CDM55 changes docs and migration query

extras/migration/v52_to_v53/README.md

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+# v5.2 to v5.3 CDM conversion
+
+The *_migration.sql scripts in this folder migrate a v5.2 CDM to a v5.3 CDM.
+These scripts follow the migration pattern already used in this repository and cover
+the structural deltas reflected by the historical v5.2 DDLs and the v5.3 DDLs under inst/ddl.
+Please replace @cdmDatabaseSchema with your schema name.

extras/migration/v52_to_v53/bigquery_migration.sql

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+-- Derived from the OMOP CDM v5.2 and v5.3 BigQuery-compatible schema deltas in this repository.
+-- BigQuery SQL references:
+--   https://cloud.google.com/bigquery/docs/reference/standard-sql/data-definition-language
+--
+-- VISIT_DETAIL
+
+create table @cdmDatabaseSchema.visit_detail (
+    visit_detail_id INT64 not null,
+    person_id INT64 not null,
+    visit_detail_concept_id INT64 not null,
+    visit_detail_start_date date not null,
+    visit_detail_start_datetime DATETIME,
+    visit_detail_end_date date not null,
+    visit_detail_end_datetime DATETIME,
+    visit_detail_type_concept_id INT64 not null,
+    provider_id INT64,
+    care_site_id INT64,
+    visit_detail_source_value STRING,
+    visit_detail_source_concept_id INT64,
+    admitting_source_value STRING,
+    admitting_source_concept_id INT64,
+    discharge_to_source_value STRING,
+    discharge_to_concept_id INT64,
+    preceding_visit_detail_id INT64,
+    visit_detail_parent_id INT64,
+    visit_occurrence_id INT64 not null
+);
+
+-- CONDITION_OCCURRENCE
+alter table @cdmDatabaseSchema.condition_occurrence alter column condition_start_datetime drop not null;
+alter table @cdmDatabaseSchema.condition_occurrence add column visit_detail_id int64;
+
+-- DRUG_EXPOSURE
+alter table @cdmDatabaseSchema.drug_exposure alter column drug_exposure_start_datetime drop not null;
+alter table @cdmDatabaseSchema.drug_exposure add column visit_detail_id int64;
+
+-- PROCEDURE_OCCURRENCE
+alter table @cdmDatabaseSchema.procedure_occurrence rename to procedure_occurrence_v52;
+create table @cdmDatabaseSchema.procedure_occurrence as
+select
+  * except(qualifier_source_value),
+  cast(null as int64) as visit_detail_id,
+  qualifier_source_value as modifier_source_value
+from @cdmDatabaseSchema.procedure_occurrence_v52;
+
+-- DEVICE_EXPOSURE
+alter table @cdmDatabaseSchema.device_exposure alter column device_exposure_start_datetime drop not null;
+alter table @cdmDatabaseSchema.device_exposure add column visit_detail_id int64;
+
+-- MEASUREMENT
+alter table @cdmDatabaseSchema.measurement add column measurement_time string;
+alter table @cdmDatabaseSchema.measurement add column visit_detail_id int64;
+
+-- OBSERVATION
+alter table @cdmDatabaseSchema.observation add column visit_detail_id int64;
+
+-- DEATH
+alter table @cdmDatabaseSchema.death alter column death_type_concept_id drop not null;
+
+-- NOTE
+alter table @cdmDatabaseSchema.note add column visit_detail_id int64;
+
+-- PAYER_PLAN_PERIOD
+alter table @cdmDatabaseSchema.payer_plan_period add column payer_concept_id int64;
+alter table @cdmDatabaseSchema.payer_plan_period add column payer_source_concept_id int64;
+alter table @cdmDatabaseSchema.payer_plan_period add column plan_concept_id int64;
+alter table @cdmDatabaseSchema.payer_plan_period add column plan_source_concept_id int64;
+alter table @cdmDatabaseSchema.payer_plan_period add column sponsor_concept_id int64;
+alter table @cdmDatabaseSchema.payer_plan_period add column sponsor_source_value string;
+alter table @cdmDatabaseSchema.payer_plan_period add column sponsor_source_concept_id int64;
+alter table @cdmDatabaseSchema.payer_plan_period add column stop_reason_concept_id int64;
+alter table @cdmDatabaseSchema.payer_plan_period add column stop_reason_source_value string;
+alter table @cdmDatabaseSchema.payer_plan_period add column stop_reason_source_concept_id int64;
+
+-- COST
+alter table @cdmDatabaseSchema.cost rename to cost_v52;
+create table @cdmDatabaseSchema.cost as
+select
+  * except(reveue_code_source_value),
+  reveue_code_source_value as revenue_code_source_value
+from @cdmDatabaseSchema.cost_v52;
+
+-- METADATA
+create table @cdmDatabaseSchema.metadata (
+    metadata_concept_id INT64 not null,
+    metadata_type_concept_id INT64 not null,
+    name STRING not null,
+    value_as_string STRING,
+    value_as_concept_id INT64,
+    metadata_date DATE,
+    metadata_datetime DATETIME
+);
+
+-- TABLES REMOVED IN v5.3
+drop table @cdmDatabaseSchema.cohort_attribute;
+drop table @cdmDatabaseSchema.cohort;

