From 2b87a263cbd4781da87041be84b0c6d89a41efc2 Mon Sep 17 00:00:00 2001
From: Charles Haynes <33608920+haynescd@users.noreply.github.com>
Date: Tue, 25 Jun 2024 09:59:52 -0400
Subject: [PATCH] :bug: Fix totalCount calculation when WES not available
 (#10858)

---
 .../service/impl/AlterationCountServiceImpl.java      | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java b/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java
index 67079dc5b63..29f94f0fd0f 100644
--- a/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java
+++ b/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java
@@ -19,7 +19,6 @@
 import org.cbioportal.web.parameter.StudyViewFilter;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.lang.NonNull;
-import org.springframework.lang.Nullable;
 import org.springframework.stereotype.Service;
 
 import java.util.ArrayList;
@@ -286,7 +285,7 @@ private < T extends AlterationCountByGene> List<T> populateAlterationCounts(@Non
                 Set<String> matchingGenePanelIds = matchingGenePanelIdsMap.get(hugoGeneSymbol) != null ?
                     matchingGenePanelIdsMap.get(hugoGeneSymbol) : Collections.emptySet();
 
-                int totalProfiledCount = getTotalProfiledCount(alterationCountByGene.getHugoGeneSymbol(),
+                int totalProfiledCount = getTotalProfiledCount(hugoGeneSymbol,
                     profiledCountsMap, profiledCountWithoutGenePanelData, matchingGenePanelIds);
 
                 alterationCountByGene.setNumberOfProfiledCases(totalProfiledCount);
@@ -297,7 +296,7 @@ private < T extends AlterationCountByGene> List<T> populateAlterationCounts(@Non
     }
 
     private int getTotalProfiledCount(@NonNull String hugoGeneSymbol, @NonNull Map<String, AlterationCountByGene> profiledCountsMap,
-                                      int profiledCountWithoutGenePanelData, @Nullable Set<String> matchingGenePanelIds) {
+                                      int profiledCountWithoutGenePanelData, @NonNull Set<String> matchingGenePanelIds) {
         int totalProfiledCount = profiledCountWithoutGenePanelData;
         
         if (hasGenePanelData(matchingGenePanelIds) && profiledCountsMap.containsKey(hugoGeneSymbol)) {
@@ -306,9 +305,9 @@ private int getTotalProfiledCount(@NonNull String hugoGeneSymbol, @NonNull Map<S
         return totalProfiledCount;
     }
     
-    private boolean hasGenePanelData(@Nullable Set<String> matchingGenePanelIds) {
-        return matchingGenePanelIds != null && matchingGenePanelIds.contains(WHOLE_EXOME_SEQUENCING) 
-            && matchingGenePanelIds.size() > 1;
+    private boolean hasGenePanelData(@NonNull Set<String> matchingGenePanelIds) {
+        return matchingGenePanelIds.contains(WHOLE_EXOME_SEQUENCING) 
+            && matchingGenePanelIds.size() > 1 || !matchingGenePanelIds.contains(WHOLE_EXOME_SEQUENCING) && !matchingGenePanelIds.isEmpty();
     }
 
     private <S extends AlterationCountBase> Pair<List<S>, Long> getAlterationGeneCounts(