From f90cf039b8aac5ef013fd77def187c4efaccfb02 Mon Sep 17 00:00:00 2001 From: TheCedarPrince Date: Tue, 11 Jul 2023 20:50:04 -0400 Subject: [PATCH 1/3] Temporarily unignored inst to track development of duckdb --- .gitignore | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 3d58222..12de2db 100644 --- a/.gitignore +++ b/.gitignore @@ -15,4 +15,5 @@ ehthumbs.db Thumbs.db extras/codeToRun.R output/ -ddl/ +# ddl/ +# NOTE: Temporarily disabling so we can track development of DuckDB From 1e16d267a0f57405d6e0b8bfe195ba7e3e32dd20 Mon Sep 17 00:00:00 2001 From: TheCedarPrince Date: Tue, 11 Jul 2023 20:51:01 -0400 Subject: [PATCH 2/3] Added new fields for COST table --- .../ddl/5.4/duckdb/OMOPCDM_duckdb_5.4_ddl.sql | 514 ++++++++++++++++++ 1 file changed, 514 insertions(+) create mode 100644 inst/ddl/5.4/duckdb/OMOPCDM_duckdb_5.4_ddl.sql diff --git a/inst/ddl/5.4/duckdb/OMOPCDM_duckdb_5.4_ddl.sql b/inst/ddl/5.4/duckdb/OMOPCDM_duckdb_5.4_ddl.sql new file mode 100644 index 0000000..4ecc8ba --- /dev/null +++ b/inst/ddl/5.4/duckdb/OMOPCDM_duckdb_5.4_ddl.sql @@ -0,0 +1,514 @@ +--postgresql CDM DDL Specification for OMOP Common Data Model 5.4 +--HINT DISTRIBUTE ON KEY (person_id) +CREATE TABLE @cdmDatabaseSchema.PERSON ( + person_id integer NOT NULL, + gender_concept_id integer NOT NULL, + year_of_birth integer NOT NULL, + month_of_birth integer NULL, + day_of_birth integer NULL, + birth_datetime TIMESTAMP NULL, + race_concept_id integer NOT NULL, + ethnicity_concept_id integer NOT NULL, + location_id integer NULL, + provider_id integer NULL, + care_site_id integer NULL, + person_source_value varchar(50) NULL, + gender_source_value varchar(50) NULL, + gender_source_concept_id integer NULL, + race_source_value varchar(50) NULL, + race_source_concept_id integer NULL, + ethnicity_source_value varchar(50) NULL, + ethnicity_source_concept_id integer NULL ); +--HINT DISTRIBUTE ON KEY (person_id) +CREATE TABLE @cdmDatabaseSchema.OBSERVATION_PERIOD ( + observation_period_id integer NOT NULL, + person_id integer NOT NULL, + observation_period_start_date date NOT NULL, + observation_period_end_date date NOT NULL, + period_type_concept_id integer NOT NULL ); +--HINT DISTRIBUTE ON KEY (person_id) +CREATE TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ( + visit_occurrence_id integer NOT NULL, + person_id integer NOT NULL, + visit_concept_id integer NOT NULL, + visit_start_date date NOT NULL, + visit_start_datetime TIMESTAMP NULL, + visit_end_date date NOT NULL, + visit_end_datetime TIMESTAMP NULL, + visit_type_concept_id Integer NOT NULL, + provider_id integer NULL, + care_site_id integer NULL, + visit_source_value varchar(50) NULL, + visit_source_concept_id integer NULL, + admitted_from_concept_id integer NULL, + admitted_from_source_value varchar(50) NULL, + discharged_to_concept_id integer NULL, + discharged_to_source_value varchar(50) NULL, + preceding_visit_occurrence_id integer NULL ); +--HINT DISTRIBUTE ON KEY (person_id) +CREATE TABLE @cdmDatabaseSchema.VISIT_DETAIL ( + visit_detail_id integer NOT NULL, + person_id integer NOT NULL, + visit_detail_concept_id integer NOT NULL, + visit_detail_start_date date NOT NULL, + visit_detail_start_datetime TIMESTAMP NULL, + visit_detail_end_date date NOT NULL, + visit_detail_end_datetime TIMESTAMP NULL, + visit_detail_type_concept_id integer NOT NULL, + provider_id integer NULL, + care_site_id integer NULL, + visit_detail_source_value varchar(50) NULL, + visit_detail_source_concept_id Integer NULL, + admitted_from_concept_id Integer NULL, + admitted_from_source_value varchar(50) NULL, + discharged_to_source_value varchar(50) NULL, + discharged_to_concept_id integer NULL, + preceding_visit_detail_id integer NULL, + parent_visit_detail_id integer NULL, + visit_occurrence_id integer NOT NULL ); +--HINT DISTRIBUTE ON KEY (person_id) +CREATE TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ( + condition_occurrence_id integer NOT NULL, + person_id integer NOT NULL, + condition_concept_id integer NOT NULL, + condition_start_date date NOT NULL, + condition_start_datetime TIMESTAMP NULL, + condition_end_date date NULL, + condition_end_datetime TIMESTAMP NULL, + condition_type_concept_id integer NOT NULL, + condition_status_concept_id integer NULL, + stop_reason varchar(20) NULL, + provider_id integer NULL, + visit_occurrence_id integer NULL, + visit_detail_id integer NULL, + condition_source_value varchar(50) NULL, + condition_source_concept_id integer NULL, + condition_status_source_value varchar(50) NULL ); +--HINT DISTRIBUTE ON KEY (person_id) +CREATE TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ( + drug_exposure_id integer NOT NULL, + person_id integer NOT NULL, + drug_concept_id integer NOT NULL, + drug_exposure_start_date date NOT NULL, + drug_exposure_start_datetime TIMESTAMP NULL, + drug_exposure_end_date date NOT NULL, + drug_exposure_end_datetime TIMESTAMP NULL, + verbatim_end_date date NULL, + drug_type_concept_id integer NOT NULL, + stop_reason varchar(20) NULL, + refills integer NULL, + quantity NUMERIC NULL, + days_supply integer NULL, + sig TEXT NULL, + route_concept_id integer NULL, + lot_number varchar(50) NULL, + provider_id integer NULL, + visit_occurrence_id integer NULL, + visit_detail_id integer NULL, + drug_source_value varchar(50) NULL, + drug_source_concept_id integer NULL, + route_source_value varchar(50) NULL, + dose_unit_source_value varchar(50) NULL ); +--HINT DISTRIBUTE ON KEY (person_id) +CREATE TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE ( + procedure_occurrence_id integer NOT NULL, + person_id integer NOT NULL, + procedure_concept_id integer NOT NULL, + procedure_date date NOT NULL, + procedure_datetime TIMESTAMP NULL, + procedure_end_date date NULL, + procedure_end_datetime TIMESTAMP NULL, + procedure_type_concept_id integer NOT NULL, + modifier_concept_id integer NULL, + quantity integer NULL, + provider_id integer NULL, + visit_occurrence_id integer NULL, + visit_detail_id integer NULL, + procedure_source_value varchar(50) NULL, + procedure_source_concept_id integer NULL, + modifier_source_value varchar(50) NULL ); +--HINT DISTRIBUTE ON KEY (person_id) +CREATE TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ( + device_exposure_id