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Clickhousify samples endpoint (cBioPortal#11393)
* add sample column store controller, service, repository, and mapper classes * add sample_type, sequenced, and copy_number_segment_present to sample_derived * add fields required for detailed projection * add meta samples mappers * add remaining endpoints * reorganize files in favor of the clickhouse only clean architecture * reduce number of sample_derived columns by using join for the detailed projection * replace sample service with individual use cases * use ArrayType Handler wherever possible * add tests * add support for sample filter in hasPermission
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-24
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‎src/main/java/org/cbioportal/application/rest/vcolumnstore/ColumnStoreSampleController.java‎

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package org.cbioportal.application.rest.vcolumnstore;
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import io.swagger.v3.oas.annotations.Operation;
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import io.swagger.v3.oas.annotations.Parameter;
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import io.swagger.v3.oas.annotations.media.ArraySchema;
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import io.swagger.v3.oas.annotations.media.Content;
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import io.swagger.v3.oas.annotations.media.Schema;
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import io.swagger.v3.oas.annotations.responses.ApiResponse;
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import jakarta.validation.Valid;
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import jakarta.validation.constraints.Max;
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import jakarta.validation.constraints.Min;
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import org.cbioportal.application.rest.mapper.SampleMapper;
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import org.cbioportal.application.rest.response.SampleDTO;
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import org.cbioportal.legacy.model.CancerStudy;
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import org.cbioportal.domain.sample.Sample;
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import org.cbioportal.domain.sample.usecase.SampleUseCases;
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import org.cbioportal.legacy.model.meta.BaseMeta;
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import org.cbioportal.legacy.service.StudyService;
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import org.cbioportal.legacy.service.exception.PatientNotFoundException;
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import org.cbioportal.legacy.service.exception.SampleNotFoundException;
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import org.cbioportal.legacy.service.exception.StudyNotFoundException;
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import org.cbioportal.legacy.utils.security.AccessLevel;
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import org.cbioportal.legacy.utils.security.PortalSecurityConfig;
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import org.cbioportal.legacy.web.parameter.Direction;
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import org.cbioportal.legacy.web.parameter.HeaderKeyConstants;
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import org.cbioportal.legacy.web.parameter.PagingConstants;
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import org.cbioportal.legacy.web.parameter.SampleFilter;
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import org.cbioportal.legacy.web.parameter.sort.SampleSortBy;
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import org.cbioportal.shared.enums.ProjectionType;
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import org.springframework.beans.factory.annotation.Value;
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import org.springframework.context.annotation.Profile;
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import org.springframework.http.HttpHeaders;
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import org.springframework.http.HttpStatus;
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import org.springframework.http.MediaType;
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import org.springframework.http.ResponseEntity;
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import org.springframework.security.access.prepost.PreAuthorize;
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import org.springframework.validation.annotation.Validated;
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import org.springframework.web.bind.annotation.GetMapping;
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import org.springframework.web.bind.annotation.PathVariable;
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import org.springframework.web.bind.annotation.PostMapping;
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import org.springframework.web.bind.annotation.RequestBody;
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import org.springframework.web.bind.annotation.RequestMapping;
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import org.springframework.web.bind.annotation.RequestParam;
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import org.springframework.web.bind.annotation.RestController;
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import java.util.List;
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@RestController
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@RequestMapping("/api/column-store")
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@Validated
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@Profile("clickhouse")
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public class ColumnStoreSampleController {
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public static final int SAMPLE_MAX_PAGE_SIZE = 10000000;
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private static final String SAMPLE_DEFAULT_PAGE_SIZE = "10000000";
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private final SampleUseCases sampleUseCases;
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private final StudyService studyService;
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@Value("${authenticate}")
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private String authenticate;
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public ColumnStoreSampleController(
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SampleUseCases sampleUseCases,
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StudyService studyService
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) {
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this.sampleUseCases = sampleUseCases;
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this.studyService = studyService;
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}
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@GetMapping(value = "/samples", produces = MediaType.APPLICATION_JSON_VALUE)
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@Operation(description = "Get all samples matching keyword")
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@ApiResponse(
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responseCode = "200",
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description = "OK",
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content = @Content(array = @ArraySchema(schema = @Schema(implementation = Sample.class)))
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)
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public ResponseEntity<List<SampleDTO>> getSamplesByKeyword(
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@Parameter(description = "Search keyword that applies to the study ID")
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@RequestParam(required = false)
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String keyword,
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@Parameter(description = "Level of detail of the response")
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@RequestParam(defaultValue = "SUMMARY")
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ProjectionType projection,
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@Parameter(description = "Page size of the result list")
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@Max(PagingConstants.MAX_PAGE_SIZE)
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@Min(PagingConstants.MIN_PAGE_SIZE)
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@RequestParam(defaultValue = PagingConstants.DEFAULT_PAGE_SIZE)
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Integer pageSize,
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@Parameter(description = "Page number of the result list")
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@Min(PagingConstants.MIN_PAGE_NUMBER)
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@RequestParam(defaultValue = PagingConstants.DEFAULT_PAGE_NUMBER)
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Integer pageNumber,
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@Parameter(description = "Name of the property that the result list is sorted by")
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@RequestParam(required = false)
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SampleSortBy sortBy,
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@Parameter(description = "Direction of the sort")
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@RequestParam(defaultValue = "ASC")
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Direction direction
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) {
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String sort = sortBy == null ? null : sortBy.getOriginalValue();
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List<String> studyIds = null;
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// TODO is there a better way to do this? something like @PreAuthorize?
