CDM v5.3 to v5.4 conversion scripts, initial commit
This commit is contained in:
AnthonyMolinaro
parent
15f5fb1ed5
commit
2456c66c62
|
|
@ -0,0 +1,13 @@
|
|||
|
||||
README
|
||||
------
|
||||
|
||||
v5.3 to v5.4 CDM conversion
|
||||
|
||||
NOTES
|
||||
-----
|
||||
|
||||
The *_v53_to_v54_migration.sql scripts are SQL scripts that migrate a v5.3 CDM to a v5.4 CDM.
|
||||
The changes implemented are found here: http://ohdsi.github.io/CommonDataModel/cdm54Changes.html.
|
||||
Please replace @cdmDatabaseSchema with your schema name.
|
||||
Links to database documentation are included in each script to facilitate debugging.
|
||||
|
|
@ -0,0 +1,188 @@
|
|||
-- http://ohdsi.github.io/CommonDataModel/cdm54Changes.html
|
||||
-- BigQuery SQL references:
|
||||
-- https://cloud.google.com/bigquery/docs/reference/standard-sql/data-definition-language#creating_a_new_table_from_an_existing_table
|
||||
-- https://cloud.google.com/bigquery/docs/manually-changing-schemas
|
||||
-- https://cloud.google.com/bigquery/docs/reference/standard-sql/data-definition-language#alter_column_set_data_type_statement
|
||||
-- https://cloud.google.com/bigquery/docs/managing-tables#renaming-table
|
||||
--
|
||||
|
||||
-- VISIT_OCCURRENCE
|
||||
-- admitting_source_concept_id -> admitted_from_concept_id
|
||||
-- admitting_source_value -> admitted_from_source_value
|
||||
-- discharge_to_concept_id -> discharged_to_concept_id
|
||||
-- discharge_to_source_value -> discharged_to_source_value
|
||||
|
||||
alter table @cdmDatabaseSchema.visit_occurrence rename to visit_occurrence_old;
|
||||
create table @cdmDatabaseSchema.visit_occurrence
|
||||
as
|
||||
select * EXCEPT(admitting_source_concept_id,admitting_source_value,discharge_to_concept_id,discharge_to_source_value),
|
||||
admitting_source_concept_id as admitted_from_concept_id,
|
||||
admitting_source_value as admitted_from_source_value,
|
||||
discharge_to_concept_id as discharged_to_concept_id,
|
||||
discharge_to_source_value as discharged_to_source_value
|
||||
from visit_occurrence_old;
|
||||
|
||||
--
|
||||
-- VISIT_DETAIL
|
||||
-- admitting_source_concept_id -> admitted_from_concept_id
|
||||
-- admitting_source_value -> admitted_from_source_value
|
||||
-- discharge_to_concept_id -> discharged_to_concept_id
|
||||
-- discharge_to_source_value -> discharged_to_source_value
|
||||
-- visit_detail_parent_id -> parent_visit_detail_id
|
||||
|
||||
alter table @cdmDatabaseSchema.visit_detail rename to visit_detail_old;
|
||||
create table @cdmDatabaseSchema.visit_occurrence
|
||||
as
|
||||
select * EXCEPT(admitting_source_concept_id,admitting_source_value,discharge_to_concept_id,discharge_to_source_value,visit_detail_parent_id),
|
||||
admitting_source_concept_id as admitted_from_concept_id,
|
||||
admitting_source_value as admitted_from_source_value,
|
||||
discharge_to_concept_id as discharged_to_concept_id,
|
||||
discharge_to_source_value as discharged_to_source_value,
|
||||
visit_detail_parent_id as parent_visit_detail_id
|
||||
from visit_detail_old;
|
||||
|
||||
-- PROCEDURE_OCCURRENCE
|
||||
-- + Procedure_end_date
|
||||
-- + Procedure_end_datetime
|
||||
|
||||
alter table @cdmDatabaseSchema.procedure_occurrence add column procedure_end_date date;
|
||||
alter table @cdmDatabaseSchema.procedure_occurrence add column procedure_end_datetime datetime;
|
||||
|
||||
-- DEVICE_EXPOSURE
|
||||
-- Unique_device_id -> Changed to varchar(255) (already a STRING on bigquery)
|
||||
-- + Production_id
|
||||
-- + Unit_concept_id
|
||||
-- + Unit_source_value
|
||||
-- + Unit_source_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.device_exposure add column production_id int64;
|
||||
alter table @cdmDatabaseSchema.device_exposure add column unit_concept_id int64;
|
||||
alter table @cdmDatabaseSchema.device_exposure add column unit_source_value string;
|
||||
alter table @cdmDatabaseSchema.device_exposure add column unit_source_concept_id int64;
|
||||
|
||||
-- MEASUREMENT
|
||||
-- + Unit_source_concept_id
|
||||
-- + Measurement_event_id
|
||||
-- + Meas_event_field_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.measurement add column unit_source_id int64;
|
||||
alter table @cdmDatabaseSchema.measurement add column measurement_event_id int64;
|
||||
alter table @cdmDatabaseSchema.measurement add column meas_event_field_concept_id int64;
|
||||
|
||||
-- OBSERVATION
|
||||
-- + Value_source_value
|
||||
-- + Observation_event_id
|
||||
-- + Obs_event_field_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.observation add column value_source_value string;
|
||||
alter table @cdmDatabaseSchema.observation add column observation_event_id int64;
|
||||
alter table @cdmDatabaseSchema.observation add column obs_event_field_concept_id int64;
|
||||
|
||||
-- NOTE
|
||||
-- + Note_event_id
|
||||
-- + Note_event_field_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.note add column note_event_id int64;
|
||||
alter table @cdmDatabaseSchema.note add column note_event_field_concept_id int64;
|
||||
|
||||
-- LOCATION
|
||||
-- + Country_concept_id
|
||||
-- + Country_source_value
|
||||
-- + Latitude
|
||||
-- + Longitude
|
||||
|
||||
alter table @cdmDatabaseSchema.location add column country_concept_id int64;
|
||||
alter table @cdmDatabaseSchema.location add column country_source_value string;
|
||||
alter table @cdmDatabaseSchema.location add column latitude float64;
|
||||
alter table @cdmDatabaseSchema.location add column longitude float64;
|
||||
|
||||
-- EPISODE
|
||||
create table @cdmDatabaseSchema.episode (
|
||||
episode_id INT64 not null,
|
||||
person_id INT64 not null,
|
||||
episode_concept_id INT64 not null,
|
||||
episode_start_date date not null,
|
||||
episode_start_datetime datetime null,
|
||||
episode_end_date date null,
|
||||
episode_end_datetime datetime null,
|
||||
episode_parent_id INT64,
|
||||
episode_number INT64,
|
||||
episode_object_concept_id INT64 not null,
|
||||
episode_type_concept_id INT64 not null,
|
||||
episode_source_value STRING,
|
||||
episode_source_concept_id INT64 );
|
||||
|
||||
-- EPISODE_EVENT
|
||||
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
|
||||
episode_id int64 NOT NULL,
|
||||
event_id int64 NOT NULL,
|
||||
episode_event_field_concept_id int64 NOT NULL );
|
||||
|
||||
|
||||
-- METADATA
|
||||
-- + Metadata_id
|
||||
-- + Value_as_number
|
||||
|
||||
alter table @cdmDatabaseSchema.metadata add column metadata_id int64;
|
||||
alter table @cdmDatabaseSchema.metadata add column value_as_number float64;
|
||||
|
||||
-- CDM_SOURCE
|
||||
-- Cdm_source_name -> Mandatory field
|
||||
-- Cdm_source_abbreviation -> Mandatory field
|
||||
-- Cdm_holder -> Mandatory field
|
||||
-- Source_release_date -> Mandatory field
|
||||
-- Cdm_release_date -> Mandatory field
|
||||
-- + Cdm_version_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.cdm_source rename to cdm_source_v53;
|
||||
|
||||
CREATE TABLE @cdmDatabaseSchema.cdm_source (
|
||||
cdm_source_name string NOT NULL,
|
||||
cdm_source_abbreviation string NOT NULL,
|
||||
cdm_holder string NOT NULL,
|
||||
source_description string NULL,
|
||||
source_documentation_reference string NULL,
|
||||
cdm_etl_reference string NULL,
|
||||
source_release_date datetime NOT NULL,
