/*********************************************************************************

# 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





*********************************************************************************/

/* 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;