Arvados

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.