Including the 'Type Concept' domain_id from the latest version of the vocabulary
This commit is contained in:
Anthony Sena
parent
11188fee37
commit
021c9f5a14
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@ -1,38 +0,0 @@
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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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@ -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 ilbyrix0concept_map';
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EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0concept_map';
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EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmconcept_map';
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EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmconcept_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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@ -120,9 +120,8 @@ END;
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/* / */
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CREATE GLOBAL TEMPORARY TABLE ilbyrix0concept_map
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ON COMMIT PRESERVE ROWS
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AS
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CREATE TABLE g8iauhqmconcept_map
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AS
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SELECT
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concept_id AS source_concept_id
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,concept_id AS target_concept_id
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@ -134,7 +133,7 @@ FROM
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/* / */
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INSERT INTO ilbyrix0concept_map
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INSERT INTO g8iauhqmconcept_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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@ -269,11 +268,11 @@ INNER JOIN [TARGET_CDMV5].[SCHEMA].concept c2 ON cr1.concept_id_2 = c2.concept_i
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WHERE c2.standard_concept = 'S'
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AND c2.invalid_reason IS NULL
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AND cr1.relationship_id IN ('Is a')
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AND cr1.invalid_reason IS NULL FROM DUAL FROM DUAL FROM DUAL;
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AND cr1.invalid_reason IS NULL ;
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BEGIN
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EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0concept_map_distinct';
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EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0concept_map_distinct';
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EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmconcept_map_distinct';
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EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmconcept_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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@ -283,27 +282,26 @@ END;
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/* / */
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CREATE GLOBAL TEMPORARY TABLE ilbyrix0concept_map_distinct
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ON COMMIT PRESERVE ROWS
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AS
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CREATE TABLE g8iauhqmconcept_map_distinct
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AS
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SELECT
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source_concept_id
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,domain_id
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,COUNT(*) AS targetConceptCount
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FROM
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ilbyrix0concept_map
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g8iauhqmconcept_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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INSERT INTO ilbyrix0concept_map_distinct
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INSERT INTO g8iauhqmconcept_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 ilbyrix0concept_map
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FROM g8iauhqmconcept_map
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GROUP BY source_concept_id
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,domain_id ;
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@ -416,11 +414,11 @@ 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 ilbyrix0concept_map gender ON LOWER(gender.DOMAIN_ID) IN ('gender')
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LEFT JOIN g8iauhqmconcept_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 ilbyrix0concept_map race ON LOWER(race.DOMAIN_ID) IN ('race')
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LEFT JOIN g8iauhqmconcept_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 ilbyrix0concept_map ethnicity ON LOWER(ethnicity.DOMAIN_ID) IN ('ethnicity')
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LEFT JOIN g8iauhqmconcept_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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@ -496,8 +494,8 @@ 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 ilbyrix0concept_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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LEFT JOIN g8iauhqmconcept_map_distinct cm1 ON DEATH.DEATH_TYPE_CONCEPT_ID = CM1.SOURCE_CONCEPT_ID
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AND LOWER(DOMAIN_ID) IN ('death type', 'Type Concept') ;
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INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE)
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SELECT 'DEATH: ' || TO_CHAR(NUM_INVALID_RECORDS ) || ' records in the source CDMv4 database have invalid DEATH_TYPE_CONCEPT_ID'
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@ -508,7 +506,7 @@ SELECT 'DEATH: ' || TO_CHAR(NUM_INVALID_RECORDS ) || ' records in the source C
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WHERE CONCEPT_ID = 0
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OR (
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STANDARD_CONCEPT = 'S'
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AND LOWER(DOMAIN_ID) IN ('death type')
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AND LOWER(DOMAIN_ID) IN ('death type', 'Type Concept')
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)
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)
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HAVING COUNT(PERSON_ID) > 0
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@ -533,7 +531,7 @@ 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 ilbyrix0concept_map cm1 ON VISIT_OCCURRENCE.PLACE_OF_SERVICE_CONCEPT_ID = cm1.source_concept_id
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LEFT JOIN g8iauhqmconcept_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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@ -557,8 +555,8 @@ SELECT 'VISIT_OCCURRENCE: ' || TO_CHAR(NUM_INVALID_RECORDS ) || ' records in t
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****/
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BEGIN
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EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0po_map';
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EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0po_map';
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EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmpo_map';
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EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmpo_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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@ -568,9 +566,8 @@ END;
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/* / */
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CREATE GLOBAL TEMPORARY TABLE ilbyrix0po_map
