draft schema for paramter restrictions extension

Author: mr-c

MANIFEST.in

@@ -57,6 +57,7 @@ include cwltool/cwlNodeEngineJSConsole.js
 include cwltool/cwlNodeEngineWithContext.js
 include cwltool/extensions.yml
 include cwltool/extensions-v1.1.yml
+include cwltool/extensions-v1.2.yml
 include cwltool/jshint/jshint_wrapper.js
 include cwltool/jshint/jshint.js
 include cwltool/hello.simg

cwltool/extensions-v1.2.yml

@@ -0,0 +1,272 @@
+$base: http://commonwl.org/cwltool#
+$namespaces:
+  cwl: "https://w3id.org/cwl/cwl#"
+  cwltool: "http://commonwl.org/cwltool#"
+$graph:
+- $import: https://w3id.org/cwl/CommonWorkflowLanguage.yml
+
+- name: Secrets
+  type: record
+  inVocab: false
+  extends: cwl:ProcessRequirement
+  fields:
+    class:
+      type: string
+      doc: "Always 'Secrets'"
+      jsonldPredicate:
+        "_id": "@type"
+        "_type": "@vocab"
+    secrets:
+      type: string[]
+      doc: |
+        List one or more input parameters that are sensitive (such as passwords)
+        which will be deliberately obscured from logging.
+      jsonldPredicate:
+        "_type": "@id"
+        refScope: 0
+
+
+- name: ProcessGenerator
+  type: record
+  inVocab: true
+  extends: cwl:Process
+  documentRoot: true
+  fields:
+    - name: class
+      jsonldPredicate:
+        "_id": "@type"
+        "_type": "@vocab"
+      type: string
+    - name: run
+      type: [string, cwl:Process]
+      jsonldPredicate:
+        _id: "cwl:run"
+        _type: "@id"
+        subscope: run
+      doc: |
+        Specifies the process to run.
+
+- name: MPIRequirement
+  type: record
+  inVocab: false
+  extends: cwl:ProcessRequirement
+  doc: |
+    Indicates that a process requires an MPI runtime.
+  fields:
+    - name: class
+      type: string
+      doc: "Always 'MPIRequirement'"
+      jsonldPredicate:
+        "_id": "@type"
+        "_type": "@vocab"
+    - name: processes
+      type: [int, cwl:Expression]
+      doc: |
+        The number of MPI processes to start. If you give a string,
+        this will be evaluated as a CWL Expression and it must
+        evaluate to an integer.
+
+- name: CUDARequirement
+  type: record
+  extends: cwl:ProcessRequirement
+  inVocab: false
+  doc: |
+    Require support for NVIDA CUDA (GPU hardware acceleration).
+  fields:
+    class:
+      type: string
+      doc: 'cwltool:CUDARequirement'
+      jsonldPredicate:
+        _id: "@type"
+        _type: "@vocab"
+    cudaVersionMin:
+      type: string
+      doc: |
+        Minimum CUDA version to run the software, in X.Y format.  This
+        corresponds to a CUDA SDK release.  When running directly on
+        the host (not in a container) the host must have a compatible
+        CUDA SDK (matching the exact version, or, starting with CUDA
+        11.3, matching major version).  When run in a container, the
+        container image should provide the CUDA runtime, and the host
+        driver is injected into the container.  In this case, because
+        CUDA drivers are backwards compatible, it is possible to
+        use an older SDK with a newer driver across major versions.
+
+        See https://docs.nvidia.com/deploy/cuda-compatibility/ for
+        details.
+    cudaComputeCapability:
+      type:
+        - 'string'
+        - 'string[]'
+      doc: |
+        CUDA hardware capability required to run the software, in X.Y
+        format.
+
+        * If this is a single value, it defines only the minimum
+          compute capability.  GPUs with higher capability are also
+          accepted.
+
+        * If it is an array value, then only select GPUs with compute
+          capabilities that explicitly appear in the array.
+    cudaDeviceCountMin:
+      type: ['null', int, cwl:Expression]
+      default: 1
+      doc: |
+        Minimum number of GPU devices to request.  If not specified,
+        same as `cudaDeviceCountMax`.  If neither are specified,
+        default 1.
+    cudaDeviceCountMax:
+      type: ['null', int, cwl:Expression]
+      doc: |
+        Maximum number of GPU devices to request.  If not specified,
+        same as `cudaDeviceCountMin`.
+
+- name: intervalBase
+  type: record
+  abstract: true
+  fields:
+    low:
+      type: [int, float, double]
+      default: -.inf  # negative infinity
+      jsonldPredicate: "cwltool:low"
+    high:
+      type: [int, float, double]
+      default: .inf  # positive infinity
+      jsonldPredicate: "cwltool:high"
+
+- name: intInterval
+  type: record
+  extends: intervalBase
+  doc: |
+    Integer number interval specification. All integer intervals are inclusive.
+  fields:
+    class:
+      type:
+        type: enum
+        name: intInterval_class
+        symbols:
+          - cwltool:intInterval
+      jsonldPredicate:
+        _id: "@type"
+        _type: "@vocab"
+    low:
+      type: int
+      default: -.inf  # negative infinity
+      jsonldPredicate: "cwltool:low"
+    high:
+      type: int
+      default: .inf  # positive infinity
+      jsonldPredicate: "cwltool:high"
+    # compact form proposal
+        # doc: |
+        #   Examples:
+        #   "[0,3)" any real number between 0 (inclusive) and 3 (exclusive)
+        #   "[6,)" any real number greater than or equal to 6
+        #   "(0,1)" any real number between 0 and 1 (exclusive)
+
+
+- name: realInterval
+  type: record
+  extends: intervalBase
+  doc: |
+    Integer number interval
+  fields:
+    class:
+      type:
+        type: enum
+        name: realInterval_class
+        symbols:
+          - cwltool:realInterval
+      jsonldPredicate:
+        _id: "@type"
+        _type: "@vocab"
+    low_inclusive:
+      type: boolean
+      default: true
+    high_inclusive:
+      type: boolean
+      default: true
+    # compact form proposal
+        # doc: |
+        #   Use "(" or "[" to indicate an exclusive or inclusive beginning,
+        #   and ")" or "]" to indicate an exclusive or inclusive end.
+        #   Default is inclusive.
+        #   Examples:
+        #   "[0,3)" any real number between 0 (inclusive) and 3 (exclusive)
+        #   "[6,)" any real number greater than or equal to 6
+        #   "(0,1)" any real number between 0 and 1 (exclusive)
+
+- name: regex
+  type: record
+  doc: |
+    Regular Expression
+    TODO: what type of regex?
+  fields:
+    class:
+      type:
+        type: enum
+        name: regex_class
+        symbols:
+          - cwltool:regex
+      jsonldPredicate:
+        _id: "@type"
+        _type: "@vocab"
+    rpattern:
+      type: string
+      
+
+- name: Restrictions
+  type: record
+  fields:
+    input:
+      type: string
+      jsonldPredicate:
+        "_type": "@id"
+        refScope: 2
+    constraints:
+      type:
+        type: array
+        items: 
+          - string
+          - int
+          - float
+          - double
+          - regex
+          - cwl:Expression
+          - intInterval
+          - realInterval
+
+- name: ParameterRestrictions
+  type: record
+  extends: cwl:ProcessRequirement
+  inVocab: false
+  doc: |
+    Prototype of input value restrictions construct.
+  fields:
+    class:
+      type:
+        type: enum
+        name: ParameterRestrictions_class
+        symbols:
+          - cwltool:ParameterRestrictions
+      jsonldPredicate:
+        _id: "@type"
+        _type: "@vocab"
+    restrictions:
+      type: Restrictions[]
+      jsonldPredicate:
+        _id: "cwltool:restrictions"
+        mapSubject: input
+        mapPredicate: constraints
+      doc: |
+        (Only applicable for string, int, long, float and double parameters)
+        List of restrictions that apply to the input parameter "id".
+        A given parameter value should be accepted if any of the restrictions
+        match the input. Restrictions can be
+        single values (applies to all types),
+        ranges of the same type (applies to int, float and double),
+        regular expressions (for string parameters)
+        or Expressions (if an expression is provided, the expression must
+        return a boolean representing a match).
+        If the parameter is an array type, every value has to match at least
+        one of the restrictions.

