OMOP/CodeExcerpts/DerivedTables/GenerateEra.sql

/*********************************************************************************
# 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
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#     http://www.apache.org/licenses/LICENSE-2.0
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# 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
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********************************************************************************/
/*******************************************************************************

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
    (@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.

<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 */

	
	{DEFAULT @TARGET_CDMV5 = '[CDM]' } -- The target CDMv5 database name
	{DEFAULT @TARGET_CDMV5_SCHEMA = '[CDM].[CDMSCHEMA]' } -- the target CDMv5 database plus schema

USE @TARGET_CDMV5;



/****

DRUG ERA
Note: Eras derived from DRUG_EXPOSURE table, using 30d gap

 ****/
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
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
INTO #cteDrugTarget
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 OBJECT_ID('tempdb..#cteEndDates', 'U') IS NOT NULL
	DROP TABLE #cteEndDates;

/* / */

SELECT PERSON_ID
	,INGREDIENT_CONCEPT_ID
	,DATEADD(day, - 30, EVENT_DATE) AS END_DATE -- unpad the end date
INTO #cteEndDates
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 OBJECT_ID('tempdb..#cteDrugExpEnds', 'U') IS NOT NULL
	DROP TABLE #cteDrugExpEnds;

/* / */

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
INTO #cteDrugExpEnds
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 OBJECT_ID('tempdb..#condition_era_phase_1', 'U') IS NOT NULL
	DROP TABLE #condition_era_phase_1;

/* / */

IF OBJECT_ID('tempdb..#cteConditionTarget', 'U') IS NOT NULL
	DROP TABLE #cteConditionTarget;

/* / */

-- create base eras from the concepts found in condition_occurrence
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
INTO #cteConditionTarget
FROM @TARGET_CDMV5_SCHEMA.CONDITION_OCCURRENCE co;

/* / */

IF OBJECT_ID('tempdb..#cteCondEndDates', 'U') IS NOT NULL
	DROP TABLE #cteCondEndDates;

/* / */

SELECT PERSON_ID
	,CONDITION_CONCEPT_ID
	,DATEADD(day, - 30, EVENT_DATE) AS END_DATE -- unpad the end date
INTO #cteCondEndDates
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 OBJECT_ID('tempdb..#cteConditionEnds', 'U') IS NOT NULL
	DROP TABLE #cteConditionEnds;

/* / */

SELECT c.PERSON_ID
	,c.CONDITION_CONCEPT_ID
	,c.CONDITION_START_DATE
	,MIN(e.END_DATE) AS ERA_END_DATE
INTO #cteConditionEnds
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;