fix loadContents for File[]

[fmigneault]

When a type: File[] is provided with loadContents: true, the contents property of the respective files are NOT loaded. This does not respect the specification https://www.commonwl.org/v1.2/CommandLineTool.html#CommandInputParameter that indicates they should be loaded.

• Fixes loadContents does not load contents for an array of files #1246
• Relates to A Workflow with two steps of the same ExpressionTool fails if the tool inputs an array of files with loadContents #1094

@mr-c
I would really like to have this integrated as soon as possible, since this is blocking me for many integrations with geospatial community tools. Feel free to adjust, or let me know what I just adjust, to make this integrated quickly (I do not remember the procedure to integrate the test to the test pipeline).

The expected output of the provided test is {"data": [1,2]}.
Without the changes, it results in {"data":[null,null]} (since contents is missing).

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 83.77%. Comparing base (4046c49) to head (a492285).
Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2036      +/-   ##
==========================================
- Coverage   83.80%   83.77%   -0.03%     
==========================================
  Files          46       46              
  Lines        8267     8267              
  Branches     2201     2201              
==========================================
- Hits         6928     6926       -2     
- Misses        859      861       +2     
  Partials      480      480              

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[mr-c]

Thank you @fmigneault ! Did you mean to add test code that uses the new test data in this PR?

[fmigneault]

Yes. The test data submitted is used by the test CWL.

[fmigneault]

@mr-c
I think I might have misunderstood your question originally.
Indeed, there was no Python script added to run the test.
Now added.

[fmigneault]

@mr-c All tests resolved and working.

[fmigneault]

@mr-c
When is the next planned release with this PR integrated?

[mr-c]

@mr-c
When is the next planned release with this PR integrated?

We don't have scheduled releases. Can you install from your fork?

[fmigneault]

Yes, I can work with the fork in the meantime.
No rush for the release. Just trying to estimate when a tag would become available to pin the official repository.

[mr-c]

@fmigneault https://github.com/common-workflow-language/cwltool/releases/tag/3.1.20240909164951 :-)

[fmigneault]

@mr-c Thanks!