feature/add consent models and fix temporal type

mex/common/models/__init__.py

@@ -5,6 +5,7 @@
 - AccessPlatform
 - Activity
 - BibliographicResource
+- Consent
 - ContactPoint
 - Distribution
 - Organization
@@ -106,6 +107,16 @@
     PreventiveBibliographicResource,
     SubtractiveBibliographicResource,
 )
+from mex.common.models.consent import (
+    AdditiveConsent,
+    BaseConsent,
+    ConsentRuleSetRequest,
+    ConsentRuleSetResponse,
+    ExtractedConsent,
+    MergedConsent,
+    PreventiveConsent,
+    SubtractiveConsent,
+)
 from mex.common.models.contact_point import (
     AdditiveContactPoint,
     BaseContactPoint,
@@ -211,6 +222,7 @@
     "AdditiveAccessPlatform",
     "AdditiveActivity",
     "AdditiveBibliographicResource",
+    "AdditiveConsent",
     "AdditiveContactPoint",
     "AdditiveDistribution",
     "AdditiveOrganization",
@@ -230,11 +242,12 @@
     "AnyRuleSetRequest",
     "AnyRuleSetResponse",
     "AnySubtractiveModel",
-    "BaseBibliographicResource",
     "BASE_MODEL_CLASSES_BY_NAME",
     "BASE_MODEL_CLASSES",
     "BaseAccessPlatform",
     "BaseActivity",
+    "BaseBibliographicResource",
+    "BaseConsent",
     "BaseContactPoint",
     "BaseDistribution",
     "BaseModel",
@@ -245,6 +258,8 @@
     "BaseResource",
     "BaseVariable",
     "BaseVariableGroup",
+    "ConsentRuleSetRequest",
+    "ConsentRuleSetResponse",
     "ContactPointRuleSetRequest",
     "ContactPointRuleSetResponse",
     "DistributionRuleSetRequest",
@@ -254,6 +269,7 @@
     "ExtractedAccessPlatform",
     "ExtractedActivity",
     "ExtractedBibliographicResource",
+    "ExtractedConsent",
     "ExtractedContactPoint",
     "ExtractedData",
     "ExtractedDistribution",
@@ -275,6 +291,7 @@
     "MergedAccessPlatform",
     "MergedActivity",
     "MergedBibliographicResource",
+    "MergedConsent",
     "MergedContactPoint",
     "MergedDistribution",
     "MergedItem",
@@ -300,6 +317,7 @@
     "PreventiveAccessPlatform",
     "PreventiveActivity",
     "PreventiveBibliographicResource",
+    "PreventiveConsent",
     "PreventiveContactPoint",
     "PreventiveDistribution",
     "PreventiveOrganization",
@@ -325,6 +343,7 @@
     "SubtractiveAccessPlatform",
     "SubtractiveActivity",
     "SubtractiveBibliographicResource",
+    "SubtractiveConsent",
     "SubtractiveContactPoint",
     "SubtractiveDistribution",
     "SubtractiveOrganization",
@@ -349,6 +368,7 @@
     BaseAccessPlatform
     | BaseActivity
     | BaseBibliographicResource
+    | BaseConsent
     | BaseContactPoint
     | BaseDistribution
     | BaseOrganization
@@ -368,6 +388,7 @@
     ExtractedAccessPlatform
     | ExtractedActivity
     | ExtractedBibliographicResource
+    | ExtractedConsent
     | ExtractedContactPoint
     | ExtractedDistribution
     | ExtractedOrganization
@@ -389,6 +410,7 @@
     MergedAccessPlatform
     | MergedActivity
     | MergedBibliographicResource
+    | MergedConsent
     | MergedContactPoint
     | MergedDistribution
     | MergedOrganization
@@ -408,6 +430,7 @@
     AdditiveAccessPlatform
     | AdditiveActivity
     | AdditiveBibliographicResource
+    | AdditiveConsent
     | AdditiveContactPoint
     | AdditiveDistribution
     | AdditiveOrganization
@@ -429,6 +452,7 @@
     SubtractiveAccessPlatform
     | SubtractiveActivity
     | SubtractiveBibliographicResource
+    | SubtractiveConsent
     | SubtractiveContactPoint
     | SubtractiveDistribution
     | SubtractiveOrganization
@@ -450,6 +474,7 @@
     PreventiveAccessPlatform
     | PreventiveActivity
     | PreventiveBibliographicResource
+    | PreventiveConsent
     | PreventiveContactPoint
     | PreventiveDistribution
     | PreventiveOrganization
@@ -477,6 +502,7 @@
     AccessPlatformRuleSetRequest
     | ActivityRuleSetRequest
     | BibliographicResourceRuleSetRequest
+    | ConsentRuleSetRequest
     | ContactPointRuleSetRequest
     | DistributionRuleSetRequest
     | OrganizationRuleSetRequest
@@ -498,6 +524,7 @@
     AccessPlatformRuleSetResponse
     | ActivityRuleSetResponse
     | BibliographicResourceRuleSetResponse
+    | ConsentRuleSetResponse
     | ContactPointRuleSetResponse
     | DistributionRuleSetResponse
     | OrganizationRuleSetResponse

