separate mutated and mutation types service

model/src/main/java/org/cbioportal/model/MutationFilterOption.java

@@ -1,9 +1,9 @@
 package org.cbioportal.model;
 
 public enum MutationFilterOption {
-    MUTATED("Mutated"),
-    NOT_MUTATED("Not Mutated"),
-    NOT_PROFILED("Not Profiled"),
+    MUTATED("Mutated vs. Wild Type"),
+    WILD_TYPE("Wild Type"),
+    NA("NA"),
     ;
 
     private final String mutationFilterOption;
@@ -12,7 +12,7 @@ public enum MutationFilterOption {
         this.mutationFilterOption = mutationFilterOption;
     }
 
-    public String getMutationType() {
+    public String getMutationFilterOption() {
         return mutationFilterOption;
     }
 }

service/src/main/java/org/cbioportal/service/StudyViewService.java

@@ -12,7 +12,7 @@ public interface StudyViewService {
     List<AlterationCountByGene> getMutationAlterationCountByGenes(List<String> studyIds, List<String> sampleIds, AlterationFilter annotationFilter)
         throws StudyNotFoundException;
 
-    List<GenomicDataCountItem> getMutationCountsByGeneSpecific(List<String> studyIds, List<String> sampleIds, List<Pair<String, String>> genomicDataFilters, AlterationFilter annotationFilter, String projection);
+    List<GenomicDataCountItem> getMutationCountsByGeneSpecific(List<String> studyIds, List<String> sampleIds, List<Pair<String, String>> genomicDataFilters, AlterationFilter annotationFilter);
 
     List<GenomicDataCountItem> getMutationTypeCountsByGeneSpecific(List<String> studyIds, List<String> sampleIds, List<Pair<String, String>> genomicDataFilters);
 

service/src/main/java/org/cbioportal/service/impl/StudyViewServiceImpl.java

@@ -1,6 +1,5 @@
 package org.cbioportal.service.impl;
 
-import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.collections4.map.MultiKeyMap;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.math3.util.Pair;
@@ -112,8 +111,7 @@ public List<AlterationCountByGene> getMutationAlterationCountByGenes(List<String
     public List<GenomicDataCountItem> getMutationCountsByGeneSpecific(List<String> studyIds,
                                                                       List<String> sampleIds,
                                                                       List<Pair<String, String>> genomicDataFilters,
-                                                                      AlterationFilter alterationFilter,
-                                                                      String projection) {
+                                                                      AlterationFilter alterationFilter) {
         List<MolecularProfileCaseIdentifier> caseIdentifiers =
             molecularProfileService.getMutationProfileCaseIdentifiers(studyIds, sampleIds);
 
@@ -134,13 +132,6 @@ public List<GenomicDataCountItem> getMutationCountsByGeneSpecific(List<String> s
             false,
             alterationFilter).getFirst();
 
-        List<GenomicDataCountItem> mutationTypeCountItems;
-        if (projection.equals("DETAILED")) {
-            mutationTypeCountItems = getMutationTypeCountsByGeneSpecific(studyIds, sampleIds, genomicDataFilters);
-        } else {
-            mutationTypeCountItems = new ArrayList<>();
-        }
-
         return genomicDataFilters
             .stream()
             .flatMap(gdFilter -> {
@@ -164,33 +155,24 @@ public List<GenomicDataCountItem> getMutationCountsByGeneSpecific(List<String> s
                 int totalCount = sampleIds.size();
 
