/* Need to replace  
@vocabulary_database_schema
@cdm_database_schema
@target_database_schema
*/

IF OBJECT_ID( '@target_database_schema.t1d_controls', 'U') IS NOT NULL 
DROP TABLE @target_database_schema.t1d_controls;

CREATE TABLE @target_database_schema.t1d_controls (
  person_id						        VARCHAR(10)	  	NOT NULL ,
  age_days		  INTEGER		NOT NULL
)
;

ALTER TABLE @target_database_schema.t1d_controls 
ADD CONSTRAINT pk_t1d_controls PRIMARY KEY NONCLUSTERED (person_id);


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 (201820)
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 (201820)
  and c.invalid_reason is null

) I
) C;
INSERT INTO #Codesets (codeset_id, concept_id)
SELECT 1 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 (1529331,1530014,44816332,43013884,43526465,1594973,44785829,45774435,45774751,1583722,1597756,1560171,1559684,40239216,40170911,44506754,1503297,1510202,1502826,1525215,1516766,1547504,40166035,1580747,1502809,1502855,1515249)
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 (1529331,1530014,44816332,43013884,43526465,1594973,44785829,45774435,45774751,1583722,1597756,1560171,1559684,40239216,40170911,44506754,1503297,1510202,1502826,1525215,1516766,1547504,40166035,1580747,1502809,1502855,1515249)
  and c.invalid_reason is null

) I
) C;
INSERT INTO #Codesets (codeset_id, concept_id)
SELECT 2 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 (35198096,1531601,1567198,35602717,1516976,1502905,1544838,1588986,46221581,1550023,1513876,42899447,19013951,1590165,1596977,1586346,1586369)
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 (35198096,1531601,1567198,35602717,1516976,1502905,1544838,1588986,46221581,1550023,1513876,42899447,19013951,1590165,1596977,1586346,1586369)
  and c.invalid_reason is null

) I
) C;
INSERT INTO #Codesets (codeset_id, concept_id)
SELECT 3 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 (42538542,42538541,4341770,254320,44802279,36714965,193174,434615,4143529,44808532,45769170,37110724)
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 (42538542,42538541,4341770,254320,44802279,36714965,193174,434615,4143529,44808532,45769170,37110724)
  and c.invalid_reason is null

) I
) C;
INSERT INTO #Codesets (codeset_id, concept_id)
SELECT 4 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 (443392)
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 (443392)
  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 Condition Occurrence Criteria
SELECT C.person_id, C.condition_occurrence_id as event_id, C.condition_start_date as start_date, COALESCE(C.condition_end_date, DATEADD(day,1,C.condition_start_date)) as end_date,
       C.CONDITION_CONCEPT_ID as TARGET_CONCEPT_ID, C.visit_occurrence_id,
       C.condition_start_date as sort_date
FROM 
(
  SELECT co.* 
  FROM @cdm_database_schema.CONDITION_OCCURRENCE co
  
) C


-- End Condition Occurrence 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,0,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
  
JOIN (
-- Begin Criteria Group
select 0 as index_id, person_id, event_id
FROM
(
  select E.person_id, E.event_id 
  FROM primary_events E
  INNER JOIN
  (
    -- Begin Demographic Criteria
SELECT 0 as index_id, e.person_id, e.event_id
FROM primary_events E
JOIN @cdm_database_schema.PERSON P ON P.PERSON_ID = E.PERSON_ID
WHERE YEAR(E.start_date) - P.year_of_birth > 4
GROUP BY e.person_id, e.event_id
-- End Demographic Criteria

  ) CQ on E.person_id = CQ.person_id and E.event_id = CQ.event_id
  GROUP BY E.person_id, E.event_id
  HAVING COUNT(index_id) = 1
) G
-- End Criteria Group
) AC on AC.person_id = pe.person_id and AC.event_id = pe.event_id

) QE
WHERE QE.ordinal = 1
;

--- Inclusion Rule Inserts

select 0 as inclusion_rule_id, person_id, event_id
INTO #Inclusion_0
FROM 
(
  select pe.person_id, pe.event_id
  FROM #qualified_events pe
  
