From cb116a29a0427b9c86ed4d0d277dcab7c1dbda27 Mon Sep 17 00:00:00 2001 From: Anthony Sena Date: Tue, 1 Sep 2015 13:18:42 -0400 Subject: [PATCH] Adding in Redshift and SQL Server PDW translations along with a bug fix to the era logic --- .../Convert-OHDSI-Sql-To-Dialect-Local.R | 38 + .../OMOP CDMv4 to CDMv5 - OHDSI-SQL.sql | 4 +- .../Oracle/OMOP CDMv4 to CDMv5 - Oracle.sql | 318 +-- .../OMOP CDMv4 to CDMv5 - PostgreSQL.sql | 6 +- Version4 To Version5 Conversion/README.md | 2 + .../OMOP CDMv4 to CDMv5 - Redshift.sql | 2408 +++++++++++++++++ .../OMOP CDMv4 to CDMv5 - Sql Server PDW.dsql | 2388 ++++++++++++++++ .../OMOP CDMv4 to CDMv5 - SQL Server.sql | 6 +- 8 files changed, 5005 insertions(+), 165 deletions(-) create mode 100644 Version4 To Version5 Conversion/Convert-OHDSI-Sql-To-Dialect-Local.R create mode 100644 Version4 To Version5 Conversion/Redshift/OMOP CDMv4 to CDMv5 - Redshift.sql create mode 100644 Version4 To Version5 Conversion/Sql Server PDW/OMOP CDMv4 to CDMv5 - Sql Server PDW.dsql diff --git a/Version4 To Version5 Conversion/Convert-OHDSI-Sql-To-Dialect-Local.R b/Version4 To Version5 Conversion/Convert-OHDSI-Sql-To-Dialect-Local.R new file mode 100644 index 0000000..edf4613 --- /dev/null +++ b/Version4 To Version5 Conversion/Convert-OHDSI-Sql-To-Dialect-Local.R @@ -0,0 +1,38 @@ +# Load Libraries +install.packages(devtools) +library(devtools) +install_github("OHDSI/SqlRender") +library(SqlRender) +# Variables +ohdsiSqlFile <- "C:/Git/CommonDataModel/Version4 To Version5 Conversion/OMOP CDMv4 to CDMv5 - OHDSI-SQL.sql" +targetSqlServerFile <- "C:/Git/CommonDataModel/Version4 To Version5 Conversion/Sql Server/OMOP CDMv4 to CDMv5 - SQL Server.sql" +targetPostgreSqlFile <- "C:/Git/CommonDataModel/Version4 To Version5 Conversion/PostgreSQL/OMOP CDMv4 to CDMv5 - PostgreSQL.sql" +targetOracleFile <- "C:/Git/CommonDataModel/Version4 To Version5 Conversion/Oracle/OMOP CDMv4 to CDMv5 - Oracle.sql" +targetSqlServerPDWFile <- "C:/Git/CommonDataModel/Version4 To Version5 Conversion/Sql Server PDW/OMOP CDMv4 to CDMv5 - Sql Server PDW.dsql" +targetRedshiftFile <- "C:/Git/CommonDataModel/Version4 To Version5 Conversion/Redshift/OMOP CDMv4 to CDMv5 - Redshift.sql" + +##### LOCAL - SQL Server Testing +#renderSqlFile(ohdsiSqlFile, targetSqlServerFile, SOURCE_CDMV4 = "[CDMV4]", SOURCE_CDMV4_SCHEMA = "[CDMV4].[dbo]", TARGET_CDMV5 = "[CDMV5]", TARGET_CDMV5_SCHEMA = "[CDMV5].[dbo]") + +##### SQL Server Testing +#renderSqlFile(ohdsiSqlFile, targetSqlServerFile, SOURCE_CDMV4 = "[CDM_TRUVEN_CCAE_6k]", SOURCE_CDMV4_SCHEMA = "[CDM_TRUVEN_CCAE_6k].[dbo]", TARGET_CDMV5 = "[CDMV5_Conversion_Target]", TARGET_CDMV5_SCHEMA = "[CDMV5_Conversion_Target].[dbo]") + +##### PostgreSql Testing +#renderSqlFile(ohdsiSqlFile, targetSqlServerFile, SOURCE_CDMV4 = "sandbox", SOURCE_CDMV4_SCHEMA = "sandbox.cdmv4", TARGET_CDMV5 = "sandbox", TARGET_CDMV5_SCHEMA = "sandbox.cdmv5") +#translateSqlFile(sourceFile = targetSqlServerFile, targetFile = targetPostgreSqlFile, targetDialect = "postgresql") + +##### Oracle Testing +#renderSqlFile(ohdsiSqlFile, targetSqlServerFile, SOURCE_CDMV4 = "CDMV4", SOURCE_CDMV4_SCHEMA = "CDMV4", TARGET_CDMV5 = "CDMV5", TARGET_CDMV5_SCHEMA = "CDMV5") +#translateSqlFile(sourceFile = targetSqlServerFile, targetFile = targetOracleFile, targetDialect = "oracle") + +##### APS Testing +#renderSqlFile(ohdsiSqlFile, targetSqlServerFile, SOURCE_CDMV4 = "[CDM_THIN]", SOURCE_CDMV4_SCHEMA = "[CDM_THIN].[dbo]", TARGET_CDMV5 = "[CDM_THIN_V5_asena5]", TARGET_CDMV5_SCHEMA = "[CDM_THIN_V5_asena5].[dbo]") +#translateSqlFile(sourceFile = targetSqlServerFile, targetFile = targetSqlServerPDWFile, targetDialect = "pdw") + +##### Push to GitHub +renderSqlFile(ohdsiSqlFile, targetSqlServerFile) +translateSqlFile(sourceFile = targetSqlServerFile, targetFile = targetPostgreSqlFile, targetDialect = "postgresql") +translateSqlFile(sourceFile = targetSqlServerFile, targetFile = targetOracleFile, targetDialect = "oracle") +translateSqlFile(sourceFile = targetSqlServerFile, targetFile = targetSqlServerPDWFile, targetDialect = "pdw") +translateSqlFile(sourceFile = targetSqlServerFile, targetFile = targetRedshiftFile, targetDialect = "redshift") + diff --git a/Version4 To Version5 Conversion/OMOP CDMv4 to CDMv5 - OHDSI-SQL.sql b/Version4 To Version5 Conversion/OMOP CDMv4 to CDMv5 - OHDSI-SQL.sql index 30e8aed..7ebe47a 100644 --- a/Version4 To Version5 Conversion/OMOP CDMv4 to CDMv5 - OHDSI-SQL.sql +++ b/Version4 To Version5 Conversion/OMOP CDMv4 to CDMv5 - OHDSI-SQL.sql @@ -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 diff --git a/Version4 To Version5 Conversion/Oracle/OMOP CDMv4 to CDMv5 - Oracle.sql b/Version4 To Version5 Conversion/Oracle/OMOP CDMv4 to CDMv5 - Oracle.sql index 5d3a13c..f143127 100644 --- a/Version4 To Version5 Conversion/Oracle/OMOP CDMv4 to CDMv5 - Oracle.sql +++ b/Version4 To Version5 Conversion/Oracle/OMOP CDMv4 to CDMv5 - Oracle.sql @@ -109,8 +109,8 @@ ALTER SESSION SET current_schema = [TARGET_CDMV5]; * Also, as of the date which this script was authored, no source_concept_ids map to multiple domains */ BEGIN - EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0oconcept_map'; - EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0oconcept_map'; + EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78aconcept_map'; + EXECUTE IMMEDIATE 'DROP TABLE ra2pz78aconcept_map'; EXCEPTION WHEN OTHERS THEN IF SQLCODE != -942 THEN @@ -118,9 +118,9 @@ EXCEPTION END IF; END; -/ +/* / */ -CREATE GLOBAL TEMPORARY TABLE q7a3ac0oconcept_map +CREATE GLOBAL TEMPORARY TABLE ra2pz78aconcept_map ON COMMIT PRESERVE ROWS AS SELECT @@ -132,9 +132,9 @@ FROM [TARGET_CDMV5].[SCHEMA].concept WHERE 1 = 0; -/ +/* / */ -INSERT INTO q7a3ac0oconcept_map +INSERT INTO ra2pz78aconcept_map --standard concepts SELECT concept_id AS source_concept_id ,concept_id AS target_concept_id @@ -279,8 +279,8 @@ INNER JOIN [TARGET_CDMV5].[SCHEMA].concept c2 ON cr1.concept_id_2 = c2.concept_i AND cr1.invalid_reason IS NULL; BEGIN - EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0oconcept_map_distinct'; - EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0oconcept_map_distinct'; + EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78aconcept_map_distinct'; + EXECUTE IMMEDIATE 'DROP TABLE ra2pz78aconcept_map_distinct'; EXCEPTION WHEN OTHERS THEN IF SQLCODE != -942 THEN @@ -288,9 +288,9 @@ EXCEPTION END IF; END; -/ +/* / */ -CREATE GLOBAL TEMPORARY TABLE q7a3ac0oconcept_map_distinct +CREATE GLOBAL TEMPORARY TABLE ra2pz78aconcept_map_distinct ON COMMIT PRESERVE ROWS AS SELECT @@ -299,18 +299,18 @@ SELECT ,COUNT(*) AS targetConceptCount FROM - q7a3ac0oconcept_map + ra2pz78aconcept_map WHERE 1 = 0 GROUP BY source_concept_id ,domain_id; -/ +/* / */ -INSERT INTO q7a3ac0oconcept_map_distinct +INSERT INTO ra2pz78aconcept_map_distinct SELECT source_concept_id ,domain_id ,COUNT(*) -FROM q7a3ac0oconcept_map +FROM ra2pz78aconcept_map GROUP BY source_concept_id ,domain_id; @@ -324,10 +324,10 @@ EXCEPTION END IF; END; -/ +/* / */ CREATE TABLE [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE VARCHAR(4000)); -/ +/* / */ /**** @@ -423,11 +423,11 @@ SELECT person_id ,ethnicity_source_value ,CAST(NULL AS INT) ethnicity_source_concept_id FROM [SOURCE_CDMV4].[SCHEMA].PERSON p -LEFT JOIN q7a3ac0oconcept_map gender ON LOWER(gender.DOMAIN_ID) IN ('gender') +LEFT JOIN ra2pz78aconcept_map gender ON LOWER(gender.DOMAIN_ID) IN ('gender') AND p.gender_concept_id = gender.source_concept_id -LEFT JOIN q7a3ac0oconcept_map race ON LOWER(race.DOMAIN_ID) IN ('race') +LEFT JOIN ra2pz78aconcept_map race ON LOWER(race.DOMAIN_ID) IN ('race') AND p.race_concept_id = race.source_concept_id -LEFT JOIN q7a3ac0oconcept_map ethnicity ON LOWER(ethnicity.DOMAIN_ID) IN ('ethnicity') +LEFT JOIN ra2pz78aconcept_map ethnicity ON LOWER(ethnicity.DOMAIN_ID) IN ('ethnicity') AND p.ETHNICITY_CONCEPT_ID = ethnicity.source_concept_id; INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) @@ -509,7 +509,7 @@ SELECT person_id ,cause_of_death_source_value AS cause_source_value ,CAST(NULL AS INT) AS cause_source_concept_id FROM [SOURCE_CDMV4].[SCHEMA].DEATH -LEFT JOIN q7a3ac0oconcept_map_distinct cm1 ON DEATH.DEATH_TYPE_CONCEPT_ID = CM1.SOURCE_CONCEPT_ID +LEFT JOIN ra2pz78aconcept_map_distinct cm1 ON DEATH.DEATH_TYPE_CONCEPT_ID = CM1.SOURCE_CONCEPT_ID AND LOWER(DOMAIN_ID) IN ('death type'); INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) @@ -548,7 +548,7 @@ SELECT visit_occurrence_id ,place_of_service_source_value AS visit_source_value ,CAST(NULL AS INT) visit_source_concept_id FROM [SOURCE_CDMV4].[SCHEMA].VISIT_OCCURRENCE -LEFT JOIN q7a3ac0oconcept_map cm1 ON VISIT_OCCURRENCE.PLACE_OF_SERVICE_CONCEPT_ID = cm1.source_concept_id +LEFT JOIN ra2pz78aconcept_map cm1 ON VISIT_OCCURRENCE.PLACE_OF_SERVICE_CONCEPT_ID = cm1.source_concept_id AND LOWER(cm1.domain_id) IN ('visit'); INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) @@ -574,8 +574,8 @@ FROM ( ****/ BEGIN - EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0opo_map'; - EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0opo_map'; + EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78apo_map'; + EXECUTE IMMEDIATE 'DROP TABLE ra2pz78apo_map'; EXCEPTION WHEN OTHERS THEN IF SQLCODE != -942 THEN @@ -583,9 +583,9 @@ EXCEPTION END IF; END; -/ +/* / */ -CREATE GLOBAL TEMPORARY TABLE q7a3ac0opo_map +CREATE GLOBAL TEMPORARY TABLE ra2pz78apo_map ON COMMIT PRESERVE ROWS AS SELECT @@ -608,10 +608,10 @@ FROM LEFT JOIN [TARGET_CDMV5].[SCHEMA].drug_exposure de ON 1 = 0 WHERE 0 = 1; -/ +/* / */ --find valid procedures from procedure table -INSERT INTO q7a3ac0opo_map +INSERT INTO ra2pz78apo_map SELECT procedure_occurrence_id ,person_id ,COALESCE(cm1.target_concept_id, 0) AS procedure_concept_id @@ -626,14 +626,14 @@ SELECT procedure_occurrence_id ,NULL AS qualifier_source_value ,CAST(NULL AS INT) AS origional_drug_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 ('procedure') -INNER JOIN q7a3ac0oconcept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id +INNER JOIN ra2pz78aconcept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id AND cm1.domain_id = cmdis.domain_id AND cmdis.targetConceptCount = 1 -LEFT JOIN q7a3ac0oconcept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id +LEFT JOIN ra2pz78aconcept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id AND LOWER(cm2.domain_id) IN ('procedure type') -LEFT JOIN q7a3ac0oconcept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id +LEFT JOIN ra2pz78aconcept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id AND cm2.domain_id = cmdis2.domain_id AND cmdis2.targetConceptCount = 1 @@ -654,11 +654,15 @@ SELECT procedure_occurrence_id ,NULL qualifier_source_value ,CAST(NULL AS INT) AS origional_drug_id FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE + FROM + DUAL + FROM + DUAL 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 @@ -673,8 +677,8 @@ SELECT procedure_occurrence_id ,NULL qualifier_source_value ,CAST(NULL AS INT) AS origional_drug_id FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE -LEFT JOIN q7a3ac0oconcept_map cm1 ON procedure_concept_id = cm1.source_concept_id -LEFT JOIN q7a3ac0oconcept_map cm2 ON procedure_concept_id = cm2.source_concept_id +LEFT JOIN ra2pz78aconcept_map cm1 ON procedure_concept_id = cm1.source_concept_id +LEFT JOIN ra2pz78aconcept_map cm2 ON procedure_concept_id = cm2.source_concept_id AND LOWER(cm2.domain_id) IN ('procedure type') WHERE procedure_concept_id <> 0 AND cm1.domain_id IS NULL @@ -717,12 +721,12 @@ FROM ( ,CAST(NULL AS INT) AS origional_drug_id ,CAST(NULL AS INT) 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 ('procedure') - INNER JOIN q7a3ac0oconcept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id + INNER JOIN ra2pz78aconcept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_concept_id AND cm1.domain_id = cmdis.domain_id AND cmdis.targetConceptCount > 1 - LEFT JOIN q7a3ac0oconcept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id + LEFT JOIN ra2pz78aconcept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id AND LOWER(cm2.domain_id) IN ('procedure type') UNION ALL @@ -742,7 +746,7 @@ FROM ( ,CAST(NULL AS INT) AS origional_drug_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 ('procedure') UNION ALL @@ -762,7 +766,7 @@ FROM ( ,drug_exposure_id AS origional_drug_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 ('procedure') --find procedures that were previously classified as observation @@ -782,7 +786,7 @@ FROM ( ,CAST(NULL AS INT) AS origional_drug_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 ('procedure') ) OTHERS ,( @@ -816,7 +820,7 @@ SELECT procedure_occurrence_id ,procedure_source_value ,procedure_source_concept_id ,qualifier_source_value -FROM q7a3ac0opo_map; +FROM ra2pz78apo_map; --warnings of invalid records INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) @@ -857,8 +861,8 @@ FROM ( ****/ --find valid drugs from drug_exposure table BEGIN - EXECUTE IMMEDIATE 'TRUNCATE TABLE q7a3ac0odrgexp_map'; - EXECUTE IMMEDIATE 'DROP TABLE q7a3ac0odrgexp_map'; + EXECUTE IMMEDIATE 'TRUNCATE TABLE ra2pz78adrgexp_map'; + EXECUTE IMMEDIATE 'DROP TABLE ra2pz78adrgexp_map'; EXCEPTION WHEN OTHERS THEN IF SQLCODE != -942 THEN @@ -866,9 +870,9 @@ EXCEPTION END IF; END; -/ +/* / */ -CREATE GLOBAL TEMPORARY TABLE q7a3ac0odrgexp_map +CREATE GLOBAL TEMPORARY TABLE ra2pz78adrgexp_map ON COMMIT PRESERVE ROWS AS SELECT @@ -900,9 +904,9 @@ FROM LEFT JOIN [TARGET_CDMV5].[SCHEMA].procedure_occurrence po ON 1 = 0 WHERE 0 = 1; -/ +/* / */ -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; \ No newline at end of file diff --git a/Version4 To Version5 Conversion/PostgreSQL/OMOP CDMv4 to CDMv5 - PostgreSQL.sql b/Version4 To Version5 Conversion/PostgreSQL/OMOP CDMv4 to CDMv5 - PostgreSQL.sql index dba70f3..51198d5 100644 --- a/Version4 To Version5 Conversion/PostgreSQL/OMOP CDMv4 to CDMv5 - PostgreSQL.sql +++ b/Version4 To Version5 Conversion/PostgreSQL/OMOP CDMv4 to CDMv5 - PostgreSQL.sql @@ -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 diff --git a/Version4 To Version5 Conversion/README.md b/Version4 To Version5 Conversion/README.md index 58c14e4..013fafe 100644 --- a/Version4 To Version5 Conversion/README.md +++ b/Version4 To Version5 Conversion/README.md @@ -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 diff --git a/Version4 To Version5 Conversion/Redshift/OMOP CDMv4 to CDMv5 - Redshift.sql b/Version4 To Version5 Conversion/Redshift/OMOP CDMv4 to CDMv5 - Redshift.sql new file mode 100644 index 0000000..6395c26 --- /dev/null +++ b/Version4 To Version5 Conversion/Redshift/OMOP CDMv4 to CDMv5 - Redshift.sql @@ -0,0 +1,2408 @@ +/********************************************************************************* +# Copyright 2015 Observational Health Data Sciences and Informatics +# +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +********************************************************************************/ +/******************************************************************************* + +PURPOSE: Use this script to convert your OMOP V4 common data model to CDM V5. + +last revised: 04 August 2015 +authors: Patrick Ryan, Chris Knoll, Anthony Sena + +!!!!!!!!!!!!!!!!!!!!! PLEASE READ THESE INSTRUCTIONS !!!!!!!!!!!!!!!!!!!!!!!!!!! + +This script was authored using OHDSI-SQL which will require you to run this +script through SqlRender to creat a version that is compatible with your target +RDBMS. We have pre-generated these scripts using SQL Render and have placed +them in folders for each RDBMS. Depending on which script you are viewing, your +instructions will be slightly different. + +General Assumptions +------------------- + +This script assumes that your V4 and V5 database are located on the same +RDBMS server. It also assumes that the V4 and V5 databases were created +using the standard data definition scripts for these databases. If you +altered your V4 database in any way, this script will likely require +some mo + +Getting Started +--------------- + +Before you can use this script, there are some prerequisites: + + 1. Create a target CDMv5 database on your database server using the + appropriate script from https://github.com/OHDSI/CommonDataModel + 2. Load VocabV5 into the target database/schema that will contain CDMv5 using + Athena: http://ohdsi.org/web/ATHENA + +OHDSI-SQL File Instructions +----------------------------- + + 1. Set parameter name of schema that contains CDMv4 instance + ([SOURCE_CDMV4], [SOURCE_CDMV4].[SCHEMA]) + 2. Set parameter name of schema that contains CDMv5 instance + ([TARGET_CDMV5], [TARGET_CDMV5].[SCHEMA]) + 3. Run this script through SqlRender to produce a script that will work in your + source dialect. SqlRender can be found here: https://github.com/OHDSI/SqlRender + 4. Run the script produced by SQL Render on your target RDBDMS. + + File Instructions +------------------------- + + 1. This script will hold a number of placeholders for your CDM V4 and CDMV5 + database/schema. In order to make this file work in your environment, you + should plan to do a global "FIND AND REPLACE" on this file 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: + + a. [SOURCE_CDMV4] + b. [SOURCE_CDMV4].[SCHEMA] + c. [TARGET_CDMV5] + d. [TARGET_CDMV5].[SCHEMA] + + 2. Run the resulting script on your target RDBDMS. + +*********************************************************************************/ +/* SCRIPT PARAMETERS */ + -- The CDMv4 database name + -- The CDMv4 database plus schema + -- The target CDMv5 database name + -- the target CDMv5 database plus schema + +SET search_path TO [TARGET_CDMV5]; + +/* + * The #concept_map table will hold the mapping of source_concept_ids to target_concept_ids + * and their respective domain_ids. As a result, the results of this table will have + * some source_concept_ids that map to multiple target_concept_ids which is expected. + * + * In some of the conversion queries below, we will use the distinct values from the + * #concept_map table since our need in those instances is to understand the domain_id + * that will provide the destination table in the target V5 database. To make the code + * easier to read, we dervied a #concept_map_distinct table that holds the distinct + * source_concept_id and target domain_id. + * + * As of the dateof this script, the following domains contain source_concept_ids that + * map to multiple target_concept_ids: + * + * Condition + * Device + * Drug + * Measurement + * Observation + * Procedure + * Spec Anatomic Site + * + * Also, as of the date which this script was authored, no source_concept_ids map to multiple domains + */ +DROP TABLE IF EXISTS concept_map; + +/* / */ + +CREATE TEMP TABLE concept_map + +AS +SELECT + concept_id AS source_concept_id + ,concept_id AS target_concept_id + ,domain_id AS domain_id + +FROM + [TARGET_CDMV5].[SCHEMA].concept +WHERE 1 = 0; + +/* / */ + +INSERT INTO concept_map +--standard concepts +SELECT concept_id AS source_concept_id + ,concept_id AS target_concept_id + ,domain_id +FROM [TARGET_CDMV5].[SCHEMA].concept +WHERE standard_concept = 'S' + AND invalid_reason IS NULL + +UNION + +--concepts with 'map to' standard +SELECT DISTINCT c1.concept_id AS source_concept_id + ,c2.concept_id AS target_concept_id + ,c2.domain_id +FROM ( + SELECT concept_id + FROM [TARGET_CDMV5].[SCHEMA].concept + WHERE ( + ( + standard_concept <> 'S' + OR standard_concept IS NULL + ) + OR invalid_reason IS NOT NULL + ) + ) c1 +INNER JOIN [TARGET_CDMV5].