                 List<GenomicDataCount> genomicDataCounts = new ArrayList<>();
-
-                if (CollectionUtils.isNotEmpty(mutationTypeCountItems)) {
-                    Optional<GenomicDataCountItem> genomicDataCountItemType = mutationTypeCountItems.stream()
-                        .filter(item -> item.getHugoGeneSymbol().equals(hugoGeneSymbol) && item.getProfileType().equals(profileType))
-                        .findFirst();
-                    genomicDataCountItemType.ifPresent(dataCountItem -> genomicDataCounts.addAll(dataCountItem.getCounts()));
-                }
-
-                if (CollectionUtils.isEmpty(genomicDataCounts)) {
-                    GenomicDataCount genomicDataCountMutated = new GenomicDataCount();
-                    genomicDataCountMutated.setLabel(MutationFilterOption.MUTATED.getMutationType());
-                    genomicDataCountMutated.setValue(MutationFilterOption.MUTATED.name());
-                    genomicDataCountMutated.setCount(mutatedCount);
-                    genomicDataCountMutated.setUniqueCount(mutatedCount);
-                    if (genomicDataCountMutated.getCount() > 0) genomicDataCounts.add(genomicDataCountMutated);
-                }
-
-                GenomicDataCount genomicDataCountNotMutated = new GenomicDataCount();
-                genomicDataCountNotMutated.setLabel(MutationFilterOption.NOT_MUTATED.getMutationType());
-                genomicDataCountNotMutated.setValue(MutationFilterOption.NOT_MUTATED.name());
-                genomicDataCountNotMutated.setCount(profiledCount - mutatedCount);
-                genomicDataCountNotMutated.setUniqueCount(profiledCount - mutatedCount);
-                if (genomicDataCountNotMutated.getCount() > 0) genomicDataCounts.add(genomicDataCountNotMutated);
+
+                GenomicDataCount genomicDataCountMutated = new GenomicDataCount();
+                genomicDataCountMutated.setLabel(MutationFilterOption.MUTATED.getMutationFilterOption());
+                genomicDataCountMutated.setValue(MutationFilterOption.MUTATED.name());
+                genomicDataCountMutated.setCount(mutatedCount);
+                genomicDataCountMutated.setUniqueCount(mutatedCount);
+                if (genomicDataCountMutated.getCount() > 0) genomicDataCounts.add(genomicDataCountMutated);
+
+                GenomicDataCount genomicDataCountWildType = new GenomicDataCount();
+                genomicDataCountWildType.setLabel(MutationFilterOption.WILD_TYPE.getMutationFilterOption());
+                genomicDataCountWildType.setValue(MutationFilterOption.WILD_TYPE.name());
+                genomicDataCountWildType.setCount(profiledCount - mutatedCount);
+                genomicDataCountWildType.setUniqueCount(profiledCount - mutatedCount);
+                if (genomicDataCountWildType.getCount() > 0) genomicDataCounts.add(genomicDataCountWildType);
 
                 GenomicDataCount genomicDataCountNotProfiled = new GenomicDataCount();
-                genomicDataCountNotProfiled.setLabel(MutationFilterOption.NOT_PROFILED.getMutationType());
-                genomicDataCountNotProfiled.setValue(MutationFilterOption.NOT_PROFILED.name());
+                genomicDataCountNotProfiled.setLabel(MutationFilterOption.NA.getMutationFilterOption());
+                genomicDataCountNotProfiled.setValue(MutationFilterOption.NA.name());
                 genomicDataCountNotProfiled.setCount(totalCount - profiledCount);
                 genomicDataCountNotProfiled.setUniqueCount(totalCount - profiledCount);
                 if (genomicDataCountNotProfiled.getCount() > 0) genomicDataCounts.add(genomicDataCountNotProfiled);

service/src/test/java/org/cbioportal/service/impl/StudyViewServiceImplTest.java

@@ -235,37 +235,11 @@ public void getMutationCountsByGeneSpecific() {
         List<Pair<String, String>> genomicDataFilters = new ArrayList<>();
         Pair<String, String> genomicDataFilter = new Pair<>(BaseServiceImplTest.HUGO_GENE_SYMBOL_1, BaseServiceImplTest.PROFILE_TYPE_1);
         genomicDataFilters.add(genomicDataFilter);
-
-        GenomicDataCountItem genomicDataCountItem = new GenomicDataCountItem();
-        genomicDataCountItem.setHugoGeneSymbol(BaseServiceImplTest.HUGO_GENE_SYMBOL_1);
-        genomicDataCountItem.setProfileType(BaseServiceImplTest.PROFILE_TYPE_1);
-        List<GenomicDataCount> genomicDataCounts = new ArrayList<>();
-        GenomicDataCount genomicDataCount1 = new GenomicDataCount();
-        genomicDataCount1.setLabel(MutationEventType.missense_mutation.getMutationType());
-        genomicDataCount1.setValue(MutationEventType.missense_mutation.getMutationType());
-        genomicDataCount1.setCount(2);
-        genomicDataCount1.setUniqueCount(1);
-        genomicDataCounts.add(genomicDataCount1);
-        GenomicDataCount genomicDataCount2 = new GenomicDataCount();
-        genomicDataCount2.setLabel(MutationEventType.splice_site_indel.getMutationType());
-        genomicDataCount2.setValue(MutationEventType.splice_site_indel.getMutationType());
-        genomicDataCount2.setCount(2);
-        genomicDataCount2.setUniqueCount(1);
-        genomicDataCounts.add(genomicDataCount2);
-        genomicDataCountItem.setCounts(genomicDataCounts);
-
-        Mockito.doReturn(Collections.singletonList(genomicDataCountItem))
-            .when(studyViewService).getMutationTypeCountsByGeneSpecific(anyList(), anyList(), anyList());
 