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ON COMMIT PRESERVE ROWS
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AS
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CREATE TABLE g8iauhqmpo_map
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AS
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SELECT
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po.procedure_occurrence_id
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,po.person_id
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@ -594,7 +591,7 @@ LEFT JOIN [TARGET_CDMV5].[SCHEMA].drug_exposure de ON 1 = 0
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/* / */
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--find valid procedures from procedure table
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INSERT INTO ilbyrix0po_map
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INSERT INTO g8iauhqmpo_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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@ -609,14 +606,14 @@ 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 ilbyrix0concept_map cm1 ON PROCEDURE_OCCURRENCE.PROCEDURE_CONCEPT_ID = cm1.source_concept_id
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INNER JOIN g8iauhqmconcept_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 ilbyrix0concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id
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INNER JOIN g8iauhqmconcept_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 ilbyrix0concept_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 ilbyrix0concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id
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LEFT JOIN g8iauhqmconcept_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', 'Type Concept')
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LEFT JOIN g8iauhqmconcept_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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@ -656,9 +653,9 @@ 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 ilbyrix0concept_map cm1 ON procedure_concept_id = cm1.source_concept_id
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LEFT JOIN ilbyrix0concept_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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LEFT JOIN g8iauhqmconcept_map cm1 ON procedure_concept_id = cm1.source_concept_id
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LEFT JOIN g8iauhqmconcept_map cm2 ON procedure_concept_id = cm2.source_concept_id
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AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
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WHERE procedure_concept_id <> 0
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AND cm1.domain_id IS NULL
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@ -697,13 +694,13 @@ SELECT CASE
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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 ilbyrix0concept_map cm1 ON PROCEDURE_OCCURRENCE.PROCEDURE_CONCEPT_ID = cm1.source_concept_id
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INNER JOIN g8iauhqmconcept_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 ilbyrix0concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id
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INNER JOIN g8iauhqmconcept_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 ilbyrix0concept_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 g8iauhqmconcept_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', 'Type Concept')
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UNION ALL
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@ -722,7 +719,7 @@ SELECT CASE
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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 ilbyrix0concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
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INNER JOIN g8iauhqmconcept_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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@ -742,7 +739,7 @@ SELECT CASE
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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 ilbyrix0concept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id
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INNER JOIN g8iauhqmconcept_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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@ -762,12 +759,12 @@ SELECT CASE
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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 ilbyrix0concept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id
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INNER JOIN g8iauhqmconcept_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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,(SELECT MAX(PROCEDURE_OCCURRENCE_ID) AS MAXROWID
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FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
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) MAXROW FROM DUAL FROM DUAL;
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) MAXROW ;
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INSERT INTO [TARGET_CDMV5].[SCHEMA].procedure_occurrence (
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procedure_occurrence_id
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@ -795,7 +792,7 @@ 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 ilbyrix0po_map ;
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FROM g8iauhqmpo_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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@ -819,7 +816,7 @@ SELECT 'PROCEDURE_OCCURRENCE: ' || TO_CHAR(NUM_INVALID_RECORDS ) || ' records
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WHERE CONCEPT_ID = 0
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OR (
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STANDARD_CONCEPT = 'S'
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AND LOWER(DOMAIN_ID) IN ('procedure type')
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AND LOWER(DOMAIN_ID) IN ('procedure type', 'Type Concept')
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)
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)
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HAVING COUNT(PERSON_ID) > 0
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@ -832,8 +829,8 @@ SELECT 'PROCEDURE_OCCURRENCE: ' || TO_CHAR(NUM_INVALID_RECORDS ) || ' records
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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 ilbyrix0drgexp_map';
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EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0drgexp_map';
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EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmdrgexp_map';
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EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmdrgexp_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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@ -843,9 +840,8 @@ END;
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/* / */
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CREATE GLOBAL TEMPORARY TABLE ilbyrix0drgexp_map
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ON COMMIT PRESERVE ROWS
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AS
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CREATE TABLE g8iauhqmdrgexp_map
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AS
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SELECT
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de.drug_exposure_id
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,de.person_id
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@ -877,7 +873,7 @@ LEFT JOIN [TARGET_CDMV5].[SCHEMA].procedure_occurrence po ON 1 = 0
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/* / */
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INSERT INTO ilbyrix0drgexp_map
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INSERT INTO g8iauhqmdrgexp_map
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SELECT drug_exposure_id
