======================================================================
ERROR: test_fine_tuned (tests.integration.test_clients.test_openai_client.TestCompletion)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_clients/test_openai_client.py", line 221, in test_fine_tuned
    ann = client.complete(TUNED_TEST_PROMPT)
  File "/home/harry/ontogpt/src/ontogpt/clients/openai_client.py", line 74, in complete
    raise e
  File "/home/harry/ontogpt/src/ontogpt/clients/openai_client.py", line 53, in complete
    response = openai.ChatCompletion.create(
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/openai/api_resources/chat_completion.py", line 25, in create
    return super().create(*args, **kwargs)
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/openai/api_resources/abstract/engine_api_resource.py", line 153, in create
    response, _, api_key = requestor.request(
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/openai/api_requestor.py", line 298, in request
    resp, got_stream = self._interpret_response(result, stream)
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/openai/api_requestor.py", line 700, in _interpret_response
    self._interpret_response_line(
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/openai/api_requestor.py", line 765, in _interpret_response_line
    raise self.handle_error_response(
openai.error.InvalidRequestError: This is not a chat model and thus not supported in the v1/chat/completions endpoint. Did you mean to use v1/completions?

======================================================================
ERROR: test_eval (tests.integration.test_evaluation.test_eval_ctd.TestCTD)
----------------------------------------------------------------------
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

======================================================================
ERROR: test_load_test_sets (tests.integration.test_evaluation.test_eval_ctd.TestCTD)
----------------------------------------------------------------------
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

======================================================================
ERROR: tests.integration.test_evaluation.test_eval_drugmechdb (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: tests.integration.test_evaluation.test_eval_drugmechdb
Traceback (most recent call last):
  File "/usr/lib/python3.9/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
  File "/usr/lib/python3.9/unittest/loader.py", line 377, in _get_module_from_name
    __import__(name)
  File "/home/harry/ontogpt/tests/integration/test_evaluation/test_eval_drugmechdb.py", line 7, in <module>
    from ontogpt.evaluation.drugmechdb.datamodel.drugmechdb import Graph, Mechanism
  File "/home/harry/ontogpt/src/ontogpt/evaluation/drugmechdb/datamodel/drugmechdb.py", line 18, in <module>
    class ConfiguredBaseModel(
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/pydantic/_internal/_model_construction.py", line 123, in __new__
    cls: type[BaseModel] = super().__new__(mcs, cls_name, bases, namespace, **kwargs)  # type: ignore
  File "/usr/lib/python3.9/abc.py", line 106, in __new__
    cls = super().__new__(mcls, name, bases, namespace, **kwargs)
TypeError: ConfiguredBaseModel.__init_subclass__() takes no keyword arguments


======================================================================
ERROR: test_closure (tests.integration.test_evaluation.test_eval_enrichment.TestEvalEnrichment)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_evaluation/test_eval_enrichment.py", line 356, in setUp
    self.evaluator = EvalEnrichment()
  File "<string>", line 7, in __init__
  File "/home/harry/ontogpt/src/ontogpt/evaluation/enrichment/eval_enrichment.py", line 100, in __post_init__
    model = modelname["names"][0]
TypeError: string indices must be integers

======================================================================
ERROR: test_full (tests.integration.test_evaluation.test_eval_enrichment.TestEvalEnrichment)
Tests complete all by all comparisons.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_evaluation/test_eval_enrichment.py", line 356, in setUp
    self.evaluator = EvalEnrichment()
  File "<string>", line 7, in __init__
  File "/home/harry/ontogpt/src/ontogpt/evaluation/enrichment/eval_enrichment.py", line 100, in __post_init__
    model = modelname["names"][0]
TypeError: string indices must be integers

======================================================================
ERROR: test_full_mini (tests.integration.test_evaluation.test_eval_enrichment.TestEvalEnrichment)
Tests complete all by all comparisons.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_evaluation/test_eval_enrichment.py", line 356, in setUp
    self.evaluator = EvalEnrichment()
  File "<string>", line 7, in __init__
  File "/home/harry/ontogpt/src/ontogpt/evaluation/enrichment/eval_enrichment.py", line 100, in __post_init__
    model = modelname["names"][0]
TypeError: string indices must be integers

