Class PreboardedExperimentServiceImpl

java.lang.Object

ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentServiceImpl

All Implemented Interfaces:

PreboardedExperimentService

@Service
public class PreboardedExperimentServiceImpl
extends Object
implements PreboardedExperimentService

Default PreboardedExperimentService implementation.

The promotion path is the substantive piece: it calls into AnnotationSetService.rebindInvestigation(Investigation, Investigation) to point every AnnotationSet row at the loaded EE rather than the preboarded, then advances both rows' workflow state. Audit events are emitted declaratively via @Audited. The create path delegates to PreboardedAuditService so the proxy-intercepted return triggers the aspect against the freshly constructed preboarded — direct annotation on createPreboarded would not work because the AuditedAspect locates the auditable target on the argument list (the new preboarded is built inside the method body).

Nested Class Summary

Nested classes/interfaces inherited from interface PreboardedExperimentService

PreboardedExperimentService.AccessionAlreadyExistsException, PreboardedExperimentService.PreboardedAlreadyPromotedException, PreboardedExperimentService.PromotionResult

Constructor Summary

Constructors

Constructor	Description
PreboardedExperimentServiceImpl(SessionFactory sessionFactory, AnnotationSetService annotationSetService, ExpressionExperimentService expressionExperimentService, PreboardedAuditService preboardedAuditService)

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.

Methods inherited from class Object

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

Constructor Details

PreboardedExperimentServiceImpl

@Autowired
public PreboardedExperimentServiceImpl(SessionFactory sessionFactory,
 AnnotationSetService annotationSetService,
 ExpressionExperimentService expressionExperimentService,
 PreboardedAuditService preboardedAuditService)

Method Details

createPreboarded

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

Description copied from interface: PreboardedExperimentService

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.

Specified by:

createPreboarded in interface PreboardedExperimentService

Throws:

PreboardedExperimentService.AccessionAlreadyExistsException

load

@Nullable
@Transactional(readOnly=true)
public PreboardedExperiment load(Long id)

Specified by:

load in interface PreboardedExperimentService

Returns:

the preboarded with the given id, or null.

loadAccessions

@Transactional(readOnly=true)
public Map<Long,String> loadAccessions(Collection<Long> ids)

Description copied from interface: PreboardedExperimentService

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.

Specified by:

loadAccessions in interface PreboardedExperimentService

Returns:

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

findByAccession

@Nullable
@Transactional(readOnly=true)
public PreboardedExperiment findByAccession(String accession)

Specified by:

findByAccession in interface PreboardedExperimentService

Returns:

the preboarded with the given accession, or null.

findAllByAccession

@Transactional(readOnly=true)
public List<PreboardedExperiment> findAllByAccession(String accession)

Specified by:

findAllByAccession in interface PreboardedExperimentService

Returns:

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

findExpressionExperimentByAccession

@Nullable
@Transactional(readOnly=true)
public ExpressionExperiment findExpressionExperimentByAccession(String accession)

Description copied from interface: PreboardedExperimentService

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.

Specified by:

findExpressionExperimentByAccession in interface PreboardedExperimentService

Returns:

the existing EE with this accession, or null.

promote

@Transactional
@Audited(value=PreboardedPromotedEvent.class,
         messageSpel="'Preboarded#' + #preboarded.id + ' promoted to ExpressionExperiment#' + #ee.id + ' (annotation_sets_rebound=' + #result.annotationSetsRebound + ')'")
public PreboardedExperimentService.PromotionResult promote(ExpressionExperiment ee,
 PreboardedExperiment preboarded)
                                                    throws PreboardedExperimentService.PreboardedAlreadyPromotedException

Description copied from interface: PreboardedExperimentService

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).

Specified by:

promote in interface PreboardedExperimentService

Returns:

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

Throws:

PreboardedExperimentService.PreboardedAlreadyPromotedException