Interface EeWriteService

All Known Implementing Classes:

EeWriteServiceImpl

public interface EeWriteService

Write service for ExpressionExperiment graphs.

This is the strangler-fig replacement for the EE-related portions of the former ExpressionPersister (deleted in Persister-shrink S1; the remaining polymorphic EE dispatch arms used only by test fixtures have been folded into PersisterHelperImpl.doPersist).

Author:

pavlidis

Method Summary

Modifier and Type	Method	Description
ExpressionExperiment	create(ExpressionExperiment ee)	Persist an ExpressionExperiment graph, synthesising the ArrayDesignsForExperimentCache via ExpressionExperimentPrePersistService.prepare(ExpressionExperiment) in the same transaction.
ExpressionExperiment	create(ExpressionExperiment ee, ArrayDesignsForExperimentCache cache)	Persist an ExpressionExperiment graph.
BioAssay	persistBioAssay(BioAssay bioAssay)	Persist a standalone BioAssay.
BioMaterial	persistBioMaterial(BioMaterial bioMaterial)	Persist a standalone BioMaterial.

Method Details

create

ExpressionExperiment create(ExpressionExperiment ee,
 @Nullable
 ArrayDesignsForExperimentCache cache)

Persist an ExpressionExperiment graph.

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

Parameters:

ee - the expression experiment to persist

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

Returns:

the persisted entity

create

ExpressionExperiment create(ExpressionExperiment ee)

Persist an ExpressionExperiment graph, synthesising the ArrayDesignsForExperimentCache via ExpressionExperimentPrePersistService.prepare(ExpressionExperiment) in the same transaction.

Prefer the two-argument create(ExpressionExperiment, ArrayDesignsForExperimentCache) overload when a cache is available from a prior, separate transaction (recommended for large platforms). This single-argument overload exists for the few callers (CellXGene, SplitExperiment, etc.) that build the EE graph in one transaction and accept the in-transaction prepare.

Parameters:

ee - the expression experiment to persist

Returns:

the persisted entity

persistBioAssay

BioAssay persistBioAssay(BioAssay bioAssay)

Persist a standalone BioAssay.

Persister-shrink S4c: public typed entry point added so test fixtures (notably PersistentDummyObjectHelper) can stop routing through the polymorphic PersisterHelper.persist(BioAssay) dispatch. The caller's BioAssay must reference an already-persistent ArrayDesign; this entry point allocates fresh per-call caches (xdb / taxon) and a null ArrayDesignsForExperimentCache — matching the prior persisterHelper.persist(BioAssay) semantics for stand-alone BA fixtures.

Parameters:

bioAssay - the bioassay to persist

Returns:

the persisted entity

persistBioMaterial

BioMaterial persistBioMaterial(BioMaterial bioMaterial)

Persist a standalone BioMaterial.

Persister-shrink S4c: public typed entry point added so test fixtures (notably PersistentDummyObjectHelper) can stop routing through the polymorphic PersisterHelper.persist(BioMaterial) dispatch. Allocates fresh per-call caches (xdb / taxon) — matches the prior persisterHelper.persist(BioMaterial) semantics.

Parameters:

bioMaterial - the biomaterial to persist

Returns:

the persisted entity