Added constraints
This commit is contained in:
clairblacketer
parent
97a97f3bcb
commit
73a87c3b4a
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# Generated by roxygen2: do not edit by hand
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export(writeConstraints)
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export(writeDDL)
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export(writeIndex)
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export(writePDF)
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# Copyright 2017 Observational Health Data Sciences and Informatics
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#
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# This file is part of DDLGeneratr
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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#' Write constraint script
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#'
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#' @param targetdialect The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"
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#'
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#' @export
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writeConstraints <- function(targetdialect) {
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if(!dir.exists("output")){
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dir.create("output")
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}
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if(!dir.exists(paste0("output/",targetdialect))){
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dir.create(paste0("output/",targetdialect))
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}
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sql <- SqlRender::loadRenderTranslateSql(sqlFilename = "OMOP CDM constraints.sql",
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packageName = "DDLGeneratr",
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dbms = targetdialect,
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targetdialect = targetdialect)
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SqlRender::writeSql(sql = sql,
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targetFile = paste0("output/",targetdialect,"/OMOP CDM ",targetdialect," constraints.txt"))
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}
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@ -34,6 +34,6 @@ sql <- SqlRender::loadRenderTranslateSql(sqlFilename = "OMOP CDM indexes require
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targetdialect = targetdialect)
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SqlRender::writeSql(sql = sql,
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targetFile = paste0("output/",targetdialect,"/OMOP CDM ",targetdialect," indices.txt"))
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targetFile = paste0("output/",targetdialect,"/OMOP CDM ",targetdialect," indexes.txt"))
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}
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@ -17,9 +17,17 @@ writeDDL("sql server")
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# Step 3: Run the following code to create indices for Oracle, Postgres, PDW and Sql Server
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writeIndex("oracle")
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writeIndex("postgresql")
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writeIndex("pdw")
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writeIndex("sql server")
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# Step 3: Update the .md wiki files with the changes for the new version
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# Step 4: Run the following code to create constraints for Oracle, Postgres, PDW and Sql Server
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# step 4: Run the following code to create the pdf documentation. It will be written to the reports folder.
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writeConstraints("oracle")
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writeConstraints("postgresql")
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writeConstraints("pdw")
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writeConstraints("sql server")
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# step 5: Run the following code to create the pdf documentation. It will be written to the reports folder.
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writePDF(mdFilesLocation = "../../Documentation/CommonDataModel_Wiki_Files", cdmVersion = "v5_3")
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/*********************************************************************************
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# Copyright 2014 Observational Health Data Sciences and Informatics
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#
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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********************************************************************************/
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/************************
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####### # # ####### ###### ##### ###### # # ####### ##### #####
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# # ## ## # # # # # # # # ## ## # # # # # # # #### # # #### ##### ##### ## # # # ##### ####
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# # # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # ## # # #
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# # # # # # # ###### # # # # # # # # ###### ##### # # # # # # #### # # # # # # # # # # ####
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# # # # # # # # # # # # # # # ### # # # # # # # # # ##### ###### # # # # # #
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# # # # # # # # # # # # # # # # # ### # # # # # # # ## # # # # # # # # # ## # # #
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####### # # ####### # ##### ###### # # ## ##### ### ##### ##### #### # # #### # # # # # # # # # ####
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@targetdialect script to create constraints within OMOP common data model, version 5.3.0
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last revised: 15-November-2017
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author: Patrick Ryan, Clair Blacketer
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*************************/
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/************************
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*************************
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*************************
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*************************
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Primary key constraints
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*************************
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*************************
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*************************
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************************/
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/************************
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Standardized vocabulary
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************************/
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ALTER TABLE concept ADD CONSTRAINT xpk_concept PRIMARY KEY NONCLUSTERED (concept_id);
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ALTER TABLE vocabulary ADD CONSTRAINT xpk_vocabulary PRIMARY KEY NONCLUSTERED (vocabulary_id);
