Added code for index
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Blacketer
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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 Index 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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writeIndex <- 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 indexes required.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," indices.txt"))
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}
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@ -14,6 +14,10 @@ writeDDL("postgresql")
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writeDDL("redshift")
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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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# 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 the pdf documentation. It will be written to the reports folder.
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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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@targetdialect script to create the required indexes within OMOP common data model, version 5.3
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last revised: 14-November-2017
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author: Patrick Ryan, Clair Blacketer
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description: These indices are considered a minimal requirement to ensure adequate performance of analyses.
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*************************/
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/************************
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Standardized vocabulary
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************************/
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CREATE UNIQUE CLUSTERED INDEX idx_concept_concept_id ON concept (concept_id ASC);
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CREATE INDEX idx_concept_code ON concept (concept_code ASC);
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CREATE INDEX idx_concept_vocabluary_id ON concept (vocabulary_id ASC);
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CREATE INDEX idx_concept_domain_id ON concept (domain_id ASC);
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CREATE INDEX idx_concept_class_id ON concept (concept_class_id ASC);
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CREATE UNIQUE CLUSTERED INDEX idx_vocabulary_vocabulary_id ON vocabulary (vocabulary_id ASC);
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CREATE UNIQUE CLUSTERED INDEX idx_domain_domain_id ON domain (domain_id ASC);
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CREATE UNIQUE CLUSTERED INDEX idx_concept_class_class_id ON concept_class (concept_class_id ASC);
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CREATE INDEX idx_concept_relationship_id_1 ON concept_relationship (concept_id_1 ASC);
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CREATE INDEX idx_concept_relationship_id_2 ON concept_relationship (concept_id_2 ASC);
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CREATE INDEX idx_concept_relationship_id_3 ON concept_relationship (relationship_id ASC);
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CREATE UNIQUE CLUSTERED INDEX idx_relationship_rel_id ON relationship (relationship_id ASC);
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CREATE CLUSTERED INDEX idx_concept_synonym_id ON concept_synonym (concept_id ASC);
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CREATE CLUSTERED INDEX idx_concept_ancestor_id_1 ON concept_ancestor (ancestor_concept_id ASC);
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CREATE INDEX idx_concept_ancestor_id_2 ON concept_ancestor (descendant_concept_id ASC);
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CREATE CLUSTERED INDEX idx_source_to_concept_map_id_3 ON source_to_concept_map (target_concept_id ASC);
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CREATE INDEX idx_source_to_concept_map_id_1 ON source_to_concept_map (source_vocabulary_id ASC);
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CREATE INDEX idx_source_to_concept_map_id_2 ON source_to_concept_map (target_vocabulary_id ASC);
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CREATE INDEX idx_source_to_concept_map_code ON source_to_concept_map (source_code ASC);
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CREATE CLUSTERED INDEX idx_drug_strength_id_1 ON drug_strength (drug_concept_id ASC);
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CREATE INDEX idx_drug_strength_id_2 ON drug_strength (ingredient_concept_id ASC);
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CREATE CLUSTERED INDEX idx_cohort_definition_id ON cohort_definition (cohort_definition_id ASC);
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CREATE CLUSTERED INDEX idx_attribute_definition_id ON attribute_definition (attribute_definition_id ASC);
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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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CREATE UNIQUE CLUSTERED INDEX idx_person_id ON person (person_id ASC);
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CREATE CLUSTERED INDEX idx_observation_period_id ON observation_period (person_id ASC);
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CREATE CLUSTERED INDEX idx_specimen_person_id ON specimen (person_id ASC);
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CREATE INDEX idx_specimen_concept_id ON specimen (specimen_concept_id ASC);
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CREATE CLUSTERED INDEX idx_death_person_id ON death (person_id ASC);
