text: -- Creates the target drug cohorts to be used in SVVEHDEN-sprint, according to updated study protocol.
  -- Note: cohort exit based on end of continuous drug exposure with death as censoring event
  -- Note: based on template OHDSI.SQL generated from ATLAS 
  --       see cohort-id 1778164 for example butalbital cohort (concept-id: 1139699)
  -- TODO: add cohort with target drug and event to target database schema
  /* 
  ##################################################################################
  */
  
  CREATE TABLE #Codesets (
    codeset_id int NOT NULL,
    concept_id bigint NOT NULL
  )
  ;
  
  INSERT INTO #Codesets (codeset_id, concept_id)
  SELECT 0 as codeset_id, c.concept_id FROM (select distinct I.concept_id FROM
  ( 
    select concept_id from @vocabulary_database_schema.CONCEPT where concept_id in (@generic_concept_id)
  UNION  select c.concept_id
    from @vocabulary_database_schema.CONCEPT c
    join @vocabulary_database_schema.CONCEPT_ANCESTOR ca on c.concept_id = ca.descendant_concept_id
    and ca.ancestor_concept_id in (@generic_concept_id)
    and c.invalid_reason is null
  
  ) I
  ) C
  ;
  
  with primary_events (event_id, person_id, start_date, end_date, op_start_date, op_end_date, visit_occurrence_id) as
  (
  -- Begin Primary Events
  select P.ordinal as event_id, P.person_id, P.start_date, P.end_date, op_start_date, op_end_date, cast(P.visit_occurrence_id as bigint) as visit_occurrence_id
  FROM
  (
    select E.person_id, E.start_date, E.end_date,
           row_number() OVER (PARTITION BY E.person_id ORDER BY E.sort_date ASC) ordinal,
           OP.observation_period_start_date as op_start_date, OP.observation_period_end_date as op_end_date, cast(E.visit_occurrence_id as bigint) as visit_occurrence_id
    FROM 
    (
    -- Begin Drug Exposure Criteria
  select C.person_id, C.drug_exposure_id as event_id, C.drug_exposure_start_date as start_date,
         COALESCE(C.DRUG_EXPOSURE_END_DATE, DATEADD(day,C.DAYS_SUPPLY,DRUG_EXPOSURE_START_DATE), DATEADD(day,1,C.DRUG_EXPOSURE_START_DATE)) as end_date,
         C.visit_occurrence_id,C.drug_exposure_start_date as sort_date
  from 
  (
    select de.* 
    FROM @cdm_database_schema.DRUG_EXPOSURE de
  JOIN #Codesets cs on (de.drug_concept_id = cs.concept_id and cs.codeset_id = 0)
  ) C
  
  
  -- End Drug Exposure Criteria
  
    ) E
  	JOIN @cdm_database_schema.observation_period OP on E.person_id = OP.person_id and E.start_date >=  OP.observation_period_start_date and E.start_date <= op.observation_period_end_date
    WHERE DATEADD(day,365,OP.OBSERVATION_PERIOD_START_DATE) <= E.START_DATE AND DATEADD(day,0,E.START_DATE) <= OP.OBSERVATION_PERIOD_END_DATE
  ) P
  WHERE P.ordinal = 1
  -- End Primary Events
  
  )
  SELECT event_id, person_id, start_date, end_date, op_start_date, op_end_date, visit_occurrence_id
  INTO #qualified_events
  FROM 
  (
    select pe.event_id, pe.person_id, pe.start_date, pe.end_date, pe.op_start_date, pe.op_end_date, row_number() over (partition by pe.person_id order by pe.start_date ASC) as ordinal, cast(pe.visit_occurrence_id as bigint) as visit_occurrence_id
    FROM primary_events pe
    
  ) QE
  
  ;
  