======================================================================
ERROR: test_full_v2 (tests.integration.test_evaluation.test_eval_enrichment.TestEvalEnrichment)
Tests complete all by all comparisons.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_evaluation/test_eval_enrichment.py", line 356, in setUp
    self.evaluator = EvalEnrichment()
  File "<string>", line 7, in __init__
  File "/home/harry/ontogpt/src/ontogpt/evaluation/enrichment/eval_enrichment.py", line 100, in __post_init__
    model = modelname["names"][0]
TypeError: string indices must be integers

======================================================================
ERROR: test_load (tests.integration.test_evaluation.test_eval_enrichment.TestEvalEnrichment)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_evaluation/test_eval_enrichment.py", line 356, in setUp
    self.evaluator = EvalEnrichment()
  File "<string>", line 7, in __init__
  File "/home/harry/ontogpt/src/ontogpt/evaluation/enrichment/eval_enrichment.py", line 100, in __post_init__
    model = modelname["names"][0]
TypeError: string indices must be integers

======================================================================
ERROR: test_null_enrichment (tests.integration.test_evaluation.test_eval_enrichment.TestEvalEnrichment)
Tests null enrichment terms.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_evaluation/test_eval_enrichment.py", line 356, in setUp
    self.evaluator = EvalEnrichment()
  File "<string>", line 7, in __init__
  File "/home/harry/ontogpt/src/ontogpt/evaluation/enrichment/eval_enrichment.py", line 100, in __post_init__
    model = modelname["names"][0]
TypeError: string indices must be integers

======================================================================
ERROR: test_pairwise (tests.integration.test_evaluation.test_eval_enrichment.TestEvalEnrichment)
Tests template and module is loaded.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_evaluation/test_eval_enrichment.py", line 356, in setUp
    self.evaluator = EvalEnrichment()
  File "<string>", line 7, in __init__
  File "/home/harry/ontogpt/src/ontogpt/evaluation/enrichment/eval_enrichment.py", line 100, in __post_init__
    model = modelname["names"][0]
TypeError: string indices must be integers

======================================================================
ERROR: test_random_enrichment (tests.integration.test_evaluation.test_eval_enrichment.TestEvalEnrichment)
Tests random terms.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_evaluation/test_eval_enrichment.py", line 356, in setUp
    self.evaluator = EvalEnrichment()
  File "<string>", line 7, in __init__
  File "/home/harry/ontogpt/src/ontogpt/evaluation/enrichment/eval_enrichment.py", line 100, in __post_init__
    model = modelname["names"][0]
TypeError: string indices must be integers

======================================================================
ERROR: test_random_gene_id (tests.integration.test_evaluation.test_eval_enrichment.TestEvalEnrichment)
Tests random gene id.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_evaluation/test_eval_enrichment.py", line 356, in setUp
    self.evaluator = EvalEnrichment()
  File "<string>", line 7, in __init__
  File "/home/harry/ontogpt/src/ontogpt/evaluation/enrichment/eval_enrichment.py", line 100, in __post_init__
    model = modelname["names"][0]
TypeError: string indices must be integers

======================================================================
ERROR: test_standard_enrichment (tests.integration.test_evaluation.test_eval_enrichment.TestEvalEnrichment)
Tests normal OAK enrichment.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_evaluation/test_eval_enrichment.py", line 356, in setUp
    self.evaluator = EvalEnrichment()
  File "<string>", line 7, in __init__
  File "/home/harry/ontogpt/src/ontogpt/evaluation/enrichment/eval_enrichment.py", line 100, in __post_init__
    model = modelname["names"][0]
TypeError: string indices must be integers

