Overload methods

cBioPortal · Sep 5, 2024 · a73857b · a73857b
1 parent 942e443
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Showing 7 changed files with 84 additions and 41 deletions.
diff --git a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java b/src/main/java/org/cbioportal/persistence/StudyViewRepository.java
@@ -27,7 +27,9 @@ public interface StudyViewRepository {
 
     List<ClinicalData> getPatientClinicalData(StudyViewFilterContext studyViewFilterContext, List<String> attributeIds);
 
-    List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext, String specificHugoGeneSymbol);
+    List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext);
+
+    List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext, List<String> hugoGeneSymbols);
 
     List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilterContext studyViewFilterContext);
     List<CopyNumberCountByGene> getCnaGenes(StudyViewFilterContext studyViewFilterContext);
@@ -42,11 +44,15 @@ public interface StudyViewRepository {
 
     List<CaseListDataCount> getCaseListDataCountsPerStudy(StudyViewFilterContext studyViewFilterContext);
 
-    Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType, String specificHugoGeneSymbol);
+    Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType);
+
+    Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType, List<String> hugoGeneSymbols);
 
     int getFilteredSamplesCount(StudyViewFilterContext studyViewFilterContext);
 
-    Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilterContext studyViewFilterContext, String alterationType, String specificHugoGeneSymbol);
+    Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilterContext studyViewFilterContext, String alterationType);
+
+    Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilterContext studyViewFilterContext, String alterationType, List<String> hugoGeneSymbols);
 
     int getTotalProfiledCountsByAlterationType(StudyViewFilterContext studyViewFilterContext, String alterationType);
 
@@ -65,6 +71,4 @@ 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, String specificHugoGeneSymbol);
+    List<AlterationCountByGene> getMutatedGenes(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper, List<String> hugoGeneSymbols);
 
     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, String specificHugoGeneSymbol);
+    List<AlterationCountByGene> getTotalProfiledCounts(StudyViewFilterHelper studyViewFilterHelper, String alterationType, List<String> hugoGeneSymbols);
 
     int getFilteredSamplesCount(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);
 
-    List<GenePanelToGene> getMatchingGenePanelIds(StudyViewFilterHelper studyViewFilterHelper, String alterationType, String specificHugoGeneSymbol);
+    List<GenePanelToGene> getMatchingGenePanelIds(StudyViewFilterHelper studyViewFilterHelper, String alterationType, List<String> hugoGeneSymbols);
 
     int getTotalProfiledCountByAlterationType(StudyViewFilterHelper studyViewFilterHelper, String alterationType);
 

diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
@@ -50,9 +50,15 @@ public List<Sample> getFilteredSamples(StudyViewFilterContext studyViewFilterCon
     }
 
     @Override
-    public List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext, String specificHugoGeneSymbol) {
+    public List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext) {
         return mapper.getMutatedGenes(createStudyViewFilterHelper(studyViewFilterContext),
-            AlterationFilterHelper.build(studyViewFilterContext.studyViewFilter().getAlterationFilter()), specificHugoGeneSymbol);
+            AlterationFilterHelper.build(studyViewFilterContext.studyViewFilter().getAlterationFilter()), null);
+    }
+
+    @Override
+    public List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext, List<String> hugoGeneSymbols) {
+        return mapper.getMutatedGenes(createStudyViewFilterHelper(studyViewFilterContext),
+            AlterationFilterHelper.build(studyViewFilterContext.studyViewFilter().getAlterationFilter()), hugoGeneSymbols);
     }
 
     @Override
@@ -142,10 +148,18 @@ public List<ClinicalData> getSampleClinicalData(StudyViewFilterContext studyView
     public List<ClinicalData> getPatientClinicalData(StudyViewFilterContext studyViewFilterContext, List<String> attributeIds) {
         return mapper.getPatientClinicalDataFromStudyViewFilter(createStudyViewFilterHelper(studyViewFilterContext), attributeIds);
     }
+
+    @Override
+    public Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType) {
+        return mapper.getTotalProfiledCounts(createStudyViewFilterHelper(studyViewFilterContext), alterationType, null)
+            .stream()
+            .collect(Collectors.groupingBy(AlterationCountByGene::getHugoGeneSymbol,
+                Collectors.mapping(AlterationCountByGene::getNumberOfProfiledCases, Collectors.summingInt(Integer::intValue))));
+    }
 
