omop-constructs 0.3.0__tar.gz → 0.3.2__tar.gz

{omop_constructs-0.3.0 → omop_constructs-0.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: omop-constructs
-Version: 0.3.0
+Version: 0.3.2
 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-0.3.0 → omop_constructs-0.3.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "omop-constructs"
-version = "0.3.0"
+version = "0.3.2"
 description = "For building complex constructs on top of the omop-alchemy library."
 readme = "README.md"
 authors = [

{omop_constructs-0.3.0 → omop_constructs-0.3.2}/src/omop_constructs/alchemy/episodes/__init__.py

@@ -1,9 +1,12 @@
-from .condition_episode_mv import OverarchingDiseaseEpisodeMV, TreatmentRegimenCycleMV, ConditionEpisodeMV
+from .condition_episode_mv import OverarchingDiseaseEpisodeMV, TreatmentRegimenCycleMV, ConditionEpisodeMV, DxTreatStartMV
 from .condition_episode_objects import ConditionEpisodeObject
+from .surgical_procedure_mv import SurgicalProcedureMV
 
 __all__ = [
     "OverarchingDiseaseEpisodeMV",
     "TreatmentRegimenCycleMV",
     "ConditionEpisodeMV",
     "ConditionEpisodeObject",
+    "SurgicalProcedureMV",
+    "DxTreatStartMV",
 ]

{omop_constructs-0.3.0 → omop_constructs-0.3.2}/src/omop_constructs/alchemy/episodes/condition_episode_mv.py

@@ -3,7 +3,7 @@ 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, condition_episode_select
+from .episode_joins import overarching_disease_episode, treatment_regimen_with_cycles, condition_episode_select, dx_window_select
 from ...core.materialized import MaterializedViewMixin
 from ...core.constructs import register_construct
 
@@ -116,6 +116,8 @@ class TreatmentRegimenCycleMV(
     episode_start_date: so.Mapped[date] = so.mapped_column(sa.Date)
     episode_end_date: so.Mapped[Optional[date]] = so.mapped_column(sa.Date, nullable=True)
 
+    episode_parent_id: so.Mapped[Optional[int]] = so.mapped_column(sa.Integer, 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)
@@ -143,4 +145,21 @@ class TreatmentRegimenCycleMV(
     def cycle_interval(self):
         if self.cycle_episode_id is None:
             return None
-        return (self.cycle_episode_start_date, self.cycle_episode_end_date)
+        return (self.cycle_episode_start_date, self.cycle_episode_end_date)
+    
+
+@register_construct
+class DxTreatStartMV(MaterializedViewMixin, Base):
+    __mv_name__ = "dx_treat_start_mv"
+    __mv_select__ = dx_window_select.select()
+    __mv_index__ = "dx_episode_id"
+    __deps__ = (ConditionEpisodeMV.__mv_name__, TreatmentRegimenCycleMV.__mv_name__,)
+    __tablename__ = __mv_name__
+
+    dx_episode_id: so.Mapped[int] = so.mapped_column(primary_key=True)
+    person_id: so.Mapped[int] = so.mapped_column(sa.Integer)
+    dx_start_date: so.Mapped[date] = so.mapped_column(sa.Date)
+
+    treatment_start: so.Mapped[Optional[date]] = so.mapped_column(sa.Date)
+    treatment_end: so.Mapped[Optional[date]] = so.mapped_column(sa.Date)
+    treatment_regimen_count: so.Mapped[Optional[int]] = so.mapped_column(sa.Integer)

{omop_constructs-0.3.0 → omop_constructs-0.3.2}/src/omop_constructs/alchemy/episodes/episode_factories.py

@@ -6,8 +6,9 @@ from omop_alchemy.cdm.model import (
     Concept
 )
 
-episode_concept = so.aliased(Concept, name="episode_concept")
+from omop_semantics.runtime.default_valuesets import runtime # type: ignore
 
