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Adding support for InterSystems IRIS dialect #717

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Adding support for InterSystems IRIS dialect #717

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b68423f
default DDL for IRIS
bdeboe Jul 1, 2024
afe69e3
fix directory structure
bdeboe Jul 8, 2024
cfaf26b
add 5.3 DDL
bdeboe Jul 8, 2024
42f645f
default DDL for IRIS
bdeboe Jul 1, 2024
61dc576
fix directory structure
bdeboe Jul 8, 2024
677d0c9
add 5.3 DDL
bdeboe Jul 8, 2024
589f143
Merge branch 'main' of github.com:intersystems-community/OHDSI-Common…
bdeboe Sep 16, 2024
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158 changes: 158 additions & 0 deletions ddl/5.3/iris/OMOPCDM_iris_5.3_constraints.sql
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471 changes: 471 additions & 0 deletions ddl/5.3/iris/OMOPCDM_iris_5.3_ddl.sql
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98 changes: 98 additions & 0 deletions ddl/5.3/iris/OMOPCDM_iris_5.3_indices.sql
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/*iris OMOP CDM Indices
There are no unique indices created because it is assumed that the primary key constraints have been run prior to
implementing indices.
*/
/************************
Standardized clinical data
************************/
CREATE INDEX idx_person_id ON @cdmDatabaseSchema.person (person_id ASC);
CREATE INDEX idx_gender ON @cdmDatabaseSchema.person (gender_concept_id ASC);
CREATE INDEX idx_observation_period_id_1 ON @cdmDatabaseSchema.observation_period (person_id ASC);
CREATE INDEX idx_visit_person_id_1 ON @cdmDatabaseSchema.visit_occurrence (person_id ASC);
CREATE INDEX idx_visit_concept_id_1 ON @cdmDatabaseSchema.visit_occurrence (visit_concept_id ASC);
CREATE INDEX idx_visit_det_person_id_1 ON @cdmDatabaseSchema.visit_detail (person_id ASC);
CREATE INDEX idx_visit_det_concept_id_1 ON @cdmDatabaseSchema.visit_detail (visit_detail_concept_id ASC);
CREATE INDEX idx_visit_det_occ_id ON @cdmDatabaseSchema.visit_detail (visit_occurrence_id ASC);
CREATE INDEX idx_condition_person_id_1 ON @cdmDatabaseSchema.condition_occurrence (person_id ASC);
CREATE INDEX idx_condition_concept_id_1 ON @cdmDatabaseSchema.condition_occurrence (condition_concept_id ASC);
CREATE INDEX idx_condition_visit_id_1 ON @cdmDatabaseSchema.condition_occurrence (visit_occurrence_id ASC);
CREATE INDEX idx_drug_person_id_1 ON @cdmDatabaseSchema.drug_exposure (person_id ASC);
CREATE INDEX idx_drug_concept_id_1 ON @cdmDatabaseSchema.drug_exposure (drug_concept_id ASC);
CREATE INDEX idx_drug_visit_id_1 ON @cdmDatabaseSchema.drug_exposure (visit_occurrence_id ASC);
CREATE INDEX idx_procedure_person_id_1 ON @cdmDatabaseSchema.procedure_occurrence (person_id ASC);
CREATE INDEX idx_procedure_concept_id_1 ON @cdmDatabaseSchema.procedure_occurrence (procedure_concept_id ASC);
CREATE INDEX idx_procedure_visit_id_1 ON @cdmDatabaseSchema.procedure_occurrence (visit_occurrence_id ASC);
