ubic.gemma.persistence.service.common.description

Interface CharacteristicService

All Superinterfaces:

BaseReadOnlyService<Characteristic>, BaseService<Characteristic>, BaseVoEnabledService<Characteristic,CharacteristicValueObject>, FilteringService<Characteristic>

All Known Implementing Classes:

CharacteristicServiceImpl

public interface CharacteristicService
extends BaseVoEnabledService<Characteristic,CharacteristicValueObject>, FilteringService<Characteristic>

Author:

paul

Method Summary

Modifier and Type	Method and Description
List<Characteristic>	browse(int start, int limit) Browse through the characteristics, excluding GO annotations.
List<Characteristic>	browse(int start, int limit, String sortField, boolean descending) Browse through the characteristics, excluding GO annotations.
Map<String,Long>	countCharacteristicsByValueUri(Collection<String> uris)
Characteristic	create(Characteristic c) Creates the given entity in the persistent storage.
Collection<? extends Characteristic>	findByCategory(String queryPrefix)
Collection<Characteristic>	findByUri(Collection<String> uris) given a collection of strings that represent URI's will find all the characteristics that are used in the system with URI's matching anyone in the given collection
Collection<Characteristic>	findByUri(String searchString) Looks for an exact match of the give string to a valueUri in the characteristic database
Collection<Characteristic>	findByValue(String search) Returns a collection of characteristics that have a Value that match the given search string.
Map<String,Characteristic>	findCharacteristicsByValueUriOrValueLike(String search)
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>	findExperimentsByUris(Collection<String> uris, Taxon taxon, int limit)
Map<Characteristic,Long>	getParentIds(Class<?> parentClass, Collection<Characteristic> characteristics) Optimized version that only retrieves the IDs of the owning object.
Map<Characteristic,Object>	getParents(Collection<Characteristic> characteristics)
Map<Characteristic,Object>	getParents(Collection<Class<?>> classes, Collection<Characteristic> characteristics)
void	remove(Characteristic c) Removes the given entity from the persistent storage.
void	remove(Long id) Removes the entity with given ID from the persistent storage.
void	update(Characteristic c) Updates the given entity in the persistent storage.

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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

getObjectFilter, getObjectFilter, getSort

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

create, findOrCreate, remove, removeAllInBatch, save, save, update

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

countAll, find, findOrFail, load, load, loadAll, loadOrFail

Method Detail

browse

List<Characteristic> browse(int start,
                            int limit)

Browse through the characteristics, excluding GO annotations.

Parameters:

start - How far into the list to start

limit - Maximum records to retrieve

Returns:

characteristics

browse

List<Characteristic> browse(int start,
                            int limit,
                            String sortField,
                            boolean descending)

Browse through the characteristics, excluding GO annotations.

Parameters:

start - How far into the list to start

limit - Maximum records to retrieve

sortField - sort field

descending - sor order

Returns:

characteristics

findExperimentsByUris

Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>> findExperimentsByUris(Collection<String> uris,
                                                                                               @Nullable
                                                                                               Taxon taxon,
                                                                                               int limit)

See Also:

CharacteristicDao.findExperimentsByUris(Collection, Taxon, int)

findByUri

Collection<Characteristic> findByUri(Collection<String> uris)

given a collection of strings that represent URI's will find all the characteristics that are used in the system with URI's matching anyone in the given collection

Parameters:

uris - uris

Returns:

characteristics

findByUri

Collection<Characteristic> findByUri(String searchString)

Looks for an exact match of the give string to a valueUri in the characteristic database

Parameters:

searchString - search string

Returns:

characteristics

findByValue

Collection<Characteristic> findByValue(String search)

Returns a collection of characteristics that have a Value that match the given search string. The value is usually a human readable form of the termURI

Parameters:

search - search

Returns:

characteristics

findCharacteristicsByValueUriOrValueLike

Map<String,Characteristic> findCharacteristicsByValueUriOrValueLike(String search)

See Also:

CharacteristicDao.findCharacteristicsByValueUriOrValueLikeGroupedByNormalizedValue(String)

countCharacteristicsByValueUri

Map<String,Long> countCharacteristicsByValueUri(Collection<String> uris)

getParents

@Secured(value={"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_MAP_VALUES_READ"})
Map<Characteristic,Object> getParents(Collection<Characteristic> characteristics)

Parameters:

characteristics - characteristics

Returns:

a map of the specified characteristics to their annotated objects.

getParents

@Secured(value={"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_MAP_VALUES_READ"})
Map<Characteristic,Object> getParents(Collection<Class<?>> classes,
                                                                                                                   @Nullable
                                                                                                                   Collection<Characteristic> characteristics)

Parameters:

characteristics - characteristics

classes - classes

Returns:

a map of the specified characteristics to their parent objects, constrained to be among the classes given.

findByCategory

Collection<? extends Characteristic> findByCategory(String queryPrefix)

create

@Secured(value="GROUP_USER")
Characteristic create(Characteristic c)

Description copied from interface: BaseService

Creates the given entity in the persistent storage.

Specified by:

create in interface BaseService<Characteristic>

Parameters:

c - the entity to be created.

Returns:

object referencing the persistent instance of the given entity.

remove

@Secured(value="GROUP_USER")
void remove(Long id)

Description copied from interface: BaseService

Removes the entity with given ID from the persistent storage.

Specified by:

remove in interface BaseService<Characteristic>

Parameters:

id - the ID of entity to be removed.

remove

@Secured(value="GROUP_USER")
void remove(Characteristic c)

Description copied from interface: BaseService

Removes the given entity from the persistent storage.

Specified by:

remove in interface BaseService<Characteristic>

Parameters:

c - the entity to be removed.

update

@Secured(value="GROUP_USER")
void update(Characteristic c)

Description copied from interface: BaseService

Updates the given entity in the persistent storage.

Specified by:

update in interface BaseService<Characteristic>

Parameters:

c - the entity to be updated.

getParentIds

Map<Characteristic,Long> getParentIds(Class<?> parentClass,
                                      @Nullable
                                      Collection<Characteristic> characteristics)

Optimized version that only retrieves the IDs of the owning object. The caller has to keep track of the parentClass

Parameters:

parentClass - the type of object sought associated with the characteristic