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

…ect frequencies
pughlab · May 14, 2019 · ebafefa · ebafefa
1 parent 4ccece8
commit ebafefa
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Showing 8 changed files with 154 additions and 4 deletions.
diff --git a/persistence/persistence-api/src/main/java/org/cbioportal/persistence/MutationRepository.java b/persistence/persistence-api/src/main/java/org/cbioportal/persistence/MutationRepository.java
@@ -41,6 +41,11 @@ List<MutationCountByGene> getSampleCountByEntrezGeneIdsAndSampleIds(String molec
     List<MutationCountByGene> getSampleCountInMultipleMolecularProfiles(List<String> molecularProfileIds,
                                                                         List<String> sampleIds,
                                                                         List<Integer> entrezGeneIds);
+
+    List<MutationCountByGene> getSampleCountInMultipleMolecularProfilesForMutationOrFusion(List<String> molecularProfileIds,
+                                                                        List<String> sampleIds,
+                                                                        List<Integer> entrezGeneIds,
+                                                                        Boolean fusionOnly);
 
     List<MutationCountByGene> getPatientCountByEntrezGeneIdsAndSampleIds(String molecularProfileId,
                                                                          List<String> patientIds,

diff --git a/.../persistence-mybatis/src/main/java/org/cbioportal/persistence/mybatis/MutationMapper.java b/.../persistence-mybatis/src/main/java/org/cbioportal/persistence/mybatis/MutationMapper.java
@@ -45,6 +45,11 @@ List<MutationCountByGene> getPatientCountByEntrezGeneIdsAndSampleIds(String mole
                                                                          List<String> patientIds,
                                                                          List<Integer> entrezGeneIds,
                                                                          Boolean snpOnly);
+
+    List<MutationCountByGene> getSampleCountInMultipleMolecularProfilesForMutationOrFusion(List<String> molecularProfileIds,
+                                                                                           List<String> sampleIds,
+                                                                                           List<Integer> entrezGeneIds,
+                                                                                           Boolean fusionOnly);
 
     MutationCountByPosition getMutationCountByPosition(Integer entrezGeneId, Integer proteinPosStart, 
                                                        Integer proteinPosEnd);

diff --git a/...e-mybatis/src/main/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepository.java b/...e-mybatis/src/main/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepository.java
@@ -89,6 +89,15 @@ public List<MutationCountByGene> getSampleCountInMultipleMolecularProfiles(List<
         return mutationMapper.getSampleCountInMultipleMolecularProfiles(molecularProfileIds, sampleIds, entrezGeneIds, null);
 	}
 
+    @Override
+    public List<MutationCountByGene> getSampleCountInMultipleMolecularProfilesForMutationOrFusion(List<String> molecularProfileIds,
+                                                                               List<String> sampleIds, List<Integer> entrezGeneIds, 
+                                                                               Boolean fusionOnly) {
+
+        return mutationMapper.getSampleCountInMultipleMolecularProfilesForMutationOrFusion(molecularProfileIds, 
+                        sampleIds, entrezGeneIds, fusionOnly);
+    }
+
     @Override
     public List<MutationCountByGene> getPatientCountByEntrezGeneIdsAndSampleIds(String molecularProfileId,
                                                                                 List<String> patientIds,

diff --git a/...sistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/MutationMapper.xml b/...sistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/MutationMapper.xml
@@ -268,6 +268,65 @@
         GROUP BY mutation.ENTREZ_GENE_ID
     </select>
 
