Feature/mutated genes total profiled counts and gene panels (#10824)

* Add Support for TotalProfiledCase Counts for Mutated-genes endpoint. * Create sql files to create new tables * Add unit test for totalProfiledCount * Add matching gene panel ids * Add TotalProfiledCountsWithoutPanelData * Add profileCount for genes without gene panel data * Add Comments for SQL * Update matching Gene Panel Ids * Clean up code * Fix test * Add query to get correct Gene Panels * Fix unit test * Add comments
cBioPortal · Nov 24, 2024 · f566075 · f566075
1 parent b5fb29e
commit f566075
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Showing 19 changed files with 363 additions and 225 deletions.
diff --git a/pom.xml b/pom.xml
@@ -447,6 +447,7 @@
                     <include>clickhouse/clickhouse.sql</include>
                     <include>clickhouse/clickhouse_views.sql</include>
                     <include>clickhouse/clickhouse_migration.sql</include>
+                    <include>clickhouse/materialized_views.sql</include>
 				</includes>
 			</resource>
 		</resources>
@@ -458,6 +459,7 @@
                     <include>clickhouse/clickhouse.sql</include>
                     <include>clickhouse/views.sql</include>
                     <include>clickhouse/clickhouse_migration.sql</include>
+                    <include>clickhouse/materialized_views.sql</include>
                 </includes> 
             </testResource>
             <testResource>

diff --git a/src/main/java/org/cbioportal/model/AlterationType.java b/src/main/java/org/cbioportal/model/AlterationType.java
@@ -1,6 +1,8 @@
 package org.cbioportal.model;
 
 public enum AlterationType {
-    MUTATION,
-    COPY_NUMBER_ALTERATION
+    MUTATION_EXTENDED,
+    COPY_NUMBER_ALTERATION,
+    STRUCTURAL_VARIANT,
+    GENERIC_ASSAY;
 }
diff --git a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java b/src/main/java/org/cbioportal/persistence/StudyViewRepository.java
@@ -10,6 +10,7 @@
 import org.cbioportal.web.parameter.StudyViewFilter;
 
 import java.util.List;
+import java.util.Map;
 
 public interface StudyViewRepository {
     List<Sample> getFilteredSamples(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
@@ -28,4 +29,10 @@ public interface StudyViewRepository {
 
     List<String> getClinicalDataAttributeNames(ClinicalAttributeDataSource clinicalAttributeDataSource, ClinicalAttributeDataType dataType);
 
+    Map<String, AlterationCountByGene> getTotalProfiledCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, String alterationType);
+
+    int getFilteredSamplesCount(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
+
+    Map<String, AlterationCountByGene> getMatchingGenePanelIds(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, String alterationType);
+
 }
diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
@@ -1,5 +1,6 @@
 package org.cbioportal.persistence.mybatisclickhouse;
 
+import org.apache.ibatis.annotations.MapKey;
 import org.cbioportal.model.AlterationCountByGene;
 import org.cbioportal.model.ClinicalData;
 import org.cbioportal.model.ClinicalDataCount;
@@ -9,6 +10,7 @@
 import org.cbioportal.web.parameter.StudyViewFilter;
 
 import java.util.List;
+import java.util.Map;
 
 public interface StudyViewMapper {
     List<Sample> getFilteredSamples(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
@@ -31,4 +33,12 @@ List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, C
 
     List<ClinicalData> getPatientClinicalDataFromStudyViewFilter(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, List<String> attributeIds);
 
+    @MapKey("hugoGeneSymbol")
+    Map<String, AlterationCountByGene> getTotalProfiledCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, String alterationType);
+
+    int getFilteredSamplesCount(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
+
+    @MapKey("hugoGeneSymbol")
+    Map<String, AlterationCountByGene> getMatchingGenePanelIds(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, String alterationType);
+
 }
diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
@@ -14,6 +14,7 @@
 import org.springframework.stereotype.Repository;
 
 import java.util.List;
+import java.util.Map;
 
