resolve issue cBioPortal#5613 fixing mutated genes table shows incorr…

…ect frequencies

persistence/persistence-api/src/main/java/org/cbioportal/persistence/MutationRepository.java

@@ -51,6 +51,11 @@ List<MutationCountByGene> getSampleCountByEntrezGeneIdsAndSampleIds(String molec
     List<MutationCountByGene> getSampleCountInMultipleMolecularProfiles(List<String> molecularProfileIds,
                                                                         List<String> sampleIds,
                                                                         List<Integer> entrezGeneIds);
+
+    @Cacheable(cacheNames = "GeneralRepositoryCache", condition = "@cacheEnabledConfig.getEnabled()")
+    List<MutationCountByGene> getSampleCountInMultipleMolecularProfilesForFusions(List<String> molecularProfileIds,
+                                                                        List<String> sampleIds,
+                                                                        List<Integer> entrezGeneIds);
 
     @Cacheable(cacheNames = "GeneralRepositoryCache", condition = "@cacheEnabledConfig.getEnabled()")
     List<MutationCountByGene> getPatientCountInMultipleMolecularProfiles(List<String> molecularProfileIds,

persistence/persistence-mybatis/src/main/java/org/cbioportal/persistence/mybatis/MutationMapper.java

@@ -45,6 +45,13 @@ List<MutationCountByGene> getPatientCountInMultipleMolecularProfiles(List<String
                                                                          List<String> patientIds,
                                                                          List<Integer> entrezGeneIds,
                                                                          Boolean snpOnly);
+
+    List<MutationCountByGene> getSampleCountInMultipleMolecularProfilesForFusions(List<String> molecularProfileIds,
+                                                                                           List<String> sampleIds,
+                                                                                           List<Integer> entrezGeneIds,
+                                                                                           Boolean snpOnly);
+
+
 
     MutationCountByPosition getMutationCountByPosition(Integer entrezGeneId, Integer proteinPosStart, 
                                                        Integer proteinPosEnd);

persistence/persistence-mybatis/src/main/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepository.java

@@ -89,6 +89,14 @@ public List<MutationCountByGene> getSampleCountInMultipleMolecularProfiles(List<
         return mutationMapper.getSampleCountInMultipleMolecularProfiles(molecularProfileIds, sampleIds, entrezGeneIds, null);
 	}
 
+    @Override
+    public List<MutationCountByGene> getSampleCountInMultipleMolecularProfilesForFusions(List<String> molecularProfileIds,
+                                                                               List<String> sampleIds, List<Integer> entrezGeneIds) {
+
+        return mutationMapper.getSampleCountInMultipleMolecularProfilesForFusions(molecularProfileIds, 
+                        sampleIds, entrezGeneIds, null);
+    }
+
     @Override
     public List<MutationCountByGene> getPatientCountInMultipleMolecularProfiles(List<String> molecularProfileIds,
                                                                                 List<String> patientIds,

persistence/persistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/MutationMapper.xml

@@ -262,6 +262,22 @@
         COUNT(*) AS totalCount,
         COUNT(DISTINCT(mutation.SAMPLE_ID)) AS numberOfAlteredCases
         FROM mutation
+        INNER JOIN mutation_event ON mutation_event.MUTATION_EVENT_ID = mutation.MUTATION_EVENT_ID AND mutation_event.MUTATION_TYPE != 'Fusion'
+        INNER JOIN genetic_profile ON mutation.GENETIC_PROFILE_ID = genetic_profile.GENETIC_PROFILE_ID
+        INNER JOIN sample ON mutation.SAMPLE_ID = sample.INTERNAL_ID
+        INNER JOIN gene ON mutation.ENTREZ_GENE_ID = gene.ENTREZ_GENE_ID
+        <include refid="whereInMultipleMolecularProfiles"/>
+        GROUP BY mutation.ENTREZ_GENE_ID
+    </select>
+
+    <select id="getSampleCountInMultipleMolecularProfilesForFusions" resultType="org.cbioportal.model.MutationCountByGene">
+        SELECT
+        mutation.ENTREZ_GENE_ID AS entrezGeneId,
+        gene.HUGO_GENE_SYMBOL AS hugoGeneSymbol,
+        COUNT(*) AS totalCount,
+        COUNT(DISTINCT(mutation.SAMPLE_ID)) AS numberOfAlteredCases
+        FROM mutation
+        INNER JOIN mutation_event ON mutation_event.MUTATION_EVENT_ID = mutation.MUTATION_EVENT_ID AND mutation_event.MUTATION_TYPE = 'Fusion'
         INNER JOIN genetic_profile ON mutation.GENETIC_PROFILE_ID = genetic_profile.GENETIC_PROFILE_ID
         INNER JOIN sample ON mutation.SAMPLE_ID = sample.INTERNAL_ID
         INNER JOIN gene ON mutation.ENTREZ_GENE_ID = gene.ENTREZ_GENE_ID

