Add optional specific gene parameter for populateAlterationCounts

cBioPortal · Sep 4, 2024 · 942e443 · 942e443
1 parent ea7e6e0
commit 942e443
Show file tree

Hide file tree

Showing 8 changed files with 50 additions and 29 deletions.
diff --git a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java b/src/main/java/org/cbioportal/persistence/StudyViewRepository.java
@@ -27,7 +27,7 @@ public interface StudyViewRepository {
 
     List<ClinicalData> getPatientClinicalData(StudyViewFilterContext studyViewFilterContext, List<String> attributeIds);
 
-    List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext);
+    List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext, String specificHugoGeneSymbol);
 
     List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilterContext studyViewFilterContext);
     List<CopyNumberCountByGene> getCnaGenes(StudyViewFilterContext studyViewFilterContext);
@@ -42,11 +42,11 @@ public interface StudyViewRepository {
 
     List<CaseListDataCount> getCaseListDataCountsPerStudy(StudyViewFilterContext studyViewFilterContext);
 
-    Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType);
+    Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType, String specificHugoGeneSymbol);
 
     int getFilteredSamplesCount(StudyViewFilterContext studyViewFilterContext);
 
-    Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilterContext studyViewFilterContext, String alterationType);
+    Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilterContext studyViewFilterContext, String alterationType, String specificHugoGeneSymbol);
 
     int getTotalProfiledCountsByAlterationType(StudyViewFilterContext studyViewFilterContext, String alterationType);
 
@@ -65,4 +65,6 @@ public interface StudyViewRepository {
     List<GenomicDataCountItem> getCNACounts(StudyViewFilterContext studyViewFilterContext, List<GenomicDataFilter> genomicDataFilters);
 
     List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilterContext studyViewFilterContext, List<GenomicDataFilter> genomicDataFilters);
+
+    AlterationCountByGene getMutatedGene(StudyViewFilterContext studyViewFilterContext, String specificHugoGeneSymbol);
 }
diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
@@ -26,7 +26,7 @@ public interface StudyViewMapper {
 
     List<GenomicDataCount> getMolecularProfileSampleCounts(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);
 
-    List<AlterationCountByGene> getMutatedGenes(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper);
+    List<AlterationCountByGene> getMutatedGenes(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper, String specificHugoGeneSymbol);
 
     List<CopyNumberCountByGene> getCnaGenes(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper);
 
@@ -42,11 +42,11 @@ public interface StudyViewMapper {
 
     List<ClinicalData> getPatientClinicalDataFromStudyViewFilter(StudyViewFilterHelper studyViewFilterHelper, List<String> attributeIds);
 
-    List<AlterationCountByGene> getTotalProfiledCounts(StudyViewFilterHelper studyViewFilterHelper, String alterationType);
+    List<AlterationCountByGene> getTotalProfiledCounts(StudyViewFilterHelper studyViewFilterHelper, String alterationType, String specificHugoGeneSymbol);
 
     int getFilteredSamplesCount(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);
 
-    List<GenePanelToGene> getMatchingGenePanelIds(StudyViewFilterHelper studyViewFilterHelper, String alterationType);
+    List<GenePanelToGene> getMatchingGenePanelIds(StudyViewFilterHelper studyViewFilterHelper, String alterationType, String specificHugoGeneSymbol);
 
     int getTotalProfiledCountByAlterationType(StudyViewFilterHelper studyViewFilterHelper, String alterationType);
 
@@ -62,4 +62,6 @@ public interface StudyViewMapper {
     List<GenomicDataCountItem> getCNACounts(StudyViewFilterHelper studyViewFilterHelper, List<GenomicDataFilter> genomicDataFilters);
 
     List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilterHelper studyViewFilterHelper, List<GenomicDataFilter> genomicDataFilters);
+
+    AlterationCountByGene getMutatedGene(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper, String specificHugoGeneSymbol);
 }
diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
@@ -50,9 +50,9 @@ public List<Sample> getFilteredSamples(StudyViewFilterContext studyViewFilterCon
     }
 
