Add mutation domain classes and use cases

src/main/java/org/cbioportal/application/rest/mapper/AlleleSpecificCopyNumberMapper.java

@@ -0,0 +1,15 @@
+package org.cbioportal.application.rest.mapper;
+import org.cbioportal.application.rest.response.AlleleSpecificCopyNumberDTO;
+import org.cbioportal.legacy.model.AlleleSpecificCopyNumber;
+import org.mapstruct.Mapper;
+import org.mapstruct.factory.Mappers;
+
+@Mapper
+public interface AlleleSpecificCopyNumberMapper {
+    AlleleSpecificCopyNumberMapper INSTANCE =
+        Mappers.getMapper(AlleleSpecificCopyNumberMapper.class);
+
+    AlleleSpecificCopyNumberDTO toAlleleSpecificCopyNumberDTO(
+        AlleleSpecificCopyNumber alleleSpecificCopyNumber
+    );
+}

src/main/java/org/cbioportal/application/rest/mapper/GeneMapper.java

@@ -0,0 +1,13 @@
+package org.cbioportal.application.rest.mapper;
+
+import org.cbioportal.application.rest.response.GeneDTO;
+import org.cbioportal.legacy.model.Gene;
+import org.mapstruct.Mapper;
+import org.mapstruct.factory.Mappers;
+
+@Mapper
+public interface GeneMapper {
+    GeneMapper INSTANCE = Mappers.getMapper(GeneMapper.class);
+
+    GeneDTO toGeneDTO(Gene gene);
+}

src/main/java/org/cbioportal/application/rest/mapper/MutationMapper.java

@@ -0,0 +1,31 @@
+package org.cbioportal.application.rest.mapper;
+
+import org.cbioportal.application.rest.response.MutationDTO;
+
+import org.cbioportal.legacy.model.Mutation;
+import org.cbioportal.legacy.utils.Encoder;
+import org.mapstruct.Mapper;
+import org.mapstruct.Mapping;
+import org.mapstruct.factory.Mappers;
+
+import java.util.List;
+
+@Mapper(
+    imports = Encoder.class,
+    uses = { GeneMapper.class, AlleleSpecificCopyNumberMapper.class }
+)
+public interface MutationMapper {
+    MutationMapper INSTANCE = Mappers.getMapper(MutationMapper.class);
+
+    @Mapping(
+        target = "uniqueSampleKey",
+        expression =
+            "java( Encoder.calculateBase64(mutation.getSampleId()," + "mutation.getStudyId()) )")
+    @Mapping(
+        target = "uniquePatientKey",
+        expression =
+            "java( Encoder.calculateBase64(mutation.getPatientId(), " + "mutation.getStudyId()) )")
+    MutationDTO toMutationDTOO(Mutation mutation);
+
+    List<MutationDTO> toDTOs(List<Mutation> mutationList);
+}

src/main/java/org/cbioportal/application/rest/response/AlleleSpecificCopyNumberDTO.java

@@ -0,0 +1,13 @@
+package org.cbioportal.application.rest.response;
+
+public record AlleleSpecificCopyNumberDTO(
+    Integer ascnIntegerCopyNumber,
+    String ascnMethod,
+    Float ccfExpectedCopiesUpper,
+    Float ccfExpectedCopies,
+    String clonal,
+    Integer minorCopyNumber,
+    Integer expectedAltCopies,
+    Integer totalCopyNumber
+) {
+}

src/main/java/org/cbioportal/application/rest/response/GeneDTO.java

@@ -0,0 +1,8 @@
+package org.cbioportal.application.rest.response;
+
+public record GeneDTO(
+    Integer entrezGeneId,
+    String hugoGeneSymbol,
+    String type
+        ) {
+}

