feature/model update v3 (#207)

# PR Context # Added - added new consent and bibliography reference models and vocabs - added `doi` field to resource models # Changes - split up YearMonth and Year temporal types and improved patterns - applied all changes to model fields according to model v3 - update LOINC pattern # Fixed - fix temporal entity schemas --------- Signed-off-by: Nicolas Drebenstedt <[email protected]> Signed-off-by: Janina Esins <[email protected]> Co-authored-by: RKIMetadataExchange <[email protected]> Co-authored-by: erichesse <[email protected]> Co-authored-by: Kamran Ali <[email protected]> Co-authored-by: esinsj <[email protected]>
robert-koch-institut · Oct 28, 2024 · 6ad5e05 · 6ad5e05
1 parent 16a8f03
commit 6ad5e05
Show file tree

Hide file tree

Showing 27 changed files with 874 additions and 329 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,16 +9,30 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- added new consent and bibliography reference models and vocabs
+- added doi field to resource models
+- helper function for primary source look up
+
 ### Changes
 
+- upgrade mex-model dependency to version 3
 - make ruff linter config opt-out, instead of opt-in
+- make instances of extracted data hashable
+- BREAKING: Wikidata convenience function refactored and renamed to 'helper'
+- wikidata helper function split between mex-common and mex-extractors
+- code de-duplication: fixture extracted_primary_sources now uses function-part of primary sources helper
+- split up YearMonth and Year temporal types and improved patterns
+- applied all changes to model fields according to model v3
+- update LOINC pattern
 
 ### Deprecated
 
 ### Removed
 
 ### Fixed
 
+- fix temporal entity schemas
+
 ### Security
 
 ## [0.38.0] - 2024-10-11

diff --git a/mex/common/models/__init__.py b/mex/common/models/__init__.py
@@ -4,6 +4,8 @@
 
 - AccessPlatform
 - Activity
+- BibliographicResource
+- Consent
 - ContactPoint
 - Distribution
 - Organization
@@ -95,6 +97,26 @@
 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, SubtractiveRule
+from mex.common.models.bibliographic_resource import (
+    AdditiveBibliographicResource,
+    BaseBibliographicResource,
+    BibliographicResourceRuleSetRequest,
+    BibliographicResourceRuleSetResponse,
+    ExtractedBibliographicResource,
+    MergedBibliographicResource,
+    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,
@@ -199,6 +221,8 @@
     "ADDITIVE_MODEL_CLASSES",
     "AdditiveAccessPlatform",
     "AdditiveActivity",
+    "AdditiveBibliographicResource",
+    "AdditiveConsent",
     "AdditiveContactPoint",
     "AdditiveDistribution",
     "AdditiveOrganization",
@@ -222,6 +246,8 @@
     "BASE_MODEL_CLASSES",
     "BaseAccessPlatform",
     "BaseActivity",
+    "BaseBibliographicResource",
+    "BaseConsent",
     "BaseContactPoint",
     "BaseDistribution",
     "BaseModel",
@@ -232,6 +258,8 @@
     "BaseResource",
     "BaseVariable",
     "BaseVariableGroup",
+    "ConsentRuleSetRequest",
+    "ConsentRuleSetResponse",
     "ContactPointRuleSetRequest",
     "ContactPointRuleSetResponse",
     "DistributionRuleSetRequest",
@@ -240,6 +268,8 @@
     "EXTRACTED_MODEL_CLASSES",
     "ExtractedAccessPlatform",
     "ExtractedActivity",
+    "ExtractedBibliographicResource",
+    "ExtractedConsent",
     "ExtractedContactPoint",
     "ExtractedData",
     "ExtractedDistribution",
@@ -260,6 +290,8 @@
     "MERGED_MODEL_CLASSES",
     "MergedAccessPlatform",
     "MergedActivity",
+    "MergedBibliographicResource",
+    "MergedConsent",
     "MergedContactPoint",
     "MergedDistribution",
     "MergedItem",
@@ -284,6 +316,8 @@
     "PREVENTIVE_MODEL_CLASSES",
     "PreventiveAccessPlatform",
     "PreventiveActivity",
+    "PreventiveBibliographicResource",
+    "PreventiveConsent",
     "PreventiveContactPoint",
     "PreventiveDistribution",
     "PreventiveOrganization",
@@ -308,6 +342,8 @@
     "SUBTRACTIVE_MODEL_CLASSES",
     "SubtractiveAccessPlatform",
     "SubtractiveActivity",
+    "SubtractiveBibliographicResource",
+    "SubtractiveConsent",
     "SubtractiveContactPoint",
     "SubtractiveDistribution",
     "SubtractiveOrganization",
@@ -331,6 +367,8 @@
 AnyBaseModel = (
     BaseAccessPlatform
     | BaseActivity
+    | BaseBibliographicResource
+    | BaseConsent
     | BaseContactPoint
     | BaseDistribution
     | BaseOrganization
@@ -349,6 +387,8 @@
 AnyExtractedModel = (
     ExtractedAccessPlatform
     | ExtractedActivity
+    | ExtractedBibliographicResource
+    | ExtractedConsent
     | ExtractedContactPoint
     | ExtractedDistribution
     | ExtractedOrganization
@@ -369,6 +409,8 @@
 AnyMergedModel = (
     MergedAccessPlatform
     | MergedActivity
+    | MergedBibliographicResource
+    | MergedConsent
     | MergedContactPoint
     | MergedDistribution
     | MergedOrganization
@@ -387,6 +429,8 @@
 AnyAdditiveModel = (
     AdditiveAccessPlatform
     | AdditiveActivity
+    | AdditiveBibliographicResource
+    | AdditiveConsent
     | AdditiveContactPoint
     | AdditiveDistribution
     | AdditiveOrganization
@@ -407,6 +451,8 @@
 AnySubtractiveModel = (
     SubtractiveAccessPlatform
     | SubtractiveActivity
+    | SubtractiveBibliographicResource
+    | SubtractiveConsent
     | SubtractiveContactPoint
     | SubtractiveDistribution
     | SubtractiveOrganization
@@ -427,6 +473,8 @@
 AnyPreventiveModel = (
     PreventiveAccessPlatform
     | PreventiveActivity
+    | PreventiveBibliographicResource
+    | PreventiveConsent
     | PreventiveContactPoint
     | PreventiveDistribution
     | PreventiveOrganization
@@ -453,6 +501,8 @@
 AnyRuleSetRequest = (
     AccessPlatformRuleSetRequest
     | ActivityRuleSetRequest
+    | BibliographicResourceRuleSetRequest
+    | ConsentRuleSetRequest
     | ContactPointRuleSetRequest
     | DistributionRuleSetRequest
     | OrganizationRuleSetRequest
@@ -473,6 +523,8 @@
 AnyRuleSetResponse = (
     AccessPlatformRuleSetResponse
     | ActivityRuleSetResponse
+    | BibliographicResourceRuleSetResponse
+    | ConsentRuleSetResponse
     | ContactPointRuleSetResponse
     | DistributionRuleSetResponse
     | OrganizationRuleSetResponse

