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Merge pull request #22 from anthonysena/V5ConversionImprovement 

Adding Redshift & SQL Server PDW translations and fixing era logic bug
This commit is contained in:
Patrick Ryan 2015-09-01 13:21:58 -04:00
parent 69a9555b50 cb116a29a0
commit 101c632072
8 changed files with 5005 additions and 165 deletions
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38
Version4 To Version5 Conversion/Convert-OHDSI-Sql-To-Dialect-Local.R Normal file
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@ -0,0 +1,38 @@
# 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")

4
Version4 To Version5 Conversion/OMOP CDMv4 to CDMv5 - OHDSI-SQL.sql
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@ -2008,7 +2008,7 @@ FROM (
FROM #cteDrugTarget FROM #cteDrugTarget
) 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
GROUP BY E1.PERSON_ID GROUP BY E1.PERSON_ID
,E1.INGREDIENT_CONCEPT_ID ,E1.INGREDIENT_CONCEPT_ID
,E1.EVENT_DATE ,E1.EVENT_DATE
@ -2143,7 +2143,7 @@ FROM (
FROM #cteConditionTarget FROM #cteConditionTarget
) 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
GROUP BY E1.PERSON_ID GROUP BY E1.PERSON_ID
,E1.CONDITION_CONCEPT_ID ,E1.CONDITION_CONCEPT_ID
,E1.EVENT_DATE ,E1.EVENT_DATE

318
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 q7a3ac0oconcept_map'; EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78aconcept_map';
EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0oconcept_map'; EXECUTE IMMEDIATE 'DROP TABLE ra2pz78aconcept_map';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -118,9 +118,9 @@ EXCEPTION
END IF; END IF;
END; END;
/ /* / */
CREATE GLOBAL TEMPORARY TABLE q7a3ac0oconcept_map CREATE GLOBAL TEMPORARY TABLE ra2pz78aconcept_map
ON COMMIT PRESERVE ROWS ON COMMIT PRESERVE ROWS
AS AS
SELECT SELECT
@ -132,9 +132,9 @@ FROM
[TARGET_CDMV5].[SCHEMA].concept [TARGET_CDMV5].[SCHEMA].concept
WHERE 1 = 0; WHERE 1 = 0;
/ /* / */
INSERT INTO q7a3ac0oconcept_map INSERT INTO ra2pz78aconcept_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
@ -279,8 +279,8 @@ INNER JOIN [TARGET_CDMV5].[SCHEMA].concept c2 ON cr1.concept_id_2 = c2.concept_i
AND cr1.invalid_reason IS NULL; AND cr1.invalid_reason IS NULL;
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0oconcept_map_distinct'; EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78aconcept_map_distinct';
EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0oconcept_map_distinct'; EXECUTE IMMEDIATE 'DROP TABLE ra2pz78aconcept_map_distinct';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -288,9 +288,9 @@ EXCEPTION
END IF; END IF;
END; END;
/ /* / */
CREATE GLOBAL TEMPORARY TABLE q7a3ac0oconcept_map_distinct CREATE GLOBAL TEMPORARY TABLE ra2pz78aconcept_map_distinct
ON COMMIT PRESERVE ROWS ON COMMIT PRESERVE ROWS
AS AS
SELECT SELECT
@ -299,18 +299,18 @@ SELECT
,COUNT(*) AS targetConceptCount ,COUNT(*) AS targetConceptCount
FROM FROM
q7a3ac0oconcept_map ra2pz78aconcept_map
WHERE 1 = 0 WHERE 1 = 0
GROUP BY source_concept_id GROUP BY source_concept_id
,domain_id; ,domain_id;
/ /* / */
INSERT INTO q7a3ac0oconcept_map_distinct INSERT INTO ra2pz78aconcept_map_distinct
SELECT source_concept_id SELECT source_concept_id
,domain_id ,domain_id
,COUNT(*) ,COUNT(*)
FROM q7a3ac0oconcept_map FROM ra2pz78aconcept_map
GROUP BY source_concept_id GROUP BY source_concept_id
,domain_id; ,domain_id;
@ -324,10 +324,10 @@ EXCEPTION
END IF; END IF;
END; END;
/ /* / */
CREATE TABLE [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE VARCHAR(4000)); CREATE TABLE [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE VARCHAR(4000));
/ /* / */
/**** /****
@ -423,11 +423,11 @@ 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 q7a3ac0oconcept_map gender ON LOWER(gender.DOMAIN_ID) IN ('gender') LEFT JOIN ra2pz78aconcept_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 q7a3ac0oconcept_map race ON LOWER(race.DOMAIN_ID) IN ('race') LEFT JOIN ra2pz78aconcept_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 q7a3ac0oconcept_map ethnicity ON LOWER(ethnicity.DOMAIN_ID) IN ('ethnicity') LEFT JOIN ra2pz78aconcept_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)
@ -509,7 +509,7 @@ 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 q7a3ac0oconcept_map_distinct cm1 ON DEATH.DEATH_TYPE_CONCEPT_ID = CM1.SOURCE_CONCEPT_ID LEFT JOIN ra2pz78aconcept_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');
INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE)
@ -548,7 +548,7 @@ 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 q7a3ac0oconcept_map cm1 ON VISIT_OCCURRENCE.PLACE_OF_SERVICE_CONCEPT_ID = cm1.source_concept_id LEFT JOIN ra2pz78aconcept_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)
@ -574,8 +574,8 @@ FROM (
****/ ****/
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0opo_map'; EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78apo_map';
EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0opo_map'; EXECUTE IMMEDIATE 'DROP TABLE ra2pz78apo_map';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -583,9 +583,9 @@ EXCEPTION
END IF; END IF;
END; END;
/ /* / */
CREATE GLOBAL TEMPORARY TABLE q7a3ac0opo_map CREATE GLOBAL TEMPORARY TABLE ra2pz78apo_map
ON COMMIT PRESERVE ROWS ON COMMIT PRESERVE ROWS
AS AS
SELECT SELECT
@ -608,10 +608,10 @@ FROM
LEFT JOIN [TARGET_CDMV5].[SCHEMA].drug_exposure de ON 1 = 0 LEFT JOIN [TARGET_CDMV5].[SCHEMA].drug_exposure de ON 1 = 0
WHERE 0 = 1; WHERE 0 = 1;
/ /* / */
--find valid procedures from procedure table --find valid procedures from procedure table
INSERT INTO q7a3ac0opo_map INSERT INTO ra2pz78apo_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
@ -626,14 +626,14 @@ 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 q7a3ac0oconcept_map cm1 ON PROCEDURE_OCCURRENCE.PROCEDURE_CONCEPT_ID = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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 q7a3ac0oconcept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id INNER JOIN ra2pz78aconcept_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 q7a3ac0oconcept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id LEFT JOIN ra2pz78aconcept_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')
LEFT JOIN q7a3ac0oconcept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id LEFT JOIN ra2pz78aconcept_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
@ -654,11 +654,15 @@ 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
FROM
DUAL
FROM
DUAL
WHERE procedure_concept_id = 0 WHERE procedure_concept_id = 0
UNION ALL UNION ALL
-- All drug exposures that do not map to a standard concept in V5 should also carry over with condition_concept_id = 0 -- All PROCEDURE_OCCURRENCE that do not map to a standard concept in V5 should also carry over with procedure_concept_id = 0
SELECT procedure_occurrence_id SELECT procedure_occurrence_id
,person_id ,person_id
,0 AS procedure_concept_id ,0 AS procedure_concept_id
@ -673,8 +677,8 @@ 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 q7a3ac0oconcept_map cm1 ON procedure_concept_id = cm1.source_concept_id LEFT JOIN ra2pz78aconcept_map cm1 ON procedure_concept_id = cm1.source_concept_id
LEFT JOIN q7a3ac0oconcept_map cm2 ON procedure_concept_id = cm2.source_concept_id LEFT JOIN ra2pz78aconcept_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')
WHERE procedure_concept_id <> 0 WHERE procedure_concept_id <> 0
AND cm1.domain_id IS NULL AND cm1.domain_id IS NULL
@ -717,12 +721,12 @@ FROM (
,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 q7a3ac0oconcept_map cm1 ON PROCEDURE_OCCURRENCE.PROCEDURE_CONCEPT_ID = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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 q7a3ac0oconcept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id INNER JOIN ra2pz78aconcept_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 q7a3ac0oconcept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id LEFT JOIN ra2pz78aconcept_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')
UNION ALL UNION ALL
@ -742,7 +746,7 @@ FROM (
,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 q7a3ac0oconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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
@ -762,7 +766,7 @@ FROM (
,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 q7a3ac0oconcept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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
@ -782,7 +786,7 @@ FROM (
,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 q7a3ac0oconcept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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
,( ,(
@ -816,7 +820,7 @@ 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 q7a3ac0opo_map; FROM ra2pz78apo_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)
