: - is_a: NamedThing - description: >- - A person (alive, dead, undead, or fictional). - class_uri: schema:Person - mixins: - - HasAliases - slots: - - primary_email - - birth_date - - age_in_years - - gender - - current_address - - has_employment_history - - has_familial_relationships - - has_medical_history - slot_usage: - primary_email: - pattern: "^\\S+@[\\S+\\.]+\\S+" - in_subset: - - basic_subset - - HasAliases: - description: >- - A mixin applied to any class that can have aliases/alternateNames - mixin: true - attributes: - aliases: - multivalued: true - exact_mappings: - - schema:alternateName - - - Organization: - description: >- - An organization such as a company or university - is_a: NamedThing - class_uri: schema:Organization - mixins: - - HasAliases - slots: - - mission_statement - - founding_date - - founding_location - - Place: - mixins: - - HasAliases - slots: - - id - - name - - Address: - class_uri: schema:PostalAddress - slots: - - street - - city - - postal_code - - Event: - slots: - - started_at_time - - ended_at_time - - duration - - is_current - close_mappings: - - schema:Event - - Concept: - is_a: NamedThing - - DiagnosisConcept: - is_a: Concept - - ProcedureConcept: - is_a: Concept - - - Relationship: - slots: - - started_at_time - - ended_at_time - - related_to - - FamilialRelationship: - is_a: Relationship - slots: - - type - slot_usage: - type: - range: FamilialRelationshipType - required: true - related_to: - range: Person - required: true - - EmploymentEvent: - is_a: Event - slots: - - employed_at - - type - - MedicalEvent: - is_a: Event - slots: - - in_location - - diagnosis - - procedure - - type - - WithLocation: - mixin: true - slots: - - in_location - - # TODO: annotate that this is a container/root class - Container: - tree_root: true - slots: - - persons - - organizations - -slots: - id: - identifier: true - slot_uri: schema:identifier - name: - slot_uri: schema:name - description: - slot_uri: schema:description - image: - slot_uri: schema:image - gender: - slot_uri: schema:gender - range: GenderType - primary_email: - slot_uri: schema:email - birth_date: - slot_uri: schema:birthDate - employed_at: - range: Organization - is_current: - range: boolean - has_employment_history: - range: EmploymentEvent - multivalued: true - inlined_as_list: true - has_medical_history: - range: MedicalEvent - multivalued: true - inlined_as_list: true - has_familial_relationships: - range: FamilialRelationship - multivalued: true - inlined_as_list: true - in_location: - range: Place - current_address: - description: >- - The address at which a person currently lives - range: Address - age_in_years: - range: integer - minimum_value: 0 - maximum_value: 999 - related_to: - type: - range: RelationshipType - street: - city: - mission_statement: - founding_date: - founding_location: - range: Place - postal_code: - range: string - started_at_time: - slot_uri: prov:startedAtTime - range: date - duration: - range: float - diagnosis: - range: DiagnosisConcept - inlined: true - procedure: - range: ProcedureConcept - inlined: true - - ended_at_time: - slot_uri: prov:endedAtTime - range: date - - persons: - range: Person - inlined: true - inlined_as_list: true - multivalued: true - organizations: - range: Organization - inlined_as_list: true - inlined: true - multivalued: true - -enums: - RelationshipType: - FamilialRelationshipType: - is_a: RelationshipType - permissible_values: - SIBLING_OF: - meaning: famrel:01 - PARENT_OF: - meaning: famrel:02 - CHILD_OF: - meaning: famrel:01 - FATHER_OF: - meaning: famrel:11 - GenderType: - permissible_values: - nonbinary man: - meaning: GSSO:009254 - nonbinary woman: - meaning: GSSO:009253 - transgender woman: - meaning: GSSO:000384 - transgender man: - meaning: GSSO:000372 - cisgender man: - meaning: GSSO:000371 - cisgender woman: - meaning: GSSO:000385 - DiagnosisType: - -subsets: - basic_subset: - description: A subset of the schema that handles basic information diff --git a/tests/input/attic/personinfo_s2.yaml b/tests/input/attic/personinfo_s2.yaml deleted file mode 100644 index 2e2d59a..0000000 --- a/tests/input/attic/personinfo_s2.yaml +++ /dev/null @@ -1,273 +0,0 @@ -id: https://w3id.org/linkml/examples/personinfo -name: personinfo -description: |- - Information about people, based on [schema.org](http://schema.org) -license: https://creativecommons.org/publicdomain/zero/1.0/ -default_curi_maps: - - semweb_context -imports: - - linkml:types -prefixes: - personinfo: https://w3id.org/linkml/examples/personinfo/ - linkml: https://w3id.org/linkml/ - schema: http://schema.org/ - rdfs: http://www.w3.org/2000/01/rdf-schema# - prov: http://www.w3.org/ns/prov# - GSSO: http://purl.obolibrary.org/obo/GSSO_ - famrel: https://example.org/FamilialRelations# - # DATA PREFIXES - P: http://example.org/P/ - ROR: http://example.org/ror/ - CODE: http://example.org/code/ - GEO: http://example.org/geoloc/ -default_prefix: personinfo -default_range: string - -emit_prefixes: - - rdf - - rdfs - - xsd - - skos - -classes: - - NamedThing: - description: >- - A generic grouping for any identifiable entity - slots: - - id - - label - - description - - image - close_mappings: - - schema:Thing - - Agent: - is_a: NamedThing - description: >- - A person (alive, dead, undead, or fictional). - class_uri: schema:Person - mixins: - - HasAliases - slots: - - primary_email - - birth_date - - age - - gender - - current_address - - has_employment_history - - has_familial_relationships - - has_medical_history - slot_usage: - primary_email: - pattern: "^\\S+@[\\S+\\.]+\\S+" - in_subset: - - basic_subset - - HasAliases: - description: >- - A mixin applied to any class that can have aliases/alternateNames - mixin: true - attributes: - aliases: - multivalued: true - exact_mappings: - - schema:alternateName - - - Organization: - description: >- - An organization such as a company or university - is_a: NamedThing - class_uri: schema:Organization - mixins: - - HasAliases - slots: - - mission_statement - - founding_date - - founding_location - - Place: - mixins: - - HasAliases - slots: - - id - - label - - Address: - class_uri: schema:PostalAddress - slots: - - street - - city - - postal_code - - address_of - - Event: - slots: - - started_at_time - - ended_at_time - - duration - - is_current - close_mappings: - - schema:Event - - Concept: - is_a: NamedThing - - DiagnosisConcept: - is_a: Concept - - ProcedureConcept: - is_a: Concept - - - Relationship: - slots: - - started_at_time - - ended_at_time - - related_to - - type - - FamilialRelationship: - is_a: Relationship - slot_usage: - type: - range: FamilialRelationshipType - required: true - related to: - range: Agent - required: true - - EmploymentEvent: - is_a: Event - slots: - - employed_at - - MedicalEvent: - is_a: Event - slots: - - in_location - - diagnosis - - procedure - - WithLocation: - mixin: true - slots: - - in_location - - # TODO: annotate that this is a container/root class - Container: - tree_root: true - slots: - - agents - - organizations - -slots: - id: - identifier: true - slot_uri: schema:identifier - label: - slot_uri: schema:name - description: - slot_uri: schema:description - image: - slot_uri: schema:image - gender: - slot_uri: schema:gender - range: GenderType - primary_email: - slot_uri: schema:email - birth_date: - slot_uri: schema:birthDate - employed_at: - range: Organization - is_current: - range: boolean - has_employment_history: - range: EmploymentEvent - multivalued: true - inlined_as_list: true - has_medical_history: - range: MedicalEvent - multivalued: true - inlined_as_list: true - has_familial_relationships: - range: FamilialRelationship - multivalued: true - inlined_as_list: true - in_location: - range: Place - current_address: - description: >- - The address at which a Agent currently lives - range: Address - age: - range: string - pattern: "\\d+ \\S+" - related_to: - type: - street: - city: - mission_statement: - founding_date: - founding_location: - range: Place - postal_code: - range: string - address_of: - range: Agent - started_at_time: - slot_uri: prov:startedAtTime - range: date - duration: - range: float - diagnosis: - range: DiagnosisConcept - inlined: true - procedure: - range: ProcedureConcept - inlined: true - - ended_at_time: - slot_uri: prov:endedAtTime - range: date - - agents: - range: Agent - inlined: true - inlined_as_list: true - multivalued: true - organizations: - range: Organization - inlined_as_list: true - inlined: true - multivalued: true - -enums: - FamilialRelationshipType: - permissible_values: - SIBLING_OF: - meaning: famrel:01 - parent of: - meaning: famrel:02 - child of: - meaning: famrel:01 - GenderType: - permissible_values: - nonbinary man: - meaning: GSSO:009254 - nonbinary woman: - meaning: GSSO:009253 - transgender woman: - meaning: GSSO:000384 - transgender man: - meaning: GSSO:000372 - cisgender man: - meaning: GSSO:000371 - cisgender woman: - meaning: GSSO:000385 - DiagnosisType: - -subsets: - basic_subset: - description: A subset of the schema that handles basic information diff --git a/tests/input/attic/transform-s1-to-s2.yaml b/tests/input/attic/transform-s1-to-s2.yaml deleted file mode 100644 index e8bbf46..0000000 --- a/tests/input/attic/transform-s1-to-s2.yaml +++ /dev/null @@ -1,126 +0,0 @@ -id: my-mappings -title: my mappings -prefixes: - foo: foo -source_schema: s1 -target_schema: s2 -class_derivations: - Container: - populated_from: Container - slot_derivations: - agents: - populated_from: persons - copy_directives: - "*": - copy_all: true - Entity: - Agent: - is_a: Entity - populated_from: Person - slot_derivations: - - ## implicitly same name in Agent - id: - - label: - populated_from: name - - age: - expr: "str({age_in_years})+' years'" - - primary_email: - - gender: - expr: "None" - - current_address: - - ## expressions - #full_name: - # expr: "{first} {last}" - - ## unit conversion - #age_in_years: - # expr: "units.convert(age.value, age.unit, units.YEARS)" - - ## nested to flat - #friends: - # expr: "[x.id for x in {friends}]" - - ## copy recursively, flat to nested - #jobs: - # populated_from: jobs - - ## copy recursively - #diagnoses: - # populated_from: diagnoses - - has_familial_relationships: - populated_from: has_familial_relationships - Job: - #primitive: uriorcurie - slot_derivations: - type: - # this: true ## use input primitive - current: - expr: "True" - - Address: - populated_from: Address - slot_derivations: - address_of: - expr: "'foo'" - inverse_of: - class_name: Agent - slot_name: current_address - street: - city: - expr: "'foo'" - - FamilialRelationship: - populated_from: FamilialRelationship - slot_derivations: - type: - related_to: - #person_id: - # # inverse of has_familial_relationships - # inverse_of: - # slot_name: has_familial_relationships - # class_name: Person - - SequenceFeature: - slot_derivations: - type: - type_designator: true - hide: true - populated_from: feature_type - - DenormMapping: - populated_from: Mapping - #joins: - # subject: Entity - # object: Entity - slot_derivations: - id: ## implicitly mapping.id - creator: - license: - subject_id: - expr: subject.id - subject_name: - expr: subject.name - object_id: - expr: object.id - object_name: - expr: object.name - predicate_id: - ## implicitly: mapping.predicate - populated_from: predicate - predicate_label: - expr: "lookup(predicate)" - -enum_derivations: - FamilialRelationshipType: - populated_from: FamilialRelationshipType - permissible_value_derivations: - #sibling of: - # populated_from: SIBLING_OF diff --git a/tests/input/examples/README.md b/tests/input/examples/README.md deleted file mode 100644 index 945563e..0000000 --- a/tests/input/examples/README.md +++ /dev/null @@ -1,31 +0,0 @@ -# Transformer Examples - -This folder contains examples that serve as both documentation and unit tests. - -Each subfolder contains independent examples, that contain at least: - - - 1 source schema - - 1 transformation - - 1 test input data file (conforming to source schema) - -when the test suite is executed, it will include a derived schema for each source schema, plus one output file -for every input file. If these files exist, then the contents of a fresh derivation is checked against them. - -The folder layout is: - - - `foobar` - - `source` - - `foo.yaml` ## source schema - - `transform` - - `foo-to-bar.transform.yaml` ## transformer spec - - `target` - - `bar.yaml` ## target schema (autogenerated if not present) - - `data` - - `Foo-001.yaml` ## Example file 1, instantiating Foo class for foo schema - - `Foo-002.yaml` ## Example file 2, instantiating Foo class for foo schema - - ... - - `output` ## derived files, conforming to bar (autogenerated if not present) - - `Bar-001.yaml` - - `Bar-002.yaml` - -Optionally, an `instructions.yaml` file may be present. If not the structure of the folder is inferred. \ No newline at end of file diff --git a/tests/input/examples/__init__.py b/tests/input/examples/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/tests/input/examples/biolink/data/gene-001.yaml b/tests/input/examples/biolink/data/gene-001.yaml deleted file mode 100644 index adbcc82..0000000 --- a/tests/input/examples/biolink/data/gene-001.yaml +++ /dev/null @@ -1,3 +0,0 @@ -id: HGNC:1 -symbol: foo -name: foo bar \ No newline at end of file diff --git a/tests/input/examples/biolink/output/gene-001.transformed.yaml b/tests/input/examples/biolink/output/gene-001.transformed.yaml deleted file mode 100644 index 2e24149..0000000 --- a/tests/input/examples/biolink/output/gene-001.transformed.yaml +++ /dev/null @@ -1 +0,0 @@ -symbol: foo diff --git a/tests/input/examples/biolink/source/biolink-model.yaml b/tests/input/examples/biolink/source/biolink-model.yaml deleted file mode 100644 index 0065382..0000000 --- a/tests/input/examples/biolink/source/biolink-model.yaml +++ /dev/null @@ -1,10652 +0,0 @@ -id: https://w3id.org/biolink/biolink-model -name: Biolink-Model -description: Entity and association taxonomy and datamodel for life-sciences data -license: https://creativecommons.org/publicdomain/zero/1.0/ - -# Version should be kept in sync with primary Git repository release tag - -version: 3.2.0 - - -## ------------ -## -## PREFIXES -## ------------ -# CURIE namespaces (prefixes/base URI's) mappings of prefixes used in the body of the Biolink Model specification -# are resolved using a specific precedence order, for use in the generation of the Biolink Model context.jsonld -# mappings to namespaces. Any prefixes encountered in the Biolink Model but not resolved by the following -# precedence sources, are anonymously declared by linkml as http://example.org/UNKNOWN/ rooted base URI's -# which should ideally be repaired in one of the precedence lists. -# -# 1. The following 'prefixes:' delimited list has first precedence in resolution. -# -prefixes: - AGRKB: 'https://www.alliancegenome.org/' - apollo: 'https://github.com/GMOD/Apollo' - AspGD: 'http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=' - biolink: 'https://w3id.org/biolink/vocab/' - bioschemas: 'https://bioschemas.org/' - linkml: 'https://w3id.org/linkml/' - CAID: 'http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=' - # Placeholder: just points to GMOD Chado wiki - CHADO: 'http://gmod.org/wiki/Chado/' - # Placeholders: not sure how 'chembio'and CHEMBL.MECHANISM really resolve - ChemBank: 'http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=' - CHEMBL.MECHANISM: 'https://www.ebi.ac.uk/chembl/mechanism/inspect/' - CID: 'http://pubchem.ncbi.nlm.nih.gov/compound/' - CLINVAR: 'http://identifiers.org/clinvar' - COAR_RESOURCE: 'http://purl.org/coar/resource_type/' - COG: 'https://www.ncbi.nlm.nih.gov/research/cog-project/' - ComplexPortal: 'https://www.ebi.ac.uk/complexportal/complex/' - CPT: 'https://www.ama-assn.org/practice-management/cpt/' - CTD.CHEMICAL: 'http://ctdbase.org/detail.go?type=chem&acc=' - CTD.DISEASE: 'http://ctdbase.org/detail.go?type=disease&db=MESH&acc=' - CTD.GENE: 'http://ctdbase.org/detail.go?type=gene&acc=' - CTD: 'http://ctdbase.org/' - DGIdb: 'https://www.dgidb.org/interaction_types' - dcat: 'http://www.w3.org/ns/dcat#' - dct: 'http://purl.org/dc/terms/' - dcid: 'https://datacommons.org/browser/' - doi: 'https://doi.org/' - DOID-PROPERTY: 'http://purl.obolibrary.org/obo/doid#' - DrugCentral: 'http://drugcentral.org/drugcard/' - ECTO: 'http://purl.obolibrary.org/obo/ECTO_' - EDAM-DATA: 'http://edamontology.org/data_' - EDAM-FORMAT: 'http://edamontology.org/format_' - EDAM-OPERATION: 'http://edamontology.org/operation_' - EDAM-TOPIC: 'http://edamontology.org/topic_' - EFO: 'http://www.ebi.ac.uk/efo/EFO_' - ExO: 'http://purl.obolibrary.org/obo/ExO_' - fabio: 'http://purl.org/spar/fabio/' - foaf: 'http://xmlns.com/foaf/0.1/' - foodb.food: 'http://foodb.ca/compounds/' - foodb.compound: 'http://foodb.ca/foods/' - FYECO: 'https://www.pombase.org/term/' - FYPO: 'http://purl.obolibrary.org/obo/FYPO_' # Fission Yeast Phenotype Ontology - gff3: 'https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#' - GOREL: 'http://purl.obolibrary.org/obo/GOREL_' - # GOP: Gene Ontology Property (not really a GO term but an associated metadatum) - GOP: 'http://purl.obolibrary.org/obo/go#' - gpi: 'https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#' - GSID: 'https://scholar.google.com/citations?user=' - GTEx: 'https://www.gtexportal.org/home/gene/' - GTOPDB: 'https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=' - gtpo: 'https://rdf.guidetopharmacology.org/ns/gtpo#' - HANCESTRO: 'http://www.ebi.ac.uk/ancestro/ancestro_' - HCPCS: 'http://purl.bioontology.org/ontology/HCPCS/' - HsapDv: 'http://purl.obolibrary.org/obo/HsapDv_' - ICD10: 'https://icd.codes/icd9cm/' - ICD9: 'http://translator.ncats.nih.gov/ICD9_' - interpro: 'https://www.ebi.ac.uk/interpro/entry/' - INO: 'http://purl.obolibrary.org/obo/INO_' - isbn: 'https://www.isbn-international.org/identifier/' # note: a resolvable base URI not available from isbn-international - isni: 'https://isni.org/isni/' - issn: 'https://portal.issn.org/resource/ISSN/' - ncats.drug: 'https://drugs.ncats.io/drug/' - KEGG.BRITE: 'http://www.kegg.jp/entry/' - KEGG.DGROUP: 'http://www.kegg.jp/entry/' - KEGG.ENZYME: 'http://www.kegg.jp/entry/' - KEGG.GENE: 'http://www.kegg.jp/entry/' - KEGG.PATHWAY: 'https://www.kegg.jp/entry/' - KEGG.RCLASS: 'http://www.kegg.jp/entry/' - LOINC: 'http://loinc.org/rdf/' - MAXO: 'http://purl.obolibrary.org/obo/MAXO_' - medgen: 'https://www.ncbi.nlm.nih.gov/medgen/' - metacyc.reaction: 'http://identifiers.org/metacyc.reaction:' - METANETX.REACTION: 'https://www.metanetx.org/equa_info/' - MESH: 'http://id.nlm.nih.gov/mesh/' - MI: 'http://purl.obolibrary.org/obo/MI_' - mirbase: 'http://identifiers.org/mirbase' - mmmp.biomaps: 'https://bioregistry.io/mmmp.biomaps:' - MmusDv: 'http://purl.obolibrary.org/obo/MMUSDV_' - MSigDB: 'https://www.gsea-msigdb.org/gsea/msigdb/' - NBO-PROPERTY: 'http://purl.obolibrary.org/obo/nbo#' - ncats.bioplanet: 'https://tripod.nih.gov/bioplanet/detail.jsp?pid=' - NCBIGene: 'http://identifiers.org/ncbigene/' - NCIT-OBO: 'http://purl.obolibrary.org/obo/ncit#' - NDDF: 'http://purl.bioontology.org/ontology/NDDF/' - NLMID: 'https://www.ncbi.nlm.nih.gov/nlmcatalog/?term=' - OBAN: 'http://purl.org/oban/' - oboformat: 'http://www.geneontology.org/formats/oboInOwl#' - OMIM.PS: 'https://www.omim.org/phenotypicSeries/' - ORCID: 'https://orcid.org/' - orphanet: 'http://www.orpha.net/ORDO/Orphanet_' - os: 'https://github.com/cmungall/owlstar/blob/master/owlstar.ttl' - PANTHER.FAMILY: 'http://www.pantherdb.org/panther/family.do?clsAccession=' - PathWhiz: 'http://smpdb.ca/pathways/#' # See also https://smpdb.ca/pathwhiz/ - pav: 'http://purl.org/pav/' - PHAROS: 'http://pharos.nih.gov/' - PomBase: 'https://www.pombase.org/gene/' - prov: 'http://www.w3.org/ns/prov#' - qud: 'http://qudt.org/1.1/schema/qudt#' - REPODB: 'http://apps.chiragjpgroup.org/repoDB/' - ResearchID: 'https://publons.com/researcher/' - RO: 'http://purl.obolibrary.org/obo/RO_' - RXNORM: 'http://purl.bioontology.org/ontology/RXNORM/' - RXCUI: 'https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=' - schema: 'http://schema.org/' - ScopusID: 'https://www.scopus.com/authid/detail.uri?authorId=' - SEED.REACTION: 'https://modelseed.org/biochem/reactions/' - SEMMEDDB: 'https://skr3.nlm.nih.gov/SemMedDB' - SIO: 'http://semanticscience.org/resource/SIO_' - SNOMEDCT: 'http://snomed.info/id/' - SPDI: 'https://api.ncbi.nlm.nih.gov/variation/v0/spdi/' - UBERGRAPH: 'http://translator.renci.org/ubergraph-axioms.ofn#' - UBERON_CORE: 'http://purl.obolibrary.org/obo/uberon/core#' - UBERON_NONAMESPACE: 'http://purl.obolibrary.org/obo/core#' - # The UMLS Semantic types and groups namespaces don't have a directly - # resolvable Base URI, but we point to a pair of sensible web documents - STY: 'http://purl.bioontology.org/ontology/STY/' - UMLSSG: 'https://lhncbc.nlm.nih.gov/semanticnetwork/download/sg_archive/SemGroups-v04.txt' - UniProtKB: 'http://purl.uniprot.org/uniprot/' - UNIPROT.ISOFORM: 'http://purl.uniprot.org/isoforms/' - VANDF: 'https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/' - UO-PROPERTY: 'http://purl.obolibrary.org/obo/uo#' - # The "Variation Modelling Collaboration" (VMC) is not (yet) a conventional namespace so we point to its Github repo - # See also: https://www.ga4gh.org/work_stream/genomic-knowledge-standards/#existing-standards and - # https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153148/ - VMC: 'https://github.com/ga4gh/vr-spec/' - WBls: 'http://purl.obolibrary.org/obo/WBBL_' - WBbt: 'http://purl.obolibrary.org/obo/WBBT_' - WBVocab: 'http://bio2rdf.org/wormbase_vocabulary' - WIKIDATA: 'https://www.wikidata.org/wiki/' # Wikidata Entity - WIKIDATA_PROPERTY: 'https://www.wikidata.org/wiki/Property:' # Wikidata Property - not a conventional namespace prefix - wgs: 'http://www.w3.org/2003/01/geo/wgs84_pos' - XPO: 'http://purl.obolibrary.org/obo/XPO_' # Xenopus Phenotype Ontology - Xenbase: 'http://www.xenbase.org/gene/showgene.do?method=display&geneId=' - -default_prefix: biolink -default_range: string - -# 2. The following prefix maps are retrieved from the -# specified contexts defined at https://prefixcommons.org/ -default_curi_maps: - - obo_context - - idot_context - - monarch_context - - semweb_context - -# The following 'standard' prefixes are also used. -emit_prefixes: - - rdf - - rdfs - - xsd - - skos - - OIO - - BIOGRID - - SO - -## ------------ -## SUBSETS -## ------------ - - -subsets: - - model_organism_database: - description: >- - Subset that is relevant for a typical Model Organism Database (MOD) - - translator_minimal: - description: >- - Minimum subset of translator work - - samples: - description: >- - Sample/biosample datamodel - - testing: - description: >- - TBD - - -## ------------ -## TYPES -## ------------ - -imports: - - linkml:types - -types: - - chemical formula value: - uri: xsd:string - base: str - description: A chemical formula - notes: - - Should be implemented as a stronger type - - category type: - typeof: uriorcurie - description: >- - A primitive type in which the value denotes a class within the biolink model. - The value must be a URI or a CURIE. In a Neo4j representation, the value should - be the CURIE for the biolink class, for example biolink:Gene. For an RDF representation, - the value should be a URI such as https://w3id.org/biolink/vocab/Gene - - iri type: - typeof: uriorcurie - description: >- - An IRI - - label type: - typeof: string - description: >- - A string that provides a human-readable name for an entity - - predicate type: - typeof: uriorcurie - description: >- - A CURIE from the biolink related_to hierarchy. - For example, biolink:related_to, biolink:causes, biolink:treats. - - narrative text: - typeof: string - description: >- - A string that provides a human-readable description of something - - symbol type: - typeof: string - - frequency value: - typeof: string - uri: UO:0000105 - - percentage frequency value: - typeof: double - uri: UO:0000187 - - quotient: - aliases: [ 'ratio' ] - typeof: double - uri: UO:0010006 - - unit: - typeof: string - uri: UO:0000000 - id_prefixes: - - UO - exact_mappings: - - qud:Unit - - time type: - typeof: time - - biological sequence: - typeof: string - -## ------------ -## SLOTS -## ------------ - -slots: - - ## --------------- - ## ATTRIBUTE SLOTS - ## --------------- - - has attribute: - description: >- - connects any entity to an attribute - domain: entity - range: attribute - multivalued: true - in_subset: - - samples - close_mappings: - # RTX term meaning 'specifies value of' tagged as inverse of 'biolink:has attribute' - - OBI:0001927 - exact_mappings: - - SIO:000008 - narrow_mappings: - # if 'has attribute' annotates a NamedThing as subject or - # object of an association, these OBAN mappings may apply - - OBAN:association_has_subject_property - - OBAN:association_has_object_property - - CPT:has_possibly_included_panel_element - - DRUGBANK:category - # RTX contributed terms. Could perhaps review for more semantically precise mappings? - - EFO:is_executed_in - - HANCESTRO:0301 - - LOINC:has_action_guidance - - LOINC:has_adjustment - - LOINC:has_aggregation_view - - LOINC:has_approach_guidance - - LOINC:has_divisor - - LOINC:has_exam - - LOINC:has_method - - LOINC:has_modality_subtype - - LOINC:has_object_guidance - - LOINC:has_scale - - LOINC:has_suffix - - LOINC:has_time_aspect - - LOINC:has_time_modifier - - LOINC:has_timing_of - # disease is stage - - NCIT:R88 - - NCIT:eo_disease_has_property_or_attribute - - NCIT:has_data_element - - NCIT:has_pharmaceutical_administration_method - - NCIT:has_pharmaceutical_basic_dose_form - - NCIT:has_pharmaceutical_intended_site - - NCIT:has_pharmaceutical_release_characteristics - - NCIT:has_pharmaceutical_state_of_matter - - NCIT:has_pharmaceutical_transformation - - NCIT:is_qualified_by - - NCIT:qualifier_applies_to - - NCIT:role_has_domain - - NCIT:role_has_range - - INO:0000154 - - HANCESTRO:0308 - - OMIM:has_inheritance_type - - orphanet:C016 - - orphanet:C017 - - RO:0000053 - # RTX tagged a few RO terms as 'biolink:related_to' but semantics suggest a better mapping here - - RO:0000086 - - RO:0000087 - - SNOMED:has_access - - SNOMED:has_clinical_course - - SNOMED:has_count_of_base_of_active_ingredient - - SNOMED:has_dose_form_administration_method - - SNOMED:has_dose_form_release_characteristic - - SNOMED:has_dose_form_transformation - - SNOMED:has_finding_context - - SNOMED:has_finding_informer - - SNOMED:has_inherent_attribute - - SNOMED:has_intent - - SNOMED:has_interpretation - - SNOMED:has_laterality - - SNOMED:has_measurement_method - - SNOMED:has_method - - SNOMED:has_priority - - SNOMED:has_procedure_context - - SNOMED:has_process_duration - - SNOMED:has_property - - SNOMED:has_revision_status - - SNOMED:has_scale_type - - SNOMED:has_severity - - SNOMED:has_specimen - - SNOMED:has_state_of_matter - - SNOMED:has_subject_relationship_context - - SNOMED:has_surgical_approach - - SNOMED:has_technique - - SNOMED:has_temporal_context - - SNOMED:has_time_aspect - - SNOMED:has_units - - UMLS:has_structural_class - - UMLS:has_supported_concept_property - - UMLS:has_supported_concept_relationship - - UMLS:may_be_qualified_by - - has attribute type: - description: >- - connects an attribute to a class that describes it - domain: attribute - range: ontology class - multivalued: false - required: true - in_subset: - - samples - narrow_mappings: - - LOINC:has_modality_type - - LOINC:has_view_type - - # TRAPI Attribute schema alignment: - # value: NamedThing.name - # value_type: NamedThing.category - # value_type_name: quantity_value.NamedThing.name - has qualitative value: - description: >- - connects an attribute to a value - domain: attribute - range: named thing - multivalued: false - in_subset: - - samples - - # TRAPI Attribute schema alignment: - # value: quantity_value.has_numeric_value[double] - may be a vector? - # value_type: quantity_value.has_unit.unit.uri - # value_type_name: quantity_value.has_unit.unit.name[string] - has quantitative value: - description: >- - connects an attribute to a value - domain: attribute - range: quantity value - multivalued: true - exact_mappings: - - qud:quantityValue - narrow_mappings: - - SNOMED:has_concentration_strength_numerator_value - - SNOMED:has_presentation_strength_denominator_value - - SNOMED:has_presentation_strength_numerator_value - in_subset: - - samples - - has numeric value: - description: >- - connects a quantity value to a number - domain: quantity value - range: double - multivalued: false - exact_mappings: - - qud:quantityValue - in_subset: - - samples - - has unit: - description: >- - connects a quantity value to a unit - domain: quantity value - range: unit - multivalued: false - close_mappings: - # These RTX contributed terms mean "is unit of" which is the semantic inverse of this biolink:has_unit term - - EFO:0001697 - - UO-PROPERTY:is_unit_of - exact_mappings: - - qud:unit - - IAO:0000039 - narrow_mappings: - - SNOMED:has_concentration_strength_denominator_unit - - SNOMED:has_concentration_strength_numerator_unit - - SNOMED:has_presentation_strength_denominator_unit - - SNOMED:has_presentation_strength_numerator_unit - - SNOMED:has_unit_of_presentation - in_subset: - - samples - - base coordinate: - is_a: sequence localization attribute - aliases: [ 'one-based', 'fully-closed' ] - description: >- - A position in the base coordinate system. Base coordinates start at position 1 instead of position 0. - range: integer - - ## -------------------- - ## NODE PROPERTY SLOTS - ## -------------------- - - node property: - description: >- - A grouping for any property that holds between a node and a value - domain: named thing - - id: - identifier: true - domain: entity - description: >- - A unique identifier for an entity. - Must be either a CURIE shorthand for a URI or a complete URI - in_subset: - - translator_minimal - required: true - exact_mappings: - - AGRKB:primaryId - - gff3:ID - - gpi:DB_Object_ID - - iri: - description: >- - An IRI for an entity. This is determined by the id using expansion rules. - range: iri type - in_subset: - - translator_minimal - - samples - exact_mappings: - - WIKIDATA_PROPERTY:P854 - - type: - slot_uri: rdf:type - domain: entity - exact_mappings: - - AGRKB:soTermId - - gff3:type - - gpi:DB_Object_Type - multivalued: true - - category: - is_a: type - domain: entity - range: category type - designates_type: true - description: >- - Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the - biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. - This field is multi-valued. It should include values for ancestors of the biolink class; for example, - a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... - - In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink - class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` - may have a rdf:type assertion to a SO class such as TF_binding_site, - which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, - biolink:MolecularEntity, biolink:NamedThing} - is_class_field: true - multivalued: true - in_subset: - - translator_minimal - - publication type: - slot_uri: dct:type - description: >- - Ontology term for publication type may be drawn from - Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), - FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), - the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), - the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres - (http://vocabularies.coar-repositories.org/documentation/resource_types/), - Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or - equivalent publication type ontology. When a given publication type ontology term - is used within a given knowledge graph, then the CURIE identified term must be - documented in the graph as a concept node of biolink:category biolink:OntologyClass. - values_from: # Not sure which takes precedence, if any... - - dctypes - - fabio - - MESH_PUB - - COAR_RESOURCE - - WIKIDATA - - name: - aliases: [ 'label', 'display name', 'title' ] - description: >- - A human-readable name for an attribute or entity. - domain: entity - range: label type - in_subset: - - translator_minimal - - samples - slot_uri: rdfs:label - exact_mappings: - - gff3:Name - - gpi:DB_Object_Name - narrow_mappings: - - dct:title - - WIKIDATA_PROPERTY:P1476 - - stoichiometry: - description: >- - the relationship between the relative quantities of substances taking part in a reaction or - forming a compound, typically a ratio of whole integers. - is_a: association slot - range: integer - - reaction direction: - description: >- - the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.) - is_a: association slot - range: ReactionDirectionEnum - narrow_mappings: - - NCIT:C42677 - - reaction balanced: - is_a: association slot - range: boolean - - reaction side: - description: >- - the side of a reaction being modeled (ie: left or right) - is_a: association slot - range: ReactionSideEnum - - symbol: - is_a: node property - domain: named thing - description: >- - Symbol for a particular thing - exact_mappings: - - AGRKB:symbol - - gpi:DB_Object_Symbol - - synonym: - is_a: node property - aliases: [ 'alias' ] - domain: named thing - range: label type - description: >- - Alternate human-readable names for a thing - multivalued: true - in_subset: - - translator_minimal - narrow_mappings: - # there is an interesting debate here: are these terms "narrower" a.k.a. more specialized instances of - # 'biolink:synonym' or should they be binned into their respective namesake class of mappings? - # namely, is 'oboInOwl:hasExactSynonym' an instance 'exact_mappings', etc. - - skos:altLabel - - gff3:Alias - - AGRKB:synonyms - - gpi:DB_Object_Synonyms - # TODO: RTX contributed terms mapped here... May need review? - - HANCESTRO:0330 - - IAO:0000136 - - RXNORM:has_tradename - - exact synonym: - is_a: synonym - exact_mappings: - - oboInOwl:hasExactSynonym - - broad synonym: - is_a: synonym - exact_mappings: - - oboInOwl:hasBroadSynonym - - narrow synonym: - is_a: synonym - exact_mappings: - - oboInOwl:hasNarrowSynonym - - related synonym: - is_a: synonym - exact_mappings: - - oboInOwl:hasRelatedSynonym - - has topic: - aliases: [ 'topic', 'descriptors' ] - is_a: node property - range: ontology class - exact_mappings: - - foaf:topic - description: >- - Connects a node to a vocabulary term or ontology class that describes some aspect of the entity. In general specific characterization is preferred. - See https://github.com/biolink/biolink-model/issues/238 - - xref: - is_a: node property - aliases: [ 'dbxref', 'Dbxref', 'DbXref' ] - domain: named thing - range: uriorcurie - description: >- - Alternate CURIEs for a thing - multivalued: true - in_subset: - - translator_minimal - narrow_mappings: - - gff3:Dbxref - - gpi:DB_Xrefs - - full name: - is_a: node property - domain: named thing - range: label type - description: >- - a long-form human readable name for a thing - - description: - aliases: [ 'definition' ] - range: narrative text - description: >- - a human-readable description of an entity - in_subset: - - translator_minimal - slot_uri: dct:description - exact_mappings: - - IAO:0000115 - - skos:definitions - narrow_mappings: - - gff3:Description - - systematic synonym: - is_a: node property - domain: named thing - range: label type - multivalued: true - slot_uri: GOP:systematic_synonym - description: >- - more commonly used for gene symbols in yeast - - affiliation: - is_a: node property - description: >- - a professional relationship between one provider (often a person) within another provider (often an organization). - Target provider identity should be specified by a CURIE. Providers may have multiple affiliations. - domain: agent - range: uriorcurie - multivalued: true - - address: - is_a: node property - description: >- - the particulars of the place where someone or an organization is situated. For now, this slot is a - simple text "blob" containing all relevant details of the given location for fitness of purpose. - For the moment, this "address" can include other contact details such as email and phone number(?). - - ## Space - - latitude: - is_a: node property - range: float - description: >- - latitude - exact_mappings: - - wgs:lat - - longitude: - is_a: node property - range: float - description: >- - longitude - exact_mappings: - - wgs:long - - ## Time - - timepoint: - aliases: [ 'duration' ] - range: time type - description: >- - a point in time - - creation date: - is_a: node property - aliases: [ 'publication date' ] - range: date - description: >- - date on which an entity was created. This can be applied to nodes or edges - exact_mappings: - - dct:createdOn - - WIKIDATA_PROPERTY:P577 - - update date: - is_a: node property - range: date - description: >- - date on which an entity was updated. This can be applied to nodes or edges - - ## Statistics - - aggregate statistic: - is_a: node property - abstract: true - - has count: - description: >- - number of things with a particular property - is_a: aggregate statistic - range: integer - exact_mappings: - - LOINC:has_count - - has total: - description: >- - total number of things in a particular reference set - is_a: aggregate statistic - range: integer - - has quotient: - is_a: aggregate statistic - range: double - - has percentage: - description: >- - equivalent to has quotient multiplied by 100 - is_a: aggregate statistic - range: double - - ## Properties for Information Content Entity and Publication Nodes - - has taxonomic rank: - is_a: node property - range: taxonomic rank - multivalued: false - mappings: - - WIKIDATA:P105 - - has dataset: - is_a: node property - domain: dataset version - range: dataset - slot_uri: dct:source - - source web page: - is_a: node property - domain: dataset summary - broad_mappings: - - dct:source - - source logo: - is_a: node property - domain: dataset summary - slot_uri: schema:logo - - retrieved on: - is_a: node property - domain: dataset - range: date - exact_mappings: - - pav:retrievedOn - - version of: - is_a: node property - domain: dataset version - range: dataset summary - exact_mappings: - - dct:isVersionOf - - version: - is_a: node property - domain: dataset - broad_mappings: - - pav:version - - owl:versionInfo - - license: - is_a: node property - domain: information content entity - exact_mappings: - - dct:license - narrow_mappings: - - WIKIDATA_PROPERTY:P275 - - rights: - is_a: node property - domain: information content entity - exact_mappings: - - dct:rights - - format: - is_a: node property - domain: information content entity - exact_mappings: - - dct:format - - WIKIDATA_PROPERTY:P2701 - - created with: - is_a: node property - domain: dataset - exact_mappings: - - pav:createdWith - - download url: - is_a: node property - domain: information content entity - slot_uri: dcat:downloadURL - - dataset download url: - is_a: node property - domain: dataset - slot_uri: dcat:downloadURL - - distribution download url: - is_a: node property - domain: dataset distribution - exact_mappings: - - dcat:downloadURL - - ingest date: - is_a: node property - domain: dataset version - slot_uri: pav:version - - has distribution: - is_a: node property - domain: dataset version - range: dataset distribution - slot_uri: dct:distribution - - published in: - is_a: node property - description: >- - CURIE identifier of a broader publication context within which the publication may be placed, - e.g. a specified book or journal. - domain: publication - range: uriorcurie - values_from: - - NLMID - - issn - - isbn - exact_mappings: - - WIKIDATA_PROPERTY:P1433 - - iso abbreviation: - is_a: node property - description: >- - Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system - See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, - then the iso abbreviation pertains to the broader publication context (the journal) within which the given - publication node is embedded, not the publication itself. - domain: publication - exact_mappings: - - WIKIDATA_PROPERTY:P1160 - - authors: - is_a: node property - singular_name: author - description: >- - connects an publication to the list of authors who contributed to the publication. - This property should be a comma-delimited list of author names. It is recommended that an author's name - be formatted as "surname, firstname initial.". Note that this property is a node annotation expressing - the citation list of authorship which might typically otherwise be more completely documented in - biolink:PublicationToProviderAssociation defined edges which point to full details about an author - and possibly, some qualifiers which clarify the specific status of a given author in the publication. - multivalued: true - domain: publication - - volume: - is_a: node property - description: >- - volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication - domain: publication - exact_mappings: - - WIKIDATA_PROPERTY:P478 - - chapter: - is_a: node property - description: >- - chapter of a book - domain: book chapter - exact_mappings: - - WIKIDATA:Q1980247 - - issue: - is_a: node property - description: >- - issue of a newspaper, a scientific journal or magazine for reference purpose - domain: publication - exact_mappings: - - WIKIDATA_PROPERTY:P433 - - pages: - is_a: node property - description: >- - page number of source referenced for statement or publication - domain: publication - multivalued: true - exact_mappings: - - WIKIDATA_PROPERTY:P304 - - summary: - is_a: node property - # since 'abstract' is a linkML keyword denoting a non-instantiable class or slot, - # it is generally recommended that knowledge graphs use 'summary' instead to tag a Publication 'abstract' - aliases: [ 'abstract' ] - description: >- - executive summary of a publication - domain: publication - exact_mappings: - - dct:abstract - - WIKIDATA:Q333291 - - keywords: - is_a: node property - description: >- - keywords tagging a publication - domain: publication - multivalued: true - - mesh terms: - is_a: node property - description: >- - mesh terms tagging a publication - domain: publication - range: uriorcurie - values_from: - - MESH - multivalued: true - exact_mappings: - - dcid:MeSHTerm - - ## Biology - - has biological sequence: - is_a: node property - description: >- - connects a genomic feature to its sequence - range: biological sequence - - has gene or gene product: - is_a: node property - description: >- - connects an entity with one or more gene or gene products - range: gene - multivalued: true - - has gene: - is_a: has gene or gene product - description: >- - connects an entity associated with one or more genes - range: gene - multivalued: true - - has zygosity: - is_a: node property - domain: nucleic acid entity - range: zygosity - - ## Chemistry, drugs and food - - has chemical formula: - is_a: node property - range: chemical formula value - description: >- - description of chemical compound based on element symbols - exact_mappings: - - WIKIDATA_PROPERTY:P274 - - is metabolite: - is_a: node property - domain: molecular entity - range: boolean - description: >- - indicates whether a molecular entity is a metabolite - exact_mappings: - - CHEBI:25212 - - has constituent: - description: >- - one or more molecular entities within a chemical mixture - is_a: node property - range: molecular entity - multivalued: true - - has drug: - is_a: node property - description: >- - connects an entity to one or more drugs - range: drug - multivalued: true - - has device: - is_a: node property - description: >- - connects an entity to one or more (medical) devices - range: device - multivalued: true - - has procedure: - is_a: node property - description: >- - connects an entity to one or more (medical) procedures - range: procedure - multivalued: true - - ## Clinical exposures - - has receptor: - is_a: node property - domain: exposure event - range: organismal entity - description: >- - the organism or organism part being exposed - exact_mappings: - - ExO:0000001 - - has stressor: - is_a: node property - domain: exposure event - aliases: [ 'has stimulus' ] - description: >- - the process or entity that the receptor is being exposed to - exact_mappings: - - ExO:0000000 - - has route: - is_a: node property - domain: exposure event - description: >- - the process that results in the stressor coming into direct contact with the receptor - exact_mappings: - - ExO:0000055 - narrow_mappings: - - LOINC:has_pharmaceutical_route - - SNOMED:has_dose_form_intended_site - - SNOMED:has_route_of_administration - - - population context qualifier: - description: >- - a biological population (general, study, cohort, etc.) with a specific - set of characteristics to constrain an association. - is_a: qualifier - range: population of individual organisms - - temporal context qualifier: - description: >- - a constraint of time placed upon the truth value of an association. - for time intervales, use temporal interval qualifier. - is_a: qualifier - range: time type - - temporal interval qualifier: - is_a: temporal context qualifier - description: >- - a constraint of a time interval placed upon the truth value of an - association. - - is supplement: - description: >- - is_a: node property - range: chemical mixture - - trade name: - description: >- - is_a: node property - range: chemical entity - - available from: - description: >- - is_a: node property - multivalued: true - range: DrugAvailabilityEnum - - is toxic: - description: >- - is_a: node property - multivalued: false - range: boolean - - has chemical role: - is_a: related to at concept level - description: >- - A role is particular behaviour which a chemical entity may exhibit. - range: chemical role - multivalued: true - - max tolerated dose: - description: >- - The highest dose of a drug or treatment that does not cause unacceptable side effects. - The maximum tolerated dose is determined in clinical trials by testing increasing doses - on different groups of people until the highest dose with acceptable side effects is - found. Also called MTD. - is_a: node property - multivalued: false - range: string - - animal model available from: - description: >- - is_a: node property - multivalued: true - range: disease or phenotypic feature - - FDA adverse event level: - description: >- - is_a: association slot - range: FDAIDAAdverseEventEnum - - highest FDA approval status: - description: >- - Should be the highest level of FDA approval this chemical entity or device has, regardless of which - disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA - approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.' - - drug regulatory status world wide: - aliases: [ 'max phase' ] - description: >- - An agglomeration of drug regulatory status worldwide. Not specific to FDA. - exact_mappings: - - NCIT:C172573 - narrow_mappings: - - NCIT:R172 - - NCIT:regimen_has_accepted_use_for_disease - # RTX mapped REPODB terms - - REPODB:clinically_tested_approved_unknown_phase - - REPODB:clinically_tested_suspended_phase_0 - - REPODB:clinically_tested_suspended_phase_1 - - REPODB:clinically_tested_suspended_phase_1_or_phase_2 - - REPODB:clinically_tested_suspended_phase_2 - - REPODB:clinically_tested_suspended_phase_2_or_phase_3 - - REPODB:clinically_tested_suspended_phase_3 - - REPODB:clinically_tested_terminated_phase_0 - - REPODB:clinically_tested_terminated_phase_1 - - REPODB:clinically_tested_terminated_phase_1_or_phase_2 - - REPODB:clinically_tested_terminated_phase_2 - - REPODB:clinically_tested_terminated_phase_2_or_phase_3 - - REPODB:clinically_tested_terminated_phase_3 - - REPODB:clinically_tested_withdrawn_phase_0 - - REPODB:clinically_tested_withdrawn_phase_1 - - REPODB:clinically_tested_withdrawn_phase_1_or_phase_2 - - REPODB:clinically_tested_withdrawn_phase_2 - - REPODB:clinically_tested_withdrawn_phase_2_or_phase_3 - - REPODB:clinically_tested_withdrawn_phase_3 - - routes of delivery: - description: >- - the method or process of administering a pharmaceutical compound to achieve a therapeutic - effect in humans or animals. - multivalued: true - range: DrugDeliveryEnum - - ## ------------------- - ## QUALIFIERS - ## ------------------- - - form or variant qualifier: - is_a: qualifier - abstract: true - description: >- - A qualifier that composes with a core subject/object concept to define a specific type, variant, - alternative version of this concept. The composed concept remains a subtype or instance of the core concept. - For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept - ‘a mutation of Gene X’. - examples: - - value: mutation - - value: late stage - - value: severe - - value: transplant - - value: chemical analog - notes: >- - please see the ChemicalOrGeneOrGeneProductFormOrVariantEnum (below) for examples of 'form or variant qualifier' - terms in the gene->chemical association space. - the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘Mutated forms of Gene X’. - the qualifier ‘late stage’ combines with a core concept of ‘Disease X’ to express the more specific concept ‘Late Stage forms of Disease X’ - the qualifier ‘recombinant’ combines with a core concept of ‘FLT1 Gene’ to express the composed concept ‘Recombinant forms of the FLT1 gene’ - the qualifier ‘chemical analog’ combines with a core concept of ‘Ditiocarb’ to express the composed concept ‘analog forms of Ditiocarb’ - in_subset: - - translator_minimal - - aspect qualifier: - is_a: qualifier - abstract: true - description: >- - Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which - the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that - inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an - 'affects' association. - examples: - - value: stability - - value: abundance - - value: expression - - value: exposure - notes: >- - for good examples of aspects in the gene-> chemical space, please see the - GeneOrGeneProductOrChemicalEntityAspectEnum (below) which lists many aspects that can be used to qualify - the gene making the full subject a different ontological type. - the qualifier ‘expression’ combines with a core concept of ‘Gene X’ to express the composed concept ‘expression of Gene X’ (Gene → Biological Process) - the qualifier ‘exposure’ combines with a core concept of ‘Chemical X’ to express the composed concept ‘exposure to Chemical X’ (Chemical → Exposure Process) - the qualifier ‘activity’ combines with a core concept of ‘PPARG’ to express the concept ‘activity of PPARG’ (Gene → function/activity) - the qualifier ‘emergency Department Visit’ combines with a core concept of ‘Disease X’ to express the concept ‘Emergency Department visits for Disease X’ (Disease → Clinical Event) - the qualifier ‘infection’ combines with a core concept of ‘Giardia’ to express the concept ‘Infection with Giardia’ (Taxon → Biological / Pathological Process) - the qualifier ‘severity’ combines with a core concept of ‘DILI’ to express the concept ‘the severity level of DILI’ (Disease → (intrinsic) Characteristic/Quality) - the qualifier ‘abundance’ combines with a core concept of ‘BRCA2’ to express the concept ‘abundance of BRCA2’ (Gene → (extrinsic) characteristic/quality) - in_subset: - - translator_minimal - - derivative qualifier: - is_a: qualifier - abstract: true - description: >- - A qualifier that composes with a core subject/object concept to describe something that is derived from the - core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express - the composed concept ‘a metabolite of Chemical X’. - examples: - - value: metabolite - in_subset: - - translator_minimal - - part qualifier: - is_a: qualifier - abstract: true - description: >- - defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can - use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). - examples: - - value: polyA tail - - value: upstream control region - in_subset: - - translator_minimal - - context qualifier: - is_a: qualifier - abstract: true - description: >- - Restricts the setting/context/location where the core concept (or qualified core concept) resides or occurs. - examples: - - value: cohort x (e.g. a specific population, referenced by an identifier) - - value: gut microbiome # OHMI:0000020 - in_subset: - - translator_minimal - - direction qualifier: - is_a: qualifier - abstract: true - description: >- - Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. - notes: >- - the qualifier ‘increased’ combines with a core concept of ‘Gene X’ and an aspect of ‘expression’ to express the composed concept ‘increased expression of Gene X’ - the qualifier ‘decreased’ combines with a core concept of ‘Protein X’ and an aspect of ‘abundance’ to express the composed concept ‘decreased abundance of Protein X’ - in_subset: - - translator_minimal - - mapped predicate: - description: >- - The predicate that is being replaced by the fully qualified representation of predicate + subject and object - qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified - predicate model. Not to be used in knowledge graphs. - - predicate mappings: - description: >- - A collection of relationships that are not used in biolink, but have biolink patterns that can - be used to replace them. This is a temporary slot to help with the transition to the fully qualified predicate - model in Biolink3. - multivalued: true - range: predicate mapping - inlined_as_list: true - - exact matches: - description: >- - A list of terms from different schemas or terminology systems that have - an identical meaning. Such terms often describe the same concept from - different ontological perspectives. - multivalued: true - - narrow matches: - description: >- - A list of terms from different schemas or terminology systems that have - a narrower meaning. Such terms often describe a more specific concept - from different ontological perspectives. - multivalued: true - - broad matches: - description: >- - A list of terms from different schemas or terminology systems that have - a broader meaning. Such terms often describe a more general concept - from different ontological perspectives. - multivalued: true - - subject aspect qualifier: - is_a: aspect qualifier - in_subset: - - translator_minimal - - subject form or variant qualifier: - is_a: form or variant qualifier - in_subset: - - translator_minimal - - subject part qualifier: - is_a: part qualifier - in_subset: - - translator_minimal - - subject derivative qualifier: - is_a: derivative qualifier - in_subset: - - translator_minimal - - subject context qualifier: - is_a: context qualifier - in_subset: - - translator_minimal - - subject direction qualifier: - is_a: direction qualifier - range: DirectionQualifierEnum - in_subset: - - translator_minimal - - object aspect qualifier: - is_a: aspect qualifier - in_subset: - - translator_minimal - - object form or variant qualifier: - is_a: form or variant qualifier - in_subset: - - translator_minimal - - object part qualifier: - is_a: part qualifier - in_subset: - - translator_minimal - - object derivative qualifier: - is_a: derivative qualifier - in_subset: - - translator_minimal - - object context qualifier: - is_a: context qualifier - in_subset: - - translator_minimal - - object direction qualifier: - is_a: direction qualifier - range: DirectionQualifierEnum - in_subset: - - translator_minimal - - qualified predicate: - is_a: qualifier - description: >- - Predicate to be used in an association when subject and object qualifiers are present and the full - reading of the statement requires a qualification to the predicate in use in order to refine or - increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that - expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based - semantics are included. This is necessary only in cases where the primary predicate does not work in a - full statement reading. - notes: >- - to express the statement that “Chemical X causes increased expression of Gene Y”, the core triple is read - using the fields subject:ChemX, predicate:affects, object:GeneY . . . and the full statement is read using - the fields subject:ChemX, qualified_predicate:causes, object:GeneY, object_aspect: expression, - object_direction:increased. The predicate ‘affects’ is needed for the core triple reading, but doesn't make - sense in the full statement reading (because “Chemical X affects increased expression of Gene Y'' is not - what we mean to say here: it causes increased expression of Gene Y) - - qualifier: - is_a: association slot - description: >- - grouping slot for all qualifiers on an edge. useful for testing compliance with association classes - in_subset: - - translator_minimal - - statement qualifier: - is_a: qualifier - description: >- - in_subset: - - translator_minimal - - causal mechanism qualifier: - is_a: statement qualifier - description: >- - A statement qualifier representing a type of molecular control mechanism through which an - effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', - 'allosteric modulation', 'channel blocker') - range: CausalMechanismQualifierEnum - in_subset: - - translator_minimal - - anatomical context qualifier: - is_a: statement qualifier - description: >- - A statement qualifier representing an anatomical location where an relationship expressed in an - association took place (can be a tissue, cell type, or sub-cellular location). - range: AnatomicalContextQualifierEnum - notes: >- - Anatomical context values can be any term from UBERON. For example, the context qualifier ‘cerebral cortext’ - combines with a core concept of ‘neuron’ - to express the composed concept ‘neuron in the cerebral cortext’. The species_context_qualifier applies - taxonomic context, e.g. species-specific molecular activity. Ontology CURIEs are expected as values - here, the examples below are intended to help clarify the content of the CURIEs. - examples: - - value: blood # UBERON:0000178 - - value: cerebral cortext # UBERON:0000956 - in_subset: - - translator_minimal - - species context qualifier: - is_a: statement qualifier - description: >- - A statement qualifier representing a taxonomic category of species in which a relationship - expressed in an association took place. - range: organism taxon - examples: - - value: zebrafish # NCBITaxon:7955 - - value: human # NCBITaxon:9606 - notes: >- - Ontology CURIEs are expected as values - here, the examples below are intended to help clarify the content of the CURIEs. - in_subset: - - translator_minimal - - qualifiers: - singular_name: qualifier - description: >- - connects an association to qualifiers that modify or - qualify the meaning of that association - local_names: - ga4gh: annotation qualifier - is_a: association slot - multivalued: true - range: ontology class - - frequency qualifier: - is_a: qualifier - description: >- - a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject - range: frequency value - in_subset: - - translator_minimal - - severity qualifier: - description: >- - a qualifier used in a phenotypic association to state - how severe the phenotype is in the subject - is_a: qualifier - range: severity value - in_subset: - - translator_minimal - - sex qualifier: - description: >- - a qualifier used in a phenotypic association to state whether - the association is specific to a particular sex. - is_a: qualifier - range: biological sex - in_subset: - - translator_minimal - - onset qualifier: - description: >- - a qualifier used in a phenotypic association to state - when the phenotype appears is in the subject - is_a: qualifier - range: onset - in_subset: - - translator_minimal - - clinical modifier qualifier: - description: >- - the method or process of administering a pharmaceutical compound to achieve a therapeutic - effect in humans or animals. - is_a: association slot - range: clinical modifier - - sequence variant qualifier: - description: >- - a qualifier used in an association with the variant - is_a: association slot - range: sequence variant - - quantifier qualifier: - is_a: association slot - range: ontology class - description: >- - A measurable quantity for the object of the association - narrow_mappings: - # TODO: RTX contributed terms mapped here... May need review? - - LOINC:analyzes - - LOINC:measured_by - - LOINC:property_of - - SEMMEDDB:MEASURES - - UMLS:measures - - catalyst qualifier: - is_a: association slot - multivalued: true - range: macromolecular machine mixin - description: >- - a qualifier that connects an association between two causally connected - entities (for example, two chemical entities, or a chemical entity in - that changes location) and the gene product, gene, or complex that - enables or catalyzes the change. - - stage qualifier: - description: >- - stage during which gene or protein expression of takes place. - is_a: association slot - range: life stage - # path: "object/during" - examples: - - value: UBERON:0000069 - description: larval stage - in_subset: - - translator_minimal - - ## -------------------- - ## PREDICATES/RELATIONS - ## -------------------- - - related to: - description: >- - A relationship that is asserted between two named things - domain: named thing - range: named thing - multivalued: true - inherited: true - symmetric: true - annotations: - canonical_predicate: true - exact_mappings: - - skos:relatedMatch - - UMLS:related_to - broad_mappings: - - owl:topObjectProperty - narrow_mappings: - - SEMMEDDB:ASSOCIATED_WITH - - SEMMEDDB:compared_with - - SEMMEDDB:higher_than - - SEMMEDDB:lower_than - - BFO:0000054 - - UBERON_CORE:protects - - GOREL:0002005 - - GOREL:0012006 - # several of the following terms mapped here by RTX could merit upgrade to new Biolink terms - - BTO:related_to - - CHEBI:is_conjugate_acid_of - - CHEBI:is_conjugate_base_of - - CPT:has_add_on_code - - CPT:mapped_to - - EFO:0006351 - - FMA:connected_to - - FMA:continuous_with - - FMA:homonym_of - - FMA:related_developmental_entity_of - - RO:0002093 - - RO:0002092 - - RO:0002084 - - HCPCS:mapped_to - # RTX contributed terms, perhaps belong somewhere else with more precise semantics? - - HMDB:disease - - HMDB:has_protein_association - - IAO:0000136 - - LOINC:has_answer - - LOINC:has_challenge - - LOINC:has_evaluation - - LOINC:mapped_to - - LOINC:mth_has_expanded_form - - MESH:RO - - MESH:has_mapping_qualifier - - MESH:mapped_to - - MONDO:disease_shares_features_of - - NCIT:disease_may_have_associated_disease - - NCIT:human_disease_maps_to_eo_disease - - NCIT:is_abnormal_cell_of_disease - - NCIT:is_related_to_endogenous_product - - UBERON_NONAMESPACE:connected_to - - UBERON_NONAMESPACE:innervated_by - - NBO-PROPERTY:is_about - - RO:0000053 # bearer_of - - PATO:reciprocal_of - - RO:0000052 - - RO:0002001 - - RO:0002002 - - RO:0002003 - - RO:0002008 - - RO:0002134 - - RO:0002150 - - RO:0002159 - - RO:0002176 - - RO:0002177 - - RO:0002178 - - RO:0002179 - - RO:0002314 - - RO:0002322 - # functionally related to - - RO:0002328 - - RO:0002332 - - RO:0002338 - - RO:0002339 - - RO:0002341 - - RO:0002342 - - RO:0002344 - - RO:0002348 - - RO:0002349 - - RO:0002356 - - RO:0002371 - - RO:0002372 - - RO:0002373 - - RO:0002374 - - RO:0002385 - - RO:0002387 - - RO:0002451 - - RO:0002494 - - RO:0002495 - - RO:0002568 - - RO:0002573 - - RO:0004026 - - RO:0004027 - - RO:0009001 - - RO:0009004 - - RXNORM:has_form - - RXNORM:reformulated_to - - SNOMED:has_associated_morphology - - SNOMED:has_associated_procedure - - SNOMED:has_direct_morphology - - SNOMED:has_disposition - - SNOMED:has_indirect_morphology - - SNOMED:has_modification - - SNOMED:has_procedure_morphology - - SNOMED:has_specimen_source_morphology - - SNOMED:inheres_in - - SNOMED:is_interpreted_by - - SNOMED:relative_to_part_of - - UBERON:synapsed_by - - UMLS:RO - - UMLS:RQ - - UMLS:class_code_classified_by - - UMLS:exhibited_by - - UMLS:has_context_binding - - UMLS:has_form - - UMLS:has_mapping_qualifier - - UMLS:larger_than - - UMLS:mapped_to - - UMLS:owning_section_of - - related to at concept level: - is_a: related to - description: >- - Represents a relationship held between terminology components that describe the conceptual model of a domain. - annotations: - canonical_predicate: true - symmetric: true - - related to at instance level: - is_a: related to - description: >- - Represents a relationship held between two instances of a data classes. Much like an assertion component, - in an ABox, these represent facts associated with the conceptual model. - annotations: - canonical_predicate: true - symmetric: true - - associated with: - is_a: related to at instance level - description: >- - Expresses a relationship between two named things where the relationship is typically generated statistically - (though not in all cases), and is weaker than its child, 'correlated with', but stronger than its parent, - 'related to'. This relationship holds between two concepts represented by variables for which a statistical - dependence is demonstrated. E.g. the statement “Atrial Fibrillation (Afib) is associated with Myocardial - Infarction (MI)” asserts that having Afib is not statistically independent from whether a patient - will also have MI. Note that in Translator associations, the subject and object concepts may map exactly to - the statistical variables, or represent related entities for which the variables serve as proxies in an - Association (e.g. diseases, chemical entities or processes). - annotations: - canonical_predicate: true - symmetric: true - domain: named thing - range: named thing - narrow_mappings: - - RO:0004029 - - SNOMEDCT:47429007 - - superclass of: - is_a: related to at concept level - description: >- - holds between two classes where the domain class is a super class of the range class - domain: ontology class - range: ontology class - multivalued: True - in_subset: - - translator_minimal - exact_mappings: - - WIKIDATA:Q66088480 - - CHEMBL.MECHANISM:superset_of - - GO:inverse_isa - - MESH:inverse_isa - - RXNORM:inverse_isa - - VANDF:inverse_isa - narrow_mappings: - - NCIT:cdrh_parent_of - - NCIT:ctcae_5_parent_of - - NCIT:subset_includes_concept - - OMIM:has_manifestation - - SNOMED:has_basic_dose_form - - UMLS:RB - - subclass of: - is_a: related to at concept level - description: >- - holds between two classes where the domain class is a specialization of the range class - domain: ontology class - range: ontology class - multivalued: True - in_subset: - - translator_minimal - annotations: - canonical_predicate: true - close_mappings: - # RTX - - LOINC:class_of - - LOINC:has_class - exact_mappings: - - rdfs:subClassOf - - SEMMEDDB:ISA - - WIKIDATA_PROPERTY:P279 - - CHEMBL.MECHANISM:subset_of - - GO:isa - - MESH:isa - - RXNORM:isa - - VANDF:isa - narrow_mappings: - - CHEBI:has_parent_hydride - - LOINC:has_archetype - - LOINC:has_parent_group - - LOINC:is_presence_guidance_for - - NCIT:gene_product_has_chemical_classification - # RTX mapped terms classes for biomarkers - - NCIT:R36 - - NCIT:R42 - - NCIT:A16 - - NCIT:A11 - - NCIT:A14 - - NCIT:A3 - - NDDF:has_dose_form - - RXNORM:has_dose_form - - RXNORM:has_doseformgroup - - SNOMED:entire_anatomy_structure_of - - SNOMED:has_dose_form - # RTX mapping - - rdfs:subPropertyOf - - same as: - is_a: exact match - description: >- - holds between two entities that are considered equivalent to each other - in_subset: - - translator_minimal - symmetric: true - annotations: - canonical_predicate: true - close_mappings: - # identical class extension with identical sets of individuals - - owl:equivalentClass - exact_mappings: - # identical individual, or identical class concept/meaning - - owl:sameAs - - skos:exactMatch - # Semantic Medline definition: "comparative predicate" where the equivalence could simply be functional - # RTX suggests mapping this to proposed new "biolink:close_match" predicate instead - #- SEMMEDDB:same_as - - WIKIDATA_PROPERTY:P2888 - - CHEMBL.MECHANISM:equivalent_to - - MONDO:equivalentTo - narrow_mappings: - - DRUGBANK:external-identifier - - close match: - is_a: related to at concept level - description: >- - a list of terms from different schemas or terminology systems that have - a semantically similar but not strictly equivalent, broader, or narrower - meaning. Such terms often describe the same general concept from - different ontological perspectives (e.g. drug as a type of chemical - entity versus drug as a type of role borne by a chemical entity). - in_subset: - - translator_minimal - symmetric: true - annotations: - canonical_predicate: true - exact_mappings: - - skos:closeMatch - # Semantic Medline definition: "comparative predicate" where the equivalence could simply be functional - - SEMMEDDB:same_as - narrow_mappings: - - CHEBI:is_enantiomer_of - - CHEBI:is_tautomer_of - - MEDDRA:classified_as - - OIO:hasDbXref - - oboformat:xref - - RXNORM:has_quantified_form - - UMLS:SY - - exact match: - is_a: close match - description: >- - holds between two entities that have strictly equivalent - meanings, with a high degree of confidence - in_subset: - - translator_minimal - symmetric: true - annotations: - canonical_predicate: true - exact_mappings: - - skos:exactMatch - - WIKIDATA:Q39893449 - - WIKIDATA:P2888 - - broad match: - description: >- - a list of terms from different schemas or terminology systems - that have a broader, more general meaning. Broader terms are - typically shown as parents in a hierarchy or tree. - is_a: related to at concept level - in_subset: - - translator_minimal - annotations: - canonical_predicate: true - opposite_of: narrow match - exact_mappings: - - skos:broadMatch - - WIKIDATA:Q39894595 - - narrow match: - description: >- - a list of terms from different schemas or terminology systems - that have a narrower, more specific meaning. Narrower terms are - typically shown as children in a hierarchy or tree. - is_a: related to at concept level - inverse: broad match - in_subset: - - translator_minimal - exact_mappings: - - skos:narrowMatch - - WIKIDATA:Q39893967 - annotations: - opposite_of: broad match - - member of: - description: >- - Defines a mereological relation between a item and a collection. - is_a: related to at concept level - inverse: has member - in_subset: - - translator_minimal - exact_mappings: - - RO:0002350 - close_mappings: - - skos:member - - has member: - description: >- - Defines a mereological relation between a collection and an item. - is_a: related to at concept level - in_subset: - - translator_minimal - exact_mappings: - - RO:0002351 - - skos:member - - opposite of: - description: >- - x is the opposite of y if there exists some distance metric M, and there exists - no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). (This description is from RO. Needs to be rephrased). - is_a: related to at instance level - symmetric: true - annotations: - canonical_predicate: true - exact_mappings: - - RO:0002604 - see_also: - - https://doi.org/10.1101/108977 - - https://github.com/biolink/biolink-model/issues/657 - - - associated with likelihood of: - is_a: associated with - description: >- - A a relationship that holds between two concepts represented by variables for which a statistical - dependence is demonstrated, wherein the state or value of one variable predicts the future state - or value of the other. E.g. the statement “An Atrial Fibrillation (Afib) diagnosis is associated - with likelihood of a Myocardial Infarction (MI) diagnosis” asserts that the state of having Afib - is associated with an increased or decreased likelihood that a patient will later exhibit MI. - annotations: - canonical_predicate: true - - likelihood associated with: - is_a: associated with - description: >- - inverse: associated with likelihood of - - associated with increased likelihood of: - is_a: associated with likelihood of - description: >- - Expresses a relationship between two named things where the relationship is typically generated statistically - and the state or fact of something is more probable. - annotations: - canonical_predicate: true - - increased likelihood associated with: - is_a: likelihood associated with - description: >- - inverse: associated with increased likelihood of - - associated with decreased likelihood of: - is_a: associated with likelihood of - description: >- - Expresses a relationship between two named things where the relationship is typically generated statistically - and the state or fact of something is less probable. - annotations: - canonical_predicate: true - - decreased likelihood associated with: - is_a: likelihood associated with - description: >- - inverse: associated with decreased likelihood of - - target for: - is_a: related to at instance level - description: >- - A gene is a target of a disease when its products are druggable and when a drug interaction with the gene - product could have a therapeutic effect - annotations: - canonical_predicate: true - domain: gene - range: disease - - has target: - is_a: related to at instance level - inverse: target for - domain: disease - range: gene - - active in: - is_a: related to at instance level - domain: gene or gene product - range: cellular component - annotations: - canonical_predicate: true - exact_mappings: - - RO:0002432 - - has active component: - is_a: related to at instance level - inverse: active in - domain: cellular component - range: gene or gene product - - acts upstream of: - is_a: related to at instance level - domain: gene or gene product - range: biological process - annotations: - canonical_predicate: true - exact_mappings: - - RO:0002263 - - has upstream actor: - is_a: related to at instance level - inverse: acts upstream of - domain: biological process - range: gene or gene product - - acts upstream of positive effect: - is_a: acts upstream of - domain: gene or gene product - range: biological process - annotations: - canonical_predicate: true - exact_mappings: - - RO:0004034 - - has positive upstream actor: - is_a: has upstream actor - inverse: acts upstream of positive effect - domain: biological process - range: gene or gene product - - acts upstream of negative effect: - is_a: acts upstream of - domain: gene or gene product - range: biological process - annotations: - canonical_predicate: true - exact_mappings: - - RO:0004035 - - has negative upstream actor: - is_a: has upstream actor - inverse: acts upstream of negative effect - domain: biological process - range: gene or gene product - - acts upstream of or within: - is_a: acts upstream of - domain: gene or gene product - range: biological process - annotations: - canonical_predicate: true - exact_mappings: - - RO:0002264 - - has upstream or within actor: - is_a: has upstream actor - inverse: acts upstream of or within - domain: biological process - range: gene or gene product - - acts upstream of or within positive effect: - is_a: acts upstream of or within - domain: gene or gene product - range: biological process - annotations: - canonical_predicate: true - exact_mappings: - - RO:0004032 - - has positive upstream or within actor: - is_a: has upstream or within actor - inverse: acts upstream of or within positive effect - domain: biological process - range: gene or gene product - - acts upstream of or within negative effect: - is_a: acts upstream of or within - domain: gene or gene product - range: biological process - annotations: - canonical_predicate: true - exact_mappings: - - RO:0004033 - - has negative upstream or within actor: - is_a: has upstream or within actor - inverse: acts upstream of or within negative effect - domain: biological process - range: gene or gene product - - ## Publication related predicates - mentions: - description: >- - refers to is a relation between one information content entity and the named thing - that it makes reference to. - is_a: related to at instance level - exact_mappings: - - IAO:0000142 - narrow_mappings: - - SIO:000628 - - mentioned by: - description: >- - refers to is a relation between one named thing and the information content entity - that it makes reference to. - is_a: related to at instance level - inverse: mentions - - ## Publication related predicates - - contributor: - is_a: related to at instance level - domain: agent - range: information content entity - comments: - - This is a grouping for predicates relating entities to their associated contributors realizing them - abstract: true - exact_mappings: - - dct:contributor - - has contributor: - inverse: contributor - is_a: related to at instance level - domain: information content entity - range: agent - - provider: - is_a: contributor - description: >- - person, group, organization or project that provides a piece of information (e.g. a knowledge association). - - has provider: - inverse: provider - is_a: has contributor - domain: information content entity - range: agent - - publisher: - is_a: contributor - domain: agent - range: publication - description: >- - organization or person responsible for publishing books, periodicals, podcasts, games or software. - Note that in the case of publications which have a containing "published in" node property, the publisher - association may not be attached directly to the embedded child publication, but only made in between the - parent's publication node and the publisher agent of the encompassing publication - (e.g. only from the Journal referenced by the 'published_in' property of an journal article Publication node). - exact_mappings: - - dct:publisher - - WIKIDATA_PROPERTY:P123 - - has publisher: - is_a: has contributor - inverse: publisher - domain: publication - range: agent - - editor: - is_a: contributor - domain: agent - range: publication - description: >- - editor of a compiled work such as a book or a periodical (newspaper or an academic journal). - Note that in the case of publications which have a containing "published in" node property, the editor - association may not be attached directly to the embedded child publication, but only made in between the - parent's publication node and the editorial agent of the encompassing publication - (e.g. only from the Book referenced by the 'published_in' property of a book chapter Publication node). - exact_mappings: - - WIKIDATA_PROPERTY:P98 - - has editor: - inverse: editor - is_a: has contributor - domain: publication - range: agent - - author: - is_a: contributor - domain: agent - range: publication - description: >- - an instance of one (co-)creator primarily responsible for a written work - exact_mappings: - - dct:creator - - WIKIDATA_PROPERTY:P50 - - has author: - inverse: author - is_a: has contributor - domain: publication - range: agent - - ## end of Publication related predicates - - assesses: - is_a: related to at instance level - aliases: [ 'was assayed against' ] - description: >- - The effect of a thing on a target was interrogated in some assay. - A relationship between some perturbing agent (usually a chemical compound) and some target entity, - where the affect of the perturbing agent on the target entity was interrogated in a particular assay. - The target might be a particular protein, tissue, phenotype, whole organism, cell line, or other type - of biological entity. - domain: named thing - range: named thing - annotations: - canonical_predicate: true - - is assessed by: - is_a: related to at instance level - inverse: assesses - domain: named thing - range: named thing - - interacts with: - domain: named thing - range: named thing - description: >- - holds between any two entities that directly or indirectly interact with each other - is_a: related to at instance level - in_subset: - - translator_minimal - symmetric: true - mixin: true - exact_mappings: - - SEMMEDDB:INTERACTS_WITH - notes: >- - please use a more specific child predicate of interacts with, either physically interacts with - or genetically interacts with. - - physically interacts with: - is_a: interacts with - description: >- - holds between two entities that make physical contact as part of some interaction. - does not imply a causal relationship. - in_subset: - - translator_minimal - symmetric: true - annotations: - canonical_predicate: true - broad_mappings: - - WIKIDATA_PROPERTY:P129 - close_mappings: - - CHEMBL.MECHANISM:binding_agent - - CHEMBL.MECHANISM:chelating_agent - - CHEMBL.MECHANISM:cross-linking_agent - - CHEMBL.MECHANISM:oxidative_enzyme - - CHEMBL.MECHANISM:sequestering_agent - - CHEMBL.MECHANISM:substrate - - DRUGBANK:target - narrow_mappings: - # Defined more narrowly as "substance interaction", thus specific applies to a subclass entities - - DRUGBANK:drug-interaction - - FMA:adheres_to - - NCIT:A7 - - PR:non-covalently_bound_to - mixins: - - interacts with - - directly physically interacts with: - is_a: physically interacts with - description: >- - A causal mechanism mediated by a direct contact between the effector and target entities (this contact may - be weak or strong, transient or stable). - symmetric: true - exact_mappings: - - RO:0002436 - broad_mappings: - # Definition of this term is more generic than direct physical molecular interactions: - # A is connected to B iff there exists a fiat, material or temporal path between A and B. - - SIO:000203 - - RO:0002578 - narrow_mappings: - - PHAROS:drug_targets - - DRUGBANK:chelator - - CTD:affects_binding - - DGIdb:cofactor - annotations: - canonical_predicate: true - - binds: - deprecated: true - is_a: directly physically interacts with - description: >- - A causal mechanism mediated by the direct contact between effector and target chemical or biomolecular entity, - which form a stable physical interaction. - symmetric: true - annotations: - canonical_predicate: true - close_mappings: - - DGIdb:binder - - indirectly physically interacts with: - is_a: physically interacts with - symmetric: true - annotations: - canonical_predicate: true - - genetically interacts with: - is_a: interacts with - description: >- - holds between two genes whose phenotypic effects are dependent on each - other in some way - such that their combined phenotypic effects are the - result of some interaction between the activity of their gene products. - Examples include epistasis and synthetic lethality. - domain: gene - range: gene - in_subset: - - translator_minimal - annotations: - canonical_predicate: true - symmetric: true - exact_mappings: - - RO:0002435 - - affects: - is_a: related to at instance level - description: >- - describes an entity that has a direct affect on the state or quality - of another existing entity. Use of the 'affects' predicate implies that - the affected entity already exists, unlike predicates such as - 'affects risk for' and 'prevents, where the outcome is something - that may or may not come to be. - in_subset: - - translator_minimal - annotations: - canonical_predicate: true - related_mappings: - # Contributed by RTX. Seems possible that a new predicate "biolink:in_pathway" could be justified? - - DRUGBANK:pathway - exact_mappings: - - SEMMEDDB:AFFECTS - - DGIdb:affects - narrow_mappings: - - SEMMEDDB:ADMINISTERED_TO - - CTD:prediction_hypothesis - - GOREL:0001006 - - CTD:inferred - - UPHENO:0000001 - - RO:0002263 - - RO:0002264 - - NCIT:R158 - - NCIT:R160 - - NCIT:R30 - - NCIT:R150 - - NCIT:R72 - - NCIT:R146 - - NCIT:R124 - - NCIT:R173 - - NCIT:R100 - - NCIT:R102 - - NCIT:R101 - - NCIT:R113 - - NCIT:R23 - - NCIT:R25 - - NCIT:gene_mapped_to_disease - - NCIT:R133 - - RO:0002343 - - RO:0002355 - - RO:0002591 - - RO:0002592 - - RO:0012003 - - SNOMED:has_pathological_process - - UBERGRAPH:is_increase_of # talked to Jim Balhoff, this is a valid mapping - - UBERGRAPH:is_decrease_of # talked to Jim Balhoff, this is a valid mapping - - affected by: - is_a: related to at instance level - description: >- - describes an entity of which the state or quality is affected by - another existing entity. - inverse: affects - - associated with sensitivity to: - is_a: associated with - description: >- - A relation that holds between a named thing and a chemical - that specifies that the change in the named - thing is found to be associated with the degree of sensitivity to treatment by the chemical. - domain: named thing - range: chemical entity - annotations: - canonical_predicate: true - broad_mappings: - - PATO:0000085 # sensitivity toward - narrow_mappings: - - SNOMEDCT:418038007 # propensity to adverse reaction - - sensitivity associated with: - is_a: associated with - inverse: associated with sensitivity to - range: named thing - domain: chemical entity - - associated with resistance to: - is_a: associated with - description: >- - A relation that holds between a named thing and a chemical - that specifies that the change in the named - thing is found to be associated with the degree of resistance to treatment by the chemical. - domain: named thing - range: chemical entity - annotations: - canonical_predicate: true - - resistance associated with: - is_a: associated with - inverse: associated with resistance to - range: named thing - domain: chemical entity - - diagnoses: - is_a: related to at instance level - description: >- - a relationship that identifies the nature of (an illness or other problem) by examination of the symptoms. - domain: chemical or drug or treatment - range: disease or phenotypic feature - annotations: - canonical_predicate: true - close_mappings: - - NCIT:C15220 # diagnosis - - SIO:001331 # diagnosis - exact_mappings: - - DrugCentral:5271 - - SEMMEDDB:DIAGNOSES - - is diagnosed by: - is_a: related to at instance level - inverse: diagnoses - range: chemical or drug or treatment - domain: disease or phenotypic feature - - increases amount or activity of: - deprecated: true - is_a: related to at instance level - mixin: true - description: >- - A grouping mixin to help with searching for all the predicates that increase the amount - or activity of the object. - - amount or activity increased by: - deprecated: true - is_a: related to at instance level - inverse: increases amount or activity of - - decreases amount or activity of: - deprecated: true - is_a: related to at instance level - mixin: true - description: >- - A grouping mixin to help with searching for all the predicates that decrease the amount - or activity of the object. - - amount or activity decreased by: - deprecated: true - is_a: related to at instance level - inverse: decreases amount or activity of - - ## role mixins for use in tagging corresponding role predicates - - chemical role mixin: - description: >- - A role played by the chemical entity or part thereof within a chemical context. - mixin: true - exact_mappings: - - CHEBI:51086 - - biological role mixin: - description: >- - A role played by the chemical entity or part thereof within a biological context. - mixin: true - narrow_mappings: - - CHEBI:24432 - - affects response to: - is_a: affects - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: response affected by - annotations: - canonical_predicate: true - exact_mappings: - - CTD:affects_response_to - - response affected by: - description: >- - holds between two chemical entities where the susceptibility of a biological entity or system - (e.g. an organism, cell, cellular component, macromolecular machine mixin, - biological or pathological process) of one is affected by the action of the other. - is_a: affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - - increases response to: - description: >- - holds between two chemical entities where the action or effect of one - increases the susceptibility of a biological entity or system (e.g. an - organism, cell, cellular component, macromolecular machine mixin, biological - or pathological process) to the other - is_a: affects response to - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - annotations: - canonical_predicate: true - opposite_of: decreases response to - exact_mappings: - - CTD:increases_response_to - - response increased by: - is_a: response affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: increases response to - - decreases response to: - description: >- - holds between two chemical entities where the action or effect of one - decreases the susceptibility of a biological entity or system (e.g. an - organism, cell, cellular component, macromolecular machine mixin, biological - or pathological process) to the other - is_a: affects response to - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - annotations: - canonical_predicate: true - opposite_of: increases response to - exact_mappings: - - CTD:decreases_response_to - narrow_mappings: - - CTD:decreases_response_to_substance - - response decreased by: - is_a: response affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: decreases response to - - regulates: - is_a: affects - description: >- - A more specific form of affects, that implies the effect results from a biologically evolved control mechanism. - Gene-affects-gene relationships will (almost) always involve regulation. Exogenous/environmental chemical-affects-gene relationships - are not cases of regulation in this definition. Instead these would be captured using the 'affects' predicate, or - possibly one of the 'interacts with' predicates depending on the nature of the interaction. - domain: physical essence or occurrent - range: physical essence or occurrent - annotations: - canonical_predicate: true - exact_mappings: - - RO:0002448 - broad_mappings: - # https://www.wikidata.org/wiki/Property:P128 - regulates (molecular biology) - - WIKIDATA_PROPERTY:P128 - - CHEMBL.MECHANISM:modulator - - RO:0002295 - - RO:0002332 - - RO:0002448 - notes: >- - The RO definition of 'directly regulates the activity of' is an exact_mapping here because - it describes genetic regulation from the point of view of one genetic entity regulating another, as opposed to - "RO:0002211" which describes process to process regulation. - mixins: - - interacts with - - regulated by: - is_a: affected by - domain: physical essence or occurrent - range: physical essence or occurrent - inverse: regulates - - disrupts: - is_a: affects - aliases: [ 'disease causes disruption of' ] - description: >- - describes a relationship where one entity degrades or interferes - with the structure, function, or occurrence of another. - in_subset: - - translator_minimal - annotations: - canonical_predicate: true - opposite_of: enables - exact_mappings: - - SEMMEDDB:DISRUPTS - - CHEMBL.MECHANISM:disrupting_agent - narrow_mappings: - - RO:0004024 - - RO:0004025 - - disrupted by: - is_a: affected by - description: >- - describes a relationship where the structure, function, or occurrence - of one entity is degraded or interfered with by another. - inverse: disrupts - - gene product of: - is_a: related to at instance level - description: >- - definition x has gene product of y if and only if y is a gene (SO:0000704) - that participates in some gene expression process (GO:0010467) where the output of thatf - process is either y or something that is ribosomally translated from x - exact_mappings: - - RO:0002204 - domain: gene product mixin - range: gene - annotations: - canonical_predicate: true - inverse: has gene product - in_subset: - - translator_minimal - - has gene product: - is_a: related to at instance level - description: >- - holds between a gene and a transcribed and/or - translated product generated from it - domain: gene - range: gene product mixin - inverse: gene product of - in_subset: - - translator_minimal - close_mappings: - # RTX term tagged as inverse mapping - - PR:has_gene_template - exact_mappings: - - RO:0002205 - - WIKIDATA_PROPERTY:P688 - - NCIT:gene_encodes_gene_product - narrow_mappings: - - NCIT:R178 - - transcribed to: - is_a: related to at instance level - domain: gene - range: transcript - description: >- - inverse of transcribed from - inverse: transcribed from - exact_mappings: - - RO:0002511 - - SIO:010080 - - transcribed from: - is_a: related to at instance level - domain: transcript - range: gene - annotations: - canonical_predicate: true - inverse: transcribed to - description: >- - x is transcribed from y if and only if x is synthesized from template y - exact_mappings: - - RO:0002510 - - SIO:010081 - - translates to: - is_a: related to at instance level - domain: transcript - range: protein - annotations: - canonical_predicate: true - inverse: translation of - description: >- - x (amino acid chain/polypeptide) is the ribosomal translation of y (transcript) if and only if a ribosome - reads y (transcript) through a series of triplet codon-amino acid adaptor activities (GO:0030533) - and produces x (amino acid chain/polypeptide) - close_mappings: - - RO:0002513 - - SIO:010082 - - translation of: - is_a: related to at instance level - domain: protein - range: transcript - description: >- - inverse of translates to - inverse: translates to - close_mappings: - - RO:0002512 - - SIO:010083 - - homologous to: - is_a: similar to - aliases: [ 'in homology relationship with' ] - description: >- - holds between two biological entities that have common evolutionary origin - comments: - - typically used to describe homology relationships between genes or gene products - in_subset: - - translator_minimal - symmetric: true - annotations: - canonical_predicate: true - exact_mappings: - - RO:HOM0000001 - - SIO:010302 - narrow_mappings: - # This is a tricky one to place; seems narrower than the RO mapping but that mapping, RO:0002158 - - UBERON_CORE:sexually_homologous_to - - paralogous to: - is_a: homologous to - description: >- - a homology relationship that holds between entities (typically genes) that diverged after a duplication event. - in_subset: - - translator_minimal - symmetric: true - annotations: - canonical_predicate: true - exact_mappings: - - RO:HOM0000011 - - orthologous to: - is_a: homologous to - description: >- - a homology relationship between entities (typically genes) that diverged after a speciation event. - in_subset: - - translator_minimal - symmetric: true - annotations: - canonical_predicate: true - exact_mappings: - - RO:HOM0000017 - - WIKIDATA_PROPERTY:P684 - - xenologous to: - is_a: homologous to - description: >- - a homology relationship characterized by an interspecies (horizontal) transfer since the common ancestor. - in_subset: - - translator_minimal - symmetric: true - annotations: - canonical_predicate: true - exact_mappings: - - RO:HOM0000018 - - coexists with: - is_a: related to at instance level - description: >- - holds between two entities that are co-located in the same aggregate object, process, or spatio-temporal region - in_subset: - - translator_minimal - symmetric: true - annotations: - canonical_predicate: true - exact_mappings: - - SEMMEDDB:COEXISTS_WITH - narrow_mappings: - - BSPO:0000096 - - BSPO:0000097 - - BSPO:0000098 - - BSPO:0000099 - - BSPO:0000100 - - BSPO:0000102 - - BSPO:0000104 - - BSPO:0000110 - - BSPO:0000113 - - BSPO:0015001 - - BSPO:0015002 - - BSPO:0015003 - - BSPO:0015005 - - BSPO:0015006 - - BSPO:0015007 - - BSPO:0015008 - - BSPO:0015009 - - BSPO:0015012 - - BSPO:0015014 - - BSPO:parallel_to - - UBERON_CORE:anastomoses_with - - UBERON_CORE:anteriorly_connected_to - - UBERON_CORE:posteriorly_connected_to - - UBERON_CORE:channel_for - - UBERON_CORE:channels_from - - UBERON_CORE:channels_into - - UBERON_CORE:conduit_for - - UBERON_CORE:distally_connected_to - - UBERON_CORE:extends_fibers_into - - UBERON_CORE:filtered_through - - UBERON_CORE:indirectly_supplies - - UBERON_CORE:proximally_connected_to - - UBERON_CORE:synapsed_by - - UBERON_CORE:transitively_anteriorly_connected_to - - UBERON_CORE:transitively_connected_to - - UBERON_CORE:transitively_distally_connected_to - - UBERON_CORE:transitively_proximally_connected_to - # RTX contributed Environmental Ontology term meaning "partially surrounded by" - - ENVO:01001307 - - FMA:adjacent_to - - FMA:afferent_to - - FMA:anterior_to - - FMA:anteroinferior_to - - FMA:anterolateral_to - - FMA:anteromedial_to - - FMA:anterosuperior_to - # RTX contributed terms (also inverses to one another?) might better be mapped to another term with more precise functional semantics? - # Some of these terms also seem to be semantic inverses of one another, thus, perhaps not simple narrow_mappings to Biolink - - FMA:arterial_supply_of - - FMA:has_arterial_supply - - FMA:articulates_with - - FMA:attaches_to - - FMA:bounded_by - - FMA:bounds - - FMA:branch_of - - FMA:connection_type_of - - FMA:continuation_branch_of - - FMA:continuous_distally_with - - FMA:continuous_proximally_with - - FMA:corresponds_to - - FMA:development_type_of - - FMA:developmental_stage_of - - FMA:direct_cell_shape_of - - FMA:direct_left_of - - FMA:direct_right_of - - FMA:distal_to - - FMA:drains_into - - FMA:efferent_to - - FMA:external_to - - FMA:formed_by - - FMA:forms - # these next two RTX mapped terms also seem to be inverses of one another - - FMA:full_grown_phenotype_of - - FMA:has_full_grown_phenotype - # these next two RTX mapped terms also seem to be inverses of one another - - FMA:fuses_with - - FMA:fusion_of - - FMA:has_fusion - - FMA:germ_origin_of - - FMA:has_germ_origin - - FMA:has_adherent - - FMA:has_branch - - FMA:has_connection_type - - FMA:has_continuation_branch - - FMA:has_development_type - - FMA:has_developmental_stage - - FMA:has_direct_cell_shape - - FMA:has_inherent_3d_shape - - FMA:has_insertion - - FMA:has_lymphatic_drainage - - FMA:has_nerve_supply - - FMA:has_observed_anatomical_entity - - FMA:has_origin - - FMA:has_primary_segmental_supply - - FMA:has_projection - - FMA:has_regional_part - - FMA:has_related_developmental_entity - - FMA:has_secondary_segmental_supply - - FMA:has_segmental_composition - - FMA:has_segmental_supply - - FMA:has_tributary - - FMA:has_venous_drainage - - FMA:inferior_to - - FMA:inferolateral_to - - FMA:inferomedial_to - - FMA:inherent_3d_shape_of - - FMA:insertion_of - - FMA:internal_to - - FMA:lateral_to - - FMA:left_lateral_to - - FMA:left_medial_to - - FMA:lymphatic_drainage_of - - FMA:matures_from - - FMA:matures_into - - FMA:medial_to - - FMA:merges_with - - FMA:nerve_supply_of - - FMA:origin_of - - FMA:posterior_to - - FMA:posteroinferior_to - - FMA:posterolateral_to - - FMA:posteromedial_to - - FMA:posterosuperior_to - - FMA:primary_segmental_supply_of - - FMA:projects_from - - FMA:projects_to - - FMA:proximal_to - - FMA:receives_attachment_from - - FMA:receives_drainage_from - - FMA:receives_input_from - - FMA:receives_projection - - FMA:related_part - - FMA:right_lateral_to - - FMA:right_medial_to - - FMA:secondary_segmental_supply_of - - FMA:segmental_composition_of - - FMA:segmental_supply_of - - FMA:sends_output_to - - FMA:superior_to - - FMA:superolateral_to - - FMA:superomedial_to - - FMA:surrounded_by - - FMA:surrounds - - FMA:tributary_of - - FMA:venous_drainage_of - # These LOINC: terms contributed by RTX were only tagged as 'biolink:has_attribute' - # but seem more aligned to the FMA entries in this biolink term, so I leave them here for now - - LOINC:has_lateral_anatomic_location - - LOINC:has_lateral_location_presence - - UBERON_NONAMESPACE:distally_connected_to - - UBERON_NONAMESPACE:subdivision_of - # These RO terms seem similar to the FMA terms above, so I place them here rather than under 'biolink:related_to' - - RO:0002219 - - RO:0002220 - - RO:0002221 - - SO:has_origin - # RTX mapped these UBERON terms all here - - UBERON:anastomoses_with - - UBERON:anteriorly_connected_to - - UBERON:channel_for - - UBERON:channels_from - - UBERON:channels_into - - UBERON:conduit_for - - UBERON:distally_connected_to - - UBERON:existence_starts_and_ends_during - - UBERON:extends_fibers_into - - UBERON:filtered_through - - UBERON:in_central_side_of - - UBERON:in_innermost_side_of - - UBERON:in_outermost_side_of - - UBERON:indirectly_supplies - - UBERON:posteriorly_connected_to - - UBERON:protects - - UBERON:proximally_connected_to - - UBERON:sexually_homologous_to - - in pathway with: - description: >- - holds between two genes or gene products that are part of in the same biological pathway - is_a: coexists with - domain: gene or gene product - range: gene or gene product - in_subset: - - translator_minimal - symmetric: true - annotations: - canonical_predicate: true - related_mappings: - # generally pertains to membership of a (subject) component - gene, - # metabolite, etc? - in an (object) metabolic pathway - - SIO:010532 - - in complex with: - description: >- - holds between two genes or gene products that are part of (or code for - products that are part of) in the same macromolecular complex - is_a: coexists with - domain: gene or gene product - range: gene or gene product - in_subset: - - translator_minimal - symmetric: true - annotations: - canonical_predicate: true - related_mappings: - # generally pertains to membership of a (subject) protein in an (object) protein complex (doesn't cover RNA-Protein, Lipid-Protein, etc complexes though) - - SIO:010497 - broad_mappings: - # generally pertains to membership of any (subject) constituent molecule in an (object) molecular complex (might also generically cover RNA-Protein, Lipid-Protein, etc complexes) - - SIO:010285 - - in cell population with: - description: >- - holds between two genes or gene products that are expressed in the same cell type or population - is_a: coexists with - domain: gene or gene product - range: gene or gene product - in_subset: - - translator_minimal - symmetric: true - annotations: - canonical_predicate: true - - colocalizes with: - description: >- - holds between two entities that are observed to be located in the same place. - is_a: coexists with - in_subset: - - translator_minimal - symmetric: true - annotations: - canonical_predicate: true - exact_mappings: - - RO:00002325 - - # Despite the name, note that this particular entity is - # NOT a biolink:Association but rather, a biolink:predicate - genetic association: - is_a: related to at instance level - symmetric: true - annotations: - canonical_predicate: true - description: >- - Co-occurrence of a certain allele of a genetic marker and the phenotype - of interest in the same individuals at above-chance level - exact_mappings: - - WIKIDATA_PROPERTY:P2293 - - gene associated with condition: - is_a: genetic association - description: >- - holds between a gene and a disease or phenotypic feature that the gene or its alleles/products may influence, - contribute to, or correlate with - domain: disease or phenotypic feature - range: gene - annotations: - canonical_predicate: true - in_subset: - - translator_minimal - broad_mappings: - - GENO:0000840 # broader than a single gene: 'genotype' pathogenic for condition - - GENO:0000841 - narrow_mappings: - # narrower: just diseases, not phenotypic features as well - - NCIT:R38 - - NCIT:R175 - - NCIT:R48 - - condition associated with gene: - is_a: genetic association - aliases: [ 'disease associated with gene' ] - description: >- - holds between a gene and a disease or phenotypic feature that may be influenced, contribute to, or be correlated with the gene or its alleles/products - domain: gene - range: disease or phenotypic feature - in_subset: - - translator_minimal - inverse: gene associated with condition - narrow_mappings: - # narrower since just diseases, not phenotypic features as well - - NCIT:R176 - - affects risk for: - is_a: related to at instance level - description: >- - holds between two entities where exposure to one entity alters the chance of developing the other - annotations: - canonical_predicate: true - in_subset: - - translator_minimal - - risk affected by: - is_a: related to at instance level - inverse: affects risk for - - predisposes: - is_a: affects risk for - description: >- - holds between two entities where exposure to one entity increases the chance of developing the other - in_subset: - - translator_minimal - annotations: - canonical_predicate: true - opposite_of: prevents - exact_mappings: - - SEMMEDDB:PREDISPOSES - - has predisposing factor: - is_a: risk affected by - inverse: predisposes - in_subset: - - translator_minimal - - contributes to: - is_a: related to at instance level - description: >- - holds between two entities where the occurrence, existence, or activity of one causes or contributes to the - occurrence or generation of the other - in_subset: - - translator_minimal - annotations: - canonical_predicate: true - close_mappings: - # RTX contributed mapping tagged as 'inverse' of this Biolink predicate - - IDO:0000664 - exact_mappings: - - RO:0002326 - narrow_mappings: - - CTD:marker_mechanism - - MONDO:predisposes_towards - # RTX mapped this to 'biolink:related_to' but this term seems a more precise mapping - - RO:0002255 - # RTX term 'contributes to condition' mapped to 'biolink:causes' seems more suitable here - - RO:0003304 - - contribution from: - is_a: related to at instance level - in_subset: - - translator_minimal - inverse: contributes to - - causes: - description: >- - holds between two entities where the occurrence, existence, or activity of one causes the occurrence - or generation of the other - is_a: contributes to - in_subset: - - translator_minimal - annotations: - canonical_predicate: true - opposite_of: prevents - exact_mappings: - - SEMMEDDB:CAUSES - - WIKIDATA_PROPERTY:P1542 - - SNOMED:cause_of - - RO:0003303 - broad_mappings: - - RO:0002410 - - RO:0002506 - narrow_mappings: - - MONDO:disease_triggers - - GOREL:0000040 - - MONDO:disease_causes_feature - - MONDO:disease_triggers - - NCIT:allele_has_abnormality - - NCIT:biological_process_has_result_biological_process - - NCIT:chemical_or_drug_has_physiologic_effect - # RTX mapped terms as 'biolink:part_of' but implied sequence of causality suggests 'biolink:causes'? - - NCIT:chemical_or_drug_initiates_biological_process - - NCIT:process_initiates_biological_process - - NCIT:chromosome_mapped_to_disease - - NCIT:disease_has_normal_tissue_origin - - NBO-PROPERTY:in_response_to - - orphanet:317343 - - orphanet:317344 - - orphanet:317346 - - orphanet:410295 - - orphanet:410296 - # RTX mapped this term to 'biolink:related_to' but this term seems a more precise mapping - - RO:0002256 - - RO:0002315 - - RO:0002507 - - RO:0002509 - - RO:0004001 - - SNOMED:causative_agent_of - - SNOMED:has_realization - - UMLS:has_physiologic_effect - - caused by: - description: >- - holds between two entities where the occurrence, existence, - or activity of one is caused by the occurrence or generation of the other - is_a: contribution from - aliases: [ 'disease caused by disruption of', 'disease has basis in dysfunction of', - 'realized in response to', 'realized in response to stimulus' ] - in_subset: - - translator_minimal - inverse: causes - exact_mappings: - - WIKIDATA_PROPERTY:P828 - narrow_mappings: - - RO:0001022 - - RO:0002608 - - RO:0004019 - - RO:0004020 - - RO:0004028 - - RO:0009501 - - # TODO: ameliorates and exacerbates inverses. - ameliorates: - is_a: affects - description: >- - A relationship between an entity (e.g. a genotype, - genetic variation, chemical, or environmental exposure, clinical intervention) - and a condition (a phenotype or disease), where the - presence of the entity reduces or eliminates some or - all aspects of the condition. - # 'biological entity' currently includes 'exposure event' which covers a lot of related ground - domain: named thing - range: disease or phenotypic feature - annotations: - canonical_predicate: true - opposite_of: exacerbates - exact_mappings: - - RO:0003307 - - is ameliorated by: - inverse: ameliorates - is_a: affected by - domain: disease or phenotypic feature - range: named thing - - exacerbates: - is_a: affects - description: >- - A relationship between an entity (e.g. a chemical, - environmental exposure, or some form of genetic variation) - and a condition (a phenotype or disease), where the presence - of the entity worsens some or all aspects of the condition. - # 'biological entity' currently includes 'exposure event' which covers a lot of related ground - domain: biological entity - range: disease or phenotypic feature - annotations: - canonical_predicate: true - exact_mappings: - - RO:0003309 - broad_mappings: - - SEMMEDDB:COMPLICATES - - is exacerbated by: - inverse: exacerbates - is_a: affected by - domain: disease or phenotypic feature - range: biological entity - in_subset: - - translator_minimal - - treats: - aliases: [ 'is substance that treats', 'indicated for' ] - is_a: ameliorates - description: >- - holds between a therapeutic procedure or chemical entity - and a disease or phenotypic feature that it is used to treat - domain: chemical or drug or treatment - range: disease or phenotypic feature - annotations: - canonical_predicate: true - opposite_of: contraindicated for - in_subset: - - translator_minimal - related_mappings: - - MONDO:disease_responds_to - exact_mappings: - - DRUGBANK:treats - - SEMMEDDB:TREATS - - WIKIDATA_PROPERTY:P2175 - narrow_mappings: - # "is substance that treats" constrains statements to - # a subset of the universe of all possible treatments - - RO:0002606 - - NCIT:regimen_has_accepted_use_for_disease - # RTX mapped REPODB terms - - REPODB:clinically_tested_approved_unknown_phase - - REPODB:clinically_tested_suspended_phase_0 - - REPODB:clinically_tested_suspended_phase_1 - - REPODB:clinically_tested_suspended_phase_1_or_phase_2 - - REPODB:clinically_tested_suspended_phase_2 - - REPODB:clinically_tested_suspended_phase_2_or_phase_3 - - REPODB:clinically_tested_suspended_phase_3 - - REPODB:clinically_tested_terminated_phase_0 - - REPODB:clinically_tested_terminated_phase_1 - - REPODB:clinically_tested_terminated_phase_1_or_phase_2 - - REPODB:clinically_tested_terminated_phase_2 - - REPODB:clinically_tested_terminated_phase_2_or_phase_3 - - REPODB:clinically_tested_terminated_phase_3 - - REPODB:clinically_tested_withdrawn_phase_0 - - REPODB:clinically_tested_withdrawn_phase_1 - - REPODB:clinically_tested_withdrawn_phase_1_or_phase_2 - - REPODB:clinically_tested_withdrawn_phase_2 - - REPODB:clinically_tested_withdrawn_phase_2_or_phase_3 - - REPODB:clinically_tested_withdrawn_phase_3 - - SNOMED:plays_role - - treated by: - is_a: is ameliorated by - description: >- - holds between a disease or phenotypic feature and a therapeutic - process or chemical entity that is used to treat the condition - domain: disease or phenotypic feature - range: chemical or drug or treatment - # range: chemical or drug or treatment - in_subset: - - translator_minimal - inverse: treats - exact_mappings: - - WIKIDATA_PROPERTY:P2176 - # RTX contributed term tagged as inverse of 'biolink:treats' - - MONDO:disease_responds_to - narrow_mappings: - # "is treated by substance" constrains statements to - # subset of the universe of all possible treatments - - RO:0002302 - - prevents: - is_a: affects risk for - description: >- - holds between an entity whose application or use reduces - the likelihood of a potential outcome. Typically used to associate - a chemical entity, exposure, activity, or medical intervention - that can prevent the onset a disease or phenotypic feature. - annotations: - canonical_predicate: true - opposite_of: predisposes - in_subset: - - translator_minimal - exact_mappings: - - SEMMEDDB:PREVENTS - narrow_mappings: - # more restricted case of a material entity mitigating a pathological process - - RO:0002599 - - prevented by: - is_a: risk affected by - description: >- - holds between a potential outcome of which the likelihood - was reduced by the application or use of an entity. - inverse: prevents - annotations: - opposite_of: enabled by - - correlated with: - is_a: associated with - description: >- - A relationship that holds between two concepts represented by variables for which a statistical dependence is - demonstrated using a correlation analysis method. - notes: >- - These concepts may map exactly to the statistical variables, or represent related entities for which the - variables serve as proxies in an Association (e.g. diseases, chemical entities or processes). - domain: named thing - range: named thing - in_subset: - - translator_minimal - symmetric: true - annotations: - canonical_predicate: true - exact_mappings: - - RO:0002610 - - PATO:correlates_with - - # proposed positive and negative semantic extensions to the general "correlated with" predicate - - positively correlated with: - is_a: correlated with - description: >- - A relationship that holds between two concepts represented by variables for which a statistical correlation - is demonstrated, wherein variable values move together in the same direction (i.e. increased in one or - presence of one correlates with an increase or presence of the other). - domain: named thing - range: named thing - in_subset: - - translator_minimal - symmetric: true - annotations: - canonical_predicate: true - opposite_of: negatively correlated with - exact_mappings: - - CTD:positive_correlation - - negatively correlated with: - is_a: correlated with - description: >- - A relationship that holds between two concepts represented by variables for which a statistical correlation - is demonstrated, wherein variable values move in opposite directions (i.e. increased in one or presence of - one correlates with a decrease or absence of the other). - domain: named thing - range: named thing - in_subset: - - translator_minimal - symmetric: true - annotations: - canonical_predicate: true - opposite_of: positively correlated with - exact_mappings: - - CTD:negative_correlation - - occurs together in literature with: - is_a: correlated with - description: >- - holds between two entities where their co-occurrence is correlated by counts of publications - in which both occur, using some threshold of occurrence as defined by the edge provider. - domain: named thing - range: named thing - in_subset: translator_minimal - symmetric: true - annotations: - canonical_predicate: true - - coexpressed with: - is_a: correlated with - description: >- - holds between any two genes or gene products, in which both are - generally expressed within a single defined experimental context. - domain: gene or gene product - range: gene or gene product - symmetric: true - annotations: - canonical_predicate: true - - has biomarker: - is_a: correlated with - description: >- - holds between a disease or phenotypic feature and a measurable - chemical entity that is used as an indicator of the presence - or state of the disease or feature. - # metabolite - domain: disease or phenotypic feature - range: chemical entity or gene or gene product - in_subset: - - translator_minimal - inverse: biomarker for - narrow_mappings: - # some RTX terms contributed as inverses of 'biolink:biomarker_for' - - NCIT:disease_has_molecular_abnormality - - NCIT:disease_is_marked_by_gene - - biomarker for: - is_a: correlated with - description: >- - holds between a measurable chemical entity and a disease - or phenotypic feature, where the entity is used as an indicator - of the presence or state of the disease or feature. - domain: chemical entity or gene or gene product - range: disease or phenotypic feature - annotations: - canonical_predicate: true - in_subset: - - translator_minimal - exact_mappings: - - NCIT:R39 - broad_mappings: - # Generic marker definition not specific to biomarkers per say - - RO:0002607 - narrow_mappings: - - NCIT:R47 - # RTX term was tagged as 'biolink:actively_involved_in' but maps better here? - - NCIT:genetic_biomarker_related_to - - NCIT:is_molecular_abnormality_of_disease - - orphanet:465410 - - # It may be helpful to introduce an intermediate predicate in between 'related_to' and 'expressed in' - # which would have a domain of 'biological entity' and range of 'anatomical entity', to map predicates - # which are biological which have manifestation in an anatomical site, e.g. RO:0004026, RO:0004027 and others - expressed in: - is_a: located in - description: >- - holds between a gene or gene product and an anatomical entity in which it is expressed - domain: gene or gene product - range: anatomical entity - multivalued: true - annotations: - canonical_predicate: true - in_subset: - - translator_minimal - exact_mappings: - - RO:0002206 - narrow_mappings: - - NCIT:R49 - - NCIT:R46 - - expresses: - is_a: location of - aliases: [ 'anatomy expresses gene' ] - description: >- - holds between an anatomical entity and gene or gene product that is expressed there - domain: anatomical entity - range: gene or gene product - multivalued: true - in_subset: - - translator_minimal - inverse: expressed in - exact_mappings: - - RO:0002292 - - has phenotype: - is_a: related to at instance level - aliases: [ 'disease presents symptom' ] - description: >- - holds between a biological entity and a phenotype, where a phenotype - is construed broadly as any kind of quality of an organism part, - a collection of these qualities, or a change in quality or qualities - (e.g. abnormally increased temperature). In SNOMEDCT, disorders with keyword 'characterized by' should - translate into this predicate. - domain: biological entity - range: phenotypic feature - multivalued: true - annotations: - canonical_predicate: true - notes: - - check the range - in_subset: - - translator_minimal - exact_mappings: - - RO:0002200 - broad_mappings: - - NCIT:R115 - - NCIT:R108 - narrow_mappings: - - NCIT:R89 - - DOID-PROPERTY:has_symptom - - RO:0004022 - - phenotype of: - is_a: related to at instance level - domain: phenotypic feature - range: biological entity - multivalued: true - inverse: has phenotype - - # TODO: predicate inverse for occurs in - occurs in: - is_a: related to at instance level - description: >- - holds between a process and a material entity or site within which the process occurs - in_subset: - - translator_minimal - annotations: - canonical_predicate: true - close_mappings: - # These RTX mapped terms tagged as the inverse of "biolink:occurs_in", i.e. Entity/Site contains Process - - BFO:0000067 - - SNOMED:has_occurrence - - UBERON:site_of - exact_mappings: - - BFO:0000066 - - PathWhiz:has_location - - SNOMED:occurs_in - narrow_mappings: - # SemMedDb term 'OCCURS_IN' constrained to something (other than process) occurring in a group or population - - SEMMEDDB:OCCURS_IN - # SemMedDb term 'PROCESS_IN' constrained specifically to a process occurring in the object concept entity - - SEMMEDDB:PROCESS_OF - # Uberon term constrained to a 'site' as object concept - - UBERON_CORE:site_of - - LOINC:has_imaged_location - - PathWhiz:in_species - - RO:0002231 - - RO:0002232 - - SNOMED:has_direct_procedure_site - - SNOMED:has_direct_site - - SNOMED:has_procedure_site - - contains process: - is_a: related to at instance level - inverse: occurs in - - located in: - is_a: related to at instance level - description: >- - holds between a material entity and a material entity or site - within which it is located (but of which it is not considered a part) - in_subset: - - translator_minimal - annotations: - canonical_predicate: true - exact_mappings: - - RO:0001025 - - FMA:has_location - narrow_mappings: - - GOREL:0001004 - - BSPO:0000107 - - BSPO:0000108 - - BSPO:0000120 - - BSPO:0000121 - - BSPO:0000122 - - BSPO:0000123 - - BSPO:0000124 - - BSPO:0000125 - - BSPO:0000126 - - BSPO:0001100 - - BSPO:0001101 - - BSPO:0001107 - - BSPO:0015101 - - BSPO:0015102 - - BSPO:0015202 - - UBERON_CORE:in_central_side_of - - UBERON_CORE:in_innermost_side_of - - UBERON_CORE:in_outermost_side_of - - NCIT:R100 - - EFO:0000784 - - FMA:has_location - - HMDB:at_cellular_location - - HMDB:at_tissue - - HMDB:in_biospecimen - - LOINC:has_imaging_focus - - NCIT:R156 - - NCIT:R155 - - NCIT:R145 - - NCIT:R40 - - NCIT:R171 - - NCIT:R167 - - NCIT:R165 - - NCIT:R169 - - NCIT:R170 - - NCIT:R166 - - NCIT:R168 - - RO:0002303 - - SNOMED:has_finding_site - - SNOMED:has_indirect_procedure_site - - SNOMED:has_inherent_location - domain: named thing - range: named thing - - location of: - is_a: related to at instance level - aliases: [ 'site of' ] - domain: named thing - range: named thing - description: >- - holds between material entity or site and a material entity - that is located within it (but not considered a part of it) - in_subset: - - translator_minimal - inverse: located in - exact_mappings: - - RO:0001015 - - SEMMEDDB:LOCATION_OF - - WIKIDATA_PROPERTY:P276 - # RTX tagged this as an inverse of biolink:located_in - - FMA:location_of - narrow_mappings: - - SNOMED:inherent_location_of - - NCIT:Anatomic_Structure_Has_Location_Role - - disease has location: - description: >- - A relationship between a disease and an anatomical entity where the - disease has one or more features that are located in that entity. - is_a: related to - exact_mappings: - - RO:0004026 - - MONDO:disease_has_location - - location of disease: - is_a: related to - inverse: disease has location - - similar to: - is_a: related to at instance level - description: >- - holds between an entity and some other entity with similar features. - in_subset: - - translator_minimal - symmetric: true - annotations: - canonical_predicate: true - exact_mappings: - - RO:HOM0000000 #I don't understand this identifier, but I think it's equivalent - - SO:similar_to #equivalent - - chemically similar to: - is_a: similar to - description: >- - holds between one small molecule entity and another that it approximates - for purposes of scientific study, in virtue of its exhibiting - similar features of the studied entity. - in_subset: - - translator_minimal - symmetric: true - annotations: - canonical_predicate: true - narrow_mappings: - - CHEBI:has_parent_hydride #subproperty - - CHEBI:has_functional_parent #subproperty - - CHEBI:is_conjugate_acid_of #subproperty - - CHEBI:is_conjugate_base_of #subproperty - - CHEBI:is_enantiomer_of #subproperty - - CHEBI:is_tautomer_of #subproperty - - NCIT:has_salt_form - - has sequence location: - is_a: related to at instance level - description: >- - holds between two nucleic acid entities when the subject can be localized - in sequence coordinates on the object. For example, between - an exon and a chromosome/contig. - domain: nucleic acid entity - range: nucleic acid entity - annotations: - canonical_predicate: true - exact_mappings: - - faldo:location - - sequence location of: - is_a: related to at instance level - domain: nucleic acid entity - range: nucleic acid entity - inverse: has sequence location - - model of: - is_a: related to at instance level - description: >- - holds between a thing and some other thing it approximates - for purposes of scientific study, in virtue of its exhibiting - similar features of the studied entity. - annotations: - canonical_predicate: true - in_subset: - - translator_minimal - exact_mappings: - - RO:0003301 - narrow_mappings: - - FOODON:00001301 - - models: - is_a: related to at instance level - inverse: model of - - overlaps: - is_a: related to at instance level - description: >- - holds between entities that overlap in their extents (materials or processes) - in_subset: - - translator_minimal - symmetric: true - annotations: - canonical_predicate: true - exact_mappings: - - RO:0002131 - narrow_mappings: - - BSPO:0005001 - - CHEMBL.MECHANISM:overlaps_with - - RO:0002100 - - RO:0002102 - - RO:0002433 - - has part: - is_a: overlaps - annotations: - canonical_predicate: true - opposite_of: lacks part - description: >- - holds between wholes and their parts (material entities or processes) - in_subset: - - translator_minimal - exact_mappings: - - BFO:0000051 - # term name seems to be 'realizes' but RTX maps this term here - - BFO:0000055 - - WIKIDATA_PROPERTY:P527 - - RO:0001019 - - RXNORM:consists_of - - RXNORM:has_part - broad_mappings: - # To 'contain' is 'to have something inside or include something as a part'; slightly broader? - - RO:0001019 - - FMA:contains - - RXNORM:contains - narrow_mappings: - - BFO:0000117 - # RTX term originally mapped to 'biolink:coexists_with'? - - FMA:has_constitutional_part - - FMA:has_part - # Several of the following RTX terms were originally mapped as inverses to 'biolink:part_of'? - - FMA:has_member - - FOODON:00001563 - - FOODON:00002420 - - LOINC:has_component - - LOINC:has_member - - MEDDRA:has_member - - MONDO:disease_has_major_feature - - NCIT:complex_has_physical_part - - NDDF:has_ingredient - - PathWhiz:has_element_in_bound - # This RTX contributed term was tagged as 'biolink:has_gene_product' but seems more compositional in nature - - NCIT:R50 - - PathWhiz:has_protein_in_complex - - RO:0002104 - - RO:0002180 - - RO:0002351 - - RO:0002473 - - RO:0002524 - - RO:0002551 - - RXNORM:has_ingredient - - SNOMED:has_component - - UMLS:has_component - - has plasma membrane part: - is_a: has part - description: >- - Holds between a cell c and a protein complex or protein p if - and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - exact_mappings: - - RO:0002104 - annotations: - canonical_predicate: true - in_subset: - - translator_minimal - - composed primarily of: - is_a: related to - description: >- - x composed_primarily_of_y if:more than half of the mass of x is made from parts of y. - exact_mappings: - - RO:0002473 - annotations: - canonical_predicate: true - in_subset: - - translator_minimal - - primarily composed of: - inverse: composed primarily of - is_a: related to - - plasma membrane part of: - is_a: part of - inverse: has plasma membrane part - - part of: - is_a: overlaps - description: >- - holds between parts and wholes (material entities or processes) - in_subset: - - translator_minimal - inverse: has part - exact_mappings: - - BFO:0000050 - - SEMMEDDB:PART_OF - - WIKIDATA_PROPERTY:P361 - - FMA:part_of - - RXNORM:constitutes - - RXNORM:part_of - broad_mappings: - # To 'contain' is 'to have something inside or include something as a part' - - RO:0001018 - - FMA:contained_in - - RXNORM:contained_in - narrow_mappings: - - BSPO:0001106 - - BSPO:0001108 - - BSPO:0001113 - - BSPO:0001115 - - UBERON_CORE:layer_part_of - - UBERON_CORE:subdivision_of - - UBERON_CORE:trunk_part_of - - CHEBI:is_substituent_group_from - - CPT:panel_element_of - - CPT:panel_element_of_possibly_included - - DRUGBANK:component_of - - FMA:constitutional_part_of - - FMA:member_of - - FMA:regional_part_of - - FMA:related_developmental_entity_of - - LOINC:component_of - - LOINC:has_supersystem - - LOINC:member_of - - LOINC:multipart_of - - MEDDRA:member_of - - MONDO:part_of_progression_of_disease - - NCIT:R82 - - NCIT:R27 - - NCIT:is_component_of_chemotherapy_regimen - - NDDF:ingredient_of - - RO:0002007 - - RO:0002350 - - RO:0002376 - - RO:0002380 - - RO:0002571 - - RO:0002572 - - RO:0002576 - - RXNORM:ingredient_of - - RXNORM:ingredients_of - - RXNORM:precise_ingredient_of - - SNOMED:active_ingredient_of - - SNOMED:basis_of_strength_substance_of - - SNOMED:component_of - - SNOMED:direct_substance_of - - SNOMED:during - - SNOMED:focus_of - - SNOMED:has_dependent - - SNOMED:part_anatomy_structure_of - - SNOMED:precise_active_ingredient_of - - UBERON:subdivision_of - - UMLS:component_of - - UMLS:has_owning_affiliate - - UMLS:owning_subsection_of - - VANDF:ingredient_of - - has input: - is_a: has participant - description: >- - holds between a process and a continuant, where the continuant is an input into the process - domain: biological process or activity - range: occurrent - annotations: - canonical_predicate: true - opposite_of: has output - in_subset: - - translator_minimal - close_mappings: - # RTX inverse mapping to 'biolink:has_input' - - RO:0002352 - exact_mappings: - - RO:0002233 - - SEMMEDDB:USES - narrow_mappings: - - LOINC:has_fragments_for_synonyms - - LOINC:has_system - - PathWhiz:has_left_element - - RO:0002590 - - RO:0004009 - - SNOMED:has_finding_method - - SNOMED:has_precondition - - SNOMED:has_specimen_source_identity - - SNOMED:has_specimen_substance - - SNOMED:uses_access_device - - SNOMED:uses_device - - SNOMED:uses_energy - - SNOMED:uses_substance - - is input of: - is_a: participates in - domain: occurrent - range: biological process or activity - inverse: has input - in_subset: - - translator_minimal - - has output: - is_a: has participant - description: >- - holds between a process and a continuant, where the continuant is an output of the process - domain: biological process or activity - range: occurrent - annotations: - canonical_predicate: true - opposite_of: has input - in_subset: - - translator_minimal - close_mappings: - - RO:0002353 - - RO:0002354 - exact_mappings: - - RO:0002234 - narrow_mappings: - - NCIT:R31 - - OBI:0000299 - - PathWhiz:has_right_element - - RO:0002296 - - RO:0002297 - - RO:0002298 - - RO:0002299 - - RO:0002588 - - RO:0004008 - - is output of: - is_a: participates in - domain: occurrent - range: biological process or activity - inverse: has output - in_subset: - - translator_minimal - - has participant: - is_a: related to at instance level - description: >- - holds between a process and a continuant, where the continuant is somehow involved in the process - domain: biological process or activity - range: occurrent - annotations: - canonical_predicate: true - in_subset: - - translator_minimal - close_mappings: - - WIKIDATA_PROPERTY:P2283 - exact_mappings: - - RO:0000057 - - RO:has_participant - narrow_mappings: - - BFO:0000167 - # Several of the following RTX terms tagged as inverse to 'biolink:participates_in' - - LOINC:has_subject - - NCIT:process_involves_gene - - NBO-PROPERTY:has_participant - - PathWhiz:has_bound - - PathWhiz:has_compound - - PathWhiz:has_element_collection - - PathWhiz:has_enzyme - - OBI:0000293 - - PathWhiz:has_nucleic_acid - - PathWhiz:has_protein - - PathWhiz:has_reaction - - RO:0004007 - - RO:0004020 - - RO:0004021 - - SNOMED:has_indirect_device - - SNOMED:has_procedure_device - - SNOMED:has_recipient_category - - catalyzes: - is_a: participates in - domain: nucleic acid entity - range: molecular activity - annotations: - canonical_predicate: true - - has catalyst: - is_a: has participant - inverse: catalyzes - domain: molecular activity - range: nucleic acid entity - - has substrate: - is_a: has participant - domain: molecular activity - range: chemical entity or gene or gene product - annotations: - canonical_predicate: true - - is substrate of: - is_a: participates in - inverse: has substrate - domain: chemical entity or gene or gene product - range: molecular activity - - participates in: - is_a: related to at instance level - description: >- - holds between a continuant and a process, where the continuant is somehow involved - in the process - range: biological process or activity - domain: occurrent - inverse: has participant - in_subset: - - translator_minimal - exact_mappings: - - RO:0000056 - - BFO:0000056 - narrow_mappings: - - DRUGBANK:pathway - - HMDB:in_pathway - - LOINC:is_given_pharmaceutical_substance_for - - NCIT:R130 - - NCIT:R37 - - NCIT:R131 - - NCIT:R51 - - NCIT:R53 - - OBI:0000295 - - RO:0002216 - - RO:0002505 - - RO:0002565 - - SNOMED:has_direct_device - - actively involved in: - is_a: participates in - aliases: [ 'involved in' ] - description: >- - holds between a continuant and a process or function, where - the continuant actively contributes to part or all of - the process or function it realizes - domain: occurrent - range: molecular activity - annotations: - canonical_predicate: true - in_subset: - - translator_minimal - exact_mappings: - - RO:0002331 - - RO:0002432 - narrow_mappings: - - NBO-PROPERTY:by_means - - orphanet:317348 - - orphanet:317349 - - orphanet:327767 - - RO:0002503 - - actively involves: - is_a: has participant - domain: molecular activity - range: occurrent - inverse: actively involved in - exact_mappings: - - RO:0002331 - in_subset: - - translator_minimal - - capable of: - is_a: actively involved in - description: >- - holds between a physical entity and process or function, where the - continuant alone has the ability to carry out the process or function. - range: occurrent - annotations: - canonical_predicate: true - in_subset: - - translator_minimal - exact_mappings: - - RO:0002215 - narrow_mappings: - - NCIT:R52 - - RO:0002500 - - can be carried out by: - is_a: actively involves - inverse: capable of - domain: occurrent - - enables: - is_a: participates in - description: >- - holds between a physical entity and a process, where the physical entity executes the process - domain: physical entity - range: biological process or activity - annotations: - canonical_predicate: true - opposite_of: prevents - in_subset: - - translator_minimal - inverse: enabled by - exact_mappings: - - RO:0002327 - - enabled by: - is_a: has participant - description: >- - holds between a process and a physical entity, where the physical entity executes the process - domain: biological process or activity - range: physical entity - in_subset: - - translator_minimal - inverse: enables - exact_mappings: - - RO:0002333 - annotations: - opposite_of: prevented by - - derives into: - is_a: related to at instance level - aliases: [ 'is normal cell origin of disease', 'may be normal cell origin of disease' ] - description: >- - holds between two distinct material entities, the old entity and - the new entity, in which the new entity begins to exist when - the old entity ceases to exist, and the new entity inherits - the significant portion of the matter of the old entity - in_subset: - - translator_minimal - inverse: derives from - # TODO: fix this according to WG notes. Example of both opposite and inverse - # Commenting as it feels very wrong. A good example with both opposite and inverse is `has active ingredient` - # annotations: - # opposite_of: subclass of - exact_mappings: - - RO:0001001 - - SEMMEDDB:CONVERTS_TO - # RTX posted terms as inverse of 'biolink:derives_from' - - FMA:derives - - derives from: - is_a: related to at instance level - annotations: - canonical_predicate: true - description: >- - holds between two distinct material entities, the new entity - and the old entity, in which the new entity begins to exist - when the old entity ceases to exist, and the new entity - inherits the significant portion of the matter of the old entity - in_subset: - - translator_minimal - - samples - inverse: derives into - exact_mappings: - - RO:0001000 - - FMA:derives_from - - DOID-PROPERTY:derives_from - narrow_mappings: - - CHEBI:has_functional_parent - - SNOMED:has_specimen_source_topography - - is metabolite of: - is_a: derives from - description: >- - holds between two molecular entities in which the first one is derived - from the second one as a product of metabolism - domain: molecular entity - range: molecular entity - in_subset: - - translator_minimal - inverse: has metabolite - comments: - - The CHEBI ID represents a role rather than a predicate - exact_mappings: - - CHEBI:25212 - - has metabolite: - is_a: derives into - description: >- - holds between two molecular entities in which the second one is derived from the first - one as a product of metabolism - domain: molecular entity - range: molecular entity - annotations: - canonical_predicate: true - in_subset: - - translator_minimal - comments: - - The CHEBI ID represents a role rather than a predicate - exact_mappings: - - CHEBI:25212 - - food component of: - is_a: part of - description: >- - holds between a one or more chemical entities present in food, - irrespective of nutritional value (i.e. could also be a contaminant or additive) - domain: chemical entity - range: chemical entity - in_subset: - - translator_minimal - inverse: has food component - #mappings: - # - - - has food component: - is_a: has part - description: >- - holds between food and one or more chemical entities composing it, - irrespective of nutritional value (i.e. could also be a contaminant or additive) - domain: chemical entity - range: chemical entity - annotations: - canonical_predicate: true - in_subset: - - translator_minimal - - nutrient of: - is_a: food component of - description: >- - holds between a one or more chemical entities present in food, - irrespective of nutritional value (i.e. could also be a contaminant or additive) - domain: chemical entity - range: chemical entity - in_subset: - - translator_minimal - inverse: has nutrient - #exact_mappings: - # - - - has nutrient: - is_a: has food component - description: >- - one or more nutrients which are growth factors for a living organism - domain: chemical entity - range: chemical entity - annotations: - canonical_predicate: true - in_subset: - - translator_minimal - exact_mappings: - - WIKIDATA:Q181394 - - is active ingredient of: - is_a: part of - description: >- - holds between a molecular entity and a drug, in which the former - is a part of the latter, and is a biologically active component - domain: molecular entity - range: drug - in_subset: - - translator_minimal - inverse: has active ingredient - mappings: - - RO:0002249 - - has active ingredient: - is_a: has part - description: >- - holds between a drug and a molecular entity in which the latter - is a part of the former, and is a biologically active component - domain: drug - range: molecular entity - annotations: - canonical_predicate: true - opposite_of: is excipient of - in_subset: - - translator_minimal - inverse: is active ingredient of - mappings: - - RO:0002248 - - is excipient of: - is_a: part of - description: >- - holds between a molecular entity and a drug in which the former is - a part of the latter, and is a biologically inactive component - domain: molecular entity - range: drug - in_subset: - - translator_minimal - inverse: has excipient - mappings: - - WIKIDATA:Q902638 - - has excipient: - is_a: has part - description: >- - holds between a drug and a molecular entities in which the latter - is a part of the former, and is a biologically inactive component - domain: drug - range: molecular entity - annotations: - canonical_predicate: true - in_subset: - - translator_minimal - mappings: - - WIKIDATA:Q902638 - - manifestation of: - is_a: related to at instance level - description: >- - that part of a phenomenon which is directly observable or - visibly expressed, or which gives evidence to the underlying - process; used in SemMedDB for linking things like dysfunctions - and processes to some disease or syndrome - range: disease - annotations: - canonical_predicate: true - in_subset: - - translator_minimal - exact_mappings: - - SEMMEDDB:MANIFESTATION_OF - - OMIM:manifestation_of - broad_mappings: - # Wikidata's definition is slightly broader: "inherent and characteristic embodiment of a given concept" - - WIKIDATA_PROPERTY:P1557 - narrow_mappings: - - SNOMED:has_definitional_manifestation - - has manifestation: - is_a: related to at instance level - domain: disease - inverse: manifestation of - - mode of inheritance of: - is_a: manifestation of - domain: genetic inheritance - range: disease or phenotypic feature - inverse: has mode of inheritance - - has mode of inheritance: - is_a: has manifestation - description: >- - Relates a disease or phenotypic feature to its observed genetic segregation and assumed - associated underlying DNA manifestation (i.e. autosomal, sex or mitochondrial chromosome). - domain: disease or phenotypic feature - range: genetic inheritance - annotations: - # This canonical order reverses that of its parent 'has manifestation' class - # but seems a more natural direction in the pertinent edge relationships. - canonical_predicate: true - in_subset: - - translator_minimal - - produces: - is_a: related to at instance level - description: >- - holds between a material entity and a product that is generated - through the intentional actions or functioning of the material entity - in_subset: - - translator_minimal - annotations: - canonical_predicate: true - related_mappings: - - GOREL:0001010 - exact_mappings: - - RO:0003000 - - WIKIDATA_PROPERTY:P1056 - - SEMMEDDB:PRODUCES - narrow_mappings: - - NCIT:R29 - - SNOMED:has_process_output - - SNOMED:specimen_procedure_of - - produced by: - is_a: related to at instance level - inverse: produces - exact_mappings: - - RO:0003001 - - consumes: - is_a: has input - annotations: - canonical_predicate: true - narrow_mappings: - - RO:0004009 - - consumed by: - is_a: is input of - inverse: consumes - - temporally related to: - is_a: related to at instance level - description: >- - holds between two entities with a temporal relationship - domain: occurrent - range: occurrent - symmetric: true - annotations: - canonical_predicate: true - exact_mappings: - - SNOMED:temporally_related_to - narrow_mappings: - # The These RTX mappings are temporal in nature, but not with precedes ordering, so mapped here - - RO:0002082 - - RO:0002083 - - RO:0002092 - - RO:0002093 - - RO:0002223 - - RO:0002224 - - RO:0002229 - - RO:0002230 - - RO:0002488 - - RO:0002489 - - RO:0002492 - - RO:0002493 - - RO:0002496 - - RO:0002497 - - precedes: - is_a: temporally related to - description: >- - holds between two processes, where one completes before the other begins - domain: occurrent - range: occurrent - annotations: - canonical_predicate: true - inverse: preceded by - in_subset: - - translator_minimal - close_mappings: - # the subject of these terms is a material entity, not a process, - # but affects a process which causes a second process to occur - - RO:0002263 - - RO:0002264 - exact_mappings: - - BFO:0000063 - - SEMMEDDB:PRECEDES - - SNOMED:occurs_before - broad_mappings: - # the Wikidata definition is subtly broader, focusing on a series not strictly temporal in nature - - WIKIDATA_PROPERTY:P156 - narrow_mappings: - - FMA:transforms_into - - RO:0002090 - - RO:0002411 - - RO:0002412 - - preceded by: - is_a: temporally related to - description: >- - holds between two processes, where the other is completed before the one begins - domain: occurrent - range: occurrent - inverse: precedes - in_subset: - - translator_minimal - exact_mappings: - - BFO:0000062 - broad_mappings: - # Contributed by RTX as inverse of 'precedes'. Seems more generic to just processes, so we tag it as 'broad'? - - GENEPIO:0001739 - narrow_mappings: - # RTX contributed mapping was given as the inverse of 'biolink:precedes' - - FMA:transforms_from - - RO:0002087 - - RO:0002285 - - has variant part: - is_a: has part - description: holds between a nucleic acid entity and a nucleic acid entity that is a sub-component of it - annotations: - canonical_predicate: true - exact_mappings: - - GENO:0000382 - - variant part of: - is_a: part of - inverse: has variant part - - related condition: - is_a: related to at instance level - symmetric: true - annotations: - canonical_predicate: true - exact_mappings: - - GENO:0000790 - - ## Predicates relating variants to genes - - is sequence variant of: - is_a: related to at instance level - aliases: [ 'gene product sequence variation encoded by gene mutant', 'allelic variant of', 'gene product variant of gene product' ] - description: holds between a sequence variant and a nucleic acid entity - domain: sequence variant - range: genomic entity - annotations: - canonical_predicate: true - narrow_mappings: - - WIKIDATA:P3433 - - has sequence variant: - is_a: related to at instance level - inverse: is sequence variant of - domain: genomic entity - range: sequence variant - - is missense variant of: - is_a: is sequence variant of - description: holds between a gene and a sequence variant, such the sequence variant - results in a different amino acid sequence but where the length is preserved. - domain: sequence variant - range: genomic entity - annotations: - canonical_predicate: true - exact_mappings: - - SO:0001583 - - has missense variant: - is_a: has sequence variant - domain: genomic entity - range: sequence variant - inverse: is missense variant of - - is synonymous variant of: - is_a: is sequence variant of - description: holds between a sequence variant and a gene, such the sequence variant - is in the coding sequence of the gene, but results in the same amino acid sequence - domain: sequence variant - range: genomic entity - annotations: - canonical_predicate: true - exact_mappings: - - SO:0001819 - - has synonymous variant: - is_a: has sequence variant - domain: genomic entity - range: sequence variant - inverse: is synonymous variant of - aliases: [ 'stop gained' ] - - is nonsense variant of: - is_a: is sequence variant of - description: holds between a sequence variant and a gene, such the sequence variant - results in a premature stop codon - domain: sequence variant - range: genomic entity - annotations: - canonical_predicate: true - broad_mappings: - # Term definition broader than nonsense codon: A sequence variant whereby - # the gene product has diminished or abolished function. - - SO:0002054 - - has nonsense variant: - is_a: has sequence variant - domain: genomic entity - range: sequence variant - inverse: is nonsense variant of - - is frameshift variant of: - is_a: is sequence variant of - description: holds between a sequence variant and a gene, such the sequence variant - causes a disruption of the translational reading frame, because the number of - nucleotides inserted or deleted is not a multiple of three. - domain: sequence variant - range: genomic entity - annotations: - canonical_predicate: true - exact_mappings: - - SO:0001589 - aliases: [ 'frameshift variant', 'start lost', 'stop lost' ] - - has frameshift variant: - is_a: has sequence variant - inverse: is frameshift variant of - domain: genomic entity - range: sequence variant - aliases: [ 'splice region variant', 'splice acceptor variant', 'splice donor variant' ] - - is splice site variant of: - is_a: is sequence variant of - description: holds between a sequence variant and a gene, such the sequence variant - is in the canonical splice site of one of the gene's exons. - domain: sequence variant - range: genomic entity - annotations: - canonical_predicate: true - exact_mappings: - - SO:0001629 - - - has splice site variant: - is_a: has sequence variant - domain: genomic entity - range: sequence variant - inverse: is splice site variant of - aliases: [ 'downstream gene variant', 'upstream gene variant' ] - - is nearby variant of: - is_a: is sequence variant of - description: holds between a sequence variant and a gene sequence that the variant - is genomically close to. - domain: sequence variant - range: genomic entity - annotations: - canonical_predicate: true - - has nearby variant: - is_a: has sequence variant - domain: genomic entity - range: sequence variant - inverse: is nearby variant of - aliases: [ 'intron variant', '3 prime UTR variant', '5 prime UTR variant', '5 prime UTR premature start codon gain variant', 'non coding transcript exon variant' ] - - is non coding variant of: - is_a: is sequence variant of - description: holds between a sequence variant and a gene, where the variant does - not affect the coding sequence - domain: sequence variant - range: genomic entity - annotations: - canonical_predicate: true - - has non coding variant: - is_a: has sequence variant - domain: genomic entity - range: sequence variant - inverse: is non coding variant of - - # relating disease to process - - disease has basis in: - description: A relation that holds between a disease and an entity where the state - of the entity has contribution to the disease. - is_a: related to at instance level - annotations: - canonical_predicate: true - narrow_mappings: - # These two MONDO terms seem more particular than the predicate - - MONDO:disease_has_basis_in_development_of - - MONDO:disease_has_basis_in_accumulation_of - - occurs in disease: - is_a: related to at instance level - inverse: disease has basis in - - - has adverse event: - is_a: affects - aliases: [ 'adverse effect'] - description: >- - An untoward medical occurrence in a patient or clinical investigation subject that happens during treatment - with a therapeutic agent. Adverse events may be caused by something - other than the drug or therapy being given and may include abnormal laboratory finding, symptoms, or - diseases temporally associated with the treatment, whether or not considered related to the treatment. - Adverse events are unintended effects that occur when a medication is administered correctly. - domain: chemical or drug or treatment - range: disease or phenotypic feature - annotations: - canonical_predicate: true - - adverse event of: - is_a: affected by - domain: disease or phenotypic feature - range: chemical or drug or treatment - inverse: has adverse event - - has side effect: - aliases: [ 'adverse drug reaction'] - is_a: affects - description: >- - An unintended, but predictable, secondary effect shown to be correlated with a therapeutic agent, drug or treatment. - Side effects happen at normal, recommended doses or treatments, and are unrelated to the intended purpose of - the medication. - notes: >- - Side effects are listed on drug labels. There can be positive side effects, while adverse events are always negative. - Aeolus, Sider are both resources that provide side effects. - domain: chemical or drug or treatment - range: disease or phenotypic feature - annotations: - canonical_predicate: true - exact_mappings: - - NCIT:C2861 # side effect - - is side effect of: - is_a: affected by - domain: disease or phenotypic feature - range: chemical or drug or treatment - inverse: has side effect - - contraindicated for: - is_a: related to at instance level - description: Holds between a drug and a disease or phenotype, such that a person - with that disease should not be treated with the drug. - domain: drug - range: disease or phenotypic feature - annotations: - canonical_predicate: true - opposite_of: treats - exact_mappings: - - NCIT:C37933 - - has contraindication: - is_a: related to at instance level - domain: disease or phenotypic feature - range: drug - inverse: contraindicated for - - # The remaining new slots are here because we ran across them somewhere and - # they didn't seem to map well to anything else. - - has not completed: - is_a: related to at instance level - description: holds between an entity and a process that the entity is capable of, - but has not completed - exact_mappings: - - CL:has_not_completed - annotations: - opposite_of: has completed - canonical_predicate: true - - not completed by: - is_a: related to at instance level - inverse: has not completed - - has completed: - is_a: related to at instance level - description: holds between an entity and a process that the entity is capable of - and has completed - annotations: - canonical_predicate: true - opposite_of: has not completed - exact_mappings: - - CL:has_completed - - completed by: - is_a: related to at instance level - inverse: has completed - - - in linkage disequilibrium with: - is_a: related to at instance level - description: holds between two sequence variants, the presence of which are correlated - in a population - symmetric: true - annotations: - canonical_predicate: true - exact_mappings: - - NCIT:C16798 - - has increased amount: - is_a: related to at instance level - annotations: - canonical_predicate: true - opposite_of: has decreased amount - narrow_mappings: - - CL:has_high_plasma_membrane_amount - - increased amount of: - is_a: related to at instance level - inverse: has increased amount - - has decreased amount: - is_a: related to at instance level - annotations: - canonical_predicate: true - opposite_of: has increased amount - narrow_mappings: - - CL:has_low_plasma_membrane_amount - - decreased amount in: - is_a: related to at instance level - inverse: has decreased amount - - lacks part: - is_a: related to at instance level - annotations: - canonical_predicate: true - opposite_of: has part - exact_mappings: - - CL:lacks_part - - PR:lacks_part - narrow_mappings: - - CL:lacks_plasma_membrane_part - - missing from: - is_a: related to at instance level - inverse: lacks part - - develops from: - is_a: related to at instance level - annotations: - canonical_predicate: true - close_mappings: - # RTX mapping seems to be inverse of 'biolink:develops_from' - - RO:0002203 - - FMA:develops_into - exact_mappings: - - BTO:develops_from - - DDANAT:develops_from - - FMA:develops_from - - RO:0002202 - narrow_mappings: - - RO:0002207 - - RO:0002225 # x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - - RO:0002226 # x develops_in y if x is located in y whilst x is developing - - develops into: - is_a: related to at instance level - inverse: develops from - - in taxon: - aliases: [ 'instance of', 'is organism source of gene product', 'organism has gene', 'gene found in organism', 'gene product has organism source' ] - is_a: related to at instance level - domain: thing with taxon - range: organism taxon - annotations: - canonical_predicate: true - description: >- - connects an entity to its taxonomic classification. Only certain kinds - of entities can be taxonomically classified; see 'thing with taxon' - in_subset: - - translator_minimal - exact_mappings: - - RO:0002162 - - WIKIDATA_PROPERTY:P703 - narrow_mappings: - - RO:0002160 - - taxon of: - is_a: related to at instance level - inverse: in taxon - domain: organism taxon - range: thing with taxon - - has molecular consequence: - is_a: related to at instance level - aliases: [ 'allele has activity' ] - description: >- - connects a sequence variant to a class describing the molecular - consequence. E.g. SO:0001583 - range: ontology class - annotations: - canonical_predicate: true - narrow_mappings: - - NCIT:allele_has_activity - - is molecular consequence of: - is_a: related to at instance level - domain: ontology class - inverse: has molecular consequence - - ## -------------------- - ## ASSOCIATION SLOTS - ## -------------------- - - association slot: - abstract: true - domain: association - aliases: [ 'edge property', 'statement property', 'node qualifier', 'edge qualifier', 'statement qualifier' ] - description: >- - any slot that relates an association to another entity - - original subject: - is_a: association slot - description: >- - used to hold the original subject of a relation (or predicate) that an external knowledge - source uses before transformation to match the biolink-model specification. - - original object: - is_a: association slot - description: >- - used to hold the original object of a relation (or predicate) that an external knowledge - source uses before transformation to match the biolink-model specification. - - original predicate: - aliases: [ 'original relation', 'relation' ] - is_a: association slot - description: >- - used to hold the original relation/predicate that an external knowledge - source uses before transformation to match the biolink-model specification. - id_prefixes: - - RO - - BSPO - - SIO - domain: association - range: uriorcurie - - subject: - is_a: association slot - local_names: - ga4gh: annotation subject - neo4j: node with outgoing relationship - description: >- - connects an association to the subject of the association. - For example, in a gene-to-phenotype association, the gene is subject and phenotype is object. - required: true - domain: association - range: named thing - slot_uri: rdf:subject - exact_mappings: - - owl:annotatedSource - - OBAN:association_has_subject - - object: - is_a: association slot - description: >- - connects an association to the object of the association. - For example, in a gene-to-phenotype association, the gene is subject and phenotype is object. - required: true - domain: association - range: named thing - local_names: - ga4gh: descriptor - neo4j: node with incoming relationship - slot_uri: rdf:object - exact_mappings: - - owl:annotatedTarget - - OBAN:association_has_object - - predicate: - is_a: association slot - description: >- - A high-level grouping for the relationship type. AKA minimal predicate. - This is analogous to category for nodes. - domain: association - notes: >- - Has a value from the Biolink related_to hierarchy. In RDF, this - corresponds to rdf:predicate and in Neo4j this corresponds to the - relationship type. The convention is for an edge label in snake_case - form. For example, biolink:related_to, biolink:causes, biolink:treats - range: predicate type - required: true - local_names: - ga4gh: annotation predicate - translator: predicate - slot_uri: rdf:predicate - exact_mappings: - - owl:annotatedProperty - - OBAN:association_has_predicate - - logical interpretation: - is_a: association slot - required: false - domain: association - range: LogicalInterpretationEnum - exact_mappings: - - os:LogicalInterpretation - - relation: - deprecated: true - - negated: - is_a: association slot - range: boolean - description: >- - if set to true, then the association is negated i.e. is not true - - has confidence level: - is_a: association slot - range: confidence level - description: >- - connects an association to a qualitative term denoting the level of confidence - - has evidence: - is_a: association slot - range: evidence type - description: >- - connects an association to an instance of supporting evidence - exact_mappings: - - RO:0002558 - multivalued: true - - has supporting study result: - is_a: association slot - description: >- - connects an association to an instance of supporting study result - - mechanism of action: - is_a: association slot - range: boolean - description: >- - a boolean flag to indicate if the edge is part of a path or subgraph of a knowledge graph that constitutes - the mechanism of action for a result. - exact_mappings: - - NCIT:C54680 - - MI:2044 - - LOINC:MTHU019741 - - knowledge source: - is_a: association slot - description: >- - An Information Resource from which the knowledge expressed in an Association was - retrieved, directly or indirectly. This can be any resource through which the - knowledge passed on its way to its currently serialized form. In practice, - implementers should use one of the more specific subtypes of this generic property. - range: information resource - close_mappings: - - pav:providedBy - - provided by: - is_a: node property - description: >- - The value in this node property represents the knowledge provider that created or assembled the - node and all of its attributes. Used internally to represent how a particular node made its way into a - knowledge provider or graph. - multivalued: true - - primary knowledge source: - is_a: knowledge source - description: >- - The most upstream source of the knowledge expressed in an Association that an - implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort - is made to catalog the most upstream source of data in this property. Only one data source should be declared - primary in any association. "aggregator knowledge source" can be used to capture non-primary sources. - range: information resource - notes: >- - For example: a single ChemicalToGene Edge originally curated by ClinicalTrials.org, is aggregated by ChEMBL, then - incorporated into the MolePro KP, then sent via TRAPI message to the ARAGORN ARA, and finally sent to - the NCATS ARS. The retrieval path for this Edge is as follows: - ARS--retrieved_from--> ARAGORN --retrieved_from--> MolePro --retrieved_from--> ChEMBL --retrieved_from--> ClinicalTrials.gov - The "primary knowledge source" for this edge is "infores:clinical-trials-gov". "infores:chembl" and "infores:molecular_data_provider" - are listed in the "aggregator knowledge source" property. - multivalued: false - - aggregator knowledge source: - is_a: knowledge source - description: >- - An intermediate aggregator resource from which knowledge expressed in an Association was - retrieved downstream of the original source, on its path to its current serialized form. - range: information resource - multivalued: true - notes: >- - For example, in this Feature Variable Association Edge generated by the Exposure Agent’s ICEES KP, - through statistical analysis of clinical and environmental data supplied by the UNC Clinical Data Warehouse, - the Edge is passed to the Ranking Agent’s ARAGORN ARA, - and then on to the ARS. The retrieval path for this Edge is as follows: - ARS--retrieved_from--> ARAGORN --retrieved_from--> ICEES --supporting_data_from--> UNC Data Warehouse - This example illustrates how to represent the source provenance of KP-generated knowledge, including the source of - data from which the knowledge was derived. - The "primary knowledge source" for this edge is "infores:icees-asthma". A "supporting data source" for this KP- - generated knowledge is "infores:unc-cdw-health." The "aggregator knowledge source" for this data is "infores:aragorn-ara" - - supporting data source: - is_a: association slot - description: >- - An Information Resource from which data was retrieved and subsequently used as - evidence to generate the knowledge expressed in an Association (e.g. through - computation on, reasoning or inference over the retrieved data). - range: information resource - multivalued: true - notes: >- - For example, in this Feature Variable Association Edge generated by the Exposure Agent’s ICEES KP, - through statistical analysis of clinical and environmental data supplied by the UNC Clinical Data Warehouse, - the Edge is passed to the Ranking Agent’s ARAGORN ARA, - and then on to the ARS. The retrieval path for this Edge is as follows: - ARS--retrieved_from--> ARAGORN --retrieved_from--> ICEES --supporting_data_from--> UNC Data Warehouse - This example illustrates how to represent the source provenance of KP-generated knowledge, including the source of - data from which the knowledge was derived. - The "primary knowledge source" for this edge is "infores:icees-asthma". A "supporting data source" for this KP- - generated knowledge is "infores:unc-cdw-health." The "aggregator knowledge source" for this data is "infores:aragorn-ara" - - supporting data set: - is_a: association slot - description: >- - A set of data used as evidence to generate the knowledge expressed in an Association (e.g. through - computation on, reasoning or inference over the retrieved data). - range: information resource - multivalued: true - - chi squared statistic: - is_a: association slot - range: float - description: >- - represents the chi-squared statistic computed from observations - exact_mappings: - - STATO:0000030 - - p value: - aliases: ['unadjusted p value'] - is_a: association slot - range: float - description: >- - A quantitative confidence value that represents the probability of - obtaining a result at least as extreme as that actually obtained, - assuming that the actual value was the result of chance alone. - exact_mappings: - - OBI:0000175 - - NCIT:C44185 - - EDAM-DATA:1669 - - evidence count: - is_a: association slot - description: >- - The number of evidence instances that are connected to an association. - range: integer - - concept count subject: - is_a: association slot - description: >- - The number of instances in a dataset/cohort whose records contain - the concept in the subject slot of an association. - range: integer - examples: - - value: 489 - - concept count object: - is_a: association slot - description: >- - The number of instances in a dataset/cohort whose records contain - the concept in the object slot of an association. - range: integer - - concept pair count: - is_a: association slot - description: >- - The number of instances in a dataset/cohort whose records contain - both the subject and object concept of an association. - range: integer - examples: - - value: 1731 - - expected count: - is_a: association slot - description: >- - The expected (calculated) number of instances in a dataset/cohort whose records contain both the subject and - object concept of an association if the subject and object concepts are independent. - - relative frequency subject: - is_a: association slot - description: >- - The frequency at which subject and object concepts co-occur in - records within a dataset/cohort, relative to the frequency at which the subject - concept appears in these same records. - range: float - examples: - - value: 0.01840490798 - - relative frequency object: - is_a: association slot - description: >- - The frequency at which subject and object concepts co-occur in - records within a dataset/cohort, relative to the frequency at which the object - concept appears in these same records. - range: string - - relative frequency subject confidence interval: - is_a: association slot - description: >- - The 99% confidence interval for the relative_frequency_subject calculation - (i.e. the range of values within which the true value has a 99% chance of falling) - range: string - - relative frequency object confidence interval: - is_a: association slot - description: >- - The 99% confidence interval for the relative_frequency_object calculation - (i.e. the range of values within which the true value has a 99% chance of falling) - range: string - - adjusted p value: - is_a: p value - description: >- - The adjusted p-value is the probability of obtaining test results - at least as extreme as the results actually observed, under the assumption that - the null hypothesis is correct, adjusted for multiple comparisons. - P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) - rather than expressing a statement of inequality (P<. 