omop-constructs 0.3.2__tar.gz → 0.3.4__tar.gz

{omop_constructs-0.3.2 → omop_constructs-0.3.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: omop-constructs
-Version: 0.3.2
+Version: 0.3.4
 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-0.3.2 → omop_constructs-0.3.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "omop-constructs"
-version = "0.3.2"
+version = "0.3.4"
 description = "For building complex constructs on top of the omop-alchemy library."
 readme = "README.md"
 authors = [

{omop_constructs-0.3.2 → omop_constructs-0.3.4}/src/omop_constructs/alchemy/events/__init__.py

@@ -9,6 +9,7 @@ from .dx_linked_event_mv import (
     DistressThermometerDxMV,
     ECOGDxMV,
     SmokingPYHDxMV,
+    DxMeasurementMV
 )
 
 __all__ = [
@@ -21,5 +22,6 @@ __all__ = [
     "FEV1DxMV",
     "DistressThermometerDxMV",
     "ECOGDxMV",
-    "SmokingPYHDxMV"
+    "SmokingPYHDxMV",
+    "DxMeasurementMV"
 ]

{omop_constructs-0.3.2 → omop_constructs-0.3.4}/src/omop_constructs/alchemy/events/dx_linked_event_mv.py

@@ -18,9 +18,13 @@ from .event_queries import (
     fev1_dx,
     dtherm_dx,
     ecog_dx,
-    pyh_dx
+    pyh_dx,
+    dx_all_measurements
 )
 
+
+
+
 class ConditionEpisodeMeasurementCols:
     __table_args__ = {"extend_existing": True}
 
@@ -167,4 +171,15 @@ class SmokingPYHDxMV(
     __mv_select__ = pyh_dx.select()
     __mv_index__ = "person_id"
     __deps__ = (ConditionEpisodeMV.__mv_name__,)
-    __tablename__ = __mv_name__
+    __tablename__ = __mv_name__
+
+@register_construct
+class DxMeasurementMV(ConditionEpisodeMeasurementCols, MaterializedViewMixin, Base):
+    # todo: the other measurement MVs could be slices of this one instead of 
+    # re-creating from fresh joins every time...
+    __mv_name__ = "dx_measurement_mv"
+    __mv_select__ = dx_all_measurements.select()
+    __mv_index__ = "person_id"
+    __deps__ = (ConditionEpisodeMV.__mv_name__,)
+    __tablename__ = __mv_name__
+    value_as_concept_id: so.Mapped[Optional[int]] = so.mapped_column(sa.Integer, nullable=True)

{omop_constructs-0.3.2 → omop_constructs-0.3.4}/src/omop_constructs/alchemy/events/event_queries.py

@@ -72,4 +72,20 @@ egfr_dx = episode_relevant_window(est_gfr_query, max_days_post=90, max_days_prio
 fev1_dx = episode_relevant_window(fev1_query, max_days_post=90, max_days_prior=30, name="fev1_dx")
 dtherm_dx = episode_relevant_window(distress_thermometer_query, max_days_post=90, max_days_prior=30, name="dtherm_dx")
 ecog_dx = episode_relevant_window(ecog_query, max_days_post=90, max_days_prior=30, name="ecog_dx")
-pyh_dx = episode_relevant_window(smoking_pyh_query, max_days_post=90, max_days_prior=30, name="pyh_dx")
+pyh_dx = episode_relevant_window(smoking_pyh_query, max_days_post=90, max_days_prior=30, name="pyh_dx")
+
+dx_all_measurements = episode_relevant_window(
+    measurement_attached_to_condition_episode(
+        concept_ids=None,  
+        include_cols=[
+            Measurement.value_as_number,
+            Measurement.value_as_concept_id,
+            Measurement.unit_concept_id,
+        ],
+        name="dx_all_measurements",
+        unlinked_only=False,  
+    ),
+    max_days_post=90,
+    max_days_prior=30,
+    name="dx_all_measurements_windowed",
+)

{omop_constructs-0.3.2 → omop_constructs-0.3.4}/src/omop_constructs/alchemy/modifiers/modifier_mappers.py

@@ -27,7 +27,7 @@ diagnosis, bespoke queries and/or mapper objects will be necessary.
 class StageColumns:
     __table_args__ = {"extend_existing": True}
     person_id = sa.Column(sa.Integer)
-    stage_id = sa.Column(primary_key=True)
+    stage_id = sa.Column(sa.Integer, primary_key=True) 
     stage_date = sa.Column(sa.Date)
     stage_datetime = sa.Column(sa.DateTime)
     stage_concept_id = sa.Column(sa.Integer)