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,person_id
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,COALESCE(cm1.target_concept_id, 0) AS drug_concept_id
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@ -901,14 +897,14 @@ SELECT drug_exposure_id
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,NULL AS dose_unit_source_value
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,CAST(NULL AS INT) AS origional_procedure_id
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FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE
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INNER JOIN ilbyrix0concept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id
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INNER JOIN g8iauhqmconcept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id
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AND LOWER(cm1.domain_id) IN ('drug')
|
||||
INNER JOIN ilbyrix0concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id
|
||||
INNER JOIN g8iauhqmconcept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id
|
||||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount = 1
|
||||
LEFT JOIN ilbyrix0concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('drug type')
|
||||
INNER JOIN ilbyrix0concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id
|
||||
LEFT JOIN g8iauhqmconcept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
|
||||
INNER JOIN g8iauhqmconcept_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
|
||||
|
|
@ -967,9 +963,9 @@ 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 ilbyrix0concept_map cm1 ON drug_concept_id = cm1.source_concept_id
|
||||
LEFT JOIN ilbyrix0concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('drug type')
|
||||
LEFT JOIN g8iauhqmconcept_map cm1 ON drug_concept_id = cm1.source_concept_id
|
||||
LEFT JOIN g8iauhqmconcept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
|
||||
WHERE drug_concept_id <> 0
|
||||
AND cm1.domain_id IS NULL
|
||||
|
||||
|
|
@ -1026,13 +1022,13 @@ SELECT CASE
|
|||
,CAST(NULL AS INT) AS origional_procedure_id
|
||||
,CAST(NULL AS INT) AS OCCURRENCE_ID
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE
|
||||
INNER JOIN ilbyrix0concept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id
|
||||
INNER JOIN g8iauhqmconcept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id
|
||||
AND LOWER(cm1.domain_id) IN ('drug')
|
||||
INNER JOIN ilbyrix0concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id
|
||||
INNER JOIN g8iauhqmconcept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id
|
||||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount > 1
|
||||
LEFT JOIN ilbyrix0concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('drug type')
|
||||
LEFT JOIN g8iauhqmconcept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
|
||||
|
||||
UNION ALL
|
||||
|
||||
|
|
@ -1060,7 +1056,7 @@ SELECT CASE
|
|||
,CAST(NULL AS INT) AS origional_procedure_id
|
||||
,condition_occurrence_id AS occurrence_id
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
|
||||
INNER JOIN ilbyrix0concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
|
||||
INNER JOIN g8iauhqmconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
|
||||
AND LOWER(cm1.domain_id) IN ('drug')
|
||||
--find drugs that were previously classified as procedure
|
||||
|
||||
|
|
@ -1089,7 +1085,7 @@ SELECT CASE
|
|||
,procedure_occurrence_id AS origional_procedure_id
|
||||
,procedure_occurrence_id AS occurrence_id
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
|
||||
INNER JOIN ilbyrix0concept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id
|
||||
INNER JOIN g8iauhqmconcept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id
|
||||
AND LOWER(cm1.domain_id) IN ('drug')
|
||||
--find drugs that were previously classified as observation
|
||||
|
||||
|
|
@ -1118,12 +1114,12 @@ SELECT CASE
|
|||
,CAST(NULL AS INT) AS origional_procedure_id
|
||||
,observation_id AS occurrence_id
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION
|
||||
INNER JOIN ilbyrix0concept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id
|
||||
INNER JOIN g8iauhqmconcept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id
|
||||
AND LOWER(cm1.domain_id) IN ('drug')
|
||||
) OTHERS
|
||||
,(SELECT MAX(DRUG_EXPOSURE_ID) AS MAXROWID
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE
|
||||
) MAXROW FROM DUAL FROM DUAL;
|
||||
) MAXROW ;
|
||||
|
||||
INSERT INTO [TARGET_CDMV5].[SCHEMA].drug_exposure (
|
||||
drug_exposure_id
|
||||
|
|
@ -1169,7 +1165,7 @@ SELECT drug_exposure_id
|
|||
,drug_source_concept_id
|
||||
,route_source_value
|
||||
,dose_unit_source_value
|
||||
FROM ilbyrix0drgexp_map ;
|
||||
FROM g8iauhqmdrgexp_map ;
|
||||
|
||||
--warnings of invalid records
|
||||
INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE)
|
||||
|
|
@ -1193,7 +1189,7 @@ SELECT 'DRUG_EXPOSURE: ' || TO_CHAR(NUM_INVALID_RECORDS ) || ' records in the
|
|||
WHERE CONCEPT_ID = 0
|
||||
OR (
|
||||
STANDARD_CONCEPT = 'S'
|
||||
AND LOWER(DOMAIN_ID) IN ('drug type')
|
||||
AND LOWER(DOMAIN_ID) IN ('drug type', 'Type Concept')
|
||||
)
|
||||
)
|
||||
HAVING COUNT(PERSON_ID) > 0
|
||||
|
|
@ -1218,13 +1214,13 @@ SELECT condition_occurrence_id
|
|||
,condition_source_value
|
||||
,CAST(NULL AS INT) condition_source_concept_id
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
|
||||
INNER JOIN ilbyrix0concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
|
||||
INNER JOIN g8iauhqmconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
|
||||
AND LOWER(cm1.domain_id) IN ('condition')
|
||||
INNER JOIN ilbyrix0concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id
|
||||
INNER JOIN g8iauhqmconcept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id
|
||||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount = 1
|
||||
LEFT JOIN ilbyrix0concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('condition type')
|
||||
LEFT JOIN g8iauhqmconcept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
|
||||
WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4
|
||||
|
||||
UNION ALL
|
||||
|
|
@ -1259,9 +1255,9 @@ SELECT condition_occurrence_id
|
|||
,condition_source_value
|
||||
,CAST(NULL AS INT) condition_source_concept_id
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
|
||||
LEFT JOIN ilbyrix0concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
|
||||
LEFT JOIN ilbyrix0concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('condition type')
|
||||
LEFT JOIN g8iauhqmconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
|
||||
LEFT JOIN g8iauhqmconcept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
|
||||
WHERE condition_concept_id <> 0
|
||||
AND cm1.domain_id IS NULL
|
||||
|
||||
|
|
@ -1296,13 +1292,13 @@ SELECT CASE
|
|||
,CAST(NULL AS INT) condition_source_concept_id
|
||||
,NULL AS OCCURRENCE_ID
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
|
||||
INNER JOIN ilbyrix0concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
|
||||
INNER JOIN g8iauhqmconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
|
||||
AND LOWER(cm1.domain_id) IN ('condition')
|
||||
INNER JOIN ilbyrix0concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id
|
||||
INNER JOIN g8iauhqmconcept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id
|
||||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount > 1
|
||||
LEFT JOIN ilbyrix0concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('condition type')
|
||||
LEFT JOIN g8iauhqmconcept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
|
||||
WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4
|
||||
|
||||
UNION ALL
|
||||
|
|
@ -1320,7 +1316,7 @@ SELECT CASE
|
|||
,CAST(NULL AS INT) condition_source_concept_id
|
||||
,procedure_occurrence_id AS OCCURRENCE_ID
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
|
||||
INNER JOIN ilbyrix0concept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id
|
||||
INNER JOIN g8iauhqmconcept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id
|
||||
AND LOWER(cm1.domain_id) IN ('condition')
|
||||
--find conditions that were previously classified as drug
|
||||
|
||||
|
|
@ -1338,7 +1334,7 @@ SELECT CASE
|
|||
,CAST(NULL AS INT) condition_source_concept_id
|
||||
,drug_exposure_id AS OCCURRENCE_ID
