Package ubic.gemma.persistence.service

Class AbstractService<O extends Identifiable>

java.lang.Object

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

Type Parameters:

O - the Identifiable Object type that this service is handling.

All Implemented Interfaces:

BaseImmutableService<O>, BaseReadOnlyService<O>, BaseService<O>

Direct Known Subclasses:

AbstractBulkExpressionDataVectorService, AbstractFilteringVoEnabledService, AbstractVoEnabledService, AnnotationAssociationServiceImpl, AuditTrailServiceImpl, BlatAssociationServiceImpl, ChromosomeServiceImpl, CoexpressionAnalysisServiceImpl, CompoundServiceImpl, ContactServiceImpl, DifferentialExpressionAnalysisServiceImpl, DifferentialExpressionResultServiceImpl, ExperimentalDesignServiceImpl, ExpressionExperimentSubSetServiceImpl, ExternalDatabaseServiceImpl, Gene2GOAssociationServiceImpl, GeneDiffExMetaAnalysisServiceImpl, PrincipalComponentAnalysisServiceImpl, ProtocolServiceImpl

public abstract class AbstractService<O extends Identifiable>
extends Object
implements BaseService<O>

Base for all services handling DAO access.

Author:

tesarst

Field Summary

Fields

Modifier and Type	Field	Description
protected static final org.apache.commons.logging.Log	log

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	AbstractService(BaseDao<O> mainDao)

Method Summary

Modifier and Type	Method	Description
long	countAll()
Collection<O>	create(Collection<O> entities)	Creates all the given entities in a persistent storage
O	create(O entity)	Creates the given entity in the persistent storage.
protected Collection<O>	ensureInSession(Collection<O> entities)	Deprecated. avoid using this if possible and ensure that all operations are properly enclosed by a single Hibernate session
protected O	ensureInSession(O entity)	Deprecated. avoid using this if possible and ensure that all operations are properly enclosed by a single Hibernate session
O	find(O entity)	Does a search for the entity in the persistent storage
O	findOrCreate(O entity)	Does a search for the entity in the persistent storage, and if not found, creates it.
O	findOrFail(O entity)	Does a search for the entity in the persistent storage, raising a NullPointerException if not found.
Class<? extends O>	getElementClass()
O	load(Long id)	Loads object with given ID.
Collection<O>	load(Collection<Long> ids)	Loads objects with given ids.
Collection<O>	loadAll()	Loads all the entities of specific type.
O	loadOrFail(Long id)	Convenience for running BaseReadOnlyService.load(Long) and checking if the result is null.
<T extends Exception> O	loadOrFail(Long id, Function<String,T> exceptionSupplier)	Load an entity or fail with the supplied exception; the message is generated automatically.
<T extends Exception> O	loadOrFail(Long id, Function<String,T> exceptionSupplier, String message)	Load an entity or fail with the supplied exception and message.
<T extends Exception> O	loadOrFail(Long id, Supplier<T> exceptionSupplier)	Load an entity or fail with the supplied exception.
Collection<O>	loadOrFail(Collection<Long> ids)	Load multiple objects or fail with a NullPointerException if any of the objects does not exist in the persistent storage.
<T extends Exception> Collection<O>	loadOrFail(Collection<Long> ids, Function<String,T> exceptionSupplier)
void	remove(Long id)	Removes the entity with given ID from the persistent storage.
void	remove(Collection<O> entities)	Removes all the given entities from persistent storage.
void	remove(O entity)	Removes the given entity from the persistent storage.
Collection<O>	save(Collection<O> entities)
O	save(O entity)
Stream<O>	streamAll()
Stream<O>	streamAll(boolean createNewSession)
void	update(Collection<O> entities)	Updates all entities in the given collection in the persistent storage.
void	update(O entity)	Updates the given entity in the persistent storage.