mex/common/models/base/schema.py

@@ -1,7 +1,10 @@
+from typing import Any
+
 from pydantic.json_schema import (
     GenerateJsonSchema as PydanticJsonSchemaGenerator,
 )
 from pydantic.json_schema import JsonSchemaValue
+from pydantic_core.core_schema import ComplexSchema
 
 
 class JsonSchemaGenerator(PydanticJsonSchemaGenerator):
@@ -18,3 +21,10 @@ def handle_ref_overrides(self, json_schema: JsonSchemaValue) -> JsonSchemaValue:
         to stay compatible with mex-editor and mex-model.
         """
         return json_schema
+
+    def complex_schema(self, schema: ComplexSchema) -> dict[str, Any]:
+        """Returns a schema that matches a complex value."""
+        # TODO: clean this up in MX-1704 (stop-gap)
+        raise NotImplementedError(
+            "Method for generating JsonSchema for 'complex' schemas is not implemented."
+        )

mex/common/models/consent.py

@@ -0,0 +1,155 @@
+"""A consent - for example, an interdepartmental project."""
+
+from typing import Annotated, ClassVar, Literal
+
+from pydantic import Field, computed_field
+
+from mex.common.models.base.extracted_data import ExtractedData
+from mex.common.models.base.merged_item import MergedItem
+from mex.common.models.base.model import BaseModel
+from mex.common.models.base.rules import (
+    AdditiveRule,
+    PreventiveRule,
+    RuleSet,
+    SubtractiveRule,
+)
+from mex.common.types import (
+    ConsentStatus,
+    ConsentType,
+    ExtractedConsentIdentifier,
+    MergedConsentIdentifier,
+    MergedPersonIdentifier,
+    MergedPrimarySourceIdentifier,
+    YearMonthDayTime,
+)
+
+
+class _Stem(BaseModel):
+    stemType: ClassVar[Annotated[Literal["Consent"], Field(frozen=True)]] = "Consent"
+
+
+class _OptionalValues(_Stem):
+    hasConsentType: (
+        Annotated[
+            ConsentType, Field(examples=["https://mex.rki.de/item/consent-type-1"])
+        ]
+        | None
+    ) = None
+
+
+class _RequiredValues(_Stem):
+    hasConsentStatus: Annotated[
+        ConsentStatus, Field(examples=["https://mex.rki.de/item/consent-status-1"])
+    ]
+    hasDataSubject: MergedPersonIdentifier
+    isIndicatedAtTime: YearMonthDayTime
+
+
+class _SparseValues(_Stem):
+    hasConsentStatus: (
+        Annotated[
+            ConsentStatus, Field(examples=["https://mex.rki.de/item/consent-status-1"])
+        ]
+        | None
+    ) = None
+    hasDataSubject: MergedPersonIdentifier | None = None
+    isIndicatedAtTime: YearMonthDayTime | None = None
+
+
+class _VariadicValues(_Stem):
+    hasConsentType: list[
+        Annotated[
+            ConsentType, Field(examples=["https://mex.rki.de/item/consent-type-1"])
+        ]
+    ] = []
+    hasConsentStatus: list[
+        Annotated[
+            ConsentStatus, Field(examples=["https://mex.rki.de/item/consent-status-1"])
+        ]
+    ] = []
+    hasDataSubject: list[MergedPersonIdentifier] = []
+    isIndicatedAtTime: list[YearMonthDayTime] = []
+
+
+class BaseConsent(_OptionalValues, _RequiredValues):
+    """All fields for a valid consent except for provenance."""
+
+
+class ExtractedConsent(BaseConsent, ExtractedData):
+    """An automatically extracted metadata set describing a consent."""
+
+    entityType: Annotated[
+        Literal["ExtractedConsent"], Field(alias="$type", frozen=True)
+    ] = "ExtractedConsent"
+
+    @computed_field  # type: ignore[prop-decorator]
+    @property
+    def identifier(self) -> ExtractedConsentIdentifier:
+        """Return the computed identifier for this extracted data item."""
+        return self._get_identifier(ExtractedConsentIdentifier)
+
+    @computed_field  # type: ignore[prop-decorator]
+    @property
+    def stableTargetId(self) -> MergedConsentIdentifier:  # noqa: N802
+        """Return the computed stableTargetId for this extracted data item."""
+        return self._get_stable_target_id(MergedConsentIdentifier)
+
+
+class MergedConsent(BaseConsent, MergedItem):
+    """The result of merging all extracted data and rules for a consent."""
+
+    entityType: Annotated[
+        Literal["MergedConsent"], Field(alias="$type", frozen=True)
+    ] = "MergedConsent"
+    identifier: Annotated[MergedConsentIdentifier, Field(frozen=True)]
+
+
+class AdditiveConsent(_OptionalValues, _SparseValues, AdditiveRule):
+    """Rule to add values to merged consent items."""
+
+    entityType: Annotated[
+        Literal["AdditiveConsent"], Field(alias="$type", frozen=True)
+    ] = "AdditiveConsent"
+
+
+class SubtractiveConsent(_VariadicValues, SubtractiveRule):
+    """Rule to subtract values from merged consent items."""
+
+    entityType: Annotated[
+        Literal["SubtractiveConsent"], Field(alias="$type", frozen=True)
+    ] = "SubtractiveConsent"
+
+
+class PreventiveConsent(_Stem, PreventiveRule):
+    """Rule to prevent primary sources for fields of merged consent items."""
+
+    entityType: Annotated[
+        Literal["PreventiveConsent"], Field(alias="$type", frozen=True)
+    ] = "PreventiveConsent"
+    hasConsentType: list[MergedPrimarySourceIdentifier] = []
+    hasConsentStatus: list[MergedPrimarySourceIdentifier] = []
+    hasDataSubject: list[MergedPrimarySourceIdentifier] = []
+    isIndicatedAtTime: list[MergedPrimarySourceIdentifier] = []
+
+
+class _BaseRuleSet(_Stem, RuleSet):
+    additive: AdditiveConsent
+    subtractive: SubtractiveConsent
+    preventive: PreventiveConsent
+
+
+class ConsentRuleSetRequest(_BaseRuleSet):
+    """Set of rules to create or update a consent item."""
+
+    entityType: Annotated[
+        Literal["ConsentRuleSetRequest"], Field(alias="$type", frozen=True)
+    ] = "ConsentRuleSetRequest"
+
+
+class ConsentRuleSetResponse(_BaseRuleSet):
+    """Set of rules to retrieve a consent item."""
+
+    entityType: Annotated[
+        Literal["ConsentRuleSetResponse"], Field(alias="$type", frozen=True)
+    ] = "ConsentRuleSetResponse"
+    stableTargetId: MergedConsentIdentifier

