omop-constructs 0.2.6__tar.gz → 0.2.8__tar.gz

{omop_constructs-0.2.6 → omop_constructs-0.2.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: omop-constructs
-Version: 0.2.6
+Version: 0.2.8
 Summary: For building complex constructs on top of the omop-alchemy library.
 Author: Georgie Kennedy
 Author-email: Georgie Kennedy <georgina.kennedy@unsw.edu.au>

{omop_constructs-0.2.6 → omop_constructs-0.2.8}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "omop-constructs"
-version = "0.2.6"
+version = "0.2.8"
 description = "For building complex constructs on top of the omop-alchemy library."
 readme = "README.md"
 authors = [

{omop_constructs-0.2.6 → omop_constructs-0.2.8}/src/omop_constructs/alchemy/episodes/__init__.py

@@ -1,13 +1,16 @@
-from .condition_episode_mv import OverarchingDiseaseEpisodeMV, TreatmentRegimenCycleMV
+from .condition_episode_mv import OverarchingDiseaseEpisodeMV, TreatmentRegimenCycleMV, ConditionEpisodeMV
 from .episode_joins import episode_of_care_select, disease_extent_select, overarching_disease_episode
 from .episode_factories import get_episode_query, get_episode_hierarchy_query
+from .condition_episode_objects import ConditionEpisodeObject
 
 __all__ = [
     "OverarchingDiseaseEpisodeMV",
     "TreatmentRegimenCycleMV",
+    "ConditionEpisodeMV",
     "episode_of_care_select",
     "disease_extent_select",
     "overarching_disease_episode",
     "get_episode_query",
     "get_episode_hierarchy_query",
+    "ConditionEpisodeObject",
 ]

{omop_constructs-0.2.6 → omop_constructs-0.2.8}/src/omop_constructs/alchemy/episodes/condition_episode_mv.py

@@ -3,12 +3,45 @@ import sqlalchemy.orm as so
 from orm_loader.helpers import Base
 from datetime import date
 from typing import Optional
-from .episode_joins import overarching_disease_episode, treatment_regimen_with_cycles
+from .episode_joins import overarching_disease_episode, treatment_regimen_with_cycles, condition_episode_select
 from ...core.materialized import MaterializedViewMixin
 from ...core.constructs import register_construct
 
+class DiseaseEpisodeCols:
+
+    disease_episode_id: so.Mapped[int] = so.mapped_column(sa.Integer, primary_key=True)
+    person_id: so.Mapped[int] = so.mapped_column(sa.Integer)
+
+    disease_episode_concept_id: so.Mapped[int] = so.mapped_column(sa.Integer)
+    disease_episode_label: so.Mapped[str] = so.mapped_column(sa.String)
+
+    disease_episode_start_date: so.Mapped[date] = so.mapped_column(sa.Date)
+    disease_episode_end_date: so.Mapped[Optional[date]] = so.mapped_column(sa.Date, nullable=True)
+
+@register_construct
+class ConditionEpisodeMV(
+    DiseaseEpisodeCols,
+    MaterializedViewMixin,
+    Base,
+):
+    """
+    Materialized view representing all disease episodes (irrespective of type).
+
+    Used for resolving linkages between clinical events and disease episodes 
+    when there is no explicit link in the source data, and we must therefore use
+    time-windowing logic.
+    """
+    __mv_name__ = "condition_episode_mv"
+    __mv_select__ = condition_episode_select.select()
+    __mv_index__ = "disease_episode_id"
+    __deps__ = ()
+    __tablename__ = __mv_name__
+    __table_args__ = {"extend_existing": True}
+
+
 @register_construct
 class OverarchingDiseaseEpisodeMV(
+    DiseaseEpisodeCols,
     MaterializedViewMixin,
     Base,
 ):
@@ -16,7 +49,7 @@ class OverarchingDiseaseEpisodeMV(
     Materialized view representing overarching disease episodes
     with optional child disease-extent episodes.
 
-    One row per (episode_of_care, disease_extent_episode?) pair.
+    One row per (episode_of_care, disease_extent_episode) pair.
     """
 
     __mv_name__ = "overarching_disease_episode_mv"
@@ -26,21 +59,12 @@ class OverarchingDiseaseEpisodeMV(
     __tablename__ = __mv_name__
     __table_args__ = {"extend_existing": True}
 
-    disease_episode_id: so.Mapped[int] = so.mapped_column(sa.Integer, primary_key=True)
-    person_id: so.Mapped[int] = so.mapped_column(sa.Integer)
-
-    disease_episode_concept_id: so.Mapped[int] = so.mapped_column(sa.Integer)
-    disease_episode_label: so.Mapped[str] = so.mapped_column(sa.String)
-
-    disease_episode_start_date: so.Mapped[date] = so.mapped_column(sa.Date)
-    disease_episode_end_date: so.Mapped[Optional[date]] = so.mapped_column(sa.Date, nullable=True)
-
     extent_episode_id: so.Mapped[Optional[int]] = so.mapped_column(sa.Integer, nullable=True)
     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 +86,7 @@ class OverarchingDiseaseEpisodeMV(
     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 +113,15 @@ 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 +138,10 @@ class TreatmentRegimenCycleMV(
 