  --- Inclusion Rule Inserts
  
  create table #inclusion_events (inclusion_rule_id bigint,
  	person_id bigint,
  	event_id bigint
  );
  
  with cteIncludedEvents(event_id, person_id, start_date, end_date, op_start_date, op_end_date, ordinal) as
  (
    SELECT event_id, person_id, start_date, end_date, op_start_date, op_end_date, row_number() over (partition by person_id order by start_date ASC) as ordinal
    from
    (
      select Q.event_id, Q.person_id, Q.start_date, Q.end_date, Q.op_start_date, Q.op_end_date, SUM(coalesce(POWER(cast(2 as bigint), I.inclusion_rule_id), 0)) as inclusion_rule_mask
      from #qualified_events Q
      LEFT JOIN #inclusion_events I on I.person_id = Q.person_id and I.event_id = Q.event_id
      GROUP BY Q.event_id, Q.person_id, Q.start_date, Q.end_date, Q.op_start_date, Q.op_end_date
    ) MG -- matching groups
  
  )
  select event_id, person_id, start_date, end_date, op_start_date, op_end_date
  into #included_events
  FROM cteIncludedEvents Results
  WHERE Results.ordinal = 1
  ;
  
  -- custom era strategy
  
  with ctePersons(person_id) as (
  	select distinct person_id from #included_events
  )
  
  select person_id, drug_exposure_start_date, drug_exposure_end_date
  INTO #drugTarget
  FROM (
  	select de.PERSON_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 
  	FROM @cdm_database_schema.DRUG_EXPOSURE de
  	JOIN ctePersons p on de.person_id = p.person_id
  	JOIN #Codesets cs on cs.codeset_id = 0 AND de.drug_concept_id = cs.concept_id
  
  	UNION ALL
  
  	select de.PERSON_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 
  	FROM @cdm_database_schema.DRUG_EXPOSURE de
  	JOIN ctePersons p on de.person_id = p.person_id
  	JOIN #Codesets cs on cs.codeset_id = 0 AND de.drug_source_concept_id = cs.concept_id
  ) E
  ;
  
  select et.event_id, et.person_id, ERAS.era_end_date as end_date
  INTO #strategy_ends
  from #included_events et
  JOIN 
  (
    select ENDS.person_id, min(drug_exposure_start_date) as era_start_date, DATEADD(day,90, ENDS.era_end_date) as era_end_date
    from
    (
      select de.person_id, de.drug_exposure_start_date, MIN(e.END_DATE) as era_end_date
      FROM #drugTarget DE
      JOIN 
      (
        --cteEndDates
        select PERSON_ID, DATEADD(day,-1 * 30,EVENT_DATE) as END_DATE -- unpad the end date by 30
        FROM
        (
  				select PERSON_ID, EVENT_DATE, EVENT_TYPE, 
  				MAX(START_ORDINAL) OVER (PARTITION BY PERSON_ID ORDER BY event_date, event_type ROWS UNBOUNDED PRECEDING) AS start_ordinal,
  				ROW_NUMBER() OVER (PARTITION BY PERSON_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, DRUG_EXPOSURE_START_DATE AS EVENT_DATE, 0 as EVENT_TYPE, ROW_NUMBER() OVER (PARTITION BY PERSON_ID ORDER BY DRUG_EXPOSURE_START_DATE) as START_ORDINAL
  					from #drugTarget D
  
  					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, DATEADD(day,30,DRUG_EXPOSURE_END_DATE), 1 as EVENT_TYPE, NULL
  					FROM #drugTarget D
  				) RAWDATA
        ) E
        WHERE 2 * E.START_ORDINAL - E.OVERALL_ORD = 0
      ) E on DE.PERSON_ID = E.PERSON_ID and E.END_DATE >= DE.DRUG_EXPOSURE_START_DATE
      GROUP BY de.person_id, de.drug_exposure_start_date
    ) ENDS
    GROUP BY ENDS.person_id, ENDS.era_end_date
  ) ERAS on ERAS.person_id = et.person_id 
  WHERE et.start_date between ERAS.era_start_date and ERAS.era_end_date;
  
  TRUNCATE TABLE #drugTarget;
  DROP TABLE #drugTarget;
  
  
  -- generate cohort periods into #final_cohort
  with cohort_ends (event_id, person_id, end_date) as
  (
  	-- cohort exit dates
    -- By default, cohort exit at the event's op end date
  select event_id, person_id, op_end_date as end_date from #included_events
  UNION ALL
  -- End Date Strategy
  SELECT event_id, person_id, end_date from #strategy_ends
  