|
||||
cdm_release_date datetime NOT NULL,
|
||||
cdm_version string NULL,
|
||||
cdm_version_concept_id int64 NOT NULL,
|
||||
vocabulary_version string NOT NULL );
|
||||
|
||||
insert into @cdmDatabaseSchema.cdm_source
|
||||
select cdm_source_name,cdm_source_abbreviation,cdm_holder,
|
||||
source_description,source_documentation_reference,cdm_etl_reference,
|
||||
source_release_date,cdm_release_date,'5.4',
|
||||
756265,vocabulary_version
|
||||
from @cdmDatabaseSchema.cdm_source_v53;
|
||||
|
||||
|
||||
-- VOCABULARY
|
||||
-- Vocabulary_reference -> Non-mandatory field
|
||||
-- Vocabulary_version -> Non-mandatory field
|
||||
alter table @cdmDatabaseSchema.vocabulary rename to vocabulary_v53;
|
||||
|
||||
CREATE TABLE @cdmDatabaseSchema.vocabulary (
|
||||
vocabulary_id string NOT NULL,
|
||||
vocabulary_name string NOT NULL,
|
||||
vocabulary_reference string NULL,
|
||||
vocabulary_version string NULL,
|
||||
vocabulary_concept_id int64 NOT NULL );
|
||||
|
||||
insert into @cdmDatabaseSchema.vocabulary
|
||||
select vocabulary_id,vocabulary_name,vocabulary_reference,
|
||||
vocabulary_version, vocabulary_concept_id
|
||||
from @cdmDatabaseSchema.vocabulary_v53;
|
||||
|
||||
|
||||
-- ATTRIBUTE_DEFINITION
|
||||
drop table @cdmDatabaseSchema.attribute_definition;
|
||||
|
||||
-- COHORT
|
||||
CREATE TABLE @cdmDatabaseSchema.cohort (
|
||||
cohort_definition_id int64 NOT NULL,
|
||||
subject_id int64 NOT NULL,
|
||||
cohort_start_date datetime NOT NULL,
|
||||
cohort_end_date datetime NOT NULL );
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,176 @@
|
|||
-- http://ohdsi.github.io/CommonDataModel/cdm54Changes.html
|
||||
-- Impala SQL references:
|
||||
-- https://docs.cloudera.com/documentation/enterprise/6/6.3/topics/impala_alter_table.html
|
||||
--
|
||||
-- VISIT_OCCURRENCE
|
||||
-- admitting_source_concept_id -> admitted_from_concept_id
|
||||
-- admitting_source_value -> admitted_from_source_value
|
||||
-- discharge_to_concept_id -> discharged_to_concept_id
|
||||
-- discharge_to_source_value -> discharged_to_source_value
|
||||
|
||||
alter table @cdmDatabaseSchema.visit_occurrence change admitting_source_concept_id admitted_from_concept_id int;
|
||||
alter table @cdmDatabaseSchema.visit_occurrence change admitting_source_value admitted_from_source_value int;
|
||||
alter table @cdmDatabaseSchema.visit_occurrence change discharge_to_concept_id discharged_to_concept_id int;
|
||||
alter table @cdmDatabaseSchema.visit_occurrence change discharge_to_source_value discharged_to_source_value int;
|
||||
|
||||
--
|
||||
-- VISIT_DETAIL
|
||||
-- admitting_source_concept_id -> admitted_from_concept_id
|
||||
-- admitting_source_value -> admitted_from_source_value
|
||||
-- discharge_to_concept_id -> discharged_to_concept_id
|
||||
-- discharge_to_source_value -> discharged_to_source_value
|
||||
-- visit_detail_parent_id -> parent_visit_detail_id
|
||||
|
||||
alter table @cdmDatabaseSchema.visit_detail change admitting_source_concept_id admitted_from_concept_id int;
|
||||
alter table @cdmDatabaseSchema.visit_detail change admitting_source_value admitted_from_source_value int;
|
||||
alter table @cdmDatabaseSchema.visit_detail change discharge_to_concept_id discharged_to_concept_id int;
|
||||
alter table @cdmDatabaseSchema.visit_detail change discharge_to_source_value discharged_to_source_value int;
|
||||
alter table @cdmDatabaseSchema.visit_detail change visit_detail_parent_id parent_visit_detail_id int;
|
||||
|
||||
-- PROCEDURE_OCCURRENCE
|
||||
-- + Procedure_end_date
|
||||
-- + Procedure_end_datetime
|
||||
|
||||
alter table @cdmDatabaseSchema.procedure_occurrence add columns (procedure_end_date timestamp);
|
||||
alter table @cdmDatabaseSchema.procedure_occurrence add columns (procedure_end_datetime timestamp);
|
||||
|
||||
-- DEVICE_EXPOSURE
|
||||
-- Unique_device_id -> Changed to varchar(255)
|
||||
-- + Production_id
|
||||
-- + Unit_concept_id
|
||||
-- + Unit_source_value
|
||||
-- + Unit_source_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.device_exposure change unique_device_id unique_device_id varchar(300);
|
||||
alter table @cdmDatabaseSchema.device_exposure add columns (production_id int);
|
||||
alter table @cdmDatabaseSchema.device_exposure add columns (unit_concept_id int);
|
||||
alter table @cdmDatabaseSchema.device_exposure add columns (unit_source_value int);
|
||||
alter table @cdmDatabaseSchema.device_exposure add columns (unit_source_concept_id int);
|
||||
|
||||
-- MEASUREMENT
|
||||
-- + Unit_source_concept_id
|
||||
-- + Measurement_event_id
|
||||
-- + Meas_event_field_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.measurement add columns (unit_source_id int);
|
||||
alter table @cdmDatabaseSchema.measurement add columns (measurement_event_id int);
|
||||
alter table @cdmDatabaseSchema.measurement add columns (meas_event_field_concept_id int);
|
||||
|
||||
-- OBSERVATION
|
||||
-- + Value_source_value
|
||||
-- + Observation_event_id
|
||||
-- + Obs_event_field_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.observation add columns (value_source_value varchar(50));
|
||||
alter table @cdmDatabaseSchema.observation add columns (observation_event_id int);
|
||||
alter table @cdmDatabaseSchema.observation add columns (obs_event_field_concept_id int);
|
||||
|
||||
-- NOTE
|
||||
-- + Note_event_id
|
||||
-- + Note_event_field_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.note add columns (note_event_id int);
|
||||
alter table @cdmDatabaseSchema.note add columns (note_event_field_concept_id int);
|
||||
|
||||
-- LOCATION
|
||||
-- + Country_concept_id
|
||||
-- + Country_source_value
|
||||
-- + Latitude
|
||||
-- + Longitude
|
||||
|
||||
alter table @cdmDatabaseSchema.location add columns (country_concept_id int);
|
||||
alter table @cdmDatabaseSchema.location add columns (country_source_value varchar(80));
|
||||
alter table @cdmDatabaseSchema.location add columns (latitude float);
|
||||
alter table @cdmDatabaseSchema.location add columns (longitude float);
|
||||
|
||||
-- EPISODE
|
||||
CREATE TABLE @cdmDatabaseSchema.EPISODE (
|
||||
episode_id int,
|
||||
person_id int,
|
||||
episode_concept_id int,
|
||||
episode_start_date timestamp,
|
||||
episode_start_datetime TIMESTAMP,
|
||||
episode_end_date timestamp,
|
||||
episode_end_datetime timestamp,
|
||||
episode_parent_id int,
|
||||
episode_number int,
|
||||
episode_object_concept_id int,
|
||||
episode_type_concept_id int,
|
||||
episode_source_value varchar(50),
|
||||
episode_source_concept_id int );
|
||||
|
||||
-- EPISODE_EVENT
|
||||
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
|
||||
episode_id int,
|
||||
event_id int,
|
||||
episode_event_field_concept_id int );
|
||||
|
||||
|
||||
-- METADATA
|
||||
-- + Metadata_id
|
||||
-- + Value_as_number
|
||||
|
||||
alter table @cdmDatabaseSchema.metadata add columns (metadata_id int);
|
||||
alter table @cdmDatabaseSchema.metadata add columns (value_as_number float);
|
||||
|
||||
-- CDM_SOURCE
|
||||
-- Cdm_source_name -> Mandatory field
|
||||
-- Cdm_source_abbreviation -> Mandatory field
|
||||
-- Cdm_holder -> Mandatory field
|
||||
-- Source_release_date -> Mandatory field
|
||||
-- Cdm_release_date -> Mandatory field