@ -857,8 +861,8 @@ FROM (
****/ ****/
--find valid drugs from drug_exposure table --find valid drugs from drug_exposure table
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0odrgexp_map'; EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78adrgexp_map';
EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0odrgexp_map'; EXECUTE IMMEDIATE 'DROP TABLE ra2pz78adrgexp_map';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -866,9 +870,9 @@ EXCEPTION
END IF; END IF;
END; END;
/ /* / */
CREATE GLOBAL TEMPORARY TABLE q7a3ac0odrgexp_map CREATE GLOBAL TEMPORARY TABLE ra2pz78adrgexp_map
ON COMMIT PRESERVE ROWS ON COMMIT PRESERVE ROWS
AS AS
SELECT SELECT
@ -900,9 +904,9 @@ FROM
LEFT JOIN [TARGET_CDMV5].[SCHEMA].procedure_occurrence po ON 1 = 0 LEFT JOIN [TARGET_CDMV5].[SCHEMA].procedure_occurrence po ON 1 = 0
WHERE 0 = 1; WHERE 0 = 1;
/ /* / */
INSERT INTO q7a3ac0odrgexp_map INSERT INTO ra2pz78adrgexp_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
@ -926,14 +930,14 @@ 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 q7a3ac0oconcept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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 q7a3ac0oconcept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id INNER JOIN ra2pz78aconcept_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 q7a3ac0oconcept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id LEFT JOIN ra2pz78aconcept_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')
INNER JOIN q7a3ac0oconcept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id INNER JOIN ra2pz78aconcept_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
@ -992,8 +996,8 @@ 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 q7a3ac0oconcept_map cm1 ON drug_concept_id = cm1.source_concept_id LEFT JOIN ra2pz78aconcept_map cm1 ON drug_concept_id = cm1.source_concept_id
LEFT JOIN q7a3ac0oconcept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id LEFT JOIN ra2pz78aconcept_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')
WHERE drug_concept_id <> 0 WHERE drug_concept_id <> 0
AND cm1.domain_id IS NULL AND cm1.domain_id IS NULL
@ -1053,12 +1057,12 @@ FROM (
,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 q7a3ac0oconcept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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 q7a3ac0oconcept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id INNER JOIN ra2pz78aconcept_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 q7a3ac0oconcept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id LEFT JOIN ra2pz78aconcept_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')
UNION ALL UNION ALL
@ -1087,7 +1091,7 @@ FROM (
,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 q7a3ac0oconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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
@ -1116,7 +1120,7 @@ FROM (
,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 q7a3ac0oconcept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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
@ -1145,7 +1149,7 @@ FROM (
,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 q7a3ac0oconcept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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
,( ,(
@ -1197,7 +1201,7 @@ 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 q7a3ac0odrgexp_map; FROM ra2pz78adrgexp_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)
@ -1250,12 +1254,12 @@ 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 q7a3ac0oconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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 q7a3ac0oconcept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id INNER JOIN ra2pz78aconcept_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 q7a3ac0oconcept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id LEFT JOIN ra2pz78aconcept_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')
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
@ -1291,8 +1295,8 @@ 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 q7a3ac0oconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id LEFT JOIN ra2pz78aconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
LEFT JOIN q7a3ac0oconcept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id LEFT JOIN ra2pz78aconcept_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')