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ALTER TABLE domain ADD CONSTRAINT xpk_domain PRIMARY KEY NONCLUSTERED (domain_id);
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ALTER TABLE concept_class ADD CONSTRAINT xpk_concept_class PRIMARY KEY NONCLUSTERED (concept_class_id);
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ALTER TABLE concept_relationship ADD CONSTRAINT xpk_concept_relationship PRIMARY KEY NONCLUSTERED (concept_id_1,concept_id_2,relationship_id);
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ALTER TABLE relationship ADD CONSTRAINT xpk_relationship PRIMARY KEY NONCLUSTERED (relationship_id);
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ALTER TABLE concept_ancestor ADD CONSTRAINT xpk_concept_ancestor PRIMARY KEY NONCLUSTERED (ancestor_concept_id,descendant_concept_id);
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ALTER TABLE source_to_concept_map ADD CONSTRAINT xpk_source_to_concept_map PRIMARY KEY NONCLUSTERED (source_vocabulary_id,target_concept_id,source_code,valid_end_date);
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ALTER TABLE drug_strength ADD CONSTRAINT xpk_drug_strength PRIMARY KEY NONCLUSTERED (drug_concept_id, ingredient_concept_id);
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ALTER TABLE cohort_definition ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY NONCLUSTERED (cohort_definition_id);
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ALTER TABLE attribute_definition ADD CONSTRAINT xpk_attribute_definition PRIMARY KEY NONCLUSTERED (attribute_definition_id);
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/**************************
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Standardized meta-data
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***************************/
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/************************
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Standardized clinical data
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************************/
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/**PRIMARY KEY NONCLUSTERED constraints**/
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ALTER TABLE person ADD CONSTRAINT xpk_person PRIMARY KEY NONCLUSTERED ( person_id ) ;
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ALTER TABLE observation_period ADD CONSTRAINT xpk_observation_period PRIMARY KEY NONCLUSTERED ( observation_period_id ) ;
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ALTER TABLE specimen ADD CONSTRAINT xpk_specimen PRIMARY KEY NONCLUSTERED ( specimen_id ) ;
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ALTER TABLE death ADD CONSTRAINT xpk_death PRIMARY KEY NONCLUSTERED ( person_id ) ;
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ALTER TABLE visit_occurrence ADD CONSTRAINT xpk_visit_occurrence PRIMARY KEY NONCLUSTERED ( visit_occurrence_id ) ;
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ALTER TABLE procedure_occurrence ADD CONSTRAINT xpk_procedure_occurrence PRIMARY KEY NONCLUSTERED ( procedure_occurrence_id ) ;
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ALTER TABLE drug_exposure ADD CONSTRAINT xpk_drug_exposure PRIMARY KEY NONCLUSTERED ( drug_exposure_id ) ;
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ALTER TABLE device_exposure ADD CONSTRAINT xpk_device_exposure PRIMARY KEY NONCLUSTERED ( device_exposure_id ) ;
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ALTER TABLE condition_occurrence ADD CONSTRAINT xpk_condition_occurrence PRIMARY KEY NONCLUSTERED ( condition_occurrence_id ) ;
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ALTER TABLE measurement ADD CONSTRAINT xpk_measurement PRIMARY KEY NONCLUSTERED ( measurement_id ) ;
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ALTER TABLE note ADD CONSTRAINT xpk_note PRIMARY KEY NONCLUSTERED ( note_id ) ;
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ALTER TABLE note_nlp ADD CONSTRAINT xpk_note_nlp PRIMARY KEY NONCLUSTERED ( note_nlp_id ) ;
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ALTER TABLE observation ADD CONSTRAINT xpk_observation PRIMARY KEY NONCLUSTERED ( observation_id ) ;
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/************************
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Standardized health system data
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************************/
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ALTER TABLE location ADD CONSTRAINT xpk_location PRIMARY KEY NONCLUSTERED ( location_id ) ;
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ALTER TABLE care_site ADD CONSTRAINT xpk_care_site PRIMARY KEY NONCLUSTERED ( care_site_id ) ;
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ALTER TABLE provider ADD CONSTRAINT xpk_provider PRIMARY KEY NONCLUSTERED ( provider_id ) ;
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/************************
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Standardized health economics
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************************/
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ALTER TABLE payer_plan_period ADD CONSTRAINT xpk_payer_plan_period PRIMARY KEY NONCLUSTERED ( payer_plan_period_id ) ;
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ALTER TABLE cost ADD CONSTRAINT xpk_visit_cost PRIMARY KEY NONCLUSTERED ( cost_id ) ;
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/************************
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Standardized derived elements
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************************/
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ALTER TABLE cohort ADD CONSTRAINT xpk_cohort PRIMARY KEY NONCLUSTERED ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date ) ;
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ALTER TABLE cohort_attribute ADD CONSTRAINT xpk_cohort_attribute PRIMARY KEY NONCLUSTERED ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date, attribute_definition_id ) ;
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ALTER TABLE drug_era ADD CONSTRAINT xpk_drug_era PRIMARY KEY NONCLUSTERED ( drug_era_id ) ;
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ALTER TABLE dose_era ADD CONSTRAINT xpk_dose_era PRIMARY KEY NONCLUSTERED ( dose_era_id ) ;
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ALTER TABLE condition_era ADD CONSTRAINT xpk_condition_era PRIMARY KEY NONCLUSTERED ( condition_era_id ) ;
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/************************
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*************************
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*************************
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*************************
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Foreign key constraints
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*************************
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*************************
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************************/
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/************************
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Standardized vocabulary
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************************/
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ALTER TABLE concept ADD CONSTRAINT fpk_concept_domain FOREIGN KEY (domain_id) REFERENCES domain (domain_id);
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ALTER TABLE concept ADD CONSTRAINT fpk_concept_class FOREIGN KEY (concept_class_id) REFERENCES concept_class (concept_class_id);