|
||||
-- + Cdm_version_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.cdm_source rename to cdm_source_v53;
|
||||
|
||||
CREATE TABLE @cdmDatabaseSchema.cdm_source (
|
||||
cdm_source_name varchar(255),
|
||||
cdm_source_abbreviation varchar(25),
|
||||
cdm_holder varchar(255),
|
||||
source_description varchar(max),
|
||||
source_documentation_reference varchar(255),
|
||||
cdm_etl_reference varchar(255),
|
||||
source_release_date timestamp,
|
||||
cdm_release_date timestamp,
|
||||
cdm_version varchar(10),
|
||||
cdm_version_concept_id int,
|
||||
vocabulary_version varchar(20));
|
||||
|
||||
insert into @cdmDatabaseSchema.cdm_source
|
||||
select cdm_source_name,cdm_source_abbreviation,cdm_holder,
|
||||
source_description,source_documentation_reference,cdm_etl_reference,
|
||||
source_release_date,cdm_release_date,'5.4',
|
||||
756265,vocabulary_version
|
||||
from @cdmDatabaseSchema.cdm_source_v53;
|
||||
|
||||
|
||||
-- VOCABULARY
|
||||
-- Vocabulary_reference -> Non-mandatory field
|
||||
-- Vocabulary_version -> Non-mandatory field
|
||||
|
||||
alter table @cdmDatabaseSchema.vocabulary rename to vocabulary_v53;
|
||||
|
||||
CREATE TABLE @cdmDatabaseSchema.vocabulary (
|
||||
vocabulary_id varchar(20),
|
||||
vocabulary_name varchar(255),
|
||||
vocabulary_reference varchar(255),
|
||||
vocabulary_version varchar(255),
|
||||
vocabulary_concept_id int );
|
||||
|
||||
insert into @cdmDatabaseSchema.vocabulary
|
||||
select vocabulary_id,vocabulary_name,vocabulary_reference,
|
||||
vocabulary_version, vocabulary_concept_id
|
||||
from @cdmDatabaseSchema.vocabulary_v53;
|
||||
|
||||
|
||||
-- ATTRIBUTE_DEFINITION
|
||||
drop table @cdmDatabaseSchema.attribute_definition;
|
||||
|
||||
-- COHORT
|
||||
CREATE TABLE @cdmDatabaseSchema.cohort (
|
||||
cohort_definition_id int,
|
||||
subject_id int,
|
||||
cohort_start_date timestamp,
|
||||
cohort_end_date timestamp );
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,176 @@
|
|||
-- http://ohdsi.github.io/CommonDataModel/cdm54Changes.html
|
||||
-- Netezza SQL references:
|
||||
-- https://www.ibm.com/docs/en/psfa/7.2.1?topic=reference-alter-table
|
||||
-- https://www.ibm.com/docs/en/psfa/7.2.1?topic=tables-add-drop-column
|
||||
--
|
||||
-- VISIT_OCCURRENCE
|
||||
-- admitting_source_concept_id -> admitted_from_concept_id
|
||||
-- admitting_source_value -> admitted_from_source_value
|
||||
-- discharge_to_concept_id -> discharged_to_concept_id
|
||||
-- discharge_to_source_value -> discharged_to_source_value
|
||||
|
||||
alter table @cdmDatabaseSchema.visit_occurrence rename column admitting_source_concept_id to admitted_from_concept_id;
|
||||
alter table @cdmDatabaseSchema.visit_occurrence rename column admitting_source_value to admitted_from_source_value;
|
||||
alter table @cdmDatabaseSchema.visit_occurrence rename column discharge_to_concept_id to discharged_to_concept_id;
|
||||
alter table @cdmDatabaseSchema.visit_occurrence rename column discharge_to_source_value to discharged_to_source_value;
|
||||
|
||||
--
|
||||
-- VISIT_DETAIL
|
||||
-- admitting_source_concept_id -> admitted_from_concept_id
|
||||
-- admitting_source_value -> admitted_from_source_value
|
||||
-- discharge_to_concept_id -> discharged_to_concept_id
|
||||
-- discharge_to_source_value -> discharged_to_source_value
|
||||
-- visit_detail_parent_id -> parent_visit_detail_id
|
||||
|
||||
alter table @cdmDatabaseSchema.visit_detail rename column admitting_source_concept_id to admitted_from_concept_id;
|
||||
alter table @cdmDatabaseSchema.visit_detail rename column admitting_source_value to admitted_from_source_value;
|
||||
alter table @cdmDatabaseSchema.visit_detail rename column discharge_to_concept_id to discharged_to_concept_id;
|
||||
alter table @cdmDatabaseSchema.visit_detail rename column discharge_to_source_value to discharged_to_source_value;
|
||||
alter table @cdmDatabaseSchema.visit_detail rename column visit_detail_parent_id to parent_visit_detail_id;
|
||||
|
||||
-- PROCEDURE_OCCURRENCE
|
||||
-- + Procedure_end_date
|
||||
-- + Procedure_end_datetime
|
||||
|
||||
alter table @cdmDatabaseSchema.procedure_occurrence add column procedure_end_date timestamp null;
|
||||
alter table @cdmDatabaseSchema.procedure_occurrence add column procedure_end_datetime timestamp null;
|
||||
|
||||
-- DEVICE_EXPOSURE
|
||||
-- Unique_device_id -> Changed to varchar(255)
|
||||
-- + Production_id
|
||||
-- + Unit_concept_id
|
||||
-- + Unit_source_value
|
||||
-- + Unit_source_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.device_exposure modify column (unique_device_id varchar(300);
|
||||
alter table @cdmDatabaseSchema.device_exposure add column production_id integer null;
|
||||
alter table @cdmDatabaseSchema.device_exposure add column unit_concept_id integer null;
|
||||
alter table @cdmDatabaseSchema.device_exposure add column unit_source_value varchar(50) null;
|
||||
alter table @cdmDatabaseSchema.device_exposure add column unit_source_concept_id integer null;
|
||||
|
||||
-- MEASUREMENT
|
||||
-- + Unit_source_concept_id
|
||||
-- + Measurement_event_id
|
||||
-- + Meas_event_field_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.measurement add column unit_source_id integer default null;
|
||||
alter table @cdmDatabaseSchema.measurement add column measurement_event_id bigint null;
|
||||
alter table @cdmDatabaseSchema.measurement add column meas_event_field_concept_id integer null;
|
||||
|
||||
-- OBSERVATION
|
||||
-- + Value_source_value
|
||||
-- + Observation_event_id
|
||||
-- + Obs_event_field_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.observation add column value_source_value varchar(50) null;
|
||||
alter table @cdmDatabaseSchema.observation add column observation_event_id bigint null;
|
||||
alter table @cdmDatabaseSchema.observation add column obs_event_field_concept_id integer null;
|
||||
|
||||
-- NOTE
|
||||
-- + Note_event_id
|
||||
-- + Note_event_field_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.note add column note_event_id bigint null;
|
||||
alter table @cdmDatabaseSchema.note add column note_event_field_concept_id integer null;
|
||||
|
||||
-- LOCATION
|
||||
-- + Country_concept_id
|
||||
-- + Country_source_value
|
||||
-- + Latitude
|
||||
-- + Longitude
|
||||
|
||||
alter table @cdmDatabaseSchema.location add column country_concept_id integer null;
|
||||
alter table @cdmDatabaseSchema.location add column country_source_value varchar(80) null;
|
||||
alter table @cdmDatabaseSchema.location add column latitude float null;
|
||||
alter table @cdmDatabaseSchema.location add column longitude float null;
|
||||
|
||||
-- EPISODE
|
||||
CREATE TABLE @cdmDatabaseSchema.EPISODE (
|
||||
episode_id bigint NOT NULL,
|
||||
person_id bigint NOT NULL,
|
||||
episode_concept_id integer NOT NULL,
|
||||
episode_start_date timestamp NOT NULL,
|
||||
episode_start_datetime TIMESTAMP NULL,
|
||||
episode_end_date timestamp NULL,
|
||||
episode_end_datetime TIMESTAMP NULL,
|
||||
episode_parent_id bigint NULL,
|
||||
episode_number integer NULL,
|
||||
episode_object_concept_id integer NOT NULL,
|
||||
episode_type_concept_id integer NOT NULL,
|
||||
episode_source_value varchar(50) NULL,
|
||||
episode_source_concept_id integer NULL );
