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Add concept_id columns for country of birth and language #22

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Add concept_id columns for country of birth and language #22

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708b5aa
Add concept_id columns for country of birth and language
GhazalehNiknam Jul 23, 2026
eee6934
Regenerate stale registry schema snapshot
GhazalehNiknam Jul 23, 2026
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3 changes: 2 additions & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -13,4 +13,5 @@ wheels/
.env
.DS_Store
_temp
notebooks/
notebooks/
.ipynb_checkpoints/
2 changes: 2 additions & 0 deletions src/omop_constructs/alchemy/demography/demography_matview.py
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Expand Up @@ -38,5 +38,7 @@ class PersonDemography(MaterializedViewMixin, Base):
death_datetime: Mapped[datetime | None] = mapped_column(sa.DateTime)

language_spoken: Mapped[str | None] = mapped_column(sa.String)
language_spoken_concept_id: Mapped[int | None] = mapped_column(sa.Integer)
country_of_birth: Mapped[str | None] = mapped_column(sa.String)
country_of_birth_concept_id: Mapped[int | None] = mapped_column(sa.Integer)
post_code: Mapped[int | None] = mapped_column(sa.Integer)
4 changes: 4 additions & 0 deletions src/omop_constructs/alchemy/demography/demography_queries.py
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Expand Up @@ -20,6 +20,7 @@
sa.select(
Observation.person_id,
Concept.concept_name.label("country_of_birth"),
Observation.value_as_concept_id.label("country_of_birth_concept_id"),
)
.join(Concept, Concept.concept_id == Observation.value_as_concept_id)
.where(Observation.observation_concept_id.in_(list(registry['country_of_birth'].all_concepts)))
Expand All @@ -30,6 +31,7 @@
sa.select(
Observation.person_id,
Concept.concept_name.label("language_spoken"),
Observation.value_as_concept_id.label("language_spoken_concept_id"),
)
.join(Concept, Concept.concept_id == Observation.value_as_concept_id)
.where(Observation.observation_concept_id == runtime.observations.demography_concepts.language_spoken)
Expand All @@ -52,7 +54,9 @@

Concept.concept_name.label("sex"),
person_lang.c.language_spoken,
person_lang.c.language_spoken_concept_id,
person_cob.c.country_of_birth,
person_cob.c.country_of_birth_concept_id,
person_postcode.c.post_code,
)
.join(Death, Death.person_id == Person.person_id, isouter=True)
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6 changes: 4 additions & 2 deletions tests/artifacts/construct_registry_schema.csv
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Expand Up @@ -387,8 +387,10 @@ person_demography_mv,omop_constructs.alchemy.demography.demography_matview,Perso
person_demography_mv,omop_constructs.alchemy.demography.demography_matview,PersonDemography,materialized_view,condition_episode_mv,,mv_id,8,year_of_birth,INTEGER,true,false
person_demography_mv,omop_constructs.alchemy.demography.demography_matview,PersonDemography,materialized_view,condition_episode_mv,,mv_id,9,death_datetime,DATETIME,true,false
person_demography_mv,omop_constructs.alchemy.demography.demography_matview,PersonDemography,materialized_view,condition_episode_mv,,mv_id,10,language_spoken,VARCHAR,true,false
person_demography_mv,omop_constructs.alchemy.demography.demography_matview,PersonDemography,materialized_view,condition_episode_mv,,mv_id,11,country_of_birth,VARCHAR,true,false
person_demography_mv,omop_constructs.alchemy.demography.demography_matview,PersonDemography,materialized_view,condition_episode_mv,,mv_id,12,post_code,INTEGER,true,false
person_demography_mv,omop_constructs.alchemy.demography.demography_matview,PersonDemography,materialized_view,condition_episode_mv,,mv_id,11,language_spoken_concept_id,INTEGER,true,false
person_demography_mv,omop_constructs.alchemy.demography.demography_matview,PersonDemography,materialized_view,condition_episode_mv,,mv_id,12,country_of_birth,VARCHAR,true,false
person_demography_mv,omop_constructs.alchemy.demography.demography_matview,PersonDemography,materialized_view,condition_episode_mv,,mv_id,13,country_of_birth_concept_id,INTEGER,true,false
person_demography_mv,omop_constructs.alchemy.demography.demography_matview,PersonDemography,materialized_view,condition_episode_mv,,mv_id,14,post_code,INTEGER,true,false
primary_diagnosis_condition_mv,omop_constructs.alchemy.modifiers.condition_modifier_mv,PrimaryDiagnosisConditionMV,materialized_view,modified_conditions_mv|overarching_disease_episode_mv,mv_id,mv_id,1,mv_id,UNKNOWN,false,true
primary_diagnosis_condition_mv,omop_constructs.alchemy.modifiers.condition_modifier_mv,PrimaryDiagnosisConditionMV,materialized_view,modified_conditions_mv|overarching_disease_episode_mv,mv_id,mv_id,2,person_id,INTEGER,true,false
primary_diagnosis_condition_mv,omop_constructs.alchemy.modifiers.condition_modifier_mv,PrimaryDiagnosisConditionMV,materialized_view,modified_conditions_mv|overarching_disease_episode_mv,mv_id,mv_id,3,condition_start_date,DATE,true,false
Expand Down
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