Pydantic ValidationError in Chemical To Disease evaluation

[caufieldjh]

Chemical to Disease evaluation as defined in ontogpt/src/ontogpt/evaluation/ctd/eval_ctd.py encounters a pydantic_core._pydantic_core.ValidationError in tests.integration.test_evaluation.test_eval_ctd.TestCTD. I think this is specific to the types used in the evaluation rather than anything defined in the test or text fixtures.
Details:

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ERROR: test_eval (tests.integration.test_evaluation.test_eval_ctd.TestCTD)
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Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_evaluation/test_eval_ctd.py", line 47, in test_eval
    eos = evaluator.eval()
  File "/home/harry/ontogpt/src/ontogpt/evaluation/ctd/eval_ctd.py", line 187, in eval
    docs = list(self.load_test_cases())
  File "/home/harry/ontogpt/src/ontogpt/evaluation/ctd/eval_ctd.py", line 170, in load_cases
    yield ChemicalToDiseaseDocument(publication=pub, triples=triples)
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/pydantic/main.py", line 165, in __init__
    __pydantic_self__.__pydantic_validator__.validate_python(data, self_instance=__pydantic_self__)
pydantic_core._pydantic_core.ValidationError: 2 validation errors for ChemicalToDiseaseDocument
publication
  Input should be a valid dictionary or instance of Publication [type=model_type, input_value=Publication(id=None, titl...xt=None, full_text=None), input_type=Publication]
    For further information visit https://errors.pydantic.dev/2.3/v/model_type
triples.0
  Input should be a valid dictionary or instance of ChemicalToDiseaseRelationship [type=model_type, input_value=Triple(subject='MESH:D015..., object_qualifier=None), input_type=Triple]
    For further information visit https://errors.pydantic.dev/2.3/v/model_type

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ERROR: test_load_test_sets (tests.integration.test_evaluation.test_eval_ctd.TestCTD)
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Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_evaluation/test_eval_ctd.py", line 39, in test_load_test_sets
    docs = list(self.engine.load_test_cases())
  File "/home/harry/ontogpt/src/ontogpt/evaluation/ctd/eval_ctd.py", line 170, in load_cases
    yield ChemicalToDiseaseDocument(publication=pub, triples=triples)
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/pydantic/main.py", line 165, in __init__
    __pydantic_self__.__pydantic_validator__.validate_python(data, self_instance=__pydantic_self__)
pydantic_core._pydantic_core.ValidationError: 2 validation errors for ChemicalToDiseaseDocument
publication
  Input should be a valid dictionary or instance of Publication [type=model_type, input_value=Publication(id=None, titl...xt=None, full_text=None), input_type=Publication]
    For further information visit https://errors.pydantic.dev/2.3/v/model_type
triples.0
  Input should be a valid dictionary or instance of ChemicalToDiseaseRelationship [type=model_type, input_value=Triple(subject='MESH:D015..., object_qualifier=None), input_type=Triple]
    For further information visit https://errors.pydantic.dev/2.3/v/model_type

[caufieldjh]

One thing that makes a difference here, surprisingly, is that nested classes (like in this case, how one of the slots in ChemicalToDiseaseRelationship requires a Publication) need to be imported from the same set of source classes.
Importing Publication from core.py and ChemicalToDiseaseRelationship from ctd.py doesn't work despite the Publication class being identical in both - it won't validate because it isn't the "same" class.