dynamic named episode cols

Author: gkennos

CHANGELOG.md

@@ -42,4 +42,7 @@
 - treatment eps
 
 ## 0.2.6
-- update col for treatment eps
+- update col for treatment eps
+
+## 0.2.7
+- episode cols dynamic name correction

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "omop-constructs"
-version = "0.2.6"
+version = "0.2.7"
 description = "For building complex constructs on top of the omop-alchemy library."
 readme = "README.md"
 authors = [

src/omop_constructs/alchemy/episodes/condition_episode_mv.py

@@ -39,8 +39,8 @@ class OverarchingDiseaseEpisodeMV(
     extent_episode_concept_id: so.Mapped[Optional[int]] = so.mapped_column(sa.Integer, nullable=True)
     extent_episode_label: so.Mapped[Optional[str]] = so.mapped_column(sa.String, nullable=True)
 
-    extent_start_date: so.Mapped[Optional[date]] = so.mapped_column(sa.Date, nullable=True)
-    extent_end_date: so.Mapped[Optional[date]] = so.mapped_column(sa.Date, nullable=True)
+    extent_episode_start_date: so.Mapped[Optional[date]] = so.mapped_column(sa.Date, nullable=True)
+    extent_episode_end_date: so.Mapped[Optional[date]] = so.mapped_column(sa.Date, nullable=True)
 
     def __repr__(self) -> str:
         if self.has_extent:
@@ -62,7 +62,7 @@ def disease_interval(self):
     def extent_interval(self):
         if self.extent_episode_id is None:
             return None
-        return (self.extent_start_date, self.extent_end_date)
+        return (self.extent_episode_start_date, self.extent_episode_end_date)
 
 @register_construct
 class TreatmentRegimenCycleMV(
@@ -89,15 +89,15 @@ class TreatmentRegimenCycleMV(
     regimen_episode_concept_id: so.Mapped[int] = so.mapped_column(sa.Integer)
     regimen_episode_label: so.Mapped[str] = so.mapped_column(sa.String)
 
-    regimen_start_date: so.Mapped[date] = so.mapped_column(sa.Date)
-    regimen_end_date: so.Mapped[Optional[date]] = so.mapped_column(sa.Date, nullable=True)
+    regimen_episode_start_date: so.Mapped[date] = so.mapped_column(sa.Date)
+    regimen_episode_end_date: so.Mapped[Optional[date]] = so.mapped_column(sa.Date, nullable=True)
 
     cycle_episode_id: so.Mapped[Optional[int]] = so.mapped_column(sa.Integer, nullable=True)
     cycle_episode_concept_id: so.Mapped[Optional[int]] = so.mapped_column(sa.Integer, nullable=True)
     cycle_episode_label: so.Mapped[Optional[str]] = so.mapped_column(sa.String, nullable=True)
 
-    cycle_start_date: so.Mapped[Optional[date]] = so.mapped_column(sa.Date, nullable=True)
-    cycle_end_date: so.Mapped[Optional[date]] = so.mapped_column(sa.Date, nullable=True)
+    cycle_episode_start_date: so.Mapped[Optional[date]] = so.mapped_column(sa.Date, nullable=True)
+    cycle_episode_end_date: so.Mapped[Optional[date]] = so.mapped_column(sa.Date, nullable=True)
 
 
     def __repr__(self) -> str:
@@ -114,10 +114,10 @@ def has_cycle(self) -> bool:
 
     @property
     def regimen_interval(self):
-        return (self.regimen_start_date, self.regimen_end_date)
+        return (self.regimen_episode_start_date, self.regimen_episode_end_date)
 
     @property
     def cycle_interval(self):
         if self.cycle_episode_id is None:
             return None
-        return (self.cycle_start_date, self.cycle_end_date)
+        return (self.cycle_episode_start_date, self.cycle_episode_end_date)

src/omop_constructs/alchemy/episodes/episode_factories.py

@@ -48,25 +48,25 @@ def get_episode_hierarchy_query(
     parent_episode_subq: sa.Subquery,
     child_episode_subq: sa.Subquery,
     name: str = "episode_optional_children",
-    parent_label: str = 'disease',
-    child_label: str = 'extent'
+    parent_label: str = 'disease_episode',
+    child_label: str = 'extent_episode'
 ) -> sa.Subquery:
     """
     Expands an episode subquery to optionally include child episodes.
     """
 
     return (
         sa.select(
-            parent_episode_subq.c.episode_id.label(f"{parent_label}_episode_id"),
+            parent_episode_subq.c.episode_id.label(f"{parent_label}_id"),
             parent_episode_subq.c.person_id.label("person_id"),
-            parent_episode_subq.c.episode_concept_id.label(f"{parent_label}_episode_concept_id"),
-            parent_episode_subq.c.episode_label.label(f"{parent_label}_episode_label"),
-            parent_episode_subq.c.episode_start_date.label(f"{parent_label}_episode_start_date"),
-            parent_episode_subq.c.episode_end_date.label(f"{parent_label}_episode_end_date"),
+            parent_episode_subq.c.episode_concept_id.label(f"{parent_label}_concept_id"),
+            parent_episode_subq.c.episode_label.label(f"{parent_label}_label"),
+            parent_episode_subq.c.episode_start_date.label(f"{parent_label}_start_date"),
+            parent_episode_subq.c.episode_end_date.label(f"{parent_label}_end_date"),
 
-            child_episode_subq.c.episode_id.label(f"{child_label}_episode_id"),
-            child_episode_subq.c.episode_concept_id.label(f"{child_label}_episode_concept_id"),
-            child_episode_subq.c.episode_label.label(f"{child_label}_episode_label"),
+            child_episode_subq.c.episode_id.label(f"{child_label}_id"),
+            child_episode_subq.c.episode_concept_id.label(f"{child_label}_concept_id"),
+            child_episode_subq.c.episode_label.label(f"{child_label}_label"),
             child_episode_subq.c.episode_start_date.label(f"{child_label}_start_date"),
             child_episode_subq.c.episode_end_date.label(f"{child_label}_end_date"),
         )

src/omop_constructs/alchemy/episodes/episode_joins.py

@@ -31,6 +31,6 @@
     parent_episode_subq=treatment_regimen_select,
     child_episode_subq=treatment_cycle_select,
     name="treatment_regimen_with_cycles",
-    parent_label="regimen",
-    child_label="cycle"
+    parent_label="regimen_episode",
+    child_label="cycle_episode"
 )