pydantic validation failure

[grg2rsr]

seeing this currently when trying to run the conversion for processed only
@h-mayorquin

(nwb) georg@georg-laptop:~/code/IBL-to-nwb$ /home/georg/.python_envs/nwb/bin/python /home/georg/code/IBL-to-nwb/src/ibl_to_nwb/_scripts/convert_brainwide_map_processed_only.py
/home/georg/.python_envs/nwb/lib/python3.12/site-packages/one/alf/files.py:10: FutureWarning: `one.alf.files` will be removed in version 3.0. Use `one.alf.path` instead.
  warnings.warn(
Traceback (most recent call last):
  File "/home/georg/code/IBL-to-nwb/src/ibl_to_nwb/_scripts/convert_brainwide_map_processed_only.py", line 43, in <module>
    data_interfaces.append(IblSortingInterface(session=session_id, cache_folder=one_cache_folder_path / "sorting"))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/code/neuroconv/src/neuroconv/datainterfaces/ecephys/basesortingextractorinterface.py", line 22, in __init__
    super().__init__(**source_data)
  File "/home/georg/code/neuroconv/src/neuroconv/baseextractorinterface.py", line 34, in __init__
    super().__init__(**source_data)
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/_internal/_validate_call.py", line 38, in wrapper_function
    return wrapper(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/_internal/_validate_call.py", line 111, in __call__
    res = self.__pydantic_validator__.validate_python(pydantic_core.ArgsKwargs(args, kwargs))
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/code/neuroconv/src/neuroconv/basedatainterface.py", line 65, in __init__
    self._validate_source_data(source_data=source_data, verbose=verbose)
  File "/home/georg/code/neuroconv/src/neuroconv/basedatainterface.py", line 55, in _validate_source_data
    source_schema = self.get_source_schema()
                    ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/code/neuroconv/src/neuroconv/basedatainterface.py", line 41, in get_source_schema
    return get_json_schema_from_method_signature(cls, exclude=["source_data"])
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/code/neuroconv/src/neuroconv/utils/json_schema.py", line 167, in get_json_schema_from_method_signature
    temp_json_schema = model.model_json_schema()
                       ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/main.py", line 512, in model_json_schema
    return model_json_schema(
           ^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/json_schema.py", line 2374, in model_json_schema
    return schema_generator_instance.generate(cls.__pydantic_core_schema__, mode=mode)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/json_schema.py", line 397, in generate
    json_schema: JsonSchemaValue = self.generate_inner(schema)
                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/json_schema.py", line 565, in generate_inner
    json_schema = current_handler(schema)
                  ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/_internal/_schema_generation_shared.py", line 38, in __call__
    return self.handler(core_schema)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/json_schema.py", line 540, in new_handler_func
    json_schema = js_modify_function(schema_or_field, current_handler)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/main.py", line 728, in __get_pydantic_json_schema__
    return handler(core_schema)
           ^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/_internal/_schema_generation_shared.py", line 38, in __call__
    return self.handler(core_schema)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/json_schema.py", line 493, in handler_func
    json_schema = generate_for_schema_type(schema_or_field)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/json_schema.py", line 1489, in model_schema
    json_schema = self.generate_inner(schema['schema'])
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/json_schema.py", line 565, in generate_inner
    json_schema = current_handler(schema)
                  ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/_internal/_schema_generation_shared.py", line 38, in __call__
    return self.handler(core_schema)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/json_schema.py", line 493, in handler_func
    json_schema = generate_for_schema_type(schema_or_field)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/json_schema.py", line 1603, in model_fields_schema
    json_schema = self._named_required_fields_schema(named_required_fields)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/json_schema.py", line 1393, in _named_required_fields_schema
    field_json_schema = self.generate_inner(field).copy()
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/json_schema.py", line 565, in generate_inner
    json_schema = current_handler(schema)
                  ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/_internal/_schema_generation_shared.py", line 38, in __call__
    return self.handler(core_schema)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/json_schema.py", line 493, in handler_func
    json_schema = generate_for_schema_type(schema_or_field)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/json_schema.py", line 1461, in model_field_schema
    return self.generate_inner(schema['schema'])
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/json_schema.py", line 565, in generate_inner
    json_schema = current_handler(schema)
                  ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/_internal/_schema_generation_shared.py", line 38, in __call__
    return self.handler(core_schema)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/json_schema.py", line 493, in handler_func
    json_schema = generate_for_schema_type(schema_or_field)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/json_schema.py", line 1117, in default_schema
    json_schema = self.generate_inner(schema['schema'])
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/json_schema.py", line 565, in generate_inner
    json_schema = current_handler(schema)
                  ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/_internal/_schema_generation_shared.py", line 38, in __call__
    return self.handler(core_schema)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/json_schema.py", line 493, in handler_func
    json_schema = generate_for_schema_type(schema_or_field)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/json_schema.py", line 859, in is_instance_schema
    return self.handle_invalid_for_json_schema(schema, f'core_schema.IsInstanceSchema ({schema["cls"]})')
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/georg/.python_envs/nwb/lib/python3.12/site-packages/pydantic/json_schema.py", line 2279, in handle_invalid_for_json_schema
    raise PydanticInvalidForJsonSchema(f'Cannot generate a JsonSchema for {error_info}')
pydantic.errors.PydanticInvalidForJsonSchema: Cannot generate a JsonSchema for core_schema.IsInstanceSchema (<class 'inspect._empty'>)

For further information visit https://errors.pydantic.dev/2.10/u/invalid-for-json-schema

[h-mayorquin]

Hi, @grg2rsr.

I just pushed a fix to your branch here:

https://github.com/catalystneuro/IBL-to-nwb/pull/102/files#r1884077875

So this should be close when we merge #102

Moreover, this is a neuroconv issue that I will address over there but the fixes in #102 should be enough for you to avoid that error.

[h-mayorquin]

I added now a PR in neuroconv:

catalystneuro/neuroconv#1157