Clean up Pydantic v2 Migration warnings

[rdeaton-freenome]

There's quite a few warnings generated by Pydantic v2 generated models that could be cleaned up to make a lot less noise in downstream project users.

Some examples:

datamodel_code_generator/parser/jsonschema.py:1663: PydanticDeprecatedSince20: The `parse_obj` method is deprecated; use `model_validate` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.5/migration/
    root_obj = JsonSchemaObject.parse_obj(raw)

datamodel_code_generator/parser/jsonschema.py:299: PydanticDeprecatedSince20: The `__fields_set__` attribute is deprecated, use `model_fields_set` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.5/migration/
    return 'default' in self.__fields_set__ or 'default_factory' in self.extras

[koxudaxi]

@rdeaton-freenome Thank you for creating the issue. I agree with you!!