diff --git a/.gitignore b/.gitignore
index 4dda110d9ac..c2b81971328 100644
--- a/.gitignore
+++ b/.gitignore
@@ -73,7 +73,7 @@ portal/src/main/webapp/WEB-INF/logback.xml
 !src/main/resource/*.EXAMPLE
 firehose-importer/reference_data/gene_info
 portal.properties
-application.properties
+src/main/resources/application.properties
 importer.properties
 log4j.properties
 build.properties
@@ -103,7 +103,6 @@ package.json
 *.tramp_history
 pom.version.*
 pom.xml.*
-pom.xml.*
 Dockerfile.local
 .factorypath
 .retype
diff --git a/src/main/java/org/cbioportal/service/impl/MolecularProfileServiceImpl.java b/src/main/java/org/cbioportal/service/impl/MolecularProfileServiceImpl.java
index 9d46158a2e2..3a4d6c8a1d7 100644
--- a/src/main/java/org/cbioportal/service/impl/MolecularProfileServiceImpl.java
+++ b/src/main/java/org/cbioportal/service/impl/MolecularProfileServiceImpl.java
@@ -9,14 +9,17 @@
 import org.cbioportal.service.exception.MolecularProfileNotFoundException;
 import org.cbioportal.service.exception.StudyNotFoundException;
 import org.cbioportal.service.util.MolecularProfileUtil;
+import org.cbioportal.web.parameter.Projection;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.security.access.prepost.PostFilter;
 import org.springframework.stereotype.Service;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Optional;
+import java.util.Set;
 import java.util.function.Predicate;
-import java.util.stream.Collectors;
 
 @Service
 public class MolecularProfileServiceImpl implements MolecularProfileService {
@@ -145,13 +148,13 @@ public List<MolecularProfileCaseIdentifier> getFirstStructuralVariantProfileCase
 
     private List<MolecularProfileCaseIdentifier> getFirstFilteredMolecularProfileCaseIdentifiers(List<String> studyIds, List<String> sampleIds, Optional<Predicate<MolecularProfile>> profileFilter) {
         List<MolecularProfile> molecularProfiles =
-            getMolecularProfilesInStudies(studyIds.stream().distinct().collect(Collectors.toList()), "SUMMARY");
+            getMolecularProfilesInStudies(studyIds.stream().distinct().toList(), Projection.SUMMARY.name());
         return molecularProfileUtil.getFirstFilteredMolecularProfileCaseIdentifiers(molecularProfiles, studyIds, sampleIds, profileFilter);
     }
 
     private List<MolecularProfileCaseIdentifier> getFilteredMolecularProfileCaseIdentifiers(List<String> studyIds, List<String> sampleIds, Optional<Predicate<MolecularProfile>> profileFilter) {
         List<MolecularProfile> molecularProfiles =
-            getMolecularProfilesInStudies(studyIds.stream().distinct().collect(Collectors.toList()), "SUMMARY");
+            getMolecularProfilesInStudies(studyIds.stream().distinct().toList(), Projection.SUMMARY.name());
         return molecularProfileUtil.getFilteredMolecularProfileCaseIdentifiers(molecularProfiles, studyIds, sampleIds, profileFilter);
     }
 }
diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewServiceImpl.java
index dbcb40e8993..e3fdd9a27b2 100644
--- a/src/main/java/org/cbioportal/service/impl/StudyViewServiceImpl.java
+++ b/src/main/java/org/cbioportal/service/impl/StudyViewServiceImpl.java
@@ -10,6 +10,8 @@
 import org.cbioportal.service.exception.MolecularProfileNotFoundException;
 import org.cbioportal.service.exception.StudyNotFoundException;
 import org.cbioportal.service.util.MolecularProfileUtil;
+import org.cbioportal.web.parameter.GeneIdType;
+import org.cbioportal.web.parameter.Projection;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
@@ -41,20 +43,20 @@ public class StudyViewServiceImpl implements StudyViewService {
 
     @Autowired
     private GeneService geneService;
-    
-    @Autowired 
+
+    @Autowired
     private MolecularDataService molecularDataService;
-    
+
     @Autowired
     private MutationService mutationService;
-    
+
     @Override
     public List<GenomicDataCount> getGenomicDataCounts(List<String> studyIds, List<String> sampleIds) {
         List<MolecularProfileCaseIdentifier> molecularProfileSampleIdentifiers =
             molecularProfileService.getMolecularProfileCaseIdentifiers(studyIds, sampleIds);
 
         List<MolecularProfile> molecularProfiles = molecularProfileService
-            .getMolecularProfilesInStudies(new ArrayList<>(new HashSet<>(studyIds)),"SUMMARY");
+            .getMolecularProfilesInStudies(new ArrayList<>(new HashSet<>(studyIds)), Projection.SUMMARY.name());
         Map<String, MolecularProfile> molecularProfileMap = molecularProfiles
             .stream()
             .collect(Collectors.toMap(MolecularProfile::getStableId, Function.identity()));
@@ -66,8 +68,8 @@ public List<GenomicDataCount> getGenomicDataCounts(List<String> studyIds, List<S
             .collect(Collectors.groupingBy(GenePanelData::getMolecularProfileId))
             .entrySet()
             .stream()
-            .collect(Collectors.toMap(entry -> entry.getKey(), entry -> (int)entry.getValue().stream().map(d -> molecularProfileMap.get(entry.getKey()).getPatientLevel() ? d.getPatientId() : d.getSampleId()).distinct().count()));
-        
+            .collect(Collectors.toMap(entry -> entry.getKey(), entry -> (int) entry.getValue().stream().map(d -> molecularProfileMap.get(entry.getKey()).getPatientLevel() ? d.getPatientId() : d.getSampleId()).distinct().count()));
+
         return molecularProfileUtil
             .categorizeMolecularProfilesByStableIdSuffixes(molecularProfiles)
             .entrySet()
@@ -87,7 +89,7 @@ public List<GenomicDataCount> getGenomicDataCounts(List<String> studyIds, List<S
                 return dataCount;
             })
             .filter(dataCount -> dataCount.getCount() > 0)
-            .collect(Collectors.toList());
+            .toList();
     }
 
     @Override
@@ -119,11 +121,11 @@ public List<GenomicDataCountItem> getMutationCountsByGeneSpecific(List<String> s
             .collect(Collectors.toSet());
 
         List<Integer> entrezGeneIds = geneService
-            .fetchGenes(new ArrayList<>(hugoGeneSymbols), "HUGO_GENE_SYMBOL",
-                "SUMMARY")
+            .fetchGenes(new ArrayList<>(hugoGeneSymbols), GeneIdType.HUGO_GENE_SYMBOL.name(),
+                Projection.SUMMARY.name())
             .stream()
             .map(Gene::getEntrezGeneId)
-            .collect(Collectors.toList());
+            .toList();
 
         List<AlterationCountByGene> alterationCountByGenes = alterationCountService.getSampleMutationGeneCounts(
             caseIdentifiers,
@@ -155,7 +157,7 @@ public List<GenomicDataCountItem> getMutationCountsByGeneSpecific(List<String> s
                 int totalCount = sampleIds.size();
 
                 List<GenomicDataCount> genomicDataCounts = new ArrayList<>();
-       
+
                 GenomicDataCount genomicDataCountMutated = new GenomicDataCount();
                 genomicDataCountMutated.setLabel(MutationFilterOption.MUTATED.getMutationFilterOption());
                 genomicDataCountMutated.setValue(MutationFilterOption.MUTATED.name());
@@ -180,8 +182,7 @@ public List<GenomicDataCountItem> getMutationCountsByGeneSpecific(List<String> s
                 genomicDataCountItem.setCounts(genomicDataCounts);
 
                 return Stream.of(genomicDataCountItem);
-            })
-            .collect(Collectors.toList());
+            }).toList();
     }
 
     @Override
@@ -192,10 +193,10 @@ public List<GenomicDataCountItem> getMutationTypeCountsByGeneSpecific(List<Strin
             .collect(Collectors.toSet());
 
