Package ubic.gemma.rest
package ubic.gemma.rest
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ClassDescriptionAdmin REST surface for curator-driven pipeline batch submissions.Admin-only system monitoring surface for the gemma-curation-ui admin panel.Response shape for
AdminWebService.getCurationStatus().Dry-run response.Body shape forAdminWebService.refreshOntology(String, boolean)returns.Wire shape forAdminWebService.reindexSearchIndices(String): list of entity classes whose reindex was queued.Payload ofPOST /admin/tasks/platform-reports: the id of the task that was queued.Endpoint forAnalysisResultSetConcreteResponseDataObjecttype for the pvalueDistribution endpoint so Swagger has a non-generic schema to reference.REST surface for the unifiedAnnotationSetentity.Full-payload response shape.Thin metadata response shape (no payloadJson).Wire shape of one per-finding ruling.Body forAnnotationSetsWebService.finalizeAnnotationSet(Long, String, AnnotationSetsWebService.FinalizeRequest); optional, and one field.Wire shape of one triage ruling.RESTful interface for annotations.Wire shape forGET /annotations/categories— carries the ontology term info plus a preferred-prefix list per category (config-driven viaannotation.category.prefixes).A relation on the wire.Diff-and-apply summary returned by the bulk PUT.One batch item: a literal label plus its optional per-item category hint.GET /annotations/searchenvelope: the standarddataarray plus, when identity matching ran, theAnnotationsWebService.NegativeEvidenceValueObjectbeside it.Request body forAnnotationsWebService.replaceDatasetAnnotations(DatasetArg, AnnotationsWebService.AnnotationsReplaceRequest): the full desired tag set plus an optionalannotationSetIdto attach to emitted audit events (linkage is parked until the source-AnnotationSet → emitted-event audit link lands — seeSTATUS_PUT_DATASETS_DESIGN.md).One row of the canonicalization table: the URI as stored, and the URI Gemma reports instead.A single representative usage of a searched term, for showing a hit in context.What an external naming authority says a query string is, when nothing Gemma has loaded names it — plus enough provenance to check the claim.Wire shape forLexicalTermMetadata.JSON-friendly enumeration of which Lucene field produced a hit.A single synonym of an ontology term plus its scope.A term prior curators chose for the query string, with the number of distinct experiments they chose it on.One term that was retrieved for the query and rejected as not naming it.What the ontology says about this term's species applicability.An organism an entry derives from.Bearer-token auth endpoints for the curation-UI SPA.JSON body forPOST /login.Wire payload forPOST /login—{token, user}.Wire payload forGET /datasets/{id}/auditEvents?compact=true.Prefix-aware completion suggestions for CLI / curation-UI / REST clients.Wire shape for a single completion suggestion.RESTful interface for datasets.Write-shape for an annotation tag.This is an aggregated entity across value URI and value, thus theidandobjectClassare omitted.One accepted rewrite the grounding gate applied to a persisted annotation — a case/whitespace-only near-match canonicalized to the term's label, a blank label filled in from its URI, and/or a known Gemma-ontology term (e.g.Which of the two stored sample-correlation matricesDatasetsWebService.getDatasetSampleCorrelation(DatasetArg, DatasetsWebService.CorrelationMatrixChoice)should return.The server's reply — mirrors CAB'sCurationCommitReport.Wire shape of one curation decision.curationDetails section.The whole desired curation state for one dataset (CAB'sCurationDocument).Body for the bulk lock routes.One dataset's outcome in a bulk lock request.Wire shape of the curation lock.Publications section — same identifier shape and set-replace semantics asPUT /publications.Which agent run is applying this commit.Cursor full-fidelity shape forDatasetsWebService.getDatasetAuditEvents(DatasetArg, CursorArg, LimitArg, boolean, boolean)(compact=false).Cursor-mode