+    <select id="getSampleCountInMultipleMolecularProfilesForMutationOrFusion" 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 countByEntity
+        FROM mutation
+        INNER JOIN mutation_event ON mutation_event.MUTATION_EVENT_ID = mutation.MUTATION_EVENT_ID
+        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
+        WHERE
+        <if test="sampleIds != null and !sampleIds.isEmpty()">
+            mutation.SAMPLE_ID IN (
+            SELECT sample.INTERNAL_ID from sample
+            INNER JOIN patient ON sample.PATIENT_ID = patient.INTERNAL_ID
+            INNER JOIN genetic_profile ON patient.CANCER_STUDY_ID = genetic_profile.CANCER_STUDY_ID
+            WHERE
+            <if test="@java.util.Arrays@stream(molecularProfileIds.toArray()).distinct().count() == 1">
+                genetic_profile.STABLE_ID = #{molecularProfileIds[0]} AND
+                sample.STABLE_ID IN
+                <foreach item="item" collection="sampleIds" open="(" separator="," close=")">
+                    #{item}
+                </foreach>
+            </if>
+            <if test="@java.util.Arrays@stream(molecularProfileIds.toArray()).distinct().count() > 1">
+                (sample.STABLE_ID, genetic_profile.STABLE_ID) IN
+                <foreach index="i" collection="sampleIds" open="(" separator="," close=")">
+                    (#{sampleIds[${i}]}, #{molecularProfileIds[${i}]})
+                </foreach>
+                AND genetic_profile.STABLE_ID IN
+                <foreach item="item" collection="molecularProfileIds" open="(" separator="," close=")">
+                    #{item}
+                </foreach>
+            </if>
+            AND sample.INTERNAL_ID = mutation.SAMPLE_ID
+            AND genetic_profile.GENETIC_PROFILE_ID = mutation.GENETIC_PROFILE_ID)
+        </if>
+        <if test="sampleIds == null">
+            genetic_profile.STABLE_ID IN
+            <foreach item="item" collection="molecularProfileIds" open="(" separator="," close=")">
+                #{item}
+            </foreach>
+        </if>
+        <if test="entrezGeneIds != null and !entrezGeneIds.isEmpty()">
+            AND mutation.ENTREZ_GENE_ID IN
+            <foreach item="item" collection="entrezGeneIds" open="(" separator="," close=")">
+                #{item}
+            </foreach>
+        </if>
+        <if test="fusionOnly == false">
+            AND mutation_event.MUTATION_TYPE != 'Fusion'
+        </if>
+        <if test="fusionOnly == true">
+            AND mutation_event.MUTATION_TYPE = 'Fusion'
+        </if>
+        GROUP BY mutation.ENTREZ_GENE_ID
+    </select>
+
     <select id="getPatientCountByEntrezGeneIdsAndSampleIds" resultType="org.cbioportal.model.MutationCountByGene">
         SELECT
         mutation.ENTREZ_GENE_ID AS entrezGeneId,

diff --git a/service/src/main/java/org/cbioportal/service/MutationService.java b/service/src/main/java/org/cbioportal/service/MutationService.java
@@ -48,6 +48,14 @@ List<MutationCountByGene> getSampleCountInMultipleMolecularProfiles(List<String>
                                                                         List<Integer> entrezGeneIds,
                                                                         boolean includeFrequency);
 
+    List<MutationCountByGene> getSampleCountInMultipleMolecularProfilesForMutation(List<String> molecularProfileIds,
+                                                                        List<String> sampleIds,
+                                                                        List<Integer> entrezGeneId);
+
+    List<MutationCountByGene> getSampleCountInMultipleMolecularProfilesForFusion(List<String> molecularProfileIds,
+                                                                                 List<String> sampleIds,
+                                                                                 List<Integer> entrezGeneId);
+
     List<MutationCountByGene> getPatientCountByEntrezGeneIdsAndSampleIds(String molecularProfileId,
                                                                         List<String> patientIds,
                                                                         List<Integer> entrezGeneIds)

diff --git a/service/src/main/java/org/cbioportal/service/impl/MutationServiceImpl.java b/service/src/main/java/org/cbioportal/service/impl/MutationServiceImpl.java
@@ -137,6 +137,37 @@ public List<MutationCountByGene> getSampleCountInMultipleMolecularProfiles(List<
         return result;
 	}
 