======================================================================
ERROR: test_standard_enrichment_no_ontology (tests.integration.test_evaluation.test_eval_enrichment.TestEvalEnrichment)
Tests normal OAK enrichment.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_evaluation/test_eval_enrichment.py", line 356, in setUp
    self.evaluator = EvalEnrichment()
  File "<string>", line 7, in __init__
  File "/home/harry/ontogpt/src/ontogpt/evaluation/enrichment/eval_enrichment.py", line 100, in __post_init__
    model = modelname["names"][0]
TypeError: string indices must be integers

======================================================================
ERROR: test_write_gene_sets (tests.integration.test_evaluation.test_eval_enrichment.TestEvalEnrichment)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_evaluation/test_eval_enrichment.py", line 356, in setUp
    self.evaluator = EvalEnrichment()
  File "<string>", line 7, in __init__
  File "/home/harry/ontogpt/src/ontogpt/evaluation/enrichment/eval_enrichment.py", line 100, in __post_init__
    model = modelname["names"][0]
TypeError: string indices must be integers

======================================================================
ERROR: test_create_test_and_training (tests.integration.test_evaluation.test_eval_go.TestEvalGO)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_evaluation/test_eval_go.py", line 31, in test_create_test_and_training
    eos = engine.create_test_and_training()
  File "/home/harry/ontogpt/src/ontogpt/evaluation/go/eval_go.py", line 114, in create_test_and_training
    all_test_ids = set(self.valid_test_ids())
  File "/home/harry/ontogpt/src/ontogpt/evaluation/go/eval_go.py", line 85, in valid_test_ids
    with open(TEST_CASES_DIR / "go-ids-2022.txt") as f:
FileNotFoundError: [Errno 2] No such file or directory: '/home/harry/ontogpt/src/ontogpt/evaluation/go/test_cases/go-ids-2022.txt'

======================================================================
ERROR: test_eval_predictions (tests.integration.test_evaluation.test_eval_go.TestEvalGO)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_evaluation/test_eval_go.py", line 41, in test_eval_predictions
    eos = engine.eval()
  File "/home/harry/ontogpt/src/ontogpt/evaluation/go/eval_go.py", line 144, in eval
    eos = self.create_test_and_training()
  File "/home/harry/ontogpt/src/ontogpt/evaluation/go/eval_go.py", line 114, in create_test_and_training
    all_test_ids = set(self.valid_test_ids())
  File "/home/harry/ontogpt/src/ontogpt/evaluation/go/eval_go.py", line 85, in valid_test_ids
    with open(TEST_CASES_DIR / "go-ids-2022.txt") as f:
FileNotFoundError: [Errno 2] No such file or directory: '/home/harry/ontogpt/src/ontogpt/evaluation/go/test_cases/go-ids-2022.txt'

======================================================================
ERROR: test_cases (tests.integration.test_knowledge_engines.test_cases.TestCases)
Tests end to end knowledge extraction.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_knowledge_engines/test_cases.py", line 51, in test_cases
    ann = ke.extract_from_file(input_file)
  File "/home/harry/ontogpt/src/ontogpt/engines/knowledge_engine.py", line 190, in extract_from_file
    with file.open() as f:
  File "/usr/lib/python3.9/pathlib.py", line 1252, in open
    return io.open(self, mode, buffering, encoding, errors, newline,
  File "/usr/lib/python3.9/pathlib.py", line 1120, in _opener
    return self._accessor.open(self, flags, mode)
FileNotFoundError: [Errno 2] No such file or directory: '/home/harry/ontogpt/tests/input/cases/recipe-palak-paneer.txt'

======================================================================
ERROR: test_cases (tests.integration.test_knowledge_engines.test_generalizations.TestGeneralize)
Tests generalization over all cases.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1965, in _exec_single_context
    self.dialect.do_execute(
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/sqlalchemy/engine/default.py", line 921, in do_execute
    cursor.execute(statement, parameters)
sqlite3.DatabaseError: database disk image is malformed