 @Repository
 public class StudyViewMyBatisRepository implements StudyViewRepository {
@@ -74,4 +75,22 @@ public List<ClinicalData> getSampleClinicalData(StudyViewFilter studyViewFilter,
     public List<ClinicalData> getPatientClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter) {
         return mapper.getPatientClinicalDataFromStudyViewFilter(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter), attributeIds);
     }
+
+    public Map<String, AlterationCountByGene> getTotalProfiledCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, String alterationType) {
+        return mapper.getTotalProfiledCounts(studyViewFilter, categorizedClinicalDataCountFilter,
+            shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter), alterationType);
+    }
+
+    @Override
+    public int getFilteredSamplesCount(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter) {
+        return mapper.getFilteredSamplesCount(studyViewFilter, categorizedClinicalDataCountFilter,
+            shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter));
+    }
+
+    @Override
+    public Map<String, AlterationCountByGene> getMatchingGenePanelIds(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, String alterationType) {
+        return mapper.getMatchingGenePanelIds(studyViewFilter, categorizedClinicalDataCountFilter,
+            shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter), alterationType);
+    }
+
 }
diff --git a/...ava/org/cbioportal/persistence/mybatisclickhouse/typehandler/GenePanelIdsTypeHandler.java b/...ava/org/cbioportal/persistence/mybatisclickhouse/typehandler/GenePanelIdsTypeHandler.java
@@ -0,0 +1,39 @@
+package org.cbioportal.persistence.mybatisclickhouse.typehandler;
+
+import org.apache.ibatis.type.BaseTypeHandler;
+import org.apache.ibatis.type.JdbcType;
+
+import java.sql.CallableStatement;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.HashSet;
+import java.util.Set;
+import java.util.Arrays;
+
+public class GenePanelIdsTypeHandler extends BaseTypeHandler<Set<String>> {
+
+    @Override
+    public void setNonNullParameter(PreparedStatement ps, int i, Set<String> parameter, JdbcType jdbcType) throws SQLException {
+        // Convert Set to array for storage (if needed)
+        throw new UnsupportedOperationException("Storage of GenePanelIds not supported");
+    }
+
+    @Override
+    public Set<String> getNullableResult(ResultSet rs, String columnName) throws SQLException {
+        String[] array = (String[]) rs.getArray(columnName).getArray();
+        return new HashSet<>(Arrays.asList(array));
+    }
+
+    @Override
+    public Set<String> getNullableResult(ResultSet rs, int columnIndex) throws SQLException {
+        String[] array = (String[]) rs.getArray(columnIndex).getArray();
+        return new HashSet<>(Arrays.asList(array));
+    }
+
+    @Override
+    public Set<String> getNullableResult(CallableStatement cs, int columnIndex) throws SQLException {
+        String[] array = (String[]) cs.getArray(columnIndex).getArray();
+        return new HashSet<>(Arrays.asList(array));
+    }
+}
diff --git a/src/main/java/org/cbioportal/service/AlterationCountService.java b/src/main/java/org/cbioportal/service/AlterationCountService.java
@@ -3,6 +3,8 @@
 import org.apache.commons.math3.util.Pair;
 import org.cbioportal.model.*;
 import org.cbioportal.model.util.Select;
+import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
+import org.cbioportal.web.parameter.StudyViewFilter;
 
 import java.util.List;
 
@@ -75,4 +77,6 @@ Pair<List<CopyNumberCountByGene>, Long> getPatientCnaGeneCounts(List<MolecularPr
                                                                     boolean includeMissingAlterationsFromGenePanel,
                                                                     AlterationFilter alterationFilter);
 
+    List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
+
 }
diff --git a/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java b/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java
@@ -1,17 +1,35 @@
 package org.cbioportal.service.impl;
 
