From 77a08a667862f40f913379db3d0e577c0609e2df Mon Sep 17 00:00:00 2001 From: gkennos Date: Wed, 5 Aug 2026 21:31:32 +1000 Subject: [PATCH 1/4] Add robust episode event resolution and semantics extra --- omop_alchemy/cdm/base/modifier_interface.py | 5 +- .../model/clinical/procedure_occurrence.py | 13 + omop_alchemy/cdm/model/structural/__init__.py | 10 +- omop_alchemy/cdm/model/structural/episode.py | 12 + .../cdm/model/structural/episode_event.py | 138 +- pyproject.toml | 4 + tests/test_episodes_basic.py | 90 +- uv.lock | 1193 ++++++++++++++++- 8 files changed, 1450 insertions(+), 15 deletions(-) diff --git a/omop_alchemy/cdm/base/modifier_interface.py b/omop_alchemy/cdm/base/modifier_interface.py index 0fcf2ef..f128f44 100644 --- a/omop_alchemy/cdm/base/modifier_interface.py +++ b/omop_alchemy/cdm/base/modifier_interface.py @@ -28,8 +28,9 @@ def modifier_target_table(cls) -> str: def event_id(self) -> int: return getattr(self, self.__event_id_col__) - @event_id.expression - def event_id(cls): + @event_id.inplace.expression + @classmethod + def _event_id(cls): return getattr(cls, cls.__event_id_col__) @property diff --git a/omop_alchemy/cdm/model/clinical/procedure_occurrence.py b/omop_alchemy/cdm/model/clinical/procedure_occurrence.py index e3d6c07..4dfb65b 100644 --- a/omop_alchemy/cdm/model/clinical/procedure_occurrence.py +++ b/omop_alchemy/cdm/model/clinical/procedure_occurrence.py @@ -15,6 +15,8 @@ ReferenceContext, DomainValidationMixin, ExpectedDomain, + ModifierTargetMixin, + ModifierFieldConcepts, merge_table_args, omop_index, ) @@ -111,10 +113,17 @@ class Procedure_OccurrenceView( Procedure_Occurrence, Procedure_OccurrenceContext, DomainValidationMixin, + ModifierTargetMixin, ): __tablename__ = "procedure_occurrence" __mapper_args__ = {"concrete": False} + __event_id_col__ = "procedure_occurrence_id" + __concept_id_col__ = "procedure_concept_id" + __start_date_col__ = "procedure_date" + __end_date_col__ = "procedure_end_date" + __type_concept_id_col__ = "procedure_type_concept_id" + __expected_domains__ = { "procedure_concept_id": ExpectedDomain("Procedure"), "procedure_type_concept_id": ExpectedDomain("Type Concept"), @@ -125,6 +134,10 @@ def start(self): """Best-effort start datetime.""" return self.procedure_datetime or self.procedure_date + @classmethod + def modifier_field_concept_id(cls) -> int: + return ModifierFieldConcepts.PROCEDURE_OCCURRENCE + @property def end(self): """Best-effort end datetime.""" diff --git a/omop_alchemy/cdm/model/structural/__init__.py b/omop_alchemy/cdm/model/structural/__init__.py index f75d93e..0e713a1 100644 --- a/omop_alchemy/cdm/model/structural/__init__.py +++ b/omop_alchemy/cdm/model/structural/__init__.py @@ -1,5 +1,10 @@ from .episode import Episode, EpisodeContext, EpisodeView -from .episode_event import Episode_Event, Episode_EventContext, Episode_EventView +from .episode_event import ( + Episode_Event, + Episode_EventContext, + Episode_EventView, + EpisodeEventResolutionDiagnostic, +) from .fact_relationship import Fact_Relationship __all__ = [ @@ -9,5 +14,6 @@ "Episode_Event", "Episode_EventContext", "Episode_EventView", + "EpisodeEventResolutionDiagnostic", "Fact_Relationship", -] \ No newline at end of file +] diff --git a/omop_alchemy/cdm/model/structural/episode.py b/omop_alchemy/cdm/model/structural/episode.py index 0affd93..432e707 100644 --- a/omop_alchemy/cdm/model/structural/episode.py +++ b/omop_alchemy/cdm/model/structural/episode.py @@ -82,6 +82,18 @@ def parent_episode(cls) -> so.Mapped[Optional["Episode"]]: uselist=False, ) + @declared_attr + def children(cls) -> so.Mapped[List["Episode"]]: + return so.relationship( + cls.__name__, + primaryjoin=lambda: so.remote(cls.episode_parent_id) == cls.episode_id, + foreign_keys=lambda: [cls.episode_parent_id], + remote_side=lambda: [cls.episode_parent_id], + viewonly=True, + lazy="selectin", + uselist=True, + ) + class EpisodeView(Episode, EpisodeContext, DomainValidationMixin): """ Navigable Episode view. diff --git a/omop_alchemy/cdm/model/structural/episode_event.py b/omop_alchemy/cdm/model/structural/episode_event.py index ae3efb5..d422b20 100644 --- a/omop_alchemy/cdm/model/structural/episode_event.py +++ b/omop_alchemy/cdm/model/structural/episode_event.py @@ -1,14 +1,17 @@ import sqlalchemy as sa import sqlalchemy.orm as so -from typing import TYPE_CHECKING, Any, Type, cast +from dataclasses import dataclass +from typing import TYPE_CHECKING, Any, Literal, Type from functools import cached_property -from orm_loader.helpers import Base, get_model_by_tablename +from orm_loader.helpers import Base from omop_alchemy.cdm.base import ( cdm_table, CDMTableBase, ReferenceContext, DomainValidationMixin, ExpectedDomain, + ModifierFieldConcepts, + ModifierTargetMixin, merge_table_args, omop_index, ) @@ -17,6 +20,53 @@ from ..vocabulary import Concept from .episode import Episode +ResolutionDiagnosticKind = Literal[ + "unrecognized_field_concept", + "unmapped_field_concept", + "dangling_event", +] + + +@dataclass(frozen=True) +class EpisodeEventResolutionDiagnostic: + """ + Advisory detail for an episode_event row whose target cannot be resolved. + + Resolution remains best-effort: unresolved rows still return ``None`` from + ``resolved_event``. These diagnostics give maintenance and QA code enough + information to distinguish miscoded field concepts from harmless ORM + coverage gaps and genuine dangling event references. + """ + + kind: ResolutionDiagnosticKind + episode_id: int + event_id: int + episode_event_field_concept_id: int + message: str + + +def _known_modifier_field_concept_ids() -> set[int]: + return { + value + for name, value in vars(ModifierFieldConcepts).items() + if name.isupper() and isinstance(value, int) + } + + +def _modifier_target_classes_by_field_concept_id() -> dict[int, Type[Any]]: + classes: dict[int, Type[Any]] = {} + for mapper in Base.registry.mappers: + cls = mapper.class_ + if not issubclass(cls, ModifierTargetMixin): + continue + try: + field_concept_id = cls.modifier_field_concept_id() + except NotImplementedError: + continue + if field_concept_id not in classes: + classes[field_concept_id] = cls + return classes + @cdm_table class Episode_Event(CDMTableBase, Base): __tablename__ = "episode_event" @@ -51,6 +101,22 @@ class Episode_EventView(Episode_Event, Episode_EventContext, DomainValidationMix "episode_event_field_concept_id": ExpectedDomain("Metadata"), } + @classmethod + def resolved_event_target_classes(cls) -> dict[int, Type[Any]]: + """ + Map episode_event field concepts to ORM classes that can receive them. + + Subclasses may override this to prefer domain-specific mapped views + over the base CDM views. The default map is built from registered + ``ModifierTargetMixin`` classes and keyed by the field concept id + itself, avoiding the fragile concept-name table parsing that the CDM + metadata labels happen to support today. + """ + return _modifier_target_classes_by_field_concept_id() + + @classmethod + def recognized_field_concept_ids(cls) -> set[int]: + return _known_modifier_field_concept_ids() @property def event_table(self) -> str | None: @@ -58,21 +124,77 @@ def event_table(self) -> str | None: return self.event_field.concept_name.split(".", 1)[0] return None + @property + def resolved_event_class(self) -> Type[Any] | None: + return self.resolved_event_target_classes().get( + self.episode_event_field_concept_id + ) + + @property + def event_resolution_diagnostics(self) -> list[EpisodeEventResolutionDiagnostic]: + session = so.object_session(self) + field_concept_id = self.episode_event_field_concept_id + + if field_concept_id not in self.recognized_field_concept_ids(): + return [ + EpisodeEventResolutionDiagnostic( + kind="unrecognized_field_concept", + episode_id=self.episode_id, + event_id=self.event_id, + episode_event_field_concept_id=field_concept_id, + message=( + "episode_event_field_concept_id is not a known " + "ModifierFieldConcepts value" + ), + ) + ] + + cls = self.resolved_event_class + if cls is None: + return [ + EpisodeEventResolutionDiagnostic( + kind="unmapped_field_concept", + episode_id=self.episode_id, + event_id=self.event_id, + episode_event_field_concept_id=field_concept_id, + message=( + "episode_event_field_concept_id is recognized, but no " + "registered ORM target class declares it" + ), + ) + ] + + if session is None: + return [] + + if session.get(cls, self.event_id) is None: + return [ + EpisodeEventResolutionDiagnostic( + kind="dangling_event", + episode_id=self.episode_id, + event_id=self.event_id, + episode_event_field_concept_id=field_concept_id, + message=( + f"episode_event points to {cls.__name__}#{self.event_id}, " + "but no matching row exists" + ), + ) + ] + + return [] + @cached_property def resolved_event(self) -> Any | None: """ Resolve EVENT_ID to concrete OMOP row. Cached per-instance. """ - table_name = self.event_table session = so.object_session(self) - if session is None or table_name is None: + cls = self.resolved_event_class + if session is None or cls is None: return None - cls = cast(Type[Any] | None, get_model_by_tablename(table_name)) - if cls is not None: - return session.get(cls, self.event_id) - return None + return session.get(cls, self.event_id) def __repr__(self): target = self.resolved_event diff --git a/pyproject.toml b/pyproject.toml index 724d7d2..d871d5f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -44,6 +44,10 @@ postgres = [ "psycopg[binary]>=3.2", ] +semantics = [ + "omop-semantics>=0.5.0", +] + dev = [ "oa-configurator[dev,postgres]==0.1.2", "ipython>=8.0", diff --git a/tests/test_episodes_basic.py b/tests/test_episodes_basic.py index b339ac9..ffc22c1 100644 --- a/tests/test_episodes_basic.py +++ b/tests/test_episodes_basic.py @@ -1,4 +1,5 @@ -from omop_alchemy.cdm.model.structural import EpisodeView, Episode_Event +from omop_alchemy.cdm.base import ModifierFieldConcepts +from omop_alchemy.cdm.model.structural import EpisodeView, Episode_Event, Episode_EventView import sqlalchemy as sa def test_episode_view_expected_domains(): @@ -63,6 +64,84 @@ def test_episode_event_resolves_target(session): assert getattr(target, col) == ee.event_id +def test_episode_event_resolution_has_no_diagnostics_for_valid_target(session): + """Valid episode_event links resolve without advisory issues.""" + ee = ( + session.query(EpisodeView) + .filter(EpisodeView.episode_events.any()) + .first() + .episode_events[0] + ) + + assert ee.resolved_event is not None + assert ee.event_resolution_diagnostics == [] + + +def test_episode_event_resolution_reports_unrecognized_field_concept(session): + """A field concept outside ModifierFieldConcepts is surfaced separately.""" + ee = Episode_Event( + episode_id=101, + event_id=998, + episode_event_field_concept_id=201826, + ) + session.add(ee) + session.flush() + session.expire_all() + + loaded = session.get(Episode_EventView, (101, 998, 201826)) + diagnostics = loaded.event_resolution_diagnostics + + assert loaded.resolved_event is None + assert len(diagnostics) == 1 + assert diagnostics[0].kind == "unrecognized_field_concept" + + +def test_episode_event_resolution_reports_unmapped_known_field_concept( + session, + monkeypatch, +): + """Known field concepts can be valid data even before this ORM maps them.""" + ee = ( + session.query(EpisodeView) + .filter(EpisodeView.episode_events.any()) + .first() + .episode_events[0] + ) + monkeypatch.setattr( + type(ee), + "resolved_event_target_classes", + classmethod(lambda cls: {}), + ) + + diagnostics = ee.event_resolution_diagnostics + + assert ee.resolved_event is None + assert len(diagnostics) == 1 + assert diagnostics[0].kind == "unmapped_field_concept" + + +def test_episode_event_resolution_reports_dangling_target(session): + """Recognized field