diff --git a/mex/common/models/access_platform.py b/mex/common/models/access_platform.py
@@ -22,10 +22,10 @@
     MergedContactPointIdentifier,
     MergedOrganizationalUnitIdentifier,
     MergedPersonIdentifier,
+    MergedPrimarySourceIdentifier,
     TechnicalAccessibility,
     Text,
 )
-from mex.common.types.identifier import MergedPrimarySourceIdentifier
 
 
 class _Stem(BaseModel):

diff --git a/mex/common/models/activity.py b/mex/common/models/activity.py
@@ -22,13 +22,15 @@
     Identifier,
     Link,
     MergedActivityIdentifier,
+    MergedBibliographicResourceIdentifier,
     MergedContactPointIdentifier,
     MergedOrganizationalUnitIdentifier,
     MergedOrganizationIdentifier,
     MergedPersonIdentifier,
     MergedPrimarySourceIdentifier,
     Text,
     Theme,
+    Year,
     YearMonth,
     YearMonthDay,
 )
@@ -43,7 +45,7 @@ class _OptionalLists(_Stem):
     activityType: list[ActivityType] = []
     alternativeTitle: list[Text] = []
     documentation: list[Link] = []
-    end: list[YearMonthDay | YearMonth] = []
+    end: list[YearMonthDay | YearMonth | Year] = []
     externalAssociate: list[
         Annotated[
             MergedOrganizationIdentifier | MergedPersonIdentifier,
@@ -55,9 +57,9 @@ class _OptionalLists(_Stem):
     involvedPerson: list[MergedPersonIdentifier] = []
     involvedUnit: list[MergedOrganizationalUnitIdentifier] = []
     isPartOfActivity: list[MergedActivityIdentifier] = []
-    publication: list[Link] = []
+    publication: list[MergedBibliographicResourceIdentifier] = []
     shortName: list[Text] = []
-    start: list[YearMonthDay | YearMonth] = []
+    start: list[YearMonthDay | YearMonth | Year] = []
     succeeds: list[MergedActivityIdentifier] = []
     theme: list[Theme] = []
     website: list[Link] = []

diff --git a/mex/common/models/base/extracted_data.py b/mex/common/models/base/extracted_data.py
@@ -53,6 +53,8 @@ class ExtractedData(BaseEntity):
             ),
             examples=["123456", "item-501", "D7/x4/zz.final3"],
             min_length=1,
+            max_length=1000,
+            pattern=r"^[^\n\r]+$",
             frozen=True,
         ),
     ]
@@ -94,3 +96,7 @@ def _get_stable_target_id(
             .assign(self.hadPrimarySource, self.identifierInPrimarySource)
             .stableTargetId
         )
+
+    def __hash__(self) -> int:
+        """Calculates a hash value to make the object cachable."""
+        return hash(f"{self.hadPrimarySource}\n{self.identifierInPrimarySource}")