Adjust models to spec

.pre-commit-config.yaml

@@ -35,9 +35,10 @@ repos:
         additional_dependencies:
           - "backoff>=2.2.1,<3"
           - "click>=8.1.7,<9"
+          - "jinja2>=3.1.2,<4"
           - "pandas-stubs>=2.1.1,<3"
           - "pydantic-settings>=2.1.0,<3"
-          - "pydantic>=2.5.2,<3"
+          - "pydantic[email]>=2.5.2,<3"
           - "pytest>=7.4.3,<8"
           - "types-ldap3>=2.9.13,<3"
           - "types-pytz>=2023.3.1,<2024"

mex/common/ldap/models/person.py

@@ -7,14 +7,14 @@
 class LDAPPerson(LDAPActor):
     """Model class for LDAP persons."""
 
-    company: str | None = Field(None)
-    department: str | None = Field(None)
-    departmentNumber: str | None = Field(None)
-    displayName: str | None = Field(None)
-    employeeID: str = Field(...)
-    givenName: list[str] = Field(..., min_length=1)
-    ou: list[str] = Field([])
-    sn: str = Field(...)
+    company: str | None = None
+    department: str | None = None
+    departmentNumber: str | None = None
+    displayName: str | None = None
+    employeeID: str
+    givenName: list[str] = Field(min_length=1)
+    ou: list[str] = []
+    sn: str
 
     @classmethod
     def get_ldap_fields(cls) -> tuple[str, ...]:

mex/common/models/access_platform.py

@@ -1,31 +1,22 @@
+from typing import Annotated
+
 from pydantic import Field
 
 from mex.common.models.base import BaseModel
 from mex.common.models.extracted_data import ExtractedData
 from mex.common.models.merged_item import MergedItem
 from mex.common.types import (
     AccessPlatformID,
+    APIType,
     ContactPointID,
     Link,
     OrganizationalUnitID,
     PersonID,
+    TechnicalAccessibility,
     Text,
-    VocabularyEnum,
 )
 
 
-class TechnicalAccessibility(VocabularyEnum):
-    """Technical accessibility within RKI and outside of RKI."""
-
-    __vocabulary__ = "technical-accessibility"
-
-
-class APIType(VocabularyEnum):
-    """Technical standard or style of a network API."""
-
-    __vocabulary__ = "api-type"
-
-
 class BaseAccessPlatform(BaseModel):
     """A way of physically accessing the Resource for re-use."""
 
@@ -34,14 +25,15 @@ class BaseAccessPlatform(BaseModel):
     contact: list[OrganizationalUnitID | PersonID | ContactPointID] = []
     description: list[Text] = []
     endpointDescription: Link | None = None
-    endpointType: APIType | None = Field(
-        None, examples=["https://mex.rki.de/item/api-type-1"]
-    )
+    endpointType: Annotated[
+        APIType, Field(examples=["https://mex.rki.de/item/api-type-1"])
+    ] | None = None
     endpointURL: Link | None = None
     landingPage: list[Link] = []
-    technicalAccessibility: TechnicalAccessibility = Field(
-        ..., examples=["https://mex.rki.de/item/technical-accessibility-1"]
-    )
+    technicalAccessibility: Annotated[
+        TechnicalAccessibility,
+        Field(examples=["https://mex.rki.de/item/technical-accessibility-1"]),
+    ]
     title: list[Text] = []
     unitInCharge: list[OrganizationalUnitID] = []
 

mex/common/models/activity.py

@@ -7,25 +7,18 @@
 from mex.common.models.merged_item import MergedItem
 from mex.common.types import (
     ActivityID,
+    ActivityType,
     ContactPointID,
-    Identifier,
     Link,
     OrganizationalUnitID,
     OrganizationID,
     PersonID,
     Text,
     Theme,
     Timestamp,
-    VocabularyEnum,
 )
 
 
-class ActivityType(VocabularyEnum):
-    """The activity type."""
-
-    __vocabulary__ = "activity-type"
-
-
 class BaseActivity(BaseModel):
     """The context a resource was generated in.
 
