mz-health/OMOP
mz-health
/
OMOP
mirror of https://github.com/OHDSI/CommonDataModel.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Including the 'Type Concept' domain_id from the latest version of the vocabulary

This commit is contained in:
Anthony Sena 2015-12-15 10:08:59 -05:00
parent 11188fee37
commit 021c9f5a14
6 changed files with 212 additions and 263 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

38
Version4 To Version5 Conversion/Convert-OHDSI-Sql-To-Dialect-Local.R
View File

@ -1,38 +0,0 @@
# Load Libraries
install.packages(devtools)
library(devtools)
install_github("OHDSI/SqlRender")
library(SqlRender)
# Variables
ohdsiSqlFile <- "C:/Git/CommonDataModel/Version4 To Version5 Conversion/OMOP CDMv4 to CDMv5 - OHDSI-SQL.sql"
targetSqlServerFile <- "C:/Git/CommonDataModel/Version4 To Version5 Conversion/Sql Server/OMOP CDMv4 to CDMv5 - SQL Server.sql"
targetPostgreSqlFile <- "C:/Git/CommonDataModel/Version4 To Version5 Conversion/PostgreSQL/OMOP CDMv4 to CDMv5 - PostgreSQL.sql"
targetOracleFile <- "C:/Git/CommonDataModel/Version4 To Version5 Conversion/Oracle/OMOP CDMv4 to CDMv5 - Oracle.sql"
targetSqlServerPDWFile <- "C:/Git/CommonDataModel/Version4 To Version5 Conversion/Sql Server PDW/OMOP CDMv4 to CDMv5 - Sql Server PDW.dsql"
targetRedshiftFile <- "C:/Git/CommonDataModel/Version4 To Version5 Conversion/Redshift/OMOP CDMv4 to CDMv5 - Redshift.sql"
##### LOCAL - SQL Server Testing
#renderSqlFile(ohdsiSqlFile, targetSqlServerFile, SOURCE_CDMV4 = "[CDMV4]", SOURCE_CDMV4_SCHEMA = "[CDMV4].[dbo]", TARGET_CDMV5 = "[CDMV5]", TARGET_CDMV5_SCHEMA = "[CDMV5].[dbo]")
##### SQL Server Testing
#renderSqlFile(ohdsiSqlFile, targetSqlServerFile, SOURCE_CDMV4 = "[CDM_TRUVEN_CCAE_6k]", SOURCE_CDMV4_SCHEMA = "[CDM_TRUVEN_CCAE_6k].[dbo]", TARGET_CDMV5 = "[CDMV5_Conversion_Target]", TARGET_CDMV5_SCHEMA = "[CDMV5_Conversion_Target].[dbo]")
##### PostgreSql Testing
#renderSqlFile(ohdsiSqlFile, targetSqlServerFile, SOURCE_CDMV4 = "sandbox", SOURCE_CDMV4_SCHEMA = "sandbox.cdmv4", TARGET_CDMV5 = "sandbox", TARGET_CDMV5_SCHEMA = "sandbox.cdmv5")
#translateSqlFile(sourceFile = targetSqlServerFile, targetFile = targetPostgreSqlFile, targetDialect = "postgresql")
##### Oracle Testing
#renderSqlFile(ohdsiSqlFile, targetSqlServerFile, SOURCE_CDMV4 = "CDMV4", SOURCE_CDMV4_SCHEMA = "CDMV4", TARGET_CDMV5 = "CDMV5", TARGET_CDMV5_SCHEMA = "CDMV5")
#translateSqlFile(sourceFile = targetSqlServerFile, targetFile = targetOracleFile, targetDialect = "oracle")
##### APS Testing
#renderSqlFile(ohdsiSqlFile, targetSqlServerFile, SOURCE_CDMV4 = "[CDM_THIN]", SOURCE_CDMV4_SCHEMA = "[CDM_THIN].[dbo]", TARGET_CDMV5 = "[CDM_THIN_V5_asena5]", TARGET_CDMV5_SCHEMA = "[CDM_THIN_V5_asena5].[dbo]")
#translateSqlFile(sourceFile = targetSqlServerFile, targetFile = targetSqlServerPDWFile, targetDialect = "pdw")
##### Push to GitHub
renderSqlFile(ohdsiSqlFile, targetSqlServerFile)
translateSqlFile(sourceFile = targetSqlServerFile, targetFile = targetPostgreSqlFile, targetDialect = "postgresql")
translateSqlFile(sourceFile = targetSqlServerFile, targetFile = targetOracleFile, targetDialect = "oracle")
translateSqlFile(sourceFile = targetSqlServerFile, targetFile = targetSqlServerPDWFile, targetDialect = "pdw")
translateSqlFile(sourceFile = targetSqlServerFile, targetFile = targetRedshiftFile, targetDialect = "redshift")

325
Version4 To Version5 Conversion/Oracle/OMOP CDMv4 to CDMv5 - Oracle.sql
View File

@ -109,8 +109,8 @@ ALTER SESSION SET current_schema = [TARGET_CDMV5];
* Also, as of the date which this script was authored, no source_concept_ids map to multiple domains * Also, as of the date which this script was authored, no source_concept_ids map to multiple domains
*/ */
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0concept_map'; EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmconcept_map';
EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0concept_map'; EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmconcept_map';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -120,9 +120,8 @@ END;
/* / */ /* / */
CREATE GLOBAL TEMPORARY TABLE ilbyrix0concept_map CREATE TABLE g8iauhqmconcept_map
ON COMMIT PRESERVE ROWS AS
AS
SELECT SELECT
concept_id AS source_concept_id concept_id AS source_concept_id
,concept_id AS target_concept_id ,concept_id AS target_concept_id
@ -134,7 +133,7 @@ FROM
/* / */ /* / */
INSERT INTO ilbyrix0concept_map INSERT INTO g8iauhqmconcept_map
--standard concepts --standard concepts
SELECT concept_id AS source_concept_id SELECT concept_id AS source_concept_id
,concept_id AS target_concept_id ,concept_id AS target_concept_id
@ -269,11 +268,11 @@ INNER JOIN [TARGET_CDMV5].[SCHEMA].concept c2 ON cr1.concept_id_2 = c2.concept_i
WHERE c2.standard_concept = 'S' WHERE c2.standard_concept = 'S'
AND c2.invalid_reason IS NULL AND c2.invalid_reason IS NULL
AND cr1.relationship_id IN ('Is a') AND cr1.relationship_id IN ('Is a')
AND cr1.invalid_reason IS NULL FROM DUAL FROM DUAL FROM DUAL; AND cr1.invalid_reason IS NULL ;
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0concept_map_distinct'; EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmconcept_map_distinct';
EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0concept_map_distinct'; EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmconcept_map_distinct';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -283,27 +282,26 @@ END;
/* / */ /* / */
CREATE GLOBAL TEMPORARY TABLE ilbyrix0concept_map_distinct CREATE TABLE g8iauhqmconcept_map_distinct
ON COMMIT PRESERVE ROWS AS
AS
SELECT SELECT
source_concept_id source_concept_id
,domain_id ,domain_id
,COUNT(*) AS targetConceptCount ,COUNT(*) AS targetConceptCount
FROM FROM
ilbyrix0concept_map g8iauhqmconcept_map
WHERE 1 = 0 WHERE 1 = 0
GROUP BY source_concept_id GROUP BY source_concept_id
,domain_id ; ,domain_id ;
/* / */ /* / */
INSERT INTO ilbyrix0concept_map_distinct INSERT INTO g8iauhqmconcept_map_distinct
SELECT source_concept_id SELECT source_concept_id
,domain_id ,domain_id
,COUNT(*) ,COUNT(*)
FROM ilbyrix0concept_map FROM g8iauhqmconcept_map
GROUP BY source_concept_id GROUP BY source_concept_id
,domain_id ; ,domain_id ;
@ -416,11 +414,11 @@ SELECT person_id
,ethnicity_source_value ,ethnicity_source_value
,CAST(NULL AS INT) ethnicity_source_concept_id ,CAST(NULL AS INT) ethnicity_source_concept_id
FROM [SOURCE_CDMV4].[SCHEMA].PERSON p FROM [SOURCE_CDMV4].[SCHEMA].PERSON p
LEFT JOIN ilbyrix0concept_map gender ON LOWER(gender.DOMAIN_ID) IN ('gender') LEFT JOIN g8iauhqmconcept_map gender ON LOWER(gender.DOMAIN_ID) IN ('gender')
AND p.gender_concept_id = gender.source_concept_id AND p.gender_concept_id = gender.source_concept_id
LEFT JOIN ilbyrix0concept_map race ON LOWER(race.DOMAIN_ID) IN ('race') LEFT JOIN g8iauhqmconcept_map race ON LOWER(race.DOMAIN_ID) IN ('race')
AND p.race_concept_id = race.source_concept_id AND p.race_concept_id = race.source_concept_id
LEFT JOIN ilbyrix0concept_map ethnicity ON LOWER(ethnicity.DOMAIN_ID) IN ('ethnicity') LEFT JOIN g8iauhqmconcept_map ethnicity ON LOWER(ethnicity.DOMAIN_ID) IN ('ethnicity')
AND p.ETHNICITY_CONCEPT_ID = ethnicity.source_concept_id ; AND p.ETHNICITY_CONCEPT_ID = ethnicity.source_concept_id ;
INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE)
@ -496,8 +494,8 @@ SELECT person_id
,cause_of_death_source_value AS cause_source_value ,cause_of_death_source_value AS cause_source_value
,CAST(NULL AS INT) AS cause_source_concept_id ,CAST(NULL AS INT) AS cause_source_concept_id
FROM [SOURCE_CDMV4].[SCHEMA].DEATH FROM [SOURCE_CDMV4].[SCHEMA].DEATH
LEFT JOIN ilbyrix0concept_map_distinct cm1 ON DEATH.DEATH_TYPE_CONCEPT_ID = CM1.SOURCE_CONCEPT_ID LEFT JOIN g8iauhqmconcept_map_distinct cm1 ON DEATH.DEATH_TYPE_CONCEPT_ID = CM1.SOURCE_CONCEPT_ID
AND LOWER(DOMAIN_ID) IN ('death type') ; AND LOWER(DOMAIN_ID) IN ('death type', 'Type Concept') ;
INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE)
SELECT 'DEATH: ' || TO_CHAR(NUM_INVALID_RECORDS ) || ' records in the source CDMv4 database have invalid DEATH_TYPE_CONCEPT_ID' SELECT 'DEATH: ' || TO_CHAR(NUM_INVALID_RECORDS ) || ' records in the source CDMv4 database have invalid DEATH_TYPE_CONCEPT_ID'
@ -508,7 +506,7 @@ SELECT 'DEATH: ' || TO_CHAR(NUM_INVALID_RECORDS ) || ' records in the source C
WHERE CONCEPT_ID = 0 WHERE CONCEPT_ID = 0
OR ( OR (
STANDARD_CONCEPT = 'S' STANDARD_CONCEPT = 'S'
AND LOWER(DOMAIN_ID) IN ('death type') AND LOWER(DOMAIN_ID) IN ('death type', 'Type Concept')
) )
) )
HAVING COUNT(PERSON_ID) > 0 HAVING COUNT(PERSON_ID) > 0
@ -533,7 +531,7 @@ SELECT visit_occurrence_id
,place_of_service_source_value AS visit_source_value ,place_of_service_source_value AS visit_source_value
,CAST(NULL AS INT) visit_source_concept_id ,CAST(NULL AS INT) visit_source_concept_id
FROM [SOURCE_CDMV4].[SCHEMA].VISIT_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].VISIT_OCCURRENCE
LEFT JOIN ilbyrix0concept_map cm1 ON VISIT_OCCURRENCE.PLACE_OF_SERVICE_CONCEPT_ID = cm1.source_concept_id LEFT JOIN g8iauhqmconcept_map cm1 ON VISIT_OCCURRENCE.PLACE_OF_SERVICE_CONCEPT_ID = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('visit') ; AND LOWER(cm1.domain_id) IN ('visit') ;
INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE)
@ -557,8 +555,8 @@ SELECT 'VISIT_OCCURRENCE: ' || TO_CHAR(NUM_INVALID_RECORDS ) || ' records in t
****/ ****/
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0po_map'; EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmpo_map';
EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0po_map'; EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmpo_map';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -568,9 +566,8 @@ END;
/* / */ /* / */
CREATE GLOBAL TEMPORARY TABLE ilbyrix0po_map CREATE TABLE g8iauhqmpo_map
ON COMMIT PRESERVE ROWS AS
AS
SELECT SELECT
po.procedure_occurrence_id po.procedure_occurrence_id
,po.person_id ,po.person_id
@ -594,7 +591,7 @@ LEFT JOIN [TARGET_CDMV5].[SCHEMA].drug_exposure de ON 1 = 0
/* / */ /* / */
--find valid procedures from procedure table --find valid procedures from procedure table
INSERT INTO ilbyrix0po_map INSERT INTO g8iauhqmpo_map
SELECT procedure_occurrence_id SELECT procedure_occurrence_id
,person_id ,person_id
,COALESCE(cm1.target_concept_id, 0) AS procedure_concept_id ,COALESCE(cm1.target_concept_id, 0) AS procedure_concept_id
@ -609,14 +606,14 @@ SELECT procedure_occurrence_id
,NULL AS qualifier_source_value ,NULL AS qualifier_source_value
,CAST(NULL AS INT) AS origional_drug_id ,CAST(NULL AS INT) AS origional_drug_id
FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
INNER JOIN ilbyrix0concept_map cm1 ON PROCEDURE_OCCURRENCE.PROCEDURE_CONCEPT_ID = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON PROCEDURE_OCCURRENCE.PROCEDURE_CONCEPT_ID = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('procedure') AND LOWER(cm1.domain_id) IN ('procedure')
INNER JOIN ilbyrix0concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id INNER JOIN g8iauhqmconcept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount = 1 AND cmdis.targetConceptCount = 1
LEFT JOIN ilbyrix0concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id LEFT JOIN g8iauhqmconcept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('procedure type') AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
LEFT JOIN ilbyrix0concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id LEFT JOIN g8iauhqmconcept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id
AND cm2.domain_id = cmdis2.domain_id AND cm2.domain_id = cmdis2.domain_id
AND cmdis2.targetConceptCount = 1 AND cmdis2.targetConceptCount = 1
@ -656,9 +653,9 @@ SELECT procedure_occurrence_id
,NULL qualifier_source_value ,NULL qualifier_source_value
,CAST(NULL AS INT) AS origional_drug_id ,CAST(NULL AS INT) AS origional_drug_id
FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
LEFT JOIN ilbyrix0concept_map cm1 ON procedure_concept_id = cm1.source_concept_id LEFT JOIN g8iauhqmconcept_map cm1 ON procedure_concept_id = cm1.source_concept_id
LEFT JOIN ilbyrix0concept_map cm2 ON procedure_concept_id = cm2.source_concept_id LEFT JOIN g8iauhqmconcept_map cm2 ON procedure_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('procedure type') AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
WHERE procedure_concept_id <> 0 WHERE procedure_concept_id <> 0
AND cm1.domain_id IS NULL AND cm1.domain_id IS NULL
@ -697,13 +694,13 @@ SELECT CASE
,CAST(NULL AS INT) AS origional_drug_id ,CAST(NULL AS INT) AS origional_drug_id
,CAST(NULL AS INT) AS OCCURRENCE_ID ,CAST(NULL AS INT) AS OCCURRENCE_ID
FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
INNER JOIN ilbyrix0concept_map cm1 ON PROCEDURE_OCCURRENCE.PROCEDURE_CONCEPT_ID = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON PROCEDURE_OCCURRENCE.PROCEDURE_CONCEPT_ID = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('procedure') AND LOWER(cm1.domain_id) IN ('procedure')
INNER JOIN ilbyrix0concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id INNER JOIN g8iauhqmconcept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount > 1 AND cmdis.targetConceptCount > 1
LEFT JOIN ilbyrix0concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id LEFT JOIN g8iauhqmconcept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('procedure type') AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
UNION ALL UNION ALL
@ -722,7 +719,7 @@ SELECT CASE
,CAST(NULL AS INT) AS origional_drug_id ,CAST(NULL AS INT) AS origional_drug_id
,condition_occurrence_id AS OCCURRENCE_ID ,condition_occurrence_id AS OCCURRENCE_ID
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
INNER JOIN ilbyrix0concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('procedure') AND LOWER(cm1.domain_id) IN ('procedure')
UNION ALL UNION ALL
@ -742,7 +739,7 @@ SELECT CASE
,drug_exposure_id AS origional_drug_id ,drug_exposure_id AS origional_drug_id
,drug_exposure_id AS OCCURRENCE_ID ,drug_exposure_id AS OCCURRENCE_ID
FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE
INNER JOIN ilbyrix0concept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('procedure') AND LOWER(cm1.domain_id) IN ('procedure')
--find procedures that were previously classified as observation --find procedures that were previously classified as observation
@ -762,12 +759,12 @@ SELECT CASE
,CAST(NULL AS INT) AS origional_drug_id ,CAST(NULL AS INT) AS origional_drug_id
,OBSERVATION_ID AS OCCURRENCE_ID ,OBSERVATION_ID AS OCCURRENCE_ID
FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION
INNER JOIN ilbyrix0concept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('procedure') AND LOWER(cm1.domain_id) IN ('procedure')
) OTHERS ) OTHERS
,(SELECT MAX(PROCEDURE_OCCURRENCE_ID) AS MAXROWID ,(SELECT MAX(PROCEDURE_OCCURRENCE_ID) AS MAXROWID
FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
) MAXROW FROM DUAL FROM DUAL; ) MAXROW ;
INSERT INTO [TARGET_CDMV5].[SCHEMA].procedure_occurrence ( INSERT INTO [TARGET_CDMV5].[SCHEMA].procedure_occurrence (
procedure_occurrence_id procedure_occurrence_id
@ -795,7 +792,7 @@ SELECT procedure_occurrence_id
,procedure_source_value ,procedure_source_value
,procedure_source_concept_id ,procedure_source_concept_id
,qualifier_source_value ,qualifier_source_value
FROM ilbyrix0po_map ; FROM g8iauhqmpo_map ;
--warnings of invalid records --warnings of invalid records
INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE)
@ -819,7 +816,7 @@ SELECT 'PROCEDURE_OCCURRENCE: ' || TO_CHAR(NUM_INVALID_RECORDS ) || ' records
WHERE CONCEPT_ID = 0 WHERE CONCEPT_ID = 0
OR ( OR (
STANDARD_CONCEPT = 'S' STANDARD_CONCEPT = 'S'
AND LOWER(DOMAIN_ID) IN ('procedure type') AND LOWER(DOMAIN_ID) IN ('procedure type', 'Type Concept')
) )
) )
HAVING COUNT(PERSON_ID) > 0 HAVING COUNT(PERSON_ID) > 0
@ -832,8 +829,8 @@ SELECT 'PROCEDURE_OCCURRENCE: ' || TO_CHAR(NUM_INVALID_RECORDS ) || ' records
****/ ****/
--find valid drugs from drug_exposure table --find valid drugs from drug_exposure table
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0drgexp_map'; EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmdrgexp_map';
EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0drgexp_map'; EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmdrgexp_map';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -843,9 +840,8 @@ END;
/* / */ /* / */
CREATE GLOBAL TEMPORARY TABLE ilbyrix0drgexp_map CREATE TABLE g8iauhqmdrgexp_map
ON COMMIT PRESERVE ROWS AS
AS
SELECT SELECT
de.drug_exposure_id de.drug_exposure_id
,de.person_id ,de.person_id
@ -877,7 +873,7 @@ LEFT JOIN [TARGET_CDMV5].[SCHEMA].procedure_occurrence po ON 1 = 0
/* / */ /* / */
INSERT INTO ilbyrix0drgexp_map INSERT INTO g8iauhqmdrgexp_map
SELECT drug_exposure_id SELECT drug_exposure_id
,person_id ,person_id
,COALESCE(cm1.target_concept_id, 0) AS drug_concept_id ,COALESCE(cm1.target_concept_id, 0) AS drug_concept_id
@ -901,14 +897,14 @@ SELECT drug_exposure_id
,NULL AS dose_unit_source_value ,NULL AS dose_unit_source_value
,CAST(NULL AS INT) AS origional_procedure_id ,CAST(NULL AS INT) AS origional_procedure_id
FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE
INNER JOIN ilbyrix0concept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('drug') AND LOWER(cm1.domain_id) IN ('drug')
INNER JOIN ilbyrix0concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id INNER JOIN g8iauhqmconcept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount = 1 AND cmdis.targetConceptCount = 1
LEFT JOIN ilbyrix0concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id LEFT JOIN g8iauhqmconcept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('drug type') AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
INNER JOIN ilbyrix0concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id INNER JOIN g8iauhqmconcept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id
AND cm2.domain_id = cmdis2.domain_id AND cm2.domain_id = cmdis2.domain_id
AND cmdis2.targetConceptCount = 1 AND cmdis2.targetConceptCount = 1
WHERE drug_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4 WHERE drug_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4
@ -967,9 +963,9 @@ SELECT drug_exposure_id
,NULL AS dose_unit_source_value ,NULL AS dose_unit_source_value
,CAST(NULL AS INT) AS origional_procedure_id ,CAST(NULL AS INT) AS origional_procedure_id
FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE
LEFT JOIN ilbyrix0concept_map cm1 ON drug_concept_id = cm1.source_concept_id LEFT JOIN g8iauhqmconcept_map cm1 ON drug_concept_id = cm1.source_concept_id
LEFT JOIN ilbyrix0concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id LEFT JOIN g8iauhqmconcept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('drug type') AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
WHERE drug_concept_id <> 0 WHERE drug_concept_id <> 0
AND cm1.domain_id IS NULL AND cm1.domain_id IS NULL
@ -1026,13 +1022,13 @@ SELECT CASE
,CAST(NULL AS INT) AS origional_procedure_id ,CAST(NULL AS INT) AS origional_procedure_id
,CAST(NULL AS INT) AS OCCURRENCE_ID ,CAST(NULL AS INT) AS OCCURRENCE_ID
FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE
INNER JOIN ilbyrix0concept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('drug') AND LOWER(cm1.domain_id) IN ('drug')
INNER JOIN ilbyrix0concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id INNER JOIN g8iauhqmconcept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount > 1 AND cmdis.targetConceptCount > 1
LEFT JOIN ilbyrix0concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id LEFT JOIN g8iauhqmconcept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('drug type') AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
UNION ALL UNION ALL
@ -1060,7 +1056,7 @@ SELECT CASE
,CAST(NULL AS INT) AS origional_procedure_id ,CAST(NULL AS INT) AS origional_procedure_id
,condition_occurrence_id AS occurrence_id ,condition_occurrence_id AS occurrence_id
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
INNER JOIN ilbyrix0concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('drug') AND LOWER(cm1.domain_id) IN ('drug')
--find drugs that were previously classified as procedure --find drugs that were previously classified as procedure
@ -1089,7 +1085,7 @@ SELECT CASE
,procedure_occurrence_id AS origional_procedure_id ,procedure_occurrence_id AS origional_procedure_id
,procedure_occurrence_id AS occurrence_id ,procedure_occurrence_id AS occurrence_id
FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
INNER JOIN ilbyrix0concept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('drug') AND LOWER(cm1.domain_id) IN ('drug')
--find drugs that were previously classified as observation --find drugs that were previously classified as observation
@ -1118,12 +1114,12 @@ SELECT CASE
,CAST(NULL AS INT) AS origional_procedure_id ,CAST(NULL AS INT) AS origional_procedure_id
,observation_id AS occurrence_id ,observation_id AS occurrence_id
FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION
INNER JOIN ilbyrix0concept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('drug') AND LOWER(cm1.domain_id) IN ('drug')
) OTHERS ) OTHERS
,(SELECT MAX(DRUG_EXPOSURE_ID) AS MAXROWID ,(SELECT MAX(DRUG_EXPOSURE_ID) AS MAXROWID
FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE
) MAXROW FROM DUAL FROM DUAL; ) MAXROW ;
INSERT INTO [TARGET_CDMV5].[SCHEMA].drug_exposure ( INSERT INTO [TARGET_CDMV5].[SCHEMA].drug_exposure (
drug_exposure_id drug_exposure_id
@ -1169,7 +1165,7 @@ SELECT drug_exposure_id
,drug_source_concept_id ,drug_source_concept_id
,route_source_value ,route_source_value
,dose_unit_source_value ,dose_unit_source_value
FROM ilbyrix0drgexp_map ; FROM g8iauhqmdrgexp_map ;
--warnings of invalid records --warnings of invalid records
INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE)
@ -1193,7 +1189,7 @@ SELECT 'DRUG_EXPOSURE: ' || TO_CHAR(NUM_INVALID_RECORDS ) || ' records in the
WHERE CONCEPT_ID = 0 WHERE CONCEPT_ID = 0
OR ( OR (
STANDARD_CONCEPT = 'S' STANDARD_CONCEPT = 'S'
AND LOWER(DOMAIN_ID) IN ('drug type') AND LOWER(DOMAIN_ID) IN ('drug type', 'Type Concept')
) )
) )
HAVING COUNT(PERSON_ID) > 0 HAVING COUNT(PERSON_ID) > 0
@ -1218,13 +1214,13 @@ SELECT condition_occurrence_id
,condition_source_value ,condition_source_value
,CAST(NULL AS INT) condition_source_concept_id ,CAST(NULL AS INT) condition_source_concept_id
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
INNER JOIN ilbyrix0concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('condition') AND LOWER(cm1.domain_id) IN ('condition')
INNER JOIN ilbyrix0concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id INNER JOIN g8iauhqmconcept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount = 1 AND cmdis.targetConceptCount = 1
LEFT JOIN ilbyrix0concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id LEFT JOIN g8iauhqmconcept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('condition type') AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4 WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4
UNION ALL UNION ALL
@ -1259,9 +1255,9 @@ SELECT condition_occurrence_id
,condition_source_value ,condition_source_value
,CAST(NULL AS INT) condition_source_concept_id ,CAST(NULL AS INT) condition_source_concept_id
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
LEFT JOIN ilbyrix0concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id LEFT JOIN g8iauhqmconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
LEFT JOIN ilbyrix0concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id LEFT JOIN g8iauhqmconcept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('condition type') AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
WHERE condition_concept_id <> 0 WHERE condition_concept_id <> 0
AND cm1.domain_id IS NULL AND cm1.domain_id IS NULL
@ -1296,13 +1292,13 @@ SELECT CASE
,CAST(NULL AS INT) condition_source_concept_id ,CAST(NULL AS INT) condition_source_concept_id
,NULL AS OCCURRENCE_ID ,NULL AS OCCURRENCE_ID
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
INNER JOIN ilbyrix0concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('condition') AND LOWER(cm1.domain_id) IN ('condition')
INNER JOIN ilbyrix0concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id INNER JOIN g8iauhqmconcept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount > 1 AND cmdis.targetConceptCount > 1
LEFT JOIN ilbyrix0concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id LEFT JOIN g8iauhqmconcept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('condition type') AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4 WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4
UNION ALL UNION ALL
@ -1320,7 +1316,7 @@ SELECT CASE
,CAST(NULL AS INT) condition_source_concept_id ,CAST(NULL AS INT) condition_source_concept_id
,procedure_occurrence_id AS OCCURRENCE_ID ,procedure_occurrence_id AS OCCURRENCE_ID
FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
INNER JOIN ilbyrix0concept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('condition') AND LOWER(cm1.domain_id) IN ('condition')
--find conditions that were previously classified as drug --find conditions that were previously classified as drug
@ -1338,7 +1334,7 @@ SELECT CASE
,CAST(NULL AS INT) condition_source_concept_id ,CAST(NULL AS INT) condition_source_concept_id
,drug_exposure_id AS OCCURRENCE_ID ,drug_exposure_id AS OCCURRENCE_ID
FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE
INNER JOIN ilbyrix0concept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('condition') AND LOWER(cm1.domain_id) IN ('condition')
--find conditions that were previously classified as observation --find conditions that were previously classified as observation
@ -1356,12 +1352,12 @@ SELECT CASE
,CAST(NULL AS INT) condition_source_concept_id ,CAST(NULL AS INT) condition_source_concept_id
,observation_id AS OCCURRENCE_ID ,observation_id AS OCCURRENCE_ID
FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION
INNER JOIN ilbyrix0concept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('condition') AND LOWER(cm1.domain_id) IN ('condition')
) OTHERS ) OTHERS
,(SELECT MAX(condition_occurrence_id) AS MAXROWID ,(SELECT MAX(condition_occurrence_id) AS MAXROWID
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
) MAXROW FROM DUAL FROM DUAL; ) MAXROW ;
--warnings of invalid records --warnings of invalid records
INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE)
@ -1385,7 +1381,7 @@ SELECT 'CONDIITON_OCCURRENCE: ' || TO_CHAR(NUM_INVALID_RECORDS ) || ' records
WHERE CONCEPT_ID = 0 WHERE CONCEPT_ID = 0
OR ( OR (
STANDARD_CONCEPT = 'S' STANDARD_CONCEPT = 'S'
AND LOWER(DOMAIN_ID) IN ('condition type') AND LOWER(DOMAIN_ID) IN ('condition type', 'Type Concept')
) )
) )
HAVING COUNT(PERSON_ID) > 0 HAVING COUNT(PERSON_ID) > 0
@ -1424,7 +1420,7 @@ SELECT row_number() OVER (
,0 AS device_source_concept_id ,0 AS device_source_concept_id
,PROCEDURE_OCCURRENCE_ID AS OCCURRENCE_ID ,PROCEDURE_OCCURRENCE_ID AS OCCURRENCE_ID
FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
INNER JOIN ilbyrix0concept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('device') AND LOWER(cm1.domain_id) IN ('device')
--find devices that were previously classified as drug exposure --find devices that were previously classified as drug exposure
@ -1443,7 +1439,7 @@ SELECT row_number() OVER (
,0 AS device_source_concept_id ,0 AS device_source_concept_id
,DRUG_EXPOSURE_ID AS OCCURRENCE_ID ,DRUG_EXPOSURE_ID AS OCCURRENCE_ID
FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE
INNER JOIN ilbyrix0concept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('device') AND LOWER(cm1.domain_id) IN ('device')
--find devices that were previously classified as conditions --find devices that were previously classified as conditions
@ -1462,7 +1458,7 @@ SELECT row_number() OVER (
,0 AS device_source_concept_id ,0 AS device_source_concept_id
,CONDITION_OCCURRENCE_ID AS OCCURRENCE_ID ,CONDITION_OCCURRENCE_ID AS OCCURRENCE_ID
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
INNER JOIN ilbyrix0concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('device') AND LOWER(cm1.domain_id) IN ('device')
--find devices that were previously classified as observations --find devices that were previously classified as observations
@ -1481,7 +1477,7 @@ SELECT row_number() OVER (
,0 AS device_source_concept_id ,0 AS device_source_concept_id
,OBSERVATION_ID AS OCCURRENCE_ID ,OBSERVATION_ID AS OCCURRENCE_ID
FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION
INNER JOIN ilbyrix0concept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('device') AND LOWER(cm1.domain_id) IN ('device')
) OTHERS ; ) OTHERS ;