integer NOT NULL, + person_id integer NOT NULL, + device_concept_id integer NOT NULL, + device_exposure_start_date date NOT NULL, + device_exposure_start_datetime TIMESTAMP NULL, + device_exposure_end_date date NULL, + device_exposure_end_datetime TIMESTAMP NULL, + device_type_concept_id integer NOT NULL, + unique_device_id varchar(255) NULL, + production_id varchar(255) NULL, + quantity integer NULL, + provider_id integer NULL, + visit_occurrence_id integer NULL, + visit_detail_id integer NULL, + device_source_value varchar(50) NULL, + device_source_concept_id integer NULL, + unit_concept_id integer NULL, + unit_source_value varchar(50) NULL, + unit_source_concept_id integer NULL ); +--HINT DISTRIBUTE ON KEY (person_id) +CREATE TABLE @cdmDatabaseSchema.MEASUREMENT ( + measurement_id integer NOT NULL, + person_id integer NOT NULL, + measurement_concept_id integer NOT NULL, + measurement_date date NOT NULL, + measurement_datetime TIMESTAMP NULL, + measurement_time varchar(10) NULL, + measurement_type_concept_id integer NOT NULL, + operator_concept_id integer NULL, + value_as_number NUMERIC NULL, + value_as_concept_id integer NULL, + unit_concept_id integer NULL, + range_low NUMERIC NULL, + range_high NUMERIC NULL, + provider_id integer NULL, + visit_occurrence_id integer NULL, + visit_detail_id integer NULL, + measurement_source_value varchar(50) NULL, + measurement_source_concept_id integer NULL, + unit_source_value varchar(50) NULL, + unit_source_concept_id integer NULL, + value_source_value varchar(50) NULL, + measurement_event_id integer NULL, + meas_event_field_concept_id integer NULL ); +--HINT DISTRIBUTE ON KEY (person_id) +CREATE TABLE @cdmDatabaseSchema.OBSERVATION ( + observation_id integer NOT NULL, + person_id integer NOT NULL, + observation_concept_id integer NOT NULL, + observation_date date NOT NULL, + observation_datetime TIMESTAMP NULL, + observation_type_concept_id integer NOT NULL, + value_as_number NUMERIC NULL, + value_as_string varchar(60) NULL, + value_as_concept_id Integer NULL, + qualifier_concept_id integer NULL, + unit_concept_id integer NULL, + provider_id integer NULL, + visit_occurrence_id integer NULL, + visit_detail_id integer NULL, + observation_source_value varchar(50) NULL, + observation_source_concept_id integer NULL, + unit_source_value varchar(50) NULL, + qualifier_source_value varchar(50) NULL, + value_source_value varchar(50) NULL, + observation_event_id integer NULL, + obs_event_field_concept_id integer NULL ); +--HINT DISTRIBUTE ON KEY (person_id) +CREATE TABLE @cdmDatabaseSchema.DEATH ( + person_id integer NOT NULL, + death_date date NOT NULL, + death_datetime TIMESTAMP NULL, + death_type_concept_id integer NULL, + cause_concept_id integer NULL, + cause_source_value varchar(50) NULL, + cause_source_concept_id integer NULL ); +--HINT DISTRIBUTE ON KEY (person_id) +CREATE TABLE @cdmDatabaseSchema.NOTE ( + note_id integer NOT NULL, + person_id integer NOT NULL, + note_date date NOT NULL, + note_datetime TIMESTAMP NULL, + note_type_concept_id integer NOT NULL, + note_class_concept_id integer NOT NULL, + note_title varchar(250) NULL, + note_text TEXT NOT NULL, + encoding_concept_id integer NOT NULL, + language_concept_id integer NOT NULL, + provider_id integer NULL, + visit_occurrence_id integer NULL, + visit_detail_id integer NULL, + note_source_value varchar(50) NULL, + note_event_id integer NULL, + note_event_field_concept_id integer NULL ); +--HINT DISTRIBUTE ON RANDOM +CREATE TABLE @cdmDatabaseSchema.NOTE_NLP ( + note_nlp_id integer NOT NULL, + note_id integer NOT NULL, + section_concept_id integer NULL, + snippet varchar(250) NULL, + "offset" varchar(50) NULL, + lexical_variant varchar(250) NOT NULL, + note_nlp_concept_id integer NULL, + note_nlp_source_concept_id integer NULL, + nlp_system varchar(250) NULL, + nlp_date date NOT NULL, + nlp_datetime TIMESTAMP NULL, + term_exists varchar(1) NULL, + term_temporal varchar(50) NULL, + term_modifiers varchar(2000) NULL ); +--HINT DISTRIBUTE ON KEY (person_id) +CREATE TABLE @cdmDatabaseSchema.SPECIMEN ( + specimen_id integer NOT NULL, + person_id integer NOT NULL, + specimen_concept_id integer NOT NULL, + specimen_type_concept_id integer NOT NULL, + specimen_date date NOT NULL, + specimen_datetime TIMESTAMP NULL, + quantity NUMERIC NULL, + unit_concept_id integer NULL, + anatomic_site_concept_id integer NULL, + disease_status_concept_id integer NULL, + specimen_source_id varchar(50) NULL, + specimen_source_value varchar(50) NULL, + unit_source_value varchar(50) NULL, + anatomic_site_source_value varchar(50) NULL, + disease_status_source_value varchar(50) NULL ); +--HINT DISTRIBUTE ON RANDOM +CREATE TABLE @cdmDatabaseSchema.FACT_RELATIONSHIP ( + domain_concept_id_1 integer NOT NULL, + fact_id_1 integer NOT NULL, + domain_concept_id_2 integer NOT NULL, + fact_id_2 integer NOT NULL, + relationship_concept_id integer NOT NULL ); +--HINT DISTRIBUTE ON RANDOM +CREATE TABLE @cdmDatabaseSchema.LOCATION ( + location_id integer NOT NULL, + address_1 varchar(50) NULL, + address_2 varchar(50) NULL, + city varchar(50) NULL, + state varchar(2) NULL, + zip varchar(9) NULL, + county varchar(20) NULL, + location_source_value varchar(50) NULL, + country_concept_id integer NULL, + country_source_value varchar(80) NULL, + latitude NUMERIC NULL, + longitude NUMERIC NULL ); +--HINT DISTRIBUTE ON RANDOM +CREATE TABLE @cdmDatabaseSchema.CARE_SITE ( + care_site_id integer NOT NULL, + care_site_name varchar(255) NULL, + place_of_service_concept_id integer NULL, + location_id integer NULL, + care_site_source_value varchar(50) NULL, + place_of_service_source_value varchar(50) NULL ); +--HINT DISTRIBUTE ON RANDOM +CREATE TABLE @cdmDatabaseSchema.PROVIDER ( + provider_id integer NOT NULL, + provider_name varchar(255) NULL, + npi varchar(20) NULL, + dea varchar(20) NULL, + specialty_concept_id integer NULL, + care_site_id integer NULL, + year_of_birth integer NULL, + gender_concept_id integer NULL, + provider_source_value varchar(50) NULL, + specialty_source_value varchar(50) NULL, + specialty_source_concept_id integer NULL, + gender_source_value varchar(50) NULL, + gender_source_concept_id integer NULL ); +--HINT DISTRIBUTE