Package ubic.gemma.persistence.service.expression.biomaterial

Class BioMaterialDaoImpl

java.lang.Object

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

ubic.gemma.persistence.service.AbstractVoEnabledDao<BioMaterial,BioMaterialValueObject>

ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoImpl

All Implemented Interfaces:

BaseDao<BioMaterial>, BaseVoEnabledDao<BioMaterial,BioMaterialValueObject>, BioMaterialDao

@Repository
public class BioMaterialDaoImpl
extends AbstractVoEnabledDao<BioMaterial,BioMaterialValueObject>
implements BioMaterialDao

Author:

pavlidis

See Also:

BioMaterial

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
BioMaterialDaoImpl(SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
BioMaterial	copy(BioMaterial bioMaterial)
BioMaterial	create(BioMaterial entity)	Create an object.
protected BioMaterialValueObject	doLoadValueObject(BioMaterial entity)	Load a value object for a given entity.
BioMaterial	find(BioMaterial bioMaterial)	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<BioMaterial>	findByExperiment(ExpressionExperiment experiment)
ExpressionExperiment	getExpressionExperiment(Long bioMaterialId)
BioMaterial	save(BioMaterial entity)	Create or update an entity whether it is transient.
void	thaw(BioMaterial bioMaterial)	Thaw the given BioMaterial.
void	update(BioMaterial entity)

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

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Constructor Detail

BioMaterialDaoImpl

@Autowired
public BioMaterialDaoImpl(SessionFactory sessionFactory)

Method Detail

create

public BioMaterial create(BioMaterial entity)

Description copied from interface: BaseDao

Create an object. If the entity type is immutable, this may also remove any existing entities identified by an appropriate 'find' method.

Specified by:

create in interface BaseDao<BioMaterial>

Overrides:

create in class AbstractDao<BioMaterial>

Parameters:

entity - the entity to create

Returns:

the persistent version of the entity

save

public BioMaterial save(BioMaterial entity)

Description copied from interface: BaseDao

Create or update an entity whether it is transient.

Unlike BaseDao.update(Object), this method does not attach the given entity to the persistence context and the returned value must be used instead.

Specified by:

save in interface BaseDao<BioMaterial>

Overrides:

save in class AbstractDao<BioMaterial>

See Also:

Session.persist(Object), Session.merge(Object)

update

public void update(BioMaterial entity)

Specified by:

update in interface BaseDao<BioMaterial>

Overrides:

update in class AbstractDao<BioMaterial>

Parameters:

entity - Update the entity. Not supported if the entity is immutable.

find

public BioMaterial find(BioMaterial bioMaterial)

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<BioMaterial>

Overrides:

find in class AbstractDao<BioMaterial>

Parameters:

bioMaterial - the entity to look for.

Returns:

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

copy

public BioMaterial copy(BioMaterial bioMaterial)

Specified by:

copy in interface BioMaterialDao

findByExperiment

public Collection<BioMaterial> findByExperiment(ExpressionExperiment experiment)

Specified by:

findByExperiment in interface BioMaterialDao

getExpressionExperiment

public ExpressionExperiment getExpressionExperiment(Long bioMaterialId)

Specified by:

getExpressionExperiment in interface BioMaterialDao

Parameters:

bioMaterialId - biomaterial id

Returns:

the experiment the biomaterial appears in

thaw

public void thaw(BioMaterial bioMaterial)

Description copied from interface: BioMaterialDao

Thaw the given BioMaterial.

The following fields are initialized: sourceTaxon, treatments and factorValues.experimentalFactor.

Specified by:

thaw in interface BioMaterialDao

doLoadValueObject

protected BioMaterialValueObject doLoadValueObject(BioMaterial 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<BioMaterial,BioMaterialValueObject>