Class BibliographicReferenceDaoImpl
- java.lang.Object
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- ubic.gemma.persistence.service.AbstractDao<O>
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- ubic.gemma.persistence.service.AbstractVoEnabledDao<BibliographicReference,BibliographicReferenceValueObject>
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- ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl
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- 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
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Field Summary
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Fields inherited from class ubic.gemma.persistence.service.AbstractVoEnabledDao
REPORT_SLOW_QUERY_AFTER_MS
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Fields inherited from class ubic.gemma.persistence.service.AbstractDao
elementClass, log
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Constructor Summary
Constructors Constructor Description BibliographicReferenceDaoImpl(SessionFactory sessionFactory)
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Method Summary
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Methods inherited from class ubic.gemma.persistence.service.AbstractVoEnabledDao
doLoadValueObjects, loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds, postProcessValueObjects
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Methods inherited from class ubic.gemma.persistence.service.AbstractDao
countAll, create, create, findByProperty, findByPropertyIn, findOneByProperty, findOrCreate, getBatchSize, getElementClass, getIdentifierPropertyName, getSessionFactory, load, load, loadAll, loadReference, loadReference, remove, remove, remove, save, save, update, update
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface ubic.gemma.persistence.service.BaseDao
countAll, create, create, findOrCreate, getElementClass, getIdentifierPropertyName, load, load, loadAll, loadReference, loadReference, remove, remove, remove, save, save, update, update
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Methods inherited from interface ubic.gemma.persistence.service.BaseVoEnabledDao
loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds
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Constructor Detail
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BibliographicReferenceDaoImpl
@Autowired public BibliographicReferenceDaoImpl(SessionFactory sessionFactory)
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Method Detail
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findByExternalId
public BibliographicReference findByExternalId(String id, String databaseName)
- Specified by:
findByExternalId
in interfaceBibliographicReferenceDao
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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 interfaceBibliographicReferenceDao
- Parameters:
externalId
- external database id- Returns:
- found bibliographic reference
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getAllExperimentLinkedReferences
public Map<ExpressionExperiment,BibliographicReference> getAllExperimentLinkedReferences()
- Specified by:
getAllExperimentLinkedReferences
in interfaceBibliographicReferenceDao
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thaw
public BibliographicReference thaw(BibliographicReference bibliographicReference)
- Specified by:
thaw
in interfaceBibliographicReferenceDao
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thaw
public Collection<BibliographicReference> thaw(Collection<BibliographicReference> bibliographicReferences)
- Specified by:
thaw
in interfaceBibliographicReferenceDao
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getRelatedExperiments
public Map<BibliographicReference,Collection<ExpressionExperiment>> getRelatedExperiments(Collection<BibliographicReference> records)
- Specified by:
getRelatedExperiments
in interfaceBibliographicReferenceDao
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listAll
public Collection<Long> listAll()
- Specified by:
listAll
in interfaceBibliographicReferenceDao
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browse
public List<BibliographicReference> browse(int start, int limit)
- Specified by:
browse
in interfaceBrowsingDao<BibliographicReference>
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browse
public List<BibliographicReference> browse(int start, int limit, String orderField, boolean descending)
- Specified by:
browse
in interfaceBrowsingDao<BibliographicReference>
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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 interfaceBaseDao<BibliographicReference>
- Overrides:
find
in classAbstractDao<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.
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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 classAbstractVoEnabledDao<BibliographicReference,BibliographicReferenceValueObject>
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