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.

Example development process

Setup python virtual environment, edit code, and test locally

  1. $ virtualenv venv
  2. $ . venv/bin/activate
  3. $ (cd ~/arvados/sdk/cwl && python setup.py develop)
  4. do your development
  5. $ arvados-cwl-runner --local

Commit code, build development docker jobs image, and test submission

  1. $ git commit
  2. $ (cd ~/arvados/sdk/cwl && python setup.py develop)
  3. $ ~/arvados/build/build-dev-docker-jobs-image.sh
  4. $ arvados-cwl-runner --submit

Important to note:

  • You need to have ARVADOS_API_HOST and 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 here 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

Testing

This section describes how to set up your testing environment and run/debug CWL conformance and Arvados integration tests. Tests can be run several different ways. You can run tests using a Python 3 virtualenv in a docker image running Python 2, vice versa, or in a pure Python 2 or 3 setup. Python 2 is the default for build-dev-docker-jobs-image.sh. Use "PYCMD=python3 arvados/build/build-dev-docker-jobs-image.sh" to get a Python 3 dev docker image. You can use the --python="path/to/python/exec/" virtualenv argument to specify your python version. You can also test both the jobs and containers APIs by changing the --api flag on run-tests.sh.

If using arvbox, you can more easily test with test_with_arvbox.sh, which is in the arvados/sdk/cwl folder. Commands include:

--pythoncmd (python|python3)

--suite (conformance|integration)

--api (jobs|containers)

Example: test_with_arvbox.sh --no-reset-container --leave-running --config dev --build --pythoncmd python3 --suite integration -j3

Environment setup

  1. $ "arvbox start" and "arvswitch" to your dev cluster or run "arvbox start dev"
  2. If ARVADOS_API_HOST and ARVADOS_API_TOKEN are not set, find the the workbench ip address from the arvbox output. Open it in a browser and add a new account with fake credentials. Click on Current token in the user dropdown menu and follow instructions. If you subsequently receive localhost match errors, use "export ARVADOS_API_HOST_INSECURE=1".
  3. $ virtualenv venv
  4. $ . venv/bin/activate
  5. $ (cd ~/arvados/sdk/cwl && python setup.py develop)
  6. $ ~/arvados/build/build-dev-docker-jobs-image.sh.

Running CWL conformance tests

run_tests.sh is located in the common-workflow-language repository. To improve speed, use -jx, where x is the number tests to run simultaneously. To run a single test, use -nx where x is the test number zero-indexed.

  1. $ pip install cwltest
  2. $ git clone https://github.com/common-workflow-language/common-workflow-language.git

Run tests

  1. $ ./run_test.sh RUNNER=arvados-cwl-runner EXTRA="--api=containers --compute-checksum --disable-reuse --local"
  2. $ ./run_test.sh RUNNER=arvados-cwl-runner EXTRA="--api=containers --compute-checksum --disable-reuse --submit"

Debug tests

When a test fails, there should be output displaying Test failed: followed by the test command. Copy the command.

  1. $ cd common-workflow-language/v1.0
  2. $ Paste the command and replace the --quiet flag with --debug

Running arvados CWL integration tests

  1. $ cd arvados/sdk/cwl/tests
  2. $ ./arvados-tests.sh