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Fixes to bigquery as a result of testing and bigquery, impala, oracle, and netezza results schema ddls.

This commit is contained in:
clairblacketer 2018-09-24 12:55:05 -04:00
parent eee81f61ad
commit 62207c4309
5 changed files with 613 additions and 447 deletions
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48
BigQuery/OMOP CDM Results bigquery ddl.txt Normal file
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/*
Copyright 2018-08 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.
OMOP CDM v6.0 DDL
bigquery script to create OMOP common data model results schema version 6.0
last revised: 27-Aug-2018
Authors: Patrick Ryan, Christian Reich, Clair Blacketer
*/
#standardsql
--HINT DISTRIBUTE_ON_KEY(subject_id)
create table cohort
(
cohort_definition_id INT64 not null ,
subject_id INT64 not null ,
cohort_start_date date not null ,
cohort_end_date date not null
)
;
create table cohort_definition (
cohort_definition_id INT64 not null,
cohort_definition_name STRING not null,
cohort_definition_description STRING null,
definition_type_concept_id INT64 not null,
cohort_definition_syntax STRING null,
subject_concept_id INT64 not null,
cohort_initiation_date date null
)
;

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BigQuery/OMOP CDM bigquery ddl.txt
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Impala/OMOP CDM Results impala ddl.txt Normal file
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/*********************************************************************************
# Copyright 2018-08 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.
********************************************************************************/
/************************
####### # # ####### ###### ##### ###### # # ##### ###
# # ## ## # # # # # # # # ## ## # # # # # #
# # # # # # # # # # # # # # # # # # # # # #
# # # # # # # ###### # # # # # # # # ###### # #
# # # # # # # # # # # # # # # # ### # #
# # # # # # # # # # # # # # # # # ### # #
####### # # ####### # ##### ###### # # ## ##### ### ###
impala script to create OMOP common data model results schema version 6.0
last revised: 27-Aug-2018
Authors: Patrick Ryan, Christian Reich, Clair Blacketer
*************************/
CREATE TABLE cohort_definition (
cohort_definition_id INTEGER ,
cohort_definition_name VARCHAR(255),
cohort_definition_description STRING,
definition_type_concept_id INTEGER ,
cohort_definition_syntax STRING,
subject_concept_id INTEGER ,
cohort_initiation_date TIMESTAMP
)
;
--HINT DISTRIBUTE_ON_KEY(subject_id)
CREATE TABLE cohort
(
cohort_definition_id BIGINT ,
subject_id BIGINT ,
cohort_start_date TIMESTAMP ,
cohort_end_date TIMESTAMP
)
;

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Netezza/OMOP CDM Results netezza ddl.txt Normal file
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/*********************************************************************************
# Copyright 2018-08 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 OMOP common data model results schema version 6.0
last revised: 27-Aug-2018
Authors: Patrick Ryan, Christian Reich, Clair Blacketer
*************************/
--HINT DISTRIBUTE_ON_KEY(subject_id)
CREATE TABLE cohort
(
cohort_definition_id BIGINT NOT NULL ,
subject_id BIGINT NOT NULL ,
cohort_start_date DATE NOT NULL ,
cohort_end_date DATE NOT NULL
)
DISTRIBUTE ON (subject_id)
;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cohort_definition (
cohort_definition_id INTEGER NOT NULL,
cohort_definition_name VARCHAR(255) NOT NULL,
cohort_definition_description VARCHAR(1000) NULL,
definition_type_concept_id INTEGER NOT NULL,
cohort_definition_syntax VARCHAR(1000) NULL,
subject_concept_id INTEGER NOT NULL,
cohort_initiation_date DATE NULL
)
DISTRIBUTE ON RANDOM
;
ALTER TABLE cohort ADD CONSTRAINT xpk_cohort PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date ) ;
ALTER TABLE cohort_definition ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY (cohort_definition_id);

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Oracle/OMOP CDM Results oracle ddl.txt Normal file
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/*********************************************************************************
# Copyright 2018-08 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.
********************************************************************************/
/************************
####### # # ####### ###### ##### ###### # # ##### ###
# # ## ## # # # # # # # # ## ## # # # # # #
# # # # # # # # # # # # # # # # # # # # # #
# # # # # # # ###### # # # # # # # # ###### # #
# # # # # # # # # # # # # # # # ### # #
# # # # # # # # # # # # # # # # # ### # #
####### # # ####### # ##### ###### # # ## ##### ### ###
oracle script to create OMOP common data model results schema version 6.0
last revised: 27-Aug-2018
Authors: Patrick Ryan, Christian Reich, Clair Blacketer
*************************/
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cohort_definition (
cohort_definition_id INTEGER NOT NULL,
cohort_definition_name VARCHAR(255) NOT NULL,
cohort_definition_description CLOB NULL,
definition_type_concept_id INTEGER NOT NULL,
cohort_definition_syntax CLOB NULL,
subject_concept_id INTEGER NOT NULL,
cohort_initiation_date DATE NULL
)
;
--HINT DISTRIBUTE_ON_KEY(subject_id)
CREATE TABLE cohort
(
cohort_definition_id NUMBER(19) NOT NULL ,
subject_id NUMBER(19) NOT NULL ,
cohort_start_date DATE NOT NULL ,
cohort_end_date DATE NOT NULL
)
;
ALTER TABLE cohort ADD CONSTRAINT xpk_cohort PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date ) ;
ALTER TABLE cohort_definition ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY ( cohort_definition_id );
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_cohort_definition_concept FOREIGN KEY ( definition_type_concept_id ) REFERENCES concept ( concept_id );
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_subject_concept FOREIGN KEY ( subject_concept_id ) REFERENCES concept ( concept_id );
ALTER TABLE cohort ADD CONSTRAINT fpk_cohort_definition FOREIGN KEY ( cohort_definition_id ) REFERENCES cohort_definition ( cohort_definition_id );
CREATE INDEX idx_cohort_subject_id ON cohort ( subject_id ASC );