Adding in Redshift and SQL Server PDW translations along with a bug fix to the era logic
This commit is contained in:
Anthony Sena
parent
bac9cebf33
commit
cb116a29a0
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@ -0,0 +1,38 @@
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# Load Libraries
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install.packages(devtools)
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library(devtools)
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install_github("OHDSI/SqlRender")
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library(SqlRender)
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# Variables
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ohdsiSqlFile <- "C:/Git/CommonDataModel/Version4 To Version5 Conversion/OMOP CDMv4 to CDMv5 - OHDSI-SQL.sql"
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targetSqlServerFile <- "C:/Git/CommonDataModel/Version4 To Version5 Conversion/Sql Server/OMOP CDMv4 to CDMv5 - SQL Server.sql"
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targetPostgreSqlFile <- "C:/Git/CommonDataModel/Version4 To Version5 Conversion/PostgreSQL/OMOP CDMv4 to CDMv5 - PostgreSQL.sql"
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targetOracleFile <- "C:/Git/CommonDataModel/Version4 To Version5 Conversion/Oracle/OMOP CDMv4 to CDMv5 - Oracle.sql"
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targetSqlServerPDWFile <- "C:/Git/CommonDataModel/Version4 To Version5 Conversion/Sql Server PDW/OMOP CDMv4 to CDMv5 - Sql Server PDW.dsql"
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targetRedshiftFile <- "C:/Git/CommonDataModel/Version4 To Version5 Conversion/Redshift/OMOP CDMv4 to CDMv5 - Redshift.sql"
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##### LOCAL - SQL Server Testing
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#renderSqlFile(ohdsiSqlFile, targetSqlServerFile, SOURCE_CDMV4 = "[CDMV4]", SOURCE_CDMV4_SCHEMA = "[CDMV4].[dbo]", TARGET_CDMV5 = "[CDMV5]", TARGET_CDMV5_SCHEMA = "[CDMV5].[dbo]")
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##### SQL Server Testing
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#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]")
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##### PostgreSql Testing
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#renderSqlFile(ohdsiSqlFile, targetSqlServerFile, SOURCE_CDMV4 = "sandbox", SOURCE_CDMV4_SCHEMA = "sandbox.cdmv4", TARGET_CDMV5 = "sandbox", TARGET_CDMV5_SCHEMA = "sandbox.cdmv5")
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#translateSqlFile(sourceFile = targetSqlServerFile, targetFile = targetPostgreSqlFile, targetDialect = "postgresql")
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##### Oracle Testing
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#renderSqlFile(ohdsiSqlFile, targetSqlServerFile, SOURCE_CDMV4 = "CDMV4", SOURCE_CDMV4_SCHEMA = "CDMV4", TARGET_CDMV5 = "CDMV5", TARGET_CDMV5_SCHEMA = "CDMV5")
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#translateSqlFile(sourceFile = targetSqlServerFile, targetFile = targetOracleFile, targetDialect = "oracle")
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##### APS Testing
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#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]")
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#translateSqlFile(sourceFile = targetSqlServerFile, targetFile = targetSqlServerPDWFile, targetDialect = "pdw")
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##### Push to GitHub
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renderSqlFile(ohdsiSqlFile, targetSqlServerFile)
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translateSqlFile(sourceFile = targetSqlServerFile, targetFile = targetPostgreSqlFile, targetDialect = "postgresql")
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translateSqlFile(sourceFile = targetSqlServerFile, targetFile = targetOracleFile, targetDialect = "oracle")
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translateSqlFile(sourceFile = targetSqlServerFile, targetFile = targetSqlServerPDWFile, targetDialect = "pdw")
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translateSqlFile(sourceFile = targetSqlServerFile, targetFile = targetRedshiftFile, targetDialect = "redshift")
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@ -2008,7 +2008,7 @@ FROM (
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FROM #cteDrugTarget
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) E2 ON E1.PERSON_ID = E2.PERSON_ID
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AND E1.INGREDIENT_CONCEPT_ID = E2.INGREDIENT_CONCEPT_ID
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AND E2.EVENT_DATE < E1.EVENT_DATE
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AND E2.EVENT_DATE <= E1.EVENT_DATE
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GROUP BY E1.PERSON_ID
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,E1.INGREDIENT_CONCEPT_ID
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,E1.EVENT_DATE
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@ -2143,7 +2143,7 @@ FROM (
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FROM #cteConditionTarget
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) E2 ON E1.PERSON_ID = E2.PERSON_ID
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AND E1.CONDITION_CONCEPT_ID = E2.CONDITION_CONCEPT_ID
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AND E2.EVENT_DATE < E1.EVENT_DATE
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AND E2.EVENT_DATE <= E1.EVENT_DATE
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GROUP BY E1.PERSON_ID
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,E1.CONDITION_CONCEPT_ID
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,E1.EVENT_DATE
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@ -109,8 +109,8 @@ ALTER SESSION SET current_schema = [TARGET_CDMV5];
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* Also, as of the date which this script was authored, no source_concept_ids map to multiple domains
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*/
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BEGIN
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EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0oconcept_map';
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EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0oconcept_map';