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

@@ -48,6 +48,11 @@ List<MutationCountByGene> getSampleCountInMultipleMolecularProfiles(List<String>
                                                                         List<Integer> entrezGeneIds,
                                                                         boolean includeFrequency);
 
+    List<MutationCountByGene> getSampleCountInMultipleMolecularProfilesForFusions(List<String> molecularProfileIds,
+                                                                                  List<String> sampleIds,
+                                                                                  List<Integer> entrezGeneId,
+                                                                                  boolean includeFrequency);
+
     List<MutationCountByGene> getPatientCountInMultipleMolecularProfiles(List<String> molecularProfileIds,
                                                                         List<String> patientIds,
                                                                         List<Integer> entrezGeneIds);

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

@@ -130,10 +130,27 @@ public List<MutationCountByGene> getSampleCountInMultipleMolecularProfiles(List<
                 profiledSamplesCounter.calculate(molecularProfileIds, sampleIds, result);
             }
         }
-
         return result;
 	}
 
+    @Override
+    public List<MutationCountByGene> getSampleCountInMultipleMolecularProfilesForFusions(List<String> molecularProfileIds,
+                                                                                        List<String> sampleIds,
+                                                                                        List<Integer> entrezGeneIds,
+                                                                                        boolean includeFrequency) {
+        List<MutationCountByGene> result;
+        if (molecularProfileIds.isEmpty()) {
+            result = Collections.emptyList();
+        } else {
+            result = mutationRepository.getSampleCountInMultipleMolecularProfilesForFusions(
+                molecularProfileIds, sampleIds, entrezGeneIds);
+            if (includeFrequency) {
+                profiledSamplesCounter.calculate(molecularProfileIds, sampleIds, result);
+            }
+        }
+        return result;
+    }
+
     @Override
     public List<MutationCountByGene> getPatientCountInMultipleMolecularProfiles(List<String> molecularProfileIds,
                                                                                 List<String> patientIds,

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

@@ -223,6 +223,43 @@ public ResponseEntity<List<MutationCountByGene>> fetchMutatedGenes(
         return new ResponseEntity<>(result, HttpStatus.OK);
     }
 
+    @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', 'read')")
+    @RequestMapping(value = "/fusion-genes/fetch", method = RequestMethod.POST,
+        consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE)
+    @ApiOperation("Fetch fusion genes by study view filter")
+    public ResponseEntity<List<MutationCountByGene>> fetchFusionGenes(
+        @ApiParam(required = true, value = "Study view filter")
+        @Valid @RequestBody(required = false) StudyViewFilter studyViewFilter,
+        @ApiIgnore // prevent reference to this attribute in the swagger-ui interface
+        @RequestAttribute(required = false, value = "involvedCancerStudies") Collection<String> involvedCancerStudies,
+        @ApiIgnore // prevent reference to this attribute in the swagger-ui interface. this attribute is needed for the @PreAuthorize tag above.
+        @Valid @RequestAttribute(required = false, value = "interceptedStudyViewFilter") StudyViewFilter interceptedStudyViewFilter) throws StudyNotFoundException {
+        List<SampleIdentifier> filteredSampleIdentifiers = studyViewFilterApplier.apply(interceptedStudyViewFilter);
+        List<MutationCountByGene> result = new ArrayList<>();
+        if (!filteredSampleIdentifiers.isEmpty()) {
+            List<String> studyIds = new ArrayList<>();
+            List<String> sampleIds = new ArrayList<>();
+            studyViewFilterUtil.extractStudyAndSampleIds(filteredSampleIdentifiers, studyIds, sampleIds);
+            result = mutationService.getSampleCountInMultipleMolecularProfilesForFusions(molecularProfileService
+                .getFirstMutationProfileIds(studyIds, sampleIds), sampleIds, null, false);
+            result.sort((a, b) -> b.getNumberOfAlteredCases() - a.getNumberOfAlteredCases());
+            List<String> distinctStudyIds = studyIds.stream().distinct().collect(Collectors.toList());
+            if (distinctStudyIds.size() == 1 && !result.isEmpty()) {
+                Map<Integer, MutSig> mutSigMap = significantlyMutatedGeneService.getSignificantlyMutatedGenes(
+                    distinctStudyIds.get(0), Projection.SUMMARY.name(), null, null, null, null).stream().collect(
+                    Collectors.toMap(MutSig::getEntrezGeneId, Function.identity()));
+                result.forEach(r -> {
+                    if (mutSigMap.containsKey(r.getEntrezGeneId())) {
+                        r.setqValue(mutSigMap.get(r.getEntrezGeneId()).getqValue());
+                    }
+                });
+            }
+        }
+
+        return new ResponseEntity<>(result, HttpStatus.OK);
+    }
+
+
     @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', 'read')")
     @RequestMapping(value = "/cna-genes/fetch", method = RequestMethod.POST,
         consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE)

