Package ubic.gemma.persistence.service.expression.arrayDesign

Interface CuratableService<C extends Curatable,VO extends AbstractCuratableValueObject<C>>

All Superinterfaces:

BaseImmutableService<C>, BaseReadOnlyService<C>, BaseService<C>, BaseVoEnabledService<C,VO>, FilteringService<C>, FilteringVoEnabledService<C,VO>

All Known Subinterfaces:

ArrayDesignService, ExpressionExperimentService

All Known Implementing Classes:

ArrayDesignServiceImpl, ExpressionExperimentServiceImpl

public interface CuratableService<C extends Curatable,VO extends AbstractCuratableValueObject<C>>
extends BaseService<C>, FilteringVoEnabledService<C,VO>

Interface for curatable services.

For now, this mainly adds Secured annotations to safeguard methods inherited from BaseService.

Author:

poirigui

Method Summary

Modifier and Type	Method	Description
C	create(C curatable)	Creates the given entity in the persistent storage.
Collection<C>	create(Collection<C> entities)	Creates all the given entities in a persistent storage
C	find(C curatable)	Does a search for the entity in the persistent storage
C	findOrCreate(C curatable)	Does a search for the entity in the persistent storage, and if not found, creates it.
C	load(Long id)	Loads object with given ID.
Collection<C>	load(Collection<Long> ids)	Loads objects with given ids.
List<C>	load(Filters filters, Sort sort)
Slice<C>	load(Filters filters, Sort sort, int offset, int limit)
Collection<C>	loadAll()	Loads all the entities of specific type.
List<VO>	loadAllValueObjects()	Loads value objects representing all the entities of specific type.
List<Long>	loadIds(Filters filters, Sort sort)
C	loadOrFail(Long id)	Convenience for running BaseReadOnlyService.load(Long) and checking if the result is null.
<T extends Exception> C	loadOrFail(Long id, Function<String,T> exceptionSupplier)	Load an entity or fail with the supplied exception; the message is generated automatically.
<T extends Exception> C	loadOrFail(Long id, Function<String,T> exceptionSupplier, String message)	Load an entity or fail with the supplied exception and message.
<T extends Exception> C	loadOrFail(Long id, Supplier<T> exceptionSupplier)	Load an entity or fail with the supplied exception.
VO	loadValueObject(C entity)
VO	loadValueObjectById(Long entityId)
List<VO>	loadValueObjects(Collection<C> entities)	Loads value objects for all given entities.
List<VO>	loadValueObjects(Filters filters, Sort sort)
Slice<VO>	loadValueObjects(Filters filters, Sort sort, int offset, int limit)
List<VO>	loadValueObjectsByIds(Collection<Long> ids)	Load value objects by a given collection of IDs.
void	remove(C expressionExperiment)	Removes the given entity from the persistent storage.
void	remove(Long id)	Removes the entity with given ID from the persistent storage.
C	save(C entity)
Collection<C>	save(Collection<C> entities)
void	update(C entity)	Updates the given entity in the persistent storage.
void	update(Collection<C> entities)	Updates all entities in the given collection in the persistent storage.

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

remove

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

countAll, findOrFail, getElementClass

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

count, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getIdentifierPropertyName, getSort

Method Detail

find

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ_QUIET"})
C find(C curatable)

Description copied from interface: BaseReadOnlyService

Does a search for the entity in the persistent storage

Specified by:

find in interface BaseReadOnlyService<C extends Curatable>

Parameters:

curatable - the entity to be searched for

Returns:

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

findOrCreate

@Secured({"GROUP_USER","AFTER_ACL_READ"})
C findOrCreate(C curatable)

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<C extends Curatable>

Parameters:

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

Returns:

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

create

@Secured("GROUP_USER")
Collection<C> create(Collection<C> entities)

Description copied from interface: BaseImmutableService

Creates all the given entities in a persistent storage

Specified by:

create in interface BaseImmutableService<C extends Curatable>

Parameters:

entities - the entities to be created.

Returns:

collection of objects referencing the persistent instances of given entities.

create

@Secured("GROUP_USER")
C create(C curatable)

Description copied from interface: BaseImmutableService

Creates the given entity in the persistent storage.

Specified by:

create in interface BaseImmutableService<C extends Curatable>

Parameters:

curatable - the entity to be created.

Returns:

object referencing the persistent instance of the given entity.

load

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<C> load(Collection<Long> ids)

Description copied from interface: BaseReadOnlyService

Loads objects with given ids.

Specified by:

load in interface BaseReadOnlyService<C extends Curatable>

Parameters:

ids - the ids of objects to be loaded.

Returns:

collection containing object with given IDs.

load

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ_QUIET"})
C load(Long id)

Description copied from interface: BaseReadOnlyService

Loads object with given ID.

Specified by:

load in interface BaseReadOnlyService<C extends Curatable>

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
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
C loadOrFail(Long id)
      throws NullPointerException

Description copied from interface: BaseReadOnlyService

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

Specified by:

loadOrFail in interface BaseReadOnlyService<C extends Curatable>

Parameters:

id - the ID used to retrieve the entity

Returns:

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

Throws:

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

loadOrFail

@Nonnull
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
<T extends Exception> C loadOrFail(Long id,
                                   Supplier<T> exceptionSupplier)
                            throws T extends Exception

Description copied from interface: BaseReadOnlyService

Load an entity or fail with the supplied exception.