[SCHEMA].concept_relationship cr1 ON c1.concept_id = cr1.concept_id_1 +INNER JOIN [TARGET_CDMV5].[SCHEMA].concept c2 ON cr1.concept_id_2 = c2.concept_id +WHERE c2.standard_concept = 'S' + AND c2.invalid_reason IS NULL + AND cr1.relationship_id IN ('Maps to') + AND cr1.invalid_reason IS NULL + +UNION + +--concepts without 'map to' standard with another non 'is a' relation to standard +SELECT DISTINCT c1.concept_id AS source_concept_id + ,c2.concept_id AS target_concept_id + ,c2.domain_id +FROM ( + SELECT A.concept_id + FROM [TARGET_CDMV5].[SCHEMA].concept A + LEFT JOIN ( + SELECT DISTINCT c1.concept_id + FROM ( + SELECT concept_id + FROM [TARGET_CDMV5].[SCHEMA].concept + WHERE ( + ( + standard_concept <> 'S' + OR standard_concept IS NULL + ) + OR invalid_reason IS NOT NULL + ) + ) c1 + INNER JOIN [TARGET_CDMV5].[SCHEMA].concept_relationship cr1 ON c1.concept_id = cr1.concept_id_1 + INNER JOIN [TARGET_CDMV5].[SCHEMA].concept c2 ON cr1.concept_id_2 = c2.concept_id + WHERE c2.standard_concept = 'S' + AND c2.invalid_reason IS NULL + AND cr1.relationship_id IN ('Maps to') + AND cr1.invalid_reason IS NULL + ) B ON A.concept_id = B.concept_id + WHERE ( + ( + A.standard_concept <> 'S' + OR A.standard_concept IS NULL + ) + OR A.invalid_reason IS NOT NULL + ) + AND B.concept_id IS NULL + ) c1 +INNER JOIN [TARGET_CDMV5].[SCHEMA].concept_relationship cr1 ON c1.concept_id = cr1.concept_id_1 +INNER JOIN [TARGET_CDMV5].[SCHEMA].concept c2 ON cr1.concept_id_2 = c2.concept_id +WHERE c2.standard_concept = 'S' + AND c2.invalid_reason IS NULL + AND cr1.relationship_id IN ( + 'RxNorm replaced by' + ,'SNOMED replaced by' + ,'UCUM replaced by' + ,'Concept replaced by' + ,'ICD9P replaced by' + ,'LOINC replaced by' + ,'Concept same_as to' + ,'Concept was_a to' + ,'Concept alt_to to' + ) + AND cr1.invalid_reason IS NULL + +UNION + +--concepts without 'map to' standard with 'is a' relation to standard +SELECT DISTINCT c1.concept_id AS source_concept_id + ,c2.concept_id AS target_concept_id + ,c2.domain_id +FROM ( + SELECT A.concept_id + FROM [TARGET_CDMV5].[SCHEMA].concept A + LEFT JOIN ( + SELECT DISTINCT c1.concept_id + FROM ( + SELECT concept_id + FROM [TARGET_CDMV5].[SCHEMA].concept + WHERE ( + ( + standard_concept <> 'S' + OR standard_concept IS NULL + ) + OR invalid_reason IS NOT NULL + ) + ) c1 + INNER JOIN [TARGET_CDMV5].[SCHEMA].concept_relationship cr1 ON c1.concept_id = cr1.concept_id_1 + INNER JOIN [TARGET_CDMV5].[SCHEMA].concept c2 ON cr1.concept_id_2 = c2.concept_id + WHERE c2.standard_concept = 'S' + AND c2.invalid_reason IS NULL + AND cr1.relationship_id IN ( + 'Maps to' + ,'RxNorm replaced by' + ,'SNOMED replaced by' + ,'UCUM replaced by' + ,'Concept replaced by' + ,'ICD9P replaced by' + ,'LOINC replaced by' + ,'Concept same_as to' + ,'Concept was_a to' + ,'Concept alt_to to' + ) + AND cr1.invalid_reason IS NULL + ) B ON A.concept_id = B.concept_id + WHERE ( + ( + standard_concept <> 'S' + OR standard_concept IS NULL + ) + OR invalid_reason IS NOT NULL + ) + AND B.concept_id IS NULL + ) c1 +INNER JOIN [TARGET_CDMV5].[SCHEMA].concept_relationship cr1 ON c1.concept_id = cr1.concept_id_1 +INNER JOIN [TARGET_CDMV5].[SCHEMA].concept c2 ON cr1.concept_id_2 = c2.concept_id +WHERE c2.standard_concept = 'S' + AND c2.invalid_reason IS NULL + AND cr1.relationship_id IN ('Is a') + AND cr1.invalid_reason IS NULL; + +DROP TABLE IF EXISTS concept_map_distinct; + +/* / */ + +CREATE TEMP TABLE concept_map_distinct + +AS +SELECT + source_concept_id + ,domain_id + ,COUNT(*) AS targetConceptCount + +FROM + concept_map +WHERE 1 = 0 +GROUP BY source_concept_id + ,domain_id; + +/* / */ + +INSERT INTO concept_map_distinct +SELECT source_concept_id + ,domain_id + ,COUNT(*) +FROM concept_map +GROUP BY source_concept_id + ,domain_id; + +DROP TABLE IF EXISTS [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS; + +/* / */ + +CREATE TABLE [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE VARCHAR(4000)); +/* / */ + +/**** + +CDM_SOURCE + + ****/ +INSERT INTO [TARGET_CDMV5].[SCHEMA].cdm_source ( + cdm_source_name + ,cdm_version + ,vocabulary_version + ,cdm_release_date + ) +SELECT '[TARGET_CDMV5]' + ,'V5' + ,v.vocabulary_version + ,CURRENT_DATE +FROM [TARGET_CDMV5].[SCHEMA].vocabulary v +WHERE vocabulary_id = 'Vocabulary'; + +/**** + +LOCATION + + ****/ +INSERT INTO [TARGET_CDMV5].[SCHEMA].location +SELECT location_id + ,address_1 + ,address_2 + ,city + ,STATE + ,zip + ,county + ,location_source_value +FROM [SOURCE_CDMV4].[SCHEMA].LOCATION; + +/**** + +CARE_SITE + + ****/ +INSERT INTO [TARGET_CDMV5].[SCHEMA].care_site +SELECT care_site_id + ,cast(NULL AS VARCHAR(255)) AS care_site_name + ,place_of_service_concept_id + ,location_id + ,care_site_source_value + ,place_of_service_source_value +FROM [SOURCE_CDMV4].[SCHEMA].CARE_SITE; + +/**** + +Provider + +****/ +INSERT INTO [TARGET_CDMV5].[SCHEMA].provider +SELECT provider_id + ,cast(NULL AS VARCHAR(255)) AS provider_name + ,NPI + ,DEA + ,specialty_concept_id + ,care_site_id + ,cast(NULL AS INT) AS year_of_birth + ,cast(NULL AS INT) AS gender_concept_id + ,provider_source_value + ,specialty_source_value + ,0 AS specialty_source_concept_id + ,cast(NULL AS VARCHAR(50)) AS gender_source_value + ,cast(NULL AS INT) AS gender_source_concept_id +FROM [SOURCE_CDMV4].[SCHEMA].provider; + +/**** + + PERSON + + ****/ +INSERT INTO [TARGET_CDMV5].[SCHEMA].person +SELECT person_id + ,coalesce(gender.target_concept_id, 0) AS gender_concept_id + ,year_of_birth + ,month_of_birth + ,day_of_birth + ,CAST(NULL AS VARCHAR(10)) time_of_birth + ,coalesce(race.target_concept_id, 0) AS race_concept_id + ,coalesce(ethnicity.target_concept_id, 0) AS ethnicity_concept_id + ,location_id + ,provider_id + ,care_site_id + ,person_source_value + ,gender_source_value + ,CAST(NULL AS INT) gender_source_concept_id + ,CAST(NULL AS INT) race_source_value + ,CAST(NULL AS INT) race_source_concept_id + ,ethnicity_source_value + ,CAST(NULL AS INT) ethnicity_source_concept_id +FROM [SOURCE_CDMV4].[SCHEMA].PERSON p +LEFT JOIN concept_map gender ON LOWER(gender.DOMAIN_ID) IN ('gender') + AND p.gender_concept_id = gender.source_concept_id +LEFT JOIN concept_map race ON LOWER(race.DOMAIN_ID) IN ('race') + AND p.race_concept_id = race.source_concept_id +LEFT JOIN concept_map ethnicity ON LOWER(ethnicity.DOMAIN_ID) IN ('ethnicity') + AND p.ETHNICITY_CONCEPT_ID = ethnicity.source_concept_id; + +INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) +SELECT 'PERSON: ' || CAST(NUM_INVALID_RECORDS AS VARCHAR) || ' records in the source CDMv4 database have invalid GENDER_CONCEPT_ID' +FROM ( + SELECT COUNT(PERSON_ID) AS NUM_INVALID_RECORDS + FROM [SOURCE_CDMV4].[SCHEMA].PERSON + WHERE GENDER_CONCEPT_ID NOT IN ( + SELECT CONCEPT_ID + FROM [TARGET_CDMV5].[SCHEMA].CONCEPT + WHERE CONCEPT_ID = 0 + OR ( + STANDARD_CONCEPT = 'S' + AND LOWER(DOMAIN_ID) IN ('gender') + ) + ) + HAVING COUNT(PERSON_ID) > 0 + ) warn; + +INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) +SELECT 'PERSON: ' || CAST(NUM_INVALID_RECORDS AS VARCHAR) || ' records in the source CDMv4 database have invalid RACE_CONCEPT_ID' +FROM ( + SELECT COUNT(PERSON_ID) AS NUM_INVALID_RECORDS + FROM [SOURCE_CDMV4].[SCHEMA].PERSON + WHERE RACE_CONCEPT_ID IS NOT NULL + AND RACE_CONCEPT_ID NOT IN ( + SELECT CONCEPT_ID + FROM [TARGET_CDMV5].[SCHEMA].CONCEPT + WHERE CONCEPT_ID = 0 + OR ( + STANDARD_CONCEPT = 'S' + AND LOWER(DOMAIN_ID) IN ('race') + ) + ) + HAVING COUNT(PERSON_ID) > 0 + ) warn; + +INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) +SELECT 'PERSON: ' || CAST(NUM_INVALID_RECORDS AS VARCHAR) || ' records in the source CDMv4 database have invalid ETHNICITY_CONCEPT_ID' +FROM ( + SELECT COUNT(PERSON_ID) AS NUM_INVALID_RECORDS + FROM [SOURCE_CDMV4].[SCHEMA].PERSON + WHERE ETHNICITY_CONCEPT_ID IS NOT NULL + AND ETHNICITY_CONCEPT_ID NOT IN ( + SELECT CONCEPT_ID + FROM [TARGET_CDMV5].[SCHEMA].CONCEPT + WHERE CONCEPT_ID = 0 + OR ( + STANDARD_CONCEPT = 'S' + AND LOWER(DOMAIN_ID) IN ('ethnicity') + ) + ) + HAVING COUNT(PERSON_ID) > 0 + ) warn; + +/**** + + OBSERVATION_PERIOD + + ****/ +INSERT INTO [TARGET_CDMV5].[SCHEMA].observation_period +SELECT observation_period_id + ,person_id + ,observation_period_start_date + ,observation_period_end_date + ,44814722 AS period_type_concept_id +FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION_PERIOD; + +/**** + + DEATH + + ****/ +INSERT INTO [TARGET_CDMV5].[SCHEMA].death +SELECT person_id + ,death_date + ,COALESCE(death_type_concept_id, 0) AS death_type_concept_id + ,cause_of_death_concept_id AS cause_concept_id + ,cause_of_death_source_value AS cause_source_value + ,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'); + +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' +FROM ( + SELECT COUNT(PERSON_ID) AS NUM_INVALID_RECORDS + FROM [SOURCE_CDMV4].[SCHEMA].DEATH + WHERE DEATH_TYPE_CONCEPT_ID NOT IN ( + SELECT CONCEPT_ID + FROM [TARGET_CDMV5].[SCHEMA].CONCEPT + WHERE CONCEPT_ID = 0 + OR ( + STANDARD_CONCEPT = 'S' + AND LOWER(DOMAIN_ID) IN ('death type') + ) + ) + HAVING COUNT(PERSON_ID) > 0 + ) warn; + +/**** + + VISIT_OCCURRENCE + + ****/ +INSERT INTO [TARGET_CDMV5].[SCHEMA].visit_occurrence +SELECT visit_occurrence_id + ,person_id + ,COALESCE(cm1.target_concept_id, 0) AS visit_concept_id + ,visit_start_date + ,CAST(NULL AS VARCHAR(10)) visit_start_time + ,visit_end_date + ,CAST(NULL AS VARCHAR(10)) visit_end_time + ,44818517 AS visit_type_concept_id + ,CAST(NULL AS INT) provider_id + ,care_site_id + ,place_of_service_source_value AS visit_source_value + ,CAST(NULL AS INT) visit_source_concept_id +FROM [SOURCE_CDMV4].[SCHEMA].VISIT_OCCURRENCE +LEFT JOIN concept_map cm1 ON VISIT_OCCURRENCE.PLACE_OF_SERVICE_CONCEPT_ID = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('visit'); + +INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) +SELECT 'VISIT_OCCURRENCE: ' || CAST(NUM_INVALID_RECORDS AS VARCHAR) || ' records in the source CDMv4 database have invalid VISIT_CONCEPT_ID (from the CDMv4 PLACE_OF_SERVICE_CONCEPT_ID field)' +FROM ( + SELECT COUNT(PERSON_ID) AS NUM_INVALID_RECORDS + FROM [SOURCE_CDMV4].[SCHEMA].VISIT_OCCURRENCE + WHERE PLACE_OF_SERVICE_CONCEPT_ID NOT IN ( + SELECT CONCEPT_ID + FROM [TARGET_CDMV5].[SCHEMA].CONCEPT + WHERE CONCEPT_ID = 0 + OR ( + STANDARD_CONCEPT = 'S' + AND LOWER(DOMAIN_ID) IN ('visit') + ) + ) + HAVING COUNT(PERSON_ID) > 0 + ) warn; + +/**** + + PROCEDURE_OCCURRENCE + + ****/ +DROP TABLE IF EXISTS po_map; + +/* / */ + +CREATE TEMP TABLE po_map + +AS +SELECT + po.procedure_occurrence_id + ,po.person_id + ,po.procedure_concept_id + ,po.procedure_date + ,po.procedure_type_concept_id + ,po.modifier_concept_id + ,po.quantity + ,po.provider_id + ,po.visit_occurrence_id + ,po.procedure_source_value + ,po.procedure_source_concept_id + ,po.qualifier_source_value + ,de.drug_exposure_id AS origional_drug_id + +FROM + [TARGET_CDMV5].[SCHEMA].procedure_occurrence po +LEFT JOIN [TARGET_CDMV5].[SCHEMA].drug_exposure de ON 1 = 0 +WHERE 0 = 1; + +/* / */ + +--find valid procedures from procedure table +INSERT INTO po_map +SELECT procedure_occurrence_id + ,person_id + ,COALESCE(cm1.target_concept_id, 0) AS procedure_concept_id + ,procedure_date + ,COALESCE(cm2.target_concept_id, 0) AS procedure_type_concept_id + ,CAST(NULL AS INT) AS modifier_concept_id + ,CAST(NULL AS INT) AS quantity + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,procedure_source_value + ,CAST(NULL AS INT) AS procedure_source_concept_id + ,NULL AS qualifier_source_value + ,CAST(NULL AS INT) AS origional_drug_id +FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE +INNER JOIN concept_map cm1 ON PROCEDURE_OCCURRENCE.PROCEDURE_CONCEPT_ID = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('procedure') +INNER JOIN concept_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 concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id + AND LOWER(cm2.domain_id) IN ('procedure type') +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 + +UNION ALL + +-- All procedures that did not map to a standard concept in V4 should also carry over to V5 +SELECT procedure_occurrence_id + ,person_id + ,procedure_concept_id + ,procedure_date + ,procedure_type_concept_id + ,CAST(NULL AS INT) AS modifier_concept_id + ,CAST(NULL AS INT) AS quantity + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,procedure_source_value + ,CAST(NULL AS INT) procedure_source_concept_id + ,NULL qualifier_source_value + ,CAST(NULL AS INT) AS origional_drug_id +FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE +WHERE procedure_concept_id = 0 + +UNION ALL + +-- 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 + ,procedure_date + ,COALESCE(cm2.target_concept_id, 0) AS procedure_type_concept_id + ,CAST(NULL AS INT) AS modifier_concept_id + ,CAST(NULL AS INT) AS quantity + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,procedure_source_value + ,CAST(NULL AS INT) procedure_source_concept_id + ,NULL qualifier_source_value + ,CAST(NULL AS INT) AS origional_drug_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') +WHERE procedure_concept_id <> 0 + AND cm1.domain_id IS NULL + +UNION ALL + +SELECT CASE + WHEN MAXROW.MAXROWID IS NULL + THEN 0 + ELSE MAXROW.MAXROWID + END + row_number() OVER ( + ORDER BY OCCURRENCE_ID + ) AS procedure_occurrence_id + ,person_id + ,procedure_concept_id + ,procedure_date + ,procedure_type_concept_id + ,modifier_concept_id + ,quantity + ,provider_id + ,visit_occurrence_id + ,procedure_source_value + ,procedure_source_concept_id + ,qualifier_source_value + ,origional_drug_id +FROM ( + --find valid procedures from procedure table that map to more than 1 + --target concept in V5 + SELECT person_id + ,COALESCE(cm1.target_concept_id, 0) AS procedure_concept_id + ,procedure_date + ,COALESCE(cm2.target_concept_id, 0) AS procedure_type_concept_id + ,CAST(NULL AS INT) AS modifier_concept_id + ,CAST(NULL AS INT) AS quantity + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,procedure_source_value + ,CAST(NULL AS INT) procedure_source_concept_id + ,NULL qualifier_source_value + ,CAST(NULL AS INT) AS origional_drug_id + ,CAST(NULL AS INT) AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE + INNER JOIN concept_map cm1 ON PROCEDURE_OCCURRENCE.PROCEDURE_CONCEPT_ID = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('procedure') + INNER JOIN concept_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 concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id + AND LOWER(cm2.domain_id) IN ('procedure type') + + UNION ALL + + --find procedures that were previously classified as condition + SELECT person_id + ,cm1.target_concept_id AS procedure_concept_id + ,condition_start_date AS procedure_date + ,0 AS procedure_type_concept_id + ,CAST(NULL AS INT) AS modifier_concept_id + ,CAST(NULL AS INT) AS quantity + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,condition_source_value AS procedure_source_value + ,CAST(NULL AS INT) AS procedure_source_concept_id + ,NULL AS qualifier_source_value + ,CAST(NULL AS INT) AS origional_drug_id + ,condition_occurrence_id AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE + INNER JOIN concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('procedure') + + UNION ALL + + --find procedures that were previously classified as drug + SELECT person_id + ,cm1.target_concept_id AS procedure_concept_id + ,drug_exposure_start_date AS procedure_date + ,0 AS procedure_type_concept_id + ,CAST(NULL AS INT) AS modifier_concept_id + ,CAST(NULL AS INT) AS quantity + ,prescribing_provider_id AS provider_id + ,visit_occurrence_id + ,drug_source_value AS procedure_source_value + ,CAST(NULL AS INT) AS procedure_source_concept_id + ,NULL AS qualifier_source_value + ,drug_exposure_id AS origional_drug_id + ,drug_exposure_id AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE + INNER JOIN concept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('procedure') + --find procedures that were previously classified as observation + + UNION ALL + + SELECT person_id + ,cm1.target_concept_id AS procedure_concept_id + ,observation_date AS procedure_date + ,0 AS procedure_type_concept_id + ,CAST(NULL AS INT) AS modifier_concept_id + ,CAST(NULL AS INT) AS quantity + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,observation_source_value AS procedure_source_value + ,CAST(NULL AS INT) AS procedure_source_concept_id + ,NULL AS qualifier_source_value + ,CAST(NULL AS INT) AS origional_drug_id + ,OBSERVATION_ID AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION + INNER JOIN concept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('procedure') + ) OTHERS + ,( + SELECT MAX(PROCEDURE_OCCURRENCE_ID) AS MAXROWID + FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE + ) MAXROW; + +INSERT INTO [TARGET_CDMV5].[SCHEMA].procedure_occurrence ( + procedure_occurrence_id + ,person_id + ,procedure_concept_id + ,procedure_date + ,procedure_type_concept_id + ,modifier_concept_id + ,quantity + ,provider_id + ,visit_occurrence_id + ,procedure_source_value + ,procedure_source_concept_id + ,qualifier_source_value + ) +SELECT procedure_occurrence_id + ,person_id + ,procedure_concept_id + ,procedure_date + ,procedure_type_concept_id + ,modifier_concept_id + ,quantity + ,provider_id + ,visit_occurrence_id + ,procedure_source_value + ,procedure_source_concept_id + ,qualifier_source_value +FROM po_map; + +--warnings of invalid records +INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) +SELECT 'PROCEDURE_OCCURRENCE: ' || CAST(NUM_INVALID_RECORDS AS VARCHAR) || ' records in the source CDMv4 database have invalid PROCOEDURE_CONCEPT_ID' +FROM ( + SELECT COUNT(PERSON_ID) AS NUM_INVALID_RECORDS + FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE + WHERE PROCEDURE_CONCEPT_ID NOT IN ( + SELECT CONCEPT_ID + FROM [TARGET_CDMV5].[SCHEMA].CONCEPT + WHERE CONCEPT_ID = 0 + OR STANDARD_CONCEPT = 'S' + ) + HAVING COUNT(PERSON_ID) > 0 + ) warn; + +INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) +SELECT 'PROCEDURE_OCCURRENCE: ' || CAST(NUM_INVALID_RECORDS AS VARCHAR) || ' records in the source CDMv4 database have invalid PROCOEDURE_TYPE_CONCEPT_ID' +FROM ( + SELECT COUNT(PERSON_ID) AS NUM_INVALID_RECORDS + FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE + WHERE PROCEDURE_TYPE_CONCEPT_ID NOT IN ( + SELECT CONCEPT_ID + FROM [TARGET_CDMV5].[SCHEMA].CONCEPT + WHERE CONCEPT_ID = 0 + OR ( + STANDARD_CONCEPT = 'S' + AND LOWER(DOMAIN_ID) IN ('procedure type') + ) + ) + HAVING COUNT(PERSON_ID) > 0 + ) warn; + +/**** + + DRUG_EXPOSURE + + ****/ +--find valid drugs from drug_exposure table +DROP TABLE IF EXISTS drgexp_map; + +/* / */ + +CREATE TEMP TABLE drgexp_map + +AS +SELECT + de.drug_exposure_id + ,de.person_id + ,de.drug_concept_id + ,de.drug_exposure_start_date + ,de.drug_exposure_end_date + ,de.drug_type_concept_id + ,de.stop_reason + ,de.refills + ,de.quantity + ,de.days_supply + ,de.sig + ,de.route_concept_id + ,de.effective_drug_dose + ,de.dose_unit_concept_id + ,de.lot_number + ,de.provider_id + ,de.visit_occurrence_id + ,de.drug_source_value + ,de.drug_source_concept_id + ,de.route_source_value + ,de.dose_unit_source_value + ,po.procedure_occurrence_id AS origional_procedure_id + +FROM + [TARGET_CDMV5].[SCHEMA].drug_exposure de +LEFT JOIN [TARGET_CDMV5].