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CREATE CLUSTERED INDEX idx_visit_person_id ON visit_occurrence (person_id ASC);
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CREATE INDEX idx_visit_concept_id ON visit_occurrence (visit_concept_id ASC);
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CREATE CLUSTERED INDEX idx_procedure_person_id ON procedure_occurrence (person_id ASC);
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CREATE INDEX idx_procedure_concept_id ON procedure_occurrence (procedure_concept_id ASC);
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CREATE INDEX idx_procedure_visit_id ON procedure_occurrence (visit_occurrence_id ASC);
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CREATE CLUSTERED INDEX idx_drug_person_id ON drug_exposure (person_id ASC);
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CREATE INDEX idx_drug_concept_id ON drug_exposure (drug_concept_id ASC);
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CREATE INDEX idx_drug_visit_id ON drug_exposure (visit_occurrence_id ASC);
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CREATE CLUSTERED INDEX idx_device_person_id ON device_exposure (person_id ASC);
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CREATE INDEX idx_device_concept_id ON device_exposure (device_concept_id ASC);
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CREATE INDEX idx_device_visit_id ON device_exposure (visit_occurrence_id ASC);
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CREATE CLUSTERED INDEX idx_condition_person_id ON condition_occurrence (person_id ASC);
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CREATE INDEX idx_condition_concept_id ON condition_occurrence (condition_concept_id ASC);
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CREATE INDEX idx_condition_visit_id ON condition_occurrence (visit_occurrence_id ASC);
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CREATE CLUSTERED INDEX idx_measurement_person_id ON measurement (person_id ASC);
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CREATE INDEX idx_measurement_concept_id ON measurement (measurement_concept_id ASC);
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CREATE INDEX idx_measurement_visit_id ON measurement (visit_occurrence_id ASC);
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CREATE CLUSTERED INDEX idx_note_person_id ON note (person_id ASC);
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CREATE INDEX idx_note_concept_id ON note (note_type_concept_id ASC);
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CREATE INDEX idx_note_visit_id ON note (visit_occurrence_id ASC);
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CREATE CLUSTERED INDEX idx_note_nlp_note_id ON note_nlp (note_id ASC);
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CREATE INDEX idx_note_nlp_concept_id ON note_nlp (note_nlp_concept_id ASC);
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CREATE CLUSTERED INDEX idx_observation_person_id ON observation (person_id ASC);
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CREATE INDEX idx_observation_concept_id ON observation (observation_concept_id ASC);
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CREATE INDEX idx_observation_visit_id ON observation (visit_occurrence_id ASC);
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CREATE INDEX idx_fact_relationship_id_1 ON fact_relationship (domain_concept_id_1 ASC);
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CREATE INDEX idx_fact_relationship_id_2 ON fact_relationship (domain_concept_id_2 ASC);
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CREATE INDEX idx_fact_relationship_id_3 ON fact_relationship (relationship_concept_id ASC);
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/************************
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Standardized health system data
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************************/
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/************************
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Standardized health economics
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************************/
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CREATE CLUSTERED INDEX idx_period_person_id ON payer_plan_period (person_id ASC);
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/************************
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Standardized derived elements
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************************/
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CREATE INDEX idx_cohort_subject_id ON cohort (subject_id ASC);
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CREATE INDEX idx_cohort_c_definition_id ON cohort (cohort_definition_id ASC);
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CREATE INDEX idx_ca_subject_id ON cohort_attribute (subject_id ASC);
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CREATE INDEX idx_ca_definition_id ON cohort_attribute (cohort_definition_id ASC);
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CREATE CLUSTERED INDEX idx_drug_era_person_id ON drug_era (person_id ASC);
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CREATE INDEX idx_drug_era_concept_id ON drug_era (drug_concept_id ASC);
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CREATE CLUSTERED INDEX idx_dose_era_person_id ON dose_era (person_id ASC);
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CREATE INDEX idx_dose_era_concept_id ON dose_era (drug_concept_id ASC);
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CREATE CLUSTERED INDEX idx_condition_era_person_id ON condition_era (person_id ASC);
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CREATE INDEX idx_condition_era_concept_id ON condition_era (condition_concept_id ASC);
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