ON KEY (person_id) +CREATE TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ( + payer_plan_period_id integer NOT NULL, + person_id integer NOT NULL, + payer_plan_period_start_date date NOT NULL, + payer_plan_period_end_date date NOT NULL, + payer_concept_id integer NULL, + payer_source_value varchar(50) NULL, + payer_source_concept_id integer NULL, + plan_concept_id integer NULL, + plan_source_value varchar(50) NULL, + plan_source_concept_id integer NULL, + sponsor_concept_id integer NULL, + sponsor_source_value varchar(50) NULL, + sponsor_source_concept_id integer NULL, + family_source_value varchar(50) NULL, + stop_reason_concept_id integer NULL, + stop_reason_source_value varchar(50) NULL, + stop_reason_source_concept_id integer NULL ); +--HINT DISTRIBUTE ON RANDOM +CREATE TABLE @cdmDatabaseSchema.COST ( + cost_id integer NOT NULL, + cost_event_id integer NOT NULL, + cost_domain_id varchar(20) NOT NULL, + cost_type_concept_id integer NOT NULL, + currency_concept_id integer NULL, + total_charge NUMERIC NULL, + total_cost NUMERIC NULL, + total_paid NUMERIC NULL, + paid_by_payer NUMERIC NULL, + paid_by_patient NUMERIC NULL, + paid_patient_copay NUMERIC NULL, + paid_patient_coinsurance NUMERIC NULL, + paid_patient_deductible NUMERIC NULL, + paid_by_primary NUMERIC NULL, + paid_ingredient_cost NUMERIC NULL, + paid_dispensing_fee NUMERIC NULL, + payer_plan_period_id integer NULL, + amount_allowed NUMERIC NULL, + revenue_code_concept_id integer NULL, + revenue_code_source_value varchar(50) NULL, + drg_concept_id integer NULL, + drg_source_value varchar(3) NULL, + cash_price FLOAT, -- NOTE: Added in field + minimum_reported_price FLOAT, -- NOTE: Added in field + maximum_reported_price FLOAT ); -- NOTE: Added in field +--HINT DISTRIBUTE ON KEY (person_id) +CREATE TABLE @cdmDatabaseSchema.DRUG_ERA ( + drug_era_id integer NOT NULL, + person_id integer NOT NULL, + drug_concept_id integer NOT NULL, + drug_era_start_date date NOT NULL, + drug_era_end_date date NOT NULL, + drug_exposure_count integer NULL, + gap_days integer NULL ); +--HINT DISTRIBUTE ON KEY (person_id) +CREATE TABLE @cdmDatabaseSchema.DOSE_ERA ( + dose_era_id integer NOT NULL, + person_id integer NOT NULL, + drug_concept_id integer NOT NULL, + unit_concept_id integer NOT NULL, + dose_value NUMERIC NOT NULL, + dose_era_start_date date NOT NULL, + dose_era_end_date date NOT NULL ); +--HINT DISTRIBUTE ON KEY (person_id) +CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA ( + condition_era_id integer NOT NULL, + person_id integer NOT NULL, + condition_concept_id integer NOT NULL, + condition_era_start_date date NOT NULL, + condition_era_end_date date NOT NULL, + condition_occurrence_count integer NULL ); +--HINT DISTRIBUTE ON KEY (person_id) +CREATE TABLE @cdmDatabaseSchema.EPISODE ( + episode_id integer NOT NULL, + person_id integer NOT NULL, + episode_concept_id integer NOT NULL, + episode_start_date date NOT NULL, + episode_start_datetime TIMESTAMP NULL, + episode_end_date date NULL, + episode_end_datetime TIMESTAMP NULL, + episode_parent_id integer NULL, + episode_number integer NULL, + episode_object_concept_id integer NOT NULL, + episode_type_concept_id integer NOT NULL, + episode_source_value varchar(50) NULL, + episode_source_concept_id integer NULL ); +--HINT DISTRIBUTE ON RANDOM +CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT ( + episode_id integer NOT NULL, + event_id integer NOT NULL, + episode_event_field_concept_id integer NOT NULL ); +--HINT DISTRIBUTE ON RANDOM +CREATE TABLE @cdmDatabaseSchema.METADATA ( + metadata_id integer NOT NULL, + metadata_concept_id integer NOT NULL, + metadata_type_concept_id integer NOT NULL, + name varchar(250) NOT NULL, + value_as_string varchar(250) NULL, + value_as_concept_id integer NULL, + value_as_number NUMERIC NULL, + metadata_date date NULL, + metadata_datetime TIMESTAMP NULL ); +--HINT DISTRIBUTE ON RANDOM +CREATE TABLE @cdmDatabaseSchema.CDM_SOURCE ( + cdm_source_name varchar(255) NOT NULL, + cdm_source_abbreviation varchar(25) NOT NULL, + cdm_holder varchar(255) NOT NULL, + source_description TEXT NULL, + source_documentation_reference varchar(255) NULL, + cdm_etl_reference varchar(255) NULL, + source_release_date date NOT NULL, + cdm_release_date date NOT NULL, + cdm_version varchar(10) NULL, + cdm_version_concept_id integer NOT NULL, + vocabulary_version varchar(20) NOT NULL ); +--HINT DISTRIBUTE ON RANDOM +CREATE TABLE @cdmDatabaseSchema.CONCEPT ( + concept_id integer NOT NULL, + concept_name varchar(255) NOT NULL, + domain_id varchar(20) NOT NULL, + vocabulary_id varchar(20) NOT NULL, + concept_class_id varchar(20) NOT NULL, + standard_concept varchar(1) NULL, + concept_code varchar(50) NOT NULL, + valid_start_date date NOT NULL, + valid_end_date date NOT NULL, + invalid_reason varchar(1) NULL ); +--HINT DISTRIBUTE ON RANDOM +CREATE TABLE @cdmDatabaseSchema.VOCABULARY ( + vocabulary_id varchar(20) NOT NULL, + vocabulary_name varchar(255) NOT NULL, + vocabulary_reference varchar(255) NULL, + vocabulary_version varchar(255) NULL, + vocabulary_concept_id integer NOT NULL ); +--HINT DISTRIBUTE ON RANDOM +CREATE TABLE @cdmDatabaseSchema.DOMAIN ( + domain_id varchar(20) NOT NULL, + domain_name varchar(255) NOT NULL, + domain_concept_id integer NOT NULL ); +--HINT DISTRIBUTE ON RANDOM +CREATE TABLE @cdmDatabaseSchema.CONCEPT_CLASS ( + concept_class_id varchar(20) NOT NULL, + concept_class_name varchar(255) NOT NULL, + concept_class_concept_id integer NOT NULL ); +--HINT DISTRIBUTE ON RANDOM +CREATE TABLE @cdmDatabaseSchema.CONCEPT_RELATIONSHIP ( + concept_id_1 integer NOT NULL, + concept_id_2 integer NOT NULL, + relationship_id varchar(20) NOT NULL, + valid_start_date date NOT NULL, + valid_end_date date NOT NULL, + invalid_reason varchar(1) NULL ); +--HINT DISTRIBUTE ON RANDOM +CREATE TABLE @cdmDatabaseSchema.RELATIONSHIP ( + relationship_id varchar(20) NOT NULL, + relationship_name varchar(255) NOT NULL, + is_hierarchical varchar(1) NOT NULL, + defines_ancestry varchar(1) NOT NULL, + reverse_relationship_id varchar(20) NOT NULL, + relationship_concept_id integer NOT NULL ); +--HINT DISTRIBUTE ON RANDOM +CREATE TABLE @cdmDatabaseSchema.CONCEPT_SYNONYM ( + concept_id integer NOT