+episode_concept = so.aliased(Concept, name="episode_concept")
 
 def get_episode_query(
     episode_concept_ids: Iterable[int],
@@ -26,8 +27,6 @@ def get_episode_query(
             Episode.episode_end_date,
             Episode.episode_end_datetime,
             Episode.episode_concept_id,
-            Episode.episode_end_datetime,
-            Episode.episode_concept_id,
             episode_concept.concept_name.label(f"episode_label"),
             Episode.episode_object_concept_id,
             Episode.episode_type_concept_id,
@@ -74,4 +73,33 @@ def get_episode_hierarchy_query(
             isouter=True,  
         )
         .subquery(name=name)        
+    )
+
+def dx_treatment_window(name="dx_treat_window"):
+    Diagnosis = Episode
+    Regimen = so.aliased(Episode, name="regimen")
+
+    return (
+        sa.select(
+            Diagnosis.episode_id.label("dx_episode_id"),
+            Diagnosis.person_id,
+            Diagnosis.episode_start_date.label("dx_start_date"),
+            sa.func.min(Regimen.episode_start_date).label("treatment_start"),
+            sa.func.max(Regimen.episode_end_date).label("treatment_end"),
+            sa.func.count(sa.distinct(Regimen.episode_id)).label("treatment_regimen_count"),
+        )
+        .join(
+            Regimen,
+            Regimen.episode_parent_id == Diagnosis.episode_id,
+        )
+        .where(
+            Diagnosis.episode_concept_id.in_(runtime.types.disease_episode_types.ids),
+            Regimen.episode_concept_id.in_(runtime.types.treatment_episode_types.ids),
+        )
+        .group_by(
+            Diagnosis.episode_id,
+            Diagnosis.person_id,
+            Diagnosis.episode_start_date,
+        )
+        .subquery(name)
     )

{omop_constructs-0.3.0 → omop_constructs-0.3.2}/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 .episode_factories import get_episode_query, get_episode_hierarchy_query, dx_treatment_window
 
 episode_of_care_select = get_episode_query(
         [runtime.types.disease_episode_types.episode_of_care],  # type: ignore
@@ -37,4 +37,6 @@ treatment_regimen_with_cycles = get_episode_hierarchy_query(
     child_episode_subq=treatment_cycle_select,
     name="treatment_regimen_with_cycles",
     child_label="cycle_episode"
-)
+)
+
+dx_window_select = dx_treatment_window()

