IndexError with `matches` command

[caufieldjh]

After setting up a new database:

$ poetry run curategpt ontology index -c biolink sqlite:obo:biolink

Running the matches command encounters an IndexError:

$ poetry run curategpt matches "model" -c biolink
/home/harry/.cache/pypoetry/virtualenvs/curategpt-BZXOC9UX-py3.12/lib/python3.12/site-packages/eutils/__init__.py:4: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  import pkg_resources
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/harry/.cache/pypoetry/virtualenvs/curategpt-BZXOC9UX-py3.12/lib/python3.12/site-packages/click/core.py", line 1442, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/harry/.cache/pypoetry/virtualenvs/curategpt-BZXOC9UX-py3.12/lib/python3.12/site-packages/click/core.py", line 1363, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/home/harry/.cache/pypoetry/virtualenvs/curategpt-BZXOC9UX-py3.12/lib/python3.12/site-packages/click/core.py", line 1830, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/harry/.cache/pypoetry/virtualenvs/curategpt-BZXOC9UX-py3.12/lib/python3.12/site-packages/click/core.py", line 1226, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/harry/.cache/pypoetry/virtualenvs/curategpt-BZXOC9UX-py3.12/lib/python3.12/site-packages/click/core.py", line 794, in invoke
    return callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/harry/curategpt/src/curategpt/cli.py", line 541, in matches
    obj = db.lookup(id, collection=collection)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/harry/curategpt/src/curategpt/store/chromadb_adapter.py", line 663, in lookup
    return self._unjson(results["metadatas"][0])
                        ~~~~~~~~~~~~~~~~~~~~^^^
IndexError: list index out of range

[caufieldjh]

A related issue, and potentially one deserving of its own ticket: the Match command in the app differs from the matches command in the CLI.
The former is invoked with

mapper = MappingAgent(knowledge_source=db, extractor=extractor)

then called as

        results = mapper.match(
            search_query,
            collection=collection,
            fields=relevant_fields,
            limit=limit,
        )

Whereas the CLI command matches uses the DBAdapter matches function directly.