🔨 Move "concept" information out

Author: RobertJCarroll

src/include_access_model/datamodel/include_access_model.py

@@ -1,5 +1,5 @@
 # Auto generated from include_access_model.yaml by pythongen.py version: 0.0.1
-# Generation date: 2025-11-11T16:08:56
+# Generation date: 2025-11-12T07:19:24
 # Schema: include-access-model
 #
 # id: https://includedcc.org/include-access-model
@@ -105,6 +105,10 @@ class SubjectAssertionAssertionId(extended_str):
     pass
 
 
+class ConceptCode(URIorCURIE):
+    pass
+
+
 @dataclass(repr=False)
 class Record(YAMLRoot):
     """
@@ -515,11 +519,9 @@ class SubjectAssertion(Record):
     age_at_assertion: Optional[int] = None
     age_at_event: Optional[int] = None
     age_at_resolution: Optional[int] = None
-    code: Optional[Union[str, URIorCURIE]] = None
-    display: Optional[str] = None
+    code: Optional[Union[Union[str, URIorCURIE], list[Union[str, URIorCURIE]]]] = empty_list()
     code_source: Optional[str] = None
     value_code: Optional[Union[str, URIorCURIE]] = None
-    value_display: Optional[str] = None
     value_number: Optional[float] = None
     value_source: Optional[str] = None
     value_units: Optional[Union[str, URIorCURIE]] = None
@@ -547,21 +549,16 @@ def __post_init__(self, *_: str, **kwargs: Any):
         if self.age_at_resolution is not None and not isinstance(self.age_at_resolution, int):
             self.age_at_resolution = int(self.age_at_resolution)
 
-        if self.code is not None and not isinstance(self.code, URIorCURIE):
-            self.code = URIorCURIE(self.code)
-
-        if self.display is not None and not isinstance(self.display, str):
-            self.display = str(self.display)
+        if not isinstance(self.code, list):
+            self.code = [self.code] if self.code is not None else []
+        self.code = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.code]
 
         if self.code_source is not None and not isinstance(self.code_source, str):
             self.code_source = str(self.code_source)
 
         if self.value_code is not None and not isinstance(self.value_code, URIorCURIE):
             self.value_code = URIorCURIE(self.value_code)
 
-        if self.value_display is not None and not isinstance(self.value_display, str):
-            self.value_display = str(self.value_display)
-
         if self.value_number is not None and not isinstance(self.value_number, float):
             self.value_number = float(self.value_number)
 
@@ -580,6 +577,34 @@ def __post_init__(self, *_: str, **kwargs: Any):
         super().__post_init__(**kwargs)
 
 
+@dataclass(repr=False)
+class Concept(YAMLRoot):
+    """
+    A standardized concept with display information.
+    """
+    _inherited_slots: ClassVar[list[str]] = []
+
+    class_class_uri: ClassVar[URIRef] = INCLUDEDCC["Concept"]
+    class_class_curie: ClassVar[str] = "includedcc:Concept"
+    class_name: ClassVar[str] = "Concept"
+    class_model_uri: ClassVar[URIRef] = INCLUDEDCC.Concept
+
+    code: Union[Union[str, ConceptCode], list[Union[str, ConceptCode]]] = None
+    display: Optional[str] = None
+
+    def __post_init__(self, *_: str, **kwargs: Any):
+        if self._is_empty(self.code):
+            self.MissingRequiredField("code")
+        if not isinstance(self.code, list):
+            self.code = [self.code] if self.code is not None else []
+        self.code = [v if isinstance(v, ConceptCode) else ConceptCode(v) for v in self.code]
+
+        if self.display is not None and not isinstance(self.display, str):
+            self.display = str(self.display)
+
+        super().__post_init__(**kwargs)
+
+
 # Enumerations
 class EnumProgram(EnumDefinitionImpl):
     """
@@ -1168,7 +1193,7 @@ class slots:
                    model_uri=INCLUDEDCC.age_at_resolution, domain=None, range=Optional[int])
 
 slots.code = Slot(uri=INCLUDEDCC.code, name="code", curie=INCLUDEDCC.curie('code'),
-                   model_uri=INCLUDEDCC.code, domain=None, range=Optional[Union[str, URIorCURIE]])
+                   model_uri=INCLUDEDCC.code, domain=None, range=Optional[Union[Union[str, URIorCURIE], list[Union[str, URIorCURIE]]]])
 
 slots.display = Slot(uri=INCLUDEDCC.display, name="display", curie=INCLUDEDCC.curie('display'),
                    model_uri=INCLUDEDCC.display, domain=None, range=Optional[str])
@@ -1179,9 +1204,6 @@ class slots:
 slots.value_code = Slot(uri=INCLUDEDCC.value_code, name="value_code", curie=INCLUDEDCC.curie('value_code'),
                    model_uri=INCLUDEDCC.value_code, domain=None, range=Optional[Union[str, URIorCURIE]])
 
-slots.value_display = Slot(uri=INCLUDEDCC.value_display, name="value_display", curie=INCLUDEDCC.curie('value_display'),
-                   model_uri=INCLUDEDCC.value_display, domain=None, range=Optional[str])
-
 slots.value_number = Slot(uri=INCLUDEDCC.value_number, name="value_number", curie=INCLUDEDCC.curie('value_number'),
                    model_uri=INCLUDEDCC.value_number, domain=None, range=Optional[float])
 
