Error when running obo-lexical-review: AttributeError: 'NoneType' object has no attribute 'strip'

[pfabry]

When using the obo-lexical-review function with the following commad:

PS C:\Users\XXX> uv run --with "pyobo[gilda]" pyobo obo-lexical-review VariO --location "C:\localPathtoOntology\VariO_1.09.owl" --skip-upper

I get the following error message:

Inferred URI prefix from given OBO CURIE prefix: http://purl.obolibrary.org/obo/VariO_
given ontology path does not end with JSON. implicitly converting to OBO Graph JSON using ROBOT
reading converted OBO Graph JSON
Loading lexical index from https://github.com/biopragmatics/biolexica/raw/main/lexica/obo/obo.ssslm.tsv.gz using SSSLM
Done loading lexical index
  0%|                                                                                         | 0/1 [00:00<?, ?graph/s]
Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "C:\Users\XXX\.venv\Scripts\pyobo.exe\__main__.py", line 10, in <module>
    sys.exit(main())
             ~~~~^^
  File "C:\Users\XXX\.venv\Lib\site-packages\click\core.py", line 1485, in __call__
    return self.main(*args, **kwargs)
           ~~~~~~~~~^^^^^^^^^^^^^^^^^
  File "C:\Users\XXX\.venv\Lib\site-packages\click\core.py", line 1406, in main
    rv = self.invoke(ctx)
  File "C:\Users\XXX\.venv\Lib\site-packages\click\core.py", line 1873, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
  File "C:\Users\XXX\.venv\Lib\site-packages\click\core.py", line 1269, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\XXX\.venv\Lib\site-packages\click\core.py", line 824, in invoke
    return callback(*args, **kwargs)
  File "C:\Users\XXX\.venv\Lib\site-packages\pyobo\cli\obo_lexical_review.py", line 78, in obo_lexical_review
    passed, failed = _get_calls(
                     ~~~~~~~~~~^
        graph_document=graph_document,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    ...<2 lines>...
        skip_upper=skip_upper,
        ^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "C:\Users\XXX\.venv\Lib\site-packages\pyobo\cli\obo_lexical_review.py", line 187, in _get_calls
    matches.extend(
    ~~~~~~~~~~~~~~^
        match
        ^^^^^
        for synonym in node.meta.synonyms
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        for match in matcher.get_matches(synonym.val)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "C:\Users\XXX\.venv\Lib\site-packages\pyobo\cli\obo_lexical_review.py", line 190, in <genexpr>
    for match in matcher.get_matches(synonym.val)
                 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
  File "C:\Users\XXX\.venv\Lib\site-packages\ssslm\ner.py", line 574, in get_matches
    for scored_match in self._grounder.ground(
                        ~~~~~~~~~~~~~~~~~~~~~^
        text, context=context, organisms=organisms, namespaces=namespaces
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "C:\Users\XXX\.venv\Lib\site-packages\gilda\grounder.py", line 280, in ground
    raw_str = raw_str.strip()
              ^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'strip'

[cthoyt]

obographs is the silliest format, how can a synonym be empty... fix incoming in #492

[cthoyt]

@pfabry new release v0.12.18 has the fix in it