Bug #10674

[Workbench] Fill in defaults when creating container request from workflow

Added by Peter Amstutz almost 5 years ago. Updated almost 5 years ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Category:
-
Target version:
Start date:
12/07/2016
Due date:
% Done:

100%

Estimated time:
(Total: 0.00 h)
Story points:
0.5

Subtasks

Task #10676: Review 10674-wb-workflow-defaultsResolvedPeter Amstutz

Associated revisions

Revision e336e28f
Added by Peter Amstutz almost 5 years ago

Merge branch '10674-wb-workflow-defaults' closes #10674

History

#1 Updated by Peter Amstutz almost 5 years ago

  • Assigned To set to Peter Amstutz

#2 Updated by Radhika Chippada almost 5 years ago

Review comments:

1. I created a workflow using the following command:

130!radhika@shell.9tee4:~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner --create-workflow bwa-mem.cwl bwa-mem-input.yml
/usr/bin/arvados-cwl-runner 0fb93082a34a92699c9be9ed4b1c991dd4003ea1 1.0.20161206185818, arvados-python-client 0.1.20161128194626, cwltool 1.0.20161128202906
Resolved 'bwa-mem.cwl' to 'file:///home/radhika/arvados/doc/user/cwl/bwa-mem/bwa-mem.cwl'
9tee4-7fd4e-i436kksnp4upnb8

I then went to 9tee4 workbench and used "Run a process" and selected this workflow. The resulting CR, 9tee4-xvhdp-fkm20ytkjp9g189, has the inputs filled in as expected.

However, the CR run failed with "Unsupported scheme in url: keep:ae480c5099b81e17267b7445e35b4bc7+180/HWI-ST1027_129_D0THKACXX.1_1.fastq"

2. It appears that we need a test for this:
  • Create a workflow with a cwl and partial input or a fixture in this state
  • Run a process using this workflow
  • Verify that the provided partial inputs are filled and the others are empty

#3 Updated by Peter Amstutz almost 5 years ago

For comment (1) this requires the fix in #10576.

For (2), I will see about adding a test.

#4 Updated by Peter Amstutz almost 5 years ago

I extended the test that creates a new pipeline/workflow to check that the parameter with a default value is filled in.

Now at @ 08271aa69aafdc92e2e8f8f25ed7fab078deb993

#5 Updated by Radhika Chippada almost 5 years ago

It would be nice to also add one more assertion to the test(s) that the Run button is disabled, since at least one required parameter is empty.

LGTM

Thanks.

#6 Updated by Peter Amstutz almost 5 years ago

  • Status changed from In Progress to Resolved
  • % Done changed from 0 to 100

Applied in changeset arvados|commit:e336e28f4ce9c13aad98d059d2befb505bff365b.

#7 Updated by Peter Amstutz almost 5 years ago

  • Status changed from Resolved to In Progress

Radhika Chippada wrote:

It would be nice to also add one more assertion to the test(s) that the Run button is disabled, since at least one required parameter is empty.

LGTM

Thanks.

Done & merged.

#8 Updated by Peter Amstutz almost 5 years ago

  • Status changed from In Progress to Resolved

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