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Bug #10674

closed

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

Added by Peter Amstutz about 7 years ago. Updated about 7 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 1 (0 open1 closed)

Task #10676: Review 10674-wb-workflow-defaultsResolvedPeter Amstutz12/07/2016

Actions
Actions #1

Updated by Peter Amstutz about 7 years ago

  • Assigned To set to Peter Amstutz
Actions #2

Updated by Radhika Chippada about 7 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
Actions #3

Updated by Peter Amstutz about 7 years ago

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

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

Actions #4

Updated by Peter Amstutz about 7 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

Actions #5

Updated by Radhika Chippada about 7 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.

Actions #6

Updated by Peter Amstutz about 7 years ago

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

Applied in changeset arvados|commit:e336e28f4ce9c13aad98d059d2befb505bff365b.

Actions #7

Updated by Peter Amstutz about 7 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.

Actions #8

Updated by Peter Amstutz about 7 years ago

  • Status changed from In Progress to Resolved
Actions

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