Extract validators from pydantic models

[kdp-cloud]

Currently, there is no way to export field validators from pydantic to JSON schema.

E.g.: For assays there are two validators

• filename => Must start with 'a_'
• comments => At least one comment must be a valid target repository

class Assay(CommentedIsaBase):
    id: Optional[str] = Field(alias="@id", default=None)
    characteristicCategories: List[MaterialAttribute] = []
    dataFiles: List[Data] = []
    filename: Optional[str] = None
    materials: Optional[AssayMaterialType] = None
    measurementType: Optional[OntologyAnnotation] = None
    processSequence: List[Process] = []
    technologyPlatform: Optional[str] = None
    technologyType: Optional[OntologyAnnotation] = None
    unitCategories: List[OntologyAnnotation] = []

    @field_validator("filename")
    def validate_filename(cls, v: str) -> Union[str, None]:
        if v is None:
            return v
        elif re.match(r"^a_", v):
            return v
        else:
            raise ValueError("'filename' should start with 'a_'")

    @field_validator("comments")
    def detect_target_repo_comments(cls, v: List[Comment]) -> Optional[List[Comment]]:
        target_repo_comments = [
            comment for comment in v if comment.name == TARGET_REPO_KEY
        ]
        if len(target_repo_comments) == 0:
            raise ValueError(f"'{TARGET_REPO_KEY}' comment is missing")
        elif len(target_repo_comments) > 1:
            raise ValueError(f"Multiple '{TARGET_REPO_KEY}' comments found")
        else:
            if target_repo_comments[0].value in [
                item.value for item in TargetRepository
            ]:
                return v
            else:
                raise ValueError(
                    f"Invalid '{TARGET_REPO_KEY}' value: '{target_repo_comments[0].value}'"
                )

Pydantic is not able to export these contstraints to json schema:

{
  "additionalProperties": false,
  "properties": {
    "comments": {
      "default": [],
      "items": {
        "$ref": "#/$defs/Comment"
      },
      "title": "Comments",
      "type": "array"
    },
    "@id": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "@Id"
    },
    "characteristicCategories": {
      "default": [],
      "items": {
        "$ref": "#/$defs/MaterialAttribute"
      },
      "title": "Characteristiccategories",
      "type": "array"
    },
    "dataFiles": {
      "default": [],
      "items": {
        "$ref": "#/$defs/Data"
      },
      "title": "Datafiles",
      "type": "array"
    },
    "filename": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Filename"
    },
    "materials": {
      "anyOf": [
        {
          "$ref": "#/$defs/AssayMaterialType"
        },
        {
          "type": "null"
        }
      ],
      "default": null
    },
    "measurementType": {
      "anyOf": [
        {
          "$ref": "#/$defs/OntologyAnnotation"
        },
        {
          "type": "null"
        }
      ],
      "default": null
    },
    "processSequence": {
      "default": [],
      "items": {
        "$ref": "#/$defs/Process"
      },
      "title": "Processsequence",
      "type": "array"
    },
    "technologyPlatform": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "title": "Technologyplatform"
    },
    "technologyType": {
      "anyOf": [
        {
          "$ref": "#/$defs/OntologyAnnotation"
        },
        {
          "type": "null"
        }
      ],
      "default": null
    },
    "unitCategories": {
      "default": [],
      "items": {
        "$ref": "#/$defs/OntologyAnnotation"
      },
      "title": "Unitcategories",
      "type": "array"
    }
  },
  "title": "Assay",
  "type": "object"
}