Update Total profile Count to filter on genetic profile

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

@@ -48,7 +48,7 @@ public interface StudyViewRepository {
 
     List<CaseListDataCount> getCaseListDataCountsPerStudy(StudyViewFilterContext studyViewFilterContext);
 
-    Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType);
+    Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType, List<MolecularProfile> molecularProfiles);
 
     List<ClinicalAttribute> getClinicalAttributes();
 
@@ -87,4 +87,6 @@ public interface StudyViewRepository {
     List<ClinicalDataCount> getGenericAssayDataBinCounts(StudyViewFilterContext studyViewFilterContext, List<GenericAssayDataBinFilter> genericAssayDataBinFilters);
 
     List<MolecularProfile> getGenericAssayProfiles();
+
+    List<MolecularProfile> getFilteredMolecularProfilesByAlterationType(StudyViewFilterContext studyViewFilterContext, String alterationType);
 }

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

@@ -53,7 +53,7 @@ public interface StudyViewMapper {
 
     List<ClinicalData> getPatientClinicalDataFromStudyViewFilter(StudyViewFilterHelper studyViewFilterHelper, List<String> attributeIds);
 
-    List<AlterationCountByGene> getTotalProfiledCounts(StudyViewFilterHelper studyViewFilterHelper, String alterationType);
+    List<AlterationCountByGene> getTotalProfiledCounts(StudyViewFilterHelper studyViewFilterHelper, String alterationType, List<MolecularProfile> molecularProfiles);
 
     int getFilteredSamplesCount(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);
 
@@ -85,4 +85,6 @@ public interface StudyViewMapper {
     List<ClinicalDataCount> getGenericAssayDataBinCounts(StudyViewFilterHelper studyViewFilterHelper, List<GenericAssayDataBinFilter> genericAssayDataBinFilters);
 
     List<MolecularProfile> getGenericAssayProfiles();
+
+    List<MolecularProfile> getFilteredMolecularProfilesByAlterationType(StudyViewFilterHelper studyViewFilterHelper, String alterationType); 
 }

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

@@ -40,15 +40,17 @@
 @Repository
 public class StudyViewMyBatisRepository implements StudyViewRepository {
 
+    private final StudyViewMapper studyViewMapper;
     private Map<DataSource, List<ClinicalAttribute>> clinicalAttributesMap = new EnumMap<>(DataSource.class);
     private Map<DataSource, List<MolecularProfile>> genericAssayProfilesMap = new EnumMap<>(DataSource.class);
 
     private static final List<String> FILTERED_CLINICAL_ATTR_VALUES = Collections.emptyList();
     private final StudyViewMapper mapper;
 
     @Autowired
-    public StudyViewMyBatisRepository(StudyViewMapper mapper) {
-        this.mapper = mapper;    
+    public StudyViewMyBatisRepository(StudyViewMapper mapper, StudyViewMapper studyViewMapper) {
+        this.mapper = mapper;
+        this.studyViewMapper = studyViewMapper;
     }
 
     @Override
@@ -126,6 +128,11 @@ public List<MolecularProfile> getGenericAssayProfiles() {
         return mapper.getGenericAssayProfiles();
     }
 
+    @Override
+    public List<MolecularProfile> getFilteredMolecularProfilesByAlterationType(StudyViewFilterContext studyViewFilterContext, String alterationType) {
+        return studyViewMapper.getFilteredMolecularProfilesByAlterationType(createStudyViewFilterHelper(studyViewFilterContext), alterationType);
+    }
+
     @Override
     public Map<String, ClinicalDataType> getClinicalAttributeDatatypeMap() {
         if (clinicalAttributesMap.isEmpty()) {
@@ -166,8 +173,8 @@ public List<ClinicalData> getPatientClinicalData(StudyViewFilterContext studyVie
     }
 
     @Override
-    public Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType) {
-        return mapper.getTotalProfiledCounts(createStudyViewFilterHelper(studyViewFilterContext), alterationType)
+    public Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType, List<MolecularProfile> molecularProfiles) {
+        return mapper.getTotalProfiledCounts(createStudyViewFilterHelper(studyViewFilterContext), alterationType, molecularProfiles)
             .stream()
             .collect(Collectors.groupingBy(AlterationCountByGene::getHugoGeneSymbol,
                 Collectors.mapping(AlterationCountByGene::getNumberOfProfiledCases, Collectors.summingInt(Integer::intValue))));

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

@@ -285,8 +285,9 @@ public List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilterCont
     private < T extends AlterationCountByGene> List<T> populateAlterationCounts(@NonNull List<T> alterationCounts,
                                                                                 @NonNull StudyViewFilterContext studyViewFilterContext,
                                                                                 @NonNull AlterationType alterationType) {
+        final var firstMolecularProfileForEachStudy = getFirstMolecularProfileGroupedByStudy(studyViewFilterContext, alterationType);
         final int totalProfiledCount = studyViewRepository.getTotalProfiledCountsByAlterationType(studyViewFilterContext, alterationType.toString());
-        var profiledCountsMap = studyViewRepository.getTotalProfiledCounts(studyViewFilterContext, alterationType.toString());
+        var profiledCountsMap = studyViewRepository.getTotalProfiledCounts(studyViewFilterContext, alterationType.toString(), firstMolecularProfileForEachStudy);
         final var matchingGenePanelIdsMap = studyViewRepository.getMatchingGenePanelIds(studyViewFilterContext, alterationType.toString());
         final int sampleProfileCountWithoutGenePanelData = studyViewRepository.getSampleProfileCountWithoutPanelData(studyViewFilterContext, alterationType.toString());
 