         Map<String, Integer> geneSymbolIdMap = geneService
-            .fetchGenes(new ArrayList<>(hugoGeneSymbols), "HUGO_GENE_SYMBOL",
-                "SUMMARY")
+            .fetchGenes(new ArrayList<>(hugoGeneSymbols), GeneIdType.HUGO_GENE_SYMBOL.name(),
+                Projection.SUMMARY.name())
             .stream().collect(Collectors.toMap(Gene::getHugoGeneSymbol, Gene::getEntrezGeneId));
-        
+
         return genomicDataFilters
             .stream()
             .flatMap(gdFilter -> {
@@ -203,7 +204,7 @@ public List<GenomicDataCountItem> getMutationTypeCountsByGeneSpecific(List<Strin
                 String profileType = gdFilter.getValue();
 
                 List<Integer> stableIds = Collections.singletonList(geneSymbolIdMap.get(hugoGeneSymbol));
-                
+
                 Pair<List<String>, List<String>> sampleAndProfileIds = getMappedSampleAndProfileIds(studyIds, sampleIds, profileType);
                 List<String> mappedSampleIds = sampleAndProfileIds.getFirst();
                 List<String> mappedProfileIds = sampleAndProfileIds.getSecond();
@@ -211,17 +212,16 @@ public List<GenomicDataCountItem> getMutationTypeCountsByGeneSpecific(List<Strin
                 if (mappedSampleIds.isEmpty() || mappedProfileIds.isEmpty()) {
                     return Stream.of();
                 }
-                
-                GenomicDataCountItem genomicDataCountItem = mutationService.getMutationCountsByType(mappedProfileIds, 
+
+                GenomicDataCountItem genomicDataCountItem = mutationService.getMutationCountsByType(mappedProfileIds,
                     mappedSampleIds, stableIds, profileType);
-                
+
                 if (genomicDataCountItem != null) {
                     return Stream.of(genomicDataCountItem);
                 } else {
                     return Stream.empty();
                 }
-            })
-            .collect(Collectors.toList());
+            }).toList();
     }
 
     @Override
@@ -259,12 +259,12 @@ private void annotateDataWithQValue(List<String> studyIds, List<AlterationCountB
         if (!alterationCountByGenes.isEmpty() && distinctStudyIds.size() == 1) {
             Map<Integer, MutSig> mutSigMap =
                 significantlyMutatedGeneService.getSignificantlyMutatedGenes(
-                    studyIds.get(0),
-                    "SUMMARY",
-                    null,
-                    null,
-                    null,
-                    null)
+                        studyIds.get(0),
+                        Projection.SUMMARY.name(),
+                        null,
+                        null,
+                        null,
+                        null)
                     .stream()
                     .collect(Collectors.toMap(MutSig::getEntrezGeneId, Function.identity()));
             alterationCountByGenes.forEach(r -> {
@@ -282,7 +282,7 @@ public List<CopyNumberCountByGene> getCNAAlterationCountByGenes(List<String> stu
         throws StudyNotFoundException {
         List<MolecularProfileCaseIdentifier> caseIdentifiers =
             molecularProfileService.getFirstDiscreteCNAProfileCaseIdentifiers(studyIds, sampleIds);
-        
+
         List<CopyNumberCountByGene> copyNumberCountByGenes = alterationCountService.getSampleCnaGeneCounts(
             caseIdentifiers,
             Select.all(),
@@ -293,7 +293,7 @@ public List<CopyNumberCountByGene> getCNAAlterationCountByGenes(List<String> stu
         if (distinctStudyIds.size() == 1 && !copyNumberCountByGenes.isEmpty()) {
             List<Gistic> gisticList = significantCopyNumberRegionService.getSignificantCopyNumberRegions(
                 studyIds.get(0),
-                "SUMMARY",
+                Projection.SUMMARY.name(),
                 null,
                 null,
                 null,
@@ -315,17 +315,17 @@ public List<CopyNumberCountByGene> getCNAAlterationCountByGenes(List<String> stu
     }
 
     @Override
-    public List<GenomicDataCountItem> getCNAAlterationCountsByGeneSpecific(List<String> studyIds, 
+    public List<GenomicDataCountItem> getCNAAlterationCountsByGeneSpecific(List<String> studyIds,
                                                                            List<String> sampleIds,
                                                                            List<Pair<String, String>> genomicDataFilters) {
         Set<String> hugoGeneSymbols = genomicDataFilters.stream().map(Pair::getKey)
             .collect(Collectors.toSet());
 
         Map<String, Integer> geneSymbolIdMap = geneService
-            .fetchGenes(new ArrayList<>(hugoGeneSymbols), "HUGO_GENE_SYMBOL",
-                "SUMMARY")
+            .fetchGenes(new ArrayList<>(hugoGeneSymbols), GeneIdType.HUGO_GENE_SYMBOL.name(),
+                Projection.SUMMARY.name())
             .stream().collect(Collectors.toMap(Gene::getHugoGeneSymbol, Gene::getEntrezGeneId));
-        
+
         return genomicDataFilters
             .stream()
             .flatMap(gdFilter -> {
@@ -334,7 +334,7 @@ public List<GenomicDataCountItem> getCNAAlterationCountsByGeneSpecific(List<Stri
                 String profileType = gdFilter.getValue();
                 genomicDataCountItem.setHugoGeneSymbol(hugoGeneSymbol);
                 genomicDataCountItem.setProfileType(profileType);
-                
+
                 List<String> stableIds = Arrays.asList(geneSymbolIdMap.get(hugoGeneSymbol).toString());
 
                 Pair<List<String>, List<String>> sampleAndProfileIds = getMappedSampleAndProfileIds(studyIds, sampleIds, profileType);
@@ -346,8 +346,8 @@ public List<GenomicDataCountItem> getCNAAlterationCountsByGeneSpecific(List<Stri
                 }
 
                 List<GeneMolecularData> geneMolecularDataList = molecularDataService.getMolecularDataInMultipleMolecularProfiles(mappedProfileIds, mappedSampleIds,
-                        stableIds.stream().map(Integer::parseInt).collect(Collectors.toList()), "SUMMARY");
-                
+                    stableIds.stream().map(Integer::parseInt).toList(), Projection.SUMMARY.name());
+
                 List<GenomicDataCount> genomicDataCounts = geneMolecularDataList
                     .stream()
                     .filter(g -> StringUtils.isNotEmpty(g.getValue()) && !g.getValue().equals("NA"))
@@ -367,11 +367,11 @@ public List<GenomicDataCountItem> getCNAAlterationCountsByGeneSpecific(List<Stri
                         genomicDataCount.setCount(count);
 
                         return genomicDataCount;
-                    }).collect(Collectors.toList());
+                    }).toList();
 
                 int totalCount = genomicDataCounts.stream().mapToInt(GenomicDataCount::getCount).sum();
                 int naCount = sampleIds.size() - totalCount;
-                
+
                 if (naCount > 0) {
                     GenomicDataCount genomicDataCount = new GenomicDataCount();
                     genomicDataCount.setLabel("NA");
@@ -379,15 +379,17 @@ public List<GenomicDataCountItem> getCNAAlterationCountsByGeneSpecific(List<Stri
                     genomicDataCount.setCount(naCount);
                     genomicDataCounts.add(genomicDataCount);
                 }
-                
+
                 genomicDataCountItem.setCounts(genomicDataCounts);
                 return Stream.of(genomicDataCountItem);
-            }).collect(Collectors.toList());
-    };
+            }).toList();
+    }
+
+    ;
 
