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‎extras/v53_v54_conversion/README.txt

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README
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------
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v5.3 to v5.4 CDM conversion
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NOTES
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-----
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The *_v53_to_v54_migration.sql scripts are SQL scripts that migrate a v5.3 CDM to a v5.4 CDM.
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The changes implemented are found here: http://ohdsi.github.io/CommonDataModel/cdm54Changes.html.
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Please replace @cdmDatabaseSchema with your schema name.
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Links to database documentation are included in each script to facilitate debugging.

‎extras/v53_v54_conversion/bigquery_migration.sql

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-- http://ohdsi.github.io/CommonDataModel/cdm54Changes.html
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-- BigQuery SQL references:
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-- https://cloud.google.com/bigquery/docs/reference/standard-sql/data-definition-language#creating_a_new_table_from_an_existing_table
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-- https://cloud.google.com/bigquery/docs/manually-changing-schemas
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-- https://cloud.google.com/bigquery/docs/reference/standard-sql/data-definition-language#alter_column_set_data_type_statement
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-- https://cloud.google.com/bigquery/docs/managing-tables#renaming-table
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--
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-- VISIT_OCCURRENCE
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-- admitting_source_concept_id -> admitted_from_concept_id
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-- admitting_source_value -> admitted_from_source_value
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-- discharge_to_concept_id -> discharged_to_concept_id
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-- discharge_to_source_value -> discharged_to_source_value
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alter table @cdmDatabaseSchema.visit_occurrence rename to visit_occurrence_old;
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create table @cdmDatabaseSchema.visit_occurrence
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as
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select * EXCEPT(admitting_source_concept_id,admitting_source_value,discharge_to_concept_id,discharge_to_source_value),
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admitting_source_concept_id as admitted_from_concept_id,
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admitting_source_value as admitted_from_source_value,
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discharge_to_concept_id as discharged_to_concept_id,
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discharge_to_source_value as discharged_to_source_value
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from visit_occurrence_old;
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--
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-- VISIT_DETAIL
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-- admitting_source_concept_id -> admitted_from_concept_id
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-- admitting_source_value -> admitted_from_source_value
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-- discharge_to_concept_id -> discharged_to_concept_id
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-- discharge_to_source_value -> discharged_to_source_value
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-- visit_detail_parent_id -> parent_visit_detail_id
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alter table @cdmDatabaseSchema.visit_detail rename to visit_detail_old;
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create table @cdmDatabaseSchema.visit_occurrence
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as
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select * EXCEPT(admitting_source_concept_id,admitting_source_value,discharge_to_concept_id,discharge_to_source_value,visit_detail_parent_id),
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admitting_source_concept_id as admitted_from_concept_id,
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admitting_source_value as admitted_from_source_value,
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discharge_to_concept_id as discharged_to_concept_id,
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discharge_to_source_value as discharged_to_source_value,
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visit_detail_parent_id as parent_visit_detail_id
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from visit_detail_old;
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-- PROCEDURE_OCCURRENCE
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-- + Procedure_end_date
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-- + Procedure_end_datetime
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alter table @cdmDatabaseSchema.procedure_occurrence add column procedure_end_date date;
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alter table @cdmDatabaseSchema.procedure_occurrence add column procedure_end_datetime datetime;
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-- DEVICE_EXPOSURE
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-- Unique_device_id -> Changed to varchar(255) (already a STRING on bigquery)
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-- + Production_id
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-- + Unit_concept_id
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-- + Unit_source_value
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-- + Unit_source_concept_id
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alter table @cdmDatabaseSchema.device_exposure add column production_id int64;
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alter table @cdmDatabaseSchema.device_exposure add column unit_concept_id int64;
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alter table @cdmDatabaseSchema.device_exposure add column unit_source_value string;
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alter table @cdmDatabaseSchema.device_exposure add column unit_source_concept_id int64;
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-- MEASUREMENT
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-- + Unit_source_concept_id
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-- + Measurement_event_id
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-- + Meas_event_field_concept_id
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alter table @cdmDatabaseSchema.measurement add column unit_source_concept_id int64;
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alter table @cdmDatabaseSchema.measurement add column measurement_event_id int64;
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alter table @cdmDatabaseSchema.measurement add column meas_event_field_concept_id int64;
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-- OBSERVATION
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-- + Value_source_value
