Stable sort structural variant genes (#11861)

* make sure to stable sort structural variant genes first by total count and then by hugo gene symbol

* also sort mutated genes and cna genes by total count and gene symbol

Author: onursumer

src/main/java/org/cbioportal/domain/alteration/usecase/GetAlterationCountByGeneUseCase.java

@@ -1,6 +1,6 @@
 package org.cbioportal.domain.alteration.usecase;
 
-import java.util.HashMap;
+import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.function.Function;
@@ -85,7 +85,7 @@ public List<AlterationCountByGene> execute(
    */
   private List<AlterationCountByGene> combineAlterationCountsWithConflictingHugoSymbols(
       List<AlterationCountByGene> alterationCounts) {
-    Map<String, AlterationCountByGene> alterationCountByGeneMap = new HashMap<>();
+    Map<String, AlterationCountByGene> alterationCountByGeneMap = new LinkedHashMap<>();
     for (var alterationCount : alterationCounts) {
       if (alterationCountByGeneMap.containsKey(alterationCount.getHugoGeneSymbol())) {
         AlterationCountByGene toUpdate =
@@ -136,7 +136,7 @@ private List<AlterationCountByGene> populateAlterationCountsWithMutSigQValue(
   private Map<String, MutSig> getMutSigs(StudyViewFilterContext studyViewFilterContext)
       throws StudyNotFoundException {
     var distinctStudyIds = getFilteredStudyIdsUseCase.execute(studyViewFilterContext);
-    Map<String, MutSig> mutSigs = new HashMap<>();
+    Map<String, MutSig> mutSigs = new LinkedHashMap<>();
     if (distinctStudyIds.size() == 1) {
       var studyId = distinctStudyIds.getFirst();
       mutSigs =

src/main/resources/mappers/clickhouse/alteration/ClickhouseAlterationMapper.xml

@@ -29,6 +29,7 @@
             </if>
         </where>
         GROUP BY entrez_gene_id, hugo_gene_symbol
+        ORDER BY totalCount DESC, hugo_gene_symbol ASC
     </select>
 
     <!-- /cna-genes/fetch (returns CopyNumberCountByGene) -->
@@ -55,6 +56,7 @@
             </if>
         </where>
         GROUP BY entrez_gene_id, hugo_gene_symbol, alteration, cytoband
+        ORDER BY totalCount DESC, hugo_gene_symbol ASC
     </select>
 
     <select
@@ -77,6 +79,7 @@
             <include refid="whereMutationStatus" />
         </where>
         GROUP BY entrez_gene_id, hugo_gene_symbol
+        ORDER BY totalCount DESC, hugo_gene_symbol ASC
     </select>
 
     <!-- Grab Total Profiled Counts. Currently, this query filters out all samples associated with a Gene Panel WES before