src/main/java/org/cbioportal/application/rest/response/MutationDTO.java

@@ -0,0 +1,40 @@
+package org.cbioportal.application.rest.response;
+
+
+public record MutationDTO(
+    String uniqueSampleKey,
+    String uniquePatientKey,
+    String molecularProfileId,
+    String sampleId,
+    String patientId,
+    Integer entrezGeneId,
+    GeneDTO gene,
+    String studyId,
+    String driverFilter,
+    String driverFilterAnnotation,
+    String driverTiersFilter,
+    String driverTiersFilterAnnotation,
+    String center,
+    String mutationStatus,
+    String validationStatus,
+    Integer tumorAltCount,
+    Integer tumorRefCount,
+    Integer normalAltCount,
+    Integer normalRefCount,
+    String aminoAcidChange,
+    String chr,
+    Long startPosition,
+    Long endPosition,
+    String referenceAllele,
+    String variantAllele,
+    String proteinChange,
+    String mutationType,
+    String ncbiBuild,
+    String variantType,
+    String refseqMrnaId,
+    Integer proteinPosStart,
+    Integer proteinPosEnd,
+    String keyword,
+    AlleleSpecificCopyNumberDTO alleleSpecificCopyNumber
+) {
+}

src/main/java/org/cbioportal/application/rest/vcolumnstore/ColumnStoreMutationController.java

