Class PreboardedWebService

java.lang.Object

ubic.gemma.rest.PreboardedWebService

@Service
@Path("/")
public class PreboardedWebService
extends Object

REST surface for the proposed-experiment workflow.

Six endpoints per HANDOFF_PROPOSED_EXPERIMENT_WORKFLOW.md:

• POST /preboarded — create a preboarded from an accession. 409 with existing entity id+type if accession is already known (either as a preboarded or a loaded EE).
• GET /preboarded/{id} — fetch preboarded + latest annotation set.
• GET /preboarded?accession=X — resolve accession to id.
• POST /preboarded/{id}/annotation-sets — attach an annotation set (typically a PROPOSAL role from an agent run), idempotent on (role, runId).
• POST /preboarded/{id}/promote — promote to a loaded EE. Restricted to GROUP_CURATOR / GROUP_ADMIN; agents cannot promote.
• GET /preboarded?state=... — list preboarded by workflow state (curator triage view).

Auth model (handoff §"Authorization"):

• POST preboarded + POST annotation-sets: GROUP_CURATOR / GROUP_ADMIN / GROUP_AGENT. Agents need to create preboarded and attach annotation sets.
• POST promote: GROUP_CURATOR / GROUP_ADMIN only. Agents MUST get 403.
• GET endpoints: any authenticated user (no @PreAuthorize on reads).

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	PreboardedWebService.AnnotationSetSnapshotResponse	Thin annotation-set summary shown inline on the preboarded GET.
static class	PreboardedWebService.AttachAnnotationSetRequest	Body of attachAnnotationSet(Long, PreboardedWebService.AttachAnnotationSetRequest).
static class	PreboardedWebService.CreatePreboardedRequest	Body of createPreboarded(PreboardedWebService.CreatePreboardedRequest).
static class	PreboardedWebService.PreboardedResponse	Response of get/create preboarded.
static class	PreboardedWebService.PromoteRequest	Body of promotePreboarded(Long, PreboardedWebService.PromoteRequest).
static class	PreboardedWebService.PromoteResponse	Response of promote.

Constructor Summary

Constructors

Constructor	Description
PreboardedWebService(PreboardedExperimentService preboardedService, AnnotationSetService annotationSetService, ExpressionExperimentService expressionExperimentService)

Method Summary

Modifier and Type	Method	Description
jakarta.ws.rs.core.Response	attachAnnotationSet(Long id, PreboardedWebService.AttachAnnotationSetRequest req)	Attach a new annotation set to a preboarded.
jakarta.ws.rs.core.Response	createPreboarded(PreboardedWebService.CreatePreboardedRequest req)	Create a new PreboardedExperiment for the supplied accession.
PreboardedWebService.PreboardedResponse	getPreboarded(Long id)	Fetch a preboarded by id + its latest annotation set (proposal role).
jakarta.ws.rs.core.Response	listOrResolvePreboarded(String accession, String stateName)	Listing endpoint: by accession (returns the single matching preboarded, 404 if none) or by state (queue view, returns the most-recent preboarded in that state — full pagination deferred).
jakarta.ws.rs.core.Response	promotePreboarded(Long id, PreboardedWebService.PromoteRequest req)	Promote a preboarded to a loaded ExpressionExperiment.

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

PreboardedWebService

@Autowired
public PreboardedWebService(PreboardedExperimentService preboardedService,
 AnnotationSetService annotationSetService,
 ExpressionExperimentService expressionExperimentService)

Method Details

createPreboarded

@POST
@Path("/preboarded")
@Consumes("application/json")
@Produces("application/json")
@PreAuthorize("hasAuthority('GROUP_CURATOR') or hasAuthority('GROUP_ADMIN') or hasAuthority('GROUP_AGENT')")
public jakarta.ws.rs.core.Response createPreboarded(@Nullable
 PreboardedWebService.CreatePreboardedRequest req)

Create a new PreboardedExperiment for the supplied accession. Returns 409 with the existing id+type if the accession already exists (as a preboarded OR an EE).

getPreboarded

@GET
@Path("/preboarded/{id}")
@Produces("application/json")
public PreboardedWebService.PreboardedResponse getPreboarded(@PathParam("id")
 Long id)

Fetch a preboarded by id + its latest annotation set (proposal role).

listOrResolvePreboarded

@GET
@Path("/preboarded")
@Produces("application/json")
public jakarta.ws.rs.core.Response listOrResolvePreboarded(@QueryParam("accession") @Nullable
 String accession,
 @QueryParam("state") @Nullable
 String stateName)

Listing endpoint: by accession (returns the single matching preboarded, 404 if none) or by state (queue view, returns the most-recent preboarded in that state — full pagination deferred).

attachAnnotationSet

@POST
@Path("/preboarded/{id}/annotation-sets")
@Consumes("application/json")
@Produces("application/json")
@PreAuthorize("hasAuthority('GROUP_CURATOR') or hasAuthority('GROUP_ADMIN') or hasAuthority('GROUP_AGENT')")
public jakarta.ws.rs.core.Response attachAnnotationSet(@PathParam("id")
 Long id,
 @Nullable
 PreboardedWebService.AttachAnnotationSetRequest req)

Attach a new annotation set to a preboarded. Idempotent on (role, runId): if a row with the same triple already exists, returns 200 OK with the existing row rather than 201 Created.

promotePreboarded

@POST
@Path("/preboarded/{id}/promote")
@Consumes("application/json")
@Produces("application/json")
@PreAuthorize("hasAuthority('GROUP_CURATOR') or hasAuthority('GROUP_ADMIN')")
public jakarta.ws.rs.core.Response promotePreboarded(@PathParam("id")
 Long id,
 @Nullable
 PreboardedWebService.PromoteRequest req)

Promote a preboarded to a loaded ExpressionExperiment.