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 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 (--local), and gets information about the container it is running in using containers().current().

When doing development related to workflow execution, you can also 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.

Here's a summary of the development process:

  1. $ virtualenv venv
  2. $ . venv/bin/activate
  3. $ (cd ~/arvados/sdk/cwl && python setup.py develop)
  4. do your development
  5. test locally
  6. $ arvados-cwl-runner --local
  7. $ git commit
  8. $ (cd ~/arvados/sdk/cwl && python setup.py develop)
  9. $ ~/arvados/build/build-dev-docker-jobs-image.sh
  10. test submit to cluster
  11. $ arvados-cwl-runner --submit

Important to note:

  • You need to have ARVADOS_API_HOST an ARVADOS_API_TOKEN in your environment
  • "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).
  • the a-c-r code which is run by the submitter and which is copied in the docker image are expected to match, and it uses the version number of the python package / docker image to enforce that.

Testing changes to Arvados Python SDK, cwltool or schema-salad

If changes

Running cwl conformance tests

  1. $ virtualenv venv
  2. $ . venv/bin/activate
  3. $ (cd ~/arvados/sdk/cwl && python setup.py develop)
  4. $ pip install cwltest
  5. $ git clone https://github.com/common-workflow-language/common-workflow-language.git
  6. $ ./run_test.sh RUNNER=arvados-cwl-runner EXTRA="--api=containers --compute-checksum --disable-reuse"

Running arvados integration tests

  1. $ virtualenv venv
  2. $ . venv/bin/activate
  3. $ (cd ~/arvados/sdk/cwl && python setup.py develop)
  4. $ cd arvados/sdk/cwl/tests
  5. $ ./arvados-tests.sh