Workflow Hub Crate Error #124
Comments
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Dear @kbarrass1252 , first of all, thanks for the feedback! I have been analysing the generated RO-Crate from WorkflowHub, and in this case, strictly following the specification, the code is complaining properly. The documentation about profile https://about.workflowhub.eu/Workflow-RO-Crate/1.0/ specifies that :
In the RO-Crate obtained from WorkflowHub, the {
"@context": "https://w3id.org/ro/crate/1.1/context",
"@graph": [
{
"@id": "ro-crate-metadata.json",
"@type": "CreativeWork",
"about": {
"@id": "./"
},
"conformsTo": {
"@id": "https://w3id.org/ro/crate/1.1"
}
},
{
"@id": "ro-crate-preview.html",
"@type": "CreativeWork",
"about": {
"@id": "./"
}
},
{
"@id": "./",
"@type": "Dataset",
"conformsTo": [
{
"@id": "https://w3id.org/ro/crate/1.1"
},
{
"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
}
],
"mainEntity": {
"@id": "x86/workflow-entrypoint.cwl"
},
"author": [
{
"@id": "#person-476"
}
],On the other hand, RO-Crate 1.2 draft specification declares that any RO-Crate profile should be referred from the @stain @fbacall I have a question, as this issue might partially fall on your side. RO-Crates obtained from WorkflowHub with URLs similar to https://workflowhub.eu/ga4gh/trs/v2/tools/471/versions/3/CWL/files?format=zip , are generated on the fly? If it is so, then either the Workflow RO-Crate profile specification should be updated in order to be conformant to RO-Crate 1.2 draft, or WorkflowHub should fix the issue about the location of |
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In any case @kbarrass1252 , I'm going to relax the detection of Workflow RO-Crate |
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@kbarrass1252 I have tagged WfExS 1.0.0rc1, where commit 61fd06a relaxes Workflow RO-Crate profile detection . Could you try using it in your usage scenario, please? |
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Hi @jmfernandez ! TY so much! However - we still have an issue as follows: "(.pyWEenv) @ip----:~/wfexs/WfExS-backend$ python3 WfExS-backend.py -L config/local_config_admin.yaml execute -W omopworkflow/omop-workflow.stage
However - our fallback test which is to run the CWL through cwltool through conda runs the CWL without any error :( |
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Mmmmmm, I see @kbarrass1252 , thanks for the tests!! As you have uncovered a different bug, I have transferred your last report to the new issue #128 |
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Perfect! TTY! |
When pulling from workflowhub.eu (both samples and our own) we encounter the following error: "JSON-LD from /home/admin/wfexs_tmpdir/ro-crate-cache/***.crate.zip is not a Workflow RO-Crate"
A dump of the error is shown below.
All pre-requisites are shown as valid. Config and stage file are taken from a working instance from another user who have patched a local copy to run from local git - but this scenario does not work for us.
Error is coming from 2686 to 2689 of this file:
[WfExS-backend/wfexs_backend/wfexs_backend.py at main · inab/WfExS-backend · GitHub]
(https://github.com/inab/WfExS-backend/blob/main/wfexs_backend/wfexs_backend.py#L2686C1-L2689C14)
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