response shape forDatasetsWebService.getDatasetSamples(DatasetArg, QuantitationTypeArg, boolean, CursorArg, LimitArg, ExcludeArg, boolean).Cursor collapsed shape forDatasetsWebService.getDatasetAuditEvents(DatasetArg, CursorArg, LimitArg, boolean, boolean)(compact=true).Cursor shape forDatasetsWebService.getDatasetTickets(DatasetArg, CursorArg, LimitArg).Response body forDatasetsWebService.updateDatasetBasics(DatasetArg, DatasetsWebService.DatasetBasicsUpdateRequest)— the persisted name and description after the update.Optional request body forDatasetsWebService.importDataset(DatasetsWebService.DatasetImportRequest).Wire shape forDatasetsWebService.getDatasetMetadataFiles(DatasetArg): one entry per available metadata file.Lightweight view of a dataset's sharing state, returned by the permissions endpoint.Thin dataset projection for the typeahead/datasets/searchendpoint.The experimental-design section (CABDesignCommit).Identity half of every committable design entity: exactly one ofgemmaIdorclientRef.A group of subsets, logically organized by aBioAssayDimension.One experimental factor.One factor value, with the samples it applies to (by GSM short name) and its statements.Cursor-mode counterpart toDatasetsWebService.FilteredAndInferredAndPaginatedResponseDataObject.Wire shape forDatasetsWebService.getDatasetMeanVariance(DatasetArg): parallel mean / variance arrays.A per-factor-value numeric measurement (continuous factors).An ontology term reference — a human label plus an optional ontology URI.Sort direction forDatasetsWebService.getDatasetSvdLoadings(DatasetArg, Integer, Integer, DatasetsWebService.PcLoadingDirection):bothsorts by |loading| desc,positivefilters to loading > 0 desc,negativefilters to loading < 0 asc.Wire shape forDatasetsWebService.getDatasetSvdLoadings(DatasetArg, Integer, Integer, DatasetsWebService.PcLoadingDirection): the top-N probe loadings on a principal component plus the bioAssay scores on the same PC.Optional request body forDatasetsWebService.runDatasetSwitchPlatform(DatasetArg, DatasetsWebService.PlatformSwitchRequest).A single publication on theDatasetsWebService.updateDatasetPublications(DatasetArg, DatasetsWebService.PublicationsUpdateRequest)wire: which paper, and why.Wire shape for one metric column ofDatasetsWebService.SequencingQcMetricsValueObject.Cursor-mode counterpart toDatasetsWebService.QueriedAndFilteredAndInferredAndPaginatedResponseDataObject.Cursor shape forDatasetsWebService.getDatasetsExpressionLevelsForGene(GeneArg, QueryArg, FilterArg, OffsetArg, LimitArg, Boolean, ExpLevelConsolidationArg, CursorArg, Boolean)/DatasetsWebService.getDatasetsExpressionLevelsForGeneInTaxon(TaxonArg, GeneArg, QueryArg, FilterArg, OffsetArg, LimitArg, Boolean, ExpLevelConsolidationArg, CursorArg, Boolean).Legacy shape forDatasetsWebService.getDatasetsExpressionLevelsForGene(GeneArg, QueryArg, FilterArg, OffsetArg, LimitArg, Boolean, ExpLevelConsolidationArg, CursorArg, Boolean)/DatasetsWebService.getDatasetsExpressionLevelsForGeneInTaxon(TaxonArg, GeneArg, QueryArg, FilterArg, OffsetArg, LimitArg, Boolean, ExpLevelConsolidationArg, CursorArg, Boolean).Legacy full-fidelity shape forDatasetsWebService.getDatasetAuditEvents(DatasetArg, CursorArg, LimitArg, boolean, boolean)(compact=false).Legacy-mode response shape forDatasetsWebService.getDatasetSamples(DatasetArg, QuantitationTypeArg, boolean, CursorArg, LimitArg, ExcludeArg, boolean).Legacy collapsed shape forDatasetsWebService.getDatasetAuditEvents(DatasetArg, CursorArg, LimitArg, boolean, boolean)(compact=true).Legacy shape forDatasetsWebService.getDatasetTickets(DatasetArg, CursorArg, LimitArg).Wire shape for one sub-sample report row ofDatasetsWebService.SampleQcMetricsValueObject.One per-sample characteristic (CABSampleCharacteristicCommit); the sample is a GSM short name.Wire shape forDatasetsWebService.getDatasetSampleCorrelation(DatasetArg, DatasetsWebService.CorrelationMatrixChoice): a symmetric N×N Pearson correlation matrix