CREATE INDEX idx_device_person_id_1 ON @cdmDatabaseSchema.device_exposure (person_id ASC);
CREATE INDEX idx_device_concept_id_1 ON @cdmDatabaseSchema.device_exposure (device_concept_id ASC);
CREATE INDEX idx_device_visit_id_1 ON @cdmDatabaseSchema.device_exposure (visit_occurrence_id ASC);
CREATE INDEX idx_measurement_person_id_1 ON @cdmDatabaseSchema.measurement (person_id ASC);
CREATE INDEX idx_measurement_concept_id_1 ON @cdmDatabaseSchema.measurement (measurement_concept_id ASC);
CREATE INDEX idx_measurement_visit_id_1 ON @cdmDatabaseSchema.measurement (visit_occurrence_id ASC);
CREATE INDEX idx_observation_person_id_1 ON @cdmDatabaseSchema.observation (person_id ASC);
CREATE INDEX idx_observation_concept_id_1 ON @cdmDatabaseSchema.observation (observation_concept_id ASC);
CREATE INDEX idx_observation_visit_id_1 ON @cdmDatabaseSchema.observation (visit_occurrence_id ASC);
CREATE INDEX idx_death_person_id_1 ON @cdmDatabaseSchema.death (person_id ASC);
CREATE INDEX idx_note_person_id_1 ON @cdmDatabaseSchema.note (person_id ASC);
CREATE INDEX idx_note_concept_id_1 ON @cdmDatabaseSchema.note (note_type_concept_id ASC);
CREATE INDEX idx_note_visit_id_1 ON @cdmDatabaseSchema.note (visit_occurrence_id ASC);
CREATE INDEX idx_note_nlp_note_id_1 ON @cdmDatabaseSchema.note_nlp (note_id ASC);
CREATE INDEX idx_note_nlp_concept_id_1 ON @cdmDatabaseSchema.note_nlp (note_nlp_concept_id ASC);
CREATE INDEX idx_specimen_person_id_1 ON @cdmDatabaseSchema.specimen (person_id ASC);
CREATE INDEX idx_specimen_concept_id_1 ON @cdmDatabaseSchema.specimen (specimen_concept_id ASC);
CREATE INDEX idx_fact_relationship_id1 ON @cdmDatabaseSchema.fact_relationship (domain_concept_id_1 ASC);
CREATE INDEX idx_fact_relationship_id2 ON @cdmDatabaseSchema.fact_relationship (domain_concept_id_2 ASC);
CREATE INDEX idx_fact_relationship_id3 ON @cdmDatabaseSchema.fact_relationship (relationship_concept_id ASC);
/************************
Standardized health system data
************************/
CREATE INDEX idx_location_id_1 ON @cdmDatabaseSchema.location (location_id ASC);
CREATE INDEX idx_care_site_id_1 ON @cdmDatabaseSchema.care_site (care_site_id ASC);
CREATE INDEX idx_provider_id_1 ON @cdmDatabaseSchema.provider (provider_id ASC);
/************************
Standardized health economics
************************/
CREATE INDEX idx_period_person_id_1 ON @cdmDatabaseSchema.payer_plan_period (person_id ASC);
CREATE INDEX idx_cost_event_id ON @cdmDatabaseSchema.cost (cost_event_id ASC);
/************************
Standardized derived elements
************************/
CREATE INDEX idx_drug_era_person_id_1 ON @cdmDatabaseSchema.drug_era (person_id ASC);
CREATE INDEX idx_drug_era_concept_id_1 ON @cdmDatabaseSchema.drug_era (drug_concept_id ASC);
CREATE INDEX idx_dose_era_person_id_1 ON @cdmDatabaseSchema.dose_era (person_id ASC);
CREATE INDEX idx_dose_era_concept_id_1 ON @cdmDatabaseSchema.dose_era (drug_concept_id ASC);
CREATE INDEX idx_condition_era_person_id_1 ON @cdmDatabaseSchema.condition_era (person_id ASC);
CREATE INDEX idx_condition_era_concept_id_1 ON @cdmDatabaseSchema.condition_era (condition_concept_id ASC);
/**************************
Standardized meta-data
***************************/
CREATE INDEX idx_metadata_concept_id_1 ON @cdmDatabaseSchema.metadata (metadata_concept_id ASC);
/**************************
Standardized vocabularies
***************************/
CREATE INDEX idx_concept_concept_id ON @cdmDatabaseSchema.concept (concept_id ASC);
CREATE INDEX idx_concept_code ON @cdmDatabaseSchema.concept (concept_code ASC);
CREATE INDEX idx_concept_vocabulary_id ON @cdmDatabaseSchema.concept (vocabulary_id ASC);
CREATE INDEX idx_concept_domain_id ON @cdmDatabaseSchema.concept (domain_id ASC);
CREATE INDEX idx_concept_class_id ON @cdmDatabaseSchema.concept (concept_class_id ASC);
CREATE INDEX idx_vocabulary_vocabulary_id ON @cdmDatabaseSchema.vocabulary (vocabulary_id ASC);
CREATE INDEX idx_domain_domain_id ON @cdmDatabaseSchema."DOMAIN" (domain_id ASC);
CREATE INDEX idx_concept_class_class_id ON @cdmDatabaseSchema.concept_class (concept_class_id ASC);
CREATE INDEX idx_concept_relationship_id_1 ON @cdmDatabaseSchema.concept_relationship (concept_id_1 ASC);
CREATE INDEX idx_concept_relationship_id_2 ON @cdmDatabaseSchema.concept_relationship (concept_id_2 ASC);
CREATE INDEX idx_concept_relationship_id_3 ON @cdmDatabaseSchema.concept_relationship (relationship_id ASC);
CREATE INDEX idx_relationship_rel_id ON @cdmDatabaseSchema.relationship (relationship_id ASC);
CREATE INDEX idx_concept_synonym_id ON @cdmDatabaseSchema.concept_synonym (concept_id ASC);
CREATE INDEX idx_concept_ancestor_id_1 ON @cdmDatabaseSchema.concept_ancestor (ancestor_concept_id ASC);
CREATE INDEX idx_concept_ancestor_id_2 ON @cdmDatabaseSchema.concept_ancestor (descendant_concept_id ASC);
CREATE INDEX idx_source_to_concept_map_3 ON @cdmDatabaseSchema.source_to_concept_map (target_concept_id ASC);
CREATE INDEX idx_source_to_concept_map_1 ON @cdmDatabaseSchema.source_to_concept_map (source_vocabulary_id ASC);
CREATE INDEX idx_source_to_concept_map_2 ON @cdmDatabaseSchema.source_to_concept_map (target_vocabulary_id ASC);
CREATE INDEX idx_source_to_concept_map_c ON @cdmDatabaseSchema.source_to_concept_map (source_code ASC);
CREATE INDEX idx_drug_strength_id_1 ON @cdmDatabaseSchema.drug_strength (drug_concept_id ASC);
CREATE INDEX idx_drug_strength_id_2 ON @cdmDatabaseSchema.drug_strength (ingredient_concept_id ASC);
--Additional v6.0 indices
--CREATE CLUSTERED INDEX idx_survey_person_id_1 ON @cdmDatabaseSchema.survey_conduct (person_id ASC);
--CREATE CLUSTERED INDEX idx_episode_person_id_1 ON @cdmDatabaseSchema.episode (person_id ASC);
--CREATE INDEX idx_episode_concept_id_1 ON @cdmDatabaseSchema.episode (episode_concept_id ASC);
--CREATE CLUSTERED INDEX idx_episode_event_id_1 ON @cdmDatabaseSchema.episode_event (episode_id ASC);
--CREATE INDEX idx_ee_field_concept_id_1 ON @cdmDatabaseSchema.episode_event (event_field_concept_id ASC);