         List<GenomicDataCountItem> result = studyViewService.getMutationCountsByGeneSpecific(
-            studyIds, sampleIds, genomicDataFilters, alterationFilter, "SUMMARY");
-        Assert.assertEquals(1, result.size());
-        Assert.assertEquals(3, result.get(0).getCounts().size());
-
-        result = studyViewService.getMutationCountsByGeneSpecific(
-            studyIds, sampleIds, genomicDataFilters, alterationFilter, "DETAILED");
+            studyIds, sampleIds, genomicDataFilters, alterationFilter);
         Assert.assertEquals(1, result.size());
-        Assert.assertEquals(4, result.get(0).getCounts().size());
+        Assert.assertEquals(1, result.get(0).getCounts().size());
     }
 
     @Test

web/src/main/java/org/cbioportal/web/StudyViewController.java

@@ -1113,13 +1113,20 @@ public ResponseEntity<List<GenomicDataCountItem>> fetchMutationDataCounts(
         List<String> sampleIds = new ArrayList<>();
         studyViewFilterUtil.extractStudyAndSampleIds(filteredSampleIdentifiers, studyIds, sampleIds);
 
-        List<GenomicDataCountItem> result = studyViewService.getMutationCountsByGeneSpecific(
-            studyIds,
-            sampleIds,
-            gdFilters.stream().map(gdFilter -> new Pair<>(gdFilter.getHugoGeneSymbol(), gdFilter.getProfileType())).collect(Collectors.toList()),
-            studyViewFilter.getAlterationFilter(),
-            projection.name()
-        );
+        List<GenomicDataCountItem> result;
+
+        result = projection == Projection.SUMMARY ?
+            studyViewService.getMutationCountsByGeneSpecific(
+                studyIds,
+                sampleIds,
+                gdFilters.stream().map(gdFilter -> new Pair<>(gdFilter.getHugoGeneSymbol(), gdFilter.getProfileType())).collect(Collectors.toList()),
+                studyViewFilter.getAlterationFilter()
+            ) : 
+            studyViewService.getMutationTypeCountsByGeneSpecific(
+                studyIds,
+                sampleIds,
+                gdFilters.stream().map(gdFilter -> new Pair<>(gdFilter.getHugoGeneSymbol(), gdFilter.getProfileType())).collect(Collectors.toList())
+            );
 
         return new ResponseEntity<>(result, HttpStatus.OK);
     }

web/src/main/java/org/cbioportal/web/util/StudyViewFilterApplier.java

@@ -1056,42 +1056,18 @@ private List<ClinicalData> fetchMutationDataAndTransformToClinicalDataList(
                 .stream().collect(Collectors.toMap(MolecularProfile::getCancerStudyIdentifier,
                     MolecularProfile::getStableId));
 
