Interface PreboardedExperimentService

All Known Implementing Classes:

PreboardedExperimentServiceImpl

public interface PreboardedExperimentService

Service surface for PreboardedExperiment CRUD + accession resolution + promotion. See HANDOFF_PROPOSED_EXPERIMENT_WORKFLOW.md §"Required endpoints".

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static class	PreboardedExperimentService.AccessionAlreadyExistsException	Thrown by createPreboarded(String, String, String) when an existing entity carries the same accession.
static class	PreboardedExperimentService.PreboardedAlreadyPromotedException	Thrown by promote(ExpressionExperiment, PreboardedExperiment) when the preboarded has already been promoted.
static class	PreboardedExperimentService.PromotionResult	Return value of promote(ExpressionExperiment, PreboardedExperiment).

Method Summary

Modifier and Type	Method	Description
PreboardedExperiment	createPreboarded(String accession, String source, String identifyingMetadata)	Create a new preboarded for the given accession.
List<PreboardedExperiment>	findAllByAccession(String accession)
PreboardedExperiment	findByAccession(String accession)
ExpressionExperiment	findExpressionExperimentByAccession(String accession)	Look up an existing ExpressionExperiment carrying the given accession.
PreboardedExperiment	load(Long id)
Map<Long,String>	loadAccessions(Collection<Long> ids)	Accessions for a set of preboarded ids, in ONE query.
PreboardedExperimentService.PromotionResult	promote(ExpressionExperiment ee, PreboardedExperiment preboarded)	Promote the preboarded to a loaded ExpressionExperiment.

Method Details

createPreboarded

PreboardedExperiment createPreboarded(String accession,
 @Nullable
 String source,
 @Nullable
 String identifyingMetadata)
                               throws PreboardedExperimentService.AccessionAlreadyExistsException

Create a new preboarded for the given accession.

Throws PreboardedExperimentService.AccessionAlreadyExistsException if an existing PreboardedExperiment OR ExpressionExperiment already carries the same accession. The exception carries the existing entity's id and type so the REST layer can mint a 409 response per spec.

Emits a PreboardedCreatedEvent audit row against the new preboarded's own audit trail.

Throws:

PreboardedExperimentService.AccessionAlreadyExistsException

load

@Nullable
PreboardedExperiment load(Long id)

Returns:

the preboarded with the given id, or null.

loadAccessions

Map<Long,String> loadAccessions(Collection<Long> ids)

Accessions for a set of preboarded ids, in ONE query.

Batched on purpose: the ticket navigator resolves the labels for a whole page of tickets at once, and a batch triage ticket carries every candidate from its scrape. Resolving one id at a time would put an N+1 on the server, which is the thing TicketsWebService.resolveTargetLabels exists to avoid.

Returns:

accession by id; ids that do not exist are simply absent

findByAccession

@Nullable
PreboardedExperiment findByAccession(String accession)

Returns:

the preboarded with the given accession, or null.

findAllByAccession

List<PreboardedExperiment> findAllByAccession(String accession)

Returns:

list of preboarded with the given accession (defensive — only one is expected; the create path enforces uniqueness).

findExpressionExperimentByAccession

@Nullable
ExpressionExperiment findExpressionExperimentByAccession(String accession)

Look up an existing ExpressionExperiment carrying the given accession. Used by the POST /preboarded 409 path: if the data is already loaded as an EE, the caller should write against the EE directly rather than create a preboarded.

Returns:

the existing EE with this accession, or null.

promote

PreboardedExperimentService.PromotionResult promote(ExpressionExperiment ee,
 PreboardedExperiment preboarded)
                                             throws PreboardedExperimentService.PreboardedAlreadyPromotedException

Promote the preboarded to a loaded ExpressionExperiment.

The implementation rebinds every AnnotationSet attached to the preboarded so it points at the EE row instead (new-row + FK rebind approach; see STATUS_PROPOSED_EXPERIMENT_WORKFLOW.md for the trade-off discussion). The preboarded's workflow state is advanced to Loaded (terminal marker — the row is retained for history; it carries no curatable artifacts) and the EE's workflow state is advanced to Loaded too.

Emits a PreboardedPromotedEvent on the EE's audit trail (post-promotion the EE is the authoritative parent of the trail). The ee argument is first so the @Audited aspect picks the EE as the audit target rather than the preboarded.

Throws PreboardedExperimentService.PreboardedAlreadyPromotedException if the preboarded's workflow state is already Loaded (or beyond).

Returns:

the promoted-from / promoted-to pair + counts the REST layer needs for the 200 response.

Throws:

PreboardedExperimentService.PreboardedAlreadyPromotedException