common-workflow-language / common-workflow-language/cwltool

Unhandled exception when scattering over a Directory.listing

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#279 5 comments 1 reaction 0 assignees View on GitHub
Dominant language
Python
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Description

There are two problems that seem to be happening:
1. cwltool doesn't generate the `listing` property for `Folder`s in the inputs.
2. this leads to a null reference in python which leads to the unhandled exception:
```
$ cwltool textures.cwl jobs/textures-job.yml
/home/undu/.config/virtualenvs/cwl/bin/cwltool 1.0.20170118141124
Resolved 'textures.cwl' to 'file:///home/undu/dev/stellaris-emblem-lab/textures/scripts/textures.cwl'
[job gradients] /tmp/tmpSLaHnL$ sh \
/tmp/tmp5oPppp/stg48a9ed53-e751-46f3-bd3d-74c9994398c2/gradients_gen.sh
[job gradients] completed success
[step gradients] completed success
Unhandled exception
Traceback (most recent call last):
File "/home/undu/.config/virtualenvs/cwl/lib/python2.7/site-packages/cwltool/workflow.py", line 306, in try_make_job
Callable[[Any], Any],callback), **kwargs)
File "/home/undu/.config/virtualenvs/cwl/lib/python2.7/site-packages/cwltool/workflow.py", line 636, in dotproduct_scatter
l = len(joborder[s])
TypeError: object of type 'NoneType' has no len()
[workflow textures.cwl] outdir is /tmp/tmpxbhiuz
{}
Final process status is permanentFail
```
Problem can be reproduced with [this repository](https://www.gitlab.com/unduthegun/stellaris-emblem-lab/tree/027c86bf9c147a7de3ba048a8dc158256b887b7f/textures/scripts), the command should be run in the linked repository and commit.

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