web/src/main/java/org/cbioportal/web/parameter/FusionGeneFilter.java

@@ -0,0 +1,17 @@
+package org.cbioportal.web.parameter;
+
+import java.io.Serializable;
+import java.util.List;
+
+public class FusionGeneFilter implements Serializable {
+
+    private List<Integer> entrezGeneIds;
+
+    public List<Integer> getEntrezGeneIds() {
+        return entrezGeneIds;
+    }
+
+    public void setEntrezGeneIds(List<Integer> entrezGeneIds) {
+        this.entrezGeneIds = entrezGeneIds;
+    }
+}

web/src/main/java/org/cbioportal/web/parameter/StudyViewFilter.java

@@ -19,11 +19,12 @@ public class StudyViewFilter implements Serializable {
     private List<String> studyIds;
     private List<ClinicalDataEqualityFilter> clinicalDataEqualityFilters;
     private List<ClinicalDataIntervalFilter> clinicalDataIntervalFilters;
-    private List<MutationGeneFilter> mutatedGenes;
-    private List<CopyNumberGeneFilter> cnaGenes;
-    private Boolean withMutationData;
-    private Boolean withCNAData;
-    private RectangleBounds mutationCountVsCNASelection;
+	private List<MutationGeneFilter> mutatedGenes;
+    private List<FusionGeneFilter> fusionGenes;
+	private List<CopyNumberGeneFilter> cnaGenes;
+	private Boolean withMutationData;
+	private Boolean withCNAData;
+	private RectangleBounds mutationCountVsCNASelection;
 
     @AssertTrue
     private boolean isEitherSampleIdentifiersOrStudyIdsPresent() {
@@ -81,8 +82,14 @@ public List<MutationGeneFilter> getMutatedGenes() {
         return mutatedGenes;
     }
 
-    public void setMutatedGenes(List<MutationGeneFilter> mutatedGenes) {
-        this.mutatedGenes = mutatedGenes;
+	public void setMutatedGenes(List<MutationGeneFilter> mutatedGenes) { this.mutatedGenes = mutatedGenes; }
+
+    public List<FusionGeneFilter> getFusionGenes() {
+        return fusionGenes;
+    }
+
+    public void setFusionGenes(List<FusionGeneFilter> fusionGenes) {
+        this.fusionGenes = fusionGenes;
     }
 