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EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78aconcept_map';
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EXECUTE IMMEDIATE 'DROP TABLE ra2pz78aconcept_map';
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EXCEPTION
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WHEN OTHERS THEN
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IF SQLCODE != -942 THEN
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@ -118,9 +118,9 @@ EXCEPTION
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END IF;
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END;
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/
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/* / */
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CREATE GLOBAL TEMPORARY TABLE q7a3ac0oconcept_map
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CREATE GLOBAL TEMPORARY TABLE ra2pz78aconcept_map
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ON COMMIT PRESERVE ROWS
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AS
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SELECT
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@ -132,9 +132,9 @@ FROM
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[TARGET_CDMV5].[SCHEMA].concept
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WHERE 1 = 0;
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/
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/* / */
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INSERT INTO q7a3ac0oconcept_map
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INSERT INTO ra2pz78aconcept_map
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--standard concepts
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SELECT concept_id AS source_concept_id
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,concept_id AS target_concept_id
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@ -279,8 +279,8 @@ INNER JOIN [TARGET_CDMV5].[SCHEMA].concept c2 ON cr1.concept_id_2 = c2.concept_i
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AND cr1.invalid_reason IS NULL;
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BEGIN
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EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0oconcept_map_distinct';
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EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0oconcept_map_distinct';
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EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78aconcept_map_distinct';
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EXECUTE IMMEDIATE 'DROP TABLE ra2pz78aconcept_map_distinct';
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EXCEPTION
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WHEN OTHERS THEN
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IF SQLCODE != -942 THEN
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@ -288,9 +288,9 @@ EXCEPTION
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END IF;
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END;
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/
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/* / */
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CREATE GLOBAL TEMPORARY TABLE q7a3ac0oconcept_map_distinct
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CREATE GLOBAL TEMPORARY TABLE ra2pz78aconcept_map_distinct
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ON COMMIT PRESERVE ROWS
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AS
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SELECT
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@ -299,18 +299,18 @@ SELECT
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,COUNT(*) AS targetConceptCount
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FROM
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q7a3ac0oconcept_map
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ra2pz78aconcept_map
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WHERE 1 = 0
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GROUP BY source_concept_id
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,domain_id;
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/
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/* / */
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INSERT INTO q7a3ac0oconcept_map_distinct
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INSERT INTO ra2pz78aconcept_map_distinct
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SELECT source_concept_id
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,domain_id
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,COUNT(*)
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FROM q7a3ac0oconcept_map
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FROM ra2pz78aconcept_map
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GROUP BY source_concept_id
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,domain_id;
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@ -324,10 +324,10 @@ EXCEPTION
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END IF;
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END;
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/
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/* / */
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CREATE TABLE [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE VARCHAR(4000));
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/
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/* / */
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/****
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@ -423,11 +423,11 @@ SELECT person_id
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,ethnicity_source_value
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,CAST(NULL AS INT) ethnicity_source_concept_id
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FROM [SOURCE_CDMV4].[SCHEMA].PERSON p
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LEFT JOIN q7a3ac0oconcept_map gender ON LOWER(gender.DOMAIN_ID) IN ('gender')
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LEFT JOIN ra2pz78aconcept_map gender ON LOWER(gender.DOMAIN_ID) IN ('gender')
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AND p.gender_concept_id = gender.source_concept_id