     @Override
     public List<GenericAssayDataCountItem> fetchGenericAssayDataCounts(List<String> sampleIds, List<String> studyIds,
-                                                               List<String> stableIds, List<String> profileTypes) {
+                                                                       List<String> stableIds, List<String> profileTypes) {
         if (stableIds.isEmpty()) {
             return new ArrayList<>();
         }
@@ -398,12 +400,12 @@ public List<GenericAssayDataCountItem> fetchGenericAssayDataCounts(List<String>
             List<String> mappedProfileIds = sampleAndProfileIds.getSecond();
 
             try {
-                return genericAssayService.fetchGenericAssayData(mappedProfileIds, mappedSampleIds, stableIds, "SUMMARY").stream();
+                return genericAssayService.fetchGenericAssayData(mappedProfileIds, mappedSampleIds, stableIds, Projection.SUMMARY.name()).stream();
             } catch (MolecularProfileNotFoundException e) {
                 return new ArrayList<GenericAssayData>().stream();
             }
-        }).collect(Collectors.toList());
-        
+        }).toList();
+
         return data
             .stream()
             .filter(g -> StringUtils.isNotEmpty(g.getValue()) && !g.getValue().equals("NA"))
@@ -422,10 +424,9 @@ public List<GenericAssayDataCountItem> fetchGenericAssayDataCounts(List<String>
                         GenericAssayDataCount dataCount = new GenericAssayDataCount();
                         dataCount.setValue(datum.getKey());
                         dataCount.setCount(datum.getValue().size());
-                        return dataCount; 
-                    })
-                    .collect(Collectors.toList());
-                
+                        return dataCount;
+                    }).toList();
+
                 if (naCount > 0) {
                     GenericAssayDataCount dataCount = new GenericAssayDataCount();
                     dataCount.setValue("NA");
@@ -437,14 +438,12 @@ public List<GenericAssayDataCountItem> fetchGenericAssayDataCounts(List<String>
                 genericAssayDataCountItem.setStableId(entry.getKey());
                 genericAssayDataCountItem.setCounts(counts);
                 return genericAssayDataCountItem;
-            })
-            .collect(Collectors.toList());
+            }).toList();
     }
-    
+
     private Pair<List<String>, List<String>> getMappedSampleAndProfileIds(List<String> studyIds, List<String> sampleIds, String profileType) {
-        // Get data from fetchGenericAssayData service
         List<MolecularProfile> molecularProfiles = molecularProfileService.getMolecularProfilesInStudies(studyIds,
-            "SUMMARY");
+            Projection.SUMMARY.name());
 
         Map<String, List<MolecularProfile>> molecularProfileMap = molecularProfileUtil
             .categorizeMolecularProfilesByStableIdSuffixes(molecularProfiles);
@@ -464,7 +463,7 @@ private Pair<List<String>, List<String>> getMappedSampleAndProfileIds(List<Strin
                 mappedProfileIds.add(studyIdToMolecularProfileIdMap.get(studyId));
             }
         }
-        
+
         return new Pair<>(mappedSampleIds, mappedProfileIds);
     }
 }
diff --git a/src/main/java/org/cbioportal/web/StudyViewController.java b/src/main/java/org/cbioportal/web/StudyViewController.java
index d5f1399f579..2a690620593 100644
--- a/src/main/java/org/cbioportal/web/StudyViewController.java
+++ b/src/main/java/org/cbioportal/web/StudyViewController.java
@@ -517,8 +517,8 @@ public ResponseEntity<DensityPlotData> fetchClinicalDataDensityPlot(
         if (CollectionUtils.isNotEmpty(patientAttributeIds)) {
             List<Sample> samples = sampleService.fetchSamples(studyIds, sampleIds, Projection.DETAILED.name());
             List<Patient> patients = patientService.getPatientsOfSamples(studyIds, sampleIds);
-            patientIds = patients.stream().map(Patient::getStableId).collect(Collectors.toList());
-            studyIdsOfPatients = patients.stream().map(Patient::getCancerStudyIdentifier).collect(Collectors.toList());
+            patientIds = patients.stream().map(Patient::getStableId).toList();
+            studyIdsOfPatients = patients.stream().map(Patient::getCancerStudyIdentifier).toList();
             patientToSamples = samples.stream().collect(
                 Collectors.groupingBy(Sample::getPatientStableId, Collectors.groupingBy(Sample::getCancerStudyIdentifier))
             );
@@ -750,8 +750,8 @@ public ResponseEntity<ClinicalViolinPlotData> fetchClinicalDataViolinPlots(
         if (CollectionUtils.isNotEmpty(patientAttributeIds)) {
             List<Sample> samplesWithoutNumericalFilter = sampleService.fetchSamples(studyIdsWithoutNumericalFilter, sampleIdsWithoutNumericalFilter, Projection.DETAILED.name());
             List<Patient> patients = patientService.getPatientsOfSamples(studyIdsWithoutNumericalFilter, sampleIdsWithoutNumericalFilter);
-            patientIds = patients.stream().map(Patient::getStableId).collect(Collectors.toList());
-            studyIdsOfPatients = patients.stream().map(Patient::getCancerStudyIdentifier).collect(Collectors.toList());
+            patientIds = patients.stream().map(Patient::getStableId).toList();
+            studyIdsOfPatients = patients.stream().map(Patient::getCancerStudyIdentifier).toList();
             patientToSamples = samplesWithoutNumericalFilter.stream().collect(
                 Collectors.groupingBy(Sample::getPatientStableId, Collectors.groupingBy(Sample::getCancerStudyIdentifier))
             );
@@ -865,7 +865,7 @@ public List<CaseListDataCount> fetchCaseListCounts(
                     return dataCount;
                 })
                 .filter(dataCount -> dataCount.getCount() > 0)
-                .collect(Collectors.toList());
+                .toList();
 
     }
     
@@ -962,7 +962,7 @@ public ResponseEntity<List<GenericAssayDataCountItem>> fetchGenericAssayDataCoun
         List<GenericAssayDataCountItem> result = studyViewService.fetchGenericAssayDataCounts(
             sampleIds,
             studyIds,
-            gaFilters.stream().map(GenericAssayDataFilter::getStableId).collect(Collectors.toList()),
+            gaFilters.stream().map(GenericAssayDataFilter::getStableId).toList(),
             gaFilters.stream().map(GenericAssayDataFilter::getProfileType).collect(Collectors.toList()));
 
         return new ResponseEntity<>(result, HttpStatus.OK);
@@ -1053,9 +1053,9 @@ public ResponseEntity<ClinicalDataCollection> fetchClinicalDataClinicalTable(
         final List<ImmutablePair<String, String>> patientIdentifiers = sampleClinicalData.stream()
             .map(d -> new ImmutablePair<>(d.getStudyId(), d.getPatientId()))
             .distinct()
-            .collect(Collectors.toList());
-        List<String> patientStudyIds = patientIdentifiers.stream().map(p -> p.getLeft()).collect(Collectors.toList());
-        List<String> patientIds = patientIdentifiers.stream().map(p -> p.getRight()).collect(Collectors.toList());
+            .toList();
+        List<String> patientStudyIds = patientIdentifiers.stream().map(p -> p.getLeft()).toList();
+        List<String> patientIds = patientIdentifiers.stream().map(p -> p.getRight()).toList();
         
         
         List<String> searchAllAttributes = null;
@@ -1154,13 +1154,13 @@ public ResponseEntity<List<GenomicDataCountItem>> fetchMutationDataCounts(
             studyViewService.getMutationCountsByGeneSpecific(
                 studyIds,
                 sampleIds,
-                gdFilters.stream().map(gdFilter -> new Pair<>(gdFilter.getHugoGeneSymbol(), gdFilter.getProfileType())).collect(Collectors.toList()),
+                gdFilters.stream().map(gdFilter -> new Pair<>(gdFilter.getHugoGeneSymbol(), gdFilter.getProfileType())).toList(),
                 studyViewFilter.getAlterationFilter()
             ) : 
             studyViewService.getMutationTypeCountsByGeneSpecific(
                 studyIds,
                 sampleIds,
-                gdFilters.stream().map(gdFilter -> new Pair<>(gdFilter.getHugoGeneSymbol(), gdFilter.getProfileType())).collect(Collectors.toList())
+                gdFilters.stream().map(gdFilter -> new Pair<>(gdFilter.getHugoGeneSymbol(), gdFilter.getProfileType())).toList()
             );
 
         return new ResponseEntity<>(result, HttpStatus.OK);
diff --git a/src/main/java/org/cbioportal/web/parameter/MutationDataFilter.java b/src/main/java/org/cbioportal/web/parameter/MutationDataFilter.java
index 7ab935cef2b..216d409355b 100644
--- a/src/main/java/org/cbioportal/web/parameter/MutationDataFilter.java
+++ b/src/main/java/org/cbioportal/web/parameter/MutationDataFilter.java
@@ -4,13 +4,15 @@
 import com.fasterxml.jackson.annotation.JsonInclude;
 
 import jakarta.validation.constraints.NotNull;
+
+import java.io.Serializable;
 import java.util.List;
 
 import static com.fasterxml.jackson.annotation.JsonInclude.Include.NON_NULL;
 