  UNION ALL
  -- Censor Events
  select i.event_id, i.person_id, MIN(c.start_date) as end_date
  FROM #included_events i
  JOIN
  (
  -- Begin Death Criteria
  select C.person_id, C.person_id as event_id, C.death_date as start_date, DATEADD(d,1,C.death_date) as end_date,
    CAST(NULL as bigint) as visit_occurrence_id, C.death_date as sort_date
  from 
  (
    select d.*
    FROM @cdm_database_schema.DEATH d
  
  ) C
  
  
  -- End Death Criteria
  
  
  ) C on C.person_id = I.person_id and C.start_date >= I.start_date and C.START_DATE <= I.op_end_date
  GROUP BY i.event_id, i.person_id
  
  
  ),
  first_ends (person_id, start_date, end_date) as
  (
  	select F.person_id, F.start_date, F.end_date
  	FROM (
  	  select I.event_id, I.person_id, I.start_date, E.end_date, row_number() over (partition by I.person_id, I.event_id order by E.end_date) as ordinal 
  	  from #included_events I
  	  join cohort_ends E on I.event_id = E.event_id and I.person_id = E.person_id and E.end_date >= I.start_date
  	) F
  	WHERE F.ordinal = 1
  )
  select person_id, start_date, end_date
  INTO #cohort_rows
  from first_ends;
  
  with cteEndDates (person_id, end_date) AS -- the magic
  (	
  	SELECT
  		person_id
  		, DATEADD(day,-1 * 0, event_date)  as end_date
  	FROM
  	(
  		SELECT
  			person_id
  			, event_date
  			, event_type
  			, MAX(start_ordinal) OVER (PARTITION BY person_id ORDER BY event_date, event_type ROWS UNBOUNDED PRECEDING) AS start_ordinal 
  			, ROW_NUMBER() OVER (PARTITION BY person_id ORDER BY event_date, event_type) AS overall_ord
  		FROM
  		(
  			SELECT
  				person_id
  				, start_date AS event_date
  				, -1 AS event_type
  				, ROW_NUMBER() OVER (PARTITION BY person_id ORDER BY start_date) AS start_ordinal
  			FROM #cohort_rows
  		
  			UNION ALL
  		
  
  			SELECT
  				person_id
  				, DATEADD(day,0,end_date) as end_date
  				, 1 AS event_type
  				, NULL
  			FROM #cohort_rows
  		) RAWDATA
  	) e
  	WHERE (2 * e.start_ordinal) - e.overall_ord = 0
  ),
  cteEnds (person_id, start_date, end_date) AS
  (
  	SELECT
  		 c.person_id
  		, c.start_date
  		, MIN(e.end_date) AS end_date
  	FROM #cohort_rows c
  	JOIN cteEndDates e ON c.person_id = e.person_id AND e.end_date >= c.start_date
  	GROUP BY c.person_id, c.start_date
  )
  select person_id, min(start_date) as start_date, end_date
  into #final_cohort
  from cteEnds
  group by person_id, end_date
  ;
  
  /* TO DO: MAY WANT TO MANUALLY ADJUST THE MAX AT RISK WINDOW HERE TO 2 YEARS FOR CHRONOGRAPH ANALYSES 
  update #final_cohort
  set end_date = dateadd(year,2,start_date)
  where end_date > dateadd(year,2,start_date);
  */
  
  DELETE FROM @target_database_schema.@target_cohort_table where cohort_definition_id = @target_cohort_id;
  INSERT INTO @target_database_schema.@target_cohort_table (cohort_definition_id, subject_id, cohort_start_date, cohort_end_date)
  select @target_cohort_id as cohort_definition_id, person_id, start_date, end_date 
  FROM #final_cohort CO
  ;
  
  
  TRUNCATE TABLE #strategy_ends;
  DROP TABLE #strategy_ends;
  
  
  TRUNCATE TABLE #cohort_rows;
  DROP TABLE #cohort_rows;
  
  TRUNCATE TABLE #final_cohort;
  DROP TABLE #final_cohort;
  
  TRUNCATE TABLE #inclusion_events;
  DROP TABLE #inclusion_events;
  
  TRUNCATE TABLE #qualified_events;
  DROP TABLE #qualified_events;
  
  TRUNCATE TABLE #included_events;
  DROP TABLE #included_events;
  
  TRUNCATE TABLE #Codesets;
  DROP TABLE #Codesets;
  