     @Override
-    public Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType, String specificHugoGeneSymbol) {
-        return mapper.getTotalProfiledCounts(createStudyViewFilterHelper(studyViewFilterContext), alterationType, specificHugoGeneSymbol)
+    public Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType, List<String> hugoGeneSymbols) {
+        return mapper.getTotalProfiledCounts(createStudyViewFilterHelper(studyViewFilterContext), alterationType, hugoGeneSymbols)
             .stream()
             .collect(Collectors.groupingBy(AlterationCountByGene::getHugoGeneSymbol,
                 Collectors.mapping(AlterationCountByGene::getNumberOfProfiledCases, Collectors.summingInt(Integer::intValue))));
@@ -157,8 +171,16 @@ public int getFilteredSamplesCount(StudyViewFilterContext studyViewFilterContext
     }
 
     @Override
-    public Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilterContext studyViewFilterContext, String alterationType, String specificHugoGeneSymbol) {
-        return mapper.getMatchingGenePanelIds(createStudyViewFilterHelper(studyViewFilterContext), alterationType, specificHugoGeneSymbol)
+    public Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilterContext studyViewFilterContext, String alterationType) {
+        return mapper.getMatchingGenePanelIds(createStudyViewFilterHelper(studyViewFilterContext), alterationType, null)
+            .stream()
+            .collect(Collectors.groupingBy(GenePanelToGene::getHugoGeneSymbol,
+                Collectors.mapping(GenePanelToGene::getGenePanelId, Collectors.toSet())));
+    }
+
+    @Override
+    public Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilterContext studyViewFilterContext, String alterationType, List<String> hugoGeneSymbols) {
+        return mapper.getMatchingGenePanelIds(createStudyViewFilterHelper(studyViewFilterContext), alterationType, hugoGeneSymbols)
             .stream()
             .collect(Collectors.groupingBy(GenePanelToGene::getHugoGeneSymbol,
                 Collectors.mapping(GenePanelToGene::getGenePanelId, Collectors.toSet())));
@@ -224,10 +246,4 @@ 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
@@ -1,14 +1,16 @@
 package org.cbioportal.service;
 
 import org.apache.commons.math3.util.Pair;
-import org.cbioportal.model.*;
+import org.cbioportal.model.AlterationCountByGene;
+import org.cbioportal.model.AlterationCountByStructuralVariant;
+import org.cbioportal.model.AlterationFilter;
+import org.cbioportal.model.CopyNumberCountByGene;
+import org.cbioportal.model.MolecularProfileCaseIdentifier;
+import org.cbioportal.model.StudyViewFilterContext;
 import org.cbioportal.model.util.Select;
-import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
-import org.cbioportal.web.parameter.CustomSampleIdentifier;
-import org.cbioportal.web.parameter.SampleIdentifier;
-import org.cbioportal.web.parameter.StudyViewFilter;
 
 import java.util.List;
+import java.util.Map;
 
 public interface AlterationCountService {
 
@@ -80,9 +82,10 @@ Pair<List<CopyNumberCountByGene>, Long> getPatientCnaGeneCounts(List<MolecularPr
                                                                     AlterationFilter alterationFilter);
 
     List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext);
+
+    Map<String, AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext, List<String> hugoGeneSymbols); 
+
     List<CopyNumberCountByGene> getCnaGenes(StudyViewFilterContext studyViewFilterContext);
 
     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
@@ -254,7 +254,7 @@ public Pair<List<CopyNumberCountByGene>, Long> getPatientCnaGeneCounts(List<Mole
 
     @Override
     public List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext) {
-        var alterationCountByGenes = studyViewRepository.getMutatedGenes(studyViewFilterContext, null);
+        var alterationCountByGenes = studyViewRepository.getMutatedGenes(studyViewFilterContext);
         return populateAlterationCounts(alterationCountByGenes, studyViewFilterContext, AlterationType.MUTATION_EXTENDED, null);
     }
 
@@ -271,10 +271,10 @@ public List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilterCont
 
     private < T extends AlterationCountByGene> List<T> populateAlterationCounts(@NonNull List<T> alterationCounts,
                                                                                 @NonNull StudyViewFilterContext studyViewFilterContext,
-                                                                                @NonNull AlterationType alterationType, String specificHugoGeneSymbol) {
+                                                                                @NonNull AlterationType alterationType, List<String> hugoGeneSymbols) {
         final int profiledCountWithoutGenePanelData = studyViewRepository.getTotalProfiledCountsByAlterationType(studyViewFilterContext, alterationType.toString());
-        var profiledCountsMap = studyViewRepository.getTotalProfiledCounts(studyViewFilterContext, alterationType.toString(), specificHugoGeneSymbol);
-        final var matchingGenePanelIdsMap = studyViewRepository.getMatchingGenePanelIds(studyViewFilterContext, alterationType.toString(), specificHugoGeneSymbol);
+        var profiledCountsMap = hugoGeneSymbols == null ? studyViewRepository.getTotalProfiledCounts(studyViewFilterContext, alterationType.toString()) : studyViewRepository.getTotalProfiledCounts(studyViewFilterContext, alterationType.toString(), hugoGeneSymbols);
+        final var matchingGenePanelIdsMap = hugoGeneSymbols == null ? studyViewRepository.getMatchingGenePanelIds(studyViewFilterContext, alterationType.toString()) : studyViewRepository.getMatchingGenePanelIds(studyViewFilterContext, alterationType.toString(), hugoGeneSymbols);
         final int sampleProfileCountWithoutGenePanelData = studyViewRepository.getSampleProfileCountWithoutPanelData(studyViewFilterContext, alterationType.toString());
 