|
||||
|
||||
-- EPISODE_EVENT
|
||||
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
|
||||
episode_id bigint NOT NULL,
|
||||
event_id bigint NOT NULL,
|
||||
episode_event_field_concept_id integer NOT NULL );
|
||||
|
||||
|
||||
-- METADATA
|
||||
-- + Metadata_id
|
||||
-- + Value_as_number
|
||||
|
||||
alter table @cdmDatabaseSchema.metadata add column metadata_id integer null;
|
||||
alter table @cdmDatabaseSchema.metadata add column value_as_number float null;
|
||||
|
||||
-- CDM_SOURCE
|
||||
-- Cdm_source_name -> Mandatory field
|
||||
-- Cdm_source_abbreviation -> Mandatory field
|
||||
-- Cdm_holder -> Mandatory field
|
||||
-- Source_release_date -> Mandatory field
|
||||
-- Cdm_release_date -> Mandatory field
|
||||
-- + Cdm_version_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.cdm_source rename to cdm_source_v53;
|
||||
|
||||
CREATE TABLE @cdmDatabaseSchema.cdm_source (
|
||||
cdm_source_name varchar(255) NOT NULL,
|
||||
cdm_source_abbreviation varchar(25) NOT NULL,
|
||||
cdm_holder varchar(255) NOT NULL,
|
||||
source_description varchar(1000) NULL,
|
||||
source_documentation_reference varchar(255) NULL,
|
||||
cdm_etl_reference varchar(255) NULL,
|
||||
source_release_date timestamp NOT NULL,
|
||||
cdm_release_date timestamp NOT NULL,
|
||||
cdm_version varchar(10) NULL,
|
||||
cdm_version_concept_id integer NOT NULL,
|
||||
vocabulary_version varchar(20) NOT NULL );
|
||||
|
||||
insert into @cdmDatabaseSchema.cdm_source
|
||||
select cdm_source_name,cdm_source_abbreviation,cdm_holder,
|
||||
source_description,source_documentation_reference,cdm_etl_reference,
|
||||
source_release_date,cdm_release_date,'5.4',
|
||||
756265,vocabulary_version
|
||||
from @cdmDatabaseSchema.cdm_source_v53;
|
||||
|
||||
|
||||
-- VOCABULARY
|
||||
-- Vocabulary_reference -> Non-mandatory field
|
||||
-- Vocabulary_version -> Non-mandatory field
|
||||
alter table @cdmDatabaseSchema.vocabulary rename to vocabulary_v53;
|
||||
|
||||
CREATE TABLE @cdmDatabaseSchema.vocabulary (
|
||||
vocabulary_id varchar(20) NOT NULL,
|
||||
vocabulary_name varchar(255) NOT NULL,
|
||||
vocabulary_reference varchar(255) NULL,
|
||||
vocabulary_version varchar(255) NULL,
|
||||
vocabulary_concept_id integer NOT NULL );
|
||||
|
||||
insert into @cdmDatabaseSchema.vocabulary
|
||||
select vocabulary_id,vocabulary_name,vocabulary_reference,
|
||||
vocabulary_version, vocabulary_concept_id
|
||||
from @cdmDatabaseSchema.vocabulary_v53;
|
||||
|
||||
|
||||
-- ATTRIBUTE_DEFINITION
|
||||
drop table @cdmDatabaseSchema.attribute_definition;
|
||||
|
||||
-- COHORT
|
||||
CREATE TABLE @cdmDatabaseSchema.cohort (
|
||||
cohort_definition_id integer NOT NULL,
|
||||
subject_id integer NOT NULL,
|
||||
cohort_start_date timestamp NOT NULL,
|
||||
cohort_end_date timestamp NOT NULL );
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,179 @@
|
|||
-- http://ohdsi.github.io/CommonDataModel/cdm54Changes.html
|
||||
-- Oracle SQL references:
|
||||
-- https://docs.oracle.com/en/database/oracle/oracle-database/19/sqlrf/ALTER-TABLE.html#GUID-552E7373-BF93-477D-9DA3-B2C9386F2877
|
||||
-- https://docs.oracle.com/en/database/oracle/oracle-database/19/sqlrf/Data-Types.html#GUID-0DC7FFAA-F03F-4448-8487-F2592496A510
|
||||
-- https://docs.oracle.com/en/database/oracle/oracle-database/19/sqlrf/RENAME.html#GUID-573347CE-3EB8-42E5-B4D5-EF71CA06FAFC
|
||||
--
|
||||
-- VISIT_OCCURRENCE
|
||||
-- admitting_source_concept_id -> admitted_from_concept_id
|
||||
-- admitting_source_value -> admitted_from_source_value
|
||||
-- discharge_to_concept_id -> discharged_to_concept_id
|
||||
-- discharge_to_source_value -> discharged_to_source_value
|
||||
|
||||
alter table @cdmDatabaseSchema.visit_occurrence rename column admitting_source_concept_id to admitted_from_concept_id;
|
||||
alter table @cdmDatabaseSchema.visit_occurrence rename column admitting_source_value to admitted_from_source_value;
|
||||
alter table @cdmDatabaseSchema.visit_occurrence rename column discharge_to_concept_id to discharged_to_concept_id;
|
||||
alter table @cdmDatabaseSchema.visit_occurrence rename column discharge_to_source_value to discharged_to_source_value;
|
||||
|
||||
--
|
||||
-- VISIT_DETAIL
|
||||
-- admitting_source_concept_id -> admitted_from_concept_id
|
||||
-- admitting_source_value -> admitted_from_source_value
|
||||
-- discharge_to_concept_id -> discharged_to_concept_id
|
||||
-- discharge_to_source_value -> discharged_to_source_value
|
||||
-- visit_detail_parent_id -> parent_visit_detail_id
|
||||
|
||||
alter table @cdmDatabaseSchema.visit_detail rename column admitting_source_concept_id to admitted_from_concept_id;
|
||||
alter table @cdmDatabaseSchema.visit_detail rename column admitting_source_value to admitted_from_source_value;
|
||||
alter table @cdmDatabaseSchema.visit_detail rename column discharge_to_concept_id to discharged_to_concept_id;
|
||||
alter table @cdmDatabaseSchema.visit_detail rename column discharge_to_source_value to discharged_to_source_value;
|
||||
alter table @cdmDatabaseSchema.visit_detail rename column visit_detail_parent_id to parent_visit_detail_id;
|
||||
|
||||
-- PROCEDURE_OCCURRENCE
|
||||
-- + Procedure_end_date
|
||||
-- + Procedure_end_datetime
|
||||
|
||||
alter table @cdmDatabaseSchema.procedure_occurrence add (procedure_end_date date default null);
|
||||
alter table @cdmDatabaseSchema.procedure_occurrence add (procedure_end_datetime timestamp default null);
|
||||
|
||||
-- DEVICE_EXPOSURE
|
||||
-- Unique_device_id -> Changed to varchar(255)
|
||||
-- + Production_id
|
||||
-- + Unit_concept_id
|
||||
-- + Unit_source_value
|
||||
-- + Unit_source_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.device_exposure modify (unique_device_id varchar2(300));
|
||||
alter table @cdmDatabaseSchema.device_exposure add (production_id number default null);
|
||||
alter table @cdmDatabaseSchema.device_exposure add (unit_concept_id number default null);
|
||||
alter table @cdmDatabaseSchema.device_exposure add (unit_source_value varchar2(50) default null);
|
||||
alter table @cdmDatabaseSchema.device_exposure add (unit_source_concept_id number default null);
|
||||
|
||||
-- MEASUREMENT
|
||||
-- + Unit_source_concept_id
|
||||
-- + Measurement_event_id
|
||||
-- + Meas_event_field_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.measurement add (unit_source_id number default null);
|
||||
alter table @cdmDatabaseSchema.measurement add (measurement_event_id number default null);
|
||||
alter table @cdmDatabaseSchema.measurement add (meas_event_field_concept_id number default null);
|
||||
|
||||
-- OBSERVATION
|
||||
-- + Value_source_value
|
||||
-- + Observation_event_id
|
||||
-- + Obs_event_field_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.observation add (value_source_value varchar2(50) default null);
|
||||
alter table @cdmDatabaseSchema.observation add (observation_event_id number default null);
|
||||
alter table @cdmDatabaseSchema.observation add (obs_event_field_concept_id number default null);
|
||||
|
||||
-- NOTE
|
||||
-- + Note_event_id
|
||||
-- + Note_event_field_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.note add (note_event_id number default null);
|
||||