     public List<CopyNumberGeneFilter> getCnaGenes() {

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

@@ -94,6 +94,7 @@ public class InvolvedCancerStudyExtractorInterceptor extends HandlerInterceptorA
     public static final String STUDY_VIEW_CNA_GENES = "/cna-genes/fetch";
     public static final String STUDY_VIEW_FILTERED_SAMPLES = "/filtered-samples/fetch";
     public static final String STUDY_VIEW_MUTATED_GENES = "/mutated-genes/fetch";
+    public static final String STUDY_VIEW_FUSION_GENES = "/fusion-genes/fetch";
     public static final String STUDY_VIEW_SAMPLE_COUNTS = "/sample-counts/fetch";
     public static final String CLINICAL_DATA_ENRICHMENT_FETCH_PATH = "/clinical-data-enrichments/fetch";
     public static final String MUTATION_ENRICHMENT_FETCH_PATH = "/mutation-enrichments/fetch";
@@ -132,7 +133,7 @@ public class InvolvedCancerStudyExtractorInterceptor extends HandlerInterceptorA
         } else if (requestPathInfo.equals(STUDY_VIEW_CLINICAL_DATA_COUNTS_PATH)) {
             return extractAttributesFromClinicalDataCountFilter(wrappedRequest);
         } else if (Arrays.asList(STUDY_VIEW_CLINICAL_DATA_DENSITY_PATH, STUDY_VIEW_CNA_GENES,
-                STUDY_VIEW_FILTERED_SAMPLES, STUDY_VIEW_MUTATED_GENES, STUDY_VIEW_SAMPLE_COUNTS)
+                STUDY_VIEW_FILTERED_SAMPLES, STUDY_VIEW_MUTATED_GENES, STUDY_VIEW_FUSION_GENES, STUDY_VIEW_SAMPLE_COUNTS)
                 .contains(requestPathInfo)) {
             return extractAttributesFromStudyViewFilter(wrappedRequest);
         }  else if (requestPathInfo.equals(CLINICAL_DATA_ENRICHMENT_FETCH_PATH)) {

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

@@ -117,6 +117,11 @@ public List<SampleIdentifier> apply(StudyViewFilter studyViewFilter, Boolean neg
             sampleIdentifiers = filterCNAGenes(cnaGenes, sampleIdentifiers);
         }
 
+        List<FusionGeneFilter> fusionGenes = studyViewFilter.getFusionGenes();
+        if (fusionGenes != null && !sampleIdentifiers.isEmpty()) {
+            sampleIdentifiers = filterFusionGenes(fusionGenes, sampleIdentifiers);
+        }
+
         Boolean withMutationData = studyViewFilter.getWithMutationData();
         if (withMutationData != null && !sampleIdentifiers.isEmpty()) {
             sampleIdentifiers = filterByProfiled(sampleIdentifiers, withMutationData, molecularProfileService::getFirstMutationProfileIds);
@@ -178,9 +183,7 @@ private List<SampleIdentifier> filterMutatedGenes(List<MutationGeneFilter> mutat
             List<String> sampleIds = new ArrayList<>();
             studyViewFilterUtil.extractStudyAndSampleIds(sampleIdentifiers, studyIds, sampleIds);
             List<Mutation> mutations = mutationService.getMutationsInMultipleMolecularProfiles(molecularProfileService
-                .getFirstMutationProfileIds(studyIds, sampleIds), sampleIds, molecularProfileGeneFilter.getEntrezGeneIds(),
-                Projection.ID.name(), null, null, null, null);
-
+                .getFirstMutationProfileIds(studyIds, sampleIds), sampleIds, molecularProfileGeneFilter.getEntrezGeneIds(), Projection.ID.name(), null, null, null, null);
             sampleIdentifiers = mutations.stream().map(m -> {
                 SampleIdentifier sampleIdentifier = new SampleIdentifier();
                 sampleIdentifier.setSampleId(m.getSampleId());
@@ -192,6 +195,24 @@ private List<SampleIdentifier> filterMutatedGenes(List<MutationGeneFilter> mutat
         return sampleIdentifiers;
     }
 
+    private List<SampleIdentifier> filterFusionGenes(List<FusionGeneFilter> fusionGenes, List<SampleIdentifier> sampleIdentifiers) {
+        for (FusionGeneFilter molecularProfileGeneFilter : fusionGenes) {
+            List<String> studyIds = new ArrayList<>();
+            List<String> sampleIds = new ArrayList<>();
+            studyViewFilterUtil.extractStudyAndSampleIds(sampleIdentifiers, studyIds, sampleIds);
+            List<Mutation> fusions = mutationService.getMutationsInMultipleMolecularProfiles(molecularProfileService
+                    .getFirstMutationProfileIds(studyIds, sampleIds), sampleIds, molecularProfileGeneFilter.getEntrezGeneIds(), Projection.ID.name(), null, null, null, null);
+            sampleIdentifiers = fusions.stream().map(m -> {
+                SampleIdentifier sampleIdentifier = new SampleIdentifier();
+                sampleIdentifier.setSampleId(m.getSampleId());
+                sampleIdentifier.setStudyId(m.getStudyId());
+                return sampleIdentifier;
+            }).distinct().collect(Collectors.toList());
+        }
+
+        return sampleIdentifiers;
+    }
+
     private List<SampleIdentifier> filterCNAGenes(List<CopyNumberGeneFilter> cnaGenes, List<SampleIdentifier> sampleIdentifiers) {
         for (CopyNumberGeneFilter copyNumberGeneFilter : cnaGenes) {
 

