fix minCharacterizationMean in query (#275)

OHDSI · Sep 11, 2024 · fe5c03c · fe5c03c
1 parent b5bb15d
commit fe5c03c
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Showing 6 changed files with 9 additions and 7 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: FeatureExtraction
 Type: Package
 Title: Generating Features for a Cohort
-Version: 3.7.0
-Date: 2024-09-02
+Version: 3.7.1
+Date: 2024-09-11
 Authors@R: c(
   person("Martijn", "Schuemie", , "schuemie@ohdsi.org", role = c("aut")),
   person("Marc", "Suchard", role = c("aut")),

diff --git a/inst/csv/jarChecksum.txt b/inst/csv/jarChecksum.txt
@@ -1 +1 @@
-d9f6ed460fb4a758786965f83b3c18f85dcdf3a1c9cb1b12319b1f7af243f9ef
+b7c50aec30a5ec21a39c02253133a4e9607c9630010123844a75d858c0ec684a
diff --git a/...java/featureExtraction-3.7.0-SNAPSHOT.jar → ...java/featureExtraction-3.7.1-SNAPSHOT.jar b/...java/featureExtraction-3.7.0-SNAPSHOT.jar → ...java/featureExtraction-3.7.1-SNAPSHOT.jar
diff --git a/java/org/ohdsi/featureExtraction/FeatureExtraction.java b/java/org/ohdsi/featureExtraction/FeatureExtraction.java
@@ -744,7 +744,7 @@ private static String createQuerySql(JSONObject jsonObject, String cohortTable,
 			sql.append("\n) all_covariates\nINNER JOIN (\nSELECT cohort_definition_id, COUNT(*) AS total_count\nFROM @cohort_table {@cohort_definition_id != -1} ? {\nWHERE cohort_definition_id IN (@cohort_definition_id)}");
 			sql.append(" GROUP BY cohort_definition_id\n) total\n  ON all_covariates.cohort_definition_id = total.cohort_definition_id");
 			if (minCharacterizationMean != 0) {
-				sql.append(" WHERE average_value >= " + minCharacterizationMean);
+				sql.append(" WHERE all_covariates.sum_value / (1.0 * total.total_count) >= " + minCharacterizationMean);
 			}
 			sql.append(";");
 		} else {

diff --git a/pom.xml b/pom.xml
@@ -5,7 +5,7 @@
 	<groupId>org.ohdsi</groupId>
 	<artifactId>featureExtraction</artifactId>
 	<packaging>jar</packaging>
-	<version>3.7.0-SNAPSHOT</version>
+	<version>3.7.1-SNAPSHOT</version>
 	<name>featureExtraction</name>
 	<scm>
 		<connection>scm:git:https://github.com/OHDSI/featureExtraction</connection>

diff --git a/tests/testthat/test-query-no-fail.R b/tests/testthat/test-query-no-fail.R
@@ -318,7 +318,8 @@ runExtractionAggregated <- function(connection, cdmDatabaseSchema, ohdsiDatabase
     cohortIds = c(1124300),
     rowIdField = "subject_id",
     covariateSettings = settings,
-    aggregated = TRUE
+    aggregated = TRUE,
+    minCharacterizationMean = 0.001
   ))
   return(covariateData)
 }
@@ -531,7 +532,8 @@ runExtractionTemporalAggregated <- function(connection, cdmDatabaseSchema, ohdsi
     cohortIds = c(1124300),
     rowIdField = "subject_id",
     covariateSettings = settings,
-    aggregated = TRUE
+    aggregated = TRUE,
+    minCharacterizationMean = 0.001
   ))
   return(covariateData)
 }
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		d9f6ed460fb4a758786965f83b3c18f85dcdf3a1c9cb1b12319b1f7af243f9ef
		b7c50aec30a5ec21a39c02253133a4e9607c9630010123844a75d858c0ec684a