NULL, + concept_synonym_name varchar(1000) NOT NULL, + language_concept_id integer NOT NULL ); +--HINT DISTRIBUTE ON RANDOM +CREATE TABLE @cdmDatabaseSchema.CONCEPT_ANCESTOR ( + ancestor_concept_id integer NOT NULL, + descendant_concept_id integer NOT NULL, + min_levels_of_separation integer NOT NULL, + max_levels_of_separation integer NOT NULL ); +--HINT DISTRIBUTE ON RANDOM +CREATE TABLE @cdmDatabaseSchema.SOURCE_TO_CONCEPT_MAP ( + source_code varchar(50) NOT NULL, + source_concept_id integer NOT NULL, + source_vocabulary_id varchar(20) NOT NULL, + source_code_description varchar(255) NULL, + target_concept_id integer NOT NULL, + target_vocabulary_id varchar(20) NOT NULL, + valid_start_date date NOT NULL, + valid_end_date date NOT NULL, + invalid_reason varchar(1) NULL ); +--HINT DISTRIBUTE ON RANDOM +CREATE TABLE @cdmDatabaseSchema.DRUG_STRENGTH ( + drug_concept_id integer NOT NULL, + ingredient_concept_id integer NOT NULL, + amount_value NUMERIC NULL, + amount_unit_concept_id integer NULL, + numerator_value NUMERIC NULL, + numerator_unit_concept_id integer NULL, + denominator_value NUMERIC NULL, + denominator_unit_concept_id integer NULL, + box_size integer NULL, + valid_start_date date NOT NULL, + valid_end_date date NOT NULL, + invalid_reason varchar(1) NULL ); +--HINT DISTRIBUTE ON RANDOM +CREATE TABLE @cdmDatabaseSchema.COHORT ( + cohort_definition_id integer NOT NULL, + subject_id integer NOT NULL, + cohort_start_date date NOT NULL, + cohort_end_date date NOT NULL ); +--HINT DISTRIBUTE ON RANDOM +CREATE TABLE @cdmDatabaseSchema.COHORT_DEFINITION ( + cohort_definition_id integer NOT NULL, + cohort_definition_name varchar(255) NOT NULL, + cohort_definition_description TEXT NULL, + definition_type_concept_id integer NOT NULL, + cohort_definition_syntax TEXT NULL, + subject_concept_id integer NOT NULL, + cohort_initiation_date date NULL ); From 96c01214e3d7cf7c6454767e20228cb4497435f1 Mon Sep 17 00:00:00 2001 From: TheCedarPrince Date: Tue, 11 Jul 2023 20:52:35 -0400 Subject: [PATCH 3/3] Created note that for COST table, no changes needed --- .../duckdb/OMOPCDM_duckdb_5.4_constraints.sql | 179 ++++++++++++++++++ .../5.4/duckdb/OMOPCDM_duckdb_5.4_indices.sql | 132 +++++++++++++ .../OMOPCDM_duckdb_5.4_primary_keys.sql | 31 +++ 3 files changed, 342 insertions(+) create mode 100644 inst/ddl/5.4/duckdb/OMOPCDM_duckdb_5.4_constraints.sql create mode 100644 inst/ddl/5.4/duckdb/OMOPCDM_duckdb_5.4_indices.sql create mode 100644 inst/ddl/5.4/duckdb/OMOPCDM_duckdb_5.4_primary_keys.sql diff --git a/inst/ddl/5.4/duckdb/OMOPCDM_duckdb_5.4_constraints.sql b/inst/ddl/5.4/duckdb/OMOPCDM_duckdb_5.4_constraints.sql new file mode 100644 index 0000000..f97484f --- /dev/null +++ b/inst/ddl/5.4/duckdb/OMOPCDM_duckdb_5.4_constraints.sql @@ -0,0 +1,179 @@ +--duckdb CDM Foreign Key Constraints for OMOP Common Data Model 5.4 +-- NOTE: Nothing needed to do here; however, DuckDB cannot create constraints except for at the create table step +-- TODO: Remove when done +ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_gender_concept_id FOREIGN KEY (gender_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_race_concept_id FOREIGN KEY (race_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_ethnicity_concept_id FOREIGN KEY (ethnicity_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_location_id FOREIGN KEY (location_id) REFERENCES @cdmDatabaseSchema.LOCATION (LOCATION_ID); +ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID); +ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_care_site_id FOREIGN KEY (care_site_id) REFERENCES @cdmDatabaseSchema.CARE_SITE (CARE_SITE_ID); +ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_gender_source_concept_id FOREIGN KEY (gender_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_race_source_concept_id FOREIGN KEY (race_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_ethnicity_source_concept_id FOREIGN KEY (ethnicity_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.OBSERVATION_PERIOD ADD CONSTRAINT fpk_OBSERVATION_PERIOD_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID); +ALTER TABLE @cdmDatabaseSchema.OBSERVATION_PERIOD ADD CONSTRAINT fpk_OBSERVATION_PERIOD_period_type_concept_id FOREIGN KEY (period_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID); +ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_visit_concept_id FOREIGN KEY (visit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_visit_type_concept_id FOREIGN KEY (visit_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID); +ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_care_site_id FOREIGN KEY (care_site_id) REFERENCES @cdmDatabaseSchema.CARE_SITE (CARE_SITE_ID); +ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_visit_source_concept_id FOREIGN KEY (visit_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_admitted_from_concept_id FOREIGN KEY (admitted_from_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_discharged_to_concept_id FOREIGN KEY (discharged_to_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_preceding_visit_occurrence_id FOREIGN KEY (preceding_visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID); +ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID); +ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_visit_detail_concept_id FOREIGN KEY (visit_detail_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_visit_detail_type_concept_id FOREIGN KEY (visit_detail_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID); +ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_care_site_id FOREIGN KEY (care_site_id) REFERENCES @cdmDatabaseSchema.CARE_SITE (CARE_SITE_ID); +ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_visit_detail_source_concept_id FOREIGN KEY (visit_detail_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_admitted_from_concept_id FOREIGN KEY (admitted_from_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_discharged_to_concept_id FOREIGN KEY (discharged_to_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_preceding_visit_detail_id FOREIGN KEY (preceding_visit_detail_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID); +ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_parent_visit_detail_id