omop-constructs 0.2.3__tar.gz → 0.2.5__tar.gz

{omop_constructs-0.2.3 → omop_constructs-0.2.5}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.3
 Name: omop-constructs
-Version: 0.2.3
+Version: 0.2.5
 Summary: For building complex constructs on top of the omop-alchemy library.
 Author: Georgie Kennedy
 Author-email: Georgie Kennedy <georgina.kennedy@unsw.edu.au>
 Requires-Dist: omop-alchemy>=0.5.12
-Requires-Dist: omop-semantics>=0.1.8
+Requires-Dist: omop-semantics>=0.1.10
 Requires-Dist: psycopg2-binary>=2.9.11
 Requires-Dist: sqlalchemy>=2.0.45
 Requires-Dist: urllib3>=2.6.3

{omop_constructs-0.2.3 → omop_constructs-0.2.5}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "omop-constructs"
-version = "0.2.3"
+version = "0.2.5"
 description = "For building complex constructs on top of the omop-alchemy library."
 readme = "README.md"
 authors = [
@@ -9,7 +9,7 @@ authors = [
 requires-python = ">=3.12"
 dependencies = [
     "omop-alchemy>=0.5.12",
-    "omop-semantics>=0.1.8",
+    "omop-semantics>=0.1.10",
     "psycopg2-binary>=2.9.11",
     "sqlalchemy>=2.0.45",
     "urllib3>=2.6.3",

omop_constructs-0.2.5/src/omop_constructs/alchemy/conditions/__init__.py

@@ -0,0 +1,7 @@
+from .condition_joins import condition_window
+from .condition_mappers import Condition_Window
+
+__all__ = [
+    "condition_window",
+    "Condition_Window"
+]

{omop_constructs-0.2.3 → omop_constructs-0.2.5}/src/omop_constructs/alchemy/episodes/__init__.py

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

omop_constructs-0.2.5/src/omop_constructs/alchemy/episodes/condition_episode_mv.py

@@ -0,0 +1,123 @@
+import sqlalchemy as sa
+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 ...core.materialized import MaterializedViewMixin
+from ...core.constructs import register_construct
+
+@register_construct
+class OverarchingDiseaseEpisodeMV(
+    MaterializedViewMixin,
+    Base,
+):
+    """
+    Materialized view representing overarching disease episodes
+    with optional child disease-extent episodes.
+
+    One row per (episode_of_care, disease_extent_episode?) pair.
+    """
+
+    __mv_name__ = "overarching_disease_episode_mv"
+    __mv_select__ = overarching_disease_episode.select()
+    __mv_index__ = "disease_episode_id"
+    __deps__ = ()
+    __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)
+
+    def __repr__(self) -> str:
+        if self.has_extent:
+            return (
+                f"<OverarchingDiseaseEpisode "
+                f"{self.disease_episode_id} -> extent {self.extent_episode_id}>"
+            )
+        return f"<OverarchingDiseaseEpisode {self.disease_episode_id}>"
+    
+    @property
+    def has_extent(self) -> bool:
+        return self.extent_episode_id is not None
+
+    @property
+    def disease_interval(self):
+        return (self.disease_episode_start_date, self.disease_episode_end_date)
+
+    @property
+    def extent_interval(self):
+        if self.extent_episode_id is None:
+            return None
+        return (self.extent_start_date, self.extent_end_date)
+    
+@register_construct
+class TreatmentRegimenCycleMV(
+    MaterializedViewMixin,
+    Base,
+):
+    """
+    Materialized view representing treatment regimens
+    with optional child treatment cycles.
+
+    One row per (treatment_regimen, treatment_cycle?) pair.
+    """
+
+    __mv_name__ = "treatment_regimen_cycle_mv"
+    __mv_select__ = treatment_regimen_with_cycles.select()
+    __mv_index__ = "regimen_episode_id"
+    __deps__ = ()
+    __tablename__ = __mv_name__
+    __table_args__ = {"extend_existing": True}
+
+    regimen_episode_id: so.Mapped[int] = so.mapped_column(sa.Integer, primary_key=True)
+    person_id: so.Mapped[int] = so.mapped_column(sa.Integer)
+
+    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)
+
+    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)
+
+
+    def __repr__(self) -> str:
+        if self.has_cycle:
+            return (
+                f"<TreatmentRegimenCycle "
+                f"{self.regimen_episode_id} -> cycle {self.cycle_episode_id}>"
+            )
+        return f"<TreatmentRegimenCycle {self.regimen_episode_id}>"
+    
+    @property
+    def has_cycle(self) -> bool:
+        return self.cycle_episode_id is not None
+
+    @property
+    def regimen_interval(self):
+        return (self.regimen_start_date, self.regimen_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)