concepts with missing target rows are true dangling links.""" + ee = Episode_Event( + episode_id=101, + event_id=999, + episode_event_field_concept_id=ModifierFieldConcepts.CONDITION_OCCURRENCE, + ) + session.add(ee) + session.flush() + session.expire_all() + + loaded = session.get( + Episode_EventView, + (101, 999, ModifierFieldConcepts.CONDITION_OCCURRENCE), + ) + diagnostics = loaded.event_resolution_diagnostics + + assert loaded.resolved_event is None + assert len(diagnostics) == 1 + assert diagnostics[0].kind == "dangling_event" + + def test_episode_view_events_property(session): """Test episode view events property.""" @@ -99,6 +178,15 @@ def test_episode_parent_relationship(session): assert child.parent_episode.episode_id == child.episode_parent_id +def test_episode_children_relationship_preserves_episode_view(session): + """Child navigation returns the concrete episode view being queried.""" + parent = session.get(EpisodeView, 100) + + assert parent is not None + assert [child.episode_id for child in parent.children] == [101] + assert 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Subject: [PATCH 2/4] compositional episode handling for body metrics, adverse events, oncology, drug episodes --- omop_alchemy/cdm/base/modifier_interface.py | 7 +- omop_alchemy/cdm/handlers/_semantics.py | 22 ++ .../cdm/handlers/adverse_events/__init__.py | 14 + .../cdm/handlers/adverse_events/ctcae.py | 27 ++ .../handlers/adverse_events/weight_loss.py | 78 ++++++ .../cdm/handlers/body_metrics/__init__.py | 54 ++++ .../cdm/handlers/body_metrics/calculators.py | 76 ++++++ .../cdm/handlers/body_metrics/concept_sets.py | 41 +++ .../body_metrics/measurement_series.py | 184 +++++++++++++ .../cdm/handlers/body_metrics/units.py | 67 +++++ .../body_metrics/weight_trajectory.py | 241 ++++++++++++++++++ .../cdm/handlers/drug_episodes/__init__.py | 18 ++ .../cdm/handlers/drug_episodes/dosing.py | 22 ++ .../handlers/drug_episodes/drug_episode.py | 37 +++ .../handlers/drug_episodes/exposure_series.py | 61 +++++ .../cdm/handlers/drug_episodes/summaries.py | 69 +++++ .../cdm/handlers/oncology/__init__.py | 81 ++++++ .../cdm/handlers/oncology/concept_sets.py | 220 ++++++++++++++++ .../oncology/oncology_critical_weight_loss.py | 52 ++++ .../oncology/oncology_drug_exposure.py | 38 +++ .../handlers/oncology/oncology_episodes.py | 211 +++++++++++++++ .../cdm/handlers/oncology/oncology_event.py | 52 ++++ .../oncology/oncology_procedure_occurrence.py | 82 ++++++ .../handlers/oncology/oncology_rt_dosing.py | 122 +++++++++ .../handlers/oncology/oncology_sact_dosing.py | 132 ++++++++++ 25 files changed, 2006 insertions(+), 2 deletions(-) create mode 100644 omop_alchemy/cdm/handlers/_semantics.py create mode 100644 omop_alchemy/cdm/handlers/adverse_events/__init__.py create mode 100644 omop_alchemy/cdm/handlers/adverse_events/ctcae.py create mode 100644 omop_alchemy/cdm/handlers/adverse_events/weight_loss.py create mode 100644 omop_alchemy/cdm/handlers/body_metrics/__init__.py create mode 100644 omop_alchemy/cdm/handlers/body_metrics/calculators.py create mode 100644 omop_alchemy/cdm/handlers/body_metrics/concept_sets.py create mode 100644 omop_alchemy/cdm/handlers/body_metrics/measurement_series.py create mode 100644 omop_alchemy/cdm/handlers/body_metrics/units.py create mode 100644 omop_alchemy/cdm/handlers/body_metrics/weight_trajectory.py create mode 100644 omop_alchemy/cdm/handlers/drug_episodes/__init__.py create mode 100644 omop_alchemy/cdm/handlers/drug_episodes/dosing.py create mode 100644 omop_alchemy/cdm/handlers/drug_episodes/drug_episode.py create mode 100644 omop_alchemy/cdm/handlers/drug_episodes/exposure_series.py create mode 100644 omop_alchemy/cdm/handlers/drug_episodes/summaries.py create mode 100644 omop_alchemy/cdm/handlers/oncology/__init__.py create mode 100644 omop_alchemy/cdm/handlers/oncology/concept_sets.py create mode 100644 omop_alchemy/cdm/handlers/oncology/oncology_critical_weight_loss.py create mode 100644 omop_alchemy/cdm/handlers/oncology/oncology_drug_exposure.py create mode 100644 omop_alchemy/cdm/handlers/oncology/oncology_episodes.py create mode 100644 omop_alchemy/cdm/handlers/oncology/oncology_event.py create mode 100644 omop_alchemy/cdm/handlers/oncology/oncology_procedure_occurrence.py create mode 100644 omop_alchemy/cdm/handlers/oncology/oncology_rt_dosing.py create mode 100644 omop_alchemy/cdm/handlers/oncology/oncology_sact_dosing.py diff --git a/omop_alchemy/cdm/base/modifier_interface.py b/omop_alchemy/cdm/base/modifier_interface.py index f128f44..f707c30 100644 --- a/omop_alchemy/cdm/base/modifier_interface.py +++ b/omop_alchemy/cdm/base/modifier_interface.py @@ -2,6 +2,7 @@ from sqlalchemy.ext.hybrid import hybrid_property from typing import ClassVar,Optional from datetime import date +from sqlalchemy.sql.elements import SQLColumnExpression class ModifierTargetMixin: """ @@ -10,6 +11,7 @@ class ModifierTargetMixin: """ __abstract__ = True + __tablename__: ClassVar[str] __event_id_col__: ClassVar[str] __concept_id_col__: ClassVar[str] __start_date_col__: ClassVar[str] @@ -28,11 +30,12 @@ def modifier_target_table(cls) -> str: def event_id(self) -> int: return getattr(self, self.__event_id_col__) + @event_id.inplace.expression @classmethod - def _event_id(cls): + def _event_id(cls) -> SQLColumnExpression[int]: return getattr(cls, cls.__event_id_col__) - + @property def concept_id(self) -> int: return getattr(self, self.__concept_id_col__) diff --git a/omop_alchemy/cdm/handlers/_semantics.py b/omop_alchemy/cdm/handlers/_semantics.py new file mode 100644 index 0000000..276085b --- /dev/null +++ b/omop_alchemy/cdm/handlers/_semantics.py @@ -0,0 +1,22 @@ +from __future__ import annotations + +from typing import Any + + +def default_semantics_runtime() -> Any: + """ + Return the bundled omop-semantics runtime, or fail with install guidance. + + omop-semantics is an optional dependency of omop-alchemy. Handler modules + that use governed default concept sets should call this lazily when those + defaults are actually needed, so importing core CDM models does not require + the semantics package. + """ + try: + from omop_semantics.runtime.default_valuesets import runtime + except ImportError as exc: + raise ImportError( + "This handler requires omop-semantics. Install omop-alchemy with " + "the 'semantics' extra, for example: omop-alchemy[semantics]." + ) from exc + return runtime diff --git a/omop_alchemy/cdm/handlers/adverse_events/__init__.py b/omop_alchemy/cdm/handlers/adverse_events/__init__.py new file mode 100644 index 0000000..8e9b9ef --- /dev/null +++ b/omop_alchemy/cdm/handlers/adverse_events/__init__.py @@ -0,0 +1,14 @@ +from .ctcae import CTCAEWeightLoss, ctcae_weight_loss_grade +from .weight_loss import ( + MartinWeightLoss, + critical_weight_loss_grade, + martin_weight_loss_grade, +) + +__all__ = [ + "CTCAEWeightLoss", + "MartinWeightLoss", + "critical_weight_loss_grade", + "ctcae_weight_loss_grade", + "martin_weight_loss_grade", +] diff --git a/omop_alchemy/cdm/handlers/adverse_events/ctcae.py b/omop_alchemy/cdm/handlers/adverse_events/ctcae.py new file mode 100644 index 0000000..11e2e84 --- /dev/null +++ b/omop_alchemy/cdm/handlers/adverse_events/ctcae.py @@ -0,0 +1,27 @@ +from __future__ import annotations + +from typing import ClassVar, Optional + + +class CTCAEWeightLoss: + """ + CTCAE-style weight-loss severity from percent weight change only. + + This implements physiological percent-loss bins. + + CTCAE intervention qualifiers such as hospitalisation, tube feeding, or TPN + are not inferred here. + """ + + THRESHOLDS: ClassVar[tuple[float, ...]] = (5.0, 10.0, 20.0) + + @classmethod + def grade(cls, pct_change: Optional[float]) -> Optional[int]: + if pct_change is None: + return None + loss_pct = max(0.0, -pct_change) + return sum(1 for threshold in cls.THRESHOLDS if loss_pct >= threshold) + + +def ctcae_weight_loss_grade(pct_change: Optional[float]) -> Optional[int]: + return CTCAEWeightLoss.grade(pct_change) diff --git a/omop_alchemy/cdm/handlers/adverse_events/weight_loss.py b/omop_alchemy/cdm/handlers/adverse_events/weight_loss.py new file mode 100644 index 0000000..a32ca6d --- /dev/null +++ b/omop_alchemy/cdm/handlers/adverse_events/weight_loss.py @@ -0,0 +1,78 @@ +from __future__ import annotations + +from typing import ClassVar, Optional + +from .ctcae import ctcae_weight_loss_grade + + +class MartinWeightLoss: + """ + Martin et al. BMI-adjusted percent-weight-loss grading. + + This matrix is kept in adverse events because it is clinical + severity policy over body measurements, not body-measurement + arithmetic itself. + """ + + BMI_CATEGORY_BOUNDARIES: ClassVar[tuple[float, ...]] = (20.0, 22.0, 25.0, 28.0) + WEIGHT_LOSS_CATEGORY_BOUNDARIES: ClassVar[tuple[float, ...]] = ( + 2.5, + 6.0, + 11.0, + 15.0, + ) + GRADE_MATRIX: ClassVar[tuple[tuple[int, int, int, int, int], ...]] = ( + (0, 0, 1, 1, 3), + (1, 2, 2, 2, 3), + (2, 3, 3, 3, 4), + (3, 3, 4, 4, 4), + (3, 4, 4, 4, 4), + ) + + @classmethod + def _bmi_category_index(cls, bmi: float) -> int: + for index, boundary in enumerate(reversed(cls.BMI_CATEGORY_BOUNDARIES)): + if bmi >= boundary: + return index + return len(cls.BMI_CATEGORY_BOUNDARIES) + + @classmethod + def _weight_loss_category_index(cls, loss_pct: float) -> int: + for index, boundary in enumerate(cls.WEIGHT_LOSS_CATEGORY_BOUNDARIES): + if loss_pct < boundary: + return index + return len(cls.WEIGHT_LOSS_CATEGORY_BOUNDARIES) + + @classmethod + def grade( + cls, + pct_change: Optional[float], + bmi: Optional[float], + ) -> Optional[int]: + if pct_change is None or bmi is None: + return None + loss_pct = max(0.0, -pct_change) + return cls.GRADE_MATRIX[ + cls._weight_loss_category_index(loss_pct) + ][cls._bmi_category_index(bmi)] + + +def martin_weight_loss_grade( + pct_change: Optional[float], + bmi: Optional[float], +) -> Optional[int]: + return MartinWeightLoss.grade(pct_change, bmi) + + +def critical_weight_loss_grade( + pct_change: Optional[float], + bmi: Optional[float], +) -> Optional[int]: + """ + Critical-weight-loss grade using Martin where BMI is available. + + Falls back to CTCAE-style percent-weight-loss grading when percent change is + evaluable but BMI is not, preserving coverage without guessing BMI. + """ + grade = martin_weight_loss_grade(pct_change, bmi) + return grade if grade is not None else ctcae_weight_loss_grade(pct_change) diff --git a/omop_alchemy/cdm/handlers/body_metrics/__init__.py b/omop_alchemy/cdm/handlers/body_metrics/__init__.py new file mode 100644 index 0000000..45d50bc --- /dev/null +++ b/omop_alchemy/cdm/handlers/body_metrics/__init__.py @@ -0,0 +1,54 @@ +from .calculators import BodyMetricRules, default_body_metric_rules +from .concept_sets import ( + BodySizeMeasurementConcepts, + BodySizeUnitConcepts, + default_body_size_measurement_concepts, + default_body_size_unit_concepts, +) +from .measurement_series import ( + MeasurementReading, + MeasurementSeriesMixin, + ReadingSource, + episode_attachment_window, + reading_from_measurement, + resolve_measurement_series, + resolve_person_measurement_series, +) +from .units import ( + INCH_TO_CM, + LB_US_TO_KG, + BodyUnitConversionRules, + default_body_unit_conversion_rules, +) +from .weight_trajectory import ( + WeightChange, + WeightTrajectoryMixin, + WeightTrajectoryPoint, + normalize_height_readings, + normalize_weight_readings, +) + +__all__ = [ + "BodyMetricRules", + "BodySizeMeasurementConcepts", + "BodySizeUnitConcepts", + "BodyUnitConversionRules", + "INCH_TO_CM", + "LB_US_TO_KG", + "MeasurementReading", + "MeasurementSeriesMixin", + "ReadingSource", + "WeightChange", + "WeightTrajectoryMixin", + "WeightTrajectoryPoint", + "default_body_metric_rules", + "default_body_size_measurement_concepts", + "default_body_size_unit_concepts", + "default_body_unit_conversion_rules", + "episode_attachment_window", + "normalize_height_readings", + "normalize_weight_readings", + "reading_from_measurement", + "resolve_measurement_series", + "resolve_person_measurement_series", +] diff --git a/omop_alchemy/cdm/handlers/body_metrics/calculators.py b/omop_alchemy/cdm/handlers/body_metrics/calculators.py new file mode 100644 index 0000000..2b324a7 --- /dev/null +++ b/omop_alchemy/cdm/handlers/body_metrics/calculators.py @@ -0,0 +1,76 @@ +from __future__ import annotations + +import math +from dataclasses import dataclass +from functools import lru_cache +from typing import Optional + +from .concept_sets import ( + BodySizeMeasurementConcepts, + BodySizeUnitConcepts, + default_body_size_measurement_concepts, +) +from .units import BodyUnitConversionRules, default_body_unit_conversion_rules + + +@dataclass(frozen=True) +class BodyMetricRules: + """ + Anthropometric unit normalisation and body-size formula rules. + """ + + measurements: BodySizeMeasurementConcepts + unit_rules: BodyUnitConversionRules + + @classmethod + def default(cls) -> "BodyMetricRules": + return default_body_metric_rules() + + @property + def units(self) -> BodySizeUnitConcepts: + return self.unit_rules.units + + @property + def weight_concept_id(self) -> int: + return self.measurements.weight + + @property + def height_concept_id(self) -> int: + return self.measurements.height + + def normalize_weight_kg( + self, + value: Optional[float], + unit_concept_id: Optional[int], + ) -> Optional[float]: + return self.unit_rules.normalize_weight_kg(value, unit_concept_id) + + def normalize_height_cm( + self, + value: Optional[float], + unit_concept_id: Optional[int], + ) -> Optional[float]: + return self.unit_rules.normalize_height_cm(value, unit_concept_id) + + @staticmethod + def bmi(weight_kg: Optional[float], height_m: Optional[float]) -> Optional[float]: + if not weight_kg or not height_m: + return None + return weight_kg / (height_m**2) + + @staticmethod + def bsa_mosteller_m2( + weight_kg: Optional[float], + height_cm: Optional[float], + ) -> Optional[float]: + if not weight_kg or not height_cm: + return None + return math.sqrt((height_cm * weight_kg) / 3600.0) + + +@lru_cache(maxsize=1) +def default_body_metric_rules() -> BodyMetricRules: + return BodyMetricRules( + measurements=default_body_size_measurement_concepts(), + unit_rules=default_body_unit_conversion_rules(), + ) diff --git a/omop_alchemy/cdm/handlers/body_metrics/concept_sets.py b/omop_alchemy/cdm/handlers/body_metrics/concept_sets.py new file mode 100644 index 0000000..31769a3 --- /dev/null +++ b/omop_alchemy/cdm/handlers/body_metrics/concept_sets.py @@ -0,0 +1,41 @@ +from __future__ import annotations + +from dataclasses import dataclass + +from omop_alchemy.cdm.handlers._semantics import default_semantics_runtime + + +@dataclass(frozen=True) +class BodySizeMeasurementConcepts: + weight: int + height: int + + +@dataclass(frozen=True) +class BodySizeUnitConcepts: + kg: int + lb: int + cm: int + inch: int + m2: int + + +def default_body_size_measurement_concepts() -> BodySizeMeasurementConcepts: + runtime = default_semantics_runtime() + measurements = runtime.measurements_numeric.body_size_measurements + return BodySizeMeasurementConcepts( + weight=measurements.weight, + height=measurements.height, + ) + + +def default_body_size_unit_concepts() -> BodySizeUnitConcepts: + runtime = default_semantics_runtime() + units = runtime.measurements_numeric.body_size_units + return BodySizeUnitConcepts( + kg=units.kg, + lb=units.lb, + cm=units.cm, + inch=units.inch, + m2=units.m2, + ) diff --git a/omop_alchemy/cdm/handlers/body_metrics/measurement_series.py b/omop_alchemy/cdm/handlers/body_metrics/measurement_series.py new file mode 100644 index 0000000..21e2428 --- /dev/null +++ b/omop_alchemy/cdm/handlers/body_metrics/measurement_series.py @@ -0,0 +1,184 @@ +from __future__ import annotations + +from dataclasses import dataclass +from datetime import date, timedelta +from functools import cached_property +from typing import ClassVar, Literal, Optional, Sequence + +from sqlalchemy import select +from sqlalchemy.orm import object_session + +from omop_alchemy.cdm.model import Measurement + +DEFAULT_EPISODE_WINDOW_DAYS_PRIOR = 90 +DEFAULT_EPISODE_OPEN_END_FALLBACK_DAYS = 365 + +ReadingSource = Literal["explicit", "window", "person"] + + +@dataclass(frozen=True) +class MeasurementReading: + """A resolved numeric measurement reduced to the fields trajectory math needs.""" + + measurement_id: int + date: date + value: Optional[float] + unit_concept_id: Optional[int] + concept_id: int + source: ReadingSource + + +def episode_attachment_window( + episode, + *, + days_prior: int = DEFAULT_EPISODE_WINDOW_DAYS_PRIOR, + open_end_fallback_days: int = DEFAULT_EPISODE_OPEN_END_FALLBACK_DAYS, +) -> tuple[date, date]: + """ + Date window used for episode-attributable body measurements. + + Weight and similar time-varying measurements use a bounded episode-relative + window. Open episodes fall back to a finite post-start window so accidental + long-running episodes do not absorb a person's entire future history. + """ + start = episode.episode_start_date + end = episode.episode_end_date + + window_start = start - timedelta(days=days_prior) + open_end_bound = start + timedelta(days=open_end_fallback_days) + window_end = min(end, open_end_bound) if end is not None else open_end_bound + + return window_start, window_end + + +def reading_from_measurement( + measurement: Measurement, + *, + source: ReadingSource, +) -> MeasurementReading: + return MeasurementReading( + measurement_id=measurement.measurement_id, + date=measurement.measurement_date, + value=measurement.value_as_number, + unit_concept_id=measurement.unit_concept_id, + concept_id=measurement.measurement_concept_id, + source=source, + ) + + +def _explicit_episode_measurements( + episode, + concept_id_set: set[int], + *, + exclude_modifiers: bool, +) -> tuple[list[MeasurementReading], set[int]]: + seen_ids: set[int] = set() + readings: list[MeasurementReading] = [] + + for event in episode.events: + if not isinstance(event, Measurement): + continue + if event.measurement_concept_id not in concept_id_set: + continue + if exclude_modifiers and event.measurement_event_id is not None: + continue + readings.append(reading_from_measurement(event, source="explicit")) + seen_ids.add(event.measurement_id) + + return readings, seen_ids + + +def resolve_measurement_series( + episode, + concept_ids: Sequence[int], + *, + exclude_modifiers: bool = True, +) -> list[MeasurementReading]: + """ + Resolve episode-attributable measurements for the supplied concepts. + + The resolver first honours explicit ``Episode_Event`` links, then adds + same-person measurements in the episode attachment window that were not + already seen. Detached episodes simply return explicit links. + """ + concept_id_set = set(concept_ids) + readings, seen_ids = _explicit_episode_measurements( + episode, + concept_id_set, + exclude_modifiers=exclude_modifiers, + ) + + session = object_session(episode) + if session is not None: + window_start, window_end = episode_attachment_window(episode) + stmt = select(Measurement).where( + Measurement.person_id == episode.person_id, + Measurement.measurement_concept_id.in_(concept_id_set), + Measurement.measurement_date.between(window_start, window_end), + ) + if exclude_modifiers: + stmt = stmt.where(Measurement.measurement_event_id.is_(None)) + + for row in session.execute(stmt).scalars(): + if row.measurement_id in seen_ids: + continue + readings.append(reading_from_measurement(row, source="window")) + seen_ids.add(row.measurement_id) + + readings.sort(key=lambda r: r.date) + return readings + + +def resolve_person_measurement_series( + episode, + concept_ids: Sequence[int], + *, + exclude_modifiers: bool = True, +) -> list[MeasurementReading]: + """ + Resolve all same-person measurements for effectively invariant concepts. + + This is appropriate for adult height, where an out-of-window reading can + still validly support BMI/BSA for an episode. Do not use it for weight. + """ + concept_id_set = set(concept_ids) + readings, seen_ids = _explicit_episode_measurements( + episode, + concept_id_set, + exclude_modifiers=exclude_modifiers, + ) + + session = object_session(episode) + if session is not None: + stmt = select(Measurement).where( + Measurement.person_id == episode.person_id, + Measurement.measurement_concept_id.in_(concept_id_set), + ) + if exclude_modifiers: + stmt = stmt.where(Measurement.measurement_event_id.is_(None)) + + for row in session.execute(stmt).scalars(): + if row.measurement_id in seen_ids: + continue + readings.append(reading_from_measurement(row, source="person")) + seen_ids.add(row.measurement_id) + + readings.sort(key=lambda r: r.date) + return readings + + +class MeasurementSeriesMixin: + """ + Mixin for episode views that need one cached measurement concept series. + """ + + _series_concept_ids: ClassVar[Sequence[int]] + _exclude_modifier_measurements: ClassVar[bool] = True + + @cached_property + def _series(self) -> list[MeasurementReading]: + return resolve_measurement_series( + self, + self._series_concept_ids, + exclude_modifiers=self._exclude_modifier_measurements, + ) diff --git a/omop_alchemy/cdm/handlers/body_metrics/units.py b/omop_alchemy/cdm/handlers/body_metrics/units.py new file mode 100644 index 0000000..cd2b82b --- /dev/null +++ b/omop_alchemy/cdm/handlers/body_metrics/units.py @@ -0,0 +1,67 @@ +from __future__ import annotations + +from dataclasses import dataclass +from functools import lru_cache +from typing import Optional + +from .concept_sets import BodySizeUnitConcepts, default_body_size_unit_concepts + +LB_US_TO_KG = 0.45359237 +INCH_TO_CM = 2.54 + + +@dataclass(frozen=True) +class BodyUnitConversionRules: + """ + Unit normalisation for anthropometric measurements. + + The handler keeps these conversions close to the body metrics that consume + them instead of introducing a premature global unit engine. + """ + + units: BodySizeUnitConcepts + lb_to_kg: float = LB_US_TO_KG + inch_to_cm: float = INCH_TO_CM + + @classmethod + def default(cls) -> "BodyUnitConversionRules": + return default_body_unit_conversion_rules() + + @property + def weight_unit_conversion_to_kg(self) -> dict[int, float]: + return { + self.units.kg: 1.0, + self.units.lb: self.lb_to_kg, + } + + @property + def height_unit_conversion_to_cm(self) -> dict[int, float]: + return { + self.units.cm: 1.0, + self.units.inch: self.inch_to_cm, + } + + def normalize_weight_kg( + self, + value: Optional[float], + unit_concept_id: Optional[int], + ) -> Optional[float]: + if value is None or unit_concept_id is None: + return None + factor = self.weight_unit_conversion_to_kg.get(unit_concept_id) + return value * factor if factor is not None else None + + def normalize_height_cm( + self, + value: Optional[float], + unit_concept_id: Optional[int], + ) -> Optional[float]: + if value is None or unit_concept_id is None: + return None + factor = self.height_unit_conversion_to_cm.get(unit_concept_id) + return value * factor if factor is not None else None + + +@lru_cache(maxsize=1) +def default_body_unit_conversion_rules() -> BodyUnitConversionRules: + return BodyUnitConversionRules(units=default_body_size_unit_concepts()) diff --git a/omop_alchemy/cdm/handlers/body_metrics/weight_trajectory.py b/omop_alchemy/cdm/handlers/body_metrics/weight_trajectory.py new file mode 100644 index 0000000..ad08d7a --- /dev/null +++ b/omop_alchemy/cdm/handlers/body_metrics/weight_trajectory.py @@ -0,0 +1,241 @@ +from __future__ import annotations + +from dataclasses import dataclass, replace +from datetime import date, timedelta +from functools