Fix on mutation counts

src/main/java/org/cbioportal/persistence/StudyViewRepository.java

@@ -63,8 +63,6 @@ public interface StudyViewRepository {
     int getTotalSampleTreatmentCount(StudyViewFilterContext studyViewFilterContext);
 
     List<GenomicDataCountItem> getCNACounts(StudyViewFilterContext studyViewFilterContext, List<GenomicDataFilter> genomicDataFilters);
-
-    Map<String, Integer> getMutationCounts(StudyViewFilterContext studyViewFilterContext, GenomicDataFilter genomicDataFilter);
 
     List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilterContext studyViewFilterContext, List<GenomicDataFilter> genomicDataFilters);
 }

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

@@ -19,7 +19,6 @@
 import org.cbioportal.web.parameter.GenomicDataFilter;
 
 import java.util.List;
-import java.util.Map;
 
 
 public interface StudyViewMapper {
@@ -62,7 +61,5 @@ public interface StudyViewMapper {
 
     List<GenomicDataCountItem> getCNACounts(StudyViewFilterHelper studyViewFilterHelper, List<GenomicDataFilter> genomicDataFilters);
 
-    Map<String, Integer> getMutationCounts(StudyViewFilterHelper studyViewFilterHelper, GenomicDataFilter genomicDataFilter);
-
     List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilterHelper studyViewFilterHelper, List<GenomicDataFilter> genomicDataFilters);
 }

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

@@ -218,11 +218,6 @@ public List<GenomicDataCountItem> getCNACounts(StudyViewFilterContext studyViewF
 
         return mapper.getCNACounts(createStudyViewFilterHelper(studyViewFilterContext), genomicDataFilters);
     }
-
-    public Map<String, Integer> getMutationCounts(StudyViewFilterContext studyViewFilterContext, GenomicDataFilter genomicDataFilter) {
-
-        return mapper.getMutationCounts(createStudyViewFilterHelper(studyViewFilterContext), genomicDataFilter);
-    }
 
     public List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilterContext studyViewFilterContext, List<GenomicDataFilter> genomicDataFilters) {
 

src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java

@@ -133,15 +133,19 @@ public List<GenomicDataCountItem> getCNACountsByGeneSpecific(StudyViewFilter stu
     @Override
     public List<GenomicDataCountItem> getMutationCountsByGeneSpecific(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters) {
         List<GenomicDataCountItem> genomicDataCountItemList = new ArrayList<>();
+        int totalCount = studyViewRepository.getFilteredSamplesCount(createContext(studyViewFilter));
+        List<AlterationCountByGene> alterationCountByGenes = alterationCountService.getMutatedGenes(createContext(studyViewFilter));
         for (GenomicDataFilter genomicDataFilter : genomicDataFilters) {
-            Map<String, Integer> counts = studyViewRepository.getMutationCounts(createContext(studyViewFilter), genomicDataFilter);
+            AlterationCountByGene filteredAlterationCount = alterationCountByGenes.stream()
+                .filter(g -> g.getHugoGeneSymbol().equals(genomicDataFilter.getHugoGeneSymbol()))
+                .findFirst()
+                .orElse(new AlterationCountByGene());
+            int mutatedCount = filteredAlterationCount.getNumberOfAlteredCases();
+            int profiledCount = filteredAlterationCount.getNumberOfProfiledCases();
             List<GenomicDataCount> genomicDataCountList = new ArrayList<>();
-            if (counts.getOrDefault("mutatedCount", 0) > 0)
-                genomicDataCountList.add(new GenomicDataCount("Mutated", "MUTATED", counts.get("mutatedCount"), counts.get("mutatedCount")));
-            if (counts.getOrDefault("notMutatedCount", 0) > 0)
-                genomicDataCountList.add(new GenomicDataCount("Not Mutated", "NOT_MUTATED", counts.get("notMutatedCount"), counts.get("notMutatedCount")));
-            if (counts.getOrDefault("notProfiledCount", 0) > 0)
-                genomicDataCountList.add(new GenomicDataCount("Not Profiled", "NOT_PROFILED", counts.get("notProfiledCount"), counts.get("notProfiledCount")));
+            genomicDataCountList.add(new GenomicDataCount("Mutated", "MUTATED", mutatedCount, mutatedCount));
+            genomicDataCountList.add(new GenomicDataCount("Not Mutated", "NOT_MUTATED", profiledCount - mutatedCount, profiledCount - mutatedCount));
+            genomicDataCountList.add(new GenomicDataCount("Not Profiled", "NOT_PROFILED", totalCount - profiledCount, totalCount - profiledCount));
             genomicDataCountItemList.add(new GenomicDataCountItem(genomicDataFilter.getHugoGeneSymbol(), "mutations", genomicDataCountList));
         }
         return genomicDataCountItemList;