{omop_constructs-0.2.3 → omop_constructs-0.2.5}/src/omop_constructs/alchemy/episodes/episode_factories.py

@@ -1,6 +1,7 @@
 import sqlalchemy as sa
 import sqlalchemy.orm as so
-from typing import Iterable
+from sqlalchemy.sql import ColumnElement
+from typing import Iterable, Any
 from omop_alchemy.cdm.model import (
     Condition_Occurrence,
     Episode,
@@ -42,28 +43,6 @@ def get_episode_query(
         .subquery(name=name)
     )
 
-def require_condition_anchor(
-    episode_subq: sa.Subquery,
-    name: str | None = None,
-) -> sa.Subquery:
-    """
-    Filters an Episode subquery to only episodes with at least one
-    linked Condition_Occurrence via Episode_Event.
-    """
-    exists_condition = sa.exists().where(
-        sa.and_(
-            Episode_Event.episode_id == episode_subq.c.episode_id,
-            Episode_Event.episode_event_field_concept_id
-            == runtime.modifiers.modifier_fields.condition_occurrence_id,
-            Condition_Occurrence.condition_occurrence_id == Episode_Event.event_id,
-        )
-    )
-    return (
-        sa.select(*episode_subq.c)
-        .where(exists_condition)
-        .subquery(name=name or episode_subq.name)
-    )
-
 
 def get_episode_hierarchy_query(
     parent_episode_subq: sa.Subquery,
@@ -76,18 +55,18 @@ def get_episode_hierarchy_query(
 
     return (
         sa.select(
-            parent_episode_subq.c.episode_id.label("parent_episode_id"),
+            parent_episode_subq.c.episode_id.label("disease_episode_id"),
             parent_episode_subq.c.person_id.label("person_id"),
-            parent_episode_subq.c.episode_concept_id.label("parent_episode_concept_id"),
-            parent_episode_subq.c.episode_label.label("parent_episode_label"),
-            parent_episode_subq.c.episode_start_date.label("parent_start_date"),
-            parent_episode_subq.c.episode_end_date.label("parent_end_date"),
+            parent_episode_subq.c.episode_concept_id.label("disease_episode_concept_id"),
+            parent_episode_subq.c.episode_label.label("disease_episode_label"),
+            parent_episode_subq.c.episode_start_date.label("disease_episode_start_date"),
+            parent_episode_subq.c.episode_end_date.label("disease_episode_end_date"),
 
-            child_episode_subq.c.episode_id.label("child_episode_id"),
-            child_episode_subq.c.episode_concept_id.label("child_episode_concept_id"),
-            child_episode_subq.c.episode_label.label("child_episode_label"),
-            child_episode_subq.c.episode_start_date.label("child_start_date"),
-            child_episode_subq.c.episode_end_date.label("child_end_date"),
+            child_episode_subq.c.episode_id.label("extent_episode_id"),
+            child_episode_subq.c.episode_concept_id.label("extent_episode_concept_id"),
+            child_episode_subq.c.episode_label.label("extent_episode_label"),
+            child_episode_subq.c.episode_start_date.label("extent_start_date"),
+            child_episode_subq.c.episode_end_date.label("extent_end_date"),
         )
         .join(
             child_episode_subq,