alter table @cdmDatabaseSchema.note add (note_event_field_concept_id number default null);
|
||||
|
||||
-- LOCATION
|
||||
-- + Country_concept_id
|
||||
-- + Country_source_value
|
||||
-- + Latitude
|
||||
-- + Longitude
|
||||
|
||||
alter table @cdmDatabaseSchema.location add (country_concept_id number default null);
|
||||
alter table @cdmDatabaseSchema.location add (country_source_value varchar2(80) default null);
|
||||
alter table @cdmDatabaseSchema.location add (latitude float default null);
|
||||
alter table @cdmDatabaseSchema.location add (longitude float default null);
|
||||
|
||||
-- EPISODE
|
||||
CREATE TABLE @cdmDatabaseSchema.EPISODE (
|
||||
episode_id number NOT NULL,
|
||||
person_id number NOT NULL,
|
||||
episode_concept_id number NOT NULL,
|
||||
episode_start_date date NOT NULL,
|
||||
episode_start_datetime TIMESTAMP NULL,
|
||||
episode_end_date date NULL,
|
||||
episode_end_datetime TIMESTAMP NULL,
|
||||
episode_parent_id number NULL,
|
||||
episode_number number NULL,
|
||||
episode_object_concept_id number NOT NULL,
|
||||
episode_type_concept_id number NOT NULL,
|
||||
episode_source_value varchar2(50) NULL,
|
||||
episode_source_concept_id number NULL );
|
||||
|
||||
-- EPISODE_EVENT
|
||||
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
|
||||
episode_id number NOT NULL,
|
||||
event_id number NOT NULL,
|
||||
episode_event_field_concept_id number NOT NULL );
|
||||
|
||||
|
||||
-- METADATA
|
||||
-- + Metadata_id
|
||||
-- + Value_as_number
|
||||
|
||||
alter table @cdmDatabaseSchema.metadata add (metadata_id number default null);
|
||||
alter table @cdmDatabaseSchema.metadata add (value_as_number float default null);
|
||||
|
||||
-- CDM_SOURCE
|
||||
-- Cdm_source_name -> Mandatory field
|
||||
-- Cdm_source_abbreviation -> Mandatory field
|
||||
-- Cdm_holder -> Mandatory field
|
||||
-- Source_release_date -> Mandatory field
|
||||
-- Cdm_release_date -> Mandatory field
|
||||
-- + Cdm_version_concept_id
|
||||
|
||||
rename @cdmDatabaseSchema.cdm_source to cdm_source_v53;
|
||||
|
||||
CREATE TABLE @cdmDatabaseSchema.cdm_source (
|
||||
cdm_source_name varchar2(255) NOT NULL,
|
||||
cdm_source_abbreviation varchar2(25) NOT NULL,
|
||||
cdm_holder varchar2(255) NOT NULL,
|
||||
-- 32767 bytes if MAX_STRING_SIZE = EXTENDED
|
||||
-- 4000 bytes if MAX_STRING_SIZE = STANDARD
|
||||
source_description varchar2(32767) NULL,
|
||||
source_documentation_reference varchar2(255) NULL,
|
||||
cdm_etl_reference varchar2(255) NULL,
|
||||
source_release_date date NOT NULL,
|
||||
cdm_release_date date NOT NULL,
|
||||
cdm_version varchar2(10) NULL,
|
||||
cdm_version_concept_id number NOT NULL,
|
||||
vocabulary_version varchar2(20) NOT NULL );
|
||||
|
||||
insert into @cdmDatabaseSchema.cdm_source
|
||||
select cdm_source_name,cdm_source_abbreviation,cdm_holder,
|
||||
source_description,source_documentation_reference,cdm_etl_reference,
|
||||
source_release_date,cdm_release_date,'5.4',
|
||||
756265,vocabulary_version
|
||||
from @cdmDatabaseSchema.cdm_source_v53;
|
||||
|
||||
|
||||
-- VOCABULARY
|
||||
-- Vocabulary_reference -> Non-mandatory field
|
||||
-- Vocabulary_version -> Non-mandatory field
|
||||
rename @cdmDatabaseSchema.vocabulary to vocabulary_v53;
|
||||
|
||||
CREATE TABLE @cdmDatabaseSchema.vocabulary (
|
||||
vocabulary_id varchar2(20) NOT NULL,
|
||||
vocabulary_name varchar2(255) NOT NULL,
|
||||
vocabulary_reference varchar2(255) NULL,
|
||||
vocabulary_version varchar2(255) NULL,
|
||||
vocabulary_concept_id number NOT NULL );
|
||||
|
||||
insert into @cdmDatabaseSchema.vocabulary
|
||||
select vocabulary_id,vocabulary_name,vocabulary_reference,
|
||||
vocabulary_version, vocabulary_concept_id
|
||||
from @cdmDatabaseSchema.vocabulary_v53;
|
||||
|
||||
|
||||
-- ATTRIBUTE_DEFINITION
|
||||
drop table @cdmDatabaseSchema.attribute_definition;
|
||||
|
||||
-- COHORT
|
||||
CREATE TABLE @cdmDatabaseSchema.cohort (
|
||||
cohort_definition_id number NOT NULL,
|
||||
subject_id number NOT NULL,
|
||||
cohort_start_date date NOT NULL,
|
||||
cohort_end_date date NOT NULL );
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,175 @@
|
|||
-- http://ohdsi.github.io/CommonDataModel/cdm54Changes.html
|
||||
-- PostgreSQL SQL references:
|
||||
-- https://www.postgresql.org/docs/current/sql-altertable.html
|
||||
--
|
||||
-- VISIT_OCCURRENCE
|
||||
-- admitting_source_concept_id -> admitted_from_concept_id
|
||||
-- admitting_source_value -> admitted_from_source_value
|
||||
-- discharge_to_concept_id -> discharged_to_concept_id
|
||||
-- discharge_to_source_value -> discharged_to_source_value
|
||||
|
||||
alter table @cdmDatabaseSchema.visit_occurrence rename column admitting_source_concept_id to admitted_from_concept_id;
|
||||
alter table @cdmDatabaseSchema.visit_occurrence rename column admitting_source_value to admitted_from_source_value;
|
||||
alter table @cdmDatabaseSchema.visit_occurrence rename column discharge_to_concept_id to discharged_to_concept_id;
|
||||
alter table @cdmDatabaseSchema.visit_occurrence rename column discharge_to_source_value to discharged_to_source_value;
|
||||
|
||||
--
|
||||
-- VISIT_DETAIL
|
||||
-- admitting_source_concept_id -> admitted_from_concept_id
|
||||
-- admitting_source_value -> admitted_from_source_value
|
||||
-- discharge_to_concept_id -> discharged_to_concept_id
|
||||
-- discharge_to_source_value -> discharged_to_source_value
|
||||
-- visit_detail_parent_id -> parent_visit_detail_id
|
||||
|
||||
alter table @cdmDatabaseSchema.visit_detail rename column admitting_source_concept_id to admitted_from_concept_id;
|
||||
alter table @cdmDatabaseSchema.visit_detail rename column admitting_source_value to admitted_from_source_value;
|
||||
alter table @cdmDatabaseSchema.visit_detail rename column discharge_to_concept_id to discharged_to_concept_id;
|
||||
alter table @cdmDatabaseSchema.visit_detail rename column discharge_to_source_value to discharged_to_source_value;
|
||||
alter table @cdmDatabaseSchema.visit_detail rename column visit_detail_parent_id to parent_visit_detail_id;
|
||||
|
||||
-- PROCEDURE_OCCURRENCE
|
||||
-- + Procedure_end_date
|
||||
-- + Procedure_end_datetime
|
||||
|
||||
alter table @cdmDatabaseSchema.procedure_occurrence add column procedure_end_date date default null;
|
||||
alter table @cdmDatabaseSchema.procedure_occurrence add column procedure_end_datetime timestamp default null;
|
||||
|
||||
-- DEVICE_EXPOSURE
|
||||
-- Unique_device_id -> Changed to varchar(255)
|
||||
-- + Production_id
|
||||
-- + Unit_concept_id
|
||||
-- + Unit_source_value
|
||||
-- + Unit_source_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.device_exposure alter column unique_device_id type varchar(300);
|
||||
alter table @cdmDatabaseSchema.device_exposure add column production_id integer default null;
|
||||
alter table @cdmDatabaseSchema.device_exposure add column unit_concept_id integer default null;
|
||||
alter table @cdmDatabaseSchema.device_exposure add column unit_source_value varchar(50) default null;
|
||||
alter table @cdmDatabaseSchema.device_exposure add column unit_source_concept_id integer default null;
|
||||
|
||||
-- MEASUREMENT
|
||||
-- + Unit_source_concept_id
|
||||
-- + Measurement_event_id
|
||||