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LEFT JOIN q7a3ac0oconcept_map race ON LOWER(race.DOMAIN_ID) IN ('race')
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LEFT JOIN ra2pz78aconcept_map race ON LOWER(race.DOMAIN_ID) IN ('race')
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AND p.race_concept_id = race.source_concept_id
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LEFT JOIN q7a3ac0oconcept_map ethnicity ON LOWER(ethnicity.DOMAIN_ID) IN ('ethnicity')
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LEFT JOIN ra2pz78aconcept_map ethnicity ON LOWER(ethnicity.DOMAIN_ID) IN ('ethnicity')
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AND p.ETHNICITY_CONCEPT_ID = ethnicity.source_concept_id;
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INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE)
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@ -509,7 +509,7 @@ SELECT person_id
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,cause_of_death_source_value AS cause_source_value
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,CAST(NULL AS INT) AS cause_source_concept_id
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FROM [SOURCE_CDMV4].[SCHEMA].DEATH
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LEFT JOIN q7a3ac0oconcept_map_distinct cm1 ON DEATH.DEATH_TYPE_CONCEPT_ID = CM1.SOURCE_CONCEPT_ID
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LEFT JOIN ra2pz78aconcept_map_distinct cm1 ON DEATH.DEATH_TYPE_CONCEPT_ID = CM1.SOURCE_CONCEPT_ID
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AND LOWER(DOMAIN_ID) IN ('death type');
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INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE)
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@ -548,7 +548,7 @@ SELECT visit_occurrence_id
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,place_of_service_source_value AS visit_source_value
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,CAST(NULL AS INT) visit_source_concept_id
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FROM [SOURCE_CDMV4].[SCHEMA].VISIT_OCCURRENCE
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LEFT JOIN q7a3ac0oconcept_map cm1 ON VISIT_OCCURRENCE.PLACE_OF_SERVICE_CONCEPT_ID = cm1.source_concept_id
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LEFT JOIN ra2pz78aconcept_map cm1 ON VISIT_OCCURRENCE.PLACE_OF_SERVICE_CONCEPT_ID = cm1.source_concept_id
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AND LOWER(cm1.domain_id) IN ('visit');
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INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE)
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@ -574,8 +574,8 @@ FROM (
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****/
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BEGIN
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EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0opo_map';
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EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0opo_map';
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EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78apo_map';
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EXECUTE IMMEDIATE 'DROP TABLE ra2pz78apo_map';
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EXCEPTION
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WHEN OTHERS THEN
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IF SQLCODE != -942 THEN
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@ -583,9 +583,9 @@ EXCEPTION
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END IF;
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END;
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/
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/* / */
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CREATE GLOBAL TEMPORARY TABLE q7a3ac0opo_map
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CREATE GLOBAL TEMPORARY TABLE ra2pz78apo_map
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ON COMMIT PRESERVE ROWS
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AS
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SELECT
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@ -608,10 +608,10 @@ FROM
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LEFT JOIN [TARGET_CDMV5].[SCHEMA].drug_exposure de ON 1 = 0
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WHERE 0 = 1;
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/
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/* / */
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--find valid procedures from procedure table
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INSERT INTO q7a3ac0opo_map
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INSERT INTO ra2pz78apo_map
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SELECT procedure_occurrence_id
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,person_id
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,COALESCE(cm1.target_concept_id, 0) AS procedure_concept_id
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@ -626,14 +626,14 @@ SELECT procedure_occurrence_id
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,NULL AS qualifier_source_value
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,CAST(NULL AS INT) AS origional_drug_id
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FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
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INNER JOIN q7a3ac0oconcept_map cm1 ON PROCEDURE_OCCURRENCE.PROCEDURE_CONCEPT_ID = cm1.source_concept_id
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INNER JOIN ra2pz78aconcept_map cm1 ON PROCEDURE_OCCURRENCE.PROCEDURE_CONCEPT_ID = cm1.source_concept_id
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AND LOWER(cm1.domain_id) IN ('procedure')
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INNER JOIN q7a3ac0oconcept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id
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INNER JOIN ra2pz78aconcept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id
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AND cm1.domain_id = cmdis.domain_id
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AND cmdis.targetConceptCount = 1
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LEFT JOIN q7a3ac0oconcept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id