omop_constructs-0.2.5/src/omop_constructs/alchemy/episodes/episode_joins.py

@@ -0,0 +1,34 @@
+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
+        name="episode_of_care"
+    )
+
+disease_extent_select = get_episode_query(
+        [runtime.types.disease_episode_types.disease_progression, runtime.types.disease_episode_types.metastatic],  # type: ignore
+        name="disease_extent"
+    )
+
+overarching_disease_episode = get_episode_hierarchy_query(
+    episode_of_care_select,
+    disease_extent_select,
+    name="overarching_disease_episode",
+)
+
+treatment_regimen_select = get_episode_query(
+    [runtime.types.treatment_episode_types.treatment_regimen],  # type: ignore
+    name="treatment_regimen",
+)
+
+treatment_cycle_select = get_episode_query(
+    [runtime.types.treatment_episode_types.treatment_cycle],  # type: ignore
+    name="treatment_cycle",
+)
+
+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",
+)

omop_constructs-0.2.3/src/omop_constructs/alchemy/episodes/condition_episode_mv.py

@@ -1,65 +0,0 @@
-import sqlalchemy as sa
-from orm_loader.helpers import Base
-from .episode_joins import overarching_disease_episode
-from ...core.materialized import MaterializedViewMixin
-from ...core.constructs import register_construct
-
-class OverarchingDiseaseEpisodeCols:
-    __table_args__ = {"extend_existing": True}
-
-    disease_episode_id = sa.Column(sa.Integer, primary_key=True)
-    person_id = sa.Column(sa.Integer)
-
-    disease_episode_concept_id = sa.Column(sa.Integer)
-    disease_episode_label = sa.Column(sa.String)
-
-    disease_episode_start_date = sa.Column(sa.Date)
-    disease_episode_end_date = sa.Column(sa.Date)
-
-    extent_episode_id = sa.Column(sa.Integer)
-    extent_episode_concept_id = sa.Column(sa.Integer)
-    extent_episode_label = sa.Column(sa.String)
-
-    extent_start_date = sa.Column(sa.Date)
-    extent_end_date = sa.Column(sa.Date)
-
-@register_construct
-class OverarchingDiseaseEpisodeMV(
-    OverarchingDiseaseEpisodeCols,
-    MaterializedViewMixin,
-    Base,
-):
-    """
-    Materialized view representing overarching disease episodes
-    with optional child disease-extent episodes.
-
-    One row per (episode_of_care, disease_extent_episode?) pair.
-    """
-
-    __mv_name__ = "overarching_disease_episode_mv"
-    __mv_select__ = overarching_disease_episode.select()
-    __mv_index__ = "disease_episode_id"
-    __deps__ = ()
-    __tablename__ = __mv_name__
-
-    def __repr__(self) -> str:
-        if self.has_extent:
-            return (
-                f"<OverarchingDiseaseEpisode "
-                f"{self.disease_episode_id} -> extent {self.extent_episode_id}>"
-            )
-        return f"<OverarchingDiseaseEpisode {self.disease_episode_id}>"
-    
-    @property
-    def has_extent(self) -> bool:
-        return self.extent_episode_id is not None
-
-    @property
-    def disease_interval(self):
-        return (self.disease_episode_start_date, self.disease_episode_end_date)
-
-    @property
-    def extent_interval(self):
-        if self.extent_episode_id is None:
-            return None
-        return (self.extent_start_date, self.extent_end_date)

omop_constructs-0.2.3/src/omop_constructs/alchemy/episodes/episode_joins.py

@@ -1,22 +0,0 @@
-from .episode_factories import require_condition_anchor, get_episode_query, get_episode_hierarchy_query
-from omop_semantics.runtime.default_valuesets import runtime
-
-episode_of_care_select = require_condition_anchor(
-    get_episode_query(
-        [runtime.episodes.disease_episode_types.episode_of_care],  # type: ignore
-        name="episode_of_care"
-    )
-)
-
-disease_extent_select = require_condition_anchor(
-    get_episode_query(
-        [runtime.episodes.disease_episode_types.metastatic, runtime.episodes.disease_episode_types.disease_progression],  # type: ignore
-        name="disease_extent"
-    )
-)   
-
-overarching_disease_episode = get_episode_hierarchy_query(
-    episode_of_care_select,
-    disease_extent_select,
-    name="overarching_disease_episode",
-)