Specified by:

loadOrFail in interface BaseReadOnlyService<C extends Curatable>

Throws:

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

T extends Exception

loadOrFail

@Nonnull
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
<T extends Exception> C loadOrFail(Long id,
                                   Function<String,T> exceptionSupplier)
                            throws T extends Exception

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<C extends Curatable>

Throws:

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

T extends Exception

loadOrFail

@Nonnull
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
<T extends Exception> C loadOrFail(Long id,
                                   Function<String,T> exceptionSupplier,
                                   String message)
                            throws T extends Exception

Description copied from interface: BaseReadOnlyService

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

Specified by:

loadOrFail in interface BaseReadOnlyService<C extends Curatable>

Throws:

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

T extends Exception

loadAll

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<C> loadAll()

Description copied from interface: BaseReadOnlyService

Loads all the entities of specific type.

Specified by:

loadAll in interface BaseReadOnlyService<C extends Curatable>

Returns:

collection of all entities currently available in the persistent storage.

loadIds

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
List<Long> loadIds(@Nullable
                   Filters filters,
                   @Nullable
                   Sort sort)

Specified by:

loadIds in interface FilteringService<C extends Curatable>

See Also:

FilteringDao.loadIds(Filters, Sort)

load

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
List<C> load(@Nullable
             Filters filters,
             @Nullable
             Sort sort)

Specified by:

load in interface FilteringService<C extends Curatable>

See Also:

FilteringDao.load(Filters, Sort)

load

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
Slice<C> load(@Nullable
              Filters filters,
              @Nullable
              Sort sort,
              int offset,
              int limit)

Specified by:

load in interface FilteringService<C extends Curatable>

See Also:

FilteringDao.load(Filters, Sort, int, int)

loadValueObjects

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
List<VO> loadValueObjects(@Nullable
                          Filters filters,
                          @Nullable
                          Sort sort)

Specified by:

loadValueObjects in interface FilteringVoEnabledService<C extends Curatable,VO extends AbstractCuratableValueObject<C>>

See Also:

FilteringVoEnabledDao.loadValueObjects(Filters, Sort)

loadValueObjects

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
Slice<VO> loadValueObjects(@Nullable
                           Filters filters,
                           @Nullable
                           Sort sort,
                           int offset,
                           int limit)

Specified by:

loadValueObjects in interface FilteringVoEnabledService<C extends Curatable,VO extends AbstractCuratableValueObject<C>>

See Also:

FilteringVoEnabledDao.loadValueObjects(Filters, Sort, int, int)

loadValueObject

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_READ"})
VO loadValueObject(C entity)

Specified by:

loadValueObject in interface BaseVoEnabledService<C extends Curatable,VO extends AbstractCuratableValueObject<C>>

See Also:

BaseVoEnabledDao.loadValueObject(Identifiable)

loadValueObjectById

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_READ"})
VO loadValueObjectById(Long entityId)

Specified by:

loadValueObjectById in interface BaseVoEnabledService<C extends Curatable,VO extends AbstractCuratableValueObject<C>>

See Also:

BaseVoEnabledDao.loadValueObjectById(Long)

loadValueObjects

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"})
List<VO> loadValueObjects(Collection<C> entities)

Description copied from interface: BaseVoEnabledService

Loads value objects for all given entities.

Specified by:

loadValueObjects in interface BaseVoEnabledService<C extends Curatable,VO extends AbstractCuratableValueObject<C>>

Parameters:

entities - the entities to be converted to value objects

Returns:

a collection of value objects representing he given entities.

loadValueObjectsByIds

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"})
List<VO> loadValueObjectsByIds(Collection<Long> ids)

Description copied from interface: BaseVoEnabledService

Load value objects by a given collection of IDs.

Specified by:

loadValueObjectsByIds in interface BaseVoEnabledService<C extends Curatable,VO extends AbstractCuratableValueObject<C>>

loadAllValueObjects

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"})
List<VO> loadAllValueObjects()

Description copied from interface: BaseVoEnabledService

Loads value objects representing all the entities of specific type.

Specified by:

loadAllValueObjects in interface BaseVoEnabledService<C extends Curatable,VO extends AbstractCuratableValueObject<C>>

Returns:

a collection of value objects

save

@Secured({"GROUP_USER","ACL_SECURABLE_COLLECTION_EDIT_IGNORE_TRANSIENT"})
Collection<C> save(Collection<C> entities)

Specified by:

save in interface BaseService<C extends Curatable>

See Also:

BaseDao.save(Collection)

save

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT_IGNORE_TRANSIENT"})
C save(C entity)

Specified by:

save in interface BaseService<C extends Curatable>

See Also:

BaseDao.save(Object)

update

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void update(C entity)

Description copied from interface: BaseService

Updates the given entity in the persistent storage.

Specified by:

update in interface BaseService<C extends Curatable>

Parameters:

entity - the entity to be updated.

update

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void update(Collection<C> entities)

Description copied from interface: BaseService

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

Specified by:

update in interface BaseService<C extends Curatable>

Parameters:

entities - the entities to be updated.

remove

@Secured("GROUP_ADMIN")
void remove(Long id)

Removes the entity with given ID from the persistent storage.

Only administrator are allowed to remove entity by ID.

Specified by:

remove in interface BaseImmutableService<C extends Curatable>

Parameters:

id - the ID of entity to be removed.

remove

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void remove(C expressionExperiment)

Description copied from interface: BaseImmutableService

Removes the given entity from the persistent storage.

Specified by:

remove in interface BaseImmutableService<C extends Curatable>

Parameters:

expressionExperiment - the entity to be removed.