Updated Era logic in final cohort and custom era strategy.

Fixes #204.

pom.xml

@@ -5,7 +5,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.ohdsi</groupId>
   <artifactId>circe</artifactId>
-  <version>1.11.2-SNAPSHOT</version>
+  <version>1.11.3-SNAPSHOT</version>
   <properties>
     <maven.compiler.source>1.8</maven.compiler.source>
     <maven.compiler.target>1.8</maven.compiler.target>

src/main/resources/resources/cohortdefinition/sql/customEraStrategy.sql

@@ -26,38 +26,20 @@ INTO #strategy_ends
 from @eventTable et
 JOIN 
 (
-  select ENDS.person_id, min(drug_exposure_start_date) as era_start_date, DATEADD(day,@offset, 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 * @gapDays,EVENT_DATE) as END_DATE -- unpad the end date by @gapDays
-      FROM
-      (
-				select PERSON_ID, EVENT_DATE, EVENT_TYPE, 
-				MAX(START_ORDINAL) OVER (PARTITION BY PERSON_ID ORDER BY event_date, event_type, START_ORDINAL ROWS UNBOUNDED PRECEDING) AS start_ordinal,
-				ROW_NUMBER() OVER (PARTITION BY PERSON_ID ORDER BY EVENT_DATE, EVENT_TYPE, START_ORDINAL) 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 @gapDays to allow a grace period for overlapping ranges.
-					select PERSON_ID, DATEADD(day,@gapDays,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
+  select person_id, min(start_date) as era_start_date, DATEADD(day,-1 * @gapDays, max(end_date)) as era_end_date
+  from (
+    select person_id, start_date, end_date, sum(is_start) over (partition by person_id order by start_date, is_start desc rows unbounded preceding) group_idx
+    from (
+      select person_id, start_date, end_date, 
+        case when max(end_date) over (partition by person_id order by start_date rows between unbounded preceding and 1 preceding) >= start_date then 0 else 1 end is_start
+      from (
+        select person_id, drug_exposure_start_date as start_date, DATEADD(day,(@gapDays + @offset),DRUG_EXPOSURE_END_DATE) as end_date
+        FROM #drugTarget
+      ) DT
+    ) ST
+  ) GR
+  group by person_id, group_idx
 ) ERAS on ERAS.person_id = et.person_id 
 WHERE et.start_date between ERAS.era_start_date and ERAS.era_end_date;
 

src/main/resources/resources/cohortdefinition/sql/generateCohort.sql

@@ -52,49 +52,21 @@ from ( -- first_ends
 	WHERE F.ordinal = 1
 ) FE;
 
-select person_id, min(start_date) as start_date, end_date
+
+select person_id, min(start_date) as start_date, DATEADD(day,-1 * @eraconstructorpad, max(end_date)) as end_date
 into #final_cohort
-from ( --cteEnds
-	SELECT
-		 c.person_id
-		, c.start_date
-		, MIN(ed.end_date) AS end_date
-	FROM #cohort_rows c
-	JOIN ( -- cteEndDates
-    SELECT
-      person_id
-      , DATEADD(day,-1 * @eraconstructorpad, event_date)  as end_date
-    FROM
-    (
-      SELECT
-        person_id
-        , event_date
-        , event_type
-        , SUM(event_type) OVER (PARTITION BY person_id ORDER BY event_date, event_type ROWS UNBOUNDED PRECEDING) AS interval_status
-      FROM
-      (
-        SELECT
-          person_id
-          , start_date AS event_date
-          , -1 AS event_type
-        FROM #cohort_rows
-
-        UNION ALL
-
-
-        SELECT
-          person_id
-          , DATEADD(day,@eraconstructorpad,end_date) as end_date
-          , 1 AS event_type
-        FROM #cohort_rows
-      ) RAWDATA
-    ) e
-    WHERE interval_status = 0
-  ) ed ON c.person_id = ed.person_id AND ed.end_date >= c.start_date
-	GROUP BY c.person_id, c.start_date
-) e
-group by person_id, end_date
-;
+from (
+  select person_id, start_date, end_date, sum(is_start) over (partition by person_id order by start_date, is_start desc rows unbounded preceding) group_idx
+  from (
+    select person_id, start_date, end_date, 
+      case when max(end_date) over (partition by person_id order by start_date rows between unbounded preceding and 1 preceding) >= start_date then 0 else 1 end is_start
+    from (
+      select person_id, start_date, DATEADD(day,@eraconstructorpad,end_date) as end_date
+      from #cohort_rows
+    ) CR
+  ) ST
+) GR
+group by person_id, group_idx;
 
 DELETE FROM @target_database_schema.@target_cohort_table where @cohort_id_field_name = @target_cohort_id;
 INSERT INTO @target_database_schema.@target_cohort_table (@cohort_id_field_name, subject_id, cohort_start_date, cohort_end_date)