Uses of Class
ubic.gemma.rest.util.ResponseDataObject

Packages that use ResponseDataObject

Package	Description
ubic.gemma.rest
ubic.gemma.rest.util

Uses of ResponseDataObject in ubic.gemma.rest

Subclasses of ResponseDataObject in ubic.gemma.rest

Modifier and Type	Class	Description
static class	AdminWebService.ResponseDataObjectBlacklistedValueObject
static class	AdminWebService.ResponseDataObjectCreateUserResponse
static class	AdminWebService.ResponseDataObjectDbPoolResponse
static class	AdminWebService.ResponseDataObjectGeoScrapeSubmitResponse
static class	AdminWebService.ResponseDataObjectImportGeoBatchResponse
static class	AdminWebService.ResponseDataObjectMultifunctionalityRecomputeResponse
static class	AdminWebService.ResponseDataObjectObsoleteTermCorrectionSubmission
static class	AdminWebService.ResponseDataObjectOntologyRefreshResponse
static class	AdminWebService.ResponseDataObjectReindexAcceptedResponse
static class	AdminWebService.ResponseDataObjectSubmittedJobResponse
static class	AnalysisResultSetsWebService.PaginatedResultsResponseDataObjectDifferentialExpressionAnalysisResultSetValueObject	Similar to PaginatedResponseDataObject, but the data.results is paginated instead of data
static class	AnalysisResultSetsWebService.PvalueDistributionResponseDataObject	Concrete ResponseDataObject type for the pvalueDistribution endpoint so Swagger has a non-generic schema to reference.
static class	AnnotationsWebService.AnnotationSearchResponseDataObject	GET /annotations/search envelope: the standard data array plus, when identity matching ran, the AnnotationsWebService.NegativeEvidenceValueObject beside it.
static class	AnnotationsWebService.ResponseDataObjectAnnotationValueObject	Response shape for AnnotationsWebService.addDatasetAnnotation(DatasetArg, AnnotationsWebService.AnnotationDto, Long, String).
static class	AuthWebService.ResponseDataObjectLoginResponse	Response shape for AuthWebService.login(AuthWebService.LoginRequest).
static class	DatasetsWebService.CursorPaginatedResponseDataObjectAuditEventValueObject	Cursor full-fidelity shape for DatasetsWebService.getDatasetAuditEvents(DatasetArg, CursorArg, LimitArg, boolean, boolean) (compact=false).
static class	DatasetsWebService.CursorPaginatedResponseDataObjectBioAssayValueObject	Cursor-mode response shape for DatasetsWebService.getDatasetSamples(DatasetArg, QuantitationTypeArg, boolean, CursorArg, LimitArg, ExcludeArg, boolean).
static class	DatasetsWebService.CursorPaginatedResponseDataObjectCompactAuditEventValueObject	Cursor collapsed shape for DatasetsWebService.getDatasetAuditEvents(DatasetArg, CursorArg, LimitArg, boolean, boolean) (compact=true).
static class	DatasetsWebService.FilteredAndInferredAndCursorPaginatedResponseDataObject<T>	Cursor-mode counterpart to DatasetsWebService.FilteredAndInferredAndPaginatedResponseDataObject.
static class	DatasetsWebService.FilteredAndInferredAndCursorPaginatedResponseDataObjectExpressionExperimentValueObject	Cursor shape for DatasetsWebService.getDatasetsByIds(DatasetArrayArg, FilterArg, OffsetArg, LimitArg, SortArg, CursorArg) / DatasetsWebService.getBlacklistedDatasets(FilterArg, SortArg, OffsetArg, LimitArg, CursorArg).
static class	DatasetsWebService.FilteredAndInferredAndPaginatedResponseDataObject<T>
static class	DatasetsWebService.FilteredAndInferredAndPaginatedResponseDataObjectExpressionExperimentValueObject	Legacy shape for DatasetsWebService.getDatasetsByIds(DatasetArrayArg, FilterArg, OffsetArg, LimitArg, SortArg, CursorArg) / DatasetsWebService.getBlacklistedDatasets(FilterArg, SortArg, OffsetArg, LimitArg, CursorArg).
static class	DatasetsWebService.QueriedAndFilteredAndInferredAndCursorPaginatedResponseDataObject<T>	Cursor-mode counterpart to DatasetsWebService.QueriedAndFilteredAndInferredAndPaginatedResponseDataObject.
static class	DatasetsWebService.QueriedAndFilteredAndInferredAndCursorPaginatedResponseDataObjectExperimentExpressionLevelsValueObject	Cursor shape for DatasetsWebService.getDatasetsExpressionLevelsForGene(GeneArg, QueryArg, FilterArg, OffsetArg, LimitArg, Boolean, ExpLevelConsolidationArg, CursorArg, Boolean) / DatasetsWebService.getDatasetsExpressionLevelsForGeneInTaxon(TaxonArg, GeneArg, QueryArg, FilterArg, OffsetArg, LimitArg, Boolean, ExpLevelConsolidationArg, CursorArg, Boolean).
static class	DatasetsWebService.QueriedAndFilteredAndInferredAndLimitedResponseDataObject<T>
static class	DatasetsWebService.QueriedAndFilteredAndInferredAndPaginatedResponseDataObject<T>
static class	DatasetsWebService.QueriedAndFilteredAndInferredAndPaginatedResponseDataObjectDifferentialExpressionAnalysisResultByGeneValueObject
static class	DatasetsWebService.QueriedAndFilteredAndInferredAndPaginatedResponseDataObjectExperimentExpressionLevelsValueObject	Legacy shape for DatasetsWebService.getDatasetsExpressionLevelsForGene(GeneArg, QueryArg, FilterArg, OffsetArg, LimitArg, Boolean, ExpLevelConsolidationArg, CursorArg, Boolean) / DatasetsWebService.getDatasetsExpressionLevelsForGeneInTaxon(TaxonArg, GeneArg, QueryArg, FilterArg, OffsetArg, LimitArg, Boolean, ExpLevelConsolidationArg, CursorArg, Boolean).
