fix: use correct model validator signature

[jsstevenson]

We had previously been using an incorrect method signature that was apparently working, but in an undefined way, and pydantic v 2.12 "fixed" (broke, for us) this -- see "after model validators" https://pydantic.dev/articles/pydantic-v2-12-release)

[theferrit32]

Confirmed tests/validation/test_models.py::test_mappable_concept succeeds with these versions:

pydantic==2.11.9
pydantic-core==2.33.2

And fails with these:

pydantic==2.12.0
pydantic-core==2.41.1

Error:

FAILED tests/validation/test_models.py::test_mappable_concept - AttributeError: 'pydantic_core._pydantic_core.ValidationInfo' object has no attribute 'primaryCoding'

I am a little confused at how it's working with pydantic 2.11 because looking at the docs, 2.11 and 2.12 have the same signature for model after validators.

https://docs.pydantic.dev/2.11/concepts/validators/#model-validators

class UserModel(BaseModel):
    username: str
    password: str
    password_repeat: str

    @model_validator(mode='after')
    def check_passwords_match(self) -> Self:
        if self.password != self.password_repeat:
            raise ValueError('Passwords do not match')
        return self

https://docs.pydantic.dev/2.11/api/functional_validators/#pydantic.functional_validators.ModelAfterValidator

ModelAfterValidator = Callable[
    [_ModelType, ValidationInfo], _ModelType
]

https://docs.pydantic.dev/2.12/concepts/validators/#model-validators

class UserModel(BaseModel):
    username: str
    password: str
    password_repeat: str

    @model_validator(mode='after')
    def check_passwords_match(self) -> Self:
        if self.password != self.password_repeat:
            raise ValueError('Passwords do not match')
        return self

https://docs.pydantic.dev/2.12/api/functional_validators/#pydantic.functional_validators.ModelAfterValidator

ModelAfterValidator = Callable[
    [_ModelType, ValidationInfo[Any]], _ModelType
]

[jsstevenson]

@theferrit32 what intrigues me is that the changelog makes it seem as though v2.12 will now raise some kind of validation error, and that's not what's happening to us -- rather, we're just getting some unexpected values and then the failure happens within the validator function

[theferrit32]

@jsstevenson If I add this assert at the bottom in your branch using pydantic 2.12

def test_mappable_concept():
    """Test the MappableConcept model validator"""
    # Does not provide required fields
    with pytest.raises(
        ValueError, match="One of `name` or `primaryCoding` must be provided."
    ):
        core_models.MappableConcept(conceptType="test")

    # Valid models
    assert core_models.MappableConcept(name="Primary Label")
    assert core_models.MappableConcept(
        primaryCoding=core_models.Coding(
            code="HGNC:1097",
            system="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/",
        )
    )
    assert core_models.MappableConcept(
        primaryCoding=core_models.Coding(
            # code="HGNC:1097",
            system="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/",
        )
    )

I get

FAILED tests/validation/test_models.py::test_mappable_concept - pydantic_core._pydantic_core.ValidationError: 1 validation error for Coding

Which I think is right?

[theferrit32]

This fix-validator-signature branch also works for

pydantic==2.11.9
pydantic-core==2.33.2

So I guess we don't need to constrain pyproject.toml to pydantic>=2.12