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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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@ -0,0 +1,48 @@
/*
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
)
;

96
BigQuery/OMOP CDM bigquery ddl.txt
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@ -135,30 +135,6 @@ create table drug_strength (
; ;
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
)
;
create table attribute_definition (
attribute_definition_id INT64 not null,
attribute_name STRING not null,
attribute_description STRING null,
attribute_type_concept_id INT64 not null,
attribute_syntax STRING null
)
;
create table cdm_source create table cdm_source
( (
cdm_source_name STRING not null , cdm_source_name STRING not null ,
@ -187,13 +163,11 @@ create table metadata
) )
; ;
insert into metadata (name, value_as_string) --Added cdm version record insert into metadata (metadata_concept_id, metadata_type_concept_id, name, value_as_string, value_as_concept_id, metadata_date, measurement_datetime) --Added cdm version record
values ('CDM Version', '6.0') values (0, 0, 'CDM Version', '6.0', 0, NULL, NULL)
; ;
--HINT DISTRIBUTE_ON_KEY(person_id) --HINT DISTRIBUTE_ON_KEY(person_id)
create table person create table person
( (
@ -253,20 +227,6 @@ create table specimen
; ;
--HINT DISTRIBUTE_ON_KEY(person_id)
create table death
(
person_id INT64 not null ,
death_date date null ,
death_datetime DATETIME not null ,
death_type_concept_id INT64 not null ,
cause_concept_id INT64 null ,
cause_source_value STRING null,
cause_source_concept_id INT64 null
)
;
--HINT DISTRIBUTE_ON_KEY(person_id) --HINT DISTRIBUTE_ON_KEY(person_id)
create table visit_occurrence create table visit_occurrence
( (
@ -333,7 +293,7 @@ create table procedure_occurrence
visit_detail_id INT64 null , visit_detail_id INT64 null ,
procedure_source_value STRING null , procedure_source_value STRING null ,
procedure_source_concept_id INT64 null , procedure_source_concept_id INT64 null ,
modifier_source_value STRING null , modifier_source_value STRING null
) )
; ;
@ -445,9 +405,8 @@ create table note
( (
note_id INT64 not null , note_id INT64 not null ,
person_id INT64 not null , person_id INT64 not null ,
note_event_id INT64 null , --This and the field below added note_event_id INT64 null ,
note_domain_id STRING null , --This field may be removed in favor of the one below note_event_field_concept_id INT64 NULL ,
--note_event_table_concept_id INT64 NULL , --This may be added based on 9/4 meeting
note_date date null , note_date date null ,
note_datetime DATETIME not null , note_datetime DATETIME not null ,
note_type_concept_id INT64 not null , note_type_concept_id INT64 not null ,
@ -506,15 +465,14 @@ create table observation
observation_source_concept_id INT64 null , observation_source_concept_id INT64 null ,
unit_source_value STRING null , unit_source_value STRING null ,
qualifier_source_value STRING null , qualifier_source_value STRING null ,
observation_event_id INT64 null , /* This will link back to the event table (SURVEY) on SURVEY_OCCURRENCE_ID, changed name to comply with COST and NOTE*/ observation_event_id INT64 null ,
observation_event_domain_id STRING null , obs_event_field_concept_id INT64 NULL ,
--obs_event_table_concept_id INT64 NULL , /* Changed name to comply with COST and NOTE. This should be 'Survey'. Had to use 'obs' for oracle restriction, may be added on 9/4*/
value_as_datetime DATETIME null value_as_datetime DATETIME null
) )
; ;
create table survey_conduct /*Should this be SURVEY_OCCURRENCE instead to comply with the other tables?*/ create table survey_conduct
( (
survey_conduct_id INT64 not null , survey_conduct_id INT64 not null ,
person_id INT64 not null , person_id INT64 not null ,
@ -540,12 +498,11 @@ create table survey_conduct /*Should this be SURVEY_OCCURRENCE instead to comply
survey_version_number STRING null , survey_version_number STRING null ,
visit_occurrence_id INT64 null , visit_occurrence_id INT64 null ,
visit_detail_id INT64 null , visit_detail_id INT64 null ,
response_to_visit_occurrence_id INT64 null response_visit_occurrence_id INT64 null
) )
; ;
create table fact_relationship create table fact_relationship
( (
domain_concept_id_1 INT64 not null , domain_concept_id_1 INT64 not null ,
@ -557,8 +514,6 @@ create table fact_relationship
; ;
create table location create table location
( (
location_id INT64 not null , location_id INT64 not null ,
@ -575,6 +530,7 @@ create table location
) )
; ;
create table location_history create table location_history
( (
location_history_id INT64 not null , location_history_id INT64 not null ,
@ -619,8 +575,6 @@ create table provider
; ;
--HINT DISTRIBUTE_ON_KEY(person_id) --HINT DISTRIBUTE_ON_KEY(person_id)
create table payer_plan_period create table payer_plan_period
( (
@ -654,8 +608,7 @@ create table cost
cost_id INT64 not null , cost_id INT64 not null ,
person_id INT64 not null, person_id INT64 not null,
cost_event_id INT64 not null , cost_event_id INT64 not null ,
cost_domain_id STRING not null , cost_event_field_concept_id INT64 NOT NULL ,
--cost_event_table_concept_id INT64 NOT NULL , /*This is still in discussion and most likely will replace cost_domain_id at 9/4 meeting*/
cost_concept_id INT64 not null , cost_concept_id INT64 not null ,
cost_type_concept_id INT64 not null , cost_type_concept_id INT64 not null ,
currency_concept_id INT64 null , currency_concept_id INT64 null ,
@ -674,33 +627,6 @@ create table cost
; ;
--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
)
;
--HINT DISTRIBUTE_ON_KEY(subject_id)
create table cohort_attribute
(
cohort_definition_id INT64 not null ,
subject_id INT64 not null ,
cohort_start_date date not null ,
cohort_end_date date not null ,
attribute_definition_id INT64 not null ,
value_as_number FLOAT64 null ,
value_as_concept_id INT64 null
)
;
--HINT DISTRIBUTE_ON_KEY(person_id) --HINT DISTRIBUTE_ON_KEY(person_id)
create table drug_era create table drug_era
( (

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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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@ -0,0 +1,65 @@
/*********************************************************************************
# 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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@ -0,0 +1,70 @@
/*********************************************************************************
# 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 );