JOIN (
-- Begin Criteria Group
select 0 as index_id, person_id, event_id
FROM
(
  select E.person_id, E.event_id 
  FROM #qualified_events E
  INNER JOIN
  (
    -- Begin Correlated Criteria
SELECT 0 as index_id, p.person_id, p.event_id
FROM #qualified_events P
INNER JOIN
(
  -- Begin Condition Occurrence Criteria
SELECT C.person_id, C.condition_occurrence_id as event_id, C.condition_start_date as start_date, COALESCE(C.condition_end_date, DATEADD(day,1,C.condition_start_date)) as end_date,
       C.CONDITION_CONCEPT_ID as TARGET_CONCEPT_ID, C.visit_occurrence_id,
       C.condition_start_date as sort_date
FROM 
(
  SELECT co.* 
  FROM @cdm_database_schema.CONDITION_OCCURRENCE co
  
) C


-- End Condition Occurrence Criteria

) A on A.person_id = P.person_id  AND A.START_DATE >= P.OP_START_DATE AND A.START_DATE <= P.OP_END_DATE AND A.START_DATE >= DATEADD(day,730,P.START_DATE) AND A.START_DATE <= P.OP_END_DATE
GROUP BY p.person_id, p.event_id
HAVING COUNT(A.TARGET_CONCEPT_ID) >= 1
-- End Correlated Criteria

  ) CQ on E.person_id = CQ.person_id and E.event_id = CQ.event_id
  GROUP BY E.person_id, E.event_id
  HAVING COUNT(index_id) = 1
) G
-- End Criteria Group
) AC on AC.person_id = pe.person_id AND AC.event_id = pe.event_id
) Results
;

select 1 as inclusion_rule_id, person_id, event_id
INTO #Inclusion_1
FROM 
(
  select pe.person_id, pe.event_id
  FROM #qualified_events pe
  
JOIN (
-- Begin Criteria Group
select 0 as index_id, person_id, event_id
FROM
(
  select E.person_id, E.event_id 
  FROM #qualified_events E
  INNER JOIN
  (
    -- Begin Correlated Criteria
SELECT 0 as index_id, p.person_id, p.event_id
FROM #qualified_events P
LEFT JOIN
(
  -- Begin Condition Occurrence Criteria
SELECT C.person_id, C.condition_occurrence_id as event_id, C.condition_start_date as start_date, COALESCE(C.condition_end_date, DATEADD(day,1,C.condition_start_date)) as end_date,
       C.CONDITION_CONCEPT_ID as TARGET_CONCEPT_ID, C.visit_occurrence_id,
       C.condition_start_date as sort_date
FROM 
(
  SELECT co.* 
  FROM @cdm_database_schema.CONDITION_OCCURRENCE co
  JOIN #Codesets codesets on ((co.condition_concept_id = codesets.concept_id and codesets.codeset_id = 0))
) C


-- End Condition Occurrence Criteria

) A on A.person_id = P.person_id  AND A.START_DATE >= P.OP_START_DATE AND A.START_DATE <= P.OP_END_DATE AND A.START_DATE >= P.OP_START_DATE AND A.START_DATE <= P.OP_END_DATE
GROUP BY p.person_id, p.event_id
HAVING COUNT(A.TARGET_CONCEPT_ID) = 0
-- End Correlated Criteria

  ) CQ on E.person_id = CQ.person_id and E.event_id = CQ.event_id
  GROUP BY E.person_id, E.event_id
  HAVING COUNT(index_id) = 1
) G
-- End Criteria Group
) AC on AC.person_id = pe.person_id AND AC.event_id = pe.event_id
) Results
;

select 2 as inclusion_rule_id, person_id, event_id
INTO #Inclusion_2
FROM 
(
  select pe.person_id, pe.event_id
  FROM #qualified_events pe
  
JOIN (
-- Begin Criteria Group
select 0 as index_id, person_id, event_id
FROM
(
  select E.person_id, E.event_id 
  FROM #qualified_events E
  INNER JOIN
  (
    -- Begin Correlated Criteria
SELECT 0 as index_id, p.person_id, p.event_id
FROM #qualified_events P
LEFT JOIN
(
  -- 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, 1, C.drug_exposure_start_date)) as end_date, C.drug_concept_id as TARGET_CONCEPT_ID, C.visit_occurrence_id,
       C.drug_exposure_start_date as sort_date
from 
(
  select de.* 
  FROM @cdm_database_schema.DRUG_EXPOSURE de
JOIN #Codesets codesets on ((de.drug_concept_id = codesets.concept_id and codesets.codeset_id = 1))
) C


