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monarch-initiative / ontogpt

LLM-based ontological extraction tools, including SPIRES
https://monarch-initiative.github.io/ontogpt/
BSD 3-Clause "New" or "Revised" License
548 stars 68 forks source link

pubmed-extract no longer works? #396

Closed cmungall closed 3 weeks ago

cmungall commented 3 weeks ago 
 ontogpt -vv pubmed-extract -t storms PMID:35173707 -m gpt-4o --get-pmc
...
  File "/Users/cjm/Library/Caches/pypoetry/virtualenvs/ontogpt-KHJsTWkT-py3.10/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Users/cjm/Library/Caches/pypoetry/virtualenvs/ontogpt-KHJsTWkT-py3.10/lib/python3.10/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/Users/cjm/repos/ontogpt/src/ontogpt/cli.py", line 546, in pubmed_extract
    write_extraction(results, output, output_format, template)
TypeError: write_extraction() missing 1 required positional argument: 'template'

looks like function signatures no longer match