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

Class BioMaterialDaoImpl

java.lang.Object

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

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

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)
Collection<BioMaterial>	findByFactor(ExperimentalFactor experimentalFactor)
List<BioMaterial>	findSubBioMaterials(Collection<BioMaterial> bioMaterials, boolean direct)	Find all the sub-biomaterials for a given biomaterial related by BioMaterial.getSourceBioMaterial().
List<BioMaterial>	findSubBioMaterials(BioMaterial bioMaterial, boolean direct)	Find all the sub-biomaterials for a given biomaterial related by BioMaterial.getSourceBioMaterial().
Map<BioMaterial,Map<BioAssay,ExpressionExperiment>>	getExpressionExperiments(BioMaterial bm)	Obtain all the experiments a biomaterial is used in from its hierarchy.
void	remove(BioMaterial entity)	Remove a persistent instance
BioMaterial	save(BioMaterial entity)	Create or update an entity whether it is transient.
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, getEntityName, getIdentifierPropertyName, getSessionFactory, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, save, streamAll, streamAll, streamQuery, 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, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, save, streamAll, streamAll, update

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Constructor Details

BioMaterialDaoImpl

@Autowired
public BioMaterialDaoImpl(SessionFactory sessionFactory)

Method Details

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(Identifiable), 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.

findSubBioMaterials

public List<BioMaterial> findSubBioMaterials(BioMaterial bioMaterial,
 boolean direct)

Description copied from interface: BioMaterialDao

Find all the sub-biomaterials for a given biomaterial related by BioMaterial.getSourceBioMaterial().

Specified by:

findSubBioMaterials in interface BioMaterialDao

Parameters:

direct - if true, only direct sub-biomaterials are retained, otherwise the entire hierarchy is visited recursively.

findSubBioMaterials

public List<BioMaterial> findSubBioMaterials(Collection<BioMaterial> bioMaterials,
 boolean direct)

Description copied from interface: BioMaterialDao

Find all the sub-biomaterials for a given biomaterial related by BioMaterial.getSourceBioMaterial().

Specified by:

findSubBioMaterials in interface BioMaterialDao

Parameters:

bioMaterials - a collection of biomaterials to visit

direct - if true, only direct sub-biomaterials are retained, otherwise the entire hierarchy is visited recursively.

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

findByFactor

public Collection<BioMaterial> findByFactor(ExperimentalFactor experimentalFactor)

Specified by:

findByFactor in interface BioMaterialDao

getExpressionExperiments

public Map<BioMaterial,Map<BioAssay,ExpressionExperiment>> getExpressionExperiments(BioMaterial bm)

Description copied from interface: BioMaterialDao

Obtain all the experiments a biomaterial is used in from its hierarchy.

This also includes experiments that are using this via one of their parent?

Specified by:

getExpressionExperiments 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>

remove

public void remove(BioMaterial entity)

Description copied from interface: BaseDao

Remove a persistent instance

Specified by:

remove in interface BaseDao<BioMaterial>

Overrides:

remove in class AbstractDao<BioMaterial>

Parameters:

entity - the entity to be removed