extras/migration/v52_to_v53/impala_migration.sql

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+-- Derived from the OMOP CDM v5.2 and v5.3 Impala DDLs in this repository.
+-- Impala SQL references:
+--   https://docs.cloudera.com/documentation/enterprise/latest/topics/impala_alter_table.html
+--
+-- VISIT_DETAIL
+
+create table @cdmDatabaseSchema.visit_detail (
+    visit_detail_id INT,
+    person_id INT,
+    visit_detail_concept_id INT,
+    visit_detail_start_date TIMESTAMP,
+    visit_detail_start_datetime TIMESTAMP,
+    visit_detail_end_date TIMESTAMP,
+    visit_detail_end_datetime TIMESTAMP,
+    visit_detail_type_concept_id INT,
+    provider_id integer NULL,
+    care_site_id integer NULL,
+    visit_detail_source_value VARCHAR(50),
+    visit_detail_source_concept_id integer NULL,
+    admitting_source_value VARCHAR(50),
+    admitting_source_concept_id integer NULL,
+    discharge_to_source_value VARCHAR(50),
+    discharge_to_concept_id integer NULL,
+    preceding_visit_detail_id integer NULL,
+    visit_detail_parent_id integer NULL,
+    visit_occurrence_id INT
+);
+
+-- CONDITION_OCCURRENCE
+alter table @cdmDatabaseSchema.condition_occurrence add columns (visit_detail_id int);
+
+-- DRUG_EXPOSURE
+alter table @cdmDatabaseSchema.drug_exposure add columns (visit_detail_id int);
+
+-- PROCEDURE_OCCURRENCE
+alter table @cdmDatabaseSchema.procedure_occurrence change qualifier_source_value modifier_source_value varchar(50);
+alter table @cdmDatabaseSchema.procedure_occurrence add columns (visit_detail_id int);
+
+-- DEVICE_EXPOSURE
+alter table @cdmDatabaseSchema.device_exposure change device_source_value device_source_value varchar(50);
+alter table @cdmDatabaseSchema.device_exposure add columns (visit_detail_id int);
+
+-- MEASUREMENT
+alter table @cdmDatabaseSchema.measurement add columns (measurement_time varchar(10));
+alter table @cdmDatabaseSchema.measurement add columns (visit_detail_id int);
+
+-- OBSERVATION
+alter table @cdmDatabaseSchema.observation add columns (visit_detail_id int);
+
+-- NOTE
+alter table @cdmDatabaseSchema.note add columns (visit_detail_id int);
+
+-- NOTE_NLP
+alter table @cdmDatabaseSchema.note_nlp change note_nlp_id note_nlp_id int;
+alter table @cdmDatabaseSchema.note_nlp change `offset` `offset` varchar(50);
+
+-- PAYER_PLAN_PERIOD
+alter table @cdmDatabaseSchema.payer_plan_period add columns (payer_concept_id int);
+alter table @cdmDatabaseSchema.payer_plan_period add columns (payer_source_concept_id int);
+alter table @cdmDatabaseSchema.payer_plan_period add columns (plan_concept_id int);
+alter table @cdmDatabaseSchema.payer_plan_period add columns (plan_source_concept_id int);
+alter table @cdmDatabaseSchema.payer_plan_period add columns (sponsor_concept_id int);
+alter table @cdmDatabaseSchema.payer_plan_period add columns (sponsor_source_value varchar(50));
+alter table @cdmDatabaseSchema.payer_plan_period add columns (sponsor_source_concept_id int);
+alter table @cdmDatabaseSchema.payer_plan_period add columns (stop_reason_concept_id int);
+alter table @cdmDatabaseSchema.payer_plan_period add columns (stop_reason_source_value varchar(50));
+alter table @cdmDatabaseSchema.payer_plan_period add columns (stop_reason_source_concept_id int);
+
+-- COST
+alter table @cdmDatabaseSchema.cost change reveue_code_source_value revenue_code_source_value varchar(50);
+
+-- METADATA
+create table @cdmDatabaseSchema.metadata (
+    metadata_concept_id INT,
+    metadata_type_concept_id INT,
+    name VARCHAR(250),
+    value_as_string VARCHAR(250),
+    value_as_concept_id integer NULL,
+    metadata_date TIMESTAMP,
+    metadata_datetime TIMESTAMP
+);
+
+-- TABLES REMOVED IN v5.3
+drop table @cdmDatabaseSchema.cohort_attribute;
+drop table @cdmDatabaseSchema.cohort;

