Feature/mutated genes

pom.xml

@@ -447,9 +447,27 @@
 				<includes>
 					<include>cgds.sql</include>
 					<include>migration.sql</include>
+                    <include>clickhouse/clickhouse.sql</include>
+                    <include>clickhouse/clickhouse_views.sql</include>
+                    <include>clickhouse/clickhouse_migration.sql</include>
 				</includes>
 			</resource>
 		</resources>
+        <testResources>
+            <testResource>
+                <directory>src/main/resources/db-scripts</directory>
+                <filtering>false</filtering>
+                <includes>
+                    <include>clickhouse/clickhouse.sql</include>
+                    <include>clickhouse/views.sql</include>
+                    <include>clickhouse/clickhouse_migration.sql</include>
+                </includes> 
+            </testResource>
+            <testResource>
+                <directory>src/test/resources</directory>
+                <filtering>false</filtering>
+            </testResource>
+        </testResources>
 
 		<plugins>
 			<plugin>

src/main/java/org/cbioportal/persistence/helper/AlterationFilterHelper.java

@@ -0,0 +1,138 @@
+package org.cbioportal.persistence.helper;
+
+import org.cbioportal.model.AlterationFilter;
+import org.cbioportal.model.CNA;
+import org.cbioportal.model.MutationEventType;
+import org.cbioportal.model.util.Select;
+import org.springframework.lang.NonNull;
+import org.springframework.lang.Nullable;
+
+import java.util.Objects;
+
+public final class AlterationFilterHelper {
+
+   public static AlterationFilterHelper build(@Nullable AlterationFilter alterationFilter) {
+       if (Objects.isNull(alterationFilter)) {
+           alterationFilter = new AlterationFilter();
+       }
+       return new AlterationFilterHelper(alterationFilter);
+   } 
+
+    private final AlterationFilter alterationFilter;
+    private final Select<String> mappedMutationTypes;
+
+    private AlterationFilterHelper(@NonNull AlterationFilter alterationFilter){
+        this.alterationFilter = alterationFilter;
+        this.mappedMutationTypes = buildMutationTypeList();
+    }
+
+    private Select<String> buildMutationTypeList() {
+        if (alterationFilter.getMutationTypeSelect().hasNone()) {
+            return Select.none();
+        }
+        if (alterationFilter.getMutationTypeSelect().hasAll()) {
+            return Select.all();
+        }
+        Select<String> typeSelects = alterationFilter.getMutationTypeSelect().map(MutationEventType::getMutationType);
+        typeSelects.inverse(alterationFilter.getMutationTypeSelect().inverse());
+
+        return typeSelects; 
+    }
+
+    public Select<String> getMutationTypeList() {
+       return mappedMutationTypes; 
+    }
+
+    public Select<Short> getCnaTypeList() {
+        if (alterationFilter.getCNAEventTypeSelect().hasNone()) {
+            return Select.none();
+        }
+        if (alterationFilter.getCNAEventTypeSelect().hasAll()) {
+            return Select.all();
+        }
+        return alterationFilter.getCNAEventTypeSelect().map(CNA::getCode);
+    }
+
+    public boolean hasDriver() {
+        return alterationFilter.getIncludeDriver();
+    }
+
+    public boolean hasVUSDriver() {
+        return alterationFilter.getIncludeVUS();
+    }
+
+    public boolean hasUnknownOncogenicity() {
+        return alterationFilter.getIncludeUnknownOncogenicity();
+    }
+
+    public boolean hasGermline() {
+        return alterationFilter.getIncludeGermline();
+    }
+
+    public boolean hasSomatic() {
+        return alterationFilter.getIncludeSomatic();
+    }
+
+    public boolean hasUnknownMutationStatus() {
+        return alterationFilter.getIncludeUnknownStatus();
+    }
+
+    public Select<String> getSelectedTiers() {
+        return alterationFilter.getSelectedTiers();
+    }
+
+    public boolean hasUnknownTier() {
+        return alterationFilter.getIncludeUnknownTier();
+    }
+
+    public boolean isAllDriverAnnotationSelected() {
+        return alterationFilter.getIncludeDriver() && alterationFilter.getIncludeVUS() && alterationFilter.getIncludeUnknownOncogenicity();
+    }
+
+    public boolean isNoDriverAnnotationSelected() {
+        return !alterationFilter.getIncludeDriver() && !alterationFilter.getIncludeVUS() && !alterationFilter.getIncludeUnknownOncogenicity();
+    }
+
+    public boolean isSomeDriverAnnotationsSelected() {
+        return !isAllDriverAnnotationSelected() && !isNoDriverAnnotationSelected();
+    }
+
+    public boolean isAllMutationStatusSelected() {
+        return alterationFilter.getIncludeGermline() 
+            && alterationFilter.getIncludeSomatic() 
+            && alterationFilter.getIncludeUnknownStatus();
+    }
+
+    public boolean isNoMutationStatusSelected() {
+        return !alterationFilter.getIncludeGermline() 
+            && !alterationFilter.getIncludeSomatic() 
+            && !alterationFilter.getIncludeUnknownStatus();
+    }
+
+    public boolean isSomeMutationStatusSelected() {
+        return !isAllMutationStatusSelected() && !isNoMutationStatusSelected();
+    } 
+
+    public boolean isAllTierOptionsSelected() {
+        return !Objects.isNull(alterationFilter.getSelectedTiers()) 
+            && alterationFilter.getSelectedTiers().hasAll() 
+            && alterationFilter.getIncludeUnknownTier();
+    }
+
+    public boolean isNoTierOptionsSelected() {
+        return (Objects.isNull(alterationFilter.getSelectedTiers()) || alterationFilter.getSelectedTiers().hasNone())
+            && !alterationFilter.getIncludeUnknownTier();
+    }
+
+    public boolean isSomeTierOptionsSelected() {
+        return !isAllTierOptionsSelected() && !isNoTierOptionsSelected();
+    }
+
+    public boolean shouldApply() {
+        return isSomeDriverAnnotationsSelected() 
+            || isSomeMutationStatusSelected() 
+            || isSomeTierOptionsSelected()
+            || mappedMutationTypes.hasNone() 
+            || (!mappedMutationTypes.hasNone() && !mappedMutationTypes.hasAll());
+    }
+}

