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Extract validators from pydantic models #12
Description
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"
}Metadata
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