extras/migration/v52_to_v53/netezza_migration.sql

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+-- Derived from the OMOP CDM v5.2 and v5.3 Netezza DDLs in this repository.
+-- Netezza SQL references:
+--   https://www.ibm.com/docs/en/psfa
+--
+-- VISIT_DETAIL
+
+create table @cdmDatabaseSchema.visit_detail (
+    visit_detail_id integer NOT NULL,
+    person_id integer NOT NULL,
+    visit_detail_concept_id integer NOT NULL,
+    visit_detail_start_date date NOT NULL,
+    visit_detail_start_datetime TIMESTAMP NULL,
+    visit_detail_end_date date NOT NULL,
+    visit_detail_end_datetime TIMESTAMP NULL,
+    visit_detail_type_concept_id integer NOT NULL,
+    provider_id integer NULL,
+    care_site_id integer NULL,
+    visit_detail_source_value varchar(50) NULL,
+    visit_detail_source_concept_id integer NULL,
+    admitting_source_value varchar(50) NULL,
+    admitting_source_concept_id integer NULL,
+    discharge_to_source_value varchar(50) NULL,
+    discharge_to_concept_id integer NULL,
+    preceding_visit_detail_id integer NULL,
+    visit_detail_parent_id integer NULL,
+    visit_occurrence_id integer NOT NULL
+);
+
+-- CONDITION_OCCURRENCE
+alter table @cdmDatabaseSchema.condition_occurrence alter column condition_start_datetime drop not null;
+alter table @cdmDatabaseSchema.condition_occurrence add column visit_detail_id integer null;
+
+-- DRUG_EXPOSURE
+alter table @cdmDatabaseSchema.drug_exposure alter column drug_exposure_start_datetime drop not null;
+alter table @cdmDatabaseSchema.drug_exposure add column visit_detail_id integer null;
+
+-- PROCEDURE_OCCURRENCE
+alter table @cdmDatabaseSchema.procedure_occurrence alter column procedure_datetime drop not null;
+alter table @cdmDatabaseSchema.procedure_occurrence rename column qualifier_source_value to modifier_source_value;
+alter table @cdmDatabaseSchema.procedure_occurrence add column visit_detail_id integer null;
+
+-- DEVICE_EXPOSURE
+alter table @cdmDatabaseSchema.device_exposure alter column device_exposure_start_datetime drop not null;
+alter table @cdmDatabaseSchema.device_exposure alter column device_source_value set data type varchar(50);
+alter table @cdmDatabaseSchema.device_exposure add column visit_detail_id integer null;
+
+-- MEASUREMENT
+alter table @cdmDatabaseSchema.measurement add column measurement_time varchar(10) null;
+alter table @cdmDatabaseSchema.measurement add column visit_detail_id integer null;
+
+-- OBSERVATION
+alter table @cdmDatabaseSchema.observation add column visit_detail_id integer null;
+
+-- DEATH
+alter table @cdmDatabaseSchema.death alter column death_type_concept_id drop not null;
+
+-- NOTE
+alter table @cdmDatabaseSchema.note add column visit_detail_id integer null;
+
+-- NOTE_NLP
+alter table @cdmDatabaseSchema.note_nlp alter column note_nlp_id set data type integer;
+alter table @cdmDatabaseSchema.note_nlp alter column "offset" set data type varchar(50);
+
+-- PAYER_PLAN_PERIOD
+alter table @cdmDatabaseSchema.payer_plan_period add column payer_concept_id integer null;
+alter table @cdmDatabaseSchema.payer_plan_period add column payer_source_concept_id integer null;
+alter table @cdmDatabaseSchema.payer_plan_period add column plan_concept_id integer null;
+alter table @cdmDatabaseSchema.payer_plan_period add column plan_source_concept_id integer null;
+alter table @cdmDatabaseSchema.payer_plan_period add column sponsor_concept_id integer null;
+alter table @cdmDatabaseSchema.payer_plan_period add column sponsor_source_value varchar(50) null;
+alter table @cdmDatabaseSchema.payer_plan_period add column sponsor_source_concept_id integer null;
+alter table @cdmDatabaseSchema.payer_plan_period add column stop_reason_concept_id integer null;
+alter table @cdmDatabaseSchema.payer_plan_period add column stop_reason_source_value varchar(50) null;
+alter table @cdmDatabaseSchema.payer_plan_period add column stop_reason_source_concept_id integer null;
+
+-- COST
+alter table @cdmDatabaseSchema.cost rename column reveue_code_source_value to revenue_code_source_value;
+
+-- METADATA
+create table @cdmDatabaseSchema.metadata (
+    metadata_concept_id integer NOT NULL,
+    metadata_type_concept_id integer NOT NULL,
+    name varchar(250) NOT NULL,
+    value_as_string varchar(250) NULL,
+    value_as_concept_id integer NULL,
+    metadata_date date NULL,
+    metadata_datetime TIMESTAMP NULL
+);
+
+-- VOCABULARY
+update @cdmDatabaseSchema.vocabulary
+set vocabulary_reference = ''
+where vocabulary_reference is null;
+
+alter table @cdmDatabaseSchema.vocabulary alter column vocabulary_reference set not null;
+
+-- TABLES REMOVED IN v5.3
+drop table @cdmDatabaseSchema.cohort_attribute;
+drop table @cdmDatabaseSchema.cohort;