05), unless P<. - range: float - - bonferonni adjusted p value: - is_a: adjusted p value - description: >- - The Bonferroni correction is an adjustment made to P values when several dependent or independent - statistical tests are being performed simultaneously on a single data set. To perform a Bonferroni - correction, divide the critical P value (α) by the number of comparisons being made. P is always italicized and - capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality - (P<. 05), unless P<. - range: float - examples: - - value: 0.018 - - supporting text: - is_a: association slot - description: The segment of text from a document that supports the mined assertion. - multivalued: true - range: string - examples: - - value: The administration of 50g/ml bupivacaine promoted maximum breast cancer. - - supporting documents: - is_a: association slot - description: >- - One or more referenceable documents that report the statement expressed in an Association, or provide - information used as evidence supporting this statement. - range: uriorcurie - multivalued: true - examples: - - value: PMID:12345678 - - subject location in text: - is_a: association slot - description: >- - Character offsets for the text span(s) in the supporting text corresponding - to the subject concept of the extracted assertion. - range: integer - examples: - - value: 15 - multivalued: true - - object location in text: - is_a: association slot - description: >- - Character offsets for the text span(s) in the supporting text corresponding - to the object concept of the extracted assertion - range: integer - examples: - - value: 15 - multivalued: true - - extraction confidence score: - is_a: association slot - description: >- - A quantitative confidence value that represents the probability of - obtaining a result at least as extreme as that actually obtained, - assuming that the actual value was the result of chance alone. - range: integer - examples: - - value: 15 - - supporting document type: - is_a: association slot - description: >- - The document type (e.g., Journal Article, Case Study, Preprint) for - the supporting document used in a Text Mining Result. - range: string - examples: - - value: Journal Article - - supporting document year: - is_a: association slot - description: >- - The document year (typically the publication year) for the supporting - document used in a Text Mining Result. - range: integer - examples: - - value: 1999 - - supporting text section type: - is_a: association slot - description: >- - The section of the supporting text of a Text Mining Result within - the supporting document. This is in the form of the name of the document section - (e.g., Abstract, Introduction) that contains the supporting text. - range: string - examples: - - value: Introduction - - ln ratio: - is_a: association slot - description: the natural log of the ratio of co-occurrence to expected - range: float - examples: - - value: 2.922827136 - - ln ratio confidence interval: - is_a: association slot - description: >- - The 99% confidence interval for the ln_ratio calculation - (i.e. the range of values within which the true value has a 99% chance of falling) - range: float - examples: - - value: 2.922827136 - - interacting molecules category: - is_a: association slot - range: ontology class - exact_mappings: - - MI:1046 - values_from: - - MI - examples: - - value: MI:1048 - description: smallmolecule-protein - - expression site: - description: >- - location in which gene or protein expression takes place. - May be cell, tissue, or organ. - is_a: association slot - range: anatomical entity - examples: - - value: UBERON:0002037 - description: cerebellum - - phenotypic state: - description: >- - in experiments (e.g. gene expression) assaying diseased or unhealthy - tissue, the phenotypic state can be put here, e.g. MONDO ID. - For healthy tissues, use XXX. - is_a: association slot - range: disease or phenotypic feature - - publications: - aliases: ["supporting publications"] - singular_name: publication - description: >- - One or more publications that report the statement expressed in an Association, or provide information used as - evidence supporting this statement. - is_a: supporting documents - multivalued: true - range: publication - - associated environmental context: - is_a: association slot - description: >- - An attribute that can be applied to an association where the association holds between two entities - located or occurring in a particular environment. For example, two microbial taxa may interact in the context of - a human gut; a disease may give rise to a particular phenotype in a particular environmental exposure. - # TODO: add examples of values for this property. - - sequence localization attribute: - is_a: association slot - domain: genomic sequence localization - description: >- - An attribute that can be applied to a genome sequence localization edge. These edges - connect a nucleic acid entity such as an exon to an entity such as a chromosome. Edge properties are used - to ascribe specific positional information and other metadata to the localization. In pragmatic terms - this can be thought of as columns in a GFF3 line. - - interbase coordinate: - is_a: sequence localization attribute - aliases: [ 'zero-based', 'half-open', 'space-based' ] - description: >- - A position in interbase coordinates. Interbase coordinates start at position 0 instead of position 1. - This is applied to a sequence localization edge. - range: integer - - start interbase coordinate: - is_a: interbase coordinate - description: >- - The position at which the subject nucleic acid entity starts - on the chromosome or other entity to which it is located on. - (ie: the start of the sequence being referenced is 0). - close_mappings: - - faldo:begin - annotations: - opposite_of: end interbase coordinate - - end interbase coordinate: - is_a: interbase coordinate - description: >- - The position at which the subject nucleic acid entity ends - on the chromosome or other entity to which it is located on. - close_mappings: - - faldo:end - annotations: - opposite_of: start interbase coordinate - - start coordinate: - is_a: base coordinate - aliases: [ 'start' ] - description: >- - The position at which the subject genomic entity starts - on the chromosome or other entity to which it is located on. - (ie: the start of the sequence being referenced is 1). - exact_mappings: - - gff3:start - close_mappings: - - faldo:begin - - end coordinate: - is_a: base coordinate - aliases: [ 'end' ] - description: >- - The position at which the subject genomic entity ends - on the chromosome or other entity to which it is located on. - exact_mappings: - - gff3:end - close_mappings: - - faldo:end - - genome build: - is_a: sequence localization attribute - description: >- - The version of the genome on which a feature is located. - For example, GRCh38 for Homo sapiens. - range: StrandEnum - exact_mappings: - - gff3:strand - - strand: - is_a: sequence localization attribute - description: >- - The strand on which a feature is located. Has a value of '+' - (sense strand or forward strand) or '-' (anti-sense strand or reverse strand). - range: StrandEnum - exact_mappings: - - gff3:strand - - phase: - is_a: sequence localization attribute - domain: coding sequence - description: >- - The phase for a coding sequence entity. For example, phase of a - CDS as represented in a GFF3 with a value of 0, 1 or 2. - range: PhaseEnum - exact_mappings: - - gff3:phase - - FDA approval status: - is_a: association slot - description: >- - range: FDAApprovalStatusEnum - - supporting study metadata: - is_a: association slot - description: >- - Information about a study used to generate information used as evidence to support the knowledge expressed in an - Association. In practice, data creators should use one of the more specific subtypes of this property. - abstract: true - - supporting study method type: - is_a: supporting study metadata - description: >- - A type of method that was applied in a study used to generate the information used as evidence (e.g. a type of - experimental assay, or statistical calculation, or computational analysis). - range: uriorcurie - - supporting study method description: - is_a: supporting study metadata - description: >- - A uri or curie pointing to information about the methodology used to generate data supporting an Association. - range: uriorcurie - - supporting study size: - is_a: supporting study metadata - description: >- - The sample size used in a study that provided evidence for the association (e.g. 'n' of a cohort for a - clinical study). - range: integer - - supporting study cohort: - is_a: supporting study metadata - description: >- - A description of a study population/cohort that was interrogated to provide evidence for the association - (e.g. the inclusion and exclusion criteria). - range: string - - supporting study date range: - is_a: supporting study metadata - description: >- - The date range over which data was collected in a study that provided evidence for an Association. - range: string - - supporting study context: - is_a: supporting study metadata - description: >- - A term or terms describing the experimental setting/context in which evidence supporting the Association was - generated ('context' may be defined by many factors, including taxon, model system (e.g. cell line type), tissue - type, disease, etc.). - range: string -classes: - - mapping collection: - description: >- - A collection of deprecated mappings. - abstract: true - slots: - - predicate mappings - - predicate mapping: - description: >- - A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should - be done to use a qualified statement in its place. - slots: - - mapped predicate - - subject aspect qualifier - - subject direction qualifier - - subject form or variant qualifier - - subject part qualifier - - subject derivative qualifier - - subject context qualifier - - predicate - - qualified predicate - - object aspect qualifier - - object direction qualifier - - object form or variant qualifier - - object part qualifier - - object derivative qualifier - - object context qualifier - - causal mechanism qualifier - - anatomical context qualifier - - species context qualifier - - exact match - - narrow match - - broad match - - - ## ---------- - ## ATTRIBUTES - ## ---------- - - ## Ontology Classes - - ontology class: - mixin: true - slots: - - id - description: >- - a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in - a biolink compatible KG can be considered both instances of biolink classes, and - OWL classes in their own right. In general you should not need to use this class directly. - Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), - use bl:BiologicalProcess as the type. - exact_mappings: - - owl:Class - - schema:Class - comments: - - >- - This is modeled as a mixin. 'ontology class' should not be the primary type of a - node in the KG. Instead you should use an informative bioloink category, such as AnatomicalEntity - (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL), etc - - >- - Note that formally this is a metaclass. Instances of this class are instances in the graph, - but can be the object of 'type' edges. For example, if we had a node in the graph representing - a specific brain of a specific patient (e.g brain001), this could have a category of bl:Sample, - and by typed more specifically with an ontology class UBERON:nnn, which has as category bl:AnatomicalEntity - see_also: - - https://github.com/biolink/biolink-model/issues/486 - examples: - - value: UBERON:0000955 - description: >- - the class 'brain' from the Uberon anatomy ontology - id_prefixes: - - MESH - - UMLS - - KEGG.BRITE ## br/ko number - - annotation: - description: >- - Biolink Model root class for entity annotations. - abstract: true - - quantity value: - is_a: annotation - description: >- - A value of an attribute that is quantitative and measurable, - expressed as a combination of a unit and a numeric value - slots: - - has unit - - has numeric value - - # Alignment attempted of the biolink:Attribute model - # to the proposed TRAPI Release 1.1 Attribute schema, i.e. - # - # attribute_name: "assertionAuthoredBy", - # attribute_type: SEPIO:0000130, - # value: "ORCID:12345", - # value_type: "wd:Q51044", - # value_type_name: "ORCID ID" - # url: https://orcid.org/12345 - # source: ORCID - - attribute: - is_a: named thing - mixins: - - ontology class - description: >- - A property or characteristic of an entity. - For example, an apple may have properties such as color, shape, age, crispiness. - An environmental sample may have attributes such as depth, lat, long, material. - slots: - - name # 'attribute_name' - - has attribute type # 'attribute_type' - # 'value', 'value_type', 'value_type_name' - # extracted from either of the next two slots - - has quantitative value - - has qualitative value - - iri # 'url' - slot_usage: - name: - description: >- - The human-readable 'attribute name' can be set to a string which reflects its context of - interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default - to the name associated with the 'has attribute type' slot ontology term. - id_prefixes: - - EDAM-DATA - - EDAM-FORMAT - - EDAM-OPERATION - - EDAM-TOPIC - exact_mappings: - - SIO:000614 - in_subset: - - samples - - chemical role: - is_a: attribute - description: >- - A role played by the molecular entity or part thereof within a chemical context. - id_prefixes: - - CHEBI - exact_mappings: - - CHEBI:51086 - examples: - - value: CHEBI:35469 # antidepressant role - - biological sex: - is_a: attribute - exact_mappings: - - PATO:0000047 - - phenotypic sex: - is_a: biological sex - description: >- - An attribute corresponding to the phenotypic sex of the individual, - based upon the reproductive organs present. - exact_mappings: - - PATO:0001894 - - genotypic sex: - is_a: biological sex - description: >- - An attribute corresponding to the genotypic sex of the individual, - based upon genotypic composition of sex chromosomes. - exact_mappings: - - PATO:0020000 - - severity value: - is_a: attribute - description: >- - describes the severity of a phenotypic feature or disease - - relationship quantifier: - mixin: true - - sensitivity quantifier: - is_a: relationship quantifier - mixin: true - - specificity quantifier: - is_a: relationship quantifier - mixin: true - - pathognomonicity quantifier: - is_a: specificity quantifier - description: >- - A relationship quantifier between a variant or symptom and a disease, which is - high when the presence of the feature implies the existence of the disease - mixin: true - - frequency quantifier: - is_a: relationship quantifier - mixin: true - slots: - - has count - - has total - - has quotient - - has percentage - - chemical or drug or treatment: - mixin: true - - ## ------ - ## THINGS - ## ------ - - entity: - description: >- - Root Biolink Model class for all things and informational relationships, real or imagined. - abstract: true - slots: - - id - - iri - - category - - type # rdf:type - - name - - description - - has attribute - # evidence code(s)? - - named thing: - is_a: entity - description: "a databased entity or concept/class" - slots: - - provided by - - xref - slot_usage: - category: - required: true - pattern: '^biolink:[A-Z][A-Za-z]+$' - exact_mappings: - - BFO:0000001 - - WIKIDATA:Q35120 - # UMLS Semantic Group "Objects" - - UMLSSG:OBJC - # Entity - - STY:T071 - - dcid:Thing - - relationship type: - is_a: ontology class - description: >- - An OWL property used as an edge label - - taxonomic rank: - description: >- - A descriptor for the rank within a taxonomic classification. - Example instance: TAXRANK:0000017 (kingdom) - is_a: ontology class - id_prefixes: - - TAXRANK - mappings: - - WIKIDATA:Q427626 - - organism taxon: - aliases: [ 'taxon', 'taxonomic classification' ] - description: >- - A classification of a set of organisms. Example instances: - NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). - Can also be used to represent strains or subspecies. - is_a: named thing - slot_usage: - has taxonomic rank: - range: taxonomic rank - multivalued: false - mappings: - - WIKIDATA:P105 - values_from: - - NCBITaxon - exact_mappings: - - WIKIDATA:Q16521 - - STY:T001 - - bioschemas:Taxon - narrow_mappings: - - dcid:BiologicalSpecies - id_prefixes: - - NCBITaxon - - MESH - - UMLS - in_subset: - - model_organism_database - - ## Temporal Entities - - event: - is_a: named thing - description: >- - Something that happens at a given place and time. - exact_mappings: - - NCIT:C25499 - # UMLS "Event" - - STY:T051 - - ## Administrative Entities - - administrative entity: - is_a: named thing - abstract: true - - study result: - abstract: true - description: >- - A collection of data items from a study that are about a particular study subject or experimental unit (the - 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation - of this data as evidence. - notes: - The data/metadata included in a Study Result object are typically a subset of data from a larger study data set, - that are selected by a curator because they may be useful as evidence for deriving knowledge about a specific - focus of the study. The notion of a 'study' here is defined broadly to include any research activity at any - scale that is aimed at generating knowledge or hypotheses. This may include a single assay or computational - analyses, or a larger scale clinical trial or experimental research investigation. - is_a: information content entity - - study: - description: a detailed investigation and/or analysis - is_a: information content entity - exact_mappings: - - NCIT:C63536 - close_mappings: - - SIO:001066 - - SEPIO:0000004 - narrow_mappings: - - SIO:000994 - - study variable: - is_a: information content entity - description: a variable that is used as a measure in the investigation of a study - narrow_mappings: - - NCIT:C142192 # specifies clinical study - close_mappings: - - STATO:0000258 - - SIO:000367 - - common data element: - is_a: information content entity - description: >- - A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable - responses, used systematically across different sites, studies, or clinical trials to ensure consistent - data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. - (https://cde.nlm.nih.gov/home) - close_mappings: - - NCIT:C19984 - - ## epc result sets - concept count analysis result: - is_a: study result - description: >- - A result of a concept count analysis. - - observed expected frequency analysis result: - is_a: study result - description: >- - A result of a observed expected frequency analysis. - - relative frequency analysis result: - is_a: study result - description: >- - A result of a relative frequency analysis. - - text mining result: - is_a: study result - description: >- - A result of text mining. - - chi squared analysis result: - is_a: study result - description: >- - A result of a chi squared analysis. - - agent: - is_a: administrative entity - aliases: [ 'group' ] - description: >- - person, group, organization or project that provides - a piece of information (i.e. a knowledge association) - slots: - - affiliation - - address - exact_mappings: - - prov:Agent - - dct:Agent - narrow_mappings: - # Organization - - UMLSSG:ORGA - - STY:T092 - # Health Care Related Organization - - STY:T093 - # Professional Society - - STY:T094 - # Self-help or Relief Organization - - STY:T095 - # Group - - STY:T096 - slot_usage: - id: - required: true - description: >- - Different classes of agents have distinct preferred identifiers. - For publishers, use the ISBN publisher code. - See https://grp.isbn-international.org/ for publisher code lookups. - For editors, authors and individual providers, use the individual's - ORCID if available; Otherwise, a ScopusID, ResearchID or - Google Scholar ID ('GSID') may be used if the author ORCID is unknown. - Institutional agents could be identified by an - International Standard Name Identifier ('ISNI') code. - values_from: - # CURIE space for publishers - - isbn - # CURIE space for authors - - ORCID - - ScopusID - - ResearchID - - GSID - # Institutional agents - - isni - name: - description: >- - it is recommended that an author's 'name' property - be formatted as "surname, firstname initial." - id_prefixes: - - isbn - - ORCID - - ScopusID - - ResearchID - - GSID - - isni - - ## General Information Entities - - information content entity: - aliases: [ 'information', 'information artefact', 'information entity' ] - abstract: true - is_a: named thing - description: >- - a piece of information that typically describes - some topic of discourse or is used as support. - slots: - - license - - rights - - format - - creation date - id_prefixes: - - doi - exact_mappings: - - IAO:0000030 - narrow_mappings: - # UMLS Semantic Group "Concepts & Ideas" - - UMLSSG:CONC - # Conceptual Entity - - STY:T077 - # Idea or Concept - - STY:T078 - # Temporal Concept - - STY:T079 - # Qualitative Concept - - STY:T080 - # Quantitative Concept - - STY:T081 - # Spatial Concept - - STY:T082 - # Regulation or Law - - STY:T089 - # Group Attribute - - STY:T102 - # Functional Concept - - STY:T169 - # Language - - STY:T171 - # Classification - - STY:T185 - - dataset: - description: >- - an item that refers to a collection of data from a data source. - is_a: information content entity - exact_mappings: - - IAO:0000100 - - dctypes:Dataset - - schema:dataset - - dcid:Dataset - - dataset distribution: - is_a: information content entity - description: >- - an item that holds distribution level information about a dataset. - slots: - - distribution download url - exact_mappings: - - dcat:Distribution - - dataset version: - description: >- - an item that holds version level information about a dataset. - is_a: information content entity - slots: - - has dataset - - ingest date - - has distribution - - dataset summary: - description: >- - an item that holds summary level information about a dataset. - is_a: information content entity - slots: - - source web page - - source logo - - confidence level: - is_a: information content entity - description: >- - Level of confidence in a statement - values_from: - - cio - exact_mappings: - - CIO:0000028 - # statement confidence - - SEPIO:0000187 - close_mappings: - # assertion confidence levels - - SEPIO:0000167 - - evidence type: - is_a: information content entity - aliases: [ 'evidence code' ] - description: >- - Class of evidence that supports an association - values_from: - - eco - exact_mappings: - - ECO:0000000 - - information resource: - is_a: information content entity - aliases: [ 'knowledgebase' ] - description: >- - A database or knowledgebase and its supporting ecosystem of interfaces - and services that deliver content to consumers (e.g. web portals, APIs, - query endpoints, streaming services, data downloads, etc.). - A single Information Resource by this definition may span many different datasets or - databases, and include many access endpoints and user - interfaces. Information Resources include project-specific resources - such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb. - in_subset: - - translator_minimal - - - ## Publications - - # TODO: to review additional ontology relating to Publications, such as http://www.sparontologies.net/ontologies - publication: - is_a: information content entity - description: >- - Any published piece of information. Can refer to a whole publication, - its encompassing publication (i.e. journal or book) or to a part of a - publication, if of significant knowledge scope (e.g. a figure, figure - legend, or section highlighted by NLP). The scope is intended to be - general and include information published on the web, as well as printed - materials, either directly or in one of the Publication Biolink - category subclasses. - slots: - - authors - - pages - - summary - - keywords - - mesh terms - - xref - # In addition to embedded slots, instances of 'contributor association' - # may be used to more extensively document publisher, editor and author details - slot_usage: - id: - description: >- - Different kinds of publication subtypes will have different preferred - identifiers (curies when feasible). Precedence of identifiers for - scientific articles is as follows: PMID if available; DOI if not; actual - alternate CURIE otherwise. Enclosing publications (i.e. referenced by - 'published in' node property) such as books and journals, should have - industry-standard identifier such as from ISBN and ISSN. - name: - description: >- - the 'title' of the publication is generally recorded in the 'name' - property (inherited from NamedThing). The field name 'title' is now also - tagged as an acceptable alias for the node property 'name' (just in case). - publication type: - required: true - pages: - multivalued: true - description: >- - When a 2-tuple of page numbers are provided, they represent - the start and end page of the publication within its parent publication context. - For books, this may be set to the total number of pages of the book. - exact_mappings: - - IAO:0000311 - narrow_mappings: - - IAO:0000013 - # UMLS Semantic Type "Intellectual Product" - - STY:T170 - id_prefixes: - - NLMID - in_subset: - - model_organism_database - - book: - is_a: publication - description: >- - This class may rarely be instantiated except if use cases - of a given knowledge graph support its utility. - slot_usage: - id: - required: true - description: >- - Books should have industry-standard identifier such as from ISBN. - type: - description: >- - Should generally be set to an ontology class defined term for 'book'. - id_prefixes: - - isbn - - NLMID - in_subset: - - model_organism_database - - book chapter: - is_a: publication - slots: - - published in - - volume - - chapter - slot_usage: - published in: - required: true - description: >- - The enclosing parent book containing the chapter - should have industry-standard identifier from ISBN. - in_subset: - - model_organism_database - - serial: - aliases: [ 'journal' ] - is_a: publication - description: >- - This class may rarely be instantiated except if use cases - of a given knowledge graph support its utility. - slots: - - iso abbreviation - - volume - - issue - slot_usage: - id: - required: true - description: >- - Serials (journals) should have industry-standard identifier such as from ISSN. - type: - description: >- - Should generally be set to an ontology class defined term for 'serial' or 'journal'. - id_prefixes: - - issn - - NLMID - in_subset: - - model_organism_database - - article: - is_a: publication - slots: - - published in - - iso abbreviation - - volume - - issue - slot_usage: - published in: - required: true - description: >- - The enclosing parent serial containing the article should - have industry-standard identifier from ISSN. - iso abbreviation: - description: >- - Optional value, if used locally as a convenience, is set - to the iso abbreviation of the 'published in' parent. - id_prefixes: - # By inheritance, a DOI may be used as a publication identifier; there may be other relevant namespaces - - PMID - in_subset: - - model_organism_database - - ## Top Level Abstractions of Material & Process Entities - - physical essence or occurrent: - description: >- - Either a physical or processual entity. - mixin: true - - - physical essence: - description: >- - Semantic mixin concept. Pertains to entities that have - physical properties such as mass, volume, or charge. - is_a: physical essence or occurrent - mixin: true - - physical entity: - is_a: named thing - mixins: - - physical essence - description: >- - An entity that has material reality (a.k.a. physical essence). - exact_mappings: - # Physical Object - - STY:T072 - narrow_mappings: - # Manufactured Object - - STY:T073 - - occurrent: - description: >- - A processual entity. - # biolink:Occurrent is most consistently used as a mixin thus it should - # be declared as such and cannot inherit from the non-mixin biolink:NamedThing - is_a: physical essence or occurrent - mixin: true - exact_mappings: - - BFO:0000003 - - activity and behavior: - is_a: occurrent - mixin: true - description: >- - Activity or behavior of any independent integral living, - organization or mechanical actor in the world - exact_mappings: - # Activities & Behaviors - - UMLSSG:ACTI - - activity: - is_a: named thing - mixins: - - activity and behavior - description: >- - An activity is something that occurs over a period of time and acts upon - or with entities; it may include consuming, processing, transforming, - modifying, relocating, using, or generating entities. - exact_mappings: - - prov:Activity - - NCIT:C43431 - # Activity - - STY:T052 - narrow_mappings: - # Daily or Recreational Activity - - STY:T056 - # Occupational Activity - - STY:T057 - # Governmental or Regulatory Activity - - STY:T064 - # Machine Activity - - STY:T066 - # Research Activity - - STY:T062 - # Educational Activity - - STY:T065 - # Health Care Activity - - STY:T058 - - procedure: - is_a: named thing - mixins: - - activity and behavior - description: >- - A series of actions conducted in a certain order or manner - exact_mappings: - # Procedures - - UMLSSG:PROC - - dcid:MedicalProcedure - narrow_mappings: - # Laboratory Procedure - - STY:T059 - # Diagnostic Procedure - - STY:T060 - # Therapeutic or Preventive Procedure - - STY:T061 - # Molecular Biology Research Technique - - STY:T063 - id_prefixes: - - CPT - - phenomenon: - is_a: named thing - mixins: - - occurrent - description: >- - a fact or situation that is observed to exist or happen, - especially one whose cause or explanation is in question - broad_mappings: - # the inclusion of 'process' in the definition of these - # terms broadens them, relative to 'phenomenon' - # Phenomenon or Process - - STY:T067 - # Human-caused Phenomenon or Process - - STY:T068 - # Natural Phenomenon or Process - - STY:T070 - exact_mappings: - # Phenomena - - UMLSSG:PHEN - narrow_mappings: - # Laboratory or Test Result - - STY:T034 - # Biologic Function - - STY:T038 - # Environmental Effect of Humans - - STY:T069 - - device: - is_a: named thing - description: >- - A thing made or adapted for a particular purpose, especially - a piece of mechanical or electronic equipment - narrow_mappings: - # Devices - - UMLSSG:DEVI - # Medical Device - - STY:T074 - # Research Device - - STY:T075 - # Drug Delivery Device - - STY:T203 - # Biomedical or Dental Material - - STY:T122 - - ## Scientific Studies - - study population: - is_a: population of individual organisms - description: >- - A group of people banded together or treated as a group as participants in a research study. - close_mappings: - - WIKIDATA:Q7229825 - - subject of investigation: - mixin: true - description: >- - An entity that has the role of being studied in an investigation, study, or experiment - - material sample: - aliases: [ 'biospecimen', 'sample', 'biosample', 'physical sample' ] - is_a: physical entity - mixins: - - subject of investigation - description: >- - A sample is a limited quantity of something (e.g. an individual or set of individuals - from a population, or a portion of a substance) to be used for testing, analysis, - inspection, investigation, demonstration, or trial use. [SIO] - exact_mappings: - - OBI:0000747 - - SIO:001050 - id_prefixes: - - BIOSAMPLE - - GOLD.META - - ## Earth Sciences - - planetary entity: - is_a: named thing - description: >- - Any entity or process that exists at the level of the whole planet - - environmental process: - is_a: planetary entity - mixins: - - occurrent - exact_mappings: - - ENVO:02500000 - - environmental feature: - is_a: planetary entity - exact_mappings: - - ENVO:01000254 - - geographic location: - is_a: planetary entity - description: >- - a location that can be described in lat/long coordinates - slots: - - latitude - - longitude - exact_mappings: - # Geographic Areas - - UMLSSG:GEOG - # Geographic Area - - STY:T083 - - geographic location at time: - is_a: geographic location - description: >- - a location that can be described in lat/long coordinates, for a particular time - slots: - - timepoint - - ## Biological Sciences - - thing with taxon: - mixin: true - description: >- - A mixin that can be used on any entity that can be taxonomically classified. - This includes individual organisms; genes, their products and other molecular - entities; body parts; biological processes - slots: - - in taxon - - biological entity: - is_a: named thing - aliases: [ 'bioentity' ] - abstract: true - mixins: - - thing with taxon - narrow_mappings: - - WIKIDATA:Q28845870 - # UMLS Semantic Type "Experimental Model of Disease" - - STY:T050 - # SIO term is 'biological entity' but less inclusive than the Biolink scope - - SIO:010046 - - genomic entity: - mixin: true - slots: - - has biological sequence - in_subset: - - translator_minimal - narrow_mappings: - - STY:T028 # Gene or Genome - - GENO:0000897 # Genomic Entity - - epigenomic entity: - mixin: true - slots: - - has biological sequence - in_subset: - - translator_minimal - narrow_mappings: - - molecular entity: - is_a: chemical entity - description: >- - A molecular entity is a chemical entity composed of individual or - covalently bonded atoms. - slots: - - is metabolite - narrow_mappings: - - STY:T088 # Carbohydrate - - STY:T085 # Molecular Sequence - - CHEBI:23367 # Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, - # radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. - - bioschemas:MolecularEntity - in_subset: - - translator_minimal - id_prefixes: - - PUBCHEM.COMPOUND - - CHEMBL.COMPOUND - - UNII - - CHEBI - - DRUGBANK - - MESH - - CAS - - DrugCentral - - GTOPDB - - HMDB - - KEGG.COMPOUND - - ChemBank - - PUBCHEM.SUBSTANCE - - SIDER.DRUG - - INCHI - - INCHIKEY - # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry - # - SMILES # is not actually a CURIE namespace but only a query language for chemistry - - KEGG.GLYCAN ## G number - - KEGG.DRUG ## D number - - KEGG.DGROUP ## DG number - - KEGG.ENVIRON ## E number - - UMLS - - chemical entity: - is_a: named thing - mixins: - - physical essence - - chemical or drug or treatment # issue 701 - - chemical entity or gene or gene product - - chemical entity or protein or polypeptide - description: >- - A chemical entity is a physical entity that pertains to chemistry or - biochemistry. - slots: - - trade name - - available from - - max tolerated dose - - is toxic - - has chemical role - exact_mappings: - - CHEBI:24431 - - SIO:010004 # Chemical entity - - WIKIDATA:Q79529 # Chemical substance - - STY:T103 # Chemical - narrow_mappings: - - WIKIDATA:Q43460564 - - STY:T129 # (imft, full name: Immunologic Factor - in_subset: - - translator_minimal - id_prefixes: - - UNII - - CHEBI - - MESH - - CAS #CAS numbers are given for things like plant extracts as well. - - UMLS - - ncats.drug - - small molecule: - is_a: molecular entity - aliases: [ 'chemical substance' ] - description: >- - A small molecule entity is a molecular entity characterized by availability - in small-molecule databases of SMILES, InChI, IUPAC, or other - unambiguous representation of its precise chemical structure; for - convenience of representation, any valid chemical representation is - included, even if it is not strictly molecular (e.g., sodium ion). - narrow_mappings: - - STY:T196 # Element, Ion, or Isotope - - CHEBI:59999 - - bioschemas:ChemicalSubstance - - STY:T123 #(bacs, full name: Biologically Active Substance) - - STY:T131 #(hops, full name: Hazardous or Poisonous Substance) - - STY:T125 #(horm, full name: Hormone) - - STY:T197 #(inch, full name: Inorganic Chemical) - - STY:T109 #(orch, full name: Organic Chemical) - - STY:T118 #(carb, full name: Carbohydrate) - note that this term is missing from newer SRDEF files (depreciated?), but is still used by the SEMMEDDB data files) - - STY:T111 #(eico, full name: Eicosanoid) - same note as above - - STY:T119 #(lipd, full name: Lipid) - same note as above - - STY:T124 #(nsba, full name: Neuroreactive Substance or Biogenic Amine) - same note as above - - STY:T115 #(opco, full name: Organophosphorus Compound) - same note as above - - STY:T110 #(strd, full name: Steroid) - same note as above - - STY:T127 # vitamin - id_prefixes: - - PUBCHEM.COMPOUND - - CHEMBL.COMPOUND - - UNII - - CHEBI - - DRUGBANK - - MESH - - CAS - - DrugCentral - - GTOPDB - - HMDB - - KEGG.COMPOUND - - ChemBank - - PUBCHEM.SUBSTANCE - - SIDER.DRUG - - INCHI - - INCHIKEY - # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry - # - SMILES # is not actually a CURIE namespace but only a query language for chemistry - - KEGG.GLYCAN ## G number - - KEGG.DRUG ## D number - - KEGG.DGROUP ## DG number - - KEGG.ENVIRON ## E number - - BIGG.METABOLITE - - UMLS - - foodb.compound - slot_usage: - id: - examples: - - value: CHEBI:29101 - description: sodium ion - in_subset: - - model_organism_database - - translator_minimal - - - chemical mixture: - is_a: chemical entity - description: >- - A chemical mixture is a chemical entity composed of two or more - molecular entities. - slots: - - is supplement - - highest FDA approval status - - drug regulatory status world wide - - routes of delivery - in_subset: - - translator_minimal - id_prefixes: - - PUBCHEM.COMPOUND - - CHEMBL.COMPOUND - - UNII - - CHEBI - - DRUGBANK - - MESH - - CAS - - DrugCentral - - GTOPDB - - HMDB - - KEGG.COMPOUND - - ChemBank - - PUBCHEM.SUBSTANCE - - SIDER.DRUG - - INCHI - - INCHIKEY - # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry - # - SMILES # is not actually a CURIE namespace but only a query language for chemistry - - KEGG.GLYCAN ## G number - - KEGG.DRUG ## D number - - KEGG.DGROUP ## DG number - - KEGG.ENVIRON ## E number - - UMLS - close_mappings: - - dcid:ChemicalCompound - narrow_mappings: - - NCIT:C20401 # monoclonal antibody - - SNOMEDCT:49616005 # monoclonal antibody (substance) - - nucleic acid entity: - is_a: molecular entity - description: >- - A nucleic acid entity is a molecular entity characterized by - availability in gene databases of nucleotide-based sequence - representations of its precise sequence; for convenience of - representation, partial sequences of various kinds are included. - aliases: [ 'sequence feature', 'genomic entity' ] - mixins: - - genomic entity - - thing with taxon - - physical essence - - ontology class - exact_mappings: - - SO:0000110 - narrow_mappings: - - STY:T086 # Nucleotide Sequence - - STY:T114 # Nucleic Acid, Nucleoside, or Nucleotide - in_subset: - - model_organism_database - - translator_minimal - id_prefixes: - - PUBCHEM.COMPOUND - - CHEMBL.COMPOUND - - UNII - - CHEBI - - MESH - - CAS - - GTOPDB - - HMDB - - KEGG.COMPOUND - - ChemBank - - PUBCHEM.SUBSTANCE - - INCHI - - INCHIKEY - # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry - # - SMILES # is not actually a CURIE namespace but only a query language for chemistry - - KEGG.GLYCAN # G number - - KEGG.ENVIRON # E number - - molecular mixture: - is_a: chemical mixture - description: >- - A molecular mixture is a chemical mixture composed of two or more - molecular entities with known concentration and stoichiometry. - in_subset: - - translator_minimal - id_prefixes: - - PUBCHEM.COMPOUND - - CHEMBL.COMPOUND - - UNII - - CHEBI - - DRUGBANK - - MESH - - CAS - - DrugCentral - - GTOPDB - - HMDB - - KEGG.COMPOUND - - ChemBank - - PUBCHEM.SUBSTANCE - - SIDER.DRUG - - INCHI - - INCHIKEY - # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry - # - SMILES # is not actually a CURIE namespace but only a query language for chemistry - - KEGG.GLYCAN ## G number - - KEGG.DRUG ## D number - - KEGG.DGROUP ## DG number - - KEGG.ENVIRON ## E number - - UMLS - - ncats.drug - - complex molecular mixture: - is_a: chemical mixture - description: >- - A complex molecular mixture is a chemical mixture composed of two or - more molecular entities with unknown concentration and stoichiometry. - in_subset: - - translator_minimal - id_prefixes: - - PUBCHEM.COMPOUND - - CHEMBL.COMPOUND - - UNII - - CHEBI - - DRUGBANK - - MESH - - CAS - - DrugCentral - - GTOPDB - - HMDB - - KEGG.COMPOUND - - ChemBank - - PUBCHEM.SUBSTANCE - - SIDER.DRUG - - INCHI - - INCHIKEY - # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry - # - SMILES # is not actually a CURIE namespace but only a query language for chemistry - - KEGG.GLYCAN ## G number - - KEGG.DRUG ## D number - - KEGG.DGROUP ## DG number - - KEGG.ENVIRON ## E number - - UMLS - - biological process or activity: - description: >- - Either an individual molecular activity, or a collection of - causally connected molecular activities in a biological system. - is_a: biological entity - mixins: - - occurrent - - ontology class - id_prefixes: - - GO - - REACT - slots: - - has input - - has output - - enabled by - - molecular activity: - description: >- - An execution of a molecular function carried out by a - gene product or macromolecular complex. - is_a: biological process or activity - aliases: [ 'molecular function', 'molecular event', 'reaction' ] - mixins: - - occurrent - - ontology class - slot_usage: - has input: - range: molecular entity - description: >- - A chemical entity that is the input for the reaction - has output: - range: molecular entity - description: >- - A chemical entity that is the output for the reaction - enabled by: - range: macromolecular machine mixin - description: >- - The gene product, gene, or complex that catalyzes the reaction - exact_mappings: - - GO:0003674 - # UMLS Semantic Type "Molecular Function" - - STY:T044 - id_prefixes: - - GO - - REACT - - RHEA - - metacyc.reaction - - EC - - TCDB - - KEGG.REACTION ## R number - - KEGG.RCLASS ## RC number - - KEGG.ENZYME ## EC number - - KEGG.ORTHOLOGY ## in particular for gut microbiome use case in issue #888 - - UMLS - - BIGG.REACTION - - SEED.REACTION - - METANETX.REACTION - - biological process: - is_a: biological process or activity - mixins: - - occurrent - - ontology class - description: >- - One or more causally connected executions of molecular functions - exact_mappings: - - GO:0008150 - - SIO:000006 - - WIKIDATA:Q2996394 - broad_mappings: - - WIKIDATA:P682 - id_prefixes: - - GO - - REACT - - metacyc.reaction - - KEGG.MODULE ## M number - - pathway: - is_a: biological process - mixins: - - ontology class - exact_mappings: - - PW:0000001 - - WIKIDATA:Q4915012 - narrow_mappings: - - SIO:010526 - - GO:0007165 - id_prefixes: - - GO - - REACT - - KEGG - - SMPDB - - MSigDB - - PHARMGKB.PATHWAYS - - WIKIPATHWAYS - - FB # FlyBase FBgg* - - PANTHER.PATHWAY - - KEGG.PATHWAY - - ncats.bioplanet - - physiological process: - aliases: [ 'physiology' ] - is_a: biological process - mixins: - - ontology class - close_mappings: - exact_mappings: - # Physiologic Function - - STY:T039 - - WIKIDATA:Q30892994 - narrow_mappings: - # Organism Function - - STY:T040 - # Organ or Tissue Function - - STY:T042 - # Cell Function - - STY:T043 - # Genetic Function - - STY:T045 - id_prefixes: - - GO - - REACT - - behavior: - is_a: biological process - mixins: - - ontology class - - activity and behavior - exact_mappings: - - GO:0007610 - # Behavior - - STY:T053 - narrow_mappings: - # Mental Process - - STY:T041 - # Social Behavior - - STY:T054 - # Individual Behavior - - STY:T055 - - ## (Bio)chemistry - - processed material: - is_a: chemical mixture - description: >- - A chemical entity (often a mixture) processed - for consumption for nutritional, medical or technical use. - Is a material entity that is created or changed during material processing. - exact_mappings: - - OBI:0000047 - id_prefixes: - - UMLS - - drug: - is_a: molecular mixture - mixins: - - chemical or drug or treatment - - ontology class - description: >- - A substance intended for use in the diagnosis, cure, - mitigation, treatment, or prevention of disease - comments: - - The CHEBI ID represents a role rather than a substance - broad_mappings: - # Pharmacologic Substance: Any natural, endogenously-derived, - # synthetic or semi synthetic compound with pharmacologic activity. - - STY:T121 - exact_mappings: - - WIKIDATA:Q12140 - - CHEBI:23888 - # UMLS Semantic Type "Clinical Drug" - - STY:T200 - - dcid:Drug - narrow_mappings: - # Antibiotic - - STY:T195 - id_prefixes: - - ncats.drug - - RXCUI - - NDC - - UMLS - - ## Food - - environmental food contaminant: - is_a: chemical entity - related_mappings: - # substance role - - CHEBI:78299 - - food additive: - is_a: chemical entity - related_mappings: - # substance role - - CHEBI:64047 - - food: - is_a: chemical mixture - description: >- - A substance consumed by a living organism as a source of nutrition - id_prefixes: - - foodb.food - - FOODON - - UMLS - - NCIT - exact_mappings: - # Food - - STY:T168 - - ## Biology and Biomedical Sciences - - ## Biological Attributes - - organism attribute: - is_a: attribute - description: >- - describes a characteristic of an organismal entity. - exact_mappings: - # Organism Attribute - - STY:T032 - - phenotypic quality: - aliases: [ 'phenotypic properties' ] - is_a: organism attribute - description: >- - A property of a phenotype - examples: - - value: weight - - mappings: - - PATO:0000001 - - genetic inheritance: - aliases: [ 'inheritance' ] - is_a: biological entity - description: >- - The pattern or 'mode' in which a particular genetic trait or disorder is passed from one - generation to the next, e.g. autosomal dominant, autosomal recessive, etc. - exact_mappings: - - HP:0000005 - - GENO:0000141 - - NCIT:C45827 - close_mappings: - - STY:T045 - id_prefixes: - - HP - - GENO - - NCIT - - ## Biological Entities - - organismal entity: - description: >- - A named entity that is either a part of an organism, a whole organism, - population or clade of organisms, excluding chemical entities - abstract: true - is_a: biological entity - mixins: - - subject of investigation - slot_usage: - has attribute: - description: >- - may often be an organism attribute - exact_mappings: - - WIKIDATA:Q7239 - # UMLS Semantic Group "Living Beings" - # Several of the associated semantic types here are probably not - # that relevant to the Biolink world, but we keep them here for now. - - UMLSSG:LIVB - - CARO:0001010 - - virus: - is_a: organismal entity - mixins: - - subject of investigation - description: >- - A virus is a microorganism that replicates itself as a microRNA - and infects the host cell. - exact_mappings: - - NCBITaxon:10239 - - cellular organism: - is_a: organismal entity - mixins: - - subject of investigation - description: >- - exact_mappings: - - NCBITaxon:131567 - - life stage: - is_a: organismal entity - description: >- - A stage of development or growth of an organism, - including post-natal adult stages - exact_mappings: - - UBERON:0000105 - narrow_mappings: - # constrained to human life cycles - - HsapDv:0000000 - in_subset: - - model_organism_database - id_prefixes: - - HsapDv - - MmusDv - - ZFS - - FBdv - - WBls - - UBERON - - individual organism: - aliases: [ 'organism' ] - description: >- - An instance of an organism. For example, Richard Nixon, - Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576 - is_a: organismal entity - mixins: - - subject of investigation - exact_mappings: - - SIO:010000 - # Organism - - STY:T001 - narrow_mappings: - # Wikidata considers its definition of 'individual' to be constrained to human persons? - - WIKIDATA:Q795052 - - foaf:Person - id_prefixes: - - ORCID - - population of individual organisms: - description: >- - A collection of individuals from the same taxonomic class - distinguished by one or more characteristics. Characteristics can - include, but are not limited to, shared geographic location, genetics, - phenotypes. - local_names: - ga4gh: population - is_a: organismal entity - mixins: - - subject of investigation - exact_mappings: - - PCO:0000001 - - SIO:001061 - # UMLS Semantic Type "Population Group" - - STY:T098 - - OBI:0000181 - id_prefixes: - - HANCESTRO - in_subset: - - model_organism_database - - disease or phenotypic feature: - aliases: [ 'phenome' ] - is_a: biological entity - description: >- - Either one of a disease or an individual phenotypic feature. - Some knowledge resources such as Monarch treat these as - distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model - for their independent descriptions. This class is helpful to enforce domains and ranges - that may involve either a disease or a phenotypic feature. - union_of: - - disease - - phenotypic feature - narrow_mappings: - # UMLS Semantic Type "Finding" - more specialized use of 'disease or phenotypic feature' - - STY:T033 - - disease: - aliases: [ 'condition', 'disorder', 'medical condition' ] - description: >- - A disorder of structure or function, especially one that produces specific - signs, phenotypes or symptoms or that affects a specific location and is not simply a - direct result of physical injury. A disposition to undergo pathological processes that exists in an - organism because of one or more disorders in that organism. - is_a: disease or phenotypic feature - exact_mappings: - - MONDO:0000001 - - DOID:4 - - NCIT:C2991 - - WIKIDATA:Q12136 - - SIO:010299 - # UMLS Semantic Group "Disorders" - - UMLSSG:DISO - # Disease or Syndrome - - STY:T047 - - dcid:Disease - narrow_mappings: - # Congenital Abnormality - - STY:T019 - # Acquired Abnormality - - STY:T020 - # Mental or Behavioral Dysfunction - - STY:T048 - # Cell or Molecular Dysfunction - - STY:T049 - # Anatomical Abnormality - - STY:T190 - # Neoplastic Process - - STY:T191 - # disease susceptibility - - MONDO:0042489 - id_prefixes: - - MONDO - - DOID - - OMIM - - OMIM.PS - - orphanet - - EFO - - UMLS - - MESH - - MEDDRA - - NCIT - - SNOMEDCT - - medgen - - ICD10 - - ICD9 - - KEGG.DISEASE ## H number - - HP - - MP - in_subset: - - model_organism_database - - phenotypic feature: - aliases: [ 'sign', 'symptom', 'phenotype', 'trait', 'endophenotype' ] - is_a: disease or phenotypic feature - description: >- - A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an - individual resulting from the interaction of its genotype with its molecular and physical environment. - examples: - - value: MP:0001262 - description: decreased body weight - exact_mappings: - - UPHENO:0001001 - - SIO:010056 - - WIKIDATA:Q104053 - - UMLS:C4021819 - - NCIT:C16977 - - SNOMEDCT:8116006 # documented as phenotypic finding and phenotype, also referred to as "SCTID:8116006" at SNOMEDCT - - MESH:D010641 # phenotype - narrow_mappings: - - STY:T184 # Sign or Symptom - - WIKIDATA:Q169872 # Sign or Symptom - # presentation of a disease in clinical medicine - - WIKIDATA:Q25203551 - - ZP:00000000 # zebrafish phenotype - - FBcv:0001347 # fly phenotype - - HP:0000118 # human phenotype - - MP:0000001 # mouse phenotype - - WBPhenotype:0000886 # worm phenotype - - XPO:00000000 # frog phenotype - - FYPO:0000001 # fission yeast phenotype - - APO:0000017 # phenotype - - TO:0000387 # more narrowly defined here for plants; our definition conflates trait and phenotype. - broad_mappings: - - BFO:0000019 # quality - - PATO:0000001 # quality - id_prefixes: - - HP - - EFO # covered by BFO quality mapping - - NCIT - - UMLS - - MEDDRA # can not find a mapping - - MP - - ZP - - UPHENO - - APO - - FBcv - - WBPhenotype - - SNOMEDCT - - MESH - - XPO - - FYPO - - TO - in_subset: - - model_organism_database - - behavioral feature: - description: >- - A phenotypic feature which is behavioral in nature. - is_a: phenotypic feature - exact_mappings: - - NBO:0000243 - - anatomical entity: - is_a: organismal entity - mixins: - - physical essence - description: >- - A subcellular location, cell type or gross anatomical part - exact_mappings: - - UBERON:0001062 - - WIKIDATA:Q4936952 - # UMLS Semantic Group "Anatomy" - - UMLSSG:ANAT - # UMLS Semantic Type "Anatomical Structure" - - STY:T017 - - FMA:62955 # anatomical entity - - CARO:0000000 # anatomical entity - - SIO:001262 # anatomical entity - narrow_mappings: - - ZFA:0100000 # zebrafish anatomical entity - - FBbt:10000000 # fly anatomical entity - - EMAPA:0 # mouse anatomical entity - - MA:0000001 # mouse anatomical entity - - XAO:0000000 # frog anatomical entity - - WBbt:0000100 # c. elegans anatomical entity - - NCIT:C12219 # human anatomical entity - - GO:0110165 # cellular anatomical entity, also used directly in CL - related_mappings: - - SNOMEDCT:123037004 # body structure - id_prefixes: - - UBERON - - GO - - CL - - UMLS - - MESH - - NCIT - - EMAPA - - ZFA - - FBbt - - WBbt - in_subset: - - model_organism_database - - cellular component: - aliases: [ 'cell component', 'cell part' ] - is_a: anatomical entity - description: >- - A location in or around a cell - exact_mappings: - - GO:0005575 - - SIO:001400 - - WIKIDATA:Q5058355 - # Cell Component - - STY:T026 - broad_mappings: - - WIKIDATA:P681 - id_prefixes: - - GO - - MESH - - UMLS - - NCIT - - SNOMEDCT - - CL - - UBERON - - cell: - is_a: anatomical entity - exact_mappings: - - GO:0005623 - - CL:0000000 - - SIO:010001 - - WIKIDATA:Q7868 - # UMLS Semantic Type "Cell" - - STY:T025 - - MESH:D002477 # cells - id_prefixes: - - CL - - PO - - UMLS - - NCIT - - MESH - - UBERON - - SNOMEDCT - - MESH - - cell line: - is_a: organismal entity - mixins: - - subject of investigation - exact_mappings: - - CLO:0000031 - id_prefixes: - - CLO - - gross anatomical structure: - aliases: [ 'tissue', 'organ' ] - is_a: anatomical entity - exact_mappings: - - UBERON:0010000 - - WIKIDATA:Q4936952 - narrow_mappings: - # UMLS Semantic Type "Body Part, Organ, or Organ Component" - - STY:T023 - # UMLS Semantic Type "Tissue" - - STY:T024 - # Embryonic Structure - - STY:T018 - id_prefixes: - - UBERON - - UMLS - - MESH - - NCIT - - PO - - FAO - - - ## entity mixins - - chemical entity or gene or gene product: - description: >- - A union of chemical entities and children, and gene or gene product. - This mixin is helpful to use when searching across - chemical entities that must include genes and their children as chemical entities. - mixin: true - - chemical entity or protein or polypeptide: - description: >- - A union of chemical entities and children, and protein and polypeptide. - This mixin is helpful to use when searching across - chemical entities that must include genes and their children as chemical entities. - mixin: true - - macromolecular machine mixin: - description: >- - A union of gene locus, gene product, and macromolecular complex. These are - the basic units of function in a cell. They either carry out individual - biological activities, or they encode molecules which do this. - mixin: true - slots: - - name - slot_usage: - name: - range: symbol type - description: >- - genes are typically designated by a short symbol and a full name. - We map the symbol to the default display name - and use an additional slot for full name - - gene or gene product: - description: >- - A union of gene loci or gene products. - Frequently an identifier for one will be used as proxy for another - is_a: macromolecular machine mixin - mixin: true - id_prefixes: - - CHEMBL.TARGET - - IUPHAR.FAMILY - - gene: - description: >- - A region (or regions) that includes all of the sequence elements - necessary to encode a functional transcript. A gene locus may include - regulatory regions, transcribed regions and/or other - functional sequence regions. - is_a: biological entity - mixins: - - gene or gene product - - genomic entity - - chemical entity or gene or gene product - - physical essence - - ontology class - slots: - - symbol - - synonym - - xref - exact_mappings: - - SO:0000704 - - SIO:010035 - - WIKIDATA:Q7187 - - dcid:Gene - id_prefixes: - - NCBIGene - - ENSEMBL - - HGNC - - MGI - - ZFIN - - dictyBase - - WB - - WormBase # we have two prefixes here as wormbase supports WormBase:WBGene00000898 - # and alliancegenome.org and identifiers.org supports WB:WBGene00000898. - - FB - - RGD - - SGD - - PomBase - - OMIM - - KEGG.GENE ## org:gene - - UMLS - - Xenbase - - AspGD - in_subset: - - translator_minimal - - model_organism_database - narrow_mappings: - - bioschemas:Gene - broad_mappings: - - NCIT:C45822 - - - gene product mixin: - description: >- - The functional molecular product of a single gene locus. - Gene products are either proteins or functional RNA molecules. - is_a: gene or gene product - mixin: true - slots: - - synonym - - xref - exact_mappings: - - WIKIDATA:Q424689 - - GENO:0000907 - - NCIT:C26548 - id_prefixes: - - UniProtKB - - gtpo - - PR - - gene product isoform mixin: - description: >- - This is an abstract class that can be mixed in with different kinds of - gene products to indicate that the gene product is intended to represent - a specific isoform rather than a canonical or reference or generic - product. The designation of canonical or reference may be arbitrary, - or it may represent the superclass of all isoforms. - is_a: gene product mixin - mixin: true - - macromolecular complex: - description: >- - A stable assembly of two or more macromolecules, i.e. proteins, - nucleic acids, carbohydrates or lipids, in which at least one - component is a protein and the constituent parts function together. - is_a: biological entity - mixins: - - macromolecular machine mixin - exact_mappings: - - GO:0032991 - - WIKIDATA:Q22325163 - id_prefixes: - - INTACT - - GO - - PR - - REACT - - ComplexPortal - in_subset: - - model_organism_database - - ## Genomic Classes - nucleosome modification: - is_a: biological entity - description: >- - A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. - e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A. - mixins: - - gene product isoform mixin - - genomic entity - - epigenomic entity - - genome: - is_a: biological entity - mixins: - - genomic entity - - physical essence - - ontology class - description: >- - A genome is the sum of genetic material within a cell or virion. - exact_mappings: - - SO:0001026 - - SIO:000984 - - WIKIDATA:Q7020 - close_mappings: - - dcid:GenomeAssemblyUnit - in_subset: - - model_organism_database - - exon: - is_a: nucleic acid entity - description: >- - A region of the transcript sequence within a gene which is not - removed from the primary RNA transcript by RNA splicing. - exact_mappings: - - SO:0000147 - - SIO:010445 - - WIKIDATA:Q373027 - - transcript: - is_a: nucleic acid entity - description: >- - An RNA synthesized on a DNA or RNA template by an RNA polymerase. - exact_mappings: - - SO:0000673 - - SIO:010450 - - WIKIDATA:Q7243183 - - dcid:RNATranscript - id_prefixes: - - ENSEMBL # ENSEMBL:ENST for human - - FB # FlyBase:FBtr - in_subset: - - model_organism_database - - coding sequence: - is_a: nucleic acid entity - exact_mappings: - - SO:0000316 - - SIO:001390 - - polypeptide: - aliases: [ 'amino acid entity' ] - is_a: biological entity - description: >- - A polypeptide is a molecular entity characterized by availability - in protein databases of amino-acid-based sequence representations - of its precise primary structure; for convenience of representation, - partial sequences of various kinds are included, even if they do not - represent a physical molecule. - mixins: - - chemical entity or gene or gene product - - chemical entity or protein or polypeptide - id_prefixes: - - UniProtKB - - PR - - ENSEMBL # ENSEMBL:ENSP* - - FB # FlyBase FBpp* - - UMLS - in_subset: - - model_organism_database - narrow_mappings: - - SO:0000104 # polypeptide defined in SO conflates protein and polypeptide - # Amino Acid, Peptide, or Protein - - STY:T116 - # Amino Acid Sequence - - STY:T087 - - protein: - description: >- - A gene product that is composed of a chain of amino acid sequences - and is produced by ribosome-mediated translation of mRNA - is_a: polypeptide - mixins: - - gene product mixin - id_prefixes: - - UniProtKB - - PR - - ENSEMBL # ENSEMBL:ENSP* - - FB # FlyBase FBpp* - - UMLS - - MESH - - ncats.drug - broad_mappings: - - bioschemas:Protein - exact_mappings: - - PR:000000001 - - SIO:010043 - - WIKIDATA:Q8054 - narrow_mappings: - # Enzyme - - STY:T126 - # Receptor - - STY:T192 - - protein isoform: - aliases: [ 'proteoform' ] - is_a: protein - description: >- - Represents a protein that is a specific isoform of the canonical or - reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/ - mixins: - - gene product isoform mixin - id_prefixes: - - UniProtKB # UniProtKB:([A-Z0-9]+-\d+) - - UNIPROT.ISOFORM - - PR - - ENSEMBL - - protein domain: - is_a: biological entity - description: >- - A conserved part of protein sequence and (tertiary) structure that can evolve, - function, and exist independently of the rest of the protein chain. - Protein domains maintain their structure and function independently of the proteins in which they are found. - e.g. an SH3 domain. - mixins: - - gene grouping mixin - - chemical entity or gene or gene product - exact_mappings: - - NCIT:C13379 - - SIO:001379 - - UMLS:C1514562 - - posttranslational modification: - is_a: biological entity - description: >- - A chemical modification of a polypeptide or protein that occurs after translation. - e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, - protein ubiquitination. - mixins: - - gene product isoform mixin - - protein family: - is_a: biological entity - exact_mappings: - - NCIT:C26004 - - WIKIDATA:Q2278983 - narrow_mappings: - - SIO:001380 - - NCIT:C20130 - - WIKIDATA:Q417841 - mixins: - - gene grouping mixin - - chemical entity or gene or gene product - - nucleic acid sequence motif: - aliases: [ 'consensus sequence' ] - is_a: biological entity - description: >- - A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, - a biological significance. e.g. the TATA box promoter motif, transcription factor binding - consensus sequences. - - RNA product: - is_a: transcript - mixins: - - gene product mixin - exact_mappings: - - CHEBI:33697 - # This SIO term here also mapped to 'biolink:Transcript'; however, - # since this 'biolink:RNAProduct' relates more to the biochemical - # essence of RNA, then map the SIO term instead to 'biolink:Transcript' - # - SIO:010450 - - WIKIDATA:Q11053 - id_prefixes: - - RNACENTRAL - - RNA product isoform: - is_a: RNA product - description: >- - Represents a protein that is a specific isoform of the canonical or reference RNA - mixins: - - gene product isoform mixin - id_prefixes: - - RNACENTRAL - - noncoding RNA product: - is_a: RNA product - id_prefixes: - - RNACENTRAL - - NCBIGene - - ENSEMBL - exact_mappings: - - SO:0000655 - - SIO:001235 - - microRNA: - is_a: noncoding RNA product - exact_mappings: - - SO:0000276 - - SIO:001397 - - WIKIDATA:Q310899 - id_prefixes: - - MIR - - HGNC - - WormBase - in_subset: - - model_organism_database - - siRNA: - aliases: [ 'small interfering RNA', 'RNAi' ] - description: >- - A small RNA molecule that is the product of a longer exogenous or - endogenous dsRNA, which is either a bimolecular duplex or very long - hairpin, processed (via the Dicer pathway) such that numerous siRNAs - accumulate from both strands of the dsRNA. SRNAs trigger the cleavage - of their target molecules. - is_a: noncoding RNA product - exact_mappings: - - SO:0000646 - - WIKIDATA:Q203221 - id_prefixes: - - MIR - - HGNC - - WormBase - in_subset: - - model_organism_database - - gene grouping mixin: - description: >- - any grouping of multiple genes or gene products - mixin: true - slots: - - has gene or gene product - - gene family: - aliases: [ 'orthogroup', 'protein family' ] - is_a: biological entity - exact_mappings: - - NCIT:C26004 - - WIKIDATA:Q2278983 - narrow_mappings: - # These term definitions focus only on proteins; - # the 'biolink:GeneFamily' term would be more inclusive - # to describe gene loci, non-coding RNA, etc. - - SIO:001380 - - NCIT:C20130 - - WIKIDATA:Q417841 - mixins: - - gene grouping mixin - - chemical entity or gene or gene product - description: >- - any grouping of multiple genes or gene products related by common descent - id_prefixes: - - PANTHER.FAMILY - - HGNC.FAMILY - - FB # FlyBase FBgg* - - interpro # note: may be better to introduce a protein domain/family - - CATH - - CDD - - HAMAP - - PFAM - - PIRSF - - PRINTS - - PRODOM - - PROSITE - - SMART - - SUPFAM - - TIGRFAM - - CATH.SUPERFAMILY - - RFAM ## RNAs only - - KEGG.ORTHOLOGY ## aka KEGG.KO: K number - - EGGNOG - - COG - in_subset: - - model_organism_database - - zygosity: - is_a: attribute - exact_mappings: - - GENO:0000133 - - genotype: - is_a: biological entity - mixins: - - physical essence - - genomic entity - - ontology class - description: >- - An information content entity that describes a genome by specifying the - total variation in genomic sequence and/or gene expression, relative to - some established background - comments: - - Consider renaming as genotypic entity - slots: - - has zygosity - exact_mappings: - - GENO:0000536 - - SIO:001079 - id_prefixes: - - ZFIN - - FB # FlyBase FBba* - in_subset: - - model_organism_database - - haplotype: - is_a: biological entity - mixins: - - genomic entity - - physical essence - - ontology class - description: >- - A set of zero or more Alleles on a single instance of a Sequence[VMC] - # slots: - # - completeness - exact_mappings: - - GENO:0000871 - - SO:0001024 - - VMC:Haplotype - - sequence variant: - aliases: [ 'allele' ] - local_names: - agr: allele - is_a: biological entity - mixins: - - genomic entity - - physical essence - - ontology class - description: >- - A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. - comments: - - This class is for modeling the specific state at a locus. - A single DBSNP rs ID could correspond to more than one sequence variants - (e.g CIViC:1252 and CIViC:1253, two distinct BRCA2 alleles for rs28897743) - exact_mappings: - # slightly broader semantics than SO:0001059 - 'sequence alteration' - # describes a sequence feature that may have 1..