[CWL] Flag "writable" InitialWorkDirRequirement as unsupported under Crunch v1
CWL on crunch v1 is failing one of the CWL conformance tests.
Test [70/73] 2016-07-17 17:17:24 arvados.cwl-runner ERROR: While getting final output object: [Errno 2] File not found 2016-07-17 17:17:24 arvados.cwl-runner 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
#5 Updated by Brett Smith over 4 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
InitialWorkDirRequirement "writable" and
work_api "jobs". I don't see much call to support additional CWL features under Crunch v1 right now.