static class	DatasetsWebService.QueriedAndFilteredAndInferredResponseDataObject<T>
static class	DatasetsWebService.ResponseDataObjectCellTypeAssignmentValueObject
static class	DatasetsWebService.ResponseDataObjectExpressionExperimentValueObject
static class	DatasetsWebService.ResponseDataObjectListAuditEventValueObject	Legacy full-fidelity shape for DatasetsWebService.getDatasetAuditEvents(DatasetArg, CursorArg, LimitArg, boolean, boolean) (compact=false).
static class	DatasetsWebService.ResponseDataObjectListBioAssayValueObject	Legacy-mode response shape for DatasetsWebService.getDatasetSamples(DatasetArg, QuantitationTypeArg, boolean, CursorArg, LimitArg, ExcludeArg, boolean).
static class	DatasetsWebService.ResponseDataObjectListCellLevelCharacteristicsValueObject
static class	DatasetsWebService.ResponseDataObjectListCompactAuditEventValueObject	Legacy collapsed shape for DatasetsWebService.getDatasetAuditEvents(DatasetArg, CursorArg, LimitArg, boolean, boolean) (compact=true).
static class	DatasetsWebService.ResponseDataObjectSingleCellDimensionValueObject
static class	ExperimentSetsWebService.ResponseDataObjectExpressionExperimentSetValueObject	Response shape for ExperimentSetsWebService.createExperimentSet(ExperimentSetsWebService.ExperimentSetRequest).
static class	GeneWebService.CursorPaginatedResponseDataObjectCompositeSequenceSummaryValueObject	Cursor-mode response shape for GeneWebService.getGeneProbes(GeneArg, OffsetArg, LimitArg, CursorArg, boolean) when summary=true.
static class	GeneWebService.PaginatedResponseDataObjectCompositeSequenceSummaryValueObject	Legacy-mode response shape for GeneWebService.getGeneProbes(GeneArg, OffsetArg, LimitArg, CursorArg, boolean) when summary=true.
static class	GroupsWebService.ResponseDataObjectGroupValueObject	Response shape for GroupsWebService.createGroup(GroupsWebService.GroupCreateRequest).
static class	SearchWebService.SearchResultsResponseDataObject
static class	TicketsWebService.ResponseDataObjectRemovedTargetResult	Response shape for TicketsWebService.removeTicketTarget(Long, TicketTargetType, Long).
static class	TicketsWebService.ResponseDataObjectTicketValueObject	The 201 body of TicketsWebService.createTicketFromAccession(CreateTicketFromAccessionRequest).
static class	WorkflowWebService.ResponseDataObjectWorkflowTransitionResponse	Response shape for WorkflowWebService.advanceDatasetWorkflow(Long, WorkflowWebService.AdvanceWorkflowRequest).

Methods in ubic.gemma.rest that return ResponseDataObject

Modifier and Type	Method	Description
ResponseDataObject<Map<Long, DatasetsWebService.CurationLockBulkResult>>	DatasetsWebService.acquireCurationLocks(Boolean steal, Integer ttlMinutes, String onBehalfOf, String runId, String agentName, DatasetsWebService.CurationLockBulkRequest body)
ResponseDataObject<GroupsWebService.GroupWithMembersValueObject>	GroupsWebService.addMember(Long id, GroupsWebService.MemberAddRequest req)	Add a member to a group.
ResponseDataObject<AnnotationValueObject>	DatasetsWebService.addSampleCharacteristic(DatasetArg<?> datasetArg, Long bioAssayId, DatasetsWebService.AnnotationTagInput body)
ResponseDataObject<TicketsWebService.AddTargetsResult>	TicketsWebService.addTicketTarget(Long id, TicketsWebService.AddTargetRequest req)	Add a target to a ticket that is open to additions.
ResponseDataObject<DatasetsWebService.BatchOutlierResponse>	DatasetsWebService.batchMarkSampleOutliers(DatasetArg<?> datasetArg, DatasetsWebService.BatchOutlierRequest body)	Batch outlier mark / unmark.
ResponseDataObject<PipelineJobBatchValueObject>	AdminPipelineWebService.cancelBatch(Long batchId)
ResponseDataObject<Boolean>	AdminPipelineWebService.cancelJob(Long batchId, Long jobId)
ResponseDataObject<TaskStatusValueObject>	TasksWebService.cancelTask(String taskId)	Cooperative task cancellation.
ResponseDataObject<DatasetsWebService.CurationCommitReport>	DatasetsWebService.commitCuration(DatasetArg<?> datasetArg, Boolean force, String onBehalfOf, DatasetsWebService.CurationDocument body)
ResponseDataObject<GoTermsWebService.GoTermGeneCountValueObject>	GoTermsWebService.countGenesByGoTerm(String termUri, TaxonArg<?> taxonArg, boolean propagate, int maxTerms)	Distinct-gene count for the given GO term, optionally including descendants.
ResponseDataObject<List<AdminWebService.CurationLockValueObject>>	AdminWebService.getAllCurationLocks()	Every advisory curation lock currently held, corpus-wide.
ResponseDataObject<List<AnnotationsWebService.AnnotationCategoryValueObject>>	AnnotationsWebService.getAnnotationCategories()	List the ontology categories allowed for use in characteristics.
ResponseDataObject<List<AnnotationsWebService.OntologyTermSimpleValueObject>>	AnnotationsWebService.getAnnotationPredicates()	List the ontology predicates allowed for use in statements.
ResponseDataObject<List<AnnotationsWebService.AnnotationRelationValueObject>>	AnnotationsWebService.getAnnotationRelations(String subject, String object, String predicate, String subjectCategory, String objectCategory, String basis, Long datasetId, String seedDirection, Long taxonId, String excludeDatasets, int minSupport, double minSpecificity, boolean includeExperimentLevel, int maxObjectBreadth, int maxSubjectBreadth, boolean includeRefuted, boolean includeCellTypeSubjects, int limit)	Relations Gemma knows between annotation terms, with the basis for each.
ResponseDataObject<List<AnnotationsWebService.AnnotationSearchResultValueObject>>	AnnotationsWebService.getAnnotationsChildren(String termUri, boolean direct)	Obtain the children of a given annotation.
