fixed output

alisman · Jan 2, 2025 · 336515b · 336515b
1 parent e4af8ef
commit 336515b
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Showing 2 changed files with 33 additions and 22 deletions.
diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
@@ -325,8 +325,29 @@ public HashMap<String, AlterationCountByGene> getAlterationEnrichmentCounts(List
         Map<String, List<String>> clumps = samplesToPanelMap.keySet().stream().collect(Collectors.groupingBy(
             sampleId->samplesToPanelMap.get(sampleId).stream().collect(Collectors.joining(","))
         ));
+
+
+        var alterationCounts = mapper.getAlterationEnrichmentCounts(sampleStableIds);
+
+        HashMap<String, AlterationCountByGene> alteredGenesWithCounts = new HashMap();
+
+        // we need map of genes to alteration counts
+        alterationCounts.stream().forEach((alterationCountByGene) -> {
+            String hugoGeneSymbol = alterationCountByGene.getHugoGeneSymbol();
+            int count = alterationCountByGene.getNumberOfAlteredCases();
+            if (!alteredGenesWithCounts.containsKey(hugoGeneSymbol)) {
+                var acg = new AlterationCountByGene();
+                acg.setHugoGeneSymbol(hugoGeneSymbol);
+                acg.setNumberOfAlteredCases(0);
+                alteredGenesWithCounts.put(hugoGeneSymbol,acg);
+            }
+            // add the count to existing tally
+            alteredGenesWithCounts.get(hugoGeneSymbol).setNumberOfAlteredCases(
+                count + alteredGenesWithCounts.get(hugoGeneSymbol).getNumberOfAlteredCases()
+            );
 
-
+        });
+
         var geneCount = new HashMap<String,AlterationCountByGene>();
 
         clumps.entrySet().stream().forEach(entry->{
@@ -351,36 +372,22 @@ public HashMap<String, AlterationCountByGene> getAlterationEnrichmentCounts(List
                         var alterationCountByGene = new AlterationCountByGene();
                         alterationCountByGene.setHugoGeneSymbol(gene);
                         alterationCountByGene.setNumberOfProfiledCases(entry.getValue().size());
+                        alterationCountByGene.setNumberOfAlteredCases(0);
                         geneCount.put(gene,alterationCountByGene);
                     }
                 });
 
         });
 
-
-        var doo = mapper.getAlterationEnrichmentCounts(sampleStableIds);
-
-        HashMap<String, Map<String, Integer>> alteredGenesWithCounts = new HashMap();
-
-        // we need map of genes to alteration counts
-        doo.stream().forEach((alterationCountByGene) -> {
-            String hugoGeneSymbol = alterationCountByGene.getHugoGeneSymbol();
-            int count = alterationCountByGene.getNumberOfAlteredCases();
-            if (!alteredGenesWithCounts.containsKey(hugoGeneSymbol)) {
-                alteredGenesWithCounts.put(hugoGeneSymbol, new HashMap<>());
-                alteredGenesWithCounts.get(hugoGeneSymbol).put("count", 0);
+        alteredGenesWithCounts.entrySet().stream().forEach(n->{
+            if (geneCount.containsKey(n.getKey())) {
+                n.getValue().setNumberOfProfiledCases(
+                    geneCount.get(n.getKey()).getNumberOfProfiledCases()
+                );
             }
-            alteredGenesWithCounts.get(hugoGeneSymbol).put("count", alteredGenesWithCounts.get(hugoGeneSymbol).get("count") + count);
         });
-
-
-
-
-//            const panelsToGeneMaps = _(panelGenes).groupBy("gene_panel_id")
-//            .mapValues(arr=>_.keyBy(arr,"gene")).value();
-
 
-        return geneCount;
+        return alteredGenesWithCounts;
     }
 
     public Map<String, Integer> getMutationCounts(StudyViewFilterContext studyViewFilterContext, GenomicDataFilter genomicDataFilter) {

diff --git a/src/main/java/org/cbioportal/web/columnar/EnrichmentsColumnStoreController.java b/src/main/java/org/cbioportal/web/columnar/EnrichmentsColumnStoreController.java
@@ -195,8 +195,12 @@ public ResponseEntity<List<AlterationEnrichment>> fetchAlterationEnrichmentsNew(
                      summary.setProfiledCount(
                         geneCount.getNumberOfProfiledCases()
                     );
+                     summary.setAlteredCount(
+                         geneCount.getNumberOfAlteredCases()
+                     );
                  } else {
                      summary.setProfiledCount(0);
+                     summary.setAlteredCount(0);
                  }
                  return summary;
              }).collect(Collectors.toList());