@ -1531,9 +1527,9 @@ SELECT row_number() OVER (
,TO_CHAR(NULL ) AS value_source_value ,TO_CHAR(NULL ) AS value_source_value
,observation_id AS occurrence_id ,observation_id AS occurrence_id
FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION
INNER JOIN ilbyrix0concept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('measurement') AND LOWER(cm1.domain_id) IN ('measurement')
LEFT JOIN ilbyrix0concept_map cm2 ON observation.unit_concept_id = cm2.source_concept_id LEFT JOIN g8iauhqmconcept_map cm2 ON observation.unit_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('unit') AND LOWER(cm2.domain_id) IN ('unit')
UNION ALL UNION ALL
@ -1557,7 +1553,7 @@ SELECT row_number() OVER (
,TO_CHAR(NULL ) AS value_source_value ,TO_CHAR(NULL ) AS value_source_value
,procedure_occurrence_id AS occurrence_id ,procedure_occurrence_id AS occurrence_id
FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
INNER JOIN ilbyrix0concept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('measurement') AND LOWER(cm1.domain_id) IN ('measurement')
UNION ALL UNION ALL
@ -1581,7 +1577,7 @@ SELECT row_number() OVER (
,TO_CHAR(NULL ) AS value_source_value ,TO_CHAR(NULL ) AS value_source_value
,condition_occurrence_id AS occurrence_id ,condition_occurrence_id AS occurrence_id
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
INNER JOIN ilbyrix0concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('measurement') AND LOWER(cm1.domain_id) IN ('measurement')
UNION ALL UNION ALL
@ -1605,7 +1601,7 @@ SELECT row_number() OVER (
,TO_CHAR(NULL ) AS value_source_value ,TO_CHAR(NULL ) AS value_source_value
,drug_exposure_id AS occurrence_id ,drug_exposure_id AS occurrence_id
FROM [SOURCE_CDMV4].[SCHEMA].drug_exposure FROM [SOURCE_CDMV4].[SCHEMA].drug_exposure
INNER JOIN ilbyrix0concept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('measurement') AND LOWER(cm1.domain_id) IN ('measurement')
) OTHERS ; ) OTHERS ;
@ -1635,7 +1631,7 @@ SELECT observation_id
,TO_CHAR(NULL ) qualifier_source_value ,TO_CHAR(NULL ) qualifier_source_value
FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION
WHERE observation_concept_id NOT IN (SELECT source_concept_id WHERE observation_concept_id NOT IN (SELECT source_concept_id
FROM ilbyrix0concept_map_distinct FROM g8iauhqmconcept_map_distinct
WHERE LOWER(domain_id) IN ( WHERE LOWER(domain_id) IN (
'condition' 'condition'
,'drug' ,'drug'
@ -1689,7 +1685,7 @@ SELECT CASE
,TO_CHAR(NULL ) qualifier_source_value ,TO_CHAR(NULL ) qualifier_source_value
,procedure_occurrence_id AS occurrence_id ,procedure_occurrence_id AS occurrence_id
FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
INNER JOIN ilbyrix0concept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('observation') AND LOWER(cm1.domain_id) IN ('observation')
--find observations that were previously classified as condition --find observations that were previously classified as condition
@ -1713,7 +1709,7 @@ SELECT CASE
,TO_CHAR(NULL ) qualifier_source_value ,TO_CHAR(NULL ) qualifier_source_value
,condition_occurrence_id AS occurrence_id ,condition_occurrence_id AS occurrence_id
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
INNER JOIN ilbyrix0concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('observation') AND LOWER(cm1.domain_id) IN ('observation')
UNION ALL UNION ALL
@ -1738,7 +1734,7 @@ SELECT CASE
,po.procedure_occurrence_id AS occurrence_id ,po.procedure_occurrence_id AS occurrence_id
FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_COST pc FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_COST pc
INNER JOIN [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE po ON pc.PROCEDURE_OCCURRENCE_ID = po.PROCEDURE_OCCURRENCE_ID INNER JOIN [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE po ON pc.PROCEDURE_OCCURRENCE_ID = po.PROCEDURE_OCCURRENCE_ID
INNER JOIN ilbyrix0concept_map cm1 ON pc.disease_class_concept_id = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON pc.disease_class_concept_id = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('observation') AND LOWER(cm1.domain_id) IN ('observation')
UNION ALL UNION ALL
@ -1762,7 +1758,7 @@ SELECT CASE
,TO_CHAR(NULL ) qualifier_source_value ,TO_CHAR(NULL ) qualifier_source_value
,drug_exposure_id AS occurrence_id ,drug_exposure_id AS occurrence_id
FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE
INNER JOIN ilbyrix0concept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id INNER JOIN g8iauhqmconcept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id
AND LOWER(cm1.domain_id) IN ('observation') AND LOWER(cm1.domain_id) IN ('observation')
) OTHERS ) OTHERS
,(SELECT MAX(OBSERVATION_ID) AS MAXROWID ,(SELECT MAX(OBSERVATION_ID) AS MAXROWID
@ -1847,7 +1843,7 @@ SELECT CASE
FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE po FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE po
INNER JOIN [SOURCE_CDMV4].[SCHEMA].PROCEDURE_COST pc ON po.procedure_occurrence_id = pc.procedure_occurrence_id INNER JOIN [SOURCE_CDMV4].[SCHEMA].PROCEDURE_COST pc ON po.procedure_occurrence_id = pc.procedure_occurrence_id
--JOIN dbo.drug_exposure de on de.person_id = po.person_id and pc.procedure_occurrence_id = de.origional_procedure_id --JOIN dbo.drug_exposure de on de.person_id = po.person_id and pc.procedure_occurrence_id = de.origional_procedure_id
INNER JOIN ilbyrix0drgexp_map de ON de.person_id = po.person_id INNER JOIN g8iauhqmdrgexp_map de ON de.person_id = po.person_id
AND pc.procedure_occurrence_id = de.origional_procedure_id AND pc.procedure_occurrence_id = de.origional_procedure_id
) OTHERS ) OTHERS
,(SELECT MAX(drug_cost_id) AS MAXROWID ,(SELECT MAX(drug_cost_id) AS MAXROWID
@ -1918,7 +1914,7 @@ SELECT CASE
FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE de FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE de
INNER JOIN [SOURCE_CDMV4].[SCHEMA].DRUG_COST dc ON de.drug_exposure_id = dc.drug_exposure_id INNER JOIN [SOURCE_CDMV4].[SCHEMA].DRUG_COST dc ON de.drug_exposure_id = dc.drug_exposure_id
--JOIN dbo.procedure_occurrence po on de.person_id = po.person_id and de.drug_exposure_id = po.origional_drug_id --JOIN dbo.procedure_occurrence po on de.person_id = po.person_id and de.drug_exposure_id = po.origional_drug_id
INNER JOIN ilbyrix0po_map po ON de.person_id = po.person_id INNER JOIN g8iauhqmpo_map po ON de.person_id = po.person_id
AND de.drug_exposure_id = po.origional_drug_id AND de.drug_exposure_id = po.origional_drug_id
) OTHERS ) OTHERS
,(SELECT MAX(drug_cost_id) AS MAXROWID ,(SELECT MAX(drug_cost_id) AS MAXROWID
@ -1932,8 +1928,8 @@ Note: Eras derived from DRUG_EXPOSURE table, using 30d gap
****/ ****/
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0cteDrugTarget'; EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmcteDrugTarget';
EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0cteDrugTarget'; EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmcteDrugTarget';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -1944,9 +1940,8 @@ END;
/* / */ /* / */
-- Normalize DRUG_EXPOSURE_END_DATE to either the existing drug exposure end date, or add days supply, or add 1 day to the start date -- Normalize DRUG_EXPOSURE_END_DATE to either the existing drug exposure end date, or add days supply, or add 1 day to the start date
CREATE GLOBAL TEMPORARY TABLE ilbyrix0cteDrugTarget CREATE TABLE g8iauhqmcteDrugTarget
ON COMMIT PRESERVE ROWS AS
AS
SELECT SELECT
d.DRUG_EXPOSURE_ID d.DRUG_EXPOSURE_ID
,d.PERSON_ID ,d.PERSON_ID
@ -1966,8 +1961,8 @@ INNER JOIN [TARGET_CDMV5].[SCHEMA].CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCE
/* / */ /* / */
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0cteEndDates'; EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmcteEndDates';
EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0cteEndDates'; EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmcteEndDates';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -1977,9 +1972,8 @@ END;
/* / */ /* / */
CREATE GLOBAL TEMPORARY TABLE ilbyrix0cteEndDates CREATE TABLE g8iauhqmcteEndDates
ON COMMIT PRESERVE ROWS AS
AS
SELECT SELECT
PERSON_ID PERSON_ID
,INGREDIENT_CONCEPT_ID ,INGREDIENT_CONCEPT_ID
@ -2009,7 +2003,7 @@ FROM
PARTITION BY PERSON_ID PARTITION BY PERSON_ID
,INGREDIENT_CONCEPT_ID ORDER BY DRUG_EXPOSURE_START_DATE ,INGREDIENT_CONCEPT_ID ORDER BY DRUG_EXPOSURE_START_DATE
) AS START_ORDINAL ) AS START_ORDINAL
FROM ilbyrix0cteDrugTarget FROM g8iauhqmcteDrugTarget
UNION ALL UNION ALL
@ -2019,7 +2013,7 @@ FROM
,( DRUG_EXPOSURE_END_DATE + 30) ,( DRUG_EXPOSURE_END_DATE + 30)
,1 AS EVENT_TYPE ,1 AS EVENT_TYPE
,NULL ,NULL
FROM ilbyrix0cteDrugTarget FROM g8iauhqmcteDrugTarget
) RAWDATA ) RAWDATA
) E1 ) E1
INNER JOIN (SELECT PERSON_ID INNER JOIN (SELECT PERSON_ID
@ -2029,7 +2023,7 @@ FROM
PARTITION BY PERSON_ID PARTITION BY PERSON_ID
,INGREDIENT_CONCEPT_ID ORDER BY DRUG_EXPOSURE_START_DATE ,INGREDIENT_CONCEPT_ID ORDER BY DRUG_EXPOSURE_START_DATE
) AS START_ORDINAL ) AS START_ORDINAL
FROM ilbyrix0cteDrugTarget FROM g8iauhqmcteDrugTarget
) E2 ON E1.PERSON_ID = E2.PERSON_ID ) E2 ON E1.PERSON_ID = E2.PERSON_ID
AND E1.INGREDIENT_CONCEPT_ID = E2.INGREDIENT_CONCEPT_ID AND E1.INGREDIENT_CONCEPT_ID = E2.INGREDIENT_CONCEPT_ID
AND E2.EVENT_DATE <= E1.EVENT_DATE AND E2.EVENT_DATE <= E1.EVENT_DATE
@ -2044,8 +2038,8 @@ FROM
/* / */ /* / */
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0cteDrugExpEnds'; EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmcteDrugExpEnds';
EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0cteDrugExpEnds'; EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmcteDrugExpEnds';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -2055,9 +2049,8 @@ END;
/* / */ /* / */
CREATE GLOBAL TEMPORARY TABLE ilbyrix0cteDrugExpEnds CREATE TABLE g8iauhqmcteDrugExpEnds
ON COMMIT PRESERVE ROWS AS
AS
SELECT SELECT
d.PERSON_ID d.PERSON_ID
,d.INGREDIENT_CONCEPT_ID ,d.INGREDIENT_CONCEPT_ID
@ -2066,8 +2059,8 @@ SELECT
,MIN(e.END_DATE) AS ERA_END_DATE ,MIN(e.END_DATE) AS ERA_END_DATE
FROM FROM
ilbyrix0cteDrugTarget d g8iauhqmcteDrugTarget d
INNER JOIN ilbyrix0cteEndDates e ON d.PERSON_ID = e.PERSON_ID INNER JOIN g8iauhqmcteEndDates e ON d.PERSON_ID = e.PERSON_ID
AND d.INGREDIENT_CONCEPT_ID = e.INGREDIENT_CONCEPT_ID AND d.INGREDIENT_CONCEPT_ID = e.INGREDIENT_CONCEPT_ID
AND e.END_DATE >= d.DRUG_EXPOSURE_START_DATE AND e.END_DATE >= d.DRUG_EXPOSURE_START_DATE
GROUP BY d.PERSON_ID GROUP BY d.PERSON_ID
@ -2087,7 +2080,7 @@ SELECT row_number() OVER (
,ERA_END_DATE ,ERA_END_DATE
,COUNT(*) AS DRUG_EXPOSURE_COUNT ,COUNT(*) AS DRUG_EXPOSURE_COUNT
,30 AS gap_days ,30 AS gap_days
FROM ilbyrix0cteDrugExpEnds FROM g8iauhqmcteDrugExpEnds
GROUP BY person_id GROUP BY person_id
,INGREDIENT_CONCEPT_ID ,INGREDIENT_CONCEPT_ID
,drug_type_concept_id ,drug_type_concept_id
@ -2100,8 +2093,8 @@ Note: Eras derived from CONDITION_OCCURRENCE table, using 30d gap
****/ ****/
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0condition_era_phase_1'; EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmcondition_era_phase_1';
EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0condition_era_phase_1'; EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmcondition_era_phase_1';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -2112,8 +2105,8 @@ END;
/* / */ /* / */
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0cteConditionTarget'; EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmcteConditionTarget';
EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0cteConditionTarget'; EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmcteConditionTarget';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -2124,9 +2117,8 @@ END;
/* / */ /* / */
-- create base eras from the concepts found in condition_occurrence -- create base eras from the concepts found in condition_occurrence
CREATE GLOBAL TEMPORARY TABLE ilbyrix0cteConditionTarget CREATE TABLE g8iauhqmcteConditionTarget
ON COMMIT PRESERVE ROWS AS
AS
SELECT SELECT
co.PERSON_ID co.PERSON_ID
,co.condition_concept_id ,co.condition_concept_id
@ -2139,8 +2131,8 @@ FROM
/* / */ /* / */
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0cteCondEndDates'; EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmcteCondEndDates';
EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0cteCondEndDates'; EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmcteCondEndDates';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -2150,9 +2142,8 @@ END;
/* / */ /* / */
CREATE GLOBAL TEMPORARY TABLE ilbyrix0cteCondEndDates CREATE TABLE g8iauhqmcteCondEndDates
ON COMMIT PRESERVE ROWS AS
AS
SELECT SELECT
PERSON_ID PERSON_ID
,CONDITION_CONCEPT_ID ,CONDITION_CONCEPT_ID
@ -2182,7 +2173,7 @@ FROM
PARTITION BY PERSON_ID PARTITION BY PERSON_ID
,CONDITION_CONCEPT_ID ORDER BY CONDITION_START_DATE ,CONDITION_CONCEPT_ID ORDER BY CONDITION_START_DATE
) AS START_ORDINAL ) AS START_ORDINAL
FROM ilbyrix0cteConditionTarget FROM g8iauhqmcteConditionTarget
UNION ALL UNION ALL
@ -2192,7 +2183,7 @@ FROM
,( CONDITION_END_DATE + 30) ,( CONDITION_END_DATE + 30)
,1 AS EVENT_TYPE ,1 AS EVENT_TYPE
,NULL ,NULL
FROM ilbyrix0cteConditionTarget FROM g8iauhqmcteConditionTarget
) RAWDATA ) RAWDATA
) E1 ) E1
INNER JOIN (SELECT PERSON_ID INNER JOIN (SELECT PERSON_ID
@ -2202,7 +2193,7 @@ FROM
PARTITION BY PERSON_ID PARTITION BY PERSON_ID
,CONDITION_CONCEPT_ID ORDER BY CONDITION_START_DATE ,CONDITION_CONCEPT_ID ORDER BY CONDITION_START_DATE
) AS START_ORDINAL ) AS START_ORDINAL
FROM ilbyrix0cteConditionTarget FROM g8iauhqmcteConditionTarget
) E2 ON E1.PERSON_ID = E2.PERSON_ID ) E2 ON E1.PERSON_ID = E2.PERSON_ID
AND E1.CONDITION_CONCEPT_ID = E2.CONDITION_CONCEPT_ID AND E1.CONDITION_CONCEPT_ID = E2.CONDITION_CONCEPT_ID
AND E2.EVENT_DATE <= E1.EVENT_DATE AND E2.EVENT_DATE <= E1.EVENT_DATE
@ -2217,8 +2208,8 @@ FROM
/* / */ /* / */
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0cteConditionEnds'; EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmcteConditionEnds';
EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0cteConditionEnds'; EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmcteConditionEnds';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -2228,9 +2219,8 @@ END;
/* / */ /* / */
CREATE GLOBAL TEMPORARY TABLE ilbyrix0cteConditionEnds CREATE TABLE g8iauhqmcteConditionEnds
ON COMMIT PRESERVE ROWS AS
AS
SELECT SELECT
c.PERSON_ID c.PERSON_ID
,c.CONDITION_CONCEPT_ID ,c.CONDITION_CONCEPT_ID
@ -2238,8 +2228,8 @@ SELECT
,MIN(e.END_DATE) AS ERA_END_DATE ,MIN(e.END_DATE) AS ERA_END_DATE
FROM FROM
ilbyrix0cteConditionTarget c g8iauhqmcteConditionTarget c
INNER JOIN ilbyrix0cteCondEndDates e ON c.PERSON_ID = e.PERSON_ID INNER JOIN g8iauhqmcteCondEndDates e ON c.PERSON_ID = e.PERSON_ID
AND c.CONDITION_CONCEPT_ID = e.CONDITION_CONCEPT_ID AND c.CONDITION_CONCEPT_ID = e.CONDITION_CONCEPT_ID
AND e.END_DATE >= c.CONDITION_START_DATE AND e.END_DATE >= c.CONDITION_START_DATE
GROUP BY c.PERSON_ID GROUP BY c.PERSON_ID
@ -2264,7 +2254,7 @@ SELECT row_number() OVER (
,min(CONDITION_START_DATE) AS CONDITION_ERA_START_DATE ,min(CONDITION_START_DATE) AS CONDITION_ERA_START_DATE
,ERA_END_DATE AS CONDITION_ERA_END_DATE ,ERA_END_DATE AS CONDITION_ERA_END_DATE
,COUNT(*) AS CONDITION_OCCURRENCE_COUNT ,COUNT(*) AS CONDITION_OCCURRENCE_COUNT
FROM ilbyrix0cteConditionEnds FROM g8iauhqmcteConditionEnds
GROUP BY person_id GROUP BY person_id
,CONDITION_CONCEPT_ID ,CONDITION_CONCEPT_ID
,ERA_END_DATE ; ,ERA_END_DATE ;
@ -2279,8 +2269,8 @@ Note: These queries are used to provide some basic stats around row counts betwe
****/ ****/
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0v5_stats'; EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmv5_stats';
EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0v5_stats'; EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmv5_stats';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -2291,8 +2281,8 @@ END;
/* / */ /* / */
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0v4_stats'; EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmv4_stats';
EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0v4_stats'; EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmv4_stats';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -2303,9 +2293,8 @@ END;
/* / */ /* / */
-- Get the row counts for each table that is in scope for the migration -- Get the row counts for each table that is in scope for the migration
CREATE GLOBAL TEMPORARY TABLE ilbyrix0v4_stats CREATE TABLE g8iauhqmv4_stats
ON COMMIT PRESERVE ROWS AS
AS
SELECT SELECT
* *
@ -2346,9 +2335,8 @@ FROM
/* / */ /* / */
CREATE GLOBAL TEMPORARY TABLE ilbyrix0v5_stats CREATE TABLE g8iauhqmv5_stats
ON COMMIT PRESERVE ROWS AS
AS
SELECT SELECT
* *
@ -2403,8 +2391,8 @@ SELECT
v5.TableName v5_table_name, v5.TableName v5_table_name,
v5.row_count v5_row_count, v5.row_count v5_row_count,
NVL(v5.row_count, 0) - NVL(v4.row_count, 0) row_count_change NVL(v5.row_count, 0) - NVL(v4.row_count, 0) row_count_change
FROM ilbyrix0v4_stats v4 FROM g8iauhqmv4_stats v4
full outer join ilbyrix0v5_stats v5 ON v4.TableName = v5.TableName full outer join g8iauhqmv5_stats v5 ON v4.TableName = v5.TableName
order by v5.TableName ; order by v5.TableName ;
/* /*
@ -2412,8 +2400,8 @@ order by v5.TableName ;
* tables to the V5 destinations * tables to the V5 destinations
*/ */
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0classification_map'; EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmclassification_map';
EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0classification_map'; EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmclassification_map';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -2423,9 +2411,8 @@ END;
/* / */ /* / */
CREATE GLOBAL TEMPORARY TABLE ilbyrix0classification_map CREATE TABLE g8iauhqmclassification_map
ON COMMIT PRESERVE ROWS AS
AS
SELECT SELECT
* *
@ -2433,22 +2420,22 @@ FROM
(SELECT 'Condition_Occurrence' TableName, NVL(LOWER(cm.domain_id), 'condition') domain_id, COUNT(*) row_count (SELECT 'Condition_Occurrence' TableName, NVL(LOWER(cm.domain_id), 'condition') domain_id, COUNT(*) row_count
FROM [SOURCE_CDMV4].[SCHEMA].Condition_Occurrence CO FROM [SOURCE_CDMV4].[SCHEMA].Condition_Occurrence CO
LEFT JOIN ilbyrix0concept_map CM ON co.condition_concept_id = cm.source_concept_id LEFT JOIN g8iauhqmconcept_map CM ON co.condition_concept_id = cm.source_concept_id
GROUP BY NVL(LOWER(cm.domain_id), 'condition') GROUP BY NVL(LOWER(cm.domain_id), 'condition')
UNION UNION
SELECT 'Drug_Exposure' TableName, NVL(LOWER(cm.domain_id), 'drug') domain_id, COUNT(*) row_count SELECT 'Drug_Exposure' TableName, NVL(LOWER(cm.domain_id), 'drug') domain_id, COUNT(*) row_count
FROM [SOURCE_CDMV4].[SCHEMA].Drug_Exposure de FROM [SOURCE_CDMV4].[SCHEMA].Drug_Exposure de
LEFT JOIN ilbyrix0concept_map CM ON de.drug_concept_id = cm.source_concept_id LEFT JOIN g8iauhqmconcept_map CM ON de.drug_concept_id = cm.source_concept_id
GROUP BY NVL(LOWER(cm.domain_id), 'drug') GROUP BY NVL(LOWER(cm.domain_id), 'drug')
UNION UNION