 @JsonIgnoreProperties(ignoreUnknown = true)
 @JsonInclude(NON_NULL)
-public class MutationDataFilter {
+public class MutationDataFilter implements Serializable {
     private String hugoGeneSymbol;
     private String profileType;
     @NotNull
diff --git a/src/main/java/org/cbioportal/web/util/ClinicalDataEqualityFilterApplier.java b/src/main/java/org/cbioportal/web/util/ClinicalDataEqualityFilterApplier.java
index 82e4617051e..c197185ab95 100644
--- a/src/main/java/org/cbioportal/web/util/ClinicalDataEqualityFilterApplier.java
+++ b/src/main/java/org/cbioportal/web/util/ClinicalDataEqualityFilterApplier.java
@@ -33,7 +33,7 @@ public Integer apply(List<ClinicalDataFilter> attributes,
         return studyViewFilterUtil.getFilteredCountByDataEquality(attributes, clinicalDataMap, entityId, studyId, negateFilters);
     }
     
-    public static MultiKeyMap buildClinicalDataMap(List<ClinicalData> clinicalDatas) {
+    public static MultiKeyMap<String, List<String>> buildClinicalDataMap(List<ClinicalData> clinicalDatas) {
         MultiKeyMap<String, List<String>> clinicalDataMap = new MultiKeyMap<>();
 
         clinicalDatas.forEach(clinicalData -> {
diff --git a/src/main/java/org/cbioportal/web/util/ClinicalDataIntervalFilterApplier.java b/src/main/java/org/cbioportal/web/util/ClinicalDataIntervalFilterApplier.java
index 49ad14f5808..2849974507a 100644
--- a/src/main/java/org/cbioportal/web/util/ClinicalDataIntervalFilterApplier.java
+++ b/src/main/java/org/cbioportal/web/util/ClinicalDataIntervalFilterApplier.java
@@ -1,10 +1,6 @@
 package org.cbioportal.web.util;
 
-import java.math.BigDecimal;
-import java.util.List;
-import java.util.Objects;
-import java.util.stream.Collectors;
-
+import com.google.common.collect.Range;
 import org.apache.commons.collections4.map.MultiKeyMap;
 import org.cbioportal.model.ClinicalData;
 import org.cbioportal.service.ClinicalDataService;
@@ -14,7 +10,10 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
-import com.google.common.collect.Range;
+import java.math.BigDecimal;
+import java.util.List;
+import java.util.Objects;
+import java.util.stream.Collectors;
 
 @Component
 public class ClinicalDataIntervalFilterApplier extends ClinicalDataFilterApplier {
@@ -134,14 +133,14 @@ private Boolean containsNA(ClinicalDataFilter filter) {
         return filter.getValues().stream().anyMatch(
             r -> r.getValue() != null && r.getValue().toUpperCase().equals("NA"));
     }
-    
-    public static MultiKeyMap buildClinicalDataMap(List<ClinicalData> clinicalDatas) {
-        MultiKeyMap clinicalDataMap = new MultiKeyMap();
 
-        clinicalDatas.forEach(clinicalData -> {
+    public static MultiKeyMap<String, String> buildClinicalDataMap(List<ClinicalData> clinicalDatas) {
+        MultiKeyMap<String, String> clinicalDataMap = new MultiKeyMap<>();
+
+        clinicalDatas.forEach(clinicalData ->
             clinicalDataMap.put(clinicalData.getStudyId(), clinicalData.getSampleId(), clinicalData.getAttrId(),
-                clinicalData.getAttrValue());
-        });
+                clinicalData.getAttrValue())
+        );
 
         return clinicalDataMap;
     }
diff --git a/src/main/java/org/cbioportal/web/util/StudyViewFilterApplier.java b/src/main/java/org/cbioportal/web/util/StudyViewFilterApplier.java
index 5c484f2883e..51e72dd959b 100644
--- a/src/main/java/org/cbioportal/web/util/StudyViewFilterApplier.java
+++ b/src/main/java/org/cbioportal/web/util/StudyViewFilterApplier.java
@@ -1,24 +1,25 @@
 package org.cbioportal.web.util;
 
-import java.util.*;
-import java.util.function.Function;
-import java.util.stream.Collectors;
-import java.util.stream.Stream;
 import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.collections4.map.MultiKeyMap;
-import org.cbioportal.model.*;
 import org.cbioportal.model.GeneFilter;
+import org.cbioportal.model.*;
 import org.cbioportal.model.MolecularProfile.MolecularAlterationType;
 import org.cbioportal.service.*;
 import org.cbioportal.service.exception.MolecularProfileNotFoundException;
 import org.cbioportal.service.util.MolecularProfileUtil;
 import org.cbioportal.web.parameter.*;
-import org.cbioportal.web.util.appliers.*;
+import org.cbioportal.web.util.appliers.StudyViewSubFilterApplier;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.cache.annotation.Cacheable;
 import org.springframework.context.ApplicationContext;
 import org.springframework.stereotype.Component;
 
+import java.util.*;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
 @Component
 public class StudyViewFilterApplier {
     @Autowired
@@ -96,14 +97,14 @@ public List<SampleIdentifier> apply(StudyViewFilter studyViewFilter, Boolean neg
             List<String> sampleIds = new ArrayList<>();
             studyViewFilterUtil.extractStudyAndSampleIds(studyViewFilter.getSampleIdentifiers(), studyIds, sampleIds);
             sampleIdentifiers = sampleService.fetchSamples(studyIds, sampleIds, Projection.ID.name()).stream()
-                .map(sampleToSampleIdentifier).collect(Collectors.toList());
+                .map(sampleToSampleIdentifier).toList();
         } else {
             sampleIdentifiers = sampleService.getAllSamplesInStudies(studyViewFilter.getStudyIds(), Projection.ID.name(),
-                null, null, null, null).stream().map(sampleToSampleIdentifier).collect(Collectors.toList());
+                null, null, null, null).stream().map(sampleToSampleIdentifier).toList();
         }
 
         List<String> studyIds = sampleIdentifiers.stream().map(SampleIdentifier::getStudyId).distinct()
-                .collect(Collectors.toList());
+                .toList();
 
         List<ClinicalDataFilter> clinicalDataEqualityFilters = new ArrayList<>();
         List<ClinicalDataFilter> clinicalDataIntervalFilters = new ArrayList<>();
@@ -112,7 +113,7 @@ public List<SampleIdentifier> apply(StudyViewFilter studyViewFilter, Boolean neg
 
         if (!CollectionUtils.isEmpty(clinicalDataFilters)) {
             List<String> attributeIds = clinicalDataFilters.stream().map(ClinicalDataFilter::getAttributeId)
-                    .collect(Collectors.toList());
+                    .toList();
             List<ClinicalAttribute> clinicalAttributes = clinicalAttributeService
                     .getClinicalAttributesByStudyIdsAndAttributeIds(studyIds, attributeIds);
 
@@ -280,7 +281,7 @@ public List<SampleIdentifier> apply(StudyViewFilter studyViewFilter, Boolean neg
                                             sampleList.getCancerStudyIdentifier(),
                                             sampleId));
                                 }))
-                        .collect(Collectors.toList());
+                        .toList();
 
                 sampleIdentifiers.retainAll(filteredSampleIdentifiers);
             }
@@ -349,7 +350,7 @@ private List<SampleIdentifier> filterMutatedGenes(List<GeneFilter> mutatedGenefi
                     .getMolecularProfileIds()
                     .stream()
                     .map(molecularProfileId -> molecularProfileMap.get(molecularProfileId))
-                    .collect(Collectors.toList());
+                    .toList();
 
             Map<String, List<MolecularProfile>> mapByStudyId = filteredMolecularProfiles
                     .stream()
@@ -362,7 +363,7 @@ private List<SampleIdentifier> filterMutatedGenes(List<GeneFilter> mutatedGenefi
                 List<String> hugoGeneSymbols = geneQueries
                         .stream()
                         .map(GeneFilterQuery::getHugoGeneSymbol)
-                        .collect(Collectors.toList());
+                        .toList();
 
