Skip to content

Harmonize collection tool not loading due to test definition #22440

@natefoo

Description

@natefoo

From .org, guessing #22236 is related:

galaxy.tool_util.toolbox.base ERROR 2026-04-09 09:50:02,681 [pN:main1-1,p:2009492,tN:MainThread] Error reading tool from path: /cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tools/harmonize_two_collections_list.xml
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tool_util/toolbox/base.py", line 950, in _load_tool_tag_set
    tool = self.load_tool(concrete_path, use_cached=False)
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tool_util/toolbox/base.py", line 1205, in load_tool
    tool = self.create_tool(
        config_file,
    ...<2 lines>...
        **kwds,
    )
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tools/__init__.py", line 617, in create_tool
    return self._create_tool_from_source(tool_source, config_file=config_file, **kwds)
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tools/__init__.py", line 632, in _create_tool_from_source
    return create_tool_from_source(self.app, tool_source, **kwds)
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tools/__init__.py", line 450, in create_tool_from_source
    tool = ToolClass(config_file, tool_source, app, **kwds)
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tools/__init__.py", line 1117, in __init__
    raise e
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tools/__init__.py", line 1114, in __init__
    self.parse(tool_source, guid=guid, dynamic=dynamic)
    ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tools/__init__.py", line 1455, in parse
    self.parse_tests()
    ~~~~~~~~~~~~~~~~^^
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tools/__init__.py", line 1601, in parse_tests
    test_descriptions = parse_tool_test_descriptions(self.tool_source, self.id)
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tool_util/verify/parse.py", line 68, in parse_tool_test_descriptions
    raw_tests_dict: ToolSourceTests = tool_source.parse_tests_to_dict()
                                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tool_util/parser/xml.py", line 710, in parse_tests_to_dict
    tests.append(_test_elem_to_dict(test_elem, i, profile))
                 ~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tool_util/parser/xml.py", line 809, in _test_elem_to_dict
    output_collections=__parse_output_collection_elems(test_elem, profile=profile),
                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tool_util/parser/xml.py", line 855, in __parse_output_collection_elems
    output_collection_def = __parse_output_collection_elem(output_collection_elem, profile=profile)
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tool_util/parser/xml.py", line 865, in __parse_output_collection_elem
    element_tests = __parse_element_tests(output_collection_elem, profile=profile)
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tool_util/parser/xml.py", line 876, in __parse_element_tests
    element_tests[identifier] = __parse_test_attributes(
                                ~~~~~~~~~~~~~~~~~~~~~~~^
        element, element_attrib, parse_elements=True, profile=profile
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tool_util/parser/xml.py", line 949, in __parse_test_attributes
    element_tests = __parse_element_tests(output_elem, profile=profile)
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tool_util/parser/xml.py", line 876, in __parse_element_tests
    element_tests[identifier] = __parse_test_attributes(
                                ~~~~~~~~~~~~~~~~~~~~~~~^
        element, element_attrib, parse_elements=True, profile=profile
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tool_util/parser/xml.py", line 964, in __parse_test_attributes
    raise Exception(
        "Test output defines nothing to check (e.g. must have a 'file' check against, assertions to check, metadata or checksum tests, etc...)"
    )
Exception: Test output defines nothing to check (e.g. must have a 'file' check against, assertions to check, metadata or checksum tests, etc...)

Metadata

Metadata

Assignees

Type

Projects

Status

Triage/Discuss

Milestone

No milestone

Relationships

None yet

Development

No branches or pull requests

Issue actions