Uses of Class
ubic.gemma.rest.util.args.DatasetArg

Packages that use DatasetArg

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

Uses of DatasetArg in ubic.gemma.rest

Methods in ubic.gemma.rest with parameters of type DatasetArg

Modifier and Type	Method	Description
jakarta.ws.rs.core.Response	DatasetsWebService.acquireCurationLock(DatasetArg<?> datasetArg, Boolean steal, Integer ttlMinutes, String onBehalfOf, String runId, String agentName)
jakarta.ws.rs.core.Response	AnnotationsWebService.addDatasetAnnotation(DatasetArg<?> datasetArg, AnnotationsWebService.AnnotationDto body, Long annotationSetId, String onBehalfOf)
jakarta.ws.rs.core.Response	DatasetsWebService.addDatasetAnnotationTag(DatasetArg<?> datasetArg, AnnotationsWebService.AnnotationDto body, Long annotationSetId, String onBehalfOf)
ResponseDataObject<AnnotationValueObject>	DatasetsWebService.addSampleCharacteristic(DatasetArg<?> datasetArg, Long bioAssayId, DatasetsWebService.AnnotationTagInput body)
ResponseDataObject<DatasetsWebService.BatchOutlierResponse>	DatasetsWebService.batchMarkSampleOutliers(DatasetArg<?> datasetArg, DatasetsWebService.BatchOutlierRequest body)	Batch outlier mark / unmark.
jakarta.ws.rs.core.Response	DatasetsWebService.clearFactorValueNeedsAttention(DatasetArg<?> datasetArg, Long factorValueId, String note)	Resolve every open needs-attention ticket on a factor value.
ResponseDataObject<DatasetsWebService.CurationCommitReport>	DatasetsWebService.commitCuration(DatasetArg<?> datasetArg, Boolean force, String onBehalfOf, DatasetsWebService.CurationDocument body)
jakarta.ws.rs.core.Response	DatasetsWebService.deleteDatasetProcessedData(DatasetArg<?> datasetArg, boolean confirm)	Delete the processed expression data vectors for a dataset (port of deleteProcessedData CLI).
jakarta.ws.rs.core.Response	DatasetsWebService.deleteDatasetRawData(DatasetArg<?> datasetArg, QuantitationTypeArg<?> quantitationTypeArg, boolean confirm)	Delete the raw expression data vectors for a dataset (port of deleteRawData CLI).
jakarta.ws.rs.core.Response	DatasetsWebService.getCurationDecisions(DatasetArg<?> datasetArg, boolean history)	The standing refusals on a dataset, or the whole decision log.
jakarta.ws.rs.core.Response	DatasetsWebService.getCurationLock(DatasetArg<?> datasetArg)	🛑 This route deliberately serves the BARE object, not the {"data": …} envelope the rest of the service uses.
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.
Object	DatasetsWebService.getDatasetAuditEvents(DatasetArg<?> datasetArg, CursorArg cursorArg, LimitArg limitArg, boolean compact, boolean excludeEmpty)
ResponseDataObject<DatasetsWebService.BatchInformationValueObject>	DatasetsWebService.getDatasetBatchInformation(DatasetArg<?> datasetArg)
Object	DatasetsWebService.getDatasetCellLevelCharacteristics(DatasetArg<?> datasetArg, QuantitationTypeArg<?> qtArg, jakarta.ws.rs.core.HttpHeaders headers)
Object	DatasetsWebService.getDatasetCellTypeAssignment(DatasetArg<?> datasetArg, QuantitationTypeArg<?> qtArg, String ctaName, String protocolName, ExcludeArg<CellTypeAssignmentValueObject> excludeArg, Boolean useBioAssayId, jakarta.ws.rs.core.HttpHeaders headers)
ResponseDataObject<CurationDetailsValueObject>	DatasetsWebService.getDatasetCurationDetails(DatasetArg<?> datasetArg)
jakarta.ws.rs.core.Response	DatasetsWebService.getDatasetDesign(DatasetArg<?> datasetArg, QuantitationTypeArg<?> quantitationTypeArg, Boolean useProcessedQuantitationType, Boolean download, Boolean force)	Retrieves the design for the given dataset.
