Package ubic.gemma.persistence.service.analysis.expression

Class ExpressionExperimentSetDaoImpl

java.lang.Object

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

ubic.gemma.persistence.service.AbstractVoEnabledDao<ExpressionExperimentSet,ExpressionExperimentSetValueObject>

ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl

All Implemented Interfaces:

ExpressionExperimentSetDao, BaseDao<ExpressionExperimentSet>, BaseVoEnabledDao<ExpressionExperimentSet,ExpressionExperimentSetValueObject>

@Repository
public class ExpressionExperimentSetDaoImpl
extends AbstractVoEnabledDao<ExpressionExperimentSet,ExpressionExperimentSetValueObject>
implements ExpressionExperimentSetDao

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

log

Constructor Summary

Constructors

Constructor	Description
ExpressionExperimentSetDaoImpl(SessionFactory sessionFactory, ExpressionExperimentDao expressionExperimentDao)

Method Summary

Modifier and Type	Method	Description
protected ExpressionExperimentSetValueObject	doLoadValueObject(ExpressionExperimentSet entity)	Load a value object for a given entity.
List<ExpressionExperimentSetValueObject>	doLoadValueObjects(Collection<ExpressionExperimentSet> entities)	Load all the value objects for the given entities.
Collection<ExpressionExperimentSet>	find(ExpressionExperiment ee)
Collection<ExpressionExperimentSet>	findByAccession(String accession)
Collection<ExpressionExperimentSet>	findByAccession(String accession, ExternalDatabase externalDatabase)
Collection<ExpressionExperimentSet>	findByName(String name)
Collection<ExpressionExperiment>	getExperimentsInSet(Long id)
Collection<ExpressionExperimentDetailsValueObject>	getExperimentValueObjectsInSet(Long id)
Collection<ExpressionExperimentSet>	loadAllExperimentSetsWithTaxon()
Collection<ExpressionExperimentSetValueObject>	loadAllValueObjects(boolean loadEEIds)
ExpressionExperimentSetValueObject	loadValueObject(Long id, boolean loadEEIds)
List<ExpressionExperimentSetValueObject>	loadValueObjects(Collection<Long> eeSetIds, boolean loadEEIds)
void	thaw(ExpressionExperimentSet expressionExperimentSet)

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

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, 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, find, findOrCreate, getElementClass, getIdentifierPropertyName, 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

ExpressionExperimentSetDaoImpl

@Autowired
public ExpressionExperimentSetDaoImpl(SessionFactory sessionFactory,
 ExpressionExperimentDao expressionExperimentDao)

Method Details

find

public Collection<ExpressionExperimentSet> find(ExpressionExperiment ee)

Specified by:

find in interface ExpressionExperimentSetDao

Parameters:

ee - bio assay set

Returns:

expressionExperimentSets that contain the given ee.

findByName

public Collection<ExpressionExperimentSet> findByName(String name)

Specified by:

findByName in interface ExpressionExperimentSetDao

findByAccession

public Collection<ExpressionExperimentSet> findByAccession(String accession)

Specified by:

findByAccession in interface ExpressionExperimentSetDao

findByAccession

public Collection<ExpressionExperimentSet> findByAccession(String accession,
 ExternalDatabase externalDatabase)

Specified by:

findByAccession in interface ExpressionExperimentSetDao

getExperimentsInSet

public Collection<ExpressionExperiment> getExperimentsInSet(Long id)

Specified by:

getExperimentsInSet in interface ExpressionExperimentSetDao

Parameters:

id - id

Returns:

the security-filtered list of experiments in a set. It is possible for the return to be empty even if the set is not (due to security filters). Use this instead of expressionExperimentSet.getExperiments.

loadAllExperimentSetsWithTaxon

public Collection<ExpressionExperimentSet> loadAllExperimentSetsWithTaxon()

Specified by:

loadAllExperimentSetsWithTaxon in interface ExpressionExperimentSetDao

Returns:

ExpressionExperimentSets that have more than 1 experiment in them & have a taxon value.

thaw

public void thaw(ExpressionExperimentSet expressionExperimentSet)

Specified by:

thaw in interface ExpressionExperimentSetDao

loadAllValueObjects

public Collection<ExpressionExperimentSetValueObject> loadAllValueObjects(boolean loadEEIds)

Specified by:

loadAllValueObjects in interface ExpressionExperimentSetDao

Parameters:

loadEEIds - whether the returned value object should have the ExpressionExperimentIds collection populated. This might be a useful information, but loading the IDs takes slightly longer, so for larger amount of EESets this might want to be avoided.

Returns:

ee vos

loadValueObjects

public List<ExpressionExperimentSetValueObject> loadValueObjects(Collection<Long> eeSetIds,
 boolean loadEEIds)

Specified by:

loadValueObjects in interface ExpressionExperimentSetDao

Parameters:

eeSetIds - ids

loadEEIds - whether the returned value object should have the ExpressionExperimentIds collection populated. This might be a useful information, but loading the IDs takes slightly longer, so for larger amount of EESets this might want to be avoided.

Returns:

ee vos

getExperimentValueObjectsInSet

public Collection<ExpressionExperimentDetailsValueObject> getExperimentValueObjectsInSet(Long id)

Specified by:

getExperimentValueObjectsInSet in interface ExpressionExperimentSetDao

loadValueObject

public ExpressionExperimentSetValueObject loadValueObject(Long id,
 boolean loadEEIds)

Specified by:

loadValueObject in interface ExpressionExperimentSetDao

Parameters:

id - id

loadEEIds - whether the returned value object should have the ExpressionExperimentIds collection populated. This might be a useful information, but loading the IDs takes slightly longer, so for larger amount of EESets this might want to be avoided.

Returns:

ee vos

doLoadValueObject

protected ExpressionExperimentSetValueObject doLoadValueObject(ExpressionExperimentSet 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<ExpressionExperimentSet,ExpressionExperimentSetValueObject>

doLoadValueObjects

public List<ExpressionExperimentSetValueObject> doLoadValueObjects(Collection<ExpressionExperimentSet> entities)

Description copied from class: AbstractVoEnabledDao

Load all the value objects for the given entities.

The default is to apply AbstractVoEnabledDao.doLoadValueObject(Identifiable) on each entry and weed out null elements.

This method should be fast and any post-processing should happen in AbstractVoEnabledDao.postProcessValueObjects(List).

Overrides:

doLoadValueObjects in class AbstractVoEnabledDao<ExpressionExperimentSet,ExpressionExperimentSetValueObject>