@@ -40,12 +33,9 @@ class BaseActivity(BaseModel):
         ]
     ] = []
     alternativeTitle: list[Text] = []
-    contact: list[
-        Annotated[
-            OrganizationalUnitID | PersonID | ContactPointID,
-            Field(examples=[Identifier.generate(seed=42)]),
-        ]
-    ] = Field(..., min_length=1)
+    contact: Annotated[
+        list[OrganizationalUnitID | PersonID | ContactPointID,], Field(min_length=1)
+    ]
     documentation: list[Link] = []
     end: list[
         Annotated[Timestamp, Field(examples=["2024-01-17", "2024", "2024-01"])]
@@ -57,7 +47,7 @@ class BaseActivity(BaseModel):
     involvedUnit: list[OrganizationalUnitID] = []
     isPartOfActivity: list[ActivityID] = []
     publication: list[Link] = []
-    responsibleUnit: list[OrganizationalUnitID] = Field(..., min_length=1)
+    responsibleUnit: Annotated[list[OrganizationalUnitID], Field(min_length=1)]
     shortName: list[Text] = []
     start: list[
         Annotated[Timestamp, Field(examples=["2023-01-16", "2023", "2023-02"])]
@@ -66,7 +56,7 @@ class BaseActivity(BaseModel):
     theme: list[
         Annotated[Theme, Field(examples=["https://mex.rki.de/item/theme-1"])]
     ] = []
-    title: list[Text] = Field(..., min_length=1)
+    title: Annotated[list[Text], Field(min_length=1)]
     website: list[Link] = []
 
 

mex/common/models/base.py

@@ -2,17 +2,39 @@
 import pickle  # nosec
 from abc import abstractmethod
 from functools import cache
-from typing import TYPE_CHECKING, Any, Optional, TypeVar, Union, get_args, get_origin
+from typing import TYPE_CHECKING, Annotated, Any, TypeVar, Union, get_args, get_origin
 
-from pydantic import BaseModel as PydanticBaseModel
+from pydantic import (
+    BaseModel as PydanticBaseModel,
+)
 from pydantic import ConfigDict, Field, TypeAdapter, ValidationError, model_validator
 from pydantic.fields import FieldInfo
+from pydantic.json_schema import DEFAULT_REF_TEMPLATE, JsonSchemaMode, JsonSchemaValue
+from pydantic.json_schema import (
+    GenerateJsonSchema as PydanticJsonSchemaGenerator,
+)
 
 from mex.common.types import Identifier
 
 ModelValuesT = TypeVar("ModelValuesT", bound=dict[str, Any])
 
 
+class JsonSchemaGenerator(PydanticJsonSchemaGenerator):
+    """Customization of the pydantic class for generating JSON schemas."""
+
+    def handle_ref_overrides(self, json_schema: JsonSchemaValue) -> JsonSchemaValue:
+        """Disable pydantic behavior to wrap top-level `$ref` keys in an `allOf`.
+
+        For example, pydantic would convert
+            {"$ref": "#/$defs/APIType", "examples": ["api-type-1"]}
+        into
+            {"allOf": {"$ref": "#/$defs/APIType"}, "examples": ["api-type-1"]}
+        which is in fact recommended by JSON schema, but we need to disable this
+        to stay compatible with mex-editor and mex-model.
+        """
+        return json_schema
+
+
 class BaseModel(PydanticBaseModel):
     """Common base class for all MEx model classes."""
 
@@ -27,6 +49,32 @@ class BaseModel(PydanticBaseModel):
         validate_assignment=True,
     )
 
+    @classmethod
+    def model_json_schema(
+        cls,
+        by_alias: bool = True,
+        ref_template: str = DEFAULT_REF_TEMPLATE,
+        schema_generator: type[PydanticJsonSchemaGenerator] = JsonSchemaGenerator,
+        mode: JsonSchemaMode = "validation",
+    ) -> dict[str, Any]:
+        """Generates a JSON schema for a model class.
+
+        Args:
+            by_alias: Whether to use attribute aliases or not.
+            ref_template: The reference template.
+            schema_generator: Overriding the logic used to generate the JSON schema
+            mode: The mode in which to generate the schema.
+
+        Returns:
+            The JSON schema for the given model class.
+        """
+        return super().model_json_schema(
+            by_alias=by_alias,
+            ref_template=ref_template,
+            schema_generator=schema_generator,
+            mode=mode,
+        )
+
     @classmethod
     @cache
     def _get_alias_lookup(cls) -> dict[str, str]:
@@ -73,7 +121,7 @@ def _get_field_names_allowing_none(cls) -> list[str]:
     @classmethod
     def _convert_non_list_to_list(
         cls, name: str, field: FieldInfo, value: Any
-    ) -> Optional[list[Any]]:
+    ) -> list[Any] | None:
         """Convert a non-list value to a list value by wrapping it in a list."""
         if value is None:
             if name in cls._get_field_names_allowing_none():
@@ -169,15 +217,16 @@ class MExModel(BaseModel):
         # also used as the foreign key for all fields containing references.
         stableTargetId: Any
 