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.
jakarta.ws.rs.core.Response	DatasetsWebService.getDatasetDifferentialExpressionAnalysisResultSets(DatasetArg<?> datasetArg, jakarta.ws.rs.core.UriInfo uriInfo)	Retrieves the result sets of all the differential expression analyses of a dataset.
jakarta.ws.rs.core.Response	DatasetsWebService.getDatasetDiffExAnalysisArchive(DatasetArg<?> datasetArg, Long analysisId, Boolean download, Boolean force)	Retrieve the differential-expression analysis archive for a dataset.
jakarta.ws.rs.core.Response	DatasetsWebService.getDatasetDraftAnnotationSet(DatasetArg<?> datasetArg, String onBehalfOf)
jakarta.ws.rs.core.Response	DatasetsWebService.getDatasetExpression(DatasetArg<?> datasetArg, Boolean filterData, Boolean download, Boolean force)	Retrieves the data 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<?>	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.
jakarta.ws.rs.core.Response	DatasetsWebService.getDatasetMetadataFile(DatasetArg<?> datasetArg, String typeArg, Boolean download)	Stream a single preprocessing-metadata file by type for a dataset.
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<List<ArrayDesignValueObject>>	DatasetsWebService.getDatasetPlatforms(DatasetArg<?> datasetArg, Boolean original)	Retrieves platforms for the given dataset.
jakarta.ws.rs.core.Response	DatasetsWebService.getDatasetProcessedExpression(DatasetArg<?> datasetArg, Boolean filtered, Boolean download, Boolean force)	Retrieve processed expression data.
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.
jakarta.ws.rs.core.Response	DatasetsWebService.getDatasetRawExpression(DatasetArg<?> datasetArg, QuantitationTypeArg<?> quantitationTypeArg, Boolean download, Boolean force)	Retrieve raw expression data.
ResponseDataObject<DatasetsWebService.SampleCorrelationMatrixValueObject>	DatasetsWebService.getDatasetSampleCorrelation(DatasetArg<?> datasetArg, DatasetsWebService.CorrelationMatrixChoice which)	Retrieves the sample-sample correlation matrix plus both outlier classifications (curator-flagged + algorithmic), unmasked.
Object	DatasetsWebService.getDatasetSamples(DatasetArg<?> datasetArg, QuantitationTypeArg<?> quantitationTypeArg, boolean useProcessedQuantitationType, CursorArg cursorArg, LimitArg limitArg, ExcludeArg<BioAssayValueObject> excludeArg, boolean includePredictedOutliers)	Retrieves the samples for the given dataset.
Object	DatasetsWebService.getDatasetSingleCellDimension(DatasetArg<?> datasetArg, QuantitationTypeArg<?> qtArg, ExcludeArg<SingleCellDimensionValueObject> excludeArg, Boolean useBioAssayIds, jakarta.ws.rs.core.HttpHeaders headers)	Retrieve the single-cell dimension for a given quantitation type.
jakarta.ws.rs.core.Response	DatasetsWebService.getDatasetSingleCellExpression(DatasetArg<?> datasetArg, QuantitationTypeArg<?> quantitationTypeArg, Boolean download, Boolean force, jakarta.ws.rs.core.HttpHeaders headers)
ResponseDataObject<com.fasterxml.jackson.databind.JsonNode>	DatasetsWebService.getDatasetSourceMetadata(DatasetArg<?> 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)
Object	DatasetsWebService.getDatasetSubSetSamples(DatasetArg<?> datasetArg, Long subSetId, CursorArg cursorArg, LimitArg limitArg, boolean includePredictedOutliers)	Retrieves the samples of a specific subset of a dataset.
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.
Object	DatasetsWebService.getDatasetTickets(DatasetArg<?> datasetArg, CursorArg cursorArg, LimitArg limitArg)