@@ -1211,3 +1233,6 @@ class slots:
 
 slots.SubjectAssertion_assertion_id = Slot(uri=INCLUDEDCC.assertion_id, name="SubjectAssertion_assertion_id", curie=INCLUDEDCC.curie('assertion_id'),
                    model_uri=INCLUDEDCC.SubjectAssertion_assertion_id, domain=SubjectAssertion, range=Union[str, SubjectAssertionAssertionId])
+
+slots.Concept_code = Slot(uri=INCLUDEDCC.code, name="Concept_code", curie=INCLUDEDCC.curie('code'),
+                   model_uri=INCLUDEDCC.Concept_code, domain=Concept, range=Union[Union[str, ConceptCode], list[Union[str, ConceptCode]]])

src/include_access_model/datamodel/include_access_model_pydantic.py

@@ -515,11 +515,9 @@ class SubjectAssertion(Record):
     age_at_assertion: Optional[int] = Field(default=None, title="Age at assertion", description="""The age in days of the Subject when the assertion was made.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion'], 'unit': {'ucum_code': 'd'}} })
     age_at_event: Optional[int] = Field(default=None, title="Age at event", description="""The age in days of the Subject at the time point which the assertion describes, | eg, age of onset or when a measurement was performed.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion'], 'unit': {'ucum_code': 'd'}} })
     age_at_resolution: Optional[int] = Field(default=None, title="Age at resolution", description="""The age in days of the Subject when the asserted state was resolved.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion'], 'unit': {'ucum_code': 'd'}} })
-    code: Optional[str] = Field(default=None, title="Assertion Code", description="""The structured term defining the meaning of the assertion.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion']} })
-    display: Optional[str] = Field(default=None, title="Display String", description="""The friendly display string of the coded term.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion']} })
+    code: Optional[list[str]] = Field(default=[], title="Assertion Code", description="""The structured term defining the meaning of the assertion.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion', 'Concept']} })
     code_source: Optional[str] = Field(default=None, title="Code Source Text", description="""The source text yielding the code.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion']} })
     value_code: Optional[str] = Field(default=None, title="Value Code", description="""The structured term defining the value of the assertion.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion']} })
-    value_display: Optional[str] = Field(default=None, title="Value Display String", description="""The friendly display string of the coded term for the value of the assertion.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion']} })
     value_number: Optional[float] = Field(default=None, title="Value Number", description="""The numeric value of the assertion.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion']} })
     value_source: Optional[str] = Field(default=None, title="Value Source Text", description="""The source text yielding the value.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion']} })
     value_units: Optional[str] = Field(default=None, title="Value Units", description="""The structured term defining the units of the value.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion']} })
@@ -528,6 +526,21 @@ class SubjectAssertion(Record):
     external_id: Optional[list[str]] = Field(default=[], title="External Identifiers", description="""Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP""", json_schema_extra = { "linkml_meta": {'domain_of': ['Record']} })
 
 
+class Concept(ConfiguredBaseModel):
+    """
+    A standardized concept with display information.
+    """
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://includedcc.org/include-access-model',
+         'slot_usage': {'code': {'identifier': True,
+                                 'multivalued': False,
+                                 'name': 'code',
+                                 'required': True}},
+         'title': 'Concept'})
+
+    code: str = Field(default=..., title="Assertion Code", description="""The structured term defining the meaning of the assertion.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SubjectAssertion', 'Concept']} })
+    display: Optional[str] = Field(default=None, title="Display String", description="""The friendly display string of the coded term.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Concept']} })
+
+
 # Model rebuild
 # see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model
 Record.model_rebuild()
@@ -539,3 +552,4 @@ class SubjectAssertion(Record):
 Subject.model_rebuild()
 Demographics.model_rebuild()
 SubjectAssertion.model_rebuild()
+Concept.model_rebuild()

src/include_access_model/schema/include_access_model.yaml

@@ -162,10 +162,11 @@ classes:
       - age_at_event
       - age_at_resolution
       - code
-      - display
+# Moved the displays into the concept
+#      - display
       - code_source
       - value_code
-      - value_display
+#      - value_display
       - value_number
       - value_source
       - value_units
@@ -175,6 +176,17 @@ classes:
       assertion_id:
         required: true
         identifier: true
+  Concept:
+    title: Concept
+    description: A standardized concept with display information.
+    slots:
+      - code
+      - display
+    slot_usage:
+      code:
+        multivalued: false
+        required: true
+        identifier: true
 
 slots: 
   uuid:
@@ -444,6 +456,7 @@ slots:
     title: Assertion Code
     description: The structured term defining the meaning of the assertion.
     range: uriorcurie
+    multivalued: true
   display:
     title: Display String
     description: The friendly display string of the coded term.
@@ -456,10 +469,6 @@ slots:
     title: Value Code
     description: The structured term defining the value of the assertion.
     range: uriorcurie
-  value_display:
-    title: Value Display String
-    description: The friendly display string of the coded term for the value of the assertion.
-    range: string
   value_number:
     title: Value Number
     description: The numeric value of the assertion.