[SCHEMA].procedure_occurrence po ON 1 = 0 +WHERE 0 = 1; + +/* / */ + +INSERT INTO drgexp_map +SELECT drug_exposure_id + ,person_id + ,COALESCE(cm1.target_concept_id, 0) AS drug_concept_id + ,drug_exposure_start_date + ,drug_exposure_end_date + ,COALESCE(cm2.target_concept_id, 0) drug_type_concept_id + ,stop_reason + ,refills + ,quantity + ,days_supply + ,sig + ,CAST(NULL AS INT) AS route_concept_id + ,CAST(NULL AS FLOAT) AS effective_drug_dose + ,CAST(NULL AS INT) AS dose_unit_concept_id + ,NULL AS lot_number + ,prescribing_provider_id AS provider_id + ,visit_occurrence_id + ,drug_source_value + ,CAST(NULL AS INT) AS drug_source_concept_id + ,NULL AS route_source_value + ,NULL AS dose_unit_source_value + ,CAST(NULL AS INT) AS origional_procedure_id +FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE +INNER JOIN concept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('drug') +INNER JOIN concept_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 concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id + AND LOWER(cm2.domain_id) IN ('drug type') +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 +WHERE drug_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4 + +UNION ALL + +-- All drug exposures that did not map to a standard concept in V4 should also carry over to V5 +SELECT drug_exposure_id + ,person_id + ,drug_concept_id + ,drug_exposure_start_date + ,drug_exposure_end_date + ,drug_type_concept_id + ,stop_reason + ,refills + ,quantity + ,days_supply + ,sig + ,CAST(NULL AS INT) AS route_concept_id + ,CAST(NULL AS FLOAT) AS effective_drug_dose + ,CAST(NULL AS INT) AS dose_unit_concept_id + ,NULL AS lot_number + ,prescribing_provider_id AS provider_id + ,visit_occurrence_id + ,drug_source_value + ,CAST(NULL AS INT) AS drug_source_concept_id + ,NULL AS route_source_value + ,NULL AS dose_unit_source_value + ,CAST(NULL AS INT) AS origional_procedure_id +FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE +WHERE drug_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 +SELECT drug_exposure_id + ,person_id + ,0 + ,drug_exposure_start_date + ,drug_exposure_end_date + ,COALESCE(cm2.target_concept_id, 0) drug_type_concept_id + ,stop_reason + ,refills + ,quantity + ,days_supply + ,sig + ,CAST(NULL AS INT) AS route_concept_id + ,CAST(NULL AS FLOAT) AS effective_drug_dose + ,CAST(NULL AS INT) AS dose_unit_concept_id + ,NULL AS lot_number + ,prescribing_provider_id AS provider_id + ,visit_occurrence_id + ,drug_source_value + ,CAST(NULL AS INT) AS drug_source_concept_id + ,NULL AS route_source_value + ,NULL AS dose_unit_source_value + ,CAST(NULL AS INT) AS origional_procedure_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') +WHERE drug_concept_id <> 0 + AND cm1.domain_id IS NULL + +UNION ALL + +SELECT CASE + WHEN MAXROW.MAXROWID IS NULL + THEN 0 + ELSE MAXROW.MAXROWID + END + row_number() OVER ( + ORDER BY OCCURRENCE_ID + ) AS drug_exposure_id + ,person_id + ,drug_concept_id + ,drug_exposure_start_date + ,drug_exposure_end_date + ,drug_type_concept_id + ,stop_reason + ,refills + ,quantity + ,days_supply + ,sig + ,route_concept_id + ,effective_drug_dose + ,dose_unit_concept_id + ,lot_number + ,provider_id + ,visit_occurrence_id + ,drug_source_value + ,drug_source_concept_id + ,route_source_value + ,dose_unit_source_value + ,origional_procedure_id +FROM ( + --find valid drugs from drug_exposure table that map to > 1 target concept + SELECT person_id + ,COALESCE(cm1.target_concept_id, 0) AS drug_concept_id + ,drug_exposure_start_date + ,drug_exposure_end_date + ,COALESCE(cm2.target_concept_id, 0) drug_type_concept_id + ,stop_reason + ,refills + ,quantity + ,days_supply + ,sig + ,CAST(NULL AS INT) AS route_concept_id + ,CAST(NULL AS FLOAT) AS effective_drug_dose + ,CAST(NULL AS INT) AS dose_unit_concept_id + ,NULL AS lot_number + ,prescribing_provider_id AS provider_id + ,visit_occurrence_id + ,drug_source_value + ,CAST(NULL AS INT) AS drug_source_concept_id + ,NULL AS route_source_value + ,NULL AS dose_unit_source_value + ,CAST(NULL AS INT) AS origional_procedure_id + ,CAST(NULL AS INT) AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE + INNER JOIN concept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('drug') + INNER JOIN concept_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 concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id + AND LOWER(cm2.domain_id) IN ('drug type') + + UNION ALL + + --find drugs that were previously classified as condition + SELECT person_id + ,cm1.target_concept_id AS drug_concept_id + ,condition_start_date AS drug_exposure_start_date + ,NULL AS drug_exposure_end_date + ,0 AS drug_type_concept_id + ,NULL AS stop_reason + ,CAST(NULL AS INT) AS refills + ,CAST(NULL AS FLOAT) AS quantity + ,CAST(NULL AS INT) AS days_supply + ,NULL AS sig + ,CAST(NULL AS INT) AS route_concept_id + ,CAST(NULL AS FLOAT) AS effective_drug_dose + ,CAST(NULL AS INT) AS dose_unit_concept_id + ,NULL AS lot_number + ,CAST(NULL AS INT) AS provider_id + ,visit_occurrence_id + ,condition_source_value AS drug_source_value + ,CAST(NULL AS INT) AS drug_source_concept_id + ,NULL AS route_source_value + ,NULL AS dose_unit_source_value + ,CAST(NULL AS INT) AS origional_procedure_id + ,condition_occurrence_id AS occurrence_id + FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE + INNER JOIN concept_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 + + UNION ALL + + SELECT person_id + ,cm1.target_concept_id AS drug_concept_id + ,procedure_date AS drug_exposure_start_date + ,TO_DATE(NULL , 'yyyymmdd') AS drug_exposure_end_date + ,0 AS drug_type_concept_id + ,NULL AS stop_reason + ,CAST(NULL AS INT) AS refills + ,CAST(NULL AS FLOAT) AS quantity + ,CAST(NULL AS INT) AS days_supply + ,NULL AS sig + ,CAST(NULL AS INT) AS route_concept_id + ,CAST(NULL AS FLOAT) AS effective_drug_dose + ,CAST(NULL AS INT) AS dose_unit_concept_id + ,NULL AS lot_number + ,CAST(NULL AS INT) AS provider_id + ,visit_occurrence_id + ,procedure_source_value AS drug_source_value + ,CAST(NULL AS INT) AS drug_source_concept_id + ,NULL AS route_source_value + ,NULL AS dose_unit_source_value + ,procedure_occurrence_id AS origional_procedure_id + ,procedure_occurrence_id AS occurrence_id + FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE + INNER JOIN concept_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 + + UNION ALL + + SELECT person_id + ,cm1.target_concept_id AS drug_concept_id + ,observation_date AS drug_exposure_start_date + ,TO_DATE(NULL , 'yyyymmdd') AS drug_exposure_end_date + ,0 AS drug_type_concept_id + ,NULL AS stop_reason + ,CAST(NULL AS INT) AS refills + ,CAST(NULL AS FLOAT) AS quantity + ,CAST(NULL AS INT) AS days_supply + ,NULL AS sig + ,CAST(NULL AS INT) AS route_concept_id + ,CAST(NULL AS FLOAT) AS effective_drug_dose + ,CAST(NULL AS INT) AS dose_unit_concept_id + ,NULL AS lot_number + ,CAST(NULL AS INT) AS provider_id + ,visit_occurrence_id + ,observation_source_value AS drug_source_value + ,CAST(NULL AS INT) AS drug_source_concept_id + ,NULL AS route_source_value + ,NULL AS dose_unit_source_value + ,CAST(NULL AS INT) AS origional_procedure_id + ,observation_id AS occurrence_id + FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION + INNER JOIN concept_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; + +INSERT INTO [TARGET_CDMV5].[SCHEMA].drug_exposure ( + drug_exposure_id + ,person_id + ,drug_concept_id + ,drug_exposure_start_date + ,drug_exposure_end_date + ,drug_type_concept_id + ,stop_reason + ,refills + ,quantity + ,days_supply + ,sig + ,route_concept_id + ,effective_drug_dose + ,dose_unit_concept_id + ,lot_number + ,provider_id + ,visit_occurrence_id + ,drug_source_value + ,drug_source_concept_id + ,route_source_value + ,dose_unit_source_value + ) +SELECT drug_exposure_id + ,person_id + ,drug_concept_id + ,drug_exposure_start_date + ,drug_exposure_end_date + ,drug_type_concept_id + ,stop_reason + ,refills + ,quantity + ,days_supply + ,sig + ,route_concept_id + ,effective_drug_dose + ,dose_unit_concept_id + ,lot_number + ,provider_id + ,visit_occurrence_id + ,drug_source_value + ,drug_source_concept_id + ,route_source_value + ,dose_unit_source_value +FROM drgexp_map; + +--warnings of invalid records +INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) +SELECT 'DRUG_EXPOSURE: ' || CAST(NUM_INVALID_RECORDS AS VARCHAR) || ' records in the source CDMv4 database have invalid DRUG_CONCEPT_ID' +FROM ( + SELECT COUNT(PERSON_ID) AS NUM_INVALID_RECORDS + FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE + WHERE DRUG_CONCEPT_ID NOT IN ( + SELECT CONCEPT_ID + FROM [TARGET_CDMV5].[SCHEMA].CONCEPT + WHERE CONCEPT_ID = 0 + OR STANDARD_CONCEPT = 'S' + ) + HAVING COUNT(PERSON_ID) > 0 + ) warn; + +INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) +SELECT 'DRUG_EXPOSURE: ' || CAST(NUM_INVALID_RECORDS AS VARCHAR) || ' records in the source CDMv4 database have invalid DRUG_TYPE_CONCEPT_ID' +FROM ( + SELECT COUNT(PERSON_ID) AS NUM_INVALID_RECORDS + FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE + WHERE DRUG_TYPE_CONCEPT_ID NOT IN ( + SELECT CONCEPT_ID + FROM [TARGET_CDMV5].[SCHEMA].CONCEPT + WHERE CONCEPT_ID = 0 + OR ( + STANDARD_CONCEPT = 'S' + AND LOWER(DOMAIN_ID) IN ('drug type') + ) + ) + HAVING COUNT(PERSON_ID) > 0 + ) warn; + +/**** + + CONDITION_OCCURRENCE + + ****/ +--find valid conditions from condition_occurrence table +INSERT INTO [TARGET_CDMV5].[SCHEMA].condition_occurrence +SELECT condition_occurrence_id + ,person_id + ,COALESCE(cm1.target_concept_id, 0) AS condition_concept_id + ,condition_start_date + ,condition_end_date + ,COALESCE(cm2.target_concept_id, 0) AS condition_type_concept_id + ,stop_reason + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,condition_source_value + ,CAST(NULL AS INT) condition_source_concept_id +FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE +INNER JOIN concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('condition') +INNER JOIN concept_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 concept_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 + +UNION ALL + +-- All conditions that did not map to a standard concept in V4 should also carry over to V5 +SELECT condition_occurrence_id + ,person_id + ,condition_concept_id + ,condition_start_date + ,condition_end_date + ,COALESCE(condition_type_concept_id, 0) AS condition_type_concept_id + ,stop_reason + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,condition_source_value + ,CAST(NULL AS INT) condition_source_concept_id +FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE +WHERE condition_concept_id = 0 + +UNION ALL + +-- All conditions that do not map to a standard concept in V5 should also carry over with condition_concept_id = 0 +SELECT condition_occurrence_id + ,person_id + ,0 AS condition_concept_id + ,condition_start_date + ,condition_end_date + ,COALESCE(cm2.target_concept_id, 0) AS condition_type_concept_id + ,stop_reason + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,condition_source_value + ,CAST(NULL AS INT) condition_source_concept_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') +WHERE condition_concept_id <> 0 + AND cm1.domain_id IS NULL + +UNION ALL + +SELECT CASE + WHEN MAXROW.MAXROWID IS NULL + THEN 0 + ELSE MAXROW.MAXROWID + END + row_number() OVER ( + ORDER BY OCCURRENCE_ID + ) AS drug_exposure_id + ,person_id + ,condition_concept_id + ,condition_start_date + ,condition_end_date + ,condition_type_concept_id + ,stop_reason + ,provider_id + ,visit_occurrence_id + ,condition_source_value + ,condition_source_concept_id +FROM ( + --find valid conditions from condition_occurrence table that map to > 1 target concept + SELECT person_id + ,COALESCE(cm1.target_concept_id, 0) AS condition_concept_id + ,condition_start_date + ,condition_end_date + ,COALESCE(cm2.target_concept_id, 0) AS condition_type_concept_id + ,stop_reason + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,condition_source_value + ,CAST(NULL AS INT) condition_source_concept_id + ,NULL AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE + INNER JOIN concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('condition') + INNER JOIN concept_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 concept_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 + + UNION ALL + + --find conditions that were previously classified as procedure + SELECT person_id + ,cm1.target_concept_id AS condition_concept_id + ,procedure_date AS condition_start_date + ,NULL AS condition_end_date + ,0 AS condition_type_concept_id + ,NULL AS stop_reason + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,procedure_source_value AS condition_source_value + ,CAST(NULL AS INT) condition_source_concept_id + ,procedure_occurrence_id AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE + INNER JOIN concept_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 + + UNION ALL + + SELECT person_id + ,cm1.target_concept_id AS condition_concept_id + ,drug_exposure_start_date AS condition_start_date + ,NULL AS condition_end_date + ,0 AS condition_type_concept_id + ,NULL AS stop_reason + ,prescribing_provider_id AS provider_id + ,visit_occurrence_id + ,drug_source_value AS condition_source_value + ,CAST(NULL AS INT) condition_source_concept_id + ,drug_exposure_id AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE + INNER JOIN concept_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 + + UNION ALL + + SELECT person_id + ,cm1.target_concept_id AS condition_concept_id + ,observation_date AS condition_start_date + ,NULL AS condition_end_date + ,0 AS condition_type_concept_id + ,NULL AS stop_reason + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,observation_source_value AS condition_source_value + ,CAST(NULL AS INT) condition_source_concept_id + ,observation_id AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION + INNER JOIN concept_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; + +--warnings of invalid records +INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) +SELECT 'CONDITION_OCCURRENCE: ' || CAST(NUM_INVALID_RECORDS AS VARCHAR) || ' records in the source CDMv4 database have invalid CONDITION_CONCEPT_ID' +FROM ( + SELECT COUNT(PERSON_ID) AS NUM_INVALID_RECORDS + FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE + WHERE CONDITION_CONCEPT_ID NOT IN ( + SELECT CONCEPT_ID + FROM [TARGET_CDMV5].[SCHEMA].CONCEPT + WHERE CONCEPT_ID = 0 + OR STANDARD_CONCEPT = 'S' + ) + HAVING COUNT(PERSON_ID) > 0 + ) warn; + +INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) +SELECT 'CONDIITON_OCCURRENCE: ' || CAST(NUM_INVALID_RECORDS AS VARCHAR) || ' records in the source CDMv4 database have invalid CONDITION_TYPE_CONCEPT_ID' +FROM ( + SELECT COUNT(PERSON_ID) AS NUM_INVALID_RECORDS + FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE + WHERE CONDITION_TYPE_CONCEPT_ID NOT IN ( + SELECT CONCEPT_ID + FROM [TARGET_CDMV5].[SCHEMA].CONCEPT + WHERE CONCEPT_ID = 0 + OR ( + STANDARD_CONCEPT = 'S' + AND LOWER(DOMAIN_ID) IN ('condition type') + ) + ) + HAVING COUNT(PERSON_ID) > 0 + ) warn; + +/**** + + DEVICE_EXPOSURE + + ****/ +INSERT INTO [TARGET_CDMV5].[SCHEMA].device_exposure +SELECT row_number() OVER ( + ORDER BY OCCURRENCE_ID + ) AS device_exposure_id + ,person_id + ,device_concept_id + ,device_exposure_start_date + ,device_exposure_end_date + ,device_type_concept_id + ,unique_device_id + ,quantity + ,provider_id + ,visit_occurrence_id + ,device_source_value + ,device_source_concept_id +FROM ( + --find devices that were previously classified as procedures + SELECT PERSON_ID + ,cm1.target_concept_id AS DEVICE_CONCEPT_ID + ,PROCEDURE_DATE AS DEVICE_EXPOSURE_START_DATE + ,TO_DATE(NULL , 'yyyymmdd') AS DEVICE_EXPOSURE_END_DATE + ,0 AS DEVICE_TYPE_CONCEPT_ID + ,CAST(NULL AS VARCHAR(50)) unique_device_id + ,CAST(NULL AS INT) quantity + ,ASSOCIATED_PROVIDER_ID AS PROVIDER_ID + ,VISIT_OCCURRENCE_ID + ,PROCEDURE_SOURCE_VALUE AS DEVICE_SOURCE_VALUE + ,0 AS device_source_concept_id + ,PROCEDURE_OCCURRENCE_ID AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE + INNER JOIN concept_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 + + UNION ALL + + SELECT PERSON_ID + ,cm1.target_concept_id AS DEVICE_CONCEPT_ID + ,DRUG_EXPOSURE_START_DATE AS DEVICE_EXPOSURE_START_DATE + ,TO_DATE(NULL , 'yyyymmdd') AS DEVICE_EXPOSURE_END_DATE + ,0 AS DEVICE_TYPE_CONCEPT_ID + ,CAST(NULL AS VARCHAR(50)) unique_device_id + ,quantity + ,PRESCRIBING_PROVIDER_ID AS PROVIDER_ID + ,VISIT_OCCURRENCE_ID + ,DRUG_SOURCE_VALUE AS DEVICE_SOURCE_VALUE + ,0 AS device_source_concept_id + ,DRUG_EXPOSURE_ID AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE + INNER JOIN concept_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 + + UNION ALL + + SELECT PERSON_ID + ,cm1.target_concept_id AS DEVICE_CONCEPT_ID + ,CONDITION_START_DATE AS DEVICE_EXPOSURE_START_DATE + ,TO_DATE(NULL , 'yyyymmdd') AS DEVICE_EXPOSURE_END_DATE + ,0 AS DEVICE_TYPE_CONCEPT_ID + ,CAST(NULL AS VARCHAR(50)) unique_device_id + ,CAST(NULL AS INT) quantity + ,ASSOCIATED_PROVIDER_ID AS PROVIDER_ID + ,VISIT_OCCURRENCE_ID + ,CONDITION_SOURCE_VALUE AS DEVICE_SOURCE_VALUE + ,0 AS device_source_concept_id + ,CONDITION_OCCURRENCE_ID AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE + INNER JOIN concept_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 + + UNION ALL + + SELECT PERSON_ID + ,cm1.target_concept_id AS DEVICE_CONCEPT_ID + ,OBSERVATION_DATE AS DEVICE_EXPOSURE_START_DATE + ,TO_DATE(NULL , 'yyyymmdd') AS DEVICE_EXPOSURE_END_DATE + ,0 AS DEVICE_TYPE_CONCEPT_ID + ,CAST(NULL AS VARCHAR(50)) unique_device_id + ,CAST(NULL AS INT) quantity + ,ASSOCIATED_PROVIDER_ID AS PROVIDER_ID + ,VISIT_OCCURRENCE_ID + ,OBSERVATION_SOURCE_VALUE AS DEVICE_SOURCE_VALUE + ,0 AS device_source_concept_id + ,OBSERVATION_ID AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION + INNER JOIN concept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('device') + ) OTHERS; + +/**** + + MEASUREMENT + + ****/ +--find valid measurements from observation table +INSERT INTO [TARGET_CDMV5].[SCHEMA].measurement +SELECT row_number() OVER ( + ORDER BY occurrence_id + ) AS measurement_id + ,person_id + ,measurement_concept_id + ,measurement_date + ,measurement_time + ,measurement_type_concept_id + ,operator_concept_id + ,value_as_number + ,value_as_concept_id + ,unit_concept_id + ,range_low + ,range_high + ,provider_id + ,visit_occurrence_id + ,measurement_source_value + ,measurement_source_concept_id + ,unit_source_value + ,value_source_value +FROM ( + --find mesaurements that were previously classified as observations + SELECT person_id + ,cm1.target_concept_id AS measurement_concept_id + ,OBSERVATION_DATE AS measurement_date + ,CAST(OBSERVATION_TIME AS VARCHAR(50)) AS measurement_time + ,0 AS measurement_type_concept_id + ,CAST(NULL AS INT) operator_concept_id + ,value_as_number + ,value_as_concept_id + ,COALESCE(cm2.target_concept_id, 0) AS unit_concept_id + ,range_low + ,range_high + ,ASSOCIATED_PROVIDER_ID AS provider_id + ,visit_occurrence_id + ,OBSERVATION_SOURCE_VALUE AS measurement_source_value + ,CAST(NULL AS INT) measurement_source_concept_id + ,unit_source_value AS unit_source_value + ,cast(NULL AS VARCHAR(50)) AS value_source_value + ,observation_id AS occurrence_id + FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION + INNER JOIN concept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('measurement') + LEFT JOIN concept_map cm2 ON observation.unit_concept_id = cm2.source_concept_id + AND LOWER(cm1.domain_id) IN ('unit') + + UNION ALL + + SELECT person_id + ,cm1.target_concept_id AS measurement_concept_id + ,procedure_date AS measurement_date + ,CAST(NULL AS VARCHAR(50)) AS measurement_time + ,0 AS measurement_type_concept_id + ,CAST(NULL AS INT) AS operator_concept_id + ,CAST(NULL AS INT) AS value_as_number + ,CAST(NULL AS INT) AS value_as_concept_id + ,CAST(NULL AS INT) AS unit_concept_id + ,CAST(NULL AS INT) AS range_low + ,CAST(NULL AS INT) AS range_high + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,procedure_source_value AS measurement_source_value + ,CAST(NULL AS INT) AS measurement_source_concept_id + ,CAST(NULL AS VARCHAR(50)) AS unit_source_value + ,CAST(NULL AS VARCHAR(50)) AS value_source_value + ,procedure_occurrence_id AS occurrence_id + FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE + INNER JOIN concept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('measurement') + + UNION ALL + + SELECT person_id + ,cm1.target_concept_id AS measurement_concept_id + ,condition_start_date AS measurement_date + ,CAST(NULL AS VARCHAR(50)) AS measurement_time + ,0 AS measurement_type_concept_id + ,CAST(NULL AS INT) AS operator_concept_id + ,CAST(NULL AS INT) AS value_as_number + ,CAST(NULL AS INT) AS value_as_concept_id + ,CAST(NULL AS INT) AS unit_concept_id + ,CAST(NULL AS INT) AS range_low + ,CAST(NULL AS INT) AS range_high + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,condition_source_value AS measurement_source_value + ,CAST(NULL AS INT) AS measurement_source_concept_id + ,CAST(NULL AS VARCHAR(50)) AS unit_source_value + ,CAST(NULL AS VARCHAR(50)) AS value_source_value + ,condition_occurrence_id AS occurrence_id + FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE + INNER JOIN concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('measurement') + + UNION ALL + + SELECT person_id + ,cm1.target_concept_id AS measurement_concept_id + ,drug_exposure_start_date AS measurement_date + ,CAST(NULL AS VARCHAR(50)) AS measurement_time + ,0 AS measurement_type_concept_id + ,CAST(NULL AS INT) AS operator_concept_id + ,CAST(NULL AS INT) AS value_as_number + ,CAST(NULL AS INT) AS value_as_concept_id + ,CAST(NULL AS INT) AS unit_concept_id + ,CAST(NULL AS INT) AS range_low + ,CAST(NULL AS INT) AS range_high + ,prescribing_provider_id AS provider_id + ,visit_occurrence_id + ,drug_source_value AS measurement_source_value + ,CAST(NULL AS INT) AS measurement_source_concept_id + ,CAST(NULL AS VARCHAR(50)) AS unit_source_value + ,CAST(NULL AS VARCHAR(50)) AS value_source_value + ,drug_exposure_id AS occurrence_id + FROM [SOURCE_CDMV4].[SCHEMA].drug_exposure + INNER JOIN concept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('measurement') + ) OTHERS; + +/**** + + OBSERVATION + + ****/ +--find valid observation from observation table +INSERT INTO [TARGET_CDMV5].[SCHEMA].observation +SELECT observation_id + ,person_id + ,observation_concept_id + ,observation_date + ,CAST(observation_time AS VARCHAR(50)) AS observation_time + ,observation_type_concept_id + ,value_as_number + ,value_as_string + ,value_as_concept_id + ,CAST(NULL AS INT) qualifier_concept_id + ,unit_concept_id + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,observation_source_value + ,CAST(NULL AS INT) observation_source_concept_id + ,unit_source_value + ,cast(NULL AS VARCHAR(50)) qualifier_source_value +FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION +WHERE observation_concept_id NOT IN ( + SELECT source_concept_id + FROM concept_map_distinct + WHERE LOWER(domain_id) IN ( + 'condition' + ,'drug' + ,'procedure' + ,'device' + ,'measurement' + ) + ) +--find observations that were previously classified as procedure + +UNION ALL + +SELECT CASE + WHEN MAXROW.MAXROWID IS NULL + THEN 0 + ELSE MAXROW.MAXROWID + END + row_number() OVER ( + ORDER BY OCCURRENCE_ID + ) AS observation_id + ,person_id + ,observation_concept_id + ,observation_date + ,observation_time + ,observation_type_concept_id + ,value_as_number + ,value_as_string + ,value_as_concept_id + ,qualifier_concept_id + ,unit_concept_id + ,provider_id + ,visit_occurrence_id + ,observation_source_value + ,observation_source_concept_id + ,unit_source_value + ,qualifier_source_value +FROM ( + SELECT person_id + ,cm1.target_concept_id AS observation_concept_id + ,procedure_date AS observation_date + ,CAST(NULL AS VARCHAR(50)) AS observation_time + ,0 AS observation_type_concept_id + ,CAST(NULL AS FLOAT) AS value_as_number + ,NULL AS value_as_string + ,CAST(NULL AS INT) AS value_as_concept_id + ,CAST(NULL AS INT) qualifier_concept_id + ,CAST(NULL AS INT) AS unit_concept_id + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,procedure_source_value AS observation_source_value + ,CAST(NULL AS INT) observation_source_concept_id + ,NULL AS unit_source_value + ,cast(NULL AS VARCHAR(50)) qualifier_source_value + ,procedure_occurrence_id AS occurrence_id + FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE + INNER JOIN concept_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 + + UNION ALL + + SELECT person_id + ,cm1.target_concept_id AS observation_concept_id + ,condition_start_date AS observation_date + ,CAST(NULL AS VARCHAR(50)) AS observation_time + ,0 AS observation_type_concept_id + ,CAST(NULL AS FLOAT) AS value_as_number + ,NULL AS value_as_string + ,CAST(NULL AS INT) AS value_as_concept_id + ,CAST(NULL AS INT) qualifier_concept_id + ,CAST(NULL AS INT) AS unit_concept_id + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,condition_source_value AS observation_source_value + ,CAST(NULL AS INT) observation_source_concept_id + ,NULL AS unit_source_value + ,cast(NULL AS VARCHAR(50)) qualifier_source_value + ,condition_occurrence_id AS occurrence_id + FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE + INNER JOIN concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('observation') + + UNION ALL + + --find DRG observations that were previously classified as procedure_cost + SELECT po.person_id + ,cm1.target_concept_id AS observation_concept_id + ,po.procedure_date AS observation_date + ,CAST(NULL AS VARCHAR(50)) AS observation_time + ,0 AS observation_type_concept_id + ,CAST(NULL AS FLOAT) AS value_as_number + ,NULL AS value_as_string + ,CAST(NULL AS INT) AS value_as_concept_id + ,CAST(NULL AS INT) qualifier_concept_id + ,CAST(NULL AS INT) AS unit_concept_id + ,po.associated_provider_id AS provider_id + ,po.visit_occurrence_id + ,pc.DISEASE_CLASS_SOURCE_VALUE AS observation_source_value + ,cm1.source_concept_id as observation_source_concept_id + ,NULL AS unit_source_value + ,cast(NULL AS VARCHAR(50)) qualifier_source_value + ,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 concept_map cm1 ON pc.disease_class_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('observation') + + UNION ALL + + --find observations that were previously classified as drug exposure + SELECT person_id + ,cm1.target_concept_id AS observation_concept_id + ,drug_exposure_start_date AS observation_date + ,CAST(NULL AS VARCHAR(10)) AS observation_time + ,0 AS observation_type_concept_id + ,CAST(NULL AS FLOAT) AS value_as_number + ,NULL AS value_as_string + ,CAST(NULL AS INT) AS value_as_concept_id + ,CAST(NULL AS INT) qualifier_concept_id + ,CAST(NULL AS INT) AS unit_concept_id + ,CAST(NULL AS INT) AS provider_id + ,visit_occurrence_id + ,drug_source_value AS observation_source_value + ,CAST(NULL AS INT) observation_source_concept_id + ,NULL AS unit_source_value + ,cast(NULL AS VARCHAR(50)) qualifier_source_value + ,drug_exposure_id AS occurrence_id + FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE + INNER JOIN concept_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 + FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION + ) MAXROW; + +/**** + + PAYER_PLAN_PERIOD + + ****/ +INSERT INTO [TARGET_CDMV5].[SCHEMA].payer_plan_period +SELECT payer_plan_period_id + ,person_id + ,payer_plan_period_start_date + ,payer_plan_period_end_date + ,payer_source_value + ,plan_source_value + ,family_source_value +FROM [SOURCE_CDMV4].[SCHEMA].PAYER_PLAN_PERIOD; + +/**** + + DRUG_COST + + note : if there were invalid drug concepts in DRUG_EXPOSURE, those records may not enter CDMv5 but costs will persist + + ****/ +INSERT INTO [TARGET_CDMV5].[SCHEMA].drug_cost +SELECT drug_cost_id + ,dc.drug_exposure_id + ,cast(NULL AS INT) currency_concept_id + ,paid_copay + ,paid_coinsurance + ,paid_toward_deductible + ,paid_by_payer + ,paid_by_coordination_benefits + ,total_out_of_pocket + ,total_paid + ,ingredient_cost + ,dispensing_fee + ,average_wholesale_price + ,payer_plan_period_id +FROM [SOURCE_CDMV4].[SCHEMA].DRUG_COST dc; + +-- insert procedure costs for procedures that were inserted into the drug_exposure table +INSERT INTO [TARGET_CDMV5].[SCHEMA].drug_cost +SELECT CASE + WHEN MAXROW.MAXROWID IS NULL + THEN 0 + ELSE MAXROW.MAXROWID + END + row_number() OVER ( + ORDER BY OCCURRENCE_ID + ) AS drug_cost_id + ,drug_exposure_id + ,cast(NULL AS INT) currency_concept_id + ,paid_copay + ,paid_coinsurance + ,paid_toward_deductible + ,paid_by_payer + ,paid_by_coordination_benefits + ,total_out_of_pocket + ,total_paid + ,ingredient_cost + ,dispensing_fee + ,average_wholesale_price + ,payer_plan_period_id +FROM ( + SELECT drug_exposure_id + ,po.person_id + ,paid_copay + ,paid_coinsurance + ,paid_toward_deductible + ,paid_by_payer + ,paid_by_coordination_benefits + ,total_out_of_pocket + ,total_paid + ,CAST(NULL AS FLOAT) AS ingredient_cost + ,CAST(NULL AS FLOAT) AS dispensing_fee + ,CAST(NULL AS FLOAT) AS average_wholesale_price + ,payer_plan_period_id + ,procedure_cost_id AS OCCURRENCE_ID + 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 drgexp_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 + FROM [SOURCE_CDMV4].[SCHEMA].DRUG_COST + ) MAXROW; + +/**** + + PROCEDURE_COST + + note : if there were invalid procedure concepts in PROCEDURE_OCCURRENCE, those records may not enter CDMv5 but costs will persist + + + ****/ +INSERT INTO [TARGET_CDMV5].[SCHEMA].procedure_cost +SELECT procedure_cost_id + ,procedure_occurrence_id + ,cast(NULL AS INT) currency_concept_id + ,paid_copay + ,paid_coinsurance + ,paid_toward_deductible + ,paid_by_payer + ,paid_by_coordination_benefits + ,total_out_of_pocket + ,total_paid + ,payer_plan_period_id + ,revenue_code_concept_id + ,revenue_code_source_value +FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_COST; + +-- insert drug costs for drugs that were inserted into the procedure_occurrence table +INSERT INTO [TARGET_CDMV5].[SCHEMA].procedure_cost +SELECT CASE + WHEN MAXROW.MAXROWID IS NULL + THEN 0 + ELSE MAXROW.MAXROWID + END + row_number() OVER ( + ORDER BY OCCURRENCE_ID + ) AS procedure_cost_id + ,procedure_occurrence_id + ,cast(NULL AS INT) currency_concept_id + ,paid_copay + ,paid_coinsurance + ,paid_toward_deductible + ,paid_by_payer + ,paid_by_coordination_benefits + ,total_out_of_pocket + ,total_paid + ,payer_plan_period_id + ,revenue_code_concept_id + ,revenue_code_source_value +FROM ( + SELECT po.procedure_occurrence_id + ,po.person_id + ,paid_copay + ,paid_coinsurance + ,paid_toward_deductible + ,paid_by_payer + ,paid_by_coordination_benefits + ,total_out_of_pocket + ,total_paid + ,CAST(NULL AS FLOAT) AS ingredient_cost + ,CAST(NULL AS FLOAT) AS dispensing_fee + ,CAST(NULL AS FLOAT) AS average_wholesale_price + ,payer_plan_period_id + ,CAST(NULL AS INT) AS revenue_code_concept_id + ,CAST(NULL AS INT) AS revenue_code_source_value + ,drug_cost_id AS OCCURRENCE_ID + 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 po_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 + FROM [SOURCE_CDMV4].[SCHEMA].DRUG_COST + ) MAXROW; + +/**** + +DRUG ERA +Note: Eras derived from DRUG_EXPOSURE table, using 30d gap + + ****/ +DROP TABLE IF EXISTS cteDrugTarget; + +/* / */ + +-- 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 TEMP TABLE cteDrugTarget + +AS +SELECT + d.DRUG_EXPOSURE_ID + ,d.PERSON_ID + ,c.CONCEPT_ID + ,d.DRUG_TYPE_CONCEPT_ID + ,DRUG_EXPOSURE_START_DATE + ,COALESCE(DRUG_EXPOSURE_END_DATE, ( DRUG_EXPOSURE_START_DATE + DAYS_SUPPLY), ( DRUG_EXPOSURE_START_DATE + 1)) AS DRUG_EXPOSURE_END_DATE + ,c.CONCEPT_ID AS INGREDIENT_CONCEPT_ID + +FROM + [TARGET_CDMV5].[SCHEMA].DRUG_EXPOSURE d +INNER JOIN [TARGET_CDMV5].[SCHEMA].CONCEPT_ANCESTOR ca ON ca.DESCENDANT_CONCEPT_ID = d.DRUG_CONCEPT_ID +INNER JOIN [TARGET_CDMV5].[SCHEMA].CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCEPT_ID +WHERE c.VOCABULARY_ID = 'RxNorm' + AND c.CONCEPT_CLASS_ID = 'Ingredient'; + +/* / */ + +DROP TABLE IF EXISTS cteEndDates; + +/* / */ + +CREATE TEMP TABLE cteEndDates + +AS +SELECT + PERSON_ID + ,INGREDIENT_CONCEPT_ID + ,( EVENT_DATE + - 30) AS END_DATE -- unpad the end date + +FROM + ( + SELECT E1.PERSON_ID + ,E1.INGREDIENT_CONCEPT_ID + ,E1.EVENT_DATE + ,COALESCE(E1.START_ORDINAL, MAX(E2.START_ORDINAL)) START_ORDINAL + ,E1.OVERALL_ORD + FROM ( + SELECT PERSON_ID + ,INGREDIENT_CONCEPT_ID + ,EVENT_DATE + ,EVENT_TYPE + ,START_ORDINAL + ,ROW_NUMBER() OVER ( + PARTITION BY PERSON_ID + ,INGREDIENT_CONCEPT_ID ORDER BY EVENT_DATE + ,EVENT_TYPE + ) AS OVERALL_ORD -- this re-numbers the inner UNION so all rows are numbered ordered by the event date + FROM ( + -- select the start dates, assigning a row number to each + SELECT PERSON_ID + ,INGREDIENT_CONCEPT_ID + ,DRUG_EXPOSURE_START_DATE AS EVENT_DATE + ,0 AS EVENT_TYPE + ,ROW_NUMBER() OVER ( + PARTITION BY PERSON_ID + ,INGREDIENT_CONCEPT_ID ORDER BY DRUG_EXPOSURE_START_DATE + ) AS START_ORDINAL + FROM cteDrugTarget + + UNION ALL + + -- add the end dates with NULL as the row number, padding the end dates by 30 to allow a grace period for overlapping ranges. + SELECT PERSON_ID + ,INGREDIENT_CONCEPT_ID + ,( DRUG_EXPOSURE_END_DATE + 30) + ,1 AS EVENT_TYPE + ,NULL + FROM cteDrugTarget + ) RAWDATA + ) E1 + INNER JOIN ( + SELECT PERSON_ID + ,INGREDIENT_CONCEPT_ID + ,DRUG_EXPOSURE_START_DATE AS EVENT_DATE + ,ROW_NUMBER() OVER ( + PARTITION BY PERSON_ID + ,INGREDIENT_CONCEPT_ID ORDER BY DRUG_EXPOSURE_START_DATE + ) AS START_ORDINAL + 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 + GROUP BY E1.PERSON_ID + ,E1.INGREDIENT_CONCEPT_ID + ,E1.EVENT_DATE + ,E1.START_ORDINAL + ,E1.OVERALL_ORD + ) E +WHERE 2 * E.START_ORDINAL - E.OVERALL_ORD = 0; + +/* / */ + +DROP TABLE IF EXISTS cteDrugExpEnds; + +/* / */ + +CREATE TEMP TABLE cteDrugExpEnds + +AS +SELECT + d.PERSON_ID + ,d.INGREDIENT_CONCEPT_ID + ,d.DRUG_TYPE_CONCEPT_ID + ,d.DRUG_EXPOSURE_START_DATE + ,MIN(e.END_DATE) AS ERA_END_DATE + +FROM + cteDrugTarget d +INNER JOIN cteEndDates 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 + ,d.INGREDIENT_CONCEPT_ID + ,d.DRUG_TYPE_CONCEPT_ID + ,d.DRUG_EXPOSURE_START_DATE; + +/* / */ + +INSERT INTO [TARGET_CDMV5].[SCHEMA].drug_era +SELECT row_number() OVER ( + ORDER BY person_id + ) AS drug_era_id + ,person_id + ,INGREDIENT_CONCEPT_ID + ,min(DRUG_EXPOSURE_START_DATE) AS drug_era_start_date + ,ERA_END_DATE + ,COUNT(*) AS DRUG_EXPOSURE_COUNT + ,30 AS gap_days +FROM cteDrugExpEnds +GROUP BY person_id + ,INGREDIENT_CONCEPT_ID + ,drug_type_concept_id + ,ERA_END_DATE; + +/**** + +CONDITION ERA +Note: Eras derived from CONDITION_OCCURRENCE table, using 30d gap + + ****/ +DROP TABLE IF EXISTS condition_era_phase_1; + +/* / */ + +DROP TABLE IF EXISTS cteConditionTarget; + +/* / */ + +-- create base eras from the concepts found in condition_occurrence +CREATE TEMP TABLE cteConditionTarget + +AS +SELECT + co.PERSON_ID + ,co.condition_concept_id + ,co.CONDITION_START_DATE + ,COALESCE(co.CONDITION_END_DATE, ( CONDITION_START_DATE + 1)) AS CONDITION_END_DATE + +FROM + [TARGET_CDMV5].[SCHEMA].CONDITION_OCCURRENCE co; + +/* / */ + +DROP TABLE IF EXISTS cteCondEndDates; + +/* / */ + +CREATE TEMP TABLE cteCondEndDates + +AS +SELECT + PERSON_ID + ,CONDITION_CONCEPT_ID + ,( EVENT_DATE + - 30) AS END_DATE -- unpad the end date + +FROM + ( + SELECT E1.PERSON_ID + ,E1.CONDITION_CONCEPT_ID + ,E1.EVENT_DATE + ,COALESCE(E1.START_ORDINAL, MAX(E2.START_ORDINAL)) START_ORDINAL + ,E1.OVERALL_ORD + FROM ( + SELECT PERSON_ID + ,CONDITION_CONCEPT_ID + ,EVENT_DATE + ,EVENT_TYPE + ,START_ORDINAL + ,ROW_NUMBER() OVER ( + PARTITION BY PERSON_ID + ,CONDITION_CONCEPT_ID ORDER BY EVENT_DATE + ,EVENT_TYPE + ) AS OVERALL_ORD -- this re-numbers the inner UNION so all rows are numbered ordered by the event date + FROM ( + -- select the start dates, assigning a row number to each + SELECT PERSON_ID + ,CONDITION_CONCEPT_ID + ,CONDITION_START_DATE AS EVENT_DATE + ,- 1 AS EVENT_TYPE + ,ROW_NUMBER() OVER ( + PARTITION BY PERSON_ID + ,CONDITION_CONCEPT_ID ORDER BY CONDITION_START_DATE + ) AS START_ORDINAL + FROM cteConditionTarget + + UNION ALL + + -- pad the end dates by 30 to allow a grace period for overlapping ranges. + SELECT PERSON_ID + ,CONDITION_CONCEPT_ID + ,( CONDITION_END_DATE + 30) + ,1 AS EVENT_TYPE + ,NULL + FROM cteConditionTarget + ) RAWDATA + ) E1 + INNER JOIN ( + SELECT PERSON_ID + ,CONDITION_CONCEPT_ID + ,CONDITION_START_DATE AS EVENT_DATE + ,ROW_NUMBER() OVER ( + PARTITION BY PERSON_ID + ,CONDITION_CONCEPT_ID ORDER BY CONDITION_START_DATE + ) AS START_ORDINAL + 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 + GROUP BY E1.PERSON_ID + ,E1.CONDITION_CONCEPT_ID + ,E1.EVENT_DATE + ,E1.START_ORDINAL + ,E1.OVERALL_ORD + ) E +WHERE (2 * E.START_ORDINAL) - E.OVERALL_ORD = 0; + +/* / */ + +DROP TABLE IF EXISTS cteConditionEnds; + +/* / */ + +CREATE TEMP TABLE cteConditionEnds + +AS +SELECT + c.PERSON_ID + ,c.CONDITION_CONCEPT_ID + ,c.CONDITION_START_DATE + ,MIN(e.END_DATE) AS ERA_END_DATE + +FROM + cteConditionTarget c +INNER JOIN cteCondEndDates 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 + ,person_id + ,condition_concept_id + ,condition_era_start_date + ,condition_era_end_date + ,condition_occurrence_count + ) +SELECT row_number() OVER ( + ORDER BY person_id + ) AS condition_era_id + ,person_id + ,CONDITION_CONCEPT_ID + ,min(CONDITION_START_DATE) AS CONDITION_ERA_START_DATE + ,ERA_END_DATE AS CONDITION_ERA_END_DATE + ,COUNT(*) AS CONDITION_OCCURRENCE_COUNT +FROM cteConditionEnds +GROUP BY person_id + ,CONDITION_CONCEPT_ID + ,ERA_END_DATE; + +/**** + +QUALITY ASSURANCE OUTPUT + +Note: These queries are used to provide some basic stats around row counts between your V4 and V5 database + to ensure that all of the data has migrated as expected. + + ****/ + +DROP TABLE IF EXISTS v5_stats; + +/* / */ + +DROP TABLE IF EXISTS v4_stats; + +/* / */ + +-- Get the row counts for each table that is in scope for the migration +CREATE TEMP TABLE v4_stats + +AS +SELECT + * + +FROM + +( + SELECT '[SOURCE_CDMV4]' AS DBName, 'care_site' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].care_site + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'condition_era' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].condition_era + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'condition_occurrence' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].condition_occurrence + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'death' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].death + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'drug_cost' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].drug_cost + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'drug_era' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].drug_era + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'drug_exposure' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].drug_exposure + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'location' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].location + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'observation' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].observation + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'observation_period' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].observation_period + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'payer_plan_period' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].payer_plan_period + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'person' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].person + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'procedure_cost' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].procedure_cost + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'procedure_occurrence' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].procedure_occurrence + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'provider' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].provider + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'visit_occurrence' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].visit_occurrence +) v4_stats; + +/* / */ + +CREATE TEMP TABLE v5_stats + +AS +SELECT + * + +FROM + +( + SELECT '[TARGET_CDMV5]' AS DBName, 'care_site' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].care_site + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'condition_era' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].condition_era + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'condition_occurrence' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].condition_occurrence + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'death' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].death + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'device_exposure' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].device_exposure + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'drug_cost' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].drug_cost + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'drug_era' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].drug_era + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'drug_exposure' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].drug_exposure + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'location' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].location + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'measurement' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].measurement + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'observation' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].observation + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'observation_period' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].observation_period + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'payer_plan_period' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].payer_plan_period + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'person' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].person + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'procedure_cost' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].procedure_cost + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'procedure_occurrence' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].procedure_occurrence + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'provider' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].provider + UNION + 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 + 'Rowcounts for each database and table', + COALESCE(V4.DBName, 'None') v4_database_name, + v4.TableName v4_table_name, + v4.row_count v4_row_count, + COALESCE(v5.DBName, 'None') v5_database_name, + v5.TableName v5_table_name, + v5.row_count v5_row_count, + COALESCE(v5.row_count, 0) - COALESCE(v4.row_count, 0) row_count_change +from v4_stats v4 +full outer join v5_stats v5 ON v4.TableName = v5.TableName +order by v5.TableName; + +/* + * Determine how the vocabulary/domains helped to map from the V4 source + * tables to the V5 destinations + */ +DROP TABLE IF EXISTS classification_map; + +/* / */ + +CREATE TEMP TABLE classification_map + +AS +SELECT + * + +FROM + +( + SELECT 'Condition_Occurrence' TableName, COALESCE(LOWER(cm.domain_id), 'condition') domain_id, COUNT(*) row_count + FROM [SOURCE_CDMV4].[SCHEMA].Condition_Occurrence CO + LEFT JOIN concept_map CM ON co.condition_concept_id = cm.source_concept_id + GROUP BY COALESCE(LOWER(cm.domain_id), 'condition') + UNION + SELECT 'Drug_Exposure' TableName, COALESCE(LOWER(cm.domain_id), 'drug') domain_id, COUNT(*) row_count + FROM [SOURCE_CDMV4].[SCHEMA].Drug_Exposure de + LEFT JOIN concept_map CM ON de.drug_concept_id = cm.source_concept_id + GROUP BY COALESCE(LOWER(cm.domain_id), 'drug') + UNION + SELECT 'Observation' TableName, COALESCE(LOWER(cm.domain_id), 'observation') domain_id, COUNT(*) row_count + FROM [SOURCE_CDMV4].[SCHEMA].Observation o + LEFT JOIN concept_map CM ON o.observation_concept_id = cm.source_concept_id + GROUP BY COALESCE(LOWER(cm.domain_id), 'observation') + UNION + SELECT 'Procedure_Occurrence' TableName, COALESCE(LOWER(cm.domain_id), 'procedure') domain_id, COUNT(*) row_count + FROM [SOURCE_CDMV4].[SCHEMA].Procedure_Occurrence po + LEFT JOIN concept_map CM ON po.PROCEDURE_CONCEPT_ID = cm.source_concept_id + GROUP BY COALESCE(LOWER(cm.domain_id), 'procedure') +) A +ORDER by A.TableName, A.domain_id; + +/* / */ + +select * +from classification_map +order by tablename, domain_id; + +select domain_id, SUM(row_count) +from classification_map +group by domain_id +order by domain_id; \ No newline at end of file diff --git a/Version4 To Version5 Conversion/Sql Server PDW/OMOP CDMv4 to CDMv5 - Sql Server PDW.dsql b/Version4 To Version5 Conversion/Sql Server PDW/OMOP CDMv4 to CDMv5 - Sql Server PDW.dsql new file mode 100644 index 0000000..cbe26c2 --- /dev/null +++ b/Version4 To Version5 Conversion/Sql Server PDW/OMOP CDMv4 to CDMv5 - Sql Server PDW.dsql @@ -0,0 +1,2388 @@ +/********************************************************************************* +# Copyright 2015 Observational Health Data Sciences and Informatics +# +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +********************************************************************************/ +/******************************************************************************* + +PURPOSE: Use this script to convert your OMOP V4 common data model to CDM V5. + +last revised: 04 August 2015 +authors: Patrick Ryan, Chris Knoll, Anthony Sena + +!!!!!!!!!!!!!!!!!!!!! PLEASE READ THESE INSTRUCTIONS !!!!!!!!!!!!!!!!!!!!!!!!!!! + +This script was authored using OHDSI-SQL which will require you to run this +script through SqlRender to creat a version that is compatible with your target +RDBMS. We have pre-generated these scripts using SQL Render and have placed +them in folders for each RDBMS. Depending on which script you are viewing, your +instructions will be slightly different. + +General Assumptions +------------------- + +This script assumes that your V4 and V5 database are located on the same +RDBMS server. It also assumes that the V4 and V5 databases were created +using the standard data definition scripts for these databases. If you +altered your V4 database in any way, this script will likely require +some mo + +Getting Started +--------------- + +Before you can use this script, there are some prerequisites: + + 1. Create a target CDMv5 database on your database server using the + appropriate script from https://github.com/OHDSI/CommonDataModel + 2. Load VocabV5 into the target database/schema that will contain CDMv5 using + Athena: http://ohdsi.org/web/ATHENA + +OHDSI-SQL File Instructions +----------------------------- + + 1. Set parameter name of schema that contains CDMv4 instance + ([SOURCE_CDMV4], [SOURCE_CDMV4].[SCHEMA]) + 2. Set parameter name of schema that contains CDMv5 instance + ([TARGET_CDMV5], [TARGET_CDMV5].[SCHEMA]) + 3. Run this script through SqlRender to produce a script that will work in your + source dialect. SqlRender can be found here: https://github.com/OHDSI/SqlRender + 4. Run the script produced by SQL Render on your target RDBDMS. + + File Instructions +------------------------- + + 1. This script will hold a number of placeholders for your CDM V4 and CDMV5 + database/schema. In order to make this file work in your environment, you + should plan to do a global "FIND AND REPLACE" on this file 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: + + a. [SOURCE_CDMV4] + b. [SOURCE_CDMV4].[SCHEMA] + c. [TARGET_CDMV5] + d. [TARGET_CDMV5].[SCHEMA] + + 2. Run the resulting script on your target RDBDMS. + +*********************************************************************************/ +/* SCRIPT PARAMETERS */ + -- The CDMv4 database name + -- The CDMv4 database plus schema + -- The target CDMv5 database name + -- the target CDMv5 database plus schema + +USE [TARGET_CDMV5]; + +/* + * The #concept_map table will hold the mapping of source_concept_ids to target_concept_ids + * and their respective domain_ids. As a result, the results of this table will have + * some source_concept_ids that map to multiple target_concept_ids which is expected. + * + * In some of the conversion queries below, we will use the distinct values from the + * #concept_map table since our need in those instances is to understand the domain_id + * that will provide the destination table in the target V5 database. To make the code + * easier to read, we dervied a #concept_map_distinct table that holds the distinct + * source_concept_id and target domain_id. + * + * As of the dateof this script, the following domains contain source_concept_ids that + * map to multiple target_concept_ids: + * + * Condition + * Device + * Drug + * Measurement + * Observation + * Procedure + * Spec Anatomic Site + * + * Also, as of the date which this script was authored, no source_concept_ids map to multiple domains + */ +IF XACT_STATE() = 1 COMMIT; IF OBJECT_ID('tempdb..#concept_map', 'U') IS NOT NULL DROP TABLE #concept_map; + +/* / */ + +IF XACT_STATE() = 1 COMMIT; CREATE TABLE #concept_map + WITH (LOCATION = USER_DB, DISTRIBUTION = REPLICATE) AS +SELECT + concept_id AS source_concept_id + ,concept_id AS target_concept_id + ,domain_id AS domain_id + +FROM + [TARGET_CDMV5].[SCHEMA].concept +WHERE 1 = 0; + +/* / */ + +INSERT INTO #concept_map +--standard concepts +SELECT concept_id AS source_concept_id + ,concept_id AS target_concept_id + ,domain_id +FROM [TARGET_CDMV5].[SCHEMA].concept +WHERE standard_concept = 'S' + AND invalid_reason IS NULL + +UNION + +--concepts with 'map to' standard +SELECT DISTINCT c1.concept_id AS source_concept_id + ,c2.concept_id AS target_concept_id + ,c2.domain_id +FROM ( + SELECT concept_id + FROM [TARGET_CDMV5].[SCHEMA].concept + WHERE ( + ( + standard_concept <> 'S' + OR standard_concept IS NULL + ) + OR invalid_reason IS NOT NULL + ) + ) c1 +INNER JOIN [TARGET_CDMV5].[SCHEMA].concept_relationship cr1 ON c1.concept_id = cr1.concept_id_1 +INNER JOIN [TARGET_CDMV5].[SCHEMA].concept c2 ON cr1.concept_id_2 = c2.concept_id +WHERE c2.standard_concept = 'S' + AND c2.invalid_reason IS NULL + AND cr1.relationship_id IN ('Maps to') + AND cr1.invalid_reason IS NULL + +UNION + +--concepts without 'map to' standard with another non 'is a' relation to standard +SELECT DISTINCT c1.concept_id AS source_concept_id + ,c2.concept_id AS target_concept_id + ,c2.domain_id +FROM ( + SELECT A.concept_id + FROM [TARGET_CDMV5].[SCHEMA].concept A + LEFT JOIN ( + SELECT DISTINCT c1.concept_id + FROM ( + SELECT concept_id + FROM [TARGET_CDMV5].[SCHEMA].concept + WHERE ( + ( + standard_concept <> 'S' + OR standard_concept IS NULL + ) + OR invalid_reason IS NOT NULL + ) + ) c1 + INNER JOIN [TARGET_CDMV5].[SCHEMA].concept_relationship cr1 ON c1.concept_id = cr1.concept_id_1 + INNER JOIN [TARGET_CDMV5].[SCHEMA].concept c2 ON cr1.concept_id_2 = c2.concept_id + WHERE c2.standard_concept = 'S' + AND c2.invalid_reason IS NULL + AND cr1.relationship_id IN ('Maps to') + AND cr1.invalid_reason IS NULL + ) B ON A.concept_id = B.concept_id + WHERE ( + ( + A.standard_concept <> 'S' + OR A.standard_concept IS NULL + ) + OR A.invalid_reason IS NOT NULL + ) + AND B.concept_id IS NULL + ) c1 +INNER JOIN [TARGET_CDMV5].[SCHEMA].concept_relationship cr1 ON c1.concept_id = cr1.concept_id_1 +INNER JOIN [TARGET_CDMV5].[SCHEMA].concept c2 ON cr1.concept_id_2 = c2.concept_id +WHERE c2.standard_concept = 'S' + AND c2.invalid_reason IS NULL + AND cr1.relationship_id IN ( + 'RxNorm replaced by' + ,'SNOMED replaced by' + ,'UCUM replaced by' + ,'Concept replaced by' + ,'ICD9P replaced by' + ,'LOINC replaced by' + ,'Concept same_as to' + ,'Concept was_a to' + ,'Concept alt_to to' + ) + AND cr1.invalid_reason IS NULL + +UNION + +--concepts without 'map to' standard with 'is a' relation to standard +SELECT DISTINCT c1.concept_id AS source_concept_id + ,c2.concept_id AS target_concept_id + ,c2.domain_id +FROM ( + SELECT A.concept_id + FROM [TARGET_CDMV5].[SCHEMA].concept A + LEFT JOIN ( + SELECT DISTINCT c1.concept_id + FROM ( + SELECT concept_id + FROM [TARGET_CDMV5].[SCHEMA].concept + WHERE ( + ( + standard_concept <> 'S' + OR standard_concept IS NULL + ) + OR invalid_reason IS NOT NULL + ) + ) c1 + INNER JOIN [TARGET_CDMV5].[SCHEMA].concept_relationship cr1 ON c1.concept_id = cr1.concept_id_1 + INNER JOIN [TARGET_CDMV5].[SCHEMA].concept c2 ON cr1.concept_id_2 = c2.concept_id + WHERE c2.standard_concept = 'S' + AND c2.invalid_reason IS NULL + AND cr1.relationship_id IN ( + 'Maps to' + ,'RxNorm replaced by' + ,'SNOMED replaced by' + ,'UCUM replaced by' + ,'Concept replaced by' + ,'ICD9P replaced by' + ,'LOINC replaced by' + ,'Concept same_as to' + ,'Concept was_a to' + ,'Concept alt_to to' + ) + AND cr1.invalid_reason IS NULL + ) B ON A.concept_id = B.concept_id + WHERE ( + ( + standard_concept <> 'S' + OR standard_concept IS NULL + ) + OR invalid_reason IS NOT NULL + ) + AND B.concept_id IS NULL + ) c1 +INNER JOIN [TARGET_CDMV5].[SCHEMA].concept_relationship cr1 ON c1.concept_id = cr1.concept_id_1 +INNER JOIN [TARGET_CDMV5].[SCHEMA].concept c2 ON cr1.concept_id_2 = c2.concept_id +WHERE c2.standard_concept = 'S' + AND c2.invalid_reason IS NULL + AND cr1.relationship_id IN ('Is a') + AND cr1.invalid_reason IS NULL; + +IF XACT_STATE() = 1 COMMIT; IF OBJECT_ID('tempdb..#concept_map_distinct', 'U') IS NOT NULL DROP TABLE #concept_map_distinct; + +/* / */ + +IF XACT_STATE() = 1 COMMIT; CREATE TABLE #concept_map_distinct + WITH (LOCATION = USER_DB, DISTRIBUTION = REPLICATE) AS +SELECT + source_concept_id + ,domain_id + ,COUNT(*) AS targetConceptCount + +FROM + #concept_map +WHERE 1 = 0 +GROUP BY source_concept_id + ,domain_id; + +/* / */ + +INSERT INTO #concept_map_distinct +SELECT source_concept_id + ,domain_id + ,COUNT(*) +FROM #concept_map +GROUP BY source_concept_id + ,domain_id; + +IF XACT_STATE() = 1 COMMIT; IF OBJECT_ID('[TARGET_CDMV5].[SCHEMA].ETL_WARNINGS', 'U') IS NOT NULL DROP TABLE [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS; + +/* / */ + +IF XACT_STATE() = 1 COMMIT; CREATE TABLE [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE VARCHAR(4000)) +WITH (DISTRIBUTION = REPLICATE); +/* / */ + +/**** + +CDM_SOURCE + + ****/ +INSERT INTO [TARGET_CDMV5].[SCHEMA].cdm_source ( + cdm_source_name + ,cdm_version + ,vocabulary_version + ,cdm_release_date + ) +SELECT '[TARGET_CDMV5]' + ,'V5' + ,v.vocabulary_version + ,getDate() +FROM [TARGET_CDMV5].[SCHEMA].vocabulary v +WHERE vocabulary_id = 'Vocabulary'; + +/**** + +LOCATION + + ****/ +INSERT INTO [TARGET_CDMV5].[SCHEMA].location +SELECT location_id + ,address_1 + ,address_2 + ,city + ,STATE + ,zip + ,county + ,location_source_value +FROM [SOURCE_CDMV4].[SCHEMA].LOCATION; + +/**** + +CARE_SITE + + ****/ +INSERT INTO [TARGET_CDMV5].[SCHEMA].care_site +SELECT care_site_id + ,cast(NULL AS VARCHAR(255)) AS care_site_name + ,place_of_service_concept_id + ,location_id + ,care_site_source_value + ,place_of_service_source_value +FROM [SOURCE_CDMV4].[SCHEMA].CARE_SITE; + +/**** + +Provider + +****/ +INSERT INTO [TARGET_CDMV5].[SCHEMA].provider +SELECT provider_id + ,cast(NULL AS VARCHAR(255)) AS provider_name + ,NPI + ,DEA + ,specialty_concept_id + ,care_site_id + ,cast(NULL AS INT) AS year_of_birth + ,cast(NULL AS INT) AS gender_concept_id + ,provider_source_value + ,specialty_source_value + ,0 AS specialty_source_concept_id + ,cast(NULL AS VARCHAR(50)) AS gender_source_value + ,cast(NULL AS INT) AS gender_source_concept_id +FROM [SOURCE_CDMV4].[SCHEMA].provider; + +/**** + + PERSON + + ****/ +INSERT INTO [TARGET_CDMV5].[SCHEMA].person +SELECT person_id + ,coalesce(gender.target_concept_id, 0) AS gender_concept_id + ,year_of_birth + ,month_of_birth + ,day_of_birth + ,CAST(NULL AS VARCHAR(10)) time_of_birth + ,coalesce(race.target_concept_id, 0) AS race_concept_id + ,coalesce(ethnicity.target_concept_id, 0) AS ethnicity_concept_id + ,location_id + ,provider_id + ,care_site_id + ,person_source_value + ,gender_source_value + ,CAST(NULL AS INT) gender_source_concept_id + ,CAST(NULL AS INT) race_source_value + ,CAST(NULL AS INT) race_source_concept_id + ,ethnicity_source_value + ,CAST(NULL AS INT) ethnicity_source_concept_id +FROM [SOURCE_CDMV4].[SCHEMA].PERSON p +LEFT JOIN #concept_map gender ON LOWER(gender.DOMAIN_ID) IN ('gender') + AND p.gender_concept_id = gender.source_concept_id +LEFT JOIN #concept_map race ON LOWER(race.DOMAIN_ID) IN ('race') + AND p.race_concept_id = race.source_concept_id +LEFT JOIN #concept_map ethnicity ON LOWER(ethnicity.DOMAIN_ID) IN ('ethnicity') + AND p.ETHNICITY_CONCEPT_ID = ethnicity.source_concept_id; + +INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) +SELECT 'PERSON: ' + CAST(NUM_INVALID_RECORDS AS VARCHAR) + ' records in the source CDMv4 database have invalid GENDER_CONCEPT_ID' +FROM ( + SELECT COUNT(PERSON_ID) AS NUM_INVALID_RECORDS + FROM [SOURCE_CDMV4].[SCHEMA].PERSON + WHERE GENDER_CONCEPT_ID NOT IN ( + SELECT CONCEPT_ID + FROM [TARGET_CDMV5].[SCHEMA].CONCEPT + WHERE CONCEPT_ID = 0 + OR ( + STANDARD_CONCEPT = 'S' + AND LOWER(DOMAIN_ID) IN ('gender') + ) + ) + HAVING COUNT(PERSON_ID) > 0 + ) warn; + +INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) +SELECT 'PERSON: ' + CAST(NUM_INVALID_RECORDS AS VARCHAR) + ' records in the source CDMv4 database have invalid RACE_CONCEPT_ID' +FROM ( + SELECT COUNT(PERSON_ID) AS NUM_INVALID_RECORDS + FROM [SOURCE_CDMV4].[SCHEMA].PERSON + WHERE RACE_CONCEPT_ID IS NOT NULL + AND RACE_CONCEPT_ID NOT IN ( + SELECT CONCEPT_ID + FROM [TARGET_CDMV5].[SCHEMA].CONCEPT + WHERE CONCEPT_ID = 0 + OR ( + STANDARD_CONCEPT = 'S' + AND LOWER(DOMAIN_ID) IN ('race') + ) + ) + HAVING COUNT(PERSON_ID) > 0 + ) warn; + +INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) +SELECT 'PERSON: ' + CAST(NUM_INVALID_RECORDS AS VARCHAR) + ' records in the source CDMv4 database have invalid ETHNICITY_CONCEPT_ID' +FROM ( + SELECT COUNT(PERSON_ID) AS NUM_INVALID_RECORDS + FROM [SOURCE_CDMV4].[SCHEMA].PERSON + WHERE ETHNICITY_CONCEPT_ID IS NOT NULL + AND ETHNICITY_CONCEPT_ID NOT IN ( + SELECT CONCEPT_ID + FROM [TARGET_CDMV5].[SCHEMA].CONCEPT + WHERE CONCEPT_ID = 0 + OR ( + STANDARD_CONCEPT = 'S' + AND LOWER(DOMAIN_ID) IN ('ethnicity') + ) + ) + HAVING COUNT(PERSON_ID) > 0 + ) warn; + +/**** + + OBSERVATION_PERIOD + + ****/ +INSERT INTO [TARGET_CDMV5].