/********************************************************************************* # Copyright 2017 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: Generate Era table (based on conversion script from V4 V5). last revised: Jun 2017 authors: Patrick Ryan, Chris Knoll, Anthony Sena, Vojtech Huser 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 ([CDM], [CDM].[CDMSCHEMA]) 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. <RDBMS> 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: [CMD] [CDM].[CDMSCHEMA] *********************************************************************************/ /* SCRIPT PARAMETERS */ -- The target CDMv5 database name -- the target CDMv5 database plus schema SET search_path TO [CDM]; /**** 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*INTERVAL'1 day'), (DRUG_EXPOSURE_START_DATE + 1*INTERVAL'1 day')) AS DRUG_EXPOSURE_END_DATE ,c.CONCEPT_ID AS INGREDIENT_CONCEPT_ID FROM [CDM].[CDMSCHEMA].DRUG_EXPOSURE d INNER JOIN [CDM].[CDMSCHEMA].CONCEPT_ANCESTOR ca ON ca.DESCENDANT_CONCEPT_ID = d.DRUG_CONCEPT_ID INNER JOIN [CDM].[CDMSCHEMA].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*INTERVAL'1 day') 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*INTERVAL'1 day') ,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 [CDM].[CDMSCHEMA].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*INTERVAL'1 day')) AS CONDITION_END_DATE FROM [CDM].[CDMSCHEMA].CONDITION_OCCURRENCE co; /* / */ DROP TABLE IF EXISTS cteCondEndDates; /* / */ CREATE TEMP TABLE cteCondEndDates AS SELECT PERSON_ID ,CONDITION_CONCEPT_ID ,(EVENT_DATE + - 30*INTERVAL'1 day') 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*INTERVAL'1 day') ,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 [CDM].[CDMSCHEMA].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;