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Fix test_deserialize_* unit tests #13208

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merged 2 commits into from Jan 20, 2022

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nsoranzo
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Fix:

    def test_deserialize_xml_tool(tool_app):

>       tool = _deserialize(tool_app, tool_source_class='XmlToolSource', raw_tool_source=XML_TOOL)

test/unit/app/tools/test_tool_deserialization.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
test/unit/app/tools/test_tool_deserialization.py:54: in _deserialize
    return create_tool_from_source(app, tool_source=tool_source)
lib/galaxy/tools/__init__.py:278: in create_tool_from_source
    tool = ToolClass(config_file, tool_source, app, **kwds)
lib/galaxy/tools/__init__.py:606: in __init__
    raise e
lib/galaxy/tools/__init__.py:603: in __init__
    self.parse(tool_source, guid=guid, dynamic=dynamic)

        if has_missing_data:
            biotools_reference = self.biotools_reference
>           metadata_source = self.app.biotools_metadata_source
E           AttributeError: 'ToolApp' object has no attribute 'biotools_metadata_source'

lib/galaxy/tools/__init__.py:1032: AttributeError

introduced merging forward #13202 .

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

Fix:

```
    def test_deserialize_xml_tool(tool_app):

>       tool = _deserialize(tool_app, tool_source_class='XmlToolSource', raw_tool_source=XML_TOOL)

test/unit/app/tools/test_tool_deserialization.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
test/unit/app/tools/test_tool_deserialization.py:54: in _deserialize
    return create_tool_from_source(app, tool_source=tool_source)
lib/galaxy/tools/__init__.py:278: in create_tool_from_source
    tool = ToolClass(config_file, tool_source, app, **kwds)
lib/galaxy/tools/__init__.py:606: in __init__
    raise e
lib/galaxy/tools/__init__.py:603: in __init__
    self.parse(tool_source, guid=guid, dynamic=dynamic)

        if has_missing_data:
            biotools_reference = self.biotools_reference
>           metadata_source = self.app.biotools_metadata_source
E           AttributeError: 'ToolApp' object has no attribute 'biotools_metadata_source'

lib/galaxy/tools/__init__.py:1032: AttributeError
```

introduced merging forward galaxyproject#13202 .
@nsoranzo nsoranzo added this to the 22.01 milestone Jan 19, 2022
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@jdavcs jdavcs left a comment

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Thank you!

@nsoranzo nsoranzo merged commit 7c34b05 into galaxyproject:dev Jan 20, 2022
@nsoranzo nsoranzo deleted the fix_test_tool_deserialization branch January 20, 2022 09:42
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3 participants