import cached_property +from typing import ClassVar, Optional + +from .calculators import BodyMetricRules +from .measurement_series import ( + MeasurementReading, + resolve_measurement_series, + resolve_person_measurement_series, +) + + +@dataclass(frozen=True) +class WeightChange: + """ + Result of a windowed weight-change computation. + + ``pct_change`` is None whenever the change is not evaluable. Keeping that + explicit prevents callers from folding "unknown" into "no loss". + """ + + pct_change: Optional[float] + evaluable: bool + reference: Optional[MeasurementReading] = None + + @classmethod + def not_evaluable(cls) -> "WeightChange": + return cls(pct_change=None, evaluable=False) + + +@dataclass(frozen=True) +class WeightTrajectoryPoint: + day_offset: int + pct_change: float + date: date + weight_kg: float + + +def normalize_weight_readings( + readings: list[MeasurementReading], + rules: BodyMetricRules, +) -> list[MeasurementReading]: + normalized: list[MeasurementReading] = [] + for reading in readings: + kg = rules.normalize_weight_kg(reading.value, reading.unit_concept_id) + if kg is None: + continue + normalized.append(replace(reading, value=kg, unit_concept_id=rules.units.kg)) + return normalized + + +def normalize_height_readings( + readings: list[MeasurementReading], + rules: BodyMetricRules, +) -> list[MeasurementReading]: + normalized: list[MeasurementReading] = [] + for reading in readings: + cm = rules.normalize_height_cm(reading.value, reading.unit_concept_id) + if cm is None: + continue + normalized.append(replace(reading, value=cm, unit_concept_id=rules.units.cm)) + return normalized + + +class WeightTrajectoryMixin: + """ + Episode mixin exposing normalized weight, height, BMI, and trajectories. + + Subclasses may set ``_body_metric_rules`` to avoid loading the default + omop-semantics-backed concept IDs. + """ + + _body_metric_rules: ClassVar[BodyMetricRules | None] = None + _exclude_modifier_measurements: ClassVar[bool] = True + episode_id: ClassVar[int] + person_id: ClassVar[int] + + @classmethod + def body_metric_rules(cls) -> BodyMetricRules: + return cls._body_metric_rules or BodyMetricRules.default() + + @cached_property + def _raw_weight_series(self) -> list[MeasurementReading]: + rules = self.body_metric_rules() + return resolve_measurement_series( + self, + (rules.weight_concept_id,), + exclude_modifiers=self._exclude_modifier_measurements, + ) + + @cached_property + def _raw_height_series(self) -> list[MeasurementReading]: + rules = self.body_metric_rules() + return resolve_person_measurement_series( + self, + (rules.height_concept_id,), + exclude_modifiers=self._exclude_modifier_measurements, + ) + + @cached_property + def weight_readings(self) -> list[MeasurementReading]: + """Weight readings normalized to kg.""" + return normalize_weight_readings(self._raw_weight_series, self.body_metric_rules()) + + @cached_property + def height_readings_cm(self) -> list[MeasurementReading]: + """Height readings normalized to cm and resolved without an episode date window.""" + return normalize_height_readings(self._raw_height_series, self.body_metric_rules()) + + @property + def height_m(self) -> Optional[float]: + readings = self.height_readings_cm + if not readings or readings[0].value is None: + return None + return readings[0].value / 100.0 + + @property + def baseline_weight(self) -> Optional[MeasurementReading]: + return self.weight_readings[0] if self.weight_readings else None + + @property + def latest_weight(self) -> Optional[MeasurementReading]: + return self.weight_readings[-1] if self.weight_readings else None + + @property + def baseline_bmi(self) -> Optional[float]: + baseline = self.baseline_weight + return self.body_metric_rules().bmi( + baseline.value if baseline else None, + self.height_m, + ) + + @property + def baseline_bsa_mosteller_m2(self) -> Optional[float]: + baseline = self.baseline_weight + height = self.height_readings_cm[0] if self.height_readings_cm else None + return self.body_metric_rules().bsa_mosteller_m2( + baseline.value if baseline else None, + height.value if height else None, + ) + + def pct_change_from_baseline( + self, + as_of: Optional[MeasurementReading] = None, + ) -> WeightChange: + baseline = self.baseline_weight + target = as_of or self.latest_weight + if ( + baseline is None + or target is None + or baseline.measurement_id == target.measurement_id + or baseline.value is None + or target.value is None + ): + return WeightChange.not_evaluable() + pct = 100.0 * (target.value - baseline.value) / baseline.value + return WeightChange(pct_change=pct, evaluable=True, reference=baseline) + + def pct_change_over(self, days: int) -> WeightChange: + readings = self.weight_readings + if len(readings) < 2: + return WeightChange.not_evaluable() + latest = readings[-1] + window_start = latest.date - timedelta(days=days) + candidates = [r for r in readings if r.date >= window_start] + earliest_in_window = candidates[0] + if ( + latest.value is None + or earliest_in_window.value is None + or earliest_in_window.measurement_id == latest.measurement_id + ): + return WeightChange.not_evaluable() + pct = 100.0 * (latest.value - earliest_in_window.value) / earliest_in_window.value + return WeightChange(pct_change=pct, evaluable=True, reference=earliest_in_window) + + def pct_change_trajectory(self) -> list[WeightTrajectoryPoint]: + baseline = self.baseline_weight + if baseline is None or baseline.value is None: + return [] + points: list[WeightTrajectoryPoint] = [] + for reading in self.weight_readings: + if reading.value is None: + continue + day_offset = (reading.date - baseline.date).days + pct = 100.0 * (reading.value - baseline.value) / baseline.value + points.append( + WeightTrajectoryPoint( + day_offset=day_offset, + pct_change=pct, + date=reading.date, + weight_kg=reading.value, + ) + ) + return points + + def sustained_loss( + self, + threshold_pct: float = 5.0, + min_consecutive: int = 2, + ) -> Optional[bool]: + baseline = self.baseline_weight + readings = self.weight_readings + if baseline is None or baseline.value is None or len(readings) < min_consecutive: + return None + tail = readings[-min_consecutive:] + if any(r.value is None for r in tail): + return None + return all( + r.value is not None + and (100.0 * (baseline.value - r.value) / baseline.value) >= threshold_pct + for r in tail + ) + + def weight_trajectory_summary(self) -> dict: + baseline = self.baseline_weight + latest = self.latest_weight + change_from_baseline = self.pct_change_from_baseline() + change_3mo = self.pct_change_over(90) + change_6mo = self.pct_change_over(180) + return { + "episode_id": self.episode_id, + "person_id": self.person_id, + "n_weight_readings": len(self.weight_readings), + "baseline_weight_kg": baseline.value if baseline else None, + "baseline_weight_date": baseline.date if baseline else None, + "latest_weight_kg": latest.value if latest else None, + "latest_weight_date": latest.date if latest else None, + "height_m": self.height_m, + "baseline_bmi": self.baseline_bmi, + "baseline_bsa_mosteller_m2": self.baseline_bsa_mosteller_m2, + "pct_change_from_baseline": change_from_baseline.pct_change, + "pct_change_from_baseline_evaluable": change_from_baseline.evaluable, + "pct_change_3mo": change_3mo.pct_change, + "pct_change_3mo_evaluable": change_3mo.evaluable, + "pct_change_6mo": change_6mo.pct_change, + "pct_change_6mo_evaluable": change_6mo.evaluable, + "sustained_5pct_loss": self.sustained_loss(), + } diff --git a/omop_alchemy/cdm/handlers/drug_episodes/__init__.py b/omop_alchemy/cdm/handlers/drug_episodes/__init__.py new file mode 100644 index 0000000..e7eec6e --- /dev/null +++ b/omop_alchemy/cdm/handlers/drug_episodes/__init__.py @@ -0,0 +1,18 @@ +from .dosing import DOSE_EVALUABLE, DoseEvaluability +from .drug_episode import DrugEpisodeMixin +from .exposure_series import resolve_drug_exposure_series +from .summaries import ( + DrugExposureSummary, + summarize_drug_exposures, + summarize_drug_exposures_by, +) + +__all__ = [ + "DOSE_EVALUABLE", + "DoseEvaluability", + "DrugEpisodeMixin", + "DrugExposureSummary", + "resolve_drug_exposure_series", + "summarize_drug_exposures", + "summarize_drug_exposures_by", +] diff --git a/omop_alchemy/cdm/handlers/drug_episodes/dosing.py b/omop_alchemy/cdm/handlers/drug_episodes/dosing.py new file mode 100644 index 0000000..faead17 --- /dev/null +++ b/omop_alchemy/cdm/handlers/drug_episodes/dosing.py @@ -0,0 +1,22 @@ +from __future__ import annotations + +from dataclasses import dataclass +from typing import Optional + + +@dataclass(frozen=True) +class DoseEvaluability: + """ + Whether a dose-like summary can be interpreted as a dose quantity. + + Drug exposure rows often carry source units and quantities without enough + normalization to compare across agents or regimens. Domain-specific dosing + modules should use this as a small shared vocabulary instead of silently + treating missing or mixed units as comparable. + """ + + evaluable: bool + reason: Optional[str] = None + + +DOSE_EVALUABLE = DoseEvaluability(evaluable=True) diff --git a/omop_alchemy/cdm/handlers/drug_episodes/drug_episode.py b/omop_alchemy/cdm/handlers/drug_episodes/drug_episode.py new file mode 100644 index 0000000..7632889 --- /dev/null +++ b/omop_alchemy/cdm/handlers/drug_episodes/drug_episode.py @@ -0,0 +1,37 @@ +from __future__ import annotations + +from functools import cached_property +from typing import Callable, ClassVar, Hashable, Sequence + +from omop_alchemy.cdm.model import Drug_Exposure + +from .exposure_series import resolve_drug_exposure_series +from .summaries import DrugExposureSummary, summarize_drug_exposures_by + + +class DrugEpisodeMixin: + """ + Episode mixin for generic linked-drug retrieval and summary. + + Domain-specific subclasses can supply concept filters, grouping keys, and + dose validity rules. This base layer only knows how to find and summarise + drug exposure rows. + """ + + _drug_concept_ids: ClassVar[Sequence[int] | None] = None + _include_window_drug_exposures: ClassVar[bool] = False + + @cached_property + def drug_exposures(self) -> list[Drug_Exposure]: + return resolve_drug_exposure_series( + self, + self._drug_concept_ids, + include_window=self._include_window_drug_exposures, + ) + + def drug_exposure_summaries_by( + self, + key: Callable[[Drug_Exposure], Hashable] | None = None, + ) -> list[DrugExposureSummary]: + key = key or (lambda exposure: exposure.drug_concept_id) + return summarize_drug_exposures_by(self.drug_exposures, key) diff --git a/omop_alchemy/cdm/handlers/drug_episodes/exposure_series.py b/omop_alchemy/cdm/handlers/drug_episodes/exposure_series.py new file mode 100644 index 0000000..a7354a6 --- /dev/null +++ b/omop_alchemy/cdm/handlers/drug_episodes/exposure_series.py @@ -0,0 +1,61 @@ +from __future__ import annotations + +from typing import Optional, Sequence + +from sqlalchemy import select +from sqlalchemy.orm import object_session + +from omop_alchemy.cdm.model import Drug_Exposure + + +def _episode_date_bounds(episode): + start = episode.episode_start_date + end = episode.episode_end_date or start + return start, end + + +def resolve_drug_exposure_series( + episode, + concept_ids: Optional[Sequence[int]] = None, + *, + include_window: bool = False, +) -> list[Drug_Exposure]: + """ + Resolve drug exposures linked to an episode. + + Explicit ``Episode_Event`` links are always honoured. A bounded episode-date + fallback can be enabled by callers that have a meaningful concept set and + want to recover unlinked rows. The default stays explicit-only to avoid + accidentally attributing unrelated same-person medications to a drug + episode. + """ + concept_id_set = set(concept_ids) if concept_ids is not None else None + seen_ids: set[int] = set() + exposures: list[Drug_Exposure] = [] + + for event in episode.events: + if not isinstance(event, Drug_Exposure): + continue + if concept_id_set is not None and event.drug_concept_id not in concept_id_set: + continue + exposures.append(event) + seen_ids.add(event.drug_exposure_id) + + session = object_session(episode) + if include_window and session is not None: + start, end = _episode_date_bounds(episode) + stmt = select(Drug_Exposure).where( + Drug_Exposure.person_id == episode.person_id, + Drug_Exposure.drug_exposure_start_date.between(start, end), + ) + if concept_id_set is not None: + stmt = stmt.where(Drug_Exposure.drug_concept_id.in_(concept_id_set)) + + for row in session.execute(stmt).scalars(): + if row.drug_exposure_id in seen_ids: + continue + exposures.append(row) + seen_ids.add(row.drug_exposure_id) + + exposures.sort(key=lambda e: e.drug_exposure_start_date) + return exposures diff --git a/omop_alchemy/cdm/handlers/drug_episodes/summaries.py b/omop_alchemy/cdm/handlers/drug_episodes/summaries.py new file mode 100644 index 0000000..7d2ff50 --- /dev/null +++ b/omop_alchemy/cdm/handlers/drug_episodes/summaries.py @@ -0,0 +1,69 @@ +from __future__ import annotations + +from collections import defaultdict +from dataclasses import dataclass +from datetime import date +from typing import Callable, Hashable, Optional, Sequence + +from omop_alchemy.cdm.model import Drug_Exposure + + +@dataclass(frozen=True) +class DrugExposureSummary: + """ + Small generic summary of drug exposures grouped by a caller-chosen key. + + The grouping key can be a drug concept, ingredient concept, regimen member, + or any downstream classifier. This type deliberately does not encode SACT or + any other clinical programme-specific policy. + """ + + group_key: object + n_exposures: int + first_start_date: Optional[date] + last_start_date: Optional[date] + total_quantity: Optional[float] + dose_unit_source_values: frozenset[str] + drug_concept_ids: frozenset[int] + + +def summarize_drug_exposures( + exposures: Sequence[Drug_Exposure], + *, + group_key: object, +) -> DrugExposureSummary: + quantities = [e.quantity for e in exposures if e.quantity is not None] + dates = [ + e.drug_exposure_start_date + for e in exposures + if e.drug_exposure_start_date is not None + ] + dose_units = frozenset( + e.dose_unit_source_value + for e in exposures + if e.dose_unit_source_value + ) + drug_concept_ids = frozenset(e.drug_concept_id for e in exposures) + + return DrugExposureSummary( + group_key=group_key, + n_exposures=len(exposures), + first_start_date=min(dates) if dates else None, + last_start_date=max(dates) if dates else None, + total_quantity=sum(quantities) if quantities else None, + dose_unit_source_values=dose_units, + drug_concept_ids=drug_concept_ids, + ) + + +def summarize_drug_exposures_by( + exposures: Sequence[Drug_Exposure], + key: Callable[[Drug_Exposure], Hashable], +) -> list[DrugExposureSummary]: + grouped: dict[Hashable, list[Drug_Exposure]] = defaultdict(list) + for exposure in exposures: + grouped[key(exposure)].append(exposure) + return [ + summarize_drug_exposures(rows, group_key=group_key) + for group_key, rows in grouped.items() + ] diff --git a/omop_alchemy/cdm/handlers/oncology/__init__.py b/omop_alchemy/cdm/handlers/oncology/__init__.py new file mode 100644 index 0000000..0fd0cce --- /dev/null +++ b/omop_alchemy/cdm/handlers/oncology/__init__.py @@ -0,0 +1,81 @@ +from .concept_sets import ( + cancer_indicating_surgery_parent_concept_ids, + cancer_indicating_surgery_point_concept_ids, + clear_concept_set_cache, + disease_episode_type_concept_ids, + diagnostic_staging_procedure_parent_concept_ids, + diagnostic_staging_procedure_point_concept_ids, + drug_concept_membership_expression, + overarching_episode_type_concept_id, + procedure_concept_membership_expression, + resolve_cancer_indicating_surgery_procedure_concept_ids, + resolve_diagnostic_staging_procedure_concept_ids, + resolve_rt_procedure_concept_ids, + resolve_sact_drug_concept_ids, + rt_procedure_parent_concept_ids, + sact_drug_excluded_parent_concept_ids, + sact_drug_parent_concept_ids, + treatment_cycle_episode_concept_id, + treatment_episode_type_concept_ids, + treatment_regimen_episode_concept_id, +) +from .oncology_critical_weight_loss import OncologyCriticalWeightLossMixin +from .oncology_drug_exposure import OncologyDrugExposure +from .oncology_episodes import OncologyEpisode, OncologyModality +from .oncology_event import OncologyEpisodeEvent, OncologyEpisodeEventMixin +from .oncology_procedure_occurrence import OncologyProcedure +from .oncology_rt_dosing import ( + OncologyRTDosingMixin, + RTDoseSummary, + rt_dose_evaluability, + rt_site_key, + summarize_rt_procedures, + summarize_rt_procedures_by, +) +from .oncology_sact_dosing import ( + OncologySACTDosingMixin, + SACTDoseSummary, + sact_dose_evaluability, + summarize_sact_exposures, + summarize_sact_exposures_by, +) + +__all__ = [ + "OncologyCriticalWeightLossMixin", + "OncologyDrugExposure", + "OncologyEpisode", + "OncologyEpisodeEvent", + "OncologyEpisodeEventMixin", + "OncologyModality", + "OncologyProcedure", + "OncologyRTDosingMixin", + "OncologySACTDosingMixin", + "RTDoseSummary", + "SACTDoseSummary", + "cancer_indicating_surgery_parent_concept_ids", + "cancer_indicating_surgery_point_concept_ids", + "clear_concept_set_cache", + "disease_episode_type_concept_ids", + "diagnostic_staging_procedure_parent_concept_ids", + "diagnostic_staging_procedure_point_concept_ids", + "drug_concept_membership_expression", + "overarching_episode_type_concept_id", + "procedure_concept_membership_expression", + "resolve_cancer_indicating_surgery_procedure_concept_ids", + "resolve_diagnostic_staging_procedure_concept_ids", + "resolve_rt_procedure_concept_ids", + "resolve_sact_drug_concept_ids", + "rt_procedure_parent_concept_ids", + "rt_dose_evaluability", + "rt_site_key", + "sact_drug_excluded_parent_concept_ids", + "sact_drug_parent_concept_ids", + "sact_dose_evaluability", + "summarize_rt_procedures", + "summarize_rt_procedures_by", + "summarize_sact_exposures", + "summarize_sact_exposures_by", + "treatment_cycle_episode_concept_id", + "treatment_episode_type_concept_ids", + "treatment_regimen_episode_concept_id", +] diff --git a/omop_alchemy/cdm/handlers/oncology/concept_sets.py b/omop_alchemy/cdm/handlers/oncology/concept_sets.py new file mode 100644 index 0000000..6f89954 --- /dev/null +++ b/omop_alchemy/cdm/handlers/oncology/concept_sets.py @@ -0,0 +1,220 @@ +from __future__ import annotations + +from collections.abc import Callable, Iterable + +import sqlalchemy.orm as so +from sqlalchemy import select + +from omop_alchemy.cdm.handlers._semantics import default_semantics_runtime +from omop_alchemy.cdm.model import Concept_Ancestor + + +def _runtime_group(value_set_name: str, semantic_unit_name: str, group_name: str): + runtime = default_semantics_runtime() + value_set = getattr(runtime, value_set_name) + semantic_unit = getattr(value_set, semantic_unit_name) + return semantic_unit.groups[group_name] + + +def rt_procedure_parent_concept_ids() -> tuple[int, ...]: + group = _runtime_group( + "cancer_procedures", + "cancer_procedure_types", + "cancer_procedure_types", + ) + mapper = group.mapper() + return ( + mapper["rt_externalbeam"], + mapper["rt_procedure"], + mapper["rt_brachytherapy"], + ) + + +def cancer_indicating_surgery_parent_concept_ids() -> tuple[int, ...]: + group = _runtime_group( + "cancer_procedures", + "cancer_indicating_surgery_parent_concepts", + "cancer_indicating_surgery_parent_concepts", + ) + return tuple(group.mapper().values()) + + +def cancer_indicating_surgery_point_concept_ids() -> tuple[int, ...]: + group = _runtime_group( + "cancer_procedures", + "cancer_indicating_surgery_point_concepts", + "cancer_indicating_surgery_point_concepts", + ) + return tuple(group.mapper().values()) + + +def diagnostic_staging_procedure_parent_concept_ids() -> tuple[int, ...]: + group = _runtime_group( + "cancer_procedures", + "diagnostic_staging_procedure_parent_concepts", + "diagnostic_staging_procedure_parent_concepts", + ) + return tuple(group.mapper().values()) + + +def diagnostic_staging_procedure_point_concept_ids() -> tuple[int, ...]: + group = _runtime_group( + "cancer_procedures", + "diagnostic_staging_procedure_point_concepts", + "diagnostic_staging_procedure_point_concepts", + ) + return tuple(group.mapper().values()) + + +def sact_drug_parent_concept_ids() -> tuple[int, ...]: + group = _runtime_group( + "sact", + "sact_drug_classification", + "sact_drug_classification", + ) + return tuple(group.ids) + + +def sact_drug_excluded_parent_concept_ids() -> tuple[int, ...]: + group = _runtime_group( + "sact", + "sact_drug_classification", + "sact_drug_classification", + ) + return tuple(group.excluded_ids) + + +def disease_episode_type_concept_ids() -> tuple[int, ...]: + return tuple(default_semantics_runtime().types.disease_episode_types.ids) + + +def overarching_episode_type_concept_id() -> int: + return default_semantics_runtime().types.disease_episode_types.episode_of_care + + +def treatment_episode_type_concept_ids() -> tuple[int, ...]: + return tuple(default_semantics_runtime().types.treatment_episode_types.ids) + + +def treatment_regimen_episode_concept_id() -> int: + return default_semantics_runtime().types.treatment_episode_types.treatment_regimen + + +def treatment_cycle_episode_concept_id() -> int: + return default_semantics_runtime().types.treatment_episode_types.treatment_cycle + + +def _descendant_concept_ids( + session: so.Session, + ancestor_concept_ids: Iterable[int], +) -> frozenset[int]: + stmt = select(Concept_Ancestor.descendant_concept_id).where( + Concept_Ancestor.ancestor_concept_id.in_(tuple(ancestor_concept_ids)) + ) + return frozenset(session.execute(stmt).scalars().all()) + + +def procedure_concept_membership_expression( + concept_id_column, + parent_ids: Iterable[int], + point_ids: Iterable[int] = (), +): + expr = concept_id_column.in_( + select(Concept_Ancestor.descendant_concept_id).where( + Concept_Ancestor.ancestor_concept_id.in_(tuple(parent_ids)) + ) + ) + point_ids = tuple(point_ids) + if point_ids: + expr = expr | concept_id_column.in_(point_ids) + return expr + + +def drug_concept_membership_expression( + concept_id_column, + include_parent_ids: Iterable[int], + exclude_parent_ids: Iterable[int] = (), +): + expr = concept_id_column.in_( + select(Concept_Ancestor.descendant_concept_id).where( + Concept_Ancestor.ancestor_concept_id.in_(tuple(include_parent_ids)) + ) + ) + exclude_parent_ids = tuple(exclude_parent_ids) + if exclude_parent_ids: + expr = expr & concept_id_column.not_in( + select(Concept_Ancestor.descendant_concept_id).where( + Concept_Ancestor.ancestor_concept_id.in_(exclude_parent_ids) + ) + ) + return expr + + +class _ConceptSetCache: + def __init__(self) -> None: + self._cache: dict[tuple[int, str], frozenset[int]] = {} + + def get( + self, + name: str, + session: so.Session, + builder: Callable[[so.Session], frozenset[int]], + ) -> frozenset[int]: + bind = session.get_bind() + key = (id(bind), name) + if key not in self._cache: + self._cache[key] = builder(session) + return self._cache[key] + + def clear(self) -> None: + self._cache.clear() + + +_cache = _ConceptSetCache() + + +def resolve_rt_procedure_concept_ids(session: so.Session) -> frozenset[int]: + return _cache.get( + "rt_procedure_concept_ids", + session, + lambda s: _descendant_concept_ids(s, rt_procedure_parent_concept_ids()), + ) + + +def resolve_cancer_indicating_surgery_procedure_concept_ids( + session: so.Session, +) -> frozenset[int]: + def _build(s: so.Session) -> frozenset[int]: + closure = _descendant_concept_ids( + s, + cancer_indicating_surgery_parent_concept_ids(), + ) + return