✨ Add StructuralVariant-genes endpoint (#10854)

* ✨ Add StructuralVariant-genes endpoint * Fix sonar issues * Update MatchingGenePanel request to return list * Create and use sample_derive * Update where sample_derived is stored to fix unit test
cBioPortal · Jun 24, 2024 · 505847b · 505847b
1 parent bb5456a
commit 505847b
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Showing 14 changed files with 146 additions and 102 deletions.
diff --git a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java b/src/main/java/org/cbioportal/persistence/StudyViewRepository.java
@@ -3,8 +3,8 @@
 import org.cbioportal.model.AlterationCountByGene;
 import org.cbioportal.model.ClinicalData;
 import org.cbioportal.model.ClinicalDataCount;
-import org.cbioportal.model.GenomicDataCount;
 import org.cbioportal.model.CopyNumberCountByGene;
+import org.cbioportal.model.GenomicDataCount;
 import org.cbioportal.model.Sample;
 import org.cbioportal.persistence.enums.ClinicalAttributeDataSource;
 import org.cbioportal.persistence.enums.ClinicalAttributeDataType;
@@ -13,6 +13,7 @@
 
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 public interface StudyViewRepository {
     List<Sample> getFilteredSamples(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
@@ -24,6 +25,7 @@ public interface StudyViewRepository {
     List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
 
     List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
+    List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
 
     List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<String> filteredAttributes);
 
@@ -39,7 +41,7 @@ public interface StudyViewRepository {
 
     int getFilteredSamplesCount(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
 
-    Map<String, AlterationCountByGene> getMatchingGenePanelIds(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, String alterationType);
+    Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, String alterationType);
 
     int getTotalProfiledCountsByAlterationType(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
@@ -24,6 +24,9 @@ List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter, Cat
 
     List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
                                             boolean applyPatientIdFilters, AlterationFilterHelper alterationFilterHelper);
+
+    List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
+                                                boolean applyPatientIdFilters, AlterationFilterHelper alterationFilterHelper);
 
     List<ClinicalDataCount> getPatientClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
                                                          boolean applyPatientIdFilters,  List<String> attributeIds, List<String> filteredAttributeValues);
@@ -45,8 +48,7 @@ List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, C
 
     int getFilteredSamplesCount(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
 
-    @MapKey("hugoGeneSymbol")
-    Map<String, AlterationCountByGene> getMatchingGenePanelIds(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, String alterationType);
+    List<GenePanelToGene> getMatchingGenePanelIds(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, String alterationType);
 
     int getTotalProfiledCountByAlterationType(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
@@ -2,6 +2,7 @@
 import org.cbioportal.model.AlterationCountByGene;
 import org.cbioportal.model.ClinicalData;
 import org.cbioportal.model.ClinicalDataCount;
+import org.cbioportal.model.GenePanelToGene;
 import org.cbioportal.model.GenomicDataCount;
 import org.cbioportal.model.CopyNumberCountByGene;
 import org.cbioportal.model.Sample;
@@ -16,6 +17,8 @@
 import java.util.Collections;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
+import java.util.stream.Collectors;
 
 @Repository
 public class StudyViewMyBatisRepository implements StudyViewRepository {
@@ -47,6 +50,13 @@ public List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter,
             AlterationFilterHelper.build(studyViewFilter.getAlterationFilter()));
     }
 
+    @Override
+    public List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter) {
+        return mapper.getStructuralVariantGenes(studyViewFilter, categorizedClinicalDataCountFilter,
+            shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter),
+            AlterationFilterHelper.build(studyViewFilter.getAlterationFilter()));
+    }
+
     @Override
     public List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<String> filteredAttributes) {
         return mapper.getClinicalDataCounts(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter),
@@ -103,9 +113,12 @@ public int getFilteredSamplesCount(StudyViewFilter studyViewFilter, CategorizedC
     }
 
     @Override
-    public Map<String, AlterationCountByGene> getMatchingGenePanelIds(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, String alterationType) {
+    public Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, String alterationType) {
         return mapper.getMatchingGenePanelIds(studyViewFilter, categorizedClinicalDataCountFilter,
-            shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter), alterationType);
+            shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter), alterationType)
+            .stream()
+            .collect(Collectors.groupingBy(GenePanelToGene::getHugoGeneSymbol,
+                Collectors.mapping(GenePanelToGene::getGenePanelId, Collectors.toSet())));
     }
 
     @Override

diff --git a/...ava/org/cbioportal/persistence/mybatisclickhouse/typehandler/GenePanelIdsTypeHandler.java b/...ava/org/cbioportal/persistence/mybatisclickhouse/typehandler/GenePanelIdsTypeHandler.java
diff --git a/src/main/java/org/cbioportal/service/AlterationCountService.java b/src/main/java/org/cbioportal/service/AlterationCountService.java
@@ -80,4 +80,6 @@ Pair<List<CopyNumberCountByGene>, Long> getPatientCnaGeneCounts(List<MolecularPr
     List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
     List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
 
+    List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
+
 }
diff --git a/src/main/java/org/cbioportal/service/StudyViewColumnarService.java b/src/main/java/org/cbioportal/service/StudyViewColumnarService.java
@@ -16,6 +16,7 @@ public interface StudyViewColumnarService {
 
     List<AlterationCountByGene> getMutatedGenes(StudyViewFilter interceptedStudyViewFilter);
     List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter interceptedStudyViewFilter);
+    List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilter studyViewFilter);
 