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// (this code segment is duplicate of the legacy SampleController)
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if (PortalSecurityConfig.userAuthorizationEnabled(authenticate)) {
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/*
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If using auth, filter the list of samples returned using the list of study ids the
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user has access to. If the user has access to no studies, the endpoint should not 403,
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but instead return an empty list.
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*/
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studyIds = studyService
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.getAllStudies(
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null,
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ProjectionType.SUMMARY.name(), // force to summary so that post filter doesn't NPE
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PagingConstants.MAX_PAGE_SIZE,
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0,
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null,
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direction.name(),
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null,
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AccessLevel.READ
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)
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.stream()
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.map(CancerStudy::getCancerStudyIdentifier)
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.toList();
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}
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if (projection == ProjectionType.META) {
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HttpHeaders responseHeaders = getMetaSamplesHeaders(keyword, studyIds);
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return new ResponseEntity<>(responseHeaders, HttpStatus.OK);
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}
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else {
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List<Sample> samples = sampleUseCases.getAllSamplesUseCase().execute(
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keyword,
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studyIds,
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projection,
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pageSize,
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pageNumber,
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sort,
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direction.name()
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);
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return new ResponseEntity<>(SampleMapper.INSTANCE.toDtos(samples), HttpStatus.OK);
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}
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}
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@PreAuthorize("hasPermission(#sampleFilter, 'SampleFilter', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)")
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@PostMapping(
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value = "/samples/fetch",
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consumes = MediaType.APPLICATION_JSON_VALUE,
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produces = MediaType.APPLICATION_JSON_VALUE
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)
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@Operation(description = "Fetch samples by ID")
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@ApiResponse(
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responseCode = "200",
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description = "OK",
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content = @Content(array = @ArraySchema(schema = @Schema(implementation = Sample.class)))
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)
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public ResponseEntity<List<SampleDTO>> fetchSamples(
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@Parameter(required = true, description = "List of sample identifiers")
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@Valid
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@RequestBody(required = false)
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SampleFilter sampleFilter,
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@Parameter(description = "Level of detail of the response")
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@RequestParam(defaultValue = "SUMMARY")
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ProjectionType projection
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) {
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if (projection == ProjectionType.META) {
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HttpHeaders responseHeaders = fetchMetaSamplesHeaders(sampleFilter);
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return new ResponseEntity<>(responseHeaders, HttpStatus.OK);
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}
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else {
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List<Sample> samples = sampleUseCases.fetchSamplesUseCase().execute(sampleFilter, projection);
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return new ResponseEntity<>(SampleMapper.INSTANCE.toDtos(samples), HttpStatus.OK);
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}
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}
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@PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)")
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@GetMapping(value = "/studies/{studyId}/samples", produces = MediaType.APPLICATION_JSON_VALUE)
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@Operation(description = "Get all samples in a study")
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@ApiResponse(
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responseCode = "200",
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description = "OK",
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content = @Content(array = @ArraySchema(schema = @Schema(implementation = Sample.class)))
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)
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public ResponseEntity<List<SampleDTO>> getAllSamplesInStudy(
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@Parameter(required = true, description = "Study ID e.g. acc_tcga")
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@PathVariable
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String studyId,
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@Parameter(description = "Level of detail of the response")
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@RequestParam(defaultValue = "SUMMARY")
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ProjectionType projection,
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@Parameter(description = "Page size of the result list")
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@Max(SAMPLE_MAX_PAGE_SIZE)
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@Min(PagingConstants.MIN_PAGE_SIZE)
