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Bug #9615

closed

[CWL] Flag "writable" InitialWorkDirRequirement as unsupported under Crunch v1

Added by Peter Amstutz over 7 years ago. Updated over 7 years ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Category:
Crunch
Target version:
Start date:
08/16/2016
Due date:
% Done:

100%

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

Description

CWL on crunch v1 is failing one of the CWL conformance tests.

Test [70/73] 2016-07-17 17:17:24 arvados.cwl-runner[63563] ERROR: While getting final output object: [Errno 2] File not found
2016-07-17 17:17:24 arvados.cwl-runner[63563] WARNING: Overall process status is permanentFail
Workflow error, try again with --debug for more information:
  Workflow failed.
Test failed: /usr/bin/cwl-runner --outdir=/tmp/tmpj2SonY --quiet v1.0/stagefile.cwl v1.0/stagefile-job.yml
Test writable staged files.
Returned non-zero

This is the test of the "writable" flag, which indicates that an input file should be copied into the output directory and directly writable by the tool (open "r+"). The test failure is accurate because this feature isn't actually supported. We should either implement it, or raise cwl.process.UnsupportedRequirement to indicate that it not a supported feature (which will cause the test suite to consider the test skipped instead of failing.)

To implement this, arvados-cwl-runner needs to indicate to crunchrunner that a file in the task.vwd object should be copied and not symlinked.

On crunch v2 we don't yet support staging files to the output directory at all, so this probably already raises UnsupportedRequirement.


Subtasks 1 (0 open1 closed)

Task #9733: Review 9615-cwl-writable-unsupportedResolved08/16/2016

Actions
Actions #1

Updated by Peter Amstutz over 7 years ago

  • Subject changed from [CWL] Doesn't support "writable" flag to [CWL] Support "writable" flag
Actions #2

Updated by Peter Amstutz over 7 years ago

  • Subject changed from [CWL] Support "writable" flag to [CWL] Support "writable" flag on InitialWorkDirRequirement
Actions #3

Updated by Peter Amstutz over 7 years ago

  • Description updated (diff)
Actions #4

Updated by Peter Amstutz over 7 years ago

  • Description updated (diff)
Actions #5

Updated by Brett Smith over 7 years ago

  • Subject changed from [CWL] Support "writable" flag on InitialWorkDirRequirement to [CWL] Flag "writable" InitialWorkDirRequirement as unsupported under Crunch v1
  • Category set to Crunch

arvados-cwl-runner should raise cwl.process.UnsupportedRequirement when InitialWorkDirRequirement "writable" and work_api "jobs". I don't see much call to support additional CWL features under Crunch v1 right now.

Actions #6

Updated by Brett Smith over 7 years ago

  • Target version set to Arvados Future Sprints
Actions #7

Updated by Tom Morris over 7 years ago

  • Story points set to 0.5
Actions #8

Updated by Peter Amstutz over 7 years ago

  • Assigned To set to Peter Amstutz
  • Target version changed from Arvados Future Sprints to 2016-08-17 sprint
Actions #9

Updated by Peter Amstutz over 7 years ago

Branch 9615-cwl-writable-unsupported is up to review

Actions #10

Updated by Peter Amstutz over 7 years ago

  • Status changed from New to Resolved
Actions

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