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-- + Observation_event_id
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-- + Obs_event_field_concept_id
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alter table @cdmDatabaseSchema.observation add column value_source_value string;
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alter table @cdmDatabaseSchema.observation add column observation_event_id int64;
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alter table @cdmDatabaseSchema.observation add column obs_event_field_concept_id int64;
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-- NOTE
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-- + Note_event_id
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-- + Note_event_field_concept_id
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alter table @cdmDatabaseSchema.note add column note_event_id int64;
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alter table @cdmDatabaseSchema.note add column note_event_field_concept_id int64;
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-- LOCATION
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-- + Country_concept_id
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-- + Country_source_value
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-- + Latitude
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-- + Longitude
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alter table @cdmDatabaseSchema.location add column country_concept_id int64;
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alter table @cdmDatabaseSchema.location add column country_source_value string;
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alter table @cdmDatabaseSchema.location add column latitude float64;
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alter table @cdmDatabaseSchema.location add column longitude float64;
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-- EPISODE
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create table @cdmDatabaseSchema.episode (
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episode_id INT64 not null,
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person_id INT64 not null,
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episode_concept_id INT64 not null,
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episode_start_date date not null,
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episode_start_datetime datetime null,
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episode_end_date date null,
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episode_end_datetime datetime null,
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episode_parent_id INT64,
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episode_number INT64,
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episode_object_concept_id INT64 not null,
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episode_type_concept_id INT64 not null,
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episode_source_value STRING,
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episode_source_concept_id INT64 );
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-- EPISODE_EVENT
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CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
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episode_id int64 NOT NULL,
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event_id int64 NOT NULL,
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episode_event_field_concept_id int64 NOT NULL );
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-- METADATA
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-- + Metadata_id
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-- + Value_as_number
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alter table @cdmDatabaseSchema.metadata add column metadata_id int64;
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alter table @cdmDatabaseSchema.metadata add column value_as_number float64;
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-- CDM_SOURCE
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-- Cdm_source_name -> Mandatory field
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-- Cdm_source_abbreviation -> Mandatory field
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-- Cdm_holder -> Mandatory field
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-- Source_release_date -> Mandatory field
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-- Cdm_release_date -> Mandatory field
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-- + Cdm_version_concept_id
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alter table @cdmDatabaseSchema.cdm_source rename to cdm_source_v53;
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CREATE TABLE @cdmDatabaseSchema.cdm_source (
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cdm_source_name string NOT NULL,
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cdm_source_abbreviation string NOT NULL,
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cdm_holder string NOT NULL,
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source_description string NULL,
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source_documentation_reference string NULL,
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cdm_etl_reference string NULL,
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source_release_date datetime NOT NULL,
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cdm_release_date datetime NOT NULL,
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cdm_version string NULL,
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cdm_version_concept_id int64 NOT NULL,
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vocabulary_version string NOT NULL );
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insert into @cdmDatabaseSchema.cdm_source
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select cdm_source_name,cdm_source_abbreviation,cdm_holder,
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source_description,source_documentation_reference,cdm_etl_reference,
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source_release_date,cdm_release_date,'5.4',
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756265,vocabulary_version
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from @cdmDatabaseSchema.cdm_source_v53;
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-- VOCABULARY
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-- Vocabulary_reference -> Non-mandatory field
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-- Vocabulary_version -> Non-mandatory field
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alter table @cdmDatabaseSchema.vocabulary rename to vocabulary_v53;
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CREATE TABLE @cdmDatabaseSchema.vocabulary (
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vocabulary_id string NOT NULL,
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vocabulary_name string NOT NULL,
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vocabulary_reference string NULL,
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vocabulary_version string NULL,
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vocabulary_concept_id int64 NOT NULL );
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insert into @cdmDatabaseSchema.vocabulary