-import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.math3.util.Pair;
-import org.cbioportal.model.*;
+import org.cbioportal.model.AlterationCountBase;
+import org.cbioportal.model.AlterationCountByGene;
+import org.cbioportal.model.AlterationCountByStructuralVariant;
+import org.cbioportal.model.AlterationFilter;
+import org.cbioportal.model.AlterationType;
+import org.cbioportal.model.CopyNumberCountByGene;
+import org.cbioportal.model.MolecularProfile;
+import org.cbioportal.model.MolecularProfileCaseIdentifier;
 import org.cbioportal.model.util.Select;
 import org.cbioportal.persistence.AlterationRepository;
 import org.cbioportal.persistence.MolecularProfileRepository;
+import org.cbioportal.persistence.StudyViewRepository;
 import org.cbioportal.service.AlterationCountService;
 import org.cbioportal.service.util.AlterationEnrichmentUtil;
+import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
+import org.cbioportal.web.parameter.StudyViewFilter;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.lang.NonNull;
+import org.springframework.lang.Nullable;
 import org.springframework.stereotype.Service;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeSet;
 import java.util.concurrent.atomic.AtomicReference;
 import java.util.function.BiFunction;
 import java.util.function.Function;
@@ -20,17 +38,30 @@
 @Service
 public class AlterationCountServiceImpl implements AlterationCountService {
 
+    private final AlterationRepository alterationRepository;
+    private final AlterationEnrichmentUtil<AlterationCountByGene> alterationEnrichmentUtil;
+    private final AlterationEnrichmentUtil<CopyNumberCountByGene> alterationEnrichmentUtilCna;
+    private final AlterationEnrichmentUtil<AlterationCountByStructuralVariant> alterationEnrichmentUtilStructVar;
+    private final MolecularProfileRepository molecularProfileRepository;
+
+    private final StudyViewRepository studyViewRepository;
+
+    private static final String WHOLE_EXOME_SEQUENCING = "WES";
+
+
     @Autowired
-    private AlterationRepository alterationRepository;
-    @Autowired
-    private AlterationEnrichmentUtil<AlterationCountByGene> alterationEnrichmentUtil;
-    @Autowired
-    private AlterationEnrichmentUtil<CopyNumberCountByGene> alterationEnrichmentUtilCna;
-    @Autowired
-    private AlterationEnrichmentUtil<AlterationCountByStructuralVariant> alterationEnrichmentUtilStructVar;
-    @Autowired
-    private MolecularProfileRepository molecularProfileRepository;
-
+    public AlterationCountServiceImpl(AlterationRepository alterationRepository, AlterationEnrichmentUtil<AlterationCountByGene> alterationEnrichmentUtil,
+                                      AlterationEnrichmentUtil<CopyNumberCountByGene> alterationEnrichmentUtilCna,
+                                      AlterationEnrichmentUtil<AlterationCountByStructuralVariant> alterationEnrichmentUtilStructVar,
+                                      MolecularProfileRepository molecularProfileRepository,
+                                      StudyViewRepository studyViewRepository) {
+        this.alterationRepository = alterationRepository;
+        this.alterationEnrichmentUtil = alterationEnrichmentUtil;
+        this.alterationEnrichmentUtilCna = alterationEnrichmentUtilCna;
+        this.alterationEnrichmentUtilStructVar = alterationEnrichmentUtilStructVar;
+        this.molecularProfileRepository = molecularProfileRepository;
+        this.studyViewRepository = studyViewRepository;
+    }
     @Override
     public Pair<List<AlterationCountByGene>, Long> getSampleAlterationGeneCounts(List<MolecularProfileCaseIdentifier> molecularProfileCaseIdentifiers,
                                                                                  Select<Integer> entrezGeneIds,
@@ -223,6 +254,48 @@ public Pair<List<CopyNumberCountByGene>, Long> getPatientCnaGeneCounts(List<Mole
         );
     }
 