FOREIGN KEY (parent_visit_detail_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID); +ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_visit_occurrence_id FOREIGN KEY (visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID); +ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT fpk_CONDITION_OCCURRENCE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID); +ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT fpk_CONDITION_OCCURRENCE_condition_concept_id FOREIGN KEY (condition_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT fpk_CONDITION_OCCURRENCE_condition_type_concept_id FOREIGN KEY (condition_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT fpk_CONDITION_OCCURRENCE_condition_status_concept_id FOREIGN KEY (condition_status_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT fpk_CONDITION_OCCURRENCE_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID); +ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT fpk_CONDITION_OCCURRENCE_visit_occurrence_id FOREIGN KEY (visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID); +ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT fpk_CONDITION_OCCURRENCE_visit_detail_id FOREIGN KEY (visit_detail_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID); +ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT fpk_CONDITION_OCCURRENCE_condition_source_concept_id FOREIGN KEY (condition_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT fpk_DRUG_EXPOSURE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID); +ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT fpk_DRUG_EXPOSURE_drug_concept_id FOREIGN KEY (drug_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT fpk_DRUG_EXPOSURE_drug_type_concept_id FOREIGN KEY (drug_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT fpk_DRUG_EXPOSURE_route_concept_id FOREIGN KEY (route_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT fpk_DRUG_EXPOSURE_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID); +ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT fpk_DRUG_EXPOSURE_visit_occurrence_id FOREIGN KEY (visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID); +ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT fpk_DRUG_EXPOSURE_visit_detail_id FOREIGN KEY (visit_detail_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID); +ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT fpk_DRUG_EXPOSURE_drug_source_concept_id FOREIGN KEY (drug_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE ADD CONSTRAINT fpk_PROCEDURE_OCCURRENCE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID); +ALTER TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE ADD CONSTRAINT fpk_PROCEDURE_OCCURRENCE_procedure_concept_id FOREIGN KEY (procedure_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE ADD CONSTRAINT fpk_PROCEDURE_OCCURRENCE_procedure_type_concept_id FOREIGN KEY (procedure_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE ADD CONSTRAINT fpk_PROCEDURE_OCCURRENCE_modifier_concept_id FOREIGN KEY (modifier_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE ADD CONSTRAINT fpk_PROCEDURE_OCCURRENCE_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID); +ALTER TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE ADD CONSTRAINT fpk_PROCEDURE_OCCURRENCE_visit_occurrence_id FOREIGN KEY (visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID); +ALTER TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE ADD CONSTRAINT fpk_PROCEDURE_OCCURRENCE_visit_detail_id FOREIGN KEY (visit_detail_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID); +ALTER TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE ADD CONSTRAINT fpk_PROCEDURE_OCCURRENCE_procedure_source_concept_id FOREIGN KEY (procedure_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT fpk_DEVICE_EXPOSURE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID); +ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT fpk_DEVICE_EXPOSURE_device_concept_id FOREIGN KEY (device_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT fpk_DEVICE_EXPOSURE_device_type_concept_id FOREIGN KEY (device_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT fpk_DEVICE_EXPOSURE_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID); +ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT fpk_DEVICE_EXPOSURE_visit_occurrence_id FOREIGN KEY (visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID); +ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT fpk_DEVICE_EXPOSURE_visit_detail_id FOREIGN KEY (visit_detail_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID); +ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT fpk_DEVICE_EXPOSURE_device_source_concept_id FOREIGN KEY (device_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT fpk_DEVICE_EXPOSURE_unit_concept_id FOREIGN KEY (unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT fpk_DEVICE_EXPOSURE_unit_source_concept_id FOREIGN KEY (unit_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID); +ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_measurement_concept_id FOREIGN KEY (measurement_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_measurement_type_concept_id FOREIGN KEY (measurement_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_operator_concept_id FOREIGN KEY (operator_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_value_as_concept_id FOREIGN KEY (value_as_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_unit_concept_id FOREIGN KEY (unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID); +ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_visit_occurrence_id FOREIGN KEY (visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID); +ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_visit_detail_id FOREIGN KEY (visit_detail_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID); +ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_measurement_source_concept_id FOREIGN KEY (measurement_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_unit_source_concept_id FOREIGN KEY (unit_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_meas_event_field_concept_id FOREIGN KEY (meas_event_field_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID); +ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_observation_concept_id