     @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)

omop_constructs-0.2.8/src/omop_constructs/alchemy/episodes/condition_episode_objects.py

@@ -0,0 +1,51 @@
+import sqlalchemy as sa
+import sqlalchemy.orm as so
+from typing import List
+
+from omop_alchemy.cdm.model.structural import Episode_Event
+from ..modifiers import ModifiedCondition
+from .condition_episode_mv import ConditionEpisodeMV   # wherever you defined it
+from omop_semantics.runtime.default_valuesets import runtime # type: ignore
+
+
+class ConditionEpisodeObject(ConditionEpisodeMV):
+    """
+    Consumption-layer wrapper around ConditionEpisodeMV that exposes
+    relationships to Episode_Event and resolved Condition_Occurrence rows.
+    """
+
+    __tablename__ = ConditionEpisodeMV.__tablename__
+    __mapper_args__ = {"concrete": False}
+    # All Episode_Event rows for this episode
+    episode_events: so.Mapped[List[Episode_Event]] = so.relationship(
+        Episode_Event,
+        primaryjoin=ConditionEpisodeMV.disease_episode_id == so.foreign(Episode_Event.episode_id),
+        viewonly=True,
+        lazy="selectin",
+    )
+
+    # Only Condition_Occurrence-linked events
+    condition_events: so.Mapped[List[Episode_Event]] = so.relationship(
+        Episode_Event,
+        primaryjoin=sa.and_(
+            ConditionEpisodeMV.disease_episode_id == so.foreign(Episode_Event.episode_id),
+            Episode_Event.episode_event_field_concept_id
+            == runtime.modifiers.modifier_fields.condition_occurrence_id,
+        ),
+        viewonly=True,
+        lazy="selectin",
+    )
+
+    # Direct relationship to ModifiedCondition MV via Episode_Event spine
+    modified_conditions: so.Mapped[List[ModifiedCondition]] = so.relationship(
+        ModifiedCondition,
+        secondary=Episode_Event.__table__,
+        primaryjoin=ConditionEpisodeMV.disease_episode_id == so.foreign(Episode_Event.episode_id),
+        secondaryjoin=sa.and_(
+            so.foreign(Episode_Event.event_id) == ModifiedCondition.condition_occurrence_id,
+            Episode_Event.episode_event_field_concept_id
+            == runtime.modifiers.modifier_fields.condition_occurrence_id,
+        ),
+        viewonly=True,
+        lazy="selectin",
+    )

{omop_constructs-0.2.6 → omop_constructs-0.2.8}/src/omop_constructs/alchemy/episodes/episode_factories.py

@@ -1,14 +1,10 @@
 import sqlalchemy as sa
 import sqlalchemy.orm as so
-from sqlalchemy.sql import ColumnElement
-from typing import Iterable, Any
+from typing import Iterable
 from omop_alchemy.cdm.model import (
-    Condition_Occurrence,
     Episode,
-    Concept,
-    Episode_Event
+    Concept
 )
-from omop_semantics.runtime.default_valuesets import runtime
 
 episode_concept = so.aliased(Concept, name="episode_concept")
 
@@ -48,8 +44,8 @@ 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.
@@ -57,16 +53,16 @@ def get_episode_hierarchy_query(
 
     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"),
         )

{omop_constructs-0.2.6 → omop_constructs-0.2.8}/src/omop_constructs/alchemy/episodes/episode_joins.py

@@ -1,5 +1,5 @@
+from omop_semantics.runtime.default_valuesets import runtime # type: ignore
 from .episode_factories import get_episode_query, get_episode_hierarchy_query
-from omop_semantics.runtime.default_valuesets import runtime
 
 episode_of_care_select = get_episode_query(
         [runtime.types.disease_episode_types.episode_of_care],  # type: ignore
@@ -17,6 +17,11 @@ overarching_disease_episode = get_episode_hierarchy_query(
     name="overarching_disease_episode",
 )
 
+condition_episode_select = get_episode_query(
+    [runtime.types.disease_episode_types.disease_progression, runtime.types.disease_episode_types.metastatic, runtime.types.disease_episode_types.episode_of_care],  # type: ignore
+    name="condition_episode",
+)
+
 treatment_regimen_select = get_episode_query(
     [runtime.types.treatment_episode_types.treatment_regimen],  # type: ignore
     name="treatment_regimen",
@@ -31,6 +36,6 @@ treatment_regimen_with_cycles = get_episode_hierarchy_query(
     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"
 )