VDJServer Backbone is a next generation immune repertoire analysis portal.

The v2-develop branch is VDJServer V2 GUI development.

• Local Machine: http://localhost:9001
• Development Server: https://vdj-dev.tacc.utexas.edu
• Staging Server: https://vdj-staging.tacc.utexas.edu
• Production Server: https://vdjserver.org

The development setup is configured to mount the local directory with the source code files inside the docker container so that they can be modified and be available without regenerating the docker image. In order to support this, an npm install will install all of the node modules into that local directory. The first time the docker image is run, the install will take a few minutes.

- Clone project and init submodules
git clone http://bitbucket.org/vdjserver/vdjserver-web-backbone.git web-backbone-v2-develop
cd web-backbone-v2-develop
git checkout v2-develop
git submodule update --init --recursive

- Setup local environment config file
cp docker/environment-config/environment-config.js.defaults component/app/scripts/config/environment-config.js
vim component/app/scripts/config/environment-config.js

- Build the docker image
docker build -t vdjserver/backbone:v2-develop .

- For Mac/Linux, run docker image (with name vdjserver-backbone) with source code directory mounted
docker run -t -p 9001:9001 --rm --name vdjserver-backbone -v $(pwd)/component:/var/www/html/vdjserver-v2-web-backbone vdjserver/backbone:v2-develop bash -c "npm install && npm run eslint app/scripts && npm run dev && npm start"

- For Windows, run docker image (with name vdjserver-backbone) with source code directory mounted
docker run -t -p 9001:9001 --rm --name vdjserver-backbone -v ${PWD}/component:/var/www/html/vdjserver-v2-web-backbone vdjserver/backbone:v2-develop bash -c "npm install && npm run eslint app/scripts && npm run dev && npm start"

Note for Windows users: If you run the Mac/Linux command with a Mac-created container, (ie. vdjserver/backbone:develop), then npm will get stuck while trying to install fsevents (which is native to MacOS FSEvents; read more). Workaround: use a Windows-created container or the following with the Mac/Linux code: npm install --no-optional

Now you can access the website from your browser by going to http://localhost:9001.

Doing a CTRL-C will not completely stop the docker container. As the next time you perform docker run, you will get an error that the container name is already in use. You need to perform docker stop to completely stop the container.

- Stop the docker container
docker stop vdjserver-backbone

Even though webpack-dev-server is watching the file system, and it says that it has recompiled when a file is changed, it doesn't seem to working correctly, nor is it able to force the browser to refresh. To force a recompile of the website, do this command from another terminal window. Then do a refresh of the browser to load the new code.

- Perform a recompile of the website within the running container
docker exec vdjserver-backbone npm run dev

There is a TestCafe-based test suite in component/tests with its own readme.

In the server environment, docker compose is used at the higher-level (vdjserver-web) to compose the web application, the web api and the web server together.

Code Style

• Code should roughly follow Google Javascript Style Guide conventions: https://google-styleguide.googlecode.com/svn/trunk/javascriptguide.xml.

• A jscs.rc file (Javascript Code Style Checker) file has been provided in the project repo for any developers who use it.

• A git pre-commit hook is available via the file pre-commit.sh. To use it, just symlink it as follows: ln -s ../../pre-commit.sh .git/hooks/pre-commit

• Spaces are preferred over tabs, and indentation is set at 4 spaces.

• Vimrc settings: set shiftwidth=4, softtabstop=4, expandtab

Git Structure

• This project uses the Git Flow methodology for code management and development: https://www.atlassian.com/git/tutorials/comparing-workflows/gitflow-workflow.

• New development and features should be done on branches that are cloned from the develop branch, and then merged into this branch when completed. New release candidates should be branched from develop, and then merged into master once they have been tested/verified. Once a release branch is ready for production, it should be merged into master and tagged appropriately.