                 Map<String, Integer> symbolToEntrezGeneId = geneService
                     .fetchGenes(new ArrayList<>(hugoGeneSymbols),
@@ -397,7 +398,7 @@ private List<SampleIdentifier> filterMutatedGenes(List<GeneFilter> mutatedGenefi
                         .stream()
                         .map(m -> studyViewFilterUtil.buildSampleIdentifier(m.getStudyId(), m.getSampleId()))
                         .distinct()
-                        .collect(Collectors.toList());
+                        .toList();
             }
 
         }
@@ -417,7 +418,7 @@ private List<SampleIdentifier> filterStructuralVariantGenes(List<GeneFilter> svG
                     .getMolecularProfileIds()
                     .stream()
                     .map(molecularProfileId -> molecularProfileMap.get(molecularProfileId))
-                    .collect(Collectors.toList());
+                    .toList();
 
             Map<String, List<MolecularProfile>> mapByStudyId = filteredMolecularProfiles
                     .stream()
@@ -430,7 +431,7 @@ private List<SampleIdentifier> filterStructuralVariantGenes(List<GeneFilter> svG
                 List<String> hugoGeneSymbols = geneQueries
                     .stream()
                     .map(GeneFilterQuery::getHugoGeneSymbol)
-                    .collect(Collectors.toList());
+                    .toList();
 
                 Map<String, Integer> symbolToEntrezGeneId = geneService
                     .fetchGenes(new ArrayList<>(hugoGeneSymbols),
@@ -465,7 +466,7 @@ private List<SampleIdentifier> filterStructuralVariantGenes(List<GeneFilter> svG
                         .stream()
                         .map(m -> studyViewFilterUtil.buildSampleIdentifier(m.getStudyId(), m.getSampleId()))
                         .distinct()
-                        .collect(Collectors.toList());
+                        .toList();
             }
 
         }
@@ -483,7 +484,7 @@ private List<SampleIdentifier> filterCNAGenes(List<GeneFilter> cnaGeneFilters,
 
             List<MolecularProfile> filteredMolecularProfiles = geneFilter.getMolecularProfileIds().stream()
                     .map(molecularProfileId -> molecularProfileMap.get(molecularProfileId))
-                    .collect(Collectors.toList());
+                    .toList();
 
             for (List<GeneFilterQuery> geneQueries : geneFilter.getGeneQueries()) {
 
@@ -512,10 +513,10 @@ private List<SampleIdentifier> filterCNAGenes(List<GeneFilter> cnaGeneFilters,
                                 .filter(geneQuery -> geneQuery.getAlterations().stream()
                                     .filter(alteration -> alteration.getCode() == alterationType)
                                     .count() > 0)
-                                .collect(Collectors.toList());
+                                .toList();
 
                             List<String> hugoGeneSymbols = filteredGeneQueries.stream()
-                                    .map(GeneFilterQuery::getHugoGeneSymbol).collect(Collectors.toList());
+                                    .map(GeneFilterQuery::getHugoGeneSymbol).toList();
 
                             Map<String, Integer> symbolToEntrezGeneId = geneService
                                 .fetchGenes(new ArrayList<>(hugoGeneSymbols),
@@ -540,11 +541,11 @@ private List<SampleIdentifier> filterCNAGenes(List<GeneFilter> cnaGeneFilters,
                                         Projection.ID.name());
                             }
                             return copyNumberDatas.stream();
-                        }).collect(Collectors.toList());
+                        }).toList();
 
                 sampleIdentifiers = resultList.stream().map(
                     d -> studyViewFilterUtil.buildSampleIdentifier(d.getStudyId(), d.getSampleId())
-                ).distinct().collect(Collectors.toList());
+                ).distinct().toList();
             }
         }
 
@@ -595,7 +596,7 @@ private List<SampleIdentifier> filterMutationData(List<SampleIdentifier> sampleI
                 }
             }
 
-            return newSampleIdentifiers.stream().distinct().collect(Collectors.toList());
+            return newSampleIdentifiers.stream().distinct().toList();
         }
         
         return sampleIdentifiers;
@@ -612,7 +613,7 @@ private void splitGeneFiltersByMolecularAlterationType(List<GeneFilter> genefilt
                     // in filter but the study might already been filtered out
                     .filter(molecularProfileMap::containsKey)
                     .map(molecularProfileMap::get)
-                    .collect(Collectors.toList());
+                    .toList();
 
             Set<MolecularAlterationType> alterationTypes = filteredMolecularProfiles.stream()
                     .map(MolecularProfile::getMolecularAlterationType)
@@ -698,7 +699,7 @@ public <T extends DataBinCountFilter, S extends DataBinFilter, U extends DataBin
                                 filteredUniqueSampleKeys, unFilteredUniqueSampleKeys)
                         .stream().map(dataBin -> (U) transform(dataBinFilter, dataBin));
 
-            }).collect(Collectors.toList());
+            }).toList();
 
         } else { // dataBinMethod == DataBinMethod.DYNAMIC
             resultDataBins = (List<U>) dataBinFilters.stream().flatMap(dataBinFilter -> {
@@ -708,7 +709,7 @@ public <T extends DataBinCountFilter, S extends DataBinFilter, U extends DataBin
                                         Collections.emptyList()),
                                 filteredUniqueSampleKeys)
                         .stream().map(dataBin -> (U) transform(dataBinFilter, dataBin));
-            }).collect(Collectors.toList());
+            }).toList();
         }
 
         return resultDataBins;
@@ -745,7 +746,7 @@ private <S extends DataBinCountFilter> List<Binnable> fetchData(
             return genomicDataBinFilters.stream().flatMap(genomicDataBinFilter -> {
 
                 Map<String, String> studyIdToMolecularProfileIdMap = molecularProfileMap
-                        .getOrDefault(genomicDataBinFilter.getProfileType(), new ArrayList<MolecularProfile>()).stream()
+                        .getOrDefault(genomicDataBinFilter.getProfileType(), new ArrayList<>()).stream()
                         .collect(Collectors.toMap(MolecularProfile::getCancerStudyIdentifier,
                                 MolecularProfile::getStableId));
                 
@@ -806,13 +807,12 @@ private interface FourParameterFunction<T, U, V, W, R> {
     }
 
     FourParameterFunction<List<String>, List<String>, List<String>, String, List<ClinicalData>> fetchMolecularData = (
-            mappedProfileIds, mappedSampleIds, stableIds, attributeId) -> {
-        return molecularDataService.getMolecularDataInMultipleMolecularProfiles(mappedProfileIds, mappedSampleIds,
-                stableIds.stream().map(Integer::parseInt).collect(Collectors.toList()), Projection.SUMMARY.name())
-                .stream().map(geneMolecularData -> 
+            mappedProfileIds, mappedSampleIds, stableIds, attributeId) ->
+        molecularDataService.getMolecularDataInMultipleMolecularProfiles(mappedProfileIds, mappedSampleIds,
+                stableIds.stream().map(Integer::parseInt).toList(), Projection.SUMMARY.name())
+            .stream().map(geneMolecularData ->
                 transformDataToClinicalData(geneMolecularData, attributeId, geneMolecularData.getValue()))
-            .collect(Collectors.toList());
-    };
+            .toList();
 
     FourParameterFunction<List<String>, List<String>, List<String>, String, List<ClinicalData>> fetchGenericAssayData = (
             mappedProfileIds, mappedSampleIds, stableIds, attributeId) -> {
@@ -822,29 +822,27 @@ private interface FourParameterFunction<T, U, V, W, R> {
                     .fetchGenericAssayData(mappedProfileIds, mappedSampleIds, stableIds, Projection.SUMMARY.name())
                     .stream().map(genericAssayData -> 
                         transformDataToClinicalData(genericAssayData, attributeId, genericAssayData.getValue())
-                    ).collect(Collectors.toList());
+                    ).toList();
         } catch (MolecularProfileNotFoundException e) {
             return new ArrayList<>();
         }
     };
 