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_knowledge_engines/test_generalizations.py", line 80, in test_cases
    nu_obj = ke.generalize(test_obj, examples)
  File "/home/harry/ontogpt/src/ontogpt/engines/spires_engine.py", line 236, in generalize
    prompt += f"{self.serialize_object(example)}\n\n"
  File "/home/harry/ontogpt/src/ontogpt/engines/spires_engine.py", line 340, in serialize_object
    v_serialized = self._serialize_value(v, slot)
  File "/home/harry/ontogpt/src/ontogpt/engines/spires_engine.py", line 348, in _serialize_value
    return "; ".join([self._serialize_value(v, slot) for v in val if v])
  File "/home/harry/ontogpt/src/ontogpt/engines/spires_engine.py", line 348, in <listcomp>
    return "; ".join([self._serialize_value(v, slot) for v in val if v])
  File "/home/harry/ontogpt/src/ontogpt/engines/spires_engine.py", line 350, in _serialize_value
    return " - ".join([self._serialize_value(v, slot) for v in val.values() if v])
  File "/home/harry/ontogpt/src/ontogpt/engines/spires_engine.py", line 350, in <listcomp>
    return " - ".join([self._serialize_value(v, slot) for v in val.values() if v])
  File "/home/harry/ontogpt/src/ontogpt/engines/spires_engine.py", line 360, in _serialize_value
    label = labeler.label(val)
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/oaklib/implementations/sqldb/sql_implementation.py", line 473, in label
    for (lbl,) in q:
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/sqlalchemy/orm/query.py", line 2828, in __iter__
    result = self._iter()
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/sqlalchemy/orm/query.py", line 2842, in _iter
    result: Union[ScalarResult[_T], Result[_T]] = self.session.execute(
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/sqlalchemy/orm/session.py", line 2262, in execute
    return self._execute_internal(
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/sqlalchemy/orm/session.py", line 2144, in _execute_internal
    result: Result[Any] = compile_state_cls.orm_execute_statement(
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/sqlalchemy/orm/context.py", line 293, in orm_execute_statement
    result = conn.execute(
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1412, in execute
    return meth(
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/sqlalchemy/sql/elements.py", line 515, in _execute_on_connection
    return connection._execute_clauseelement(
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1635, in _execute_clauseelement
    ret = self._execute_context(
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1844, in _execute_context
    return self._exec_single_context(
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1984, in _exec_single_context
    self._handle_dbapi_exception(
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 2339, in _handle_dbapi_exception
    raise sqlalchemy_exception.with_traceback(exc_info[2]) from e
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1965, in _exec_single_context
    self.dialect.do_execute(
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/sqlalchemy/engine/default.py", line 921, in do_execute
    cursor.execute(statement, parameters)
sqlalchemy.exc.DatabaseError: (sqlite3.DatabaseError) database disk image is malformed
[SQL: SELECT rdfs_label_statement.value AS rdfs_label_statement_value 
FROM rdfs_label_statement 
WHERE rdfs_label_statement.subject = ?]
[parameters: ('PR:P00519',)]
(Background on this error at: https://sqlalche.me/e/20/4xp6)

======================================================================
ERROR: test_hallucinate (tests.integration.test_knowledge_engines.test_halo_engine.TestHALO)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_knowledge_engines/test_halo_engine.py", line 64, in test_hallucinate
    elts = ke.hallucinate(["Axon", "Dendrite"], num_iterations=4)
  File "/home/harry/ontogpt/src/ontogpt/engines/halo_engine.py", line 118, in hallucinate
    if seed_elements:
  File "/home/harry/ontogpt/src/ontogpt/engines/halo_engine.py", line 227, in hallucinate_element
    prompt = self.generate_prompt(element, example_elements[0:10])
  File "/home/harry/ontogpt/src/ontogpt/clients/openai_client.py", line 74, in complete
    raise e
  File "/home/harry/ontogpt/src/ontogpt/clients/openai_client.py", line 53, in complete
    response = openai.ChatCompletion.create(
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/openai/api_resources/chat_completion.py", line 25, in create
    return super().create(*args, **kwargs)
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/openai/api_resources/abstract/engine_api_resource.py", line 153, in create
    response, _, api_key = requestor.request(
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/openai/api_requestor.py", line 298, in request
    resp, got_stream = self._interpret_response(result, stream)
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/openai/api_requestor.py", line 700, in _interpret_response
    self._interpret_response_line(
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/openai/api_requestor.py", line 765, in _interpret_response_line
    raise self.handle_error_response(
openai.error.InvalidRequestError: This model's maximum context length is 4097 tokens. However, you requested 4391 tokens (1391 in the messages, 3000 in the completion). Please reduce the length of the messages or completion.