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select vocabulary_id,vocabulary_name,vocabulary_reference,
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vocabulary_version, vocabulary_concept_id
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from @cdmDatabaseSchema.vocabulary_v53;
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-- ATTRIBUTE_DEFINITION
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drop table @cdmDatabaseSchema.attribute_definition;
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-- COHORT
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CREATE TABLE @cdmDatabaseSchema.cohort (
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cohort_definition_id int64 NOT NULL,
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subject_id int64 NOT NULL,
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cohort_start_date datetime NOT NULL,
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cohort_end_date datetime NOT NULL );
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‎extras/v53_v54_conversion/impala_migration.sql

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-- http://ohdsi.github.io/CommonDataModel/cdm54Changes.html
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-- Impala SQL references:
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-- https://docs.cloudera.com/documentation/enterprise/6/6.3/topics/impala_alter_table.html
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--
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-- VISIT_OCCURRENCE
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-- admitting_source_concept_id -> admitted_from_concept_id
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-- admitting_source_value -> admitted_from_source_value
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-- discharge_to_concept_id -> discharged_to_concept_id
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-- discharge_to_source_value -> discharged_to_source_value
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alter table @cdmDatabaseSchema.visit_occurrence change admitting_source_concept_id admitted_from_concept_id int;
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alter table @cdmDatabaseSchema.visit_occurrence change admitting_source_value admitted_from_source_value int;
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alter table @cdmDatabaseSchema.visit_occurrence change discharge_to_concept_id discharged_to_concept_id int;
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alter table @cdmDatabaseSchema.visit_occurrence change discharge_to_source_value discharged_to_source_value int;
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--
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-- VISIT_DETAIL
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-- admitting_source_concept_id -> admitted_from_concept_id
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-- admitting_source_value -> admitted_from_source_value
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-- discharge_to_concept_id -> discharged_to_concept_id
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-- discharge_to_source_value -> discharged_to_source_value
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-- visit_detail_parent_id -> parent_visit_detail_id
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alter table @cdmDatabaseSchema.visit_detail change admitting_source_concept_id admitted_from_concept_id int;
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alter table @cdmDatabaseSchema.visit_detail change admitting_source_value admitted_from_source_value int;
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alter table @cdmDatabaseSchema.visit_detail change discharge_to_concept_id discharged_to_concept_id int;
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alter table @cdmDatabaseSchema.visit_detail change discharge_to_source_value discharged_to_source_value int;
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alter table @cdmDatabaseSchema.visit_detail change visit_detail_parent_id parent_visit_detail_id int;
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-- PROCEDURE_OCCURRENCE
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-- + Procedure_end_date
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-- + Procedure_end_datetime
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alter table @cdmDatabaseSchema.procedure_occurrence add columns (procedure_end_date timestamp);
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alter table @cdmDatabaseSchema.procedure_occurrence add columns (procedure_end_datetime timestamp);
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-- DEVICE_EXPOSURE
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-- Unique_device_id -> Changed to varchar(255)
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-- + Production_id
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-- + Unit_concept_id
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-- + Unit_source_value
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-- + Unit_source_concept_id
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alter table @cdmDatabaseSchema.device_exposure change unique_device_id unique_device_id varchar(300);
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alter table @cdmDatabaseSchema.device_exposure add columns (production_id int);
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alter table @cdmDatabaseSchema.device_exposure add columns (unit_concept_id int);
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alter table @cdmDatabaseSchema.device_exposure add columns (unit_source_value int);
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alter table @cdmDatabaseSchema.device_exposure add columns (unit_source_concept_id int);
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-- MEASUREMENT
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-- + Unit_source_concept_id
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-- + Measurement_event_id
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-- + Meas_event_field_concept_id
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alter table @cdmDatabaseSchema.measurement add columns (unit_source_concept_id int);
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alter table @cdmDatabaseSchema.measurement add columns (measurement_event_id int);
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alter table @cdmDatabaseSchema.measurement add columns (meas_event_field_concept_id int);
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-- OBSERVATION
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-- + Value_source_value
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-- + Observation_event_id
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-- + Obs_event_field_concept_id
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alter table @cdmDatabaseSchema.observation add columns (value_source_value varchar(50));
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alter table @cdmDatabaseSchema.observation add columns (observation_event_id int);
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alter table @cdmDatabaseSchema.observation add columns (obs_event_field_concept_id int);
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-- NOTE
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-- + Note_event_id
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-- + Note_event_field_concept_id