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ALTER TABLE concept ADD CONSTRAINT fpk_concept_vocabulary FOREIGN KEY (vocabulary_id) REFERENCES vocabulary (vocabulary_id);
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ALTER TABLE vocabulary ADD CONSTRAINT fpk_vocabulary_concept FOREIGN KEY (vocabulary_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE domain ADD CONSTRAINT fpk_domain_concept FOREIGN KEY (domain_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE concept_class ADD CONSTRAINT fpk_concept_class_concept FOREIGN KEY (concept_class_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_1 FOREIGN KEY (concept_id_1) REFERENCES concept (concept_id);
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ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_2 FOREIGN KEY (concept_id_2) REFERENCES concept (concept_id);
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ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_id FOREIGN KEY (relationship_id) REFERENCES relationship (relationship_id);
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ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_concept FOREIGN KEY (relationship_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_reverse FOREIGN KEY (reverse_relationship_id) REFERENCES relationship (relationship_id);
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ALTER TABLE concept_synonym ADD CONSTRAINT fpk_concept_synonym_concept FOREIGN KEY (concept_id) REFERENCES concept (concept_id);
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ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_1 FOREIGN KEY (ancestor_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_2 FOREIGN KEY (descendant_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_1 FOREIGN KEY (source_vocabulary_id) REFERENCES vocabulary (vocabulary_id);
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ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_2 FOREIGN KEY (target_vocabulary_id) REFERENCES vocabulary (vocabulary_id);
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ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_c_1 FOREIGN KEY (target_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_1 FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_2 FOREIGN KEY (ingredient_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_1 FOREIGN KEY (amount_unit_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_2 FOREIGN KEY (numerator_unit_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_3 FOREIGN KEY (denominator_unit_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE cohort_definition ADD CONSTRAINT fpk_cohort_definition_concept FOREIGN KEY (definition_type_concept_id) REFERENCES concept (concept_id);
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/**************************
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Standardized meta-data
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***************************/
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/************************
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Standardized clinical data
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************************/
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ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept FOREIGN KEY (gender_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept FOREIGN KEY (race_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept FOREIGN KEY (ethnicity_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept_s FOREIGN KEY (gender_source_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept_s FOREIGN KEY (race_source_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept_s FOREIGN KEY (ethnicity_source_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE person ADD CONSTRAINT fpk_person_location FOREIGN KEY (location_id) REFERENCES location (location_id);
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ALTER TABLE person ADD CONSTRAINT fpk_person_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
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ALTER TABLE person ADD CONSTRAINT fpk_person_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
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ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_person FOREIGN KEY (person_id) REFERENCES person (person_id);
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ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_concept FOREIGN KEY (period_type_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_person FOREIGN KEY (person_id) REFERENCES person (person_id);
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ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_concept FOREIGN KEY (specimen_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_type_concept FOREIGN KEY (specimen_type_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_unit_concept FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_site_concept FOREIGN KEY (anatomic_site_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_status_concept FOREIGN KEY (disease_status_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE death ADD CONSTRAINT fpk_death_person FOREIGN KEY (person_id) REFERENCES person (person_id);
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ALTER TABLE death ADD CONSTRAINT fpk_death_type_concept FOREIGN KEY (death_type_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE death ADD CONSTRAINT fpk_death_cause_concept FOREIGN KEY (cause_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE death ADD CONSTRAINT fpk_death_cause_concept_s FOREIGN KEY (cause_source_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_person FOREIGN KEY (person_id) REFERENCES person (person_id);
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ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept FOREIGN KEY (visit_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_type_concept FOREIGN KEY (visit_type_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
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ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
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ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept_s FOREIGN KEY (visit_source_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_admitting_s FOREIGN KEY (admitting_source_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_discharge FOREIGN KEY (discharge_to_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_person FOREIGN KEY (person_id) REFERENCES person (person_id);
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ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept FOREIGN KEY (procedure_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_type_concept FOREIGN KEY (procedure_type_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_modifier FOREIGN KEY (modifier_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
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|
||||
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept_s FOREIGN KEY (procedure_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_type_concept FOREIGN KEY (drug_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_route_concept FOREIGN KEY (route_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||
|
||||
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept_s FOREIGN KEY (drug_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept FOREIGN KEY (device_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_type_concept FOREIGN KEY (device_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||
|
||||
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept_s FOREIGN KEY (device_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_type_concept FOREIGN KEY (condition_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||