with bioAssay ids + short names parallel to the rows/columns.Wire shape for one bioAssay's row ofDatasetsWebService.SequencingQcMetricsValueObject.A committable collection: authoritativeitemsplus explicitdeletedIds(the only way to remove).Wire shape forDatasetsWebService.getDatasetQcMetrics(DatasetArg).One row ofDatasetsWebService.getStaleDatasets(OffsetArg, LimitArg): a dataset owing pipeline work, and what it owes.One statement (subject / predicate / object triple with an optional category).One experiment-level tag (CABTagCommit); a statement-shaped tag rides itsstatements.One line of "what changed here recently" for a dataset: a short label, the event class it came from, when, and by whom.Dataset visualization endpoints.Experiment sets — named, ACL'd collections of datasets ("dataset groups" in the old DWR surface).Membership replacement body.Create / rename body.RESTful interface for genes.Enriched per-probe row returned byGeneWebService.getGeneProbes(GeneArg, OffsetArg, LimitArg, CursorArg, boolean)whensummary=true.One experiment's DEA results for the requested gene.RESTful interface for reverse GO-term lookup:GO term URI → genes annotated with it.Wire payload forGET /goTerms/{termUri}/genes/count.RESTful CRUD + member management for user groups (gap §3c ofGEMMA_UI_ENDPOINT_GAP.md).Body for POST /groups.Lightweight per-member projection — just the fields needed to render a member-list row.Lightweight projection for list pages — only the fields the curation UI needs to render a row.Body for PATCH /groups/{id}.Single-group response (no members list — useGroupsWebService.GroupWithMembersValueObjectfor that).Full response including member summaries; used forGET /groups/{id}?includeSummaries=trueand the membership-mutating endpoints so the caller doesn't need a follow-up GET.Body for POST /groups/{id}/members.AssemblesHeatmapDataValueObjectpayloads for theGET /datasets/{id}/heatmap-dataendpoint.Wire payload forGET /datasets/{id}/heatmap-data.OneExperimentalFactorValueObjectplus, for continuous factors, the per-sample measurement map (keyed by bioAssayId).Compact gene reference: official symbol + full name + Gemma ID + NCBI gene ID.Service-to-service push callback for scheduler-side pipelines reporting progress / terminal state.Serve the OpenAPI specification held by theopenApibean.Snapshot of every preprocessing/analysis pipeline step for a single experiment.RESTful interface for platforms.Which of the three annotation-file flavours written byArrayDesignAnnotationService.create(ArrayDesign, Boolean, boolean)to serve.REST surface for the proposed-experiment workflow.Thin annotation-set summary shown inline on the preboarded GET.Response of get/create preboarded.Response of promote.Wire payload forGET /resultSets/{id}/pvalueDistribution.Handles calls to the root API url and user info apiRequest body forRootWebService.changeMyPassword(RootWebService.ChangePasswordRequest).Provides search capabilities to the RESTful API.Representation ofSearchResultfor the RESTful API.Public statistics endpoints used by the Gemma home page and similar landing widgets.Snapshot of aSubmittedTaskfor the REST API.Machine-readable classification of a failed task, so a REST client can react to the failure (link to the existing experiment, correct the accession, retry a transient network error, or surface the raw detail) rather than parsing a free-text message.RESTful interface for polling background pipeline tasks submitted via the dispatch endpoints onDatasetsWebService(preprocess, diagnostics, batch info fetch, differential analysis run/redo/remove).RESTful interface for taxa.RESTful interface for curation tickets (Phase B-2 ofAUDIT_AS_WORKFLOW_RECCE.md).Body ofPOST /tickets/{id}/targets.Result of adding targets: which ids landed and which were already there.Result of removing a target: what went, and what state it was in.RESTful interface for the 8-state workflow lifecycle (HANDOFF_WORKFLOW_STATE_STORAGE.md).Response ofWorkflowWebService.getDatasetWorkflow(Long).