SELECT 'Observation' TableName, NVL(LOWER(cm.domain_id), 'observation') domain_id, COUNT(*) row_count SELECT 'Observation' TableName, NVL(LOWER(cm.domain_id), 'observation') domain_id, COUNT(*) row_count
FROM [SOURCE_CDMV4].[SCHEMA].Observation o FROM [SOURCE_CDMV4].[SCHEMA].Observation o
LEFT JOIN ilbyrix0concept_map CM ON o.observation_concept_id = cm.source_concept_id LEFT JOIN g8iauhqmconcept_map CM ON o.observation_concept_id = cm.source_concept_id
GROUP BY NVL(LOWER(cm.domain_id), 'observation') GROUP BY NVL(LOWER(cm.domain_id), 'observation')
UNION UNION
SELECT 'Procedure_Occurrence' TableName, NVL(LOWER(cm.domain_id), 'procedure') domain_id, COUNT(*) row_count SELECT 'Procedure_Occurrence' TableName, NVL(LOWER(cm.domain_id), 'procedure') domain_id, COUNT(*) row_count
FROM [SOURCE_CDMV4].[SCHEMA].Procedure_Occurrence po FROM [SOURCE_CDMV4].[SCHEMA].Procedure_Occurrence po
LEFT JOIN ilbyrix0concept_map CM ON po.PROCEDURE_CONCEPT_ID = cm.source_concept_id LEFT JOIN g8iauhqmconcept_map CM ON po.PROCEDURE_CONCEPT_ID = cm.source_concept_id
GROUP BY NVL(LOWER(cm.domain_id), 'procedure') GROUP BY NVL(LOWER(cm.domain_id), 'procedure')
) A ) A
ORDER by A.TableName, A.domain_id ; ORDER by A.TableName, A.domain_id ;
@ -2456,10 +2443,10 @@ ORDER by A.TableName, A.domain_id ;
/* / */ /* / */
SELECT * SELECT *
FROM ilbyrix0classification_map FROM g8iauhqmclassification_map
order by tablename, domain_id ; order by tablename, domain_id ;
SELECT domain_id, SUM(row_count) SELECT domain_id, SUM(row_count)
FROM ilbyrix0classification_map FROM g8iauhqmclassification_map
group by domain_id group by domain_id
order by domain_id ; order by domain_id ;

28
Version4 To Version5 Conversion/PostgreSQL/OMOP CDMv4 to CDMv5 - PostgreSQL.sql
View File

@ -486,7 +486,7 @@ SELECT person_id
,CAST(NULL AS INT) AS cause_source_concept_id ,CAST(NULL AS INT) AS cause_source_concept_id
FROM [SOURCE_CDMV4].[SCHEMA].DEATH FROM [SOURCE_CDMV4].[SCHEMA].DEATH
LEFT JOIN concept_map_distinct cm1 ON DEATH.DEATH_TYPE_CONCEPT_ID = CM1.SOURCE_CONCEPT_ID LEFT JOIN concept_map_distinct cm1 ON DEATH.DEATH_TYPE_CONCEPT_ID = CM1.SOURCE_CONCEPT_ID
AND LOWER(DOMAIN_ID) IN ('death type'); AND LOWER(DOMAIN_ID) IN ('death type', 'Type Concept');
INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE)
SELECT 'DEATH: ' || CAST(NUM_INVALID_RECORDS AS VARCHAR) || ' records in the source CDMv4 database have invalid DEATH_TYPE_CONCEPT_ID' SELECT 'DEATH: ' || CAST(NUM_INVALID_RECORDS AS VARCHAR) || ' records in the source CDMv4 database have invalid DEATH_TYPE_CONCEPT_ID'
@ -499,7 +499,7 @@ FROM (
WHERE CONCEPT_ID = 0 WHERE CONCEPT_ID = 0
OR ( OR (
STANDARD_CONCEPT = 'S' STANDARD_CONCEPT = 'S'
AND LOWER(DOMAIN_ID) IN ('death type') AND LOWER(DOMAIN_ID) IN ('death type', 'Type Concept')
) )
) )
HAVING COUNT(PERSON_ID) > 0 HAVING COUNT(PERSON_ID) > 0
@ -600,7 +600,7 @@ INNER JOIN concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_co
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount = 1 AND cmdis.targetConceptCount = 1
LEFT JOIN concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id LEFT JOIN concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('procedure type') AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
LEFT JOIN concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id LEFT JOIN concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id
AND cm2.domain_id = cmdis2.domain_id AND cm2.domain_id = cmdis2.domain_id
AND cmdis2.targetConceptCount = 1 AND cmdis2.targetConceptCount = 1
@ -643,7 +643,7 @@ SELECT procedure_occurrence_id
FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
LEFT JOIN concept_map cm1 ON procedure_concept_id = cm1.source_concept_id LEFT JOIN concept_map cm1 ON procedure_concept_id = cm1.source_concept_id
LEFT JOIN concept_map cm2 ON procedure_concept_id = cm2.source_concept_id LEFT JOIN concept_map cm2 ON procedure_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('procedure type') AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
WHERE procedure_concept_id <> 0 WHERE procedure_concept_id <> 0
AND cm1.domain_id IS NULL AND cm1.domain_id IS NULL
@ -691,7 +691,7 @@ FROM (
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount > 1 AND cmdis.targetConceptCount > 1
LEFT JOIN concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id LEFT JOIN concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('procedure type') AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
UNION ALL UNION ALL
@ -812,7 +812,7 @@ FROM (
WHERE CONCEPT_ID = 0 WHERE CONCEPT_ID = 0
OR ( OR (
STANDARD_CONCEPT = 'S' STANDARD_CONCEPT = 'S'
AND LOWER(DOMAIN_ID) IN ('procedure type') AND LOWER(DOMAIN_ID) IN ('procedure type', 'Type Concept')
) )
) )
HAVING COUNT(PERSON_ID) > 0 HAVING COUNT(PERSON_ID) > 0
@ -892,7 +892,7 @@ INNER JOIN concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_co
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount = 1 AND cmdis.targetConceptCount = 1
LEFT JOIN concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id LEFT JOIN concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('drug type') AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
INNER JOIN concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id INNER JOIN concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id
AND cm2.domain_id = cmdis2.domain_id AND cm2.domain_id = cmdis2.domain_id
AND cmdis2.targetConceptCount = 1 AND cmdis2.targetConceptCount = 1
@ -954,7 +954,7 @@ SELECT drug_exposure_id
FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE
LEFT JOIN concept_map cm1 ON drug_concept_id = cm1.source_concept_id LEFT JOIN concept_map cm1 ON drug_concept_id = cm1.source_concept_id
LEFT JOIN concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id LEFT JOIN concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('drug type') AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
WHERE drug_concept_id <> 0 WHERE drug_concept_id <> 0
AND cm1.domain_id IS NULL AND cm1.domain_id IS NULL
@ -1019,7 +1019,7 @@ FROM (
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount > 1 AND cmdis.targetConceptCount > 1
LEFT JOIN concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id LEFT JOIN concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('drug type') AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
UNION ALL UNION ALL
@ -1185,7 +1185,7 @@ FROM (
WHERE CONCEPT_ID = 0 WHERE CONCEPT_ID = 0
OR ( OR (
STANDARD_CONCEPT = 'S' STANDARD_CONCEPT = 'S'
AND LOWER(DOMAIN_ID) IN ('drug type') AND LOWER(DOMAIN_ID) IN ('drug type', 'Type Concept')
) )
) )
HAVING COUNT(PERSON_ID) > 0 HAVING COUNT(PERSON_ID) > 0
@ -1216,7 +1216,7 @@ INNER JOIN concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_co
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount = 1 AND cmdis.targetConceptCount = 1
LEFT JOIN concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id LEFT JOIN concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('condition type') AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4 WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4
UNION ALL UNION ALL
@ -1253,7 +1253,7 @@ SELECT condition_occurrence_id
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
LEFT JOIN concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id LEFT JOIN concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
LEFT JOIN concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id LEFT JOIN concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('condition type') AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
WHERE condition_concept_id <> 0 WHERE condition_concept_id <> 0
AND cm1.domain_id IS NULL AND cm1.domain_id IS NULL
@ -1296,7 +1296,7 @@ FROM (
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount > 1 AND cmdis.targetConceptCount > 1
LEFT JOIN concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id LEFT JOIN concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('condition type') AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4 WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4
UNION ALL UNION ALL
@ -1384,7 +1384,7 @@ FROM (
WHERE CONCEPT_ID = 0 WHERE CONCEPT_ID = 0
OR ( OR (
STANDARD_CONCEPT = 'S' STANDARD_CONCEPT = 'S'
AND LOWER(DOMAIN_ID) IN ('condition type') AND LOWER(DOMAIN_ID) IN ('condition type', 'Type Concept')
) )
) )
HAVING COUNT(PERSON_ID) > 0 HAVING COUNT(PERSON_ID) > 0

28
Version4 To Version5 Conversion/Redshift/OMOP CDMv4 to CDMv5 - Redshift.sql
View File

@ -486,7 +486,7 @@ SELECT person_id
,CAST(NULL AS INT) AS cause_source_concept_id ,CAST(NULL AS INT) AS cause_source_concept_id
FROM [SOURCE_CDMV4].[SCHEMA].DEATH FROM [SOURCE_CDMV4].[SCHEMA].DEATH
LEFT JOIN concept_map_distinct cm1 ON DEATH.DEATH_TYPE_CONCEPT_ID = CM1.SOURCE_CONCEPT_ID LEFT JOIN concept_map_distinct cm1 ON DEATH.DEATH_TYPE_CONCEPT_ID = CM1.SOURCE_CONCEPT_ID
AND LOWER(DOMAIN_ID) IN ('death type'); AND LOWER(DOMAIN_ID) IN ('death type', 'Type Concept');
INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE)
SELECT 'DEATH: ' || CAST(NUM_INVALID_RECORDS AS VARCHAR) || ' records in the source CDMv4 database have invalid DEATH_TYPE_CONCEPT_ID' SELECT 'DEATH: ' || CAST(NUM_INVALID_RECORDS AS VARCHAR) || ' records in the source CDMv4 database have invalid DEATH_TYPE_CONCEPT_ID'
@ -499,7 +499,7 @@ FROM (
WHERE CONCEPT_ID = 0 WHERE CONCEPT_ID = 0
OR ( OR (
STANDARD_CONCEPT = 'S' STANDARD_CONCEPT = 'S'
AND LOWER(DOMAIN_ID) IN ('death type') AND LOWER(DOMAIN_ID) IN ('death type', 'Type Concept')
) )
) )
HAVING COUNT(PERSON_ID) > 0 HAVING COUNT(PERSON_ID) > 0
