Address sonorcloud issues

cBioPortal · Sep 11, 2024 · 8c0f82b · 8c0f82b
1 parent 002e515
commit 8c0f82b
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Showing 4 changed files with 9 additions and 31 deletions.
diff --git a/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java b/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java
@@ -11,7 +11,7 @@
 import org.springframework.lang.Nullable;
 
 import java.util.ArrayList;
-import java.util.HashMap;
+import java.util.EnumMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Objects;
@@ -24,7 +24,7 @@ public static StudyViewFilterHelper build(@Nullable StudyViewFilter studyViewFil
             studyViewFilter = new StudyViewFilter();
         }
         if (Objects.isNull(genericAssayProfilesMap)) {
-            genericAssayProfilesMap = new HashMap<>();
+            genericAssayProfilesMap = new EnumMap<>(DataSource.class);
         }
         if (Objects.isNull(customDataSamples)) {
             customDataSamples = new ArrayList<>();

diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
@@ -37,8 +37,7 @@ public class StudyViewMyBatisRepository implements StudyViewRepository {
 
     private Map<DataSource, List<ClinicalAttribute>> clinicalAttributesMap = new EnumMap<>(DataSource.class);
     private Map<DataSource, List<MolecularProfile>> genericAssayProfilesMap = new EnumMap<>(DataSource.class);
-
-
+
     private static final List<String> FILTERED_CLINICAL_ATTR_VALUES = Collections.emptyList();
     private final StudyViewMapper mapper;
 
@@ -217,25 +216,18 @@ public List<ClinicalDataCount> getGenomicDataBinCounts(StudyViewFilterContext st
     public List<ClinicalDataCount> getGenericAssayDataBinCounts(StudyViewFilterContext studyViewFilterContext, List<String> attributeIds) {
         return mapper.getGenericAssayDataBinCounts(createStudyViewFilterHelper(studyViewFilterContext), attributeIds);
     }
-
+    
     private void buildClinicalAttributeNameMap() {
         clinicalAttributesMap = this.getClinicalAttributes()
             .stream()
-            .collect(Collectors.groupingBy(ca -> ca.getPatientAttribute() ? DataSource.PATIENT : DataSource.SAMPLE));
+            .collect(Collectors.groupingBy(ca -> ca.getPatientAttribute().booleanValue() ? DataSource.PATIENT : DataSource.SAMPLE));
     }
 
     private void buildGenericAssayProfilesMap() {
         genericAssayProfilesMap = this.getGenericAssayProfiles()
             .stream()
             .collect(Collectors.groupingBy(ca -> ca.getPatientLevel().booleanValue() ? DataSource.PATIENT : DataSource.SAMPLE));
     }
-
-    private Map<DataSource, List<ClinicalAttribute>> getClinicalAttributeNameMap() {
-        if (clinicalAttributesMap.isEmpty()) {
-            buildClinicalAttributeNameMap();
-        }
-        return clinicalAttributesMap;
-    }
 
     private Map<DataSource, List<MolecularProfile>> getGenericAssayProfilesMap() {
         if (genericAssayProfilesMap.isEmpty()) {

diff --git a/src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java b/src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java
@@ -152,28 +152,20 @@ public <T extends DataBinCountFilter, S extends DataBinFilter, U extends DataBin
 
     private <S extends DataBinFilter> void removeSelfFromFilter(S dataBinFilter, StudyViewFilter studyViewFilter) {
         switch (dataBinFilter) {
-            case ClinicalDataBinFilter clinicalDataBinFilter -> {
-                if (studyViewFilter.getClinicalDataFilters() != null) {
+            case ClinicalDataBinFilter clinicalDataBinFilter when studyViewFilter.getClinicalDataFilters() != null ->
                     studyViewFilter.getClinicalDataFilters().removeIf(f -> f.getAttributeId().equals(clinicalDataBinFilter.getAttributeId()));
-                }
-            }
-            case GenomicDataBinFilter genomicDataBinFilter -> {
-                if (studyViewFilter.getGenomicDataFilters() != null) {
+            case GenomicDataBinFilter genomicDataBinFilter when studyViewFilter.getGenomicDataFilters() != null ->
                     studyViewFilter.getGenomicDataFilters().removeIf(f ->
                         f.getHugoGeneSymbol().equals(genomicDataBinFilter.getHugoGeneSymbol())
                             && f.getProfileType().equals(genomicDataBinFilter.getProfileType())
                     );
-                }
-            }
-            case GenericAssayDataBinFilter genericAssayDataBinFilter -> {
-                if (studyViewFilter.getGenericAssayDataFilters() != null) {
+            case GenericAssayDataBinFilter genericAssayDataBinFilter when studyViewFilter.getGenericAssayDataFilters() != null ->
                     studyViewFilter.getGenericAssayDataFilters().removeIf(f ->
                         f.getStableId().equals(genericAssayDataBinFilter.getStableId())
                             && f.getProfileType().equals(genericAssayDataBinFilter.getProfileType())
                     );
-                }
-            }
             default -> {
+                // Do not remove any filters
             }
         }
     }
@@ -223,7 +215,6 @@ private <T extends DataBinFilter, U extends DataBin> List<U> calculateStaticData
 
         for (T dataBinFilter : dataBinFilters) {
             // if there is data for requested attribute
-            // TODO: consider if this is correct to passing in a empty map
             if (attributeDatatypeMap.isEmpty() || attributeDatatypeMap.containsKey(getDataBinFilterUniqueKey(dataBinFilter))) {
                 List<U> dataBins = dataBinner
                     .calculateClinicalDataBins(
@@ -252,7 +243,6 @@ private <T extends DataBinFilter, U extends DataBin> List<U> calculateDynamicDat
 
         for (T dataBinFilter : dataBinFilters) {
             // if there is data for requested attribute
-            // TODO: consider if this is correct to passing in a empty map
             if (attributeDatatypeMap.isEmpty() || attributeDatatypeMap.containsKey(getDataBinFilterUniqueKey(dataBinFilter))) {
                 List<U> dataBins = dataBinner
                     .calculateDataBins(

diff --git a/...va/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java b/...va/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java
@@ -1,8 +1,6 @@
 package org.cbioportal.persistence.mybatisclickhouse;
 
-import org.cbioportal.model.ClinicalAttribute;
 import org.cbioportal.model.ClinicalDataCount;
-import org.cbioportal.persistence.enums.DataSource;
 import org.cbioportal.persistence.helper.StudyViewFilterHelper;
 import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig;
 import org.cbioportal.web.parameter.ClinicalDataFilter;
@@ -20,9 +18,7 @@
 
 import java.math.BigDecimal;
 import java.util.Collections;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
 
 import static org.junit.Assert.assertEquals;