extras/migration/v52_to_v53/oracle_migration.sql

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+-- Derived from the OMOP CDM v5.2 and v5.3 Oracle DDLs in this repository.
+-- Oracle SQL references:
+--   https://docs.oracle.com/en/database/oracle/oracle-database/19/sqlrf/ALTER-TABLE.html
+--
+-- VISIT_DETAIL
+
+create table @cdmDatabaseSchema.visit_detail (
+    visit_detail_id integer NOT NULL,
+    person_id integer NOT NULL,
+    visit_detail_concept_id integer NOT NULL,
+    visit_detail_start_date date NOT NULL,
+    visit_detail_start_datetime TIMESTAMP NULL,
+    visit_detail_end_date date NOT NULL,
+    visit_detail_end_datetime TIMESTAMP NULL,
+    visit_detail_type_concept_id integer NOT NULL,
+    provider_id integer NULL,
+    care_site_id integer NULL,
+    visit_detail_source_value varchar2(50) NULL,
+    visit_detail_source_concept_id integer NULL,
+    admitting_source_value varchar2(50) NULL,
+    admitting_source_concept_id integer NULL,
+    discharge_to_source_value varchar2(50) NULL,
+    discharge_to_concept_id integer NULL,
+    preceding_visit_detail_id integer NULL,
+    visit_detail_parent_id integer NULL,
+    visit_occurrence_id integer NOT NULL
+);
+
+-- CONDITION_OCCURRENCE
+alter table @cdmDatabaseSchema.condition_occurrence modify (condition_start_datetime timestamp null);
+alter table @cdmDatabaseSchema.condition_occurrence add (visit_detail_id number default null);
+
+-- DRUG_EXPOSURE
+alter table @cdmDatabaseSchema.drug_exposure modify (drug_exposure_start_datetime timestamp null);
+alter table @cdmDatabaseSchema.drug_exposure add (visit_detail_id number default null);
+
+-- PROCEDURE_OCCURRENCE
+alter table @cdmDatabaseSchema.procedure_occurrence modify (procedure_datetime timestamp null);
+alter table @cdmDatabaseSchema.procedure_occurrence rename column qualifier_source_value to modifier_source_value;
+alter table @cdmDatabaseSchema.procedure_occurrence add (visit_detail_id number default null);
+
+-- DEVICE_EXPOSURE
+alter table @cdmDatabaseSchema.device_exposure modify (device_exposure_start_datetime timestamp null);
+alter table @cdmDatabaseSchema.device_exposure modify (device_source_value varchar2(50));
+alter table @cdmDatabaseSchema.device_exposure add (visit_detail_id number default null);
+
+-- MEASUREMENT
+alter table @cdmDatabaseSchema.measurement add (measurement_time varchar2(10) default null);