-- End Drug Exposure Criteria

) A on A.person_id = P.person_id  AND A.START_DATE >= P.OP_START_DATE AND A.START_DATE <= P.OP_END_DATE AND A.START_DATE >= P.OP_START_DATE AND A.START_DATE <= P.OP_END_DATE
GROUP BY p.person_id, p.event_id
HAVING COUNT(A.TARGET_CONCEPT_ID) = 0
-- End Correlated Criteria

  ) CQ on E.person_id = CQ.person_id and E.event_id = CQ.event_id
  GROUP BY E.person_id, E.event_id
  HAVING COUNT(index_id) = 1
) G
-- End Criteria Group
) AC on AC.person_id = pe.person_id AND AC.event_id = pe.event_id
) Results
;

select 3 as inclusion_rule_id, person_id, event_id
INTO #Inclusion_3
FROM 
(
  select pe.person_id, pe.event_id
  FROM #qualified_events pe
  
JOIN (
-- Begin Criteria Group
select 0 as index_id, person_id, event_id
FROM
(
  select E.person_id, E.event_id 
  FROM #qualified_events E
  INNER JOIN
  (
    -- Begin Correlated Criteria
SELECT 0 as index_id, p.person_id, p.event_id
FROM #qualified_events P
LEFT JOIN
(
  -- 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, 1, C.drug_exposure_start_date)) as end_date, C.drug_concept_id as TARGET_CONCEPT_ID, C.visit_occurrence_id,
       C.drug_exposure_start_date as sort_date
from 
(
  select de.* 
  FROM @cdm_database_schema.DRUG_EXPOSURE de
JOIN #Codesets codesets on ((de.drug_concept_id = codesets.concept_id and codesets.codeset_id = 2))
) C


-- End Drug Exposure Criteria

) A on A.person_id = P.person_id  AND A.START_DATE >= P.OP_START_DATE AND A.START_DATE <= P.OP_END_DATE AND A.START_DATE >= P.OP_START_DATE AND A.START_DATE <= P.OP_END_DATE
GROUP BY p.person_id, p.event_id
HAVING COUNT(A.TARGET_CONCEPT_ID) = 0
-- End Correlated Criteria

  ) CQ on E.person_id = CQ.person_id and E.event_id = CQ.event_id
  GROUP BY E.person_id, E.event_id
  HAVING COUNT(index_id) = 1
) G
-- End Criteria Group
) AC on AC.person_id = pe.person_id AND AC.event_id = pe.event_id
) Results
;

select 4 as inclusion_rule_id, person_id, event_id
INTO #Inclusion_4
FROM 
(
  select pe.person_id, pe.event_id
  FROM #qualified_events pe
  
JOIN (
-- Begin Criteria Group
select 0 as index_id, person_id, event_id
FROM
(
  select E.person_id, E.event_id 
  FROM #qualified_events E
  INNER JOIN
  (
    -- Begin Correlated Criteria
SELECT 0 as index_id, p.person_id, p.event_id
FROM #qualified_events P
LEFT JOIN
(
  -- Begin Condition Occurrence Criteria
SELECT C.person_id, C.condition_occurrence_id as event_id, C.condition_start_date as start_date, COALESCE(C.condition_end_date, DATEADD(day,1,C.condition_start_date)) as end_date,
       C.CONDITION_CONCEPT_ID as TARGET_CONCEPT_ID, C.visit_occurrence_id,
       C.condition_start_date as sort_date
FROM 
(
  SELECT co.* 
  FROM @cdm_database_schema.CONDITION_OCCURRENCE co
  JOIN #Codesets codesets on ((co.condition_concept_id = codesets.concept_id and codesets.codeset_id = 3))
) C


-- End Condition Occurrence Criteria

) A on A.person_id = P.person_id  AND A.START_DATE >= P.OP_START_DATE AND A.START_DATE <= P.OP_END_DATE AND A.START_DATE >= P.OP_START_DATE AND A.START_DATE <= P.OP_END_DATE
GROUP BY p.person_id, p.event_id
HAVING COUNT(A.TARGET_CONCEPT_ID) = 0
-- End Correlated Criteria