======================================================================
ERROR: test_hallucinate_element (tests.integration.test_knowledge_engines.test_halo_engine.TestHALO)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_knowledge_engines/test_halo_engine.py", line 49, in test_hallucinate_element
    elt = ke.hallucinate_element(name)
  File "/home/harry/ontogpt/src/ontogpt/engines/halo_engine.py", line 227, in hallucinate_element
    prompt = self.generate_prompt(element, example_elements[0:10])
  File "/home/harry/ontogpt/src/ontogpt/clients/openai_client.py", line 74, in complete
    raise e
  File "/home/harry/ontogpt/src/ontogpt/clients/openai_client.py", line 53, in complete
    response = openai.ChatCompletion.create(
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/openai/api_resources/chat_completion.py", line 25, in create
    return super().create(*args, **kwargs)
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/openai/api_resources/abstract/engine_api_resource.py", line 153, in create
    response, _, api_key = requestor.request(
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/openai/api_requestor.py", line 298, in request
    resp, got_stream = self._interpret_response(result, stream)
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/openai/api_requestor.py", line 700, in _interpret_response
    self._interpret_response_line(
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/openai/api_requestor.py", line 765, in _interpret_response_line
    raise self.handle_error_response(
openai.error.InvalidRequestError: This model's maximum context length is 4097 tokens. However, you requested 4391 tokens (1391 in the messages, 3000 in the completion). Please reduce the length of the messages or completion.

======================================================================
ERROR: test_hallucinate_metabolism (tests.integration.test_knowledge_engines.test_halo_engine.TestHALO)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_knowledge_engines/test_halo_engine.py", line 80, in test_hallucinate_metabolism
    elts = ke.hallucinate(
  File "/home/harry/ontogpt/src/ontogpt/engines/halo_engine.py", line 118, in hallucinate
    if seed_elements:
  File "/home/harry/ontogpt/src/ontogpt/engines/halo_engine.py", line 227, in hallucinate_element
    prompt = self.generate_prompt(element, example_elements[0:10])
  File "/home/harry/ontogpt/src/ontogpt/clients/openai_client.py", line 74, in complete
    raise e
  File "/home/harry/ontogpt/src/ontogpt/clients/openai_client.py", line 53, in complete
    response = openai.ChatCompletion.create(
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/openai/api_resources/chat_completion.py", line 25, in create
    return super().create(*args, **kwargs)
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/openai/api_resources/abstract/engine_api_resource.py", line 153, in create
    response, _, api_key = requestor.request(
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/openai/api_requestor.py", line 298, in request
    resp, got_stream = self._interpret_response(result, stream)
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/openai/api_requestor.py", line 700, in _interpret_response
    self._interpret_response_line(
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/openai/api_requestor.py", line 765, in _interpret_response_line
    raise self.handle_error_response(
openai.error.InvalidRequestError: This model's maximum context length is 4097 tokens. However, you requested 4631 tokens (1631 in the messages, 3000 in the completion). Please reduce the length of the messages or completion.