-- + Meas_event_field_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.measurement add column unit_source_id integer default null;
|
||||
alter table @cdmDatabaseSchema.measurement add column measurement_event_id bigint default null;
|
||||
alter table @cdmDatabaseSchema.measurement add column meas_event_field_concept_id integer default null;
|
||||
|
||||
-- OBSERVATION
|
||||
-- + Value_source_value
|
||||
-- + Observation_event_id
|
||||
-- + Obs_event_field_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.observation add column value_source_value varchar(50) default null;
|
||||
alter table @cdmDatabaseSchema.observation add column observation_event_id bigint default null;
|
||||
alter table @cdmDatabaseSchema.observation add column obs_event_field_concept_id integer default null;
|
||||
|
||||
-- NOTE
|
||||
-- + Note_event_id
|
||||
-- + Note_event_field_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.note add column note_event_id bigint default null;
|
||||
alter table @cdmDatabaseSchema.note add column note_event_field_concept_id integer default null;
|
||||
|
||||
-- LOCATION
|
||||
-- + Country_concept_id
|
||||
-- + Country_source_value
|
||||
-- + Latitude
|
||||
-- + Longitude
|
||||
|
||||
alter table @cdmDatabaseSchema.location add column country_concept_id integer default null;
|
||||
alter table @cdmDatabaseSchema.location add column country_source_value varchar(80) default null;
|
||||
alter table @cdmDatabaseSchema.location add column latitude numeric default null;
|
||||
alter table @cdmDatabaseSchema.location add column longitude numeric default null;
|
||||
|
||||
-- EPISODE
|
||||
CREATE TABLE @cdmDatabaseSchema.EPISODE (
|
||||
episode_id bigint NOT NULL,
|
||||
person_id bigint NOT NULL,
|
||||
episode_concept_id integer NOT NULL,
|
||||
episode_start_date date NOT NULL,
|
||||
episode_start_datetime TIMESTAMP NULL,
|
||||
episode_end_date date NULL,
|
||||
episode_end_datetime TIMESTAMP NULL,
|
||||
episode_parent_id bigint NULL,
|
||||
episode_number integer NULL,
|
||||
episode_object_concept_id integer NOT NULL,
|
||||
episode_type_concept_id integer NOT NULL,
|
||||
episode_source_value varchar(50) NULL,
|
||||
episode_source_concept_id integer NULL );
|
||||
|
||||
-- EPISODE_EVENT
|
||||
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
|
||||
episode_id bigint NOT NULL,
|
||||
event_id bigint NOT NULL,
|
||||
episode_event_field_concept_id integer NOT NULL );
|
||||
|
||||
|
||||
-- METADATA
|
||||
-- + Metadata_id
|
||||
-- + Value_as_number
|
||||
|
||||
alter table @cdmDatabaseSchema.metadata add column metadata_id integer default null;
|
||||
alter table @cdmDatabaseSchema.metadata add column value_as_number numeric default null;
|
||||
|
||||
-- CDM_SOURCE
|
||||
-- Cdm_source_name -> Mandatory field
|
||||
-- Cdm_source_abbreviation -> Mandatory field
|
||||
-- Cdm_holder -> Mandatory field
|
||||
-- Source_release_date -> Mandatory field
|
||||
-- Cdm_release_date -> Mandatory field
|
||||
-- + Cdm_version_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.cdm_source rename to cdm_source_v53;
|
||||
|
||||
CREATE TABLE @cdmDatabaseSchema.cdm_source (
|
||||
cdm_source_name varchar(255) NOT NULL,
|
||||
cdm_source_abbreviation varchar(25) NOT NULL,
|
||||
cdm_holder varchar(255) NOT NULL,
|
||||
source_description text NULL,
|
||||
source_documentation_reference varchar(255) NULL,
|
||||
cdm_etl_reference varchar(255) NULL,
|
||||
source_release_date date NOT NULL,
|
||||
cdm_release_date date NOT NULL,
|
||||
cdm_version varchar(10) NULL,
|
||||
cdm_version_concept_id integer NOT NULL,
|
||||
vocabulary_version varchar(20) NOT NULL );
|
||||
|
||||
insert into @cdmDatabaseSchema.cdm_source
|
||||
select cdm_source_name,cdm_source_abbreviation,cdm_holder,
|
||||
source_description,source_documentation_reference,cdm_etl_reference,
|
||||
source_release_date,cdm_release_date,'5.4',
|
||||
756265,vocabulary_version
|
||||
from @cdmDatabaseSchema.cdm_source_v53;
|
||||
|
||||
|
||||
-- VOCABULARY
|
||||
-- Vocabulary_reference -> Non-mandatory field
|
||||
-- Vocabulary_version -> Non-mandatory field
|
||||
alter table @cdmDatabaseSchema.vocabulary rename to vocabulary_v53;
|
||||
|
||||
CREATE TABLE @cdmDatabaseSchema.vocabulary (
|
||||
vocabulary_id varchar(20) NOT NULL,
|
||||
vocabulary_name varchar(255) NOT NULL,
|
||||
vocabulary_reference varchar(255) NULL,
|
||||
vocabulary_version varchar(255) NULL,
|
||||
vocabulary_concept_id integer NOT NULL );
|
||||
|
||||
insert into @cdmDatabaseSchema.vocabulary
|
||||
select vocabulary_id,vocabulary_name,vocabulary_reference,
|
||||
vocabulary_version, vocabulary_concept_id
|
||||
from @cdmDatabaseSchema.vocabulary_v53;
|
||||
|
||||
|
||||
-- ATTRIBUTE_DEFINITION
|
||||
drop table @cdmDatabaseSchema.attribute_definition;
|
||||
|
||||
-- COHORT
|
||||
CREATE TABLE @cdmDatabaseSchema.cohort (
|
||||
cohort_definition_id integer NOT NULL,
|
||||
subject_id integer NOT NULL,
|
||||
cohort_start_date date NOT NULL,
|
||||
cohort_end_date date NOT NULL );
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,176 @@
|
|||
-- http://ohdsi.github.io/CommonDataModel/cdm54Changes.html
|
||||
-- Redshift SQL references:
|
||||
-- https://docs.aws.amazon.com/redshift/latest/dg/r_ALTER_TABLE_examples_basic.html
|
||||
-- https://docs.aws.amazon.com/redshift/latest/dg/r_ALTER_TABLE_COL_ex-add-drop.html
|
||||
--
|
||||
-- VISIT_OCCURRENCE
|
||||
-- admitting_source_concept_id -> admitted_from_concept_id
|
||||
-- admitting_source_value -> admitted_from_source_value
|
||||
-- discharge_to_concept_id -> discharged_to_concept_id
|
||||
-- discharge_to_source_value -> discharged_to_source_value
|
||||
|
||||
alter table @cdmDatabaseSchema.visit_occurrence rename column admitting_source_concept_id to admitted_from_concept_id;
|
||||
alter table @cdmDatabaseSchema.visit_occurrence rename column admitting_source_value to admitted_from_source_value;
|
||||
alter table @cdmDatabaseSchema.visit_occurrence rename column discharge_to_concept_id to discharged_to_concept_id;
|
||||
alter table @cdmDatabaseSchema.visit_occurrence rename column discharge_to_source_value to discharged_to_source_value;
|
||||
|
||||
--
|
||||
-- VISIT_DETAIL
|
||||
-- admitting_source_concept_id -> admitted_from_concept_id
|
||||
-- admitting_source_value -> admitted_from_source_value
|
||||
-- discharge_to_concept_id -> discharged_to_concept_id
|
||||
-- discharge_to_source_value -> discharged_to_source_value
|
||||
-- visit_detail_parent_id -> parent_visit_detail_id
|
||||
|
||||
alter table @cdmDatabaseSchema.visit_detail rename column admitting_source_concept_id to admitted_from_concept_id;
|
||||
alter table @cdmDatabaseSchema.visit_detail rename column admitting_source_value to admitted_from_source_value;
|
||||
alter table @cdmDatabaseSchema.visit_detail rename column discharge_to_concept_id to discharged_to_concept_id;
|
||||
alter table @cdmDatabaseSchema.visit_detail rename column discharge_to_source_value to discharged_to_source_value;
|
||||
alter table @cdmDatabaseSchema.visit_detail rename column visit_detail_parent_id to parent_visit_detail_id;
|
||||
|
||||
-- PROCEDURE_OCCURRENCE
|
||||
-- + Procedure_end_date
|
||||
-- + Procedure_end_datetime
|
||||
|
||||