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LEFT JOIN ra2pz78aconcept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id
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AND LOWER(cm2.domain_id) IN ('procedure type')
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LEFT JOIN q7a3ac0oconcept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id
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LEFT JOIN ra2pz78aconcept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id
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AND cm2.domain_id = cmdis2.domain_id
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AND cmdis2.targetConceptCount = 1
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@ -654,11 +654,15 @@ SELECT procedure_occurrence_id
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,NULL qualifier_source_value
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,CAST(NULL AS INT) AS origional_drug_id
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FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
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FROM
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DUAL
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FROM
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DUAL
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WHERE procedure_concept_id = 0
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UNION ALL
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-- All drug exposures that do not map to a standard concept in V5 should also carry over with condition_concept_id = 0
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-- All PROCEDURE_OCCURRENCE that do not map to a standard concept in V5 should also carry over with procedure_concept_id = 0
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SELECT procedure_occurrence_id
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,person_id
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,0 AS procedure_concept_id
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@ -673,8 +677,8 @@ SELECT procedure_occurrence_id
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,NULL qualifier_source_value
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,CAST(NULL AS INT) AS origional_drug_id
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FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
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LEFT JOIN q7a3ac0oconcept_map cm1 ON procedure_concept_id = cm1.source_concept_id
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LEFT JOIN q7a3ac0oconcept_map cm2 ON procedure_concept_id = cm2.source_concept_id
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LEFT JOIN ra2pz78aconcept_map cm1 ON procedure_concept_id = cm1.source_concept_id
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LEFT JOIN ra2pz78aconcept_map cm2 ON procedure_concept_id = cm2.source_concept_id
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AND LOWER(cm2.domain_id) IN ('procedure type')
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WHERE procedure_concept_id <> 0
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AND cm1.domain_id IS NULL
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@ -717,12 +721,12 @@ FROM (
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,CAST(NULL AS INT) AS origional_drug_id
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,CAST(NULL AS INT) AS OCCURRENCE_ID
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FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
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INNER JOIN q7a3ac0oconcept_map cm1 ON PROCEDURE_OCCURRENCE.PROCEDURE_CONCEPT_ID = cm1.source_concept_id
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INNER JOIN ra2pz78aconcept_map cm1 ON PROCEDURE_OCCURRENCE.PROCEDURE_CONCEPT_ID = cm1.source_concept_id
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AND LOWER(cm1.domain_id) IN ('procedure')
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INNER JOIN q7a3ac0oconcept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id
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INNER JOIN ra2pz78aconcept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id
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AND cm1.domain_id = cmdis.domain_id
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AND cmdis.targetConceptCount > 1
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LEFT JOIN q7a3ac0oconcept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id
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LEFT JOIN ra2pz78aconcept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id
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AND LOWER(cm2.domain_id) IN ('procedure type')
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UNION ALL
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@ -742,7 +746,7 @@ FROM (
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,CAST(NULL AS INT) AS origional_drug_id
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,condition_occurrence_id AS OCCURRENCE_ID
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FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
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INNER JOIN q7a3ac0oconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
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INNER JOIN ra2pz78aconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
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AND LOWER(cm1.domain_id) IN ('procedure')
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UNION ALL
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@ -762,7 +766,7 @@ FROM (
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,drug_exposure_id AS origional_drug_id
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,drug_exposure_id AS OCCURRENCE_ID
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FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE
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INNER JOIN q7a3ac0oconcept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id
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INNER JOIN ra2pz78aconcept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id
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AND LOWER(cm1.domain_id) IN ('procedure')
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--find procedures that were previously classified as observation