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE
|
||||
INNER JOIN ilbyrix0concept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id
|
||||
INNER JOIN g8iauhqmconcept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id
|
||||
AND LOWER(cm1.domain_id) IN ('condition')
|
||||
--find conditions that were previously classified as observation
|
||||
|
||||
|
|
@ -1356,12 +1352,12 @@ SELECT CASE
|
|||
,CAST(NULL AS INT) condition_source_concept_id
|
||||
,observation_id AS OCCURRENCE_ID
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION
|
||||
INNER JOIN ilbyrix0concept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id
|
||||
INNER JOIN g8iauhqmconcept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id
|
||||
AND LOWER(cm1.domain_id) IN ('condition')
|
||||
) OTHERS
|
||||
,(SELECT MAX(condition_occurrence_id) AS MAXROWID
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
|
||||
) MAXROW FROM DUAL FROM DUAL;
|
||||
) MAXROW ;
|
||||
|
||||
--warnings of invalid records
|
||||
INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE)
|
||||
|
|
@ -1385,7 +1381,7 @@ SELECT 'CONDIITON_OCCURRENCE: ' || TO_CHAR(NUM_INVALID_RECORDS ) || ' records
|
|||
WHERE CONCEPT_ID = 0
|
||||
OR (
|
||||
STANDARD_CONCEPT = 'S'
|
||||
AND LOWER(DOMAIN_ID) IN ('condition type')
|
||||
AND LOWER(DOMAIN_ID) IN ('condition type', 'Type Concept')
|
||||
)
|
||||
)
|
||||
HAVING COUNT(PERSON_ID) > 0
|
||||
|
|
@ -1424,7 +1420,7 @@ SELECT row_number() OVER (
|
|||
,0 AS device_source_concept_id
|
||||
,PROCEDURE_OCCURRENCE_ID AS OCCURRENCE_ID
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
|
||||
INNER JOIN ilbyrix0concept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id
|
||||
INNER JOIN g8iauhqmconcept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id
|
||||
AND LOWER(cm1.domain_id) IN ('device')
|
||||
--find devices that were previously classified as drug exposure
|
||||
|
||||
|
|
@ -1443,7 +1439,7 @@ SELECT row_number() OVER (
|
|||
,0 AS device_source_concept_id
|
||||
,DRUG_EXPOSURE_ID AS OCCURRENCE_ID
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE
|
||||
INNER JOIN ilbyrix0concept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id
|
||||
INNER JOIN g8iauhqmconcept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id
|
||||
AND LOWER(cm1.domain_id) IN ('device')
|
||||
--find devices that were previously classified as conditions
|
||||
|
||||
|
|
@ -1462,7 +1458,7 @@ SELECT row_number() OVER (
|
|||
,0 AS device_source_concept_id
|
||||
,CONDITION_OCCURRENCE_ID AS OCCURRENCE_ID
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
|
||||
INNER JOIN ilbyrix0concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
|
||||
INNER JOIN g8iauhqmconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
|
||||
AND LOWER(cm1.domain_id) IN ('device')
|
||||
--find devices that were previously classified as observations
|
||||
|
||||
|
|
@ -1481,7 +1477,7 @@ SELECT row_number() OVER (
|
|||
,0 AS device_source_concept_id
|
||||
,OBSERVATION_ID AS OCCURRENCE_ID
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION
|
||||
INNER JOIN ilbyrix0concept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id
|
||||
INNER JOIN g8iauhqmconcept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id
|
||||
AND LOWER(cm1.domain_id) IN ('device')
|
||||
) OTHERS ;
|
||||
|
||||
|
|
@ -1531,9 +1527,9 @@ SELECT row_number() OVER (
|
|||
,TO_CHAR(NULL ) AS value_source_value
|
||||
,observation_id AS occurrence_id
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION
|
||||
INNER JOIN ilbyrix0concept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id
|
||||
INNER JOIN g8iauhqmconcept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id
|
||||
AND LOWER(cm1.domain_id) IN ('measurement')
|
||||
LEFT JOIN ilbyrix0concept_map cm2 ON observation.unit_concept_id = cm2.source_concept_id
|
||||
LEFT JOIN g8iauhqmconcept_map cm2 ON observation.unit_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('unit')
|
||||
|
||||
UNION ALL
|
||||
|
|
@ -1557,7 +1553,7 @@ SELECT row_number() OVER (
|
|||
,TO_CHAR(NULL ) AS value_source_value
|
||||
,procedure_occurrence_id AS occurrence_id
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
|
||||
INNER JOIN ilbyrix0concept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id
|
||||
INNER JOIN g8iauhqmconcept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id
|
||||
AND LOWER(cm1.domain_id) IN ('measurement')
|
||||
|
||||
UNION ALL
|
||||
|
|
@ -1581,7 +1577,7 @@ SELECT row_number() OVER (
|
|||
,TO_CHAR(NULL ) AS value_source_value
|
||||
,condition_occurrence_id AS occurrence_id
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
|
||||
INNER JOIN ilbyrix0concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
|
||||
INNER JOIN g8iauhqmconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
|
||||
AND LOWER(cm1.domain_id) IN ('measurement')
|
||||
|
||||
UNION ALL
|
||||
|
|
@ -1605,7 +1601,7 @@ SELECT row_number() OVER (
|
|||
,TO_CHAR(NULL ) AS value_source_value
|
||||
,drug_exposure_id AS occurrence_id
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].drug_exposure
|
||||
INNER JOIN ilbyrix0concept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id
|
||||
INNER JOIN g8iauhqmconcept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id
|
||||
AND LOWER(cm1.domain_id) IN ('measurement')
|
||||
) OTHERS ;
|
||||
|
||||
|
|
@ -1635,7 +1631,7 @@ SELECT observation_id
|
|||
,TO_CHAR(NULL ) qualifier_source_value
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION
|
||||
WHERE observation_concept_id NOT IN (SELECT source_concept_id
|
||||
FROM ilbyrix0concept_map_distinct
|
||||
FROM g8iauhqmconcept_map_distinct
|
||||
WHERE LOWER(domain_id) IN (
|
||||
'condition'
|
||||
,'drug'
|
||||
|
|
@ -1689,7 +1685,7 @@ SELECT CASE
|
|||
,TO_CHAR(NULL ) qualifier_source_value
|
||||
,procedure_occurrence_id AS occurrence_id
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
|
||||
INNER JOIN ilbyrix0concept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id
|
||||
INNER JOIN g8iauhqmconcept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id
|
||||
AND LOWER(cm1.domain_id) IN ('observation')
|
||||
--find observations that were previously classified as condition
|
||||
|
||||
|
|
@ -1713,7 +1709,7 @@ SELECT CASE
|
|||
,TO_CHAR(NULL ) qualifier_source_value
|
||||
,condition_occurrence_id AS occurrence_id
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
|
||||
INNER JOIN ilbyrix0concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
|
||||
INNER JOIN g8iauhqmconcept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
|
||||
AND LOWER(cm1.domain_id) IN ('observation')
|
||||
|
||||
UNION ALL
|
||||
|
|
@ -1738,7 +1734,7 @@ SELECT CASE
|
|||
,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 ilbyrix0concept_map cm1 ON pc.disease_class_concept_id = cm1.source_concept_id
|
||||
INNER JOIN g8iauhqmconcept_map cm1 ON pc.disease_class_concept_id = cm1.source_concept_id
|
||||
AND LOWER(cm1.domain_id) IN ('observation')
|
||||
|
||||
UNION ALL
|
||||
|
|
@ -1762,7 +1758,7 @@ SELECT CASE
|
|||
,TO_CHAR(NULL ) qualifier_source_value
|
||||
,drug_exposure_id AS occurrence_id
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE
|
||||
INNER JOIN ilbyrix0concept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id
|
||||
INNER JOIN g8iauhqmconcept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id
|
||||
AND LOWER(cm1.domain_id) IN ('observation')
|
||||
) OTHERS
|
||||
,(SELECT MAX(OBSERVATION_ID) AS MAXROWID
|
||||
|
|
@ -1847,7 +1843,7 @@ SELECT CASE
|
|||
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 ilbyrix0drgexp_map de ON de.person_id = po.person_id
|
||||
INNER JOIN g8iauhqmdrgexp_map de ON de.person_id = po.person_id
|
||||
AND pc.procedure_occurrence_id = de.origional_procedure_id
|
||||
) OTHERS
|
||||
,(SELECT MAX(drug_cost_id) AS MAXROWID
|
||||
|
|
@ -1918,7 +1914,7 @@ SELECT CASE
|
|||
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 ilbyrix0po_map po ON de.person_id = po.person_id
|
||||
INNER JOIN g8iauhqmpo_map po ON de.person_id = po.person_id
|
||||
AND de.drug_exposure_id = po.origional_drug_id
|
||||
) OTHERS
|
||||
,(SELECT MAX(drug_cost_id) AS MAXROWID
|
||||
|
|
@ -1932,8 +1928,8 @@ Note: Eras derived from DRUG_EXPOSURE table, using 30d gap