alter table @cdmDatabaseSchema.procedure_occurrence add column procedure_end_date date default null;
|
||||
alter table @cdmDatabaseSchema.procedure_occurrence add column procedure_end_datetime timestamp default null;
|
||||
|
||||
-- DEVICE_EXPOSURE
|
||||
-- Unique_device_id -> Changed to varchar(255)
|
||||
-- + Production_id
|
||||
-- + Unit_concept_id
|
||||
-- + Unit_source_value
|
||||
-- + Unit_source_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.device_exposure alter column unique_device_id varchar(300);
|
||||
alter table @cdmDatabaseSchema.device_exposure add column production_id integer default null;
|
||||
alter table @cdmDatabaseSchema.device_exposure add column unit_concept_id integer default null;
|
||||
alter table @cdmDatabaseSchema.device_exposure add column unit_source_value varchar(50) default null;
|
||||
alter table @cdmDatabaseSchema.device_exposure add column unit_source_concept_id integer default null;
|
||||
|
||||
-- MEASUREMENT
|
||||
-- + Unit_source_concept_id
|
||||
-- + Measurement_event_id
|
||||
-- + Meas_event_field_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.measurement add column unit_source_id integer default null;
|
||||
alter table @cdmDatabaseSchema.measurement add column measurement_event_id bigint default null;
|
||||
alter table @cdmDatabaseSchema.measurement add column meas_event_field_concept_id integer default null;
|
||||
|
||||
-- OBSERVATION
|
||||
-- + Value_source_value
|
||||
-- + Observation_event_id
|
||||
-- + Obs_event_field_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.observation add column value_source_value varchar(50) default null;
|
||||
alter table @cdmDatabaseSchema.observation add column observation_event_id bigint default null;
|
||||
alter table @cdmDatabaseSchema.observation add column obs_event_field_concept_id integer default null;
|
||||
|
||||
-- NOTE
|
||||
-- + Note_event_id
|
||||
-- + Note_event_field_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.note add column note_event_id bigint default null;
|
||||
alter table @cdmDatabaseSchema.note add column note_event_field_concept_id integer default null;
|
||||
|
||||
-- LOCATION
|
||||
-- + Country_concept_id
|
||||
-- + Country_source_value
|
||||
-- + Latitude
|
||||
-- + Longitude
|
||||
|
||||
alter table @cdmDatabaseSchema.location add column country_concept_id integer default null;
|
||||
alter table @cdmDatabaseSchema.location add column country_source_value varchar(80) default null;
|
||||
alter table @cdmDatabaseSchema.location add column latitude float default null;
|
||||
alter table @cdmDatabaseSchema.location add column longitude float default null;
|
||||
|
||||
-- EPISODE
|
||||
CREATE TABLE @cdmDatabaseSchema.EPISODE (
|
||||
episode_id bigint NOT NULL,
|
||||
person_id bigint NOT NULL,
|
||||
episode_concept_id integer NOT NULL,
|
||||
episode_start_date date NOT NULL,
|
||||
episode_start_datetime TIMESTAMP NULL,
|
||||
episode_end_date date NULL,
|
||||
episode_end_datetime TIMESTAMP NULL,
|
||||
episode_parent_id bigint NULL,
|
||||
episode_number integer NULL,
|
||||
episode_object_concept_id integer NOT NULL,
|
||||
episode_type_concept_id integer NOT NULL,
|
||||
episode_source_value varchar(50) NULL,
|
||||
episode_source_concept_id integer NULL );
|
||||
|
||||
-- EPISODE_EVENT
|
||||
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
|
||||
episode_id bigint NOT NULL,
|
||||
event_id bigint NOT NULL,
|
||||
episode_event_field_concept_id integer NOT NULL );
|
||||
|
||||
|
||||
-- METADATA
|
||||
-- + Metadata_id
|
||||
-- + Value_as_number
|
||||
|
||||
alter table @cdmDatabaseSchema.metadata add column metadata_id integer default null;
|
||||
alter table @cdmDatabaseSchema.metadata add column value_as_number float default null;
|
||||
|
||||
-- CDM_SOURCE
|
||||
-- Cdm_source_name -> Mandatory field
|
||||
-- Cdm_source_abbreviation -> Mandatory field
|
||||
-- Cdm_holder -> Mandatory field
|
||||
-- Source_release_date -> Mandatory field
|
||||
-- Cdm_release_date -> Mandatory field
|
||||
-- + Cdm_version_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.cdm_source rename to cdm_source_v53;
|
||||
|
||||
CREATE TABLE @cdmDatabaseSchema.cdm_source (
|
||||
cdm_source_name varchar(255) NOT NULL,
|
||||
cdm_source_abbreviation varchar(25) NOT NULL,
|
||||
cdm_holder varchar(255) NOT NULL,
|
||||
source_description varchar(MAX) NULL,
|
||||
source_documentation_reference varchar(255) NULL,
|
||||
cdm_etl_reference varchar(255) NULL,
|
||||
source_release_date date NOT NULL,
|
||||
cdm_release_date date NOT NULL,
|
||||
cdm_version varchar(10) NULL,
|
||||
cdm_version_concept_id integer NOT NULL,
|
||||
vocabulary_version varchar(20) NOT NULL );
|
||||
|
||||
insert into @cdmDatabaseSchema.cdm_source
|
||||
select cdm_source_name,cdm_source_abbreviation,cdm_holder,
|
||||
source_description,source_documentation_reference,cdm_etl_reference,
|
||||
source_release_date,cdm_release_date,'5.4',
|
||||
756265,vocabulary_version
|
||||
from @cdmDatabaseSchema.cdm_source_v53;
|
||||
|
||||
|
||||
-- VOCABULARY
|
||||
-- Vocabulary_reference -> Non-mandatory field
|
||||
-- Vocabulary_version -> Non-mandatory field
|
||||
alter table @cdmDatabaseSchema.vocabulary rename to vocabulary_v53;
|
||||
|
||||
CREATE TABLE @cdmDatabaseSchema.vocabulary (
|
||||
vocabulary_id varchar(20) NOT NULL,
|
||||
vocabulary_name varchar(255) NOT NULL,
|
||||
vocabulary_reference varchar(255) NULL,
|
||||
vocabulary_version varchar(255) NULL,
|
||||
vocabulary_concept_id integer NOT NULL );
|
||||
|
||||
insert into @cdmDatabaseSchema.vocabulary
|
||||
select vocabulary_id,vocabulary_name,vocabulary_reference,
|
||||
vocabulary_version, vocabulary_concept_id
|
||||
from @cdmDatabaseSchema.vocabulary_v53;
|
||||
|
||||
|
||||
-- ATTRIBUTE_DEFINITION
|
||||
drop table @cdmDatabaseSchema.attribute_definition;
|
||||
|
||||
-- COHORT
|
||||
CREATE TABLE @cdmDatabaseSchema.cohort (
|
||||
cohort_definition_id integer NOT NULL,
|
||||
subject_id integer NOT NULL,
|
||||
cohort_start_date date NOT NULL,
|
||||
cohort_end_date date NOT NULL );
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,179 @@
|
|||
-- http://ohdsi.github.io/CommonDataModel/cdm54Changes.html
|
||||
-- SQL SERVER SQL References:
|
||||
-- https://docs.microsoft.com/en-us/sql/relational-databases/tables/rename-columns-database-engine?view=sql-server-ver15
|
||||
-- https://docs.microsoft.com/en-us/sql/relational-databases/system-stored-procedures/sp-rename-transact-sql?view=sql-server-ver15
|
||||
-- https://docs.microsoft.com/en-us/sql/relational-databases/tables/add-columns-to-a-table-database-engine?view=sql-server-ver15
|
||||
-- https://docs.microsoft.com/en-us/sql/relational-databases/tables/modify-columns-database-engine?view=sql-server-ver15
|
||||
-- https://docs.microsoft.com/en-us/sql/t-sql/data-types/data-types-transact-sql?view=sql-server-ver15
|
||||
--
|
||||
-- VISIT_OCCURRENCE
|
||||
-- admitting_source_concept_id -> admitted_from_concept_id
|
||||
-- admitting_source_value -> admitted_from_source_value
|
||||
-- discharge_to_concept_id -> discharged_to_concept_id
|
||||
-- discharge_to_source_value -> discharged_to_source_value
|
||||
|
||||
EXEC sp_rename '@cdmDatabaseSchema.visit_occurrence.admitting_source_concept_id', 'admitted_from_concept_id', 'COLUMN';