|
||||
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept_s FOREIGN KEY (condition_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_status_concept FOREIGN KEY (condition_status_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_concept FOREIGN KEY (measurement_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_type_concept FOREIGN KEY (measurement_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_operator FOREIGN KEY (operator_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_unit FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_concept_s FOREIGN KEY (measurement_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE note ADD CONSTRAINT fpk_note_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE note ADD CONSTRAINT fpk_note_type_concept FOREIGN KEY (note_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE note ADD CONSTRAINT fpk_note_class_concept FOREIGN KEY (note_class_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE note ADD CONSTRAINT fpk_note_encoding_concept FOREIGN KEY (encoding_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE note ADD CONSTRAINT fpk_language_concept FOREIGN KEY (language_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE note ADD CONSTRAINT fpk_note_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||
|
||||
ALTER TABLE note ADD CONSTRAINT fpk_note_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
|
||||
ALTER TABLE note_nlp ADD CONSTRAINT fpk_note_nlp_note FOREIGN KEY (note_id) REFERENCES note (note_id);
|
||||
|
||||
ALTER TABLE note_nlp ADD CONSTRAINT fpk_note_nlp_section_concept FOREIGN KEY (section_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE note_nlp ADD CONSTRAINT fpk_note_nlp_concept FOREIGN KEY (note_nlp_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept FOREIGN KEY (observation_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_type_concept FOREIGN KEY (observation_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_qualifier FOREIGN KEY (qualifier_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_unit FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept_s FOREIGN KEY (observation_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_1 FOREIGN KEY (domain_concept_id_1) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_2 FOREIGN KEY (domain_concept_id_2) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_relationship FOREIGN KEY (relationship_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health system data
|
||||
|
||||
************************/
|
||||
|
||||
ALTER TABLE care_site ADD CONSTRAINT fpk_care_site_location FOREIGN KEY (location_id) REFERENCES location (location_id);
|
||||
|
||||
ALTER TABLE care_site ADD CONSTRAINT fpk_care_site_place FOREIGN KEY (place_of_service_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE provider ADD CONSTRAINT fpk_provider_specialty FOREIGN KEY (specialty_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE provider ADD CONSTRAINT fpk_provider_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
|
||||
|
||||
ALTER TABLE provider ADD CONSTRAINT fpk_provider_gender FOREIGN KEY (gender_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE provider ADD CONSTRAINT fpk_provider_specialty_s FOREIGN KEY (specialty_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE provider ADD CONSTRAINT fpk_provider_gender_s FOREIGN KEY (gender_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health economics
|
||||
|
||||
************************/
|
||||
|
||||
ALTER TABLE payer_plan_period ADD CONSTRAINT fpk_payer_plan_period FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE cost ADD CONSTRAINT fpk_visit_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE cost ADD CONSTRAINT fpk_visit_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
|
||||
|
||||
ALTER TABLE cost ADD CONSTRAINT fpk_drg_concept FOREIGN KEY (drg_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
/************************
|
||||
|
||||
Standardized derived elements
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
ALTER TABLE cohort ADD CONSTRAINT fpk_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
|
||||
|
||||
|
||||
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
|
||||
|
||||
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_attribute_definition FOREIGN KEY (attribute_definition_id) REFERENCES attribute_definition (attribute_definition_id);
|
||||
|
||||
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_unit_concept FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id);
|
||||
|
|
@ -0,0 +1,14 @@
|
|||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/writeConstraints.R
|
||||
\name{writeConstraints}
|
||||
\alias{writeConstraints}
|
||||
\title{Write constraint script}
|
||||
\usage{
|
||||
writeConstraints(targetdialect)
|
||||
}
|
||||
\arguments{
|
||||
\item{targetdialect}{The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"}
|
||||
}
|
||||
\description{
|
||||
Write constraint script
|
||||
}
|
||||
|
|
@ -0,0 +1,14 @@
|
|||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/writeIndex.R
|
||||
\name{writeIndex}
|
||||
\alias{writeIndex}
|
||||
\title{Write Index script}
|
||||
\usage{
|
||||
writeIndex(targetdialect)
|
||||
}
|
||||
\arguments{
|
||||
\item{targetdialect}{The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"}
|
||||
}
|
||||
\description{
|
||||
Write Index script
|
||||
}
|
||||
|
|
@ -0,0 +1,528 @@
|
|||
/*********************************************************************************
|
||||
# Copyright 2014 Observational Health Data Sciences and Informatics
|
||||
#
|
||||
#
|
||||
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||
# you may not use this file except in compliance with the License.
|
||||
# You may obtain a copy of the License at
|
||||
#
|
||||
# http://www.apache.org/licenses/LICENSE-2.0
|
||||
#
|
||||
# Unless required by applicable law or agreed to in writing, software
|
||||
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
# See the License for the specific language governing permissions and
|
||||
# limitations under the License.
|
||||
********************************************************************************/
|
||||
|
||||
/************************
|
||||
|
||||
####### # # ####### ###### ##### ###### # # ####### ##### #####
|
||||
# # ## ## # # # # # # # # ## ## # # # # # # # #### # # #### ##### ##### ## # # # ##### ####
|
||||
# # # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # ## # # #
|
||||
# # # # # # # ###### # # # # # # # # ###### ##### # # # # # # #### # # # # # # # # # # ####
|
||||
# # # # # # # # # # # # # # # ### # # # # # # # # # ##### ###### # # # # # #
|
||||
# # # # # # # # # # # # # # # # # ### # # # # # # # ## # # # # # # # # # ## # # #
|
||||
####### # # ####### # ##### ###### # # ## ##### ### ##### ##### #### # # #### # # # # # # # # # ####
|
||||
|
||||
|
||||
oracle script to create constraints within OMOP common data model, version 5.3.0
|
||||
|
||||
last revised: 15-November-2017
|
||||
|
||||
author: Patrick Ryan, Clair Blacketer
|
||||
|
||||
|
||||
*************************/
|
||||
|
||||
|
||||
/************************
|
||||
*************************
|
||||
*************************
|
||||
*************************
|
||||
|
||||
Primary key constraints
|
||||
|
||||
*************************
|
||||
*************************
|
||||
*************************
|
||||
************************/
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized vocabulary
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
|
||||
ALTER TABLE concept ADD CONSTRAINT xpk_concept PRIMARY KEY (concept_id);
|
||||
|
||||
ALTER TABLE vocabulary ADD CONSTRAINT xpk_vocabulary PRIMARY KEY (vocabulary_id);