omop_constructs-0.3.2/src/omop_constructs/alchemy/episodes/surgical_joins.py

@@ -0,0 +1,131 @@
+import sqlalchemy as sa
+import sqlalchemy.orm as so
+from typing import Optional
+from omop_alchemy.cdm.model import Concept, Concept_Ancestor, Procedure_Occurrence, Observation
+from omop_semantics.runtime.default_valuesets import runtime # type: ignore
+from .condition_episode_mv import ConditionEpisodeMV
+
+rth_ca = so.aliased(Concept_Ancestor, name="rth_ca")
+srg_ca = so.aliased(Concept_Ancestor, name="srg_ca")
+
+surgical_concepts = (
+    sa.select(
+        Concept.concept_id,
+        Concept.concept_name,
+        Concept.concept_code,
+    )
+    .join(srg_ca, Concept.concept_id == srg_ca.descendant_concept_id)
+    .where(srg_ca.ancestor_concept_id == runtime.cancer_procedures.cancer_procedure_types.surgical_procedure)
+)
+
+radiotherapy_concepts = (
+    sa.select(
+        Concept.concept_id,
+        Concept.concept_name,
+        Concept.concept_code,
+    )
+    .join(rth_ca, Concept.concept_id == rth_ca.descendant_concept_id)
+    .where(rth_ca.ancestor_concept_id == runtime.cancer_procedures.cancer_procedure_types.rt_procedure)
+)
+
+radioisotope_concepts = (
+    sa.select(
+        Concept.concept_id,
+        Concept.concept_name,
+        Concept.concept_code,
+    )
+    .join(rth_ca, Concept.concept_id == rth_ca.descendant_concept_id)
+    .where(rth_ca.ancestor_concept_id == runtime.cancer_procedures.cancer_procedure_types.rn_procedure)
+)
+
+surg_only = surgical_concepts.except_all(
+    radiotherapy_concepts.union_all(radioisotope_concepts)
+).subquery(name="surg_only")
+
+radioisotopes_only = radioisotope_concepts.subquery(name="radioisotopes_only")
+
+surg_obs_concept = so.aliased(Concept, name="surg_obs_concept")
+
+surgical_procedure_events = (
+    sa.select(
+        Procedure_Occurrence.person_id,
+        Procedure_Occurrence.procedure_occurrence_id.label("surgery_occurrence_id"),
+        Procedure_Occurrence.procedure_concept_id.label("surgery_concept_id"),
+        Procedure_Occurrence.procedure_datetime.label("surgery_datetime"),
+        surg_only.c.concept_name.label("surgery_name"),
+        surg_only.c.concept_code.label("surgery_concept_code"),
+        sa.literal("procedure").label("surgery_source"),
+    )
+    .join(surg_only, surg_only.c.concept_id == Procedure_Occurrence.procedure_concept_id)
+)
+
+historical_surgical_events = (
+    sa.select(
+        Observation.person_id,
+        Observation.observation_id.label("surgery_occurrence_id"),
+        Observation.value_as_concept_id.label("surgery_concept_id"),
+        Observation.observation_datetime.label("surgery_datetime"),
+        surg_obs_concept.concept_name.label("surgery_name"),
+        surg_obs_concept.concept_code.label("surgery_concept_code"),
+        sa.literal("observation").label("surgery_source"),
+    )
+    .join(surg_obs_concept, surg_obs_concept.concept_id == Observation.value_as_concept_id)
+    .where(Observation.observation_concept_id == runtime.cancer_procedures.cancer_procedure_types.historical_procedure)
+)
+
+all_cancer_relevant_surg = (
+    sa.union_all(surgical_procedure_events, historical_surgical_events)
+    .subquery(name="all_cancer_relevant_surg")
+)
+
+
+cancer_relevant_surg_select = (
+    sa.select(
+        sa.func.row_number().over().label("mv_id"),
+        ConditionEpisodeMV.person_id,
+        ConditionEpisodeMV.episode_id.label("condition_episode_id"),
+        ConditionEpisodeMV.episode_start_date.label("condition_start_date"),
+
+        all_cancer_relevant_surg.c.surgery_occurrence_id,
+        all_cancer_relevant_surg.c.surgery_concept_id,
+        all_cancer_relevant_surg.c.surgery_datetime,
+        all_cancer_relevant_surg.c.surgery_concept_code,
+        all_cancer_relevant_surg.c.surgery_name,
+        all_cancer_relevant_surg.c.surgery_source,
+    )
+    # still person-level until windowing is added
+    .join(
+        all_cancer_relevant_surg,
+        all_cancer_relevant_surg.c.person_id == ConditionEpisodeMV.person_id,
+        isouter=True,
+    )
+    .subquery(name="cancer_relevant_surg")
+)
+
+radioisotope_select = (
+    sa.select(
+        sa.func.row_number().over().label("mv_id"),
+        ConditionEpisodeMV.person_id,
+        ConditionEpisodeMV.episode_id.label("condition_episode_id"),
+        ConditionEpisodeMV.episode_start_date.label("condition_start_date"),
+
+        Procedure_Occurrence.procedure_occurrence_id.label("ri_occurrence_id"),
+        Procedure_Occurrence.procedure_concept_id.label("ri_concept_id"),
+        Procedure_Occurrence.procedure_datetime.label("ri_datetime"),
+        radioisotopes_only.c.concept_name.label("ri_name"),
+        radioisotopes_only.c.concept_code.label("ri_concept_code"),
+        sa.literal("radioisotope_procedure").label("ri_source"),
+    )
+    .join(
+        Procedure_Occurrence,
+        Procedure_Occurrence.person_id == ConditionEpisodeMV.person_id,
+        isouter=True,
+    )
+    .join(
+        radioisotopes_only,
+        radioisotopes_only.c.concept_id == Procedure_Occurrence.procedure_concept_id,
+        isouter=True,
+    )
+    .subquery(name="radioisotope_procedure")
+)
+

omop_constructs-0.3.2/src/omop_constructs/alchemy/episodes/surgical_procedure_mv.py