src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java

@@ -4,6 +4,7 @@
 import org.cbioportal.model.ClinicalData;
 import org.cbioportal.model.ClinicalDataCount;
 import org.cbioportal.model.Sample;
+import org.cbioportal.persistence.helper.AlterationFilterHelper;
 import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
 import org.cbioportal.web.parameter.StudyViewFilter;
 
@@ -12,7 +13,8 @@
 public interface StudyViewMapper {
     List<Sample> getFilteredSamples(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
 
-    List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
+    List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
+                                                boolean applyPatientIdFilters, AlterationFilterHelper alterationFilterHelper);
 
     List<ClinicalDataCount> getPatientClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
                                                          boolean applyPatientIdFilters,  List<String> attributeIds, List<String> filteredAttributeValues);

src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java

@@ -7,6 +7,7 @@
 import org.cbioportal.persistence.StudyViewRepository;
 import org.cbioportal.persistence.enums.ClinicalAttributeDataSource;
 import org.cbioportal.persistence.enums.ClinicalAttributeDataType;
+import org.cbioportal.persistence.helper.AlterationFilterHelper;
 import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
 import org.cbioportal.web.parameter.StudyViewFilter;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -32,7 +33,9 @@ public List<Sample> getFilteredSamples(StudyViewFilter studyViewFilter, Categori
 
     @Override
     public List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter) {
-        return mapper.getMutatedGenes(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter));
+        return mapper.getMutatedGenes(studyViewFilter, categorizedClinicalDataCountFilter,
+            shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter),
+            AlterationFilterHelper.build(studyViewFilter.getAlterationFilter()));
     }
 
