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

Class BibliographicReferenceDaoImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractDao<BibliographicReference>

ubic.gemma.persistence.service.AbstractVoEnabledDao<BibliographicReference,BibliographicReferenceValueObject>

ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl

All Implemented Interfaces:

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

@Repository
public class BibliographicReferenceDaoImpl
extends AbstractVoEnabledDao<BibliographicReference,BibliographicReferenceValueObject>
implements BibliographicReferenceDao

Author:

pavlidis

See Also:

• BibliographicReference

Field Summary

Fields inherited from class ubic.gemma.persistence.service.AbstractVoEnabledDao

REPORT_SLOW_QUERY_AFTER_MS

Fields inherited from class ubic.gemma.persistence.service.AbstractDao

log

Constructor Summary

Constructors

Constructor	Description
BibliographicReferenceDaoImpl(SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
List<BibliographicReference>	browse(int start, int limit)
List<BibliographicReference>	browse(int start, int limit, String orderField, boolean descending)
long	countExperimentLinkedReferences()	Count the number of distinct references that are linked to experiments.
protected BibliographicReferenceValueObject	doLoadValueObject(BibliographicReference entity)	Load a value object for a given entity.
BibliographicReference	find(BibliographicReference bibliographicReference)	Does a look up for the given entity in the persistent storage, usually looking for a specific identifier ( either id or a string property).
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 class ubic.gemma.persistence.service.AbstractVoEnabledDao

doLoadValueObjects, loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds, postProcessValueObjects

Methods inherited from class ubic.gemma.persistence.service.AbstractDao

countAll, create, create, findByProperty, findByPropertyIn, findOneByProperty, findOrCreate, getBatchSize, getElementClass, getEntityName, getIdentifierPropertyName, getSessionFactory, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, remove, save, save, streamAll, streamAll, streamQuery, update, update

Methods inherited from class java.lang.Object

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

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

countAll, create, create, 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

Constructor Details

BibliographicReferenceDaoImpl

@Autowired
public BibliographicReferenceDaoImpl(SessionFactory sessionFactory)

Method Details

findByExternalId

public BibliographicReference findByExternalId(String id,
 String databaseName)

Specified by:

findByExternalId in interface BibliographicReferenceDao

findByExternalId

public BibliographicReference findByExternalId(DatabaseEntry externalId)

Description copied from interface: BibliographicReferenceDao

Find by the external database id, such as for PubMed

Specified by:

findByExternalId in interface BibliographicReferenceDao

Parameters:

externalId - external database id

Returns:

found bibliographic reference

countExperimentLinkedReferences

public long countExperimentLinkedReferences()

Description copied from interface: BibliographicReferenceDao

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

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

Specified by:

countExperimentLinkedReferences in interface BibliographicReferenceDao

See Also:

• CitationValueObject

getAllExperimentLinkedReferences

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

Description copied from interface: BibliographicReferenceDao

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

References are sorted by author and title.

Specified by:

getAllExperimentLinkedReferences in interface BibliographicReferenceDao

thaw

public BibliographicReference thaw(BibliographicReference bibliographicReference)

Specified by:

thaw in interface BibliographicReferenceDao

thaw

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

Specified by:

thaw in interface BibliographicReferenceDao

getRelatedExperiments

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

Specified by:

getRelatedExperiments in interface BibliographicReferenceDao

listAll

public Collection<Long> listAll()

Specified by:

listAll in interface BibliographicReferenceDao

browse

public List<BibliographicReference> browse(int start,
 int limit)

Specified by:

browse in interface BrowsingDao<BibliographicReference>

browse

public List<BibliographicReference> browse(int start,
 int limit,
 String orderField,
 boolean descending)

Specified by:

browse in interface BrowsingDao<BibliographicReference>

find

public BibliographicReference find(BibliographicReference bibliographicReference)

Description copied from interface: BaseDao

Does a look up for the given entity in the persistent storage, usually looking for a specific identifier ( either id or a string property).

Specified by:

find in interface BaseDao<BibliographicReference>

Overrides:

find in class AbstractDao<BibliographicReference>

Parameters:

bibliographicReference - the entity to look for.

Returns:

an entity that was found in the persistent storage, or null if no such entity was found.

doLoadValueObject

protected BibliographicReferenceValueObject doLoadValueObject(BibliographicReference entity)

Description copied from class: AbstractVoEnabledDao

Load a value object for a given entity.

This should be fast and efficient, and avoid any database query or post-processing. If you need to perform additional queries, implement AbstractVoEnabledDao.postProcessValueObjects(List) instead.

Specified by:

doLoadValueObject in class AbstractVoEnabledDao<BibliographicReference,BibliographicReferenceValueObject>