Package ubic.gemma.persistence.service.expression.bioAssay

Class BioAssayDaoImpl

java.lang.Object

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

ubic.gemma.persistence.service.AbstractVoEnabledDao<BioAssay,BioAssayValueObject>

ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao<BioAssay,BioAssayValueObject>

ubic.gemma.persistence.service.expression.bioAssay.BioAssayDaoImpl

All Implemented Interfaces:

BaseDao<BioAssay>, BaseVoEnabledDao<BioAssay,BioAssayValueObject>, BioAssayDao, FilteringDao<BioAssay>, FilteringVoEnabledDao<BioAssay,BioAssayValueObject>

@Repository
public class BioAssayDaoImpl
extends AbstractNoopFilteringVoEnabledDao<BioAssay,BioAssayValueObject>
implements BioAssayDao

Author:

pavlidis

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
BioAssayDaoImpl(SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
protected BioAssayValueObject	doLoadValueObject(BioAssay entity)	Load a value object for a given entity.
BioAssay	find(BioAssay bioAssay)	Does a look up for the given entity in the persistent storage, usually looking for a specific identifier ( either id or a string property).
Collection<BioAssayDimension>	findBioAssayDimensions(BioAssay bioAssay)
Collection<BioAssay>	findByAccession(String accession)
BioAssay	findByShortName(String shortName)
Collection<BioAssaySet>	getBioAssaySets(BioAssay bioAssay)
List<BioAssayValueObject>	loadValueObjects(Collection<BioAssay> entities, Map<ArrayDesign,ArrayDesignValueObject> ad2vo, Map<BioAssay,BioAssay> assay2sourceAssayMap, boolean basic, boolean allFactorValues)

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

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyType, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery, load, load, loadIds, loadValueObjects, loadValueObjects

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

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

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyType, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery, load, load, loadIds

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

loadValueObjects, loadValueObjects

Constructor Details

BioAssayDaoImpl

@Autowired
public BioAssayDaoImpl(SessionFactory sessionFactory)

Method Details

find

public BioAssay find(BioAssay bioAssay)

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<BioAssay>

Overrides:

find in class AbstractDao<BioAssay>

Parameters:

bioAssay - the entity to look for.

Returns:

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

findByShortName

@Nullable
public BioAssay findByShortName(String shortName)

Specified by:

findByShortName in interface BioAssayDao

findBioAssayDimensions

public Collection<BioAssayDimension> findBioAssayDimensions(BioAssay bioAssay)

Specified by:

findBioAssayDimensions in interface BioAssayDao

findByAccession

public Collection<BioAssay> findByAccession(String accession)

Specified by:

findByAccession in interface BioAssayDao

getBioAssaySets

public Collection<BioAssaySet> getBioAssaySets(BioAssay bioAssay)

Specified by:

getBioAssaySets in interface BioAssayDao

loadValueObjects

public List<BioAssayValueObject> loadValueObjects(Collection<BioAssay> entities,
 @Nullable
 Map<ArrayDesign,ArrayDesignValueObject> ad2vo,
 @Nullable
 Map<BioAssay,BioAssay> assay2sourceAssayMap,
 boolean basic,
 boolean allFactorValues)

Specified by:

loadValueObjects in interface BioAssayDao

See Also:

• BioAssayValueObject(BioAssay, Map, BioAssay, boolean, boolean)

doLoadValueObject

protected BioAssayValueObject doLoadValueObject(BioAssay 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<BioAssay,BioAssayValueObject>