fixed all stage cols

Author: gkennos

CHANGELOG.md

@@ -78,4 +78,7 @@
 - mets cols thru to condition mods
 
 ## 0.3.0
-- all stage modifier mapper
+- all stage modifier mapper
+
+## 0.3.1
+- fixed all stage cols

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "omop-constructs"
-version = "0.3.0"
+version = "0.3.1"
 description = "For building complex constructs on top of the omop-alchemy library."
 readme = "README.md"
 authors = [

src/omop_constructs/alchemy/modifiers/__init__.py

@@ -9,7 +9,7 @@
     MetastaticDiseaseModifierMV,
     AllStageModifierMV
 )
-from .condition_modifier_mv import ModifiedCondition
+from .condition_modifier_mv import ModifiedCondition, StageModifier
 
 __all__ = [
     "TStageMV",
@@ -21,5 +21,6 @@
     "SizeModifierMV",
     "ModifiedCondition",
     "MetastaticDiseaseModifierMV",
-    "AllStageModifierMV"
+    "AllStageModifierMV",
+    "StageModifier"
 ]

src/omop_constructs/alchemy/modifiers/condition_modifier_join.py

@@ -18,6 +18,7 @@
 )
 
 condition_concept = so.aliased(Concept, name='condition_concept')
+stage_concept = so.aliased(Concept, name='stage_concept')
 
 modified_conditions_join = (
     sa.select(
@@ -147,10 +148,10 @@
         Condition_Occurrence.condition_concept_id,
         condition_concept.concept_name.label('condition_concept'),
         Episode_Event.episode_id.label('condition_episode'),
-    	AllStageModifierMV.stage_id.label('stage_id'),
-    	AllStageModifierMV.stage_date.label('stage_date'),
-    	AllStageModifierMV.stage_concept_id.label('stage_concept_id'),
-    	AllStageModifierMV.stage_label.label('stage_label'),
+    	AllStageModifierMV.measurement_id.label('stage_id'),
+    	AllStageModifierMV.measurement_date.label('stage_date'),
+    	AllStageModifierMV.measurement_concept_id.label('stage_concept_id'),
+    	stage_concept.concept_name.label('stage_label'),
     )
     .join(
         Episode_Event, 
@@ -169,4 +170,5 @@
         isouter=True
     )
     .join(condition_concept, condition_concept.concept_id==Condition_Occurrence.condition_concept_id)
+    .join(stage_concept, stage_concept.concept_id==AllStageModifierMV.measurement_concept_id)
 )

src/omop_constructs/alchemy/modifiers/modifier_mappers.py

@@ -116,7 +116,7 @@ class MetastaticDiseaseModifierMV(MeasModCols, MaterializedViewMixin, Base):
     measurement_concept_id = sa.Column(sa.Integer)
 
 @register_construct
-class AllStageModifierMV(StageColumns, MaterializedViewMixin, Base):
+class AllStageModifierMV(MeasModCols, MaterializedViewMixin, Base):
     __mv_name__ = "all_stage_modifier_mv"
     __mv_select__ = all_stage_select.select()
     __mv_index__ = "measurement_event_id"