WHERE condition_concept_id <> 0 WHERE condition_concept_id <> 0
AND cm1.domain_id IS NULL AND cm1.domain_id IS NULL
@ -1330,12 +1334,12 @@ FROM (
,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 q7a3ac0oconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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 q7a3ac0oconcept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id INNER JOIN ra2pz78aconcept_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 q7a3ac0oconcept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id LEFT JOIN ra2pz78aconcept_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')
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
@ -1354,7 +1358,7 @@ FROM (
,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 q7a3ac0oconcept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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
@ -1372,7 +1376,7 @@ FROM (
,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 q7a3ac0oconcept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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
@ -1390,7 +1394,7 @@ FROM (
,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 q7a3ac0oconcept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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
,( ,(
@ -1465,7 +1469,7 @@ FROM (
,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 q7a3ac0oconcept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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
@ -1484,7 +1488,7 @@ FROM (
,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 q7a3ac0oconcept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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
@ -1503,7 +1507,7 @@ FROM (
,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 q7a3ac0oconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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
@ -1522,7 +1526,7 @@ FROM (
,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 q7a3ac0oconcept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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;
@ -1574,9 +1578,9 @@ FROM (
,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 q7a3ac0oconcept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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 q7a3ac0oconcept_map cm2 ON observation.unit_concept_id = cm2.source_concept_id LEFT JOIN ra2pz78aconcept_map cm2 ON observation.unit_concept_id = cm2.source_concept_id
AND LOWER(cm1.domain_id) IN ('unit') AND LOWER(cm1.domain_id) IN ('unit')
UNION ALL UNION ALL
@ -1600,7 +1604,7 @@ FROM (
,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 q7a3ac0oconcept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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
@ -1624,7 +1628,7 @@ FROM (
,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 q7a3ac0oconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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
@ -1648,7 +1652,7 @@ FROM (
,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 q7a3ac0oconcept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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;
@ -1679,7 +1683,7 @@ SELECT observation_id
FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION
WHERE observation_concept_id NOT IN ( WHERE observation_concept_id NOT IN (
SELECT source_concept_id SELECT source_concept_id
FROM q7a3ac0oconcept_map_distinct FROM ra2pz78aconcept_map_distinct
WHERE LOWER(domain_id) IN ( WHERE LOWER(domain_id) IN (
'condition' 'condition'
,'drug' ,'drug'
@ -1734,7 +1738,7 @@ FROM (
,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 q7a3ac0oconcept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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
@ -1758,7 +1762,7 @@ FROM (
,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 q7a3ac0oconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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
@ -1783,7 +1787,7 @@ FROM (
,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 q7a3ac0oconcept_map cm1 ON pc.disease_class_concept_id = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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
@ -1807,7 +1811,7 @@ FROM (