+alter table @cdmDatabaseSchema.measurement add (visit_detail_id number default null);
+
+-- OBSERVATION
+alter table @cdmDatabaseSchema.observation add (visit_detail_id number default null);
+
+-- DEATH
+alter table @cdmDatabaseSchema.death modify (death_type_concept_id number null);
+
+-- NOTE
+alter table @cdmDatabaseSchema.note add (visit_detail_id number default null);
+
+-- NOTE_NLP
+alter table @cdmDatabaseSchema.note_nlp modify (note_nlp_id number);
+alter table @cdmDatabaseSchema.note_nlp modify ("offset" varchar2(50));
+
+-- PAYER_PLAN_PERIOD
+alter table @cdmDatabaseSchema.payer_plan_period add (payer_concept_id number default null);
+alter table @cdmDatabaseSchema.payer_plan_period add (payer_source_concept_id number default null);
+alter table @cdmDatabaseSchema.payer_plan_period add (plan_concept_id number default null);
+alter table @cdmDatabaseSchema.payer_plan_period add (plan_source_concept_id number default null);
+alter table @cdmDatabaseSchema.payer_plan_period add (sponsor_concept_id number default null);
+alter table @cdmDatabaseSchema.payer_plan_period add (sponsor_source_value varchar2(50) default null);
+alter table @cdmDatabaseSchema.payer_plan_period add (sponsor_source_concept_id number default null);
+alter table @cdmDatabaseSchema.payer_plan_period add (stop_reason_concept_id number default null);
+alter table @cdmDatabaseSchema.payer_plan_period add (stop_reason_source_value varchar2(50) default null);
+alter table @cdmDatabaseSchema.payer_plan_period add (stop_reason_source_concept_id number default null);
+
+-- COST
+alter table @cdmDatabaseSchema.cost rename column reveue_code_source_value to revenue_code_source_value;
+
+-- METADATA
+create table @cdmDatabaseSchema.metadata (
+    metadata_concept_id integer NOT NULL,
+    metadata_type_concept_id integer NOT NULL,
+    name varchar2(250) NOT NULL,
+    value_as_string varchar2(250) NULL,
+    value_as_concept_id integer NULL,
+    metadata_date date NULL,
+    metadata_datetime TIMESTAMP NULL
+);
+
+-- VOCABULARY
+update @cdmDatabaseSchema.vocabulary
+set vocabulary_reference = ''
+where vocabulary_reference is null;
+
+alter table @cdmDatabaseSchema.vocabulary modify (vocabulary_reference varchar2(255) not null);
+
+-- TABLES REMOVED IN v5.3
+drop table @cdmDatabaseSchema.cohort_attribute;
+drop table @cdmDatabaseSchema.cohort;