ResponseDataObject<DatasetsWebService.DatasetPermissionsValueObject>	DatasetsWebService.getDatasetVisibility(DatasetArg<?> datasetArg)	Curation-UI compatibility alias for DatasetsWebService.getDatasetPermissions(DatasetArg).
jakarta.ws.rs.core.Response	AnnotationSetsWebService.getDraftForDataset(DatasetArg<?> datasetArg, String onBehalfOf)	Fetch a curator's DRAFT for the given dataset.
ResponseDataObject<Set<AnnotationValueObject>>	DatasetsWebService.getSampleCharacteristics(DatasetArg<?> datasetArg, Long bioAssayId)
jakarta.ws.rs.core.Response	AnnotationSetsWebService.listAnnotationSets(DatasetArg<?> datasetArg, String role, String source, String createdBy, String shape)	List annotation sets attached to a dataset, newest first.
jakarta.ws.rs.core.Response	DatasetsWebService.listDatasetAnnotationSets(DatasetArg<?> datasetArg, String role, String source, String createdBy, String shape)
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.
jakarta.ws.rs.core.Response	DatasetsWebService.markFactorValueNeedsAttention(DatasetArg<?> datasetArg, Long factorValueId, DatasetsWebService.FactorValueNeedsAttentionRequest body)	Open a "needs attention" ticket against a factor value.
ResponseDataObject<QuantitationTypeValueObject>	DatasetsWebService.patchDatasetQuantitationType(DatasetArg<?> datasetArg, Long qtId, DatasetsWebService.QuantitationTypePatchRequest body)	Body-driven PATCH dispatcher for a quantitation type.
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.
jakarta.ws.rs.core.Response	DatasetsWebService.recordCurationDecision(DatasetArg<?> datasetArg, String onBehalfOf, DatasetsWebService.CurationDecisionRequest body)	Record a curator's standing ruling that a change must NOT be made -- or, rarely, that one may be.
jakarta.ws.rs.core.Response	DatasetsWebService.redoDatasetDifferentialAnalysis(DatasetArg<?> datasetArg, Long analysisId)
jakarta.ws.rs.core.Response	DatasetsWebService.redoDatasetDifferentialAnalysisAlias(DatasetArg<?> datasetArg, Long analysisId)	Curation-UI compatibility alias for DatasetsWebService.redoDatasetDifferentialAnalysis(DatasetArg, Long): UI calls POST /datasets/{id}/analyses/differential/{aid}/redo; the canonical handler lives at /tasks/redo/{analysisId}.
jakarta.ws.rs.core.Response	DatasetsWebService.refreshDataset(DatasetArg<?> datasetArg, Boolean refreshVectors, Boolean refreshReports)	Retrieve a "refreshed" dataset.
jakarta.ws.rs.core.Response	DatasetsWebService.releaseCurationLock(DatasetArg<?> datasetArg, String onBehalfOf)
jakarta.ws.rs.core.Response	AnnotationsWebService.removeDatasetAnnotation(DatasetArg<?> datasetArg, Long annotationId, String onBehalfOf)
jakarta.ws.rs.core.Response	DatasetsWebService.removeDatasetAnnotationTag(DatasetArg<?> datasetArg, Long annotationId, String onBehalfOf)
jakarta.ws.rs.core.Response	DatasetsWebService.removeDatasetDifferentialAnalysis(DatasetArg<?> datasetArg, Long analysisId)
jakarta.ws.rs.core.Response	DatasetsWebService.removeDatasetDifferentialAnalysisAlias(DatasetArg<?> datasetArg, Long analysisId)	Curation-UI compatibility alias for DatasetsWebService.removeDatasetDifferentialAnalysis(DatasetArg, Long): UI calls DELETE /datasets/{id}/analyses/differential/{aid}.
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)
jakarta.ws.rs.core.Response	DatasetsWebService.replaceDatasetDesign(DatasetArg<?> datasetArg, Boolean force, Long agentProposalId, ExperimentalDesignValueObject proposed)	Apply a proposed ExperimentalDesignValueObject as the experiment's new design.