@ -600,7 +600,7 @@ INNER JOIN concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_co
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount = 1 AND cmdis.targetConceptCount = 1
LEFT JOIN concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id LEFT JOIN concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('procedure type') AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
LEFT JOIN concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id LEFT JOIN concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id
AND cm2.domain_id = cmdis2.domain_id AND cm2.domain_id = cmdis2.domain_id
AND cmdis2.targetConceptCount = 1 AND cmdis2.targetConceptCount = 1
@ -643,7 +643,7 @@ SELECT procedure_occurrence_id
FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
LEFT JOIN concept_map cm1 ON procedure_concept_id = cm1.source_concept_id LEFT JOIN concept_map cm1 ON procedure_concept_id = cm1.source_concept_id
LEFT JOIN concept_map cm2 ON procedure_concept_id = cm2.source_concept_id LEFT JOIN concept_map cm2 ON procedure_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('procedure type') AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
WHERE procedure_concept_id <> 0 WHERE procedure_concept_id <> 0
AND cm1.domain_id IS NULL AND cm1.domain_id IS NULL
@ -691,7 +691,7 @@ FROM (
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount > 1 AND cmdis.targetConceptCount > 1
LEFT JOIN concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id LEFT JOIN concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('procedure type') AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
UNION ALL UNION ALL
@ -812,7 +812,7 @@ FROM (
WHERE CONCEPT_ID = 0 WHERE CONCEPT_ID = 0
OR ( OR (
STANDARD_CONCEPT = 'S' STANDARD_CONCEPT = 'S'
AND LOWER(DOMAIN_ID) IN ('procedure type') AND LOWER(DOMAIN_ID) IN ('procedure type', 'Type Concept')
) )
) )
HAVING COUNT(PERSON_ID) > 0 HAVING COUNT(PERSON_ID) > 0
@ -892,7 +892,7 @@ INNER JOIN concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_co
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount = 1 AND cmdis.targetConceptCount = 1
LEFT JOIN concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id LEFT JOIN concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('drug type') AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
INNER JOIN concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id INNER JOIN concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id
AND cm2.domain_id = cmdis2.domain_id AND cm2.domain_id = cmdis2.domain_id
AND cmdis2.targetConceptCount = 1 AND cmdis2.targetConceptCount = 1
@ -954,7 +954,7 @@ SELECT drug_exposure_id
FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE
LEFT JOIN concept_map cm1 ON drug_concept_id = cm1.source_concept_id LEFT JOIN concept_map cm1 ON drug_concept_id = cm1.source_concept_id
LEFT JOIN concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id LEFT JOIN concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('drug type') AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
WHERE drug_concept_id <> 0 WHERE drug_concept_id <> 0
AND cm1.domain_id IS NULL AND cm1.domain_id IS NULL
@ -1019,7 +1019,7 @@ FROM (
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount > 1 AND cmdis.targetConceptCount > 1
LEFT JOIN concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id LEFT JOIN concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('drug type') AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
UNION ALL UNION ALL
@ -1185,7 +1185,7 @@ FROM (
WHERE CONCEPT_ID = 0 WHERE CONCEPT_ID = 0
OR ( OR (
STANDARD_CONCEPT = 'S' STANDARD_CONCEPT = 'S'
AND LOWER(DOMAIN_ID) IN ('drug type') AND LOWER(DOMAIN_ID) IN ('drug type', 'Type Concept')
) )
) )
HAVING COUNT(PERSON_ID) > 0 HAVING COUNT(PERSON_ID) > 0
@ -1216,7 +1216,7 @@ INNER JOIN concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_co
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount = 1 AND cmdis.targetConceptCount = 1
LEFT JOIN concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id LEFT JOIN concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('condition type') AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4 WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4
UNION ALL UNION ALL
@ -1253,7 +1253,7 @@ SELECT condition_occurrence_id
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
LEFT JOIN concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id LEFT JOIN concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
LEFT JOIN concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id LEFT JOIN concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('condition type') AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
WHERE condition_concept_id <> 0 WHERE condition_concept_id <> 0
AND cm1.domain_id IS NULL AND cm1.domain_id IS NULL
@ -1296,7 +1296,7 @@ FROM (
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount > 1 AND cmdis.targetConceptCount > 1
LEFT JOIN concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id LEFT JOIN concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('condition type') AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4 WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4
UNION ALL UNION ALL
@ -1384,7 +1384,7 @@ FROM (
WHERE CONCEPT_ID = 0 WHERE CONCEPT_ID = 0
OR ( OR (
STANDARD_CONCEPT = 'S' STANDARD_CONCEPT = 'S'
AND LOWER(DOMAIN_ID) IN ('condition type') AND LOWER(DOMAIN_ID) IN ('condition type', 'Type Concept')
) )
) )
HAVING COUNT(PERSON_ID) > 0 HAVING COUNT(PERSON_ID) > 0

28
Version4 To Version5 Conversion/Sql Server PDW/OMOP CDMv4 to CDMv5 - Sql Server PDW.dsql
View File

@ -485,7 +485,7 @@ SELECT person_id
,CAST(NULL AS INT) AS cause_source_concept_id ,CAST(NULL AS INT) AS cause_source_concept_id
FROM [SOURCE_CDMV4].[SCHEMA].DEATH FROM [SOURCE_CDMV4].[SCHEMA].DEATH
LEFT JOIN #concept_map_distinct cm1 ON DEATH.DEATH_TYPE_CONCEPT_ID = CM1.SOURCE_CONCEPT_ID LEFT JOIN #concept_map_distinct cm1 ON DEATH.DEATH_TYPE_CONCEPT_ID = CM1.SOURCE_CONCEPT_ID
AND LOWER(DOMAIN_ID) IN ('death type'); AND LOWER(DOMAIN_ID) IN ('death type', 'Type Concept');
INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE)
SELECT 'DEATH: ' + CAST(NUM_INVALID_RECORDS AS VARCHAR) + ' records in the source CDMv4 database have invalid DEATH_TYPE_CONCEPT_ID' SELECT 'DEATH: ' + CAST(NUM_INVALID_RECORDS AS VARCHAR) + ' records in the source CDMv4 database have invalid DEATH_TYPE_CONCEPT_ID'
@ -498,7 +498,7 @@ FROM (
WHERE CONCEPT_ID = 0 WHERE CONCEPT_ID = 0
OR ( OR (
STANDARD_CONCEPT = 'S' STANDARD_CONCEPT = 'S'
AND LOWER(DOMAIN_ID) IN ('death type') AND LOWER(DOMAIN_ID) IN ('death type', 'Type Concept')
) )
) )
HAVING COUNT(PERSON_ID) > 0 HAVING COUNT(PERSON_ID) > 0
@ -597,7 +597,7 @@ INNER JOIN #concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_c
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount = 1 AND cmdis.targetConceptCount = 1
LEFT JOIN #concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id LEFT JOIN #concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('procedure type') AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
LEFT JOIN #concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id LEFT JOIN #concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id
AND cm2.domain_id = cmdis2.domain_id AND cm2.domain_id = cmdis2.domain_id
AND cmdis2.targetConceptCount = 1 AND cmdis2.targetConceptCount = 1
@ -640,7 +640,7 @@ SELECT procedure_occurrence_id
FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
LEFT JOIN #concept_map cm1 ON procedure_concept_id = cm1.source_concept_id LEFT JOIN #concept_map cm1 ON procedure_concept_id = cm1.source_concept_id
LEFT JOIN #concept_map cm2 ON procedure_concept_id = cm2.source_concept_id LEFT JOIN #concept_map cm2 ON procedure_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('procedure type') AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
WHERE procedure_concept_id <> 0 WHERE procedure_concept_id <> 0
AND cm1.domain_id IS NULL AND cm1.domain_id IS NULL
@ -688,7 +688,7 @@ FROM (
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount > 1 AND cmdis.targetConceptCount > 1
LEFT JOIN #concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id LEFT JOIN #concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('procedure type') AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
UNION ALL UNION ALL
@ -809,7 +809,7 @@ FROM (
WHERE CONCEPT_ID = 0 WHERE CONCEPT_ID = 0
OR ( OR (
STANDARD_CONCEPT = 'S' STANDARD_CONCEPT = 'S'
AND LOWER(DOMAIN_ID) IN ('procedure type') AND LOWER(DOMAIN_ID) IN ('procedure type', 'Type Concept')
) )
) )
HAVING COUNT(PERSON_ID) > 0 HAVING COUNT(PERSON_ID) > 0
@ -887,7 +887,7 @@ INNER JOIN #concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_c
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount = 1 AND cmdis.targetConceptCount = 1
LEFT JOIN #concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id LEFT JOIN #concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('drug type') AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
INNER JOIN #concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id INNER JOIN #concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id
AND cm2.domain_id = cmdis2.domain_id AND cm2.domain_id = cmdis2.domain_id
AND cmdis2.targetConceptCount = 1 AND cmdis2.targetConceptCount = 1
@ -949,7 +949,7 @@ SELECT drug_exposure_id
FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE
LEFT JOIN #concept_map cm1 ON drug_concept_id = cm1.source_concept_id LEFT JOIN #concept_map cm1 ON drug_concept_id = cm1.source_concept_id