@@ -0,0 +1,124 @@
+package org.cbioportal.application.rest.vcolumnstore;
+
+import io.swagger.v3.oas.annotations.Hidden;
+import io.swagger.v3.oas.annotations.Parameter;
+import jakarta.validation.Valid;
+import jakarta.validation.constraints.Max;
+import jakarta.validation.constraints.Min;
+import org.cbioportal.application.rest.mapper.MutationMapper;
+import org.cbioportal.application.rest.response.MutationDTO;
+import org.cbioportal.domain.mutation.usecase.GetMutationUseCases;
+import org.cbioportal.legacy.model.Mutation;
+import org.cbioportal.legacy.model.meta.MutationMeta;
+import org.cbioportal.legacy.web.parameter.*;
+import org.cbioportal.legacy.web.parameter.sort.MutationSortBy;
+import org.cbioportal.shared.MutationSearchCriteria;
+import org.cbioportal.shared.enums.ProjectionType;
+import org.springframework.context.annotation.Profile;
+import org.springframework.http.HttpHeaders;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
+import org.springframework.security.access.prepost.PreAuthorize;
+import org.springframework.web.bind.annotation.*;
+
+import java.util.Collection;
+import java.util.List;
+
+
+/**
+ * REST controller for managing and retrieving Mutation data from a column-store data
+ * source.
+ *
+ * <p>This controller provides an endpoint to fetch Mutation data with support for
+ * filtering, sorting, and controlling the level of detail in the response. It is designed to work
+ * with a column-store database, which is optimized for querying large datasets efficiently.
+ *
+ */
+
+
+@RestController
+@RequestMapping("/api/column-store")
+@Profile("clickhouse")
+public class ColumnStoreMutationController {
+    private final GetMutationUseCases getMutationUseCases;
+
+    /**
+     * Constructs a new {@link ColumnStoreMutationController} with the specified use case.
+     *
+     * @param getMutationUseCases the use case responsible for retrieving Mutation metadata or Mutation
+     *   
+     */
+    public ColumnStoreMutationController(GetMutationUseCases getMutationUseCases) {
+        this.getMutationUseCases = getMutationUseCases;
+    }
+
+
+    /**
+     * Fetch Mutation by exactly one sampleUniqueIdentifier or molecularProfileId must or entrezGeneIds
+     * @return ResponseEntity containing list of Mutation data DTOs, or empty body with count header
+     *  for META projection
+     */
+    @Hidden
+    @PreAuthorize(
+        "hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)")
+    @PostMapping(
+        value = "/mutations/fetch",
+        consumes = MediaType.APPLICATION_JSON_VALUE,
+        produces = MediaType.APPLICATION_JSON_VALUE)
+    public ResponseEntity<List<MutationDTO>> fetchMutationsInMultipleMolecularProfiles(
+        @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface
+        @RequestAttribute(required = false, value = "involvedCancerStudies")
+        Collection<String> involvedCancerStudies, 
+        @Parameter(
+            hidden =
+                true) // prevent reference to this attribute in the swagger-ui interface. this
+        // attribute is needed for now but was needed previously for @PreAuthorize .
+        @Valid
+        @RequestBody(required = false)
+        MutationMultipleStudyFilter interceptedMutationMultipleStudyFilter, // This is being intercepted will leave this 
+        @Parameter(
+            required = true,
+            description =
+                "List of Molecular Profile IDs or List of Molecular Profile ID / Sample ID pairs,"
+                    + " and List of Entrez Gene IDs")
+        @Valid
+        @RequestBody(required = false)
+        MutationMultipleStudyFilter mutationMultipleStudyFilter,
+        @Parameter(description = "Level of detail of the response")
+        @RequestParam(defaultValue = "SUMMARY")
+        ProjectionType projection,
+        @Parameter(description = "Page size of the result list")
+        @Max(PagingConstants.MAX_PAGE_SIZE)
+        @Min(PagingConstants.MIN_PAGE_SIZE)
+        @RequestParam(defaultValue = PagingConstants.DEFAULT_PAGE_SIZE)
+        Integer pageSize,
+        @Parameter(description = "Page number of the result list")
+        @Min(PagingConstants.MIN_PAGE_NUMBER)
+        @RequestParam(defaultValue = PagingConstants.DEFAULT_PAGE_NUMBER)
+        Integer pageNumber,
+        @Parameter(description = "Name of the property that the result list is sorted by")
+        @RequestParam(required = false)
+        MutationSortBy sortBy,
+        @Parameter(description = "Direction of the sort") @RequestParam(defaultValue = "ASC")
+        Direction direction) {
+
+        if (projection == ProjectionType.META) {
+            HttpHeaders responseHeaders = new HttpHeaders();
+            MutationMeta mutationMeta=getMutationUseCases.fetchMetaMutationsUseCase().execute(interceptedMutationMultipleStudyFilter);
+            responseHeaders.add(HeaderKeyConstants.TOTAL_COUNT, mutationMeta.getTotalCount().toString());
+            responseHeaders.add(
+                HeaderKeyConstants.SAMPLE_COUNT, mutationMeta.getSampleCount().toString());
+            return new ResponseEntity<>(responseHeaders, HttpStatus.OK);
+        }
+        MutationSearchCriteria mutationSearchCriteria = new MutationSearchCriteria(projection,pageSize,
+            pageNumber,
+            sortBy == null ? null : sortBy.getOriginalValue(),
+            direction);
+        List<MutationDTO> mutations= MutationMapper.INSTANCE.toDTOs(getMutationUseCases.fetchAllMutationsInProfileUseCase()
+            .execute(
+            interceptedMutationMultipleStudyFilter,
+            mutationSearchCriteria));
+        return ResponseEntity.ok(mutations);
+    }
+}

src/main/java/org/cbioportal/domain/mutation/AlleleSpecificCopyNumber.java

@@ -0,0 +1,13 @@
+package org.cbioportal.domain.mutation;
+
+public record AlleleSpecificCopyNumber(
+    Integer ascnIntegerCopyNumber,
+    String ascnMethod,
+    Float ccfExpectedCopiesUpper,
+    Float ccfExpectedCopies,
+    String clonal,
+    Integer minorCopyNumber,
+    Integer expectedAltCopies,
+    Integer totalCopyNumber
+) {
+}

src/main/java/org/cbioportal/domain/mutation/Gene.java

@@ -0,0 +1,8 @@
+package org.cbioportal.domain.mutation;
+
+public record Gene(
+    Integer entrezGeneId,
+    String hugoGeneSymbol,
+    String type
+        ) {
+}

