/*********************************************************************************
# 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
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#     http://www.apache.org/licenses/LICENSE-2.0
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# 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
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********************************************************************************/

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postgresql script to create the required primary keys and indices within the OMOP common data model, version 6.0

last revised: 30-Aug-2017

author:  Patrick Ryan, Clair Blacketer

description:  These primary keys and indices are considered a minimal requirement to ensure adequate performance of analyses.

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Primary key constraints

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

Standardized vocabulary

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ALTER TABLE ohdsi.concept ADD CONSTRAINT xpk_concept PRIMARY KEY (concept_id);

ALTER TABLE ohdsi.vocabulary ADD CONSTRAINT xpk_vocabulary PRIMARY KEY (vocabulary_id);

ALTER TABLE ohdsi.domain ADD CONSTRAINT xpk_domain PRIMARY KEY (domain_id);

ALTER TABLE ohdsi.concept_class ADD CONSTRAINT xpk_concept_class PRIMARY KEY (concept_class_id);

ALTER TABLE ohdsi.concept_relationship ADD CONSTRAINT xpk_concept_relationship PRIMARY KEY (concept_id_1,concept_id_2,relationship_id);

ALTER TABLE ohdsi.relationship ADD CONSTRAINT xpk_relationship PRIMARY KEY (relationship_id);

ALTER TABLE ohdsi.concept_ancestor ADD CONSTRAINT xpk_concept_ancestor PRIMARY KEY (ancestor_concept_id,descendant_concept_id);

ALTER TABLE ohdsi.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 ohdsi.drug_strength ADD CONSTRAINT xpk_drug_strength PRIMARY KEY (drug_concept_id, ingredient_concept_id);


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

Standardized meta-data

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

Standardized clinical data

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/**PRIMARY KEY NONCLUSTERED constraints**/

ALTER TABLE ohdsi.person ADD CONSTRAINT xpk_person PRIMARY KEY ( person_id ) ;

ALTER TABLE ohdsi.observation_period ADD CONSTRAINT xpk_observation_period PRIMARY KEY ( observation_period_id ) ;

ALTER TABLE ohdsi.specimen ADD CONSTRAINT xpk_specimen PRIMARY KEY ( specimen_id ) ;

ALTER TABLE ohdsi.visit_occurrence ADD CONSTRAINT xpk_visit_occurrence PRIMARY KEY ( visit_occurrence_id ) ;

ALTER TABLE ohdsi.visit_detail ADD CONSTRAINT xpk_visit_detail PRIMARY KEY ( visit_detail_id ) ;

ALTER TABLE ohdsi.procedure_occurrence ADD CONSTRAINT xpk_procedure_occurrence PRIMARY KEY ( procedure_occurrence_id ) ;

ALTER TABLE ohdsi.drug_exposure ADD CONSTRAINT xpk_drug_exposure PRIMARY KEY ( drug_exposure_id ) ;

ALTER TABLE ohdsi.device_exposure ADD CONSTRAINT xpk_device_exposure PRIMARY KEY ( device_exposure_id ) ;

ALTER TABLE ohdsi.condition_occurrence ADD CONSTRAINT xpk_condition_occurrence PRIMARY KEY ( condition_occurrence_id ) ;

ALTER TABLE ohdsi.measurement ADD CONSTRAINT xpk_measurement PRIMARY KEY ( measurement_id ) ;

ALTER TABLE ohdsi.note ADD CONSTRAINT xpk_note PRIMARY KEY ( note_id ) ;

ALTER TABLE ohdsi.note_nlp ADD CONSTRAINT xpk_note_nlp PRIMARY KEY ( note_nlp_id ) ;

ALTER TABLE ohdsi.observation  ADD CONSTRAINT xpk_observation PRIMARY KEY ( observation_id ) ;

ALTER TABLE ohdsi.survey_conduct ADD CONSTRAINT xpk_survey PRIMARY KEY ( survey_conduct_id ) ;

ALTER TABLE ohdsi.episode ADD CONSTRAINT episode_pk PRIMARY KEY ( episode_id);