LEFT JOIN #concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id LEFT JOIN #concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('drug type') AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
WHERE drug_concept_id <> 0 WHERE drug_concept_id <> 0
AND cm1.domain_id IS NULL AND cm1.domain_id IS NULL
@ -1014,7 +1014,7 @@ FROM (
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount > 1 AND cmdis.targetConceptCount > 1
LEFT JOIN #concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id LEFT JOIN #concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('drug type') AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
UNION ALL UNION ALL
@ -1180,7 +1180,7 @@ FROM (
WHERE CONCEPT_ID = 0 WHERE CONCEPT_ID = 0
OR ( OR (
STANDARD_CONCEPT = 'S' STANDARD_CONCEPT = 'S'
AND LOWER(DOMAIN_ID) IN ('drug type') AND LOWER(DOMAIN_ID) IN ('drug type', 'Type Concept')
) )
) )
HAVING COUNT(PERSON_ID) > 0 HAVING COUNT(PERSON_ID) > 0
@ -1211,7 +1211,7 @@ INNER JOIN #concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_c
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount = 1 AND cmdis.targetConceptCount = 1
LEFT JOIN #concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id LEFT JOIN #concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('condition type') AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4 WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4
UNION ALL UNION ALL
@ -1248,7 +1248,7 @@ SELECT condition_occurrence_id
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
LEFT JOIN #concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id LEFT JOIN #concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
LEFT JOIN #concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id LEFT JOIN #concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('condition type') AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
WHERE condition_concept_id <> 0 WHERE condition_concept_id <> 0
AND cm1.domain_id IS NULL AND cm1.domain_id IS NULL
@ -1291,7 +1291,7 @@ FROM (
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount > 1 AND cmdis.targetConceptCount > 1
LEFT JOIN #concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id LEFT JOIN #concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('condition type') AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4 WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4
UNION ALL UNION ALL
@ -1379,7 +1379,7 @@ FROM (
WHERE CONCEPT_ID = 0 WHERE CONCEPT_ID = 0
OR ( OR (
STANDARD_CONCEPT = 'S' STANDARD_CONCEPT = 'S'
AND LOWER(DOMAIN_ID) IN ('condition type') AND LOWER(DOMAIN_ID) IN ('condition type', 'Type Concept')
) )
) )
HAVING COUNT(PERSON_ID) > 0 HAVING COUNT(PERSON_ID) > 0

28
Version4 To Version5 Conversion/Sql Server/OMOP CDMv4 to CDMv5 - SQL Server.sql
View File

@ -479,7 +479,7 @@ SELECT person_id
,CAST(NULL AS INT) AS cause_source_concept_id ,CAST(NULL AS INT) AS cause_source_concept_id
FROM [SOURCE_CDMV4].[SCHEMA].DEATH FROM [SOURCE_CDMV4].[SCHEMA].DEATH
LEFT JOIN #concept_map_distinct cm1 ON DEATH.DEATH_TYPE_CONCEPT_ID = CM1.SOURCE_CONCEPT_ID LEFT JOIN #concept_map_distinct cm1 ON DEATH.DEATH_TYPE_CONCEPT_ID = CM1.SOURCE_CONCEPT_ID
AND LOWER(DOMAIN_ID) IN ('death type'); AND LOWER(DOMAIN_ID) IN ('death type', 'Type Concept');
INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE)
SELECT 'DEATH: ' + CAST(NUM_INVALID_RECORDS AS VARCHAR) + ' records in the source CDMv4 database have invalid DEATH_TYPE_CONCEPT_ID' SELECT 'DEATH: ' + CAST(NUM_INVALID_RECORDS AS VARCHAR) + ' records in the source CDMv4 database have invalid DEATH_TYPE_CONCEPT_ID'
@ -492,7 +492,7 @@ FROM (
WHERE CONCEPT_ID = 0 WHERE CONCEPT_ID = 0
OR ( OR (
STANDARD_CONCEPT = 'S' STANDARD_CONCEPT = 'S'
AND LOWER(DOMAIN_ID) IN ('death type') AND LOWER(DOMAIN_ID) IN ('death type', 'Type Concept')
) )
) )
HAVING COUNT(PERSON_ID) > 0 HAVING COUNT(PERSON_ID) > 0
@ -589,7 +589,7 @@ INNER JOIN #concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_c
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount = 1 AND cmdis.targetConceptCount = 1
LEFT JOIN #concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id LEFT JOIN #concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('procedure type') AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
LEFT JOIN #concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id LEFT JOIN #concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id
AND cm2.domain_id = cmdis2.domain_id AND cm2.domain_id = cmdis2.domain_id
AND cmdis2.targetConceptCount = 1 AND cmdis2.targetConceptCount = 1
@ -632,7 +632,7 @@ SELECT procedure_occurrence_id
FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
LEFT JOIN #concept_map cm1 ON procedure_concept_id = cm1.source_concept_id LEFT JOIN #concept_map cm1 ON procedure_concept_id = cm1.source_concept_id
LEFT JOIN #concept_map cm2 ON procedure_concept_id = cm2.source_concept_id LEFT JOIN #concept_map cm2 ON procedure_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('procedure type') AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
WHERE procedure_concept_id <> 0 WHERE procedure_concept_id <> 0
AND cm1.domain_id IS NULL AND cm1.domain_id IS NULL
@ -680,7 +680,7 @@ FROM (
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount > 1 AND cmdis.targetConceptCount > 1
LEFT JOIN #concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id LEFT JOIN #concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('procedure type') AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
UNION ALL UNION ALL
@ -801,7 +801,7 @@ FROM (
WHERE CONCEPT_ID = 0 WHERE CONCEPT_ID = 0
OR ( OR (
STANDARD_CONCEPT = 'S' STANDARD_CONCEPT = 'S'
AND LOWER(DOMAIN_ID) IN ('procedure type') AND LOWER(DOMAIN_ID) IN ('procedure type', 'Type Concept')
) )
) )
HAVING COUNT(PERSON_ID) > 0 HAVING COUNT(PERSON_ID) > 0
@ -877,7 +877,7 @@ INNER JOIN #concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_c
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount = 1 AND cmdis.targetConceptCount = 1
LEFT JOIN #concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id LEFT JOIN #concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('drug type') AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
INNER JOIN #concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id INNER JOIN #concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id
AND cm2.domain_id = cmdis2.domain_id AND cm2.domain_id = cmdis2.domain_id
AND cmdis2.targetConceptCount = 1 AND cmdis2.targetConceptCount = 1
@ -939,7 +939,7 @@ SELECT drug_exposure_id
FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE
LEFT JOIN #concept_map cm1 ON drug_concept_id = cm1.source_concept_id LEFT JOIN #concept_map cm1 ON drug_concept_id = cm1.source_concept_id
LEFT JOIN #concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id LEFT JOIN #concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('drug type') AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
WHERE drug_concept_id <> 0 WHERE drug_concept_id <> 0
AND cm1.domain_id IS NULL AND cm1.domain_id IS NULL
@ -1004,7 +1004,7 @@ FROM (
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount > 1 AND cmdis.targetConceptCount > 1
LEFT JOIN #concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id LEFT JOIN #concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('drug type') AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
UNION ALL UNION ALL
@ -1170,7 +1170,7 @@ FROM (
WHERE CONCEPT_ID = 0 WHERE CONCEPT_ID = 0
OR ( OR (
STANDARD_CONCEPT = 'S' STANDARD_CONCEPT = 'S'
AND LOWER(DOMAIN_ID) IN ('drug type') AND LOWER(DOMAIN_ID) IN ('drug type', 'Type Concept')
) )
) )
HAVING COUNT(PERSON_ID) > 0 HAVING COUNT(PERSON_ID) > 0
@ -1201,7 +1201,7 @@ INNER JOIN #concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_c
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount = 1 AND cmdis.targetConceptCount = 1
LEFT JOIN #concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id LEFT JOIN #concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('condition type') AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4 WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4
UNION ALL UNION ALL
@ -1238,7 +1238,7 @@ SELECT condition_occurrence_id
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
LEFT JOIN #concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id LEFT JOIN #concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
LEFT JOIN #concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id LEFT JOIN #concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('condition type') AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
WHERE condition_concept_id <> 0 WHERE condition_concept_id <> 0
AND cm1.domain_id IS NULL AND cm1.domain_id IS NULL
@ -1281,7 +1281,7 @@ FROM (
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount > 1 AND cmdis.targetConceptCount > 1
LEFT JOIN #concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id LEFT JOIN #concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
AND LOWER(cm2.domain_id) IN ('condition type') AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4 WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4
UNION ALL UNION ALL
@ -1369,7 +1369,7 @@ FROM (
WHERE CONCEPT_ID = 0 WHERE CONCEPT_ID = 0
OR ( OR (
STANDARD_CONCEPT = 'S' STANDARD_CONCEPT = 'S'
AND LOWER(DOMAIN_ID) IN ('condition type') AND LOWER(DOMAIN_ID) IN ('condition type', 'Type Concept')
) )
) )
HAVING COUNT(PERSON_ID) > 0 HAVING COUNT(PERSON_ID) > 0