Add mutation domain classes and use cases

src/e2e/java/org/cbioportal/ColumnStoreMutationControllerE2ETest.java

@@ -0,0 +1,132 @@
+package org.cbioportal;
+
+
+import org.cbioportal.application.rest.response.MutationDTO;
+import org.cbioportal.shared.enums.ProjectionType;
+import org.springframework.http.HttpHeaders;
+import org.springframework.http.MediaType;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.web.client.TestRestTemplate;
+import org.springframework.boot.test.web.server.LocalServerPort;
+import org.springframework.http.HttpEntity;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.http.HttpMethod;
+import org.springframework.test.context.junit.jupiter.SpringExtension;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+@ExtendWith(SpringExtension.class)
+public class ColumnStoreMutationControllerE2ETest extends AbstractE2ETest{
+
+    @Autowired
+    private TestRestTemplate restTemplate;
+
+    @LocalServerPort
+    private int port;
+
+    private static final com.fasterxml.jackson.databind.ObjectMapper OBJECT_MAPPER = new com.fasterxml.jackson.databind.ObjectMapper();
+
+
+    private MutationDTO[] callFetchMutationEndPoint(String testDataJson, ProjectionType projectionType)throws Exception{
+        HttpHeaders headers = new HttpHeaders();
+        headers.setContentType(MediaType.APPLICATION_JSON);
+        HttpEntity<String> requestEntity = new HttpEntity<>(testDataJson, headers);
+
+        ResponseEntity<String> response = restTemplate.exchange(
+            "http://localhost:" + port + "/api/column-store/mutations/fetch?projection=" 
+                    + projectionType.name(),
+            HttpMethod.POST,
+            requestEntity,
+            String.class
+        );
+
+        assertEquals(HttpStatus.OK, response.getStatusCode());
+        assertNotNull(response.getBody());
+
+        return OBJECT_MAPPER.readValue(response.getBody(), MutationDTO[].class);
+
+    }
+
+    private String loadTestData(String filename) throws Exception {
+        return new String(java.nio.file.Files.readAllBytes(
+            java.nio.file.Paths.get("src/e2e/java/org/cbioportal/ColumnStoreMutationControllerE2ETest/" + filename)));
+    }
+
+    @Test
+    void testFetchMutationEndPointWithDataJson_IdProjection() throws Exception {
+        // The json has two molecularProfileId and a sampleId and entrezGeneIds to restrict search  
+        // Two profiles meet this criteria 
+
+        String testDataJson = loadTestData("mutation_filter.json");
+        MutationDTO[] mutationResultID = callFetchMutationEndPoint(testDataJson, ProjectionType.ID);
+
+        assertNotNull(mutationResultID, "Response should have mutation DTO");
+        assertEquals(2, mutationResultID.length, "Two mutations meet the search criteria of the json file");
+
+
+        //Compare the fields that should be equal
+        //MolecularProfile id should be identical
+        assertEquals(mutationResultID[0].molecularProfileId(), mutationResultID[1].molecularProfileId(), "molecularProfile IDs should match");
+        //study id should be identical; 
+        assertEquals(mutationResultID[0].studyId(), mutationResultID[1].studyId(), "study IDs should match");
+
+
+    }
+    @Test
+    void testFetchMutationEndPointWithDataJson_SummaryProjection() throws Exception {
+        // The json has two molecularProfileId and a sampleId and entrezGeneIds to restrict search  
+        // Two profiles meet this criteria 
+
+        String testDataJson = loadTestData("mutation_filter.json");
+        MutationDTO[] mutationResultSummary = callFetchMutationEndPoint(testDataJson,ProjectionType.SUMMARY);
+
+        assertNotNull(mutationResultSummary, "Response should have mutation DTO");
+        assertEquals(2, mutationResultSummary.length, "SUMMARY projection should not add or remove records");
+
+
+        //Compare the fields that should be equal
+        //MolecularProfile id should be identical
+        assertEquals(mutationResultSummary[0].molecularProfileId(), mutationResultSummary[1].molecularProfileId(), "molecularProfile IDs should match");
+
+        //study id should be identical; 
+        assertEquals(mutationResultSummary[0].studyId(), mutationResultSummary[1].studyId(), "study IDs should match");
+
+        // Testing different projection expose different fields 
+        // SUMMARY projection should not have gene present or any AlleleSpecificCopyNumber. AlleleSpecificCopyNumber is null for this mutation profile
+        for (MutationDTO mutationDTO : mutationResultSummary) {
+            assertNull(mutationDTO.gene(), "Response should not have gene present");
+            assertNull(mutationDTO.alleleSpecificCopyNumber(), "Response should not have AlleleSpecificCopyNumber present");
+        }
+
+    }
+
+    @Test
+    void testFetchMutationEndPointWithDataJson_DetailedProjection() throws Exception {
+        // The json has two molecularProfileId and a sampleId and entrezGeneIds to restrict search  
+        // Two profiles meet this criteria 
+
+        String testDataJson = loadTestData("mutation_filter.json");
+        MutationDTO[] mutationResultDetailed = callFetchMutationEndPoint(testDataJson,ProjectionType.DETAILED);
+
+        assertNotNull(mutationResultDetailed, "Response should have mutation DTO");
+        assertEquals(2, mutationResultDetailed.length, "DETAILED projection should not add or remove records");
+
+
+        //Compare the fields that should be equal 
+
+        //MolecularProfile id should be identical
+        assertEquals(mutationResultDetailed[0].molecularProfileId(), mutationResultDetailed[1].molecularProfileId(), "molecularProfile IDs should match");
+        //study id should be identical; 
+        assertEquals(mutationResultDetailed[0].studyId(), mutationResultDetailed[1].studyId(), "study IDs should match");
+
+        // Testing different projection expose different fields 
+        // Detailed projection should have gene present or any AlleleSpecificCopyNumber. AlleleSpecificCopyNumber is null for this mutation profile
+        for (MutationDTO mutationDTO : mutationResultDetailed) {
+            assertNotNull(mutationDTO.gene(), "Response should have gene present");
+            assertNull(mutationDTO.alleleSpecificCopyNumber(), "Response should not have AlleleSpecificCopyNumber present ");
+        }
+    }
+}

src/e2e/java/org/cbioportal/ColumnStoreMutationControllerE2ETest/mutation_filter.JSON

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+ {
+   "sampleMolecularIdentifiers": [
+     {"sampleId": "P01_Pri", "molecularProfileId": "lgg_ucsf_2014_mutations"},
+     {"sampleId": "P05_Rec", "molecularProfileId": "lgg_ucsf_2014_mutations"}
+   ],
+   "entrezGeneIds": [287,2]
+ }

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

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+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 +1,32 @@
+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()) )")
+    @Mapping(source = "tumorSeqAllele", target = "variantAllele")
+    MutationDTO toMutationDTOO(Mutation mutation);
+
+    List<MutationDTO> toDTOs(List<Mutation> mutationList);
+}

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

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+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

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+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
+) {
+}