ResponseDataObject<AnnotationSetsWebService.AnnotationSetResponse>	AnnotationSetsWebService.getAnnotationSet(Long id)	Single annotation set (full payload).
ResponseDataObject<List<AnnotationsWebService.AnnotationSearchResultValueObject>>	AnnotationsWebService.getAnnotationsParents(String termUri, boolean direct)
ResponseDataObject<AnnotationsWebService.OntologyTermValueObject>	AnnotationsWebService.getAnnotationTerm(String termUri, boolean includeCitationXrefs)
ResponseDataObject<RootWebService.ApiInfoValueObject>	RootWebService.getApiInfo(jakarta.ws.rs.core.UriInfo uriInfo)	Returns an object with API information.
ResponseDataObject<PipelineJobBatchValueObject>	AdminPipelineWebService.getBatch(Long batchId)
ResponseDataObject<AdminWebService.CacheListResponse>	AdminWebService.getCaches()	Lists the registered Spring caches by name.
ResponseDataObject<List<AnnotationsWebService.CanonicalUriValueObject>>	AnnotationsWebService.getCanonicalUris(String uri)	Every URI Gemma resolves to a different one on read, so a caller can hold the same answer we do instead of a hand-copied subset of it.
ResponseDataObject<AdminWebService.CurationAgentHealthResponse>	AdminWebService.getCurationAgentHealth()	Out-of-process liveness probe for the gemma-curation-agents Python service.
ResponseDataObject<Map<Long, DatasetsWebService.CurationLockResponse>>	DatasetsWebService.getCurationLocks(DatasetArrayArg datasets)
ResponseDataObject<Map<Long, DatasetsWebService.CurationLockResponse>>	DatasetsWebService.getCurationLocksBulk(DatasetsWebService.CurationLockBulkRequest body)
ResponseDataObject<AdminWebService.CurationStatusResponse>	AdminWebService.getCurationStatus()	Snapshot of the annotation-set -> ticket lifecycle: per-role AnnotationSet counts in the recent windows, open-ticket counts by TicketType, distinct agent run id count, and latest-createdAt timestamp.
ResponseDataObject<List<DatasetPublicationValueObject>>	DatasetsWebService.getDatasetAllPublications(DatasetArg<?> datasetArg, Boolean includeRejected)
ResponseDataObject<Set<AnnotationValueObject>>	DatasetsWebService.getDatasetAnnotations(DatasetArg<?> datasetArg, Boolean includeFreeText)	Retrieves the annotations for the given dataset.
ResponseDataObject<DatasetsWebService.BatchInformationValueObject>	DatasetsWebService.getDatasetBatchInformation(DatasetArg<?> datasetArg)
ResponseDataObject<List<CompletionsWebService.CompletionValueObject>>	CompletionsWebService.getDatasetCompletions(String prefix, int limit)
ResponseDataObject<CurationDetailsValueObject>	DatasetsWebService.getDatasetCurationDetails(DatasetArg<?> datasetArg)
ResponseDataObject<ExperimentalDesignValueObject>	DatasetsWebService.getDatasetDesignJson(DatasetArg<?> datasetArg)	Retrieves the structured experimental design for the given dataset as JSON.
ResponseDataObject<List<DifferentialExpressionAnalysisValueObject>>	DatasetsWebService.getDatasetDifferentialExpressionAnalyses(DatasetArg<?> datasetArg, OffsetArg offsetArg, LimitArg limitArg, boolean includeAssays)	Retrieves the differential analysis results for the given dataset.
ResponseDataObject<GeeqValueObject>	DatasetsWebService.getDatasetGeeq(DatasetArg<?> datasetArg)
ResponseDataObject<GeeqValueObject>	DatasetsWebService.getDatasetGeeqPublic(DatasetArg<?> datasetArg)	Public sibling of DatasetsWebService.getDatasetGeeq(DatasetArg): returns the per-factor GEEQ breakdown without exposing the admin-only detected/manual override scores or the free-text otherIssues curator field, which live on GeeqAdminValueObject.
ResponseDataObject<List<CompletionsWebService.CompletionValueObject>>	CompletionsWebService.getDatasetGroupCompletions(String prefix, int limit)
ResponseDataObject<?>	DatasetsWebService.getDatasetGroups(DatasetArg<?> datasetArg, boolean includeSummaries, boolean includeSummariesLegacy)	Groups that have ANY permission (read or admin) on the given dataset (gap §3c of GEMMA_UI_ENDPOINT_GAP.md).
ResponseDataObject<Boolean>	DatasetsWebService.getDatasetHasBatchInformation(DatasetArg<?> datasetArg)	Indicate if the experiment has batch information.
ResponseDataObject<HeatmapDataValueObject>	DatasetVisualizationWebService.getDatasetHeatmapData(DatasetArg<?> datasetArg, String genesCsv, String probesCsv, Long resultSetId, Double threshold, Integer pcaComponent, Integer pcaCount, Integer sampleSize, String encoding, Long subSetId, QuantitationTypeArg<?> quantitationTypeArg, boolean maskOutliers)	Resolve raw matrix + metadata for a client-rendered heatmap.
ResponseDataObject<DatasetsWebService.MeanVarianceValueObject>	DatasetsWebService.getDatasetMeanVariance(DatasetArg<?> datasetArg)	Retrieves the per-probe mean / variance pre-computed by MeanVarianceService.
ResponseDataObject<List<DatasetsWebService.DatasetMetadataFileValueObject>>	DatasetsWebService.getDatasetMetadataFiles(DatasetArg<?> datasetArg)	List the preprocessing-metadata files available for a dataset.
ResponseDataObject<DatasetsWebService.DatasetPermissionsValueObject>	DatasetsWebService.getDatasetPermissions(DatasetArg<?> datasetArg)	Retrieve the current sharing state of a dataset.