     @Override

src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java

@@ -75,15 +75,8 @@ public ResponseEntity<List<AlterationCountByGene>> fetchMutatedGenes(
         @RequestAttribute(required = false, value = "interceptedStudyViewFilter") StudyViewFilter interceptedStudyViewFilter
     ) throws StudyNotFoundException {
         AlterationFilter annotationFilters = interceptedStudyViewFilter.getAlterationFilter();
-        List<Sample> samples = studyViewColumnarService.getFilteredSamples(interceptedStudyViewFilter);
-        List<String> studyIds = new ArrayList<>();
-        List<String> sampleIds = new ArrayList<>();
-        for(Sample sample : samples) {
-            studyIds.add(sample.getCancerStudyIdentifier());
-            sampleIds.add(sample.getStableId());
-        }
         return new ResponseEntity<>(
-            studyViewService.getMutationAlterationCountByGenes(studyIds, sampleIds, annotationFilters),
+            studyViewColumnarService.getMutatedGenes(interceptedStudyViewFilter),
             HttpStatus.OK
         );
     }

src/main/resources/db-scripts/clickhouse/clickhouse.sql

@@ -0,0 +1,29 @@
+DROP TABLE IF EXISTS genomic_event_mutation;
+DROP TABLE IF EXISTS genomic_event;
+
+CREATE TABLE IF NOT EXISTS genomic_event
+(
+    sample_unique_id          String,
+    variant                   String,
+    variant_type              String,
+    hugo_gene_symbol          String,
+    gene_panel_stable_id      String,
+    cancer_study_identifier   String,
+    genetic_profile_stable_id String
+) ENGINE = MergeTree
+      ORDER BY ( variant_type, sample_unique_id, hugo_gene_symbol);
+
+CREATE TABLE IF NOT EXISTS genomic_event_mutation
+(
+    sample_unique_id          String,
+    variant                   String,
+    hugo_gene_symbol          String,
+    gene_panel_stable_id      String,
+    cancer_study_identifier   String,
+    genetic_profile_stable_id String,
+    mutation_type             String,
+    mutation_status           String,
+    driver_filter             String,
+    driver_tiers_filter       String
+) ENGINE = MergeTree
+ORDER BY ( hugo_gene_symbol, genetic_profile_stable_id);

