Package ubic.gemma.persistence.service.expression.experiment

Class BlacklistedEntityDaoImpl

java.lang.Object

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

ubic.gemma.persistence.service.AbstractVoEnabledDao<BlacklistedEntity,BlacklistedValueObject>

ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityDaoImpl

All Implemented Interfaces:

BaseDao<BlacklistedEntity>, BaseVoEnabledDao<BlacklistedEntity,BlacklistedValueObject>, BlacklistedEntityDao

@Repository
public class BlacklistedEntityDaoImpl
extends AbstractVoEnabledDao<BlacklistedEntity,BlacklistedValueObject>
implements BlacklistedEntityDao

Author:

paul

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

elementClass, log

Constructor Summary

Constructors

Constructor	Description
BlacklistedEntityDaoImpl(SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
protected BlacklistedValueObject	doLoadValueObject(BlacklistedEntity entity)	Load a value object for a given entity.
BlacklistedEntity	findByAccession(String accession)
Collection<ExpressionExperiment>	getNonBlacklistedExpressionExperiments(ArrayDesign arrayDesign)
boolean	isBlacklisted(String accession)
boolean	isBlacklisted(ArrayDesign platform)
boolean	isBlacklisted(ExpressionExperiment dataset)
int	removeAll()

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, find, findByProperty, findByPropertyIn, findOneByProperty, findOrCreate, getBatchSize, getElementClass, getIdentifierPropertyName, getSessionFactory, load, load, loadAll, loadReference, loadReference, remove, remove, remove, save, save, 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, find, findOrCreate, getElementClass, getIdentifierPropertyName, load, load, loadAll, loadReference, loadReference, remove, remove, remove, save, save, update, update

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Constructor Detail

BlacklistedEntityDaoImpl

@Autowired
public BlacklistedEntityDaoImpl(SessionFactory sessionFactory)

Method Detail

findByAccession

public BlacklistedEntity findByAccession(String accession)

Specified by:

findByAccession in interface BlacklistedEntityDao

Parameters:

accession - accession to search for (typically either a GPL or GSE)

Returns:

null if not blacklisted, or a BlackListedPlatform or BlackListedExperiment.

isBlacklisted

public boolean isBlacklisted(ArrayDesign platform)

Specified by:

isBlacklisted in interface BlacklistedEntityDao

isBlacklisted

public boolean isBlacklisted(ExpressionExperiment dataset)

Specified by:

isBlacklisted in interface BlacklistedEntityDao

isBlacklisted

public boolean isBlacklisted(String accession)

Specified by:

isBlacklisted in interface BlacklistedEntityDao

doLoadValueObject

protected BlacklistedValueObject doLoadValueObject(BlacklistedEntity 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<BlacklistedEntity,BlacklistedValueObject>

getNonBlacklistedExpressionExperiments

public Collection<ExpressionExperiment> getNonBlacklistedExpressionExperiments(ArrayDesign arrayDesign)

Specified by:

getNonBlacklistedExpressionExperiments in interface BlacklistedEntityDao

removeAll

public int removeAll()

Specified by:

removeAll in interface BlacklistedEntityDao