ALTER TABLE ohdsi.episode_event ADD CONSTRAINT episode_event_pk PRIMARY KEY ( episode_id, event_id, event_field_concept_id );


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

Standardized health system data

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ALTER TABLE ohdsi.location ADD CONSTRAINT xpk_location PRIMARY KEY ( location_id ) ;

ALTER TABLE ohdsi.location_history ADD CONSTRAINT xpk_location_history PRIMARY KEY ( location_history_id ) ;

ALTER TABLE ohdsi.care_site ADD CONSTRAINT xpk_care_site PRIMARY KEY ( care_site_id ) ;

ALTER TABLE ohdsi.provider ADD CONSTRAINT xpk_provider PRIMARY KEY ( provider_id ) ;



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

Standardized health economics

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ALTER TABLE ohdsi.payer_plan_period ADD CONSTRAINT xpk_payer_plan_period PRIMARY KEY ( payer_plan_period_id ) ;

ALTER TABLE ohdsi.cost ADD CONSTRAINT xpk_visit_cost PRIMARY KEY ( cost_id ) ;


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

Standardized derived elements

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ALTER TABLE ohdsi.drug_era ADD CONSTRAINT xpk_drug_era PRIMARY KEY ( drug_era_id ) ;

ALTER TABLE ohdsi.dose_era  ADD CONSTRAINT xpk_dose_era PRIMARY KEY ( dose_era_id ) ;

ALTER TABLE ohdsi.condition_era ADD CONSTRAINT xpk_condition_era PRIMARY KEY ( condition_era_id ) ;


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Indices

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

Standardized vocabulary

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CREATE UNIQUE INDEX idx_concept_concept_id  ON ohdsi.concept  (concept_id ASC);
CLUSTER ohdsi.concept  USING idx_concept_concept_id ;
CREATE INDEX idx_concept_code ON ohdsi.concept (concept_code ASC);
CREATE INDEX idx_concept_vocabluary_id ON ohdsi.concept (vocabulary_id ASC);
CREATE INDEX idx_concept_domain_id ON ohdsi.concept (domain_id ASC);
CREATE INDEX idx_concept_class_id ON ohdsi.concept (concept_class_id ASC);

CREATE UNIQUE INDEX idx_vocabulary_vocabulary_id  ON ohdsi.vocabulary  (vocabulary_id ASC);
CLUSTER ohdsi.vocabulary  USING idx_vocabulary_vocabulary_id ;

CREATE UNIQUE INDEX idx_domain_domain_id  ON ohdsi.domain  (domain_id ASC);
CLUSTER ohdsi.domain  USING idx_domain_domain_id ;

CREATE UNIQUE INDEX idx_concept_class_class_id  ON ohdsi.concept_class  (concept_class_id ASC);
CLUSTER ohdsi.concept_class  USING idx_concept_class_class_id ;

CREATE INDEX idx_concept_relationship_id_1 ON ohdsi.concept_relationship (concept_id_1 ASC);
CREATE INDEX idx_concept_relationship_id_2 ON ohdsi.concept_relationship (concept_id_2 ASC);
CREATE INDEX idx_concept_relationship_id_3 ON ohdsi.concept_relationship (relationship_id ASC);

CREATE UNIQUE INDEX idx_relationship_rel_id  ON ohdsi.relationship  (relationship_id ASC);
CLUSTER ohdsi.relationship  USING idx_relationship_rel_id ;

CREATE INDEX idx_concept_synonym_id  ON ohdsi.concept_synonym  (concept_id ASC);
CLUSTER ohdsi.concept_synonym  USING idx_concept_synonym_id ;

CREATE INDEX idx_concept_ancestor_id_1  ON ohdsi.concept_ancestor  (ancestor_concept_id ASC);
CLUSTER ohdsi.concept_ancestor  USING idx_concept_ancestor_id_1 ;
CREATE INDEX idx_concept_ancestor_id_2 ON ohdsi.concept_ancestor (descendant_concept_id ASC);

