From 98911c6e19a8b013fd433d28acd885b9e83b3ae5 Mon Sep 17 00:00:00 2001
From: Vitaly Koulakov <vitaly.koulakov@gmail.com>
Date: Wed, 23 Jan 2019 00:14:48 +0300
Subject: [PATCH] Fix inclusion impact analysis where censor period is being
 used (#66)

* Added cohort_censor_stats table.
* censor stats only calculated when there is a censor window specified.
---
 .../cohortdefinition/CohortExpressionQueryBuilder.java | 10 ++++++++--
 .../cohortdefinition/sql/cohortCensoredStats.sql       |  7 +++++++
 .../resources/cohortdefinition/sql/generateCohort.sql  |  4 ++++
 3 files changed, 19 insertions(+), 2 deletions(-)
 create mode 100644 src/main/resources/resources/cohortdefinition/sql/cohortCensoredStats.sql

diff --git a/src/main/java/org/ohdsi/circe/cohortdefinition/CohortExpressionQueryBuilder.java b/src/main/java/org/ohdsi/circe/cohortdefinition/CohortExpressionQueryBuilder.java
index bb0b5f43..8134f491 100644
--- a/src/main/java/org/ohdsi/circe/cohortdefinition/CohortExpressionQueryBuilder.java
+++ b/src/main/java/org/ohdsi/circe/cohortdefinition/CohortExpressionQueryBuilder.java
@@ -68,6 +68,7 @@ public class CohortExpressionQueryBuilder implements IGetCriteriaSqlDispatcher,
 	private final static String CODESET_JOIN_TEMPLATE = "JOIN #Codesets codesets on (@codesetClauses)";
   
 	private final static String COHORT_INCLUSION_ANALYSIS_TEMPALTE = ResourceHelper.GetResourceAsString("/resources/cohortdefinition/sql/cohortInclusionAnalysis.sql");
+	private final static String COHORT_CENSORED_STATS_TEMPLATE = ResourceHelper.GetResourceAsString("/resources/cohortdefinition/sql/cohortCensoredStats.sql");
 
   // Strategy templates
   private final static String DATE_OFFSET_STRATEGY_TEMPLATE = ResourceHelper.GetResourceAsString("/resources/cohortdefinition/sql/dateOffsetStrategy.sql");
@@ -365,7 +366,7 @@ private String getInclusionAnalysisQuery(String eventTable, int modeId) {
 		resultSql = StringUtils.replace(resultSql, "@eventTable", eventTable);
 		return resultSql;
 	}
-	
+
   public String buildExpressionQuery(CohortExpression expression, BuildExpressionQueryOptions options) {
     String resultSql = COHORT_QUERY_TEMPLATE;
 
@@ -463,7 +464,12 @@ public String buildExpressionQuery(CohortExpression expression, BuildExpressionQ
 	
 		resultSql = StringUtils.replace(resultSql, "@inclusionImpactAnalysisByEventQuery", getInclusionAnalysisQuery("#qualified_events", 0));
 		resultSql = StringUtils.replace(resultSql, "@inclusionImpactAnalysisByPersonQuery", getInclusionAnalysisQuery("#best_events", 1));
-		
+
+		resultSql = StringUtils.replace(resultSql, "@cohortCensoredStatsQuery",
+			(expression.censorWindow != null && (!StringUtils.isEmpty(expression.censorWindow.startDate) || !StringUtils.isEmpty(expression.censorWindow.endDate))) 
+				? COHORT_CENSORED_STATS_TEMPLATE 
+				: "");
+
     if (options != null)
     {
       // replease query parameters with tokens
diff --git a/src/main/resources/resources/cohortdefinition/sql/cohortCensoredStats.sql b/src/main/resources/resources/cohortdefinition/sql/cohortCensoredStats.sql
new file mode 100644
index 00000000..5826970e
--- /dev/null
+++ b/src/main/resources/resources/cohortdefinition/sql/cohortCensoredStats.sql
@@ -0,0 +1,7 @@
+-- calculate censored
+delete from @results_database_schema.cohort_censor_stats where cohort_definition_id = @target_cohort_id;
+insert into @results_database_schema.cohort_censor_stats (cohort_definition_id, lost_count)
+	select @target_cohort_id as cohort_definition_id, coalesce(FCC.total_people - TC.total, 0) as lost_count
+	FROM
+		(select count_big(distinct person_id) as total_people from #final_cohort) FCC,
+		(select count_big(distinct subject_id) as total from @target_database_schema.@target_cohort_table t where t.cohort_definition_id = @target_cohort_id) TC;
\ No newline at end of file
diff --git a/src/main/resources/resources/cohortdefinition/sql/generateCohort.sql b/src/main/resources/resources/cohortdefinition/sql/generateCohort.sql
index 1660b4bf..9ad9f9fd 100644
--- a/src/main/resources/resources/cohortdefinition/sql/generateCohort.sql
+++ b/src/main/resources/resources/cohortdefinition/sql/generateCohort.sql
@@ -151,6 +151,10 @@ WHERE ranked.rank_value = 1
 @inclusionImpactAnalysisByPersonQuery
 -- END: Inclusion Impact Analysis - person
 
+-- BEGIN: Censored Stats
+@cohortCensoredStatsQuery
+-- END: Censored Stats
+
 TRUNCATE TABLE #best_events;
 DROP TABLE #best_events;