ResponseDataObject<PipelineStatusValueObject>	DatasetsWebService.getDatasetPipelineStatus(DatasetArg<?> datasetArg)
ResponseDataObject<PipelineStatusValueObject>	DatasetsWebService.getDatasetPipelineStatusAlias(DatasetArg<?> datasetArg)	Curation-UI compatibility alias for DatasetsWebService.getDatasetPipelineStatus(DatasetArg): the UI uses the flatter, hyphenated path /datasets/{id}/pipeline-status; the canonical handler lives at /pipelineStatus.
ResponseDataObject<Map<Long, PipelineStatusValueObject>>	DatasetsWebService.getDatasetPipelineStatusBulk(DatasetsWebService.PipelineStatusBulkRequest body)
ResponseDataObject<List<ArrayDesignValueObject>>	DatasetsWebService.getDatasetPlatforms(DatasetArg<?> datasetArg, Boolean original)	Retrieves platforms for the given dataset.
ResponseDataObject<DatasetsWebService.SequencingQcMetricsValueObject>	DatasetsWebService.getDatasetQcMetrics(DatasetArg<?> datasetArg)	Retrieves the per-sample sequencing QC metrics for a dataset — read depth, mapping rate, duplication and the rest of the RNA-Seq pipeline's MultiQC general statistics — keyed by bioAssay id.
ResponseDataObject<Set<QuantitationTypeValueObject>>	DatasetsWebService.getDatasetQuantitationTypes(DatasetArg<?> datasetArg)	Retrieve all available quantitation types for a dataset.
ResponseDataObject<DatasetsWebService.SampleCorrelationMatrixValueObject>	DatasetsWebService.getDatasetSampleCorrelation(DatasetArg<?> datasetArg, DatasetsWebService.CorrelationMatrixChoice which)	Retrieves the sample-sample correlation matrix plus both outlier classifications (curator-flagged + algorithmic), unmasked.
ResponseDataObject<List<ExperimentExpressionLevelsValueObject>>	DatasetsWebService.getDatasetsDifferentialExpression(DatasetArrayArg datasets, Long diffExSet, Double threshold, LimitArg limit, Boolean keepNonSpecific, ExpLevelConsolidationArg consolidate, Boolean precise)	Retrieves the expression levels of genes highly expressed in the given component on given datasets.
ResponseDataObject<List<ExperimentExpressionLevelsValueObject>>	DatasetsWebService.getDatasetsExpressionLevelsForGenes(DatasetArrayArg datasets, GeneArrayArg genes, Boolean keepNonSpecific, ExpLevelConsolidationArg consolidate, Boolean precise)
ResponseDataObject<List<ExperimentExpressionLevelsValueObject>>	DatasetsWebService.getDatasetsExpressionLevelsForGenesInTaxon(DatasetArrayArg datasets, TaxonArg<?> taxonArg, GeneArrayArg genes, Boolean keepNonSpecific, ExpLevelConsolidationArg consolidate, Boolean precise)	Retrieves the expression levels of given genes on given datasets.
ResponseDataObject<List<ExperimentExpressionLevelsValueObject>>	DatasetsWebService.getDatasetsExpressionPca(DatasetArrayArg datasets, Integer component, LimitArg limit, Boolean keepNonSpecific, ExpLevelConsolidationArg consolidate, Boolean precise)	Retrieves the expression levels of genes highly expressed in the given component on given datasets.
ResponseDataObject<com.fasterxml.jackson.databind.JsonNode>	DatasetsWebService.getDatasetSourceMetadata(DatasetArg<?> datasetArg)
ResponseDataObject<List<PipelineStatusValueObject>>	DatasetsWebService.getDatasetsPipelineStatus(DatasetArrayArg datasets)	Bulk sibling of DatasetsWebService.getDatasetPipelineStatus(DatasetArg).
ResponseDataObject<DatasetsWebService.ExpressionExperimentSubSetWithGroupsValueObject>	DatasetsWebService.getDatasetSubSetById(DatasetArg<?> datasetArg, Long subSetId)
ResponseDataObject<DatasetsWebService.ExpressionExperimentSubSetGroupValueObject>	DatasetsWebService.getDatasetSubSetGroup(DatasetArg<?> datasetArg, Long bioAssayDimensionId, boolean includePredictedOutliers)
ResponseDataObject<List<DatasetsWebService.ExpressionExperimentSubSetGroupValueObject>>	DatasetsWebService.getDatasetSubSetGroups(DatasetArg<?> datasetArg)	Retrieve all the "groups" of subsets of a dataset.
ResponseDataObject<List<DatasetsWebService.ExpressionExperimentSubSetWithGroupsValueObject>>	DatasetsWebService.getDatasetSubSets(DatasetArg<?> datasetArg)
ResponseDataObject<DatasetsWebService.SimpleSVDValueObject>	DatasetsWebService.getDatasetSvd(DatasetArg<?> datasetArg)	Retrieves the design for the given dataset.
ResponseDataObject<DatasetsWebService.PcLoadingsValueObject>	DatasetsWebService.getDatasetSvdLoadings(DatasetArg<?> datasetArg, Integer pc, Integer top, DatasetsWebService.PcLoadingDirection direction)	Retrieve the top-N probe loadings on a chosen principal component, plus the bioAssay scores on that PC.
ResponseDataObject<Map<Long, List<TicketSummaryForTargetValueObject>>>	DatasetsWebService.getDatasetTicketsBulk(DatasetsWebService.DatasetTicketsBulkRequest body)
ResponseDataObject<DatasetsWebService.DatasetPermissionsValueObject>	DatasetsWebService.getDatasetVisibility(DatasetArg<?> datasetArg)	Curation-UI compatibility alias for DatasetsWebService.getDatasetPermissions(DatasetArg).
ResponseDataObject<WorkflowWebService.WorkflowStateResponse>	WorkflowWebService.getDatasetWorkflow(Long datasetId)	Retrieve the current workflow state and full transition history of a dataset.
