Add ARIC height variables and expand IntegratedHeight001

src/bdc_variable_library/datamodel/bdc_variable_library.py

@@ -1,5 +1,5 @@
 # Auto generated from bdc_variable_library.yaml by pythongen.py version: 0.0.1
-# Generation date: 2026-07-14T11:45:29
+# Generation date: 2026-07-21T15:37:17
 # Schema: bdc-variable-library
 #
 # id: https://w3id.org/linkml/bdc-variable-library
@@ -124,6 +124,10 @@ class CompoundHeight002Id(CompoundVariableId):
     pass
 
 
+class CompoundHeight001Id(CompoundVariableId):
+    pass
+
+
 class IntegratedHeight001Id(IntegratedVariableId):
     pass
 
@@ -457,6 +461,29 @@ def __post_init__(self, *_: str, **kwargs: Any):
         super().__post_init__(**kwargs)
 
 
+@dataclass(repr=False)
+class CompoundHeight001(CompoundVariable):
+    """
+    Height variable with metadata, measured in cm and collected using a wall-mounted stadiometer
+    """
+    _inherited_slots: ClassVar[list[str]] = []
+
+    class_class_uri: ClassVar[URIRef] = BDC_VARIABLE_LIBRARY["CompoundHeight001"]
+    class_class_curie: ClassVar[str] = "bdc_variable_library:CompoundHeight001"
+    class_name: ClassVar[str] = "CompoundHeight001"
+    class_model_uri: ClassVar[URIRef] = BDC_VARIABLE_LIBRARY.CompoundHeight001
+
+    id: Union[str, CompoundHeight001Id] = None
+
+    def __post_init__(self, *_: str, **kwargs: Any):
+        if self._is_empty(self.id):
+            self.MissingRequiredField("id")
+        if not isinstance(self.id, CompoundHeight001Id):
+            self.id = CompoundHeight001Id(self.id)
+
+        super().__post_init__(**kwargs)
+
+
 @dataclass(repr=False)
 class IntegratedHeight001(IntegratedVariable):
     """

src/bdc_variable_library/datamodel/bdc_variable_library_pydantic.py

@@ -2265,6 +2265,26 @@ class CompoundHeight002(CompoundVariable):
     id: str = Field(default=..., description="""A unique identifier for a variable within BDC""", json_schema_extra = { "linkml_meta": {'domain_of': ['Entity'], 'slot_uri': 'schema:identifier'} })
 
 
+class CompoundHeight001(CompoundVariable):
+    """
+    Height variable with metadata, measured in cm and collected using a wall-mounted stadiometer
+    """
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/linkml/bdc-variable-library',
+         'instantiates': ['HumanBodyHeightRecord001']})
+
+    cde_id: Optional[str] = Field(default=None, description="""CURIE from Condor""", json_schema_extra = { "linkml_meta": {'domain_of': ['CompoundVariable', 'IntegratedVariable']} })
+    bdchm_type: Optional[BdchmTypeEnum] = Field(default=None, description="""Entity type from BDCHM that defines the variable type""", json_schema_extra = { "linkml_meta": {'domain_of': ['CompoundVariable', 'IntegratedVariable']} })
+    metadata: Optional[list[MetadataVariable]] = Field(default=None, description="""List of variable identifiers providing metadata for a compound variable""", json_schema_extra = { "linkml_meta": {'domain_of': ['CompoundVariable']} })
+    alert_value: Optional[list[str]] = Field(default=None, description="""List of values that provide extra optional information about a variable. Often this is used to indicate a violation of QA/QC""", json_schema_extra = { "linkml_meta": {'domain_of': ['CompoundVariable']} })
+    associated_study: Optional[str] = Field(default=None, description="""The study that produced the variable data""", json_schema_extra = { "linkml_meta": {'domain_of': ['Variable'], 'slot_uri': 'bdchm:ResearchStudy'} })
+    variable_description: Optional[str] = Field(default=None, description="""Human readable description of the variable.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Variable']} })
+    concept_type: Optional[str] = Field(default=None, description="""CURIE describing the main content of the variable. This can be from OBA, OMOP, or LOINC""", json_schema_extra = { "linkml_meta": {'domain_of': ['Variable']} })
+    variable_label: Optional[str] = Field(default=None, description="""Human readable label describing the variable""", json_schema_extra = { "linkml_meta": {'domain_of': ['Variable']} })
+    unit: Optional[str] = Field(default=None, description="""A unit from UCUM""", json_schema_extra = { "linkml_meta": {'domain_of': ['ClinicalMeasurementRecord', 'Variable'],
+         'slot_uri': 'bdchm:unit'} })
+    id: str = Field(default=..., description="""A unique identifier for a variable within BDC""", json_schema_extra = { "linkml_meta": {'domain_of': ['Entity'], 'slot_uri': 'schema:identifier'} })
+
+
 class IntegratedHeight001(IntegratedVariable):
     """
     Height variable containing data from multiple studies, normalized to cm
@@ -2358,5 +2378,6 @@ class ResearchStudy(Entity):
 AlertValue.model_rebuild()
 MetadataVariable.model_rebuild()
 CompoundHeight002.model_rebuild()
+CompoundHeight001.model_rebuild()
 IntegratedHeight001.model_rebuild()
 ResearchStudy.model_rebuild()