|
||||
|
||||
ALTER TABLE domain ADD CONSTRAINT xpk_domain PRIMARY KEY (domain_id);
|
||||
|
||||
ALTER TABLE concept_class ADD CONSTRAINT xpk_concept_class PRIMARY KEY (concept_class_id);
|
||||
|
||||
ALTER TABLE concept_relationship ADD CONSTRAINT xpk_concept_relationship PRIMARY KEY (concept_id_1,concept_id_2,relationship_id);
|
||||
|
||||
ALTER TABLE relationship ADD CONSTRAINT xpk_relationship PRIMARY KEY (relationship_id);
|
||||
|
||||
ALTER TABLE concept_ancestor ADD CONSTRAINT xpk_concept_ancestor PRIMARY KEY (ancestor_concept_id,descendant_concept_id);
|
||||
|
||||
ALTER TABLE source_to_concept_map ADD CONSTRAINT xpk_source_to_concept_map PRIMARY KEY (source_vocabulary_id,target_concept_id,source_code,valid_end_date);
|
||||
|
||||
ALTER TABLE drug_strength ADD CONSTRAINT xpk_drug_strength PRIMARY KEY (drug_concept_id, ingredient_concept_id);
|
||||
|
||||
ALTER TABLE cohort_definition ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY (cohort_definition_id);
|
||||
|
||||
ALTER TABLE attribute_definition ADD CONSTRAINT xpk_attribute_definition PRIMARY KEY (attribute_definition_id);
|
||||
|
||||
|
||||
/**************************
|
||||
|
||||
Standardized meta-data
|
||||
|
||||
***************************/
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized clinical data
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
/**PRIMARY KEY NONCLUSTERED constraints**/
|
||||
|
||||
ALTER TABLE person ADD CONSTRAINT xpk_person PRIMARY KEY ( person_id ) ;
|
||||
|
||||
ALTER TABLE observation_period ADD CONSTRAINT xpk_observation_period PRIMARY KEY ( observation_period_id ) ;
|
||||
|
||||
ALTER TABLE specimen ADD CONSTRAINT xpk_specimen PRIMARY KEY ( specimen_id ) ;
|
||||
|
||||
ALTER TABLE death ADD CONSTRAINT xpk_death PRIMARY KEY ( person_id ) ;
|
||||
|
||||
ALTER TABLE visit_occurrence ADD CONSTRAINT xpk_visit_occurrence PRIMARY KEY ( visit_occurrence_id ) ;
|
||||
|
||||
ALTER TABLE procedure_occurrence ADD CONSTRAINT xpk_procedure_occurrence PRIMARY KEY ( procedure_occurrence_id ) ;
|
||||
|
||||
ALTER TABLE drug_exposure ADD CONSTRAINT xpk_drug_exposure PRIMARY KEY ( drug_exposure_id ) ;
|
||||
|
||||
ALTER TABLE device_exposure ADD CONSTRAINT xpk_device_exposure PRIMARY KEY ( device_exposure_id ) ;
|
||||
|
||||
ALTER TABLE condition_occurrence ADD CONSTRAINT xpk_condition_occurrence PRIMARY KEY ( condition_occurrence_id ) ;
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT xpk_measurement PRIMARY KEY ( measurement_id ) ;
|
||||
|
||||
ALTER TABLE note ADD CONSTRAINT xpk_note PRIMARY KEY ( note_id ) ;
|
||||
|
||||
ALTER TABLE note_nlp ADD CONSTRAINT xpk_note_nlp PRIMARY KEY ( note_nlp_id ) ;
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT xpk_observation PRIMARY KEY ( observation_id ) ;
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health system data
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
ALTER TABLE location ADD CONSTRAINT xpk_location PRIMARY KEY ( location_id ) ;
|
||||
|
||||
ALTER TABLE care_site ADD CONSTRAINT xpk_care_site PRIMARY KEY ( care_site_id ) ;
|
||||
|
||||
ALTER TABLE provider ADD CONSTRAINT xpk_provider PRIMARY KEY ( provider_id ) ;
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health economics
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
ALTER TABLE payer_plan_period ADD CONSTRAINT xpk_payer_plan_period PRIMARY KEY ( payer_plan_period_id ) ;
|
||||
|
||||
ALTER TABLE cost ADD CONSTRAINT xpk_visit_cost PRIMARY KEY ( cost_id ) ;
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized derived elements
|
||||
|
||||
************************/
|
||||
|
||||
ALTER TABLE cohort ADD CONSTRAINT xpk_cohort PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date ) ;
|
||||
|
||||
ALTER TABLE cohort_attribute ADD CONSTRAINT xpk_cohort_attribute PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date, attribute_definition_id ) ;
|
||||
|
||||
ALTER TABLE drug_era ADD CONSTRAINT xpk_drug_era PRIMARY KEY ( drug_era_id ) ;
|
||||
|
||||
ALTER TABLE dose_era ADD CONSTRAINT xpk_dose_era PRIMARY KEY ( dose_era_id ) ;
|
||||
|
||||
ALTER TABLE condition_era ADD CONSTRAINT xpk_condition_era PRIMARY KEY ( condition_era_id ) ;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
*************************
|
||||
*************************
|
||||
*************************
|
||||
|
||||
Foreign key constraints
|
||||
|
||||
*************************
|
||||
*************************
|
||||
*************************
|
||||
************************/
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized vocabulary
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
ALTER TABLE concept ADD CONSTRAINT fpk_concept_domain FOREIGN KEY (domain_id) REFERENCES domain (domain_id);
|
||||
|
||||
ALTER TABLE concept ADD CONSTRAINT fpk_concept_class FOREIGN KEY (concept_class_id) REFERENCES concept_class (concept_class_id);
|
||||
|
||||
ALTER TABLE concept ADD CONSTRAINT fpk_concept_vocabulary FOREIGN KEY (vocabulary_id) REFERENCES vocabulary (vocabulary_id);
|
||||
|
||||
ALTER TABLE vocabulary ADD CONSTRAINT fpk_vocabulary_concept FOREIGN KEY (vocabulary_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE domain ADD CONSTRAINT fpk_domain_concept FOREIGN KEY (domain_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE concept_class ADD CONSTRAINT fpk_concept_class_concept FOREIGN KEY (concept_class_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_1 FOREIGN KEY (concept_id_1) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_2 FOREIGN KEY (concept_id_2) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_id FOREIGN KEY (relationship_id) REFERENCES relationship (relationship_id);
|
||||
|
||||
ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_concept FOREIGN KEY (relationship_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_reverse FOREIGN KEY (reverse_relationship_id) REFERENCES relationship (relationship_id);
|
||||
|
||||
ALTER TABLE concept_synonym ADD CONSTRAINT fpk_concept_synonym_concept FOREIGN KEY (concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_1 FOREIGN KEY (ancestor_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_2 FOREIGN KEY (descendant_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_1 FOREIGN KEY (source_vocabulary_id) REFERENCES vocabulary (vocabulary_id);
|
||||
|
||||
ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_2 FOREIGN KEY (target_vocabulary_id) REFERENCES vocabulary (vocabulary_id);
|
||||
|
||||
ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_c_1 FOREIGN KEY (target_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_1 FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_2 FOREIGN KEY (ingredient_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_1 FOREIGN KEY (amount_unit_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_2 FOREIGN KEY (numerator_unit_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_3 FOREIGN KEY (denominator_unit_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_cohort_definition_concept FOREIGN KEY (definition_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
/**************************
|
||||
|
||||
Standardized meta-data
|
||||
|
||||
***************************/
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized clinical data
|
||||
|
||||
************************/
|
||||
|
||||
ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept FOREIGN KEY (gender_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept FOREIGN KEY (race_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept FOREIGN KEY (ethnicity_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept_s FOREIGN KEY (gender_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept_s FOREIGN KEY (race_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept_s FOREIGN KEY (ethnicity_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE person ADD CONSTRAINT fpk_person_location FOREIGN KEY (location_id) REFERENCES location (location_id);