Methods inherited from class java.lang.Object

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

Field Details

log

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

Constructor Details

AbstractService

protected AbstractService(BaseDao<O> mainDao)

Method Details

getElementClass

public Class<? extends O> getElementClass()

Specified by:

getElementClass in interface BaseReadOnlyService<O extends Identifiable>

find

@Transactional(readOnly=true)
public O find(O entity)

Description copied from interface: BaseReadOnlyService

Does a search for the entity in the persistent storage

Specified by:

find in interface BaseReadOnlyService<O extends Identifiable>

Parameters:

entity - the entity to be searched for

Returns:

the version of entity retrieved from the persistent storage, if found, otherwise null.

findOrFail

@Nonnull
@Transactional(readOnly=true)
public O findOrFail(O entity)

Description copied from interface: BaseReadOnlyService

Does a search for the entity in the persistent storage, raising a NullPointerException if not found.

Specified by:

findOrFail in interface BaseReadOnlyService<O extends Identifiable>

Parameters:

entity - the entity to be searched for

Returns:

the version of entity retrieved from persistent storage

findOrCreate

@Transactional
public O findOrCreate(O entity)

Description copied from interface: BaseImmutableService

Does a search for the entity in the persistent storage, and if not found, creates it.

Specified by:

findOrCreate in interface BaseImmutableService<O extends Identifiable>

Parameters:

entity - the entity to look for, and create if not found.

Returns:

the entity retrieved from the persistent storage, either found or created.

create

@Transactional
public Collection<O> create(Collection<O> entities)

Description copied from interface: BaseImmutableService

Creates all the given entities in a persistent storage

Specified by:

create in interface BaseImmutableService<O extends Identifiable>

Parameters:

entities - the entities to be created.

Returns:

collection of objects referencing the persistent instances of given entities.

create

@Transactional
@OverridingMethodsMustInvokeSuper
public O create(O entity)

Description copied from interface: BaseImmutableService

Creates the given entity in the persistent storage.

Specified by:

create in interface BaseImmutableService<O extends Identifiable>

Parameters:

entity - the entity to be created.

Returns:

object referencing the persistent instance of the given entity.

save

@Transactional
public Collection<O> save(Collection<O> entities)

Specified by:

save in interface BaseService<O extends Identifiable>

See Also:

• BaseDao.save(Collection)

save

@Transactional
@OverridingMethodsMustInvokeSuper
public O save(O entity)

Specified by:

save in interface BaseService<O extends Identifiable>

See Also:

• invalid reference

  BaseDao#save(Object)

load

@Transactional(readOnly=true)
public Collection<O> load(Collection<Long> ids)

Description copied from interface: BaseReadOnlyService

Loads objects with given ids.

Specified by:

load in interface BaseReadOnlyService<O extends Identifiable>

Parameters:

ids - the ids of objects to be loaded.

Returns:

collection containing object with given IDs.

loadOrFail

@Transactional(readOnly=true)
public Collection<O> loadOrFail(Collection<Long> ids)
                         throws NullPointerException

Description copied from interface: BaseReadOnlyService

Load multiple objects or fail with a NullPointerException if any of the objects does not exist in the persistent storage.

Specified by:

loadOrFail in interface BaseReadOnlyService<O extends Identifiable>

Throws:

NullPointerException

loadOrFail

@Transactional(readOnly=true)
public <T extends Exception> Collection<O> loadOrFail(Collection<Long> ids,
 Function<String,T> exceptionSupplier)
                                               throws T

Specified by:

loadOrFail in interface BaseReadOnlyService<O extends Identifiable>

Throws:

T

load

@Transactional(readOnly=true)
public O load(Long id)

Description copied from interface: BaseReadOnlyService

Loads object with given ID.

Specified by:

load in interface BaseReadOnlyService<O extends Identifiable>

Parameters:

id - the ID of entity to be loaded.

Returns:

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

loadOrFail

@Nonnull
@Transactional(readOnly=true)
public O loadOrFail(Long id)

Description copied from interface: BaseReadOnlyService

Convenience for running BaseReadOnlyService.load(Long) and checking if the result is null.

Specified by:

loadOrFail in interface BaseReadOnlyService<O extends Identifiable>

Parameters:

id - the ID used to retrieve the entity

Returns:

the entity as per BaseReadOnlyService.load(Long), never null

loadOrFail

@Nonnull
@Transactional(readOnly=true)
public <T extends Exception> O loadOrFail(Long id,
 Supplier<T> exceptionSupplier)
                                   throws T

Description copied from interface: BaseReadOnlyService

Load an entity or fail with the supplied exception.