     @Override
-    public List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext) {
+    public List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext, String specificHugoGeneSymbol) {
         return mapper.getMutatedGenes(createStudyViewFilterHelper(studyViewFilterContext),
-            AlterationFilterHelper.build(studyViewFilterContext.studyViewFilter().getAlterationFilter()));
+            AlterationFilterHelper.build(studyViewFilterContext.studyViewFilter().getAlterationFilter()), specificHugoGeneSymbol);
     }
 
     @Override
@@ -144,8 +144,8 @@ public List<ClinicalData> getPatientClinicalData(StudyViewFilterContext studyVie
     }
 
     @Override
-    public Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType) {
-        return mapper.getTotalProfiledCounts(createStudyViewFilterHelper(studyViewFilterContext), alterationType)
+    public Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType, String specificHugoGeneSymbol) {
+        return mapper.getTotalProfiledCounts(createStudyViewFilterHelper(studyViewFilterContext), alterationType, specificHugoGeneSymbol)
             .stream()
             .collect(Collectors.groupingBy(AlterationCountByGene::getHugoGeneSymbol,
                 Collectors.mapping(AlterationCountByGene::getNumberOfProfiledCases, Collectors.summingInt(Integer::intValue))));
@@ -157,8 +157,8 @@ public int getFilteredSamplesCount(StudyViewFilterContext studyViewFilterContext
     }
 
     @Override
-    public Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilterContext studyViewFilterContext, String alterationType) {
-        return mapper.getMatchingGenePanelIds(createStudyViewFilterHelper(studyViewFilterContext), alterationType)
+    public Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilterContext studyViewFilterContext, String alterationType, String specificHugoGeneSymbol) {
+        return mapper.getMatchingGenePanelIds(createStudyViewFilterHelper(studyViewFilterContext), alterationType, specificHugoGeneSymbol)
             .stream()
             .collect(Collectors.groupingBy(GenePanelToGene::getHugoGeneSymbol,
                 Collectors.mapping(GenePanelToGene::getGenePanelId, Collectors.toSet())));
@@ -224,4 +224,10 @@ public List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilterContext
         return mapper.getMutationCountsByType(createStudyViewFilterHelper(studyViewFilterContext), genomicDataFilters);
     }
 
+    @Override
+    public AlterationCountByGene getMutatedGene(StudyViewFilterContext studyViewFilterContext, String specificHugoGeneSymbol) {
+        return mapper.getMutatedGene(createStudyViewFilterHelper(studyViewFilterContext),
+            AlterationFilterHelper.build(studyViewFilterContext.studyViewFilter().getAlterationFilter()), specificHugoGeneSymbol);
+    }
+
 }
diff --git a/src/main/java/org/cbioportal/service/AlterationCountService.java b/src/main/java/org/cbioportal/service/AlterationCountService.java
@@ -84,4 +84,5 @@ Pair<List<CopyNumberCountByGene>, Long> getPatientCnaGeneCounts(List<MolecularPr
 
     List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilterContext studyViewFilterContext);
 
+    AlterationCountByGene getMutatedGene(StudyViewFilterContext studyViewFilterContext, String specificHugoGeneSymbol);
 }
diff --git a/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java b/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java
@@ -254,27 +254,27 @@ public Pair<List<CopyNumberCountByGene>, Long> getPatientCnaGeneCounts(List<Mole
 
     @Override
     public List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext) {
-        var alterationCountByGenes = studyViewRepository.getMutatedGenes(studyViewFilterContext);
-        return populateAlterationCounts(alterationCountByGenes, studyViewFilterContext, AlterationType.MUTATION_EXTENDED);
+        var alterationCountByGenes = studyViewRepository.getMutatedGenes(studyViewFilterContext, null);
+        return populateAlterationCounts(alterationCountByGenes, studyViewFilterContext, AlterationType.MUTATION_EXTENDED, null);
     }
 
     public List<CopyNumberCountByGene> getCnaGenes(StudyViewFilterContext studyViewFilterContext) {
         var copyNumberCountByGenes = studyViewRepository.getCnaGenes(studyViewFilterContext);
-        return populateAlterationCounts(copyNumberCountByGenes, studyViewFilterContext, AlterationType.COPY_NUMBER_ALTERATION);
+        return populateAlterationCounts(copyNumberCountByGenes, studyViewFilterContext, AlterationType.COPY_NUMBER_ALTERATION, null);
     }
 
