Skip to content

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

Open
@audrium

Description

@audrium
[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   --

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions