era
This commit is contained in:
vojtechhuser
parent
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/*********************************************************************************
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# Copyright 2017 Observational Health Data Sciences and Informatics
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#
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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********************************************************************************/
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/*******************************************************************************
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PURPOSE: Use this script to convert your OMOP V4 common data model to CDM V5.
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last revised: Jun 2017
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authors: Patrick Ryan, Chris Knoll, Anthony Sena, Vojtech Huser
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!!!!!!!!!!!!!!!!!!!!! PLEASE READ THESE INSTRUCTIONS !!!!!!!!!!!!!!!!!!!!!!!!!!!
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This script was authored using OHDSI-SQL which will require you to run this
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script through SqlRender to creat a version that is compatible with your target
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RDBMS. We have pre-generated these scripts using SQL Render and have placed
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them in folders for each RDBMS. Depending on which script you are viewing, your
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instructions will be slightly different.
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General Assumptions
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-------------------
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This script assumes that your V4 and V5 database are located on the same
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RDBMS server. It also assumes that the V4 and V5 databases were created
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using the standard data definition scripts for these databases. If you
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altered your V4 database in any way, this script will likely require
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some mo
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Getting Started
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---------------
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Before you can use this script, there are some prerequisites:
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1. Create a target CDMv5 database on your database server using the
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appropriate script from https://github.com/OHDSI/CommonDataModel
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2. Load VocabV5 into the target database/schema that will contain CDMv5 using
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Athena: http://ohdsi.org/web/ATHENA
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OHDSI-SQL File Instructions
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-----------------------------
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1. Set parameter name of schema that contains CDMv4 instance
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(@SOURCE_CDMV4, @SOURCE_CDMV4_SCHEMA)
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2. Set parameter name of schema that contains CDMv5 instance
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(@TARGET_CDMV5, @TARGET_CDMV5_SCHEMA)
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3. Run this script through SqlRender to produce a script that will work in your
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source dialect. SqlRender can be found here: https://github.com/OHDSI/SqlRender
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4. Run the script produced by SQL Render on your target RDBDMS.
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<RDBMS> File Instructions
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-------------------------
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1. This script will hold a number of placeholders for your CDM V4 and CDMV5
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database/schema. In order to make this file work in your environment, you
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should plan to do a global "FIND AND REPLACE" on this file to fill in the
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file with values that pertain to your environment. The following are the
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tokens you should use when doing your "FIND AND REPLACE" operation:
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a. [SOURCE_CDMV4]
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b. [SOURCE_CDMV4].[SCHEMA]
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c. [TARGET_CDMV5]
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d. [TARGET_CDMV5].[SCHEMA]
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2. Run the resulting script on your target RDBDMS.
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*********************************************************************************/
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/* SCRIPT PARAMETERS */
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{DEFAULT @SOURCE_CDMV4 = '[SOURCE_CDMV4]' } -- The CDMv4 database name
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{DEFAULT @SOURCE_CDMV4_SCHEMA = '[SOURCE_CDMV4].[SCHEMA]' } -- The CDMv4 database plus schema
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{DEFAULT @TARGET_CDMV5 = '[TARGET_CDMV5]' } -- The target CDMv5 database name
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{DEFAULT @TARGET_CDMV5_SCHEMA = '[TARGET_CDMV5].[SCHEMA]' } -- the target CDMv5 database plus schema
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USE @TARGET_CDMV5;
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/****
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DRUG ERA
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Note: Eras derived from DRUG_EXPOSURE table, using 30d gap
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****/
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IF OBJECT_ID('tempdb..#cteDrugTarget', 'U') IS NOT NULL
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DROP TABLE #cteDrugTarget;
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/* / */
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-- 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