+    @Override
+    public List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter) {
+        var alterationCountByGenes = studyViewRepository.getMutatedGenes(studyViewFilter, categorizedClinicalDataCountFilter);
+        var profiledCountsMap = studyViewRepository.getTotalProfiledCounts(studyViewFilter,
+            categorizedClinicalDataCountFilter,
+            AlterationType.MUTATION_EXTENDED.toString());
+        var profiledCountWithoutGenePanelData = studyViewRepository.getFilteredSamplesCount(studyViewFilter, categorizedClinicalDataCountFilter);
+        var matchingGenePanelIdsMap = studyViewRepository.getMatchingGenePanelIds(studyViewFilter,
+            categorizedClinicalDataCountFilter, AlterationType.MUTATION_EXTENDED.toString());
+
+        alterationCountByGenes.parallelStream()
+            .forEach(alterationCountByGene ->  {
+                String hugoGeneSymbol = alterationCountByGene.getHugoGeneSymbol();
+                var matchingGenePanelIds = matchingGenePanelIdsMap.get(hugoGeneSymbol) != null ? 
+                    matchingGenePanelIdsMap.get(hugoGeneSymbol).getMatchingGenePanelIds() : null;
+
+                int totalProfiledCount = getTotalProfiledCount(alterationCountByGene.getHugoGeneSymbol(),
+                    profiledCountsMap, profiledCountWithoutGenePanelData, matchingGenePanelIds);
+
+                alterationCountByGene.setNumberOfProfiledCases(totalProfiledCount);
+
+                alterationCountByGene.setMatchingGenePanelIds(matchingGenePanelIds);
+            });
+
+        return alterationCountByGenes;
+    }
+
+    private int getTotalProfiledCount(@NonNull String hugoGeneSymbol, @NonNull Map<String, AlterationCountByGene> profiledCountsMap,
+                                      int profiledCountWithoutGenePanelData, @Nullable Set<String> matchingGenePanelIds) {
+        int totalProfiledCount = profiledCountWithoutGenePanelData;
+
+        if (hasGenePanelData(matchingGenePanelIds)) {
+            totalProfiledCount  = profiledCountsMap.get(hugoGeneSymbol).getNumberOfProfiledCases();
+        }
+        return totalProfiledCount;
+    }
+
+    private boolean hasGenePanelData(@Nullable Set<String> matchingGenePanelIds) {
+        return matchingGenePanelIds != null && matchingGenePanelIds.contains(WHOLE_EXOME_SEQUENCING) 
+            && matchingGenePanelIds.size() > 1;
+    }
+
     private <S extends AlterationCountBase> Pair<List<S>, Long> getAlterationGeneCounts(
         List<MolecularProfileCaseIdentifier> molecularProfileCaseIdentifiers,
         boolean includeFrequency,

diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
@@ -8,6 +8,7 @@
 import org.cbioportal.persistence.StudyViewRepository;
 import org.cbioportal.persistence.enums.ClinicalAttributeDataSource;
 import org.cbioportal.persistence.enums.ClinicalAttributeDataType;
+import org.cbioportal.service.AlterationCountService;
 import org.cbioportal.service.StudyViewColumnarService;
 import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
 import org.cbioportal.web.parameter.StudyViewFilter;
@@ -27,21 +28,24 @@ public class StudyViewColumnarServiceImpl implements StudyViewColumnarService {
 
     private final StudyViewRepository studyViewRepository;
 
+    private final AlterationCountService alterationCountService;
+
     @Autowired
-    public StudyViewColumnarServiceImpl(StudyViewRepository studyViewRepository) {
+    public StudyViewColumnarServiceImpl(StudyViewRepository studyViewRepository, AlterationCountService alterationCountService) {
         this.studyViewRepository = studyViewRepository;
+        this.alterationCountService = alterationCountService;
     }
-    
+
     @Override
     public List<Sample> getFilteredSamples(StudyViewFilter studyViewFilter) {
         CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
-        return studyViewRepository.getFilteredSamples(studyViewFilter, categorizedClinicalDataCountFilter);    
+        return studyViewRepository.getFilteredSamples(studyViewFilter, categorizedClinicalDataCountFilter);
     }
-    
+
     @Override
     public List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter) {
         CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
-        return studyViewRepository.getMutatedGenes(studyViewFilter, categorizedClinicalDataCountFilter);
+        return alterationCountService.getMutatedGenes(studyViewFilter, categorizedClinicalDataCountFilter);
     }
 
