Fix pydot tests

[lkk7]

No description provided.

[codecov]

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Project coverage is 54.92%. Comparing base (6d8c2a4) to head (5dd4d08).

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@@             Coverage Diff             @@
##             main    #2019       +/-   ##
===========================================
- Coverage   83.78%   54.92%   -28.86%     
===========================================
  Files          46       46               
  Lines        8262     8260        -2     
  Branches     2199     2103       -96     
===========================================
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- Misses        858     3185     +2327     
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[lkk7]

The test fails for the same reason it failed for me locally: https://github.com/common-workflow-language/cwltool/actions/runs/9964048376/job/27541027817

The reason is that cwltool returns these strings with a path attached to them, while it wasn't expected.
It doesn't seem to be pydot related, does it?

[mr-c]

@lkk7 Interesting, I've triggered a re-run of the CI on the main branch to see if there has been a regression related to one of our dependencies since July 12th

https://github.com/common-workflow-language/cwltool/actions/runs/9905754128

[mr-c]

@lkk7 When we pin to a pydot before version 3, all the CI tests still pass: https://github.com/common-workflow-language/cwltool/actions/runs/9976419287/job/27568552139

[lkk7]

That's an old issue, but could we retry the CI now? Or has this been solved already?

[mr-c]

@lkk7 Since you started this PR we capped the pydot version to be less than 3. So now that we've rebased the PR I had to add a revert of that pydot version cap commit. We can now compare the pending test results (with pydot 3.x) to the results without pydot 3.x.

[mr-c]

@lkk7 Looks like there is a behavior change with pydot 3.x (3.0.1, specifically)

    [
        (
  -         '"command_line_tool"',
  -         '"file_output"',
  +         'file:"///home/runner/work/cwltool/cwltool/tests/wf/three_step_color.cwl#command_line_tool"',
  +         'file:"///home/runner/work/cwltool/cwltool/tests/wf/three_step_color.cwl#file_output"',
        ),
        (
  -         '"file_input"',
  -         '"nested_workflow"',
  +         'file:"///home/runner/work/cwltool/cwltool/tests/wf/three_step_color.cwl#file_input"',
  +         'file:"///home/runner/work/cwltool/cwltool/tests/wf/three_step_color.cwl#nested_workflow"',
        ),
        (
  -         '"nested_workflow"',
  -         '"operation"',
  +         'file:"///home/runner/work/cwltool/cwltool/tests/wf/three_step_color.cwl#nested_workflow"',
  +         'file:"///home/runner/work/cwltool/cwltool/tests/wf/three_step_color.cwl#operation"',
        ),
        (
  -         '"operation"',
  -         '"command_line_tool"',
  +         'file:"///home/runner/work/cwltool/cwltool/tests/wf/three_step_color.cwl#operation"',
  +         'file:"///home/runner/work/cwltool/cwltool/tests/wf/three_step_color.cwl#command_line_tool"',
        ),
        (
  -         '"operation"',
  -         '"string_output"',
  +         'file:"///home/runner/work/cwltool/cwltool/tests/wf/three_step_color.cwl#operation"',
  +         'file:"///home/runner/work/cwltool/cwltool/tests/wf/three_step_color.cwl#string_output"',
        ),
    ]

https://github.com/common-workflow-language/cwltool/actions/runs/10468140236/job/28988377402?pr=2019#step:8:82

[lkk7]

I can't pinpoint the exact fix yet, but the bug appears in cwlrdf.py in this function:

def printdot(
    wf: Process,
    ctx: ContextType,
    stdout: IO[str],
) -> None:
    cwl_viewer: CWLViewer = CWLViewer(printrdf(wf, ctx, "n3"))
    stdout.write(cwl_viewer.dot().replace(f"{wf.metadata['id']}#", ""))  ###  <<< HERE 

It's all about those file paths.

wf.metadata['id'] equals 'file:///<your_path>/three_step_color.cwl', and in pydot 2.0.0 it's removed from the string as expected.

In 3.0.0+ the cwl_viewer.dot() contains these paths in a changed form: file:"///<your_path>/three_step_color.cwl#string_output". There is an additional quote that causes the replacement not to work.

@ferdnyc, Could you confirm my suspicion. I know you were not involved in this one, but you made the change that affect this (ea0131517db2a0dbf58ec0f8bb3bd7b40bbd279d). The context of this bug is not important, but – file:///<path>#<...> changed to file:"///<path>#<...>". Is it because now pydot thinks it's a port, like node1:port1?