Package ubic.gemma.persistence.service.common.description

Interface BibliographicReferenceDao

All Superinterfaces:

BaseDao<BibliographicReference>, BaseVoEnabledDao<BibliographicReference,BibliographicReferenceValueObject>, BrowsingDao<BibliographicReference>

All Known Implementing Classes:

BibliographicReferenceDaoImpl

public interface BibliographicReferenceDao
extends BrowsingDao<BibliographicReference>, BaseVoEnabledDao<BibliographicReference,BibliographicReferenceValueObject>

See Also:

• BibliographicReference

Method Summary

Modifier and Type	Method	Description
long	countExperimentLinkedReferences()	Count the number of distinct references that are linked to experiments.
BibliographicReference	findByExternalId(String id, String databaseName)
BibliographicReference	findByExternalId(DatabaseEntry externalId)	Find by the external database id, such as for PubMed
Map<BibliographicReference,Set<ExpressionExperiment>>	getAllExperimentLinkedReferences(int offset, int limit)	To save some space, the EEs only have their ID and short name filled.
Map<BibliographicReference,Collection<ExpressionExperiment>>	getRelatedExperiments(Collection<BibliographicReference> records)
Collection<Long>	listAll()
Collection<BibliographicReference>	thaw(Collection<BibliographicReference> bibliographicReferences)
BibliographicReference	thaw(BibliographicReference bibliographicReference)

Methods inherited from interface ubic.gemma.persistence.service.BaseDao

countAll, create, create, find, findOrCreate, getElementClass, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, remove, save, save, streamAll, streamAll, update, update

Methods inherited from interface ubic.gemma.persistence.service.BaseVoEnabledDao

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from interface ubic.gemma.persistence.service.BrowsingDao

browse, browse

Method Details

findByExternalId

BibliographicReference findByExternalId(String id,
 String databaseName)

findByExternalId

BibliographicReference findByExternalId(DatabaseEntry externalId)

Find by the external database id, such as for PubMed

Parameters:

externalId - external database id

Returns:

found bibliographic reference

countExperimentLinkedReferences

long countExperimentLinkedReferences()

Count the number of distinct references that are linked to experiments.

To be distinct, two references must have different author lists and titles.

See Also:

• CitationValueObject

getAllExperimentLinkedReferences

Map<BibliographicReference,Set<ExpressionExperiment>> getAllExperimentLinkedReferences(int offset,
 int limit)

To save some space, the EEs only have their ID and short name filled.

References are sorted by author and title.

thaw

BibliographicReference thaw(BibliographicReference bibliographicReference)

thaw

Collection<BibliographicReference> thaw(Collection<BibliographicReference> bibliographicReferences)

getRelatedExperiments

Map<BibliographicReference,Collection<ExpressionExperiment>> getRelatedExperiments(Collection<BibliographicReference> records)

listAll

Collection<Long> listAll()