,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 q7a3ac0oconcept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id INNER JOIN ra2pz78aconcept_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
,( ,(
@ -1894,7 +1898,7 @@ FROM (
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 q7a3ac0odrgexp_map de ON de.person_id = po.person_id INNER JOIN ra2pz78adrgexp_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
,( ,(
@ -1967,7 +1971,7 @@ FROM (
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 q7a3ac0opo_map po ON de.person_id = po.person_id INNER JOIN ra2pz78apo_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
,( ,(
@ -1982,8 +1986,8 @@ Note: Eras derived from DRUG_EXPOSURE table, using 30d gap
****/ ****/
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0octeDrugTarget'; EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78acteDrugTarget';
EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0octeDrugTarget'; EXECUTE IMMEDIATE 'DROP TABLE ra2pz78acteDrugTarget';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -1991,10 +1995,10 @@ EXCEPTION
END IF; END IF;
END; 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 q7a3ac0octeDrugTarget CREATE GLOBAL TEMPORARY TABLE ra2pz78acteDrugTarget
ON COMMIT PRESERVE ROWS ON COMMIT PRESERVE ROWS
AS AS
SELECT SELECT
@ -2013,11 +2017,11 @@ INNER JOIN [TARGET_CDMV5].[SCHEMA].CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCE
WHERE c.VOCABULARY_ID = 'RxNorm' WHERE c.VOCABULARY_ID = 'RxNorm'
AND c.CONCEPT_CLASS_ID = 'Ingredient'; AND c.CONCEPT_CLASS_ID = 'Ingredient';
/ /* / */
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0octeEndDates'; EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78acteEndDates';
EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0octeEndDates'; EXECUTE IMMEDIATE 'DROP TABLE ra2pz78acteEndDates';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -2025,9 +2029,9 @@ EXCEPTION
END IF; END IF;
END; END;
/ /* / */
CREATE GLOBAL TEMPORARY TABLE q7a3ac0octeEndDates CREATE GLOBAL TEMPORARY TABLE ra2pz78acteEndDates
ON COMMIT PRESERVE ROWS ON COMMIT PRESERVE ROWS
AS AS
SELECT SELECT
@ -2063,7 +2067,7 @@ 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 q7a3ac0octeDrugTarget FROM ra2pz78acteDrugTarget
UNION ALL UNION ALL
@ -2073,7 +2077,7 @@ FROM
,( DRUG_EXPOSURE_END_DATE + 30) ,( DRUG_EXPOSURE_END_DATE + 30)
,1 AS EVENT_TYPE ,1 AS EVENT_TYPE
,NULL ,NULL
FROM q7a3ac0octeDrugTarget FROM ra2pz78acteDrugTarget
) RAWDATA ) RAWDATA
) E1 ) E1
INNER JOIN ( INNER JOIN (
@ -2084,10 +2088,10 @@ 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 q7a3ac0octeDrugTarget FROM ra2pz78acteDrugTarget
) 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
GROUP BY E1.PERSON_ID GROUP BY E1.PERSON_ID
,E1.INGREDIENT_CONCEPT_ID ,E1.INGREDIENT_CONCEPT_ID
,E1.EVENT_DATE ,E1.EVENT_DATE
@ -2096,11 +2100,11 @@ FROM
) E ) E
WHERE 2 * E.START_ORDINAL - E.OVERALL_ORD = 0; WHERE 2 * E.START_ORDINAL - E.OVERALL_ORD = 0;
/ /* / */
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0octeDrugExpEnds'; EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78acteDrugExpEnds';
EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0octeDrugExpEnds'; EXECUTE IMMEDIATE 'DROP TABLE ra2pz78acteDrugExpEnds';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -2108,9 +2112,9 @@ EXCEPTION
END IF; END IF;
END; END;
/ /* / */
CREATE GLOBAL TEMPORARY TABLE q7a3ac0octeDrugExpEnds CREATE GLOBAL TEMPORARY TABLE ra2pz78acteDrugExpEnds
ON COMMIT PRESERVE ROWS ON COMMIT PRESERVE ROWS
AS AS
SELECT SELECT
@ -2121,8 +2125,8 @@ SELECT
,MIN(e.END_DATE) AS ERA_END_DATE ,MIN(e.END_DATE) AS ERA_END_DATE
FROM FROM
q7a3ac0octeDrugTarget d ra2pz78acteDrugTarget d
INNER JOIN q7a3ac0octeEndDates e ON d.PERSON_ID = e.PERSON_ID INNER JOIN ra2pz78acteEndDates 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
@ -2130,7 +2134,7 @@ GROUP BY d.PERSON_ID
,d.DRUG_TYPE_CONCEPT_ID ,d.DRUG_TYPE_CONCEPT_ID
,d.DRUG_EXPOSURE_START_DATE; ,d.DRUG_EXPOSURE_START_DATE;
/ /* / */
INSERT INTO [TARGET_CDMV5].[SCHEMA].drug_era INSERT INTO [TARGET_CDMV5].[SCHEMA].drug_era
SELECT row_number() OVER ( SELECT row_number() OVER (
@ -2142,7 +2146,7 @@ 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 q7a3ac0octeDrugExpEnds FROM ra2pz78acteDrugExpEnds
GROUP BY person_id GROUP BY person_id
,INGREDIENT_CONCEPT_ID ,INGREDIENT_CONCEPT_ID
,drug_type_concept_id ,drug_type_concept_id
@ -2155,8 +2159,8 @@ Note: Eras derived from CONDITION_OCCURRENCE table, using 30d gap