27 changes: 27 additions & 0 deletions ddl/5.3/iris/OMOPCDM_iris_5.3_primary_keys.sql
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--iris CDM Primary Key Constraints for OMOP Common Data Model 5.3
ALTER TABLE @cdmDatabaseSchema.person ADD CONSTRAINT xpk_person PRIMARY KEY (person_id);
ALTER TABLE @cdmDatabaseSchema.observation_period ADD CONSTRAINT xpk_observation_period PRIMARY KEY (observation_period_id);
ALTER TABLE @cdmDatabaseSchema.visit_occurrence ADD CONSTRAINT xpk_visit_occurrence PRIMARY KEY (visit_occurrence_id);
ALTER TABLE @cdmDatabaseSchema.visit_detail ADD CONSTRAINT xpk_visit_detail PRIMARY KEY (visit_detail_id);
ALTER TABLE @cdmDatabaseSchema.condition_occurrence ADD CONSTRAINT xpk_condition_occurrence PRIMARY KEY (condition_occurrence_id);
ALTER TABLE @cdmDatabaseSchema.drug_exposure ADD CONSTRAINT xpk_drug_exposure PRIMARY KEY (drug_exposure_id);
ALTER TABLE @cdmDatabaseSchema.procedure_occurrence ADD CONSTRAINT xpk_procedure_occurrence PRIMARY KEY (procedure_occurrence_id);
ALTER TABLE @cdmDatabaseSchema.device_exposure ADD CONSTRAINT xpk_device_exposure PRIMARY KEY (device_exposure_id);
ALTER TABLE @cdmDatabaseSchema.measurement ADD CONSTRAINT xpk_measurement PRIMARY KEY (measurement_id);
ALTER TABLE @cdmDatabaseSchema.observation ADD CONSTRAINT xpk_observation PRIMARY KEY (observation_id);
ALTER TABLE @cdmDatabaseSchema.note ADD CONSTRAINT xpk_note PRIMARY KEY (note_id);
ALTER TABLE @cdmDatabaseSchema.note_nlp ADD CONSTRAINT xpk_note_nlp PRIMARY KEY (note_nlp_id);
ALTER TABLE @cdmDatabaseSchema.specimen ADD CONSTRAINT xpk_specimen PRIMARY KEY (specimen_id);
ALTER TABLE @cdmDatabaseSchema.location ADD CONSTRAINT xpk_location PRIMARY KEY (location_id);
ALTER TABLE @cdmDatabaseSchema.care_site ADD CONSTRAINT xpk_care_site PRIMARY KEY (care_site_id);
ALTER TABLE @cdmDatabaseSchema.provider ADD CONSTRAINT xpk_provider PRIMARY KEY (provider_id);
ALTER TABLE @cdmDatabaseSchema.payer_plan_period ADD CONSTRAINT xpk_payer_plan_period PRIMARY KEY (payer_plan_period_id);
ALTER TABLE @cdmDatabaseSchema.cost ADD CONSTRAINT xpk_cost PRIMARY KEY (cost_id);
ALTER TABLE @cdmDatabaseSchema.drug_era ADD CONSTRAINT xpk_drug_era PRIMARY KEY (drug_era_id);
ALTER TABLE @cdmDatabaseSchema.dose_era ADD CONSTRAINT xpk_dose_era PRIMARY KEY (dose_era_id);
ALTER TABLE @cdmDatabaseSchema.condition_era ADD CONSTRAINT xpk_condition_era PRIMARY KEY (condition_era_id);
ALTER TABLE @cdmDatabaseSchema.concept ADD CONSTRAINT xpk_concept PRIMARY KEY (concept_id);
ALTER TABLE @cdmDatabaseSchema.vocabulary ADD CONSTRAINT xpk_vocabulary PRIMARY KEY (vocabulary_id);
ALTER TABLE @cdmDatabaseSchema."DOMAIN" ADD CONSTRAINT xpk_domain PRIMARY KEY (domain_id);
ALTER TABLE @cdmDatabaseSchema.concept_class ADD CONSTRAINT xpk_concept_class PRIMARY KEY (concept_class_id);
ALTER TABLE @cdmDatabaseSchema.relationship ADD CONSTRAINT xpk_relationship PRIMARY KEY (relationship_id);
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