-    identifier: Identifier = Field(
-        ...,
-        description=(
-            "A globally unique identifier for this item. Regardless of the entity-type "
-            "or whether this item was extracted, merged, etc. identifiers will be "
-            "assigned just once."
+    identifier: Annotated[
+        Identifier,
+        Field(
+            description=(
+                "A globally unique identifier for this item. Regardless of the "
+                "entity-type or whether this item was extracted, merged, etc. "
+                "identifiers will be assigned just once."
+            ),
         ),
-        examples=[Identifier.generate(seed=42)],
-    )
+    ]
 
     @classmethod
     @abstractmethod

mex/common/models/contact_point.py

@@ -12,17 +12,7 @@ class BaseContactPoint(BaseModel):
     """A contact point - for example, an interdepartmental project."""
 
     stableTargetId: ContactPointID
-    email: list[
-        Annotated[
-            Email,
-            Field(
-                examples=["[email protected]"],
-            ),
-        ]
-    ] = Field(
-        ...,
-        min_length=1,
-    )
+    email: Annotated[list[Email], Field(min_length=1)]
 
 
 class ExtractedContactPoint(BaseContactPoint, ExtractedData):

mex/common/models/distribution.py

@@ -1,3 +1,5 @@
+from typing import Annotated
+
 from pydantic import Field
 
 from mex.common.models.base import BaseModel
@@ -9,53 +11,51 @@
     DistributionID,
     License,
     Link,
+    MIMEType,
     OrganizationID,
     PersonID,
     Timestamp,
-    VocabularyEnum,
 )
 
 
-class MIMEType(VocabularyEnum):
-    """The mime type."""
-
-    __vocabulary__ = "mime-type"
-
-
 class BaseDistribution(BaseModel):
     """A specific representation of a dataset."""
 
     stableTargetId: DistributionID
     accessService: AccessPlatformID | None = None
-    accessRestriction: AccessRestriction = Field(
-        ...,
-        examples=["https://mex.rki.de/item/access-restriction-1"],
-    )
+    accessRestriction: Annotated[
+        AccessRestriction,
+        Field(examples=["https://mex.rki.de/item/access-restriction-1"]),
+    ]
     accessURL: Link | None = None
     author: list[PersonID] = []
     contactPerson: list[PersonID] = []
     dataCurator: list[PersonID] = []
     dataManager: list[PersonID] = []
     downloadURL: Link | None = None
     issued: Timestamp
-    license: License | None = Field(
-        None, examples=["https://mex.rki.de/item/license-1"]
-    )
-    mediaType: MIMEType | None = Field(
-        None,
-        examples=["https://mex.rki.de/item/mime-type-1"],
-    )
+    license: Annotated[
+        License, Field(examples=["https://mex.rki.de/item/license-1"])
+    ] | None = None
+    mediaType: Annotated[
+        MIMEType,
+        Field(
+            examples=["https://mex.rki.de/item/mime-type-1"],
+        ),
+    ] | None = None
     modified: Timestamp | None = None
     otherContributor: list[PersonID] = []
     projectLeader: list[PersonID] = []
     projectManager: list[PersonID] = []
-    publisher: list[OrganizationID] = Field(..., min_length=1)
+    publisher: Annotated[list[OrganizationID], Field(min_length=1)]
     researcher: list[PersonID] = []
-    title: str = Field(
-        ...,
-        examples=["theNameOfTheFile"],
-        min_length=1,
-    )
+    title: Annotated[
+        str,
+        Field(
+            examples=["theNameOfTheFile"],
+            min_length=1,
+        ),
+    ]
 
 
 class ExtractedDistribution(BaseDistribution, ExtractedData):