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alter table @cdmDatabaseSchema.note add columns (note_event_id int);
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alter table @cdmDatabaseSchema.note add columns (note_event_field_concept_id int);
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-- LOCATION
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-- + Country_concept_id
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-- + Country_source_value
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-- + Latitude
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-- + Longitude
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alter table @cdmDatabaseSchema.location add columns (country_concept_id int);
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alter table @cdmDatabaseSchema.location add columns (country_source_value varchar(80));
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alter table @cdmDatabaseSchema.location add columns (latitude float);
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alter table @cdmDatabaseSchema.location add columns (longitude float);
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-- EPISODE
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CREATE TABLE @cdmDatabaseSchema.EPISODE (
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episode_id int,
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person_id int,
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episode_concept_id int,
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episode_start_date timestamp,
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episode_start_datetime TIMESTAMP,
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episode_end_date timestamp,
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episode_end_datetime timestamp,
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episode_parent_id int,
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episode_number int,
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episode_object_concept_id int,
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episode_type_concept_id int,
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episode_source_value varchar(50),
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episode_source_concept_id int );
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-- EPISODE_EVENT
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CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
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episode_id int,
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event_id int,
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episode_event_field_concept_id int );
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-- METADATA
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-- + Metadata_id
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-- + Value_as_number
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alter table @cdmDatabaseSchema.metadata add columns (metadata_id int);
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alter table @cdmDatabaseSchema.metadata add columns (value_as_number float);
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-- CDM_SOURCE
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-- Cdm_source_name -> Mandatory field
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-- Cdm_source_abbreviation -> Mandatory field
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-- Cdm_holder -> Mandatory field
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-- Source_release_date -> Mandatory field
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-- Cdm_release_date -> Mandatory field
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-- + Cdm_version_concept_id
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alter table @cdmDatabaseSchema.cdm_source rename to cdm_source_v53;
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CREATE TABLE @cdmDatabaseSchema.cdm_source (
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cdm_source_name varchar(255),
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cdm_source_abbreviation varchar(25),
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cdm_holder varchar(255),
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source_description varchar(max),
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source_documentation_reference varchar(255),
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cdm_etl_reference varchar(255),
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source_release_date timestamp,
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cdm_release_date timestamp,
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cdm_version varchar(10),
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cdm_version_concept_id int,
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vocabulary_version varchar(20));
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insert into @cdmDatabaseSchema.cdm_source
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select cdm_source_name,cdm_source_abbreviation,cdm_holder,
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source_description,source_documentation_reference,cdm_etl_reference,
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source_release_date,cdm_release_date,'5.4',
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756265,vocabulary_version
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from @cdmDatabaseSchema.cdm_source_v53;
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-- VOCABULARY
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-- Vocabulary_reference -> Non-mandatory field
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-- Vocabulary_version -> Non-mandatory field
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alter table @cdmDatabaseSchema.vocabulary rename to vocabulary_v53;
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CREATE TABLE @cdmDatabaseSchema.vocabulary (
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vocabulary_id varchar(20),
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vocabulary_name varchar(255),
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vocabulary_reference varchar(255),
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vocabulary_version varchar(255),
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vocabulary_concept_id int );
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insert into @cdmDatabaseSchema.vocabulary
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select vocabulary_id,vocabulary_name,vocabulary_reference,
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vocabulary_version, vocabulary_concept_id
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from @cdmDatabaseSchema.vocabulary_v53;
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-- ATTRIBUTE_DEFINITION
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drop table @cdmDatabaseSchema.attribute_definition;
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-- COHORT
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CREATE TABLE @cdmDatabaseSchema.cohort (
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cohort_definition_id int,
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subject_id int,
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cohort_start_date timestamp,
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cohort_end_date timestamp );
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