Class ArrayDesignPersister

java.lang.Object

ubic.gemma.persistence.persister.ArrayDesignPersister

@Component("arrayDesignPersister")
public class ArrayDesignPersister
extends Object

Handles persisting array designs.

Persister-shrink S2c: lifted out of the GenomePersister inheritance chain into a concrete @Component. Genome and Common collaboration is via @Autowired fields (genome, common); the protected doPersist entry point remains so the still-extant RelationshipPersister chain keeps compiling (delegates to persistArrayDesign(ArrayDesign) for the AD arm, falls through to genome.doGenome / common.doCommon, then throws).

Phase 3 persister retirement: rewired to BusinessKey.find(Session, ArrayDesign) for the root-level "find existing" lookup, with the compositeSequences and externalReferences collections flowing through Hibernate's cascade="all" on ArrayDesign.getCompositeSequences() and ArrayDesign.getExternalReferences() (see ArrayDesign.hbm.xml). The remaining responsibilities here are:

• Pre-resolve BioSequence per composite sequence — BioSequences have their own lifecycle (shared across array designs) and are not cascaded from CompositeSequence; they must be looked up / created before dao.create.
• Pre-resolve the design provider, primary taxon, and the external database for each external reference — these are many-to-one associations without cascade.

The ArrayDesignsForExperimentCache contract is unaffected: that cache is populated explicitly by ExpressionExperimentPrePersistServiceImpl and GeoServiceImpl, never as a side effect of this persister.

Author:

pavlidis

Constructor Summary

Constructors

Constructor	Description
ArrayDesignPersister()

Method Summary

Modifier and Type	Method	Description
ArrayDesign	doArrayDesign(Object entity, Map<String, ExternalDatabase> xdbCache)	Persister-shrink S2c typed dispatch: returns null if the entity is not an ArrayDesign.
protected <T extends Identifiable> T	doPersist(T entity, Map<String, ExternalDatabase> xdbCache)	Polymorphic dispatch entry point reached by RelationshipPersister via the still-extant inheritance chain.
protected <T extends Identifiable> T	doPersistOrUpdate(T entity, Map<String, ExternalDatabase> xdbCache)	Polymorphic persist-or-update dispatch entry point reached by the chain.
protected SessionFactory	getSessionFactory()
ArrayDesign	persistArrayDesign(ArrayDesign arrayDesign)	Persister-shrink S3 public entry point: find an existing ArrayDesign by business key, else create.
ArrayDesign	persistArrayDesign(ArrayDesign arrayDesign, Map<String, ExternalDatabase> xdbCache, Map<Object,Taxon> taxonCache, Map<Integer, Chromosome> chromosomeCache)	Look up an existing ArrayDesign by business key (shortName, alternate names, or name — see BusinessKey.matches(CriteriaBuilder, From, ArrayDesign)); otherwise create a new one along with its full graph.

Methods inherited from class Object

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

Constructor Details

ArrayDesignPersister

public ArrayDesignPersister()

Method Details

getSessionFactory

protected SessionFactory getSessionFactory()

doPersist

@Nullable
protected <T extends Identifiable> T doPersist(T entity,
 Map<String, ExternalDatabase> xdbCache)

Polymorphic dispatch entry point reached by RelationshipPersister via the still-extant inheritance chain. Handles the AD arm itself; everything else falls through to GenomePersister.doGenome(T, Map) then CommonPersister.doCommon(T, Map), else throws.

doPersistOrUpdate

protected <T extends Identifiable> T doPersistOrUpdate(T entity,
 Map<String, ExternalDatabase> xdbCache)

Polymorphic persist-or-update dispatch entry point reached by the chain. AD does not own any update arm of its own; everything routes through Genome.

doArrayDesign

@Nullable
public ArrayDesign doArrayDesign(Object entity,
 Map<String, ExternalDatabase> xdbCache)

Persister-shrink S2c typed dispatch: returns null if the entity is not an ArrayDesign. Used by the S2e dispatcher.

persistArrayDesign

@Transactional
public ArrayDesign persistArrayDesign(ArrayDesign arrayDesign)

Persister-shrink S3 public entry point: find an existing ArrayDesign by business key, else create. Owns the FlushMode.MANUAL window formerly carried by PersisterHelperImpl.persist(ubic.gemma.model.common.Identifiable); caches are fresh per call (matches prior PHI semantics).

persistArrayDesign

public ArrayDesign persistArrayDesign(ArrayDesign arrayDesign,
 Map<String, ExternalDatabase> xdbCache,
 Map<Object,Taxon> taxonCache,
 Map<Integer, Chromosome> chromosomeCache)

Look up an existing ArrayDesign by business key (shortName, alternate names, or name — see BusinessKey.matches(CriteriaBuilder, From, ArrayDesign)); otherwise create a new one along with its full graph. Public after S2c so the S2e dispatcher (and future direct callers) can reach it.