Fix class detection for namespaced classes (Py)

[GlassOfWhiskey]

This commit asjusts the Python generated parser to correctly deal with namespaced classes (e.g., those coming from cwltool extensions).

[mr-c]

Thank you @GlassOfWhiskey !

I regenerated the cwl-utils parsers and ran the tests, I get one error:

_________________________________________ test_static_checker_fail[v1_0] _________________________________________

cwlVersion = 'v1_0'

    @pytest.mark.parametrize("cwlVersion", ["v1_0", "v1_1", "v1_2"])
    def test_static_checker_fail(cwlVersion: str) -> None:
        """Confirm that static type checker raises expected exception."""
        if cwlVersion == "v1_0":
            uri = Path(get_data("testdata/checker_wf/broken-wf.cwl")).resolve().as_uri()
            cwl_obj = load_document_by_uri(uri)
            with pytest.raises(
                ValidationException,
                match="\nSource .* of type .* is incompatible\n.*with sink .* of type .*",
            ):
                cwl_utils.parser.utils.static_checker(cwl_obj)
    
            uri = Path(get_data("testdata/checker_wf/broken-wf2.cwl")).resolve().as_uri()
            cwl_obj = load_document_by_uri(uri)
            with pytest.raises(
                ValidationException, match="param .* not found in class: CommandLineTool"
            ):
>               cwl_utils.parser.utils.static_checker(cwl_obj)

tests/test_parser_utils.py:42: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
cwl_utils/parser/utils.py:193: in static_checker
    {
cwl_utils/parser/utils.py:194: in <dictcomp>
    s.id: type_for_step_output(step, s.id, workflow.cwlVersion)
cwl_utils/parser/utils.py:410: in type_for_step_output
    return cwl_v1_0_utils.type_for_step_output(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

step = <cwl_utils.parser.cwl_v1_0.WorkflowStep object at 0x7f2025d3fc10>
sourcename = 'file:///home/michael/cwl-utils/testdata/checker_wf/broken-wf2.cwl#echo_w/other'

    def type_for_step_output(
        step: cwl.WorkflowStep,
        sourcename: str,
    ) -> Any:
        """Determine the type for the given step output."""
        step_run = cwl_utils.parser.utils.load_step(step)
        cwl_utils.parser.utils.convert_stdstreams_to_files(step_run)
        if step_run and step_run.outputs:
            for step_output in step_run.outputs:
                if (
                    step_output.id.split("#")[-1].split("/")[-1]
                    == sourcename.split("#")[-1].split("/")[-1]
                ):
                    output_type = step_output.type_
                    if step.scatter is not None:
                        if step.scatterMethod == "nested_crossproduct":
                            for _ in range(len(aslist(step.scatter))):
                                output_type = cwl.ArraySchema(
                                    items=output_type, type_="array"
                                )
                        else:
                            output_type = cwl.ArraySchema(items=output_type, type_="array")
                    return output_type
>       raise ValidationException(
            "param {} not found in {}.".format(
                sourcename,
                yaml_dumps(cwl.save(step_run)),
            )
        )
E       schema_salad.exceptions.ValidationException: param file:///home/michael/cwl-utils/testdata/checker_wf/broken-wf2.cwl#echo_w/other not found in id: file:///home/michael/cwl-utils/testdata/checker_wf/echo.cwl
E       class: CommandLineTool
E       inputs:
E       - id: echo_in
E         inputBinding: {}
E         type:
E         - string
E         - items: string
E           type: array
E       outputs:
E       - id: txt
E         outputBinding:
E           glob: out.txt
E         type: File
E       cwlVersion: v1.0
E       baseCommand: echo
E       stdout: out.txt
E       .

cwl_utils/parser/cwl_v1_0_utils.py:417: ValidationException

During handling of the above exception, another exception occurred:

cwlVersion = 'v1_0'

    @pytest.mark.parametrize("cwlVersion", ["v1_0", "v1_1", "v1_2"])
    def test_static_checker_fail(cwlVersion: str) -> None:
        """Confirm that static type checker raises expected exception."""
        if cwlVersion == "v1_0":
            uri = Path(get_data("testdata/checker_wf/broken-wf.cwl")).resolve().as_uri()
            cwl_obj = load_document_by_uri(uri)
            with pytest.raises(
                ValidationException,
                match="\nSource .* of type .* is incompatible\n.*with sink .* of type .*",
            ):
                cwl_utils.parser.utils.static_checker(cwl_obj)
    
            uri = Path(get_data("testdata/checker_wf/broken-wf2.cwl")).resolve().as_uri()
            cwl_obj = load_document_by_uri(uri)
>           with pytest.raises(
                ValidationException, match="param .* not found in class: CommandLineTool"
            ):
E           AssertionError: Regex pattern did not match.
E            Regex: 'param .* not found in class: CommandLineTool'
E            Input: 'param file:///home/michael/cwl-utils/testdata/checker_wf/broken-wf2.cwl#echo_w/other not found in id: file:///home/michael/cwl-utils/testdata/checker_wf/echo.cwl\nclass: CommandLineTool\ninputs:\n- id: echo_in\n  inputBinding: {}\n  type:\n  - string\n  - items: string\n    type: array\noutputs:\n- id: txt\n  outputBinding:\n    glob: out.txt\n  type: File\ncwlVersion: v1.0\nbaseCommand: echo\nstdout: out.txt\n.'

tests/test_parser_utils.py:39: AssertionError

[mr-c]

That error looks harmless, we just need to update the other test to match the re-ordered output.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 83.13%. Comparing base (f3518e2) to head (daf7967).
Report is 26 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #897      +/-   ##
==========================================
- Coverage   83.14%   83.13%   -0.01%     
==========================================
  Files          22       22              
  Lines        4900     4899       -1     
  Branches     1178     1177       -1     
==========================================
- Hits         4074     4073       -1     
  Misses        548      548              
  Partials      278      278              

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