FOREIGN KEY (observation_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_observation_type_concept_id FOREIGN KEY (observation_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_value_as_concept_id FOREIGN KEY (value_as_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_qualifier_concept_id FOREIGN KEY (qualifier_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_unit_concept_id FOREIGN KEY (unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID); +ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_visit_occurrence_id FOREIGN KEY (visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID); +ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_visit_detail_id FOREIGN KEY (visit_detail_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID); +ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_observation_source_concept_id FOREIGN KEY (observation_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_obs_event_field_concept_id FOREIGN KEY (obs_event_field_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.DEATH ADD CONSTRAINT fpk_DEATH_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID); +ALTER TABLE @cdmDatabaseSchema.DEATH ADD CONSTRAINT fpk_DEATH_death_type_concept_id FOREIGN KEY (death_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.DEATH ADD CONSTRAINT fpk_DEATH_cause_concept_id FOREIGN KEY (cause_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.DEATH ADD CONSTRAINT fpk_DEATH_cause_source_concept_id FOREIGN KEY (cause_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID); +ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_note_type_concept_id FOREIGN KEY (note_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_note_class_concept_id FOREIGN KEY (note_class_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_encoding_concept_id FOREIGN KEY (encoding_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_language_concept_id FOREIGN KEY (language_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID); +ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_visit_occurrence_id FOREIGN KEY (visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID); +ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_visit_detail_id FOREIGN KEY (visit_detail_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID); +ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_note_event_field_concept_id FOREIGN KEY (note_event_field_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.NOTE_NLP ADD CONSTRAINT fpk_NOTE_NLP_section_concept_id FOREIGN KEY (section_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.NOTE_NLP ADD CONSTRAINT fpk_NOTE_NLP_note_nlp_concept_id FOREIGN KEY (note_nlp_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.NOTE_NLP ADD CONSTRAINT fpk_NOTE_NLP_note_nlp_source_concept_id FOREIGN KEY (note_nlp_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.SPECIMEN ADD CONSTRAINT fpk_SPECIMEN_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID); +ALTER TABLE @cdmDatabaseSchema.SPECIMEN ADD CONSTRAINT fpk_SPECIMEN_specimen_concept_id FOREIGN KEY (specimen_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.SPECIMEN ADD CONSTRAINT fpk_SPECIMEN_specimen_type_concept_id FOREIGN KEY (specimen_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.SPECIMEN ADD CONSTRAINT fpk_SPECIMEN_unit_concept_id FOREIGN KEY (unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.SPECIMEN ADD CONSTRAINT fpk_SPECIMEN_anatomic_site_concept_id FOREIGN KEY (anatomic_site_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.SPECIMEN ADD CONSTRAINT fpk_SPECIMEN_disease_status_concept_id FOREIGN KEY (disease_status_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.FACT_RELATIONSHIP ADD CONSTRAINT fpk_FACT_RELATIONSHIP_domain_concept_id_1 FOREIGN KEY (domain_concept_id_1) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.FACT_RELATIONSHIP ADD CONSTRAINT fpk_FACT_RELATIONSHIP_domain_concept_id_2 FOREIGN KEY (domain_concept_id_2) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.FACT_RELATIONSHIP ADD CONSTRAINT fpk_FACT_RELATIONSHIP_relationship_concept_id FOREIGN KEY (relationship_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.LOCATION ADD CONSTRAINT fpk_LOCATION_country_concept_id FOREIGN KEY (country_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.CARE_SITE ADD CONSTRAINT fpk_CARE_SITE_place_of_service_concept_id FOREIGN KEY (place_of_service_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.CARE_SITE ADD CONSTRAINT fpk_CARE_SITE_location_id FOREIGN KEY (location_id) REFERENCES @cdmDatabaseSchema.LOCATION (LOCATION_ID); +ALTER TABLE @cdmDatabaseSchema.PROVIDER ADD CONSTRAINT fpk_PROVIDER_specialty_concept_id FOREIGN KEY (specialty_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.PROVIDER ADD CONSTRAINT fpk_PROVIDER_care_site_id FOREIGN KEY (care_site_id) REFERENCES @cdmDatabaseSchema.CARE_SITE (CARE_SITE_ID); +ALTER TABLE @cdmDatabaseSchema.PROVIDER ADD CONSTRAINT fpk_PROVIDER_gender_concept_id FOREIGN KEY (gender_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.PROVIDER ADD CONSTRAINT fpk_PROVIDER_specialty_source_concept_id FOREIGN KEY (specialty_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.PROVIDER ADD CONSTRAINT fpk_PROVIDER_gender_source_concept_id FOREIGN KEY (gender_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID); +ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_payer_concept_id FOREIGN KEY (payer_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_payer_source_concept_id FOREIGN KEY (payer_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_plan_concept_id FOREIGN KEY (plan_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_plan_source_concept_id FOREIGN KEY (plan_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_sponsor_concept_id FOREIGN KEY (sponsor_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_sponsor_source_concept_id FOREIGN KEY (sponsor_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_stop_reason_concept_id FOREIGN KEY (stop_reason_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_stop_reason_source_concept_id FOREIGN KEY (stop_reason_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.COST ADD