Fix Sonar issues

cBioPortal · Nov 14, 2024 · 0436da7 · 0436da7
1 parent 1e641db
commit 0436da7
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Showing 3 changed files with 7 additions and 9 deletions.
diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
@@ -170,7 +170,7 @@ public List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilter studyVi
             var attributes = getClinicalAttributesForStudies(involvedCancerStudies)
                 .stream()
                 .filter(attribute -> filteredAttributes.contains(attribute.getAttrId()))
-                .collect(Collectors.toList());
+                .toList();
 
             Integer filteredSampleCount = studyViewRepository.getFilteredSamplesCount(createContext(studyViewFilter));
             Integer filteredPatientCount = studyViewRepository.getFilteredPatientCount(createContext(studyViewFilter));
@@ -192,8 +192,7 @@ public List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilter studyVi
         condition = "@cacheEnabledConfig.getEnabledClickhouse()"
     )
     public List<ClinicalAttribute> getClinicalAttributesForStudies(List<String> studyIds) {
-        return studyViewRepository.getClinicalAttributesForStudies(studyIds).stream()
-            .collect(Collectors.toList());
+        return studyViewRepository.getClinicalAttributesForStudies(studyIds).stream().toList();
     }
 
     @Cacheable(

diff --git a/src/main/java/org/cbioportal/service/util/StudyViewColumnarServiceUtil.java b/src/main/java/org/cbioportal/service/util/StudyViewColumnarServiceUtil.java
@@ -3,28 +3,28 @@
 import org.cbioportal.model.ClinicalAttribute;
 import org.cbioportal.model.ClinicalDataCount;
 import org.cbioportal.model.ClinicalDataCountItem;
-import org.cbioportal.model.Sample;
-
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 import java.util.stream.Collectors;
 
 public class StudyViewColumnarServiceUtil {
 
+    private StudyViewColumnarServiceUtil() {}
+
     public static List<ClinicalDataCountItem> mergeClinicalDataCounts(
         List<ClinicalDataCountItem> items
     ) {
         items.forEach(attr -> {
             Map<String, List<ClinicalDataCount>> countsPerType = attr.getCounts().stream()
                 .collect(Collectors.groupingBy(ClinicalDataCount::getValue));
-            List<ClinicalDataCount> res = countsPerType.entrySet().stream().map((entry) -> {
+            List<ClinicalDataCount> res = countsPerType.entrySet().stream().map(entry -> {
                 ClinicalDataCount mergedCount = new ClinicalDataCount();
                 mergedCount.setAttributeId(attr.getAttributeId());
                 mergedCount.setValue(entry.getKey());
                 mergedCount.setCount(entry.getValue().stream().mapToInt(ClinicalDataCount::getCount).sum());
                 return mergedCount;
-            }).collect(Collectors.toList());
+            }).toList();
             attr.setCounts(res);
         });
         return items;
@@ -42,7 +42,7 @@ public static List<ClinicalDataCountItem> addClinicalDataCountsForMissingAttribu
         List<ClinicalDataCountItem> result = new ArrayList<>(counts);
 
         attributes.forEach(attr -> {
-            Integer count = attr.getPatientAttribute() ? filteredPatientCount : filteredSampleCount;
+            Integer count = attr.getPatientAttribute().booleanValue() == true ? filteredPatientCount : filteredSampleCount;
 
             if (!map.containsKey(attr.getAttrId())) {
                 ClinicalDataCountItem newItem = new ClinicalDataCountItem();

diff --git a/src/test/java/org/cbioportal/service/util/StudyViewColumnarServiceUtilTest.java b/src/test/java/org/cbioportal/service/util/StudyViewColumnarServiceUtilTest.java
@@ -3,7 +3,6 @@
 import org.cbioportal.model.ClinicalAttribute;
 import org.cbioportal.model.ClinicalDataCount;
 import org.cbioportal.model.ClinicalDataCountItem;
-import org.cbioportal.model.Sample;
 import org.junit.Assert;
 import org.junit.Test;