ResponseDataObject<ExpressionExperimentSetValueObject>	ExperimentSetsWebService.getExperimentSet(Long id, boolean includeMembers)
ResponseDataObject<List<ExpressionExperimentDetailsValueObject>>	ExperimentSetsWebService.getExperimentSetDatasets(Long id)
ResponseDataObject<List<GeneWebService.GeneDifferentialExpressionGroupValueObject>>	GeneWebService.getGeneDifferentialExpression(GeneArg<?> geneArg, double threshold, int limit)	Retrieves the differential expression results for the given gene across all experiments the caller has access to (ACL-filtered downstream).
ResponseDataObject<List<GeneOntologyTermValueObject>>	GeneWebService.getGeneGoTerms(GeneArg<?> geneArg)	Retrieves the GO terms of the given gene.
ResponseDataObject<Collection<GeneValueObject>>	GeneWebService.getGeneHomologues(GeneArg<?> geneArg)	Retrieves the homologues of the given gene.
ResponseDataObject<List<PhysicalLocationValueObject>>	GeneWebService.getGeneLocations(GeneArg<?> geneArg)	Retrieves the physical location of the given gene.
ResponseDataObject<GeneValueObject>	GeneWebService.getGeneOverview(GeneArg<?> geneArg)	Retrieves a fully-populated overview of the given gene, suitable for rendering the gene-page header in gemma-curation-ui.
ResponseDataObject<List<GeneValueObject>>	GeneWebService.getGenesByIds(GeneArrayArg genes)
ResponseDataObject<? extends GroupsWebService.GroupValueObject>	GroupsWebService.getGroup(Long id, boolean includeSummaries, boolean includeSummariesLegacy)	Retrieve a single group by id.
ResponseDataObject<AdminWebService.HibernateStatsResponse>	AdminWebService.getHibernateStats()	Returns a structured snapshot of Hibernate statistics.
ResponseDataObject<HomeStats>	StatsWebService.getHomeStats()
ResponseDataObject<List<AnnotationsWebService.AnnotationRelationValueObject>>	AnnotationsWebService.getImpliedAnnotations(String from, String to, String excludeDatasets, String basis, Long taxonId, int maxObjectBreadth, boolean includeExperimentLevel, int limit)	Is a term already implied by the terms an experiment carries?
ResponseDataObject<AdminWebService.JobsListResponse>	AdminWebService.getJobs()	Aggregated admin view of the in-memory background task queue.
ResponseDataObject<AdminWebService.GeoScrapeWatermarkValueObject>	AdminWebService.getLastGeoScrape()	Deprecated. Reads the watermark written by the deprecated in-Gemma scrape.
ResponseDataObject<TicketsWebService.MyQueueResponse>	TicketsWebService.getMyQueue(int limit, int resolvedWithinDays)	Calling admin's own ticket queue: assigned-to-me + the few cheap counters that back a "My Queue" card in the curation-UI.
ResponseDataObject<TicketsWebService.MyQueueSummaryResponse>	TicketsWebService.getMyQueueSummary()	Lightweight counters about the calling admin's ticket workload.
ResponseDataObject<RootWebService.UserValueObject>	RootWebService.getMyself()	Retrieve user information for the current user.
ResponseDataObject<Long>	DatasetsWebService.getNumberOfAnnotations(QueryArg query, FilterArg<ExpressionExperiment> filter, String category, Integer minFrequency, Boolean excludeFreeText)
ResponseDataObject<Long>	DatasetsWebService.getNumberOfDatasets(QueryArg query, FilterArg<ExpressionExperiment> filter)
ResponseDataObject<Long>	PlatformsWebService.getNumberOfPlatforms(FilterArg<ArrayDesign> filter)
ResponseDataObject<Long>	AnalysisResultSetsWebService.getNumberOfResultSets(FilterArg<ExpressionAnalysisResultSet> filter)
ResponseDataObject<Long>	DatasetsWebService.getNumberOfSamples(FilterArg<ExpressionExperiment> filter)
ResponseDataObject<List<ObsoleteTermUsage>>	AdminWebService.getObsoleteTerms(Integer timeoutSeconds)	In-application port of FindObsoleteTermsCli: which obsolete ontology terms do Gemma's annotations still use, and what does each owning ontology say should replace them.
ResponseDataObject<AdminWebService.OntologiesResponse>	AdminWebService.getOntologies(boolean includeTermCount)	Per-ontology load status.
ResponseDataObject<List<CompletionsWebService.CompletionValueObject>>	CompletionsWebService.getOntologyTermCompletions(String prefix, int limit)
ResponseDataObject<TicketsWebService.OpenTicketSummaryResponse>	TicketsWebService.getOpenTicketSummary()	Global open-ticket roll-up for the admin dashboard's TicketsSection.
ResponseDataObject<List<CompletionsWebService.CompletionValueObject>>	CompletionsWebService.getPlatformCompletions(String prefix, int limit, boolean generic)
ResponseDataObject<CompositeSequenceValueObject>	PlatformsWebService.getPlatformElementMappingSummary(PlatformArg<?> platformArg, CompositeSequenceArg<?> probeArg)	Retrieves the per-probe gene-mapping summary (BLAT alignments + biological-sequence metadata + supported genes) for a single probe on a given platform.
ResponseDataObject<List<CompletionsWebService.CompletionValueObject>>	CompletionsWebService.getProtocolCompletions(String prefix, int limit)
ResponseDataObject<Set<AnnotationValueObject>>	DatasetsWebService.getSampleCharacteristics(DatasetArg<?> datasetArg, Long bioAssayId)
ResponseDataObject<TicketValueObject>	TicketsWebService.getScratchpad()	The calling curator's scratchpad, provisioned on first access.
ResponseDataObject<AdminWebService.SearchIndicesResponse>	AdminWebService.getSearchIndices()	Per-@Indexed-entity Hibernate Search 7 index status.
ResponseDataObject<AdminWebService.SessionsResponse>	AdminWebService.getSessions()	Authenticated session listing.
ResponseDataObject<AdminWebService.SystemSnapshotResponse>	AdminWebService.getSystem()	Process-level memory / GC / thread / load snapshot.
ResponseDataObject<TaskStatusValueObject>	TasksWebService.getTaskStatus(String taskId)
ResponseDataObject<List<TaxonValueObject>>	TaxaWebService.getTaxa()	Lists all available taxa.
