Added code for index

This commit is contained in:
Blacketer 2017-11-14 15:19:03 -05:00
parent f298b0c446
commit 97a97f3bcb
3 changed files with 233 additions and 0 deletions

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# Copyright 2017 Observational Health Data Sciences and Informatics
#
# This file is part of DDLGeneratr
#
# 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.
#' Write Index script
#'
#' @param targetdialect The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"
#'
#' @export
writeIndex <- function(targetdialect) {
if(!dir.exists("output")){
dir.create("output")
}
if(!dir.exists(paste0("output/",targetdialect))){
dir.create(paste0("output/",targetdialect))
}
sql <- SqlRender::loadRenderTranslateSql(sqlFilename = "OMOP CDM indexes required.sql",
packageName = "DDLGeneratr",
dbms = targetdialect,
targetdialect = targetdialect)
SqlRender::writeSql(sql = sql,
targetFile = paste0("output/",targetdialect,"/OMOP CDM ",targetdialect," indices.txt"))
}

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@ -14,6 +14,10 @@ writeDDL("postgresql")
writeDDL("redshift") writeDDL("redshift")
writeDDL("sql server") writeDDL("sql server")
# Step 3: Run the following code to create indices for Oracle, Postgres, PDW and Sql Server
writeIndex("oracle")
# Step 3: Update the .md wiki files with the changes for the new version # Step 3: Update the .md wiki files with the changes for the new version
# step 4: Run the following code to create the pdf documentation. It will be written to the reports folder. # step 4: Run the following code to create the pdf documentation. It will be written to the reports folder.

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/*********************************************************************************
# 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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@targetdialect 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
************************/
CREATE UNIQUE CLUSTERED INDEX idx_concept_concept_id ON concept (concept_id ASC);
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);
CREATE UNIQUE CLUSTERED INDEX idx_vocabulary_vocabulary_id ON vocabulary (vocabulary_id ASC);
CREATE UNIQUE CLUSTERED INDEX idx_domain_domain_id ON domain (domain_id ASC);
CREATE UNIQUE CLUSTERED INDEX idx_concept_class_class_id ON concept_class (concept_class_id ASC);
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);
CREATE UNIQUE CLUSTERED INDEX idx_relationship_rel_id ON relationship (relationship_id ASC);
CREATE CLUSTERED INDEX idx_concept_synonym_id ON concept_synonym (concept_id ASC);
CREATE CLUSTERED 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 CLUSTERED 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 CLUSTERED 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 CLUSTERED INDEX idx_cohort_definition_id ON cohort_definition (cohort_definition_id ASC);
CREATE CLUSTERED INDEX idx_attribute_definition_id ON attribute_definition (attribute_definition_id ASC);
/**************************
Standardized meta-data
***************************/
/************************
Standardized clinical data
************************/
CREATE UNIQUE CLUSTERED INDEX idx_person_id ON person (person_id ASC);
CREATE CLUSTERED INDEX idx_observation_period_id ON observation_period (person_id ASC);
CREATE CLUSTERED INDEX idx_specimen_person_id ON specimen (person_id ASC);
CREATE INDEX idx_specimen_concept_id ON specimen (specimen_concept_id ASC);
CREATE CLUSTERED INDEX idx_death_person_id ON death (person_id ASC);
CREATE CLUSTERED 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 CLUSTERED 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 CLUSTERED 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 CLUSTERED 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 CLUSTERED 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 CLUSTERED 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 CLUSTERED 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 CLUSTERED 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 CLUSTERED 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 CLUSTERED 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 CLUSTERED 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 CLUSTERED 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 CLUSTERED 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);