omop-constructs 0.3.4__tar.gz → 0.3.6__tar.gz

{omop_constructs-0.3.4 → omop_constructs-0.3.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: omop-constructs
-Version: 0.3.4
+Version: 0.3.6
 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-0.3.4 → omop_constructs-0.3.6}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "omop-constructs"
-version = "0.3.4"
+version = "0.3.6"
 description = "For building complex constructs on top of the omop-alchemy library."
 readme = "README.md"
 authors = [

{omop_constructs-0.3.4 → omop_constructs-0.3.6}/src/omop_constructs/alchemy/concepts/concept_standardisation.py

@@ -1,5 +1,4 @@
-from orm_loader.helpers import Base
-from collections import defaultdict
+
 import sqlalchemy.orm as so
 import sqlalchemy as sa
 from omop_alchemy.cdm.model.vocabulary import Concept, Concept_Relationship

{omop_constructs-0.3.4 → omop_constructs-0.3.6}/src/omop_constructs/alchemy/episodes/surgical_joins.py

@@ -78,7 +78,6 @@ all_cancer_relevant_surg = (
     .subquery(name="all_cancer_relevant_surg")
 )
 
-
 cancer_relevant_surg_select = (
     sa.select(
         sa.func.row_number().over().label("mv_id"),

{omop_constructs-0.3.4 → omop_constructs-0.3.6}/src/omop_constructs/alchemy/events/__init__.py

@@ -12,6 +12,13 @@ from .dx_linked_event_mv import (
     DxMeasurementMV
 )
 
+from .dx_linked_procedure_mv import (
+    DxProcedureMV,
+)
+from .dx_linked_obs_mv import (
+    DxObservationMV,
+)
+
 __all__ = [
     "WeightDxMV",
     "WeightChangeDxMV",         
@@ -23,5 +30,7 @@ __all__ = [
     "DistressThermometerDxMV",
     "ECOGDxMV",
     "SmokingPYHDxMV",
-    "DxMeasurementMV"
+    "DxMeasurementMV",
+    "DxProcedureMV",
+    "DxObservationMV",
 ]

{omop_constructs-0.3.4 → omop_constructs-0.3.6}/src/omop_constructs/alchemy/events/dx_linked_event_mv.py

@@ -22,9 +22,6 @@ from .event_queries import (
     dx_all_measurements
 )
 
-
-
-
 class ConditionEpisodeMeasurementCols:
     __table_args__ = {"extend_existing": True}
 

omop_constructs-0.3.6/src/omop_constructs/alchemy/events/dx_linked_obs_mv.py

@@ -0,0 +1,51 @@
+import sqlalchemy as sa
+import sqlalchemy.orm as so
+from datetime import date
+from typing import Optional
+from orm_loader.helpers import Base
+
+from omop_constructs.alchemy.episodes.condition_episode_mv import ConditionEpisodeMV
+from ...core.materialized import MaterializedViewMixin
+from ...core.constructs import register_construct
+from ..episodes import ConditionEpisodeMV
+from .observation_queries import (
+    dx_all_observations
+)
+
+class ConditionEpisodeObservationCols:
+    __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)
+    event_id: so.Mapped[int] = so.mapped_column(sa.Integer)
+    event_date: so.Mapped[date] = so.mapped_column(sa.Date)
+    event_concept_id: so.Mapped[int] = so.mapped_column(sa.Integer)
+    event_label: so.Mapped[Optional[str]] = so.mapped_column(sa.String, nullable=True)
+
+    value_as_number: so.Mapped[Optional[float]] = so.mapped_column(sa.Float, nullable=True)
+    qualifier_concept_id: so.Mapped[Optional[int]] = so.mapped_column(sa.Integer, nullable=True)
+    value_concept_id: so.Mapped[Optional[int]] = so.mapped_column(sa.Integer, nullable=True)
+
+    episode_id: so.Mapped[Optional[int]] = so.mapped_column(sa.Integer, nullable=True)
+    episode_concept_id: so.Mapped[Optional[int]] = so.mapped_column(sa.Integer, nullable=True)
+    episode_label: so.Mapped[Optional[str]] = so.mapped_column(sa.String, nullable=True)
+
+    episode_start_date: so.Mapped[Optional[date]] = so.mapped_column(sa.Date, nullable=True)
+    episode_end_date: so.Mapped[Optional[date]] = so.mapped_column(sa.Date, nullable=True)
+
+    episode_delta_days: so.Mapped[Optional[int]] = so.mapped_column(sa.Integer, nullable=True)
+
+
+@register_construct
+class DxObservationMV(ConditionEpisodeObservationCols, MaterializedViewMixin, Base):
+    __mv_name__ = "dx_observation_mv"
+    __mv_select__ = dx_all_observations.select()
+    __mv_index__ = "person_id"
+    __deps__ = (ConditionEpisodeMV.__mv_name__,)
+    __tablename__ = __mv_name__
+
+    observation_concept_id: so.Mapped[int] = so.mapped_column(sa.Integer)
+    observation_date: so.Mapped[Optional[date]] = so.mapped_column(sa.DateTime)
+    value_concept_id: so.Mapped[Optional[int]] = so.mapped_column(sa.Integer, nullable=True)
+    qualifier_concept_id: so.Mapped[Optional[int]] = so.mapped_column(sa.Integer, nullable=True)