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@ -782,7 +786,7 @@ FROM (
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,CAST(NULL AS INT) AS origional_drug_id
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,OBSERVATION_ID AS OCCURRENCE_ID
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FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION
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INNER JOIN q7a3ac0oconcept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id
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INNER JOIN ra2pz78aconcept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id
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AND LOWER(cm1.domain_id) IN ('procedure')
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) OTHERS
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,(
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@ -816,7 +820,7 @@ SELECT procedure_occurrence_id
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,procedure_source_value
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,procedure_source_concept_id
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,qualifier_source_value
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FROM q7a3ac0opo_map;
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FROM ra2pz78apo_map;
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--warnings of invalid records
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INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE)
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@ -857,8 +861,8 @@ FROM (
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****/
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--find valid drugs from drug_exposure table
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BEGIN
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EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0odrgexp_map';
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EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0odrgexp_map';
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EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78adrgexp_map';
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EXECUTE IMMEDIATE 'DROP TABLE ra2pz78adrgexp_map';
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EXCEPTION
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WHEN OTHERS THEN
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IF SQLCODE != -942 THEN
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@ -866,9 +870,9 @@ EXCEPTION
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END IF;
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END;
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/
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/* / */
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CREATE GLOBAL TEMPORARY TABLE q7a3ac0odrgexp_map
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CREATE GLOBAL TEMPORARY TABLE ra2pz78adrgexp_map
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ON COMMIT PRESERVE ROWS
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AS
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SELECT
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@ -900,9 +904,9 @@ FROM
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LEFT JOIN [TARGET_CDMV5].[SCHEMA].procedure_occurrence po ON 1 = 0
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WHERE 0 = 1;
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/
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/* / */
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INSERT INTO q7a3ac0odrgexp_map
|
||||
INSERT INTO ra2pz78adrgexp_map
|
||||
SELECT drug_exposure_id
|
||||
,person_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
|
||||
,CAST(NULL AS INT) AS origional_procedure_id
|
||||
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')
|
||||
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 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')
|
||||
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 cmdis2.targetConceptCount = 1
|
||||
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
|
||||
,CAST(NULL AS INT) AS origional_procedure_id
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE
|
||||
LEFT JOIN q7a3ac0oconcept_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 cm1 ON drug_concept_id = cm1.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')
|
||||
WHERE drug_concept_id <> 0
|
||||
AND cm1.domain_id IS NULL
|
||||
|
|
@ -1053,12 +1057,12 @@ FROM (
|
|||
,CAST(NULL AS INT) AS origional_procedure_id
|
||||
,CAST(NULL AS INT) AS OCCURRENCE_ID
|
||||
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')
|
||||
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 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')
|
||||
|
||||
UNION ALL
|
||||
|
|
@ -1087,7 +1091,7 @@ FROM (
|
|||
,CAST(NULL AS INT) AS origional_procedure_id
|
||||
,condition_occurrence_id AS occurrence_id
|
||||
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')
|
||||
--find drugs that were previously classified as procedure
|
||||
|
||||
|
|
@ -1116,7 +1120,7 @@ FROM (
|
|||
,procedure_occurrence_id AS origional_procedure_id
|
||||
,procedure_occurrence_id AS occurrence_id
|
||||
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')
|
||||
--find drugs that were previously classified as observation
|
||||
|
||||
|
|
@ -1145,7 +1149,7 @@ FROM (
|
|||
,CAST(NULL AS INT) AS origional_procedure_id
|
||||
,observation_id AS occurrence_id
|
||||
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')
|
||||
) OTHERS
|
||||
,(
|
||||
|
|
@ -1197,7 +1201,7 @@ SELECT drug_exposure_id
|
|||
,drug_source_concept_id
|
||||
,route_source_value
|
||||
,dose_unit_source_value
|
||||
FROM q7a3ac0odrgexp_map;
|
||||
FROM ra2pz78adrgexp_map;
|
||||
|
||||
--warnings of invalid records
|
||||
INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE)
|
||||
|
|
@ -1250,12 +1254,12 @@ SELECT condition_occurrence_id
|
|||
,condition_source_value
|
||||
,CAST(NULL AS INT) condition_source_concept_id
|
||||
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')
|
||||
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 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')
|
||||
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
|
||||
,CAST(NULL AS INT) condition_source_concept_id
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
|
||||