ResponseDataObject<DatasetsWebService.CurationCommitReport>	DatasetsWebService.restoreDatasetCurationFromSnapshot(DatasetArg<?> datasetArg, Long setId, Boolean dryRun, Boolean force, String onBehalfOf)
jakarta.ws.rs.core.Response	DatasetsWebService.runDatasetBatchInformationFetch(DatasetArg<?> datasetArg)
jakarta.ws.rs.core.Response	DatasetsWebService.runDatasetBatchInformationFetchAlias(DatasetArg<?> datasetArg)	Curation-UI compatibility alias for DatasetsWebService.runDatasetBatchInformationFetch(DatasetArg): UI calls POST /datasets/{id}/batchInformation/fetch.
jakarta.ws.rs.core.Response	DatasetsWebService.runDatasetDiagnostics(DatasetArg<?> datasetArg)
jakarta.ws.rs.core.Response	DatasetsWebService.runDatasetDiagnosticsAlias(DatasetArg<?> datasetArg)	Curation-UI compatibility alias for DatasetsWebService.runDatasetDiagnostics(DatasetArg): UI calls POST /datasets/{id}/preprocess/diagnostics.
jakarta.ws.rs.core.Response	DatasetsWebService.runDatasetDifferentialAnalysis(DatasetArg<?> datasetArg, DatasetsWebService.DifferentialAnalysisRunRequest body)
jakarta.ws.rs.core.Response	DatasetsWebService.runDatasetDifferentialAnalysisAlias(DatasetArg<?> datasetArg, DatasetsWebService.DifferentialAnalysisRunRequest body)	Alias for DatasetsWebService.runDatasetDifferentialAnalysis(DatasetArg, DifferentialAnalysisRunRequest) that exposes the DEA dispatch under /datasets/{id}/analyses/differential.
jakarta.ws.rs.core.Response	DatasetsWebService.runDatasetGeeq(DatasetArg<?> datasetArg, GeeqService.ScoreMode mode)
jakarta.ws.rs.core.Response	DatasetsWebService.runDatasetPreprocess(DatasetArg<?> datasetArg)
jakarta.ws.rs.core.Response	DatasetsWebService.runDatasetPreprocessAlias(DatasetArg<?> datasetArg)	Curation-UI compatibility alias for DatasetsWebService.runDatasetPreprocess(DatasetArg): UI calls POST /datasets/{id}/preprocess.
jakarta.ws.rs.core.Response	DatasetsWebService.runDatasetSvd(DatasetArg<?> datasetArg)
jakarta.ws.rs.core.Response	DatasetsWebService.runDatasetSwitchPlatform(DatasetArg<?> datasetArg, DatasetsWebService.PlatformSwitchRequest body)
SearchWebService.SearchResultsResponseDataObject	SearchWebService.search(QueryArg query, DatasetArg<?> datasetArg, TaxonArg<?> taxonArg, PlatformArg<?> platformArg, List<String> resultTypes, LimitArg limit, ExcludeArg<SearchResult<?>> excludeArg, boolean useGeneOntology, boolean inferRelations)	Search everything subject to taxon and platform constraints.
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)
jakarta.ws.rs.core.Response	DatasetsWebService.snapshotDatasetCuration(DatasetArg<?> datasetArg, String createdBy)
jakarta.ws.rs.core.Response	AnnotationSetsWebService.submitAnnotationSet(DatasetArg<?> datasetArg, AnnotationSetsWebService.AnnotationSetRequest body)	Create or upsert an annotation set on a dataset.
jakarta.ws.rs.core.Response	DatasetsWebService.submitDatasetAnnotationSet(DatasetArg<?> datasetArg, AnnotationSetsWebService.AnnotationSetRequest body)
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<Set<AnnotationValueObject>>	DatasetsWebService.updateSampleCharacteristics(DatasetArg<?> datasetArg, Long bioAssayId, DatasetsWebService.AnnotationsUpdateRequest body)
jakarta.ws.rs.core.Response	DatasetsWebService.upsertDatasetDraftAnnotationSet(DatasetArg<?> datasetArg, String onBehalfOf, AnnotationSetsWebService.UpsertDraftRequest body)
jakarta.ws.rs.core.Response	AnnotationSetsWebService.upsertDraftForDataset(DatasetArg<?> datasetArg, String onBehalfOf, AnnotationSetsWebService.UpsertDraftRequest body)	Upsert a curator's DRAFT for the given dataset.