     FourParameterFunction<List<String>, List<String>, List<String>, String, List<ClinicalData>> fetchMutationData = (
-        mappedProfileIds, mappedSampleIds, stableIds, attributeId) -> {
-        return mutationService.getMutationsInMultipleMolecularProfiles(mappedProfileIds, mappedSampleIds,
-                stableIds.stream().map(Integer::parseInt).collect(Collectors.toList()), Projection.DETAILED.name(),
+        mappedProfileIds, mappedSampleIds, stableIds, attributeId) ->
+        mutationService.getMutationsInMultipleMolecularProfiles(mappedProfileIds, mappedSampleIds,
+                stableIds.stream().map(Integer::parseInt).toList(), Projection.DETAILED.name(),
                 null, null, null, null)
             .stream().map(mutationData -> transformDataToClinicalData(mutationData, attributeId, mutationData.getMutationType().toUpperCase())
-            ).collect(Collectors.toList());
-    };
+            ).toList();
 
     FourParameterFunction<List<String>, List<String>, List<String>, String, List<ClinicalData>> fetchMutatedData = (
-        mappedProfileIds, mappedSampleIds, stableIds, attributeId) -> {
-        return mutationService.getMutationsInMultipleMolecularProfiles(mappedProfileIds, mappedSampleIds,
-                stableIds.stream().map(Integer::parseInt).collect(Collectors.toList()), Projection.DETAILED.name(),
+        mappedProfileIds, mappedSampleIds, stableIds, attributeId) ->
+        mutationService.getMutationsInMultipleMolecularProfiles(mappedProfileIds, mappedSampleIds,
+                stableIds.stream().map(Integer::parseInt).toList(), Projection.DETAILED.name(),
                 null, null, null, null)
             .stream().map(mutationData -> transformDataToClinicalData(mutationData, attributeId, MutationFilterOption.MUTATED.name())
-             ).collect(Collectors.toList());
-    };
+            ).toList();
 
     private <S extends DataBinFilter, T extends DataBinCountFilter> List<S> fetchDataBinFilters(T dataBinCountFilter) {
         if (dataBinCountFilter instanceof GenomicDataBinCountFilter) {
@@ -963,7 +961,7 @@ public <S extends DataFilter> List<SampleIdentifier> filterExpressionData(
                 }
             }
 
-            return newSampleIdentifiers.stream().distinct().collect(Collectors.toList());
+            return newSampleIdentifiers.stream().distinct().toList();
         }
          
         return sampleIdentifiers;
@@ -999,7 +997,7 @@ private <S extends DataFilter> List<ClinicalData> fetchDataAndTransformToClinica
                     Collections.singletonList(geneNameIdMap.get(genomicDataFilter.getHugoGeneSymbol()).toString()),
                     studyIdToMolecularProfileIdMap, studyViewFilterUtil.getDataFilterUniqueKey(genomicDataFilter), 
                     fetchMolecularData);
-            }).collect(Collectors.toList());
+            }).toList();
 
         } else {
             return ((List<GenericAssayDataFilter>) dataFilters).stream().flatMap(genericAssayDataFilter -> {
@@ -1020,7 +1018,7 @@ private <S extends DataFilter> List<ClinicalData> fetchDataAndTransformToClinica
                 }
                 // don't change anything for non patient level data
                 return dataStream;
-            }).collect(Collectors.toList());
+            }).toList();
         }
     }
 
@@ -1060,7 +1058,7 @@ private List<ClinicalData> fetchMutationDataAndTransformToClinicalDataList(
                     studyViewFilterUtil.getMutationDataFilterUniqueKey(mutationDataFilter),
                     fetchMutationData);
             }
-        }).collect(Collectors.toList());
+        }).toList();
     }
     private <S extends DataFilter> List<ClinicalDataFilter> transformToClinicalDataFilter(List<S> dataFilters) {
         List<ClinicalDataFilter> attributes;
@@ -1069,7 +1067,7 @@ private <S extends DataFilter> List<ClinicalDataFilter> transformToClinicalDataF
             clinicalDataFilter.setAttributeId(studyViewFilterUtil.getDataFilterUniqueKey(dataFilter));
             clinicalDataFilter.setValues(dataFilter.getValues());
             return clinicalDataFilter;
-        }).collect(Collectors.toList());
+        }).toList();
         return attributes;
     }
 
@@ -1102,7 +1100,7 @@ private List<SampleIdentifier> fetchMutationOptionDataByGene(List<String> studyI
         List<GenePanelData> genePanelData = genePanelDataList
             .stream()
             .filter(GenePanelData::getProfiled)
-            .collect(Collectors.toList());
+            .toList();
 
         Set<SampleIdentifier> profiledCases = genePanelData
             .stream()
@@ -1138,7 +1136,7 @@ private List<SampleIdentifier> fetchMutationOptionDataByGene(List<String> studyI
                 .stream()
                 .filter(genePanelToGene -> genePanelToGene.getEntrezGeneId().equals(entrezGeneId))
                 .map(GenePanelToGene::getGenePanelId);
-        }).collect(Collectors.toList());
+        }).toList();
         
         List<SampleIdentifier> newSampleIdentifiers = new ArrayList<>();
         // different calculations depending on if gene is linked to gene panels
@@ -1170,12 +1168,12 @@ private Stream<ClinicalData> fetchMutatedAndWildTypeData(
         List<ClinicalData> mutatedClinicalDatas = invokeDataFunc(sampleIds, studyIds,
             Collections.singletonList(geneNameIdMap.get(mutationDataFilter.getHugoGeneSymbol()).toString()),
             studyIdToMolecularProfileIdMap, studyViewFilterUtil.getMutationDataFilterUniqueKey(mutationDataFilter),
-            fetchMutatedData).collect(Collectors.toList());
+            fetchMutatedData).toList();
 
         List<SampleIdentifier> mutatedSampleIdentifiers = mutatedClinicalDatas
             .stream()
             .map(datum -> studyViewFilterUtil.buildSampleIdentifier(datum.getStudyId(), datum.getSampleId())
-            ).collect(Collectors.toList());
+            ).toList();
 
         List<ClinicalData> clinicalDatas = new ArrayList<>(mutatedClinicalDatas);
 
@@ -1186,7 +1184,7 @@ private Stream<ClinicalData> fetchMutatedAndWildTypeData(
         List<SampleIdentifier> notProfiledSampleIdentifiers = sampleIdentifiers
             .stream()
             .filter(s -> profiledSampleIdentifiers.stream().noneMatch(p -> p.equals(s)))
-            .collect(Collectors.toList());
+            .toList();
 
         List<ClinicalData> notProfiledClinicalDatas = transformSampleIdentifiersToClinicalData(
             notProfiledSampleIdentifiers,
@@ -1200,7 +1198,7 @@ private Stream<ClinicalData> fetchMutatedAndWildTypeData(
         List<SampleIdentifier> notMutatedSampleIdentifiers = profiledSampleIdentifiers
             .stream()
             .filter(p -> mutatedSampleIdentifiers.stream().noneMatch(m -> m.equals(p)))
-            .collect(Collectors.toList());
+            .toList();
 
         List<ClinicalData> notMutatedClinicalDatas = transformSampleIdentifiersToClinicalData(
             notMutatedSampleIdentifiers,
@@ -1242,6 +1240,6 @@ private List<ClinicalData> transformSampleIdentifiersToClinicalData(List<SampleI
                 clinicalData.setSampleId(sampleIdentifier.getSampleId());
                 clinicalData.setStudyId(sampleIdentifier.getStudyId());
                 return clinicalData;
-            }).collect(Collectors.toList());
+            }).toList();
     }
 }
diff --git a/src/main/java/org/cbioportal/web/util/StudyViewFilterUtil.java b/src/main/java/org/cbioportal/web/util/StudyViewFilterUtil.java
index 10306462a94..e23ae60f114 100644
--- a/src/main/java/org/cbioportal/web/util/StudyViewFilterUtil.java
+++ b/src/main/java/org/cbioportal/web/util/StudyViewFilterUtil.java
@@ -22,10 +22,10 @@ public class StudyViewFilterUtil {
 
