Class EeWriteServiceImpl

java.lang.Object

ubic.gemma.persistence.persister.EeWriteServiceImpl

All Implemented Interfaces:

EeWriteService

@Component
public class EeWriteServiceImpl
extends Object
implements EeWriteService

Strangler-fig replacement for the EE-graph write path historically owned by ExpressionPersister (now removed; the polymorphic EE dispatch arms have been folded into PersisterHelperImpl.doPersist(Collection, Map)). Per-call caches are plumbed as explicit Map<KEY, VALUE> parameters (Phase 3 lift; formerly all carried on the now-deleted AbstractPersister.Caches POJO).

Persister-shrink S4a: this class autowires the typed leaf persister beans (CommonPersister, GenomePersister) directly rather than routing through PersisterHelperImpl. The former persister() AOP-unwrap helper and the PersisterHelper field are gone.

Author:

pavlidis

See Also:

• EeWriteService

Constructor Summary

Constructors

Constructor	Description
EeWriteServiceImpl()

Method Summary

Modifier and Type	Method	Description
ExpressionExperiment	create(ExpressionExperiment ee)	No-cache overload: synthesises the ArrayDesignsForExperimentCache via ExpressionExperimentPrePersistService.prepare(ExpressionExperiment) in the same transaction.
ExpressionExperiment	create(ExpressionExperiment ee, ArrayDesignsForExperimentCache cache)	Persist an ExpressionExperiment graph.
BioAssay	persistBioAssay(BioAssay bioAssay)	Persister-shrink S4c: public typed entry point for standalone BioAssay persistence.
BioMaterial	persistBioMaterial(BioMaterial bioMaterial)	Persister-shrink S4c: public typed entry point for standalone BioMaterial persistence.

Methods inherited from class Object

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

Constructor Details

EeWriteServiceImpl

public EeWriteServiceImpl()

Method Details

create

@Transactional
public ExpressionExperiment create(ExpressionExperiment ee,
 @Nullable
 ArrayDesignsForExperimentCache cache)

Description copied from interface: EeWriteService

Persist an ExpressionExperiment graph.

The cache should be obtained from a prior, separate transaction via ExpressionExperimentPrePersistService.prepare(ExpressionExperiment).

Specified by:

create in interface EeWriteService

Parameters:

ee - the expression experiment to persist

cache - cache of array designs already persisted in a prior transaction

Returns:

the persisted entity

create

@Transactional
public ExpressionExperiment create(ExpressionExperiment ee)

No-cache overload: synthesises the ArrayDesignsForExperimentCache via ExpressionExperimentPrePersistService.prepare(ExpressionExperiment) in the same transaction. Matches the historical behaviour of the polymorphic persisterHelper.persist(ee) dispatch (the former ExpressionPersister.doPersist EE arm did the same synthesis and emitted a warning recommending a separate transaction). The warning is preserved here.

Specified by:

create in interface EeWriteService

Parameters:

ee - the expression experiment to persist

Returns:

the persisted entity

persistBioAssay

@Transactional
public BioAssay persistBioAssay(BioAssay bioAssay)

Persister-shrink S4c: public typed entry point for standalone BioAssay persistence. Opens a FlushMode.MANUAL window matching the prior PersisterHelperImpl.persist(BioAssay) semantics, allocates fresh per-call caches, and delegates to the package-private persistBioAssay(BioAssay, Map, ArrayDesignsForExperimentCache, Map) helper. The ArrayDesignsForExperimentCache is null because the caller is providing an already-persistent platform on the BioAssay; see fillInBioAssayAssociations(BioAssay, Map, ArrayDesignsForExperimentCache, Map).

Specified by:

persistBioAssay in interface EeWriteService

Parameters:

bioAssay - the bioassay to persist

Returns:

the persisted entity

persistBioMaterial

@Transactional
public BioMaterial persistBioMaterial(BioMaterial bioMaterial)

Persister-shrink S4c: public typed entry point for standalone BioMaterial persistence. Opens a FlushMode.MANUAL window matching the prior PersisterHelperImpl.persist(BioMaterial) semantics, allocates fresh per-call caches, and delegates to the package-private persistBioMaterial(BioMaterial, Map, Map) helper.

Specified by:

persistBioMaterial in interface EeWriteService

Parameters:

bioMaterial - the biomaterial to persist

Returns:

the persisted entity