======================================================================
ERROR: test_different_from (tests.integration.test_knowledge_engines.test_mapping.TestMapping)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_knowledge_engines/test_mapping.py", line 108, in test_different_from
    meval = mapper.categorize_mapping(subject, object)
  File "/home/harry/ontogpt/src/ontogpt/engines/mapping_engine.py", line 123, in categorize_mapping
    with open(template_path) as file:
FileNotFoundError: [Errno 2] No such file or directory: ''

======================================================================
ERROR: test_from_sssom (tests.integration.test_knowledge_engines.test_mapping.TestMapping)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_knowledge_engines/test_mapping.py", line 66, in test_from_sssom
    tc = mapper.from_sssom(
  File "/home/harry/ontogpt/src/ontogpt/engines/mapping_engine.py", line 238, in from_sssom
    msdf = parse_sssom_table(path)
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/sssom/parsers.py", line 290, in parse_sssom_table
    msdf = from_sssom_dataframe(df, prefix_map=meta_all.prefix_map, meta=meta_all.metadata)
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/sssom/parsers.py", line 471, in from_sssom_dataframe
    prefix_map = _ensure_prefix_map(prefix_map)
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/sssom/parsers.py", line 817, in _ensure_prefix_map
    return add_built_in_prefixes_to_prefix_map(prefix_map)
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/sssom/context.py", line 86, in add_built_in_prefixes_to_prefix_map
    raise ValueError(
ValueError: Built-in prefix semapv is specified (https://w3id.org/semapv/) but differs from default (https://w3id.org/semapv/vocab/)

======================================================================
ERROR: test_from_sssom2 (tests.integration.test_knowledge_engines.test_mapping.TestMapping)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_knowledge_engines/test_mapping.py", line 80, in test_from_sssom2
    msdf = parse_sssom_table(INPUT_DIR / "mondo-exact-ncit.sssom.tsv")
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/sssom/parsers.py", line 290, in parse_sssom_table
    msdf = from_sssom_dataframe(df, prefix_map=meta_all.prefix_map, meta=meta_all.metadata)
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/sssom/parsers.py", line 471, in from_sssom_dataframe
    prefix_map = _ensure_prefix_map(prefix_map)
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/sssom/parsers.py", line 817, in _ensure_prefix_map
    return add_built_in_prefixes_to_prefix_map(prefix_map)
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/sssom/context.py", line 86, in add_built_in_prefixes_to_prefix_map
    raise ValueError(
ValueError: Built-in prefix semapv is specified (https://w3id.org/semapv/) but differs from default (https://w3id.org/semapv/vocab/)

======================================================================
ERROR: test_generate (tests.integration.test_knowledge_engines.test_mapping.TestMapping)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_knowledge_engines/test_mapping.py", line 56, in test_generate
    results = list(mapper.run_tasks(tc))
  File "/home/harry/ontogpt/src/ontogpt/engines/mapping_engine.py", line 200, in run_tasks
    cm = self.categorize_mapping(task.subject, task.object)
  File "/home/harry/ontogpt/src/ontogpt/engines/mapping_engine.py", line 123, in categorize_mapping
    with open(template_path) as file:
FileNotFoundError: [Errno 2] No such file or directory: ''

======================================================================
ERROR: test_mapping_eval (tests.integration.test_knowledge_engines.test_mapping.TestMapping)
Test evaluation of mapping on uberon.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_knowledge_engines/test_mapping.py", line 96, in test_mapping_eval
    for meval in mapper.categorize_mappings(subjects, object_sources=["ZFA"]):
  File "/home/harry/ontogpt/src/ontogpt/engines/mapping_engine.py", line 188, in categorize_mappings
    yield self.categorize_mapping(mapping.subject_id, mapping.object_id)
  File "/home/harry/ontogpt/src/ontogpt/engines/mapping_engine.py", line 123, in categorize_mapping
    with open(template_path) as file:
FileNotFoundError: [Errno 2] No such file or directory: ''

======================================================================
ERROR: test_species_identical (tests.integration.test_knowledge_engines.test_mapping.TestMapping)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_knowledge_engines/test_mapping.py", line 144, in test_species_identical
    meval = mapper.categorize_mapping(subject, object)
  File "/home/harry/ontogpt/src/ontogpt/engines/mapping_engine.py", line 123, in categorize_mapping
    with open(template_path) as file:
FileNotFoundError: [Errno 2] No such file or directory: ''