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SELECT d.DRUG_EXPOSURE_ID
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,d.PERSON_ID
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,c.CONCEPT_ID
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,d.DRUG_TYPE_CONCEPT_ID
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,DRUG_EXPOSURE_START_DATE
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,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
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,c.CONCEPT_ID AS INGREDIENT_CONCEPT_ID
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INTO #cteDrugTarget
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FROM @TARGET_CDMV5_SCHEMA.DRUG_EXPOSURE d
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INNER JOIN @TARGET_CDMV5_SCHEMA.CONCEPT_ANCESTOR ca ON ca.DESCENDANT_CONCEPT_ID = d.DRUG_CONCEPT_ID
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INNER JOIN @TARGET_CDMV5_SCHEMA.CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCEPT_ID
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WHERE c.VOCABULARY_ID = 'RxNorm'
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AND c.CONCEPT_CLASS_ID = 'Ingredient';
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/* / */
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IF OBJECT_ID('tempdb..#cteEndDates', 'U') IS NOT NULL
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DROP TABLE #cteEndDates;
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/* / */
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SELECT PERSON_ID
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,INGREDIENT_CONCEPT_ID
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,DATEADD(day, - 30, EVENT_DATE) AS END_DATE -- unpad the end date
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INTO #cteEndDates
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FROM (
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SELECT E1.PERSON_ID
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,E1.INGREDIENT_CONCEPT_ID
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,E1.EVENT_DATE
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,COALESCE(E1.START_ORDINAL, MAX(E2.START_ORDINAL)) START_ORDINAL
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,E1.OVERALL_ORD
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FROM (
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SELECT PERSON_ID
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,INGREDIENT_CONCEPT_ID
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,EVENT_DATE
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,EVENT_TYPE
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,START_ORDINAL
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,ROW_NUMBER() OVER (
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PARTITION BY PERSON_ID
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,INGREDIENT_CONCEPT_ID ORDER BY EVENT_DATE
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,EVENT_TYPE
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) AS OVERALL_ORD -- this re-numbers the inner UNION so all rows are numbered ordered by the event date
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FROM (
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-- select the start dates, assigning a row number to each
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SELECT PERSON_ID
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,INGREDIENT_CONCEPT_ID
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,DRUG_EXPOSURE_START_DATE AS EVENT_DATE
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,0 AS EVENT_TYPE
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,ROW_NUMBER() OVER (
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PARTITION BY PERSON_ID
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,INGREDIENT_CONCEPT_ID ORDER BY DRUG_EXPOSURE_START_DATE
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) AS START_ORDINAL
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FROM #cteDrugTarget
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UNION ALL
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-- add the end dates with NULL as the row number, padding the end dates by 30 to allow a grace period for overlapping ranges.
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SELECT PERSON_ID
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,INGREDIENT_CONCEPT_ID
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,DATEADD(day, 30, DRUG_EXPOSURE_END_DATE)
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,1 AS EVENT_TYPE
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,NULL
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FROM #cteDrugTarget
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) RAWDATA
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) E1
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INNER JOIN (
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SELECT PERSON_ID
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,INGREDIENT_CONCEPT_ID
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,DRUG_EXPOSURE_START_DATE AS EVENT_DATE
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,ROW_NUMBER() OVER (
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PARTITION BY PERSON_ID
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,INGREDIENT_CONCEPT_ID ORDER BY DRUG_EXPOSURE_START_DATE
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) AS START_ORDINAL
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FROM #cteDrugTarget
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) E2 ON E1.PERSON_ID = E2.PERSON_ID
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AND E1.INGREDIENT_CONCEPT_ID = E2.INGREDIENT_CONCEPT_ID
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AND E2.EVENT_DATE <= E1.EVENT_DATE
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GROUP BY E1.PERSON_ID
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,E1.INGREDIENT_CONCEPT_ID
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,E1.EVENT_DATE
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,E1.START_ORDINAL
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,E1.OVERALL_ORD
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) E
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WHERE 2 * E.START_ORDINAL - E.OVERALL_ORD = 0;
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/* / */
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IF OBJECT_ID('tempdb..#cteDrugExpEnds', 'U') IS NOT NULL
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DROP TABLE #cteDrugExpEnds;
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/* / */
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SELECT d.PERSON_ID
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,d.INGREDIENT_CONCEPT_ID
