Use id entity attribute when setting exampleOfWork property

[nsoranzo]

Fix the following error in 3 unit tests when using rocrate 0.13.0 (e.g. in test_galaxy_packages tests run on Python 3.13):

______________________ test_export_invocation_to_ro_crate ______________________

tmp_path = PosixPath('/tmp/pytest-of-runner/pytest-5/test_export_invocation_to_ro_c0')

    def test_export_invocation_to_ro_crate(tmp_path):
        app = _mock_app()
        workflow_invocation = _setup_invocation(app)
        crate_directory = tmp_path / "crate"
        with store.ROCrateModelExportStore(crate_directory, app=app) as export_store:
            export_store.export_workflow_invocation(workflow_invocation)
>       validate_invocation_crate_directory(crate_directory)

tests/data/model/test_model_store.py:627:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/data/model/test_model_store.py:564: in validate_invocation_crate_directory
    validate_create_action(crate)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

ro_crate = <rocrate.rocrate.ROCrate object at 0x7fb4673c2520>

    def validate_create_action(ro_crate: ROCrate):
        workflow = ro_crate.mainEntity
        actions = [_ for _ in ro_crate.contextual_entities if "CreateAction" in _.type]
        assert len(actions) == 1
        wf_action = actions[0]
        assert wf_action["instrument"]
        assert wf_action["instrument"] is workflow
        wf_objects = wf_action["object"]
        wf_results = wf_action["result"]
        assert len(wf_objects) == 1
        assert len(wf_results) == 1
        for entity in wf_results:
            if entity.id.endswith(".txt"):
                assert "File" in entity.type
                wf_output_file = entity
                assert wf_output_file["encodingFormat"] == "text/plain"
>               assert wf_output_file["exampleOfWork"] is workflow["output"][0]
E               AssertionError: assert '#d2ed04ef-36f8-49ae-86ce-47cb03a856c0' is <d2ed04ef-36f8-49ae-86ce-47cb03a856c0 FormalParameter>

tests/data/model/test_model_store.py:540: AssertionError

Also:

• Remove _add_step_tool_pv method, unused since commit 01782c0 .
• Uniform use of tmp_path in ro-crate tests.

How to test the changes?

(Select all options that apply)

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

[nsoranzo]

Test failures unrelated.

[davelopez]

Thank you! It looks good to me.

[nsoranzo]

If we'd like to have the test_galaxy_packages tests pass on 24.2, we can backport just the second commit, let me know!

[davelopez]

Sounds like a good idea :) 👍