src/main/java/org/cbioportal/domain/mutation/Mutation.java

@@ -0,0 +1,125 @@
+package org.cbioportal.domain.mutation;
+import java.io.Serializable;
+
+public record Mutation(
+    String uniqueSampleKey,
+    String uniquePatientKey,
+    String molecularProfileId,
+    String sampleId,
+    String patientId,
+    Integer entrezGeneId,
+    Gene gene,
+    String studyId,
+    String driverFilter,
+    String driverFilterAnnotation,
+    String driverTiersFilter,
+    String driverTiersFilterAnnotation,
+    String center,
+    String mutationStatus,
+    String validationStatus,
+    Integer tumorAltCount,
+    Integer tumorRefCount,
+    Integer normalAltCount,
+    Integer normalRefCount,
+    String aminoAcidChange,
+    String chr,
+    Long startPosition,
+    Long endPosition,
+    String referenceAllele,
+    String tumorSeqAllele,
+    String proteinChange,
+    String mutationType,
+    String ncbiBuild,
+    String variantType,
+    String refseqMrnaId,
+    Integer proteinPosStart,
+    Integer proteinPosEnd,
+    String keyword,
+    AlleleSpecificCopyNumber alleleSpecificCopyNumber
+) implements Serializable {
+
+    // Constructor for ID projection
+    public Mutation(String uniqueSampleKey, String uniquePatientKey, String molecularProfileId,
+                    String sampleId, String patientId, Integer entrezGeneId, String studyId) {
+        this(
+            uniqueSampleKey,
+            uniquePatientKey,
+            molecularProfileId,
+            sampleId,
+            patientId,
+            entrezGeneId,
+            null,  // Gene
+            studyId,
+            null,  // driverFilter
+            null,  // driverFilterAnnotation
+            null,  // driverTiersFilter
+            null,  // driverTiersFilterAnnotation
+            null,  // center
+            null,  // mutationStatus
+            null,  // validationStatus
+            null,  // tumorAltCount
+            null,  // tumorRefCount
+            null,  // normalAltCount
+            null,  // normalRefCount
+            null,  // aminoAcidChange
+            null,  // chr
+            null,  // startPosition
+            null,  // endPosition
+            null,  // referenceAllele
+            null,  // tumorSeqAllele
+            null,  // proteinChange
+            null,  // mutationType
+            null,  // ncbiBuild
+            null,  // variantType
+            null,  // refseqMrnaId
+            null,  // proteinPosStart
+            null,  // proteinPosEnd
+            null,  // keyword
+            null   // alleleSpecificCopyNumber
+        );
+    }
+
+
+    //This constructor is meant for Detailed projection something is wrong here 
+//    public Mutation(
+//        String uniqueSampleKey,
+//        String uniquePatientKey,
+//        String molecularProfileId,
+//        String sampleId,
+//        String patientId,
+//        Integer entrezGeneId,
+//        Gene gene,
+//        String studyId,
+//        String driverFilter,
+//        String driverFilterAnnotation,
+//        String driverTiersFilter,
+//        String driverTiersFilterAnnotation,
+//        String center,
+//        String mutationStatus,
+//        String validationStatus,
+//        Integer tumorAltCount,
+//        Integer tumorRefCount,
+//        Integer normalAltCount,
+//        Integer normalRefCount,
+//        String aminoAcidChange,
+//        String chr,
+//        Long startPosition,
+//        Long endPosition,
+//        String referenceAllele,
+//        String tumorSeqAllele,
+//        String proteinChange,
+//        String mutationType,
+//        String ncbiBuild,
+//        String variantType,
+//        String refseqMrnaId,
+//        Integer proteinPosStart,
+//        Integer proteinPosEnd,
+//        String keyword,
+//        AlleleSpecificCopyNumber alleleSpecificCopyNumber
+//    ) {
+//        this(
+//        );
+//    }
+
+
+}