pubmed-annotate breaks with AttributeError on some articles.

[caufieldjh]

@AgranyaGitHub reports that a run of pubmed-annotate on disease vs. cellular process relationships in the IBD literature template (ibd_literature and ibd_literature.DiseaseCellularProcessRelationship) encountered this:

  File “/Users/agranyaketha/opt/anaconda3/envs/ontogpt/bin/ontogpt”, line 6, in <module>
    sys.exit(main())
  File “/Users/agranyaketha/opt/anaconda3/envs/ontogpt/lib/python3.10/site-packages/click/core.py”, line 1130, in __call__
    return self.main(*args, **kwargs)
  File “/Users/agranyaketha/opt/anaconda3/envs/ontogpt/lib/python3.10/site-packages/click/core.py”, line 1055, in main
    rv = self.invoke(ctx)
  File “/Users/agranyaketha/opt/anaconda3/envs/ontogpt/lib/python3.10/site-packages/click/core.py”, line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File “/Users/agranyaketha/opt/anaconda3/envs/ontogpt/lib/python3.10/site-packages/click/core.py”, line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File “/Users/agranyaketha/opt/anaconda3/envs/ontogpt/lib/python3.10/site-packages/click/core.py”, line 760, in invoke
    return __callback(*args, **kwargs)
  File “/Users/agranyaketha/Documents/GitHub/ontogpt/src/ontogpt/cli.py”, line 373, in pubmed_annotate
    textlist = pmc.text(pmids[: pubmed_annotate_limit + 1])
  File “/Users/agranyaketha/Documents/GitHub/ontogpt/src/ontogpt/clients/pubmed_client.py”, line 335, in text
    these_docs = self.parse_pmxml(
  File “/Users/agranyaketha/Documents/GitHub/ontogpt/src/ontogpt/clients/pubmed_client.py”, line 468, in parse_pmxml
    pa.find(“PubmedData”).find(“ArticleIdList”).find(“ArticleId”, {“IdType”: “pmc”})
AttributeError: ‘NoneType’ object has no attribute ‘find’

My best guess is that one of the Pubmed results in the search doesn't have an ArticleIdList at all, which is pretty weird, and my guess is that the IDs are stored somewhere else in that entry.

Reproduce with:

ontogpt -vvv pubmed-annotate -t ibd_literature.DiseaseCellularProcessRelationship “inflammatory bowel disease” --limit 2000 -o output.yaml -O yaml