src/main/resources/db-scripts/clickhouse/clickhouse_migration.sql

@@ -0,0 +1,91 @@
+
+-- Genomic Event Mutation Data
+Insert into genomic_event_mutation
+SELECT  concat(cs.cancer_study_identifier, '_', sample.stable_id) as sample_unique_id,
+        me.protein_change                                         as variant,
+        gene.hugo_gene_symbol                                     as hugo_gene_symbol,
+        gp.stable_id                                              as gene_panel_stable_id,
+        cs.cancer_study_identifier                                as cancer_study_identifier,
+        g.stable_id                                               as genetic_profile_stable_id,
+        me.mutation_type                                          as mutation_type,
+        mutation.mutation_status                                  as mutation_status,
+        'NA'                                                      as driver_filter,
+        'NA'                                                      as drivet_tiers_filter
+FROM mutation
+         INNER JOIN mutation_event as me on mutation.mutation_event_id = me.mutation_event_id
+         INNER JOIN sample_profile sp
+                    on mutation.sample_id = sp.sample_id and mutation.genetic_profile_id = sp.genetic_profile_id
+         LEFT JOIN gene_panel gp on sp.panel_id = gp.internal_id
+         LEFT JOIN genetic_profile g on sp.genetic_profile_id = g.genetic_profile_id
+         INNER JOIN cancer_study cs on g.cancer_study_id = cs.cancer_study_id
+         INNER JOIN sample on mutation.sample_id = sample.internal_id
+         LEFT JOIN gene on mutation.entrez_gene_id = gene.entrez_gene_id;
+
+-- Genomic Event Data
+Insert into genomic_event
+SELECT concat(cs.cancer_study_identifier, '_', sample.stable_id) as sample_unique_id,
+       me.protein_change                                         as variant,
+       'mutation'                                                as variant_type,
+       gene.hugo_gene_symbol                                     as hugo_gene_symbol,
+       gp.stable_id                                              as gene_panel_stable_id,
+       cs.cancer_study_identifier                                as cancer_study_identifier,
+       g.stable_id                                               as genetic_profile_stable_id
+FROM mutation
+         INNER JOIN mutation_event as me on mutation.mutation_event_id = me.mutation_event_id
+         INNER JOIN sample_profile sp
+                    on mutation.sample_id = sp.sample_id and mutation.genetic_profile_id = sp.genetic_profile_id
+         LEFT JOIN gene_panel gp on sp.panel_id = gp.internal_id
+         LEFT JOIN genetic_profile g on sp.genetic_profile_id = g.genetic_profile_id
+         INNER JOIN cancer_study cs on g.cancer_study_id = cs.cancer_study_id
+         INNER JOIN sample on mutation.sample_id = sample.internal_id
+         LEFT JOIN gene on mutation.entrez_gene_id = gene.entrez_gene_id
+UNION ALL
+SELECT concat(cs.cancer_study_identifier, '_', sample.stable_id) as sample_unique_id,
+       toString(ce.alteration)                                   as variant,
+       'cna'                                                     as variant_type,
+       gene.hugo_gene_symbol                                     as hugo_gene_symbol,
+       gp.stable_id                                              as gene_panel_stable_id,
+       cs.cancer_study_identifier                                as cancer_study_identifier,
+       g.stable_id                                              as genetic_profile_stable_id
+FROM cna_event ce
+         INNER JOIN sample_cna_event sce ON ce.cna_event_id = sce.cna_event_id
+         INNER JOIN sample_profile sp ON sce.sample_id = sp.sample_id AND sce.genetic_profile_id = sp.genetic_profile_id
+         INNER JOIN gene_panel gp ON sp.panel_id = gp.internal_id
+         INNER JOIN genetic_profile g ON sp.genetic_profile_id = g.genetic_profile_id
+         INNER JOIN cancer_study cs ON g.cancer_study_id = cs.cancer_study_id
+         INNER JOIN sample ON sce.sample_id = sample.internal_id
+         INNER JOIN gene ON ce.entrez_gene_id = gene.entrez_gene_id
+UNION ALL
+SELECT
+    concat(cs.cancer_study_identifier, '_', s.stable_id) as sample_unique_id,
+    event_info as variant,
+    'structural_variant' as variant_type,
+    gene2.hugo_gene_symbol as hugo_gene_symbol,
+    gene_panel.stable_id as gene_panel_stable_id,
+    cs.cancer_study_identifier as cancer_study_identifier,
+    gp.stable_id as genetic_profile_stable_id
+FROM
+    structural_variant sv
+        INNER JOIN genetic_profile gp ON sv.genetic_profile_id = gp.genetic_profile_id
+        INNER JOIN sample s ON sv.sample_id = s.internal_id
+        INNER JOIN cancer_study cs ON gp.cancer_study_id = cs.cancer_study_id
+        INNER JOIN gene gene2 ON sv.site2_entrez_gene_id = gene2.entrez_gene_id
+        INNER JOIN sample_profile on s.internal_id = sample_profile.sample_id
+        INNER JOIN gene_panel on sample_profile.panel_id = gene_panel.internal_id
+UNION ALL
+SELECT
+    concat(cs.cancer_study_identifier, '_', s.stable_id) as sample_unique_id,
+    event_info as variant,
+    'structural_variant' as variant_type,
+    gene1.hugo_gene_symbol as hugo_gene_symbol,
+    gene_panel.stable_id as gene_panel_stable_id,
+    cs.cancer_study_identifier as cancer_study_identifier,
+    gp.stable_id as genetic_profile_stable_id
+FROM
+    structural_variant sv
+        INNER JOIN genetic_profile gp ON sv.genetic_profile_id = gp.genetic_profile_id
+        INNER JOIN sample s ON sv.sample_id = s.internal_id
+        INNER JOIN cancer_study cs ON gp.cancer_study_id = cs.cancer_study_id
+        INNER JOIN gene gene1 ON sv.site1_entrez_gene_id = gene1.entrez_gene_id
+        INNER JOIN sample_profile on s.internal_id = sample_profile.sample_id
+        INNER JOIN gene_panel on sample_profile.panel_id = gene_panel.internal_id;