Specified by:

loadOrFail in interface BaseReadOnlyService<O extends Identifiable>

Throws:

T - if the entity does not exist in the persistent storage

loadOrFail

@Nonnull
@Transactional(readOnly=true)
public <T extends Exception> O loadOrFail(Long id,
 Function<String,T> exceptionSupplier)
                                   throws T

Description copied from interface: BaseReadOnlyService

Load an entity or fail with the supplied exception; the message is generated automatically.

Specified by:

loadOrFail in interface BaseReadOnlyService<O extends Identifiable>

Throws:

T - if the entity does not exist in the persistent storage

loadOrFail

@Nonnull
@Transactional(readOnly=true)
public <T extends Exception> O loadOrFail(Long id,
 Function<String,T> exceptionSupplier,
 String message)
                                   throws T

Description copied from interface: BaseReadOnlyService

Load an entity or fail with the supplied exception and message.

Specified by:

loadOrFail in interface BaseReadOnlyService<O extends Identifiable>

Throws:

T - if the entity does not exist in the persistent storage

loadAll

@Transactional(readOnly=true)
public Collection<O> loadAll()

Description copied from interface: BaseReadOnlyService

Loads all the entities of specific type.

Specified by:

loadAll in interface BaseReadOnlyService<O extends Identifiable>

Returns:

collection of all entities currently available in the persistent storage.

countAll

@Transactional(readOnly=true)
public long countAll()

Specified by:

countAll in interface BaseReadOnlyService<O extends Identifiable>

streamAll

@Transactional(readOnly=true)
public Stream<O> streamAll()

Specified by:

streamAll in interface BaseReadOnlyService<O extends Identifiable>

streamAll

@Transactional(readOnly=true)
public Stream<O> streamAll(boolean createNewSession)

Specified by:

streamAll in interface BaseReadOnlyService<O extends Identifiable>

remove

@Transactional
public void remove(Collection<O> entities)

Description copied from interface: BaseImmutableService

Removes all the given entities from persistent storage.

Specified by:

remove in interface BaseImmutableService<O extends Identifiable>

Parameters:

entities - the entities to be removed.

remove

@Transactional
public void remove(Long id)

Description copied from interface: BaseImmutableService

Removes the entity with given ID from the persistent storage.

Specified by:

remove in interface BaseImmutableService<O extends Identifiable>

Parameters:

id - the ID of entity to be removed.

remove

@Transactional
@OverridingMethodsMustInvokeSuper
public void remove(O entity)

Description copied from interface: BaseImmutableService

Removes the given entity from the persistent storage.

Specified by:

remove in interface BaseImmutableService<O extends Identifiable>

Parameters:

entity - the entity to be removed.

update

@Transactional
public void update(Collection<O> entities)

Description copied from interface: BaseService

Updates all entities in the given collection in the persistent storage.

Specified by:

update in interface BaseService<O extends Identifiable>

Parameters:

entities - the entities to be updated.

update

@Transactional
@OverridingMethodsMustInvokeSuper
public void update(O entity)

Description copied from interface: BaseService

Updates the given entity in the persistent storage.

Specified by:

update in interface BaseService<O extends Identifiable>

Parameters:

entity - the entity to be updated.

ensureInSession

@Deprecated
@CheckReturnValue
protected O ensureInSession(O entity)

Deprecated.

avoid using this if possible and ensure that all operations are properly enclosed by a single Hibernate session

Ensure that a given entity is in the current session.

If not found in the current session, it will be retrieved from the persistent storage.

ensureInSession

@Deprecated
@CheckReturnValue
protected Collection<O> ensureInSession(Collection<O> entities)

Deprecated.

avoid using this if possible and ensure that all operations are properly enclosed by a single Hibernate session

Ensure that a collection of entities are in the current session.

Implementation note: if all entities are already in the session - or are transient, this call is very fast and does not involve any database interaction, otherwise the persistent entities are fetched in bulk.

See Also:

• ensureInSession(Identifiable)