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,d.DRUG_TYPE_CONCEPT_ID
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,d.DRUG_EXPOSURE_START_DATE
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,MIN(e.END_DATE) AS ERA_END_DATE
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INTO #cteDrugExpEnds
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FROM #cteDrugTarget d
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INNER JOIN #cteEndDates e ON d.PERSON_ID = e.PERSON_ID
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AND d.INGREDIENT_CONCEPT_ID = e.INGREDIENT_CONCEPT_ID
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AND e.END_DATE >= d.DRUG_EXPOSURE_START_DATE
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GROUP BY d.PERSON_ID
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,d.INGREDIENT_CONCEPT_ID
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,d.DRUG_TYPE_CONCEPT_ID
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,d.DRUG_EXPOSURE_START_DATE;
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/* / */
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INSERT INTO @TARGET_CDMV5_SCHEMA.drug_era
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SELECT row_number() OVER (
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ORDER BY person_id
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) AS drug_era_id
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,person_id
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,INGREDIENT_CONCEPT_ID
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,min(DRUG_EXPOSURE_START_DATE) AS drug_era_start_date
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,ERA_END_DATE
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,COUNT(*) AS DRUG_EXPOSURE_COUNT
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,30 AS gap_days
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FROM #cteDrugExpEnds
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GROUP BY person_id
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,INGREDIENT_CONCEPT_ID
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,drug_type_concept_id
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,ERA_END_DATE;
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/****
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CONDITION ERA
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Note: Eras derived from CONDITION_OCCURRENCE table, using 30d gap
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****/
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IF OBJECT_ID('tempdb..#condition_era_phase_1', 'U') IS NOT NULL
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DROP TABLE #condition_era_phase_1;
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/* / */
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IF OBJECT_ID('tempdb..#cteConditionTarget', 'U') IS NOT NULL
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DROP TABLE #cteConditionTarget;
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/* / */
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-- create base eras from the concepts found in condition_occurrence
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SELECT co.PERSON_ID
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,co.condition_concept_id
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,co.CONDITION_START_DATE
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,COALESCE(co.CONDITION_END_DATE, DATEADD(day, 1, CONDITION_START_DATE)) AS CONDITION_END_DATE
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INTO #cteConditionTarget
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FROM @TARGET_CDMV5_SCHEMA.CONDITION_OCCURRENCE co;
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/* / */
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IF OBJECT_ID('tempdb..#cteCondEndDates', 'U') IS NOT NULL
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DROP TABLE #cteCondEndDates;
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/* / */
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SELECT PERSON_ID
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,CONDITION_CONCEPT_ID
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,DATEADD(day, - 30, EVENT_DATE) AS END_DATE -- unpad the end date
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INTO #cteCondEndDates
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FROM (
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SELECT E1.PERSON_ID
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,E1.CONDITION_CONCEPT_ID
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,E1.EVENT_DATE
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,COALESCE(E1.START_ORDINAL, MAX(E2.START_ORDINAL)) START_ORDINAL
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,E1.OVERALL_ORD
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FROM (
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SELECT PERSON_ID
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,CONDITION_CONCEPT_ID
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,EVENT_DATE
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,EVENT_TYPE
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,START_ORDINAL
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,ROW_NUMBER() OVER (
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PARTITION BY PERSON_ID
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,CONDITION_CONCEPT_ID ORDER BY EVENT_DATE
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,EVENT_TYPE
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) AS OVERALL_ORD -- this re-numbers the inner UNION so all rows are numbered ordered by the event date
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FROM (
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-- select the start dates, assigning a row number to each
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SELECT PERSON_ID
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,CONDITION_CONCEPT_ID
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,CONDITION_START_DATE AS EVENT_DATE
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,- 1 AS EVENT_TYPE
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,ROW_NUMBER() OVER (
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PARTITION BY PERSON_ID
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,CONDITION_CONCEPT_ID ORDER BY CONDITION_START_DATE
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) AS START_ORDINAL
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FROM #cteConditionTarget
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UNION ALL
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-- pad the end dates by 30 to allow a grace period for overlapping ranges.