|
|||
|
||||
****/
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0cteDrugTarget';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0cteDrugTarget';
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmcteDrugTarget';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmcteDrugTarget';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -942 THEN
|
||||
|
|
@ -1944,9 +1940,8 @@ END;
|
|||
/* / */
|
||||
|
||||
-- Normalize DRUG_EXPOSURE_END_DATE to either the existing drug exposure end date, or add days supply, or add 1 day to the start date
|
||||
CREATE GLOBAL TEMPORARY TABLE ilbyrix0cteDrugTarget
|
||||
ON COMMIT PRESERVE ROWS
|
||||
AS
|
||||
CREATE TABLE g8iauhqmcteDrugTarget
|
||||
AS
|
||||
SELECT
|
||||
d.DRUG_EXPOSURE_ID
|
||||
,d.PERSON_ID
|
||||
|
|
@ -1966,8 +1961,8 @@ INNER JOIN [TARGET_CDMV5].[SCHEMA].CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCE
|
|||
/* / */
|
||||
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0cteEndDates';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0cteEndDates';
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmcteEndDates';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmcteEndDates';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -942 THEN
|
||||
|
|
@ -1977,9 +1972,8 @@ END;
|
|||
|
||||
/* / */
|
||||
|
||||
CREATE GLOBAL TEMPORARY TABLE ilbyrix0cteEndDates
|
||||
ON COMMIT PRESERVE ROWS
|
||||
AS
|
||||
CREATE TABLE g8iauhqmcteEndDates
|
||||
AS
|
||||
SELECT
|
||||
PERSON_ID
|
||||
,INGREDIENT_CONCEPT_ID
|
||||
|
|
@ -2009,7 +2003,7 @@ FROM
|
|||
PARTITION BY PERSON_ID
|
||||
,INGREDIENT_CONCEPT_ID ORDER BY DRUG_EXPOSURE_START_DATE
|
||||
) AS START_ORDINAL
|
||||
FROM ilbyrix0cteDrugTarget
|
||||
FROM g8iauhqmcteDrugTarget
|
||||
|
||||
UNION ALL
|
||||
|
||||
|
|
@ -2019,7 +2013,7 @@ FROM
|
|||
,( DRUG_EXPOSURE_END_DATE + 30)
|
||||
,1 AS EVENT_TYPE
|
||||
,NULL
|
||||
FROM ilbyrix0cteDrugTarget
|
||||
FROM g8iauhqmcteDrugTarget
|
||||
) RAWDATA
|
||||
) E1
|
||||
INNER JOIN (SELECT PERSON_ID
|
||||
|
|
@ -2029,7 +2023,7 @@ FROM
|
|||
PARTITION BY PERSON_ID
|
||||
,INGREDIENT_CONCEPT_ID ORDER BY DRUG_EXPOSURE_START_DATE
|
||||
) AS START_ORDINAL
|
||||
FROM ilbyrix0cteDrugTarget
|
||||
FROM g8iauhqmcteDrugTarget
|
||||
) E2 ON E1.PERSON_ID = E2.PERSON_ID
|
||||
AND E1.INGREDIENT_CONCEPT_ID = E2.INGREDIENT_CONCEPT_ID
|
||||
AND E2.EVENT_DATE <= E1.EVENT_DATE
|
||||
|
|
@ -2044,8 +2038,8 @@ FROM
|
|||
/* / */
|
||||
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0cteDrugExpEnds';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0cteDrugExpEnds';
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmcteDrugExpEnds';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmcteDrugExpEnds';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -942 THEN
|
||||
|
|
@ -2055,9 +2049,8 @@ END;
|
|||
|
||||
/* / */
|
||||
|
||||
CREATE GLOBAL TEMPORARY TABLE ilbyrix0cteDrugExpEnds
|
||||
ON COMMIT PRESERVE ROWS
|
||||
AS
|
||||
CREATE TABLE g8iauhqmcteDrugExpEnds
|
||||
AS
|
||||
SELECT
|
||||
d.PERSON_ID
|
||||
,d.INGREDIENT_CONCEPT_ID
|
||||
|
|
@ -2066,8 +2059,8 @@ SELECT
|
|||
,MIN(e.END_DATE) AS ERA_END_DATE
|
||||
|
||||
FROM
|
||||
ilbyrix0cteDrugTarget d
|
||||
INNER JOIN ilbyrix0cteEndDates e ON d.PERSON_ID = e.PERSON_ID
|
||||
g8iauhqmcteDrugTarget d
|
||||
INNER JOIN g8iauhqmcteEndDates 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
|
||||
|
|
@ -2087,7 +2080,7 @@ SELECT row_number() OVER (
|
|||
,ERA_END_DATE
|
||||
,COUNT(*) AS DRUG_EXPOSURE_COUNT
|
||||
,30 AS gap_days
|
||||
FROM ilbyrix0cteDrugExpEnds
|
||||
FROM g8iauhqmcteDrugExpEnds
|
||||
GROUP BY person_id
|
||||
,INGREDIENT_CONCEPT_ID
|
||||
,drug_type_concept_id
|
||||
|
|
@ -2100,8 +2093,8 @@ Note: Eras derived from CONDITION_OCCURRENCE table, using 30d gap
|
|||
|
||||
****/
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0condition_era_phase_1';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0condition_era_phase_1';
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmcondition_era_phase_1';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmcondition_era_phase_1';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -942 THEN
|
||||
|
|
@ -2112,8 +2105,8 @@ END;
|
|||
/* / */
|
||||
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0cteConditionTarget';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0cteConditionTarget';
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmcteConditionTarget';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmcteConditionTarget';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -942 THEN
|
||||
|
|
@ -2124,9 +2117,8 @@ END;
|
|||
/* / */
|
||||
|
||||
-- create base eras from the concepts found in condition_occurrence
|
||||
CREATE GLOBAL TEMPORARY TABLE ilbyrix0cteConditionTarget
|
||||
ON COMMIT PRESERVE ROWS
|
||||
AS
|
||||
CREATE TABLE g8iauhqmcteConditionTarget
|
||||
AS
|
||||
SELECT
|
||||
co.PERSON_ID
|
||||
,co.condition_concept_id
|
||||
|
|
@ -2139,8 +2131,8 @@ FROM
|
|||
/* / */
|
||||
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0cteCondEndDates';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0cteCondEndDates';
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmcteCondEndDates';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmcteCondEndDates';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -942 THEN
|
||||
|
|
@ -2150,9 +2142,8 @@ END;
|
|||
|
||||
/* / */
|
||||
|
||||
CREATE GLOBAL TEMPORARY TABLE ilbyrix0cteCondEndDates
|
||||
ON COMMIT PRESERVE ROWS
|
||||
AS
|
||||
CREATE TABLE g8iauhqmcteCondEndDates
|
||||
AS
|
||||
SELECT
|
||||
PERSON_ID
|
||||
,CONDITION_CONCEPT_ID
|
||||
|
|
@ -2182,7 +2173,7 @@ FROM
|
|||
PARTITION BY PERSON_ID
|
||||
,CONDITION_CONCEPT_ID ORDER BY CONDITION_START_DATE
|
||||
) AS START_ORDINAL
|
||||
FROM ilbyrix0cteConditionTarget
|
||||
FROM g8iauhqmcteConditionTarget
|
||||
|
||||
UNION ALL
|
||||
|
||||
|
|
@ -2192,7 +2183,7 @@ FROM
|
|||
,( CONDITION_END_DATE + 30)
|
||||
,1 AS EVENT_TYPE
|
||||
,NULL
|
||||
FROM ilbyrix0cteConditionTarget
|
||||
FROM g8iauhqmcteConditionTarget
|
||||
) RAWDATA
|
||||
) E1
|
||||
INNER JOIN (SELECT PERSON_ID
|
||||
|
|
@ -2202,7 +2193,7 @@ FROM
|
|||
PARTITION BY PERSON_ID
|
||||
,CONDITION_CONCEPT_ID ORDER BY CONDITION_START_DATE
|
||||
) AS START_ORDINAL
|
||||
FROM ilbyrix0cteConditionTarget
|
||||
FROM g8iauhqmcteConditionTarget
|
||||
) E2 ON E1.PERSON_ID = E2.PERSON_ID
|
||||
AND E1.CONDITION_CONCEPT_ID = E2.CONDITION_CONCEPT_ID
|
||||
AND E2.EVENT_DATE <= E1.EVENT_DATE
|
||||
|
|
@ -2217,8 +2208,8 @@ FROM
|
|||
/* / */
|
||||
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0cteConditionEnds';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0cteConditionEnds';
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmcteConditionEnds';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmcteConditionEnds';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -942 THEN
|
||||
|
|
@ -2228,9 +2219,8 @@ END;
|
|||
|
||||
/* / */
|
||||
|
||||
CREATE GLOBAL TEMPORARY TABLE ilbyrix0cteConditionEnds
|
||||
ON COMMIT PRESERVE ROWS
|
||||
AS
|
||||
CREATE TABLE g8iauhqmcteConditionEnds
|
||||
AS
|
||||
SELECT
|
||||
c.PERSON_ID
|
||||
,c.CONDITION_CONCEPT_ID
|
||||
|
|
@ -2238,8 +2228,8 @@ SELECT
|
|||
,MIN(e.END_DATE) AS ERA_END_DATE
|
||||
|
||||
FROM
|
||||
ilbyrix0cteConditionTarget c
|
||||
INNER JOIN ilbyrix0cteCondEndDates e ON c.PERSON_ID = e.PERSON_ID
|
||||
g8iauhqmcteConditionTarget c
|
||||
INNER JOIN g8iauhqmcteCondEndDates 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
|
||||
|
|
@ -2264,7 +2254,7 @@ 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 ilbyrix0cteConditionEnds
|
||||
FROM g8iauhqmcteConditionEnds
|
||||
GROUP BY person_id
|
||||
,CONDITION_CONCEPT_ID
|
||||
,ERA_END_DATE ;
|
||||
|
|
@ -2279,8 +2269,8 @@ Note: These queries are used to provide some basic stats around row counts betwe
|
|||
****/
|
||||
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0v5_stats';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0v5_stats';
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmv5_stats';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmv5_stats';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -942 THEN
|
||||
|
|
@ -2291,8 +2281,8 @@ END;
|
|||
/* / */
|
||||