|
||||
|
||||
ALTER TABLE person ADD CONSTRAINT fpk_person_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||
|
||||
ALTER TABLE person ADD CONSTRAINT fpk_person_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
|
||||
|
||||
|
||||
ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_concept FOREIGN KEY (period_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_concept FOREIGN KEY (specimen_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_type_concept FOREIGN KEY (specimen_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_unit_concept FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_site_concept FOREIGN KEY (anatomic_site_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_status_concept FOREIGN KEY (disease_status_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE death ADD CONSTRAINT fpk_death_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE death ADD CONSTRAINT fpk_death_type_concept FOREIGN KEY (death_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE death ADD CONSTRAINT fpk_death_cause_concept FOREIGN KEY (cause_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE death ADD CONSTRAINT fpk_death_cause_concept_s FOREIGN KEY (cause_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept FOREIGN KEY (visit_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_type_concept FOREIGN KEY (visit_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||
|
||||
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
|
||||
|
||||
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept_s FOREIGN KEY (visit_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_admitting_s FOREIGN KEY (admitting_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_discharge FOREIGN KEY (discharge_to_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept FOREIGN KEY (procedure_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_type_concept FOREIGN KEY (procedure_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_modifier FOREIGN KEY (modifier_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||
|
||||
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept_s FOREIGN KEY (procedure_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_type_concept FOREIGN KEY (drug_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_route_concept FOREIGN KEY (route_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||
|
||||
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept_s FOREIGN KEY (drug_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept FOREIGN KEY (device_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_type_concept FOREIGN KEY (device_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||
|
||||
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept_s FOREIGN KEY (device_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_type_concept FOREIGN KEY (condition_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||
|
||||
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept_s FOREIGN KEY (condition_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_status_concept FOREIGN KEY (condition_status_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_concept FOREIGN KEY (measurement_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_type_concept FOREIGN KEY (measurement_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_operator FOREIGN KEY (operator_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_unit FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_concept_s FOREIGN KEY (measurement_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE note ADD CONSTRAINT fpk_note_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE note ADD CONSTRAINT fpk_note_type_concept FOREIGN KEY (note_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE note ADD CONSTRAINT fpk_note_class_concept FOREIGN KEY (note_class_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE note ADD CONSTRAINT fpk_note_encoding_concept FOREIGN KEY (encoding_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE note ADD CONSTRAINT fpk_language_concept FOREIGN KEY (language_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE note ADD CONSTRAINT fpk_note_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||
|
||||
ALTER TABLE note ADD CONSTRAINT fpk_note_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
|
||||
ALTER TABLE note_nlp ADD CONSTRAINT fpk_note_nlp_note FOREIGN KEY (note_id) REFERENCES note (note_id);
|
||||
|
||||
ALTER TABLE note_nlp ADD CONSTRAINT fpk_note_nlp_section_concept FOREIGN KEY (section_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE note_nlp ADD CONSTRAINT fpk_note_nlp_concept FOREIGN KEY (note_nlp_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept FOREIGN KEY (observation_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_type_concept FOREIGN KEY (observation_type_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_qualifier FOREIGN KEY (qualifier_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_unit FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept_s FOREIGN KEY (observation_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_1 FOREIGN KEY (domain_concept_id_1) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_2 FOREIGN KEY (domain_concept_id_2) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_relationship FOREIGN KEY (relationship_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health system data
|
||||
|
||||
************************/
|
||||
|
||||
ALTER TABLE care_site ADD CONSTRAINT fpk_care_site_location FOREIGN KEY (location_id) REFERENCES location (location_id);
|
||||
|
||||
ALTER TABLE care_site ADD CONSTRAINT fpk_care_site_place FOREIGN KEY (place_of_service_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE provider ADD CONSTRAINT fpk_provider_specialty FOREIGN KEY (specialty_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE provider ADD CONSTRAINT fpk_provider_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
|
||||
|
||||
ALTER TABLE provider ADD CONSTRAINT fpk_provider_gender FOREIGN KEY (gender_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE provider ADD CONSTRAINT fpk_provider_specialty_s FOREIGN KEY (specialty_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE provider ADD CONSTRAINT fpk_provider_gender_s FOREIGN KEY (gender_source_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health economics
|
||||
|
||||
************************/
|
||||
|
||||
ALTER TABLE payer_plan_period ADD CONSTRAINT fpk_payer_plan_period FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE cost ADD CONSTRAINT fpk_visit_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE cost ADD CONSTRAINT fpk_visit_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
|
||||
|
||||
ALTER TABLE cost ADD CONSTRAINT fpk_drg_concept FOREIGN KEY (drg_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
/************************
|
||||
|
||||
Standardized derived elements
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
ALTER TABLE cohort ADD CONSTRAINT fpk_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
|
||||
|
||||
|
||||
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
|
||||
|
||||
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_attribute_definition FOREIGN KEY (attribute_definition_id) REFERENCES attribute_definition (attribute_definition_id);
|
||||
|
||||
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_unit_concept FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||
|
||||
ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id);
|
||||
|
|
@ -0,0 +1,232 @@
|
|||
/*********************************************************************************
