Arvados

h1. Arvados-cwl-runner development

Arvados-cwl-runner has two modes: submitting a workflow, and actively managing a workflow.

In submit mode (--submit) it creates a container request which executes arvados-cwl-runner (a-c-r) inside a container.  The container request uses the docker image "arvados/jobs" and the docker tag is the version of submitting a-c-r instance.  The a-c-r instance inside the container actively manages the workflow, and gets information about the container it is running in using containers().current().

When doing development related to workflow execution, you can use "--local" to run a locally managed workflow using your development code.  However, you still need to test that the workflow can be submitted and run in the container.  This requires building a development "arvados/jobs" image with the correct code and version tag.

h2. Example development process

_Setup python virtual environment, edit code, and test locally_

# $ virtualenv venv

# $ . venv/bin/activate

# $ (cd ~/arvados/sdk/cwl && python setup.py develop)

# _do your development_

# $ arvados-cwl-runner --local

_Commit code, build development docker jobs image, and test submission_

# $ git commit

# $ (cd ~/arvados/sdk/cwl && python setup.py develop)

# $ ~/arvados/build/build-dev-docker-jobs-image.sh

# $ arvados-cwl-runner --submit

_Important to note:_

* You need to have ARVADOS_API_HOST an ARVADOS_API_TOKEN in your environment. This can be obtained by opening workbench and clicking on _Current token_ in the user dropdown menu. 

* "setup.py develop" is convenient for editing files in place, but whenever you commit to git remember to re-run setup.py to record the new version number (which is derived from the git commit timestamp).

* If you are using arvbox, the paths above refer to your development arvados repository in the .arvbox folder

* You can specify custom schema salad, cwltool packages, and/or the python executable to use in the dev docker jobs image by doing the following:

     * $ PYCMD=python_or_python3 SALAD=/path/to/schema-salad CWLTOOL=/path/to/cwltool ~/arvados/build/build-dev-docker-jobs-image.sh

h2. Running cwl conformance tests

# $ "arvbox start" and "arvswitch" to your dev cluster  

# $ virtualenv venv

# $ . venv/bin/activate

# $ (cd ~/arvados/sdk/cwl && python setup.py develop)

# $ pip install cwltest

# $ git clone https://github.com/common-workflow-language/common-workflow-language.git

# $ ./run_test.sh RUNNER=arvados-cwl-runner EXTRA="--api=containers --compute-checksum --disable-reuse"

h2. Running arvados integration tests

# $ virtualenv venv

# $ . venv/bin/activate

# $ (cd ~/arvados/sdk/cwl && python setup.py develop)

# $ cd arvados/sdk/cwl/tests

# $ ./arvados-tests.sh