Bug #9615
Updated by Peter Amstutz almost 8 years ago
CWL on crunch v1 is failing one of the CWL conformance tests. <pre> 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 </pre> 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@. <pre> 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 </pre>