fix study view service errors

gblaih · Dec 6, 2024 · 58fee52 · 58fee52
1 parent 781d1d8
commit 58fee52
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Showing 2 changed files with 2 additions and 21 deletions.
diff --git a/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java b/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java
@@ -393,26 +393,7 @@ private <S extends AlterationCountBase> Pair<List<S>, Long> getAlterationGeneCou
                         Long studyProfiledCasesCount = includeFrequencyFunction.apply(studyMolecularProfileCaseIdentifiers, studyAlterationCountByGenes);
                         profiledCasesCount.updateAndGet(v -> v + studyProfiledCasesCount);
                     }
-                    studyAlterationCountByGenes.forEach(datum -> {
-                        String key = datum.getUniqueEventKey();
-                        if (totalResult.containsKey(key)) {
-                            S alterationCountByGene = totalResult.get(key);
-                            alterationCountByGene.setTotalCount(alterationCountByGene.getTotalCount() + datum.getTotalCount());
-                            alterationCountByGene.setNumberOfAlteredCases(alterationCountByGene.getNumberOfAlteredCases() + datum.getNumberOfAlteredCases());
-                            alterationCountByGene.setNumberOfProfiledCases(alterationCountByGene.getNumberOfProfiledCases() + datum.getNumberOfProfiledCases());
-                            Set<String> matchingGenePanelIds = new HashSet<>();
-                            if (!alterationCountByGene.getMatchingGenePanelIds().isEmpty()) {
-                                matchingGenePanelIds.addAll(alterationCountByGene.getMatchingGenePanelIds());
-                            }
-                            if (!datum.getMatchingGenePanelIds().isEmpty()) {
-                                matchingGenePanelIds.addAll(datum.getMatchingGenePanelIds());
-                            }
-                            alterationCountByGene.setMatchingGenePanelIds(matchingGenePanelIds);
-                            totalResult.put(key, alterationCountByGene);
-                        } else {
-                            totalResult.put(key, datum);
-                        }
-                    });
+                    AlterationCountServiceUtil.setupAlterationGeneCountsMap(studyAlterationCountByGenes, totalResult);
                 });
             alterationCountByGenes = new ArrayList<>(totalResult.values());
         }

diff --git a/src/main/java/org/cbioportal/service/util/StudyViewColumnarServiceUtil.java b/src/main/java/org/cbioportal/service/util/StudyViewColumnarServiceUtil.java
@@ -164,7 +164,7 @@ public static List<ClinicalDataCount> normalizeDataCounts(List<ClinicalDataCount
     public static GenomicDataCountItem createGenomicDataCountItemFromMutationCounts(GenomicDataFilter genomicDataFilter, Map<String, Integer> counts) {
         List<GenomicDataCount> genomicDataCountList = new ArrayList<>();
         if (counts.getOrDefault(MUTATED_COUNT, 0) > 0)
-            genomicDataCountList.add(new GenomicDataCount("Mutated", "MUTATED", counts.get("MUTATED_COUNT"), counts.get("MUTATED_COUNT")));
+            genomicDataCountList.add(new GenomicDataCount("Mutated", "MUTATED", counts.get(MUTATED_COUNT), counts.get(MUTATED_COUNT)));
         if (counts.getOrDefault(NOT_MUTATED_COUNT, 0) > 0)
             genomicDataCountList.add(new GenomicDataCount("Not Mutated", "NOT_MUTATED", counts.get(NOT_MUTATED_COUNT), counts.get(NOT_MUTATED_COUNT)));
         if (counts.getOrDefault(NOT_PROFILED_COUNT, 0) > 0)