-            Stream<ClinicalData> res = Stream.of();
-            List<DataFilterValue> customFilters = new ArrayList<>();
-
-            if (mutationDataFilter.getCategorization() == MutationOption.EVENT) {
-                customFilters = mutationDataFilter.getValues()
-                    .stream()
-                    .flatMap(value -> 
-                        value.stream().filter(x -> x.getValue().equalsIgnoreCase(MutationFilterOption.
-                            MUTATED
-                            .name()) ||
-                            x.getValue().equalsIgnoreCase(MutationFilterOption.
-                                NOT_PROFILED
-                                .name()) ||
-                            x.getValue().equalsIgnoreCase(MutationFilterOption.
-                                NOT_MUTATED
-                                .name()))
-                    ).collect(Collectors.toList());
-
-
+            if (mutationDataFilter.getCategorization() == MutationOption.MUTATED) {
+                return fetchMutatedAndWildTypeData(
+                    sampleIdentifiers, geneNameIdMap, mutationDataFilter,
+                    studyIdToMolecularProfileIdMap);
+            } else {
                 // fetch mutation type data
-                res = invokeDataFunc(sampleIds, studyIds, Collections.singletonList(
+                return invokeDataFunc(sampleIds, studyIds, Collections.singletonList(
                         geneNameIdMap.get(mutationDataFilter.getHugoGeneSymbol()).toString()),
                     studyIdToMolecularProfileIdMap,
                     studyViewFilterUtil.getMutationDataFilterUniqueKey(mutationDataFilter),
                     fetchMutationData);
-
-            }
-            if (mutationDataFilter.getCategorization() == MutationOption.MUTATED ||
-                CollectionUtils.isNotEmpty(customFilters)) {
-
-                Stream<ClinicalData> res1 = fetchMutatedAndProfiledMutationData(
-                    sampleIdentifiers, geneNameIdMap, mutationDataFilter,
-                    studyIdToMolecularProfileIdMap);
-                res = Stream.concat(res, res1);
             }
-            return res;
         }).collect(Collectors.toList());
     }
     private <S extends DataFilter> List<ClinicalDataFilter> transformToClinicalDataFilter(List<S> dataFilters) {
@@ -1191,7 +1167,7 @@ private List<SampleIdentifier> fetchMutationOptionDataByGene(List<String> studyI
         return newSampleIdentifiers;
     }
 
-    private Stream<ClinicalData> fetchMutatedAndProfiledMutationData(
+    private Stream<ClinicalData> fetchMutatedAndWildTypeData(
         List<SampleIdentifier> sampleIdentifiers, Map<String, Integer> geneNameIdMap, MutationDataFilter mutationDataFilter,
         Map<String, String> studyIdToMolecularProfileIdMap) {
         List<String> studyIds = new ArrayList<>();
@@ -1223,7 +1199,7 @@ private Stream<ClinicalData> fetchMutatedAndProfiledMutationData(
         List<ClinicalData> notProfiledClinicalDatas = transformSampleIdentifiersToClinicalData(
             notProfiledSampleIdentifiers,
             studyViewFilterUtil.getMutationDataFilterUniqueKey(mutationDataFilter),
-            MutationFilterOption.NOT_PROFILED.name()
+            MutationFilterOption.NA.name()
         );
 
         clinicalDatas.addAll(notProfiledClinicalDatas);
@@ -1237,7 +1213,7 @@ private Stream<ClinicalData> fetchMutatedAndProfiledMutationData(
         List<ClinicalData> notMutatedClinicalDatas = transformSampleIdentifiersToClinicalData(
             notMutatedSampleIdentifiers,
             studyViewFilterUtil.getMutationDataFilterUniqueKey(mutationDataFilter),
-            MutationFilterOption.NOT_MUTATED.name()
+            MutationFilterOption.WILD_TYPE.name()
         );
 
         clinicalDatas.addAll(notMutatedClinicalDatas);

web/src/test/java/org/cbioportal/web/StudyViewControllerTest.java

@@ -1117,8 +1117,13 @@ public void fetchMutationDataCounts() throws Exception {
             anyList(),
             anyList(),
             anyList(),
-            any(AlterationFilter.class),
-            anyString()))
+            any(AlterationFilter.class)))
+            .thenReturn(genomicDataCountItems);
+
+        when(studyViewService.getMutationTypeCountsByGeneSpecific(
+            anyList(),
+            anyList(),
+            anyList()))
             .thenReturn(genomicDataCountItems);
 
         GenomicDataCountFilter genomicDataCountFilter = new GenomicDataCountFilter();