     @Override
     public List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilterContext studyViewFilterContext) {
         var alterationCountByGenes = studyViewRepository.getStructuralVariantGenes(studyViewFilterContext);
-        return populateAlterationCounts(alterationCountByGenes, studyViewFilterContext, AlterationType.STRUCTURAL_VARIANT);
+        return populateAlterationCounts(alterationCountByGenes, studyViewFilterContext, AlterationType.STRUCTURAL_VARIANT, null);
     }
 
     private < T extends AlterationCountByGene> List<T> populateAlterationCounts(@NonNull List<T> alterationCounts,
                                                                                 @NonNull StudyViewFilterContext studyViewFilterContext,
-                                                                                @NonNull AlterationType alterationType) {
+                                                                                @NonNull AlterationType alterationType, String specificHugoGeneSymbol) {
         final int profiledCountWithoutGenePanelData = studyViewRepository.getTotalProfiledCountsByAlterationType(studyViewFilterContext, alterationType.toString());
-        var profiledCountsMap = studyViewRepository.getTotalProfiledCounts(studyViewFilterContext, alterationType.toString());
-        final var matchingGenePanelIdsMap = studyViewRepository.getMatchingGenePanelIds(studyViewFilterContext, alterationType.toString());
+        var profiledCountsMap = studyViewRepository.getTotalProfiledCounts(studyViewFilterContext, alterationType.toString(), specificHugoGeneSymbol);
+        final var matchingGenePanelIdsMap = studyViewRepository.getMatchingGenePanelIds(studyViewFilterContext, alterationType.toString(), specificHugoGeneSymbol);
         final int sampleProfileCountWithoutGenePanelData = studyViewRepository.getSampleProfileCountWithoutPanelData(studyViewFilterContext, alterationType.toString());
 
         alterationCounts.parallelStream()
@@ -294,6 +294,11 @@ private < T extends AlterationCountByGene> List<T> populateAlterationCounts(@Non
         return alterationCounts;
     }
 
+    @Override
+    public AlterationCountByGene getMutatedGene(StudyViewFilterContext studyViewFilterContext, String specificHugoGeneSymbol) {
+        List<AlterationCountByGene> alterationCountByGenes = studyViewRepository.getMutatedGenes(studyViewFilterContext, specificHugoGeneSymbol);
+        return populateAlterationCounts(alterationCountByGenes, studyViewFilterContext, AlterationType.MUTATION_EXTENDED, specificHugoGeneSymbol).getFirst();
+    }
 
     private boolean hasGenePanelData(@NonNull Set<String> matchingGenePanelIds) {
         return matchingGenePanelIds.contains(WHOLE_EXOME_SEQUENCING) 

diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
@@ -134,12 +134,8 @@ public List<GenomicDataCountItem> getCNACountsByGeneSpecific(StudyViewFilter stu
     public List<GenomicDataCountItem> getMutationCountsByGeneSpecific(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters) {
         List<GenomicDataCountItem> genomicDataCountItemList = new ArrayList<>();
         int totalCount = studyViewRepository.getFilteredSamplesCount(createContext(studyViewFilter));
-        List<AlterationCountByGene> alterationCountByGenes = alterationCountService.getMutatedGenes(createContext(studyViewFilter));
         for (GenomicDataFilter genomicDataFilter : genomicDataFilters) {
-            AlterationCountByGene filteredAlterationCount = alterationCountByGenes.stream()
-                .filter(g -> g.getHugoGeneSymbol().equals(genomicDataFilter.getHugoGeneSymbol()))
-                .findFirst()
-                .orElse(new AlterationCountByGene());
+            AlterationCountByGene filteredAlterationCount = alterationCountService.getMutatedGene(createContext(studyViewFilter), genomicDataFilter.getHugoGeneSymbol());
             int mutatedCount = filteredAlterationCount.getNumberOfAlteredCases();
             int profiledCount = filteredAlterationCount.getNumberOfProfiledCases();
             List<GenomicDataCount> genomicDataCountList = new ArrayList<>();

diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
@@ -30,6 +30,9 @@
         FROM genomic_event_derived
         <where>
             variant_type = 'mutation' AND
+            <if test="specificHugoGeneSymbol != null">
+                hugo_gene_symbol = #{specificHugoGeneSymbol} AND
+            </if>
             <include refid="applyStudyViewFilter">
                 <property name="filter_type" value="'SAMPLE_AND_PATIENT_ID'"/>
             </include>
@@ -336,6 +339,9 @@
             INNER JOIN gene_panel_to_gene_derived gptg on stgp.gene_panel_id = gptg.gene_panel_id 
         <where>
             stgp.alteration_type = '${alterationType}'
+            <if test="specificHugoGeneSymbol != null">
+                AND gptg.gene = #{specificHugoGeneSymbol}
+            </if>
             AND stgp.gene_panel_id != 'WES'
             AND
             <include refid="applyStudyViewFilter">
@@ -395,6 +401,9 @@
                     </include>
                 </where>
             )
+            <if test="specificHugoGeneSymbol != null">
+                AND gene = #{specificHugoGeneSymbol}
+            </if>
         </where>
         GROUP BY gene, gene_panel_id;
     </select>

diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperTest.java
@@ -62,7 +62,7 @@ public void getMutatedGenes() {
         StudyViewFilter studyViewFilter = new StudyViewFilter();
         studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB));
         var alterationCountByGenes = studyViewMapper.getMutatedGenes(StudyViewFilterHelper.build(studyViewFilter, null, null),
-            AlterationFilterHelper.build(studyViewFilter.getAlterationFilter()));
+            AlterationFilterHelper.build(studyViewFilter.getAlterationFilter()), null);
         assertEquals(3, alterationCountByGenes.size());
 
         var testBrca1AlterationCount = alterationCountByGenes.stream().filter(a -> Objects.equals(a.getHugoGeneSymbol(), "BRCA1")).findFirst();
@@ -83,7 +83,7 @@ public void getMutatedGenesWithAlterationFilter() {
         alterationFilter.setMutationEventTypes(mutationEventTypeFilterMap);
 
         var alterationCountByGenes = studyViewMapper.getMutatedGenes(StudyViewFilterHelper.build(studyViewFilter, null, null),
-            AlterationFilterHelper.build(alterationFilter));
+            AlterationFilterHelper.build(alterationFilter), null);
         assertEquals(2, alterationCountByGenes.size());
 
         AlterationFilter onlyMutationStatusFilter = new AlterationFilter();
@@ -93,7 +93,7 @@ public void getMutatedGenesWithAlterationFilter() {
         onlyMutationStatusFilter.setIncludeUnknownStatus(true);
 
         var alterationCountByGenes1 = studyViewMapper.getMutatedGenes(StudyViewFilterHelper.build(studyViewFilter, null, null),
-            AlterationFilterHelper.build(onlyMutationStatusFilter));
+            AlterationFilterHelper.build(onlyMutationStatusFilter), null);
         assertEquals(1, alterationCountByGenes1.size());
 
         AlterationFilter mutationTypeAndStatusFilter = new AlterationFilter();
@@ -104,7 +104,7 @@ public void getMutatedGenesWithAlterationFilter() {
         mutationTypeAndStatusFilter.setIncludeUnknownStatus(true);
 
         var alterationCountByGenes2 = studyViewMapper.getMutatedGenes(StudyViewFilterHelper.build(studyViewFilter, null, null),
-            AlterationFilterHelper.build(onlyMutationStatusFilter));
+            AlterationFilterHelper.build(onlyMutationStatusFilter), null);
         assertEquals(1, alterationCountByGenes2.size());
     }
 
@@ -114,7 +114,7 @@ public void getTotalProfiledCountsByGene() {
         studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB));
 
         var totalProfiledCountsMap = studyViewMapper.getTotalProfiledCounts(StudyViewFilterHelper.build(studyViewFilter, null, null),
-            "MUTATION_EXTENDED");
+            "MUTATION_EXTENDED", null);
 
         assertEquals(3, totalProfiledCountsMap.size());