|
||||
EXEC sp_rename '@cdmDatabaseSchema.visit_occurrence.admitting_source_value', 'admitted_from_source_value', 'COLUMN';
|
||||
EXEC sp_rename '@cdmDatabaseSchema.visit_occurrence.discharge_to_concept_id', 'discharged_to_concept_id', 'COLUMN';
|
||||
EXEC sp_rename '@cdmDatabaseSchema.visit_occurrence.discharge_to_source_value', 'discharged_to_source_value', 'COLUMN';
|
||||
|
||||
--
|
||||
-- VISIT_DETAIL
|
||||
-- admitting_source_concept_id -> admitted_from_concept_id
|
||||
-- admitting_source_value -> admitted_from_source_value
|
||||
-- discharge_to_concept_id -> discharged_to_concept_id
|
||||
-- discharge_to_source_value -> discharged_to_source_value
|
||||
-- visit_detail_parent_id -> parent_visit_detail_id
|
||||
|
||||
EXEC sp_rename '@cdmDatabaseSchema.visit_detail.admitting_source_concept_id', 'admitted_from_concept_id', 'COLUMN';
|
||||
EXEC sp_rename '@cdmDatabaseSchema.visit_detail.admitting_source_value', 'admitted_from_source_value', 'COLUMN';
|
||||
EXEC sp_rename '@cdmDatabaseSchema.visit_detail.discharge_to_concept_id', 'discharged_to_concept_id', 'COLUMN';
|
||||
EXEC sp_rename '@cdmDatabaseSchema.visit_detail.discharge_to_source_value', 'discharged_to_source_value', 'COLUMN';
|
||||
EXEC sp_rename '@cdmDatabaseSchema.visit_detail.visit_detail_parent_id', 'parent_visit_detail_id', 'COLUMN';
|
||||
|
||||
-- PROCEDURE_OCCURRENCE
|
||||
-- + Procedure_end_date
|
||||
-- + Procedure_end_datetime
|
||||
|
||||
alter table @cdmDatabaseSchema.procedure_occurrence add procedure_end_date date null;
|
||||
alter table @cdmDatabaseSchema.procedure_occurrence add procedure_end_datetime datetime null;
|
||||
|
||||
-- DEVICE_EXPOSURE
|
||||
-- Unique_device_id -> Changed to varchar(255)
|
||||
-- + Production_id
|
||||
-- + Unit_concept_id
|
||||
-- + Unit_source_value
|
||||
-- + Unit_source_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.device_exposure alter column unique_device_id varchar(300);
|
||||
alter table @cdmDatabaseSchema.device_exposure add production_id int null;
|
||||
alter table @cdmDatabaseSchema.device_exposure add unit_concept_id int null;
|
||||
alter table @cdmDatabaseSchema.device_exposure add unit_source_value varchar(50) null;
|
||||
alter table @cdmDatabaseSchema.device_exposure add unit_source_concept_id int null;
|
||||
|
||||
-- MEASUREMENT
|
||||
-- + Unit_source_concept_id
|
||||
-- + Measurement_event_id
|
||||
-- + Meas_event_field_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.measurement add unit_source_id int null;
|
||||
alter table @cdmDatabaseSchema.measurement add measurement_event_id bigint null;
|
||||
alter table @cdmDatabaseSchema.measurement add meas_event_field_concept_id int null;
|
||||
|
||||
-- OBSERVATION
|
||||
-- + Value_source_value
|
||||
-- + Observation_event_id
|
||||
-- + Obs_event_field_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.observation add value_source_value varchar(50) null;
|
||||
alter table @cdmDatabaseSchema.observation add observation_event_id bigint null;
|
||||
alter table @cdmDatabaseSchema.observation add obs_event_field_concept_id int null;
|
||||
|
||||
-- NOTE
|
||||
-- + Note_event_id
|
||||
-- + Note_event_field_concept_id
|
||||
|
||||
alter table @cdmDatabaseSchema.note add note_event_id bigint null;
|
||||
alter table @cdmDatabaseSchema.note add note_event_field_concept_id int null;
|
||||
|
||||
-- LOCATION
|
||||
-- + Country_concept_id
|
||||
-- + Country_source_value
|
||||
-- + Latitude
|
||||
-- + Longitude
|
||||
|
||||
alter table @cdmDatabaseSchema.location add country_concept_id int null;
|
||||
alter table @cdmDatabaseSchema.location add country_source_value varchar(80) null;
|
||||
alter table @cdmDatabaseSchema.location add latitude numeric null;
|
||||
alter table @cdmDatabaseSchema.location add longitude numeric null;
|
||||
|
||||
-- EPISODE
|
||||
CREATE TABLE @cdmDatabaseSchema.EPISODE (
|
||||
episode_id bigint NOT NULL,
|
||||
person_id bigint NOT NULL,
|
||||
episode_concept_id int NOT NULL,
|
||||
episode_start_date date NOT NULL,
|
||||
episode_start_datetime datetime NULL,
|
||||
episode_end_date date NULL,
|
||||
episode_end_datetime datetime NULL,
|
||||
episode_parent_id bigint NULL,
|
||||
episode_number int NULL,
|
||||
episode_object_concept_id int NOT NULL,
|
||||
episode_type_concept_id int NOT NULL,
|
||||
episode_source_value varchar(50) NULL,
|
||||
episode_source_concept_id int NULL );
|
||||
|
||||
-- EPISODE_EVENT
|
||||
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
|
||||
episode_id bigint NOT NULL,
|
||||
event_id bigint NOT NULL,
|
||||
episode_event_field_concept_id int NOT NULL );
|
||||
|
||||
|
||||
-- METADATA
|
||||
-- + Metadata_id
|
||||
-- + Value_as_number
|
||||
|
||||
alter table @cdmDatabaseSchema.metadata add metadata_id int null;
|
||||
alter table @cdmDatabaseSchema.metadata add value_as_number numeric null;
|
||||
|
||||
-- CDM_SOURCE
|
||||
-- Cdm_source_name -> Mandatory field
|
||||
-- Cdm_source_abbreviation -> Mandatory field
|
||||
-- Cdm_holder -> Mandatory field
|
||||
-- Source_release_date -> Mandatory field
|
||||
-- Cdm_release_date -> Mandatory field
|
||||
-- + Cdm_version_concept_id
|
||||
|
||||
EXEC sp_rename '@cdmDatabaseSchema.cdm_source', 'cdm_source_v53';
|
||||
|
||||
CREATE TABLE @cdmDatabaseSchema.cdm_source (
|
||||
cdm_source_name varchar(255) NOT NULL,
|
||||
cdm_source_abbreviation varchar(25) NOT NULL,
|
||||
cdm_holder varchar(255) NOT NULL,
|
||||
source_description varchar(MAX) NULL,
|
||||
source_documentation_reference varchar(255) NULL,
|
||||
cdm_etl_reference varchar(255) NULL,
|
||||
source_release_date date NOT NULL,
|
||||
cdm_release_date date NOT NULL,
|
||||
cdm_version varchar(10) NULL,
|
||||
cdm_version_concept_id int NOT NULL,
|
||||
vocabulary_version varchar(20) NOT NULL );
|
||||
|
||||
insert into @cdmDatabaseSchema.cdm_source
|
||||
select cdm_source_name,cdm_source_abbreviation,cdm_holder,
|
||||
source_description,source_documentation_reference,cdm_etl_reference,
|
||||
source_release_date,cdm_release_date,'5.4',
|
||||
756265,vocabulary_version
|
||||
from @cdmDatabaseSchema.cdm_source_v53;
|
||||
|
||||
|
||||
-- VOCABULARY
|
||||
-- Vocabulary_reference -> Non-mandatory field
|
||||
-- Vocabulary_version -> Non-mandatory field
|
||||
EXEC sp_rename '@cdmDatabaseSchema.vocabulary', 'vocabulary_v53';
|
||||
|
||||
CREATE TABLE @cdmDatabaseSchema.vocabulary (
|
||||
vocabulary_id varchar(20) NOT NULL,
|
||||
vocabulary_name varchar(255) NOT NULL,
|
||||
vocabulary_reference varchar(255) NULL,
|
||||
vocabulary_version varchar(255) NULL,
|
||||
vocabulary_concept_id int NOT NULL );
|
||||
|
||||
insert into @cdmDatabaseSchema.vocabulary
|
||||
select vocabulary_id,vocabulary_name,vocabulary_reference,
|
||||
vocabulary_version, vocabulary_concept_id
|
||||
from @cdmDatabaseSchema.vocabulary_v53;
|
||||
|
||||
|
||||
-- ATTRIBUTE_DEFINITION
|
||||
drop table @cdmDatabaseSchema.attribute_definition;
|
||||
|
||||
-- COHORT
|
||||
CREATE TABLE @cdmDatabaseSchema.cohort (
|
||||
cohort_definition_id int NOT NULL,
|
||||
subject_id int NOT NULL,
|
||||
cohort_start_date date NOT NULL,
|
||||
cohort_end_date date NOT NULL );
|
||||
|
||||
|
||||
Loading…
Reference in New Issue