     List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes);
 

diff --git a/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java b/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java
@@ -265,7 +265,13 @@ public List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter,
         var copyNumberCountByGenes = studyViewRepository.getCnaGenes(studyViewFilter, categorizedClinicalDataCountFilter);
         return populateAlterationCounts(copyNumberCountByGenes, studyViewFilter, categorizedClinicalDataCountFilter, AlterationType.COPY_NUMBER_ALTERATION);
     }
-
+
+    @Override
+    public List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter) {
+        var alterationCountByGenes = studyViewRepository.getStructuralVariantGenes(studyViewFilter, categorizedClinicalDataCountFilter);
+        return populateAlterationCounts(alterationCountByGenes, studyViewFilter, categorizedClinicalDataCountFilter, AlterationType.STRUCTURAL_VARIANT);
+    }
+
     private < T extends AlterationCountByGene> List<T> populateAlterationCounts(@NonNull List<T> alterationCounts,
                                                                                 @NonNull StudyViewFilter studyViewFilter,
                                                                                 @NonNull CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
@@ -276,13 +282,13 @@ private < T extends AlterationCountByGene> List<T> populateAlterationCounts(@Non
             alterationType.toString());
         var profiledCountWithoutGenePanelData = studyViewRepository.getTotalProfiledCountsByAlterationType(studyViewFilter, categorizedClinicalDataCountFilter, alterationType.toString());
         var matchingGenePanelIdsMap = studyViewRepository.getMatchingGenePanelIds(studyViewFilter,
-            categorizedClinicalDataCountFilter, AlterationType.MUTATION_EXTENDED.toString());
+            categorizedClinicalDataCountFilter, alterationType.toString());
 
-        updatedAlterationCounts
+        updatedAlterationCounts.parallelStream()
             .forEach(alterationCountByGene ->  {
                 String hugoGeneSymbol = alterationCountByGene.getHugoGeneSymbol();
-                var matchingGenePanelIds = matchingGenePanelIdsMap.get(hugoGeneSymbol) != null ?
-                    matchingGenePanelIdsMap.get(hugoGeneSymbol).getMatchingGenePanelIds() : null;
+                Set<String> matchingGenePanelIds = matchingGenePanelIdsMap.get(hugoGeneSymbol) != null ?
+                    matchingGenePanelIdsMap.get(hugoGeneSymbol) : Collections.emptySet();
 
                 int totalProfiledCount = getTotalProfiledCount(alterationCountByGene.getHugoGeneSymbol(),
                     profiledCountsMap, profiledCountWithoutGenePanelData, matchingGenePanelIds);

diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
@@ -61,6 +61,12 @@ public List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter)
         return alterationCountService.getCnaGenes(studyViewFilter, categorizedClinicalDataCountFilter);
     }
 
+    @Override
+    public List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilter studyViewFilter) {
+        CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
+        return alterationCountService.getStructuralVariantGenes(studyViewFilter, categorizedClinicalDataCountFilter);
+    }
+
     @Override
     public List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes) {
         CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);

diff --git a/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java b/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java
@@ -132,6 +132,22 @@ public ResponseEntity<List<CopyNumberCountByGene>> fetchCnaGenes(
         );
     }
 
+    @PostMapping(value = "/column-store/structuralvariant-genes/fetch",
+        consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE)
+    @Operation(description = "Fetch structural variant genes by study view filter")
+    @ApiResponse(responseCode = "200", description = "OK",
+        content = @Content(array = @ArraySchema(schema = @Schema(implementation = AlterationCountByGene.class))))
+    public ResponseEntity<List<AlterationCountByGene>> fetchStructuralVariantGenes(
+        @Parameter(required = true, description = "Study view filter")
+        @Valid @RequestBody(required = false) StudyViewFilter studyViewFilter,
+        @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface. This attribute is needed for the @PreAuthorize tag above.
+        @RequestAttribute(required = false, value = "involvedCancerStudies") Collection<String> involvedCancerStudies,
+        @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface.
+        @Valid @RequestAttribute(required = false, value = "interceptedStudyViewFilter") StudyViewFilter interceptedStudyViewFilter
+    ) {
+        return new ResponseEntity<>(studyViewColumnarService.getStructuralVariantGenes(interceptedStudyViewFilter), HttpStatus.OK);
+    }
+
     @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.utils.security.AccessLevel).READ)")
     @PostMapping(value = "/column-store/clinical-data-counts/fetch", 
         consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE)

diff --git a/src/main/resources/db-scripts/clickhouse/clickhouse.sql b/src/main/resources/db-scripts/clickhouse/clickhouse.sql
@@ -35,4 +35,18 @@ CREATE TABLE gene_panel_to_gene
     gene_panel_id LowCardinality(String),
     gene String
 ) ENGINE = MergeTree()
-ORDER BY (gene_panel_id);
+ORDER BY (gene_panel_id);
+
+CREATE TABLE sample_derived
+(
+    sample_unique_id         String,
+    sample_unique_id_base64  String,
+    sample_stable_id         String,
+    patient_unique_id        String,
+    patient_unique_id_base64 String,
+    patient_stable_id        String,
+    cancer_study_identifier LowCardinality(String),
+    internal_id             Int 
+)
+    ENGINE = MergeTree
+        ORDER BY (cancer_study_identifier, sample_unique_id);