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0v4_stats';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0v4_stats';
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmv4_stats';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmv4_stats';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -942 THEN
|
||||
|
|
@ -2303,9 +2293,8 @@ END;
|
|||
/* / */
|
||||
|
||||
-- Get the row counts for each table that is in scope for the migration
|
||||
CREATE GLOBAL TEMPORARY TABLE ilbyrix0v4_stats
|
||||
ON COMMIT PRESERVE ROWS
|
||||
AS
|
||||
CREATE TABLE g8iauhqmv4_stats
|
||||
AS
|
||||
SELECT
|
||||
*
|
||||
|
||||
|
|
@ -2346,9 +2335,8 @@ FROM
|
|||
|
||||
/* / */
|
||||
|
||||
CREATE GLOBAL TEMPORARY TABLE ilbyrix0v5_stats
|
||||
ON COMMIT PRESERVE ROWS
|
||||
AS
|
||||
CREATE TABLE g8iauhqmv5_stats
|
||||
AS
|
||||
SELECT
|
||||
*
|
||||
|
||||
|
|
@ -2403,8 +2391,8 @@ 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 ilbyrix0v4_stats v4
|
||||
full outer join ilbyrix0v5_stats v5 ON v4.TableName = v5.TableName
|
||||
FROM g8iauhqmv4_stats v4
|
||||
full outer join g8iauhqmv5_stats v5 ON v4.TableName = v5.TableName
|
||||
order by v5.TableName ;
|
||||
|
||||
/*
|
||||
|
|
@ -2412,8 +2400,8 @@ order by v5.TableName ;
|
|||
* tables to the V5 destinations
|
||||
*/
|
||||
BEGIN
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE ilbyrix0classification_map';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE ilbyrix0classification_map';
|
||||
EXECUTE IMMEDIATE 'TRUNCATE TABLE g8iauhqmclassification_map';
|
||||
EXECUTE IMMEDIATE 'DROP TABLE g8iauhqmclassification_map';
|
||||
EXCEPTION
|
||||
WHEN OTHERS THEN
|
||||
IF SQLCODE != -942 THEN
|
||||
|
|
@ -2423,9 +2411,8 @@ END;
|
|||
|
||||
/* / */
|
||||
|
||||
CREATE GLOBAL TEMPORARY TABLE ilbyrix0classification_map
|
||||
ON COMMIT PRESERVE ROWS
|
||||
AS
|
||||
CREATE TABLE g8iauhqmclassification_map
|
||||
AS
|
||||
SELECT
|
||||
*
|
||||
|
||||
|
|
@ -2433,22 +2420,22 @@ 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 ilbyrix0concept_map CM ON co.condition_concept_id = cm.source_concept_id
|
||||
LEFT JOIN g8iauhqmconcept_map CM ON co.condition_concept_id = cm.source_concept_id
|
||||
GROUP BY NVL(LOWER(cm.domain_id), 'condition')
|
||||
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 ilbyrix0concept_map CM ON de.drug_concept_id = cm.source_concept_id
|
||||
LEFT JOIN g8iauhqmconcept_map CM ON de.drug_concept_id = cm.source_concept_id
|
||||
GROUP BY NVL(LOWER(cm.domain_id), 'drug')
|
||||
UNION
|
||||
SELECT 'Observation' TableName, NVL(LOWER(cm.domain_id), 'observation') domain_id, COUNT(*) row_count
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].Observation o
|
||||
LEFT JOIN ilbyrix0concept_map CM ON o.observation_concept_id = cm.source_concept_id
|
||||
LEFT JOIN g8iauhqmconcept_map CM ON o.observation_concept_id = cm.source_concept_id
|
||||
GROUP BY NVL(LOWER(cm.domain_id), 'observation')
|
||||
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 ilbyrix0concept_map CM ON po.PROCEDURE_CONCEPT_ID = cm.source_concept_id
|
||||
LEFT JOIN g8iauhqmconcept_map CM ON po.PROCEDURE_CONCEPT_ID = cm.source_concept_id
|
||||
GROUP BY NVL(LOWER(cm.domain_id), 'procedure')
|
||||
) A
|
||||
ORDER by A.TableName, A.domain_id ;
|
||||
|
|
@ -2456,10 +2443,10 @@ ORDER by A.TableName, A.domain_id ;
|
|||
/* / */
|
||||
|
||||
SELECT *
|
||||
FROM ilbyrix0classification_map
|
||||
FROM g8iauhqmclassification_map
|
||||
order by tablename, domain_id ;
|
||||
|
||||
SELECT domain_id, SUM(row_count)
|
||||
FROM ilbyrix0classification_map
|
||||
FROM g8iauhqmclassification_map
|
||||
group by domain_id
|
||||
order by domain_id ;
|
||||
|
|
@ -486,7 +486,7 @@ SELECT person_id
|
|||
,CAST(NULL AS INT) AS cause_source_concept_id
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].DEATH
|
||||
LEFT JOIN concept_map_distinct cm1 ON DEATH.DEATH_TYPE_CONCEPT_ID = CM1.SOURCE_CONCEPT_ID
|
||||
AND LOWER(DOMAIN_ID) IN ('death type');
|
||||
AND LOWER(DOMAIN_ID) IN ('death type', 'Type Concept');
|
||||
|
||||
INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE)
|
||||
SELECT 'DEATH: ' || CAST(NUM_INVALID_RECORDS AS VARCHAR) || ' records in the source CDMv4 database have invalid DEATH_TYPE_CONCEPT_ID'
|
||||
|
|
@ -499,7 +499,7 @@ FROM (
|
|||
WHERE CONCEPT_ID = 0
|
||||
OR (
|
||||
STANDARD_CONCEPT = 'S'
|
||||
AND LOWER(DOMAIN_ID) IN ('death type')
|
||||
AND LOWER(DOMAIN_ID) IN ('death type', 'Type Concept')
|
||||
)
|
||||
)
|
||||
HAVING COUNT(PERSON_ID) > 0
|
||||
|
|
@ -600,7 +600,7 @@ INNER JOIN concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_co
|
|||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount = 1
|
||||
LEFT JOIN concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('procedure type')
|
||||
AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
|
||||
LEFT JOIN concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id
|
||||
AND cm2.domain_id = cmdis2.domain_id
|
||||
AND cmdis2.targetConceptCount = 1
|
||||
|
|
@ -643,7 +643,7 @@ SELECT procedure_occurrence_id
|
|||
FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
|
||||
LEFT JOIN concept_map cm1 ON procedure_concept_id = cm1.source_concept_id
|
||||
LEFT JOIN concept_map cm2 ON procedure_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('procedure type')
|
||||
AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
|
||||
WHERE procedure_concept_id <> 0
|
||||
AND cm1.domain_id IS NULL
|
||||
|
||||
|
|
@ -691,7 +691,7 @@ FROM (
|
|||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount > 1
|
||||
LEFT JOIN concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('procedure type')
|
||||
AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
|
||||
|
||||
UNION ALL
|
||||
|
||||
|
|
@ -812,7 +812,7 @@ FROM (
|
|||
WHERE CONCEPT_ID = 0
|
||||
OR (
|
||||
STANDARD_CONCEPT = 'S'
|
||||
AND LOWER(DOMAIN_ID) IN ('procedure type')
|
||||
AND LOWER(DOMAIN_ID) IN ('procedure type', 'Type Concept')
|
||||
)
|
||||
)
|
||||
HAVING COUNT(PERSON_ID) > 0
|
||||
|
|
@ -892,7 +892,7 @@ INNER JOIN concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_co
|
|||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount = 1
|
||||
LEFT JOIN concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('drug type')
|
||||
AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
|
||||
INNER JOIN concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id
|
||||
AND cm2.domain_id = cmdis2.domain_id
|
||||
AND cmdis2.targetConceptCount = 1
|
||||
|
|
@ -954,7 +954,7 @@ SELECT drug_exposure_id
|
|||
FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE
|
||||
LEFT JOIN concept_map cm1 ON drug_concept_id = cm1.source_concept_id
|
||||
LEFT JOIN concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('drug type')
|
||||
AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
|
||||
WHERE drug_concept_id <> 0
|
||||
AND cm1.domain_id IS NULL
|
||||
|
||||
|
|
@ -1019,7 +1019,7 @@ FROM (
|
|||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount > 1
|
||||
LEFT JOIN concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('drug type')
|
||||
AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
|
||||
|
||||
UNION ALL
|
||||
|
||||
|
|
@ -1185,7 +1185,7 @@ FROM (
|
|||
WHERE CONCEPT_ID = 0
|
||||
OR (
|
||||
STANDARD_CONCEPT = 'S'
|
||||
AND LOWER(DOMAIN_ID) IN ('drug type')
|
||||
AND LOWER(DOMAIN_ID) IN ('drug type', 'Type Concept')
|
||||
)
|
||||
)
|
||||
HAVING COUNT(PERSON_ID) > 0
|
||||
|
|
@ -1216,7 +1216,7 @@ INNER JOIN concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_co
|
|||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount = 1
|
||||
LEFT JOIN concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('condition type')
|
||||
AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
|
||||
WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4
|
||||
|
||||
UNION ALL
|
||||
|
|
@ -1253,7 +1253,7 @@ SELECT condition_occurrence_id
|
|||
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
|
||||
LEFT JOIN concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
|
||||
LEFT JOIN concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('condition type')
|
||||
AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
|
||||
WHERE condition_concept_id <> 0
|
||||
AND cm1.domain_id IS NULL