     @Autowired
     private GeneService geneService;
-    
+
     public void extractStudyAndSampleIds(
-        List<SampleIdentifier> sampleIdentifiers, 
-        List<String> studyIds, 
+        List<SampleIdentifier> sampleIdentifiers,
+        List<String> studyIds,
         List<String> sampleIds
     ) {
         for (SampleIdentifier sampleIdentifier : sampleIdentifiers) {
@@ -39,10 +39,10 @@ public void removeSelfFromFilter(String attributeId, StudyViewFilter studyViewFi
             studyViewFilter.getClinicalDataFilters().removeIf(f -> f.getAttributeId().equals(attributeId));
         }
     }
-    
+
     public void removeSelfFromGenomicDataFilter(String hugoGeneSymbol, String profileType, StudyViewFilter studyViewFilter) {
         if (studyViewFilter != null && studyViewFilter.getGenomicDataFilters() != null) {
-            studyViewFilter.getGenomicDataFilters().removeIf(f -> 
+            studyViewFilter.getGenomicDataFilters().removeIf(f ->
                 f.getHugoGeneSymbol().equals(hugoGeneSymbol) && f.getProfileType().equals(profileType)
             );
         }
@@ -50,9 +50,9 @@ public void removeSelfFromGenomicDataFilter(String hugoGeneSymbol, String profil
 
     public void removeSelfFromMutationDataFilter(String hugoGeneSymbol, String profileType, MutationOption categorization, StudyViewFilter studyViewFilter) {
         if (studyViewFilter != null && studyViewFilter.getMutationDataFilters() != null) {
-            studyViewFilter.getMutationDataFilters().removeIf(f -> 
-                    f.getHugoGeneSymbol().equals(hugoGeneSymbol) && 
-                    f.getProfileType().equals(profileType) && 
+            studyViewFilter.getMutationDataFilters().removeIf(f ->
+                f.getHugoGeneSymbol().equals(hugoGeneSymbol) &&
+                    f.getProfileType().equals(profileType) &&
                     f.getCategorization().equals(categorization)
             );
         }
@@ -69,32 +69,28 @@ public void removeSelfCustomDataFromFilter(String attributeId, StudyViewFilter s
             studyViewFilter.getCustomDataFilters().removeIf(f -> f.getAttributeId().equals(attributeId));
         }
     }
-    
+
     public String getCaseUniqueKey(String studyId, String caseId) {
         return studyId + caseId;
     }
 
     public <S extends DataFilter> String getDataFilterUniqueKey(S dataFilter) {
-        if (dataFilter instanceof GenomicDataFilter) {
-            GenomicDataFilter genomicDataFilter = (GenomicDataFilter) dataFilter;
+        if (dataFilter instanceof GenomicDataFilter genomicDataFilter) {
             return genomicDataFilter.getHugoGeneSymbol() + genomicDataFilter.getProfileType();
-        } else if (dataFilter instanceof GenericAssayDataFilter) {
-            GenericAssayDataFilter genericAssayDataFilter = (GenericAssayDataFilter) dataFilter;
+        } else if (dataFilter instanceof GenericAssayDataFilter genericAssayDataFilter) {
             return genericAssayDataFilter.getStableId() + genericAssayDataFilter.getProfileType();
         }
         return null;
     }
-    
+
     public String getMutationDataFilterUniqueKey(MutationDataFilter mutationDataFilter) {
         return mutationDataFilter.getHugoGeneSymbol() + mutationDataFilter.getProfileType();
     }
 
     public <S extends DataBinFilter> String getDataBinFilterUniqueKey(S dataBinFilter) {
-        if (dataBinFilter instanceof GenomicDataBinFilter) {
-            GenomicDataBinFilter genomicDataBinFilter = (GenomicDataBinFilter) dataBinFilter;
+        if (dataBinFilter instanceof GenomicDataBinFilter genomicDataBinFilter) {
             return genomicDataBinFilter.getHugoGeneSymbol() + genomicDataBinFilter.getProfileType();
-        } else if (dataBinFilter instanceof GenericAssayDataBinFilter) {
-            GenericAssayDataBinFilter genericAssayDataBinFilter = (GenericAssayDataBinFilter) dataBinFilter;
+        } else if (dataBinFilter instanceof GenericAssayDataBinFilter genericAssayDataBinFilter) {
             return genericAssayDataBinFilter.getStableId() + genericAssayDataBinFilter.getProfileType();
         }
         return null;
@@ -123,26 +119,23 @@ public Map<String, List<SampleList>> categorizeSampleLists(List<SampleList> samp
     }
 
     public <S> Integer getFilteredCountByDataEquality(List<ClinicalDataFilter> attributes, MultiKeyMap<String, S> clinicalDataMap,
-            String entityId, String studyId, Boolean negateFilters) {
+                                                      String entityId, String studyId, Boolean negateFilters) {
         Integer count = 0;
         for (ClinicalDataFilter s : attributes) {
             List<String> filteredValues = s.getValues()
-                    .stream()
-                    .map(DataFilterValue::getValue)
-                    .collect(Collectors.toList());
+                .stream()
+                .map(DataFilterValue::getValue)
+                .collect(Collectors.toList());
             filteredValues.replaceAll(String::toUpperCase);
             if (clinicalDataMap.containsKey(studyId, entityId, s.getAttributeId())) {
-//                for (String value: filteredValues) System.out.println(value);
                 S value = clinicalDataMap.get(studyId, entityId, s.getAttributeId());
                 if (value instanceof String) {
                     if (negateFilters ^ filteredValues.contains(value)) {
                         count++;
                     }
-                } else if (value instanceof List) {
-//                    for (String val : (ArrayList<String>) value) System.out.println("clinical value: " + val);
-                    if (negateFilters ^ filteredValues.stream().anyMatch(((List<?>) value)::contains)) {
-                        count++;
-                    }
+                } else if (value instanceof List &&
+                    negateFilters ^ filteredValues.stream().anyMatch(((List<?>) value)::contains)) {
+                    count++;
                 }
             } else if (negateFilters ^ filteredValues.contains("NA")) {
                 count++;
@@ -152,7 +145,7 @@ public <S> Integer getFilteredCountByDataEquality(List<ClinicalDataFilter> attri
     }
 
     public List<ClinicalDataCountItem> getClinicalDataCountsFromCustomData(Collection<CustomDataSession> customDataSessions,
-            Map<String, SampleIdentifier> filteredSamplesMap, List<Patient> patients) {
+                                                                           Map<String, SampleIdentifier> filteredSamplesMap, List<Patient> patients) {
         int totalSamplesCount = filteredSamplesMap.keySet().size();
         int totalPatientsCount = patients.size();
 
@@ -167,22 +160,22 @@ public List<ClinicalDataCountItem> getClinicalDataCountsFromCustomData(Collectio
             clinicalDataCountItem.setAttributeId(customDataSession.getId());
 
             List<ClinicalDataCount> clinicalDataCounts = groupedDatabyValue.entrySet().stream()
-                    .map(entry -> {
-                        long count = entry.getValue().stream().map(datum -> {
-                            return getCaseUniqueKey(datum.getStudyId(),
-                                    customDataSession.getData().getPatientAttribute()
-                                            ? datum.getPatientId()
-                                            : datum.getSampleId());
-        
-                        }).distinct().count();
-                        ClinicalDataCount dataCount = new ClinicalDataCount();
-                        dataCount.setValue(entry.getKey());
-                        dataCount.setCount(Math.toIntExact(count));
-                        return dataCount;
-                    })
-                    .filter(c -> !c.getValue().equalsIgnoreCase("NA") && !c.getValue().equalsIgnoreCase("NAN")
-                            && !c.getValue().equalsIgnoreCase("N/A"))
-                    .collect(Collectors.toList());
+                .map(entry -> {
+                    long count = entry.getValue().stream().map(datum -> {
+                        return getCaseUniqueKey(datum.getStudyId(),
+                            customDataSession.getData().getPatientAttribute()
+                                ? datum.getPatientId()
+                                : datum.getSampleId());
+
+                    }).distinct().count();
+                    ClinicalDataCount dataCount = new ClinicalDataCount();
+                    dataCount.setValue(entry.getKey());
+                    dataCount.setCount(Math.toIntExact(count));
+                    return dataCount;
+                })
+                .filter(c -> !c.getValue().equalsIgnoreCase("NA") && !c.getValue().equalsIgnoreCase("NAN")
+                    && !c.getValue().equalsIgnoreCase("N/A"))
+                .collect(Collectors.toList());
 