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@RequestParam(defaultValue = SAMPLE_DEFAULT_PAGE_SIZE)
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Integer pageSize,
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@Parameter(description = "Page number of the result list")
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@Min(PagingConstants.MIN_PAGE_NUMBER)
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@RequestParam(defaultValue = PagingConstants.DEFAULT_PAGE_NUMBER)
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Integer pageNumber,
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@Parameter(description = "Name of the property that the result list is sorted by")
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@RequestParam(required = false)
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SampleSortBy sortBy,
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@Parameter(description = "Direction of the sort")
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@RequestParam(defaultValue = "ASC")
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Direction direction
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) throws StudyNotFoundException {
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if (projection == ProjectionType.META) {
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HttpHeaders responseHeaders = getMetaSamplesInStudyHeaders(studyId);
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return new ResponseEntity<>(responseHeaders, HttpStatus.OK);
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} else {
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List<Sample> samples = sampleUseCases.getAllSamplesInStudyUseCase().execute(
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studyId,
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projection,
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pageSize,
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pageNumber,
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sortBy == null ? null : sortBy.getOriginalValue(),
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direction.name()
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);
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return new ResponseEntity<>(SampleMapper.INSTANCE.toDtos(samples), HttpStatus.OK);
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}
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}
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@PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)")
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@GetMapping(value = "/studies/{studyId}/samples/{sampleId}", produces = MediaType.APPLICATION_JSON_VALUE)
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@Operation(description = "Get a sample in a study")
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@ApiResponse(
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responseCode = "200",
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description = "OK",
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content = @Content(schema = @Schema(implementation = Sample.class))
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)
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public ResponseEntity<SampleDTO> getSampleInStudy(
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@Parameter(required = true, description = "Study ID e.g. acc_tcga")
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@PathVariable
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String studyId,
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@Parameter(required = true, description = "Sample ID e.g. TCGA-OR-A5J2-01")
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@PathVariable
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String sampleId
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) throws SampleNotFoundException, StudyNotFoundException {
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return new ResponseEntity<>(
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SampleMapper.INSTANCE.toSampleDTO(
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sampleUseCases.getSampleInStudyUseCase().execute(studyId, sampleId)
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),
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HttpStatus.OK
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);
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}
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@PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)")
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@GetMapping(value = "/studies/{studyId}/patients/{patientId}/samples", produces = MediaType.APPLICATION_JSON_VALUE)
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@Operation(description = "Get all samples of a patient in a study")
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@ApiResponse(
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responseCode = "200",
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description = "OK",
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content = @Content(array = @ArraySchema(schema = @Schema(implementation = Sample.class)))
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)
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public ResponseEntity<List<SampleDTO>> getAllSamplesOfPatientInStudy(
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@Parameter(required = true, description = "Study ID e.g. acc_tcga")
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@PathVariable
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String studyId,
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@Parameter(required = true, description = "Patient ID e.g. TCGA-OR-A5J2")
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@PathVariable
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String patientId,
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@Parameter(description = "Level of detail of the response")
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@RequestParam(defaultValue = "SUMMARY")
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ProjectionType projection,
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@Parameter(description = "Page size of the result list")
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@Max(SAMPLE_MAX_PAGE_SIZE)
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@Min(PagingConstants.MIN_PAGE_SIZE)
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@RequestParam(defaultValue = SAMPLE_DEFAULT_PAGE_SIZE)
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Integer pageSize,
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@Parameter(description = "Page number of the result list")
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@Min(PagingConstants.MIN_PAGE_NUMBER)
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@RequestParam(defaultValue = PagingConstants.DEFAULT_PAGE_NUMBER)
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Integer pageNumber,
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@Parameter(description = "Name of the property that the result list is sorted by")
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@RequestParam(required = false)
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SampleSortBy sortBy,
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@Parameter(description = "Direction of the sort")
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@RequestParam(defaultValue = "ASC") Direction direction