src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml

@@ -270,28 +270,6 @@
         FROM cna_sum
     </select>
 
-    <!-- for /mutation-data-counts/fetch (returns GenomicDataCountItem objects) mutation counts pie chart part -->
-    <select id="getMutationCounts">
-        WITH profiled_count as (
-            SELECT count(distinct sgp.sample_unique_id)
-            FROM sample_to_gene_panel_derived sgp
-                JOIN gene_panel_to_gene_derived gpg ON sgp.gene_panel_id = gpg.gene_panel_id
-            WHERE sample_unique_id IN (<include refid="sampleUniqueIdsFromStudyViewFilter"/>)
-                AND gpg.gene = #{genomicDataFilter.hugoGeneSymbol}
-        ),
-        mutated_count as (
-            SELECT count(distinct sample_unique_id)
-            FROM genomic_event_derived
-            WHERE sample_unique_id IN (<include refid="sampleUniqueIdsFromStudyViewFilter"/>)
-                AND hugo_gene_symbol = #{genomicDataFilter.hugoGeneSymbol}
-                AND variant_type = 'mutation'
-        )
-        SELECT
-            cast((SELECT * FROM mutated_count) as INTEGER) as mutatedCount,
-            cast(((SELECT * FROM profiled_count) - (SELECT * FROM mutated_count)) as INTEGER) as notMutatedCount,
-            cast(((SELECT * FROM (<include refid="getTotalSampleCount"/>)) - (SELECT * FROM profiled_count)) as INTEGER) as notProfiledCount
-    </select>
-
     <!-- for /mutation-data-counts/fetch - (returns GenomicDataCountItem objects) mutation type counts table part-->
     <select id="getMutationCountsByType" resultMap="GenomicDataCountItemResultMap">
         SELECT

src/test/java/org/cbioportal/persistence/mybatisclickhouse/GenomicDataFilterTest.java

@@ -16,9 +16,7 @@
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringRunner;
 
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
 
 import static org.assertj.core.api.Assertions.assertThat;
 
@@ -74,23 +72,6 @@ public void getCNACounts() {
             .isEqualTo(expectedCountsGISTIC);
     }
 
-    @Test
-    public void getMutationCounts() {
-        StudyViewFilter studyViewFilter = new StudyViewFilter();
-        studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB));
-
-        GenomicDataFilter genomicDataFilterMutation = new GenomicDataFilter("AKT1", "cna");
-        Map<String, Integer> actualMutationCounts = studyViewMapper.getMutationCounts(StudyViewFilterHelper.build(studyViewFilter, null, null), genomicDataFilterMutation);
-        Map<String, Integer> expectedMutationCounts = new HashMap<>();
-        expectedMutationCounts.put("mutatedCount", 2);
-        expectedMutationCounts.put("notMutatedCount", 2);
-        expectedMutationCounts.put("notProfiledCount", 11);
-        assertThat(actualMutationCounts)
-            .usingRecursiveComparison()
-            .ignoringCollectionOrder()
-            .isEqualTo(expectedMutationCounts);
-    }
-
     @Test
     public void getMutationCountsByType() {
         StudyViewFilter studyViewFilter = new StudyViewFilter();