|
||||
# Copyright 2014 Observational Health Data Sciences and Informatics
|
||||
#
|
||||
#
|
||||
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||
# you may not use this file except in compliance with the License.
|
||||
# You may obtain a copy of the License at
|
||||
#
|
||||
# http://www.apache.org/licenses/LICENSE-2.0
|
||||
#
|
||||
# Unless required by applicable law or agreed to in writing, software
|
||||
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
# See the License for the specific language governing permissions and
|
||||
# limitations under the License.
|
||||
********************************************************************************/
|
||||
|
||||
/************************
|
||||
|
||||
####### # # ####### ###### ##### ###### # # ####### ##### ###
|
||||
# # ## ## # # # # # # # # ## ## # # # # # # # # ##### ###### # # ###### ####
|
||||
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||||
####### # # ####### # ##### ###### # # ## ##### ### ##### ### # # ##### ###### # # ###### ####
|
||||
|
||||
|
||||
oracle script to create the required indexes within OMOP common data model, version 5.3
|
||||
|
||||
last revised: 14-November-2017
|
||||
|
||||
author: Patrick Ryan, Clair Blacketer
|
||||
|
||||
description: These indices are considered a minimal requirement to ensure adequate performance of analyses.
|
||||
|
||||
*************************/
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized vocabulary
|
||||
|
||||
************************/
|
||||
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'CREATE UNIQUE INDEX idx_concept_concept_id ON concept (concept_id ASC)';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -1408 THEN
|
||||
RAISE;
|
||||
END IF;
|
||||
END;
|
||||
CREATE INDEX idx_concept_code ON concept (concept_code ASC);
|
||||
CREATE INDEX idx_concept_vocabluary_id ON concept (vocabulary_id ASC);
|
||||
CREATE INDEX idx_concept_domain_id ON concept (domain_id ASC);
|
||||
CREATE INDEX idx_concept_class_id ON concept (concept_class_id ASC);
|
||||
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'CREATE UNIQUE INDEX idx_vocabulary_vocabulary_id ON vocabulary (vocabulary_id ASC)';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -1408 THEN
|
||||
RAISE;
|
||||
END IF;
|
||||
END;
|
||||
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'CREATE UNIQUE INDEX idx_domain_domain_id ON domain (domain_id ASC)';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -1408 THEN
|
||||
RAISE;
|
||||
END IF;
|
||||
END;
|
||||
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'CREATE UNIQUE INDEX idx_concept_class_class_id ON concept_class (concept_class_id ASC)';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -1408 THEN
|
||||
RAISE;
|
||||
END IF;
|
||||
END;
|
||||
|
||||
CREATE INDEX idx_concept_relationship_id_1 ON concept_relationship (concept_id_1 ASC);
|
||||
CREATE INDEX idx_concept_relationship_id_2 ON concept_relationship (concept_id_2 ASC);
|
||||
CREATE INDEX idx_concept_relationship_id_3 ON concept_relationship (relationship_id ASC);
|
||||
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'CREATE UNIQUE INDEX idx_relationship_rel_id ON relationship (relationship_id ASC)';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -1408 THEN
|
||||
RAISE;
|
||||
END IF;
|
||||
END;
|
||||
|
||||
CREATE INDEX idx_concept_synonym_id ON concept_synonym (concept_id ASC);
|
||||
|
||||
CREATE INDEX idx_concept_ancestor_id_1 ON concept_ancestor (ancestor_concept_id ASC);
|
||||
CREATE INDEX idx_concept_ancestor_id_2 ON concept_ancestor (descendant_concept_id ASC);
|
||||
|
||||
CREATE INDEX idx_source_to_concept_map_id_3 ON source_to_concept_map (target_concept_id ASC);
|
||||
CREATE INDEX idx_source_to_concept_map_id_1 ON source_to_concept_map (source_vocabulary_id ASC);
|
||||
CREATE INDEX idx_source_to_concept_map_id_2 ON source_to_concept_map (target_vocabulary_id ASC);
|
||||
CREATE INDEX idx_source_to_concept_map_code ON source_to_concept_map (source_code ASC);
|
||||
|
||||
CREATE INDEX idx_drug_strength_id_1 ON drug_strength (drug_concept_id ASC);
|
||||
CREATE INDEX idx_drug_strength_id_2 ON drug_strength (ingredient_concept_id ASC);
|
||||
|
||||
CREATE INDEX idx_cohort_definition_id ON cohort_definition (cohort_definition_id ASC);
|
||||
|
||||
CREATE INDEX idx_attribute_definition_id ON attribute_definition (attribute_definition_id ASC);
|
||||
|
||||
|
||||
/**************************
