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conformance tests: Did not find output file with glob pattern (103, 118, 173) #199

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audrium opened this issue Aug 30, 2021 · 0 comments

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audrium commented Aug 30, 2021

[job main] FINAL JOB STATE: failed ------------------
2021-08-30 09:08:28,656 | reana-workflow-engine-cwl | main | INFO | [job main] FINAL JOB STATE: failed ------------------
[job main] workflow job error:
("Error collecting output for parameter 'thing':\nworkflow.json:1:233: Did not find output file with glob pattern: '['thing']'", {})
2021-08-30 09:08:28,678 | reana-workflow-engine-cwl | main | ERROR | [job main] workflow job error:
("Error collecting output for parameter 'thing':\nworkflow.json:1:233: Did not find output file with glob pattern: '['thing']'", {})
FinalOutput{}FinalOutput
2021-08-30 09:08:28,735 | reana-workflow-engine-cwl | MainThread | INFO | FinalOutput{}FinalOutput
WARNING Final process status is permanentFail
2021-08-30 09:08:28,735 | cwltool | MainThread | WARNING | Final process status is permanentFail
workflow done
2021-08-30 09:08:28,736 | reana-workflow-engine-cwl | MainThread | INFO | workflow done
2021-08-30 09:08:28,736 | root | MainThread | INFO | Workflow a83bfe3c-f8ca-4024-a2a8-ab2c878d4d04 finished. Files available at /var/reana/users/00000000-0000-0000-0000-000000000000/workflows/a83bfe3c-f8ca-4024-a2a8-ab2c878d4d04.
workflow_spec: {'baseCommand': ['touch', '/other/thing'], 'class': 'CommandLineTool', 'cwlVersion': 'v1.0', 'hints': [{'class': 'ResourceRequirement', 'ramMin': 8}], 'id': '#main', 'inputs': [], 'outputs': [{'id': '#main/thing', 'outputBinding': {'glob': 'thing'}, 'type': 'File'}], 'requirements': [{'class': 'DockerRequirement', 'dockerOutputDirectory': '/other', 'dockerPull': 'debian:stretch-slim'}]}

==> Job logs
==> Step: main
==> Workflow ID: a83bfe3c-f8ca-4024-a2a8-ab2c878d4d04
==> Compute backend: Kubernetes
==> Job ID: reana-run-job-47455826-a6de-4a13-9a64-1e485ca230ff
==> Docker image: debian:stretch-slim
==> Command: /bin/sh -c 'mkdir -p /other && umask 2;export TMPDIR="/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/a83bfe3c-f8ca-4024-a2a8-ab2c878d4d04/cwl/tmpdir/pj06m964";export HOME="/other";export PATH="/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin";mkdir -p /other && cd /other && touch /other/thing ; cp -r /other /var/reana/users/00000000-0000-0000-0000-000000000000/workflows/a83bfe3c-f8ca-4024-a2a8-ab2c878d4d04/cwl/outdir/vcifhj7q; cp -r /other/* /var/reana/users/00000000-0000-0000-0000-000000000000/workflows/a83bfe3c-f8ca-4024-a2a8-ab2c878d4d04/cwl/outdir/vcifhj7q'
==> Status: failed
==> Started: 2021-08-30T09:08:23
==> Finished: 2021-08-30T09:08:28
==> Logs:
job: :
 mkdir: cannot create directory '/other': Permission denied
mkdir: cannot create directory '/other': Permission denied
cp: cannot stat '/other': No such file or directory
cp: cannot stat '/other/*': No such file or directory

Error

To reproduce:

cwltest --tool /home/amecioni/.virtualenvs/cwl/bin/reana-cwl-runner --test=conformance_test_v1.0.yaml -n103 --basedir /home/amecioni/Documents/tests/common-workflow-language/v1.0   --
@audrium audrium changed the title conformance tests: Did not find output file with glob pattern (103) conformance tests: Did not find output file with glob pattern (103, 118, 173) Aug 30, 2021
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