* sequence alterations - - WIKIDATA:Q15304597 - close_mappings: - - dcid:Allele - - SO:0001060 - - VMC:Allele - - GENO:0000002 - - SIO:010277 - - SO:0001060 - id_prefixes: - - CAID # ClinGen Allele Registry - - CLINVAR - - WIKIDATA - # - CIViC needs IRI mapping - - DBSNP - - MGI - - ZFIN - - FB - - RGD - - AGRKB - - SPDI - - WB - - WormBase - alt_descriptions: - AGR: >- - An entity that describes a single affected, endogenous allele. - These can be of any type that matches that definition - VMC: >- - A contiguous change at a Location - slots: - - has gene - slot_usage: - has gene: - multivalued: true - description: Each allele can be associated with any number of genes - has biological sequence: - description: >- - The state of the sequence w.r.t a reference sequence - id: - examples: - - value: ZFIN:ZDB-ALT-980203-1091 - description: ti282a allele from ZFIN - - value: CLINVAR:17681 - description: NM_007294.3(BRCA1):c.2521C>T (p.Arg841Trp) - in_subset: - - model_organism_database - - snv: - aliases: [ 'single nucleotide variant', 'single nucleotide polymorphism', 'snp' ] - is_a: sequence variant - description: >- - SNVs are single nucleotide positions in genomic DNA at - which different sequence alternatives exist - exact_mappings: - - SO:0001483 - - reagent targeted gene: - aliases: [ 'sequence targeting reagent' ] - is_a: biological entity - description: >- - A gene altered in its expression level in the context of some - experiment as a result of being targeted by gene-knockdown - reagent(s) such as a morpholino or RNAi. - mixins: - - genomic entity - - physical essence - - ontology class - exact_mappings: - - GENO:0000504 - in_subset: - - model_organism_database - - ## -------------------- - ## Clinical - ## Attributes, Cohort, - ## Exposures & Outcomes - ## -------------------- - - ## Clinical Attributes - - clinical attribute: - is_a: attribute - description: >- - Attributes relating to a clinical manifestation - exact_mappings: - # Clinical Attribute - - STY:T201 - - clinical measurement: - is_a: clinical attribute - description: >- - A clinical measurement is a special kind of attribute which results - from a laboratory observation from a subject individual or sample. - Measurements can be connected to their subject by the 'has attribute' slot. - slot_usage: - has attribute type: - required: true - multivalued: false - values_from: - - EFO - - LOINC - exact_mappings: - - EFO:0001444 - - clinical modifier: - is_a: clinical attribute - description: >- - Used to characterize and specify the phenotypic abnormalities - defined in the phenotypic abnormality sub-ontology, with respect - to severity, laterality, and other aspects - exact_mappings: - - - clinical course: - is_a: clinical attribute - description: >- - The course a disease typically takes from its onset, progression in time, and - eventual resolution or death of the affected individual - exact_mappings: - - HP:0031797 - - onset: - is_a: clinical course - description: >- - The age group in which (disease) symptom manifestations appear - exact_mappings: - - HP:0003674 - - clinical entity: - is_a: named thing - description: >- - Any entity or process that exists in the clinical domain and outside the - biological realm. Diseases are placed under biological entities - - clinical trial: - is_a: clinical entity - - clinical intervention: - is_a: clinical entity - - clinical finding: - is_a: phenotypic feature - description: >- - this category is currently considered broad enough to tag clinical lab - measurements and other biological attributes taken as 'clinical traits' - with some statistical score, for example, a p value in genetic associations. - slot_usage: - has attribute: - range: clinical attribute - id_prefixes: - - LOINC - - NCIT - - EFO - - hospitalization: - is_a: clinical intervention - exact_mappings: - - SNOMEDCT:32485007 - - WIKIDATA:Q3140971 - - socioeconomic attribute: - is_a: attribute - description: >- - Attributes relating to a socioeconomic manifestation - #slot_usage: - # need a suitable qualifying socioeconomic ontology target here? - # Perhaps some subset of ECTO: https://github.com/EnvironmentOntology/environmental-exposure-ontology - # has attribute type: - # range: socioeconomic ontology - # exact_mappings: - # - ?? - - ## Cohorts - - case: - aliases: [ 'patient', 'proband' ] - is_a: individual organism - description: >- - An individual (human) organism that has a patient role in some clinical context. - mixins: - - subject of investigation - - cohort: - is_a: study population - description: >- - A group of people banded together or treated as a group who share common characteristics. - A cohort 'study' is a particular form of longitudinal study that samples a cohort, - performing a cross-section at intervals through time. - mixins: - - subject of investigation - exact_mappings: - - WIKIDATA:Q1303415 - narrow_mappings: - # Professional or Occupational Group - - STY:T097 - # Family Group - - STY:T099 - # Age Group - - STY:T100 - # Patient or Disabled Group - - STY:T101 - - ## Exposures - - exposure event: - is_a: ontology class - aliases: [ 'exposure', 'experimental condition' ] - mixin: true - slots: - - timepoint - description: >- - A (possibly time bounded) incidence of a feature of the environment of an organism that - influences one or more phenotypic features of that organism, potentially mediated by genes - exact_mappings: - - XCO:0000000 - in_subset: - - model_organism_database - - # TODO - confirm that genomic backgrounds are exposures - genomic background exposure: - is_a: attribute - mixins: - - exposure event - - gene grouping mixin - - physical essence - - genomic entity - - thing with taxon - - ontology class - description: >- - A genomic background exposure is where an individual's specific genomic background - of genes, sequence variants or other pre-existing genomic conditions constitute - a kind of 'exposure' to the organism, leading to or influencing an outcome. - - pathological entity mixin: - description: >- - A pathological (abnormal) structure or process. - mixin: true - exact_mappings: - - MPATH:0 - narrow_mappings: - - HP:0000118 - - pathological process: - description: >- - A biologic function or a process having an abnormal or deleterious - effect at the subcellular, cellular, multicellular, or organismal level. - is_a: biological process - mixins: - - pathological entity mixin - exact_mappings: - - OBI:1110122 - - NCIT:C16956 - narrow_mappings: - # metastasis - - NCIT:C19151 - - EFO:0009708 - - STY:T046 - - STY:T037 - - pathological process exposure: - is_a: attribute - mixins: - - exposure event - description: >- - A pathological process, when viewed as an exposure, representing - a precondition, leading to or influencing an outcome, - e.g. autoimmunity leading to disease. - - pathological anatomical structure: - description: >- - An anatomical structure with the potential of have an abnormal or deleterious - effect at the subcellular, cellular, multicellular, or organismal level. - is_a: anatomical entity - mixins: - - pathological entity mixin - - pathological anatomical exposure: - is_a: attribute - mixins: - - exposure event - description: >- - An abnormal anatomical structure, when viewed as an exposure, - representing an precondition, leading to or influencing an outcome, - e.g. thrombosis leading to an ischemic disease outcome. - - disease or phenotypic feature exposure: - is_a: attribute - mixins: - - exposure event - - pathological entity mixin - description: >- - A disease or phenotypic feature state, when viewed as an exposure, - represents an precondition, leading to or influencing an outcome, - e.g. HIV predisposing an individual to infections; a relative deficiency - of skin pigmentation predisposing an individual to skin cancer. - - chemical exposure: - is_a: attribute - mixins: - - exposure event - slots: - - has quantitative value - description: >- - A chemical exposure is an intake of a particular - chemical entity. - exact_mappings: - # this ECTO term is not visibly defined but - # the 9000000-series identifiers seems to be the - # numeric space of chemical exposure definitions - - ECTO:9000000 - - SIO:001399 - - complex chemical exposure: - is_a: attribute - description: >- - A complex chemical exposure is an intake of a chemical - mixture (e.g. gasoline), other than a drug. - - drug exposure: - is_a: chemical exposure - aliases: [ 'drug intake', 'drug dose', 'medication intake' ] - description: >- - A drug exposure is an intake of a particular drug. - mixins: - - exposure event - broad_mappings: - # slightly broader than just drug effects on a biological system - - SIO:001005 - exact_mappings: - - ECTO:0000509 - - # TODO: deprecate? - drug to gene interaction exposure: - description: >- - drug to gene interaction exposure is a drug exposure is where the - interactions of the drug with specific genes are known to constitute - an 'exposure' to the organism, leading to or influencing an outcome. - is_a: drug exposure - mixins: - - gene grouping mixin - - treatment: - aliases: [ 'medical action', 'medical intervention' ] - # 'named thing' seems too generic here but not sure what applies better here - is_a: named thing - mixins: - - exposure event - - chemical or drug or treatment - description: >- - A treatment is targeted at a disease or phenotype and may involve - multiple drug 'exposures', medical devices and/or procedures - slots: - - has drug - - has device - - has procedure - exact_mappings: - - OGMS:0000090 - - SIO:001398 - broad_mappings: - - MAXO:0000058 - - biotic exposure: - is_a: attribute - aliases: [ 'viral exposure', 'bacterial exposure' ] - mixins: - - exposure event - description: >- - An external biotic exposure is an intake of (sometimes pathological) - biological organisms (including viruses). - - geographic exposure: - is_a: environmental exposure - mixins: - - exposure event - description: >- - A geographic exposure is a factor relating to geographic - proximity to some impactful entity. - close_mappings: - - dcid:GeologicalEvent - narrow_mappings: - - dcid:IceStoremEvent - - dcid:LakeEffectSnowEvent - - dcid:LandslideEvent - - dcid:MarineDenseFogEvent - - dcid:MarineLighteningEvent - - dcid:MarineStrongWindEvent - - dcid:MarineThunderstormWindEvent - - dcid:StormEvent - - dcid:StormSurgeTideEvent - - dcid:StrongWindEvent - - dcid:ThunderstormWindEvent - - dcid:TornadoEvent - - dcid:TropicalDepressionEvent - - dcid:WinterStoremEvent - - environmental exposure: - is_a: attribute - mixins: - - exposure event - description: >- - A environmental exposure is a factor relating to abiotic processes - in the environment including sunlight (UV-B), atmospheric (heat, - cold, general pollution) and water-born contaminants. - - behavioral exposure: - is_a: attribute - mixins: - - exposure event - description: >- - A behavioral exposure is a factor relating to behavior impacting an individual. - - socioeconomic exposure: - is_a: attribute - mixins: - - exposure event - description: >- - A socioeconomic exposure is a factor relating to social and - financial status of an affected individual (e.g. poverty). - slot_usage: - has attribute: - range: socioeconomic attribute - required: true - - ## Outcomes - - outcome: - mixin: true - description: >- - An entity that has the role of being the consequence of an exposure event. - This is an abstract mixin grouping of various categories of possible - biological or non-biological (e.g. clinical) outcomes. - - pathological process outcome: - mixins: - - outcome - description: >- - An outcome resulting from an exposure event which - is the manifestation of a pathological process. - - pathological anatomical outcome: - mixins: - - outcome - description: >- - An outcome resulting from an exposure event which - is the manifestation of an abnormal anatomical structure. - - disease or phenotypic feature outcome: - mixins: - - outcome - description: >- - Physiological outcomes resulting from an exposure event which - is the manifestation of a disease or other characteristic phenotype. - - behavioral outcome: - mixins: - - outcome - description: >- - An outcome resulting from an exposure event which is - the manifestation of human behavior. - - hospitalization outcome: - mixins: - - outcome - description: >- - An outcome resulting from an exposure event which is - the increased manifestation of acute (e.g. emergency - room visit) or chronic (inpatient) hospitalization. - - mortality outcome: - mixins: - - outcome - description: >- - An outcome of death from resulting from an exposure event. - - epidemiological outcome: - mixins: - - outcome - description: >- - An epidemiological outcome, such as societal disease - burden, resulting from an exposure event. - related_mappings: - - NCIT:C19291 - - socioeconomic outcome: - mixins: - - outcome - description: >- - An general social or economic outcome, such as - healthcare costs, utilization, etc., resulting from an exposure event - - ## ------------ - ## ASSOCIATIONS - ## ------------ - - association: - is_a: entity - description: >- - A typed association between two entities, supported by evidence - comments: - - This is roughly the model used by biolink and ontobio at the moment - slots: - - subject - - predicate - - object - - negated - - qualifiers - - publications - - has evidence - - knowledge source - - primary knowledge source - - aggregator knowledge source - - timepoint - - original subject - - original predicate - - original object - slot_usage: - type: - description: rdf:type of biolink:Association should be fixed at rdf:Statement - category: - range: category type - required: false - exact_mappings: - - OBAN:association - - rdf:Statement - - owl:Axiom - - - chemical entity assesses named thing association: - is_a: association - slot_usage: - subject: - range: chemical entity - object: - range: named thing - predicate: - subproperty_of: assesses - - - contributor association: - is_a: association - defining_slots: - - subject - - predicate - - object - description: >- - Any association between an entity (such as a publication) - and various agents that contribute to its realisation - slot_usage: - subject: - range: information content entity - description: >- - information content entity which an agent has helped realise - predicate: - subproperty_of: contributor - description: >- - generally one of the predicate values 'provider', 'publisher', 'editor' or 'author' - object: - range: agent - description: >- - agent helping to realise the given entity (e.g. such as a publication) - qualifiers: - description: >- - this field can be used to annotate special characteristics of an - agent relationship, such as the fact that a given author agent of - a publication is the 'corresponding author' - - genotype to genotype part association: - is_a: association - defining_slots: - - subject - - object - description: >- - Any association between one genotype and a genotypic entity that is a sub-component of it - slot_usage: - predicate: - subproperty_of: has variant part - subject: - range: genotype - description: >- - parent genotype - object: - range: genotype - description: >- - child genotype - - genotype to gene association: - description: >- - Any association between a genotype and a gene. - The genotype have have multiple variants in that gene or a single one. - There is no assumption of cardinality - is_a: association - defining_slots: - - subject - - object - slot_usage: - predicate: - description: >- - the relationship type used to connect genotype to gene - subject: - range: genotype - description: >- - parent genotype - object: - range: gene - description: >- - gene implicated in genotype - - genotype to variant association: - description: >- - Any association between a genotype and a sequence variant. - is_a: association - defining_slots: - - subject - - object - slot_usage: - predicate: - description: >- - the relationship type used to connect genotype to gene - subject: - range: genotype - description: >- - parent genotype - object: - range: sequence variant - description: >- - gene implicated in genotype - - gene to gene association: - aliases: [ 'molecular or genetic interaction' ] - description: >- - abstract parent class for different kinds of gene-gene or gene product - to gene product relationships. Includes homology and interaction. - abstract: true - is_a: association - defining_slots: - - subject - - object - slot_usage: - subject: - range: gene or gene product - description: >- - the subject gene in the association. If the relation is symmetric, - subject vs object is arbitrary. We allow a gene product to stand - as a proxy for the gene or vice versa. - object: - range: gene or gene product - description: >- - the object gene in the association. If the relation is symmetric, - subject vs object is arbitrary. We allow a gene product to stand - as a proxy for the gene or vice versa. - - gene to gene homology association: - description: >- - A homology association between two genes. May be orthology (in which - case the species of subject and object should differ) or paralogy - (in which case the species may be the same) - is_a: gene to gene association - defining_slots: - - subject - - predicate - - object - slot_usage: - subject: - range: gene or gene product - predicate: - subproperty_of: homologous to - symmetric: true - description: >- - homology relationship type - object: - range: gene or gene product - - gene to gene family association: - description: >- - Set membership of a gene in a family of genes related by common - evolutionary ancestry usually inferred by sequence comparisons. - The genes in a given family generally share common sequence motifs which - generally map onto shared gene product structure-function relationships. - is_a: association - defining_slots: - - subject - - predicate - - object - slot_usage: - subject: - range: gene - object: - range: gene family - predicate: - subproperty_of: member of - symmetric: false - description: >- - membership of the gene in the given gene family. - - gene expression mixin: - description: >- - Observed gene expression intensity, context (site, stage) and - associated phenotypic status within which the expression occurs. - mixin: true - slots: - - quantifier qualifier - - expression site - - stage qualifier - - phenotypic state - slot_usage: - quantifier qualifier: - description: >- - Optional quantitative value indicating degree of expression. - - gene to gene coexpression association: - description: >- - Indicates that two genes are co-expressed, - generally under the same conditions. - is_a: gene to gene association - defining_slots: - - subject - - predicate - - object - mixins: - - gene expression mixin - slot_usage: - predicate: - subproperty_of: coexpressed with - symmetric: true - - pairwise gene to gene interaction: - description: >- - An interaction between two genes or two gene products. - May be physical (e.g. protein binding) or genetic (between genes). - May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation) - is_a: gene to gene association - defining_slots: - - subject - - predicate - - object - slot_usage: - predicate: - subproperty_of: interacts with - symmetric: true - description: "interaction relationship type" - narrow_mappings: - - dcid:ProteinProteinInteraction - - pairwise molecular interaction: - description: >- - An interaction at the molecular level between two physical entities - is_a: pairwise gene to gene interaction - slots: - - interacting molecules category - defining_slots: - - subject - - predicate - - object - slot_usage: - subject: - range: molecular entity - id: - description: >- - identifier for the interaction. This may come from an interaction database such as IMEX. - examples: - - value: WB:WBInteraction000538741 - values_from: - - IMEX - - BioGRID - predicate: - subproperty_of: interacts with - description: "interaction relationship type" - examples: - - value: RO:0002447 - description: the subject molecular phosphorylates the object molecule - object: - range: molecular entity - - cell line to entity association mixin: - description: >- - An relationship between a cell line and another entity - mixin: true - defining_slots: - - subject - slot_usage: - subject: - range: cell line - - # TODO: figure out what gives with subject range - cell line to disease or phenotypic feature association: - is_a: association - mixins: - - cell line to entity association mixin - - entity to disease or phenotypic feature association mixin - description: >- - An relationship between a cell line and a disease or a phenotype, where - the cell line is derived from an individual with that disease or phenotype. - slot_usage: - subject: - # - range: cell line - # - range: disease or phenotypic feature - range: disease or phenotypic feature - - chemical entity to entity association mixin: - description: >- - An interaction between a chemical entity and another entity - mixin: true - defining_slots: - - subject - slot_usage: - subject: - range: chemical entity or gene or gene product - description: "the chemical entity that is an interactor" - - drug to entity association mixin: - description: >- - An interaction between a drug and another entity - is_a: chemical entity to entity association mixin - mixin: true - defining_slots: - - subject - slot_usage: - subject: - range: drug - description: "the drug that is an interactor" - - chemical to entity association mixin: - description: >- - An interaction between a chemical entity and another entity - is_a: chemical entity to entity association mixin - mixin: true - defining_slots: - - subject - slot_usage: - subject: - range: chemical entity or gene or gene product - description: "the chemical entity or entity that is an interactor" - - case to entity association mixin: - description: >- - An abstract association for use where the case is the subject - mixin: true - defining_slots: - - subject - slot_usage: - subject: - range: case - description: "the case (e.g. patient) that has the property" - - chemical to chemical association: - description: >- - A relationship between two chemical entities. This can encompass actual - interactions as well as temporal causal edges, e.g. one chemical converted to another. - is_a: association - defining_slots: - - subject - - object - mixins: - - chemical to entity association mixin - slot_usage: - object: - range: chemical entity - description: "the chemical element that is the target of the statement" - - reaction to participant association: - description: - is_a: chemical to chemical association - slots: - - stoichiometry - - reaction direction - - reaction side - slot_usage: - subject: - range: molecular entity - defining_slots: - - subject - - predicate - - object - - reaction to catalyst association: - description: - is_a: reaction to participant association - slot_usage: - object: - range: gene or gene product - - chemical to chemical derivation association: - description: >- - A causal relationship between two chemical entities, where the subject - represents the upstream entity and the object represents the downstream. - For any such association there is an implicit reaction: - IF - R has-input C1 AND - R has-output C2 AND - R enabled-by P AND - R type Reaction - THEN - C1 derives-into C2 <> - is_a: chemical to chemical association - defining_slots: - - subject - - predicate - - object - slots: - - catalyst qualifier - slot_usage: - subject: - range: chemical entity - description: >- - the upstream chemical entity - object: - range: chemical entity - description: >- - the downstream chemical entity - predicate: - subproperty_of: derives into - catalyst qualifier: - description: >- - this connects the derivation edge to the chemical entity that - catalyzes the reaction that causes the subject chemical to - transform into the object chemical. - - chemical to disease or phenotypic feature association: - description: >- - An interaction between a chemical entity and a phenotype or disease, - where the presence of the chemical gives rise to or exacerbates the phenotype. - is_a: association - narrow_mappings: - - SIO:000993 - defining_slots: - - subject - - object - mixins: - - chemical to entity association mixin - - entity to disease or phenotypic feature association mixin - slot_usage: - object: - range: disease or phenotypic feature - description: "the disease or phenotype that is affected by the chemical" - - chemical or drug or treatment to disease or phenotypic feature association: - description: >- - This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature - where the disesae or phenotypic feature is a secondary undesirable effect. - is_a: association - defining_slots: - - subject - - predicate - - object - mixins: - - chemical to entity association mixin - - entity to disease or phenotypic feature association mixin - slots: - - FDA adverse event level - slot_usage: - predicate: - subproperty_of: has adverse event - - chemical or drug or treatment side effect disease or phenotypic feature association: - description: >- - This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature - where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect. - is_a: chemical or drug or treatment to disease or phenotypic feature association - defining_slots: - - subject - - predicate - - object - mixins: - - chemical to entity association mixin - - entity to disease or phenotypic feature association mixin - slot_usage: - predicate: - subproperty_of: has side effect - - gene to pathway association: - description: >- - An interaction between a gene or gene product and a biological process or pathway. - is_a: association - defining_slots: - - subject - - object - mixins: - - gene to entity association mixin - slot_usage: - subject: - range: gene or gene product - description: "the gene or gene product entity that participates or influences the pathway" - object: - range: pathway - description: "the pathway that includes or is affected by the gene or gene product" - - molecular activity to pathway association: - description: >- - Association that holds the relationship between a reaction and the pathway it participates in. - is_a: association - slot_usage: - subject: - range: molecular activity - object: - range: pathway - predicate: - subproperty_of: part of - - chemical to pathway association: - description: >- - An interaction between a chemical entity and a biological process or pathway. - is_a: association - exact_mappings: - - SIO:001250 - defining_slots: - - subject - - object - mixins: - - chemical to entity association mixin - slot_usage: - subject: - range: chemical entity - description: "the chemical entity that is affecting the pathway" - object: - range: pathway - description: "the pathway that is affected by the chemical" - - named thing associated with likelihood of named thing association: - # TODO: better name - description: >- - is_a: association - defining_slots: - - subject - - subject aspect qualifier - - subject context qualifier - - predicate - - object - - object aspect qualifier - - object context qualifier - - population context qualifier - slot_usage: - predicate: - subproperty_of: associated with - subject aspect qualifier: - # TODO: range - subject context qualifier: - range: ontology class - object aspect qualifier: - # TODO: range - object context qualifier: - range: ontology class - - chemical gene interaction association: - description: >- - describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical - effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type - (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction) - is_a: association - exact_mappings: - - SIO:001257 - mixins: - - chemical to entity association mixin - slots: - - subject form or variant qualifier - - subject part qualifier - - subject derivative qualifier - - subject context qualifier - - object form or variant qualifier - - object part qualifier - - object context qualifier - - anatomical context qualifier - slot_usage: - subject: - range: chemical entity - object: - range: gene or gene product - predicate: - subproperty_of: physically interacts with - subject form or variant qualifier: - range: ChemicalOrGeneOrGeneProductFormOrVariantEnum - subject part qualifier: - range: GeneOrGeneProductOrChemicalPartQualifierEnum - subject derivative qualifier: - range: ChemicalEntityDerivativeEnum - subject context qualifier: - range: anatomical entity - object form or variant qualifier: - range: ChemicalOrGeneOrGeneProductFormOrVariantEnum - object part qualifier: - range: GeneOrGeneProductOrChemicalPartQualifierEnum - object context qualifier: - range: anatomical entity - anatomical context qualifier: - range: anatomical entity - - chemical affects gene association: - description: >- - Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity, - localization, processing, expression, etc.) - is_a: association - slots: - - subject form or variant qualifier - - subject part qualifier - - subject derivative qualifier - - subject aspect qualifier - - subject context qualifier - - subject direction qualifier - - object form or variant qualifier - - object part qualifier - - object aspect qualifier - - object context qualifier - - causal mechanism qualifier - - anatomical context qualifier - - qualified predicate - slot_usage: - subject: - range: chemical entity - subject form or variant qualifier: - range: ChemicalOrGeneOrGeneProductFormOrVariantEnum - subject part qualifier: - range: GeneOrGeneProductOrChemicalPartQualifierEnum - subject derivative qualifier: - range: ChemicalEntityDerivativeEnum - subject aspect qualifier: - range: GeneOrGeneProductOrChemicalPartQualifierEnum - subject context qualifier: - range: anatomical entity - subject direction qualifier: - range: DirectionQualifierEnum - predicate: - subproperty_of: affects - qualified predicate: - subproperty_of: causes - object: - range: gene or gene product - object form or variant qualifier: - range: ChemicalOrGeneOrGeneProductFormOrVariantEnum - object part qualifier: - range: GeneOrGeneProductOrChemicalPartQualifierEnum - object aspect qualifier: - range: GeneOrGeneProductOrChemicalPartQualifierEnum - object context qualifier: - range: anatomical entity - object direction qualifier: - range: DirectionQualifierEnum - causal mechanism qualifier: - range: CausalMechanismQualifierEnum - anatomical context qualifier: - range: anatomical entity - species context qualifier: - range: organism taxon - - drug to gene association: - description: >- - An interaction between a drug and a gene or gene product. - is_a: association - related_mappings: - - SIO:001257 - defining_slots: - - subject - - object - mixins: - - drug to entity association mixin - slot_usage: - object: - range: gene or gene product - description: "the gene or gene product that is affected by the drug" - - material sample to entity association mixin: - description: >- - An association between a material sample and something. - mixin: true - defining_slots: - - subject - slot_usage: - subject: - range: material sample - description: >- - the material sample being described - - material sample derivation association: - description: >- - An association between a material sample and - the material entity from which it is derived. - is_a: association - defining_slots: - - subject - - predicate - slot_usage: - subject: - range: material sample - description: >- - the material sample being described - object: - description: >- - the material entity the sample was derived from. This may be another - material sample, or any other material entity, including for example - an organism, a geographic feature, or some environmental material. - predicate: - description: >- - derivation relationship - subproperty_of: derives from - - material sample to disease or phenotypic feature association: - description: >- - An association between a material sample and a disease or phenotype. - is_a: association - mixins: - - material sample to entity association mixin - - entity to disease or phenotypic feature association mixin - defining_slots: - - subject - - object - - disease to entity association mixin: - mixin: true - defining_slots: - - subject - slot_usage: - subject: - range: disease - description: "disease class" - values_from: [ 'mondo', 'omim', 'orphanet', 'ncit', 'doid' ] - examples: - - value: MONDO:0017314 - description: "Ehlers-Danlos syndrome, vascular type" - - entity to exposure event association mixin: - description: >- - An association between some entity and an exposure event. - mixin: true - defining_slots: - - object - slot_usage: - object: - range: exposure event - - disease to exposure event association: - description: >- - An association between an exposure event and a disease. - is_a: association - mixins: - - disease to entity association mixin - - entity to exposure event association mixin - defining_slots: - - subject - - object - - - entity to outcome association mixin: - description: >- - An association between some entity and an outcome - mixin: true - defining_slots: - - object - slot_usage: - object: - range: outcome - - exposure event to outcome association: - description: >- - An association between an exposure event and an outcome. - is_a: association - mixins: - - entity to outcome association mixin - slots: - - population context qualifier - - temporal context qualifier - defining_slots: - - subject - - object - - frequency qualifier mixin: - mixin: true - description: >- - Qualifier for frequency type associations - slots: - - frequency qualifier - - entity to feature or disease qualifiers mixin: - description: >- - Qualifiers for entity to disease or phenotype associations. - mixin: true - is_a: frequency qualifier mixin - slots: - - severity qualifier - - onset qualifier - - entity to phenotypic feature association mixin: - mixin: true - is_a: entity to feature or disease qualifiers mixin - mixins: - - frequency quantifier - defining_slots: - - object - slot_usage: - object: - range: phenotypic feature - values_from: [ 'upheno', 'hp', 'mp', 'wbphenotype' ] - examples: - - value: HP:0002487 - description: Hyperkinesis - - value: WBPhenotype:0000180 - description: axon morphology variant - - value: MP:0001569 - description: abnormal circulating bilirubin level - slots: - - sex qualifier - - information content entity to named thing association: - description: >- - association between a named thing and a information content entity where the specific context - of the relationship between that named thing and the publication is unknown. For - example, model organisms databases often capture the knowledge that a gene is found in a - journal article, but not specifically the context in which that gene was documented in the article. - In these cases, this association with the accompanying predicate 'mentions' could be used. - Conversely, for more specific associations (like 'gene to disease association', the publication should - be captured as an edge property). - is_a: association - defining_slots: - - subject - - object - slot_usage: - subject: - domain: publication - object: - range: named thing - predicate: - subproperty_of: mentions - in_subset: - - model_organism_database - - entity to disease association mixin: - description: >- - mixin class for any association whose object (target node) is a disease - mixin: true - is_a: entity to feature or disease qualifiers mixin - defining_slots: - - object - slot_usage: - object: - range: disease - description: "disease" - examples: - - value: MONDO:0020066 - description: "Ehlers-Danlos syndrome" - - disease or phenotypic feature to entity association mixin: - mixin: true - defining_slots: - - subject - slot_usage: - subject: - range: disease or phenotypic feature - description: "disease or phenotype" - examples: - - value: MONDO:0017314 - description: "Ehlers-Danlos syndrome, vascular type" - - value: MP:0013229 - description: "abnormal brain ventricle size" - - disease or phenotypic feature to location association: - description: >- - An association between either a disease or a phenotypic feature and - an anatomical entity, where the disease/feature manifests in that site. - is_a: association - mixins: - - disease or phenotypic feature to entity association mixin - slot_usage: - object: - range: anatomical entity - description: >- - anatomical entity in which the disease or feature is found. - examples: - - value: UBERON:0002048 - description: "lung" - - disease or phenotypic feature to genetic inheritance association: - description: >- - An association between either a disease or a phenotypic feature and - its mode of (genetic) inheritance. - is_a: association - mixins: - - disease or phenotypic feature to entity association mixin - slot_usage: - predicate: - subproperty_of: has mode of inheritance - object: - range: genetic inheritance - description: >- - genetic inheritance associated with the specified disease or phenotypic feature. - examples: - - value: HP:0001417 - description: "X-linked inheritance" - - entity to disease or phenotypic feature association mixin: - mixin: true - defining_slots: - - object - slot_usage: - object: - range: disease or phenotypic feature - description: "disease or phenotype" - examples: - - value: MONDO:0017314 - description: "Ehlers-Danlos syndrome, vascular type" - - value: MP:0013229 - description: "abnormal brain ventricle size" - - genotype to entity association mixin: - mixin: true - defining_slots: - - subject - slot_usage: - subject: - range: genotype - description: "genotype that is the subject of the association" - - genotype to phenotypic feature association: - is_a: association - defining_slots: - - subject - - object - description: >- - Any association between one genotype and a phenotypic feature, where having - the genotype confers the phenotype, either in isolation or through environment - mixins: - - entity to phenotypic feature association mixin - - genotype to entity association mixin - slot_usage: - predicate: - subproperty_of: has phenotype - subject: - range: genotype - description: >- - genotype that is associated with the phenotypic feature - - # ie: smoke exposure to coughing phenotype? is this a denormalization? - exposure event to phenotypic feature association: - is_a: association - defining_slots: - - subject - - object - description: >- - Any association between an environment and a phenotypic feature, - where being in the environment influences the phenotype. - mixins: - - entity to phenotypic feature association mixin - slot_usage: - subject: - range: exposure event - - disease to phenotypic feature association: - is_a: association - defining_slots: - - subject - - object - description: >- - An association between a disease and a phenotypic feature in which the - phenotypic feature is associated with the disease in some way. - mixins: - - entity to phenotypic feature association mixin - - disease to entity association mixin - close_mappings: - - dcid:DiseaseSymptomAssociation - slot_usage: - subject: - range: disease - object: - range: phenotypic feature - - case to phenotypic feature association: - description: >- - An association between a case (e.g. individual patient) and a phenotypic - feature in which the individual has or has had the phenotype. - is_a: association - defining_slots: - - subject - - object - mixins: - - entity to phenotypic feature association mixin - - case to entity association mixin - - behavior to behavioral feature association: - description: >- - An association between an mixture behavior and - a behavioral feature manifested by - the individual exhibited or has exhibited the behavior. - is_a: association - defining_slots: - - subject - - object - slot_usage: - subject: - range: behavior - description: >- - behavior that is the subject of the association - object: - range: behavioral feature - description: >- - behavioral feature that is the object of the association - mixins: - - entity to phenotypic feature association mixin - - gene to entity association mixin: - mixin: true - defining_slots: - - subject - slot_usage: - subject: - range: gene or gene product - description: >- - gene that is the subject of the association - - variant to entity association mixin: - local_names: - ga4gh: variant annotation - mixin: true - defining_slots: - - subject - slot_usage: - subject: - range: sequence variant - description: >- - a sequence variant in which the allele state is associated with some other entity - examples: - - value: CLINVAR:38077 - description: "CLINVAR representation of NM_000059.3(BRCA2):c.7007G>A (p.Arg2336His)" - - value: ClinGen:CA024716 - description: "chr13:g.32921033G>C (hg19) in ClinGen" - - gene to phenotypic feature association: - is_a: association - exact_mappings: - - WBVocab:Gene-Phenotype-Association - defining_slots: - - subject - - object - mixins: - - entity to phenotypic feature association mixin - - gene to entity association mixin - slot_usage: - subject: - range: gene or gene product - description: "gene in which variation is correlated with the phenotypic feature" - examples: - - value: HGNC:2197 - description: "COL1A1 (Human)" - object: - range: phenotypic feature - - gene to disease association: - is_a: association - comments: - - NCIT:R176 refers to the inverse relationship - exact_mappings: - - SIO:000983 - close_mappings: - - dcid:DiseaseGeneAssociation - defining_slots: - - subject - - object - mixins: - - entity to disease association mixin - - gene to entity association mixin - slot_usage: - subject: - range: gene or gene product - description: >- - gene in which variation is correlated with the disease, - may be protective or causative or associative, or as a model - object: - range: disease - - druggable gene to disease association: - is_a: gene to disease association - slot_usage: - subject: - range: gene or gene product - description: >- - gene in which variation is correlated with the disease - in a protective manner, or if the product produced by the gene can be targeted by a small molecule and - this leads to a protective or improving disease state. - predicate: - subproperty_of: target for - has evidence: - range: DruggableGeneCategoryEnum - defining_slots: - - subject - - object - - predicate - mixins: - - entity to disease association mixin - - gene to entity association mixin - - variant to gene association: - description: >- - An association between a variant and a gene, where the variant has - a genetic association with the gene (i.e. is in linkage disequilibrium) - is_a: association - defining_slots: - - subject - - predicate - - object - mixins: - - variant to entity association mixin - slot_usage: - object: - range: gene - predicate: - subproperty_of: genetic association - - variant to gene expression association: - description: >- - An association between a variant and expression of a gene (i.e. e-QTL) - is_a: variant to gene association - defining_slots: - - subject - - predicate - - object - mixins: - - gene expression mixin - slot_usage: - predicate: - subproperty_of: affects - - variant to population association: - description: >- - An association between a variant and a population, where the variant has - particular frequency in the population - is_a: association - defining_slots: - - subject - - object - mixins: - - variant to entity association mixin - - frequency quantifier - - frequency qualifier mixin - slot_usage: - subject: - range: sequence variant - description: >- - an allele that has a certain frequency in a given population - examples: - - value: "NC_000017.11:g.43051071A>T" - description: >- - 17:41203088 A/C in gnomad - object: - range: population of individual organisms - description: >- - the population that is observed to have the frequency - examples: - - value: HANCESTRO:0010 - description: African - has quotient: - description: >- - frequency of allele in population, expressed as a number with allele - divided by number in reference population, aka allele frequency - examples: - - value: "0.0001666" - has count: - description: >- - number in object population that carry a particular allele, aka allele count - examples: - - value: "4" - description: 4 individuals in gnomad set - has total: - description: >- - number all populations that carry a particular allele, aka allele number - examples: - - value: "24014" - description: 24014 individuals in gnomad set - - population to population association: - description: >- - An association between a two populations - is_a: association - defining_slots: - - subject - - object - slot_usage: - subject: - range: population of individual organisms - description: >- - the population that form the subject of the association - object: - range: population of individual organisms - description: >- - the population that form the object of the association - predicate: - # subproperty_of: ??? - description: >- - A relationship type that holds between the subject and object - populations. Standard mereological relations can be used. - E.g. subject part-of object, subject overlaps object. - Derivation relationships can also be used - - variant to phenotypic feature association: - is_a: association - defining_slots: - - subject - - object - mixins: - - variant to entity association mixin - - entity to phenotypic feature association mixin - slot_usage: - subject: - range: sequence variant - description: >- - a sequence variant in which the allele state is - associated in some way with the phenotype state - - variant to disease association: - is_a: association - comments: - - TODO decide no how to model pathogenicity - defining_slots: - - subject - - object - mixins: - - variant to entity association mixin - - entity to disease association mixin - slot_usage: - subject: - description: >- - a sequence variant in which the allele state - is associated in some way with the disease state - examples: - - value: CLINVAR:52241 - description: "NM_000059.3(BRCA2):c.7007G>C (p.Arg2336Pro)" - predicate: - description: >- - E.g. is pathogenic for - subproperty_of: related condition - object: - description: >- - a disease that is associated with that variant - examples: - - value: MONDO:0016419 - description: hereditary breast cancer - - genotype to disease association: - is_a: association - comments: - - TODO decide no how to model pathogenicity - defining_slots: - - subject - - object - mixins: - - genotype to entity association mixin - - entity to disease association mixin - slot_usage: - subject: - description: >- - a genotype that is associated in some way with a disease state - predicate: - description: >- - E.g. is pathogenic for - subproperty_of: related condition - object: - description: >- - a disease that is associated with that genotype - examples: - - value: MONDO:0016419 - description: hereditary breast cancer - - model to disease association mixin: - description: >- - This mixin is used for any association class for which the subject - (source node) plays the role of a 'model', in that it recapitulates some - features of the disease in a way that is useful for studying the disease - outside a patient carrying the disease - mixin: true - slot_usage: - subject: - description: >- - The entity that serves as the model of the disease. This may be - an organism, a strain of organism, a genotype or variant that exhibits - similar features, or a gene that when mutated exhibits features of the disease - predicate: - subproperty_of: model of - description: >- - The relationship to the disease - - gene as a model of disease association: - is_a: gene to disease association - defining_slots: - - subject - - predicate - - object - mixins: - - model to disease association mixin - - entity to disease association mixin - slot_usage: - subject: - range: gene or gene product - description: >- - A gene that has a role in modeling the disease. This may be a model - organism ortholog of a known disease gene, or it may be a gene whose - mutants recapitulate core features of the disease. - - variant as a model of disease association: - is_a: variant to disease association - defining_slots: - - subject - - predicate - - object - mixins: - - model to disease association mixin - - entity to disease association mixin - slot_usage: - subject: - range: sequence variant - description: >- - A variant that has a role in modeling the disease. - - genotype as a model of disease association: - is_a: genotype to disease association - defining_slots: - - subject - - predicate - - object - mixins: - - model to disease association mixin - - entity to disease association mixin - slot_usage: - subject: - range: genotype - description: >- - A genotype that has a role in modeling the disease. - - cell line as a model of disease association: - is_a: cell line to disease or phenotypic feature association - defining_slots: - - subject - - predicate - - object - mixins: - - model to disease association mixin - - entity to disease association mixin - slot_usage: - subject: - range: cell line - description: >- - A cell line derived from an organismal entity with a disease state that is used - as a model of that disease. - - organismal entity as a model of disease association: - is_a: association - defining_slots: - - subject - - predicate - - object - mixins: - - model to disease association mixin - - entity to disease association mixin - slot_usage: - subject: - range: organismal entity - description: >- - A organismal entity (strain, breed) with a predisposition to a disease, or bred/created - specifically to model a disease. - - organism to organism association: - is_a: association - defining_slots: - - subject - - predicate - - object - slot_usage: - subject: - range: individual organism - object: - range: individual organism - description: >- - An association between two individual organisms. - - taxon to taxon association: - is_a: association - defining_slots: - - subject - - predicate - - object - slot_usage: - subject: - range: organism taxon - object: - range: organism taxon - description: >- - An association between individuals of different taxa. - - gene has variant that contributes to disease association: - is_a: gene to disease association - defining_slots: - - subject - - predicate - - object - slots: - - subject form or variant qualifier - slot_usage: - subject: - range: gene or gene product - description: >- - A gene that has a role in modeling the disease. This may be - a model organism ortholog of a known disease gene, or it may be - a gene whose mutants recapitulate core features of the disease. - object: - range: disease - predicate: - subproperty_of: contributes to - - gene to expression site association: - is_a: association - defining_slots: - - subject - - predicate - - object - description: >- - An association between a gene and a gene expression site, - possibly qualified by stage/timing info. - notes: - - "TBD: introduce subclasses for distinction between wild-type and experimental conditions?" - see_also: "https://github.com/monarch-initiative/ingest-artifacts/tree/master/sources/BGee" - slots: - - stage qualifier - - quantifier qualifier - slot_usage: - subject: - range: gene or gene product - description: >- - Gene or gene product positively within the specified - anatomical entity (or subclass, i.e. cellular component) location. - object: - range: anatomical entity - description: "location in which the gene is expressed" - examples: - - value: UBERON:0002037 - description: cerebellum - predicate: - description: "expression relationship" - subproperty_of: expressed in - stage qualifier: - range: life stage - description: "stage at which the gene is expressed in the site" - examples: - - value: UBERON:0000069 - description: larval stage - quantifier qualifier: - description: >- - can be used to indicate magnitude, or also ranking - - sequence variant modulates treatment association: - is_a: association - description: >- - An association between a sequence variant and a treatment or health intervention. - The treatment object itself encompasses both the disease and the drug used. - comments: - - An alternate way to model the same information could be via a qualifier - defining_slots: - - subject - - object - abstract: true - slot_usage: - subject: - range: sequence variant - description: "variant that modulates the treatment of some disease" - object: - range: treatment - description: "treatment whose efficacy is modulated by the subject variant" - - functional association: - is_a: association - description: >- - An association between a macromolecular machine mixin (gene, gene product or - complex of gene products) and either a molecular activity, a biological - process or a cellular location in which a function is executed. - slot_usage: - subject: - range: macromolecular machine mixin - description: >- - gene, product or macromolecular complex that - has the function associated with the GO term - examples: - - value: ZFIN:ZDB-GENE-050417-357 - description: twist1b - object: - range: ontology class - description: >- - class describing the activity, process or - localization of the gene product - values_from: - - go - examples: - - value: GO:0016301 - description: kinase activity - - value: GO:0045211 - description: postsynaptic membrane - - macromolecular machine to entity association mixin: - description: >- - an association which has a macromolecular machine mixin as a subject - mixin: true - slot_usage: - subject: - domain: macromolecular machine mixin - - macromolecular machine to molecular activity association: - description: >- - A functional association between a macromolecular machine (gene, - gene product or complex) and a molecular activity (as represented - in the GO molecular function branch), where the entity - carries out the activity, or contributes to its execution. - is_a: functional association - mixins: - - macromolecular machine to entity association mixin - slot_usage: - object: - range: molecular activity - - macromolecular machine to biological process association: - description: >- - A functional association between a macromolecular machine (gene, - gene product or complex) and a biological process or pathway - (as represented in the GO biological process branch), where the entity - carries out some part of the process, regulates it, or acts upstream of it. - is_a: functional association - mixins: - - macromolecular machine to entity association mixin - slot_usage: - object: - range: biological process - - macromolecular machine to cellular component association: - description: >- - A functional association between a macromolecular machine (gene, - gene product or complex) and a cellular component (as represented - in the GO cellular component branch), where the entity - carries out its function in the cellular component. - is_a: functional association - mixins: - - macromolecular machine to entity association mixin - slot_usage: - object: - range: cellular component - - molecular activity to chemical entity association: - is_a: association - description: >- - Added in response to capturing relationship between microbiome activities as measured via - measurements of blood analytes as collected via blood and stool samples - slot_usage: - subject: - range: molecular activity - object: - range: chemical entity - - molecular activity to molecular activity association: - is_a: association - description: >- - Added in response to capturing relationship between microbiome activities as measured via - measurements of blood analytes as collected via blood and stool samples - slot_usage: - subject: - range: molecular activity - object: - range: molecular activity - - - gene to go term association: - aliases: [ 'functional association' ] - is_a: functional association - exact_mappings: - - WBVocab:Gene-GO-Association - defining_slots: - - subject - - object - slot_usage: - subject: - range: gene - description: >- - gene, product or macromolecular complex that has - the function associated with the GO term - examples: - - value: ZFIN:ZDB-GENE-050417-357 - description: twist1b - object: - range: ontology class - description: >- - class describing the activity, process or - localization of the gene product - values_from: - - go - examples: - - value: GO:0016301 - description: kinase activity - - entity to disease association: - is_a: association - exact_mappings: - slots: - - FDA approval status - defining_slots: - - subject - - object - - entity to phenotypic feature association: - is_a: association - exact_mappings: - slots: - - FDA approval status - defining_slots: - - subject - - object - - ## ----------------- - ## SEQUENCE FEATURES - ## ----------------- - - sequence association: - is_a: association - description: >- - An association between a sequence feature and a nucleic acid entity it is localized to. - - genomic sequence localization: - is_a: sequence association - description: >- - A relationship between a sequence feature and a nucleic acid entity - it is localized to. The reference entity may be a chromosome, - chromosome region or information entity such as a contig. - slot_usage: - subject: - aliases: [ 'sequence feature' ] - range: nucleic acid entity - object: - aliases: [ 'reference' ] - range: nucleic acid entity # typically a chromosome use monochrom - predicate: - subproperty_of: has sequence location - slots: - - start interbase coordinate - - end interbase coordinate - - genome build - - strand - - phase - broad_mappings: - - dcid:Chromosome - exact_mappings: - - dcid:GenomeAnnotation - - sequence feature relationship: - is_a: association - defining_slots: - - subject - - object - description: >- - For example, a particular exon is part of a particular transcript or gene - slot_usage: - subject: - range: nucleic acid entity - object: - range: nucleic acid entity # typically a chromosome - exact_mappings: - - CHADO:feature_relationship - - transcript to gene relationship: - is_a: sequence feature relationship - defining_slots: - - subject - - object - description: >- - A gene is a collection of transcripts - slot_usage: - subject: - range: transcript - object: - range: gene - - gene to gene product relationship: - is_a: sequence feature relationship - defining_slots: - - subject - - object - description: >- - A gene is transcribed and potentially translated to a gene product - slot_usage: - subject: - range: gene - object: - range: gene product mixin - predicate: - subproperty_of: has gene product - - exon to transcript relationship: - is_a: sequence feature relationship - defining_slots: - - subject - - object - description: >- - A transcript is formed from multiple exons - slot_usage: - subject: - range: exon - object: - range: transcript - - chemical entity or gene or gene product regulates gene association: - is_a: association - description: >- - A regulatory relationship between two genes - slots: - - object direction qualifier - slot_usage: - predicate: - description: >- - the direction is always from regulator to regulated - subproperty_of: regulates - subject: - range: chemical entity or gene or gene product - role: regulatory gene - object: - range: gene or gene product - role: regulated gene - object direction qualifier: - range: DirectionQualifierEnum - - anatomical entity to anatomical entity association: # schema: gocam - is_a: association - abstract: true - defining_slots: - - subject - - object - slot_usage: - subject: - range: anatomical entity - object: - range: anatomical entity - - anatomical entity to anatomical entity part of association: - # schema: gocam - is_a: anatomical entity to anatomical entity association - description: >- - A relationship between two anatomical entities where the relationship - is mereological, i.e the two entities are related by parthood. This - includes relationships between cellular components and cells, between - cells and tissues, tissues and whole organisms - defining_slots: - - predicate - slot_usage: - subject: - range: anatomical entity - description: >- - the part - object: - range: anatomical entity - description: >- - the whole - predicate: - subproperty_of: part of - - anatomical entity to anatomical entity ontogenic association: - is_a: anatomical entity to anatomical entity association - description: >- - A relationship between two anatomical entities where the relationship - is ontogenic, i.e. the two entities are related by development. A number - of different relationship types can be used to specify the precise - nature of the relationship. - defining_slots: - - predicate - slot_usage: - subject: - range: anatomical entity - description: >- - the structure at a later time - object: - range: anatomical entity - description: >- - the structure at an earlier time - predicate: - subproperty_of: develops from - - organism taxon to entity association: - mixin: true - description: >- - An association between an organism taxon and another entity - defining_slots: - - subject - slot_usage: - subject: - range: organism taxon - description: >- - organism taxon that is the subject of the association - - organism taxon to organism taxon association: - is_a: association - abstract: true - mixins: - - organism taxon to entity association - description: >- - A relationship between two organism taxon nodes - defining_slots: - - subject - - object - slot_usage: - subject: - range: organism taxon - object: - range: organism taxon - - organism taxon to organism taxon specialization: - is_a: organism taxon to organism taxon association - description: >- - A child-parent relationship between two taxa. - For example: Homo sapiens subclass_of Homo - defining_slots: - - predicate - slot_usage: - subject: - range: organism taxon - role: child taxon - description: >- - the more specific taxon - object: - range: organism taxon - role: parent taxon - description: >- - the more general taxon - predicate: - subproperty_of: subclass of - - organism taxon to organism taxon interaction: - is_a: organism taxon to organism taxon association - description: >- - An interaction relationship between two taxa. This may be a symbiotic - relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. - Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens - defining_slots: - - predicate - slots: - - associated environmental context - slot_usage: - subject: - range: organism taxon - role: interactor taxon - description: >- - the taxon that is the subject of the association - object: - range: organism taxon - role: interactee taxon - description: >- - the taxon that is the subject of the association - predicate: - subproperty_of: interacts with - associated environmental context: - description: >- - the environment in which the two taxa interact - - organism taxon to environment association: - is_a: association - abstract: true - mixins: - - organism taxon to entity association - slot_usage: - subject: - range: organism taxon - role: interactor taxon - description: >- - the taxon that is the subject of the association - object: - role: environmental context - description: >- - the environment in which the organism occurs - predicate: - description: >- - predicate describing the relationship between the taxon and the environment - -enums: - - AnatomicalContextQualifierEnum: - reachable_from: - source_ontology: bioregistry:uberon - source_nodes: - - UBERON:0001062 - is_direct: false - relationship_types: - - rdfs:subClassOf - - DirectionQualifierEnum: - permissible_values: - increased: - upregulated: - is_a: increased - close_mappings: - - RO:0002336 - exact_mappings: - - RO:0002213 - narrow_mappings: - - RO:0004032 - - RO:0004034 - - RO:0002629 - decreased: - downregulated: - is_a: decreased - exact_mappings: - - RO:0004035 - - RO:0002212 - close_mappings: - # This RTX contributed term is tagged as an inverse of this Biolink predicate - - RO:0002335 - broad_mappings: - # This term is slightly broader in that it includes that A acts within B as well - - RO:0004033 - - ChemicalEntityDerivativeEnum: - permissible_values: - metabolite: - - ChemicalOrGeneOrGeneProductFormOrVariantEnum: - permissible_values: - genetic_variant_form: - is_a: modified_form - modified_form: - loss_of_function_variant_form: - is_a: genetic_variant_form - gain_of_function_variant_form: - is_a: genetic_variant_form - polymorphic_form: - is_a: genetic_variant_form - snp_form: - is_a: polymorphic_form - analog_form: - is_a: modified_form - - GeneOrGeneProductOrChemicalPartQualifierEnum: - permissible_values: - 3_prime_utr: - 5_prime_utr: - polya_tail: - promoter: - enhancer: - exon: - intron: - - GeneOrGeneProductOrChemicalEntityAspectEnum: - permissible_values: - activity_or_abundance: - description: >- - Used in cases where the specificity of the relationship can not be determined to be either activity - or abundance. In general, a more specific value from this enumeration should be used. - abundance: - is_a: activity_or_abundance - activity: - is_a: activity_or_abundance - expression: - is_a: abundance - synthesis: - is_a: abundance - degradation: - cleavage: - is_a: degradation - hydrolysis: - is_a: degradation - metabolic_processing: - mutation_rate: - stability: - folding: - localization: - transport: - secretion: - is_a: transport - uptake: - is_a: transport - molecular_modification: - acetylation: - is_a: molecular_modification - acylation: - is_a: molecular_modification - alkylation: - is_a: molecular_modification - amination: - is_a: molecular_modification - carbamoylation: - is_a: molecular_modification - ethylation: - is_a: molecular_modification - glutathionylation: - is_a: molecular_modification - glycation: - is_a: molecular_modification - glycosylation: - is_a: molecular_modification - glucuronidation: - is_a: molecular_modification - n_linked_glycosylation: - is_a: molecular_modification - o_linked_glycosylation: - is_a: molecular_modification - hydroxylation: - is_a: molecular_modification - lipidation: - is_a: molecular_modification - farnesylation: - is_a: molecular_modification - geranoylation: - is_a: molecular_modification - myristoylation: - is_a: molecular_modification - palmitoylation: - is_a: molecular_modification - prenylation: - is_a: molecular_modification - methylation: - is_a: molecular_modification - nitrosation: - is_a: molecular_modification - nucleotidylation: - is_a: molecular_modification - phosphorylation: - is_a: molecular_modification - ribosylation: - is_a: molecular_modification - ADP-ribosylation: - is_a: molecular_modification - sulfation: - is_a: molecular_modification - sumoylation: - is_a: molecular_modification - ubiquitination: - is_a: molecular_modification - oxidation: - is_a: molecular_modification - reduction: - is_a: molecular_modification - carboxylation: - is_a: molecular_modification - - CausalMechanismQualifierEnum: - permissible_values: - binding: - description: >- - A causal mechanism mediated by the direct contact between effector and target chemical or - biomolecular entity, which form a stable physical interaction. - inhibition: - is_a: binding - description: >- - A causal mechanism in which the effector binds to the target and negatively effects its normal function, - e.g. prevention of enzymatic reaction or activation of downstream pathway. - close_mappings: - - DGIdb:inhibitor - - SEMMEDDB:INHIBITS - narrow_mappings: - - DGIdb:blocker - - DGIdb:channel_blocker - - DGIdb:gating_inhibitor - - CHEMBL.MECHANISM:antisense_inhibitor - - CHEMBL.MECHANISM:blocker - - CHEMBL.MECHANISM:inhibitor - - CHEMBL.MECHANISM:negative_allosteric_modulator - - CHEMBL.MECHANISM:negative_modulator - - DGIdb:negative_modulator - antibody_inhibition: - is_a: inhibition - description: >- - A causal mechanism in which an antibody specifically binds to and interferes with the target. - antagonism: - is_a: inhibition - description: >- - A causal mechanism in which the effector binds to a receptor and prevents activation by an agonist - through competing for the binding site. - close_mappings: - - DGIdb:antagonist - - CHEMBL.MECHANISM:antagonist - narrow_mappings: - - CHEMBL.MECHANISM:allosteric_antagonist - molecular_channel_blockage: - is_a: inhibition - description: >- - A causal mechanism in which the effector binds to a molecular channel and prevents or reduces - transport of ions through it. - inverse_agonism: - is_a: inhibition - description: >- - A causal mechanism in which the effector binds to the same receptor-binding site as an agonist and antagonizes - its effects, often exerting the opposite effect of the agonist by suppressing spontaneous receptor signaling. - close_mappings: - - CHEMBL.MECHANISM:inverse_agonist - - DGIdb:inverse_agonist - negative_allosteric_modulation: - is_a: inhibition - description: >- - A causal mechanism in which the effector reduces or prevents the action of the endogenous ligand of a - receptor by binding to a site distinct from that ligand (i.e. non-competitive inhibition) - close_mappings: - - CHEMBL.MECHANISM:negative_allosteric_modulator - - DGIdb:inhibitory_allosteric_modulator - narrow_mappings: - - DGIdb:negative_modulator - agonism: - is_a: activation - description: >- - A causal mechanism in which the effector binds and activates a receptor to mimic the effect of an - endogenous ligand. - close_mappings: - - CHEMBL.MECHANISM:agonist - - DGIdb:agonist - narrow_mappings: - - CHEMBL.MECHANISM:partial_agonist - - DGIdb:partial_agonist - molecular_channel_opening: - is_a: activation - description: >- - A causal mechanism in which the effector binds to a molecular channel and facilitates transport of - ions through it. - close_mappings: - - CHEMBL.MECHANISM:opener - positive_allosteric_modulation: - is_a: activation - description: >- - A causal mechanism in which the effector enhances the action of the endogenous ligand of a receptor by - binding to a site distinct from that ligand (i.e. non-competitive inhibition) - close_mappings: - - CHEMBL.MECHANISM:positive_allosteric_modulator - - CHEMBL.MECHANISM:positive_modulator - - DGIdb:positive_allosteric_modulator - broad_mappings: - - DGIdb:modulator - - DGIdb:allosteric_modulator - potentiation: - is_a: binding - description: >- - A causal mechanism in which the effector binds to and enhances or intensifies the effect of some - other chemical or drug on its target. - close_mappings: - activation: - is_a: binding - description: >- - A causal mechanism in which the effector binds to and positively affects the normal functioning of its target. - close_mappings: - - CHEMBL.MECHANISM:activator - - DGIdb:activator - inducer: - is_a: binding - description: >- - A causal mechanism in which the effector binds to and increases the activity/rate of an enzyme that - processes drugs in the body. - close_mappings: - - DGIdb:inducer - transcriptional_regulation: - description: >- - A causal mechanism mediated by through the control of target gene transcription - signaling_mediated_control: - description: >- - A causal mechanism mediated by the activation or control of signaling events that influence the some aspect - of the target entity (e.g. its activity, processing, transport, etc) - stabilization: - is_a: activation - close_mappings: - - CHEMBL.MECHANISM:stabiliser - stimulation: - is_a: activation - close_mappings: - - DGIdb:stimulator - - SEMMEDDB:STIMULATES - - DGIdb:stimulator - releasing_activity: - is_a: activation - close_mappings: - - CHEMBL:MECHANISM:releasing_agent - - LogicalInterpretationEnum: - permissible_values: - some_some: - description: >- - A modifier on a triple that causes the triple to be interpreted as a some-some statement - meaning: os:SomeSomeInterpretation - all_some: - description: >- - A modifier on a triple that causes the triple to be interpreted as an all-some statement. - meaning: os:AllSomeInterpretation - inverse_all_some: - - ReactionDirectionEnum: - permissible_values: - left_to_right: - right_to_left: - bidirectional: - neutral: - - ReactionSideEnum: - permissible_values: - left: - right: - - PhaseEnum: - description: phase - permissible_values: - 0: - 1: - 2: - - StrandEnum: - description: strand - permissible_values: - "+": - description: Positive - "-": - description: Negative - ".": - description: Unstranded - "?": - description: Unknown - - SequenceEnum: - description: type of sequence - permissible_values: - "na": - description: nucleic acid - "aa": - description: amino acid - - DruggableGeneCategoryEnum: - permissible_values: - "tclin": - description: >- - These targets have activities in DrugCentral (ie. approved drugs) with known mechanism of action. - "tbio": - description: >- - These targets have activities in ChEMBL, Guide to Pharmacology or DrugCentral that satisfy - the activity thresholds detailed below. - "tchem": - description: >- - These targets do not have known drug or small molecule activities that satisfy the activity - thresholds detailed below AND satisfy one or more of the following criteria: - target is above the cutoff criteria for Tdark - target is annotated with a Gene Ontology Molecular Function or Biological Process leaf term(s) - with an Experimental Evidence code - "tdark": - description: >- - These are targets about which virtually nothing is known. They do not have known drug or small - molecule activities that satisfy the activity thresholds detailed below AND satisfy two or - more of the following criteria: - A PubMed text-mining score from Jensen Lab less than 5, greater than or equal TO 3 Gene RIFs, or - less than or equal to 50 Antibodies available according to http://antibodypedia.com. - - DrugAvailabilityEnum: - description: >- - permissible_values: - "over_the_counter": - description: >- - chemical entity is available over the counter without a prescription. - "prescription": - description: - chemical entity is available by prescription. - - DrugDeliveryEnum: - permissible_values: - "inhalation": - "oral": - "absorption_through_the_skin": - "intravenous_injection": - - FDAApprovalStatusEnum: - description: >- - permissible_values: - "discovery_and_development_phase": - description: >- - Discovery & Development Phase. Discovery involves researchers finding new possibilities - for medication through testing molecular compounds, noting unexpected effects from existing treatments, - or the creation of new technology that allows novel ways of targeting medical products to sites in the body. - Drug development occurs after researchers identify potential compounds for experiments. - "preclinical_research_phase": - description: >- - Preclinical Research Phase. Once researchers have examined the possibilities a new drug may contain, - they must do preliminary research to determine its potential for harm (toxicity). - This is categorized as preclinical research and can be one of two types: in vitro or in vivo. - "fda_clinical_research_phase": - description: >- - Clinical Research Phase. Clinical research involves trials of the drug on people, - and it is one of the most involved stages in the drug development and approval process. - Clinical trials must answer specific questions and follow a protocol determined by - the drug researcher or manufacturer. - "fda_review_phase_4": - description: >- - FDA Review - "fda_post_market_safety_review": - description: >- - FDA Post-Market Safety Monitoring. The last phase of drug approval is an ongoing one - while the drug is on the marketplace. If a developer wants to change anything about the - drug formulation or approve it for a new use, they must apply with the FDA. The FDA also - frequently reviews the drug’s advertising and its manufacturing facility to make sure - everything involved in its creation and marketing is in compliance with regulations. - "fda_clinical_research_phase_1": - description: >- - In the FDA Clinical Research Phase, the Clinical Research Phase 1 involves 20 – 100 study participants and - lasts several months. This phase is used to determine the safety and dosage of the drug, - and about 70% of these drugs move on to the next clinical research phase. - "fda_clinical_research_phase_2": - description: >- - In the FDA Clinical Research Phase, the Clinical Research Phase 2 involves up to several hundred people, - who must have the disease or condition the drug supposes to treat. This phase can last - from a few months to two years, and its purpose is to monitor the efficacy of the drug, - as well as note side effects that may occur. - "fda_clinical_research_phase_3": - description: >- - In the FDA Clinical Research Phase, the Clinical Research Phase 3 involves 300 – 3000 volunteers - and can last up to four years. It is used to continue monitoring the efficacy of - the drug, as well as exploring any longer-term adverse reactions. - "fda_clinical_research_phase_4": - description: >- - In the FDA Clinical Research Phase, the Clinical Research Phase 4 involves several thousands of - volunteers who have the disease or condition and continues to monitor safety and efficacy. - If a drug passes this phase, it goes on to FDA review. - "fda_fast_track": - description: >- - Fast track is a process designed to facilitate the development, and expedite the - review of drugs to treat serious conditions and fill an unmet medical need. - The purpose is to get important new drugs to the patient earlier. Fast Track - addresses a broad range of serious conditions. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/fast-track - "fda_breakthrough_therapy": - description: >- - Breakthrough Therapy designation is a process designed to expedite the - development and review of drugs that are intended to treat a serious - condition and preliminary clinical evidence indicates that the drug may - demonstrate substantial improvement over available therapy on a clinically significant endpoint(s). - For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/breakthrough-therapy - "fda_accelerated_approval": - description: >- - When studying a new drug, it can sometimes take many years to learn whether a drug actually - provides a real effect on how a patient survives, feels, or functions. A positive therapeutic - effect that is clinically meaningful in the context of a given disease is known as “clinical benefit”. - Mindful of the fact that it may take an extended period of time to measure a drug’s intended clinical - benefit, in 1992 FDA instituted the Accelerated Approval regulations. These regulations allowed drugs - for serious conditions that filled an unmet medical need to be approved based on a surrogate endpoint. - Using a surrogate endpoint enabled the FDA to approve these drugs faster. - For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/accelerated-approval - "fda_priority_review": - description: >- - Prior to approval, each drug marketed in the United States must go through a detailed FDA review process. - In 1992, under the Prescription Drug User Act (PDUFA), FDA agreed to specific goals for improving - the drug review time and created a two-tiered system of review times – Standard Review and Priority - Review. A Priority Review designation means FDA’s goal is to take action on an application - within 6 months (compared to 10 months under standard review). - For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/priority-review - "regular_fda_approval": - description: >- - Regular FDA Approval. The last phase of drug approval is an ongoing one while the drug is on the marketplace. - If a developer wants to change anything about the drug formulation or approve it for a new use, - they must apply with the FDA. The FDA also frequently reviews the drug’s advertising and its - manufacturing facility to make sure everything involved in its creation and marketing is in compliance - with regulations. - "post_approval_withdrawal": - - FDAIDAAdverseEventEnum: - description: >- - please consult with the FDA guidelines as proposed in this document: - https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?fr=312.32 - permissible_values: - "life_threatening_adverse_event": - description: >- - An adverse event or suspected adverse reaction is considered 'life-threatening' if, in the view of either - the investigator or sponsor, its occurrence places the patient or subject at immediate risk of death. - It does not include an adverse event or suspected adverse reaction that, had it occurred in a more - severe form, might have caused death. - "serious_adverse_event": - description: >- - An adverse event or suspected adverse reaction is considered 'serious' if, in the view of either the - investigator or sponsor, it results in any of the following outcomes: Death, a life-threatening adverse event, - inpatient hospitalization or prolongation of existing hospitalization, a persistent or significant incapacity - or substantial disruption of the ability to conduct normal life functions, or a congenital anomaly/birth - defect. Important medical events that may not result in death, be life-threatening, or require hospitalization - may be considered serious when, based upon appropriate medical judgment, they may jeopardize the patient or - subject and may require medical or surgical intervention to prevent one of the outcomes listed in this - definition. Examples of such medical events include allergic bronchospasm requiring intensive treatment - in an emergency room or at home, blood dyscrasias or convulsions that do not result in inpatient - hospitalization, or the development of drug dependency or drug abuse. - "suspected_adverse_reaction": - description: >- - means any adverse event for which there is a reasonable possibility that the drug caused the adverse event. - For the purposes of IND safety reporting, 'reasonable possibility' means there is evidence to suggest a - causal relationship between the drug and the adverse event. Suspected adverse reaction implies a lesser - degree of certainty about causality than adverse reaction, which means any adverse event caused by a drug. - "unexpected_adverse_event": - description: >- - An adverse event or suspected adverse reaction is considered 'unexpected' if it is not listed in the - investigator brochure or is not listed at the specificity or severity that has been observed; or, if an - investigator brochure is not required or available, is not consistent with the risk information described - in the general investigational plan or elsewhere in the current application, as amended. For example, - under this definition, hepatic necrosis would be unexpected (by virtue of greater severity) if the - investigator brochure referred only to elevated hepatic enzymes or hepatitis. Similarly, cerebral - thromboembolism and cerebral vasculitis would be unexpected (by virtue of greater specificity) if the - investigator brochure listed only cerebral vascular accidents. 