/*********************************************************************************
# 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.
********************************************************************************/

/************************

 ####### #     # ####### ######      #####  ######  #     #           #######      #####     ###                                           
 #     # ##   ## #     # #     #    #     # #     # ##   ##    #    # #           #     #     #  #    # #####  ###### #    # ######  ####  
 #     # # # # # #     # #     #    #       #     # # # # #    #    # #                 #     #  ##   # #    # #       #  #  #      #      
 #     # #  #  # #     # ######     #       #     # #  #  #    #    # ######       #####      #  # #  # #    # #####    ##   #####   ####  
 #     # #     # #     # #          #       #     # #     #    #    #       # ### #           #  #  # # #    # #        ##   #           # 
 #     # #     # #     # #          #     # #     # #     #     #  #  #     # ### #           #  #   ## #    # #       #  #  #      #    # 
 ####### #     # ####### #           #####  ######  #     #      ##    #####  ### #######    ### #    # #####  ###### #    # ######  ####  
                                                                              

script to create the required indexes within OMOP common data model, version 5.2 for SQL Server database

last revised: 14-July-2017

author:  Patrick Ryan

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);