mex/common/models/resource.py

@@ -43,11 +43,24 @@
     YearMonthDayTime,
 )
 
+DoiStr = Annotated[
+    str,
+    Field(
+        examples=[
+            "https://doi.org/10.1007/978-1-0716-2441-8_7",
+            "https://doi.org/10.2807/1560-7917.ES.2022.27.46.2200849",
+            "https://doi.org/10.3389/fmicb.2022.868887",
+            "http://dx.doi.org/10.25646/5147",
+            "https://doi.org/10.1016/j.vaccine.2022.11.065",
+        ],
+        pattern=r"^(((http)|(https))://(dx.)?doi.org/)(10.\d{4,9}/[-._;()/:A-Z0-9]+)$",
+    ),
+]
 LoincIdStr = Annotated[
     str,
     Field(
         examples=["https://loinc.org/95209-3", "https://loinc.org/LA26211-5"],
-        pattern=r"^https://loinc.org/([a-zA-z]*)|(([0-9]{5}-[0-9]*))$",
+        pattern=r"^https://loinc.org/([a-zA-z]*)|(([0-9]*(-[0-9])*))$",
         json_schema_extra={"format": "uri"},
     ),
 ]
@@ -168,6 +181,7 @@ class _OptionalValues(_Stem):
         | None
     ) = None
     created: YearMonthDayTime | YearMonthDay | YearMonth | Year | None = None
+    doi: DoiStr | None = None
     hasPersonalData: (
         Annotated[
             PersonalData,
@@ -237,6 +251,7 @@ class _VariadicValues(_Stem):
         Annotated[Frequency, Field(examples=["https://mex.rki.de/item/frequency-1"])]
     ] = []
     created: list[YearMonthDayTime | YearMonthDay | YearMonth | Year] = []
+    doi: list[DoiStr] = []
     hasPersonalData: list[
         Annotated[
             PersonalData,
@@ -339,6 +354,7 @@ class PreventiveResource(_Stem, PreventiveRule):
     contributingUnit: list[MergedPrimarySourceIdentifier] = []
     contributor: list[MergedPrimarySourceIdentifier] = []
     created: list[MergedPrimarySourceIdentifier] = []
+    doi: list[MergedPrimarySourceIdentifier] = []
     creator: list[MergedPrimarySourceIdentifier] = []
     description: list[MergedPrimarySourceIdentifier] = []
     distribution: list[MergedPrimarySourceIdentifier] = []