CREATE INDEX idx_source_to_concept_map_3  ON ohdsi.source_to_concept_map  (target_concept_id ASC);
CLUSTER ohdsi.source_to_concept_map  USING idx_source_to_concept_map_3 ;
CREATE INDEX idx_source_to_concept_map_1 ON ohdsi.source_to_concept_map (source_vocabulary_id ASC);
CREATE INDEX idx_source_to_concept_map_2 ON ohdsi.source_to_concept_map (target_vocabulary_id ASC);
CREATE INDEX idx_source_to_concept_map_c ON ohdsi.source_to_concept_map (source_code ASC);

CREATE INDEX idx_drug_strength_id_1  ON ohdsi.drug_strength  (drug_concept_id ASC);
CLUSTER ohdsi.drug_strength  USING idx_drug_strength_id_1 ;
CREATE INDEX idx_drug_strength_id_2 ON ohdsi.drug_strength (ingredient_concept_id ASC);


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

Standardized meta-data

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

CREATE INDEX idx_metadata_concept_id_1 ON ohdsi.metadata (metadata_concept_id ASC);

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

Standardized clinical data

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CREATE UNIQUE INDEX idx_person_id  ON ohdsi.person  (person_id ASC);
CLUSTER ohdsi.person  USING idx_person_id ;

CREATE INDEX idx_observation_period_id_1  ON ohdsi.observation_period  (person_id ASC);
CLUSTER ohdsi.observation_period  USING idx_observation_period_id_1 ;

CREATE INDEX idx_specimen_person_id_1  ON ohdsi.specimen  (person_id ASC);
CLUSTER ohdsi.specimen  USING idx_specimen_person_id_1 ;
CREATE INDEX idx_specimen_concept_id_1 ON ohdsi.specimen (specimen_concept_id ASC);

CREATE INDEX idx_visit_person_id_1  ON ohdsi.visit_occurrence  (person_id ASC);
CLUSTER ohdsi.visit_occurrence  USING idx_visit_person_id_1 ;
CREATE INDEX idx_visit_concept_id_1 ON ohdsi.visit_occurrence (visit_concept_id ASC);

CREATE INDEX idx_visit_det_person_id_1  ON ohdsi.visit_detail  (person_id ASC);
CLUSTER ohdsi.visit_detail  USING idx_visit_det_person_id_1 ;
CREATE INDEX idx_visit_det_concept_id_1 ON ohdsi.visit_detail (visit_detail_concept_id ASC);

CREATE INDEX idx_procedure_person_id_1  ON ohdsi.procedure_occurrence  (person_id ASC);
CLUSTER ohdsi.procedure_occurrence  USING idx_procedure_person_id_1 ;
CREATE INDEX idx_procedure_concept_id_1 ON ohdsi.procedure_occurrence (procedure_concept_id ASC);
CREATE INDEX idx_procedure_visit_id_1 ON ohdsi.procedure_occurrence (visit_occurrence_id ASC);

CREATE INDEX idx_drug_person_id_1  ON ohdsi.drug_exposure  (person_id ASC);
CLUSTER ohdsi.drug_exposure  USING idx_drug_person_id_1 ;
CREATE INDEX idx_drug_concept_id_1 ON ohdsi.drug_exposure (drug_concept_id ASC);
CREATE INDEX idx_drug_visit_id_1 ON ohdsi.drug_exposure (visit_occurrence_id ASC);

CREATE INDEX idx_device_person_id_1  ON ohdsi.device_exposure  (person_id ASC);
CLUSTER ohdsi.device_exposure  USING idx_device_person_id_1 ;
CREATE INDEX idx_device_concept_id_1 ON ohdsi.device_exposure (device_concept_id ASC);
CREATE INDEX idx_device_visit_id_1 ON ohdsi.device_exposure (visit_occurrence_id ASC);

CREATE INDEX idx_condition_person_id_1  ON ohdsi.condition_occurrence  (person_id ASC);
CLUSTER ohdsi.condition_occurrence  USING idx_condition_person_id_1 ;
CREATE INDEX idx_condition_concept_id_1 ON ohdsi.condition_occurrence (condition_concept_id ASC);
CREATE INDEX idx_condition_visit_id_1 ON ohdsi.condition_occurrence (visit_occurrence_id ASC);