omop_constructs-0.3.6/src/omop_constructs/alchemy/events/dx_linked_procedure_mv.py

@@ -0,0 +1,44 @@
+import sqlalchemy as sa
+import sqlalchemy.orm as so
+from datetime import date
+from typing import Optional
+from orm_loader.helpers import Base
+
+from omop_constructs.alchemy.episodes.condition_episode_mv import ConditionEpisodeMV
+from ...core.materialized import MaterializedViewMixin
+from ...core.constructs import register_construct
+from ..episodes import ConditionEpisodeMV
+from .procedure_queries import (
+    dx_all_procedures
+)
+
+class ConditionEpisodeProcedureCols:
+    __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)
+    event_id: so.Mapped[int] = so.mapped_column(sa.Integer)
+    event_date: so.Mapped[date] = so.mapped_column(sa.Date)
+    event_concept_id: so.Mapped[int] = so.mapped_column(sa.Integer)
+    event_label: so.Mapped[Optional[str]] = so.mapped_column(sa.String, nullable=True)
+
+    episode_id: so.Mapped[Optional[int]] = so.mapped_column(sa.Integer, nullable=True)
+    episode_concept_id: so.Mapped[Optional[int]] = so.mapped_column(sa.Integer, nullable=True)
+    episode_label: so.Mapped[Optional[str]] = so.mapped_column(sa.String, nullable=True)
+
+    episode_start_date: so.Mapped[Optional[date]] = so.mapped_column(sa.Date, nullable=True)
+    episode_end_date: so.Mapped[Optional[date]] = so.mapped_column(sa.Date, nullable=True)
+
+    episode_delta_days: so.Mapped[Optional[int]] = so.mapped_column(sa.Integer, nullable=True)
+
+@register_construct
+class DxProcedureMV(ConditionEpisodeProcedureCols, MaterializedViewMixin, Base):
+    __mv_name__ = "dx_procedure_mv"
+    __mv_select__ = dx_all_procedures.select()
+    __mv_index__ = "person_id"
+    __deps__ = (ConditionEpisodeMV.__mv_name__,)
+    __tablename__ = __mv_name__
+
+    procedure_concept_id: so.Mapped[int] = so.mapped_column(sa.Integer)
+    procedure_datetime: so.Mapped[Optional[date]] = so.mapped_column(sa.DateTime)

{omop_constructs-0.3.4 → omop_constructs-0.3.6}/src/omop_constructs/alchemy/events/event_factories.py

@@ -5,12 +5,14 @@ from typing import Iterable, Any, Sequence, Union
 from omop_constructs.alchemy.episodes import ConditionEpisodeMV
 from omop_alchemy.cdm.model.structural import Episode_Event
 from omop_semantics.runtime.default_valuesets import runtime # type: ignore
-from omop_alchemy.cdm.model import Measurement, Concept
-
+from omop_alchemy.cdm.model import Measurement, Concept, Procedure_Occurrence, Observation
 from sqlalchemy.orm.attributes import InstrumentedAttribute
+
 SQLExpr = Union[ColumnElement[Any], InstrumentedAttribute[Any]]
 
 modifier_concept = so.aliased(Concept, name="modifier_concept")
+procedure_concept = so.aliased(Concept, name="procedure_concept")
+observation_concept = so.aliased(Concept, name="observation_concept")
 
 def attach_to_condition_episode_via_episode_event(
     base_event_subq: sa.Subquery,
@@ -120,6 +122,59 @@ def attach_to_condition_episode(
         .subquery(name=name)
     )
 