'Unexpected', as used in this definition, - also refers to adverse events or suspected adverse reactions that are mentioned in the investigator brochure - as occurring with a class of drugs or as anticipated from the pharmacological properties of the drug, but - are not specifically mentioned as occurring with the particular drug under investigation. diff --git a/tests/input/examples/biolink/target/target.yaml b/tests/input/examples/biolink/target/target.yaml deleted file mode 100644 index d50e68c..0000000 --- a/tests/input/examples/biolink/target/target.yaml +++ /dev/null @@ -1,309 +0,0 @@ -name: Biolink-Model -id: https://w3id.org/biolink/biolink-model -default_prefix: https://w3id.org/biolink/biolink-model/ -classes: - NamedThing: - name: NamedThing - description: a databased entity or concept/class - from_schema: https://w3id.org/biolink/biolink-model - exact_mappings: - - BFO:0000001 - - WIKIDATA:Q35120 - - UMLSSG:OBJC - - STY:T071 - - dcid:Thing - attributes: - id: - name: id - description: A unique identifier for an entity. Must be either a CURIE shorthand - for a URI or a complete URI - in_subset: - - translator_minimal - from_schema: https://w3id.org/biolink/biolink-model - exact_mappings: - - AGRKB:primaryId - - gff3:ID - - gpi:DB_Object_ID - domain: entity - identifier: true - required: true - name: - name: name - description: A human-readable name for an attribute or entity. - in_subset: - - translator_minimal - - samples - from_schema: https://w3id.org/biolink/biolink-model - aliases: - - label - - display name - - title - exact_mappings: - - gff3:Name - - gpi:DB_Object_Name - narrow_mappings: - - dct:title - - WIKIDATA_PROPERTY:P1476 - domain: entity - slot_uri: rdfs:label - range: label type - category: - name: category - description: "Name of the high level ontology class in which this entity is\ - \ categorized. Corresponds to the label for the biolink entity type class.\n\ - \ * In a neo4j database this MAY correspond to the neo4j label tag.\n *\ - \ In an RDF database it should be a biolink model class URI.\nThis field\ - \ is multi-valued. It should include values for ancestors of the biolink\ - \ class; for example, a protein such as Shh would have category values `biolink:Protein`,\ - \ `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database,\ - \ nodes will typically have an rdf:type triples. This can be to the most\ - \ specific biolink class, or potentially to a class more specific than something\ - \ in biolink. For example, a sequence feature `f` may have a rdf:type assertion\ - \ to a SO class such as TF_binding_site, which is more specific than anything\ - \ in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,\ - \ biolink:NamedThing}" - in_subset: - - translator_minimal - from_schema: https://w3id.org/biolink/biolink-model - is_a: type - domain: entity - multivalued: true - designates_type: true - is_class_field: true - range: category type - Gene: - name: Gene - id_prefixes: - - NCBIGene - - ENSEMBL - - HGNC - - MGI - - ZFIN - - dictyBase - - WB - - WormBase - - FB - - RGD - - SGD - - PomBase - - OMIM - - KEGG.GENE - - UMLS - - Xenbase - - AspGD - description: A region (or regions) that includes all of the sequence elements - necessary to encode a functional transcript. A gene locus may include regulatory - regions, transcribed regions and/or other functional sequence regions. - in_subset: - - translator_minimal - - model_organism_database - from_schema: https://w3id.org/biolink/biolink-model - exact_mappings: - - SO:0000704 - - SIO:010035 - - WIKIDATA:Q7187 - - dcid:Gene - narrow_mappings: - - bioschemas:Gene - broad_mappings: - - NCIT:C45822 - is_a: NamedThing - attributes: - symbol: - name: symbol - description: Symbol for a particular thing - from_schema: https://w3id.org/biolink/biolink-model - exact_mappings: - - AGRKB:symbol - - gpi:DB_Object_Symbol - is_a: node property - domain: named thing - Disease: - name: Disease - id_prefixes: - - MONDO - - DOID - - OMIM - - OMIM.PS - - orphanet - - EFO - - UMLS - - MESH - - MEDDRA - - NCIT - - SNOMEDCT - - medgen - - ICD10 - - ICD9 - - KEGG.DISEASE - - HP - - MP - description: A disorder of structure or function, especially one that produces - specific signs, phenotypes or symptoms or that affects a specific location - and is not simply a direct result of physical injury. A disposition to undergo - pathological processes that exists in an organism because of one or more disorders - in that organism. - in_subset: - - model_organism_database - from_schema: https://w3id.org/biolink/biolink-model - aliases: - - condition - - disorder - - medical condition - exact_mappings: - - MONDO:0000001 - - DOID:4 - - NCIT:C2991 - - WIKIDATA:Q12136 - - SIO:010299 - - UMLSSG:DISO - - STY:T047 - - dcid:Disease - narrow_mappings: - - STY:T019 - - STY:T020 - - STY:T048 - - STY:T049 - - STY:T190 - - STY:T191 - - MONDO:0042489 - is_a: NamedThing - PhenotypicFeature: - name: PhenotypicFeature - id_prefixes: - - HP - - EFO - - NCIT - - UMLS - - MEDDRA - - MP - - ZP - - UPHENO - - APO - - FBcv - - WBPhenotype - - SNOMEDCT - - MESH - - XPO - - FYPO - - TO - description: A combination of entity and quality that makes up a phenotyping statement. - An observable characteristic of an individual resulting from the interaction - of its genotype with its molecular and physical environment. - examples: - - value: MP:0001262 - description: decreased body weight - in_subset: - - model_organism_database - from_schema: https://w3id.org/biolink/biolink-model - aliases: - - sign - - symptom - - phenotype - - trait - - endophenotype - exact_mappings: - - UPHENO:0001001 - - SIO:010056 - - WIKIDATA:Q104053 - - UMLS:C4021819 - - NCIT:C16977 - - SNOMEDCT:8116006 - - MESH:D010641 - narrow_mappings: - - STY:T184 - - WIKIDATA:Q169872 - - WIKIDATA:Q25203551 - - ZP:00000000 - - FBcv:0001347 - - HP:0000118 - - MP:0000001 - - WBPhenotype:0000886 - - XPO:00000000 - - FYPO:0000001 - - APO:0000017 - - TO:0000387 - broad_mappings: - - BFO:0000019 - - PATO:0000001 - is_a: NamedThing - Association: - name: Association - description: A typed association between two entities, supported by evidence - comments: - - This is roughly the model used by biolink and ontobio at the moment - from_schema: https://w3id.org/biolink/biolink-model - exact_mappings: - - OBAN:association - - rdf:Statement - - owl:Axiom - attributes: - subject: - name: subject - local_names: - ga4gh: - local_name_source: ga4gh - local_name_value: annotation subject - neo4j: - local_name_source: neo4j - local_name_value: node with outgoing relationship - description: connects an association to the subject of the association. For - example, in a gene-to-phenotype association, the gene is subject and phenotype - is object. - from_schema: https://w3id.org/biolink/biolink-model - exact_mappings: - - owl:annotatedSource - - OBAN:association_has_subject - is_a: association slot - domain: association - slot_uri: rdf:subject - range: named thing - required: true - predicate: - name: predicate - local_names: - ga4gh: - local_name_source: ga4gh - local_name_value: annotation predicate - translator: - local_name_source: translator - local_name_value: predicate - description: A high-level grouping for the relationship type. AKA minimal - predicate. This is analogous to category for nodes. - notes: - - Has a value from the Biolink related_to hierarchy. In RDF, this corresponds - to rdf:predicate and in Neo4j this corresponds to the relationship type. - The convention is for an edge label in snake_case form. For example, biolink:related_to, - biolink:causes, biolink:treats - from_schema: https://w3id.org/biolink/biolink-model - exact_mappings: - - owl:annotatedProperty - - OBAN:association_has_predicate - is_a: association slot - domain: association - slot_uri: rdf:predicate - range: predicate type - required: true - object: - name: object - local_names: - ga4gh: - local_name_source: ga4gh - local_name_value: descriptor - neo4j: - local_name_source: neo4j - local_name_value: node with incoming relationship - description: connects an association to the object of the association. For - example, in a gene-to-phenotype association, the gene is subject and phenotype - is object. - from_schema: https://w3id.org/biolink/biolink-model - exact_mappings: - - owl:annotatedTarget - - OBAN:association_has_object - is_a: association slot - domain: association - slot_uri: rdf:object - range: named thing - required: true - GeneToPhenotypicFeatureAssociation: - name: GeneToPhenotypicFeatureAssociation diff --git a/tests/input/examples/biolink/transform/biolink-example-profile.transform.yaml b/tests/input/examples/biolink/transform/biolink-example-profile.transform.yaml deleted file mode 100644 index db49811..0000000 --- a/tests/input/examples/biolink/transform/biolink-example-profile.transform.yaml +++ /dev/null @@ -1,43 +0,0 @@ -id: example-biolink-profile -title: Example Biolink Profile -prefixes: - biolink: https://w3id.org/biolink/vocab/ -source_schema: biolink -target_schema: monarch - -#slot_names_match: true # autopopulates slot.populated_from -#class_names_match: true # autopopulates class.populated_from - -class_derivations: - NamedThing: - populated_from: named thing - slot_derivations: - id: - name: - overrides: - category: - Gene: - populated_from: gene - slot_derivations: - symbol: - overrides: - #is_a: NamedThing # would be autopopulated - Disease: - populated_from: disease - overrides: - id_prefixes: - - MONDO - PhenotypicFeature: - populated_from: phenotypic feature - Association: - populated_from: association - slot_derivations: - subject: - predicate: - object: - GeneToPhenotypicFeatureAssociation: - populated_from: gene to phenotypic feature association - overrides: - slot_usage: - predicate: - equals_string: RO:1234567 diff --git a/tests/input/examples/flattening/__init__.py b/tests/input/examples/flattening/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/tests/input/examples/flattening/data/MappingSet-001.yaml b/tests/input/examples/flattening/data/MappingSet-001.yaml deleted file mode 100644 index 02f1240..0000000 --- a/tests/input/examples/flattening/data/MappingSet-001.yaml +++ /dev/null @@ -1,9 +0,0 @@ -mappings: - - subject: X:1 - object: Y:1 - predicate: P:1 -entities: - "X:1": - name: x1 - "Y:1": - name: y1 \ No newline at end of file diff --git a/tests/input/examples/flattening/model/__init__.py b/tests/input/examples/flattening/model/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/tests/input/examples/flattening/model/denormalized_model.py b/tests/input/examples/flattening/model/denormalized_model.py deleted file mode 100644 index 104294a..0000000 --- a/tests/input/examples/flattening/model/denormalized_model.py +++ /dev/null @@ -1,200 +0,0 @@ -# Auto generated from mapping_denorm.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-02-04T18:18:56 -# Schema: mappings_norm -# -# id: https://w3id.org/linkml/examples/mappings-norm -# description: Normalized Mappings -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -from dataclasses import dataclass -from typing import Any, ClassVar, Dict, List, Optional, Union - -from jsonasobj2 import as_dict -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.utils.dataclass_extensions_376 import ( - dataclasses_init_fn_with_kwargs, -) -from linkml_runtime.utils.metamodelcore import empty_list -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.yamlutils import YAMLRoot -from rdflib import URIRef - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -LINKML = CurieNamespace("linkml", "https://w3id.org/linkml/") -MAPPINGS = CurieNamespace("mappings", "https://w3id.org/linkml/examples/mappings-norm/") -RDF = CurieNamespace("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#") -RDFS = CurieNamespace("rdfs", "http://www.w3.org/2000/01/rdf-schema#") -SCHEMA = CurieNamespace("schema", "http://schema.org/") -SKOS = CurieNamespace("skos", "http://example.org/UNKNOWN/skos/") -XSD = CurieNamespace("xsd", "http://www.w3.org/2001/XMLSchema#") -DEFAULT_ = MAPPINGS - - -# Types - -# Class references - - -@dataclass -class MappingSet(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = MAPPINGS.MappingSet - class_class_curie: ClassVar[str] = "mappings:MappingSet" - class_name: ClassVar[str] = "MappingSet" - class_model_uri: ClassVar[URIRef] = MAPPINGS.MappingSet - - mappings: Optional[Union[Union[dict, "Mapping"], List[Union[dict, "Mapping"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.mappings, list): - self.mappings = [self.mappings] if self.mappings is not None else [] - self.mappings = [ - v if isinstance(v, Mapping) else Mapping(**as_dict(v)) for v in self.mappings - ] - - super().__post_init__(**kwargs) - - -@dataclass -class Mapping(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = MAPPINGS.Mapping - class_class_curie: ClassVar[str] = "mappings:Mapping" - class_name: ClassVar[str] = "Mapping" - class_model_uri: ClassVar[URIRef] = MAPPINGS.Mapping - - subject_id: Optional[str] = None - subject_name: Optional[str] = None - object_id: Optional[str] = None - object_name: Optional[str] = None - predicate_id: Optional[str] = None - predicate_name: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_id is not None and not isinstance(self.subject_id, str): - self.subject_id = str(self.subject_id) - - if self.subject_name is not None and not isinstance(self.subject_name, str): - self.subject_name = str(self.subject_name) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_name is not None and not isinstance(self.object_name, str): - self.object_name = str(self.object_name) - - if self.predicate_id is not None and not isinstance(self.predicate_id, str): - self.predicate_id = str(self.predicate_id) - - if self.predicate_name is not None and not isinstance(self.predicate_name, str): - self.predicate_name = str(self.predicate_name) - - super().__post_init__(**kwargs) - - -# Enumerations - - -# Slots -class slots: - pass - - -slots.id = Slot( - uri=SCHEMA.identifier, - name="id", - curie=SCHEMA.curie("identifier"), - model_uri=MAPPINGS.id, - domain=None, - range=URIRef, -) - -slots.name = Slot( - uri=RDFS.label, - name="name", - curie=RDFS.curie("label"), - model_uri=MAPPINGS.name, - domain=None, - range=Optional[str], -) - -slots.predicate = Slot( - uri=MAPPINGS.predicate, - name="predicate", - curie=MAPPINGS.curie("predicate"), - model_uri=MAPPINGS.predicate, - domain=None, - range=Optional[str], -) - -slots.subject_id = Slot( - uri=MAPPINGS.subject_id, - name="subject_id", - curie=MAPPINGS.curie("subject_id"), - model_uri=MAPPINGS.subject_id, - domain=None, - range=Optional[str], -) - -slots.subject_name = Slot( - uri=MAPPINGS.subject_name, - name="subject_name", - curie=MAPPINGS.curie("subject_name"), - model_uri=MAPPINGS.subject_name, - domain=None, - range=Optional[str], -) - -slots.object_id = Slot( - uri=MAPPINGS.object_id, - name="object_id", - curie=MAPPINGS.curie("object_id"), - model_uri=MAPPINGS.object_id, - domain=None, - range=Optional[str], -) - -slots.object_name = Slot( - uri=MAPPINGS.object_name, - name="object_name", - curie=MAPPINGS.curie("object_name"), - model_uri=MAPPINGS.object_name, - domain=None, - range=Optional[str], -) - -slots.predicate_id = Slot( - uri=MAPPINGS.predicate_id, - name="predicate_id", - curie=MAPPINGS.curie("predicate_id"), - model_uri=MAPPINGS.predicate_id, - domain=None, - range=Optional[str], -) - -slots.predicate_name = Slot( - uri=MAPPINGS.predicate_name, - name="predicate_name", - curie=MAPPINGS.curie("predicate_name"), - model_uri=MAPPINGS.predicate_name, - domain=None, - range=Optional[str], -) - -slots.mappingSet__mappings = Slot( - uri=MAPPINGS.mappings, - name="mappingSet__mappings", - curie=MAPPINGS.curie("mappings"), - model_uri=MAPPINGS.mappingSet__mappings, - domain=None, - range=Optional[Union[Union[dict, Mapping], List[Union[dict, Mapping]]]], -) diff --git a/tests/input/examples/flattening/model/normalized_model.py b/tests/input/examples/flattening/model/normalized_model.py deleted file mode 100644 index efd3896..0000000 --- a/tests/input/examples/flattening/model/normalized_model.py +++ /dev/null @@ -1,200 +0,0 @@ -# Auto generated from mapping_norm.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-10-11T21:55:30 -# Schema: mappings_norm -# -# id: https://w3id.org/linkml/examples/mappings-norm -# description: Normalized Mappings -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -from dataclasses import dataclass -from typing import Any, ClassVar, Dict, List, Optional, Union - -from jsonasobj2 import as_dict -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.utils.dataclass_extensions_376 import ( - dataclasses_init_fn_with_kwargs, -) -from linkml_runtime.utils.metamodelcore import empty_dict, empty_list -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str -from rdflib import URIRef - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -LINKML = CurieNamespace("linkml", "https://w3id.org/linkml/") -MAPPINGS = CurieNamespace("mappings", "https://w3id.org/linkml/examples/mappings-norm/") -RDF = CurieNamespace("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#") -RDFS = CurieNamespace("rdfs", "http://www.w3.org/2000/01/rdf-schema#") -SCHEMA = CurieNamespace("schema", "http://example.org/UNKNOWN/schema/") -SKOS = CurieNamespace("skos", "http://example.org/UNKNOWN/skos/") -XSD = CurieNamespace("xsd", "http://www.w3.org/2001/XMLSchema#") -DEFAULT_ = MAPPINGS - - -# Types - - -# Class references -class EntityId(extended_str): - pass - - -@dataclass -class MappingSet(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = MAPPINGS.MappingSet - class_class_curie: ClassVar[str] = "mappings:MappingSet" - class_name: ClassVar[str] = "MappingSet" - class_model_uri: ClassVar[URIRef] = MAPPINGS.MappingSet - - mappings: Optional[Union[Union[dict, "Mapping"], List[Union[dict, "Mapping"]]]] = empty_list() - entities: Optional[ - Union[ - Dict[Union[str, EntityId], Union[dict, "Entity"]], - List[Union[dict, "Entity"]], - ] - ] = empty_dict() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.mappings, list): - self.mappings = [self.mappings] if self.mappings is not None else [] - self.mappings = [ - v if isinstance(v, Mapping) else Mapping(**as_dict(v)) for v in self.mappings - ] - - self._normalize_inlined_as_dict( - slot_name="entities", slot_type=Entity, key_name="id", keyed=True - ) - - super().__post_init__(**kwargs) - - -@dataclass -class Mapping(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = MAPPINGS.Mapping - class_class_curie: ClassVar[str] = "mappings:Mapping" - class_name: ClassVar[str] = "Mapping" - class_model_uri: ClassVar[URIRef] = MAPPINGS.Mapping - - subject: Optional[Union[str, EntityId]] = None - object: Optional[Union[str, EntityId]] = None - predicate: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, EntityId): - self.subject = EntityId(self.subject) - - if self.object is not None and not isinstance(self.object, EntityId): - self.object = EntityId(self.object) - - if self.predicate is not None and not isinstance(self.predicate, str): - self.predicate = str(self.predicate) - - super().__post_init__(**kwargs) - - -@dataclass -class Entity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = MAPPINGS.Entity - class_class_curie: ClassVar[str] = "mappings:Entity" - class_name: ClassVar[str] = "Entity" - class_model_uri: ClassVar[URIRef] = MAPPINGS.Entity - - id: Union[str, EntityId] = None - name: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, EntityId): - self.id = EntityId(self.id) - - if self.name is not None and not isinstance(self.name, str): - self.name = str(self.name) - - super().__post_init__(**kwargs) - - -# Enumerations - - -# Slots -class slots: - pass - - -slots.id = Slot( - uri=SCHEMA.identifier, - name="id", - curie=SCHEMA.curie("identifier"), - model_uri=MAPPINGS.id, - domain=None, - range=URIRef, -) - -slots.name = Slot( - uri=RDFS.label, - name="name", - curie=RDFS.curie("label"), - model_uri=MAPPINGS.name, - domain=None, - range=Optional[str], -) - -slots.predicate = Slot( - uri=MAPPINGS.predicate, - name="predicate", - curie=MAPPINGS.curie("predicate"), - model_uri=MAPPINGS.predicate, - domain=None, - range=Optional[str], -) - -slots.subject = Slot( - uri=MAPPINGS.subject, - name="subject", - curie=MAPPINGS.curie("subject"), - model_uri=MAPPINGS.subject, - domain=None, - range=Optional[Union[str, EntityId]], -) - -slots.object = Slot( - uri=MAPPINGS.object, - name="object", - curie=MAPPINGS.curie("object"), - model_uri=MAPPINGS.object, - domain=None, - range=Optional[Union[str, EntityId]], -) - -slots.mappingSet__mappings = Slot( - uri=MAPPINGS.mappings, - name="mappingSet__mappings", - curie=MAPPINGS.curie("mappings"), - model_uri=MAPPINGS.mappingSet__mappings, - domain=None, - range=Optional[Union[Union[dict, Mapping], List[Union[dict, Mapping]]]], -) - -slots.mappingSet__entities = Slot( - uri=MAPPINGS.entities, - name="mappingSet__entities", - curie=MAPPINGS.curie("entities"), - model_uri=MAPPINGS.mappingSet__entities, - domain=None, - range=Optional[ - Union[Dict[Union[str, EntityId], Union[dict, Entity]], List[Union[dict, Entity]]] - ], -) diff --git a/tests/input/examples/flattening/output/MappingSet-001.transformed.yaml b/tests/input/examples/flattening/output/MappingSet-001.transformed.yaml deleted file mode 100644 index 5c165a1..0000000 --- a/tests/input/examples/flattening/output/MappingSet-001.transformed.yaml +++ /dev/null @@ -1,6 +0,0 @@ -mappings: -- subject_id: X:1 - subject_name: x1 - object_id: Y:1 - object_name: y1 - predicate_id: P:1 diff --git a/tests/input/examples/flattening/source/cmdr_normalized.yaml b/tests/input/examples/flattening/source/cmdr_normalized.yaml deleted file mode 100644 index 3a0d7fd..0000000 --- a/tests/input/examples/flattening/source/cmdr_normalized.yaml +++ /dev/null @@ -1,22 +0,0 @@ -id: https://w3id.org/linkml/examples/cmdr-normalized -name: cmdr_normalized -description: |- - Normalized CMDR model -license: https://creativecommons.org/publicdomain/zero/1.0/ -default_curi_maps: - - semweb_context -imports: - - linkml:types -prefixes: - mappings: https://w3id.org/linkml/examples/cmdr-normalized/ - linkml: https://w3id.org/linkml/ -default_prefix: cmdrnormalized -default_range: string - -emit_prefixes: - - rdf - - rdfs - - xsd - - skos - -classes: diff --git a/tests/input/examples/flattening/source/normalized.yaml b/tests/input/examples/flattening/source/normalized.yaml deleted file mode 100644 index 3d0abda..0000000 --- a/tests/input/examples/flattening/source/normalized.yaml +++ /dev/null @@ -1,56 +0,0 @@ -id: https://w3id.org/linkml/examples/mappings-norm -name: mappings_norm -description: |- - Normalized Mappings -license: https://creativecommons.org/publicdomain/zero/1.0/ -default_curi_maps: - - semweb_context -imports: - - linkml:types -prefixes: - mappings: https://w3id.org/linkml/examples/mappings-norm/ - linkml: https://w3id.org/linkml/ -default_prefix: mappings -default_range: string - -emit_prefixes: - - rdf - - rdfs - - xsd - - skos - -classes: - - MappingSet: - tree_root: true - attributes: - mappings: - range: Mapping - multivalued: true - inlined: true - entities: - range: Entity - multivalued: true - inlined: true - - Mapping: - slots: - - subject - - object - - predicate - Entity: - slots: - - id - - name - -slots: - id: - identifier: true - slot_uri: schema:identifier - name: - slot_uri: rdfs:label - predicate: - subject: - range: Entity - object: - range: Entity \ No newline at end of file diff --git a/tests/input/examples/flattening/target/cmdr_denormalized.yaml b/tests/input/examples/flattening/target/cmdr_denormalized.yaml deleted file mode 100644 index e69de29..0000000 diff --git a/tests/input/examples/flattening/target/denormalized.yaml b/tests/input/examples/flattening/target/denormalized.yaml deleted file mode 100644 index eeb1db7..0000000 --- a/tests/input/examples/flattening/target/denormalized.yaml +++ /dev/null @@ -1,53 +0,0 @@ -id: https://w3id.org/linkml/examples/mappings-norm -name: mappings_norm -description: |- - Normalized Mappings -license: https://creativecommons.org/publicdomain/zero/1.0/ -default_curi_maps: - - semweb_context -imports: - - linkml:types -prefixes: - mappings: https://w3id.org/linkml/examples/mappings-norm/ - linkml: https://w3id.org/linkml/ -default_prefix: mappings -default_range: string - -emit_prefixes: - - rdf - - rdfs - - xsd - - skos - -classes: - - MappingSet: - tree_root: true - attributes: - mappings: - range: Mapping - multivalued: true - inlined: true - - Mapping: - slots: - - subject_id - - subject_name - - object_id - - object_name - - predicate_id - - predicate_name - -slots: - id: - identifier: true - slot_uri: schema:identifier - name: - slot_uri: rdfs:label - predicate: - subject_id: - subject_name: - object_id: - object_name: - predicate_id: - predicate_name: diff --git a/tests/input/examples/flattening/transform/denormalize.transform.yaml b/tests/input/examples/flattening/transform/denormalize.transform.yaml deleted file mode 100644 index 60e5918..0000000 --- a/tests/input/examples/flattening/transform/denormalize.transform.yaml +++ /dev/null @@ -1,36 +0,0 @@ -id: denormalize-mapping -title: denormalize mappings -prefixes: - foo: foo -source_schema: s1 -target_schema: s2 -class_derivations: - MappingSet: - populated_from: MappingSet - slot_derivations: - mappings: - populated_from: mappings - - Mapping: - populated_from: Mapping - #joins: - # subject: Entity - # object: Entity - slot_derivations: -# id: ## implicitly mapping.id -# creator: -# license: - subject_id: - expr: subject.id - subject_name: - expr: subject.name - object_id: - expr: object.id - object_name: - expr: object.name - predicate_id: - ## implicitly: mapping.predicate - populated_from: predicate - #predicate_name: - # expr: "predicate.name" - diff --git a/tests/input/examples/measurements/data/PersonQuantityValue-001.yaml b/tests/input/examples/measurements/data/PersonQuantityValue-001.yaml deleted file mode 100644 index d55259b..0000000 --- a/tests/input/examples/measurements/data/PersonQuantityValue-001.yaml +++ /dev/null @@ -1,4 +0,0 @@ -id: P:1 -height: - value: 172.0 - unit: cm diff --git a/tests/input/examples/measurements/data/PersonQuantityValue-002.yaml b/tests/input/examples/measurements/data/PersonQuantityValue-002.yaml deleted file mode 100644 index 31a0d1a..0000000 --- a/tests/input/examples/measurements/data/PersonQuantityValue-002.yaml +++ /dev/null @@ -1,4 +0,0 @@ -id: P:2 -height: - value: 1.72 - unit: m diff --git a/tests/input/examples/measurements/instructions.yaml b/tests/input/examples/measurements/instructions.yaml deleted file mode 100644 index 6c78af6..0000000 --- a/tests/input/examples/measurements/instructions.yaml +++ /dev/null @@ -1,10 +0,0 @@ -description: Examples of transforming measurements -transformations: - - source_schema: source/quantity_value.yaml - target_schema: target/quantity_value_flat.yaml - transformation_specification: transform/qv-to-scalar.transform.yaml - steps: - - source_data: data/PersonQuantityValue-001.yaml - target_data: output/PersonQuantityValue-001.transformed.yaml - - source_data: data/PersonQuantityValue-002.yaml - target_data: output/PersonQuantityValue-002.transformed.yaml diff --git a/tests/input/examples/measurements/output/PersonQuantityValue-001.transformed.yaml b/tests/input/examples/measurements/output/PersonQuantityValue-001.transformed.yaml deleted file mode 100644 index e0f5c81..0000000 --- a/tests/input/examples/measurements/output/PersonQuantityValue-001.transformed.yaml +++ /dev/null @@ -1,2 +0,0 @@ -id: P:1 -height_in_cm: 172.0 diff --git a/tests/input/examples/measurements/output/PersonQuantityValue-002.transformed.yaml b/tests/input/examples/measurements/output/PersonQuantityValue-002.transformed.yaml deleted file mode 100644 index 6026b67..0000000 --- a/tests/input/examples/measurements/output/PersonQuantityValue-002.transformed.yaml +++ /dev/null @@ -1,2 +0,0 @@ -id: P:2 -height_in_cm: null diff --git a/tests/input/examples/measurements/source/quantity_value.yaml b/tests/input/examples/measurements/source/quantity_value.yaml deleted file mode 100644 index fed5b51..0000000 --- a/tests/input/examples/measurements/source/quantity_value.yaml +++ /dev/null @@ -1,26 +0,0 @@ -id: https://w3id.org/linkml/examples/quantity_value -name: quantity_value -imports: - - linkml:types -prefixes: - personinfo: https://w3id.org/linkml/examples/personinfo/ - linkml: https://w3id.org/linkml/ -default_prefix: personinfo -default_range: string - -classes: - - Person: - tree_root: true - attributes: - id: - identifier: true - height: - range: QuantityValue - - QuantityValue: - attributes: - value: - range: float - unit: - range: cm diff --git a/tests/input/examples/measurements/target/quantity_value_flat.yaml b/tests/input/examples/measurements/target/quantity_value_flat.yaml deleted file mode 100644 index 865241a..0000000 --- a/tests/input/examples/measurements/target/quantity_value_flat.yaml +++ /dev/null @@ -1,16 +0,0 @@ -name: quantity_value -id: https://w3id.org/linkml/examples/quantity_value -default_prefix: https://w3id.org/linkml/examples/quantity_value/ -classes: - Person: - name: Person - from_schema: https://w3id.org/linkml/examples/quantity_value - attributes: - id: - name: id - from_schema: https://w3id.org/linkml/examples/quantity_value - identifier: true - owner: Person - height_in_cm: - name: height_in_cm - tree_root: true diff --git a/tests/input/examples/measurements/transform/qv-to-scalar.transform.yaml b/tests/input/examples/measurements/transform/qv-to-scalar.transform.yaml deleted file mode 100644 index 53a55c9..0000000 --- a/tests/input/examples/measurements/transform/qv-to-scalar.transform.yaml +++ /dev/null @@ -1,11 +0,0 @@ -id: qv-to-scalar -class_derivations: - Person: - populated_from: Person - slot_derivations: - id: - height_in_cm: - expr: "case( ({height}.unit == 'cm', {height}.value), (True, NULL) )" - #copy_directives: - # "*": - # copy_all: true diff --git a/tests/input/examples/personinfo_basic/__init__.py b/tests/input/examples/personinfo_basic/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/tests/input/examples/personinfo_basic/data/Container-001.yaml b/tests/input/examples/personinfo_basic/data/Container-001.yaml deleted file mode 100644 index 0d0a6f7..0000000 --- a/tests/input/examples/personinfo_basic/data/Container-001.yaml +++ /dev/null @@ -1,52 +0,0 @@ -persons: - - id: P:001 - name: fred bloggs - primary_email: fred.bloggs@example.com - secondary_email: frederick.b.loggs@home.com - age_in_years: 33 - gender: nonbinary man - has_familial_relationships: - - type: SIBLING_OF - related_to: P:002 - - type: CHILD_OF - related_to: P:003 - current_address: - street: 1 oak street - city: oaktown - has_important_life_events: - - event_name: BIRTH - important_event_date: 1990-01-01 - - event_name: PASSED_DRIVING_TEST - important_event_date: 2014-03-31 - - event_name: FIRST_CAR_ACCIDENT - important_event_date: 2015-01-25 - aliases: - - a - - b - has_medical_history: - - diagnosis: - id: C:001 - name: c1 - - diagnosis: - id: C:002 - - id: P:002 - name: Alison Wu - has_familial_relationships: - - type: SIBLING_OF - related_to: P:001 - - type: CHILD_OF - related_to: P:003 - has_medical_history: - - diagnosis: - id: C:001 - name: c1 (renamed) - - id: P:003 - name: Mr. Blobby - has_familial_relationships: - - type: PARENT_OF - related_to: P:001 - - type: PARENT_OF - related_to: P:002 -organizations: - - id: ROR:1 - name: Acme diff --git a/tests/input/examples/personinfo_basic/data/Person-001.yaml b/tests/input/examples/personinfo_basic/data/Person-001.yaml deleted file mode 100644 index 4fa73f6..0000000 --- a/tests/input/examples/personinfo_basic/data/Person-001.yaml +++ /dev/null @@ -1,21 +0,0 @@ -id: P:001 -name: fred bloggs -primary_email: fred.bloggs@example.com -secondary_email: frederick.b.loggs@home.com -age_in_years: 33 -gender: nonbinary man -has_familial_relationships: - - type: SIBLING_OF - related_to: P:002 - - type: CHILD_OF - related_to: P:003 -current_address: - street: 1 oak street - city: oaktown -has_important_life_events: - - event_name: BIRTH - important_event_date: 1990-01-01 - - event_name: PASSED_DRIVING_TEST - important_event_date: 2014-03-31 - - event_name: FIRST_CAR_ACCIDENT - important_event_date: 2015-01-25 diff --git a/tests/input/examples/personinfo_basic/model/__init__.py b/tests/input/examples/personinfo_basic/model/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/tests/input/examples/personinfo_basic/model/agent_model.py b/tests/input/examples/personinfo_basic/model/agent_model.py deleted file mode 100644 index 2575d33..0000000 --- a/tests/input/examples/personinfo_basic/model/agent_model.py +++ /dev/null @@ -1,1021 +0,0 @@ -# Auto generated from agent.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-05-03T07:06:53 -# Schema: personinfo -# -# id: https://w3id.org/linkml/examples/personinfo -# description: Information about people, based on [schema.org](http://schema.org) -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import re -from dataclasses import dataclass -from typing import Any, ClassVar, Dict, List, Optional, Union - -from jsonasobj2 import as_dict -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.utils.dataclass_extensions_376 import ( - dataclasses_init_fn_with_kwargs, -) -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from linkml_runtime.utils.metamodelcore import Bool, XSDDate, empty_dict, empty_list -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str -from rdflib import URIRef - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -CODE = CurieNamespace("CODE", "http://example.org/code/") -GEO = CurieNamespace("GEO", "http://example.org/geoloc/") -GSSO = CurieNamespace("GSSO", "http://purl.obolibrary.org/obo/GSSO_") -P = CurieNamespace("P", "http://example.org/P/") -ROR = CurieNamespace("ROR", "http://example.org/ror/") -FAMREL = CurieNamespace("famrel", "https://example.org/FamilialRelations#") -LINKML = CurieNamespace("linkml", "https://w3id.org/linkml/") -PERSONINFO = CurieNamespace("personinfo", "https://w3id.org/linkml/examples/personinfo/") -PROV = CurieNamespace("prov", "http://www.w3.org/ns/prov#") -RDF = CurieNamespace("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#") -RDFS = CurieNamespace("rdfs", "http://www.w3.org/2000/01/rdf-schema#") -SCHEMA = CurieNamespace("schema", "http://schema.org/") -SKOS = CurieNamespace("skos", "http://example.org/UNKNOWN/skos/") -XSD = CurieNamespace("xsd", "http://www.w3.org/2001/XMLSchema#") -DEFAULT_ = PERSONINFO - - -# Types - - -# Class references -class NamedThingId(extended_str): - pass - - -class AgentId(NamedThingId): - pass - - -class OrganizationId(NamedThingId): - pass - - -class PlaceId(extended_str): - pass - - -class ConceptId(NamedThingId): - pass - - -class DiagnosisConceptId(ConceptId): - pass - - -class ProcedureConceptId(ConceptId): - pass - - -@dataclass -class NamedThing(YAMLRoot): - """ - A generic grouping for any identifiable entity - """ - - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.NamedThing - class_class_curie: ClassVar[str] = "personinfo:NamedThing" - class_name: ClassVar[str] = "NamedThing" - class_model_uri: ClassVar[URIRef] = PERSONINFO.NamedThing - - id: Union[str, NamedThingId] = None - label: Optional[str] = None - description: Optional[str] = None - image: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedThingId): - self.id = NamedThingId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if self.image is not None and not isinstance(self.image, str): - self.image = str(self.image) - - super().__post_init__(**kwargs) - - -@dataclass -class Agent(NamedThing): - """ - A person (alive, dead, undead, or fictional). - """ - - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = SCHEMA.Person - class_class_curie: ClassVar[str] = "schema:Person" - class_name: ClassVar[str] = "Agent" - class_model_uri: ClassVar[URIRef] = PERSONINFO.Agent - - id: Union[str, AgentId] = None - primary_email: Optional[str] = None - secondary_email: Optional[str] = None - birth_date: Optional[Union[str, XSDDate]] = None - death_date: Optional[Union[str, XSDDate]] = None - age: Optional[str] = None - gender: Optional[Union[str, "GenderType"]] = None - current_address: Optional[Union[dict, "Address"]] = None - has_employment_history: Optional[ - Union[Union[dict, "EmploymentEvent"], List[Union[dict, "EmploymentEvent"]]] - ] = empty_list() - has_familial_relationships: Optional[ - Union[Union[dict, "FamilialRelationship"], List[Union[dict, "FamilialRelationship"]]] - ] = empty_list() - has_medical_history: Optional[ - Union[Union[dict, "MedicalEvent"], List[Union[dict, "MedicalEvent"]]] - ] = empty_list() - parents: Optional[Union[str, List[str]]] = empty_list() - driving_since: Optional[Union[str, XSDDate]] = None - first_known_event: Optional[Union[str, XSDDate]] = None - aliases: Optional[Union[str, List[str]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, AgentId): - self.id = AgentId(self.id) - - if self.primary_email is not None and not isinstance(self.primary_email, str): - self.primary_email = str(self.primary_email) - - if self.secondary_email is not None and not isinstance(self.secondary_email, str): - self.secondary_email = str(self.secondary_email) - - if self.birth_date is not None and not isinstance(self.birth_date, XSDDate): - self.birth_date = XSDDate(self.birth_date) - - if self.death_date is not None and not isinstance(self.death_date, XSDDate): - self.death_date = XSDDate(self.death_date) - - if self.age is not None and not isinstance(self.age, str): - self.age = str(self.age) - - if self.gender is not None and not isinstance(self.gender, GenderType): - self.gender = GenderType(self.gender) - - if self.current_address is not None and not isinstance(self.current_address, Address): - self.current_address = Address(**as_dict(self.current_address)) - - if not isinstance(self.has_employment_history, list): - self.has_employment_history = ( - [self.has_employment_history] if self.has_employment_history is not None else [] - ) - self.has_employment_history = [ - v if isinstance(v, EmploymentEvent) else EmploymentEvent(**as_dict(v)) - for v in self.has_employment_history - ] - - if not isinstance(self.has_familial_relationships, list): - self.has_familial_relationships = ( - [self.has_familial_relationships] - if self.has_familial_relationships is not None - else [] - ) - self.has_familial_relationships = [ - v if isinstance(v, FamilialRelationship) else FamilialRelationship(**as_dict(v)) - for v in self.has_familial_relationships - ] - - if not isinstance(self.has_medical_history, list): - self.has_medical_history = ( - [self.has_medical_history] if self.has_medical_history is not None else [] - ) - self.has_medical_history = [ - v if isinstance(v, MedicalEvent) else MedicalEvent(**as_dict(v)) - for v in self.has_medical_history - ] - - if not isinstance(self.parents, list): - self.parents = [self.parents] if self.parents is not None else [] - self.parents = [v if isinstance(v, str) else str(v) for v in self.parents] - - if self.driving_since is not None and not isinstance(self.driving_since, XSDDate): - self.driving_since = XSDDate(self.driving_since) - - if self.first_known_event is not None and not isinstance(self.first_known_event, XSDDate): - self.first_known_event = XSDDate(self.first_known_event) - - if not isinstance(self.aliases, list): - self.aliases = [self.aliases] if self.aliases is not None else [] - self.aliases = [v if isinstance(v, str) else str(v) for v in self.aliases] - - super().__post_init__(**kwargs) - - -@dataclass -class HasAliases(YAMLRoot): - """ - A mixin applied to any class that can have aliases/alternateNames - """ - - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.HasAliases - class_class_curie: ClassVar[str] = "personinfo:HasAliases" - class_name: ClassVar[str] = "HasAliases" - class_model_uri: ClassVar[URIRef] = PERSONINFO.HasAliases - - aliases: Optional[Union[str, List[str]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.aliases, list): - self.aliases = [self.aliases] if self.aliases is not None else [] - self.aliases = [v if isinstance(v, str) else str(v) for v in self.aliases] - - super().__post_init__(**kwargs) - - -@dataclass -class Organization(NamedThing): - """ - An organization such as a company or university - """ - - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = SCHEMA.Organization - class_class_curie: ClassVar[str] = "schema:Organization" - class_name: ClassVar[str] = "Organization" - class_model_uri: ClassVar[URIRef] = PERSONINFO.Organization - - id: Union[str, OrganizationId] = None - mission_statement: Optional[str] = None - founding_date: Optional[str] = None - founding_location: Optional[Union[str, PlaceId]] = None - aliases: Optional[Union[str, List[str]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, OrganizationId): - self.id = OrganizationId(self.id) - - if self.mission_statement is not None and not isinstance(self.mission_statement, str): - self.mission_statement = str(self.mission_statement) - - if self.founding_date is not None and not isinstance(self.founding_date, str): - self.founding_date = str(self.founding_date) - - if self.founding_location is not None and not isinstance(self.founding_location, PlaceId): - self.founding_location = PlaceId(self.founding_location) - - if not isinstance(self.aliases, list): - self.aliases = [self.aliases] if self.aliases is not None else [] - self.aliases = [v if isinstance(v, str) else str(v) for v in self.aliases] - - super().__post_init__(**kwargs) - - -@dataclass -class Place(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.Place - class_class_curie: ClassVar[str] = "personinfo:Place" - class_name: ClassVar[str] = "Place" - class_model_uri: ClassVar[URIRef] = PERSONINFO.Place - - id: Union[str, PlaceId] = None - label: Optional[str] = None - aliases: Optional[Union[str, List[str]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PlaceId): - self.id = PlaceId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - if not isinstance(self.aliases, list): - self.aliases = [self.aliases] if self.aliases is not None else [] - self.aliases = [v if isinstance(v, str) else str(v) for v in self.aliases] - - super().__post_init__(**kwargs) - - -@dataclass -class Address(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = SCHEMA.PostalAddress - class_class_curie: ClassVar[str] = "schema:PostalAddress" - class_name: ClassVar[str] = "Address" - class_model_uri: ClassVar[URIRef] = PERSONINFO.Address - - street: Optional[str] = None - city: Optional[str] = None - postal_code: Optional[str] = None - address_of: Optional[Union[str, AgentId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.street is not None and not isinstance(self.street, str): - self.street = str(self.street) - - if self.city is not None and not isinstance(self.city, str): - self.city = str(self.city) - - if self.postal_code is not None and not isinstance(self.postal_code, str): - self.postal_code = str(self.postal_code) - - if self.address_of is not None and not isinstance(self.address_of, AgentId): - self.address_of = AgentId(self.address_of) - - super().__post_init__(**kwargs) - - -@dataclass -class Event(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.Event - class_class_curie: ClassVar[str] = "personinfo:Event" - class_name: ClassVar[str] = "Event" - class_model_uri: ClassVar[URIRef] = PERSONINFO.Event - - started_at_time: Optional[Union[str, XSDDate]] = None - ended_at_time: Optional[Union[str, XSDDate]] = None - duration: Optional[float] = None - is_current: Optional[Union[bool, Bool]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.started_at_time is not None and not isinstance(self.started_at_time, XSDDate): - self.started_at_time = XSDDate(self.started_at_time) - - if self.ended_at_time is not None and not isinstance(self.ended_at_time, XSDDate): - self.ended_at_time = XSDDate(self.ended_at_time) - - if self.duration is not None and not isinstance(self.duration, float): - self.duration = float(self.duration) - - if self.is_current is not None and not isinstance(self.is_current, Bool): - self.is_current = Bool(self.is_current) - - super().__post_init__(**kwargs) - - -@dataclass -class Concept(NamedThing): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.Concept - class_class_curie: ClassVar[str] = "personinfo:Concept" - class_name: ClassVar[str] = "Concept" - class_model_uri: ClassVar[URIRef] = PERSONINFO.Concept - - id: Union[str, ConceptId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ConceptId): - self.id = ConceptId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class DiagnosisConcept(Concept): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.DiagnosisConcept - class_class_curie: ClassVar[str] = "personinfo:DiagnosisConcept" - class_name: ClassVar[str] = "DiagnosisConcept" - class_model_uri: ClassVar[URIRef] = PERSONINFO.DiagnosisConcept - - id: Union[str, DiagnosisConceptId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, DiagnosisConceptId): - self.id = DiagnosisConceptId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class ProcedureConcept(Concept): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.ProcedureConcept - class_class_curie: ClassVar[str] = "personinfo:ProcedureConcept" - class_name: ClassVar[str] = "ProcedureConcept" - class_model_uri: ClassVar[URIRef] = PERSONINFO.ProcedureConcept - - id: Union[str, ProcedureConceptId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ProcedureConceptId): - self.id = ProcedureConceptId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Relationship(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.Relationship - class_class_curie: ClassVar[str] = "personinfo:Relationship" - class_name: ClassVar[str] = "Relationship" - class_model_uri: ClassVar[URIRef] = PERSONINFO.Relationship - - started_at_time: Optional[Union[str, XSDDate]] = None - ended_at_time: Optional[Union[str, XSDDate]] = None - related_to: Optional[str] = None - type: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.started_at_time is not None and not isinstance(self.started_at_time, XSDDate): - self.started_at_time = XSDDate(self.started_at_time) - - if self.ended_at_time is not None and not isinstance(self.ended_at_time, XSDDate): - self.ended_at_time = XSDDate(self.ended_at_time) - - if self.related_to is not None and not isinstance(self.related_to, str): - self.related_to = str(self.related_to) - - if self.type is not None and not isinstance(self.type, str): - self.type = str(self.type) - - super().__post_init__(**kwargs) - - -@dataclass -class FamilialRelationship(Relationship): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.FamilialRelationship - class_class_curie: ClassVar[str] = "personinfo:FamilialRelationship" - class_name: ClassVar[str] = "FamilialRelationship" - class_model_uri: ClassVar[URIRef] = PERSONINFO.FamilialRelationship - - type: Union[str, "FamilialRelationshipType"] = None - related_to: Union[str, AgentId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.type): - self.MissingRequiredField("type") - if not isinstance(self.type, FamilialRelationshipType): - self.type = FamilialRelationshipType(self.type) - - if self._is_empty(self.related_to): - self.MissingRequiredField("related_to") - if not isinstance(self.related_to, AgentId): - self.related_to = AgentId(self.related_to) - - super().__post_init__(**kwargs) - - -@dataclass -class EmploymentEvent(Event): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.EmploymentEvent - class_class_curie: ClassVar[str] = "personinfo:EmploymentEvent" - class_name: ClassVar[str] = "EmploymentEvent" - class_model_uri: ClassVar[URIRef] = PERSONINFO.EmploymentEvent - - employed_at: Optional[Union[str, OrganizationId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.employed_at is not None and not isinstance(self.employed_at, OrganizationId): - self.employed_at = OrganizationId(self.employed_at) - - super().__post_init__(**kwargs) - - -@dataclass -class MedicalEvent(Event): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.MedicalEvent - class_class_curie: ClassVar[str] = "personinfo:MedicalEvent" - class_name: ClassVar[str] = "MedicalEvent" - class_model_uri: ClassVar[URIRef] = PERSONINFO.MedicalEvent - - in_location: Optional[Union[str, PlaceId]] = None - diagnosis: Optional[Union[dict, DiagnosisConcept]] = None - procedure: Optional[Union[dict, ProcedureConcept]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.in_location is not None and not isinstance(self.in_location, PlaceId): - self.in_location = PlaceId(self.in_location) - - if self.diagnosis is not None and not isinstance(self.diagnosis, DiagnosisConcept): - self.diagnosis = DiagnosisConcept(**as_dict(self.diagnosis)) - - if self.procedure is not None and not isinstance(self.procedure, ProcedureConcept): - self.procedure = ProcedureConcept(**as_dict(self.procedure)) - - super().__post_init__(**kwargs) - - -@dataclass -class WithLocation(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.WithLocation - class_class_curie: ClassVar[str] = "personinfo:WithLocation" - class_name: ClassVar[str] = "WithLocation" - class_model_uri: ClassVar[URIRef] = PERSONINFO.WithLocation - - in_location: Optional[Union[str, PlaceId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.in_location is not None and not isinstance(self.in_location, PlaceId): - self.in_location = PlaceId(self.in_location) - - super().__post_init__(**kwargs) - - -@dataclass -class Container(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.Container - class_class_curie: ClassVar[str] = "personinfo:Container" - class_name: ClassVar[str] = "Container" - class_model_uri: ClassVar[URIRef] = PERSONINFO.Container - - agents: Optional[ - Union[Dict[Union[str, AgentId], Union[dict, Agent]], List[Union[dict, Agent]]] - ] = empty_dict() - organizations: Optional[ - Union[ - Dict[Union[str, OrganizationId], Union[dict, Organization]], - List[Union[dict, Organization]], - ] - ] = empty_dict() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - self._normalize_inlined_as_list( - slot_name="agents", slot_type=Agent, key_name="id", keyed=True - ) - - self._normalize_inlined_as_list( - slot_name="organizations", slot_type=Organization, key_name="id", keyed=True - ) - - super().__post_init__(**kwargs) - - -# Enumerations -class FamilialRelationshipType(EnumDefinitionImpl): - SIBLING_OF = PermissibleValue(text="SIBLING_OF", meaning=FAMREL["01"]) - CHILD_OF = PermissibleValue(text="CHILD_OF", meaning=FAMREL["05"]) - PARENT_OF = PermissibleValue(text="PARENT_OF", meaning=FAMREL["02"]) - - _defn = EnumDefinition( - name="FamilialRelationshipType", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "parent of", PermissibleValue(text="parent of", meaning=FAMREL["02"])) - - -class GenderType(EnumDefinitionImpl): - _defn = EnumDefinition( - name="GenderType", - ) - - @classmethod - def _addvals(cls): - setattr( - cls, "nonbinary man", PermissibleValue(text="nonbinary man", meaning=GSSO["009254"]) - ) - setattr( - cls, "nonbinary woman", PermissibleValue(text="nonbinary woman", meaning=GSSO["009253"]) - ) - setattr( - cls, - "transgender woman", - PermissibleValue(text="transgender woman", meaning=GSSO["000384"]), - ) - setattr( - cls, "transgender man", PermissibleValue(text="transgender man", meaning=GSSO["000372"]) - ) - setattr( - cls, "cisgender man", PermissibleValue(text="cisgender man", meaning=GSSO["000371"]) - ) - setattr( - cls, "cisgender woman", PermissibleValue(text="cisgender woman", meaning=GSSO["000385"]) - ) - setattr(cls, "None", PermissibleValue(text="None", meaning=GSSO["000283"])) - - -class DiagnosisType(EnumDefinitionImpl): - _defn = EnumDefinition( - name="DiagnosisType", - ) - - -# Slots -class slots: - pass - - -slots.id = Slot( - uri=SCHEMA.identifier, - name="id", - curie=SCHEMA.curie("identifier"), - model_uri=PERSONINFO.id, - domain=None, - range=URIRef, -) - -slots.label = Slot( - uri=SCHEMA.name, - name="label", - curie=SCHEMA.curie("name"), - model_uri=PERSONINFO.label, - domain=None, - range=Optional[str], -) - -slots.description = Slot( - uri=SCHEMA.description, - name="description", - curie=SCHEMA.curie("description"), - model_uri=PERSONINFO.description, - domain=None, - range=Optional[str], -) - -slots.image = Slot( - uri=SCHEMA.image, - name="image", - curie=SCHEMA.curie("image"), - model_uri=PERSONINFO.image, - domain=None, - range=Optional[str], -) - -slots.gender = Slot( - uri=SCHEMA.gender, - name="gender", - curie=SCHEMA.curie("gender"), - model_uri=PERSONINFO.gender, - domain=None, - range=Optional[Union[str, "GenderType"]], -) - -slots.primary_email = Slot( - uri=SCHEMA.email, - name="primary_email", - curie=SCHEMA.curie("email"), - model_uri=PERSONINFO.primary_email, - domain=None, - range=Optional[str], -) - -slots.secondary_email = Slot( - uri=SCHEMA.email, - name="secondary_email", - curie=SCHEMA.curie("email"), - model_uri=PERSONINFO.secondary_email, - domain=None, - range=Optional[str], -) - -slots.birth_date = Slot( - uri=SCHEMA.birthDate, - name="birth_date", - curie=SCHEMA.curie("birthDate"), - model_uri=PERSONINFO.birth_date, - domain=None, - range=Optional[Union[str, XSDDate]], -) - -slots.death_date = Slot( - uri=PERSONINFO.death_date, - name="death_date", - curie=PERSONINFO.curie("death_date"), - model_uri=PERSONINFO.death_date, - domain=None, - range=Optional[Union[str, XSDDate]], -) - -slots.employed_at = Slot( - uri=PERSONINFO.employed_at, - name="employed_at", - curie=PERSONINFO.curie("employed_at"), - model_uri=PERSONINFO.employed_at, - domain=None, - range=Optional[Union[str, OrganizationId]], -) - -slots.is_current = Slot( - uri=PERSONINFO.is_current, - name="is_current", - curie=PERSONINFO.curie("is_current"), - model_uri=PERSONINFO.is_current, - domain=None, - range=Optional[Union[bool, Bool]], -) - -slots.has_employment_history = Slot( - uri=PERSONINFO.has_employment_history, - name="has_employment_history", - curie=PERSONINFO.curie("has_employment_history"), - model_uri=PERSONINFO.has_employment_history, - domain=None, - range=Optional[Union[Union[dict, EmploymentEvent], List[Union[dict, EmploymentEvent]]]], -) - -slots.has_medical_history = Slot( - uri=PERSONINFO.has_medical_history, - name="has_medical_history", - curie=PERSONINFO.curie("has_medical_history"), - model_uri=PERSONINFO.has_medical_history, - domain=None, - range=Optional[Union[Union[dict, MedicalEvent], List[Union[dict, MedicalEvent]]]], -) - -slots.has_familial_relationships = Slot( - uri=PERSONINFO.has_familial_relationships, - name="has_familial_relationships", - curie=PERSONINFO.curie("has_familial_relationships"), - model_uri=PERSONINFO.has_familial_relationships, - domain=None, - range=Optional[ - Union[Union[dict, FamilialRelationship], List[Union[dict, FamilialRelationship]]] - ], -) - -slots.driving_since = Slot( - uri=PERSONINFO.driving_since, - name="driving_since", - curie=PERSONINFO.curie("driving_since"), - model_uri=PERSONINFO.driving_since, - domain=None, - range=Optional[Union[str, XSDDate]], -) - -slots.first_known_event = Slot( - uri=PERSONINFO.first_known_event, - name="first_known_event", - curie=PERSONINFO.curie("first_known_event"), - model_uri=PERSONINFO.first_known_event, - domain=None, - range=Optional[Union[str, XSDDate]], -) - -slots.parents = Slot( - uri=PERSONINFO.parents, - name="parents", - curie=PERSONINFO.curie("parents"), - model_uri=PERSONINFO.parents, - domain=None, - range=Optional[Union[str, List[str]]], -) - -slots.in_location = Slot( - uri=PERSONINFO.in_location, - name="in_location", - curie=PERSONINFO.curie("in_location"), - model_uri=PERSONINFO.in_location, - domain=None, - range=Optional[Union[str, PlaceId]], -) - -slots.current_address = Slot( - uri=PERSONINFO.current_address, - name="current_address", - curie=PERSONINFO.curie("current_address"), - model_uri=PERSONINFO.current_address, - domain=None, - range=Optional[Union[dict, Address]], -) - -slots.age = Slot( - uri=PERSONINFO.age, - name="age", - curie=PERSONINFO.curie("age"), - model_uri=PERSONINFO.age, - domain=None, - range=Optional[str], - pattern=re.compile(r"\d+ \S+"), -) - -slots.related_to = Slot( - uri=PERSONINFO.related_to, - name="related_to", - curie=PERSONINFO.curie("related_to"), - model_uri=PERSONINFO.related_to, - domain=None, - range=Optional[str], -) - -slots.type = Slot( - uri=PERSONINFO.type, - name="type", - curie=PERSONINFO.curie("type"), - model_uri=PERSONINFO.type, - domain=None, - range=Optional[str], -) - -slots.street = Slot( - uri=PERSONINFO.street, - name="street", - curie=PERSONINFO.curie("street"), - model_uri=PERSONINFO.street, - domain=None, - range=Optional[str], -) - -slots.city = Slot( - uri=PERSONINFO.city, - name="city", - curie=PERSONINFO.curie("city"), - model_uri=PERSONINFO.city, - domain=None, - range=Optional[str], -) - -slots.mission_statement = Slot( - uri=PERSONINFO.mission_statement, - name="mission_statement", - curie=PERSONINFO.curie("mission_statement"), - model_uri=PERSONINFO.mission_statement, - domain=None, - range=Optional[str], -) - -slots.founding_date = Slot( - uri=PERSONINFO.founding_date, - name="founding_date", - curie=PERSONINFO.curie("founding_date"), - model_uri=PERSONINFO.founding_date, - domain=None, - range=Optional[str], -) - -slots.founding_location = Slot( - uri=PERSONINFO.founding_location, - name="founding_location", - curie=PERSONINFO.curie("founding_location"), - model_uri=PERSONINFO.founding_location, - domain=None, - range=Optional[Union[str, PlaceId]], -) - -slots.postal_code = Slot( - uri=PERSONINFO.postal_code, - name="postal_code", - curie=PERSONINFO.curie("postal_code"), - model_uri=PERSONINFO.postal_code, - domain=None, - range=Optional[str], -) - -slots.address_of = Slot( - uri=PERSONINFO.address_of, - name="address_of", - curie=PERSONINFO.curie("address_of"), - model_uri=PERSONINFO.address_of, - domain=None, - range=Optional[Union[str, AgentId]], -) - -slots.started_at_time = Slot( - uri=PROV.startedAtTime, - name="started_at_time", - curie=PROV.curie("startedAtTime"), - model_uri=PERSONINFO.started_at_time, - domain=None, - range=Optional[Union[str, XSDDate]], -) - -slots.duration = Slot( - uri=PERSONINFO.duration, - name="duration", - curie=PERSONINFO.curie("duration"), - model_uri=PERSONINFO.duration, - domain=None, - range=Optional[float], -) - -slots.diagnosis = Slot( - uri=PERSONINFO.diagnosis, - name="diagnosis", - curie=PERSONINFO.curie("diagnosis"), - model_uri=PERSONINFO.diagnosis, - domain=None, - range=Optional[Union[dict, DiagnosisConcept]], -) - -slots.procedure = Slot( - uri=PERSONINFO.procedure, - name="procedure", - curie=PERSONINFO.curie("procedure"), - model_uri=PERSONINFO.procedure, - domain=None, - range=Optional[Union[dict, ProcedureConcept]], -) - -slots.ended_at_time = Slot( - uri=PROV.endedAtTime, - name="ended_at_time", - curie=PROV.curie("endedAtTime"), - model_uri=PERSONINFO.ended_at_time, - domain=None, - range=Optional[Union[str, XSDDate]], -) - -slots.agents = Slot( - uri=PERSONINFO.agents, - name="agents", - curie=PERSONINFO.curie("agents"), - model_uri=PERSONINFO.agents, - domain=None, - range=Optional[Union[Dict[Union[str, AgentId], Union[dict, Agent]], List[Union[dict, Agent]]]], -) - -slots.organizations = Slot( - uri=PERSONINFO.organizations, - name="organizations", - curie=PERSONINFO.curie("organizations"), - model_uri=PERSONINFO.organizations, - domain=None, - range=Optional[ - Union[ - Dict[Union[str, OrganizationId], Union[dict, Organization]], - List[Union[dict, Organization]], - ] - ], -) - -slots.hasAliases__aliases = Slot( - uri=PERSONINFO.aliases, - name="hasAliases__aliases", - curie=PERSONINFO.curie("aliases"), - model_uri=PERSONINFO.hasAliases__aliases, - domain=None, - range=Optional[Union[str, List[str]]], -) - -slots.Agent_primary_email = Slot( - uri=SCHEMA.email, - name="Agent_primary_email", - curie=SCHEMA.curie("email"), - model_uri=PERSONINFO.Agent_primary_email, - domain=Agent, - range=Optional[str], - pattern=re.compile(r"^\S+@[\S+\.]+\S+"), -) - -slots.Agent_secondary_email = Slot( - uri=SCHEMA.email, - name="Agent_secondary_email", - curie=SCHEMA.curie("email"), - model_uri=PERSONINFO.Agent_secondary_email, - domain=Agent, - range=Optional[str], - pattern=re.compile(r"^\S+@[\S+\.]+\S+"), -) - -slots.FamilialRelationship_type = Slot( - uri=PERSONINFO.type, - name="FamilialRelationship_type", - curie=PERSONINFO.curie("type"), - model_uri=PERSONINFO.FamilialRelationship_type, - domain=FamilialRelationship, - range=Union[str, "FamilialRelationshipType"], -) - -slots.FamilialRelationship_related_to = Slot( - uri=PERSONINFO.related_to, - name="FamilialRelationship_related_to", - curie=PERSONINFO.curie("related_to"), - model_uri=PERSONINFO.FamilialRelationship_related_to, - domain=FamilialRelationship, - range=Union[str, AgentId], -) diff --git a/tests/input/examples/personinfo_basic/model/personinfo_model.py b/tests/input/examples/personinfo_basic/model/personinfo_model.py deleted file mode 100644 index fd09c3a..0000000 --- a/tests/input/examples/personinfo_basic/model/personinfo_model.py +++ /dev/null @@ -1,1043 +0,0 @@ -# Auto generated from personinfo.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-05-03T07:06:21 -# Schema: personinfo -# -# id: https://w3id.org/linkml/examples/personinfo -# description: Information about people, based on [schema.org](http://schema.org) -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import re -from dataclasses import dataclass -from typing import Any, ClassVar, Dict, List, Optional, Union - -from jsonasobj2 import as_dict -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.utils.dataclass_extensions_376 import ( - dataclasses_init_fn_with_kwargs, -) -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from linkml_runtime.utils.metamodelcore import Bool, XSDDate, empty_dict, empty_list -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str -from rdflib import URIRef - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -CODE = CurieNamespace("CODE", "http://example.org/code/") -GEO = CurieNamespace("GEO", "http://example.org/geoloc/") -GSSO = CurieNamespace("GSSO", "http://purl.obolibrary.org/obo/GSSO_") -P = CurieNamespace("P", "http://example.org/P/") -ROR = CurieNamespace("ROR", "http://example.org/ror/") -FAMREL = CurieNamespace("famrel", "https://example.org/FamilialRelations#") -LINKML = CurieNamespace("linkml", "https://w3id.org/linkml/") -PERSONINFO = CurieNamespace("personinfo", "https://w3id.org/linkml/examples/personinfo/") -PROV = CurieNamespace("prov", "http://www.w3.org/ns/prov#") -RDF = CurieNamespace("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#") -RDFS = CurieNamespace("rdfs", "http://www.w3.org/2000/01/rdf-schema#") -SCHEMA = CurieNamespace("schema", "http://schema.org/") -SKOS = CurieNamespace("skos", "http://example.org/UNKNOWN/skos/") -XSD = CurieNamespace("xsd", "http://www.w3.org/2001/XMLSchema#") -DEFAULT_ = PERSONINFO - - -# Types - - -# Class references -class NamedThingId(extended_str): - pass - - -class PersonId(NamedThingId): - pass - - -class OrganizationId(NamedThingId): - pass - - -class PlaceId(extended_str): - pass - - -class ConceptId(NamedThingId): - pass - - -class DiagnosisConceptId(ConceptId): - pass - - -class ProcedureConceptId(ConceptId): - pass - - -@dataclass -class NamedThing(YAMLRoot): - """ - A generic grouping for any identifiable entity - """ - - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.NamedThing - class_class_curie: ClassVar[str] = "personinfo:NamedThing" - class_name: ClassVar[str] = "NamedThing" - class_model_uri: ClassVar[URIRef] = PERSONINFO.NamedThing - - id: Union[str, NamedThingId] = None - name: Optional[str] = None - description: Optional[str] = None - image: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedThingId): - self.id = NamedThingId(self.id) - - if self.name is not None and not isinstance(self.name, str): - self.name = str(self.name) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if self.image is not None and not isinstance(self.image, str): - self.image = str(self.image) - - super().__post_init__(**kwargs) - - -@dataclass -class Person(NamedThing): - """ - A person (alive, dead, undead, or fictional). - """ - - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = SCHEMA.Person - class_class_curie: ClassVar[str] = "schema:Person" - class_name: ClassVar[str] = "Person" - class_model_uri: ClassVar[URIRef] = PERSONINFO.Person - - id: Union[str, PersonId] = None - primary_email: Optional[str] = None - secondary_email: Optional[str] = None - birth_date: Optional[str] = None - age_in_years: Optional[int] = None - gender: Optional[Union[str, "GenderType"]] = None - current_address: Optional[Union[dict, "Address"]] = None - has_employment_history: Optional[ - Union[Union[dict, "EmploymentEvent"], List[Union[dict, "EmploymentEvent"]]] - ] = empty_list() - has_familial_relationships: Optional[ - Union[Union[dict, "FamilialRelationship"], List[Union[dict, "FamilialRelationship"]]] - ] = empty_list() - has_medical_history: Optional[ - Union[Union[dict, "MedicalEvent"], List[Union[dict, "MedicalEvent"]]] - ] = empty_list() - has_important_life_events: Optional[ - Union[Union[dict, "ImportantLifeEvent"], List[Union[dict, "ImportantLifeEvent"]]] - ] = empty_list() - aliases: Optional[Union[str, List[str]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PersonId): - self.id = PersonId(self.id) - - if self.primary_email is not None and not isinstance(self.primary_email, str): - self.primary_email = str(self.primary_email) - - if self.secondary_email is not None and not isinstance(self.secondary_email, str): - self.secondary_email = str(self.secondary_email) - - if self.birth_date is not None and not isinstance(self.birth_date, str): - self.birth_date = str(self.birth_date) - - if self.age_in_years is not None and not isinstance(self.age_in_years, int): - self.age_in_years = int(self.age_in_years) - - if self.gender is not None and not isinstance(self.gender, GenderType): - self.gender = GenderType(self.gender) - - if self.current_address is not None and not isinstance(self.current_address, Address): - self.current_address = Address(**as_dict(self.current_address)) - - if not isinstance(self.has_employment_history, list): - self.has_employment_history = ( - [self.has_employment_history] if self.has_employment_history is not None else [] - ) - self.has_employment_history = [ - v if isinstance(v, EmploymentEvent) else EmploymentEvent(**as_dict(v)) - for v in self.has_employment_history - ] - - if not isinstance(self.has_familial_relationships, list): - self.has_familial_relationships = ( - [self.has_familial_relationships] - if self.has_familial_relationships is not None - else [] - ) - self.has_familial_relationships = [ - v if isinstance(v, FamilialRelationship) else FamilialRelationship(**as_dict(v)) - for v in self.has_familial_relationships - ] - - if not isinstance(self.has_medical_history, list): - self.has_medical_history = ( - [self.has_medical_history] if self.has_medical_history is not None else [] - ) - self.has_medical_history = [ - v if isinstance(v, MedicalEvent) else MedicalEvent(**as_dict(v)) - for v in self.has_medical_history - ] - - if not isinstance(self.has_important_life_events, list): - self.has_important_life_events = ( - [self.has_important_life_events] - if self.has_important_life_events is not None - else [] - ) - self.has_important_life_events = [ - v if isinstance(v, ImportantLifeEvent) else ImportantLifeEvent(**as_dict(v)) - for v in self.has_important_life_events - ] - - if not isinstance(self.aliases, list): - self.aliases = [self.aliases] if self.aliases is not None else [] - self.aliases = [v if isinstance(v, str) else str(v) for v in self.aliases] - - super().__post_init__(**kwargs) - - -@dataclass -class HasAliases(YAMLRoot): - """ - A mixin applied to any class that can have aliases/alternateNames - """ - - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.HasAliases - class_class_curie: ClassVar[str] = "personinfo:HasAliases" - class_name: ClassVar[str] = "HasAliases" - class_model_uri: ClassVar[URIRef] = PERSONINFO.HasAliases - - aliases: Optional[Union[str, List[str]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.aliases, list): - self.aliases = [self.aliases] if self.aliases is not None else [] - self.aliases = [v if isinstance(v, str) else str(v) for v in self.aliases] - - super().__post_init__(**kwargs) - - -@dataclass -class Organization(NamedThing): - """ - An organization such as a company or university - """ - - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = SCHEMA.Organization - class_class_curie: ClassVar[str] = "schema:Organization" - class_name: ClassVar[str] = "Organization" - class_model_uri: ClassVar[URIRef] = PERSONINFO.Organization - - id: Union[str, OrganizationId] = None - mission_statement: Optional[str] = None - founding_date: Optional[str] = None - founding_location: Optional[Union[str, PlaceId]] = None - aliases: Optional[Union[str, List[str]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, OrganizationId): - self.id = OrganizationId(self.id) - - if self.mission_statement is not None and not isinstance(self.mission_statement, str): - self.mission_statement = str(self.mission_statement) - - if self.founding_date is not None and not isinstance(self.founding_date, str): - self.founding_date = str(self.founding_date) - - if self.founding_location is not None and not isinstance(self.founding_location, PlaceId): - self.founding_location = PlaceId(self.founding_location) - - if not isinstance(self.aliases, list): - self.aliases = [self.aliases] if self.aliases is not None else [] - self.aliases = [v if isinstance(v, str) else str(v) for v in self.aliases] - - super().__post_init__(**kwargs) - - -@dataclass -class Place(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.Place - class_class_curie: ClassVar[str] = "personinfo:Place" - class_name: ClassVar[str] = "Place" - class_model_uri: ClassVar[URIRef] = PERSONINFO.Place - - id: Union[str, PlaceId] = None - name: Optional[str] = None - aliases: Optional[Union[str, List[str]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PlaceId): - self.id = PlaceId(self.id) - - if self.name is not None and not isinstance(self.name, str): - self.name = str(self.name) - - if not isinstance(self.aliases, list): - self.aliases = [self.aliases] if self.aliases is not None else [] - self.aliases = [v if isinstance(v, str) else str(v) for v in self.aliases] - - super().__post_init__(**kwargs) - - -@dataclass -class Address(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = SCHEMA.PostalAddress - class_class_curie: ClassVar[str] = "schema:PostalAddress" - class_name: ClassVar[str] = "Address" - class_model_uri: ClassVar[URIRef] = PERSONINFO.Address - - street: Optional[str] = None - city: Optional[str] = None - postal_code: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.street is not None and not isinstance(self.street, str): - self.street = str(self.street) - - if self.city is not None and not isinstance(self.city, str): - self.city = str(self.city) - - if self.postal_code is not None and not isinstance(self.postal_code, str): - self.postal_code = str(self.postal_code) - - super().__post_init__(**kwargs) - - -@dataclass -class Event(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.Event - class_class_curie: ClassVar[str] = "personinfo:Event" - class_name: ClassVar[str] = "Event" - class_model_uri: ClassVar[URIRef] = PERSONINFO.Event - - started_at_time: Optional[Union[str, XSDDate]] = None - ended_at_time: Optional[Union[str, XSDDate]] = None - duration: Optional[float] = None - is_current: Optional[Union[bool, Bool]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.started_at_time is not None and not isinstance(self.started_at_time, XSDDate): - self.started_at_time = XSDDate(self.started_at_time) - - if self.ended_at_time is not None and not isinstance(self.ended_at_time, XSDDate): - self.ended_at_time = XSDDate(self.ended_at_time) - - if self.duration is not None and not isinstance(self.duration, float): - self.duration = float(self.duration) - - if self.is_current is not None and not isinstance(self.is_current, Bool): - self.is_current = Bool(self.is_current) - - super().__post_init__(**kwargs) - - -@dataclass -class Concept(NamedThing): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.Concept - class_class_curie: ClassVar[str] = "personinfo:Concept" - class_name: ClassVar[str] = "Concept" - class_model_uri: ClassVar[URIRef] = PERSONINFO.Concept - - id: Union[str, ConceptId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ConceptId): - self.id = ConceptId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class DiagnosisConcept(Concept): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.DiagnosisConcept - class_class_curie: ClassVar[str] = "personinfo:DiagnosisConcept" - class_name: ClassVar[str] = "DiagnosisConcept" - class_model_uri: ClassVar[URIRef] = PERSONINFO.DiagnosisConcept - - id: Union[str, DiagnosisConceptId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, DiagnosisConceptId): - self.id = DiagnosisConceptId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class ProcedureConcept(Concept): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.ProcedureConcept - class_class_curie: ClassVar[str] = "personinfo:ProcedureConcept" - class_name: ClassVar[str] = "ProcedureConcept" - class_model_uri: ClassVar[URIRef] = PERSONINFO.ProcedureConcept - - id: Union[str, ProcedureConceptId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ProcedureConceptId): - self.id = ProcedureConceptId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Relationship(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.Relationship - class_class_curie: ClassVar[str] = "personinfo:Relationship" - class_name: ClassVar[str] = "Relationship" - class_model_uri: ClassVar[URIRef] = PERSONINFO.Relationship - - started_at_time: Optional[Union[str, XSDDate]] = None - ended_at_time: Optional[Union[str, XSDDate]] = None - related_to: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.started_at_time is not None and not isinstance(self.started_at_time, XSDDate): - self.started_at_time = XSDDate(self.started_at_time) - - if self.ended_at_time is not None and not isinstance(self.ended_at_time, XSDDate): - self.ended_at_time = XSDDate(self.ended_at_time) - - if self.related_to is not None and not isinstance(self.related_to, str): - self.related_to = str(self.related_to) - - super().__post_init__(**kwargs) - - -@dataclass -class FamilialRelationship(Relationship): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.FamilialRelationship - class_class_curie: ClassVar[str] = "personinfo:FamilialRelationship" - class_name: ClassVar[str] = "FamilialRelationship" - class_model_uri: ClassVar[URIRef] = PERSONINFO.FamilialRelationship - - type: Union[str, "FamilialRelationshipType"] = None - related_to: Union[str, PersonId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.type): - self.MissingRequiredField("type") - if not isinstance(self.type, FamilialRelationshipType): - self.type = FamilialRelationshipType(self.type) - - if self._is_empty(self.related_to): - self.MissingRequiredField("related_to") - if not isinstance(self.related_to, PersonId): - self.related_to = PersonId(self.related_to) - - super().__post_init__(**kwargs) - - -@dataclass -class EmploymentEvent(Event): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.EmploymentEvent - class_class_curie: ClassVar[str] = "personinfo:EmploymentEvent" - class_name: ClassVar[str] = "EmploymentEvent" - class_model_uri: ClassVar[URIRef] = PERSONINFO.EmploymentEvent - - employed_at: Optional[Union[str, OrganizationId]] = None - type: Optional[Union[str, "RelationshipType"]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.employed_at is not None and not isinstance(self.employed_at, OrganizationId): - self.employed_at = OrganizationId(self.employed_at) - - if self.type is not None and not isinstance(self.type, RelationshipType): - self.type = RelationshipType(self.type) - - super().__post_init__(**kwargs) - - -@dataclass -class MedicalEvent(Event): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.MedicalEvent - class_class_curie: ClassVar[str] = "personinfo:MedicalEvent" - class_name: ClassVar[str] = "MedicalEvent" - class_model_uri: ClassVar[URIRef] = PERSONINFO.MedicalEvent - - in_location: Optional[Union[str, PlaceId]] = None - diagnosis: Optional[Union[dict, DiagnosisConcept]] = None - procedure: Optional[Union[dict, ProcedureConcept]] = None - type: Optional[Union[str, "RelationshipType"]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.in_location is not None and not isinstance(self.in_location, PlaceId): - self.in_location = PlaceId(self.in_location) - - if self.diagnosis is not None and not isinstance(self.diagnosis, DiagnosisConcept): - self.diagnosis = DiagnosisConcept(**as_dict(self.diagnosis)) - - if self.procedure is not None and not isinstance(self.procedure, ProcedureConcept): - self.procedure = ProcedureConcept(**as_dict(self.procedure)) - - if self.type is not None and not isinstance(self.type, RelationshipType): - self.type = RelationshipType(self.type) - - super().__post_init__(**kwargs) - - -@dataclass -class ImportantLifeEvent(Event): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.ImportantLifeEvent - class_class_curie: ClassVar[str] = "personinfo:ImportantLifeEvent" - class_name: ClassVar[str] = "ImportantLifeEvent" - class_model_uri: ClassVar[URIRef] = PERSONINFO.ImportantLifeEvent - - important_event_date: Union[str, XSDDate] = None - event_name: Union[str, "ImportantLifeEventType"] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.important_event_date): - self.MissingRequiredField("important_event_date") - if not isinstance(self.important_event_date, XSDDate): - self.important_event_date = XSDDate(self.important_event_date) - - if self._is_empty(self.event_name): - self.MissingRequiredField("event_name") - if not isinstance(self.event_name, ImportantLifeEventType): - self.event_name = ImportantLifeEventType(self.event_name) - - super().__post_init__(**kwargs) - - -@dataclass -class WithLocation(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.WithLocation - class_class_curie: ClassVar[str] = "personinfo:WithLocation" - class_name: ClassVar[str] = "WithLocation" - class_model_uri: ClassVar[URIRef] = PERSONINFO.WithLocation - - in_location: Optional[Union[str, PlaceId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.in_location is not None and not isinstance(self.in_location, PlaceId): - self.in_location = PlaceId(self.in_location) - - super().__post_init__(**kwargs) - - -@dataclass -class Container(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PERSONINFO.Container - class_class_curie: ClassVar[str] = "personinfo:Container" - class_name: ClassVar[str] = "Container" - class_model_uri: ClassVar[URIRef] = PERSONINFO.Container - - persons: Optional[ - Union[Dict[Union[str, PersonId], Union[dict, Person]], List[Union[dict, Person]]] - ] = empty_dict() - organizations: Optional[ - Union[ - Dict[Union[str, OrganizationId], Union[dict, Organization]], - List[Union[dict, Organization]], - ] - ] = empty_dict() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - self._normalize_inlined_as_list( - slot_name="persons", slot_type=Person, key_name="id", keyed=True - ) - - self._normalize_inlined_as_list( - slot_name="organizations", slot_type=Organization, key_name="id", keyed=True - ) - - super().