CONSTRAINT fpk_COST_cost_domain_id FOREIGN KEY (cost_domain_id) REFERENCES @cdmDatabaseSchema.DOMAIN (DOMAIN_ID); +ALTER TABLE @cdmDatabaseSchema.COST ADD CONSTRAINT fpk_COST_cost_type_concept_id FOREIGN KEY (cost_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.COST ADD CONSTRAINT fpk_COST_currency_concept_id FOREIGN KEY (currency_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.COST ADD CONSTRAINT fpk_COST_revenue_code_concept_id FOREIGN KEY (revenue_code_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.COST ADD CONSTRAINT fpk_COST_drg_concept_id FOREIGN KEY (drg_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.DRUG_ERA ADD CONSTRAINT fpk_DRUG_ERA_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID); +ALTER TABLE @cdmDatabaseSchema.DRUG_ERA ADD CONSTRAINT fpk_DRUG_ERA_drug_concept_id FOREIGN KEY (drug_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.DOSE_ERA ADD CONSTRAINT fpk_DOSE_ERA_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID); +ALTER TABLE @cdmDatabaseSchema.DOSE_ERA ADD CONSTRAINT fpk_DOSE_ERA_drug_concept_id FOREIGN KEY (drug_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.DOSE_ERA ADD CONSTRAINT fpk_DOSE_ERA_unit_concept_id FOREIGN KEY (unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.CONDITION_ERA ADD CONSTRAINT fpk_CONDITION_ERA_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID); +ALTER TABLE @cdmDatabaseSchema.CONDITION_ERA ADD CONSTRAINT fpk_CONDITION_ERA_condition_concept_id FOREIGN KEY (condition_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID); +ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_concept_id FOREIGN KEY (episode_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_object_concept_id FOREIGN KEY (episode_object_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_type_concept_id FOREIGN KEY (episode_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_source_concept_id FOREIGN KEY (episode_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.EPISODE_EVENT ADD CONSTRAINT fpk_EPISODE_EVENT_episode_id FOREIGN KEY (episode_id) REFERENCES @cdmDatabaseSchema.EPISODE (EPISODE_ID); +ALTER TABLE @cdmDatabaseSchema.EPISODE_EVENT ADD CONSTRAINT fpk_EPISODE_EVENT_episode_event_field_concept_id FOREIGN KEY (episode_event_field_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.METADATA ADD CONSTRAINT fpk_METADATA_metadata_concept_id FOREIGN KEY (metadata_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.METADATA ADD CONSTRAINT fpk_METADATA_metadata_type_concept_id FOREIGN KEY (metadata_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.METADATA ADD CONSTRAINT fpk_METADATA_value_as_concept_id FOREIGN KEY (value_as_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.CDM_SOURCE ADD CONSTRAINT fpk_CDM_SOURCE_cdm_version_concept_id FOREIGN KEY (cdm_version_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.CONCEPT ADD CONSTRAINT fpk_CONCEPT_domain_id FOREIGN KEY (domain_id) REFERENCES @cdmDatabaseSchema.DOMAIN (DOMAIN_ID); +ALTER TABLE @cdmDatabaseSchema.CONCEPT ADD CONSTRAINT fpk_CONCEPT_vocabulary_id FOREIGN KEY (vocabulary_id) REFERENCES @cdmDatabaseSchema.VOCABULARY (VOCABULARY_ID); +ALTER TABLE @cdmDatabaseSchema.CONCEPT ADD CONSTRAINT fpk_CONCEPT_concept_class_id FOREIGN KEY (concept_class_id) REFERENCES @cdmDatabaseSchema.CONCEPT_CLASS (CONCEPT_CLASS_ID); +ALTER TABLE @cdmDatabaseSchema.VOCABULARY ADD CONSTRAINT fpk_VOCABULARY_vocabulary_concept_id FOREIGN KEY (vocabulary_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.DOMAIN ADD CONSTRAINT fpk_DOMAIN_domain_concept_id FOREIGN KEY (domain_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.CONCEPT_CLASS ADD CONSTRAINT fpk_CONCEPT_CLASS_concept_class_concept_id FOREIGN KEY (concept_class_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.CONCEPT_RELATIONSHIP ADD CONSTRAINT fpk_CONCEPT_RELATIONSHIP_concept_id_1 FOREIGN KEY (concept_id_1) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.CONCEPT_RELATIONSHIP ADD CONSTRAINT fpk_CONCEPT_RELATIONSHIP_concept_id_2 FOREIGN KEY (concept_id_2) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.CONCEPT_RELATIONSHIP ADD CONSTRAINT fpk_CONCEPT_RELATIONSHIP_relationship_id FOREIGN KEY (relationship_id) REFERENCES @cdmDatabaseSchema.RELATIONSHIP (RELATIONSHIP_ID); +ALTER TABLE @cdmDatabaseSchema.RELATIONSHIP ADD CONSTRAINT fpk_RELATIONSHIP_relationship_concept_id FOREIGN KEY (relationship_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.CONCEPT_SYNONYM ADD CONSTRAINT fpk_CONCEPT_SYNONYM_concept_id FOREIGN KEY (concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.CONCEPT_SYNONYM ADD CONSTRAINT fpk_CONCEPT_SYNONYM_language_concept_id FOREIGN KEY (language_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.CONCEPT_ANCESTOR ADD CONSTRAINT fpk_CONCEPT_ANCESTOR_ancestor_concept_id FOREIGN KEY (ancestor_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.CONCEPT_ANCESTOR ADD CONSTRAINT fpk_CONCEPT_ANCESTOR_descendant_concept_id FOREIGN KEY (descendant_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.SOURCE_TO_CONCEPT_MAP ADD CONSTRAINT fpk_SOURCE_TO_CONCEPT_MAP_source_concept_id FOREIGN KEY (source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.SOURCE_TO_CONCEPT_MAP ADD CONSTRAINT fpk_SOURCE_TO_CONCEPT_MAP_target_concept_id FOREIGN KEY (target_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.SOURCE_TO_CONCEPT_MAP ADD CONSTRAINT fpk_SOURCE_TO_CONCEPT_MAP_target_vocabulary_id FOREIGN KEY (target_vocabulary_id) REFERENCES @cdmDatabaseSchema.VOCABULARY (VOCABULARY_ID); +ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_drug_concept_id FOREIGN KEY (drug_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_ingredient_concept_id FOREIGN KEY (ingredient_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_amount_unit_concept_id FOREIGN KEY (amount_unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_numerator_unit_concept_id FOREIGN KEY (numerator_unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_denominator_unit_concept_id FOREIGN KEY (denominator_unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_definition_type_concept_id FOREIGN KEY (definition_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); +ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_subject_concept_id