src/bdc_variable_library/schema/bdc_variable_library.yaml

@@ -125,6 +125,14 @@ classes:
       wall-mounted stadiometer
     instantiates:
       - HumanBodyHeightRecord002
+
+  CompoundHeight001:
+    is_a: CompoundVariable
+    description: >-
+      Height variable with metadata, measured in cm and collected using a
+      wall-mounted stadiometer
+    instantiates:
+      - HumanBodyHeightRecord001
 
   IntegratedHeight001:
     is_a: IntegratedVariable

tests/data/valid/CompoundHeight001-test.yml

@@ -0,0 +1,15 @@
+id: ARICABI5phv00294492c
+associated_study: ARIC000280
+variable_description: "Height"
+concept_type: OBA:VT0001253
+variable_label: "Height"
+cde_id: CONDOR:00003
+bdchm_type: observation
+unit: https://units-of-measurement.org/cm
+metadata:
+  - id: ARICABI5phv00294492s
+    microschema_slot: measurement_value
+  - id: ARICABI4phv00294491s
+    microschema_slot: age_at_measurement
+  - id: ARICSUBJECT_IDphv00294489s
+    microschema_slot: subject_identifier

tests/data/valid/IntegratedHeight001-test.yaml

@@ -3,8 +3,9 @@ associated_study: DMCPilotv1
 variable_description: "Height"
 concept_type: OBA:VT0001253
 variable_label: "Height"
-cde_id: CONDOR:00001
+cde_id: CONDOR:00003
 bdchm_type: observation
 unit: UCUM:cm
 integrates:
-  - FHSg3b0483phv00177539c
+  - FHSg3b0483phv00177539c
+  - ARICABI5phv00294492c

tests/data/valid/SingleVariable-004test.yaml

@@ -0,0 +1,12 @@
+id: ARICABI5phv00294492s
+associated_study: ARIC000280
+variable_description: "Height"
+concept_type: OBA:VT0001253
+variable_label: "Height"
+source_id: phv00294492v3p3
+file_id: pht006414v3p3
+file_name: ABI
+variable_name: ABI5
+source_variable_description: "Body height, height [Ankle Brachial BP index. ABI. Visit 5]"
+data_type: decimal
+unit: https://units-of-measurement.org/cm

tests/data/valid/SingleVariable-005test.yaml

@@ -0,0 +1,10 @@
+id: ARICSUBJECT_IDphv00294489s
+associated_study: ARIC000280
+variable_description: "Participant Identifier"
+variable_label: "Participant Identifier"
+source_id: phv00294489v3p3
+file_id: pht006414v3p3
+file_name: ABI
+variable_name: shareid
+source_variable_description: "De-identified ARIC subject ID [Ankle Brachial BP Index, ABI. Visit 5]"
+data_type: uriorcurie

tests/data/valid/SingleVariable-006test.yaml

@@ -0,0 +1,11 @@
+id: ARICABI4phv00294491s
+associated_study: ARIC000280
+variable_description: "Participant age at visit 5"
+variable_label: "Participant Age"
+source_id: phv00294491v3p3
+file_id: pht006414v3p3
+file_name: ABI
+variable_name: ABI4
+source_variable_description: "Age [Ankle Brachial BP index, ABI. Visit 5]"
+data_type: integer
+unit: UCUM:a