ResponseDataObject<List<TaxonValueObject>>	TaxaWebService.getTaxaByIds(TaxonArrayArg taxaArg)	Retrieves single taxon based on the given identifier.
ResponseDataObject<List<CompletionsWebService.CompletionValueObject>>	CompletionsWebService.getTaxonCompletions(String prefix, int limit)
ResponseDataObject<List<GeneOntologyTermValueObject>>	TaxaWebService.getTaxonGeneGoTerms(TaxonArg<?> taxonArg, GeneArg<?> geneArg)
ResponseDataObject<List<PhysicalLocationValueObject>>	TaxaWebService.getTaxonGeneLocations(TaxonArg<?> taxonArg, GeneArg<?> geneArg)	Retrieves gene location for the gene on the given taxon.
ResponseDataObject<List<GeneValueObject>>	TaxaWebService.getTaxonGenesByIds(TaxonArg<?> taxonArg, GeneArrayArg geneArg)	Retrieves genes matching the identifier on the given taxon.
ResponseDataObject<List<GeneValueObject>>	TaxaWebService.getTaxonGenesOverlappingChromosome(TaxonArg<?> taxonArg, String chromosomeName, String strand, Long start, Integer size)	Finds genes overlapping a given region.
ResponseDataObject<TicketValueObject>	TicketsWebService.getTicket(Long id)	Retrieve a single ticket, including its full event log.
ResponseDataObject<RootWebService.UserValueObject>	RootWebService.getUser(String username)	Retrieve user information.
ResponseDataObject<AdminWebService.UsersListResponse>	AdminWebService.getUsers(boolean includeDeleted)	Admin user listing.
ResponseDataObject<AdminWebService.GeoGrabResponse>	AdminWebService.grabGeoRecords(AdminWebService.GeoGrabRequest req)	Scrape GEO record metadata by accession without importing into Gemma.
ResponseDataObject<List<PipelineJobEventValueObject>>	AdminPipelineWebService.jobEvents(Long batchId, Long jobId, Long sinceMillis, Integer limit)
ResponseDataObject<AdminWebService.BlacklistListResponse>	AdminWebService.listBlacklistEntries(int limit, int offset)	Lists current blacklist entries.
ResponseDataObject<List<PipelineJobBatchValueObject>>	AdminPipelineWebService.listMyBatches(PipelineJobBatch.BatchState state, Integer limit)
ResponseDataObject<DatasetsWebService.DatasetPermissionsValueObject>	DatasetsWebService.makeDatasetPrivate(DatasetArg<?> datasetArg)	Curation-UI workflow-step endpoint: raw ACL flip to make a dataset private.
ResponseDataObject<DatasetsWebService.DatasetPermissionsValueObject>	DatasetsWebService.makeDatasetPublic(DatasetArg<?> datasetArg)	Curation-UI workflow-step endpoint: raw ACL flip to make a dataset publicly readable.
ResponseDataObject<BioAssayValueObject>	DatasetsWebService.markDatasetSampleOutlier(DatasetArg<?> datasetArg, Long bioAssayId, DatasetsWebService.SampleOutlierRequest body)	Mark (or unmark) a BioAssay as a sample outlier.
ResponseDataObject<RootWebService.UserValueObject>	AuthWebService.me()	Convenience alias for GET /rest/v2/users/me; the curation-UI SPA's useMe() hook points at /rest/v2/me verbatim, so we mirror the shape here rather than asking the SPA to track the longer path.
ResponseDataObject<QuantitationTypeValueObject>	DatasetsWebService.patchDatasetQuantitationType(DatasetArg<?> datasetArg, Long qtId, DatasetsWebService.QuantitationTypePatchRequest body)	Body-driven PATCH dispatcher for a quantitation type.
ResponseDataObject<TicketValueObject>	TicketsWebService.patchTicket(Long id, TicketsWebService.UpdateTicketRequest req)	PATCH alias for TicketsWebService.updateTicket(Long, UpdateTicketRequest).
ResponseDataObject<AdminWebService.UserValueObject>	AdminWebService.patchUser(String username, AdminWebService.UpdateUserRequest req)	Partial update — toggle the enabled flag (lock/unlock) and/or admin role.
ResponseDataObject<List<String>>	AdminPipelineWebService.pipelineRegistry()
ResponseDataObject<PipelineJobEventValueObject>	InternalPipelineWebService.postEvent(Long jobId, String authHeader, InternalPipelineWebService.PostEventRequest req)
ResponseDataObject<DatasetsWebService.CurationCommitReport>	DatasetsWebService.preflightCuration(DatasetArg<?> datasetArg, String onBehalfOf, DatasetsWebService.CurationDocument body)
ResponseDataObject<DesignPreflightReport>	DatasetsWebService.previewDatasetDesignChange(DatasetArg<?> datasetArg, ExperimentalDesignValueObject proposed)	Dry-run preflight for a proposed design replacement.
ResponseDataObject<DatasetsWebService.DatasetPermissionsValueObject>	DatasetsWebService.publishDataset(DatasetArg<?> datasetArg, String reviewer)	Curation-UI workflow-step endpoint: curator-state-machine transition that publishes a dataset under a named reviewer.
ResponseDataObject<GeeqValueObject>	DatasetsWebService.recomputeDatasetGeeq(DatasetArg<?> datasetArg, GeeqService.ScoreMode mode)
ResponseDataObject<GeeqValueObject>	DatasetsWebService.recomputeDatasetGeeqViaPost(DatasetArg<?> datasetArg, DatasetsWebService.GeeqRecomputeRequest body)	Alias for DatasetsWebService.recomputeDatasetGeeq(DatasetArg, GeeqService.ScoreMode) that exposes the GEEQ recompute under POST /datasets/{id}/geeq/recompute with a JSON body.
ResponseDataObject<GeeqValueObject>	DatasetsWebService.recomputeDatasetGeeqViaPostAlias(DatasetArg<?> datasetArg, DatasetsWebService.GeeqRecomputeRequest body)	Curation-UI compatibility alias for DatasetsWebService.recomputeDatasetGeeqViaPost(DatasetArg, DatasetsWebService.GeeqRecomputeRequest): UI calls POST /datasets/{id}/geeq/recalculate with the same body shape.
