Arvados-cwl-runner development » History » Revision 8
Revision 7 (Peter Amstutz, 01/11/2019 09:36 PM) → Revision 8/14 (Peter Amstutz, 01/11/2019 09:37 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. Building a jobs image with custom cwltool or schema-salad When you build a "dev" jobs image, it generates custom arvados-python-client and arvados-cwl-runner packages from the working directory and injects them into the docker image build. You can also specify custom schema salad and/or cwltool packages this way: $ 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