Extract UseCases

src/main/java/org/cbioportal/domain/alteration/usecase/AbstractAlterationCountByGeneUseCase.java

@@ -0,0 +1,108 @@
+package org.cbioportal.domain.alteration.usecase;
+
+import org.cbioportal.domain.alteration.repository.AlterationRepository;
+import org.cbioportal.domain.generic_assay.usecase.GetFilteredMolecularProfilesByAlterationType;
+import org.cbioportal.domain.studyview.StudyViewFilterContext;
+import org.cbioportal.legacy.model.AlterationCountByGene;
+import org.cbioportal.legacy.model.AlterationType;
+import org.cbioportal.legacy.model.MolecularProfile;
+import org.springframework.lang.NonNull;
+
+import java.util.Collections;
+import java.util.List;
+import java.util.Set;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+
+abstract class AbstractAlterationCountByGeneUseCase {
+
+    private static final String WHOLE_EXOME_SEQUENCING = "WES";
+
+    private final AlterationRepository alterationRepository;
+    private final GetFilteredMolecularProfilesByAlterationType getFilteredMolecularProfilesByAlterationType;
+
+    AbstractAlterationCountByGeneUseCase(AlterationRepository alterationRepository, GetFilteredMolecularProfilesByAlterationType getFilteredMolecularProfilesByAlterationType){
+        this.alterationRepository = alterationRepository;
+        this.getFilteredMolecularProfilesByAlterationType = getFilteredMolecularProfilesByAlterationType;
+    }
+
+    /**
+     * Populates alteration counts with profile data, including the total profiled count and matching gene panel IDs.
+     *
+     * @param alterationCounts       List of alteration counts to enrich.
+     * @param studyViewFilterContext Context containing filter criteria.
+     * @param alterationType         Type of alteration (e.g., mutation, CNA, structural variant).
+     * @param <T>                    The type of alteration count.
+     * @return List of enriched alteration counts.
+     */
+    <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 = alterationRepository.getTotalProfiledCountsByAlterationType(studyViewFilterContext,
+                alterationType.toString());
+        var profiledCountsMap = alterationRepository.getTotalProfiledCounts(studyViewFilterContext, alterationType.toString(),
+                firstMolecularProfileForEachStudy);
+        final var matchingGenePanelIdsMap = alterationRepository.getMatchingGenePanelIds(studyViewFilterContext,
+                alterationType.toString());
+        final int sampleProfileCountWithoutGenePanelData =
+                alterationRepository.getSampleProfileCountWithoutPanelData(studyViewFilterContext, alterationType.toString());
+
+        alterationCounts.parallelStream()
+                .forEach(alterationCountByGene -> {
+                    String hugoGeneSymbol = alterationCountByGene.getHugoGeneSymbol();
+                    Set<String> matchingGenePanelIds = matchingGenePanelIdsMap.get(hugoGeneSymbol) != null ?
+                            matchingGenePanelIdsMap.get(hugoGeneSymbol) : Collections.emptySet();
+
+                    int alterationTotalProfiledCount = computeTotalProfiledCount(hasGenePanelData(matchingGenePanelIds),
+                            profiledCountsMap.getOrDefault(hugoGeneSymbol, 0),
+                            sampleProfileCountWithoutGenePanelData, totalProfiledCount);
+
+                    alterationCountByGene.setNumberOfProfiledCases(alterationTotalProfiledCount);
+
+                    alterationCountByGene.setMatchingGenePanelIds(matchingGenePanelIds);
+
+                });
+        return alterationCounts;
+    }
+
+
+     private boolean hasGenePanelData(@NonNull Set<String> matchingGenePanelIds) {
+        return matchingGenePanelIds.contains(WHOLE_EXOME_SEQUENCING)
+                && matchingGenePanelIds.size() > 1 || !matchingGenePanelIds.contains(WHOLE_EXOME_SEQUENCING) && !matchingGenePanelIds.isEmpty();
+    }
+
+    private int computeTotalProfiledCount(boolean hasGenePanelData, int alterationsProfiledCount,
+                                           int sampleProfileCountWithoutGenePanelData, int totalProfiledCount) {
+        int profiledCount = hasGenePanelData ? alterationsProfiledCount + sampleProfileCountWithoutGenePanelData
+                : sampleProfileCountWithoutGenePanelData;
+        return profiledCount == 0 ? totalProfiledCount : profiledCount;
+    }
+
+    /**
+     * Retrieves the first molecular profile for each study based on the alteration type.
+     *
+     * @param studyViewFilterContext Context containing filter criteria.
+     * @param alterationType Type of alteration (e.g., mutation, CNA, structural variant).
+     * @return List of MolecularProfile objects representing the first profile for each study.
+     */
+    private List<MolecularProfile> getFirstMolecularProfileGroupedByStudy(StudyViewFilterContext studyViewFilterContext, AlterationType alterationType) {
+        final var molecularProfiles =
+                getFilteredMolecularProfilesByAlterationType.execute(studyViewFilterContext, alterationType.toString());
+        return getFirstMolecularProfileGroupedByStudy(molecularProfiles);
+    }
+
+    private List<MolecularProfile> getFirstMolecularProfileGroupedByStudy(List<MolecularProfile> molecularProfiles) {
+        return molecularProfiles.stream()
+                .collect(Collectors.toMap(
+                        MolecularProfile::getCancerStudyIdentifier,
+                        Function.identity(),
+                        (existing, replacement) -> existing  // Keep the first occurrence
+                ))
+                .values()
+                .stream()
+                .toList();
+    }
+
+}

src/main/java/org/cbioportal/domain/alteration/usecase/AlterationCountByGeneUseCases.java

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+package org.cbioportal.domain.alteration.usecase;
+
+import org.springframework.context.annotation.Profile;
+import org.springframework.stereotype.Service;
+
+@Service
+@Profile("clickhouse")
+public record AlterationCountByGeneUseCases(
+        GetAlterationCountByGeneUseCase getAlterationCountByGeneUseCase,
+        GetCnaAlterationCountByGeneUseCase getCnaAlterationCountByGeneUseCase) {
+
+
+}