ResponseDataObject<HomeStats>	StatsWebService.refreshHomeStats()
ResponseDataObject<ArrayDesignValueObject>	AdminWebService.regeneratePlatformReport(PlatformArg<?> platformArg)	Regenerate the cached report for ONE platform, synchronously.
ResponseDataObject<Map<Long,Boolean>>	DatasetsWebService.releaseCurationLocks(String onBehalfOf, DatasetsWebService.CurationLockBulkRequest body)
ResponseDataObject<AnnotationValueObject>	DatasetsWebService.removeSampleCharacteristic(DatasetArg<?> datasetArg, Long bioAssayId, Long characteristicId)
ResponseDataObject<DatasetsWebService.RenameDatasetResponse>	DatasetsWebService.renameDatasetShortName(DatasetArg<?> datasetArg, DatasetsWebService.RenameDatasetRequest body)
ResponseDataObject<AnnotationsWebService.AnnotationReplaceReport>	AnnotationsWebService.replaceDatasetAnnotations(DatasetArg<?> datasetArg, AnnotationsWebService.AnnotationsReplaceRequest body, String onBehalfOf)
ResponseDataObject<AdminWebService.ResetPasswordResponse>	AdminWebService.resetUserPassword(String username)	Administrative password reset — set a user's password to a fresh server-generated one-time temporary password.
ResponseDataObject<DatasetsWebService.CurationCommitReport>	DatasetsWebService.restoreDatasetCurationFromSnapshot(DatasetArg<?> datasetArg, Long setId, Boolean dryRun, Boolean force, String onBehalfOf)
ResponseDataObject<List<AnnotationsWebService.AnnotationSearchBatchResultValueObject>>	AnnotationsWebService.searchAnnotationsBatch(AnnotationsWebService.AnnotationSearchBatchRequest body)
ResponseDataObject<List<AnnotationsWebService.AnnotationSearchResultValueObject>>	AnnotationsWebService.searchAnnotationsByPathQuery(StringArrayArg query)
ResponseDataObject<List<DatasetsWebService.DatasetSearchHitValueObject>>	DatasetsWebService.searchDatasets(QueryArg query, LimitArg limit)	Deprecated. redundant with GET /datasets?query=... (the paginated catalogue runs the same search), which every known client uses instead — no caller of this endpoint was found across gemma-ui, gemma-curation-agents, or gemma.R.
ResponseDataObject<List<GeneValueObject>>	GeneWebService.searchGenes(String query, TaxonArg<?> taxonArg, int limit)	Free-text typeahead for genes.
ResponseDataObject<List<TicketSearchHitValueObject>>	TicketsWebService.searchTickets(String query, boolean openOnly, LimitArg limitArg)	Ticket picker: "choose a ticket by typing".
ResponseDataObject<QuantitationTypeValueObject>	DatasetsWebService.setDatasetQuantitationTypePreferred(DatasetArg<?> datasetArg, Long qtId, DatasetsWebService.QuantitationTypePreferredRequest body)	Mark a QuantitationType as the preferred one (within its vector-type bucket) for the given dataset.
ResponseDataObject<DatasetsWebService.CurationCommitReport>	DatasetsWebService.signDatasetCuration(DatasetArg<?> datasetArg, String onBehalfOf, Boolean dryRun, Boolean keepLock, DatasetsWebService.CurationDocument body)
ResponseDataObject<PipelineJobBatchValueObject>	AdminPipelineWebService.submitBatch(AdminPipelineWebService.SubmitBatchRequest req)
ResponseDataObject<Set<AnnotationValueObject>>	DatasetsWebService.updateDatasetAnnotations(DatasetArg<?> datasetArg, DatasetsWebService.AnnotationsUpdateRequest body, String onBehalfOf)
ResponseDataObject<DatasetsWebService.DatasetBasicsResponse>	DatasetsWebService.updateDatasetBasics(DatasetArg<?> datasetArg, DatasetsWebService.DatasetBasicsUpdateRequest body)
ResponseDataObject<CurationDetailsValueObject>	DatasetsWebService.updateDatasetCurationDetails(DatasetArg<?> datasetArg, DatasetsWebService.CurationDetailsUpdateRequest body)	Deprecated. per Decision 1 of AUDIT_AS_WORKFLOW_RECCE.md the troubled / needsAttention flips are now backed by TicketService: a troubled=true flip opens a TicketType.QUALITY_REVIEW ticket, troubled=false resolves the matching open ticket(s), and analogously for needsAttention (mapped to TicketType.GENERIC on open).
ResponseDataObject<DatasetsWebService.DatasetPermissionsValueObject>	DatasetsWebService.updateDatasetPermissions(DatasetArg<?> datasetArg, DatasetsWebService.PermissionsUpdateRequest body)
ResponseDataObject<List<DatasetPublicationValueObject>>	DatasetsWebService.updateDatasetPublications(DatasetArg<?> datasetArg, DatasetsWebService.PublicationsUpdateRequest body)
ResponseDataObject<DatasetsWebService.SampleMetadataResponse>	DatasetsWebService.updateDatasetSampleMetadata(DatasetArg<?> datasetArg, DatasetsWebService.SampleMetadataRequest body)	Set the upstream-derived metadata on a dataset's samples.
ResponseDataObject<ExpressionExperimentSetValueObject>	ExperimentSetsWebService.updateExperimentSet(Long id, ExperimentSetsWebService.ExperimentSetRequest req)
ResponseDataObject<ExpressionExperimentSetValueObject>	ExperimentSetsWebService.updateExperimentSetMembers(Long id, ExperimentSetsWebService.ExperimentSetMembersRequest req)
ResponseDataObject<GroupsWebService.GroupValueObject>	GroupsWebService.updateGroup(Long id, GroupsWebService.GroupUpdateRequest req)	Partial update — currently name (rename) and description.