     @Override
@@ -59,11 +63,11 @@ public List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilter studyVi
     }
 
     private CategorizedClinicalDataCountFilter extractClinicalDataCountFilters(final StudyViewFilter studyViewFilter) {
-        if(clinicalAttributeNameMap.isEmpty()) {
+        if (clinicalAttributeNameMap.isEmpty()) {
             buildClinicalAttributeNameMap();
         }
 
-        if(studyViewFilter.getClinicalDataFilters() == null) {
+        if (studyViewFilter.getClinicalDataFilters() == null) {
             return CategorizedClinicalDataCountFilter.getBuilder().build();
         }
 
@@ -90,7 +94,7 @@ private CategorizedClinicalDataCountFilter extractClinicalDataCountFilters(final
 
     private void buildClinicalAttributeNameMap() {
         List<ClinicalAttributeDataSource> clinicalAttributeDataSources = List.of(ClinicalAttributeDataSource.values());
-        for(ClinicalAttributeDataSource clinicalAttributeDataSource : clinicalAttributeDataSources) {
+        for (ClinicalAttributeDataSource clinicalAttributeDataSource : clinicalAttributeDataSources) {
             String categoricalKey = clinicalAttributeDataSource.getValue() + ClinicalAttributeDataType.CATEGORICAL;
             String numericKey = clinicalAttributeDataSource.getValue() + ClinicalAttributeDataType.NUMERIC;
             clinicalAttributeNameMap.put(categoricalKey, studyViewRepository.getClinicalDataAttributeNames(clinicalAttributeDataSource, ClinicalAttributeDataType.CATEGORICAL));

diff --git a/src/main/resources/db-scripts/clickhouse/clickhouse.sql b/src/main/resources/db-scripts/clickhouse/clickhouse.sql
@@ -1,5 +1,7 @@
 DROP TABLE IF EXISTS genomic_event_mutation;
 DROP TABLE IF EXISTS genomic_event;
+DROP TABLE IF EXISTS sample_to_gene_panel;
+DROP TABLE IF EXISTS gene_panel_to_gene;
 
 CREATE TABLE IF NOT EXISTS genomic_event
 (
@@ -11,7 +13,7 @@ CREATE TABLE IF NOT EXISTS genomic_event
     cancer_study_identifier   String,
     genetic_profile_stable_id String
 ) ENGINE = MergeTree
-      ORDER BY ( variant_type, sample_unique_id, hugo_gene_symbol);
+ORDER BY ( variant_type, sample_unique_id, hugo_gene_symbol);
 
 CREATE TABLE IF NOT EXISTS genomic_event_mutation
 (
@@ -26,4 +28,20 @@ CREATE TABLE IF NOT EXISTS genomic_event_mutation
     driver_filter             String,
     driver_tiers_filter       String
 ) ENGINE = MergeTree
-ORDER BY ( hugo_gene_symbol, genetic_profile_stable_id);
+ORDER BY ( hugo_gene_symbol, genetic_profile_stable_id);
+
+CREATE TABLE sample_to_gene_panel
+(
+    sample_unique_id String,
+    alteration_type String,
+    gene_panel_id String,
+    cancer_study_identifier String
+) ENGINE = MergeTree()
+ORDER BY (gene_panel_id, alteration_type, sample_unique_id);
+
+CREATE TABLE gene_panel_to_gene
+(
+    gene_panel_id String,
+    gene String
+) ENGINE = MergeTree()
+ORDER BY (gene_panel_id);