+def procedure_event_core(
+    *,
+    concept_ids: Iterable[int] | None = None,
+    name: str = "procedure_core",
+    include_cols: Sequence[SQLExpr] = (),
+) -> sa.Subquery:
+    """
+    Minimal procedure event surface (person/id/date/concept/label + extras).
+    """
+    q = (
+        sa.select(
+            Procedure_Occurrence.person_id.label("person_id"),
+            Procedure_Occurrence.procedure_occurrence_id.label("event_id"),
+            Procedure_Occurrence.procedure_date.label("event_date"),
+            Procedure_Occurrence.procedure_concept_id.label("event_concept_id"),
+            procedure_concept.concept_name.label("event_label"),
+            *include_cols,
+        )
+        .join(
+            procedure_concept,
+            procedure_concept.concept_id == Procedure_Occurrence.procedure_concept_id,
+            isouter=True,
+        )
+    )
+
+    if concept_ids is not None:
+        q = q.where(Procedure_Occurrence.procedure_concept_id.in_(list(concept_ids)))
+
+    return q.subquery(name=name)
+
+def procedure_attached_to_condition_episode(
+    *,
+    concept_ids: Iterable[int] | None = None,
+    include_cols: Sequence[SQLExpr] = (),
+    name: str,
+    prefer_explicit_link: bool = True,
+) -> sa.Subquery:
+    core = procedure_event_core(
+        concept_ids=concept_ids,
+        include_cols=include_cols,
+        name=f"{name}_core",
+    )
+
+    return attach_to_condition_episode(
+        core,
+        event_id_col=core.c.event_id,
+        date_col=core.c.event_date,
+        person_col=core.c.person_id,
+        name=name,
+        prefer_explicit_link=prefer_explicit_link,
+    )
+
+
 def measurement_event_core(
     *,
     concept_ids: Iterable[int] | None = None,
@@ -176,6 +231,66 @@ def measurement_attached_to_condition_episode(
         name=name,
     )
 
+def observation_event_core(
+    *,
+    concept_ids: Iterable[int] | None = None,
+    name: str = "observation_core",
+    include_cols: Sequence[SQLExpr] = (),
+    unlinked_only: bool = True,
+) -> sa.Subquery:
+    """
+    Minimal observation event surface (person/id/date/concept/label + extras).
+    """
+    q = (
+        sa.select(
+            Observation.person_id.label("person_id"),
+            Observation.observation_id.label("event_id"),
+            Observation.observation_date.label("event_date"),
+            Observation.observation_concept_id.label("event_concept_id"),
+            observation_concept.concept_name.label("event_label"),
+            Observation.value_as_concept_id.label("value_concept_id"),
+            Observation.qualifier_concept_id.label("qualifier_concept_id"),
+            *include_cols,
+        )
+        .join(
+            observation_concept,
+            observation_concept.concept_id == Observation.observation_concept_id,
+            isouter=True,
+        )
+    )
+
+    if unlinked_only:
+        q = q.where(Observation.observation_event_id == None)
+
+    if concept_ids is not None:
+        q = q.where(Observation.observation_concept_id.in_(list(concept_ids)))
+
+    return q.subquery(name=name)
+
+def observation_attached_to_condition_episode(
+    *,
+    concept_ids: Iterable[int] | None = None,
+    include_cols: Sequence[SQLExpr] = (),
+    name: str,
+    unlinked_only: bool = True,
+    prefer_explicit_link: bool = True,
+) -> sa.Subquery:
+    core = observation_event_core(
+        concept_ids=concept_ids,
+        include_cols=include_cols,
+        name=f"{name}_core",
+        unlinked_only=unlinked_only,
+    )
+
+    return attach_to_condition_episode(
+        core,
+        event_id_col=core.c.event_id,
+        date_col=core.c.event_date,
+        person_col=core.c.person_id,
+        name=name,
+        prefer_explicit_link=prefer_explicit_link,
+    )
+
 def episode_relevant_window(
     starting_query: sa.Subquery,
     *,

omop_constructs-0.3.6/src/omop_constructs/alchemy/events/observation_queries.py

@@ -0,0 +1,16 @@
+from .event_factories import observation_attached_to_condition_episode, episode_relevant_window
+from omop_alchemy.cdm.model import Observation
+dx_all_observations = episode_relevant_window(
+    observation_attached_to_condition_episode(
+        concept_ids=None,  # all obs
+        include_cols=[
+            Observation.value_as_number,
+            Observation.qualifier_concept_id,
+        ],
+        name="dx_all_observations",
+        unlinked_only=False,
+    ),
+    max_days_post=365,
+    max_days_prior=30,
+    name="dx_all_observations_windowed",
+)

omop_constructs-0.3.6/src/omop_constructs/alchemy/events/procedure_queries.py

@@ -0,0 +1,12 @@
+from .event_factories import procedure_attached_to_condition_episode, episode_relevant_window
+
+dx_all_procedures = episode_relevant_window(
+    procedure_attached_to_condition_episode(
+        concept_ids=None,
+        include_cols=[],
+        name="dx_all_procedures",
+    ),
+    max_days_post=90,
+    max_days_prior=30,
+    name="dx_all_procedures_windowed",
+)