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) throws PatientNotFoundException, StudyNotFoundException {
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if (projection == ProjectionType.META) {
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HttpHeaders responseHeaders = getMetaSamplesOfPatientInStudyHeaders(studyId, patientId);
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return new ResponseEntity<>(responseHeaders, HttpStatus.OK);
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} else {
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List<Sample> samples = sampleUseCases.getAllSamplesOfPatientInStudyUseCase().execute(
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studyId,
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patientId,
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projection,
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pageSize,
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pageNumber,
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sortBy == null ? null : sortBy.getOriginalValue(),
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direction.name()
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);
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return new ResponseEntity<>(SampleMapper.INSTANCE.toDtos(samples), HttpStatus.OK);
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}
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}
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private HttpHeaders fetchMetaSamplesHeaders(
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SampleFilter sampleFilter
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) {
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HttpHeaders httpHeaders = new HttpHeaders();
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BaseMeta baseMeta = sampleUseCases.fetchMetaSamplesUseCase().execute(sampleFilter);
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httpHeaders.add(HeaderKeyConstants.TOTAL_COUNT, baseMeta.getTotalCount().toString());
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return httpHeaders;
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}
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private HttpHeaders getMetaSamplesHeaders(String keyword, List<String> studyIds) {
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HttpHeaders httpHeaders = new HttpHeaders();
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httpHeaders.add(
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HeaderKeyConstants.TOTAL_COUNT,
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sampleUseCases.getMetaSamplesUseCase().execute(keyword, studyIds).getTotalCount().toString()
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);
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return httpHeaders;
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}
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private HttpHeaders getMetaSamplesInStudyHeaders(String studyId) throws StudyNotFoundException {
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HttpHeaders httpHeaders = new HttpHeaders();
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httpHeaders.add(
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HeaderKeyConstants.TOTAL_COUNT,
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sampleUseCases.getMetaSamplesInStudyUseCase().execute(studyId).getTotalCount().toString()
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);
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return httpHeaders;
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}
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private HttpHeaders getMetaSamplesOfPatientInStudyHeaders(
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String studyId,
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String patientId
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) throws StudyNotFoundException, PatientNotFoundException
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{
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HttpHeaders httpHeaders = new HttpHeaders();
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httpHeaders.add(
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HeaderKeyConstants.TOTAL_COUNT,
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sampleUseCases.getMetaSamplesOfPatientInStudyUseCase().execute(studyId, patientId).getTotalCount().toString()
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);
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return httpHeaders;
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}
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}

‎src/main/java/org/cbioportal/application/security/CancerStudyPermissionEvaluator.java‎

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Original file line numberDiff line numberDiff line change
@@ -36,6 +36,7 @@
3636
import java.util.*;
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import java.util.stream.Collectors;
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import org.cbioportal.application.security.util.CancerStudyExtractorUtil;
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import org.cbioportal.legacy.model.CancerStudy;
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import org.cbioportal.legacy.model.MolecularProfile;
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import org.cbioportal.legacy.model.MolecularProfileCaseIdentifier;
@@ -48,6 +49,7 @@
4849
import org.cbioportal.legacy.web.parameter.GenericAssayDataCountFilter;
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import org.cbioportal.legacy.web.parameter.GenomicDataCountFilter;
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import org.cbioportal.legacy.web.parameter.MolecularProfileCasesGroupAndAlterationTypeFilter;
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import org.cbioportal.legacy.web.parameter.SampleFilter;
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import org.cbioportal.legacy.web.parameter.StudyViewFilter;
5254
import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
@@ -194,6 +196,13 @@ public boolean hasPermission(Authentication authentication, Serializable targetI
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return hasAccessToSampleLists(authentication, (Collection<String>) targetId, permission);
195197
} else if (targetType.contains("Filter")) {
196198
switch (targetId) {
199+
case SampleFilter sampleFilter -> {
200+
return hasAccessToCancerStudies(
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authentication,
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CancerStudyExtractorUtil.extractCancerStudyIdsFromSampleFilter(sampleFilter, this.cacheMapUtil),
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permission
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);
205+
}
197206
case StudyViewFilter studyViewFilter -> {
198207
return hasAccessToCancerStudies(authentication, studyViewFilter.getUniqueStudyIds(), permission);
199208
}
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218227
}
219228
return hasAccessToCancerStudies(authentication, studyIds, permission);
220229
}
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case GenericAssayDataCountFilter genericAssayDataCountFilter -> {
223231
Set<String> studyIds = new HashSet<>();
224232
if (genericAssayDataCountFilter.getStudyViewFilter() != null) {

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