Package ubic.gemma.persistence.service

Class AbstractDao<T extends Identifiable>

java.lang.Object

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

All Implemented Interfaces:

BaseDao<T>

Direct Known Subclasses:

AbstractDesignElementDataVectorDao, AbstractVoEnabledDao, AnnotationAssociationDaoImpl, AuditEventDaoImpl, AuditTrailDaoImpl, BlatAssociationDaoImpl, ChromosomeDaoImpl, CoexpressionNodeDegreeDaoImpl, CompoundDaoImpl, ContactDaoImpl, DifferentialExpressionEvidenceDaoImpl, DifferentialExpressionResultDaoImpl, ExperimentalDesignDaoImpl, ExperimentalEvidenceDaoImpl, ExpressionExperimentSubSetDaoImpl, ExternalDatabaseDaoImpl, Gene2GOAssociationDaoImpl, GeneAliasDaoImpl, GeneDiffExMetaAnalysisDaoImpl, GenericEvidenceDaoImpl, GenericExperimentDaoImpl, GeneSetDaoImpl, GeneSetMemberDaoImpl, LiteratureEvidenceDaoImpl, PersonDaoImpl, PhenotypeAssociationDaoImpl, PrincipalComponentAnalysisDaoImpl, ProtocolDaoImpl, ReferenceAssociationDaoImpl, SingleExperimentAnalysisDaoBase, StatementDaoImpl, UnitDaoImpl, UserDaoImpl, UserGroupDaoImpl

public abstract class AbstractDao<T extends Identifiable>
extends Object
implements BaseDao<T>

AbstractDao can find the generic type at runtime and simplify the code implementation of the BaseDao interface

Author:

Anton, Nicolas

Field Summary

Fields

Modifier and Type	Field	Description
protected Class<? extends T>	elementClass
protected static org.apache.commons.logging.Log	log

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	AbstractDao(Class<? extends T> elementClass, SessionFactory sessionFactory)
protected	AbstractDao(Class<? extends T> elementClass, SessionFactory sessionFactory, ClassMetadata classMetadata)

Method Summary

Modifier and Type	Method	Description
long	countAll()	Counts all instances of specific class in the persitent storage.
Collection<T>	create(Collection<T> entities)	Crates all the given entities in the persistent storage.
T	create(T entity)	Create an object.
T	find(T entity)	Does a look up for the given entity in the persistent storage, usually looking for a specific identifier ( either id or a string property).
protected List<T>	findByProperty(String propertyName, Object propertyValue)	Does a search on given property and its value.
protected List<T>	findByPropertyIn(String propertyName, Collection<?> propertyValues)	Perform a search on a given property and all its possible values.
protected T	findOneByProperty(String propertyName, Object propertyValue)	Retrieve one entity whose given property matches the given value.
T	findOrCreate(T entity)	Calls the find method, and if this method returns null, creates a new instance in the persistent storage.
protected int	getBatchSize()
Class<? extends T>	getElementClass()	Obtain the element class of BaseDao.
String	getIdentifierPropertyName()	Obtain the identifiable property name for BaseDao.
protected SessionFactory	getSessionFactory()
T	load(Long id)	Loads the entity with given id from the persistent storage.
Collection<T>	load(Collection<Long> ids)	This implementation is temporary and attempts to best replicate the behaviour of loading entities by multiple IDs introduced in Hibernate 5.
Collection<T>	loadAll()	Loads all instanced of specific class from the persistent storage.
T	loadReference(Long id)	Load reference for an entity.
Collection<T>	loadReference(Collection<Long> ids)	Load references for all the given IDs.
void	remove(Long id)	Remove a persistent instance based on its ID.
void	remove(Collection<T> entities)
void	remove(T entity)	Remove a persistent instance
Collection<T>	save(Collection<T> entities)	Save all the given entities in the persistent storage.
T	save(T entity)	Create or update an entity whether it is transient.
void	update(Collection<T> entities)
void	update(T entity)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

log

protected static final org.apache.commons.logging.Log log

elementClass

protected final Class<? extends T extends Identifiable> elementClass

Constructor Detail

AbstractDao

protected AbstractDao(Class<? extends T> elementClass,
                      SessionFactory sessionFactory)

AbstractDao

protected AbstractDao(Class<? extends T> elementClass,
                      SessionFactory sessionFactory,
                      ClassMetadata classMetadata)

Parameters:

classMetadata - the class metadata to use to retrieve information about AbstractDao

Method Detail

getElementClass

public Class<? extends T> getElementClass()

Description copied from interface: BaseDao

Obtain the element class of BaseDao.

Specified by:

getElementClass in interface BaseDao<T extends Identifiable>

getIdentifierPropertyName

public String getIdentifierPropertyName()

Description copied from interface: BaseDao

Obtain the identifiable property name for BaseDao.

Specified by:

getIdentifierPropertyName in interface BaseDao<T extends Identifiable>

create

public Collection<T> create(Collection<T> entities)

Description copied from interface: BaseDao

Crates all the given entities in the persistent storage.

Specified by:

create in interface BaseDao<T extends Identifiable>

Parameters:

entities - the entities to be crated.