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

@@ -286,6 +286,56 @@ public void fetchMutatedGenes() throws Exception {
             .andExpect(MockMvcResultMatchers.jsonPath("$[1].totalCount").value(3));
     }
 
+    @Test
+    public void fetchFusionGenes() throws Exception {
+
+        MolecularProfile molecularProfile = new MolecularProfile();
+        molecularProfile.setCancerStudyIdentifier(TEST_STUDY_ID);
+        Mockito.when(molecularProfileService.getMolecularProfile(Mockito.anyString())).thenReturn(molecularProfile);
+
+        List<SampleIdentifier> filteredSampleIdentifiers = new ArrayList<>();
+        SampleIdentifier sampleIdentifier = new SampleIdentifier();
+        sampleIdentifier.setSampleId(TEST_SAMPLE_ID_1);
+        sampleIdentifier.setStudyId(TEST_STUDY_ID);
+        filteredSampleIdentifiers.add(sampleIdentifier);
+        Mockito.when(studyViewFilterApplier.apply(Mockito.anyObject())).thenReturn(filteredSampleIdentifiers);
+
+        List<MutationCountByGene> fusionCounts = new ArrayList<>();
+        MutationCountByGene fusionCount1 = new MutationCountByGene();
+        fusionCount1.setEntrezGeneId(TEST_ENTREZ_GENE_ID_1);
+        fusionCount1.setHugoGeneSymbol(TEST_HUGO_GENE_SYMBOL_1);
+        fusionCount1.setNumberOfAlteredCases(1);
+        fusionCount1.setTotalCount(1);
+        fusionCounts.add(fusionCount1);
+        MutationCountByGene fusionCount2 = new MutationCountByGene();
+        fusionCount2.setEntrezGeneId(TEST_ENTREZ_GENE_ID_2);
+        fusionCount2.setHugoGeneSymbol(TEST_HUGO_GENE_SYMBOL_2);
+        fusionCount2.setNumberOfAlteredCases(2);
+        fusionCount2.setTotalCount(2);
+        fusionCounts.add(fusionCount2);
+
+        Mockito.when(mutationService.getSampleCountInMultipleMolecularProfilesForFusions(Mockito.anyListOf(String.class),
+            Mockito.anyListOf(String.class), Mockito.anyListOf(Integer.class), Mockito.anyBoolean())).thenReturn(fusionCounts);
+
+        StudyViewFilter studyViewFilter = new StudyViewFilter();
+        studyViewFilter.setStudyIds(Arrays.asList(TEST_STUDY_ID));
+
+        mockMvc.perform(MockMvcRequestBuilders.post("/fusion-genes/fetch")
+            .accept(MediaType.APPLICATION_JSON)
+            .contentType(MediaType.APPLICATION_JSON)
+            .content(objectMapper.writeValueAsString(studyViewFilter)))
+            .andExpect(MockMvcResultMatchers.status().isOk())
+            .andExpect(MockMvcResultMatchers.content().contentTypeCompatibleWith(MediaType.APPLICATION_JSON))
+            .andExpect(MockMvcResultMatchers.jsonPath("$[0].entrezGeneId").value(TEST_ENTREZ_GENE_ID_2))
+            .andExpect(MockMvcResultMatchers.jsonPath("$[0].hugoGeneSymbol").value(TEST_HUGO_GENE_SYMBOL_2))
+            .andExpect(MockMvcResultMatchers.jsonPath("$[0].numberOfAlteredCases").value(2))
+            .andExpect(MockMvcResultMatchers.jsonPath("$[0].totalCount").value(2))
+            .andExpect(MockMvcResultMatchers.jsonPath("$[1].entrezGeneId").value(TEST_ENTREZ_GENE_ID_1))
+            .andExpect(MockMvcResultMatchers.jsonPath("$[1].hugoGeneSymbol").value(TEST_HUGO_GENE_SYMBOL_1))
+            .andExpect(MockMvcResultMatchers.jsonPath("$[1].numberOfAlteredCases").value(1))
+            .andExpect(MockMvcResultMatchers.jsonPath("$[1].totalCount").value(1));
+    }
+
     @Test
     public void fetchCNAGenes() throws Exception {