****/ ****/
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0ocondition_era_phase_1'; EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78acondition_era_phase_1';
EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0ocondition_era_phase_1'; EXECUTE IMMEDIATE 'DROP TABLE ra2pz78acondition_era_phase_1';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -2164,11 +2168,11 @@ EXCEPTION
END IF; END IF;
END; END;
/ /* / */
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0octeConditionTarget'; EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78acteConditionTarget';
EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0octeConditionTarget'; EXECUTE IMMEDIATE 'DROP TABLE ra2pz78acteConditionTarget';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -2176,10 +2180,10 @@ EXCEPTION
END IF; END IF;
END; 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 q7a3ac0octeConditionTarget CREATE GLOBAL TEMPORARY TABLE ra2pz78acteConditionTarget
ON COMMIT PRESERVE ROWS ON COMMIT PRESERVE ROWS
AS AS
SELECT SELECT
@ -2191,11 +2195,11 @@ SELECT
FROM FROM
[TARGET_CDMV5].[SCHEMA].CONDITION_OCCURRENCE co; [TARGET_CDMV5].[SCHEMA].CONDITION_OCCURRENCE co;
/ /* / */
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0octeCondEndDates'; EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78acteCondEndDates';
EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0octeCondEndDates'; EXECUTE IMMEDIATE 'DROP TABLE ra2pz78acteCondEndDates';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -2203,9 +2207,9 @@ EXCEPTION
END IF; END IF;
END; END;
/ /* / */
CREATE GLOBAL TEMPORARY TABLE q7a3ac0octeCondEndDates CREATE GLOBAL TEMPORARY TABLE ra2pz78acteCondEndDates
ON COMMIT PRESERVE ROWS ON COMMIT PRESERVE ROWS
AS AS
SELECT SELECT
@ -2241,7 +2245,7 @@ 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 q7a3ac0octeConditionTarget FROM ra2pz78acteConditionTarget
UNION ALL UNION ALL
@ -2251,7 +2255,7 @@ FROM
,( CONDITION_END_DATE + 30) ,( CONDITION_END_DATE + 30)
,1 AS EVENT_TYPE ,1 AS EVENT_TYPE
,NULL ,NULL
FROM q7a3ac0octeConditionTarget FROM ra2pz78acteConditionTarget
) RAWDATA ) RAWDATA
) E1 ) E1
INNER JOIN ( INNER JOIN (
@ -2262,10 +2266,10 @@ 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 q7a3ac0octeConditionTarget FROM ra2pz78acteConditionTarget
) 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
GROUP BY E1.PERSON_ID GROUP BY E1.PERSON_ID
,E1.CONDITION_CONCEPT_ID ,E1.CONDITION_CONCEPT_ID
,E1.EVENT_DATE ,E1.EVENT_DATE
@ -2274,11 +2278,11 @@ FROM
) E ) E
WHERE (2 * E.START_ORDINAL) - E.OVERALL_ORD = 0; WHERE (2 * E.START_ORDINAL) - E.OVERALL_ORD = 0;
/ /* / */
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0octeConditionEnds'; EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78acteConditionEnds';
EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0octeConditionEnds'; EXECUTE IMMEDIATE 'DROP TABLE ra2pz78acteConditionEnds';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -2286,9 +2290,9 @@ EXCEPTION
END IF; END IF;
END; END;
/ /* / */
CREATE GLOBAL TEMPORARY TABLE q7a3ac0octeConditionEnds CREATE GLOBAL TEMPORARY TABLE ra2pz78acteConditionEnds
ON COMMIT PRESERVE ROWS ON COMMIT PRESERVE ROWS
AS AS
SELECT SELECT
@ -2298,15 +2302,15 @@ SELECT
,MIN(e.END_DATE) AS ERA_END_DATE ,MIN(e.END_DATE) AS ERA_END_DATE
FROM FROM
q7a3ac0octeConditionTarget c ra2pz78acteConditionTarget c
INNER JOIN q7a3ac0octeCondEndDates e ON c.PERSON_ID = e.PERSON_ID INNER JOIN ra2pz78acteCondEndDates 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
,c.CONDITION_CONCEPT_ID ,c.CONDITION_CONCEPT_ID
,c.CONDITION_START_DATE; ,c.CONDITION_START_DATE;
/ /* / */
INSERT INTO [TARGET_CDMV5].[SCHEMA].condition_era ( INSERT INTO [TARGET_CDMV5].[SCHEMA].condition_era (
condition_era_id condition_era_id
@ -2324,7 +2328,7 @@ 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 q7a3ac0octeConditionEnds FROM ra2pz78acteConditionEnds
GROUP BY person_id GROUP BY person_id
,CONDITION_CONCEPT_ID ,CONDITION_CONCEPT_ID
,ERA_END_DATE; ,ERA_END_DATE;
@ -2339,8 +2343,8 @@ Note: These queries are used to provide some basic stats around row counts betwe
****/ ****/
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0ov5_stats'; EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78av5_stats';
EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0ov5_stats'; EXECUTE IMMEDIATE 'DROP TABLE ra2pz78av5_stats';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -2348,11 +2352,11 @@ EXCEPTION