             int totalCount = clinicalDataCounts.stream().mapToInt(ClinicalDataCount::getCount).sum();
             int naCount = 0;
@@ -203,38 +196,38 @@ public List<ClinicalDataCountItem> getClinicalDataCountsFromCustomData(Collectio
             return clinicalDataCountItem;
         }).collect(Collectors.toList());
     }
-    
+
     public boolean isSingleStudyUnfiltered(StudyViewFilter filter) {
-            return filter.getStudyIds() != null &&
-                filter.getStudyIds().size() == 1 &&
-                (filter.getClinicalDataFilters() == null || filter.getClinicalDataFilters().isEmpty()) &&
-                (filter.getGeneFilters() == null || filter.getGeneFilters().isEmpty()) &&
-                (filter.getSampleTreatmentFilters() == null || filter.getSampleTreatmentFilters().getFilters().isEmpty()) &&
-                (filter.getPatientTreatmentFilters() == null || filter.getPatientTreatmentFilters().getFilters().isEmpty()) &&
-                (filter.getGenomicProfiles() == null || filter.getGenomicProfiles().isEmpty()) &&
-                (filter.getGenomicDataFilters() == null || filter.getGenomicDataFilters().isEmpty()) &&
-                (filter.getGenericAssayDataFilters() == null || filter.getGenericAssayDataFilters().isEmpty()) &&
-                (filter.getCaseLists() == null || filter.getCaseLists().isEmpty()) &&
-                (filter.getCustomDataFilters() == null || filter.getCustomDataFilters().isEmpty());
+        return filter.getStudyIds() != null &&
+            filter.getStudyIds().size() == 1 &&
+            (filter.getClinicalDataFilters() == null || filter.getClinicalDataFilters().isEmpty()) &&
+            (filter.getGeneFilters() == null || filter.getGeneFilters().isEmpty()) &&
+            (filter.getSampleTreatmentFilters() == null || filter.getSampleTreatmentFilters().getFilters().isEmpty()) &&
+            (filter.getPatientTreatmentFilters() == null || filter.getPatientTreatmentFilters().getFilters().isEmpty()) &&
+            (filter.getGenomicProfiles() == null || filter.getGenomicProfiles().isEmpty()) &&
+            (filter.getGenomicDataFilters() == null || filter.getGenomicDataFilters().isEmpty()) &&
+            (filter.getGenericAssayDataFilters() == null || filter.getGenericAssayDataFilters().isEmpty()) &&
+            (filter.getCaseLists() == null || filter.getCaseLists().isEmpty()) &&
+            (filter.getCustomDataFilters() == null || filter.getCustomDataFilters().isEmpty());
     }
-    
+
     public boolean shouldSkipFilterForClinicalDataBins(StudyViewFilter filter) {
         // if everything other than study ids and sample identifiers is null,
         // we can skip the filter for data bin calculation
         return (
             filter != null &&
-            filter.getClinicalDataFilters() == null &&
-            filter.getGeneFilters() == null &&
-            filter.getSampleTreatmentFilters() == null &&
-            filter.getPatientTreatmentFilters() == null &&
-            filter.getGenomicProfiles() == null &&
-            filter.getGenomicDataFilters() == null &&
-            filter.getGenericAssayDataFilters() == null &&
-            filter.getCaseLists() == null &&
-            filter.getCustomDataFilters() == null
+                filter.getClinicalDataFilters() == null &&
+                filter.getGeneFilters() == null &&
+                filter.getSampleTreatmentFilters() == null &&
+                filter.getPatientTreatmentFilters() == null &&
+                filter.getGenomicProfiles() == null &&
+                filter.getGenomicDataFilters() == null &&
+                filter.getGenericAssayDataFilters() == null &&
+                filter.getCaseLists() == null &&
+                filter.getCustomDataFilters() == null
         );
     }
-    
+
     public List<Binnable> filterClinicalData(
         List<Binnable> unfilteredClinicalDataForSamples,
         List<Binnable> unfilteredClinicalDataForPatients,
@@ -248,9 +241,9 @@ public List<Binnable> filterClinicalData(
         List<String> conflictingPatientAttributes
     ) {
         List<Binnable> combinedResult = new ArrayList<>();
-        
+
         Map<String, String> patientIdToStudyId = null;
-            
+
         if (CollectionUtils.isNotEmpty(sampleAttributeIds)) {
             // create lookups for faster filtering
             Map<String, String> sampleIdToStudyId = mapCaseToStudy(sampleIds, studyIds);
@@ -269,7 +262,7 @@ public List<Binnable> filterClinicalData(
             // create lookups for faster filtering
             Map<String, Boolean> patientAttributeIdLookup = listToMap(patientAttributeIds);
             patientIdToStudyId = mapCaseToStudy(patientIds, studyIdsOfPatients);
-            
+
             combinedResult.addAll(
                 filterClinicalDataByStudyAndPatientAndAttribute(
                     unfilteredClinicalDataForPatients,
@@ -285,7 +278,7 @@ public List<Binnable> filterClinicalData(
             if (patientIdToStudyId == null) {
                 patientIdToStudyId = mapCaseToStudy(patientIds, studyIdsOfPatients);
             }
-            
+
             combinedResult.addAll(
                 filterClinicalDataByStudyAndPatientAndAttribute(
                     unfilteredClinicalDataForConflictingPatientAttributes,
@@ -349,7 +342,7 @@ public List<StructuralVariantFilterQuery> resolveEntrezGeneIds(List<StructuralVa
 
         // Remove any genes where the Entrez gene id is needed, but translation failed.
         structVarQueries.removeIf(
-            q ->   (q.getGene1Query().getSpecialValue() != StructuralVariantSpecialValue.NO_GENE
+            q -> (q.getGene1Query().getSpecialValue() != StructuralVariantSpecialValue.NO_GENE
                 && q.getGene1Query().getSpecialValue() != StructuralVariantSpecialValue.ANY_GENE
                 && q.getGene1Query().getEntrezId() == null)
                 || (q.getGene2Query().getSpecialValue() != StructuralVariantSpecialValue.NO_GENE
@@ -378,7 +371,7 @@ private List<Binnable> filterClinicalDataByStudyAndSampleAndAttribute(
             .stream()
             .filter(d ->
                 sampleToStudyId.getOrDefault(generateSampleToStudyKey(d), "").equals(d.getStudyId()) &&
-                attributeIdLookup.getOrDefault(d.getAttrId(), false)
+                    attributeIdLookup.getOrDefault(d.getAttrId(), false)
             )
             .collect(Collectors.toList());
     }
@@ -392,40 +385,40 @@ private List<Binnable> filterClinicalDataByStudyAndPatientAndAttribute(
             .stream()
             .filter(d ->
                 patientToStudyId.getOrDefault(generatePatientToStudyKey(d), "").equals(d.getStudyId()) &&
-                attributeIdLookup.getOrDefault(d.getAttrId(), false)
+                    attributeIdLookup.getOrDefault(d.getAttrId(), false)
             )
             .collect(Collectors.toList());
     }
-    
+
     private <T> Map<T, Boolean> listToMap(List<T> list) {
         return list.stream().collect(Collectors.toMap(s -> s, s -> true, (s1, s2) -> s1));
     }
 
-    private  Map<String, String> mapCaseToStudy(List<String> caseIds, List<String> studyIds) {
+    private Map<String, String> mapCaseToStudy(List<String> caseIds, List<String> studyIds) {
         Map<String, String> caseToStudy = new HashMap<>();
-        
-        for (int i =0; i < caseIds.size(); i++) {
+
+        for (int i = 0; i < caseIds.size(); i++) {
             String studyId = studyIds.get(i);
             String caseId = caseIds.get(i);
             String key = generateCaseToStudyKey(studyId, caseId);
             caseToStudy.put(key, studyId);
         }
-        
+
         return caseToStudy;
     }
 
     private String generateSampleToStudyKey(Binnable clinicalData) {
         return generateCaseToStudyKey(clinicalData.getStudyId(), clinicalData.getSampleId());
     }
-    
+
     private String generatePatientToStudyKey(Binnable clinicalData) {
         return generateCaseToStudyKey(clinicalData.getStudyId(), clinicalData.getPatientId());
     }
-    
+
     private String generateCaseToStudyKey(String studyId, String caseId) {
         return studyId + ":" + caseId;
     }
-    
+
     public SampleIdentifier buildSampleIdentifier(String studyId, String sampleId) {
         SampleIdentifier sampleIdentifier = new SampleIdentifier();
         sampleIdentifier.setStudyId(studyId);