|
||||
|
||||
|
|
@ -1296,7 +1296,7 @@ FROM (
|
|||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount > 1
|
||||
LEFT JOIN concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('condition type')
|
||||
AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
|
||||
WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4
|
||||
|
||||
UNION ALL
|
||||
|
|
@ -1384,7 +1384,7 @@ FROM (
|
|||
WHERE CONCEPT_ID = 0
|
||||
OR (
|
||||
STANDARD_CONCEPT = 'S'
|
||||
AND LOWER(DOMAIN_ID) IN ('condition type')
|
||||
AND LOWER(DOMAIN_ID) IN ('condition type', 'Type Concept')
|
||||
)
|
||||
)
|
||||
HAVING COUNT(PERSON_ID) > 0
|
||||
|
|
|
|||
|
|
@ -486,7 +486,7 @@ SELECT person_id
|
|||
,CAST(NULL AS INT) AS cause_source_concept_id
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].DEATH
|
||||
LEFT JOIN concept_map_distinct cm1 ON DEATH.DEATH_TYPE_CONCEPT_ID = CM1.SOURCE_CONCEPT_ID
|
||||
AND LOWER(DOMAIN_ID) IN ('death type');
|
||||
AND LOWER(DOMAIN_ID) IN ('death type', 'Type Concept');
|
||||
|
||||
INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE)
|
||||
SELECT 'DEATH: ' || CAST(NUM_INVALID_RECORDS AS VARCHAR) || ' records in the source CDMv4 database have invalid DEATH_TYPE_CONCEPT_ID'
|
||||
|
|
@ -499,7 +499,7 @@ FROM (
|
|||
WHERE CONCEPT_ID = 0
|
||||
OR (
|
||||
STANDARD_CONCEPT = 'S'
|
||||
AND LOWER(DOMAIN_ID) IN ('death type')
|
||||
AND LOWER(DOMAIN_ID) IN ('death type', 'Type Concept')
|
||||
)
|
||||
)
|
||||
HAVING COUNT(PERSON_ID) > 0
|
||||
|
|
@ -600,7 +600,7 @@ INNER JOIN concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_co
|
|||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount = 1
|
||||
LEFT JOIN concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('procedure type')
|
||||
AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
|
||||
LEFT JOIN concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id
|
||||
AND cm2.domain_id = cmdis2.domain_id
|
||||
AND cmdis2.targetConceptCount = 1
|
||||
|
|
@ -643,7 +643,7 @@ SELECT procedure_occurrence_id
|
|||
FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
|
||||
LEFT JOIN concept_map cm1 ON procedure_concept_id = cm1.source_concept_id
|
||||
LEFT JOIN concept_map cm2 ON procedure_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('procedure type')
|
||||
AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
|
||||
WHERE procedure_concept_id <> 0
|
||||
AND cm1.domain_id IS NULL
|
||||
|
||||
|
|
@ -691,7 +691,7 @@ FROM (
|
|||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount > 1
|
||||
LEFT JOIN concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('procedure type')
|
||||
AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
|
||||
|
||||
UNION ALL
|
||||
|
||||
|
|
@ -812,7 +812,7 @@ FROM (
|
|||
WHERE CONCEPT_ID = 0
|
||||
OR (
|
||||
STANDARD_CONCEPT = 'S'
|
||||
AND LOWER(DOMAIN_ID) IN ('procedure type')
|
||||
AND LOWER(DOMAIN_ID) IN ('procedure type', 'Type Concept')
|
||||
)
|
||||
)
|
||||
HAVING COUNT(PERSON_ID) > 0
|
||||
|
|
@ -892,7 +892,7 @@ INNER JOIN concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_co
|
|||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount = 1
|
||||
LEFT JOIN concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('drug type')
|
||||
AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
|
||||
INNER JOIN concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id
|
||||
AND cm2.domain_id = cmdis2.domain_id
|
||||
AND cmdis2.targetConceptCount = 1
|
||||
|
|
@ -954,7 +954,7 @@ SELECT drug_exposure_id
|
|||
FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE
|
||||
LEFT JOIN concept_map cm1 ON drug_concept_id = cm1.source_concept_id
|
||||
LEFT JOIN concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('drug type')
|
||||
AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
|
||||
WHERE drug_concept_id <> 0
|
||||
AND cm1.domain_id IS NULL
|
||||
|
||||
|
|
@ -1019,7 +1019,7 @@ FROM (
|
|||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount > 1
|
||||
LEFT JOIN concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('drug type')
|
||||
AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
|
||||
|
||||
UNION ALL
|
||||
|
||||
|
|
@ -1185,7 +1185,7 @@ FROM (
|
|||
WHERE CONCEPT_ID = 0
|
||||
OR (
|
||||
STANDARD_CONCEPT = 'S'
|
||||
AND LOWER(DOMAIN_ID) IN ('drug type')
|
||||
AND LOWER(DOMAIN_ID) IN ('drug type', 'Type Concept')
|
||||
)
|
||||
)
|
||||
HAVING COUNT(PERSON_ID) > 0
|
||||
|
|
@ -1216,7 +1216,7 @@ INNER JOIN concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_co
|
|||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount = 1
|
||||
LEFT JOIN concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('condition type')
|
||||
AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
|
||||
WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4
|
||||
|
||||
UNION ALL
|
||||
|
|
@ -1253,7 +1253,7 @@ SELECT condition_occurrence_id
|
|||
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
|
||||
LEFT JOIN concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
|
||||
LEFT JOIN concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('condition type')
|
||||
AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
|
||||
WHERE condition_concept_id <> 0
|
||||
AND cm1.domain_id IS NULL
|
||||
|
||||
|
|
@ -1296,7 +1296,7 @@ FROM (
|
|||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount > 1
|
||||
LEFT JOIN concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('condition type')
|
||||
AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
|
||||
WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4
|
||||
|
||||
UNION ALL
|
||||
|
|
@ -1384,7 +1384,7 @@ FROM (
|
|||
WHERE CONCEPT_ID = 0
|
||||
OR (
|
||||
STANDARD_CONCEPT = 'S'
|
||||
AND LOWER(DOMAIN_ID) IN ('condition type')
|
||||
AND LOWER(DOMAIN_ID) IN ('condition type', 'Type Concept')
|
||||
)
|
||||
)
|
||||
HAVING COUNT(PERSON_ID) > 0
|
||||
|
|
|
|||
|
|
@ -485,7 +485,7 @@ SELECT person_id
|
|||
,CAST(NULL AS INT) AS cause_source_concept_id
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].DEATH
|
||||
LEFT JOIN #concept_map_distinct cm1 ON DEATH.DEATH_TYPE_CONCEPT_ID = CM1.SOURCE_CONCEPT_ID
|
||||
AND LOWER(DOMAIN_ID) IN ('death type');
|
||||
AND LOWER(DOMAIN_ID) IN ('death type', 'Type Concept');
|
||||
|
||||
INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE)
|
||||
SELECT 'DEATH: ' + CAST(NUM_INVALID_RECORDS AS VARCHAR) + ' records in the source CDMv4 database have invalid DEATH_TYPE_CONCEPT_ID'
|
||||
|
|
@ -498,7 +498,7 @@ FROM (
|
|||
WHERE CONCEPT_ID = 0
|
||||
OR (
|
||||
STANDARD_CONCEPT = 'S'
|
||||
AND LOWER(DOMAIN_ID) IN ('death type')
|
||||
AND LOWER(DOMAIN_ID) IN ('death type', 'Type Concept')
|
||||
)
|
||||
)
|
||||
HAVING COUNT(PERSON_ID) > 0
|
||||
|
|
@ -597,7 +597,7 @@ INNER JOIN #concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_c
|
|||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount = 1
|
||||
LEFT JOIN #concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('procedure type')
|
||||
AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
|
||||
LEFT JOIN #concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id
|
||||
AND cm2.domain_id = cmdis2.domain_id
|
||||
AND cmdis2.targetConceptCount = 1
|
||||
|
|
@ -640,7 +640,7 @@ SELECT procedure_occurrence_id
|
|||
FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
|
||||
LEFT JOIN #concept_map cm1 ON procedure_concept_id = cm1.source_concept_id
|
||||
LEFT JOIN #concept_map cm2 ON procedure_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('procedure type')
|
||||
AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
|
||||
WHERE procedure_concept_id <> 0
|
||||
AND cm1.domain_id IS NULL
|
||||
|
||||
|
|
@ -688,7 +688,7 @@ FROM (
|
|||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount > 1
|
||||
LEFT JOIN #concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('procedure type')
|
||||
AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
|
||||
|
||||
UNION ALL
|
||||
|
||||
|
|
@ -809,7 +809,7 @@ FROM (
|
|||
WHERE CONCEPT_ID = 0
|
||||
OR (
|
||||
STANDARD_CONCEPT = 'S'
|
||||
AND LOWER(DOMAIN_ID) IN ('procedure type')
|
||||
AND LOWER(DOMAIN_ID) IN ('procedure type', 'Type Concept')
|
||||
)
|
||||
)
|
||||
HAVING COUNT(PERSON_ID) > 0
|
||||
|
|