__post_init__(**kwargs) - - -# Enumerations -class RelationshipType(EnumDefinitionImpl): - _defn = EnumDefinition( - name="RelationshipType", - ) - - -class FamilialRelationshipType(EnumDefinitionImpl): - SIBLING_OF = PermissibleValue(text="SIBLING_OF", meaning=FAMREL["01"]) - PARENT_OF = PermissibleValue(text="PARENT_OF", meaning=FAMREL["02"]) - CHILD_OF = PermissibleValue(text="CHILD_OF", meaning=FAMREL["05"]) - FATHER_OF = PermissibleValue(text="FATHER_OF", meaning=FAMREL["11"]) - - _defn = EnumDefinition( - name="FamilialRelationshipType", - ) - - -class GenderType(EnumDefinitionImpl): - _defn = EnumDefinition( - name="GenderType", - ) - - @classmethod - def _addvals(cls): - setattr( - cls, "nonbinary man", PermissibleValue(text="nonbinary man", meaning=GSSO["009254"]) - ) - setattr( - cls, "nonbinary woman", PermissibleValue(text="nonbinary woman", meaning=GSSO["009253"]) - ) - setattr( - cls, - "transgender woman", - PermissibleValue(text="transgender woman", meaning=GSSO["000384"]), - ) - setattr( - cls, "transgender man", PermissibleValue(text="transgender man", meaning=GSSO["000372"]) - ) - setattr( - cls, "cisgender man", PermissibleValue(text="cisgender man", meaning=GSSO["000371"]) - ) - setattr( - cls, "cisgender woman", PermissibleValue(text="cisgender woman", meaning=GSSO["000385"]) - ) - setattr(cls, "None", PermissibleValue(text="None", meaning=GSSO["000283"])) - - -class DiagnosisType(EnumDefinitionImpl): - _defn = EnumDefinition( - name="DiagnosisType", - ) - - -class ImportantLifeEventType(EnumDefinitionImpl): - BIRTH = PermissibleValue(text="BIRTH") - DEATH = PermissibleValue(text="DEATH") - PASSED_DRIVING_TEST = PermissibleValue(text="PASSED_DRIVING_TEST") - FIRST_CAR_ACCIDENT = PermissibleValue(text="FIRST_CAR_ACCIDENT") - MARRIAGE = PermissibleValue(text="MARRIAGE") - DIVORCE = PermissibleValue(text="DIVORCE") - - _defn = EnumDefinition( - name="ImportantLifeEventType", - ) - - -# Slots -class slots: - pass - - -slots.id = Slot( - uri=SCHEMA.identifier, - name="id", - curie=SCHEMA.curie("identifier"), - model_uri=PERSONINFO.id, - domain=None, - range=URIRef, -) - -slots.name = Slot( - uri=SCHEMA.name, - name="name", - curie=SCHEMA.curie("name"), - model_uri=PERSONINFO.name, - domain=None, - range=Optional[str], -) - -slots.description = Slot( - uri=SCHEMA.description, - name="description", - curie=SCHEMA.curie("description"), - model_uri=PERSONINFO.description, - domain=None, - range=Optional[str], -) - -slots.image = Slot( - uri=SCHEMA.image, - name="image", - curie=SCHEMA.curie("image"), - model_uri=PERSONINFO.image, - domain=None, - range=Optional[str], -) - -slots.gender = Slot( - uri=SCHEMA.gender, - name="gender", - curie=SCHEMA.curie("gender"), - model_uri=PERSONINFO.gender, - domain=None, - range=Optional[Union[str, "GenderType"]], -) - -slots.primary_email = Slot( - uri=SCHEMA.email, - name="primary_email", - curie=SCHEMA.curie("email"), - model_uri=PERSONINFO.primary_email, - domain=None, - range=Optional[str], -) - -slots.secondary_email = Slot( - uri=SCHEMA.email, - name="secondary_email", - curie=SCHEMA.curie("email"), - model_uri=PERSONINFO.secondary_email, - domain=None, - range=Optional[str], -) - -slots.birth_date = Slot( - uri=SCHEMA.birthDate, - name="birth_date", - curie=SCHEMA.curie("birthDate"), - model_uri=PERSONINFO.birth_date, - domain=None, - range=Optional[str], -) - -slots.employed_at = Slot( - uri=PERSONINFO.employed_at, - name="employed_at", - curie=PERSONINFO.curie("employed_at"), - model_uri=PERSONINFO.employed_at, - domain=None, - range=Optional[Union[str, OrganizationId]], -) - -slots.is_current = Slot( - uri=PERSONINFO.is_current, - name="is_current", - curie=PERSONINFO.curie("is_current"), - model_uri=PERSONINFO.is_current, - domain=None, - range=Optional[Union[bool, Bool]], -) - -slots.has_employment_history = Slot( - uri=PERSONINFO.has_employment_history, - name="has_employment_history", - curie=PERSONINFO.curie("has_employment_history"), - model_uri=PERSONINFO.has_employment_history, - domain=None, - range=Optional[Union[Union[dict, EmploymentEvent], List[Union[dict, EmploymentEvent]]]], -) - -slots.has_medical_history = Slot( - uri=PERSONINFO.has_medical_history, - name="has_medical_history", - curie=PERSONINFO.curie("has_medical_history"), - model_uri=PERSONINFO.has_medical_history, - domain=None, - range=Optional[Union[Union[dict, MedicalEvent], List[Union[dict, MedicalEvent]]]], -) - -slots.has_familial_relationships = Slot( - uri=PERSONINFO.has_familial_relationships, - name="has_familial_relationships", - curie=PERSONINFO.curie("has_familial_relationships"), - model_uri=PERSONINFO.has_familial_relationships, - domain=None, - range=Optional[ - Union[Union[dict, FamilialRelationship], List[Union[dict, FamilialRelationship]]] - ], -) - -slots.has_important_life_events = Slot( - uri=PERSONINFO.has_important_life_events, - name="has_important_life_events", - curie=PERSONINFO.curie("has_important_life_events"), - model_uri=PERSONINFO.has_important_life_events, - domain=None, - range=Optional[Union[Union[dict, ImportantLifeEvent], List[Union[dict, ImportantLifeEvent]]]], -) - -slots.important_event_date = Slot( - uri=PERSONINFO.important_event_date, - name="important_event_date", - curie=PERSONINFO.curie("important_event_date"), - model_uri=PERSONINFO.important_event_date, - domain=None, - range=Union[str, XSDDate], -) - -slots.event_name = Slot( - uri=PERSONINFO.event_name, - name="event_name", - curie=PERSONINFO.curie("event_name"), - model_uri=PERSONINFO.event_name, - domain=None, - range=Union[str, "ImportantLifeEventType"], -) - -slots.in_location = Slot( - uri=PERSONINFO.in_location, - name="in_location", - curie=PERSONINFO.curie("in_location"), - model_uri=PERSONINFO.in_location, - domain=None, - range=Optional[Union[str, PlaceId]], -) - -slots.current_address = Slot( - uri=PERSONINFO.current_address, - name="current_address", - curie=PERSONINFO.curie("current_address"), - model_uri=PERSONINFO.current_address, - domain=None, - range=Optional[Union[dict, Address]], -) - -slots.age_in_years = Slot( - uri=PERSONINFO.age_in_years, - name="age_in_years", - curie=PERSONINFO.curie("age_in_years"), - model_uri=PERSONINFO.age_in_years, - domain=None, - range=Optional[int], -) - -slots.related_to = Slot( - uri=PERSONINFO.related_to, - name="related_to", - curie=PERSONINFO.curie("related_to"), - model_uri=PERSONINFO.related_to, - domain=None, - range=Optional[str], -) - -slots.type = Slot( - uri=PERSONINFO.type, - name="type", - curie=PERSONINFO.curie("type"), - model_uri=PERSONINFO.type, - domain=None, - range=Optional[Union[str, "RelationshipType"]], -) - -slots.street = Slot( - uri=PERSONINFO.street, - name="street", - curie=PERSONINFO.curie("street"), - model_uri=PERSONINFO.street, - domain=None, - range=Optional[str], -) - -slots.city = Slot( - uri=PERSONINFO.city, - name="city", - curie=PERSONINFO.curie("city"), - model_uri=PERSONINFO.city, - domain=None, - range=Optional[str], -) - -slots.mission_statement = Slot( - uri=PERSONINFO.mission_statement, - name="mission_statement", - curie=PERSONINFO.curie("mission_statement"), - model_uri=PERSONINFO.mission_statement, - domain=None, - range=Optional[str], -) - -slots.founding_date = Slot( - uri=PERSONINFO.founding_date, - name="founding_date", - curie=PERSONINFO.curie("founding_date"), - model_uri=PERSONINFO.founding_date, - domain=None, - range=Optional[str], -) - -slots.founding_location = Slot( - uri=PERSONINFO.founding_location, - name="founding_location", - curie=PERSONINFO.curie("founding_location"), - model_uri=PERSONINFO.founding_location, - domain=None, - range=Optional[Union[str, PlaceId]], -) - -slots.postal_code = Slot( - uri=PERSONINFO.postal_code, - name="postal_code", - curie=PERSONINFO.curie("postal_code"), - model_uri=PERSONINFO.postal_code, - domain=None, - range=Optional[str], -) - -slots.started_at_time = Slot( - uri=PROV.startedAtTime, - name="started_at_time", - curie=PROV.curie("startedAtTime"), - model_uri=PERSONINFO.started_at_time, - domain=None, - range=Optional[Union[str, XSDDate]], -) - -slots.duration = Slot( - uri=PERSONINFO.duration, - name="duration", - curie=PERSONINFO.curie("duration"), - model_uri=PERSONINFO.duration, - domain=None, - range=Optional[float], -) - -slots.diagnosis = Slot( - uri=PERSONINFO.diagnosis, - name="diagnosis", - curie=PERSONINFO.curie("diagnosis"), - model_uri=PERSONINFO.diagnosis, - domain=None, - range=Optional[Union[dict, DiagnosisConcept]], -) - -slots.procedure = Slot( - uri=PERSONINFO.procedure, - name="procedure", - curie=PERSONINFO.curie("procedure"), - model_uri=PERSONINFO.procedure, - domain=None, - range=Optional[Union[dict, ProcedureConcept]], -) - -slots.ended_at_time = Slot( - uri=PROV.endedAtTime, - name="ended_at_time", - curie=PROV.curie("endedAtTime"), - model_uri=PERSONINFO.ended_at_time, - domain=None, - range=Optional[Union[str, XSDDate]], -) - -slots.persons = Slot( - uri=PERSONINFO.persons, - name="persons", - curie=PERSONINFO.curie("persons"), - model_uri=PERSONINFO.persons, - domain=None, - range=Optional[ - Union[Dict[Union[str, PersonId], Union[dict, Person]], List[Union[dict, Person]]] - ], -) - -slots.organizations = Slot( - uri=PERSONINFO.organizations, - name="organizations", - curie=PERSONINFO.curie("organizations"), - model_uri=PERSONINFO.organizations, - domain=None, - range=Optional[ - Union[ - Dict[Union[str, OrganizationId], Union[dict, Organization]], - List[Union[dict, Organization]], - ] - ], -) - -slots.hasAliases__aliases = Slot( - uri=PERSONINFO.aliases, - name="hasAliases__aliases", - curie=PERSONINFO.curie("aliases"), - model_uri=PERSONINFO.hasAliases__aliases, - domain=None, - range=Optional[Union[str, List[str]]], -) - -slots.Person_primary_email = Slot( - uri=SCHEMA.email, - name="Person_primary_email", - curie=SCHEMA.curie("email"), - model_uri=PERSONINFO.Person_primary_email, - domain=Person, - range=Optional[str], - pattern=re.compile(r"^\S+@[\S+\.]+\S+"), -) - -slots.Person_secondary_email = Slot( - uri=SCHEMA.email, - name="Person_secondary_email", - curie=SCHEMA.curie("email"), - model_uri=PERSONINFO.Person_secondary_email, - domain=Person, - range=Optional[str], - pattern=re.compile(r"^\S+@[\S+\.]+\S+"), -) - -slots.FamilialRelationship_type = Slot( - uri=PERSONINFO.type, - name="FamilialRelationship_type", - curie=PERSONINFO.curie("type"), - model_uri=PERSONINFO.FamilialRelationship_type, - domain=FamilialRelationship, - range=Union[str, "FamilialRelationshipType"], -) - -slots.FamilialRelationship_related_to = Slot( - uri=PERSONINFO.related_to, - name="FamilialRelationship_related_to", - curie=PERSONINFO.curie("related_to"), - model_uri=PERSONINFO.FamilialRelationship_related_to, - domain=FamilialRelationship, - range=Union[str, PersonId], -) diff --git a/tests/input/examples/personinfo_basic/output/Container-001.transformed.yaml b/tests/input/examples/personinfo_basic/output/Container-001.transformed.yaml deleted file mode 100644 index bd8d179..0000000 --- a/tests/input/examples/personinfo_basic/output/Container-001.transformed.yaml +++ /dev/null @@ -1,49 +0,0 @@ -agents: -- id: P:001 - label: fred bloggs - age: 33 years - primary_email: fred.bloggs@example.com - secondary_email: null - gender: null - driving_since: 2014-03-31 - first_known_event: 1990-01-01 - death_date: null - current_address: - address_of: foo - street: 1 oak street - city: oaktown - has_familial_relationships: - - type: SIBLING_OF - related_to: P:002 - - type: CHILD_OF - related_to: P:003 -- id: P:002 - label: Alison Wu - age: null - primary_email: null - secondary_email: null - gender: null - driving_since: null - first_known_event: null - death_date: null - current_address: null - has_familial_relationships: - - type: SIBLING_OF - related_to: P:001 - - type: CHILD_OF - related_to: P:003 -- id: P:003 - label: Mr. Blobby - age: null - primary_email: null - secondary_email: null - gender: null - driving_since: null - first_known_event: null - death_date: null - current_address: null - has_familial_relationships: - - type: PARENT_OF - related_to: P:001 - - type: PARENT_OF - related_to: P:002 diff --git a/tests/input/examples/personinfo_basic/output/Person-001.transformed.yaml b/tests/input/examples/personinfo_basic/output/Person-001.transformed.yaml deleted file mode 100644 index 4632b8c..0000000 --- a/tests/input/examples/personinfo_basic/output/Person-001.transformed.yaml +++ /dev/null @@ -1,18 +0,0 @@ -id: P:001 -label: fred bloggs -age: 33 years -primary_email: fred.bloggs@example.com -secondary_email: null -gender: null -driving_since: 2014-03-31 -first_known_event: 1990-01-01 -death_date: null -current_address: - address_of: foo - street: 1 oak street - city: oaktown -has_familial_relationships: -- type: SIBLING_OF - related_to: P:002 -- type: CHILD_OF - related_to: P:003 diff --git a/tests/input/examples/personinfo_basic/output/personinfo_compiled.md b/tests/input/examples/personinfo_basic/output/personinfo_compiled.md deleted file mode 100644 index 6b1b384..0000000 --- a/tests/input/examples/personinfo_basic/output/personinfo_compiled.md +++ /dev/null @@ -1,83 +0,0 @@ -# my mappings - -## Class Mappings - - -### Container `<-` Container - -| Target | Target Range | Source | Source Range | Info | -| ------ | ------ | ---- | ---- | ---- | -| agents | | None | persons | . | . | - -### Entity `<-` None - -| Target | Target Range | Source | Source Range | Info | -| ------ | ------ | ---- | ---- | ---- | - -### Agent `<-` Person - -| Target | Target Range | Source | Source Range | Info | -| ------ | ------ | ---- | ---- | ---- | -| id | | None | None | . | . | -| label | | None | name | . | . | -| age | | None | [expression] | . | . | -| primary_email | | None | None | . | . | -| secondary_email | | None | [expression] | . | . | -| gender | | None | [expression] | . | . | -| driving_since | | None | [expression] | . | . | -| first_known_event | | None | [expression] | . | . | -| death_date | | None | [expression] | . | . | -| current_address | | None | None | . | . | -| has_familial_relationships | | None | has_familial_relationships | . | . | - -### Job `<-` None - -| Target | Target Range | Source | Source Range | Info | -| ------ | ------ | ---- | ---- | ---- | -| type | | None | None | . | . | -| current | | None | [expression] | . | . | - -### Address `<-` Address - -| Target | Target Range | Source | Source Range | Info | -| ------ | ------ | ---- | ---- | ---- | -| address_of | | None | [expression] | . | . | -| street | | None | None | . | . | -| city | | None | None | . | . | - -### FamilialRelationship `<-` FamilialRelationship - -| Target | Target Range | Source | Source Range | Info | -| ------ | ------ | ---- | ---- | ---- | -| type | | None | None | . | . | -| related_to | | None | None | . | . | - -### SequenceFeature `<-` None - -| Target | Target Range | Source | Source Range | Info | -| ------ | ------ | ---- | ---- | ---- | -| type | | None | feature_type | . | . | - -### DenormMapping `<-` Mapping - -| Target | Target Range | Source | Source Range | Info | -| ------ | ------ | ---- | ---- | ---- | -| id | | None | None | . | . | -| creator | | None | None | . | . | -| license | | None | None | . | . | -| subject_id | | None | [expression] | . | . | -| subject_name | | None | [expression] | . | . | -| object_id | | None | [expression] | . | . | -| object_name | | None | [expression] | . | . | -| predicate_id | | None | predicate | . | . | -| predicate_label | | None | [expression] | . | . | - -## Enum Mappings - - -### Target enum MyFamilialRelationshipType - -| Target | Source | Info | -| ------ | ------ | ---- | -| SIBLING_OF | SIBLING_OF | . | -| CHILD_OF | CHILD_OF | . | \ No newline at end of file diff --git a/tests/input/examples/personinfo_basic/output/personinfo_compiled.py b/tests/input/examples/personinfo_basic/output/personinfo_compiled.py deleted file mode 100644 index a512538..0000000 --- a/tests/input/examples/personinfo_basic/output/personinfo_compiled.py +++ /dev/null @@ -1,108 +0,0 @@ - -NULL = None - - - - - -def derive_Container( - source_object: src.Container - ) -> tgt.Container: - # assign slots - persons = source_object.persons - organizations = source_object.organizations - - return tgt.Container( - agents=[ derive_Agent(x) for x in source_object.persons ], - ) - - - -def derive_Agent( - source_object: src.Person - ) -> tgt.Agent: - # assign slots - primary_email = source_object.primary_email - secondary_email = source_object.secondary_email - birth_date = source_object.birth_date - age_in_years = source_object.age_in_years - gender = source_object.gender - current_address = source_object.current_address - has_employment_history = source_object.has_employment_history - has_familial_relationships = source_object.has_familial_relationships - has_medical_history = source_object.has_medical_history - has_important_life_events = source_object.has_important_life_events - aliases = source_object.aliases - id = source_object.id - name = source_object.name - description = source_object.description - image = source_object.image - - def gen_driving_since(src): - target = None - d_test = [x.important_event_date for x in src.has_important_life_events if str(x.event_name) == "PASSED_DRIVING_TEST"] - if len(d_test): - target = d_test[0] - return target - - - def gen_first_known_event(src): - target = None - if src.has_important_life_events: - target = src.has_important_life_events[0].important_event_date - return target - - - def gen_death_date(src): - target = None - death_dates = [x.important_event_date for x in src.has_important_life_events if str(x.event_name) == "DEATH"] - if len(death_dates): - target = death_dates[0] - return target - - - return tgt.Agent( - id=source_object.id, - label=source_object.name, - age=str(age_in_years) + ' years', - primary_email=source_object.primary_email, - secondary_email=NULL, - gender=None, - driving_since=gen_driving_since(source_object), - first_known_event=gen_first_known_event(source_object), - death_date=gen_death_date(source_object), - current_address=source_object.current_address, - has_familial_relationships=[ derive_FamilialRelationship(x) for x in source_object.has_familial_relationships ], - ) - - - -def derive_Address( - source_object: src.Address - ) -> tgt.Address: - # assign slots - street = source_object.street - city = source_object.city - postal_code = source_object.postal_code - - return tgt.Address( - address_of='foo', - street=source_object.street, - city=source_object.city, - ) - - - -def derive_FamilialRelationship( - source_object: src.FamilialRelationship - ) -> tgt.FamilialRelationship: - # assign slots - type = source_object.type - started_at_time = source_object.started_at_time - ended_at_time = source_object.ended_at_time - related_to = source_object.related_to - - return tgt.FamilialRelationship( - type=source_object.type, - related_to=source_object.related_to, - ) \ No newline at end of file diff --git a/tests/input/examples/personinfo_basic/output/personinfo_derived.yaml b/tests/input/examples/personinfo_basic/output/personinfo_derived.yaml deleted file mode 100644 index 87eaa9a..0000000 --- a/tests/input/examples/personinfo_basic/output/personinfo_derived.yaml +++ /dev/null @@ -1,163 +0,0 @@ -name: personinfo-derived -id: https://w3id.org/linkml/examples/personinfo-derived -imports: -- linkml:types -prefixes: - personinfo: - prefix_prefix: personinfo - prefix_reference: https://w3id.org/linkml/examples/personinfo/ - linkml: - prefix_prefix: linkml - prefix_reference: https://w3id.org/linkml/ - schema: - prefix_prefix: schema - prefix_reference: http://schema.org/ - rdfs: - prefix_prefix: rdfs - prefix_reference: http://www.w3.org/2000/01/rdf-schema# - prov: - prefix_prefix: prov - prefix_reference: http://www.w3.org/ns/prov# - GSSO: - prefix_prefix: GSSO - prefix_reference: http://purl.obolibrary.org/obo/GSSO_ - famrel: - prefix_prefix: famrel - prefix_reference: https://example.org/FamilialRelations# - P: - prefix_prefix: P - prefix_reference: http://example.org/P/ - ROR: - prefix_prefix: ROR - prefix_reference: http://example.org/ror/ - CODE: - prefix_prefix: CODE - prefix_reference: http://example.org/code/ - GEO: - prefix_prefix: GEO - prefix_reference: http://example.org/geoloc/ -default_prefix: https://w3id.org/linkml/examples/personinfo-derived/ -default_range: string -enums: - MyFamilialRelationshipType: - name: MyFamilialRelationshipType - is_a: RelationshipType - permissible_values: - SIBLING_OF: - text: SIBLING_OF - PARENT_OF: - text: PARENT_OF - meaning: famrel:02 - CHILD_OF: - text: CHILD_OF - FATHER_OF: - text: FATHER_OF - meaning: famrel:11 -classes: - Container: - name: Container - attributes: - agents: - name: agents - range: Person - multivalued: true - inlined: true - inlined_as_list: true - tree_root: true - Entity: - name: Entity - Agent: - name: Agent - description: A person (alive, dead, undead, or fictional). - in_subset: - - basic_subset - is_a: Entity - attributes: - id: - name: id - slot_uri: schema:identifier - identifier: true - label: - name: label - slot_uri: schema:name - age: - name: age - primary_email: - name: primary_email - slot_uri: schema:email - secondary_email: - name: secondary_email - gender: - name: gender - slot_uri: schema:gender - range: GenderType - driving_since: - name: driving_since - first_known_event: - name: first_known_event - death_date: - name: death_date - current_address: - name: current_address - description: The address at which a person currently lives - range: Address - has_familial_relationships: - name: has_familial_relationships - range: FamilialRelationship - multivalued: true - inlined_as_list: true - class_uri: schema:Person - Job: - name: Job - attributes: - type: - name: type - range: RelationshipType - current: - name: current - Address: - name: Address - attributes: - address_of: - name: address_of - street: - name: street - city: - name: city - class_uri: schema:PostalAddress - FamilialRelationship: - name: FamilialRelationship - attributes: - type: - name: type - range: RelationshipType - related_to: - name: related_to - SequenceFeature: - name: SequenceFeature - attributes: - type: - name: type - DenormMapping: - name: DenormMapping - attributes: - id: - name: id - slot_uri: schema:identifier - identifier: true - creator: - name: creator - license: - name: license - subject_id: - name: subject_id - subject_name: - name: subject_name - object_id: - name: object_id - object_name: - name: object_name - predicate_id: - name: predicate_id - predicate_label: - name: predicate_label diff --git a/tests/input/examples/personinfo_basic/source/personinfo.yaml b/tests/input/examples/personinfo_basic/source/personinfo.yaml deleted file mode 100644 index ac0fe8c..0000000 --- a/tests/input/examples/personinfo_basic/source/personinfo.yaml +++ /dev/null @@ -1,308 +0,0 @@ -id: https://w3id.org/linkml/examples/personinfo -name: personinfo -description: |- - Information about people, based on [schema.org](http://schema.org) -license: https://creativecommons.org/publicdomain/zero/1.0/ -default_curi_maps: - - semweb_context -imports: - - linkml:types -prefixes: - personinfo: https://w3id.org/linkml/examples/personinfo/ - linkml: https://w3id.org/linkml/ - schema: http://schema.org/ - rdfs: http://www.w3.org/2000/01/rdf-schema# - prov: http://www.w3.org/ns/prov# - GSSO: http://purl.obolibrary.org/obo/GSSO_ - famrel: https://example.org/FamilialRelations# - # DATA PREFIXES - P: http://example.org/P/ - ROR: http://example.org/ror/ - CODE: http://example.org/code/ - GEO: http://example.org/geoloc/ -default_prefix: personinfo -default_range: string - -emit_prefixes: - - rdf - - rdfs - - xsd - - skos - -classes: - - NamedThing: - description: >- - A generic grouping for any identifiable entity - slots: - - id - - name - - description - - image - close_mappings: - - schema:Thing - - Person: - is_a: NamedThing - description: >- - A person (alive, dead, undead, or fictional). - class_uri: schema:Person - mixins: - - HasAliases - slots: - - primary_email - - secondary_email - - birth_date - - age_in_years - - gender - - current_address - - has_employment_history - - has_familial_relationships - - has_medical_history - - has_important_life_events - slot_usage: - primary_email: - pattern: "^\\S+@[\\S+\\.]+\\S+" - secondary_email: - pattern: "^\\S+@[\\S+\\.]+\\S+" - in_subset: - - basic_subset - - HasAliases: - description: >- - A mixin applied to any class that can have aliases/alternateNames - mixin: true - attributes: - aliases: - multivalued: true - exact_mappings: - - schema:alternateName - - Organization: - description: >- - An organization such as a company or university - is_a: NamedThing - class_uri: schema:Organization - mixins: - - HasAliases - slots: - - mission_statement - - founding_date - - founding_location - - Place: - mixins: - - HasAliases - slots: - - id - - name - - Address: - class_uri: schema:PostalAddress - slots: - - street - - city - - postal_code - - Event: - slots: - - started_at_time - - ended_at_time - - duration - - is_current - close_mappings: - - schema:Event - - Concept: - is_a: NamedThing - - DiagnosisConcept: - is_a: Concept - - ProcedureConcept: - is_a: Concept - - Relationship: - slots: - - started_at_time - - ended_at_time - - related_to - - FamilialRelationship: - is_a: Relationship - slots: - - type - slot_usage: - type: - range: FamilialRelationshipType - required: true - related_to: - range: Person - required: true - - EmploymentEvent: - is_a: Event - slots: - - employed_at - - type - - MedicalEvent: - is_a: Event - slots: - - in_location - - diagnosis - - procedure - - type - - ImportantLifeEvent: - is_a: Event - slots: - - important_event_date - - event_name - - WithLocation: - mixin: true - slots: - - in_location - - Container: - tree_root: true - slots: - - persons - - organizations - -slots: - id: - identifier: true - slot_uri: schema:identifier - name: - slot_uri: schema:name - description: - slot_uri: schema:description - image: - slot_uri: schema:image - gender: - slot_uri: schema:gender - range: GenderType - primary_email: - slot_uri: schema:email - secondary_email: - birth_date: - slot_uri: schema:birthDate - employed_at: - range: Organization - is_current: - range: boolean - has_employment_history: - range: EmploymentEvent - multivalued: true - inlined_as_list: true - has_medical_history: - range: MedicalEvent - multivalued: true - inlined_as_list: true - has_familial_relationships: - range: FamilialRelationship - multivalued: true - inlined_as_list: true - has_important_life_events: - range: ImportantLifeEvent - multivalued: true - inlined_as_list: true - important_event_date: - range: date - required: true - event_name: - range: ImportantLifeEventType - required: true - - in_location: - range: Place - current_address: - description: >- - The address at which a person currently lives - range: Address - age_in_years: - range: integer - minimum_value: 0 - maximum_value: 999 - related_to: - type: - range: RelationshipType - street: - city: - mission_statement: - founding_date: - founding_location: - range: Place - postal_code: - range: string - started_at_time: - slot_uri: prov:startedAtTime - range: date - duration: - range: float - diagnosis: - range: DiagnosisConcept - inlined: true - procedure: - range: ProcedureConcept - inlined: true - - ended_at_time: - slot_uri: prov:endedAtTime - range: date - - persons: - range: Person - inlined: true - inlined_as_list: true - multivalued: true - organizations: - range: Organization - inlined_as_list: true - inlined: true - multivalued: true - -enums: - RelationshipType: - FamilialRelationshipType: - is_a: RelationshipType - permissible_values: - SIBLING_OF: - meaning: famrel:01 - PARENT_OF: - meaning: famrel:02 - CHILD_OF: - meaning: famrel:05 - FATHER_OF: - meaning: famrel:11 - GenderType: - permissible_values: - nonbinary man: - meaning: GSSO:009254 - nonbinary woman: - meaning: GSSO:009253 - transgender woman: - meaning: GSSO:000384 - transgender man: - meaning: GSSO:000372 - cisgender man: - meaning: GSSO:000371 - cisgender woman: - meaning: GSSO:000385 - None: - meaning: GSSO:000283 - DiagnosisType: - ImportantLifeEventType: - permissible_values: - BIRTH: - DEATH: - PASSED_DRIVING_TEST: - FIRST_CAR_ACCIDENT: - MARRIAGE: - DIVORCE: - -subsets: - basic_subset: - description: A subset of the schema that handles basic information diff --git a/tests/input/examples/personinfo_basic/target/agent.yaml b/tests/input/examples/personinfo_basic/target/agent.yaml deleted file mode 100644 index f804eb1..0000000 --- a/tests/input/examples/personinfo_basic/target/agent.yaml +++ /dev/null @@ -1,294 +0,0 @@ -id: https://w3id.org/linkml/examples/personinfo -name: personinfo -description: |- - Information about people, based on [schema.org](http://schema.org) -license: https://creativecommons.org/publicdomain/zero/1.0/ -default_curi_maps: - - semweb_context -imports: - - linkml:types -prefixes: - personinfo: https://w3id.org/linkml/examples/personinfo/ - linkml: https://w3id.org/linkml/ - schema: http://schema.org/ - rdfs: http://www.w3.org/2000/01/rdf-schema# - prov: http://www.w3.org/ns/prov# - GSSO: http://purl.obolibrary.org/obo/GSSO_ - famrel: https://example.org/FamilialRelations# - # DATA PREFIXES - P: http://example.org/P/ - ROR: http://example.org/ror/ - CODE: http://example.org/code/ - GEO: http://example.org/geoloc/ -default_prefix: personinfo -default_range: string - -emit_prefixes: - - rdf - - rdfs - - xsd - - skos - -classes: - - NamedThing: - description: >- - A generic grouping for any identifiable entity - slots: - - id - - label - - description - - image - close_mappings: - - schema:Thing - - Agent: - is_a: NamedThing - description: >- - A person (alive, dead, undead, or fictional). - class_uri: schema:Person - mixins: - - HasAliases - slots: - - primary_email - - secondary_email - - birth_date - - death_date - - age - - gender - - current_address - - has_employment_history - - has_familial_relationships - - has_medical_history - - parents - - driving_since - - first_known_event - slot_usage: - primary_email: - pattern: "^\\S+@[\\S+\\.]+\\S+" - secondary_email: - pattern: "^\\S+@[\\S+\\.]+\\S+" - in_subset: - - basic_subset - - HasAliases: - description: >- - A mixin applied to any class that can have aliases/alternateNames - mixin: true - attributes: - aliases: - multivalued: true - exact_mappings: - - schema:alternateName - - - Organization: - description: >- - An organization such as a company or university - is_a: NamedThing - class_uri: schema:Organization - mixins: - - HasAliases - slots: - - mission_statement - - founding_date - - founding_location - - Place: - mixins: - - HasAliases - slots: - - id - - label - - Address: - class_uri: schema:PostalAddress - slots: - - street - - city - - postal_code - - address_of - - Event: - slots: - - started_at_time - - ended_at_time - - duration - - is_current - close_mappings: - - schema:Event - - Concept: - is_a: NamedThing - - DiagnosisConcept: - is_a: Concept - - ProcedureConcept: - is_a: Concept - - Relationship: - slots: - - started_at_time - - ended_at_time - - related_to - - type - - FamilialRelationship: - is_a: Relationship - slot_usage: - type: - range: FamilialRelationshipType - required: true - related_to: - range: Agent - required: true - - EmploymentEvent: - is_a: Event - slots: - - employed_at - - MedicalEvent: - is_a: Event - slots: - - in_location - - diagnosis - - procedure - - WithLocation: - mixin: true - slots: - - in_location - - # TODO: annotate that this is a container/root class - Container: - tree_root: true - slots: - - agents - - organizations - -slots: - id: - identifier: true - slot_uri: schema:identifier - label: - slot_uri: schema:name - description: - slot_uri: schema:description - image: - slot_uri: schema:image - gender: - slot_uri: schema:gender - range: GenderType - primary_email: - slot_uri: schema:email - secondary_email: - slot_uri: schema:email - birth_date: - slot_uri: schema:birthDate - range: date - death_date: - range: date - employed_at: - range: Organization - is_current: - range: boolean - has_employment_history: - range: EmploymentEvent - multivalued: true - inlined_as_list: true - has_medical_history: - range: MedicalEvent - multivalued: true - inlined_as_list: true - has_familial_relationships: - range: FamilialRelationship - multivalued: true - inlined_as_list: true - driving_since: - range: date - first_known_event: - range: date - parents: - range: string - multivalued: true - inlined_as_list: true - in_location: - range: Place - current_address: - description: >- - The address at which a Agent currently lives - range: Address - age: - range: string - pattern: "\\d+ \\S+" - related_to: - type: - street: - city: - mission_statement: - founding_date: - founding_location: - range: Place - postal_code: - range: string - address_of: - range: Agent - started_at_time: - slot_uri: prov:startedAtTime - range: date - duration: - range: float - diagnosis: - range: DiagnosisConcept - inlined: true - procedure: - range: ProcedureConcept - inlined: true - - ended_at_time: - slot_uri: prov:endedAtTime - range: date - - agents: - range: Agent - inlined: true - inlined_as_list: true - multivalued: true - organizations: - range: Organization - inlined_as_list: true - inlined: true - multivalued: true - -enums: - FamilialRelationshipType: - permissible_values: - SIBLING_OF: - meaning: famrel:01 - PARENT_OF: - meaning: famrel:02 - CHILD_OF: - meaning: famrel:05 - GenderType: - permissible_values: - nonbinary man: - meaning: GSSO:009254 - nonbinary woman: - meaning: GSSO:009253 - transgender woman: - meaning: GSSO:000384 - transgender man: - meaning: GSSO:000372 - cisgender man: - meaning: GSSO:000371 - cisgender woman: - meaning: GSSO:000385 - None: - meaning: GSSO:000283 - DiagnosisType: - -subsets: - basic_subset: - description: A subset of the schema that handles basic information diff --git a/tests/input/examples/personinfo_basic/transform/personinfo-to-agent.transform.yaml b/tests/input/examples/personinfo_basic/transform/personinfo-to-agent.transform.yaml deleted file mode 100644 index d16593b..0000000 --- a/tests/input/examples/personinfo_basic/transform/personinfo-to-agent.transform.yaml +++ /dev/null @@ -1,156 +0,0 @@ -id: my-mappings -title: my mappings -prefixes: - foo: foo -source_schema: s1 -target_schema: s2 -class_derivations: - Container: - populated_from: Container - slot_derivations: - agents: - populated_from: persons - #copy_directives: - # "*": - # copy_all: true - Entity: - Agent: - is_a: Entity - populated_from: Person - slot_derivations: - ## implicitly same name in Agent - id: - - label: - populated_from: name - - age: - expr: "str({age_in_years}) + ' years'" - - # YAML interprets this as expr = None - # no transformation is performed - primary_email: - expr: NULL - - # this is the string "NULL", which will set this field to null - secondary_email: - #expr: "'NULL'" - expr: "NULL" - - # FIXME: this should return the type "None", rather than null - gender: - expr: "None" - - driving_since: - expr: | - d_test = [x.important_event_date for x in src.has_important_life_events if str(x.event_name) == "PASSED_DRIVING_TEST"] - if len(d_test): - target = d_test[0] - - first_known_event: - expr: | - if src.has_important_life_events: - target = src.has_important_life_events[0].important_event_date - - death_date: - expr: | - death_dates = [x.important_event_date for x in src.has_important_life_events if str(x.event_name) == "DEATH"] - if len(death_dates): - target = death_dates[0] - - - current_address: - - ## expressions - #full_name: - # expr: "{first} {last}" - - ## unit conversion - #age_in_years: - # expr: "units.convert(age.value, age.unit, units.YEARS)" - - ## nested to flat - #friends: - # expr: "[x.id for x in {friends}]" - - ## copy recursively, flat to nested - #jobs: - # populated_from: jobs - - ## copy recursively - #diagnoses: - # populated_from: diagnoses - - has_familial_relationships: - populated_from: has_familial_relationships - - Job: - #primitive: uriorcurie - slot_derivations: - type: - # this: true ## use input primitive - current: - expr: "True" - - Address: - populated_from: Address - slot_derivations: - address_of: - expr: "'foo'" - inverse_of: - class_name: Agent - slot_name: current_address - street: - city: - # expr: "'foo'" - - FamilialRelationship: - populated_from: FamilialRelationship - slot_derivations: - type: - related_to: - #person_id: - # # inverse of has_familial_relationships - # inverse_of: - # slot_name: has_familial_relationships - # class_name: Person - - SequenceFeature: - slot_derivations: - type: - type_designator: true - hide: true - populated_from: feature_type - - DenormMapping: - populated_from: Mapping - #joins: - # subject: Entity - # object: Entity - slot_derivations: - id: ## implicitly mapping.id - creator: - license: - subject_id: - expr: subject.id - subject_name: - expr: subject.name - object_id: - expr: object.id - object_name: - expr: object.name - predicate_id: - ## implicitly: mapping.predicate - populated_from: predicate - predicate_label: - expr: "lookup(predicate)" - -enum_derivations: - MyFamilialRelationshipType: - populated_from: FamilialRelationshipType - mirror_source: true - permissible_value_derivations: - SIBLING_OF: - populated_from: SIBLING_OF - CHILD_OF: - populated_from: CHILD_OF diff --git a/tests/input/examples/single_value_for_multivalued/data/Container-001.yaml b/tests/input/examples/single_value_for_multivalued/data/Container-001.yaml deleted file mode 100644 index 90823b4..0000000 --- a/tests/input/examples/single_value_for_multivalued/data/Container-001.yaml +++ /dev/null @@ -1,8 +0,0 @@ -my_greetings: - - greeting: - - konnichiwa - - hello - - bonjour - - greeting: - - ciao - - greeting: namaste diff --git a/tests/input/examples/single_value_for_multivalued/output/Container-001.transformed.yaml b/tests/input/examples/single_value_for_multivalued/output/Container-001.transformed.yaml deleted file mode 100644 index ca85ad5..0000000 --- a/tests/input/examples/single_value_for_multivalued/output/Container-001.transformed.yaml +++ /dev/null @@ -1,9 +0,0 @@ -my_languages: -- language: - - Japanese - - English - - French -- language: - - Italian -- language: - - Hindi diff --git a/tests/input/examples/single_value_for_multivalued/source/greetings.yaml b/tests/input/examples/single_value_for_multivalued/source/greetings.yaml deleted file mode 100644 index c0ff399..0000000 --- a/tests/input/examples/single_value_for_multivalued/source/greetings.yaml +++ /dev/null @@ -1,31 +0,0 @@ -name: greetings -id: greetings -description: Greetings from different languages -imports: -- linkml:types -default_range: string -enums: - greetings: - permissible_values: - bonjour: - ciao: - hello: - hola: - konnichiwa: - namaste: -classes: - my_greetings: - slots: - - greeting - Container: - tree_root: True - attributes: - my_greetings: - range: my_greetings - multivalued: True - inlined_as_list: True -slots: - greeting: - range: greetings - multivalued: True - inlined_as_list: True diff --git a/tests/input/examples/single_value_for_multivalued/target/languages.yaml b/tests/input/examples/single_value_for_multivalued/target/languages.yaml deleted file mode 100644 index b657010..0000000 --- a/tests/input/examples/single_value_for_multivalued/target/languages.yaml +++ /dev/null @@ -1,31 +0,0 @@ -name: languages -id: languages -description: Names of languages -imports: -- linkml:types -default_range: string -enums: - languages: - permissible_values: - English: - French: - Hindi: - Italian: - Japanese: - Spanish: -classes: - my_languages: - slots: - - language - Container: - tree_root: True - attributes: - my_languages: - range: my_languages - multivalued: True - inlined_as_list: True -slots: - language: - range: languages - multivalued: True - inlined_as_list: True diff --git a/tests/input/examples/single_value_for_multivalued/transform/greetings-to-languages.transform.yaml b/tests/input/examples/single_value_for_multivalued/transform/greetings-to-languages.transform.yaml deleted file mode 100644 index 27903dc..0000000 --- a/tests/input/examples/single_value_for_multivalued/transform/greetings-to-languages.transform.yaml +++ /dev/null @@ -1,38 +0,0 @@ -class_derivations: - my_languages: - name: my_languages - populated_from: my_greetings - slot_derivations: - language: - name: language - populated_from: greeting - Container: - name: Container - slot_derivations: - my_languages: - populated_from: my_greetings -enum_derivations: - languages: - name: languages - mirror_source: false - populated_from: greetings - permissible_value_derivations: - English: - name: English - populated_from: hello - French: - name: French - populated_from: bonjour - Hindi: - name: Hindi - populated_from: namaste - Italian: - name: Italian - populated_from: ciao - Japanese: - name: Japanese - populated_from: konnichiwa - Spanish: - name: Spanish - populated_from: hola - \ No newline at end of file diff --git a/tests/input/examples/type_coercion/data/MyRecord-001.yaml b/tests/input/examples/type_coercion/data/MyRecord-001.yaml deleted file mode 100644 index 6341fc7..0000000 --- a/tests/input/examples/type_coercion/data/MyRecord-001.yaml +++ /dev/null @@ -1,4 +0,0 @@ -id: P:1 -name: my name -age_as_integer: 33 -url: https://example.org/foo diff --git a/tests/input/examples/type_coercion/output/MyRecord-001.transformed.yaml b/tests/input/examples/type_coercion/output/MyRecord-001.transformed.yaml deleted file mode 100644 index 27771bb..0000000 --- a/tests/input/examples/type_coercion/output/MyRecord-001.transformed.yaml +++ /dev/null @@ -1,10 +0,0 @@ -id: P:1 -id_as_string: P:1 -id_as_url: https://example.org/person/1 -url: https://example.org/foo -url_as_string: https://example.org/foo -url_as_curie: example:foo -name: my name -age_as_integer: 33 -age_as_float: 33.0 -age_as_string: '33' diff --git a/tests/input/examples/type_coercion/source/type_coercion.yaml b/tests/input/examples/type_coercion/source/type_coercion.yaml deleted file mode 100644 index e7d447a..0000000 --- a/tests/input/examples/type_coercion/source/type_coercion.yaml +++ /dev/null @@ -1,36 +0,0 @@ -id: https://w3id.org/linkml/examples/type_coercion -name: quantity_value -imports: - - linkml:types -prefixes: - tc: https://w3id.org/linkml/examples/type_coercion/ - linkml: https://w3id.org/linkml/ - example: https://example.org/ - P: https://example.org/person/ -default_prefix: tc -default_range: string - -classes: - - MyRecord: - tree_root: true - attributes: - id: - identifier: true - range: uriorcurie - id_as_string: - range: string - url: - range: uri - url_as_string: - range: string - name: - range: string - age_as_integer: - range: integer - age_as_float: - range: float - age_as_string: - range: string - - diff --git a/tests/input/examples/type_coercion/target/target.yaml b/tests/input/examples/type_coercion/target/target.yaml deleted file mode 100644 index 7ede85f..0000000 --- a/tests/input/examples/type_coercion/target/target.yaml +++ /dev/null @@ -1,51 +0,0 @@ -name: quantity_value -id: https://w3id.org/linkml/examples/type_coercion -default_prefix: https://w3id.org/linkml/examples/type_coercion/ -classes: - MyRecord: - name: MyRecord - from_schema: https://w3id.org/linkml/examples/type_coercion - attributes: - id: - name: id - from_schema: https://w3id.org/linkml/examples/type_coercion - identifier: true - owner: MyRecord - range: uriorcurie - id_as_string: - name: id_as_string - from_schema: https://w3id.org/linkml/examples/type_coercion - identifier: true - owner: MyRecord - range: uriorcurie - url: - name: url - from_schema: https://w3id.org/linkml/examples/type_coercion - owner: MyRecord - range: uri - url_as_string: - name: url_as_string - from_schema: https://w3id.org/linkml/examples/type_coercion - owner: MyRecord - range: uri - name: - name: name - from_schema: https://w3id.org/linkml/examples/type_coercion - owner: MyRecord - range: string - age_as_integer: - name: age_as_integer - from_schema: https://w3id.org/linkml/examples/type_coercion - owner: MyRecord - range: integer - age_as_float: - name: age_as_float - from_schema: https://w3id.org/linkml/examples/type_coercion - owner: MyRecord - range: integer - age_as_string: - name: age_as_string - from_schema: https://w3id.org/linkml/examples/type_coercion - owner: MyRecord - range: integer - tree_root: true diff --git a/tests/input/examples/type_coercion/transform/type_coercion.transform.yaml b/tests/input/examples/type_coercion/transform/type_coercion.transform.yaml deleted file mode 100644 index 50c4d0b..0000000 --- a/tests/input/examples/type_coercion/transform/type_coercion.transform.yaml +++ /dev/null @@ -1,32 +0,0 @@ -id: qv-to-scalar -class_derivations: - MyRecord: - populated_from: MyRecord - slot_derivations: - id: - id_as_string: - range: string - populated_from: id - id_as_url: - range: uri - populated_from: id - url: - url_as_string: - range: string - populated_from: url - url_as_curie: - range: curie - populated_from: url - name: - range: string - age_as_integer: - range: integer - age_as_float: - range: float - populated_from: age_as_integer - age_as_string: - range: string - populated_from: age_as_integer -# copy_directives: -# "*": -# copy_all: true diff --git a/tests/scaffold/__init__.py b/tests/scaffold/__init__.py deleted file mode 100644 index 8fb6872..0000000 --- a/tests/scaffold/__init__.py +++ /dev/null @@ -1,16 +0,0 @@ -from pathlib import Path - -SOURCE = "source" -TARGET = "target" -TRANSFORM = "transform" -DATA = "data" -EXPECTED = "expected" - -SCAFFOLD_DIR = Path(__file__).parent.resolve() - -SOURCE_SCHEMA = SCAFFOLD_DIR / SOURCE / "person.yaml" -TARGET_SCHEMA = SCAFFOLD_DIR / TARGET / "agent.yaml" -TRANSFORM_SPEC = SCAFFOLD_DIR / TRANSFORM / "person_to_agent.transform.yaml" - -INPUT_DATA = SCAFFOLD_DIR / DATA / "Person-001.yaml" -EXPECTED_DATA = SCAFFOLD_DIR / EXPECTED / "Person-001.transformed.yaml" diff --git a/tests/scaffold/data/Person-001.yaml b/tests/scaffold/data/Person-001.yaml deleted file mode 100644 index 96f9221..0000000 --- a/tests/scaffold/data/Person-001.yaml +++ /dev/null @@ -1,2 +0,0 @@ -id: P:001 -name: alice adams diff --git a/tests/scaffold/expected/Person-001.transformed.yaml b/tests/scaffold/expected/Person-001.transformed.yaml deleted file mode 100644 index ef8e4a9..0000000 --- a/tests/scaffold/expected/Person-001.transformed.yaml +++ /dev/null @@ -1,2 +0,0 @@ -id: P:001 -label: alice adams diff --git a/tests/scaffold/source/person.yaml b/tests/scaffold/source/person.yaml deleted file mode 100644 index 15c2961..0000000 --- a/tests/scaffold/source/person.yaml +++ /dev/null @@ -1,33 +0,0 @@ -id: https://example.org/linkml/scaffold/person -name: person -description: |- - Minimal person schema for LinkML-Map testing, based on [schema.org](http://schema.org) -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - person: https://example.org/linkml/scaffold/person - linkml: https://w3id.org/linkml/ -default_prefix: person -default_range: string - -imports: - - linkml:types - -classes: - NamedThing: - description: >- - A generic grouping for any identifiable entity - slots: - - id - - name - - Person: - is_a: NamedThing - description: >- - A person (alive, dead, undead, or fictional). - -slots: - id: - identifier: true - range: string - name: - range: string diff --git a/tests/scaffold/target/agent.yaml b/tests/scaffold/target/agent.yaml deleted file mode 100644 index fa91e70..0000000 --- a/tests/scaffold/target/agent.yaml +++ /dev/null @@ -1,33 +0,0 @@ -id: https://example.org/linkml/scaffold/agent -name: agent -description: |- - Minimal agent target schema for LinkML-Map testing, based on Person from [schema.org](http://schema.org) -license: https://creativecommons.org/publicdomain/zero/1.0/ -prefixes: - agent: https://example.org/linkml/scaffold/agent/ - linkml: https://w3id.org/linkml/ -default_prefix: agent -default_range: string - -imports: - - linkml:types - -classes: - Element: - description: >- - A generic grouping for any identifiable entity - slots: - - id - - label - - Agent: - is_a: Element - description: >- - An agent (person, animal, digital, or fictional). - slots: - -slots: - id: - range: string - label: - range: string diff --git a/tests/scaffold/transform/person_to_agent.transform.yaml b/tests/scaffold/transform/person_to_agent.transform.yaml deleted file mode 100644 index 29257ee..0000000 --- a/tests/scaffold/transform/person_to_agent.transform.yaml +++ /dev/null @@ -1,15 +0,0 @@ -id: scaffold-mapping -title: Minimal scaffold mapping -prefixes: - src: https://example.org/test-source-scaffold/ - tgt: https://example.org/test-target-scaffold/ -source_schema: https://example.org/test-source-scaffold -target_schema: https://example.org/test-target-scaffold - -class_derivations: - Agent: - populated_from: Person - slot_derivations: - id: - label: - populated_from: name diff --git a/tests/scaffold/utils/apply_patch.py b/tests/scaffold/utils/apply_patch.py deleted file mode 100644 index fdefab3..0000000 --- a/tests/scaffold/utils/apply_patch.py +++ /dev/null @@ -1,64 +0,0 @@ -from linkml_runtime import SchemaView -from linkml_runtime.linkml_model import ( - ClassDefinition, EnumDefinition, Prefix, SlotDefinition, SubsetDefinition, TypeDefinition -) -import yaml - -def apply_schema_patch(schemaview: SchemaView, yaml_str: str): - """Patch a SchemaView.schema from a YAML fragment.""" - patch = yaml.safe_load(yaml_str) - schema = schemaview.schema - - for field in ["id", "name", "description", "default_prefix"]: - if field in patch: - setattr(schema, field, patch[field]) - - if "imports" in patch: - for imp in patch["imports"]: - if imp not in schema.imports: - schema.imports.append(imp) - - for pname, ppatch in patch.get("prefixes", {}).items(): - schema.prefixes[pname] = Prefix(prefix_prefix=pname, prefix_reference=ppatch["prefix_reference"]) - - for cname, cpatch in patch.get("classes", {}).items(): - if cname not in schema.classes: - schema.classes[cname] = ClassDefinition( - name=cname, **{k: v for k, v in cpatch.items() if k != "slots"} - ) - existing = schema.classes[cname] - for slot in cpatch.get("slots", []): - if slot not in existing.slots: - existing.slots.append(slot) - - simple_definitions = { - "slots": SlotDefinition, - "enums": EnumDefinition, - "types": TypeDefinition, - "subsets": SubsetDefinition, - } - - for key, cls in simple_definitions.items(): - for name, patch_data in patch.get(key, {}).items(): - if name not in getattr(schema, key): - getattr(schema, key)[name] = cls(name=name, **patch_data) - else: - existing = getattr(schema, key)[name] - for field, value in patch_data.items(): - setattr(existing, field, value) - -def apply_transform_patch(transform: dict, yaml_str: str): - """Merge a YAML fragment into the scaffold['transform_spec'].""" - patch = yaml.safe_load(yaml_str) or {} - - def merge(d, p): - for k, v in p.items(): - if isinstance(v, dict) and isinstance(d.get(k), dict): - merge(d[k], v) - elif isinstance(v, list) and isinstance(d.get(k), list): - d[k].extend(v) - else: - d[k] = v - - merge(transform, patch) - return transform \ No newline at end of file diff --git a/tests/scaffold/utils/test_apply_schema_patch.py b/tests/scaffold/utils/test_apply_schema_patch.py deleted file mode 100644 index 51ce1b9..0000000 --- a/tests/scaffold/utils/test_apply_schema_patch.py +++ /dev/null @@ -1,66 +0,0 @@ -import pytest -from linkml_runtime import SchemaView -from linkml_runtime.linkml_model import SchemaDefinition, Prefix, SlotDefinition, EnumDefinition, TypeDefinition - -from tests.scaffold.utils.apply_patch import apply_schema_patch - -@pytest.fixture -def empty_schemaview(): - return SchemaView(SchemaDefinition(id="http://example.org/schema", name="test_schema")) - -def test_add_slot(empty_schemaview): - apply_schema_patch(empty_schemaview, """ - slots: - age: - range: integer - """) - assert "age" in empty_schemaview.schema.slots - assert empty_schemaview.schema.slots["age"].range == "integer" - -def test_patch_existing_slot(empty_schemaview): - empty_schemaview.schema.slots["age"] = SlotDefinition(name="age", range="integer") - apply_schema_patch(empty_schemaview, """ - slots: - age: - description: "Age of the person" - """) - assert empty_schemaview.schema.slots["age"].description == "Age of the person" - assert empty_schemaview.schema.slots["age"].range == "integer" # unchanged - -def test_add_class_with_slot(empty_schemaview): - apply_schema_patch(empty_schemaview, """ - classes: - Person: - slots: - - name - slots: - name: - range: string - """) - assert "Person" in empty_schemaview.schema.classes - assert "name" in empty_schemaview.schema.slots - assert "name" in empty_schemaview.schema.classes["Person"].slots - -def test_add_prefix_and_import(empty_schemaview): - apply_schema_patch(empty_schemaview, """ - imports: - - linkml:types - prefixes: - ex: - prefix_reference: http://example.org/ - """) - assert "linkml:types" in empty_schemaview.schema.imports - assert "ex" in empty_schemaview.schema.prefixes - assert empty_schemaview.schema.prefixes["ex"].prefix_reference == "http://example.org/" - -def test_patch_top_level_fields(empty_schemaview): - apply_schema_patch(empty_schemaview, """ - id: http://example.org/schema - name: PatchedSchema - description: "Patched schema for testing" - default_prefix: ex - """) - assert empty_schemaview.schema.id == "http://example.org/schema" - assert empty_schemaview.schema.name == "PatchedSchema" - assert empty_schemaview.schema.description == "Patched schema for testing" - assert empty_schemaview.schema.default_prefix == "ex" diff --git a/tests/scaffold/utils/test_apply_transform_patch.py b/tests/scaffold/utils/test_apply_transform_patch.py deleted file mode 100644 index f8897a6..0000000 --- a/tests/scaffold/utils/test_apply_transform_patch.py +++ /dev/null @@ -1,53 +0,0 @@ -import pytest -from tests.scaffold.utils.apply_patch import apply_transform_patch - -def test_apply_transform_patch_merges_dicts(): - transform = { - "class_derivations": { - "Agent": { - "slot_derivations": { - "name": {"value": "Alice"} - } - } - } - } - - patch = """ -class_derivations: - Agent: - slot_derivations: - age: - value: 30 -""" - - expected = { - "class_derivations": { - "Agent": { - "slot_derivations": { - "name": {"value": "Alice"}, - "age": {"value": 30}, - } - } - } - } - - result = apply_transform_patch(transform, patch) - assert result == expected - -def test_apply_transform_patch_overwrites_scalar(): - transform = {"key": "old"} - patch = "key: new" - result = apply_transform_patch(transform, patch) - assert result["key"] == "new" - -def test_apply_transform_patch_extends_list(): - transform = {"items": [1, 2]} - patch = "items:\n - 3\n - 4" - result = apply_transform_patch(transform, patch) - assert result["items"] == [1, 2, 3, 4] - -def test_apply_transform_patch_empty_patch(): - transform = {"key": "value"} - patch = "" - result = apply_transform_patch(transform, patch) - assert result == transform diff --git a/tests/test_cli/__init__.py b/tests/test_cli/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/tests/test_cli/test_cli.py b/tests/test_cli/test_cli.py deleted file mode 100644 index 870fbd4..0000000 --- a/tests/test_cli/test_cli.py +++ /dev/null @@ -1,250 +0,0 @@ -"""Tests all command-line subcommands.""" - -from collections.abc import Generator -from pathlib import Path -import re -from typing import Any, Optional, Union - -import pytest -import yaml -from click.testing import CliRunner, Result -from linkml_runtime import SchemaView - -from linkml_map.cli.cli import dump_output, main -from tests import ( - DENORM_SPECIFICATION, - FLATTENING_DATA, - NORM_SCHEMA, - PERSONINFO_CONTAINER_DATA, - PERSONINFO_DERIVED, - PERSONINFO_SRC_SCHEMA, - PERSONINFO_TR, - PERSONINFO_TR_COMPILED_MD, - PERSONINFO_TR_COMPILED_PY, -) - -DERIVED_SCHEMA_NAME_LINE = "name: personinfo-derived" - - -@pytest.fixture -def runner() -> CliRunner: - """ - Command line interface test runner. - - :return: command line interface runner - :rtype: CliRunner - """ - return CliRunner(mix_stderr=False) - - -def test_main_help(runner: CliRunner) -> None: - """ - Ensure that the help command contains the appropriate text. - - :param runner: command line interface runner - :type runner: CliRunner - """ - result = runner.invoke(main, ["--help"]) - out = result.stdout - assert "derive-schema" in out - assert "map-data" in out - assert result.exit_code == 0 - - -def check_result(result: Result, expected_file: Path, output_param: Optional[str] = None) -> None: - """ - Check that the result of running a function matches the expected output. - - :param result: result object from the CliRunner - :type result: Result - :param expected_file: path to the expected result - :type expected_file: Path - :param output_param: output param supplied to the function, defaults to None - :type output_param: Optional[str], optional - """ - if output_param: - with output_param.open() as fh: - function_output = fh.read() - else: - function_output = result.stdout - - with expected_file.open() as fh: - assert fh.read() == function_output - - -@pytest.mark.parametrize("output", [None, "output.py"]) -@pytest.mark.parametrize("target", [None, "python", "markdown", "klingon"]) -def test_compile( - runner: CliRunner, - target: Optional[str], - output: Optional[str], - tmp_path: Generator[Path, None, None], -) -> None: - """ - Basic test of the python compiler functionality. - - :param runner: command line interface runner - :type runner: CliRunner - :param target: target language for compiled transformer - :type target: Optional[str] - :param output: output file, optional - :type output: Optional[str] - :param tmp_path: tmp dir for writing output to (if appropriate) - :type tmp_path: Generator[Path, None, None] - """ - cmd = [ - "compile", - "-T", - str(PERSONINFO_TR), - "-s", - str(PERSONINFO_SRC_SCHEMA), - ] - if target: - cmd.extend(["--target", target]) - if output: - output = tmp_path / output - cmd.extend(["--output", str(output)]) - - result = runner.invoke(main, cmd) - if target and target == "klingon": - assert result.exit_code != 0 - assert isinstance(result.exception, NotImplementedError) - assert result.exception.args[0] == "Compiler klingon not implemented" - return - - assert result.exit_code == 0 - if target and target == "markdown": - check_result(result, PERSONINFO_TR_COMPILED_MD, output) - else: - check_result(result, PERSONINFO_TR_COMPILED_PY, output) - - -@pytest.mark.parametrize("output", [None, "output.yaml"]) -def test_derive_schema( - runner: CliRunner, output: Optional[str], tmp_path: Generator[Path, None, None] -) -> None: - """ - Test schema derivation. - - :param runner: command line interface runner - :type runner: CliRunner - :param output: output file, optional - :type output: Optional[str] - :param tmp_path: tmp dir for writing output to (if appropriate) - :type tmp_path: Generator[Path, None, None] - """ - cmd = ["derive-schema", "-T", str(PERSONINFO_TR), str(PERSONINFO_SRC_SCHEMA)] - if output: - output = tmp_path / output - cmd.extend(["--output", str(output)]) - result = runner.invoke(main, cmd) - assert result.exit_code == 0 - check_result(result, PERSONINFO_DERIVED, output) - result_schema = result.stdout - if output: - with output.open() as fh: - result_schema = fh.read() - assert DERIVED_SCHEMA_NAME_LINE in result_schema - sv = SchemaView(result_schema) - assert "Agent" in sv.all_classes() - - -def test_map_data(runner: CliRunner) -> None: - cmd = [ - "map-data", - "--unrestricted-eval", - "-T", - str(PERSONINFO_TR), - "-s", - str(PERSONINFO_SRC_SCHEMA), - str(PERSONINFO_CONTAINER_DATA), - ] - result = runner.invoke(main, cmd) - assert result.exit_code == 0 - out = result.stdout - tr_data = yaml.safe_load(out) - assert tr_data["agents"][0]["label"] == "fred bloggs" - - -def test_map_data_norm_denorm(runner: CliRunner) -> None: - cmd = [ - "map-data", - "-T", - str(DENORM_SPECIFICATION), - "-s", - str(NORM_SCHEMA), - str(FLATTENING_DATA), - ] - result = runner.invoke(main, cmd) - assert result.exit_code == 0 - out = result.stdout - tr_data = yaml.safe_load(out) - m = tr_data["mappings"][0] - assert m["subject_id"] == "X:1" - assert m["subject_name"] == "x1" - - -EXPECTED_OUTPUT = { - "dict": {"input": {"that": "this"}, "yaml": "that: this\n"}, - "list": { - "input": ["this", "that", "the other"], - "yaml": "- this\n- that\n- the other\n", - }, - "string": { - "input": "But how long is it?", - "yaml": "But how long is it?\n...\n", # eh?? - None: "But how long is it?", - }, -} - - -@pytest.mark.parametrize("file_path", [None, "output.txt"]) -@pytest.mark.parametrize("output_format", [None, "yaml"]) -@pytest.mark.parametrize("output_data", EXPECTED_OUTPUT.keys()) -def test_dump_output( - capsys: Generator[pytest.CaptureFixture, None, None], - tmp_path: Generator[Path, None, None], - file_path: Optional[str], - output_format: Optional[str], - output_data: Union[dict, list], -) -> None: - """Ensure that the dump_output function does what it says.""" - if file_path: - file_path = str(tmp_path / file_path) - - # if there is no `output_format` key, this data cannot be dumped - if output_format not in EXPECTED_OUTPUT[output_data]: - with pytest.raises( - TypeError, match=re.escape(f"write() argument must be str, not {output_data}") - ): - dump_output(EXPECTED_OUTPUT[output_data]["input"], output_format, file_path) - return - - dump_output(EXPECTED_OUTPUT[output_data]["input"], output_format, file_path) - expected_text = EXPECTED_OUTPUT[output_data][output_format] - if not file_path: - captured = capsys.readouterr() - assert captured.err == "" - assert captured.out == expected_text - return - - with Path(file_path).open() as f: - assert f.read() == expected_text - - -@pytest.mark.parametrize( - ("param", "value", "error", "message"), - [ - ("output_format", "json", NotImplementedError, "Output format json is not supported"), - ("output_data", None, ValueError, "No output to be printed"), - ("file_path", "path/to/a/dir", FileNotFoundError, "No such file or directory"), - ], -) -def test_dump_output_fail(param: str, value: Optional[str], error: Exception, message: str) -> None: - """ - Ensure that invalid input causes dump_output to fail. - """ - default_params = {"output_data": {"this": "that"}, "output_format": "yaml", "file_path": None} - test_params = {**default_params, param: value} - with pytest.raises(error, match=message): - dump_output(**test_params) diff --git a/tests/test_compiler/__init__.py b/tests/test_compiler/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/tests/test_compiler/test_duckdb_compiler.py b/tests/test_compiler/test_duckdb_compiler.py deleted file mode 100644 index 32d56b0..0000000 --- a/tests/test_compiler/test_duckdb_compiler.py +++ /dev/null @@ -1,45 +0,0 @@ -""" -Tests compilation of a specification to python. -""" - -import duckdb -import pytest -from linkml_runtime import SchemaView -from linkml_runtime.dumpers import yaml_dumper - -from linkml_map.compiler.sql_compiler import SQLCompiler -from linkml_map.session import Session -from tests import SCHEMA1, SPECIFICATION - - -@pytest.fixture -def session() -> Session: - """LinkML transformer session with schema and spec set.""" - session = Session() - session.set_source_schema(SCHEMA1) - session.set_transformer_specification(SPECIFICATION) - return session - - -def test_compile(session: Session) -> None: - """Test the DuckDb compiler.""" - compiler = SQLCompiler() - assert session.transformer_specification is not None - compiled = compiler.compile(session.transformer_specification) - # TODO: include imports so that code compiles - print("Compiled SQL:") - print(compiled.serialization) - source_sv = SchemaView(SCHEMA1) - source_ddl = compiler.create_ddl(source_sv) - print("Source DDL:") - print(source_ddl) - target_sv = session.target_schemaview - print("Target Schema:") - print(yaml_dumper.dumps(target_sv.schema)) - target_ddl = compiler.create_ddl(target_sv) - print("Target DDL:") - print(target_ddl) - - conn = duckdb.connect(":memory:") - conn.execute(target_ddl) - conn.execute(compiled.serialization) diff --git a/tests/test_compiler/test_graphviz_compiler.py b/tests/test_compiler/test_graphviz_compiler.py deleted file mode 100644 index 62a387b..0000000 --- a/tests/test_compiler/test_graphviz_compiler.py +++ /dev/null @@ -1,29 +0,0 @@ -""" -Tests compilation of a specification to graphviz. -""" - -import pytest -from linkml_runtime import SchemaView - -from linkml_map.compiler.graphviz_compiler import GraphvizCompiler -from linkml_map.utils.loaders import load_specification -from tests import OUTPUT_DIR, SCHEMA1, SPECIFICATION - - -@pytest.fixture -def compiler() -> GraphvizCompiler: - """Instantiate a GraphvizCompiler.""" - return GraphvizCompiler( - source_schemaview=SchemaView(SCHEMA1), - ) - - -def test_compile(compiler: GraphvizCompiler) -> None: - """Basic test of the graphviz compiler functionality.""" - spec = load_specification(SPECIFICATION) - compiled = compiler.compile(spec) - assert ( - "sourceMapping:id -> targetDenormMapping:subject_id [style=dashed]" - in compiled.serialization - ) - compiled.render(OUTPUT_DIR / "test.png", view=False) diff --git a/tests/test_compiler/test_markdown_compiler.py b/tests/test_compiler/test_markdown_compiler.py deleted file mode 100644 index fbc0d8a..0000000 --- a/tests/test_compiler/test_markdown_compiler.py +++ /dev/null @@ -1,26 +0,0 @@ -""" -Tests compilation of a specification to markdown. -""" - -import pytest -from linkml_runtime import SchemaView - -from linkml_map.compiler.markdown_compiler import MarkdownCompiler -from linkml_map.utils.loaders import load_specification -from tests import SCHEMA1, SPECIFICATION - - -@pytest.fixture -def compiler() -> MarkdownCompiler: - """Instantiate a MarkdownCompiler.""" - return MarkdownCompiler( - source_schemaview=SchemaView(SCHEMA1), - ) - - -def test_compile(compiler: MarkdownCompiler) -> None: - """Basic test of Markdown Compiler functioning.""" - assert compiler.template_name is not None - spec = load_specification(SPECIFICATION) - markdown = compiler.compile(spec).serialization - print(markdown) diff --git a/tests/test_compiler/test_python_compiler.py b/tests/test_compiler/test_python_compiler.py deleted file mode 100644 index e059c64..0000000 --- a/tests/test_compiler/test_python_compiler.py +++ /dev/null @@ -1,41 +0,0 @@ -""" -Tests compilation of a specification to python. -""" - -import pytest -from linkml_runtime import SchemaView -from linkml_runtime.utils.compile_python import compile_python - -import tests.input.examples.personinfo_basic.model.personinfo_model as src -from linkml_map.compiler.python_compiler import PythonCompiler -from linkml_map.utils.loaders import load_specification -from tests import SCHEMA1, SPECIFICATION - - -@pytest.fixture -def compiler() -> PythonCompiler: - """Instantiate a Python Compiler.""" - return PythonCompiler( - source_schemaview=SchemaView(SCHEMA1), - source_python_module="tests.input.examples.personinfo_basic.model.personinfo_model", - target_python_module="tests.input.examples.personinfo_basic.model.agent_model", - ) - - -def test_compile(compiler: PythonCompiler) -> None: - """Basic test of Python Compiler functionality.""" - spec = load_specification(SPECIFICATION) - pycode = compiler.compile(spec) - # TODO: include imports so that code compiles - print(pycode.serialization) - mod = compile_python(pycode.serialization) - person = src.Person( - id="http://example.org/person/1", - name="Name McNameface", - age_in_years=23, - ) - agent = mod.derive_Agent(person) - print(agent) - assert agent.id == person.id - assert agent.label == person.name - assert agent.age == "23 years" diff --git a/tests/test_compliance/test_compliance_suite.py b/tests/test_compliance/test_compliance_suite.py deleted file mode 100644 index a93b559..0000000 --- a/tests/test_compliance/test_compliance_suite.py +++ /dev/null @@ -1,1203 +0,0 @@ -""" -Transformers compliance test suite. - -This is intended to test all features of the LinkML-Transformers language. -Each test focuses on a single feature, and explores different combinations -of schema, transformation specification, and source/target object pairs. - -Note that "print" statements are used intentionally here; when this -test is run via pytest with ``-s -q --tb no --disable-warnings`` settings, -the output is a markdown document that can be used as documentation, for -both end users and developers. - -This can also be helpful for developers of this test suite: due to -the use of combinatorial exploration using pytest parametrization, -it can be hard to reason through combinations, and some of the generative -code can be abstract. You are encouraged to look at the markdown outputs -to see what is being generated for each test. -""" - -import logging -import re -from dataclasses import dataclass -from datetime import date -from types import ModuleType -from typing import Any, Optional, Union - -import pytest -from deepdiff import DeepDiff -from linkml.validator import JsonschemaValidationPlugin, Validator -from linkml_runtime import SchemaView -from linkml_runtime.dumpers import yaml_dumper -from linkml_runtime.linkml_model import Prefix, SchemaDefinition - -from linkml_map.compiler.python_compiler import PythonCompiler -from linkml_map.compiler.sql_compiler import SQLCompiler -from linkml_map.datamodel.transformer_model import ( - CollectionType, - SerializationSyntaxType, - TransformationSpecification, -) -from linkml_map.functions.unit_conversion import DimensionalityError, UndefinedUnitError -from linkml_map.inference.inverter import TransformationSpecificationInverter -from linkml_map.inference.schema_mapper import SchemaMapper -from linkml_map.transformer.object_transformer import ObjectTransformer - -today = date.today() -formatted_date = today.strftime("%Y-%m-%d") - -logger = logging.getLogger(__name__) - -print( - f""" -# LinkML-Map Compliance Suite - -This is the output from running the full compliance test suite. - -```yaml -Time_executed: {formatted_date} -Package: {__file__} -``` - -It is organized into **Feature Sets** that test a particular feature or group of features, -and **combinations** of different schemas, input objects, and transformation specifications. -This is intended to exhaustively test all combinations of features, and provide informative -output. - -Each test is designed to demonstrate: - -- data mapping (transformation) -- derived schemas -- inversion (reverse transformation) (in some cases) -- compilation to other frameworks (coming soon) - -""" -) - - -def print_yaml(obj: Any) -> None: - print("```yaml") - print(yaml_dumper.dumps(obj)) - print("```\n") - - -def build_schema(name: str, **kwargs: dict[str, Any]) -> SchemaDefinition: - schema = SchemaDefinition(id=name, name=name, **kwargs) - schema.imports.append("linkml:types") - schema.default_prefix = "test" - for k, v in [("linkml", "https://w3id.org/linkml/"), ("test", "http://example.org/test/")]: - schema.prefixes[k] = Prefix(k, v) - print("**Source Schema**: \n\n") - print_yaml(schema) - return schema - - -def build_transformer(**kwargs: dict[str, Any]) -> TransformationSpecification: - mapper = ObjectTransformer() - mapper.create_transformer_specification(kwargs) - print("**Transformer Specification**:\n\n") - print_yaml(mapper.specification) - return mapper.specification - - -def create_compilers( - spec: TransformationSpecification, expected_map: dict[ModuleType, str] -) -> None: - """ - Test compilation of transformation specifications to other languages. - - This test is a placeholder for future development, where the - transformation specification will be compiled to other languages - (e.g. SQL, R2RML, etc.) - - :param spec: transformation specification - :return: - """ - for compiler_type, expected in expected_map.items(): - compiler = compiler_type() - compiled_spec = compiler.compile(spec) - print(f"**Compiled Specification ({compiler_type.__name__})**:\n\n") - print(compiled_spec.serialization) - assert expected in compiled_spec.serialization - - -@dataclass -class State: - schema_mapper: SchemaMapper = None - object_transformer: ObjectTransformer = None - target_object: Any = None - - -def map_object( - spec: TransformationSpecification, - source_object: dict[str, Any], - expected_target_object: dict[str, Any], - source_sv: SchemaView, - invertible: bool = False, # noqa: FBT001, FBT002 - index: bool = False, # noqa: FBT001, FBT002 - source_root: Optional[str] = "Container", - roundtrip_object: Optional[Any] = None, - raises_error: Optional[Exception] = None, - supply_source_schema: Optional[bool] = True, -) -> State: - """ - Map a source object to a target object, and optionally invert the transformation and perform roundtrip. - - :param spec: transformation specification to use in mapping - :param source_object: object to convert - :param expected_target_object: expected value of output of transformation - :param source_sv: source schema view - :param invertible: True if the transformation is reversible, via derived inverted transformation - :param index: True if the source object should use an Object Index - :param source_root: tree root for source schema, if non-default - :param roundtrip_object: the expected value of passing target object back through inverted transformation - (defaults to source object) - :param raises_error: if not None, the expected error to be raised during transformation - :return: state object including transformed object plus intermediate objects - """ - pc = PythonCompiler(source_schemaview=source_sv) - python_code = pc.compile(spec) - logger.debug(f"Python Code: {python_code}\n\n") - # TODO: enable this - # print("Python Code (Generated)\n\n") - # print("```python") - # print(python_code.serialization) - # print("```\n") - # mod = python_code.module - schema_mapper = SchemaMapper(source_schemaview=source_sv) - target_schema = schema_mapper.derive_schema(spec) - target_sv = SchemaView(yaml_dumper.dumps(target_schema)) - if supply_source_schema: - mapper = ObjectTransformer(source_schemaview=source_sv, specification=spec) - else: - mapper = ObjectTransformer(specification=spec) - if index: - mapper.index(source_object, target=source_root) - if raises_error: - with pytest.raises(raises_error): - target_object = mapper.map_object(source_object) - # FIXME: should only have a single line in a `pytest.raises` block - logger.debug(f"Unexpected Target Object: {target_object}") - target_object = None - else: - target_object = mapper.map_object(source_object) - assert target_object == expected_target_object, ( - f"failed to map {source_object} to {expected_target_object}" - ) - assert not DeepDiff(target_object, expected_target_object), "unexpected differences" - print("**Object Transformation**:\n") - if raises_error: - print(f"**Expected Error**: {raises_error.__name__}") - print(" * Source Object:") - print_yaml(source_object) - print(" * Target Object:") - print_yaml(target_object) - print("**Target Schema (Derived)**:\n\n") - print_yaml(target_schema) - if target_object is not None: - # remove `foo: None` entries - target_object = {k: v for k, v in target_object.items() if v is not None} - ensure_validates(target_sv.schema, target_object) - if invertible and target_object is not None: - inverter = TransformationSpecificationInverter( - source_schemaview=source_sv, - target_schemaview=target_sv, - ) - inv_spec = inverter.invert(spec) - print("**Inverted Transformation Specification** (Derived):\n\n") - print_yaml(inv_spec) - inv_mapper = ObjectTransformer(source_schemaview=target_sv, specification=inv_spec) - inv_target_object = inv_mapper.map_object(target_object) - if roundtrip_object is None: - roundtrip_object = source_object - assert inv_target_object == roundtrip_object, ( - f"failed to invert {target_object} to {source_object}" - ) - return State( - schema_mapper=schema_mapper, - object_transformer=mapper, - target_object=target_object, - ) - - -def ensure_validates(target_schema: SchemaDefinition, target_object: Any) -> None: - """Run the JsonSchema validator on a target_object.""" - target_validator = Validator( - yaml_dumper.dumps(target_schema), validation_plugins=[JsonschemaValidationPlugin()] - ) - assert list(target_validator.iter_results(target_object)) == [], ( - f"failed to validate {target_object}" - ) - - -@pytest.fixture -def invocation_tracker(request: pytest.FixtureRequest) -> bool: - """ - Emit metadata for each invocation of a test function. - - Also emits the docstring for the test function. - - :param request: - :return: - """ - node = request.node - key = "first_invocation_" + node.originalname - first_invocation = False - if not hasattr(request.config, key): - setattr(request.config, key, True) - test_function = node.function - print(f"## Feature Set: {node.originalname}\n") - docstring = test_function.__doc__ - if not docstring: - msg = f"Test {node.originalname} has no docstring" - raise AssertionError(msg) - for line in docstring.split("\n"): - line = line.strip() - if line.startswith(":return:"): - continue - match = re.match(r":param (\w+):\s*(.