  ) CQ on E.person_id = CQ.person_id and E.event_id = CQ.event_id
  GROUP BY E.person_id, E.event_id
  HAVING COUNT(index_id) = 1
) G
-- End Criteria Group
) AC on AC.person_id = pe.person_id AND AC.event_id = pe.event_id
) Results
;

select 5 as inclusion_rule_id, person_id, event_id
INTO #Inclusion_5
FROM 
(
  select pe.person_id, pe.event_id
  FROM #qualified_events pe
  
JOIN (
-- Begin Criteria Group
select 0 as index_id, person_id, event_id
FROM
(
  select E.person_id, E.event_id 
  FROM #qualified_events E
  INNER JOIN
  (
    -- Begin Correlated Criteria
SELECT 0 as index_id, p.person_id, p.event_id
FROM #qualified_events P
LEFT JOIN
(
  -- Begin Condition Occurrence Criteria
SELECT C.person_id, C.condition_occurrence_id as event_id, C.condition_start_date as start_date, COALESCE(C.condition_end_date, DATEADD(day,1,C.condition_start_date)) as end_date,
       C.CONDITION_CONCEPT_ID as TARGET_CONCEPT_ID, C.visit_occurrence_id,
       C.condition_start_date as sort_date
FROM 
(
  SELECT co.* 
  FROM @cdm_database_schema.CONDITION_OCCURRENCE co
  JOIN #Codesets codesets on ((co.condition_concept_id = codesets.concept_id and codesets.codeset_id = 4))
) C


-- End Condition Occurrence Criteria

) A on A.person_id = P.person_id  AND A.START_DATE >= P.OP_START_DATE AND A.START_DATE <= P.OP_END_DATE AND A.START_DATE >= P.OP_START_DATE AND A.START_DATE <= P.OP_END_DATE
GROUP BY p.person_id, p.event_id
HAVING COUNT(A.TARGET_CONCEPT_ID) = 0
-- End Correlated Criteria

  ) CQ on E.person_id = CQ.person_id and E.event_id = CQ.event_id
  GROUP BY E.person_id, E.event_id
  HAVING COUNT(index_id) = 1
) G
-- End Criteria Group
) AC on AC.person_id = pe.person_id AND AC.event_id = pe.event_id
) Results
;

SELECT inclusion_rule_id, person_id, event_id
INTO #inclusion_events
FROM (select inclusion_rule_id, person_id, event_id from #Inclusion_0
UNION ALL
select inclusion_rule_id, person_id, event_id from #Inclusion_1
UNION ALL
select inclusion_rule_id, person_id, event_id from #Inclusion_2
UNION ALL
select inclusion_rule_id, person_id, event_id from #Inclusion_3
UNION ALL
select inclusion_rule_id, person_id, event_id from #Inclusion_4
UNION ALL
select inclusion_rule_id, person_id, event_id from #Inclusion_5) I;
TRUNCATE TABLE #Inclusion_0;
DROP TABLE #Inclusion_0;

TRUNCATE TABLE #Inclusion_1;
DROP TABLE #Inclusion_1;

TRUNCATE TABLE #Inclusion_2;
DROP TABLE #Inclusion_2;

TRUNCATE TABLE #Inclusion_3;
DROP TABLE #Inclusion_3;

TRUNCATE TABLE #Inclusion_4;
DROP TABLE #Inclusion_4;

TRUNCATE TABLE #Inclusion_5;
DROP TABLE #Inclusion_5;


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

  -- the matching group with all bits set ( POWER(2,# of inclusion rules) - 1 = inclusion_rule_mask
  WHERE (MG.inclusion_rule_mask = POWER(cast(2 as bigint),6)-1)

)
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
;



-- 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
),
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
;

TRUNCATE TABLE @target_database_schema.t1d_controls;

INSERT INTO @target_database_schema.t1d_controls (person_id, age_days)
select CO.person_id, DATEDIFF(DAY, 
CONVERT(DATE,CAST([year_of_birth] AS VARCHAR(4))+'-'+
			 CAST(isnull([month_of_birth],7) AS VARCHAR(2))+'-'+
			 CAST(isnull([day_of_birth],1) AS VARCHAR(2))) , start_date) AS age_days
FROM #final_cohort CO
join @cdm_database_schema.person p on p.person_id = co.person_id
;



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;