@ -887,7 +887,7 @@ INNER JOIN #concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_c
|
|||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount = 1
|
||||
LEFT JOIN #concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('drug type')
|
||||
AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
|
||||
INNER JOIN #concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id
|
||||
AND cm2.domain_id = cmdis2.domain_id
|
||||
AND cmdis2.targetConceptCount = 1
|
||||
|
|
@ -949,7 +949,7 @@ SELECT drug_exposure_id
|
|||
FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE
|
||||
LEFT JOIN #concept_map cm1 ON drug_concept_id = cm1.source_concept_id
|
||||
LEFT JOIN #concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('drug type')
|
||||
AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
|
||||
WHERE drug_concept_id <> 0
|
||||
AND cm1.domain_id IS NULL
|
||||
|
||||
|
|
@ -1014,7 +1014,7 @@ FROM (
|
|||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount > 1
|
||||
LEFT JOIN #concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('drug type')
|
||||
AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
|
||||
|
||||
UNION ALL
|
||||
|
||||
|
|
@ -1180,7 +1180,7 @@ FROM (
|
|||
WHERE CONCEPT_ID = 0
|
||||
OR (
|
||||
STANDARD_CONCEPT = 'S'
|
||||
AND LOWER(DOMAIN_ID) IN ('drug type')
|
||||
AND LOWER(DOMAIN_ID) IN ('drug type', 'Type Concept')
|
||||
)
|
||||
)
|
||||
HAVING COUNT(PERSON_ID) > 0
|
||||
|
|
@ -1211,7 +1211,7 @@ INNER JOIN #concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_c
|
|||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount = 1
|
||||
LEFT JOIN #concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('condition type')
|
||||
AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
|
||||
WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4
|
||||
|
||||
UNION ALL
|
||||
|
|
@ -1248,7 +1248,7 @@ SELECT condition_occurrence_id
|
|||
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
|
||||
LEFT JOIN #concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
|
||||
LEFT JOIN #concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('condition type')
|
||||
AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
|
||||
WHERE condition_concept_id <> 0
|
||||
AND cm1.domain_id IS NULL
|
||||
|
||||
|
|
@ -1291,7 +1291,7 @@ FROM (
|
|||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount > 1
|
||||
LEFT JOIN #concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('condition type')
|
||||
AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
|
||||
WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4
|
||||
|
||||
UNION ALL
|
||||
|
|
@ -1379,7 +1379,7 @@ FROM (
|
|||
WHERE CONCEPT_ID = 0
|
||||
OR (
|
||||
STANDARD_CONCEPT = 'S'
|
||||
AND LOWER(DOMAIN_ID) IN ('condition type')
|
||||
AND LOWER(DOMAIN_ID) IN ('condition type', 'Type Concept')
|
||||
)
|
||||
)
|
||||
HAVING COUNT(PERSON_ID) > 0
|
||||
|
|
|
|||
|
|
@ -479,7 +479,7 @@ SELECT person_id
|
|||
,CAST(NULL AS INT) AS cause_source_concept_id
|
||||
FROM [SOURCE_CDMV4].[SCHEMA].DEATH
|
||||
LEFT JOIN #concept_map_distinct cm1 ON DEATH.DEATH_TYPE_CONCEPT_ID = CM1.SOURCE_CONCEPT_ID
|
||||
AND LOWER(DOMAIN_ID) IN ('death type');
|
||||
AND LOWER(DOMAIN_ID) IN ('death type', 'Type Concept');
|
||||
|
||||
INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE)
|
||||
SELECT 'DEATH: ' + CAST(NUM_INVALID_RECORDS AS VARCHAR) + ' records in the source CDMv4 database have invalid DEATH_TYPE_CONCEPT_ID'
|
||||
|
|
@ -492,7 +492,7 @@ FROM (
|
|||
WHERE CONCEPT_ID = 0
|
||||
OR (
|
||||
STANDARD_CONCEPT = 'S'
|
||||
AND LOWER(DOMAIN_ID) IN ('death type')
|
||||
AND LOWER(DOMAIN_ID) IN ('death type', 'Type Concept')
|
||||
)
|
||||
)
|
||||
HAVING COUNT(PERSON_ID) > 0
|
||||
|
|
@ -589,7 +589,7 @@ INNER JOIN #concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_c
|
|||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount = 1
|
||||
LEFT JOIN #concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('procedure type')
|
||||
AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
|
||||
LEFT JOIN #concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id
|
||||
AND cm2.domain_id = cmdis2.domain_id
|
||||
AND cmdis2.targetConceptCount = 1
|
||||
|
|
@ -632,7 +632,7 @@ SELECT procedure_occurrence_id
|
|||
FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE
|
||||
LEFT JOIN #concept_map cm1 ON procedure_concept_id = cm1.source_concept_id
|
||||
LEFT JOIN #concept_map cm2 ON procedure_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('procedure type')
|
||||
AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
|
||||
WHERE procedure_concept_id <> 0
|
||||
AND cm1.domain_id IS NULL
|
||||
|
||||
|
|
@ -680,7 +680,7 @@ FROM (
|
|||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount > 1
|
||||
LEFT JOIN #concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('procedure type')
|
||||
AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept')
|
||||
|
||||
UNION ALL
|
||||
|
||||
|
|
@ -801,7 +801,7 @@ FROM (
|
|||
WHERE CONCEPT_ID = 0
|
||||
OR (
|
||||
STANDARD_CONCEPT = 'S'
|
||||
AND LOWER(DOMAIN_ID) IN ('procedure type')
|
||||
AND LOWER(DOMAIN_ID) IN ('procedure type', 'Type Concept')
|
||||
)
|
||||
)
|
||||
HAVING COUNT(PERSON_ID) > 0
|
||||
|
|
@ -877,7 +877,7 @@ INNER JOIN #concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_c
|
|||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount = 1
|
||||
LEFT JOIN #concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('drug type')
|
||||
AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
|
||||
INNER JOIN #concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id
|
||||
AND cm2.domain_id = cmdis2.domain_id
|
||||
AND cmdis2.targetConceptCount = 1
|
||||
|
|
@ -939,7 +939,7 @@ SELECT drug_exposure_id
|
|||
FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE
|
||||
LEFT JOIN #concept_map cm1 ON drug_concept_id = cm1.source_concept_id
|
||||
LEFT JOIN #concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('drug type')
|
||||
AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
|
||||
WHERE drug_concept_id <> 0
|
||||
AND cm1.domain_id IS NULL
|
||||
|
||||
|
|
@ -1004,7 +1004,7 @@ FROM (
|
|||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount > 1
|
||||
LEFT JOIN #concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('drug type')
|
||||
AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept')
|
||||
|
||||
UNION ALL
|
||||
|
||||
|
|
@ -1170,7 +1170,7 @@ FROM (
|
|||
WHERE CONCEPT_ID = 0
|
||||
OR (
|
||||
STANDARD_CONCEPT = 'S'
|
||||
AND LOWER(DOMAIN_ID) IN ('drug type')
|
||||
AND LOWER(DOMAIN_ID) IN ('drug type', 'Type Concept')
|
||||
)
|
||||
)
|
||||
HAVING COUNT(PERSON_ID) > 0
|
||||
|
|
@ -1201,7 +1201,7 @@ INNER JOIN #concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_c
|
|||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount = 1
|
||||
LEFT JOIN #concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('condition type')
|
||||
AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
|
||||
WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4
|
||||
|
||||
UNION ALL
|
||||
|
|
@ -1238,7 +1238,7 @@ SELECT condition_occurrence_id
|
|||
FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE
|
||||
LEFT JOIN #concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id
|
||||
LEFT JOIN #concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('condition type')
|
||||
AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
|
||||
WHERE condition_concept_id <> 0
|
||||
AND cm1.domain_id IS NULL
|
||||
|
||||
|
|
@ -1281,7 +1281,7 @@ FROM (
|
|||
AND cm1.domain_id = cmdis.domain_id
|
||||
AND cmdis.targetConceptCount > 1
|
||||
LEFT JOIN #concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id
|
||||
AND LOWER(cm2.domain_id) IN ('condition type')
|
||||
AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept')
|
||||
WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4
|
||||
|
||||
UNION ALL
|
||||
|
|
@ -1369,7 +1369,7 @@ FROM (
|
|||
WHERE CONCEPT_ID = 0
|
||||
OR (
|
||||
STANDARD_CONCEPT = 'S'
|
||||
AND LOWER(DOMAIN_ID) IN ('condition type')
|
||||
AND LOWER(DOMAIN_ID) IN ('condition type', 'Type Concept')
|
||||
)
|
||||
)
|
||||
HAVING COUNT(PERSON_ID) > 0
|
||||
|
|
|
|||
Loading…
Reference in New Issue