|
||||
|
||||
Standardized meta-data
|
||||
|
||||
***************************/
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized clinical data
|
||||
|
||||
************************/
|
||||
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'CREATE UNIQUE INDEX idx_person_id ON person (person_id ASC)';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -1408 THEN
|
||||
RAISE;
|
||||
END IF;
|
||||
END;
|
||||
|
||||
CREATE INDEX idx_observation_period_id ON observation_period (person_id ASC);
|
||||
|
||||
CREATE INDEX idx_specimen_person_id ON specimen (person_id ASC);
|
||||
CREATE INDEX idx_specimen_concept_id ON specimen (specimen_concept_id ASC);
|
||||
|
||||
CREATE INDEX idx_death_person_id ON death (person_id ASC);
|
||||
|
||||
CREATE INDEX idx_visit_person_id ON visit_occurrence (person_id ASC);
|
||||
CREATE INDEX idx_visit_concept_id ON visit_occurrence (visit_concept_id ASC);
|
||||
|
||||
CREATE INDEX idx_procedure_person_id ON procedure_occurrence (person_id ASC);
|
||||
CREATE INDEX idx_procedure_concept_id ON procedure_occurrence (procedure_concept_id ASC);
|
||||
CREATE INDEX idx_procedure_visit_id ON procedure_occurrence (visit_occurrence_id ASC);
|
||||
|
||||
CREATE INDEX idx_drug_person_id ON drug_exposure (person_id ASC);
|
||||
CREATE INDEX idx_drug_concept_id ON drug_exposure (drug_concept_id ASC);
|
||||
CREATE INDEX idx_drug_visit_id ON drug_exposure (visit_occurrence_id ASC);
|
||||
|
||||
CREATE INDEX idx_device_person_id ON device_exposure (person_id ASC);
|
||||
CREATE INDEX idx_device_concept_id ON device_exposure (device_concept_id ASC);
|
||||
CREATE INDEX idx_device_visit_id ON device_exposure (visit_occurrence_id ASC);
|
||||
|
||||
CREATE INDEX idx_condition_person_id ON condition_occurrence (person_id ASC);
|
||||
CREATE INDEX idx_condition_concept_id ON condition_occurrence (condition_concept_id ASC);
|
||||
CREATE INDEX idx_condition_visit_id ON condition_occurrence (visit_occurrence_id ASC);
|
||||
|
||||
CREATE INDEX idx_measurement_person_id ON measurement (person_id ASC);
|
||||
CREATE INDEX idx_measurement_concept_id ON measurement (measurement_concept_id ASC);
|
||||
CREATE INDEX idx_measurement_visit_id ON measurement (visit_occurrence_id ASC);
|
||||
|
||||
CREATE INDEX idx_note_person_id ON note (person_id ASC);
|
||||
CREATE INDEX idx_note_concept_id ON note (note_type_concept_id ASC);
|
||||
CREATE INDEX idx_note_visit_id ON note (visit_occurrence_id ASC);
|
||||
|
||||
CREATE INDEX idx_note_nlp_note_id ON note_nlp (note_id ASC);
|
||||
CREATE INDEX idx_note_nlp_concept_id ON note_nlp (note_nlp_concept_id ASC);
|
||||
|
||||
CREATE INDEX idx_observation_person_id ON observation (person_id ASC);
|
||||
CREATE INDEX idx_observation_concept_id ON observation (observation_concept_id ASC);
|
||||
CREATE INDEX idx_observation_visit_id ON observation (visit_occurrence_id ASC);
|
||||
|
||||
CREATE INDEX idx_fact_relationship_id_1 ON fact_relationship (domain_concept_id_1 ASC);
|
||||
CREATE INDEX idx_fact_relationship_id_2 ON fact_relationship (domain_concept_id_2 ASC);
|
||||
CREATE INDEX idx_fact_relationship_id_3 ON fact_relationship (relationship_concept_id ASC);
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health system data
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health economics
|
||||
|
||||
************************/
|
||||
|
||||
CREATE INDEX idx_period_person_id ON payer_plan_period (person_id ASC);
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized derived elements
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
CREATE INDEX idx_cohort_subject_id ON cohort (subject_id ASC);
|
||||
CREATE INDEX idx_cohort_c_definition_id ON cohort (cohort_definition_id ASC);
|
||||
|
||||
CREATE INDEX idx_ca_subject_id ON cohort_attribute (subject_id ASC);
|
||||
CREATE INDEX idx_ca_definition_id ON cohort_attribute (cohort_definition_id ASC);
|
||||
|
||||
CREATE INDEX idx_drug_era_person_id ON drug_era (person_id ASC);
|
||||
CREATE INDEX idx_drug_era_concept_id ON drug_era (drug_concept_id ASC);
|
||||
|
||||
CREATE INDEX idx_dose_era_person_id ON dose_era (person_id ASC);
|
||||
CREATE INDEX idx_dose_era_concept_id ON dose_era (drug_concept_id ASC);
|
||||
|
||||
CREATE INDEX idx_condition_era_person_id ON condition_era (person_id ASC);
|
||||
CREATE INDEX idx_condition_era_concept_id ON condition_era (condition_concept_id ASC);
|
||||
|
||||
Loading…
Reference in New Issue