         alterationCounts.parallelStream()
@@ -295,9 +295,15 @@ private < T extends AlterationCountByGene> List<T> populateAlterationCounts(@Non
     }
 
     @Override
-    public AlterationCountByGene getMutatedGene(StudyViewFilterContext studyViewFilterContext, String specificHugoGeneSymbol) {
-        List<AlterationCountByGene> alterationCountByGenes = studyViewRepository.getMutatedGenes(studyViewFilterContext, specificHugoGeneSymbol);
-        return populateAlterationCounts(alterationCountByGenes, studyViewFilterContext, AlterationType.MUTATION_EXTENDED, specificHugoGeneSymbol).getFirst();
+    public Map<String, AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext, List<String> hugoGeneSymbols) {
+        List<AlterationCountByGene> alterationCounts = studyViewRepository.getMutatedGenes(studyViewFilterContext, hugoGeneSymbols);
+        List<AlterationCountByGene> alterationCountByGenes = populateAlterationCounts(alterationCounts, studyViewFilterContext, AlterationType.MUTATION_EXTENDED, hugoGeneSymbols);
+        return alterationCountByGenes.stream()
+            .collect(Collectors.toMap(
+                AlterationCountByGene::getHugoGeneSymbol,
+                alterationCountByGene -> alterationCountByGene,
+                (existing, replacement) -> existing
+            ));
     }
 
     private boolean hasGenePanelData(@NonNull Set<String> matchingGenePanelIds) {

diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
@@ -134,8 +134,12 @@ 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<String> hugoGeneSymbols = genomicDataFilters.stream()
+            .map(GenomicDataFilter::getHugoGeneSymbol)
+            .toList();
+        Map<String, AlterationCountByGene> alterationCountByGenes = alterationCountService.getMutatedGenes(createContext(studyViewFilter), hugoGeneSymbols);
         for (GenomicDataFilter genomicDataFilter : genomicDataFilters) {
-            AlterationCountByGene filteredAlterationCount = alterationCountService.getMutatedGene(createContext(studyViewFilter), genomicDataFilter.getHugoGeneSymbol());
+            AlterationCountByGene filteredAlterationCount = alterationCountByGenes.getOrDefault(genomicDataFilter.getHugoGeneSymbol(), new AlterationCountByGene());
             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
@@ -30,8 +30,12 @@
         FROM genomic_event_derived
         <where>
             variant_type = 'mutation' AND
-            <if test="specificHugoGeneSymbol != null">
-                hugo_gene_symbol = #{specificHugoGeneSymbol} AND
+            <if test="hugoGeneSymbols != null">
+                hugo_gene_symbol IN
+                <foreach item="hugoGeneSymbol" collection="hugoGeneSymbols" open="(" separator="," close=")">
+                    #{hugoGeneSymbol}
+                </foreach>
+                AND
             </if>
             <include refid="applyStudyViewFilter">
                 <property name="filter_type" value="'SAMPLE_AND_PATIENT_ID'"/>
@@ -339,8 +343,11 @@
             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 test="hugoGeneSymbols != null">
+                AND gptg.gene IN
+                <foreach item="hugoGeneSymbol" collection="hugoGeneSymbols" open="(" separator="," close=")">
+                    #{hugoGeneSymbol}
+                </foreach>
             </if>
             AND stgp.gene_panel_id != 'WES'
             AND
@@ -401,8 +408,11 @@
                     </include>
                 </where>
             )
-            <if test="specificHugoGeneSymbol != null">
-                AND gene = #{specificHugoGeneSymbol}
+            <if test="hugoGeneSymbols != null">
+                AND gene IN
+                <foreach item="hugoGeneSymbol" collection="hugoGeneSymbols" open="(" separator="," close=")">
+                    #{hugoGeneSymbol}
+                </foreach>
             </if>
         </where>
         GROUP BY gene, gene_panel_id;