Merge branch 'refs/heads/demo-rfc80-poc' into demo-rfc80-poc-mutation…

…_type_count # Conflicts: # src/main/java/org/cbioportal/persistence/StudyViewRepository.java # src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java # src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java # src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java # src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java # src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml # src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
cBioPortal · Jun 25, 2024 · cd477b6 · cd477b6
2 parents 6bc6e47 + 2b87a26
commit cd477b6
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Showing 19 changed files with 639 additions and 620 deletions.
diff --git a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java b/src/main/java/org/cbioportal/persistence/StudyViewRepository.java
@@ -1,44 +1,49 @@
 package org.cbioportal.persistence;
 
 import org.cbioportal.model.AlterationCountByGene;
+import org.cbioportal.model.ClinicalAttribute;
+import org.cbioportal.model.CaseListDataCount;
 import org.cbioportal.model.ClinicalData;
 import org.cbioportal.model.ClinicalDataCount;
+import org.cbioportal.model.CopyNumberCountByGene;
 import org.cbioportal.model.GenomicDataCountItem;
 import org.cbioportal.model.GenomicDataCount;
 import org.cbioportal.model.Sample;
-import org.cbioportal.persistence.enums.ClinicalAttributeDataSource;
-import org.cbioportal.persistence.enums.ClinicalAttributeDataType;
 import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
 import org.cbioportal.web.parameter.GenomicDataFilter;
 import org.cbioportal.web.parameter.StudyViewFilter;
 
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 public interface StudyViewRepository {
-    List<Sample> getFilteredSamples(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
+    List<Sample> getFilteredSamples(StudyViewFilter studyViewFilter);
 
-    List<ClinicalData> getSampleClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
+    List<ClinicalData> getSampleClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds);
 
-    List<ClinicalData> getPatientClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
+    List<ClinicalData> getPatientClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds);
 
-    List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
+    List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter);
 
-    List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<String> filteredAttributes);
+    List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilter studyViewFilter);
+    List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter);
 
-    List<ClinicalDataCount> getSampleClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<String> filteredAttributes);
+    List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes);
 
-    List<ClinicalDataCount> getPatientClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<String> filteredAttributes);
+    List<GenomicDataCount> getGenomicDataCounts(StudyViewFilter studyViewFilter);
 
-    List<GenomicDataCount> getGenomicDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
-    
-    List<String> getClinicalDataAttributeNames(ClinicalAttributeDataSource clinicalAttributeDataSource, ClinicalAttributeDataType dataType);
+    List<ClinicalAttribute> getClinicalAttributes();
+
+    List<CaseListDataCount> getCaseListDataCounts(StudyViewFilter studyViewFilter);
 
-    Map<String, AlterationCountByGene> getTotalProfiledCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, String alterationType);
+    Map<String, AlterationCountByGene> getTotalProfiledCounts(StudyViewFilter studyViewFilter, String alterationType);
+
+    int getFilteredSamplesCount(StudyViewFilter studyViewFilter);
 
-    int getFilteredSamplesCount(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
+    Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilter studyViewFilter, String alterationType);
 
-    Map<String, AlterationCountByGene> getMatchingGenePanelIds(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, String alterationType);
+    int getTotalProfiledCountsByAlterationType(StudyViewFilter studyViewFilter, String alterationType);
 
     List<GenomicDataCountItem> getCNAAlterationCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<GenomicDataFilter> genomicDataFilters);
 

diff --git a/src/main/java/org/cbioportal/persistence/helper/AlterationFilterHelper.java b/src/main/java/org/cbioportal/persistence/helper/AlterationFilterHelper.java
@@ -20,10 +20,13 @@ public static AlterationFilterHelper build(@Nullable AlterationFilter alteration
 
     private final AlterationFilter alterationFilter;
     private final Select<String> mappedMutationTypes;
+
+    private final Select<Short> mappedCnaTypes;
 
     private AlterationFilterHelper(@NonNull AlterationFilter alterationFilter){
         this.alterationFilter = alterationFilter;
         this.mappedMutationTypes = buildMutationTypeList();
+        this.mappedCnaTypes = buildCnaTypeList();
     }
 
     private Select<String> buildMutationTypeList() {
@@ -42,8 +45,12 @@ private Select<String> buildMutationTypeList() {
     public Select<String> getMutationTypeList() {
        return mappedMutationTypes; 
     }
-
+    
     public Select<Short> getCnaTypeList() {
+        return mappedCnaTypes;
+    }
+
+    public Select<Short> buildCnaTypeList() {
         if (alterationFilter.getCNAEventTypeSelect().hasNone()) {
             return Select.none();
         }
@@ -128,11 +135,17 @@ public boolean isSomeTierOptionsSelected() {
         return !isAllTierOptionsSelected() && !isNoTierOptionsSelected();
     }
 
-    public boolean shouldApply() {
+    public boolean shouldApplyMutationAlterationFilter() {
         return isSomeDriverAnnotationsSelected() 
             || isSomeMutationStatusSelected() 
             || isSomeTierOptionsSelected()
             || mappedMutationTypes.hasNone() 
             || (!mappedMutationTypes.hasNone() && !mappedMutationTypes.hasAll());
     }
+
+    public boolean shouldApplyCnaAlterationFilter() {
+        return isSomeDriverAnnotationsSelected()
+            || mappedCnaTypes.hasNone() 
+            || (!mappedCnaTypes.hasNone() && !mappedCnaTypes.hasAll());
+    }
 }
diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
@@ -1,10 +1,14 @@
 package org.cbioportal.persistence.mybatisclickhouse;
 
-import org.cbioportal.model.*;
 import org.apache.ibatis.annotations.MapKey;
 import org.cbioportal.model.AlterationCountByGene;
+import org.cbioportal.model.CaseListDataCount;
+import org.cbioportal.model.ClinicalAttribute;
 import org.cbioportal.model.ClinicalData;
 import org.cbioportal.model.ClinicalDataCount;
+import org.cbioportal.model.CopyNumberCountByGene;
+import org.cbioportal.model.GenePanelToGene;
+import org.cbioportal.model.GenomicDataCount;
 import org.cbioportal.model.GenomicDataCountItem;
 import org.cbioportal.model.Sample;
 import org.cbioportal.persistence.helper.AlterationFilterHelper;
@@ -15,6 +19,7 @@
 import java.util.List;
 import java.util.Map;
 
+
 public interface StudyViewMapper {
     List<Sample> getFilteredSamples(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
 
@@ -23,6 +28,12 @@ public interface StudyViewMapper {
     List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
                                                 boolean applyPatientIdFilters, AlterationFilterHelper alterationFilterHelper);
 
+    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);
 
@@ -31,8 +42,10 @@ List<ClinicalDataCount> getSampleClinicalDataCounts(StudyViewFilter studyViewFil
 
     List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
                                                   boolean applyPatientIdFilters, List<String> attributeIds, List<String> filteredAttributeValues);
+
+    List<CaseListDataCount> getCaseListDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
 
-    List<String> getClinicalAttributeNames(String tableName);
+    List<ClinicalAttribute> getClinicalAttributes();
 
     List<ClinicalData> getSampleClinicalDataFromStudyViewFilter(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, List<String> attributeIds);
 
@@ -43,12 +56,13 @@ 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);
 
     List<GenomicDataCountItem> getCNAAlterationCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<GenomicDataFilter> genomicDataFilters);
 
     Map<String, Integer> getMutationCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, GenomicDataFilter genomicDataFilter);
-    
+
     List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<GenomicDataFilter> genomicDataFilters);
 }