Arvados-cwl-runner development » History » Revision 5
Revision 4 (Peter Amstutz, 05/10/2018 02:55 PM) → Revision 5/14 (Peter Amstutz, 08/10/2018 03:36 PM)
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 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:
# $ virtualenv venv
# $ . venv/bin/activate
# $ (cd ~/arvados/sdk/cwl && python setup.py develop)
# _do your development_
# _test locally_
# $ arvados-cwl-runner --local
# $ git commit
# $ (cd ~/arvados/sdk/cwl && python setup.py develop)
# $ ~/arvados/build/build-dev-docker-jobs-image.sh
# _test submit to cluster_
# $ 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.
h2. Testing changes to Arvados Python SDK, cwltool or schema-salad
If changes
h2. Running cwl conformance tests
# $ 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