Feature #9766
closed
[Crunch2] Submit to workflows table
Description
arvados-cwl-runner --create-workflow workflow.cwl [defaults.yml]
arvados-cwl-runner --update-workflow=uuid workflow.cwl [defaults.yml]
Similar to --create-template:
- Upload dependent files to keep
- Rewrite file locations to keep locations
- Pack dependent tools into single document & rewrite cross references
- Create workflow record with packed workflow object, label -> name, doc -> description
Updated by Tom Morris over 7 years ago
Create workflow object. Take all the dependent files and make sure that they're. If workflow has multiple tools, package them all up.
Updated by Peter Amstutz over 7 years ago
- Target version set to 2016-08-31 sprint
Updated by Peter Amstutz over 7 years ago
- Status changed from New to In Progress
- Assigned To set to Peter Amstutz
Updated by Radhika Chippada over 7 years ago
- Target version changed from 2016-08-31 sprint to 2016-09-14 sprint
Updated by Radhika Chippada over 7 years ago
- 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?
Updated by Peter Amstutz over 7 years ago
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.
Updated by Peter Amstutz over 7 years ago
- Status changed from In Progress to Resolved
Applied in changeset arvados|commit:cae94f22b760c6c6899fc4d23db15d389535ff0a.