LEFT JOIN q7a3ac0oconcept_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 cm1 ON condition_occurrence.condition_concept_id = cm1.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')
|
||||
WHERE condition_concept_id <> 0
|
||||
AND cm1.domain_id IS NULL
|
||||
|
|
@ -1330,12 +1334,12 @@ FROM (
|
|||
,CAST(NULL AS INT) condition_source_concept_id
|
||||
,NULL AS OCCURRENCE_ID
|
||||
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')
|
||||
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 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')
|
||||
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
|
||||
,procedure_occurrence_id AS OCCURRENCE_ID
|
||||
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')
|
||||
--find conditions that were previously classified as drug
|
||||
|
||||
|
|
@ -1372,7 +1376,7 @@ FROM (
|
|||
,CAST(NULL AS INT) condition_source_concept_id
|
||||
,drug_exposure_id AS OCCURRENCE_ID
|
||||
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')
|
||||
--find conditions that were previously classified as observation
|
||||
|
||||
|
|
@ -1390,7 +1394,7 @@ FROM (
|
|||
,CAST(NULL AS INT) condition_source_concept_id
|
||||
,observation_id AS OCCURRENCE_ID
|
||||
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')
|
||||
) OTHERS
|
||||
,(
|
||||
|
|
@ -1465,7 +1469,7 @@ FROM (
|
|||
,0 AS device_source_concept_id
|
||||
,PROCEDURE_OCCURRENCE_ID AS OCCURRENCE_ID
|
||||
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')
|
||||
--find devices that were previously classified as drug exposure
|
||||
|
||||
|
|
@ -1484,7 +1488,7 @@ FROM (
|
|||
,0 AS device_source_concept_id
|
||||
,DRUG_EXPOSURE_ID AS OCCURRENCE_ID
|
||||
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')
|
||||
--find devices that were previously classified as conditions
|
||||
|
||||
|
|
@ -1503,7 +1507,7 @@ FROM (
|
|||
,0 AS device_source_concept_id
|
||||
,CONDITION_OCCURRENCE_ID AS OCCURRENCE_ID
|
||||
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')
|
||||
--find devices that were previously classified as observations
|
||||
|
||||
|
|
@ -1522,7 +1526,7 @@ FROM (
|
|||
,0 AS device_source_concept_id
|
||||
,OBSERVATION_ID AS OCCURRENCE_ID
|
||||
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')
|
||||
) OTHERS;
|
||||
|
||||
|
|
@ -1574,9 +1578,9 @@ FROM (
|
|||
,TO_CHAR(NULL ) AS value_source_value
|
||||
,observation_id AS occurrence_id
|
||||
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')
|
||||
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')
|
||||
|
||||
UNION ALL
|
||||
|
|
@ -1600,7 +1604,7 @@ FROM (
|
|||
,TO_CHAR(NULL ) AS value_source_value
|
||||
,procedure_occurrence_id AS occurrence_id
|
||||
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')
|
||||
|
||||
UNION ALL
|
||||
|
|
@ -1624,7 +1628,7 @@ FROM (
|
|||
,TO_CHAR(NULL ) AS value_source_value
|
||||
,condition_occurrence_id AS occurrence_id
|
||||
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')
|
||||
|
||||
UNION ALL
|
||||
|
|
@ -1648,7 +1652,7 @@ FROM (
|
|||
,TO_CHAR(NULL ) AS value_source_value
|
||||
,drug_exposure_id AS occurrence_id
|
||||
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')
|
||||
) OTHERS;
|
||||
|
||||
|
|
@ -1679,7 +1683,7 @@ SELECT observation_id
|
|||
FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION
|
||||
WHERE observation_concept_id NOT IN (
|
||||
SELECT source_concept_id
|
||||
FROM q7a3ac0oconcept_map_distinct
|
||||
FROM ra2pz78aconcept_map_distinct
|
||||
WHERE LOWER(domain_id) IN (
|
||||
'condition'
|
||||
,'drug'
|
||||
|
|
@ -1734,7 +1738,7 @@ FROM (
|
|||
,TO_CHAR(NULL ) qualifier_source_value
|
||||
,procedure_occurrence_id AS occurrence_id
|
||||
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')
|
||||
--find observations that were previously classified as condition
|
||||
|
||||
|
|
@ -1758,7 +1762,7 @@ FROM (
|
|||
,TO_CHAR(NULL ) qualifier_source_value
|
||||
,condition_occurrence_id AS occurrence_id
|
||||
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')
|
||||
|
||||
UNION ALL
|
||||
|
|
@ -1783,7 +1787,7 @@ FROM (
|
|||
,po.procedure_occurrence_id AS occurrence_id
|
||||
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 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')
|
||||
|
||||
UNION ALL
|
||||
|
|
@ -1807,7 +1811,7 @@ FROM (
|
|||
,TO_CHAR(NULL ) qualifier_source_value
|
||||
,drug_exposure_id AS occurrence_id
|
||||
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')
|
||||
) OTHERS
|
||||
,(
|
||||
|
|
@ -1894,7 +1898,7 @@ FROM (
|
|||
FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE po
|
||||
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
|
||||
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
|
||||
) OTHERS
|
||||
,(
|
||||
|
|
@ -1967,7 +1971,7 @@ FROM (
|
|||
FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE de
|
||||
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
|
||||
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
|
||||
) OTHERS
|
||||
,(
|
||||
|
|
@ -1982,8 +1986,8 @@ Note: Eras derived from DRUG_EXPOSURE table, using 30d gap
|
|||
|
||||
****/
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0octeDrugTarget';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0octeDrugTarget';
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78acteDrugTarget';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE ra2pz78acteDrugTarget';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -942 THEN
|
||||
|
|
@ -1991,10 +1995,10 @@ EXCEPTION
|
|||
END IF;
|
||||
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
|
||||
CREATE GLOBAL TEMPORARY TABLE q7a3ac0octeDrugTarget
|
||||
CREATE GLOBAL TEMPORARY TABLE ra2pz78acteDrugTarget
|
||||
ON COMMIT PRESERVE ROWS
|
||||
AS
|
||||
SELECT
|
||||
|
|
@ -2013,11 +2017,11 @@ INNER JOIN [TARGET_CDMV5].[SCHEMA].CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCE
|
|||
WHERE c.VOCABULARY_ID = 'RxNorm'
|
||||
AND c.CONCEPT_CLASS_ID = 'Ingredient';
|
||||
|
||||
/
|
||||
/* / */
|
||||
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0octeEndDates';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0octeEndDates';
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78acteEndDates';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE ra2pz78acteEndDates';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -942 THEN
|
||||
|
|
@ -2025,9 +2029,9 @@ EXCEPTION
|
|||
END IF;
|
||||
END;
|
||||
|
||||
/
|
||||
/* / */
|
||||
|
||||