======================================================================
ERROR: test_very_different_from (tests.integration.test_knowledge_engines.test_mapping.TestMapping)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_knowledge_engines/test_mapping.py", line 120, in test_very_different_from
    meval = mapper.categorize_mapping(subject, object)
  File "/home/harry/ontogpt/src/ontogpt/engines/mapping_engine.py", line 123, in categorize_mapping
    with open(template_path) as file:
FileNotFoundError: [Errno 2] No such file or directory: ''

======================================================================
ERROR: test_very_different_from2 (tests.integration.test_knowledge_engines.test_mapping.TestMapping)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_knowledge_engines/test_mapping.py", line 132, in test_very_different_from2
    meval = mapper.categorize_mapping(subject, object)
  File "/home/harry/ontogpt/src/ontogpt/engines/mapping_engine.py", line 123, in categorize_mapping
    with open(template_path) as file:
FileNotFoundError: [Errno 2] No such file or directory: ''

======================================================================
ERROR: test_reason (tests.integration.test_knowledge_engines.test_reasoning.TestReasoning)
Test basic reasoning, no explanations.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_knowledge_engines/test_reasoning.py", line 146, in test_reason
    for task in self.tasks():
  File "/home/harry/ontogpt/tests/integration/test_knowledge_engines/test_reasoning.py", line 133, in tasks
    yield extractor.extract_incoherent_ontology_task(
  File "/home/harry/ontogpt/src/ontogpt/ontex/extractor.py", line 1538, in extract_incoherent_ontology_task
    raise ValueError("Must specify incoherents, siblings, and disjoints")
ValueError: Must specify incoherents, siblings, and disjoints

======================================================================
ERROR: test_reason_with_chain_of_thought (tests.integration.test_knowledge_engines.test_reasoning.TestReasoning)
Test reasoning with explicit chain-of-thought trigger.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_knowledge_engines/test_reasoning.py", line 178, in test_reason_with_chain_of_thought
    for task in self.tasks():
  File "/home/harry/ontogpt/tests/integration/test_knowledge_engines/test_reasoning.py", line 133, in tasks
    yield extractor.extract_incoherent_ontology_task(
  File "/home/harry/ontogpt/src/ontogpt/ontex/extractor.py", line 1538, in extract_incoherent_ontology_task
    raise ValueError("Must specify incoherents, siblings, and disjoints")
ValueError: Must specify incoherents, siblings, and disjoints

======================================================================
ERROR: test_reason_with_explanations (tests.integration.test_knowledge_engines.test_reasoning.TestReasoning)
Test reasoning with explanations included.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/integration/test_knowledge_engines/test_reasoning.py", line 162, in test_reason_with_explanations
    for task in self.tasks():
  File "/home/harry/ontogpt/tests/integration/test_knowledge_engines/test_reasoning.py", line 133, in tasks
    yield extractor.extract_incoherent_ontology_task(
  File "/home/harry/ontogpt/src/ontogpt/ontex/extractor.py", line 1538, in extract_incoherent_ontology_task
    raise ValueError("Must specify incoherents, siblings, and disjoints")
ValueError: Must specify incoherents, siblings, and disjoints

======================================================================
ERROR: tests.integration.test_knowledge_engines.test_spires_engine (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: tests.integration.test_knowledge_engines.test_spires_engine
Traceback (most recent call last):
  File "/usr/lib/python3.9/unittest/loader.py", line 436, in _find_test_path
    module = self._get_module_from_name(name)
  File "/usr/lib/python3.9/unittest/loader.py", line 377, in _get_module_from_name
    __import__(name)
  File "/home/harry/ontogpt/tests/integration/test_knowledge_engines/test_spires_engine.py", line 93, in <module>
    TEST_PROCESS = BiologicalProcess(
  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: 1 validation error for BiologicalProcess
id
  Field required [type=missing, input_value={'label': 'autophagosome ...utputs': ['GO:0005776']}, input_type=dict]
    For further information visit https://errors.pydantic.dev/2.3/v/missing