@@ -340,6 +341,19 @@ private List<CopyNumberCountByGene> populateAlterationCountsWithCNASigQValue(Lis
        return alterationCountByGenes; 
     }
 
+   private List<MolecularProfile> getFirstMolecularProfileGroupedByStudy(StudyViewFilterContext studyViewFilterContext, AlterationType alterationType) {
+        final var molecularProfiles = studyViewRepository.getFilteredMolecularProfilesByAlterationType(studyViewFilterContext, alterationType.toString());
+
+       return molecularProfiles.stream()
+           .collect(Collectors.toMap(
+               MolecularProfile::getCancerStudyIdentifier,
+               Function.identity(),
+               (existing, replacement) -> existing  // Keep the first occurrence
+           ))
+           .values()
+           .stream()
+           .toList();
+   } 
 
     /**
      * Combines alteration counts by Hugo gene symbols. If multiple entries exist for the same 

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

@@ -11,17 +11,19 @@ CREATE TABLE sample_to_gene_panel_derived
     sample_unique_id String,
     alteration_type LowCardinality(String),
     gene_panel_id LowCardinality(String),
-    cancer_study_identifier LowCardinality(String)
+    cancer_study_identifier LowCardinality(String),
+    genetic_profile_id LowCardinality(String)
 ) ENGINE = MergeTree()
-ORDER BY (gene_panel_id, alteration_type, sample_unique_id);
+ORDER BY (gene_panel_id, alteration_type, genetic_profile_id, sample_unique_id);
 
 INSERT INTO sample_to_gene_panel_derived
 SELECT
     concat(cs.cancer_study_identifier, '_', sample.stable_id) AS sample_unique_id,
     genetic_alteration_type AS alteration_type,
     -- If a mutation is found in a gene that is not in a gene panel we assume Whole Exome Sequencing WES
     ifnull(gene_panel.stable_id, 'WES') AS gene_panel_id,
-    cs.cancer_study_identifier AS cancer_study_identifier
+    cs.cancer_study_identifier AS cancer_study_identifier,
+    gp.stable_id AS genetic_profile_id
 FROM sample_profile sp
          INNER JOIN genetic_profile gp ON sample_profile.genetic_profile_id = gp.genetic_profile_id
          LEFT JOIN gene_panel ON sp.panel_id = gene_panel.internal_id

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

@@ -471,12 +471,18 @@
     <select id="getTotalProfiledCounts" resultType="org.cbioportal.model.AlterationCountByGene">
         SELECT
         gene as hugoGeneSymbol,
-        COUNT(DISTINCT sample_unique_id) as numberOfProfiledCases
+        COUNT(*) as numberOfProfiledCases
         FROM sample_to_gene_panel_derived stgp
             INNER JOIN gene_panel_to_gene_derived gptg on stgp.gene_panel_id = gptg.gene_panel_id
         <where>
             stgp.alteration_type = #{alterationType}
             AND stgp.gene_panel_id != 'WES'
+            <if test="molecularProfiles != null and !molecularProfiles.isEmpty()">
+              AND stgp.genetic_profile_id IN
+                <foreach item="molecularProfile" collection="molecularProfiles" open="(" separator="," close=")">
+                   #{molecularProfile.stableId} 
+                </foreach>
+            </if>
             AND
             <include refid="applyStudyViewFilter">
                 <property name="filter_type" value="'SAMPLE_ID_ONLY'"/>
@@ -781,6 +787,31 @@
         INNER JOIN reference_genome ON cancer_study.reference_genome_id = reference_genome.reference_genome_id
         WHERE genetic_profile.genetic_alteration_type = 'GENERIC_ASSAY'
     </select>
+
+    <select id="getFilteredMolecularProfilesByAlterationType" resultType="org.cbioportal.model.MolecularProfile">
+        WITH unique_study_ids AS (
+            SELECT
+                DISTINCT cancer_study_identifier
+            FROM sample_derived
+            <where>
+                <include refid="applyStudyViewFilter">
+                    <property name="filter_type" value="'SAMPLE_ID_ONLY'"/>
+                </include>
+            </where>
+        )
+        SELECT
+            gp.stable_id AS stableId,
+            gp.datatype AS datatype,
+            cancer_study.cancer_study_identifier AS cancerStudyIdentifier
+        FROM genetic_profile gp
+        INNER JOIN cancer_study ON gp.cancer_study_id = cancer_study.cancer_study_id
+        <where>
+            gp.genetic_alteration_type = #{alterationType}
+            <!-- Currently we only look at CNA dataType Discrete -->
+            AND gp.datatype != 'CONTINUOUS'
+            AND cancer_study.cancer_study_identifier IN (unique_study_ids);
+        </where>
+    </select>
 
     <!--
         Abstraction for StudyViewFilter. Currently, we have many ch tables that have both

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

@@ -229,7 +229,7 @@ public void getTotalProfiledCountsByGene() {
         studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB));
 
         var totalProfiledCountsMap = studyViewMapper.getTotalProfiledCounts(StudyViewFilterHelper.build(studyViewFilter, null, null),
-            "MUTATION_EXTENDED");
+            "MUTATION_EXTENDED", List.of());
 
         assertEquals(3, totalProfiledCountsMap.size());