CREATE GLOBAL TEMPORARY TABLE q7a3ac0octeEndDates
|
||||
CREATE GLOBAL TEMPORARY TABLE ra2pz78acteEndDates
|
||||
ON COMMIT PRESERVE ROWS
|
||||
AS
|
||||
SELECT
|
||||
|
|
@ -2063,7 +2067,7 @@ FROM
|
|||
PARTITION BY PERSON_ID
|
||||
,INGREDIENT_CONCEPT_ID ORDER BY DRUG_EXPOSURE_START_DATE
|
||||
) AS START_ORDINAL
|
||||
FROM q7a3ac0octeDrugTarget
|
||||
FROM ra2pz78acteDrugTarget
|
||||
|
||||
UNION ALL
|
||||
|
||||
|
|
@ -2073,7 +2077,7 @@ FROM
|
|||
,( DRUG_EXPOSURE_END_DATE + 30)
|
||||
,1 AS EVENT_TYPE
|
||||
,NULL
|
||||
FROM q7a3ac0octeDrugTarget
|
||||
FROM ra2pz78acteDrugTarget
|
||||
) RAWDATA
|
||||
) E1
|
||||
INNER JOIN (
|
||||
|
|
@ -2084,10 +2088,10 @@ FROM
|
|||
PARTITION BY PERSON_ID
|
||||
,INGREDIENT_CONCEPT_ID ORDER BY DRUG_EXPOSURE_START_DATE
|
||||
) AS START_ORDINAL
|
||||
FROM q7a3ac0octeDrugTarget
|
||||
FROM ra2pz78acteDrugTarget
|
||||
) E2 ON E1.PERSON_ID = E2.PERSON_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
|
||||
,E1.INGREDIENT_CONCEPT_ID
|
||||
,E1.EVENT_DATE
|
||||
|
|
@ -2096,11 +2100,11 @@ FROM
|
|||
) E
|
||||
WHERE 2 * E.START_ORDINAL - E.OVERALL_ORD = 0;
|
||||
|
||||
/
|
||||
/* / */
|
||||
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0octeDrugExpEnds';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0octeDrugExpEnds';
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78acteDrugExpEnds';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE ra2pz78acteDrugExpEnds';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -942 THEN
|
||||
|
|
@ -2108,9 +2112,9 @@ EXCEPTION
|
|||
END IF;
|
||||
END;
|
||||
|
||||
/
|
||||
/* / */
|
||||
|
||||
CREATE GLOBAL TEMPORARY TABLE q7a3ac0octeDrugExpEnds
|
||||
CREATE GLOBAL TEMPORARY TABLE ra2pz78acteDrugExpEnds
|
||||
ON COMMIT PRESERVE ROWS
|
||||
AS
|
||||
SELECT
|
||||
|
|
@ -2121,8 +2125,8 @@ SELECT
|
|||
,MIN(e.END_DATE) AS ERA_END_DATE
|
||||
|
||||
FROM
|
||||
q7a3ac0octeDrugTarget d
|
||||
INNER JOIN q7a3ac0octeEndDates e ON d.PERSON_ID = e.PERSON_ID
|
||||
ra2pz78acteDrugTarget d
|
||||
INNER JOIN ra2pz78acteEndDates e ON d.PERSON_ID = e.PERSON_ID
|
||||
AND d.INGREDIENT_CONCEPT_ID = e.INGREDIENT_CONCEPT_ID
|
||||
AND e.END_DATE >= d.DRUG_EXPOSURE_START_DATE
|
||||
GROUP BY d.PERSON_ID
|
||||
|
|
@ -2130,7 +2134,7 @@ GROUP BY d.PERSON_ID
|
|||
,d.DRUG_TYPE_CONCEPT_ID
|
||||
,d.DRUG_EXPOSURE_START_DATE;
|
||||
|
||||
/
|
||||
/* / */
|
||||
|
||||
INSERT INTO [TARGET_CDMV5].[SCHEMA].drug_era
|
||||
SELECT row_number() OVER (
|
||||
|
|
@ -2142,7 +2146,7 @@ SELECT row_number() OVER (
|
|||
,ERA_END_DATE
|
||||
,COUNT(*) AS DRUG_EXPOSURE_COUNT
|
||||
,30 AS gap_days
|
||||
FROM q7a3ac0octeDrugExpEnds
|
||||
FROM ra2pz78acteDrugExpEnds
|
||||
GROUP BY person_id
|
||||
,INGREDIENT_CONCEPT_ID
|
||||
,drug_type_concept_id
|
||||
|
|
@ -2155,8 +2159,8 @@ Note: Eras derived from CONDITION_OCCURRENCE table, using 30d gap
|
|||
|
||||
****/
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0ocondition_era_phase_1';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0ocondition_era_phase_1';
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78acondition_era_phase_1';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE ra2pz78acondition_era_phase_1';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -942 THEN
|
||||
|
|
@ -2164,11 +2168,11 @@ EXCEPTION
|
|||
END IF;
|
||||
END;
|
||||
|
||||
/
|
||||
/* / */
|
||||
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0octeConditionTarget';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0octeConditionTarget';
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78acteConditionTarget';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE ra2pz78acteConditionTarget';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -942 THEN
|
||||
|
|
@ -2176,10 +2180,10 @@ EXCEPTION
|
|||
END IF;
|
||||
END;
|
||||
|
||||
/
|
||||
/* / */
|
||||
|
||||
-- create base eras from the concepts found in condition_occurrence
|
||||
CREATE GLOBAL TEMPORARY TABLE q7a3ac0octeConditionTarget
|
||||
CREATE GLOBAL TEMPORARY TABLE ra2pz78acteConditionTarget
|
||||
ON COMMIT PRESERVE ROWS
|
||||
AS
|
||||
SELECT
|
||||
|
|
@ -2191,11 +2195,11 @@ SELECT
|
|||
FROM
|
||||
[TARGET_CDMV5].[SCHEMA].CONDITION_OCCURRENCE co;
|
||||
|
||||
/
|
||||
/* / */
|
||||
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0octeCondEndDates';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0octeCondEndDates';
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78acteCondEndDates';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE ra2pz78acteCondEndDates';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -942 THEN
|
||||
|
|
@ -2203,9 +2207,9 @@ EXCEPTION
|
|||
END IF;
|
||||
END;
|
||||
|
||||
/
|
||||
/* / */
|
||||
|
||||
CREATE GLOBAL TEMPORARY TABLE q7a3ac0octeCondEndDates
|
||||
CREATE GLOBAL TEMPORARY TABLE ra2pz78acteCondEndDates
|
||||
ON COMMIT PRESERVE ROWS
|
||||
AS
|
||||
SELECT
|
||||
|
|
@ -2241,7 +2245,7 @@ FROM
|
|||
PARTITION BY PERSON_ID
|
||||
,CONDITION_CONCEPT_ID ORDER BY CONDITION_START_DATE
|
||||
) AS START_ORDINAL
|
||||
FROM q7a3ac0octeConditionTarget
|
||||
FROM ra2pz78acteConditionTarget
|
||||
|
||||
UNION ALL
|
||||
|
||||
|
|
@ -2251,7 +2255,7 @@ FROM
|
|||
,( CONDITION_END_DATE + 30)
|
||||
,1 AS EVENT_TYPE
|
||||
,NULL
|
||||
FROM q7a3ac0octeConditionTarget
|
||||
FROM ra2pz78acteConditionTarget
|
||||
) RAWDATA
|
||||
) E1
|
||||
INNER JOIN (
|
||||
|
|
@ -2262,10 +2266,10 @@ FROM
|
|||
PARTITION BY PERSON_ID
|
||||
,CONDITION_CONCEPT_ID ORDER BY CONDITION_START_DATE
|
||||
) AS START_ORDINAL
|
||||
FROM q7a3ac0octeConditionTarget
|
||||
FROM ra2pz78acteConditionTarget
|
||||
) E2 ON E1.PERSON_ID = E2.PERSON_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
|
||||
,E1.CONDITION_CONCEPT_ID
|
||||
,E1.EVENT_DATE
|
||||
|
|
@ -2274,11 +2278,11 @@ FROM
|
|||
) E
|
||||
WHERE (2 * E.START_ORDINAL) - E.OVERALL_ORD = 0;
|
||||
|
||||
/
|
||||
/* / */
|
||||
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0octeConditionEnds';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0octeConditionEnds';
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78acteConditionEnds';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE ra2pz78acteConditionEnds';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -942 THEN
|
||||
|
|
@ -2286,9 +2290,9 @@ EXCEPTION
|
|||
END IF;
|
||||
END;
|
||||
|
||||
/
|
||||
/* / */
|
||||
|
||||
CREATE GLOBAL TEMPORARY TABLE q7a3ac0octeConditionEnds
|
||||
CREATE GLOBAL TEMPORARY TABLE ra2pz78acteConditionEnds