[SCHEMA].observation_period +SELECT observation_period_id + ,person_id + ,observation_period_start_date + ,observation_period_end_date + ,44814722 AS period_type_concept_id +FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION_PERIOD; + +/**** + + DEATH + + ****/ +INSERT INTO [TARGET_CDMV5].[SCHEMA].death +SELECT person_id + ,death_date + ,COALESCE(death_type_concept_id, 0) AS death_type_concept_id + ,cause_of_death_concept_id AS cause_concept_id + ,cause_of_death_source_value AS cause_source_value + ,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'); + +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' +FROM ( + SELECT COUNT(PERSON_ID) AS NUM_INVALID_RECORDS + FROM [SOURCE_CDMV4].[SCHEMA].DEATH + WHERE DEATH_TYPE_CONCEPT_ID NOT IN ( + SELECT CONCEPT_ID + FROM [TARGET_CDMV5].[SCHEMA].CONCEPT + WHERE CONCEPT_ID = 0 + OR ( + STANDARD_CONCEPT = 'S' + AND LOWER(DOMAIN_ID) IN ('death type') + ) + ) + HAVING COUNT(PERSON_ID) > 0 + ) warn; + +/**** + + VISIT_OCCURRENCE + + ****/ +INSERT INTO [TARGET_CDMV5].[SCHEMA].visit_occurrence +SELECT visit_occurrence_id + ,person_id + ,COALESCE(cm1.target_concept_id, 0) AS visit_concept_id + ,visit_start_date + ,CAST(NULL AS VARCHAR(10)) visit_start_time + ,visit_end_date + ,CAST(NULL AS VARCHAR(10)) visit_end_time + ,44818517 AS visit_type_concept_id + ,CAST(NULL AS INT) provider_id + ,care_site_id + ,place_of_service_source_value AS visit_source_value + ,CAST(NULL AS INT) visit_source_concept_id +FROM [SOURCE_CDMV4].[SCHEMA].VISIT_OCCURRENCE +LEFT JOIN #concept_map cm1 ON VISIT_OCCURRENCE.PLACE_OF_SERVICE_CONCEPT_ID = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('visit'); + +INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) +SELECT 'VISIT_OCCURRENCE: ' + CAST(NUM_INVALID_RECORDS AS VARCHAR) + ' records in the source CDMv4 database have invalid VISIT_CONCEPT_ID (from the CDMv4 PLACE_OF_SERVICE_CONCEPT_ID field)' +FROM ( + SELECT COUNT(PERSON_ID) AS NUM_INVALID_RECORDS + FROM [SOURCE_CDMV4].[SCHEMA].VISIT_OCCURRENCE + WHERE PLACE_OF_SERVICE_CONCEPT_ID NOT IN ( + SELECT CONCEPT_ID + FROM [TARGET_CDMV5].[SCHEMA].CONCEPT + WHERE CONCEPT_ID = 0 + OR ( + STANDARD_CONCEPT = 'S' + AND LOWER(DOMAIN_ID) IN ('visit') + ) + ) + HAVING COUNT(PERSON_ID) > 0 + ) warn; + +/**** + + PROCEDURE_OCCURRENCE + + ****/ +IF XACT_STATE() = 1 COMMIT; IF OBJECT_ID('tempdb..#po_map', 'U') IS NOT NULL DROP TABLE #po_map; + +/* / */ + +IF XACT_STATE() = 1 COMMIT; CREATE TABLE #po_map + WITH (LOCATION = USER_DB, DISTRIBUTION = HASH(person_id)) AS +SELECT + po.procedure_occurrence_id + ,po. person_id, po.procedure_concept_id + ,po.procedure_date + ,po.procedure_type_concept_id + ,po.modifier_concept_id + ,po.quantity + ,po.provider_id + ,po.visit_occurrence_id + ,po.procedure_source_value + ,po.procedure_source_concept_id + ,po.qualifier_source_value + ,de.drug_exposure_id AS origional_drug_id + +FROM + [TARGET_CDMV5].[SCHEMA].procedure_occurrence po +LEFT JOIN [TARGET_CDMV5].[SCHEMA].drug_exposure de ON 1 = 0 +WHERE 0 = 1; + +/* / */ + +--find valid procedures from procedure table +INSERT INTO #po_map +SELECT procedure_occurrence_id + ,person_id + ,COALESCE(cm1.target_concept_id, 0) AS procedure_concept_id + ,procedure_date + ,COALESCE(cm2.target_concept_id, 0) AS procedure_type_concept_id + ,CAST(NULL AS INT) AS modifier_concept_id + ,CAST(NULL AS INT) AS quantity + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,procedure_source_value + ,CAST(NULL AS INT) AS procedure_source_concept_id + ,NULL AS qualifier_source_value + ,CAST(NULL AS INT) AS origional_drug_id +FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE +INNER JOIN #concept_map cm1 ON PROCEDURE_OCCURRENCE.PROCEDURE_CONCEPT_ID = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('procedure') +INNER JOIN #concept_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 #concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id + AND LOWER(cm2.domain_id) IN ('procedure type') +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 + +UNION ALL + +-- All procedures that did not map to a standard concept in V4 should also carry over to V5 +SELECT procedure_occurrence_id + ,person_id + ,procedure_concept_id + ,procedure_date + ,procedure_type_concept_id + ,CAST(NULL AS INT) AS modifier_concept_id + ,CAST(NULL AS INT) AS quantity + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,procedure_source_value + ,CAST(NULL AS INT) procedure_source_concept_id + ,NULL qualifier_source_value + ,CAST(NULL AS INT) AS origional_drug_id +FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE +WHERE procedure_concept_id = 0 + +UNION ALL + +-- 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 + ,procedure_date + ,COALESCE(cm2.target_concept_id, 0) AS procedure_type_concept_id + ,CAST(NULL AS INT) AS modifier_concept_id + ,CAST(NULL AS INT) AS quantity + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,procedure_source_value + ,CAST(NULL AS INT) procedure_source_concept_id + ,NULL qualifier_source_value + ,CAST(NULL AS INT) AS origional_drug_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') +WHERE procedure_concept_id <> 0 + AND cm1.domain_id IS NULL + +UNION ALL + +SELECT CASE + WHEN MAXROW.MAXROWID IS NULL + THEN 0 + ELSE MAXROW.MAXROWID + END + row_number() OVER ( + ORDER BY OCCURRENCE_ID + ) AS procedure_occurrence_id + ,person_id + ,procedure_concept_id + ,procedure_date + ,procedure_type_concept_id + ,modifier_concept_id + ,quantity + ,provider_id + ,visit_occurrence_id + ,procedure_source_value + ,procedure_source_concept_id + ,qualifier_source_value + ,origional_drug_id +FROM ( + --find valid procedures from procedure table that map to more than 1 + --target concept in V5 + SELECT person_id + ,COALESCE(cm1.target_concept_id, 0) AS procedure_concept_id + ,procedure_date + ,COALESCE(cm2.target_concept_id, 0) AS procedure_type_concept_id + ,CAST(NULL AS INT) AS modifier_concept_id + ,CAST(NULL AS INT) AS quantity + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,procedure_source_value + ,CAST(NULL AS INT) procedure_source_concept_id + ,NULL qualifier_source_value + ,CAST(NULL AS INT) AS origional_drug_id + ,CAST(NULL AS INT) AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE + INNER JOIN #concept_map cm1 ON PROCEDURE_OCCURRENCE.PROCEDURE_CONCEPT_ID = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('procedure') + INNER JOIN #concept_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 #concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id + AND LOWER(cm2.domain_id) IN ('procedure type') + + UNION ALL + + --find procedures that were previously classified as condition + SELECT person_id + ,cm1.target_concept_id AS procedure_concept_id + ,condition_start_date AS procedure_date + ,0 AS procedure_type_concept_id + ,CAST(NULL AS INT) AS modifier_concept_id + ,CAST(NULL AS INT) AS quantity + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,condition_source_value AS procedure_source_value + ,CAST(NULL AS INT) AS procedure_source_concept_id + ,NULL AS qualifier_source_value + ,CAST(NULL AS INT) AS origional_drug_id + ,condition_occurrence_id AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE + INNER JOIN #concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('procedure') + + UNION ALL + + --find procedures that were previously classified as drug + SELECT person_id + ,cm1.target_concept_id AS procedure_concept_id + ,drug_exposure_start_date AS procedure_date + ,0 AS procedure_type_concept_id + ,CAST(NULL AS INT) AS modifier_concept_id + ,CAST(NULL AS INT) AS quantity + ,prescribing_provider_id AS provider_id + ,visit_occurrence_id + ,drug_source_value AS procedure_source_value + ,CAST(NULL AS INT) AS procedure_source_concept_id + ,NULL AS qualifier_source_value + ,drug_exposure_id AS origional_drug_id + ,drug_exposure_id AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE + INNER JOIN #concept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('procedure') + --find procedures that were previously classified as observation + + UNION ALL + + SELECT person_id + ,cm1.target_concept_id AS procedure_concept_id + ,observation_date AS procedure_date + ,0 AS procedure_type_concept_id + ,CAST(NULL AS INT) AS modifier_concept_id + ,CAST(NULL AS INT) AS quantity + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,observation_source_value AS procedure_source_value + ,CAST(NULL AS INT) AS procedure_source_concept_id + ,NULL AS qualifier_source_value + ,CAST(NULL AS INT) AS origional_drug_id + ,OBSERVATION_ID AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION + INNER JOIN #concept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('procedure') + ) OTHERS + ,( + SELECT MAX(PROCEDURE_OCCURRENCE_ID) AS MAXROWID + FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE + ) MAXROW; + +INSERT INTO [TARGET_CDMV5].[SCHEMA].procedure_occurrence ( + procedure_occurrence_id + ,person_id + ,procedure_concept_id + ,procedure_date + ,procedure_type_concept_id + ,modifier_concept_id + ,quantity + ,provider_id + ,visit_occurrence_id + ,procedure_source_value + ,procedure_source_concept_id + ,qualifier_source_value + ) +SELECT procedure_occurrence_id + ,person_id + ,procedure_concept_id + ,procedure_date + ,procedure_type_concept_id + ,modifier_concept_id + ,quantity + ,provider_id + ,visit_occurrence_id + ,procedure_source_value + ,procedure_source_concept_id + ,qualifier_source_value +FROM #po_map; + +--warnings of invalid records +INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) +SELECT 'PROCEDURE_OCCURRENCE: ' + CAST(NUM_INVALID_RECORDS AS VARCHAR) + ' records in the source CDMv4 database have invalid PROCOEDURE_CONCEPT_ID' +FROM ( + SELECT COUNT(PERSON_ID) AS NUM_INVALID_RECORDS + FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE + WHERE PROCEDURE_CONCEPT_ID NOT IN ( + SELECT CONCEPT_ID + FROM [TARGET_CDMV5].[SCHEMA].CONCEPT + WHERE CONCEPT_ID = 0 + OR STANDARD_CONCEPT = 'S' + ) + HAVING COUNT(PERSON_ID) > 0 + ) warn; + +INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) +SELECT 'PROCEDURE_OCCURRENCE: ' + CAST(NUM_INVALID_RECORDS AS VARCHAR) + ' records in the source CDMv4 database have invalid PROCOEDURE_TYPE_CONCEPT_ID' +FROM ( + SELECT COUNT(PERSON_ID) AS NUM_INVALID_RECORDS + FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE + WHERE PROCEDURE_TYPE_CONCEPT_ID NOT IN ( + SELECT CONCEPT_ID + FROM [TARGET_CDMV5].[SCHEMA].CONCEPT + WHERE CONCEPT_ID = 0 + OR ( + STANDARD_CONCEPT = 'S' + AND LOWER(DOMAIN_ID) IN ('procedure type') + ) + ) + HAVING COUNT(PERSON_ID) > 0 + ) warn; + +/**** + + DRUG_EXPOSURE + + ****/ +--find valid drugs from drug_exposure table +IF XACT_STATE() = 1 COMMIT; IF OBJECT_ID('tempdb..#drgexp_map', 'U') IS NOT NULL DROP TABLE #drgexp_map; + +/* / */ + +IF XACT_STATE() = 1 COMMIT; CREATE TABLE #drgexp_map + WITH (LOCATION = USER_DB, DISTRIBUTION = HASH(person_id)) AS +SELECT + de.drug_exposure_id + ,de. person_id, de.drug_concept_id + ,de.drug_exposure_start_date + ,de.drug_exposure_end_date + ,de.drug_type_concept_id + ,de.stop_reason + ,de.refills + ,de.quantity + ,de.days_supply + ,de.sig + ,de.route_concept_id + ,de.effective_drug_dose + ,de.dose_unit_concept_id + ,de.lot_number + ,de.provider_id + ,de.visit_occurrence_id + ,de.drug_source_value + ,de.drug_source_concept_id + ,de.route_source_value + ,de.dose_unit_source_value + ,po.procedure_occurrence_id AS origional_procedure_id + +FROM + [TARGET_CDMV5].[SCHEMA].drug_exposure de +LEFT JOIN [TARGET_CDMV5].[SCHEMA].procedure_occurrence po ON 1 = 0 +WHERE 0 = 1; + +/* / */ + +INSERT INTO #drgexp_map +SELECT drug_exposure_id + ,person_id + ,COALESCE(cm1.target_concept_id, 0) AS drug_concept_id + ,drug_exposure_start_date + ,drug_exposure_end_date + ,COALESCE(cm2.target_concept_id, 0) drug_type_concept_id + ,stop_reason + ,refills + ,quantity + ,days_supply + ,sig + ,CAST(NULL AS INT) AS route_concept_id + ,CAST(NULL AS FLOAT) AS effective_drug_dose + ,CAST(NULL AS INT) AS dose_unit_concept_id + ,NULL AS lot_number + ,prescribing_provider_id AS provider_id + ,visit_occurrence_id + ,drug_source_value + ,CAST(NULL AS INT) AS drug_source_concept_id + ,NULL AS route_source_value + ,NULL AS dose_unit_source_value + ,CAST(NULL AS INT) AS origional_procedure_id +FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE +INNER JOIN #concept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('drug') +INNER JOIN #concept_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 #concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id + AND LOWER(cm2.domain_id) IN ('drug type') +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 +WHERE drug_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4 + +UNION ALL + +-- All drug exposures that did not map to a standard concept in V4 should also carry over to V5 +SELECT drug_exposure_id + ,person_id + ,drug_concept_id + ,drug_exposure_start_date + ,drug_exposure_end_date + ,drug_type_concept_id + ,stop_reason + ,refills + ,quantity + ,days_supply + ,sig + ,CAST(NULL AS INT) AS route_concept_id + ,CAST(NULL AS FLOAT) AS effective_drug_dose + ,CAST(NULL AS INT) AS dose_unit_concept_id + ,NULL AS lot_number + ,prescribing_provider_id AS provider_id + ,visit_occurrence_id + ,drug_source_value + ,CAST(NULL AS INT) AS drug_source_concept_id + ,NULL AS route_source_value + ,NULL AS dose_unit_source_value + ,CAST(NULL AS INT) AS origional_procedure_id +FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE +WHERE drug_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 +SELECT drug_exposure_id + ,person_id + ,0 + ,drug_exposure_start_date + ,drug_exposure_end_date + ,COALESCE(cm2.target_concept_id, 0) drug_type_concept_id + ,stop_reason + ,refills + ,quantity + ,days_supply + ,sig + ,CAST(NULL AS INT) AS route_concept_id + ,CAST(NULL AS FLOAT) AS effective_drug_dose + ,CAST(NULL AS INT) AS dose_unit_concept_id + ,NULL AS lot_number + ,prescribing_provider_id AS provider_id + ,visit_occurrence_id + ,drug_source_value + ,CAST(NULL AS INT) AS drug_source_concept_id + ,NULL AS route_source_value + ,NULL AS dose_unit_source_value + ,CAST(NULL AS INT) AS origional_procedure_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') +WHERE drug_concept_id <> 0 + AND cm1.domain_id IS NULL + +UNION ALL + +SELECT CASE + WHEN MAXROW.MAXROWID IS NULL + THEN 0 + ELSE MAXROW.MAXROWID + END + row_number() OVER ( + ORDER BY OCCURRENCE_ID + ) AS drug_exposure_id + ,person_id + ,drug_concept_id + ,drug_exposure_start_date + ,drug_exposure_end_date + ,drug_type_concept_id + ,stop_reason + ,refills + ,quantity + ,days_supply + ,sig + ,route_concept_id + ,effective_drug_dose + ,dose_unit_concept_id + ,lot_number + ,provider_id + ,visit_occurrence_id + ,drug_source_value + ,drug_source_concept_id + ,route_source_value + ,dose_unit_source_value + ,origional_procedure_id +FROM ( + --find valid drugs from drug_exposure table that map to > 1 target concept + SELECT person_id + ,COALESCE(cm1.target_concept_id, 0) AS drug_concept_id + ,drug_exposure_start_date + ,drug_exposure_end_date + ,COALESCE(cm2.target_concept_id, 0) drug_type_concept_id + ,stop_reason + ,refills + ,quantity + ,days_supply + ,sig + ,CAST(NULL AS INT) AS route_concept_id + ,CAST(NULL AS FLOAT) AS effective_drug_dose + ,CAST(NULL AS INT) AS dose_unit_concept_id + ,NULL AS lot_number + ,prescribing_provider_id AS provider_id + ,visit_occurrence_id + ,drug_source_value + ,CAST(NULL AS INT) AS drug_source_concept_id + ,NULL AS route_source_value + ,NULL AS dose_unit_source_value + ,CAST(NULL AS INT) AS origional_procedure_id + ,CAST(NULL AS INT) AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE + INNER JOIN #concept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('drug') + INNER JOIN #concept_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 #concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id + AND LOWER(cm2.domain_id) IN ('drug type') + + UNION ALL + + --find drugs that were previously classified as condition + SELECT person_id + ,cm1.target_concept_id AS drug_concept_id + ,condition_start_date AS drug_exposure_start_date + ,NULL AS drug_exposure_end_date + ,0 AS drug_type_concept_id + ,NULL AS stop_reason + ,CAST(NULL AS INT) AS refills + ,CAST(NULL AS FLOAT) AS quantity + ,CAST(NULL AS INT) AS days_supply + ,NULL AS sig + ,CAST(NULL AS INT) AS route_concept_id + ,CAST(NULL AS FLOAT) AS effective_drug_dose + ,CAST(NULL AS INT) AS dose_unit_concept_id + ,NULL AS lot_number + ,CAST(NULL AS INT) AS provider_id + ,visit_occurrence_id + ,condition_source_value AS drug_source_value + ,CAST(NULL AS INT) AS drug_source_concept_id + ,NULL AS route_source_value + ,NULL AS dose_unit_source_value + ,CAST(NULL AS INT) AS origional_procedure_id + ,condition_occurrence_id AS occurrence_id + FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE + INNER JOIN #concept_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 + + UNION ALL + + SELECT person_id + ,cm1.target_concept_id AS drug_concept_id + ,procedure_date AS drug_exposure_start_date + ,CAST(NULL AS DATE) AS drug_exposure_end_date + ,0 AS drug_type_concept_id + ,NULL AS stop_reason + ,CAST(NULL AS INT) AS refills + ,CAST(NULL AS FLOAT) AS quantity + ,CAST(NULL AS INT) AS days_supply + ,NULL AS sig + ,CAST(NULL AS INT) AS route_concept_id + ,CAST(NULL AS FLOAT) AS effective_drug_dose + ,CAST(NULL AS INT) AS dose_unit_concept_id + ,NULL AS lot_number + ,CAST(NULL AS INT) AS provider_id + ,visit_occurrence_id + ,procedure_source_value AS drug_source_value + ,CAST(NULL AS INT) AS drug_source_concept_id + ,NULL AS route_source_value + ,NULL AS dose_unit_source_value + ,procedure_occurrence_id AS origional_procedure_id + ,procedure_occurrence_id AS occurrence_id + FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE + INNER JOIN #concept_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 + + UNION ALL + + SELECT person_id + ,cm1.target_concept_id AS drug_concept_id + ,observation_date AS drug_exposure_start_date + ,CAST(NULL AS DATE) AS drug_exposure_end_date + ,0 AS drug_type_concept_id + ,NULL AS stop_reason + ,CAST(NULL AS INT) AS refills + ,CAST(NULL AS FLOAT) AS quantity + ,CAST(NULL AS INT) AS days_supply + ,NULL AS sig + ,CAST(NULL AS INT) AS route_concept_id + ,CAST(NULL AS FLOAT) AS effective_drug_dose + ,CAST(NULL AS INT) AS dose_unit_concept_id + ,NULL AS lot_number + ,CAST(NULL AS INT) AS provider_id + ,visit_occurrence_id + ,observation_source_value AS drug_source_value + ,CAST(NULL AS INT) AS drug_source_concept_id + ,NULL AS route_source_value + ,NULL AS dose_unit_source_value + ,CAST(NULL AS INT) AS origional_procedure_id + ,observation_id AS occurrence_id + FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION + INNER JOIN #concept_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; + +INSERT INTO [TARGET_CDMV5].