*)", line) - if match: - pname, pdesc = match.groups() - if pname == "invocation_tracker": - continue - print(f"* **{pname}**: {pdesc}") - else: - print(line) - first_invocation = True - print(f"### Combo: {node.name}\n") - return first_invocation - - -@pytest.mark.parametrize( - ("source_datatype", "target_datatype", "source_value", "target_value", "invertible"), - [ - ("string", "string", "foo", "foo", True), - ("integer", "integer", 5, 5, True), - ("string", "integer", "5", 5, True), - ("integer", "float", 5, 5.0, True), - ("float", "integer", 5.0, 5, True), - ("float", "integer", 5.2, 5, False), - ("integer", "boolean", 5, True, False), - ("integer", "boolean", 0, False, False), - ], -) -def test_map_types( - invocation_tracker, - source_datatype: str, - target_datatype: str, - source_value: Union[str, float], - target_value: Union[str, float, bool], - invertible: bool, # noqa: FBT001 -) -> None: - """ - Test mapping between basic data types. - - This test uses an ultra-minimal schema with a single class and a single attribute, - the transformation specification maps that attribute onto itself, with a different - type, demonstrating type coercion. - - Some cases will be trivially isomorphic (where `source_datatype` == `target_datatype`), - but these are executed anyway. - - :param invocation_tracker: pytest fixture to emit metadata - :param source_datatype: linkml datatype of source object - :param target_datatype: linkml datatype of target object - :param source_value: value of source object - :param target_value: expected value of slot in target object - :param invertible: True if the transformation is invertible - :return: - """ - print(f"Mapping `{source_datatype}` => `{target_datatype}`\n\n") - if source_datatype == target_datatype: - print("Isomorphic mapping: input should equal output\n") - else: - print("Should coerce datatype\n") - classes = {"C": {"attributes": {"s1": {"range": source_datatype}}}} - schema = build_schema( - "types", - classes=classes, - description="Minimal single-attribute schema for testing datatype mapping", - ) - source_sv = SchemaView(schema) - cds = { - "C": { - "slot_derivations": { - "s1": { - "populated_from": "s1", - "range": target_datatype, - } - } - } - } - spec = build_transformer(class_derivations=cds) - - source_object = {"s1": source_value} - map_object( - spec=spec, - source_object=source_object, - expected_target_object={"s1": target_value}, - source_sv=source_sv, - invertible=invertible, - ) - - -@pytest.mark.parametrize( - ("source_datatype", "target_datatype", "source_value", "target_value", "invertible"), - [ - ( - "string", - "string", - [{"id": "X", "s1": "foo"}, {"id": "Y", "s1": "bar"}], - {"X": {"s1": "foo"}, "Y": {"s1": "bar"}}, - True, - ), - ( - "string", - "string", - {"X": {"s1": "foo"}, "Y": {"s1": "bar"}}, - [{"id": "X", "s1": "foo"}, {"id": "Y", "s1": "bar"}], - True, - ), - ], -) -def test_map_collections( - invocation_tracker, - source_datatype: str, - target_datatype: str, - source_value: Union[list[dict[str, Any]], dict[str, Any]], - target_value: Union[list[dict[str, Any]], dict[str, Any]], - invertible: bool, -) -> None: - """ - Test mapping between collection data types (lists and dicts). - - This makes use of the `cast_collection_as` construct - - :param invocation_tracker: - :param source_datatype: linkml datatype of source object - :param target_datatype: linkml datatype of target object - :param source_value: value of source object - :param target_value: expected value of slot in target object - :param invertible: True if the transformation is invertible - :return: - """ - print(f"Mapping `{source_datatype}` => `{target_datatype}`\n\n") - if source_datatype == target_datatype: - print("Isomorphic mapping: **input must equal output**\n") - else: - print("Should coerce datatype\n") - source_collection_type = ( - CollectionType.MultiValuedList - if isinstance(source_value, list) - else CollectionType.MultiValuedDict - ) - target_collection_type = ( - CollectionType.MultiValuedList - if isinstance(target_value, list) - else CollectionType.MultiValuedDict - ) - classes = { - "C": { - "tree_root": True, - "attributes": { - "ds": { - "range": "D", - "inlined": True, - "inlined_as_list": source_collection_type == CollectionType.MultiValuedList, - "multivalued": True, - } - }, - }, - "D": {"attributes": {"id": {"identifier": True}, "s1": {"range": source_datatype}}}, - } - schema = build_schema( - "types", - classes=classes, - description="Mapping between collection types", - ) - source_sv = SchemaView(schema) - cds = { - "C": { - "slot_derivations": { - "ds": { - "populated_from": "ds", - "dictionary_key": "id" if isinstance(source_value, list) else None, - "cast_collection_as": target_collection_type.value, - } - } - }, - "D": { - "slot_derivations": { - "id": { - "populated_from": "id", - }, - "s1": { - "populated_from": "s1", - "range": target_datatype, - }, - } - }, - } - spec = build_transformer(class_derivations=cds) - - source_object = {"ds": source_value} - map_object( - spec=spec, - source_object=source_object, - expected_target_object={"ds": target_value}, - source_sv=source_sv, - invertible=invertible, - ) - - -@pytest.mark.parametrize( - ("expr", "source_object", "target_value"), - [ - ("s1 + s2", {"s1": 5, "s2": 6}, 11), - ("{s1} + {s2}", {"s1": 5, "s2": 6}, 11), - ("{s1} + {s2}", {"s1": 5}, None), - ("s1 + s2.s3", {"s1": 5, "s2": {"s3": 6}}, 11), - ("s1 + s2.s3.s4", {"s1": 5, "s2": {"s3": {"s4": 6}}}, 11), - ("s1 + s2", {"s1": "a", "s2": "b"}, "ab"), - ("s1 + s2", {"s1": ["a"], "s2": ["b"]}, ["a", "b"]), - ("len(s1)", {"s1": ["a"]}, 1), - ("s1 < s2", {"s1": 5, "s2": 6}, True), - ], -) -def test_expr(invocation_tracker, expr: str, source_object: Any, target_value: Any) -> None: - """ - Test transformation using pythonic expressions. - - This test uses a simple source schema with two slots (`s1` and `s2`). - These are combined using a pythonic expression, to populate the only - slot in the target schema (called `derived`). - - The values of `s1` and `s2` can be numbers or strings. - - If the expression wraps a slot in `{...}` then the presence of a None - forces the entire expression to be `None` - - Limitations: At this time, the framework cannot generate a complete - derived schema or inversion for expressions. This will be fixed - in future. - - - See also: [LinkML Expressions](https://linkml.io/linkml/schemas/expression-language.html) - - :param invocation_tracker: pytest fixture to emit metadata - :param expr: pythonic expression - :param source_object: source object - :param target_value: expected value of slot in target object - :return: - """ - classes = {"C": {"tree_root": True, "attributes": {}}} - - def infer_range(v: Any, typ: Optional[str] = None) -> str: - if isinstance(v, dict): - if not typ: - typ = v.get("type", "D") - if typ not in classes: - classes[typ] = {"attributes": {}} - for k1, v1 in v.items(): - r = infer_range(v1) - if not isinstance(r, dict): - r = {"range": r} - classes[typ]["attributes"][k1] = r - return typ - if isinstance(v, list): - r = infer_range(v[0]) - return {"range": r, "multivalued": True} - if isinstance(v, int): - return "integer" - if isinstance(v, float): - return "float" - if isinstance(v, bool): - return "boolean" - if isinstance(v, str): - return "string" - msg = f"Unknown type {type(v)}" - raise ValueError(msg) - - infer_range(source_object, typ="C") - schema = build_schema("expr", classes=classes) - - source_sv = SchemaView(schema) - cds = { - "C": { - "populated_from": "C", - "slot_derivations": { - "derived": { - "expr": expr, - } - }, - } - } - spec = build_transformer(class_derivations=cds) - map_object( - spec=spec, - source_object=source_object, - expected_target_object={"derived": target_value}, - source_sv=source_sv, - invertible=False, - ) - - -@pytest.mark.parametrize( - ( - "source_slot", - "target_slot", - "source_unit", - "target_unit", - "unit_metaslot", - "source_value", - "target_value", - "err", - "skip", - ), - [ - ("s1", "s1", "m", "cm", "ucum_code", 1.0, 100.0, None, None), - ("s1", "s1", "m", "cm", "symbol", 1.0, 100.0, None, None), - ("s1", "s1", "m", "m", "ucum_code", 1.0, 1.0, None, None), - ("s1", "s1", "a", "mo", "ucum_code", 10.0, 120.0, None, None), - ("s1", "s1", "a", "mo", "symbol", 10.0, None, UndefinedUnitError, None), - ("s1", "s1", "m", "ml", "ucum_code", 1.0, None, DimensionalityError, None), - ("s1", "s1", "m", "pinknoodles", "ucum_code", 1.0, None, UndefinedUnitError, None), - ("s1", "s1", "ml", "m", "ucum_code", 1.0, None, DimensionalityError, None), - ("s1", "s1", "pinknoodles", "m", "ucum_code", 1.0, None, UndefinedUnitError, None), - ("s1", "s1", "m/s", "cm/s", "ucum_code", 1.0, 100.0, None, None), - ("s1", "s1", "m.s-1", "cm.s-1", "ucum_code", 1.0, 100.0, None, None), - ( - "s1", - "s1", - "g.m2-1", - "kg.m2-1", - "ucum_code", - 1.0, - 0.001, - None, - "https://github.com/dalito/ucumvert/issues/8", - ), - ("height_in_m", "height_in_cm", "m", "cm", "ucum_code", 1.0, 100.0, None, None), - ("s1", "s1", "m[H2O]{35Cel}", "m[H2O]{35Cel}", "ucum_code", 1.0, 1.0, None, None), - ], -) -def test_simple_unit_conversion( - invocation_tracker, - source_slot: str, - target_slot: str, - source_unit: str, - target_unit: str, - unit_metaslot: str, - source_value: float, - target_value: Optional[float], - err: Optional[Exception], - skip: Optional[str], -) -> None: - """ - Test unit conversion. - - This test uses a simple source schema with a single class and a single attribute, where the attribute - is described using the [units](https://w3id.org/linkml/units) metaslot. - - The recommended way to describe unit slots in LinkML is with UCUM, but a number of other schemes - can be used. We explicitly test for some known cases where UCUM uses non-standard units (e.g. Cel, mo), - as well as UCUM-specific syntax (e.g. `m.s-1`) and extensions (e.g. using annotations like `{Cre}`). - - :param invocation_tracker: pytest fixture to emit metadata - :param source_slot: name of slot in source schema - :param target_slot: name of slot in target schema - :param source_unit: unit of source slot - :param target_unit: unit of target slot - :param source_value: magnitude of source slot (to be converted) - :param target_value: expected magnitude of target slot (output of conversion) - :param err: - :return: - """ - if skip: - pytest.skip(f"TODO: {skip}") - print( - f"Unit Conversion: `{source_value}` `{source_unit}` => " - f"`{target_value}` `{target_unit}` [with {source_slot}]\n\n" - ) - if source_unit == target_unit: - print("Isomorphic mapping: **input must equal output**") - classes = { - "C": { - "attributes": { - source_slot: { - "range": "float", - "unit": { - unit_metaslot: source_unit, - }, - } - } - } - } - schema = build_schema("types", classes=classes) - source_sv = SchemaView(schema) - cds = { - "C": { - "slot_derivations": { - target_slot: { - "populated_from": source_slot, - "unit_conversion": { - "target_unit": target_unit, - }, - } - } - } - } - spec = build_transformer(class_derivations=cds) - - source_object = {source_slot: source_value} - map_object( - spec=spec, - source_object=source_object, - expected_target_object={target_slot: target_value} if target_value is not None else None, - source_sv=source_sv, - invertible=True, - raises_error=err, - ) - - -@pytest.mark.parametrize( - ("source_unit", "target_unit", "source_value", "target_value", "roundtrip_object", "err"), - [ - ("m", "cm", 1.0, 100.0, {"q": {"unit": "cm", "magnitude": 100.0}}, None), - ("cm", "cm", 100.0, 100.0, {"q": {"unit": "cm", "magnitude": 100.0}}, None), - ("cm", "ml", 100.0, None, None, DimensionalityError), - ("cm", "pinknoodles", 100.0, None, None, UndefinedUnitError), - ], -) -def test_complex_unit_conversion( - invocation_tracker, - source_unit: str, - target_unit: str, - source_value: float, - target_value: Optional[float], - roundtrip_object: Optional[dict[str, Any]], - err: Optional[Exception], -) -> None: - """ - Test unit conversion, from complex object to simple scalar. - - An example complex object would be an object with separate attributes for - representing magnitude (value) and unit. - - For example `magnitude: 1.0, unit: "m"` - - :param invocation_tracker: - :param source_unit: unit of source slot - :param target_unit: unit of target slot - :param source_value: magnitude of source slot (to be converted) - :param target_value: expected magnitude of target slot (output of conversion) - :param roundtrip_object: expected value of passing target object back through inverted transformation - :param err: True if expected to raise an Error - :return: - """ - target_slot = f"q_in_{target_unit}" - classes = { - "Q": { - "attributes": { - "magnitude": { - "range": "float", - }, - "unit": { - "range": "string", - }, - }, - }, - "C": { - "tree_root": True, - "attributes": { - "q": { - "range": "Q", - } - }, - }, - } - schema = build_schema("types", classes=classes) - source_sv = SchemaView(schema) - cds = { - "D": { - "populated_from": "C", - "slot_derivations": { - target_slot: { - "populated_from": "q", - "unit_conversion": { - "target_unit": target_unit, - "source_unit_slot": "unit", - "source_magnitude_slot": "magnitude", - }, - } - }, - } - } - spec = build_transformer(class_derivations=cds) - - source_object = { - "q": { - "magnitude": source_value, - "unit": source_unit, - } - } - map_object( - spec=spec, - source_object=source_object, - expected_target_object={target_slot: target_value} if target_value is not None else None, - source_sv=source_sv, - invertible=True, - roundtrip_object=roundtrip_object, - raises_error=err, - ) - - -@pytest.mark.parametrize( - ("syntax", "delimiter", "source_value", "target_value"), - [ - (None, ",", ["a", "b"], "a,b"), - (None, "|", ["a", "b"], "a|b"), - (None, "|", ["a"], "a"), - (None, "|", [], ""), - (SerializationSyntaxType.JSON, None, ["a", "b"], '["a", "b"]'), - (SerializationSyntaxType.JSON, None, [], "[]"), - (SerializationSyntaxType.YAML, None, ["a", "b"], "[a, b]"), - ], -) -def test_stringify( - invocation_tracker, - syntax: Optional[SerializationSyntaxType], - delimiter: Optional[str], - source_value: list[str], - target_value: str, -) -> None: - """ - Test compaction of multivalued slots into a string. - - Stringification is primarily intended for mapping from complex nested formats to - simple tabular TSV formats, where some of the following methodologies can be used: - - - flattening lists using an (internal) delimiter - - flattening lists or more complex objects using JSON or YAML - - For example, `["a", "b"]` => `"a,b"` - - As a convention we use `s1_verbatim` as a slot/attribute name for the - stringified form. - - :param invocation_tracker: pytest fixture to emit metadata - :param syntax: SerializationSyntaxType - :param delimiter: delimiter to use in stringification - :param source_value: source value (a list) - :param target_value: expected value of slot in target object (a string) - :return: - """ - classes = { - "C": { - "attributes": { - "s1": {"range": "string", "multivalued": True}, - } - }, - } - schema = build_schema("types", classes=classes) - source_sv = SchemaView(schema) - cds = { - "D": { - "populated_from": "C", - "slot_derivations": { - "s1_verbatim": { - "populated_from": "s1", - "stringification": { - "syntax": syntax, - "delimiter": delimiter, - }, - } - }, - } - } - spec = build_transformer(class_derivations=cds) - source_object = {"s1": source_value} - map_object( - spec=spec, - source_object=source_object, - expected_target_object={"s1_verbatim": target_value}, - source_sv=source_sv, - invertible=True, - ) - create_compilers(spec, {SQLCompiler: ""}) - - -@pytest.mark.parametrize( - "source_object", - [ - ({"c_list": [{"s1": "a", "s2": "b"}, {"s1": "c", "s2": "d"}], "d": {"s3": "e"}}), - ], -) -@pytest.mark.parametrize("use_expr", [True, False]) -@pytest.mark.parametrize("supply_source_schema", [True]) # TODO -def test_isomorphic( - invocation_tracker, - source_object: dict[str, Any], - use_expr: bool, # noqa: FBT001 - supply_source_schema: bool, # noqa: FBT001 -) -> None: - """ - Test mapping a schema to an identical schema (i.e copy). - - This also tests for the ability to recursively descend a nested structure. - - :param invocation_tracker: - :param source_object: - :param use_expr: - :param supply_source_schema: TODO: always True for now - :return: - """ - classes = { - "Container": { - "tree_root": True, - "attributes": { - "c_list": { - "range": "C", - "multivalued": True, - }, - "d": { - "range": "D", - }, - }, - }, - "C": { - "attributes": { - "s1": { - "range": "string", - }, - "s2": { - "range": "string", - }, - } - }, - "D": { - "attributes": { - "s3": { - "range": "string", - }, - }, - }, - } - schema = build_schema("isomorphic", classes=classes) - source_sv = SchemaView(schema) - mapping_key = "expr" if use_expr else "populated_from" - cds = { - "Container": { - "populated_from": "Container", - "slot_derivations": { - "c_list": { - "populated_from": "c_list", - "range": "C", - }, - "d": { - "populated_from": "d", - "range": "D", - }, - }, - }, - "C": { - "populated_from": "C", - "slot_derivations": { - "s1": { - "populated_from": "s1", - }, - "s2": { - "populated_from": "s2", - }, - }, - }, - "D": { - "populated_from": "D", - "slot_derivations": { - "s3": { - mapping_key: "s3", - } - }, - }, - } - spec = build_transformer(class_derivations=cds) - map_object( - spec=spec, - source_object=source_object, - expected_target_object=source_object, - source_sv=source_sv, - invertible=True, - supply_source_schema=supply_source_schema, - ) - - -@pytest.mark.parametrize("inlined", [True, False]) -@pytest.mark.parametrize( - ("source_object", "target_object"), - [ - ( - {"s1": {"id": "x1", "name": "foo"}, "s2": {"id": "x2", "name": "bar"}}, - {"s1_id": "x1", "s1_name": "foo", "s2_id": "x2", "s2_name": "bar"}, - ), - ], -) -def test_join( - invocation_tracker, - source_object: dict[str, Any], - target_object: dict[str, Any], - inlined: bool, # noqa: FBT001 -) -> None: - """ - Test joining two objects into a single object, aka denormalization. - - :param invocation_tracker: - :param source_object: normalized source object - :param target_object: denormalized target object - :param inlined: True if the source objects are inlined - :return: - """ - classes = { - "R": { - "tree_root": inlined, - "attributes": { - "s1": { - "range": "E", - "inlined": inlined, - }, - "s2": { - "range": "E", - "inlined": inlined, - }, - }, - }, - "E": { - "attributes": { - "id": { - "range": "string", - "identifier": True, - }, - "name": { - "range": "string", - }, - }, - }, - } - cds = { - "R": { - "populated_from": "R", - "slot_derivations": { - "s1_id": { - "expr": "s1.id", - }, - "s1_name": { - "expr": "s1.name", - }, - "s2_id": { - "expr": "s2.id", - }, - "s2_name": { - "expr": "s2.name", - }, - }, - }, - } - if not inlined: - classes["Container"] = { - "tree_root": True, - "attributes": { - "r_list": { - "range": "R", - "multivalued": True, - }, - "e_list": { - "range": "E", - "multivalued": True, - "inlined_as_list": True, - }, - }, - } - source_object = { - "r_list": [{"s1": source_object["s1"]["id"], "s2": source_object["s2"]["id"]}], - "e_list": [source_object["s1"], source_object["s2"]], - } - target_object = {"r_list": [target_object]} - cds["Container"] = { - "populated_from": "Container", - "slot_derivations": { - "r_list": { - "populated_from": "r_list", - }, - }, - } - schema = build_schema("types", classes=classes) - source_sv = SchemaView(schema) - - spec = build_transformer(class_derivations=cds) - map_object( - spec=spec, - source_object=source_object, - expected_target_object=target_object, - source_sv=source_sv, - invertible=False, - index=not inlined, - ) - - -@pytest.mark.parametrize( - ("source_value", "mapping", "target_value", "mirror_source"), - [ - ("A", {"B": "A"}, "B", False), - ("Z", {"B": "A"}, None, False), - ("C", {"B": "A"}, "C", True), - ("A", {"B": ["A", "C"]}, "B", False), - ("C", {"B": ["A", "C"]}, "B", False), - ], -) -def test_map_enum( - invocation_tracker, - source_value: str, - mapping: dict[str, Any], - target_value: Optional[str], - mirror_source: bool, # noqa: FBT001 -) -> None: - """ - Test mapping between enum values. - - Currently this only supports simple dictionary-style mapping between permissible values, - akin to SSSOM, but in future additional expressivity will be supported, including: - - - mapping ranges to categorical values - - boolean/branching logic - - :param invocation_tracker: - :param source_value: source enum permissible value to be mapped - :param mapping: mapping from source to target enum permissible values - :param target_value: expected target enum permissible value - :return: - """ - classes = { - "C": { - "attributes": { - "s1": { - "range": "E", - } - } - } - } - enums = {"E": {"permissible_values": ["A", "B", "C"]}} - schema = build_schema("enums", classes=classes, enums=enums) - source_sv = SchemaView(schema) - cds = { - "C": { - "slot_derivations": { - "s1": { - "populated_from": "s1", - } - } - } - } - pv_derivs = {} - invertible = True - for k, v in mapping.items(): - if isinstance(v, list): - pv_derivs[k] = {"sources": v} - invertible = False - else: - pv_derivs[k] = {"populated_from": v} - - eds = { - "E": { - "populated_from": "E", - "mirror_source": mirror_source, - "permissible_value_derivations": pv_derivs, - }, - } - spec = build_transformer(class_derivations=cds, enum_derivations=eds) - source_object = {"s1": source_value} - if target_value is None: - invertible = False - if mirror_source: - pytest.skip("TODO: mirror_source") - map_object( - spec=spec, - source_object=source_object, - expected_target_object={"s1": target_value}, - source_sv=source_sv, - invertible=invertible, - ) - - -@pytest.mark.parametrize("is_a", [True, False]) -@pytest.mark.parametrize("flatten", [False, True]) -def test_inheritance(invocation_tracker, is_a: bool, flatten: bool) -> None: # noqa: FBT001 - """ - Test inheritance. - - Transformation specifications can utilize inheritance, in the same way that LinkML schemas can. - - :param invocation_tracker: pytest fixture to emit metadata - :param is_a: use is_as instead of mixins in test schema - :param flatten: roll down inherited slots - :return: - """ - classes = { - "C": { - "tree_root": True, - "attributes": { - "s1": { - "range": "integer", - } - }, - }, - "D": { - "attributes": { - "s2": { - "range": "integer", - } - }, - }, - } - if is_a: - classes["C"]["is_a"] = "D" - else: - classes["C"]["mixins"] = ["D"] - - schema = build_schema("expr", classes=classes) - - source_sv = SchemaView(schema) - cds = { - "C": { - "populated_from": "C", - "slot_derivations": { - "s1": { - "expr": "s1 + 1", - }, - }, - }, - "D": { - "populated_from": "D", - "slot_derivations": { - "s2": { - "expr": "s2 + 1", - } - }, - }, - } - if flatten: - cds["C"]["slot_derivations"]["s2"] = { - "expr": "s2 + 1", - } - del cds["D"] - elif is_a: - cds["C"]["is_a"] = "D" - else: - cds["C"]["mixins"] = ["D"] - spec = build_transformer(class_derivations=cds) - source_object = {"s1": 1, "s2": 2} - target_object = {"s1": 2, "s2": 3} - map_object( - spec=spec, - source_object=source_object, - expected_target_object=target_object, - source_sv=source_sv, - invertible=False, - ) diff --git a/tests/test_datamodel.py b/tests/test_datamodel.py deleted file mode 100644 index a6532d3..0000000 --- a/tests/test_datamodel.py +++ /dev/null @@ -1,60 +0,0 @@ -"""Tests the data model.""" - -from linkml_map.transformer.object_transformer import ObjectTransformer -from tests import PERSONINFO_TR - - -def test_datamodel() -> None: - """Check loading/retrieval.""" - tr = ObjectTransformer() - tr.load_transformer_specification(PERSONINFO_TR) - trs = tr.specification - assert trs.model_dump_json() != "" - assert trs.source_schema == "s1" - assert trs.target_schema == "s2" - - # class derivations - class_derivs = { - "Container": "Container", - "Entity": None, - "Agent": "Person", - "Job": None, - "Address": "Address", - "FamilialRelationship": "FamilialRelationship", - "SequenceFeature": None, - "DenormMapping": "Mapping", - } - for clss, spec in trs.class_derivations.items(): - assert class_derivs[clss] == spec.populated_from - - # slot derivations - agent_slots = trs.class_derivations["Agent"].slot_derivations - # populated from - assert agent_slots["label"].populated_from == "name" - - # one line expression - assert agent_slots["age"].expr == "str({age_in_years}) + ' years'" - - # multi-line expr - assert ( - agent_slots["driving_since"].expr - == 'd_test = [x.important_event_date for x in src.has_important_life_events if str(x.event_name) == "PASSED_DRIVING_TEST"]\nif len(d_test):\n target = d_test[0]\n' - ) - - assert agent_slots["primary_email"].expr is None - assert agent_slots["secondary_email"].expr == "NULL" - # this should be fixed! - assert agent_slots["gender"].expr == "None" - - assert agent_slots["id"].populated_from is None - assert agent_slots["id"].expr is None - - # enum derivations - assert len(trs.enum_derivations) == 1 - assert ( - trs.enum_derivations["MyFamilialRelationshipType"].populated_from - == "FamilialRelationshipType" - ) - assert {"SIBLING_OF", "CHILD_OF"} == set( - trs.enum_derivations["MyFamilialRelationshipType"].permissible_value_derivations.keys() - ) diff --git a/tests/test_schema_mapper/__init__.py b/tests/test_schema_mapper/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/tests/test_schema_mapper/test_schema_mapper.py b/tests/test_schema_mapper/test_schema_mapper.py deleted file mode 100644 index 6366753..0000000 --- a/tests/test_schema_mapper/test_schema_mapper.py +++ /dev/null @@ -1,412 +0,0 @@ -""" -Tests engine for deriving schemas (profiling) from a specification and a source. -""" - -import pytest -from linkml_runtime import SchemaView -from linkml_runtime.dumpers import yaml_dumper -from linkml_runtime.utils.schema_builder import SchemaBuilder - -from linkml_map.datamodel.transformer_model import ( - ClassDerivation, - CopyDirective, - SlotDerivation, - TransformationSpecification, -) -from linkml_map.inference.schema_mapper import SchemaMapper -from linkml_map.transformer.object_transformer import ObjectTransformer -from tests import SCHEMA1, SPECIFICATION - - -@pytest.fixture -def source_schemaview() -> SchemaView: - """Instantiate a schemaview with Schema1.""" - return SchemaView(SCHEMA1) - - -@pytest.fixture -def mapper(source_schemaview: SchemaView) -> SchemaMapper: - """Instantiate a mapper with Schema1 as the source schema.""" - mapper = SchemaMapper() - mapper.source_schemaview = source_schemaview - return mapper - - -def test_derive_schema(mapper: SchemaMapper, source_schemaview: SchemaView) -> None: - """Tests deriving a schema from a specification and a source.""" - tr = ObjectTransformer() - tr.source_schemaview = source_schemaview - tr.load_transformer_specification(SPECIFICATION) - target_schema = mapper.derive_schema(tr.specification) - cases = [ - ( - "Agent", - [ - "id", - "age", - "label", - "has_familial_relationships", - "primary_email", - "gender", - "current_address", - ], - ), - ("FamilialRelationship", ["related_to", "type"]), - ] - for cn, ex_slots in cases: - assert cn in target_schema.classes - c = target_schema.classes[cn] - atts = c.attributes - for s in ex_slots: - assert s in atts - agent = target_schema.classes["Agent"] - assert agent.is_a == "Entity" - - -def test_null_specification(mapper: SchemaMapper) -> None: - """ - Tests empty spec limit case. - - An empty spec should return an empty schema. - """ - specification = TransformationSpecification(id="test") - target_schema = mapper.derive_schema(specification) - assert list(target_schema.classes.values()) == [] - - -def test_null_specification_and_source() -> None: - """ - Tests empty spec and source schema limit case. - - An empty spec and source schema should return an empty schema. - """ - tr = SchemaMapper() - tr.source_schemaview = SchemaView(SCHEMA1) - specification = TransformationSpecification(id="test") - target_schema = tr.derive_schema(specification) - assert list(target_schema.classes.values()) == [] - - -def test_definition_in_derivation() -> None: - """ - Test where the derived schema is entirely specified by the spec. - """ - tr = SchemaMapper() - tr.source_schemaview = SchemaView(SCHEMA1) - specification = TransformationSpecification( - id="test", - class_derivations={ - "Thing": ClassDerivation( - name="Thing", - slot_derivations={ - "id": SlotDerivation( - name="id", - target_definition={"identifier": "true", "range": "uriorcurie"}, - ), - }, - ), - "Agent": ClassDerivation( - name="Agent", - slot_derivations={ - "age": SlotDerivation(name="role", target_definition={"range": "integer"}), - }, - target_definition={ - "description": "A person or organization.", - "is_a": "Thing", - }, - ), - }, - ) - target_schema = tr.derive_schema(specification) - assert {"Agent", "Thing"} == set(target_schema.classes.keys()) - - thing = target_schema.classes["Thing"] - atts = thing.attributes - assert list(atts.keys()) == ["id"] - id_att = atts["id"] - assert id_att.range == "uriorcurie" - assert id_att.identifier - agent = target_schema.classes["Agent"] - assert agent.is_a == "Thing" - - -def test_derive_partial(mapper: SchemaMapper) -> None: - """ - Tests partial spec limit case. - """ - specification = TransformationSpecification(id="test") - derivations = [ - ClassDerivation(name="Agent", populated_from="Person"), - ] - for derivation in derivations: - specification.class_derivations[derivation.name] = derivation - target_schema = mapper.derive_schema(specification) - print(yaml_dumper.dumps(target_schema)) - assert list(target_schema.classes.keys()) == ["Agent"] - - -def test_rewire() -> None: - """ - Tests rewire. - - An empty spec and source schema should return an empty schema. - """ - tr = SchemaMapper() - sb = SchemaBuilder() - sb.add_slot("id", range="string", identifier=True) - sb.add_slot("name", range="string") - sb.add_slot("pets", range="Pet", multivalued=True) - sb.add_slot("salary", range="integer") - sb.add_class("Thing", slots=["id", "name"]) - sb.add_class("Person", is_a="Thing", slots=["pets"]) - sb.add_class("Employee", is_a="Person", slots=["salary"]) - sb.add_class("Pet", is_a="Thing", slots=["pets"]) - tr.source_schemaview = SchemaView(sb.schema) - specification = TransformationSpecification( - id="test", - ) - target_schema = tr.derive_schema(specification) - assert list(target_schema.classes.values()) == [] - specification = TransformationSpecification( - id="test", - class_derivations={ - "TrEmployee": ClassDerivation( - name="TrEmployee", - slot_derivations={ - "tr_salary": SlotDerivation( - name="tr_salary", - range="decimal", - ) - }, - ) - }, - ) - target_schema = tr.derive_schema(specification) - assert list(target_schema.classes.keys()) == ["TrEmployee"] - emp = target_schema.classes["TrEmployee"] - assert list(emp.attributes.keys()) == ["tr_salary"] - specification.class_derivations["TrEmployee"].is_a = "Person" - target_schema = tr.derive_schema(specification) - assert list(target_schema.classes.keys()) == ["TrEmployee"] - emp = target_schema.classes["TrEmployee"] - assert list(emp.attributes.keys()) == ["tr_salary"] - - -def test_full_copy_specification(mapper: SchemaMapper) -> None: - """Tests copy isomorphism.""" - copy_all_directive = {"*": CopyDirective(element_name="*", copy_all=True)} - specification = TransformationSpecification(id="test", copy_directives=copy_all_directive) - source_schema = mapper.source_schemaview.schema - - target_schema = mapper.derive_schema(specification) - # classes, slots and enums must be exactly the same - assert yaml_dumper.dumps(source_schema.classes) == yaml_dumper.dumps(target_schema.classes) - assert yaml_dumper.dumps(source_schema.slots) == yaml_dumper.dumps(target_schema.slots) - assert yaml_dumper.dumps(source_schema.enums) == yaml_dumper.dumps(target_schema.enums) - - -def test_partial_copy_specification(mapper: SchemaMapper) -> None: - """Tests copy isomorphism excluding derivations.""" - copy_all_directive = {"*": CopyDirective(element_name="*", copy_all=True)} - specification = TransformationSpecification(id="test", copy_directives=copy_all_directive) - source_schema = mapper.source_schemaview.schema - - derivations = [ - ClassDerivation(name="Agent", populated_from="Person"), - ] - for derivation in derivations: - specification.class_derivations[derivation.name] = derivation - target_schema = mapper.derive_schema(specification) - # classes must be the same with addition - for schema_class in source_schema.classes: - assert schema_class in target_schema.classes, f"Class '{schema_class}' is missing in target" - assert "Agent" in target_schema.classes, "Derived class 'Agent' is missing in target" - # slots and enums must be exactly the same - assert yaml_dumper.dumps(source_schema.slots) == yaml_dumper.dumps(target_schema.slots) - assert yaml_dumper.dumps(source_schema.enums) == yaml_dumper.dumps(target_schema.enums) - - -def test_full_copy_class(mapper: SchemaMapper) -> None: - """Tests copy isomorphism with class derivation.""" - copy_all_directive = {"*": CopyDirective(element_name="*", copy_all=True)} - specification = TransformationSpecification(id="test", copy_directives=copy_all_directive) - source_schema = mapper.source_schemaview.schema - - derivations = [ - ClassDerivation(name="Agent", populated_from="Person", copy_directives=copy_all_directive), - ] - for derivation in derivations: - specification.class_derivations[derivation.name] = derivation - target_schema = mapper.derive_schema(specification) - # classes must be the same with addition - for schema_class in source_schema.classes: - assert schema_class in target_schema.classes, f"Class '{schema_class}' is missing in target" - assert "Agent" in target_schema.classes, "Derived class 'Agent' is missing in target" - assert yaml_dumper.dumps(source_schema.classes["Person"].slots) == yaml_dumper.dumps( - target_schema.classes["Agent"].slots - ) - assert yaml_dumper.dumps(source_schema.classes["Person"].attributes) == yaml_dumper.dumps( - target_schema.classes["Agent"].attributes - ) - # slots and enums must be exactly the same - assert yaml_dumper.dumps(source_schema.slots) == yaml_dumper.dumps(target_schema.slots) - assert yaml_dumper.dumps(source_schema.enums) == yaml_dumper.dumps(target_schema.enums) - - -def test_copy_blacklisting(mapper: SchemaMapper) -> None: - """Tests copy on a blacklist approach.""" - blacklist = ["Person"] - copy_all_directive = {"*": CopyDirective(element_name="*", copy_all=True, exclude=blacklist)} - specification = TransformationSpecification(id="test", copy_directives=copy_all_directive) - source_schema = mapper.source_schemaview.schema - - derivations = [ - ClassDerivation(name="Agent", populated_from="Person"), - ] - for derivation in derivations: - specification.class_derivations[derivation.name] = derivation - target_schema = mapper.derive_schema(specification) - # classes must be the same with addition - for schema_class in source_schema.classes: - if schema_class in blacklist: - assert schema_class not in target_schema.classes, ( - f"Class '{schema_class}' is missing in target" - ) - else: - assert schema_class in target_schema.classes, ( - f"Class '{schema_class}' is missing in target" - ) - assert "Agent" in target_schema.classes, "Derived class 'Agent' is missing in target" - - # slots and enums must be exactly the same - assert yaml_dumper.dumps(source_schema.slots) == yaml_dumper.dumps(target_schema.slots) - assert yaml_dumper.dumps(source_schema.enums) == yaml_dumper.dumps(target_schema.enums) - - -def test_copy_whitelisting(mapper: SchemaMapper) -> None: - """Tests copy on a whitelist approach.""" - whitelist = ["NamedThing"] - whitelist_directive = { - "Whitelist": CopyDirective( - element_name="*", copy_all=True, exclude_all=True, include=whitelist - ) - } - specification = TransformationSpecification(id="test", copy_directives=whitelist_directive) - source_schema = mapper.source_schemaview.schema - - derivations = [ - ClassDerivation(name="Agent", populated_from="Person"), - ] - for derivation in derivations: - specification.class_derivations[derivation.name] = derivation - target_schema = mapper.derive_schema(specification) - # classes, slots and enums must have only what explicitly included - for schema_class in source_schema.classes: - if schema_class in whitelist: - assert schema_class in target_schema.classes, ( - f"Class '{schema_class}' is missing in target" - ) - else: - assert schema_class not in target_schema.classes, ( - f"Class '{schema_class}' is missing in target" - ) - assert "Agent" in target_schema.classes, "Derived class 'Agent' is missing in target" - for schema_slot in source_schema.slots: - if schema_slot in whitelist: - assert schema_slot in target_schema.slots, f"Slot '{schema_slot}' is missing in target" - else: - assert schema_slot not in target_schema.slots, ( - f"Slot '{schema_slot}' is missing in target" - ) - for schema_enum in source_schema.enums: - if schema_enum in whitelist: - assert schema_enum in target_schema.enums, f"Enum '{schema_enum}' is missing in target" - else: - assert schema_enum not in target_schema.enums, ( - f"Enum '{schema_enum}' is missing in target" - ) - - -def test_overrides_in_class_derivation(mapper: SchemaMapper) -> None: - """Test that overrides in ClassDerivation are applied.""" - specification = TransformationSpecification( - id="test", - class_derivations={ - "Agent": ClassDerivation( - name="Agent", - populated_from="Person", - overrides={ - "description": "Like Person, but not in a subset", - "in_subset": None, - }, - ) - }, - ) - target_schema = mapper.derive_schema(specification) - agent = target_schema.classes["Agent"] - assert agent.description == "Like Person, but not in a subset" - assert agent.class_uri == "schema:Person" - - -def test_overrides_in_slot_derivation(mapper: SchemaMapper) -> None: - """Test that overrides in SlotDerivation are applied.""" - specification = TransformationSpecification( - id="test", - class_derivations={ - "Agent": ClassDerivation( - name="Agent", - populated_from="Person", - slot_derivations={ - "age_in_years": SlotDerivation( - name="age_in_years", - overrides={ - "required": True, - "maximum_value": 120, - "description": "Age in years, but required and more realistic", - }, - ) - }, - ) - }, - ) - target_schema = mapper.derive_schema(specification) - agent = target_schema.classes["Agent"] - age = agent.attributes["age_in_years"] - assert age.required is True - assert age.minimum_value == 0 - assert age.maximum_value == 120 - assert age.description == "Age in years, but required and more realistic" - - -def test_overrides_errors_with_unknown_attribute(mapper: SchemaMapper) -> None: - """Test that an error is raised if overrides contains attributes not part of the metamodel.""" - specification = TransformationSpecification( - id="test", - class_derivations={ - "Agent": ClassDerivation( - name="Agent", - populated_from="Person", - overrides={"unknown_attribute": "This should raise an error"}, - ) - }, - ) - with pytest.raises(TypeError, match="got an unexpected keyword argument 'unknown_attribute'"): - mapper.derive_schema(specification) - - specification = TransformationSpecification( - id="test", - class_derivations={ - "Agent": ClassDerivation( - name="Agent", - populated_from="Person", - slot_derivations={ - "age_in_years": SlotDerivation( - name="age_in_years", - overrides={"unknown_attribute": "This should raise an error"}, - ) - }, - ) - }, - ) - with pytest.raises(TypeError, match="got an unexpected keyword argument 'unknown_attribute'"): - mapper.derive_schema(specification) diff --git a/tests/test_strictdict.py b/tests/test_strictdict.py deleted file mode 100644 index 4458842..0000000 --- a/tests/test_strictdict.py +++ /dev/null @@ -1,23 +0,0 @@ -import pytest -from tests.conftest import StrictDict - -def test_strictdict_allows_same_value(): - d = StrictDict() - d["x"] = 1 - d["x"] = 1 # ok - assert d["x"] == 1 - -def test_strictdict_rejects_conflicting_value(): - d = StrictDict() - d["x"] = 1 - with pytest.raises(ValueError): - d["x"] = 2 - -def test_strictdict_update_respects_strictness(): - d = StrictDict() - d["x"] = 1 - d.update({"x": 1, "y": 2}) - assert d == {"x": 1, "y": 2} - - with pytest.raises(ValueError): - d.update({"x": 99}) diff --git a/tests/test_transformer/__init__.py b/tests/test_transformer/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/tests/test_transformer/test_biolink_subsetting.py b/tests/test_transformer/test_biolink_subsetting.py deleted file mode 100644 index 7a2eee8..0000000 --- a/tests/test_transformer/test_biolink_subsetting.py +++ /dev/null @@ -1,150 +0,0 @@ -"""Tests of biolink subsetting.""" - -from collections.abc import Generator -from pathlib import Path - -import pytest -from linkml_runtime.dumpers import yaml_dumper -from linkml_runtime.utils.formatutils import camelcase, underscore -from linkml_runtime.utils.schemaview import SchemaView - -from linkml_map.datamodel.transformer_model import ( - ClassDerivation, - CopyDirective, - SlotDerivation, - TransformationSpecification, -) -from linkml_map.inference.schema_mapper import SchemaMapper -from linkml_map.session import Session -from src.linkml_map.utils.loaders import load_specification - -REPO_ROOT = Path(__file__).resolve().parent.parent - - -def get_biolink_class_derivations(sv: SchemaView, subset_classes: list) -> dict: - """ - Get Biolink class definitions. - - :param sv: SchemaView object - :param subset_classes: List of classes to subset - :return: Dictionary of class derivations incl slot derivations - """ - # Example implementation to fetch class definitions - # This should be replaced with the actual implementation - class_derivations = {} - for class_name in subset_classes: - class_derivation = ClassDerivation(populated_from=class_name, name=camelcase(class_name)) - induced_slots = sv.class_induced_slots(class_name) - for slot in induced_slots: - slot_derivation = SlotDerivation(populated_from=slot.name, name=underscore(slot.name)) - class_derivation.slot_derivations[underscore(slot.name)] = slot_derivation - class_derivations[camelcase(class_name)] = class_derivation - return class_derivations - - -@pytest.fixture -def biolink_schema() -> SchemaView: - """ - Fixture to load Biolink schema. - - :return: SchemaView object named `biolink-schema` - """ - schema_url = "https://raw.githubusercontent.com/biolink/biolink-model/master/biolink-model.yaml" - return SchemaView(schema_url) - - -def test_biolink_subsetting_manual( - biolink_schema: SchemaView, tmp_path: Generator[Path, None, None] -) -> None: - """ - Test to subset the Biolink schema manually. - - :param biolink_schema: Fixture to load Biolink schema - """ - transform_file = ( - REPO_ROOT / "input/examples/biolink/transform/biolink-example-profile.transform.yaml" - ) - # Initialize Session and SchemaBuilder - session = Session() - - # Set the source schema in the session - session.set_source_schema(biolink_schema) - - tr_spec = load_specification(transform_file) - mapper = SchemaMapper() - mapper.source_schemaview = biolink_schema - - target_schema_obj = mapper.derive_schema( - specification=tr_spec, - target_schema_id="biolink-profile", - target_schema_name="BiolinkProfile", - ) - - dump_output = str(tmp_path / "biolink-profile.yaml") - yaml_dumper.dump(target_schema_obj, dump_output) - - transformed_sv = SchemaView(dump_output) - - for class_name in transformed_sv.all_classes(): - print(class_name) - print() - for slot_name in transformed_sv.all_slots(): - print(slot_name) - - -def test_biolink_subset_auto(biolink_schema: SchemaView, tmp_path: Path) -> None: - """ - Test to subset the Biolink schema automatically by deriving the class definitions from biolink via a collection of class names to subset. - - :param biolink_schema: Fixture to load Biolink schema - """ - # Initialize Session and SchemaBuilder - session = Session() - - # Set the source schema in the session - session.set_source_schema(biolink_schema) - - subset_classes = [ - "gene", - "disease", - "case to phenotypic feature association", - "gene to disease association", - "gene to phenotypic feature association", - "case", - "phenotypic feature", - ] - - class_derivations = get_biolink_class_derivations(biolink_schema, subset_classes) - copy_type_directives = { - type_name: CopyDirective(element_name=type_name, copy_all=False) - for type_name, type_def in biolink_schema.all_types().items() - } - - ts = TransformationSpecification( - class_derivations=class_derivations, copy_directives=copy_type_directives - ) - - mapper = SchemaMapper() - mapper.source_schemaview = biolink_schema - - target_schema_obj = mapper.derive_schema( - specification=ts, target_schema_id="biolink-subset", target_schema_name="BiolinkSubset" - ) - - # ugly bit of hacking to demonstrate end-to-end functionality - target_schema_obj.types = biolink_schema.all_types() - - dump_output = str(tmp_path / "biolink-subset.yaml") - yaml_dumper.dump(target_schema_obj, dump_output) - - transformed_sv = SchemaView(dump_output) - - for class_name in transformed_sv.all_classes(): - print(class_name) - for slot_name in transformed_sv.all_slots(): - print(slot_name) - for type_name in transformed_sv.all_types(): - print(type_name) - - for slot in transformed_sv.get_class("Gene").slots: - print(slot) diff --git a/tests/test_transformer/test_cmdr_transformation.py b/tests/test_transformer/test_cmdr_transformation.py deleted file mode 100644 index 0fc5cfc..0000000 --- a/tests/test_transformer/test_cmdr_transformation.py +++ /dev/null @@ -1,53 +0,0 @@ -"""Test conversion of normalised to denormalised schema.""" - -from collections.abc import Generator -from pathlib import Path - -from linkml_runtime.dumpers import yaml_dumper -from linkml_runtime.utils.schemaview import SchemaView - -from linkml_map.inference.schema_mapper import SchemaMapper -from linkml_map.session import Session -from src.linkml_map.utils.loaders import load_specification - -REPO_ROOT = Path(__file__).resolve().parent.parent - - -def test_denormalizingl(tmp_path: Generator[Path, None, None]) -> None: - """ - Test to convert a normalized mapping set schema to a denormalized one. - - """ - input_schema = REPO_ROOT / "input/examples/flattening/source/normalized.yaml" - # output_schema = REPO_ROOT / "input/examples/flattening/target/denormalized.yaml" - transformation_specification_file = ( - REPO_ROOT / "input/examples/flattening/transform/denormalize.transform.yaml" - ) - # Initialize Session and SchemaBuilder - session = Session() - - source_schema_view = SchemaView(input_schema) - # target_schema_view = SchemaView(output_schema) - # Set the source schema in the session - session.set_source_schema(source_schema_view) - - tr_spec = load_specification(transformation_specification_file) - mapper = SchemaMapper() - mapper.source_schemaview = source_schema_view - - target_schema_obj = mapper.derive_schema( - specification=tr_spec, - target_schema_id="denormalized-view", - target_schema_name="DenormalizedView", - ) - - dump_output = str(tmp_path / "denormalized_view.yaml") - yaml_dumper.dump(target_schema_obj, dump_output) - - transformed_sv = SchemaView(dump_output) - - for class_name in transformed_sv.all_classes(): - print(class_name) - print() - for slot_name in transformed_sv.all_slots(): - print(slot_name) diff --git a/tests/test_transformer/test_duckdb_transformer.py b/tests/test_transformer/test_duckdb_transformer.py deleted file mode 100644 index 3a943d1..0000000 --- a/tests/test_transformer/test_duckdb_transformer.py +++ /dev/null @@ -1,33 +0,0 @@ -""" -Tests compilation of a specification to python. -""" - -import pytest -from linkml_runtime import SchemaView - -from linkml_map.session import Session -from linkml_map.transformer.duckdb_transformer import DuckDBTransformer -from tests import PERSONINFO_SRC_SCHEMA, PERSONINFO_TGT_SCHEMA, PERSONINFO_TR - - -@pytest.fixture -def session() -> Session: - """Instantiate a transformer session.""" - session = Session() - session.set_source_schema(PERSONINFO_SRC_SCHEMA) - session.set_transformer_specification(PERSONINFO_TR) - if not session.transformer_specification: - msg = "No specification provided." - raise ValueError(msg) - tr = DuckDBTransformer() - session.set_transformer(tr) - tr.specification = session.transformer_specification - tr.source_schemaview = SchemaView(str(PERSONINFO_SRC_SCHEMA)) - tr.target_schemaview = SchemaView(str(PERSONINFO_TGT_SCHEMA)) - return session - - -def test_compile(session: Session) -> None: - """Test compilation using the DuckDb transformer.""" - pytest.skip("TODO") - session.transformer.map_database(":memory:") diff --git a/tests/test_transformer/test_object_transformer.py b/tests/test_transformer/test_object_transformer.py deleted file mode 100644 index 75c3f64..0000000 --- a/tests/test_transformer/test_object_transformer.py +++ /dev/null @@ -1,705 +0,0 @@ -"""Test the object transformer.""" - -from typing import Any - -import pytest -import yaml -from unittest.mock import MagicMock -from linkml_runtime import SchemaView -from linkml_runtime.linkml_model import ( - ClassDefinition, - SchemaDefinition, - SlotDefinition, -) -from linkml_runtime.loaders import yaml_loader -from linkml.utils.schema_builder import SchemaBuilder -from linkml_runtime.processing.referencevalidator import ReferenceValidator -from linkml_runtime.utils.introspection import package_schemaview - -import tests.input.examples.flattening.model.denormalized_model as sssom_tgt_dm -import tests.input.examples.flattening.model.normalized_model as sssom_src_dm -import tests.input.examples.personinfo_basic.model.agent_model as tgt_dm -import tests.input.examples.personinfo_basic.model.personinfo_model as src_dm -from linkml_map.compiler.tr import TR_TO_MAPPING_TABLES -from linkml_map.datamodel import TR_SCHEMA -from linkml_map.datamodel.transformer_model import ( - ClassDerivation, - CollectionType, - SlotDerivation, - TransformationSpecification, -) -from linkml_map.transformer.object_transformer import ObjectTransformer -from linkml_map.utils.dynamic_object import dynamic_object -from tests import ( - DENORM_SCHEMA, - DENORM_SPECIFICATION, - FLATTENING_DATA, - NORM_SCHEMA, - PERSONINFO_CONTAINER_DATA, - PERSONINFO_CONTAINER_TGT_DATA, - PERSONINFO_DATA, - PERSONINFO_SRC_SCHEMA, - PERSONINFO_TGT_DATA, - PERSONINFO_TGT_SCHEMA, - PERSONINFO_TR, -) - -AGE_STRING = "33 years" -AGE_INT = 33 - -TARGET_DATA = yaml.safe_load(open(str(PERSONINFO_TGT_DATA))) -TARGET_OBJECT = yaml_loader.load(str(PERSONINFO_TGT_DATA), target_class=tgt_dm.Agent) - -CONTAINER_DATA = yaml.safe_load(open(str(PERSONINFO_CONTAINER_TGT_DATA))) -CONTAINER_OBJECT = yaml_loader.load( - str(PERSONINFO_CONTAINER_TGT_DATA), target_class=tgt_dm.Container -) - -def inject_slot(schema_dict: dict, class_name: str, slot_name: str, slot_def: dict): - schema_dict.setdefault("slots", {})[slot_name] = slot_def - schema_dict["classes"][class_name].setdefault("slots", []).append(slot_name) - -def inject_enum(schema: dict, enum_name: str, values: list[str]) -> None: - schema["enums"][enum_name] = { "permissible_values": {val: {} for val in values} } - -@pytest.fixture -def obj_tr() -> ObjectTransformer: - """Instantiate an object transformer.""" - obj_tr = ObjectTransformer(unrestricted_eval=True) - obj_tr.source_schemaview = SchemaView(str(PERSONINFO_SRC_SCHEMA)) - obj_tr.target_schemaview = SchemaView(str(PERSONINFO_TGT_SCHEMA)) - obj_tr.load_transformer_specification(PERSONINFO_TR) - return obj_tr - - -def test_transform_dict(obj_tr: ObjectTransformer) -> None: - """ - Tests transforming a dictionary of Person data into a dictionary of Agent data. - """ - person_dict: dict[str, Any] = yaml.safe_load(open(str(PERSONINFO_DATA))) - assert person_dict["age_in_years"] == AGE_INT - target_dict: dict[str, Any] = obj_tr.map_object(person_dict, source_type="Person") - assert isinstance(target_dict, type(TARGET_DATA)) - assert target_dict["age"] == AGE_STRING - assert target_dict == TARGET_DATA - - -def test_transform_dict_in_container(obj_tr: ObjectTransformer) -> None: - """ - Tests transforming a Person data dict in a Container into an Agent data dict in a Container dict. - """ - person_dict: dict[str, Any] = yaml.safe_load(open(str(PERSONINFO_DATA))) - container_dict = {"persons": [person_dict]} - target_dict = obj_tr.map_object(container_dict, source_type="Container") - assert target_dict == {"agents": [TARGET_DATA]} - - -def test_transform_multiple_dicts_in_container(obj_tr: ObjectTransformer) -> None: - """ - Tests transforming several Person data dicts in a Container into Agent data dicts in a Container dicts. - """ - container_dict: dict[str, Any] = yaml.safe_load(open(str(PERSONINFO_CONTAINER_DATA))) - target_dict: dict[str, Any] = obj_tr.map_object(container_dict, source_type="Container") - assert target_dict == CONTAINER_DATA - - -def check_familial_relationships(obj, data_model, expected) -> None: - """Check FamilialRelationships in a data model.""" - assert len(expected) == len(obj.has_familial_relationships) - for n in range(len(expected)): - fr = obj.has_familial_relationships[n] - assert isinstance(fr, data_model.FamilialRelationship) - assert expected[n]["related_to"] == fr.related_to - assert expected[n]["type"] == str(fr.type) - - -def test_coerce(obj_tr: ObjectTransformer) -> None: - """Test datatype coercion.""" - x = obj_tr._coerce_datatype("5", "integer") # noqa: SLF001 - assert x == 5 - x = obj_tr._coerce_datatype(5, "string") # noqa: SLF001 - assert x == "5" - x = obj_tr._coerce_datatype(5, "integer") # noqa: SLF001 - assert x == 5 - -def test_constant_value_slot_derivation() -> None: - """ - Tests transforming using a constant value (via `value:` field). - """ - source_schema: dict[str, Any] = yaml.safe_load(open(str(PERSONINFO_SRC_SCHEMA))) - # No need to inject a source slot since `value:` doesn't need source data - - target_schema: dict[str, Any] = yaml.safe_load(open(str(PERSONINFO_TGT_SCHEMA))) - inject_slot(target_schema, "Agent", "study_name", {"range": "string"}) - - transform_spec: dict[str, Any] = yaml.safe_load(open(str(PERSONINFO_TR))) - transform_spec.setdefault("class_derivations", {}).setdefault("Agent", {}) \ - .setdefault("slot_derivations", {})["study_name"] = { - "value": "Framingham", - "range": "string", - } - - obj_tr = ObjectTransformer(unrestricted_eval=True) - obj_tr.source_schemaview = SchemaView(yaml.dump(source_schema)) - obj_tr.target_schemaview = SchemaView(yaml.dump(target_schema)) - obj_tr.create_transformer_specification(transform_spec) - - person_dict: dict[str, Any] = yaml.safe_load(open(str(PERSONINFO_DATA))) - target_dict: dict[str, Any] = obj_tr.map_object(person_dict, source_type="Person") - - expected = dict(TARGET_DATA) - expected["study_name"] = "Framingham" - assert target_dict == expected - -def test_value_mappings() -> None: - """ - Tests transforming using value mappings. - """ - source_schema: dict[str, Any] = yaml.safe_load(open(str(PERSONINFO_SRC_SCHEMA))) - work_int_dict = { "range": "integer", "minimum_value": 1, "maximum_value": 2} - inject_slot(source_schema, "Person", "work_type", work_int_dict) - - target_schema: dict[str, Any] = yaml.safe_load(open(str(PERSONINFO_TGT_SCHEMA))) - inject_enum(target_schema, "WorkEnum", ["Home", "Office", "None"]) - work_enum_dict = {"range": "WorkEnum"} - inject_slot(target_schema, "Agent", "work_value", work_enum_dict) - - transform_spec: dict[str, Any] = yaml.safe_load(open(str(PERSONINFO_TR))) - transform_spec_dict = { - "populated_from": "work_type", - "value_mappings": { "1": "Home", "2": "Office" } - } - transform_spec.setdefault("class_derivations", {}).setdefault("Agent", {}) \ - .setdefault("slot_derivations", {})["work_value"] = transform_spec_dict - - obj_tr = ObjectTransformer(unrestricted_eval=True) - obj_tr.source_schemaview = SchemaView(yaml.dump(source_schema)) - obj_tr.target_schemaview = SchemaView(yaml.dump(target_schema)) - obj_tr.create_transformer_specification(transform_spec) - - person_dict: dict[str, Any] = yaml.safe_load(open(str(PERSONINFO_DATA))) - person_dict["work_type"] = 1 - target_dict: dict[str, Any] = obj_tr.map_object(person_dict, source_type="Person") - assert target_dict["work_value"] == "Home" - TARGET_DATA["work_value"] = "Home" - assert target_dict == TARGET_DATA - -def test_object_derivations() -> None: - """ - Test nested object_derivations inside slot_derivations using YAML transform spec. - """ - - # Build source schema - sb_source = SchemaBuilder() - sb_source.add_slot("phv00159563", range="string") - sb_source.add_slot("phv00159568", range="integer") - sb_source.add_slot("phv00159569", range="string") - sb_source.add_slot("phv00159573", range="string") - sb_source.add_slot("phv00159578", range="integer") - sb_source.add_slot("phv00159579", range="string") - sb_source.add_class("Person", slots=["phv00159563", "phv00159568", "phv00159569", "phv00159573", "phv00159578", "phv00159579"]) - sb_source.add_defaults() - source_schema = sb_source.schema - - # Build target schema - sb_target = SchemaBuilder() - sb_target.add_slot("id", range="integer") - sb_target.add_slot("conditions", range="Condition", multivalued=True, inlined=True) - sb_target.add_slot("condition_concept", range="string") - sb_target.add_slot("condition_status", range="string") - sb_target.add_slot("condition_providence", range="string") - sb_target.add_class("Participant", slots=["id", "conditions"]) - sb_target.add_class("Condition", slots=["condition_concept", "condition_status", "condition_providence"]) - sb_target.add_defaults() - target_schema = sb_target.schema - - # Transformation spec in YAML - transform_spec_yaml = """ - class_derivations: - Participant: - populated_from: Person - slot_derivations: - id: - populated_from: phv00159568 - conditions: - object_derivations: - - class_derivations: - Condition: - populated_from: Person - slot_derivations: - condition_concept: - expr: "'HP:0001681'" - condition_status: - populated_from: phv00159563 - condition_providence: - populated_from: phv00159569 - - class_derivations: - Condition: - populated_from: Person - slot_derivations: - condition_concept: - expr: "'HP:0001683'" - condition_status: - populated_from: phv00159573 - condition_providence: - populated_from: phv00159579 - """ - - transform_spec = yaml.safe_load(transform_spec_yaml) - - # Source input - input_data = { - "phv00159563": "PRESENT", - "phv00159568": 123947, - "phv00159569": "1", - "phv00159573": "ABSENT", - "phv00159578": 123947, - "phv00159579": "2", - } - - # Expected target output - expected_output = { - "id": 123947, - "conditions": [ - { - "condition_concept": "HP:0001681", - "condition_status": "PRESENT", - "condition_providence": "1", - }, - { - "condition_concept": "HP:0001683", - "condition_status": "ABSENT", - "condition_providence": "2", - } - ] - } - - # Create ObjectTransformer and apply transformation - transformer = ObjectTransformer(unrestricted_eval=True) - transformer.source_schemaview = SchemaView(source_schema) - transformer.target_schemaview = SchemaView(target_schema) - transformer.create_transformer_specification(transform_spec) - - result = transformer.map_object(input_data, source_type="Person") - - assert result == expected_output - - -def test_transform_simple_object(obj_tr: ObjectTransformer) -> None: - """ - Tests transforming a Person object into an Agent object. - """ - person_obj: src_dm.Person = yaml_loader.load(str(PERSONINFO_DATA), target_class=src_dm.Person) - assert isinstance(person_obj, src_dm.Person) - assert person_obj.age_in_years == AGE_INT - - expected = [ - { - "related_to": "P:002", - "type": "SIBLING_OF", - "enum": src_dm.FamilialRelationshipType.SIBLING_OF, - }, - { - "related_to": "P:003", - "type": "CHILD_OF", - "enum": src_dm.FamilialRelationshipType.CHILD_OF, - }, - ] - check_familial_relationships(person_obj, src_dm, expected) - # TODO: move these tests to `check_familial_relationships` once - # enum derivations are implemented - for n in range(len(expected)): - fr = person_obj.has_familial_relationships[n] - assert src_dm.FamilialRelationshipType(expected[n]["enum"]) == fr.type - - target_obj = obj_tr.transform_object(person_obj, target_class=tgt_dm.Agent) - assert isinstance(target_obj, tgt_dm.Agent) - assert person_obj.name == target_obj.label - assert target_obj.age == AGE_STRING - assert target_obj.gender is None - - expected = [ - { - "related_to": "P:002", - "type": "SIBLING_OF", - # TODO: enum derivations - # "enum": tgt_dm.MyFamilialRelationshipType.SIBLING_OF, - }, - { - "related_to": "P:003", - "type": "CHILD_OF", - # TODO: enum derivations - # "enum": tgt_dm.MyFamilialRelationshipType.CHILD_OF, - }, - ] - check_familial_relationships(target_obj, tgt_dm, expected) - assert target_obj == TARGET_OBJECT - - -def test_transform_container_object(obj_tr: ObjectTransformer) -> None: - """ - Tests transforming a Container object holding a Person object into Container object holding an Agent object. - """ - person = yaml_loader.load(str(PERSONINFO_DATA), target_class=src_dm.Person) - container_obj = src_dm.Container(persons=[person]) - result: tgt_dm.Container = obj_tr.transform_object(container_obj, target_class=tgt_dm.Container) - assert isinstance(result, tgt_dm.Container) - agents = result.agents - agent = agents[0] - assert agent.label == person.name - assert agent.age == AGE_STRING - assert agent == TARGET_OBJECT - for rel in [0, 1]: - person_fr1 = person.has_familial_relationships[rel] - agent_fr1 = agent.has_familial_relationships[rel] - assert person_fr1.related_to == agent_fr1.related_to - - -def test_transform_object_container(obj_tr: ObjectTransformer) -> None: - """ - Tests transforming a Container object holding several Person objects into Container object holding several Agent objects. - """ - container_obj = yaml_loader.load(str(PERSONINFO_CONTAINER_DATA), target_class=src_dm.Container) - target_obj = obj_tr.transform_object(container_obj, target_class=tgt_dm.Container) - assert target_obj.agents[0] == TARGET_OBJECT - assert target_obj == CONTAINER_OBJECT - - -def check_subject_object_predicate( - obj, - expected, -) -> None: - assert expected["subject_id"] == obj.subject.id - assert expected["subject_name"] == obj.subject.name - assert expected["object_id"] == obj.object.id - assert expected["object_name"] == obj.object.name - assert expected["predicate"] == obj.predicate - - -def test_index_dict() -> None: - sv = SchemaView(NORM_SCHEMA) - container = yaml.safe_load(open(str(FLATTENING_DATA))) - dynobj = dynamic_object(container, sv, "MappingSet") - m = dynobj.mappings[0] - tr = ObjectTransformer() - tr.source_schemaview = sv - tr.index(container, "MappingSet") - ix = tr.object_index - mp = ix.bless(m) - check_subject_object_predicate( - mp, - { - "subject_id": "X:1", - "subject_name": "x1", - "object_id": "Y:1", - "object_name": "y1", - "predicate": "P:1", - }, - ) - container["mappings"][0]["subject"] = "U:1" - tr.index(container, "MappingSet") - dynobj = dynamic_object(container, sv, "MappingSet") - mset = ix.bless(dynobj) - assert mset.mappings[0].subject == "U:1" - assert mset.mappings[0].object.id == "Y:1" - assert mset.mappings[0].object.name == "y1" - assert mset.mappings[0].predicate == "P:1" - - -def test_index_obj() -> None: - sv = SchemaView(NORM_SCHEMA) - mset: sssom_src_dm.MappingSet = yaml_loader.load( - str(FLATTENING_DATA), target_class=sssom_src_dm.MappingSet - ) - m = mset.mappings[0] - tr = ObjectTransformer() - tr.source_schemaview = sv - tr.index(mset, "MappingSet") - ix = tr.object_index - mp = ix.bless(m) - check_subject_object_predicate( - mp, - { - "subject_id": "X:1", - "subject_name": "x1", - "object_id": "Y:1", - "object_name": "y1", - "predicate": "P:1", - }, - ) - - mset.mappings[0].subject = "U:1" - tr.index(mset, "MappingSet") - mset = ix.bless(mset) - expected = { - "subject_id": "U:1", - "subject_name": None, - "object_id": "Y:1", - "object_name": "y1", - "predicate": "P:1", - } - check_subject_object_predicate(mset.mappings[0], expected) - - -def test_denormalized_transform_dict() -> None: - """ - Tests denormalizing transformation. - - The test input is a normalized Mapping class with subject and object that reference a separate - entities class, which has id and name fields. - - The denormalized output has fields like subject_id - """ - tr = ObjectTransformer() - tr.source_schemaview = SchemaView(NORM_SCHEMA) - tr.target_schemaview = SchemaView(DENORM_SCHEMA) - tr.load_transformer_specification(DENORM_SPECIFICATION) - mset = yaml.safe_load(open(str(FLATTENING_DATA))) - assert mset["mappings"] == [{"subject": "X:1", "object": "Y:1", "predicate": "P:1"}] - assert mset["entities"] == {"X:1": {"name": "x1"}, "Y:1": {"name": "y1"}} - tr.index(mset, "MappingSet") - target_obj = tr.map_object(mset, source_type="MappingSet") - assert isinstance(target_obj, dict) - assert target_obj["mappings"][0] == { - "subject_id": "X:1", - "subject_name": "x1", - "object_id": "Y:1", - "object_name": "y1", - "predicate_id": "P:1", - } - - -def test_denormalized_object_transform() -> None: - """ - Tests denormalizing transformation. - - The test input is a normalized Mapping class with subject and object that reference a separate - entities class, which has id and name fields. - - The denormalized output has fields like subject_id - """ - tr = ObjectTransformer() - tr.source_schemaview = SchemaView(NORM_SCHEMA) - tr.target_schemaview = SchemaView(DENORM_SCHEMA) - tr.target_module = sssom_tgt_dm - tr.load_transformer_specification(DENORM_SPECIFICATION) - mset: sssom_src_dm.MappingSet = yaml_loader.load( - str(FLATTENING_DATA), target_class=sssom_src_dm.MappingSet - ) - mapping = mset.mappings[0] - assert mapping.subject == "X:1" - assert mapping.object == "Y:1" - assert mset.entities["X:1"].name == "x1" - assert mset.entities["Y:1"].name == "y1" - tr.index(mset) - mset_proxy = tr.object_index.bless(mset) - assert mset_proxy.mappings[0].subject.id == "X:1" - assert mset_proxy.mappings[0].subject.name == "x1" - target_obj: sssom_tgt_dm.MappingSet = tr.transform_object( - mset, target_class=sssom_tgt_dm.MappingSet - ) - mapping = target_obj.mappings[0] - assert mapping.subject_id == "X:1" - assert mapping.subject_name == "x1" - assert mapping.object_id == "Y:1" - assert mapping.object_name == "y1" - # dangling reference - mset.mappings[0].subject = "U:1" - tr.index(mset) - mset_proxy = tr.object_index.bless(mset) - assert mset_proxy.mappings[0].subject.id == "U:1" - assert mset_proxy.mappings[0].subject.name is None - target_obj = tr.transform_object(mset, target_class=sssom_tgt_dm.MappingSet) - mapping = target_obj.mappings[0] - assert mapping.subject_id == "U:1" - assert mapping.subject_name is None - assert mapping.object_id == "Y:1" - assert mapping.object_name == "y1" - - -@pytest.mark.parametrize("source_multivalued", [True, False]) -@pytest.mark.parametrize("target_multivalued", [True, False]) -@pytest.mark.parametrize("explicit", [True, False]) -def test_cardinalities(source_multivalued: bool, target_multivalued: bool, explicit: bool) -> None: # noqa: FBT001 - """ - Tests enforcing cardinality. - """ - class_name = "MyClass" - att_name = "my_att" - val = "v1" - - def mk(mv: bool, ex: bool = False) -> SchemaDefinition: - """ - Generate a schema with a class with an attribute. - - :param mv: whether or not the attribute is multivalued - :type mv: bool - :param ex: whether or not the attribute is explicitly defined as multivalued, defaults to False - :type ex: bool, optional - :return: _description_ - :rtype: _type_ - """ - cls = ClassDefinition(class_name) - # TODO: it should not be necessary to set this if present in Transformation - # att = SlotDefinition(att_name, multivalued=mv and not ex) - att = SlotDefinition(att_name, multivalued=mv) - cls.attributes[att.name] = att - return SchemaDefinition(name="test", id="test", classes=[cls], default_range="string") - - source_schema = mk(source_multivalued) - target_schema = mk(target_multivalued, explicit) - specification = TransformationSpecification(id="test") - cd = ClassDerivation(name=class_name, populated_from=class_name) - sd = SlotDerivation(name=att_name, populated_from=att_name) - if explicit: - sd.cast_collection_as = ( - CollectionType.MultiValued if target_multivalued else CollectionType.SingleValued - ) - specification.class_derivations[class_name] = cd - cd.slot_derivations[att_name] = sd - source_instance = {att_name: [val] if source_multivalued else val} - tr = ObjectTransformer( - specification=specification, - source_schemaview=SchemaView(source_schema), - target_schemaview=SchemaView(target_schema), - ) - target_instance = tr.map_object(source_instance, class_name) - assert [val] if target_multivalued else val == target_instance[att_name] - - -def test_self_transform() -> None: - tr = ObjectTransformer() - tr.source_schemaview = SchemaView(str(TR_SCHEMA)) - tr.load_transformer_specification(TR_TO_MAPPING_TABLES) - source_object = yaml.safe_load(open(str(PERSONINFO_TR))) - normalizer = ReferenceValidator(package_schemaview("linkml_map.datamodel.transformer_model")) - normalizer.expand_all = True - source_object = normalizer.normalize(source_object) - derived = tr.map_object(source_object) - print(derived) - print(yaml.dump(derived)) - -def test_perform_unit_conversion_basic(obj_tr: ObjectTransformer): - # Prepare a SlotDerivation with a unit_conversion object mock - uc_mock = MagicMock() - uc_mock.source_unit = "cm" - uc_mock.target_unit = "m" - uc_mock.source_unit_slot = None - uc_mock.source_magnitude_slot = None - uc_mock.target_magnitude_slot = None - uc_mock.target_unit_slot = None - - slot_derivation = MagicMock() - slot_derivation.unit_conversion = uc_mock - slot_derivation.populated_from = "length" - - # Prepare source_obj with a numeric value for 'length' - source_obj = {"length": 120} - - # Mock SchemaView and Slot - slot_mock = MagicMock() - slot_mock.unit.ucum_code = "cm" - slot_mock.unit.iec61360code = None - slot_mock.unit.symbol = None - slot_mock.unit.abbreviation = None - slot_mock.unit.descriptive_name = None - slot_mock.name = "length" - - # Patch induced_slot to return slot_mock when called - obj_tr.source_schemaview.induced_slot = MagicMock(return_value=slot_mock) - - # Call the method - result = obj_tr._perform_unit_conversion(slot_derivation, source_obj, obj_tr.source_schemaview, source_type="SomeType") - - # 120 cm -> 1.2 m expected (assuming convert_units works as expected) - # If convert_units not mocked, this test depends on it. - assert abs(result - 1.2) < 1e-6 - - -def test_perform_unit_conversion_structured_value(obj_tr: ObjectTransformer): - # Prepare unit_conversion with structured input slots - uc_mock = MagicMock() - uc_mock.source_unit = "cm" - uc_mock.target_unit = "m" - uc_mock.source_unit_slot = "unit" - uc_mock.source_magnitude_slot = "value" - uc_mock.target_magnitude_slot = "value_converted" - uc_mock.target_unit_slot = "unit_converted" - - slot_derivation = MagicMock() - slot_derivation.unit_conversion = uc_mock - slot_derivation.populated_from = "measurement" - - # Prepare a structured source_obj with unit and value keys - source_obj = {"measurement": {"value": 200, "unit": "cm"}} - - # Mock Slot with unit info - slot_mock = MagicMock() - slot_mock.unit.ucum_code = "cm" - slot_mock.unit.iec61360code = None - slot_mock.unit.symbol = None - slot_mock.unit.abbreviation = None - slot_mock.unit.descriptive_name = None - slot_mock.name = "measurement" - - obj_tr.source_schemaview.induced_slot = MagicMock(return_value=slot_mock) - - result = obj_tr._perform_unit_conversion(slot_derivation, source_obj, obj_tr.source_schemaview, source_type="SomeType") - - # Should return a dict with converted value and unit - assert isinstance(result, dict) - assert "value_converted" in result - assert "unit_converted" in result - # Check that the converted value is numeric and unit matches target_unit - assert isinstance(result["value_converted"], (int, float)) - assert result["unit_converted"] == "m" - - -def test_perform_unit_conversion_missing_value(obj_tr: ObjectTransformer): - uc_mock = MagicMock() - uc_mock.source_unit = "cm" - uc_mock.target_unit = "m" - uc_mock.source_unit_slot = None - uc_mock.source_magnitude_slot = None - uc_mock.target_magnitude_slot = None - uc_mock.target_unit_slot = None - - slot_derivation = MagicMock() - slot_derivation.unit_conversion = uc_mock - slot_derivation.populated_from = "missing_length" - - source_obj = {} # no 'missing_length' key - - # Should return None if source value missing - result = obj_tr._perform_unit_conversion(slot_derivation, source_obj, obj_tr.source_schemaview, source_type="SomeType") - assert result is None - - -def test_perform_unit_conversion_raise_on_unit_mismatch(obj_tr: ObjectTransformer): - uc_mock = MagicMock() - uc_mock.source_unit = "mm" - uc_mock.target_unit = "m" - uc_mock.source_unit_slot = None - uc_mock.source_magnitude_slot = None - uc_mock.target_magnitude_slot = None - uc_mock.target_unit_slot = None - - slot_derivation = MagicMock() - slot_derivation.unit_conversion = uc_mock - slot_derivation.populated_from = "length" - - source_obj = {"length": 100} - - # Mock Slot with unit 'cm' which conflicts with uc.source_unit 'mm' - slot_mock = MagicMock() - slot_mock.unit.ucum_code = "cm" - slot_mock.unit.iec61360code = None - slot_mock.unit.symbol = None - slot_mock.unit.abbreviation = None - slot_mock.unit.descriptive_name = None - slot_mock.name = "length" - - obj_tr.source_schemaview.induced_slot = MagicMock(return_value=slot_mock) - - with pytest.raises(ValueError, match="Mismatch in source units"): - obj_tr._perform_unit_conversion(slot_derivation, source_obj, obj_tr.source_schemaview, source_type="SomeType") diff --git a/tests/test_transformer/test_object_transformer_new.py b/tests/test_transformer/test_object_transformer_new.py deleted file mode 100644 index 1a10d4f..0000000 --- a/tests/test_transformer/test_object_transformer_new.py +++ /dev/null @@ -1,101 +0,0 @@ -"""Test the object transformer. -- New framework""" -import pytest - -from linkml_map.transformer.object_transformer import ObjectTransformer -from tests.conftest import add_to_test_setup, TEST_SETUP_FUNCTIONS -from tests.scaffold.utils.apply_patch import apply_schema_patch, apply_transform_patch - -def run_transformer(scaffold): - """Helper function to run the object transformer with the given scaffold.""" - source = scaffold["source_schema"] - target = scaffold["target_schema"] - - obj_tr = ObjectTransformer(unrestricted_eval=True) - obj_tr.source_schemaview = source - obj_tr.target_schemaview = target - obj_tr.create_transformer_specification(scaffold["transform_spec"]) - - return obj_tr.map_object(scaffold["input_data"], source_type="Person") - -def test_basic_person_to_agent(scaffold): - """Ensure Person is transformed into Agent with expected slot mappings.""" - - result = run_transformer(scaffold) - assert result == scaffold["expected"] - -# Each setup function should adjust the scaffold (schemas, transform spec, and expected output). -# Mark with @add_to_test_setup to include in both parameterized unit tests and integration tests. -# -# @add_to_test_setup -# def setup_your_test_name(scaffold): -# # Your test setup code modifying the scaffold here -# # apply_schema_patch(...) (source and target) -# # apply_transform_patch(...) -# # scaffold["expected"]... - -@add_to_test_setup -def setup_value_slot_derivation(scaffold): - """Derive slot from constant value.""" - - apply_schema_patch(scaffold["target_schema"], -""" - classes: - Agent: - slots: - - study_name - slots: - study_name: - range: string -""" - ) - - apply_transform_patch(scaffold["transform_spec"], -""" - class_derivations: - Agent: - slot_derivations: - study_name: - value: Framingham Heart Study -""" - ) - - scaffold["expected"]["study_name"] = "Framingham Heart Study" - -@add_to_test_setup -def setup_value_attribute_slot_derivation(scaffold): - """Derive attribute from constant value.""" - apply_schema_patch(scaffold["target_schema"], -""" - classes: - Agent: - attributes: - location: - range: string -""" - ) - - apply_transform_patch(scaffold["transform_spec"], -""" - class_derivations: - Agent: - slot_derivations: - location: - value: Framingham -""") - - scaffold["expected"]["location"] = "Framingham" - -@pytest.mark.parametrize( - "setup_func", - TEST_SETUP_FUNCTIONS, - ids=[f.__doc__ or f.__name__.removeprefix("setup_") for f in TEST_SETUP_FUNCTIONS], -) -def test_unit(scaffold, setup_func): - """Apply a setup function, run transformer, and assert expected output.""" - setup_func(scaffold) - result = run_transformer(scaffold) - assert result == scaffold["expected"] - -def test_integration(integration_scaffold): - result = run_transformer(integration_scaffold) - assert result == integration_scaffold["expected"] diff --git a/tests/test_transformer/test_transformer_examples.py b/tests/test_transformer/test_transformer_examples.py deleted file mode 100644 index 97456cb..0000000 --- a/tests/test_transformer/test_transformer_examples.py +++ /dev/null @@ -1,53 +0,0 @@ -"""Tests ObjectTransformer using examples.""" - -import pytest - -from linkml_map.utils.multi_file_transformer import MultiFileTransformer -from tests import EXAMPLE_DIR - -EXAMPLE_PROJECTS = [ - "measurements", - "personinfo_basic", - "single_value_for_multivalued", -] - - -""" -Tests ObjectTransformer using examples. - -Assumes folder structures: - -- input/examples - - {package} - - source/{source_schema}.yaml :: the schema to transform from - - transform/{transform_spec}.transform.yaml :: mapping spec - - data/{SourceClassName}-{LocalId}.yaml :: data to transform - - target/{SourceClassName}-{LocalId}.yaml :: expected output data -""" - - -def test_all() -> None: - """ - Iterates through all examples. - - This uses the MultiFileProcessor in test_mode - if the outputs differ - then the test will fail - """ - mft = MultiFileTransformer() - for directory in EXAMPLE_PROJECTS: - full_dir = EXAMPLE_DIR / directory - instructions = mft.infer_instructions(full_dir) - mft.process_instructions(instructions, full_dir, test_mode=True) - - -@pytest.mark.skip("Uncomment this to regenerate examples") -def test_regenerate() -> None: - """ - Use this to regenerate test examples. - """ - mft = MultiFileTransformer() - dirs = EXAMPLE_PROJECTS - for directory in dirs: - full_dir = EXAMPLE_DIR / directory - instructions = mft.infer_instructions(full_dir) - mft.process_instructions(instructions, full_dir, test_mode=False) diff --git a/tests/test_utils/__init__.py b/tests/test_utils/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/tests/test_utils/test_dynamic_object.py b/tests/test_utils/test_dynamic_object.py deleted file mode 100644 index 19f10f0..0000000 --- a/tests/test_utils/test_dynamic_object.py +++ /dev/null @@ -1,19 +0,0 @@ -"""Test dynamic objects.""" - -import yaml -from linkml_runtime import SchemaView - -from linkml_map.utils.dynamic_object import dynamic_object -from tests import FLATTENING_DATA, NORM_SCHEMA - - -def test_dynamic_object() -> None: - """Basic test for generating a dynamic object.""" - sv = SchemaView(NORM_SCHEMA) - container = yaml.safe_load(open(str(FLATTENING_DATA))) - dynobj = dynamic_object(container, sv, "MappingSet") - assert type(dynobj).__name__ == "MappingSet" - assert type(dynobj.entities["X:1"]).__name__ == "Entity" - assert isinstance(dynobj.entities, dict) - m = dynobj.mappings[0] - assert type(m).__name__ == "Mapping" diff --git a/title/index.html b/title/index.html new file mode 100644 index 0000000..4642909 --- /dev/null +++ b/title/index.html @@ -0,0 +1,126 @@ + + + + + + + + + + + + + + Slot: title - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + +

    Slot: title

    +

    human readable title for this transformation specification

    +

    URI: dcterms:title

    + + +

    Applicable Classes

    + + + + + + + + + + + + + + + +
    NameDescriptionModifies Slot
    TransformationSpecificationA collection of mappings between source and target classesno
    +

    Properties

    +
      +
    • Range: NONE
    • +
    +

    Identifier and Mapping Information

    +

    Schema Source

    +
      +
    • from schema: https://w3id.org/linkml/transformer
    • +
    +

    LinkML Source

    +
    + +
    name: title
    +description: human readable title for this transformation specification
    +from_schema: https://w3id.org/linkml/transformer
    +rank: 1000
    +slot_uri: dcterms:title
    +alias: title
    +owner: TransformationSpecification
    +domain_of:
    +- TransformationSpecification
    +
    +
    + +
    + +
    + + +
    +
    + + + + + \ No newline at end of file diff --git a/tox.ini b/tox.ini deleted file mode 100644 index 7d61bc2..0000000 --- a/tox.ini +++ /dev/null @@ -1,35 +0,0 @@ -# Tox (http://tox.testrun.org/) is a tool for running tests -# in multiple virtualenvs. This configuration file will run the -# test suite on all supported python versions. To use it, "pip install tox" -# and then run "tox" from this directory. - -[tox] -isolated_build = true -envlist = - format - lint - lint_stats - -[testenv:format] -deps = - ruff -skip_install = true -commands = - ruff format . -description = Run code formatter. - -[testenv:lint] -skip_install = true -deps = - ruff -commands = - ruff check src/ tests/ -description = Run ruff code linter. - -[testenv:lint_stats] -skip_install = true -deps = - ruff -commands = - ruff check src/ tests/ --statistics --exit-zero -description = Run ruff code linter and output statistics about lint errors. Ruff will exit with a non-zero exit code if it terminates abnormally, but lint errors will not cause failure. diff --git a/type_designator/index.html b/type_designator/index.html new file mode 100644 index 0000000..075f96f --- /dev/null +++ b/type_designator/index.html @@ -0,0 +1,124 @@ + + + + + + + + + + + + + + Slot: type_designator - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + +

    Slot: type_designator

    +

    URI: linkmltr:type_designator

    + + +

    Applicable Classes

    + + + + + + + + + + + + + + + +
    NameDescriptionModifies Slot
    SlotDerivationA specification of how to derive the value of a target slot from a source slo...no
    +

    Properties

    + +

    Identifier and Mapping Information

    +

    Schema Source

    +
      +
    • from schema: https://w3id.org/linkml/transformer
    • +
    +

    LinkML Source

    +
    + +
    name: type_designator
    +from_schema: https://w3id.org/linkml/transformer
    +rank: 1000
    +alias: type_designator
    +owner: SlotDerivation
    +domain_of:
    +- SlotDerivation
    +range: boolean
    +
    +
    + +
    + +
    + + +
    +
    + + + + + \ No newline at end of file diff --git a/unit_conversion/index.html b/unit_conversion/index.html new file mode 100644 index 0000000..3f487a4 --- /dev/null +++ b/unit_conversion/index.html @@ -0,0 +1,124 @@ + + + + + + + + + + + + + + Slot: unit_conversion - LinkML-Map + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + +

    Slot: unit_conversion

    +

    URI: linkmltr:unit_conversion

    + + +

    Applicable Classes

    + + + + + + + + + + + + + + + +
    NameDescriptionModifies Slot
    SlotDerivationA specification of how to derive the value of a target slot from a source slo...no
    +

    Properties

    + +

    Identifier and Mapping Information

    +

    Schema Source

    +
      +
    • from schema: https://w3id.org/linkml/transformer
    • +
    +

    LinkML Source

    +
    + +
    name: unit_conversion
    +from_schema: https://w3id.org/linkml/transformer
    +rank: 1000
    +alias: unit_conversion
    +owner: SlotDerivation
    +domain_of:
    +- SlotDerivation
    +range: UnitConversionConfiguration
    +
    +
    + +
    + +
    + + +
    +
    + + + + + \ No newline at end of file diff --git a/utils/get-value.sh b/utils/get-value.sh deleted file mode 100644 index de8c96f..0000000 --- a/utils/get-value.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/usr/bin/env bash -# get the value of a key in the about.yaml file -# https://stackoverflow.com/questions/1221833/pipe-output-and-capture-exit-status-in-bash -grep $1 about.yaml | sed "s/$1:[[:space:]]//" ; test ${PIPESTATUS[0]} -eq 0 diff --git a/uv.lock b/uv.lock deleted file mode 100644 index c9998bd..0000000 --- a/uv.lock +++ /dev/null @@ -1,3481 +0,0 @@ -version = 1 -revision = 2 -requires-python = ">=3.9, <=3.13" -resolution-markers = [ - "python_full_version >= '3.11'", - "python_full_version == '3.10.*'", - "python_full_version < '3.10'", -] - -[[package]] -name = "annotated-types" -version = "0.7.0" -source = { registry = "https://pypi.org/simple" } -sdist = { url = "https://files.pythonhosted.org/packages/ee/67/531ea369ba64dcff5ec9c3402f9f51bf748cec26dde048a2f973a4eea7f5/annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89", size = 16081, upload-time = "2024-05-20T21:33:25.928Z" } -wheels = [ - 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