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SELECT PERSON_ID
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,CONDITION_CONCEPT_ID
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,DATEADD(day, 30, CONDITION_END_DATE)
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,1 AS EVENT_TYPE
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,NULL
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FROM #cteConditionTarget
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) RAWDATA
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) E1
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INNER JOIN (
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SELECT PERSON_ID
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,CONDITION_CONCEPT_ID
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,CONDITION_START_DATE AS EVENT_DATE
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,ROW_NUMBER() OVER (
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PARTITION BY PERSON_ID
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,CONDITION_CONCEPT_ID ORDER BY CONDITION_START_DATE
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) AS START_ORDINAL
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FROM #cteConditionTarget
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) E2 ON E1.PERSON_ID = E2.PERSON_ID
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AND E1.CONDITION_CONCEPT_ID = E2.CONDITION_CONCEPT_ID
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AND E2.EVENT_DATE <= E1.EVENT_DATE
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GROUP BY E1.PERSON_ID
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,E1.CONDITION_CONCEPT_ID
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,E1.EVENT_DATE
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,E1.START_ORDINAL
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,E1.OVERALL_ORD
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) E
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WHERE (2 * E.START_ORDINAL) - E.OVERALL_ORD = 0;
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/* / */
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IF OBJECT_ID('tempdb..#cteConditionEnds', 'U') IS NOT NULL
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DROP TABLE #cteConditionEnds;
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/* / */
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SELECT c.PERSON_ID
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,c.CONDITION_CONCEPT_ID
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,c.CONDITION_START_DATE
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,MIN(e.END_DATE) AS ERA_END_DATE
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INTO #cteConditionEnds
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FROM #cteConditionTarget c
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INNER JOIN #cteCondEndDates e ON c.PERSON_ID = e.PERSON_ID
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AND c.CONDITION_CONCEPT_ID = e.CONDITION_CONCEPT_ID
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AND e.END_DATE >= c.CONDITION_START_DATE
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GROUP BY c.PERSON_ID
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,c.CONDITION_CONCEPT_ID
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,c.CONDITION_START_DATE;
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/* / */
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INSERT INTO @TARGET_CDMV5_SCHEMA.condition_era (
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condition_era_id
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,person_id
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,condition_concept_id
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,condition_era_start_date
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,condition_era_end_date
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,condition_occurrence_count
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)
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SELECT row_number() OVER (
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ORDER BY person_id
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) AS condition_era_id
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,person_id
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,CONDITION_CONCEPT_ID
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,min(CONDITION_START_DATE) AS CONDITION_ERA_START_DATE
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,ERA_END_DATE AS CONDITION_ERA_END_DATE
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,COUNT(*) AS CONDITION_OCCURRENCE_COUNT
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FROM #cteConditionEnds
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GROUP BY person_id
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,CONDITION_CONCEPT_ID
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,ERA_END_DATE;
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@ -0,0 +1,34 @@
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library(SqlRender);library(RCurl)
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#specify URL of sql code written in parametized SQL (see some examples below)
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# url<-'https://raw.githubusercontent.com/OHDSI/CommonDataModel/master/Version4%20To%20Version5%20Conversion/OMOP%20CDMv4%20to%20CDMv5%20-%20OHDSI-SQL.sql'
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url<-'https://raw.githubusercontent.com/OHDSI/Achilles/master/inst/sql/sql_server/export_v5/drugera/sqlPrevalenceByGenderAgeYear.sql'
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#get the code
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sql<-getURL(url)
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#inspect what parameters are needed by searching for @
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#decide your parameters
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results='ccae'
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vocab='public'
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#fill in parameters
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tta<-SqlRender::renderSql(sql,results_database_schema=results,vocab_database_schema=vocab)
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#translate into target dialect
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ttb<-SqlRender::translateSql(tta$sql,targetDialect = 'postgresql')
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#write final SQL to a local file
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cat(ttb$sql,file='c:/temp/drug_era_2017.sql')
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sql<-ttb$sql
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