END IF; END IF;
END; END;
/ /* / */
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0ov4_stats'; EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78av4_stats';
EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0ov4_stats'; EXECUTE IMMEDIATE 'DROP TABLE ra2pz78av4_stats';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -2360,10 +2364,10 @@ EXCEPTION
END IF; END IF;
END; 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 q7a3ac0ov4_stats CREATE GLOBAL TEMPORARY TABLE ra2pz78av4_stats
ON COMMIT PRESERVE ROWS ON COMMIT PRESERVE ROWS
AS AS
SELECT SELECT
@ -2405,9 +2409,9 @@ FROM
SELECT '[SOURCE_CDMV4]' AS DBName, 'visit_occurrence' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].visit_occurrence SELECT '[SOURCE_CDMV4]' AS DBName, 'visit_occurrence' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].visit_occurrence
) v4_stats; ) v4_stats;
/ /* / */
CREATE GLOBAL TEMPORARY TABLE q7a3ac0ov5_stats CREATE GLOBAL TEMPORARY TABLE ra2pz78av5_stats
ON COMMIT PRESERVE ROWS ON COMMIT PRESERVE ROWS
AS AS
SELECT SELECT
@ -2453,7 +2457,7 @@ FROM
SELECT '[TARGET_CDMV5]' AS DBName, 'visit_occurrence' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].visit_occurrence SELECT '[TARGET_CDMV5]' AS DBName, 'visit_occurrence' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].visit_occurrence
) v5_stats; ) v5_stats;
/ /* / */
-- Show the results -- Show the results
select select
@ -2465,8 +2469,8 @@ 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 q7a3ac0ov4_stats v4 from ra2pz78av4_stats v4
full outer join q7a3ac0ov5_stats v5 ON v4.TableName = v5.TableName full outer join ra2pz78av5_stats v5 ON v4.TableName = v5.TableName
order by v5.TableName; order by v5.TableName;
/* /*
@ -2474,8 +2478,8 @@ order by v5.TableName;
* tables to the V5 destinations * tables to the V5 destinations
*/ */
BEGIN BEGIN
EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0oclassification_map'; EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78aclassification_map';
EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0oclassification_map'; EXECUTE IMMEDIATE 'DROP TABLE ra2pz78aclassification_map';
EXCEPTION EXCEPTION
WHEN OTHERS THEN WHEN OTHERS THEN
IF SQLCODE != -942 THEN IF SQLCODE != -942 THEN
@ -2483,9 +2487,9 @@ EXCEPTION
END IF; END IF;
END; END;
/ /* / */
CREATE GLOBAL TEMPORARY TABLE q7a3ac0oclassification_map CREATE GLOBAL TEMPORARY TABLE ra2pz78aclassification_map
ON COMMIT PRESERVE ROWS ON COMMIT PRESERVE ROWS
AS AS
SELECT SELECT
@ -2496,33 +2500,33 @@ 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 q7a3ac0oconcept_map CM ON co.condition_concept_id = cm.source_concept_id LEFT JOIN ra2pz78aconcept_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 q7a3ac0oconcept_map CM ON de.drug_concept_id = cm.source_concept_id LEFT JOIN ra2pz78aconcept_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 q7a3ac0oconcept_map CM ON o.observation_concept_id = cm.source_concept_id LEFT JOIN ra2pz78aconcept_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 q7a3ac0oconcept_map CM ON po.PROCEDURE_CONCEPT_ID = cm.source_concept_id LEFT JOIN ra2pz78aconcept_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;
/ /* / */
select * select *
from q7a3ac0oclassification_map from ra2pz78aclassification_map
order by tablename, domain_id; order by tablename, domain_id;
select domain_id, SUM(row_count) select domain_id, SUM(row_count)
from q7a3ac0oclassification_map from ra2pz78aclassification_map
group by domain_id group by domain_id
order by domain_id; order by domain_id;

6
Version4 To Version5 Conversion/PostgreSQL/OMOP CDMv4 to CDMv5 - PostgreSQL.sql
View File

@ -626,7 +626,7 @@ WHERE procedure_concept_id = 0
UNION ALL UNION ALL
-- All drug exposures that do not map to a standard concept in V5 should also carry over with condition_concept_id = 0 -- All PROCEDURE_OCCURRENCE that do not map to a standard concept in V5 should also carry over with procedure_concept_id = 0
SELECT procedure_occurrence_id SELECT procedure_occurrence_id
,person_id ,person_id
,0 AS procedure_concept_id ,0 AS procedure_concept_id
@ -2031,7 +2031,7 @@ FROM
FROM cteDrugTarget FROM cteDrugTarget
) 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
GROUP BY E1.PERSON_ID GROUP BY E1.PERSON_ID
,E1.INGREDIENT_CONCEPT_ID ,E1.INGREDIENT_CONCEPT_ID