ResponseDataObject<Set<AnnotationValueObject>>	DatasetsWebService.updateSampleCharacteristics(DatasetArg<?> datasetArg, Long bioAssayId, DatasetsWebService.AnnotationsUpdateRequest body)
ResponseDataObject<TicketValueObject>	TicketsWebService.updateTargetStatus(Long id, Long targetRowId, TicketsWebService.UpdateTargetStatusRequest req)
ResponseDataObject<TicketValueObject>	TicketsWebService.updateTicket(Long id, TicketsWebService.UpdateTicketRequest req)	Update mutable fields of a ticket.

Uses of ResponseDataObject in ubic.gemma.rest.util

Subclasses of ResponseDataObject in ubic.gemma.rest.util

Modifier and Type	Class	Description
class	CursorPaginatedResponseDataObject<T>	Response wrapper for cursor-paginated results.
class	FilteredAndCursorPaginatedResponseDataObject<T>	Cursor-mode counterpart to FilteredAndPaginatedResponseDataObject.
class	FilteredAndLimitedResponseDataObject<T>
class	FilteredAndPaginatedResponseDataObject<T>
class	FilteredResponseDataObject<T>
static class	OpenApiResponseTypes.CursorPaginatedResponseDataObjectCompositeSequenceValueObject	Cursor shape for GET /genes/{gene}/probes and GET /taxa/{taxon}/genes/{gene}/probes.
static class	OpenApiResponseTypes.CursorPaginatedResponseDataObjectExpressionExperimentValueObject	Cursor shape for GET /platforms/{platform}/datasets.
static class	OpenApiResponseTypes.CursorPaginatedResponseDataObjectGeneValueObject	Cursor shape for GET /genes and GET /taxa/{taxon}/genes.
static class	OpenApiResponseTypes.CursorPaginatedResponseDataObjectTicketEventValueObject	Cursor shape for GET /tickets/{id}/events.
static class	OpenApiResponseTypes.CursorPaginatedResponseDataObjectTicketValueObject	Cursor shape for GET /tickets, GET /datasets/{dataset}/tickets and GET /platforms/{platform}/tickets.
static class	OpenApiResponseTypes.FilteredAndCursorPaginatedResponseDataObjectArrayDesignValueObject	Cursor shape for GET /platforms, GET /platforms/{platform} and GET /platforms/blacklisted.
static class	OpenApiResponseTypes.FilteredAndCursorPaginatedResponseDataObjectCompositeSequenceValueObject	Cursor shape for GET /platforms/{platform}/elements and GET /platforms/{platform}/elements/{probes}.
static class	OpenApiResponseTypes.FilteredAndCursorPaginatedResponseDataObjectDifferentialExpressionAnalysisResultSetValueObject	Cursor shape for GET /resultSets.
static class	OpenApiResponseTypes.FilteredAndCursorPaginatedResponseDataObjectExpressionExperimentValueObject	Cursor shape for GET /taxa/{taxon}/datasets.
static class	OpenApiResponseTypes.FilteredAndCursorPaginatedResponseDataObjectGeneValueObject	Cursor shape for GET /platforms/{platform}/elements/{probe}/genes.
static class	OpenApiResponseTypes.FilteredAndPaginatedResponseDataObjectArrayDesignValueObject	Legacy shape for GET /platforms, GET /platforms/{platform} and GET /platforms/blacklisted.
static class	OpenApiResponseTypes.FilteredAndPaginatedResponseDataObjectCompositeSequenceValueObject	Legacy shape for GET /platforms/{platform}/elements and GET /platforms/{platform}/elements/{probes}.
static class	OpenApiResponseTypes.FilteredAndPaginatedResponseDataObjectDifferentialExpressionAnalysisResultSetValueObject	Legacy shape for GET /resultSets.
static class	OpenApiResponseTypes.FilteredAndPaginatedResponseDataObjectExpressionExperimentValueObject	Legacy shape for GET /taxa/{taxon}/datasets.
static class	OpenApiResponseTypes.FilteredAndPaginatedResponseDataObjectGeneValueObject	Legacy shape for GET /platforms/{platform}/elements/{probe}/genes.
static class	OpenApiResponseTypes.PaginatedResponseDataObjectCompositeSequenceValueObject	Legacy shape for GET /genes/{gene}/probes and GET /taxa/{taxon}/genes/{gene}/probes.
static class	OpenApiResponseTypes.PaginatedResponseDataObjectExpressionExperimentValueObject	Legacy shape for GET /platforms/{platform}/datasets.
static class	OpenApiResponseTypes.PaginatedResponseDataObjectGeneValueObject	Legacy shape for GET /genes and GET /taxa/{taxon}/genes.
static class	OpenApiResponseTypes.PaginatedResponseDataObjectTicketValueObject	Legacy shape for GET /tickets.
static class	OpenApiResponseTypes.ResponseDataObjectListTicketEventValueObject	Legacy shape for GET /tickets/{id}/events.
static class	OpenApiResponseTypes.ResponseDataObjectListTicketValueObject	Legacy shape for GET /datasets/{dataset}/tickets and GET /platforms/{platform}/tickets.
class	PaginatedResponseDataObject<T>	Represents paginated results with offset and limit.
class	QueriedAndFilteredAndCursorPaginatedResponseDataObject<T>	Cursor-mode counterpart to QueriedAndFilteredAndPaginatedResponseDataObject.
class	QueriedAndFilteredAndLimitedResponseDataObject<T>	Represents a payload with a limited number of results.
class	QueriedAndFilteredAndPaginatedResponseDataObject<T>
class	QueriedAndFilteredResponseDataObject<T>

Methods in ubic.gemma.rest.util with type parameters of type ResponseDataObject

Modifier and Type	Method	Description
<S extends ResponseDataObject<T>> S	ResponseDataObject.addWarnings(Iterable<Throwable> throwables, String location, LocationType locationType)	Add a bunch of warnings to ResponseDataObject.getWarnings().

Methods in ubic.gemma.rest.util that return ResponseDataObject

Modifier and Type	Method	Description
static <T> ResponseDataObject<T>	Responders.respond(T payload)	Produce a ResponseDataObject that wraps the given argument.