Returns:

collection of entities representing the instances in the persistent storage that were created.

create

@OverridingMethodsMustInvokeSuper
public T create(T 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<T extends Identifiable>

Parameters:

entity - the entity to create

Returns:

the persistent version of the entity

save

public Collection<T> save(Collection<T> entities)

Description copied from interface: BaseDao

Save all the given entities in the persistent storage.

Unlike BaseDao.update(Collection), this method does not attach the given entities to the persistence context; the returned values must be used instead.

Specified by:

save in interface BaseDao<T extends Identifiable>

See Also:

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

save

@OverridingMethodsMustInvokeSuper
public T save(T 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<T extends Identifiable>

See Also:

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

load

public Collection<T> load(Collection<Long> ids)

This implementation is temporary and attempts to best replicate the behaviour of loading entities by multiple IDs introduced in Hibernate 5. Read more about this.

Specified by:

load in interface BaseDao<T extends Identifiable>

Parameters:

ids - the IDs of entities to be loaded. If some IDs are not found or null, they are skipped.

Returns:

collection of entities with given ids.

load

public T load(Long id)

Description copied from interface: BaseDao

Loads the entity with given id from the persistent storage.

Specified by:

load in interface BaseDao<T extends Identifiable>

Parameters:

id - the id of entity to load.

Returns:

the entity with given ID, or null if such entity does not exist or if the passed ID was null

See Also:

Session.get(Class, Serializable)

loadAll

public Collection<T> loadAll()

Description copied from interface: BaseDao

Loads all instanced of specific class from the persistent storage.

Specified by:

loadAll in interface BaseDao<T extends Identifiable>

Returns:

a collection containing all instances that are currently accessible.

loadReference

public Collection<T> loadReference(Collection<Long> ids)

Description copied from interface: BaseDao

Load references for all the given IDs.

Entities already in the session will be returned directly.

Specified by:

loadReference in interface BaseDao<T extends Identifiable>

loadReference

@Nonnull
public T loadReference(Long id)

Description copied from interface: BaseDao

Load reference for an entity.

If the entity is already in the session, it will be returned instead. Note that unlike BaseDao.load(Long), this method will not return null if the entity does not exist.

You may freely access the Identifiable.getId() field without triggering proxy initialization.

Specified by:

loadReference in interface BaseDao<T extends Identifiable>

See Also:

Session.load(Object, Serializable)

countAll

public long countAll()

Description copied from interface: BaseDao

Counts all instances of specific class in the persitent storage.

Specified by:

countAll in interface BaseDao<T extends Identifiable>

Returns:

number that is the amount of instances currently accessible.

remove

public void remove(Collection<T> entities)

Specified by:

remove in interface BaseDao<T extends Identifiable>

remove

public void remove(Long id)

Description copied from interface: BaseDao

Remove a persistent instance based on its ID. The implementer is trusted to know what type of object to remove. Note that this method is to be avoided for Securable, because it will leave cruft in the ACL tables. We may fix this by having this method return the removed object.

Specified by:

remove in interface BaseDao<T extends Identifiable>

Parameters:

id - the ID of the entity to be removed

remove

@OverridingMethodsMustInvokeSuper
public void remove(T entity)

Description copied from interface: BaseDao

Remove a persistent instance

Specified by:

remove in interface BaseDao<T extends Identifiable>

Parameters:

entity - the entity to be removed

update

public void update(Collection<T> entities)

Specified by:

update in interface BaseDao<T extends Identifiable>

Parameters:

entities - Update the entities. Not supported if the entities are immutable.

update

@OverridingMethodsMustInvokeSuper
public void update(T entity)

Specified by:

update in interface BaseDao<T extends Identifiable>

Parameters:

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

find

public T find(T entity)

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<T extends Identifiable>

Parameters:

entity - the entity to look for.

Returns:

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

findOrCreate

public T findOrCreate(T entity)

Description copied from interface: BaseDao

Calls the find method, and if this method returns null, creates a new instance in the persistent storage.

Specified by:

findOrCreate in interface BaseDao<T extends Identifiable>

Parameters:

entity - the entity to look for and persist if not found.

Returns:

the given entity, guaranteed to be representing an entity present in the persistent storage.

getSessionFactory

protected final SessionFactory getSessionFactory()

getBatchSize

protected final int getBatchSize()

findOneByProperty

protected T findOneByProperty(String propertyName,
                              Object propertyValue)

Retrieve one entity whose given property matches the given value.

Note: the property should have a unique index, otherwise a NonUniqueResultException will be raised.

Parameters:

propertyName - the name of property to be matched.

propertyValue - the value to look for.

Returns:

an entity whose property matched the given value

findByProperty

protected List<T> findByProperty(String propertyName,
                                 Object propertyValue)

Does a search on given property and its value.

Parameters:

propertyName - the name of property to be matched.

propertyValue - the value to look for.

Returns:

an entity whose property first matched the given value.

findByPropertyIn

protected List<T> findByPropertyIn(String propertyName,
                                   Collection<?> propertyValues)

Perform a search on a given property and all its possible values.