@@ -0,0 +1,57 @@
+import sqlalchemy as sa
+import sqlalchemy.orm as so
+from datetime import date
+from typing import Optional
+from orm_loader.helpers import Base
+from ...core.materialized import MaterializedViewMixin
+from ...core.constructs import register_construct
+from .surgical_joins import all_cancer_relevant_surg, cancer_relevant_surg_select, radioisotope_select
+from .condition_episode_mv import ConditionEpisodeMV
+
+
+@register_construct
+class SurgicalProcedureMV(MaterializedViewMixin, Base):
+    __mv_name__ = "surgical_procedure_mv"
+    __mv_select__ = cancer_relevant_surg_select.select()
+    __mv_index__ = "mv_id"
+    __deps__ = (ConditionEpisodeMV.__mv_name__,)
+    __tablename__ = __mv_name__
+    __table_args__ = {"extend_existing": True}
+
+    mv_id: so.Mapped[int] = so.mapped_column(primary_key=True)
+
+    person_id: so.Mapped[int] = so.mapped_column(sa.Integer)
+    condition_episode_id: so.Mapped[int] = so.mapped_column(sa.Integer)
+    condition_start_date: so.Mapped[date] = so.mapped_column(sa.Date)
+
+    surgery_occurrence_id: so.Mapped[int] = so.mapped_column(sa.Integer)
+    surgery_concept_id: so.Mapped[int] = so.mapped_column(sa.Integer)
+    surgery_datetime: so.Mapped[Optional[date]] = so.mapped_column(sa.DateTime)
+
+    surgery_name: so.Mapped[str] = so.mapped_column(sa.String)
+    surgery_concept_code: so.Mapped[str] = so.mapped_column(sa.String)
+    surgery_source: so.Mapped[str] = so.mapped_column(sa.String)
+
+
+@register_construct
+class RadioisotopeMV(MaterializedViewMixin, Base):
+    __mv_name__ = "radioisotope_mv"
+    __mv_select__ = radioisotope_select.select()
+    __mv_index__ = "mv_id"
+    __deps__ = (ConditionEpisodeMV.__mv_name__,)
+    __tablename__ = __mv_name__
+    __table_args__ = {"extend_existing": True}
+
+    mv_id: so.Mapped[int] = so.mapped_column(primary_key=True)
+
+    person_id: so.Mapped[int] = so.mapped_column(sa.Integer)
+    condition_episode_id: so.Mapped[int] = so.mapped_column(sa.Integer)
+    condition_start_date: so.Mapped[date] = so.mapped_column(sa.Date)
+
+    ri_occurrence_id: so.Mapped[int] = so.mapped_column(sa.Integer)
+    ri_concept_id: so.Mapped[int] = so.mapped_column(sa.Integer)
+    ri_datetime: so.Mapped[Optional[date]] = so.mapped_column(sa.DateTime)
+
+    ri_name: so.Mapped[str] = so.mapped_column(sa.String)
+    ri_concept_code: so.Mapped[str] = so.mapped_column(sa.String)
+    ri_source: so.Mapped[str] = so.mapped_column(sa.String)

omop_constructs-0.3.2/src/omop_constructs/alchemy/episodes/treatment_summary_joins.py

@@ -0,0 +1,25 @@
+import sqlalchemy as sa
+from omop_semantics.runtime.default_valuesets import runtime
+from .condition_episode_mv import TreatmentRegimenCycleMV
+
+treatment_summary = (
+    sa.select(
+        TreatmentRegimenCycleMV.person_id,
+        TreatmentRegimenCycleMV.episode_parent_id.label("condition_episode_id"),
+        TreatmentRegimenCycleMV.episode_concept_id,
+        TreatmentRegimenCycleMV.episode_label,
+
+        sa.func.min(TreatmentRegimenCycleMV.episode_start_date).label("treatment_start_date"),
+        sa.func.max(TreatmentRegimenCycleMV.episode_end_date).label("treatment_end_date"),
+
+        sa.func.count(sa.distinct(TreatmentRegimenCycleMV.episode_id)).label("regimen_count"),
+        sa.func.count(sa.distinct(TreatmentRegimenCycleMV.cycle_episode_id)).label("cycle_count"),
+    )
+    .group_by(
+        TreatmentRegimenCycleMV.person_id,
+        TreatmentRegimenCycleMV.episode_parent_id,
+        TreatmentRegimenCycleMV.episode_concept_id,
+        TreatmentRegimenCycleMV.episode_label,
+    )
+    .subquery("treatment_summary")
+)

{omop_constructs-0.3.0 → omop_constructs-0.3.2}/src/omop_constructs/alchemy/modifiers/__init__.py

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

{omop_constructs-0.3.0 → omop_constructs-0.3.2}/src/omop_constructs/alchemy/modifiers/condition_modifier_join.py

@@ -18,6 +18,7 @@ from .modifier_mappers import (
 )
 
 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 @@ all_stage_join = (
         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 @@ all_stage_join = (
         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)
 )

{omop_constructs-0.3.0 → omop_constructs-0.3.2}/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"