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[23.2] Don't check availability of shellescape #18954

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nsoranzo
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@nsoranzo nsoranzo commented Oct 8, 2024

It is not used in the CWL branch any more.

cwltool removed shellescape as dependency in 3.1.20241007082533 , which causes errors like the following in test_galaxy_packages tests:

_______________________________ test_tool_proxy ________________________________

    def test_tool_proxy():
        """Test that tool proxies load some valid tools correctly."""
>       tool_proxy(_cwl_tool_path("v1.0/v1.0/cat1-testcli.cwl"))

tests/tool_util/test_cwl.py:35:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
galaxy/tool_util/cwl/parser.py:726: in tool_proxy
    ensure_cwltool_available()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

    def ensure_cwltool_available():
        """Assert optional dependencies proxied via this module are available at runtime.

        Throw an ImportError with a description of the problem if they do not exist.
        """
        if main is None or workflow is None or shellescape is None:
            message = "This feature requires cwltool and dependencies to be available, they are not."
            if main is None:
                message += " cwltool is not unavailable."
            elif resolve_and_validate_document is None:
                message += " cwltool.load_tool.resolve_and_validate_document is unavailable - cwltool version is too old."
            if requests is None:
                message += " Library 'requests' unavailable."
            if shellescape is None:
                message += " Library 'shellescape' unavailable."
            if schema_salad is None:
                message += " Library 'schema_salad' unavailable."
>           raise ImportError(message)
E           ImportError: This feature requires cwltool and dependencies to be available, they are not. Library 'shellescape' unavailable.

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.

It is not used in the CWL branch any more.

cwltool removed shellescape as dependency in 3.1.20241007082533 , which causes
errors like the following in test_galaxy_packages tests:

```
_______________________________ test_tool_proxy ________________________________

    def test_tool_proxy():
        """Test that tool proxies load some valid tools correctly."""
>       tool_proxy(_cwl_tool_path("v1.0/v1.0/cat1-testcli.cwl"))

tests/tool_util/test_cwl.py:35:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
galaxy/tool_util/cwl/parser.py:726: in tool_proxy
    ensure_cwltool_available()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

    def ensure_cwltool_available():
        """Assert optional dependencies proxied via this module are available at runtime.

        Throw an ImportError with a description of the problem if they do not exist.
        """
        if main is None or workflow is None or shellescape is None:
            message = "This feature requires cwltool and dependencies to be available, they are not."
            if main is None:
                message += " cwltool is not unavailable."
            elif resolve_and_validate_document is None:
                message += " cwltool.load_tool.resolve_and_validate_document is unavailable - cwltool version is too old."
            if requests is None:
                message += " Library 'requests' unavailable."
            if shellescape is None:
                message += " Library 'shellescape' unavailable."
            if schema_salad is None:
                message += " Library 'schema_salad' unavailable."
>           raise ImportError(message)
E           ImportError: This feature requires cwltool and dependencies to be available, they are not. Library 'shellescape' unavailable.
```
@github-actions github-actions bot added this to the 23.2 milestone Oct 8, 2024
@nsoranzo
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nsoranzo commented Oct 8, 2024

Test failures unrelated.

@mvdbeek mvdbeek merged commit 8cc3604 into galaxyproject:release_23.2 Oct 9, 2024
33 of 46 checks passed
@nsoranzo nsoranzo deleted the release_23.2_drop_shellescape branch October 9, 2024 09:02
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