Arvados

Create workflow object. Take all the dependent files and make sure that they're. If workflow has multiple tools, package them all up.

• exgroup.add_argument("--update-workflow", type=str, help="Update Arvados workflow." => Can we call it --update-workflow-uuid? Please expand the description to say uuid of the workflow specified.

• main = [p for p in packed["$graph"] if p["id"] == "#main"][0] => Is it always guaranteed that $graph is present here? Do we need any error handling in make_workflow?

• It appears that the workflow being used is surrounded in a ”$graph": []. How does this compare with what we have in our fixtures? Do we need a fixture with a format similar to what you have here and verify how running such a workflow using workbench would work and how the inputs in workbench are rendered in such a case? Also, the code and examples are using multiple steps and I am wondering if you checked how such a workflow will be rendered in workbench.

• Do we need a test with invalid cwl?

• Does it make sense to add a yaml file based test?

Radhika Chippada wrote:

• exgroup.add_argument("--update-workflow", type=str, help="Update Arvados workflow." => Can we call it --update-workflow-uuid? Please expand the description to say uuid of the workflow specified.

Tweaked description and set metavar="UUID".

• main = [p for p in packed["$graph"] if p["id"] == "#main"][0] => Is it always guaranteed that $graph is present here?

Yes.

Do we need any error handling in make_workflow?

No, I don't think so. Exceptions are caught higher up.

• It appears that the workflow being used is surrounded in a ”$graph": []. How does this compare with what we have in our fixtures? Do we need a fixture with a format similar to what you have here and verify how running such a workflow using workbench would work and how the inputs in workbench are rendered in such a case? Also, the code and examples are using multiple steps and I am wondering if you checked how such a workflow will be rendered in workbench.

I adjusted the "uncommitted" fixture to use the $graph/#main pattern form that

• Do we need a test with invalid cwl?

arvados-cwl-runner validates the file before it uploads it. Teaching workbench how to validate CWL is out of the scope of this ticket.

• Does it make sense to add a yaml file based test?

I changed it to dump yaml text instead of json, and updated the test.

LGTM