From 461a85fb6d90f60b3ace5dfb3972b75031821bc8 Mon Sep 17 00:00:00 2001 From: Blacketer Date: Fri, 1 Dec 2017 13:37:53 -0500 Subject: [PATCH] Updated netezza with distribution --- .../output/netezza/OMOP CDM netezza ddl.txt | 19 ++ .../netezza/OMOP CDM netezza primary keys.txt | 174 ++++++++++++++++++ 2 files changed, 193 insertions(+) create mode 100644 DDLGeneratr/output/netezza/OMOP CDM netezza primary keys.txt diff --git a/DDLGeneratr/output/netezza/OMOP CDM netezza ddl.txt b/DDLGeneratr/output/netezza/OMOP CDM netezza ddl.txt index cc56aa0..5561434 100644 --- a/DDLGeneratr/output/netezza/OMOP CDM netezza ddl.txt +++ b/DDLGeneratr/output/netezza/OMOP CDM netezza ddl.txt @@ -243,6 +243,7 @@ CREATE TABLE person ethnicity_source_value VARCHAR(50) NULL, ethnicity_source_concept_id INTEGER NULL ) +DISTRIBUTE ON (person_id) ; @@ -255,6 +256,7 @@ CREATE TABLE observation_period observation_period_end_date DATE NOT NULL , period_type_concept_id INTEGER NOT NULL ) +DISTRIBUTE ON (person_id) ; @@ -277,6 +279,7 @@ CREATE TABLE specimen anatomic_site_source_value VARCHAR(50) NULL , disease_status_source_value VARCHAR(50) NULL ) +DISTRIBUTE ON (person_id) ; @@ -291,6 +294,7 @@ CREATE TABLE death cause_source_value VARCHAR(50) NULL, cause_source_concept_id INTEGER NULL ) +DISTRIBUTE ON (person_id) ; @@ -315,6 +319,7 @@ CREATE TABLE visit_occurrence discharge_to_source_value VARCHAR(50) NULL , preceding_visit_occurrence_id INTEGER NULL ) +DISTRIBUTE ON (person_id) ; @@ -341,6 +346,7 @@ CREATE TABLE visit_detail visit_detail_parent_id INTEGER NULL , visit_occurrence_id INTEGER NOT NULL ) +DISTRIBUTE ON (person_id) ; @@ -362,6 +368,7 @@ CREATE TABLE procedure_occurrence procedure_source_concept_id INTEGER NULL , modifier_source_value VARCHAR(50) NULL ) +DISTRIBUTE ON (person_id) ; @@ -392,6 +399,7 @@ CREATE TABLE drug_exposure route_source_value VARCHAR(50) NULL , dose_unit_source_value VARCHAR(50) NULL ) +DISTRIBUTE ON (person_id) ; @@ -414,6 +422,7 @@ CREATE TABLE device_exposure device_source_value VARCHAR(100) NULL , device_source_concept_id INTEGER NULL ) +DISTRIBUTE ON (person_id) ; @@ -437,6 +446,7 @@ CREATE TABLE condition_occurrence condition_status_source_value VARCHAR(50) NULL , condition_status_concept_id INTEGER NULL ) +DISTRIBUTE ON (person_id) ; @@ -464,6 +474,7 @@ CREATE TABLE measurement unit_source_value VARCHAR(50) NULL , value_source_value VARCHAR(50) NULL ) +DISTRIBUTE ON (person_id) ; @@ -485,6 +496,7 @@ CREATE TABLE note visit_detail_id INTEGER NULL , note_source_value VARCHAR(50) NULL ) +DISTRIBUTE ON (person_id) ; @@ -531,6 +543,7 @@ CREATE TABLE observation unit_source_value VARCHAR(50) NULL , qualifier_source_value VARCHAR(50) NULL ) +DISTRIBUTE ON (person_id) ; @@ -626,6 +639,7 @@ CREATE TABLE payer_plan_period stop_reason_source_value INTEGER NULL , stop_reason_source_concept_id INTEGER NULL ) +DISTRIBUTE ON (person_id) ; @@ -672,6 +686,7 @@ CREATE TABLE cohort cohort_start_date DATE NOT NULL , cohort_end_date DATE NOT NULL ) +DISTRIBUTE ON (subject_id) ; @@ -686,6 +701,7 @@ CREATE TABLE cohort_attribute value_as_number NUMERIC NULL , value_as_concept_id INTEGER NULL ) +DISTRIBUTE ON (subject_id) ; @@ -700,6 +716,7 @@ CREATE TABLE drug_era drug_exposure_count INTEGER NULL , gap_days INTEGER NULL ) +DISTRIBUTE ON (person_id) ; @@ -714,6 +731,7 @@ CREATE TABLE dose_era dose_era_start_date DATE NOT NULL , dose_era_end_date DATE NOT NULL ) +DISTRIBUTE ON (person_id) ; @@ -727,4 +745,5 @@ CREATE TABLE condition_era condition_era_end_date DATE NOT NULL , condition_occurrence_count INTEGER NULL ) +DISTRIBUTE ON (person_id) ; diff --git a/DDLGeneratr/output/netezza/OMOP CDM netezza primary keys.txt b/DDLGeneratr/output/netezza/OMOP CDM netezza primary keys.txt new file mode 100644 index 0000000..3a14d7e --- /dev/null +++ b/DDLGeneratr/output/netezza/OMOP CDM netezza primary keys.txt @@ -0,0 +1,174 @@ +/********************************************************************************* +# 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. +********************************************************************************/ + +/************************ + + ####### # # ####### ###### ##### ###### # # ####### ##### ##### + # # ## ## # # # # # # # # ## ## # # # # # # # #### # # #### ##### ##### ## # # # ##### #### + # # # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # ## # # # + # # # # # # # ###### # # # # # # # # ###### ##### # # # # # # #### # # # # # # # # # # #### + # # # # # # # # # # # # # # # ### # # # # # # # # # ##### ###### # # # # # # + # # # # # # # # # # # # # # # # # ### # # # # # # # ## # # # # # # # # # ## # # # + ####### # # ####### # ##### ###### # # ## ##### ### ##### ##### #### # # #### # # # # # # # # # #### + + +netezza 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 primary keys and indices are considered a minimal requirement to ensure adequate performance of analyses. + +*************************/ + + +/************************ +************************* +************************* +************************* + +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 visit_detail ADD CONSTRAINT xpk_visit_detail PRIMARY KEY ( visit_detail_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 ) ;