,E1.EVENT_DATE ,E1.EVENT_DATE
@ -2177,7 +2177,7 @@ FROM
FROM cteConditionTarget FROM cteConditionTarget
) 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
GROUP BY E1.PERSON_ID GROUP BY E1.PERSON_ID
,E1.CONDITION_CONCEPT_ID ,E1.CONDITION_CONCEPT_ID
,E1.EVENT_DATE ,E1.EVENT_DATE

2
Version4 To Version5 Conversion/README.md
View File

@ -24,6 +24,8 @@ Usage
1. **Create your V5 Target Database:** Create a CDM V5 database on the same server as your CDM V4 database by using the **[Common Data Model Scripts](https://github.com/OHDSI/CommonDataModel "Common Data Model Scripts")** for your RDBMS. **NOTE: Please review the data types that exist on your V4 database and ensure you carry forward any data type changes from V4 to V5. For example, if you converted columns from an INT to a BIGINT to accommodate tables with > 2.1 Billion Rows, you will need to make the corresponding changes in your V5 Database and potentially to this conversion script** 1. **Create your V5 Target Database:** Create a CDM V5 database on the same server as your CDM V4 database by using the **[Common Data Model Scripts](https://github.com/OHDSI/CommonDataModel "Common Data Model Scripts")** for your RDBMS. **NOTE: Please review the data types that exist on your V4 database and ensure you carry forward any data type changes from V4 to V5. For example, if you converted columns from an INT to a BIGINT to accommodate tables with > 2.1 Billion Rows, you will need to make the corresponding changes in your V5 Database and potentially to this conversion script**
2. **Load the V5 Vocabulary**: Download the V5 vocabulary from **[Athena](http://www.ohdsi.org/web/athena/ "Athena")** and load them into the V5 database created in step 1 above.
2. **Download the conversion script:** The **[CDM V4 to V5 Conversion](https://github.com/OHDSI/CommonDataModel/tree/master/Version4%20To%20Version5%20Conversion "CDM V4 to V5 Conversion Directory")** folder has subfolders with scripts that will work on each RDBMS. In order to make this file work in your environment, you will need to perform a global "FIND AND REPLACE" on the conversion script to fill in the file with values that pertain to your environment. The following are the tokens you should use when doing your "FIND AND REPLACE" operation: 2. **Download the conversion script:** The **[CDM V4 to V5 Conversion](https://github.com/OHDSI/CommonDataModel/tree/master/Version4%20To%20Version5%20Conversion "CDM V4 to V5 Conversion Directory")** folder has subfolders with scripts that will work on each RDBMS. In order to make this file work in your environment, you will need to perform a global "FIND AND REPLACE" on the conversion script to fill in the file with values that pertain to your environment. The following are the tokens you should use when doing your "FIND AND REPLACE" operation:
* [SOURCE_CDMV4] - Your V4 database name * [SOURCE_CDMV4] - Your V4 database name

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Version4 To Version5 Conversion/Redshift/OMOP CDMv4 to CDMv5 - Redshift.sql Normal file
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Version4 To Version5 Conversion/Sql Server PDW/OMOP CDMv4 to CDMv5 - Sql Server PDW.dsql Normal file
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6
Version4 To Version5 Conversion/Sql Server/OMOP CDMv4 to CDMv5 - SQL Server.sql
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@ -615,7 +615,7 @@ WHERE procedure_concept_id = 0
UNION ALL UNION ALL
-- All drug exposures that do not map to a standard concept in V5 should also carry over with condition_concept_id = 0 -- All PROCEDURE_OCCURRENCE that do not map to a standard concept in V5 should also carry over with procedure_concept_id = 0
SELECT procedure_occurrence_id SELECT procedure_occurrence_id
,person_id ,person_id
,0 AS procedure_concept_id ,0 AS procedure_concept_id
@ -2008,7 +2008,7 @@ FROM (
FROM #cteDrugTarget FROM #cteDrugTarget
) 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
GROUP BY E1.PERSON_ID GROUP BY E1.PERSON_ID
,E1.INGREDIENT_CONCEPT_ID ,E1.INGREDIENT_CONCEPT_ID
,E1.EVENT_DATE ,E1.EVENT_DATE
@ -2143,7 +2143,7 @@ FROM (
FROM #cteConditionTarget FROM #cteConditionTarget
) 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
GROUP BY E1.PERSON_ID GROUP BY E1.PERSON_ID
,E1.CONDITION_CONCEPT_ID ,E1.CONDITION_CONCEPT_ID
,E1.EVENT_DATE ,E1.EVENT_DATE