CREATE INDEX idx_measurement_person_id_1  ON ohdsi.measurement  (person_id ASC);
CLUSTER ohdsi.measurement  USING idx_measurement_person_id_1 ;
CREATE INDEX idx_measurement_concept_id_1 ON ohdsi.measurement (measurement_concept_id ASC);
CREATE INDEX idx_measurement_visit_id_1 ON ohdsi.measurement (visit_occurrence_id ASC);

CREATE INDEX idx_note_person_id_1  ON ohdsi.note  (person_id ASC);
CLUSTER ohdsi.note  USING idx_note_person_id_1 ;
CREATE INDEX idx_note_concept_id_1 ON ohdsi.note (note_type_concept_id ASC);
CREATE INDEX idx_note_visit_id_1 ON ohdsi.note (visit_occurrence_id ASC);

CREATE INDEX idx_note_nlp_note_id_1  ON ohdsi.note_nlp  (note_id ASC);
CLUSTER ohdsi.note_nlp  USING idx_note_nlp_note_id_1 ;
CREATE INDEX idx_note_nlp_concept_id_1 ON ohdsi.note_nlp (note_nlp_concept_id ASC);

CREATE INDEX idx_observation_person_id_1  ON ohdsi.observation  (person_id ASC);
CLUSTER ohdsi.observation  USING idx_observation_person_id_1 ;
CREATE INDEX idx_observation_concept_id_1 ON ohdsi.observation (observation_concept_id ASC);
CREATE INDEX idx_observation_visit_id_1 ON ohdsi.observation (visit_occurrence_id ASC);

CREATE INDEX idx_survey_person_id_1  ON ohdsi.survey_conduct  (person_id ASC);
CLUSTER ohdsi.survey_conduct  USING idx_survey_person_id_1 ;

CREATE INDEX idx_fact_relationship_id1 ON ohdsi.fact_relationship (domain_concept_id_1 ASC);
CREATE INDEX idx_fact_relationship_id2 ON ohdsi.fact_relationship (domain_concept_id_2 ASC);
CREATE INDEX idx_fact_relationship_id3 ON ohdsi.fact_relationship (relationship_concept_id ASC);

CREATE INDEX idx_episode_person_id_1  ON ohdsi.episode  (person_id ASC);
CLUSTER ohdsi.episode  USING idx_episode_person_id_1 ;
CREATE INDEX idx_episode_concept_id_1 ON ohdsi.episode (episode_concept_id ASC);

CREATE INDEX idx_episode_event_id_1  ON ohdsi.episode_event  (episode_id ASC);
CLUSTER ohdsi.episode_event  USING idx_episode_event_id_1 ;
CREATE INDEX idx_ee_field_concept_id_1 ON ohdsi.episode_event (event_field_concept_id ASC);

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

Standardized health system data

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

Standardized health economics

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CREATE INDEX idx_period_person_id_1  ON ohdsi.payer_plan_period  (person_id ASC);
CLUSTER ohdsi.payer_plan_period  USING idx_period_person_id_1 ;

CREATE INDEX idx_cost_person_id_1  ON ohdsi.cost  (person_id ASC);
CLUSTER ohdsi.cost  USING idx_cost_person_id_1 ;


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

Standardized derived elements

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CREATE INDEX idx_drug_era_person_id_1  ON ohdsi.drug_era  (person_id ASC);
CLUSTER ohdsi.drug_era  USING idx_drug_era_person_id_1 ;
CREATE INDEX idx_drug_era_concept_id_1 ON ohdsi.drug_era (drug_concept_id ASC);

CREATE INDEX idx_dose_era_person_id_1  ON ohdsi.dose_era  (person_id ASC);
CLUSTER ohdsi.dose_era  USING idx_dose_era_person_id_1 ;
CREATE INDEX idx_dose_era_concept_id_1 ON ohdsi.dose_era (drug_concept_id ASC);

CREATE INDEX idx_condition_era_person_id_1  ON ohdsi.condition_era  (person_id ASC);
CLUSTER ohdsi.condition_era  USING idx_condition_era_person_id_1 ;
CREATE INDEX idx_condition_era_concept_id_1 ON ohdsi.condition_era (condition_concept_id ASC);