|
||||
ON COMMIT PRESERVE ROWS
|
||||
AS
|
||||
SELECT
|
||||
|
|
@ -2298,15 +2302,15 @@ SELECT
|
|||
,MIN(e.END_DATE) AS ERA_END_DATE
|
||||
|
||||
FROM
|
||||
q7a3ac0octeConditionTarget c
|
||||
INNER JOIN q7a3ac0octeCondEndDates e ON c.PERSON_ID = e.PERSON_ID
|
||||
ra2pz78acteConditionTarget c
|
||||
INNER JOIN ra2pz78acteCondEndDates e ON c.PERSON_ID = e.PERSON_ID
|
||||
AND c.CONDITION_CONCEPT_ID = e.CONDITION_CONCEPT_ID
|
||||
AND e.END_DATE >= c.CONDITION_START_DATE
|
||||
GROUP BY c.PERSON_ID
|
||||
,c.CONDITION_CONCEPT_ID
|
||||
,c.CONDITION_START_DATE;
|
||||
|
||||
/
|
||||
/* / */
|
||||
|
||||
INSERT INTO [TARGET_CDMV5].[SCHEMA].condition_era (
|
||||
condition_era_id
|
||||
|
|
@ -2324,7 +2328,7 @@ SELECT row_number() OVER (
|
|||
,min(CONDITION_START_DATE) AS CONDITION_ERA_START_DATE
|
||||
,ERA_END_DATE AS CONDITION_ERA_END_DATE
|
||||
,COUNT(*) AS CONDITION_OCCURRENCE_COUNT
|
||||
FROM q7a3ac0octeConditionEnds
|
||||
FROM ra2pz78acteConditionEnds
|
||||
GROUP BY person_id
|
||||
,CONDITION_CONCEPT_ID
|
||||
,ERA_END_DATE;
|
||||
|
|
@ -2339,8 +2343,8 @@ Note: These queries are used to provide some basic stats around row counts betwe
|
|||
****/
|
||||
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0ov5_stats';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0ov5_stats';
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78av5_stats';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE ra2pz78av5_stats';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -942 THEN
|
||||
|
|
@ -2348,11 +2352,11 @@ EXCEPTION
|
|||
END IF;
|
||||
END;
|
||||
|
||||
/
|
||||
/* / */
|
||||
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0ov4_stats';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0ov4_stats';
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78av4_stats';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE ra2pz78av4_stats';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -942 THEN
|
||||
|
|
@ -2360,10 +2364,10 @@ EXCEPTION
|
|||
END IF;
|
||||
END;
|
||||
|
||||
/
|
||||
/* / */
|
||||
|
||||
-- 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
|
||||
AS
|
||||
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
|
||||
) v4_stats;
|
||||
|
||||
/
|
||||
/* / */
|
||||
|
||||
CREATE GLOBAL TEMPORARY TABLE q7a3ac0ov5_stats
|
||||
CREATE GLOBAL TEMPORARY TABLE ra2pz78av5_stats
|
||||
ON COMMIT PRESERVE ROWS
|
||||
AS
|
||||
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
|
||||
) v5_stats;
|
||||
|
||||
/
|
||||
/* / */
|
||||
|
||||
-- Show the results
|
||||
select
|
||||
|
|
@ -2465,8 +2469,8 @@ select
|
|||
v5.TableName v5_table_name,
|
||||
v5.row_count v5_row_count,
|
||||
NVL(v5.row_count, 0) - NVL(v4.row_count, 0) row_count_change
|
||||
from q7a3ac0ov4_stats v4
|
||||
full outer join q7a3ac0ov5_stats v5 ON v4.TableName = v5.TableName
|
||||
from ra2pz78av4_stats v4
|
||||
full outer join ra2pz78av5_stats v5 ON v4.TableName = v5.TableName
|
||||
order by v5.TableName;
|
||||
|
||||
/*
|
||||
|
|
@ -2474,8 +2478,8 @@ order by v5.TableName;
|
|||
* tables to the V5 destinations
|
||||
*/
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0oclassification_map';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0oclassification_map';
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78aclassification_map';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE ra2pz78aclassification_map';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -942 THEN
|
||||
|
|
@ -2483,9 +2487,9 @@ EXCEPTION
|
|||
END IF;
|
||||
END;
|
||||
|
||||
/
|
||||
/* / */
|
||||
|
||||
CREATE GLOBAL TEMPORARY TABLE q7a3ac0oclassification_map
|
||||
CREATE GLOBAL TEMPORARY TABLE ra2pz78aclassification_map
|
||||
ON COMMIT PRESERVE ROWS
|
||||
AS
|
||||
SELECT
|
||||
|
|
@ -2496,33 +2500,33 @@ FROM
|
|||
(
|
||||
SELECT 'Condition_Occurrence' TableName, NVL(LOWER(cm.domain_id), 'condition') domain_id, COUNT(*) row_count
|
||||
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')
|
||||
UNION
|
||||
SELECT 'Drug_Exposure' TableName, NVL(LOWER(cm.domain_id), 'drug') domain_id, COUNT(*) row_count
|
||||
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')
|
||||
UNION
|
||||
SELECT 'Observation' TableName, NVL(LOWER(cm.domain_id), 'observation') domain_id, COUNT(*) row_count
|
||||
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')
|
||||
UNION
|
||||
SELECT 'Procedure_Occurrence' TableName, NVL(LOWER(cm.domain_id), 'procedure') domain_id, COUNT(*) row_count
|
||||
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')
|
||||
) A
|
||||
ORDER by A.TableName, A.domain_id;
|
||||
|
||||
/
|
||||
/* / */
|
||||
|
||||
select *
|
||||
from q7a3ac0oclassification_map
|
||||
from ra2pz78aclassification_map
|
||||
order by tablename, domain_id;
|
||||
|
||||
select domain_id, SUM(row_count)
|
||||
from q7a3ac0oclassification_map
|
||||
from ra2pz78aclassification_map
|
||||
group by domain_id
|
||||
order by domain_id;
|
||||
|
|
@ -626,7 +626,7 @@ WHERE procedure_concept_id = 0
|
|||
|
||||
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
|
||||
,person_id
|
||||
,0 AS procedure_concept_id
|
||||
|
|
@ -2031,7 +2031,7 @@ FROM
|
|||
FROM cteDrugTarget
|
||||
) E2 ON E1.PERSON_ID = E2.PERSON_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
|
||||
,E1.INGREDIENT_CONCEPT_ID
|
||||
,E1.EVENT_DATE
|
||||
|
|
@ -2177,7 +2177,7 @@ FROM
|
|||
FROM cteConditionTarget
|
||||
) E2 ON E1.PERSON_ID = E2.PERSON_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
|
||||
,E1.CONDITION_CONCEPT_ID
|
||||
,E1.EVENT_DATE
|
||||
|
|
|
|||
|
|
@ -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**
|
||||
|
||||
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:
|
||||
|
||||
* [SOURCE_CDMV4] - Your V4 database name
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -615,7 +615,7 @@ WHERE procedure_concept_id = 0
|
|||
|
||||
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
|
||||
,person_id
|
||||
,0 AS procedure_concept_id
|
||||
|
|
@ -2008,7 +2008,7 @@ FROM (
|
|||
FROM #cteDrugTarget
|
||||
) E2 ON E1.PERSON_ID = E2.PERSON_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
|
||||
,E1.INGREDIENT_CONCEPT_ID
|
||||
,E1.EVENT_DATE
|
||||
|
|
@ -2143,7 +2143,7 @@ FROM (
|
|||
FROM #cteConditionTarget
|
||||
) E2 ON E1.PERSON_ID = E2.PERSON_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
|
||||
,E1.CONDITION_CONCEPT_ID
|
||||
,E1.EVENT_DATE
|
||||
|
|
|
|||
Loading…
Reference in New Issue