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Merged
gkennos merged 1 commit into from
Jul 13, 2026
Merged

added support for precoordinated measurements #20

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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -191,3 +191,5 @@
## 0.5.0
- integrated oa-configurator package configuration and adapted omop-constructs to current orm-loader / omop-alchemy compatibility changes

## 0.5.2
- ecog_dx_mv now also carries value_as_concept_id: ECOG performance status is a precoordinated-concept answer (OHDSI convention), not a plain number, so downstream measure logic needs the concept alongside (or instead of) value_as_number
2 changes: 1 addition & 1 deletion pyproject.toml
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@@ -1,6 +1,6 @@
[project]
name = "omop-constructs"
version = "0.5.1"
version = "0.5.2"
description = "For building complex constructs on top of the omop-alchemy library."
readme = "README.md"
authors = [
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1 change: 1 addition & 0 deletions src/omop_constructs/alchemy/events/dx_linked_event_mv.py
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Expand Up @@ -157,6 +157,7 @@ class ECOGDxMV(
__mv_index__ = "person_id"
__deps__ = (ConditionEpisodeMV.__mv_name__,)
__tablename__ = __mv_name__
value_as_concept_id: so.Mapped[Optional[int]] = so.mapped_column(sa.Integer, nullable=True)

@register_construct
class SmokingPYHDxMV(
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2 changes: 1 addition & 1 deletion src/omop_constructs/alchemy/events/event_queries.py
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Expand Up @@ -52,7 +52,7 @@

ecog_query = measurement_attached_to_condition_episode(
concept_ids=[runtime.measurements_numeric.performance_status_measurements.ecog_performance_status], # type: ignore
include_cols=[Measurement.value_as_number, Measurement.unit_concept_id],
include_cols=[Measurement.value_as_number, Measurement.value_as_concept_id, Measurement.unit_concept_id],
name="ecog",
)

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29 changes: 15 additions & 14 deletions tests/artifacts/construct_registry_schema.csv
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Expand Up @@ -185,20 +185,21 @@ dx_visit_mv,omop_constructs.alchemy.events.dx_linked_visit_mv,DxRelevantVisitMV,
dx_visit_mv,omop_constructs.alchemy.events.dx_linked_visit_mv,DxRelevantVisitMV,materialized_view,,person_id,,11,episode_prior,INTEGER,false,false
dx_visit_mv,omop_constructs.alchemy.events.dx_linked_visit_mv,DxRelevantVisitMV,materialized_view,,person_id,,12,diff_days,FLOAT,false,false
dx_visit_mv,omop_constructs.alchemy.events.dx_linked_visit_mv,DxRelevantVisitMV,materialized_view,,person_id,,13,rank,INTEGER,false,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,1,mv_id,INTEGER,false,true
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,2,person_id,INTEGER,false,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,3,event_id,INTEGER,false,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,4,event_date,DATE,false,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,5,event_concept_id,INTEGER,false,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,6,event_label,VARCHAR,true,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,7,value_as_number,FLOAT,true,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,8,unit_concept_id,INTEGER,true,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,9,episode_id,INTEGER,true,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,10,episode_concept_id,INTEGER,true,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,11,episode_label,VARCHAR,true,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,12,episode_start_date,DATE,true,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,13,episode_end_date,DATE,true,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,14,episode_delta_days,INTEGER,true,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,1,value_as_concept_id,INTEGER,true,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,2,mv_id,INTEGER,false,true
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,3,person_id,INTEGER,false,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,4,event_id,INTEGER,false,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,5,event_date,DATE,false,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,6,event_concept_id,INTEGER,false,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,7,event_label,VARCHAR,true,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,8,value_as_number,FLOAT,true,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,9,unit_concept_id,INTEGER,true,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,10,episode_id,INTEGER,true,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,11,episode_concept_id,INTEGER,true,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,12,episode_label,VARCHAR,true,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,13,episode_start_date,DATE,true,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,14,episode_end_date,DATE,true,false
ecog_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,ECOGDxMV,materialized_view,condition_episode_mv,person_id,,15,episode_delta_days,INTEGER,true,false
egfr_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,EGFRDxMV,materialized_view,condition_episode_mv,person_id,,1,mv_id,INTEGER,false,true
egfr_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,EGFRDxMV,materialized_view,condition_episode_mv,person_id,,2,person_id,INTEGER,false,false
egfr_dx_mv,omop_constructs.alchemy.events.dx_linked_event_mv,EGFRDxMV,materialized_view,condition_episode_mv,person_id,,3,event_id,INTEGER,false,false
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