closure | frozenset(cancer_indicating_surgery_point_concept_ids()) + + return _cache.get("cancer_indicating_surgery_procedure_concept_ids", session, _build) + + +def resolve_diagnostic_staging_procedure_concept_ids( + session: so.Session, +) -> frozenset[int]: + def _build(s: so.Session) -> frozenset[int]: + closure = _descendant_concept_ids( + s, + diagnostic_staging_procedure_parent_concept_ids(), + ) + return closure | frozenset(diagnostic_staging_procedure_point_concept_ids()) + + return _cache.get("diagnostic_staging_procedure_concept_ids", session, _build) + + +def resolve_sact_drug_concept_ids(session: so.Session) -> frozenset[int]: + def _build(s: so.Session) -> frozenset[int]: + included = _descendant_concept_ids(s, sact_drug_parent_concept_ids()) + excluded = _descendant_concept_ids(s, sact_drug_excluded_parent_concept_ids()) + return included - excluded + + return _cache.get("sact_drug_concept_ids", session, _build) + + +def clear_concept_set_cache() -> None: + _cache.clear() diff --git a/omop_alchemy/cdm/handlers/oncology/oncology_critical_weight_loss.py b/omop_alchemy/cdm/handlers/oncology/oncology_critical_weight_loss.py new file mode 100644 index 0000000..8b2df8a --- /dev/null +++ b/omop_alchemy/cdm/handlers/oncology/oncology_critical_weight_loss.py @@ -0,0 +1,52 @@ +from __future__ import annotations + +from functools import cached_property +from typing import Any + +from omop_alchemy.cdm.handlers.adverse_events import ( + critical_weight_loss_grade, + ctcae_weight_loss_grade, + martin_weight_loss_grade, +) +from omop_alchemy.cdm.handlers.body_metrics import WeightTrajectoryMixin + + +class OncologyCriticalWeightLossMixin(WeightTrajectoryMixin): + """ + Critical-weight-loss support for oncology episodes. + + Body measurements stay in ``body_metrics`` and grading policy stays in + ``adverse_events``. This mixin only composes those reusable pieces onto the + oncology episode surface. + """ + + @cached_property + def ctcae_weight_loss_grade(self) -> int | None: + return ctcae_weight_loss_grade( + self.pct_change_from_baseline().pct_change, + ) + + @cached_property + def martin_weight_loss_grade(self) -> int | None: + return martin_weight_loss_grade( + self.pct_change_from_baseline().pct_change, + self.baseline_bmi, + ) + + @cached_property + def critical_weight_loss_grade(self) -> int | None: + return critical_weight_loss_grade( + self.pct_change_from_baseline().pct_change, + self.baseline_bmi, + ) + + def critical_weight_loss_summary(self) -> dict[str, Any]: + summary = self.weight_trajectory_summary() + summary.update( + { + "ctcae_weight_loss_grade": self.ctcae_weight_loss_grade, + "martin_weight_loss_grade": self.martin_weight_loss_grade, + "critical_weight_loss_grade": self.critical_weight_loss_grade, + } + ) + return summary diff --git a/omop_alchemy/cdm/handlers/oncology/oncology_drug_exposure.py b/omop_alchemy/cdm/handlers/oncology/oncology_drug_exposure.py new file mode 100644 index 0000000..3a27293 --- /dev/null +++ b/omop_alchemy/cdm/handlers/oncology/oncology_drug_exposure.py @@ -0,0 +1,38 @@ +from __future__ import annotations + +from sqlalchemy.ext.hybrid import hybrid_property +from sqlalchemy.orm import object_session + +from omop_alchemy.cdm.model.clinical.drug_exposure import Drug_ExposureView + +from .concept_sets import ( + drug_concept_membership_expression, + resolve_sact_drug_concept_ids, + sact_drug_excluded_parent_concept_ids, + sact_drug_parent_concept_ids, +) + + +class OncologyDrugExposure(Drug_ExposureView): + """ + Oncology-aware drug exposure view. + + SACT classification is governed by omop-semantics and intentionally kept + separate from generic drug episode summaries. + """ + + @hybrid_property + def is_sact(self) -> bool: + session = object_session(self) + if session is None: + return False + return self.drug_concept_id in resolve_sact_drug_concept_ids(session) + + @is_sact.inplace.expression + @classmethod + def _is_sact_expression(cls): + return drug_concept_membership_expression( + cls.drug_concept_id, + sact_drug_parent_concept_ids(), + sact_drug_excluded_parent_concept_ids(), + ) diff --git a/omop_alchemy/cdm/handlers/oncology/oncology_episodes.py b/omop_alchemy/cdm/handlers/oncology/oncology_episodes.py new file mode 100644 index 0000000..c5a1911 --- /dev/null +++ b/omop_alchemy/cdm/handlers/oncology/oncology_episodes.py @@ -0,0 +1,211 @@ +from __future__ import annotations + +from enum import StrEnum +from functools import cached_property +from typing import Self, cast + +import sqlalchemy.orm as so +from sqlalchemy.ext.declarative import declared_attr +from sqlalchemy.ext.hybrid import hybrid_property +from sqlalchemy.orm import object_session + +from omop_alchemy.cdm.handlers.drug_episodes import DrugEpisodeMixin +from omop_alchemy.cdm.model.structural import EpisodeView + +from .concept_sets import ( + disease_episode_type_concept_ids, + overarching_episode_type_concept_id, + treatment_cycle_episode_concept_id, + treatment_episode_type_concept_ids, + treatment_regimen_episode_concept_id, +) +from .oncology_critical_weight_loss import OncologyCriticalWeightLossMixin +from .oncology_drug_exposure import OncologyDrugExposure +from .oncology_event import OncologyEpisodeEventMixin +from .oncology_procedure_occurrence import OncologyProcedure +from .oncology_rt_dosing import OncologyRTDosingMixin +from .oncology_sact_dosing import OncologySACTDosingMixin + + +class OncologyModality(StrEnum): + SACT = "sact" + RADIOTHERAPY = "radiotherapy" + SURGERY = "surgery" + DIAGNOSTIC_STAGING = "diagnostic_staging" + UNKNOWN = "unknown" + + +class OncologyEpisode( + OncologyCriticalWeightLossMixin, + OncologySACTDosingMixin, + OncologyRTDosingMixin, + DrugEpisodeMixin, + OncologyEpisodeEventMixin, + EpisodeView, +): + """ + Oncology-aware episode view. + + This composes generic episode hierarchy support, oncology-aware + ``Episode_Event`` resolution, body-metric adverse-event grading, and + treatment dose-summary interfaces. Modality classification exposes both + structural treatment evidence, such as linked drug exposures, and governed + concept evidence, such as SACT-classified drug concepts, so callers can + audit disagreements. + """ + + @declared_attr + def children(cls) -> so.Mapped[list["OncologyEpisode"]]: + episode_id = cls.__table__.c.episode_id + episode_parent_id = cls.__table__.c.episode_parent_id + return so.relationship( + cls.__name__, + primaryjoin=lambda: so.remote(episode_parent_id) == episode_id, + foreign_keys=lambda: [episode_parent_id], + remote_side=lambda: [episode_parent_id], + viewonly=True, + lazy="selectin", + uselist=True, + ) + + @hybrid_property + def is_disease_episode(self) -> bool: + return self.episode_concept_id in disease_episode_type_concept_ids() + + @is_disease_episode.inplace.expression + @classmethod + def _is_disease_episode_expression(cls): + return cls.episode_concept_id.in_(disease_episode_type_concept_ids()) + + @hybrid_property + def is_overarching(self) -> bool: + return self.episode_concept_id == overarching_episode_type_concept_id() + + @is_overarching.inplace.expression + @classmethod + def _is_overarching_expression(cls): + return cls.episode_concept_id == overarching_episode_type_concept_id() + + @hybrid_property + def is_treatment_episode(self) -> bool: + return self.episode_concept_id in treatment_episode_type_concept_ids() + + @is_treatment_episode.inplace.expression + @classmethod + def _is_treatment_episode_expression(cls): + return cls.episode_concept_id.in_(treatment_episode_type_concept_ids()) + + @hybrid_property + def is_treatment_regimen(self) -> bool: + return self.episode_concept_id == treatment_regimen_episode_concept_id() + + @is_treatment_regimen.inplace.expression + @classmethod + def _is_treatment_regimen_expression(cls): + return cls.episode_concept_id == treatment_regimen_episode_concept_id() + + @hybrid_property + def is_treatment_cycle(self) -> bool: + return self.episode_concept_id == treatment_cycle_episode_concept_id() + + @is_treatment_cycle.inplace.expression + @classmethod + def _is_treatment_cycle_expression(cls): + return cls.episode_concept_id == treatment_cycle_episode_concept_id() + + @property + def primary_episode(self) -> Self: + current = self + while not current.is_overarching and current.episode_parent_id is not None: + session = object_session(current) + if session is None: + break + parent = session.get(type(self), current.episode_parent_id) + if parent is None: + break + current = parent + return current + + @cached_property + def child_treatment_episodes(self) -> list[Self]: + return [ + child + for child in cast(list[Self], self.children) + if child.is_treatment_episode + ] + + def _linked_oncology_events(self, *, include_child_events: bool = True) -> list[object]: + resolved: list[object] = list(self.events) + if include_child_events: + for child in cast(list[Self], self.children): + resolved.extend(child.events) + return resolved + + @cached_property + def structural_modality(self) -> OncologyModality: + """ + Classify modality from linked event structure. + + Any linked drug exposure is treated as structural SACT evidence, while + radiotherapy, surgery, and diagnostic/staging require governed procedure + concept membership. + """ + has_drug_exposure = False + for event in self._linked_oncology_events(): + if isinstance(event, OncologyDrugExposure): + has_drug_exposure = True + continue + if not isinstance(event, OncologyProcedure): + continue + if event.is_radiotherapy: + return OncologyModality.RADIOTHERAPY + if event.is_surgery: + return OncologyModality.SURGERY + if event.is_diagnostic_staging: + return OncologyModality.DIAGNOSTIC_STAGING + return OncologyModality.SACT if has_drug_exposure else OncologyModality.UNKNOWN + + @cached_property + def concept_modality(self) -> OncologyModality: + """ + Classify modality from linked procedure/drug concept identity. + + This is intentionally distinct from ``structural_modality`` so SACT + disagreements remain visible. + """ + for event in self._linked_oncology_events(): + if isinstance(event, OncologyDrugExposure): + if event.is_sact: + return OncologyModality.SACT + elif isinstance(event, OncologyProcedure): + if event.is_radiotherapy: + return OncologyModality.RADIOTHERAPY + if event.is_surgery: + return OncologyModality.SURGERY + if event.is_diagnostic_staging: + return OncologyModality.DIAGNOSTIC_STAGING + return OncologyModality.UNKNOWN + + @cached_property + def child_treatment_episodes_by_modality( + self, + ) -> dict[OncologyModality, list[Self]]: + groups: dict[OncologyModality, list[Self]] = { + modality: [] + for modality in OncologyModality + } + for child in self.child_treatment_episodes: + groups[child.structural_modality].append(child) + return groups + + @cached_property + def child_treatment_episodes_by_concept_modality( + self, + ) -> dict[OncologyModality, list[Self]]: + groups: dict[OncologyModality, list[Self]] = { + modality: [] + for modality in OncologyModality + } + for child in self.child_treatment_episodes: + groups[child.concept_modality].append(child) + return groups diff --git a/omop_alchemy/cdm/handlers/oncology/oncology_event.py b/omop_alchemy/cdm/handlers/oncology/oncology_event.py new file mode 100644 index 0000000..9d49c7c --- /dev/null +++ b/omop_alchemy/cdm/handlers/oncology/oncology_event.py @@ -0,0 +1,52 @@ +from __future__ import annotations + +from typing import Any, cast + +import sqlalchemy.orm as so +from sqlalchemy.ext.declarative import declared_attr + +from omop_alchemy.cdm.base import ModifierFieldConcepts +from omop_alchemy.cdm.model.structural.episode_event import Episode_EventView + +from .oncology_drug_exposure import OncologyDrugExposure +from .oncology_procedure_occurrence import OncologyProcedure + + +class OncologyEpisodeEvent(Episode_EventView): + """ + Episode-event view that prefers oncology-aware fact table views. + + Non-oncology targets continue to use the base resolver map from + ``Episode_EventView``. Procedure and drug targets resolve to oncology + subclasses so episode traversal can ask domain-specific questions such as + ``is_radiotherapy`` and ``is_sact``. + """ + + @classmethod + def resolved_event_target_classes(cls) -> dict[int, type[Any]]: + base_resolver = getattr(Episode_EventView, "resolved_event_target_classes") + targets = dict(base_resolver()) + targets.update( + { + ModifierFieldConcepts.PROCEDURE_OCCURRENCE: OncologyProcedure, + ModifierFieldConcepts.DRUG_EXPOSURE: OncologyDrugExposure, + } + ) + return targets + + +class OncologyEpisodeEventMixin: + """ + Relationship override for episode classes that need oncology event targets. + """ + + @declared_attr + def episode_events(cls) -> so.Mapped[list["OncologyEpisodeEvent"]]: + owner_episode_id = cast(Any, cls).