cwltool/main.py

@@ -661,9 +661,11 @@ def setup_schema(
             ext10 = res.read().decode("utf-8")
         with pkg_resources.resource_stream(__name__, "extensions-v1.1.yml") as res:
             ext11 = res.read().decode("utf-8")
+        with pkg_resources.resource_stream(__name__, "extensions-v1.2.yml") as res:
+            ext12 = res.read().decode("utf-8")
         use_custom_schema("v1.0", "http://commonwl.org/cwltool", ext10)
         use_custom_schema("v1.1", "http://commonwl.org/cwltool", ext11)
-        use_custom_schema("v1.2", "http://commonwl.org/cwltool", ext11)
+        use_custom_schema("v1.2", "http://commonwl.org/cwltool", ext12)
         use_custom_schema("v1.2.0-dev1", "http://commonwl.org/cwltool", ext11)
         use_custom_schema("v1.2.0-dev2", "http://commonwl.org/cwltool", ext11)
         use_custom_schema("v1.2.0-dev3", "http://commonwl.org/cwltool", ext11)

cwltool/process.py

@@ -121,6 +121,7 @@ def filter(self, record: logging.LogRecord) -> bool:
     "http://commonwl.org/cwltool#LoadListingRequirement",
     "http://commonwl.org/cwltool#InplaceUpdateRequirement",
     "http://commonwl.org/cwltool#CUDARequirement",
+    "http://commonwl.org/cwltool#ParameterRestrictions",
 ]
 
 cwl_files = (

tests/parameter_restrictions.cwl

@@ -0,0 +1,40 @@
+cwlVersion: v1.2
+class: CommandLineTool
+
+doc: |
+  Tests of paramater restrictions extension
+
+inputs:
+  one: double
+  two: string
+
+
+hints:
+  cwltool:ParameterRestrictions:
+    restrictions:
+      one:
+       - class: cwltool:realInterval
+         low: 0
+         high: 3
+         high_inclusive: false
+       - class: cwltool:realInterval
+         low: 6
+         # high should be the default of positive infinity
+         high_inclusive: false
+      two:
+       - class: cwltool:regex
+         rpattern: "foo.*bar"
+
+
+baseCommand: echo
+
+arguments:
+ - $(inputs.one) 
+ - $(inputs.two) 
+
+outputs:
+  result: stdout
+
+$namespaces:
+  cwltool: "http://commonwl.org/cwltool#"
+