FOREIGN KEY (subject_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID); diff --git a/inst/ddl/5.4/duckdb/OMOPCDM_duckdb_5.4_indices.sql b/inst/ddl/5.4/duckdb/OMOPCDM_duckdb_5.4_indices.sql new file mode 100644 index 0000000..0b70ad4 --- /dev/null +++ b/inst/ddl/5.4/duckdb/OMOPCDM_duckdb_5.4_indices.sql @@ -0,0 +1,132 @@ +/*duckdb 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. + NOTE: Nothing needs to be added here for COST table + TODO: Remove note when done +*/ +/************************ +Standardized clinical data +************************/ +CREATE INDEX idx_person_id ON @cdmDatabaseSchema.person (person_id ASC); +CLUSTER @cdmDatabaseSchema.person USING idx_person_id ; +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); +CLUSTER @cdmDatabaseSchema.observation_period USING idx_observation_period_id_1 ; +CREATE INDEX idx_visit_person_id_1 ON @cdmDatabaseSchema.visit_occurrence (person_id ASC); +CLUSTER @cdmDatabaseSchema.visit_occurrence USING idx_visit_person_id_1 ; +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); +CLUSTER @cdmDatabaseSchema.visit_detail USING idx_visit_det_person_id_1 ; +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); +CLUSTER @cdmDatabaseSchema.condition_occurrence USING idx_condition_person_id_1 ; +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); +CLUSTER @cdmDatabaseSchema.drug_exposure USING idx_drug_person_id_1 ; +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); +CLUSTER @cdmDatabaseSchema.procedure_occurrence USING idx_procedure_person_id_1 ; +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); +CLUSTER @cdmDatabaseSchema.device_exposure USING idx_device_person_id_1 ; +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); +CLUSTER @cdmDatabaseSchema.measurement USING idx_measurement_person_id_1 ; +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); +CLUSTER @cdmDatabaseSchema.observation USING idx_observation_person_id_1 ; +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); +CLUSTER @cdmDatabaseSchema.death USING idx_death_person_id_1 ; +CREATE INDEX idx_note_person_id_1 ON @cdmDatabaseSchema.note (person_id ASC); +CLUSTER @cdmDatabaseSchema.note USING idx_note_person_id_1 ; +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); +CLUSTER @cdmDatabaseSchema.note_nlp USING idx_note_nlp_note_id_1 ; +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); +CLUSTER @cdmDatabaseSchema.specimen USING idx_specimen_person_id_1 ; +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); +CLUSTER @cdmDatabaseSchema.location USING idx_location_id_1 ; +CREATE INDEX idx_care_site_id_1 ON @cdmDatabaseSchema.care_site (care_site_id ASC); +CLUSTER @cdmDatabaseSchema.care_site USING idx_care_site_id_1 ; +CREATE INDEX idx_provider_id_1 ON @cdmDatabaseSchema.provider (provider_id ASC); +CLUSTER @cdmDatabaseSchema.provider USING idx_provider_id_1 ; +/************************ +Standardized health economics +************************/ +CREATE INDEX idx_period_person_id_1 ON @cdmDatabaseSchema.payer_plan_period (person_id ASC); +CLUSTER @cdmDatabaseSchema.payer_plan_period USING idx_period_person_id_1 ; +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); +CLUSTER @cdmDatabaseSchema.drug_era USING idx_drug_era_person_id_1 ; +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); +CLUSTER @cdmDatabaseSchema.dose_era USING idx_dose_era_person_id_1 ; +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); +CLUSTER @cdmDatabaseSchema.condition_era USING idx_condition_era_person_id_1 ; +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); +CLUSTER @cdmDatabaseSchema.metadata USING idx_metadata_concept_id_1 ; +/************************** +Standardized vocabularies +***************************/ +CREATE INDEX idx_concept_concept_id ON @cdmDatabaseSchema.concept (concept_id ASC); +CLUSTER @cdmDatabaseSchema.concept USING idx_concept_concept_id ; +CREATE INDEX idx_concept_code ON @cdmDatabaseSchema.concept (concept_code ASC); +CREATE INDEX idx_concept_vocabluary_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); +CLUSTER @cdmDatabaseSchema.vocabulary USING idx_vocabulary_vocabulary_id ; +CREATE INDEX idx_domain_domain_id ON @cdmDatabaseSchema.domain (domain_id ASC); +CLUSTER @cdmDatabaseSchema.domain USING idx_domain_domain_id ; +CREATE INDEX idx_concept_class_class_id ON @cdmDatabaseSchema.concept_class (concept_class_id ASC); +CLUSTER @cdmDatabaseSchema.concept_class USING idx_concept_class_class_id ; +CREATE INDEX idx_concept_relationship_id_1 ON @cdmDatabaseSchema.concept_relationship (concept_id_1 ASC); +CLUSTER @cdmDatabaseSchema.concept_relationship USING idx_concept_relationship_id_1 ; +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); +CLUSTER @cdmDatabaseSchema.relationship USING idx_relationship_rel_id ; +CREATE INDEX idx_concept_synonym_id ON @cdmDatabaseSchema.concept_synonym (concept_id ASC); +CLUSTER @cdmDatabaseSchema.concept_synonym USING idx_concept_synonym_id ; +CREATE INDEX idx_concept_ancestor_id_1 ON @cdmDatabaseSchema.concept_ancestor (ancestor_concept_id ASC); +CLUSTER @cdmDatabaseSchema.concept_ancestor USING idx_concept_ancestor_id_1 ; +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); +CLUSTER @cdmDatabaseSchema.source_to_concept_map USING idx_source_to_concept_map_3 ; +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); +CLUSTER @cdmDatabaseSchema.drug_strength USING idx_drug_strength_id_1 ; +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); diff --git a/inst/ddl/5.4/duckdb/OMOPCDM_duckdb_5.4_primary_keys.sql b/inst/ddl/5.4/duckdb/OMOPCDM_duckdb_5.4_primary_keys.sql new file mode 100644 index 0000000..6ccda85 --- /dev/null +++ b/inst/ddl/5.4/duckdb/OMOPCDM_duckdb_5.4_primary_keys.sql @@ -0,0 +1,31 @@ +--postgresql CDM Primary Key Constraints for OMOP Common Data Model 5.4 +-- NOTE: Nothing needed to do here; however, DuckDB cannot create constraints except for at the create table step +-- TODO: Remove when done +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.EPISODE ADD CONSTRAINT xpk_EPISODE PRIMARY KEY (episode_id); +ALTER TABLE @cdmDatabaseSchema.METADATA ADD CONSTRAINT xpk_METADATA PRIMARY KEY (metadata_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);