[SCHEMA].drug_exposure ( + drug_exposure_id + ,person_id + ,drug_concept_id + ,drug_exposure_start_date + ,drug_exposure_end_date + ,drug_type_concept_id + ,stop_reason + ,refills + ,quantity + ,days_supply + ,sig + ,route_concept_id + ,effective_drug_dose + ,dose_unit_concept_id + ,lot_number + ,provider_id + ,visit_occurrence_id + ,drug_source_value + ,drug_source_concept_id + ,route_source_value + ,dose_unit_source_value + ) +SELECT drug_exposure_id + ,person_id + ,drug_concept_id + ,drug_exposure_start_date + ,drug_exposure_end_date + ,drug_type_concept_id + ,stop_reason + ,refills + ,quantity + ,days_supply + ,sig + ,route_concept_id + ,effective_drug_dose + ,dose_unit_concept_id + ,lot_number + ,provider_id + ,visit_occurrence_id + ,drug_source_value + ,drug_source_concept_id + ,route_source_value + ,dose_unit_source_value +FROM #drgexp_map; + +--warnings of invalid records +INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) +SELECT 'DRUG_EXPOSURE: ' + CAST(NUM_INVALID_RECORDS AS VARCHAR) + ' records in the source CDMv4 database have invalid DRUG_CONCEPT_ID' +FROM ( + SELECT COUNT(PERSON_ID) AS NUM_INVALID_RECORDS + FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE + WHERE DRUG_CONCEPT_ID NOT IN ( + SELECT CONCEPT_ID + FROM [TARGET_CDMV5].[SCHEMA].CONCEPT + WHERE CONCEPT_ID = 0 + OR STANDARD_CONCEPT = 'S' + ) + HAVING COUNT(PERSON_ID) > 0 + ) warn; + +INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) +SELECT 'DRUG_EXPOSURE: ' + CAST(NUM_INVALID_RECORDS AS VARCHAR) + ' records in the source CDMv4 database have invalid DRUG_TYPE_CONCEPT_ID' +FROM ( + SELECT COUNT(PERSON_ID) AS NUM_INVALID_RECORDS + FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE + WHERE DRUG_TYPE_CONCEPT_ID NOT IN ( + SELECT CONCEPT_ID + FROM [TARGET_CDMV5].[SCHEMA].CONCEPT + WHERE CONCEPT_ID = 0 + OR ( + STANDARD_CONCEPT = 'S' + AND LOWER(DOMAIN_ID) IN ('drug type') + ) + ) + HAVING COUNT(PERSON_ID) > 0 + ) warn; + +/**** + + CONDITION_OCCURRENCE + + ****/ +--find valid conditions from condition_occurrence table +INSERT INTO [TARGET_CDMV5].[SCHEMA].condition_occurrence +SELECT condition_occurrence_id + ,person_id + ,COALESCE(cm1.target_concept_id, 0) AS condition_concept_id + ,condition_start_date + ,condition_end_date + ,COALESCE(cm2.target_concept_id, 0) AS condition_type_concept_id + ,stop_reason + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,condition_source_value + ,CAST(NULL AS INT) condition_source_concept_id +FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE +INNER JOIN #concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('condition') +INNER JOIN #concept_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 #concept_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 + +UNION ALL + +-- All conditions that did not map to a standard concept in V4 should also carry over to V5 +SELECT condition_occurrence_id + ,person_id + ,condition_concept_id + ,condition_start_date + ,condition_end_date + ,COALESCE(condition_type_concept_id, 0) AS condition_type_concept_id + ,stop_reason + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,condition_source_value + ,CAST(NULL AS INT) condition_source_concept_id +FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE +WHERE condition_concept_id = 0 + +UNION ALL + +-- All conditions that do not map to a standard concept in V5 should also carry over with condition_concept_id = 0 +SELECT condition_occurrence_id + ,person_id + ,0 AS condition_concept_id + ,condition_start_date + ,condition_end_date + ,COALESCE(cm2.target_concept_id, 0) AS condition_type_concept_id + ,stop_reason + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,condition_source_value + ,CAST(NULL AS INT) condition_source_concept_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') +WHERE condition_concept_id <> 0 + AND cm1.domain_id IS NULL + +UNION ALL + +SELECT CASE + WHEN MAXROW.MAXROWID IS NULL + THEN 0 + ELSE MAXROW.MAXROWID + END + row_number() OVER ( + ORDER BY OCCURRENCE_ID + ) AS drug_exposure_id + ,person_id + ,condition_concept_id + ,condition_start_date + ,condition_end_date + ,condition_type_concept_id + ,stop_reason + ,provider_id + ,visit_occurrence_id + ,condition_source_value + ,condition_source_concept_id +FROM ( + --find valid conditions from condition_occurrence table that map to > 1 target concept + SELECT person_id + ,COALESCE(cm1.target_concept_id, 0) AS condition_concept_id + ,condition_start_date + ,condition_end_date + ,COALESCE(cm2.target_concept_id, 0) AS condition_type_concept_id + ,stop_reason + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,condition_source_value + ,CAST(NULL AS INT) condition_source_concept_id + ,NULL AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE + INNER JOIN #concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('condition') + INNER JOIN #concept_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 #concept_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 + + UNION ALL + + --find conditions that were previously classified as procedure + SELECT person_id + ,cm1.target_concept_id AS condition_concept_id + ,procedure_date AS condition_start_date + ,NULL AS condition_end_date + ,0 AS condition_type_concept_id + ,NULL AS stop_reason + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,procedure_source_value AS condition_source_value + ,CAST(NULL AS INT) condition_source_concept_id + ,procedure_occurrence_id AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE + INNER JOIN #concept_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 + + UNION ALL + + SELECT person_id + ,cm1.target_concept_id AS condition_concept_id + ,drug_exposure_start_date AS condition_start_date + ,NULL AS condition_end_date + ,0 AS condition_type_concept_id + ,NULL AS stop_reason + ,prescribing_provider_id AS provider_id + ,visit_occurrence_id + ,drug_source_value AS condition_source_value + ,CAST(NULL AS INT) condition_source_concept_id + ,drug_exposure_id AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE + INNER JOIN #concept_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 + + UNION ALL + + SELECT person_id + ,cm1.target_concept_id AS condition_concept_id + ,observation_date AS condition_start_date + ,NULL AS condition_end_date + ,0 AS condition_type_concept_id + ,NULL AS stop_reason + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,observation_source_value AS condition_source_value + ,CAST(NULL AS INT) condition_source_concept_id + ,observation_id AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION + INNER JOIN #concept_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; + +--warnings of invalid records +INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) +SELECT 'CONDITION_OCCURRENCE: ' + CAST(NUM_INVALID_RECORDS AS VARCHAR) + ' records in the source CDMv4 database have invalid CONDITION_CONCEPT_ID' +FROM ( + SELECT COUNT(PERSON_ID) AS NUM_INVALID_RECORDS + FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE + WHERE CONDITION_CONCEPT_ID NOT IN ( + SELECT CONCEPT_ID + FROM [TARGET_CDMV5].[SCHEMA].CONCEPT + WHERE CONCEPT_ID = 0 + OR STANDARD_CONCEPT = 'S' + ) + HAVING COUNT(PERSON_ID) > 0 + ) warn; + +INSERT INTO [TARGET_CDMV5].[SCHEMA].ETL_WARNINGS (WARNING_MESSAGE) +SELECT 'CONDIITON_OCCURRENCE: ' + CAST(NUM_INVALID_RECORDS AS VARCHAR) + ' records in the source CDMv4 database have invalid CONDITION_TYPE_CONCEPT_ID' +FROM ( + SELECT COUNT(PERSON_ID) AS NUM_INVALID_RECORDS + FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE + WHERE CONDITION_TYPE_CONCEPT_ID NOT IN ( + SELECT CONCEPT_ID + FROM [TARGET_CDMV5].[SCHEMA].CONCEPT + WHERE CONCEPT_ID = 0 + OR ( + STANDARD_CONCEPT = 'S' + AND LOWER(DOMAIN_ID) IN ('condition type') + ) + ) + HAVING COUNT(PERSON_ID) > 0 + ) warn; + +/**** + + DEVICE_EXPOSURE + + ****/ +INSERT INTO [TARGET_CDMV5].[SCHEMA].device_exposure +SELECT row_number() OVER ( + ORDER BY OCCURRENCE_ID + ) AS device_exposure_id + ,person_id + ,device_concept_id + ,device_exposure_start_date + ,device_exposure_end_date + ,device_type_concept_id + ,unique_device_id + ,quantity + ,provider_id + ,visit_occurrence_id + ,device_source_value + ,device_source_concept_id +FROM ( + --find devices that were previously classified as procedures + SELECT PERSON_ID + ,cm1.target_concept_id AS DEVICE_CONCEPT_ID + ,PROCEDURE_DATE AS DEVICE_EXPOSURE_START_DATE + ,CAST(NULL AS DATE) AS DEVICE_EXPOSURE_END_DATE + ,0 AS DEVICE_TYPE_CONCEPT_ID + ,CAST(NULL AS VARCHAR(50)) unique_device_id + ,CAST(NULL AS INT) quantity + ,ASSOCIATED_PROVIDER_ID AS PROVIDER_ID + ,VISIT_OCCURRENCE_ID + ,PROCEDURE_SOURCE_VALUE AS DEVICE_SOURCE_VALUE + ,0 AS device_source_concept_id + ,PROCEDURE_OCCURRENCE_ID AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE + INNER JOIN #concept_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 + + UNION ALL + + SELECT PERSON_ID + ,cm1.target_concept_id AS DEVICE_CONCEPT_ID + ,DRUG_EXPOSURE_START_DATE AS DEVICE_EXPOSURE_START_DATE + ,CAST(NULL AS DATE) AS DEVICE_EXPOSURE_END_DATE + ,0 AS DEVICE_TYPE_CONCEPT_ID + ,CAST(NULL AS VARCHAR(50)) unique_device_id + ,quantity + ,PRESCRIBING_PROVIDER_ID AS PROVIDER_ID + ,VISIT_OCCURRENCE_ID + ,DRUG_SOURCE_VALUE AS DEVICE_SOURCE_VALUE + ,0 AS device_source_concept_id + ,DRUG_EXPOSURE_ID AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE + INNER JOIN #concept_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 + + UNION ALL + + SELECT PERSON_ID + ,cm1.target_concept_id AS DEVICE_CONCEPT_ID + ,CONDITION_START_DATE AS DEVICE_EXPOSURE_START_DATE + ,CAST(NULL AS DATE) AS DEVICE_EXPOSURE_END_DATE + ,0 AS DEVICE_TYPE_CONCEPT_ID + ,CAST(NULL AS VARCHAR(50)) unique_device_id + ,CAST(NULL AS INT) quantity + ,ASSOCIATED_PROVIDER_ID AS PROVIDER_ID + ,VISIT_OCCURRENCE_ID + ,CONDITION_SOURCE_VALUE AS DEVICE_SOURCE_VALUE + ,0 AS device_source_concept_id + ,CONDITION_OCCURRENCE_ID AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE + INNER JOIN #concept_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 + + UNION ALL + + SELECT PERSON_ID + ,cm1.target_concept_id AS DEVICE_CONCEPT_ID + ,OBSERVATION_DATE AS DEVICE_EXPOSURE_START_DATE + ,CAST(NULL AS DATE) AS DEVICE_EXPOSURE_END_DATE + ,0 AS DEVICE_TYPE_CONCEPT_ID + ,CAST(NULL AS VARCHAR(50)) unique_device_id + ,CAST(NULL AS INT) quantity + ,ASSOCIATED_PROVIDER_ID AS PROVIDER_ID + ,VISIT_OCCURRENCE_ID + ,OBSERVATION_SOURCE_VALUE AS DEVICE_SOURCE_VALUE + ,0 AS device_source_concept_id + ,OBSERVATION_ID AS OCCURRENCE_ID + FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION + INNER JOIN #concept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('device') + ) OTHERS; + +/**** + + MEASUREMENT + + ****/ +--find valid measurements from observation table +INSERT INTO [TARGET_CDMV5].[SCHEMA].measurement +SELECT row_number() OVER ( + ORDER BY occurrence_id + ) AS measurement_id + ,person_id + ,measurement_concept_id + ,measurement_date + ,measurement_time + ,measurement_type_concept_id + ,operator_concept_id + ,value_as_number + ,value_as_concept_id + ,unit_concept_id + ,range_low + ,range_high + ,provider_id + ,visit_occurrence_id + ,measurement_source_value + ,measurement_source_concept_id + ,unit_source_value + ,value_source_value +FROM ( + --find mesaurements that were previously classified as observations + SELECT person_id + ,cm1.target_concept_id AS measurement_concept_id + ,OBSERVATION_DATE AS measurement_date + ,CAST(OBSERVATION_TIME AS VARCHAR(50)) AS measurement_time + ,0 AS measurement_type_concept_id + ,CAST(NULL AS INT) operator_concept_id + ,value_as_number + ,value_as_concept_id + ,COALESCE(cm2.target_concept_id, 0) AS unit_concept_id + ,range_low + ,range_high + ,ASSOCIATED_PROVIDER_ID AS provider_id + ,visit_occurrence_id + ,OBSERVATION_SOURCE_VALUE AS measurement_source_value + ,CAST(NULL AS INT) measurement_source_concept_id + ,unit_source_value AS unit_source_value + ,cast(NULL AS VARCHAR(50)) AS value_source_value + ,observation_id AS occurrence_id + FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION + INNER JOIN #concept_map cm1 ON observation.observation_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('measurement') + LEFT JOIN #concept_map cm2 ON observation.unit_concept_id = cm2.source_concept_id + AND LOWER(cm1.domain_id) IN ('unit') + + UNION ALL + + SELECT person_id + ,cm1.target_concept_id AS measurement_concept_id + ,procedure_date AS measurement_date + ,CAST(NULL AS VARCHAR(50)) AS measurement_time + ,0 AS measurement_type_concept_id + ,CAST(NULL AS INT) AS operator_concept_id + ,CAST(NULL AS INT) AS value_as_number + ,CAST(NULL AS INT) AS value_as_concept_id + ,CAST(NULL AS INT) AS unit_concept_id + ,CAST(NULL AS INT) AS range_low + ,CAST(NULL AS INT) AS range_high + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,procedure_source_value AS measurement_source_value + ,CAST(NULL AS INT) AS measurement_source_concept_id + ,CAST(NULL AS VARCHAR(50)) AS unit_source_value + ,CAST(NULL AS VARCHAR(50)) AS value_source_value + ,procedure_occurrence_id AS occurrence_id + FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE + INNER JOIN #concept_map cm1 ON procedure_occurrence.procedure_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('measurement') + + UNION ALL + + SELECT person_id + ,cm1.target_concept_id AS measurement_concept_id + ,condition_start_date AS measurement_date + ,CAST(NULL AS VARCHAR(50)) AS measurement_time + ,0 AS measurement_type_concept_id + ,CAST(NULL AS INT) AS operator_concept_id + ,CAST(NULL AS INT) AS value_as_number + ,CAST(NULL AS INT) AS value_as_concept_id + ,CAST(NULL AS INT) AS unit_concept_id + ,CAST(NULL AS INT) AS range_low + ,CAST(NULL AS INT) AS range_high + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,condition_source_value AS measurement_source_value + ,CAST(NULL AS INT) AS measurement_source_concept_id + ,CAST(NULL AS VARCHAR(50)) AS unit_source_value + ,CAST(NULL AS VARCHAR(50)) AS value_source_value + ,condition_occurrence_id AS occurrence_id + FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE + INNER JOIN #concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('measurement') + + UNION ALL + + SELECT person_id + ,cm1.target_concept_id AS measurement_concept_id + ,drug_exposure_start_date AS measurement_date + ,CAST(NULL AS VARCHAR(50)) AS measurement_time + ,0 AS measurement_type_concept_id + ,CAST(NULL AS INT) AS operator_concept_id + ,CAST(NULL AS INT) AS value_as_number + ,CAST(NULL AS INT) AS value_as_concept_id + ,CAST(NULL AS INT) AS unit_concept_id + ,CAST(NULL AS INT) AS range_low + ,CAST(NULL AS INT) AS range_high + ,prescribing_provider_id AS provider_id + ,visit_occurrence_id + ,drug_source_value AS measurement_source_value + ,CAST(NULL AS INT) AS measurement_source_concept_id + ,CAST(NULL AS VARCHAR(50)) AS unit_source_value + ,CAST(NULL AS VARCHAR(50)) AS value_source_value + ,drug_exposure_id AS occurrence_id + FROM [SOURCE_CDMV4].[SCHEMA].drug_exposure + INNER JOIN #concept_map cm1 ON drug_exposure.drug_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('measurement') + ) OTHERS; + +/**** + + OBSERVATION + + ****/ +--find valid observation from observation table +INSERT INTO [TARGET_CDMV5].[SCHEMA].observation +SELECT observation_id + ,person_id + ,observation_concept_id + ,observation_date + ,CAST(observation_time AS VARCHAR(50)) AS observation_time + ,observation_type_concept_id + ,value_as_number + ,value_as_string + ,value_as_concept_id + ,CAST(NULL AS INT) qualifier_concept_id + ,unit_concept_id + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,observation_source_value + ,CAST(NULL AS INT) observation_source_concept_id + ,unit_source_value + ,cast(NULL AS VARCHAR(50)) qualifier_source_value +FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION +WHERE observation_concept_id NOT IN ( + SELECT source_concept_id + FROM #concept_map_distinct + WHERE LOWER(domain_id) IN ( + 'condition' + ,'drug' + ,'procedure' + ,'device' + ,'measurement' + ) + ) +--find observations that were previously classified as procedure + +UNION ALL + +SELECT CASE + WHEN MAXROW.MAXROWID IS NULL + THEN 0 + ELSE MAXROW.MAXROWID + END + row_number() OVER ( + ORDER BY OCCURRENCE_ID + ) AS observation_id + ,person_id + ,observation_concept_id + ,observation_date + ,observation_time + ,observation_type_concept_id + ,value_as_number + ,value_as_string + ,value_as_concept_id + ,qualifier_concept_id + ,unit_concept_id + ,provider_id + ,visit_occurrence_id + ,observation_source_value + ,observation_source_concept_id + ,unit_source_value + ,qualifier_source_value +FROM ( + SELECT person_id + ,cm1.target_concept_id AS observation_concept_id + ,procedure_date AS observation_date + ,CAST(NULL AS VARCHAR(50)) AS observation_time + ,0 AS observation_type_concept_id + ,CAST(NULL AS FLOAT) AS value_as_number + ,NULL AS value_as_string + ,CAST(NULL AS INT) AS value_as_concept_id + ,CAST(NULL AS INT) qualifier_concept_id + ,CAST(NULL AS INT) AS unit_concept_id + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,procedure_source_value AS observation_source_value + ,CAST(NULL AS INT) observation_source_concept_id + ,NULL AS unit_source_value + ,cast(NULL AS VARCHAR(50)) qualifier_source_value + ,procedure_occurrence_id AS occurrence_id + FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_OCCURRENCE + INNER JOIN #concept_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 + + UNION ALL + + SELECT person_id + ,cm1.target_concept_id AS observation_concept_id + ,condition_start_date AS observation_date + ,CAST(NULL AS VARCHAR(50)) AS observation_time + ,0 AS observation_type_concept_id + ,CAST(NULL AS FLOAT) AS value_as_number + ,NULL AS value_as_string + ,CAST(NULL AS INT) AS value_as_concept_id + ,CAST(NULL AS INT) qualifier_concept_id + ,CAST(NULL AS INT) AS unit_concept_id + ,associated_provider_id AS provider_id + ,visit_occurrence_id + ,condition_source_value AS observation_source_value + ,CAST(NULL AS INT) observation_source_concept_id + ,NULL AS unit_source_value + ,cast(NULL AS VARCHAR(50)) qualifier_source_value + ,condition_occurrence_id AS occurrence_id + FROM [SOURCE_CDMV4].[SCHEMA].CONDITION_OCCURRENCE + INNER JOIN #concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('observation') + + UNION ALL + + --find DRG observations that were previously classified as procedure_cost + SELECT po.person_id + ,cm1.target_concept_id AS observation_concept_id + ,po.procedure_date AS observation_date + ,CAST(NULL AS VARCHAR(50)) AS observation_time + ,0 AS observation_type_concept_id + ,CAST(NULL AS FLOAT) AS value_as_number + ,NULL AS value_as_string + ,CAST(NULL AS INT) AS value_as_concept_id + ,CAST(NULL AS INT) qualifier_concept_id + ,CAST(NULL AS INT) AS unit_concept_id + ,po.associated_provider_id AS provider_id + ,po.visit_occurrence_id + ,pc.DISEASE_CLASS_SOURCE_VALUE AS observation_source_value + ,cm1.source_concept_id as observation_source_concept_id + ,NULL AS unit_source_value + ,cast(NULL AS VARCHAR(50)) qualifier_source_value + ,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 #concept_map cm1 ON pc.disease_class_concept_id = cm1.source_concept_id + AND LOWER(cm1.domain_id) IN ('observation') + + UNION ALL + + --find observations that were previously classified as drug exposure + SELECT person_id + ,cm1.target_concept_id AS observation_concept_id + ,drug_exposure_start_date AS observation_date + ,CAST(NULL AS VARCHAR(10)) AS observation_time + ,0 AS observation_type_concept_id + ,CAST(NULL AS FLOAT) AS value_as_number + ,NULL AS value_as_string + ,CAST(NULL AS INT) AS value_as_concept_id + ,CAST(NULL AS INT) qualifier_concept_id + ,CAST(NULL AS INT) AS unit_concept_id + ,CAST(NULL AS INT) AS provider_id + ,visit_occurrence_id + ,drug_source_value AS observation_source_value + ,CAST(NULL AS INT) observation_source_concept_id + ,NULL AS unit_source_value + ,cast(NULL AS VARCHAR(50)) qualifier_source_value + ,drug_exposure_id AS occurrence_id + FROM [SOURCE_CDMV4].[SCHEMA].DRUG_EXPOSURE + INNER JOIN #concept_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 + FROM [SOURCE_CDMV4].[SCHEMA].OBSERVATION + ) MAXROW; + +/**** + + PAYER_PLAN_PERIOD + + ****/ +INSERT INTO [TARGET_CDMV5].