Uses of DatasetArg in ubic.gemma.rest.util.args

Subclasses of DatasetArg in ubic.gemma.rest.util.args

Modifier and Type	Class	Description
class	DatasetIdArg	Long argument type for dataset API, referencing the Dataset ID.
class	DatasetStringArg	String argument type for dataset API, referencing the Dataset short name.

Methods in ubic.gemma.rest.util.args that return DatasetArg

Modifier and Type	Method	Description
static DatasetArg<?>	DatasetArg.valueOf(String s)	Used by RS to parse value of request parameters.

Methods in ubic.gemma.rest.util.args with parameters of type DatasetArg

Modifier and Type	Method	Description
DatasetArgService.DesignChangeResult	DatasetArgService.applyDesignChange(DatasetArg<?> arg, ExperimentalDesignValueObject proposed, boolean force)	Validate and apply a proposed design replacement.
Set<AnnotationValueObject>	DatasetArgService.getAnnotations(DatasetArg<?> arg)
Set<AnnotationValueObject>	DatasetArgService.getAnnotations(DatasetArg<?> arg, boolean includeFreeText)
Long	DatasetArgService.getEntityId(DatasetArg<?> datasetArg)	Retrieve an ID for a given dataset argument.
ExperimentalDesignValueObject	DatasetArgService.getExperimentalDesign(DatasetArg<?> arg)
List<ArrayDesignValueObject>	DatasetArgService.getOriginalPlatforms(DatasetArg<?> arg)	The platforms the dataset was originally submitted on, before any switch — empty when it was never switched.
List<ArrayDesignValueObject>	DatasetArgService.getPlatforms(DatasetArg<?> arg)	Retrieves the Platforms of the Dataset that this argument represents.
QuantitationType	DatasetArgService.getPreferredQuantitationType(DatasetArg<?> datasetArg)
List<DatasetPublicationValueObject>	DatasetArgService.getPublications(DatasetArg<?> datasetArg)
List<DatasetPublicationValueObject>	DatasetArgService.getPublications(DatasetArg<?> datasetArg, boolean includeRejected)	A dataset's publications, each carrying the evidenced claim that attaches it.
Set<QuantitationTypeValueObject>	DatasetArgService.getQuantitationTypes(DatasetArg<?> arg)	Retrieve a dataset with quantitation type initialized.
List<BioAssayValueObject>	DatasetArgService.getSamples(DatasetArg<?> arg, boolean includePredictedOutliers)
List<BioAssayValueObject>	DatasetArgService.getSamples(DatasetArg<?> datasetArg, QuantitationType qt, boolean includePredictedOutliers)	Obtain a collection of BioAssays that represent the experiments samples for a particular quantitation type.
CursorPage<BioAssayValueObject>	DatasetArgService.getSamplesByCursor(DatasetArg<?> arg, Cursor cursor, int limit, boolean includePredictedOutliers)	Cursor-mode counterpart to DatasetArgService.getSamples(DatasetArg, boolean) for the GET /datasets/{dataset}/samples endpoint — see CURSOR_PAGINATION_STEP1_PLAN.md step 1k.
ExpressionExperimentSubSet	DatasetArgService.getSubSet(DatasetArg<?> datasetArg, Long subSetId)
List<Long>	DatasetArgService.getSubSetGroupIds(DatasetArg<?> datasetArg, ExpressionExperimentSubSet subset)
List<ExpressionExperimentSubSet>	DatasetArgService.getSubSets(DatasetArg<?> datasetArg)
List<BioAssayValueObject>	DatasetArgService.getSubSetSamples(DatasetArg<?> datasetArg, Long subSetId, boolean includePredictedOutliers)
CursorPage<BioAssayValueObject>	DatasetArgService.getSubSetSamplesByCursor(DatasetArg<?> datasetArg, Long subSetId, Cursor cursor, int limit, boolean includePredictedOutliers)	Cursor-mode counterpart to DatasetArgService.getSubSetSamples(DatasetArg, Long, boolean) for the GET /datasets/{dataset}/subSets/{subSet}/samples endpoint — see CURSOR_PAGINATION_STEP1_PLAN.md step 1u (the subset-scoped twin of step 1k for GET /datasets/{dataset}/samples).
Map<ExpressionExperimentSubSet, List<Long>>	DatasetArgService.getSubSetsGroupIds(DatasetArg<?> datasetArg)
DesignPreflightReport	DatasetArgService.previewDesignChange(DatasetArg<?> arg, ExperimentalDesignValueObject proposed)	Run a dry-run preflight for the proposed design replacement.
DesignPreflightReport	DatasetArgService.previewDesignChange(DatasetArg<?> arg, ExperimentalDesignValueObject proposed, DesignCommitPlan plan)	Run a dry-run preflight for a design commit, counting the bindings plan defers to a second apply pass.