__table__.c.episode_id + event_episode_id = OncologyEpisodeEvent.__table__.c.episode_id + return so.relationship( + "OncologyEpisodeEvent", + primaryjoin=lambda: owner_episode_id == event_episode_id, + viewonly=True, + lazy="selectin", + ) diff --git a/omop_alchemy/cdm/handlers/oncology/oncology_procedure_occurrence.py b/omop_alchemy/cdm/handlers/oncology/oncology_procedure_occurrence.py new file mode 100644 index 0000000..d948374 --- /dev/null +++ b/omop_alchemy/cdm/handlers/oncology/oncology_procedure_occurrence.py @@ -0,0 +1,82 @@ +from __future__ import annotations + +from sqlalchemy.ext.hybrid import hybrid_property +from sqlalchemy.orm import object_session + +from omop_alchemy.cdm.model.clinical.procedure_occurrence import ( + Procedure_OccurrenceView, +) + +from .concept_sets import ( + cancer_indicating_surgery_parent_concept_ids, + cancer_indicating_surgery_point_concept_ids, + diagnostic_staging_procedure_parent_concept_ids, + diagnostic_staging_procedure_point_concept_ids, + procedure_concept_membership_expression, + resolve_cancer_indicating_surgery_procedure_concept_ids, + resolve_diagnostic_staging_procedure_concept_ids, + resolve_rt_procedure_concept_ids, + rt_procedure_parent_concept_ids, +) + + +class OncologyProcedure(Procedure_OccurrenceView): + """ + Oncology-aware procedure occurrence view. + + This maps the standard ``procedure_occurrence`` table and adds governed + concept-set membership checks used by oncology episode classification. + """ + + @hybrid_property + def is_radiotherapy(self) -> bool: + session = object_session(self) + if session is None: + return False + return self.procedure_concept_id in resolve_rt_procedure_concept_ids(session) + + @is_radiotherapy.inplace.expression + @classmethod + def _is_radiotherapy_expression(cls): + return procedure_concept_membership_expression( + cls.procedure_concept_id, + rt_procedure_parent_concept_ids(), + ) + + @hybrid_property + def is_surgery(self) -> bool: + session = object_session(self) + if session is None: + return False + return ( + self.procedure_concept_id + in resolve_cancer_indicating_surgery_procedure_concept_ids(session) + ) + + @is_surgery.inplace.expression + @classmethod + def _is_surgery_expression(cls): + return procedure_concept_membership_expression( + cls.procedure_concept_id, + cancer_indicating_surgery_parent_concept_ids(), + cancer_indicating_surgery_point_concept_ids(), + ) + + @hybrid_property + def is_diagnostic_staging(self) -> bool: + session = object_session(self) + if session is None: + return False + return ( + self.procedure_concept_id + in resolve_diagnostic_staging_procedure_concept_ids(session) + ) + + @is_diagnostic_staging.inplace.expression + @classmethod + def _is_diagnostic_staging_expression(cls): + return procedure_concept_membership_expression( + cls.procedure_concept_id, + diagnostic_staging_procedure_parent_concept_ids(), + diagnostic_staging_procedure_point_concept_ids(), + ) diff --git a/omop_alchemy/cdm/handlers/oncology/oncology_rt_dosing.py b/omop_alchemy/cdm/handlers/oncology/oncology_rt_dosing.py new file mode 100644 index 0000000..98627ea --- /dev/null +++ b/omop_alchemy/cdm/handlers/oncology/oncology_rt_dosing.py @@ -0,0 +1,122 @@ +from __future__ import annotations + +from collections import defaultdict +from dataclasses import dataclass +from datetime import date +from functools import cached_property +from typing import Any, Callable, Hashable, Sequence + +from omop_alchemy.cdm.handlers.drug_episodes import DoseEvaluability + +from .oncology_procedure_occurrence import OncologyProcedure + + +@dataclass(frozen=True) +class RTDoseSummary: + """ + Radiotherapy procedure summary for one caller-chosen site/group key. + + OMOP procedure rows do not provide one universal RT dose model. This summary + exposes dates, procedure concepts, modifiers, counts, and evaluability so a + site-specific RT policy can decide what is clinically meaningful. + """ + + group_key: object + n_procedures: int + first_date: date | None + last_date: date | None + total_quantity: int | None + procedure_concept_ids: frozenset[int] + modifier_concept_ids: frozenset[int] + evaluability: DoseEvaluability + + +def rt_dose_evaluability( + procedures: Sequence[OncologyProcedure], +) -> DoseEvaluability: + if not procedures: + return DoseEvaluability(False, "no_rt_procedures") + if any(procedure.quantity is None for procedure in procedures): + return DoseEvaluability(False, "missing_quantity") + return DoseEvaluability(True) + + +def summarize_rt_procedures( + procedures: Sequence[OncologyProcedure], + *, + group_key: object, +) -> RTDoseSummary: + dates = [ + procedure.procedure_date + for procedure in procedures + if procedure.procedure_date is not None + ] + quantities = [ + procedure.quantity + for procedure in procedures + if procedure.quantity is not None + ] + return RTDoseSummary( + group_key=group_key, + n_procedures=len(procedures), + first_date=min(dates) if dates else None, + last_date=max(dates) if dates else None, + total_quantity=sum(quantities) if quantities else None, + procedure_concept_ids=frozenset( + procedure.procedure_concept_id + for procedure in procedures + ), + modifier_concept_ids=frozenset( + procedure.modifier_concept_id + for procedure in procedures + if procedure.modifier_concept_id is not None + ), + evaluability=rt_dose_evaluability(procedures), + ) + + +def summarize_rt_procedures_by( + procedures: Sequence[OncologyProcedure], + key: Callable[[OncologyProcedure], Hashable], +) -> list[RTDoseSummary]: + grouped: dict[Hashable, list[OncologyProcedure]] = defaultdict(list) + for procedure in procedures: + grouped[key(procedure)].append(procedure) + return [ + summarize_rt_procedures(rows, group_key=group_key) + for group_key, rows in grouped.items() + ] + + +def rt_site_key(procedure: OncologyProcedure) -> object: + return procedure.modifier_concept_id or procedure.procedure_source_value or "unknown_site" + + +class OncologyRTDosingMixin: + """ + RT dose/site summary interface for oncology treatment episodes. + """ + + def _linked_oncology_events(self, *, include_child_events: bool = True) -> list[Any]: + raise NotImplementedError + + @cached_property + def rt_procedures(self) -> list[OncologyProcedure]: + procedures = [ + event + for event in self._linked_oncology_events() + if isinstance(event, OncologyProcedure) and event.is_radiotherapy + ] + procedures.sort(key=lambda procedure: procedure.procedure_date) + return procedures + + @cached_property + def rt_dose_summaries_by_site(self) -> list[RTDoseSummary]: + return summarize_rt_procedures_by(self.rt_procedures, rt_site_key) + + @cached_property + def rt_dose_summary(self) -> RTDoseSummary: + return summarize_rt_procedures( + self.rt_procedures, + group_key="all_rt", + ) diff --git a/omop_alchemy/cdm/handlers/oncology/oncology_sact_dosing.py b/omop_alchemy/cdm/handlers/oncology/oncology_sact_dosing.py new file mode 100644 index 0000000..712668c --- /dev/null +++ b/omop_alchemy/cdm/handlers/oncology/oncology_sact_dosing.py @@ -0,0 +1,132 @@ +from __future__ import annotations + +from collections import defaultdict +from dataclasses import dataclass +from datetime import date +from functools import cached_property +from typing import Any, Callable, Hashable, Sequence + +from omop_alchemy.cdm.handlers.drug_episodes import ( + DOSE_EVALUABLE, + DoseEvaluability, + DrugExposureSummary, + summarize_drug_exposures, +) + +from .oncology_drug_exposure import OncologyDrugExposure + + +@dataclass(frozen=True) +class SACTDoseSummary: + """ + SACT dose summary for one caller-chosen drug grouping. + + This is deliberately a summary interface, not a dose-reduction rule. It + preserves mixed/missing units as evaluability states for downstream SACT + policy to interpret. + """ + + exposure_summary: DrugExposureSummary + evaluability: DoseEvaluability + + @property + def group_key(self) -> object: + return self.exposure_summary.group_key + + @property + def n_exposures(self) -> int: + return self.exposure_summary.n_exposures + + @property + def first_start_date(self) -> date | None: + return self.exposure_summary.first_start_date + + @property + def last_start_date(self) -> date | None: + return self.exposure_summary.last_start_date + + @property + def total_quantity(self) -> float | None: + return self.exposure_summary.total_quantity + + @property + def dose_unit_source_values(self) -> frozenset[str]: + return self.exposure_summary.dose_unit_source_values + + @property + def drug_concept_ids(self) -> frozenset[int]: + return self.exposure_summary.drug_concept_ids + + +def sact_dose_evaluability( + exposures: Sequence[OncologyDrugExposure], +) -> DoseEvaluability: + if not exposures: + return DoseEvaluability(False, "no_sact_exposures") + if any(exposure.quantity is None for exposure in exposures): + return DoseEvaluability(False, "missing_quantity") + units = { + exposure.dose_unit_source_value + for exposure in exposures + if exposure.dose_unit_source_value + } + if len(units) > 1: + return DoseEvaluability(False, "mixed_dose_units") + return DOSE_EVALUABLE + + +def summarize_sact_exposures( + exposures: Sequence[OncologyDrugExposure], + *, + group_key: object, +) -> SACTDoseSummary: + return SACTDoseSummary( + exposure_summary=summarize_drug_exposures(exposures, group_key=group_key), + evaluability=sact_dose_evaluability(exposures), + ) + + +def summarize_sact_exposures_by( + exposures: Sequence[OncologyDrugExposure], + key: Callable[[OncologyDrugExposure], Hashable], +) -> list[SACTDoseSummary]: + grouped: dict[Hashable, list[OncologyDrugExposure]] = defaultdict(list) + for exposure in exposures: + grouped[key(exposure)].append(exposure) + return [ + summarize_sact_exposures(rows, group_key=group_key) + for group_key, rows in grouped.items() + ] + + +class OncologySACTDosingMixin: + """ + SACT dose-summary interface for oncology treatment episodes. + """ + + def _linked_oncology_events(self, *, include_child_events: bool = True) -> list[Any]: + raise NotImplementedError + + @cached_property + def sact_exposures(self) -> list[OncologyDrugExposure]: + exposures = [ + event + for event in self._linked_oncology_events() + if isinstance(event, OncologyDrugExposure) and event.is_sact + ] + exposures.sort(key=lambda exposure: exposure.drug_exposure_start_date) + return exposures + + @cached_property + def sact_dose_summaries_by_drug_concept(self) -> list[SACTDoseSummary]: + return summarize_sact_exposures_by( + self.sact_exposures, + lambda exposure: exposure.drug_concept_id, + ) + + @cached_property + def sact_dose_summary(self) -> SACTDoseSummary: + return summarize_sact_exposures( + self.sact_exposures, + group_key="all_sact", + ) From 996a7eb525d7a864de3608ea9950713cc3632bef Mon Sep 17 00:00:00 2001 From: gkennos Date: Wed, 5 Aug 2026 23:18:52 +1000 Subject: [PATCH 3/4] performance caching for episode event resolution --- omop_alchemy/cdm/base/modifier_interface.py | 2 +- .../handlers/oncology/oncology_episodes.py | 1 + .../cdm/handlers/oncology/oncology_event.py | 1 + omop_alchemy/cdm/model/structural/__init__.py | 2 + omop_alchemy/cdm/model/structural/episode.py | 9 +- .../cdm/model/structural/episode_event.py | 30 ++++- tests/test_adverse_events.py | 40 ++++++ tests/test_body_metrics.py | 114 ++++++++++++++++++ tests/test_episodes_basic.py | 21 +++- 9 files changed, 214 insertions(+), 6 deletions(-) create mode 100644 tests/test_adverse_events.py create mode 100644 tests/test_body_metrics.py diff --git a/omop_alchemy/cdm/base/modifier_interface.py b/omop_alchemy/cdm/base/modifier_interface.py index f707c30..87f8c8a 100644 --- a/omop_alchemy/cdm/base/modifier_interface.py +++ b/omop_alchemy/cdm/base/modifier_interface.py @@ -24,7 +24,7 @@ def modifier_field_concept_id(cls) -> int: @classmethod def modifier_target_table(cls) -> str: - return cls.