[SCHEMA].payer_plan_period +SELECT payer_plan_period_id + ,person_id + ,payer_plan_period_start_date + ,payer_plan_period_end_date + ,payer_source_value + ,plan_source_value + ,family_source_value +FROM [SOURCE_CDMV4].[SCHEMA].PAYER_PLAN_PERIOD; + +/**** + + DRUG_COST + + note : if there were invalid drug concepts in DRUG_EXPOSURE, those records may not enter CDMv5 but costs will persist + + ****/ +INSERT INTO [TARGET_CDMV5].[SCHEMA].drug_cost +SELECT drug_cost_id + ,dc.drug_exposure_id + ,cast(NULL AS INT) currency_concept_id + ,paid_copay + ,paid_coinsurance + ,paid_toward_deductible + ,paid_by_payer + ,paid_by_coordination_benefits + ,total_out_of_pocket + ,total_paid + ,ingredient_cost + ,dispensing_fee + ,average_wholesale_price + ,payer_plan_period_id +FROM [SOURCE_CDMV4].[SCHEMA].DRUG_COST dc; + +-- insert procedure costs for procedures that were inserted into the drug_exposure table +INSERT INTO [TARGET_CDMV5].[SCHEMA].drug_cost +SELECT CASE + WHEN MAXROW.MAXROWID IS NULL + THEN 0 + ELSE MAXROW.MAXROWID + END + row_number() OVER ( + ORDER BY OCCURRENCE_ID + ) AS drug_cost_id + ,drug_exposure_id + ,cast(NULL AS INT) currency_concept_id + ,paid_copay + ,paid_coinsurance + ,paid_toward_deductible + ,paid_by_payer + ,paid_by_coordination_benefits + ,total_out_of_pocket + ,total_paid + ,ingredient_cost + ,dispensing_fee + ,average_wholesale_price + ,payer_plan_period_id +FROM ( + SELECT drug_exposure_id + ,po.person_id + ,paid_copay + ,paid_coinsurance + ,paid_toward_deductible + ,paid_by_payer + ,paid_by_coordination_benefits + ,total_out_of_pocket + ,total_paid + ,CAST(NULL AS FLOAT) AS ingredient_cost + ,CAST(NULL AS FLOAT) AS dispensing_fee + ,CAST(NULL AS FLOAT) AS average_wholesale_price + ,payer_plan_period_id + ,procedure_cost_id AS OCCURRENCE_ID + 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 #drgexp_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 + FROM [SOURCE_CDMV4].[SCHEMA].DRUG_COST + ) MAXROW; + +/**** + + PROCEDURE_COST + + note : if there were invalid procedure concepts in PROCEDURE_OCCURRENCE, those records may not enter CDMv5 but costs will persist + + + ****/ +INSERT INTO [TARGET_CDMV5].[SCHEMA].procedure_cost +SELECT procedure_cost_id + ,procedure_occurrence_id + ,cast(NULL AS INT) currency_concept_id + ,paid_copay + ,paid_coinsurance + ,paid_toward_deductible + ,paid_by_payer + ,paid_by_coordination_benefits + ,total_out_of_pocket + ,total_paid + ,payer_plan_period_id + ,revenue_code_concept_id + ,revenue_code_source_value +FROM [SOURCE_CDMV4].[SCHEMA].PROCEDURE_COST; + +-- insert drug costs for drugs that were inserted into the procedure_occurrence table +INSERT INTO [TARGET_CDMV5].[SCHEMA].procedure_cost +SELECT CASE + WHEN MAXROW.MAXROWID IS NULL + THEN 0 + ELSE MAXROW.MAXROWID + END + row_number() OVER ( + ORDER BY OCCURRENCE_ID + ) AS procedure_cost_id + ,procedure_occurrence_id + ,cast(NULL AS INT) currency_concept_id + ,paid_copay + ,paid_coinsurance + ,paid_toward_deductible + ,paid_by_payer + ,paid_by_coordination_benefits + ,total_out_of_pocket + ,total_paid + ,payer_plan_period_id + ,revenue_code_concept_id + ,revenue_code_source_value +FROM ( + SELECT po.procedure_occurrence_id + ,po.person_id + ,paid_copay + ,paid_coinsurance + ,paid_toward_deductible + ,paid_by_payer + ,paid_by_coordination_benefits + ,total_out_of_pocket + ,total_paid + ,CAST(NULL AS FLOAT) AS ingredient_cost + ,CAST(NULL AS FLOAT) AS dispensing_fee + ,CAST(NULL AS FLOAT) AS average_wholesale_price + ,payer_plan_period_id + ,CAST(NULL AS INT) AS revenue_code_concept_id + ,CAST(NULL AS INT) AS revenue_code_source_value + ,drug_cost_id AS OCCURRENCE_ID + 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 #po_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 + FROM [SOURCE_CDMV4].[SCHEMA].DRUG_COST + ) MAXROW; + +/**** + +DRUG ERA +Note: Eras derived from DRUG_EXPOSURE table, using 30d gap + + ****/ +IF XACT_STATE() = 1 COMMIT; IF OBJECT_ID('tempdb..#cteDrugTarget', 'U') IS NOT NULL DROP TABLE #cteDrugTarget; + +/* / */ + +-- 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 +IF XACT_STATE() = 1 COMMIT; CREATE TABLE #cteDrugTarget + WITH (LOCATION = USER_DB, DISTRIBUTION = HASH(person_id)) AS +SELECT + d.DRUG_EXPOSURE_ID + ,d. person_id, c.CONCEPT_ID + ,d.DRUG_TYPE_CONCEPT_ID + ,DRUG_EXPOSURE_START_DATE + ,COALESCE(DRUG_EXPOSURE_END_DATE, DATEADD(day, DAYS_SUPPLY, DRUG_EXPOSURE_START_DATE), DATEADD(day, 1, DRUG_EXPOSURE_START_DATE)) AS DRUG_EXPOSURE_END_DATE + ,c.CONCEPT_ID AS INGREDIENT_CONCEPT_ID + +FROM + [TARGET_CDMV5].[SCHEMA].DRUG_EXPOSURE d +INNER JOIN [TARGET_CDMV5].[SCHEMA].CONCEPT_ANCESTOR ca ON ca.DESCENDANT_CONCEPT_ID = d.DRUG_CONCEPT_ID +INNER JOIN [TARGET_CDMV5].[SCHEMA].CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCEPT_ID +WHERE c.VOCABULARY_ID = 'RxNorm' + AND c.CONCEPT_CLASS_ID = 'Ingredient'; + +/* / */ + +IF XACT_STATE() = 1 COMMIT; IF OBJECT_ID('tempdb..#cteEndDates', 'U') IS NOT NULL DROP TABLE #cteEndDates; + +/* / */ + +IF XACT_STATE() = 1 COMMIT; CREATE TABLE #cteEndDates + WITH (LOCATION = USER_DB, DISTRIBUTION = HASH(person_id)) AS +SELECT + person_id, INGREDIENT_CONCEPT_ID + ,DATEADD(day, - 30, EVENT_DATE) AS END_DATE -- unpad the end date + +FROM + ( + SELECT E1.PERSON_ID + ,E1.INGREDIENT_CONCEPT_ID + ,E1.EVENT_DATE + ,COALESCE(E1.START_ORDINAL, MAX(E2.START_ORDINAL)) START_ORDINAL + ,E1.OVERALL_ORD + FROM ( + SELECT PERSON_ID + ,INGREDIENT_CONCEPT_ID + ,EVENT_DATE + ,EVENT_TYPE + ,START_ORDINAL + ,ROW_NUMBER() OVER ( + PARTITION BY PERSON_ID + ,INGREDIENT_CONCEPT_ID ORDER BY EVENT_DATE + ,EVENT_TYPE + ) AS OVERALL_ORD -- this re-numbers the inner UNION so all rows are numbered ordered by the event date + FROM ( + -- select the start dates, assigning a row number to each + SELECT PERSON_ID + ,INGREDIENT_CONCEPT_ID + ,DRUG_EXPOSURE_START_DATE AS EVENT_DATE + ,0 AS EVENT_TYPE + ,ROW_NUMBER() OVER ( + PARTITION BY PERSON_ID + ,INGREDIENT_CONCEPT_ID ORDER BY DRUG_EXPOSURE_START_DATE + ) AS START_ORDINAL + FROM #cteDrugTarget + + UNION ALL + + -- add the end dates with NULL as the row number, padding the end dates by 30 to allow a grace period for overlapping ranges. + SELECT PERSON_ID + ,INGREDIENT_CONCEPT_ID + ,DATEADD(day, 30, DRUG_EXPOSURE_END_DATE) + ,1 AS EVENT_TYPE + ,NULL + FROM #cteDrugTarget + ) RAWDATA + ) E1 + INNER JOIN ( + SELECT PERSON_ID + ,INGREDIENT_CONCEPT_ID + ,DRUG_EXPOSURE_START_DATE AS EVENT_DATE + ,ROW_NUMBER() OVER ( + PARTITION BY PERSON_ID + ,INGREDIENT_CONCEPT_ID ORDER BY DRUG_EXPOSURE_START_DATE + ) AS START_ORDINAL + 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 + GROUP BY E1.PERSON_ID + ,E1.INGREDIENT_CONCEPT_ID + ,E1.EVENT_DATE + ,E1.START_ORDINAL + ,E1.OVERALL_ORD + ) E +WHERE 2 * E.START_ORDINAL - E.OVERALL_ORD = 0; + +/* / */ + +IF XACT_STATE() = 1 COMMIT; IF OBJECT_ID('tempdb..#cteDrugExpEnds', 'U') IS NOT NULL DROP TABLE #cteDrugExpEnds; + +/* / */ + +IF XACT_STATE() = 1 COMMIT; CREATE TABLE #cteDrugExpEnds + WITH (LOCATION = USER_DB, DISTRIBUTION = HASH(person_id)) AS +SELECT + d. person_id, d.INGREDIENT_CONCEPT_ID + ,d.DRUG_TYPE_CONCEPT_ID + ,d.DRUG_EXPOSURE_START_DATE + ,MIN(e.END_DATE) AS ERA_END_DATE + +FROM + #cteDrugTarget d +INNER JOIN #cteEndDates 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 + ,d.INGREDIENT_CONCEPT_ID + ,d.DRUG_TYPE_CONCEPT_ID + ,d.DRUG_EXPOSURE_START_DATE; + +/* / */ + +INSERT INTO [TARGET_CDMV5].[SCHEMA].drug_era +SELECT row_number() OVER ( + ORDER BY person_id + ) AS drug_era_id + ,person_id + ,INGREDIENT_CONCEPT_ID + ,min(DRUG_EXPOSURE_START_DATE) AS drug_era_start_date + ,ERA_END_DATE + ,COUNT(*) AS DRUG_EXPOSURE_COUNT + ,30 AS gap_days +FROM #cteDrugExpEnds +GROUP BY person_id + ,INGREDIENT_CONCEPT_ID + ,drug_type_concept_id + ,ERA_END_DATE; + +/**** + +CONDITION ERA +Note: Eras derived from CONDITION_OCCURRENCE table, using 30d gap + + ****/ +IF XACT_STATE() = 1 COMMIT; IF OBJECT_ID('tempdb..#condition_era_phase_1', 'U') IS NOT NULL DROP TABLE #condition_era_phase_1; + +/* / */ + +IF XACT_STATE() = 1 COMMIT; IF OBJECT_ID('tempdb..#cteConditionTarget', 'U') IS NOT NULL DROP TABLE #cteConditionTarget; + +/* / */ + +-- create base eras from the concepts found in condition_occurrence +IF XACT_STATE() = 1 COMMIT; CREATE TABLE #cteConditionTarget + WITH (LOCATION = USER_DB, DISTRIBUTION = HASH(person_id)) AS +SELECT + co. person_id, co.condition_concept_id + ,co.CONDITION_START_DATE + ,COALESCE(co.CONDITION_END_DATE, DATEADD(day, 1, CONDITION_START_DATE)) AS CONDITION_END_DATE + +FROM + [TARGET_CDMV5].[SCHEMA].CONDITION_OCCURRENCE co; + +/* / */ + +IF XACT_STATE() = 1 COMMIT; IF OBJECT_ID('tempdb..#cteCondEndDates', 'U') IS NOT NULL DROP TABLE #cteCondEndDates; + +/* / */ + +IF XACT_STATE() = 1 COMMIT; CREATE TABLE #cteCondEndDates + WITH (LOCATION = USER_DB, DISTRIBUTION = HASH(person_id)) AS +SELECT + person_id, CONDITION_CONCEPT_ID + ,DATEADD(day, - 30, EVENT_DATE) AS END_DATE -- unpad the end date + +FROM + ( + SELECT E1.PERSON_ID + ,E1.CONDITION_CONCEPT_ID + ,E1.EVENT_DATE + ,COALESCE(E1.START_ORDINAL, MAX(E2.START_ORDINAL)) START_ORDINAL + ,E1.OVERALL_ORD + FROM ( + SELECT PERSON_ID + ,CONDITION_CONCEPT_ID + ,EVENT_DATE + ,EVENT_TYPE + ,START_ORDINAL + ,ROW_NUMBER() OVER ( + PARTITION BY PERSON_ID + ,CONDITION_CONCEPT_ID ORDER BY EVENT_DATE + ,EVENT_TYPE + ) AS OVERALL_ORD -- this re-numbers the inner UNION so all rows are numbered ordered by the event date + FROM ( + -- select the start dates, assigning a row number to each + SELECT PERSON_ID + ,CONDITION_CONCEPT_ID + ,CONDITION_START_DATE AS EVENT_DATE + ,- 1 AS EVENT_TYPE + ,ROW_NUMBER() OVER ( + PARTITION BY PERSON_ID + ,CONDITION_CONCEPT_ID ORDER BY CONDITION_START_DATE + ) AS START_ORDINAL + FROM #cteConditionTarget + + UNION ALL + + -- pad the end dates by 30 to allow a grace period for overlapping ranges. + SELECT PERSON_ID + ,CONDITION_CONCEPT_ID + ,DATEADD(day, 30, CONDITION_END_DATE) + ,1 AS EVENT_TYPE + ,NULL + FROM #cteConditionTarget + ) RAWDATA + ) E1 + INNER JOIN ( + SELECT PERSON_ID + ,CONDITION_CONCEPT_ID + ,CONDITION_START_DATE AS EVENT_DATE + ,ROW_NUMBER() OVER ( + PARTITION BY PERSON_ID + ,CONDITION_CONCEPT_ID ORDER BY CONDITION_START_DATE + ) AS START_ORDINAL + 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 + GROUP BY E1.PERSON_ID + ,E1.CONDITION_CONCEPT_ID + ,E1.EVENT_DATE + ,E1.START_ORDINAL + ,E1.OVERALL_ORD + ) E +WHERE (2 * E.START_ORDINAL) - E.OVERALL_ORD = 0; + +/* / */ + +IF XACT_STATE() = 1 COMMIT; IF OBJECT_ID('tempdb..#cteConditionEnds', 'U') IS NOT NULL DROP TABLE #cteConditionEnds; + +/* / */ + +IF XACT_STATE() = 1 COMMIT; CREATE TABLE #cteConditionEnds + WITH (LOCATION = USER_DB, DISTRIBUTION = HASH(person_id)) AS +SELECT + c. person_id, c.CONDITION_CONCEPT_ID + ,c.CONDITION_START_DATE + ,MIN(e.END_DATE) AS ERA_END_DATE + +FROM + #cteConditionTarget c +INNER JOIN #cteCondEndDates 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 + ,person_id + ,condition_concept_id + ,condition_era_start_date + ,condition_era_end_date + ,condition_occurrence_count + ) +SELECT row_number() OVER ( + ORDER BY person_id + ) AS condition_era_id + ,person_id + ,CONDITION_CONCEPT_ID + ,min(CONDITION_START_DATE) AS CONDITION_ERA_START_DATE + ,ERA_END_DATE AS CONDITION_ERA_END_DATE + ,COUNT(*) AS CONDITION_OCCURRENCE_COUNT +FROM #cteConditionEnds +GROUP BY person_id + ,CONDITION_CONCEPT_ID + ,ERA_END_DATE; + +/**** + +QUALITY ASSURANCE OUTPUT + +Note: These queries are used to provide some basic stats around row counts between your V4 and V5 database + to ensure that all of the data has migrated as expected. + + ****/ + +IF XACT_STATE() = 1 COMMIT; IF OBJECT_ID('tempdb..#v5_stats', 'U') IS NOT NULL DROP TABLE #v5_stats; + +/* / */ + +IF XACT_STATE() = 1 COMMIT; IF OBJECT_ID('tempdb..#v4_stats', 'U') IS NOT NULL DROP TABLE #v4_stats; + +/* / */ + +-- Get the row counts for each table that is in scope for the migration +IF XACT_STATE() = 1 COMMIT; CREATE TABLE #v4_stats + WITH (LOCATION = USER_DB, DISTRIBUTION = REPLICATE) AS +SELECT + * + +FROM + +( + SELECT '[SOURCE_CDMV4]' AS DBName, 'care_site' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].care_site + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'condition_era' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].condition_era + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'condition_occurrence' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].condition_occurrence + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'death' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].death + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'drug_cost' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].drug_cost + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'drug_era' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].drug_era + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'drug_exposure' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].drug_exposure + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'location' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].location + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'observation' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].observation + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'observation_period' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].observation_period + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'payer_plan_period' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].payer_plan_period + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'person' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].person + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'procedure_cost' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].procedure_cost + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'procedure_occurrence' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].procedure_occurrence + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'provider' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].provider + UNION + SELECT '[SOURCE_CDMV4]' AS DBName, 'visit_occurrence' AS TableName, COUNT(*) as row_count FROM [SOURCE_CDMV4].[SCHEMA].visit_occurrence +) v4_stats; + +/* / */ + +IF XACT_STATE() = 1 COMMIT; CREATE TABLE #v5_stats + WITH (LOCATION = USER_DB, DISTRIBUTION = REPLICATE) AS +SELECT + * + +FROM + +( + SELECT '[TARGET_CDMV5]' AS DBName, 'care_site' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].care_site + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'condition_era' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].condition_era + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'condition_occurrence' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].condition_occurrence + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'death' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].death + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'device_exposure' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].device_exposure + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'drug_cost' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].drug_cost + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'drug_era' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].drug_era + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'drug_exposure' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].drug_exposure + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'location' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].location + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'measurement' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].measurement + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'observation' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].observation + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'observation_period' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].observation_period + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'payer_plan_period' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].payer_plan_period + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'person' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].person + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'procedure_cost' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].procedure_cost + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'procedure_occurrence' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].procedure_occurrence + UNION + SELECT '[TARGET_CDMV5]' AS DBName, 'provider' AS TableName, COUNT(*) as row_count FROM [TARGET_CDMV5].[SCHEMA].provider + UNION + 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 + 'Rowcounts for each database and table', + ISNULL(V4.DBName, 'None') v4_database_name, + v4.TableName v4_table_name, + v4.row_count v4_row_count, + ISNULL(v5.DBName, 'None') v5_database_name, + v5.TableName v5_table_name, + v5.row_count v5_row_count, + ISNULL(v5.row_count, 0) - ISNULL(v4.row_count, 0) row_count_change +from #v4_stats v4 +full outer join #v5_stats v5 ON v4.TableName = v5.TableName +order by v5.TableName; + +/* + * Determine how the vocabulary/domains helped to map from the V4 source + * tables to the V5 destinations + */ +IF XACT_STATE() = 1 COMMIT; IF OBJECT_ID('tempdb..#classification_map', 'U') IS NOT NULL DROP TABLE #classification_map; + +/* / */ + +IF XACT_STATE() = 1 COMMIT; CREATE TABLE #classification_map + WITH (LOCATION = USER_DB, DISTRIBUTION = REPLICATE) AS +SELECT + * + +FROM + +( + SELECT 'Condition_Occurrence' TableName, ISNULL(LOWER(cm.domain_id), 'condition') domain_id, COUNT(*) row_count + FROM [SOURCE_CDMV4].[SCHEMA].Condition_Occurrence CO + LEFT JOIN #concept_map CM ON co.condition_concept_id = cm.source_concept_id + GROUP BY ISNULL(LOWER(cm.domain_id), 'condition') + UNION + SELECT 'Drug_Exposure' TableName, ISNULL(LOWER(cm.domain_id), 'drug') domain_id, COUNT(*) row_count + FROM [SOURCE_CDMV4].[SCHEMA].Drug_Exposure de + LEFT JOIN #concept_map CM ON de.drug_concept_id = cm.source_concept_id + GROUP BY ISNULL(LOWER(cm.domain_id), 'drug') + UNION + SELECT 'Observation' TableName, ISNULL(LOWER(cm.domain_id), 'observation') domain_id, COUNT(*) row_count + FROM [SOURCE_CDMV4].[SCHEMA].Observation o + LEFT JOIN #concept_map CM ON o.observation_concept_id = cm.source_concept_id + GROUP BY ISNULL(LOWER(cm.domain_id), 'observation') + UNION + SELECT 'Procedure_Occurrence' TableName, ISNULL(LOWER(cm.domain_id), 'procedure') domain_id, COUNT(*) row_count + FROM [SOURCE_CDMV4].[SCHEMA].Procedure_Occurrence po + LEFT JOIN #concept_map CM ON po.PROCEDURE_CONCEPT_ID = cm.source_concept_id + GROUP BY ISNULL(LOWER(cm.domain_id), 'procedure') +) A +ORDER by A.TableName, A.domain_id; + +/* / */ + +select * +from #classification_map +order by tablename, domain_id; + +select domain_id, SUM(row_count) +from #classification_map +group by domain_id +order by domain_id; \ No newline at end of file diff --git a/Version4 To Version5 Conversion/Sql Server/OMOP CDMv4 to CDMv5 - SQL Server.sql b/Version4 To Version5 Conversion/Sql Server/OMOP CDMv4 to CDMv5 - SQL Server.sql index 1fc6366..3757a6e 100644 --- a/Version4 To Version5 Conversion/Sql Server/OMOP CDMv4 to CDMv5 - SQL Server.sql +++ b/Version4 To Version5 Conversion/Sql Server/OMOP CDMv4 to CDMv5 - SQL Server.sql @@ -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