+    @Override
+    public List<MutationCountByGene> getSampleCountInMultipleMolecularProfilesForMutation(List<String> molecularProfileIds,
+                                                                               List<String> sampleIds, 
+                                                                               List<Integer> entrezGeneIds) {
+        List<MutationCountByGene> result;
+        if (molecularProfileIds.isEmpty()) {
+            result = Collections.emptyList();
+        } else {
+            result = mutationRepository.getSampleCountInMultipleMolecularProfilesForMutationOrFusion(
+                molecularProfileIds, sampleIds, entrezGeneIds, false);
+            geneFrequencyCalculator.calculate(molecularProfileIds, sampleIds, result);
+        }
+        return result;
+    }
+
+    @Override
+    public List<MutationCountByGene> getSampleCountInMultipleMolecularProfilesForFusion(List<String> molecularProfileIds,
+                                                                                        List<String> sampleIds,
+                                                                                        List<Integer> entrezGeneIds) {
+
+        List<MutationCountByGene> result;
+        if (molecularProfileIds.isEmpty()) {
+            result = Collections.emptyList();
+        } else {
+            result = mutationRepository.getSampleCountInMultipleMolecularProfilesForMutationOrFusion(
+                molecularProfileIds, sampleIds, entrezGeneIds,true);
+        }
+
+        return result;
+    }
+
     @Override
     public List<MutationCountByGene> getPatientCountByEntrezGeneIdsAndSampleIds(String molecularProfileId,
                                                                                 List<String> patientIds,

diff --git a/web/src/main/java/org/cbioportal/web/StudyViewController.java b/web/src/main/java/org/cbioportal/web/StudyViewController.java
@@ -190,8 +190,8 @@ public ResponseEntity<List<MutationCountByGene>> fetchMutatedGenes(
             List<String> studyIds = new ArrayList<>();
             List<String> sampleIds = new ArrayList<>();
             studyViewFilterUtil.extractStudyAndSampleIds(filteredSampleIdentifiers, studyIds, sampleIds);
-            result = mutationService.getSampleCountInMultipleMolecularProfiles(molecularProfileService
-                .getFirstMutationProfileIds(studyIds, sampleIds), sampleIds, null, true);
+            result = mutationService.getSampleCountInMultipleMolecularProfilesForMutation(molecularProfileService
+                .getFirstMutationProfileIds(studyIds, sampleIds), sampleIds, null);
             result.sort((a, b) -> b.getCountByEntity() - a.getCountByEntity());
             List<String> distinctStudyIds = studyIds.stream().distinct().collect(Collectors.toList());
             if (distinctStudyIds.size() == 1 && !result.isEmpty()) {
@@ -208,6 +208,39 @@ public ResponseEntity<List<MutationCountByGene>> fetchMutatedGenes(
 
         return new ResponseEntity<>(result, HttpStatus.OK);
     }
+
+    @PreAuthorize("hasPermission(#studyViewFilter, 'StudyViewFilter', '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 StudyViewFilter studyViewFilter) throws StudyNotFoundException {
+
+        List<SampleIdentifier> filteredSampleIdentifiers = studyViewFilterApplier.apply(studyViewFilter);
+        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.getSampleCountInMultipleMolecularProfilesForFusion(molecularProfileService
+                .getFirstMutationProfileIds(studyIds, sampleIds), sampleIds, null);
+            result.sort((a, b) -> b.getCountByEntity() - a.getCountByEntity());
+            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(#studyViewFilter, 'StudyViewFilter', 'read')")
     @RequestMapping(value = "/cna-genes/fetch", method = RequestMethod.POST, 

diff --git a/web/src/test/java/org/cbioportal/web/StudyViewControllerTest.java b/web/src/test/java/org/cbioportal/web/StudyViewControllerTest.java
@@ -265,8 +265,8 @@ public void fetchMutatedGenes() throws Exception {
         mutationCount2.setTotalCount(2);
         mutationCounts.add(mutationCount2);
 
-        Mockito.when(mutationService.getSampleCountInMultipleMolecularProfiles(Mockito.anyListOf(String.class), 
-            Mockito.anyListOf(String.class), Mockito.anyListOf(Integer.class), Mockito.anyBoolean())).thenReturn(mutationCounts);
+        Mockito.when(mutationService.getSampleCountInMultipleMolecularProfilesForMutation(Mockito.anyListOf(String.class), 
+            Mockito.anyListOf(String.class), Mockito.anyListOf(Integer.class))).thenReturn(mutationCounts);
 
         StudyViewFilter studyViewFilter = new StudyViewFilter();
         studyViewFilter.setStudyIds(Arrays.asList(TEST_STUDY_ID));