__tablename__ # ty: ignore[unresolved-attribute] + return cls.__tablename__ @hybrid_property def event_id(self) -> int: diff --git a/omop_alchemy/cdm/handlers/oncology/oncology_episodes.py b/omop_alchemy/cdm/handlers/oncology/oncology_episodes.py index c5a1911..53bd3be 100644 --- a/omop_alchemy/cdm/handlers/oncology/oncology_episodes.py +++ b/omop_alchemy/cdm/handlers/oncology/oncology_episodes.py @@ -55,6 +55,7 @@ class OncologyEpisode( """ @declared_attr + @classmethod def children(cls) -> so.Mapped[list["OncologyEpisode"]]: episode_id = cls.__table__.c.episode_id episode_parent_id = cls.__table__.c.episode_parent_id diff --git a/omop_alchemy/cdm/handlers/oncology/oncology_event.py b/omop_alchemy/cdm/handlers/oncology/oncology_event.py index 9d49c7c..e5be5d6 100644 --- a/omop_alchemy/cdm/handlers/oncology/oncology_event.py +++ b/omop_alchemy/cdm/handlers/oncology/oncology_event.py @@ -41,6 +41,7 @@ class OncologyEpisodeEventMixin: """ @declared_attr + @classmethod def episode_events(cls) -> so.Mapped[list["OncologyEpisodeEvent"]]: owner_episode_id = cast(Any, cls).__table__.c.episode_id event_episode_id = OncologyEpisodeEvent.__table__.c.episode_id diff --git a/omop_alchemy/cdm/model/structural/__init__.py b/omop_alchemy/cdm/model/structural/__init__.py index 0e713a1..6fe80f4 100644 --- a/omop_alchemy/cdm/model/structural/__init__.py +++ b/omop_alchemy/cdm/model/structural/__init__.py @@ -4,6 +4,7 @@ Episode_EventContext, Episode_EventView, EpisodeEventResolutionDiagnostic, + clear_episode_event_target_class_cache, ) from .fact_relationship import Fact_Relationship @@ -15,5 +16,6 @@ "Episode_EventContext", "Episode_EventView", "EpisodeEventResolutionDiagnostic", + "clear_episode_event_target_class_cache", "Fact_Relationship", ] diff --git a/omop_alchemy/cdm/model/structural/episode.py b/omop_alchemy/cdm/model/structural/episode.py index 432e707..3f19f71 100644 --- a/omop_alchemy/cdm/model/structural/episode.py +++ b/omop_alchemy/cdm/model/structural/episode.py @@ -83,12 +83,15 @@ def parent_episode(cls) -> so.Mapped[Optional["Episode"]]: ) @declared_attr + @classmethod def children(cls) -> so.Mapped[List["Episode"]]: + episode_id = cls.__table__.c.episode_id + episode_parent_id = cls.__table__.c.episode_parent_id return so.relationship( cls.__name__, - primaryjoin=lambda: so.remote(cls.episode_parent_id) == cls.episode_id, - foreign_keys=lambda: [cls.episode_parent_id], - remote_side=lambda: [cls.episode_parent_id], + primaryjoin=lambda: so.remote(episode_parent_id) == episode_id, + foreign_keys=lambda: [episode_parent_id], + remote_side=lambda: [episode_parent_id], viewonly=True, lazy="selectin", uselist=True, diff --git a/omop_alchemy/cdm/model/structural/episode_event.py b/omop_alchemy/cdm/model/structural/episode_event.py index d422b20..0f42961 100644 --- a/omop_alchemy/cdm/model/structural/episode_event.py +++ b/omop_alchemy/cdm/model/structural/episode_event.py @@ -67,6 +67,34 @@ def _modifier_target_classes_by_field_concept_id() -> dict[int, Type[Any]]: classes[field_concept_id] = cls return classes + +class _EpisodeEventTargetClassCache: + def __init__(self) -> None: + self._cache: dict[int, Type[Any]] | None = None + + def get(self) -> dict[int, Type[Any]]: + if self._cache is None: + self._cache = _modifier_target_classes_by_field_concept_id() + return self._cache + + def clear(self) -> None: + self._cache = None + + +_target_class_cache = _EpisodeEventTargetClassCache() + + +def clear_episode_event_target_class_cache() -> None: + """ + Clear cached episode_event field-concept target mappings. + + Most applications import all mapped classes before resolving episode events. + Long-running processes that register additional modifier-target classes + later can call this before resolving through the new class surface. + """ + _target_class_cache.clear() + + @cdm_table class Episode_Event(CDMTableBase, Base): __tablename__ = "episode_event" @@ -112,7 +140,7 @@ def resolved_event_target_classes(cls) -> dict[int, Type[Any]]: itself, avoiding the fragile concept-name table parsing that the CDM metadata labels happen to support today. """ - return _modifier_target_classes_by_field_concept_id() + return _target_class_cache.get() @classmethod def recognized_field_concept_ids(cls) -> set[int]: diff --git a/tests/test_adverse_events.py b/tests/test_adverse_events.py new file mode 100644 index 0000000..6a2596b --- /dev/null +++ b/tests/test_adverse_events.py @@ -0,0 +1,40 @@ +from __future__ import annotations + +from omop_alchemy.cdm.handlers.adverse_events import ( + CTCAEWeightLoss, + MartinWeightLoss, + critical_weight_loss_grade, + ctcae_weight_loss_grade, +) + + +def test_martin_weight_loss_reference_cells(): + assert MartinWeightLoss.grade(pct_change=-1, bmi=30) == 0 + assert MartinWeightLoss.grade(pct_change=-20, bmi=18) == 4 + + +def test_martin_bmi_category_boundaries(): + assert [ + MartinWeightLoss._bmi_category_index(bmi) + for bmi in (30, 26, 23, 21, 18) + ] == [0, 1, 2, 3, 4] + + +def test_martin_weight_loss_category_boundaries(): + assert [ + MartinWeightLoss._weight_loss_category_index(loss_pct) + for loss_pct in (0, 2, 4, 8, 12, 20) + ] == [0, 0, 1, 2, 3, 4] + + +def test_ctcae_weight_loss_grade_counts_crossed_thresholds(): + assert CTCAEWeightLoss.grade(-12) == 2 + assert ctcae_weight_loss_grade(-12) == 2 + + +def test_critical_weight_loss_grade_falls_back_to_ctcae_without_bmi(): + assert critical_weight_loss_grade(pct_change=-12, bmi=None) == 2 + + +def test_critical_weight_loss_grade_requires_percent_change(): + assert critical_weight_loss_grade(pct_change=None, bmi=30) is None diff --git a/tests/test_body_metrics.py b/tests/test_body_metrics.py new file mode 100644 index 0000000..582a499 --- /dev/null +++ b/tests/test_body_metrics.py @@ -0,0 +1,114 @@ +from __future__ import annotations + +from datetime import date + +import pytest + +from omop_alchemy.cdm.handlers.body_metrics import ( + BodyMetricRules, + BodySizeMeasurementConcepts, + BodySizeUnitConcepts, + BodyUnitConversionRules, + MeasurementReading, + WeightTrajectoryMixin, +) + + +def _body_metric_rules() -> BodyMetricRules: + return BodyMetricRules( + measurements=BodySizeMeasurementConcepts(weight=1, height=2), + unit_rules=BodyUnitConversionRules( + units=BodySizeUnitConcepts(kg=10, lb=11, cm=12, inch=13, m2=14), + ), + ) + + +def test_body_metric_rules_normalize_weight_kg(): + rules = _body_metric_rules() + + assert rules.normalize_weight_kg(70, rules.units.kg) == 70 + assert rules.normalize_weight_kg(150, rules.units.lb) == pytest.approx(68.0388555) + assert rules.normalize_weight_kg(70, 999) is None + assert rules.normalize_weight_kg(None, rules.units.kg) is None + assert rules.normalize_weight_kg(70, None) is None + + +def test_body_metric_rules_normalize_height_cm(): + rules = _body_metric_rules() + + assert rules.normalize_height_cm(170, rules.units.cm) == 170 + assert rules.normalize_height_cm(67, rules.units.inch) == pytest.approx(170.18) + assert rules.normalize_height_cm(170, 999) is None + assert rules.normalize_height_cm(None, rules.units.cm) is None + assert rules.normalize_height_cm(170, None) is None + + +def test_body_metric_rules_bmi(): + assert BodyMetricRules.bmi(70, 1.7) == pytest.approx(24.22, abs=0.01) + assert BodyMetricRules.bmi(None, 1.7) is None + assert BodyMetricRules.bmi(70, None) is None + assert BodyMetricRules.bmi(0, 1.7) is None + + +def test_body_metric_rules_bsa_mosteller_m2(): + assert BodyMetricRules.bsa_mosteller_m2(70, 170) == pytest.approx(1.818, abs=0.001) + + +class WeightTrajectoryStub(WeightTrajectoryMixin): + def __init__(self, readings: list[MeasurementReading]) -> None: + self.episode_id = 1 + self.person_id = 1 + self._readings = readings + + @property + def weight_readings(self) -> list[MeasurementReading]: + return self._readings + + +def _weight_reading( + measurement_id: int, + value: float, + reading_date: date = date(2020, 1, 1), +) -> MeasurementReading: + return MeasurementReading( + measurement_id=measurement_id, + date=reading_date, + value=value, + unit_concept_id=10, + concept_id=1, + source="explicit", + ) + + +def test_weight_change_single_reading_is_not_evaluable(): + episode = WeightTrajectoryStub([_weight_reading(1, 100)]) + + change = episode.pct_change_from_baseline() + + assert not change.evaluable + assert change.pct_change is None + + +def test_weight_change_same_measurement_id_is_not_evaluable(): + baseline = _weight_reading(1, 100) + same_measurement = _weight_reading(1, 95, date(2020, 1, 5)) + episode = WeightTrajectoryStub([baseline]) + + change = episode.pct_change_from_baseline(as_of=same_measurement) + + assert not change.evaluable + assert change.pct_change is None + + +def test_weight_change_near_zero_change_remains_evaluable(): + episode = WeightTrajectoryStub( + [ + _weight_reading(1, 100, date(2020, 1, 1)), + _weight_reading(2, 100.01, date(2020, 1, 5)), + ] + ) + + change = episode.pct_change_from_baseline() + + assert change.evaluable + assert change.pct_change == pytest.approx(0.01) diff --git a/tests/test_episodes_basic.py b/tests/test_episodes_basic.py index ffc22c1..1b3faa7 100644 --- a/tests/test_episodes_basic.py +++ b/tests/test_episodes_basic.py @@ -1,5 +1,10 @@ from omop_alchemy.cdm.base import ModifierFieldConcepts -from omop_alchemy.cdm.model.structural import EpisodeView, Episode_Event, Episode_EventView +from omop_alchemy.cdm.model.structural import ( + EpisodeView, + Episode_Event, + Episode_EventView, + clear_episode_event_target_class_cache, +) import sqlalchemy as sa def test_episode_view_expected_domains(): @@ -142,6 +147,20 @@ def test_episode_event_resolution_reports_dangling_target(session): assert diagnostics[0].kind == "dangling_event" +def test_episode_event_target_class_cache_can_be_cleared(): + """The resolver map is memoized but explicitly invalidatable.""" + clear_episode_event_target_class_cache() + first = Episode_EventView.resolved_event_target_classes() + second = Episode_EventView.resolved_event_target_classes() + + assert first is second + + clear_episode_event_target_class_cache() + third = Episode_EventView.resolved_event_target_classes() + + assert third is not first + assert third == first + def test_episode_view_events_property(session): """Test episode view events property.""" From bf86731015327498ac7539a13bc25288e7ff8848 Mon Sep 17 00:00:00 2001 From: gkennos Date: Fri, 7 Aug 2026 13:55:51 +1000 Subject: [PATCH 4/4] updated ignore --- .gitignore | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 92ea8da..1002bd7 100644 --- a/.gitignore +++ b/.gitignore @@ -72,4 +72,5 @@ temp/ *.bak notebooks/ .dockerignore -docker/ \ No newline at end of file +docker/ +tests/test_meds* \ No newline at end of file