Package ubic.gemma.persistence.service.common.description

Interface CharacteristicService

All Superinterfaces:

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

All Known Implementing Classes:

CharacteristicServiceImpl

public interface CharacteristicService
extends BaseService<Characteristic>, FilteringVoEnabledService<Characteristic,CharacteristicValueObject>

Author:

paul

Method Summary

Modifier and Type	Method	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>	countByValueUri(Collection<String> uris, Collection<Class<?>> parentClasses)
Characteristic	create(Characteristic c)	Creates the given entity in the persistent storage.
Characteristic	findBestByUri(String uri)	Find the best possible characteristic for a given URI.
Collection<? extends Characteristic>	findByAnyUri(String uri)	Find a characteristic or statement by any URI it contains including its category, value, predicates and objects.
Collection<? extends Characteristic>	findByAnyValue(String value)	Find a characteristic by any value it contains including its category, value, predicates and objects.
Collection<? extends Characteristic>	findByAnyValueStartingWith(String value)	Find a characteristic by any value it contains including its category, value, predicates and objects that starts with the given query.
Collection<Characteristic>	findByCategoryStartingWith(String queryPrefix)
Collection<Characteristic>	findByCategoryUri(String query)
Collection<Statement>	findByObject(String value)
Collection<Statement>	findByObjectUri(String uri)
Collection<Statement>	findByPredicate(String value)
Collection<Statement>	findByPredicateUri(String uri)
Collection<Characteristic>	findByUri(String searchString)	Looks for an exact match of the give string to a valueUri in the characteristic database
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>	findByValueLike(String search)	Returns a collection of characteristics that have a value matching the given SQL LIKE pattern.
Collection<Characteristic>	findByValueStartingWith(String search)	Returns a collection of characteristics that have a value starting with the given string.
Map<String,Characteristic>	findByValueUriOrValueLike(String search, Collection<Class<?>> parentClasses)
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>	findExperimentsByUris(Collection<String> uris, Taxon taxon, int limit, boolean loadEEs, boolean rankByLevel)
Map<Characteristic,Identifiable>	getParents(Collection<Characteristic> characteristics, Collection<Class<?>> parentClasses, int maxResults)
void	remove(Long id)	Removes the entity with given ID from the persistent storage.
void	remove(Characteristic c)	Removes the given entity from the persistent storage.

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

create, findOrCreate, remove

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

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

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

save, save, update, update

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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

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

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

loadValueObjects, loadValueObjects

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,
                                                                                                           boolean loadEEs,
                                                                                                           boolean rankByLevel)

See Also:

CharacteristicDao.findExperimentsByUris(Collection, Taxon, int, boolean)

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

findBestByUri

@Nullable
Characteristic findBestByUri(String uri)

Find the best possible characteristic for a given URI.

findByValueStartingWith

Collection<Characteristic> findByValueStartingWith(String search)

Returns a collection of characteristics that have a value starting with the given string.

The value is usually a human-readable form of the termURI. SQL LIKE patterns are escaped. Use findByValueLike(String) to do wildcard searches instead.

findByValueLike

Collection<Characteristic> findByValueLike(String search)

Returns a collection of characteristics that have a value matching the given SQL LIKE pattern.

findByValueUriOrValueLike

Map<String,Characteristic> findByValueUriOrValueLike(String search,
                                                           @Nullable
                                                           Collection<Class<?>> parentClasses)

See Also:

CharacteristicDao#findCharacteristicsByValueUriOrValueLikeGroupedByNormalizedValue(String, String, Collection)

countByValueUri

Map<String,Long> countByValueUri(Collection<String> uris,
                                       @Nullable
                                       Collection<Class<?>> parentClasses)

getParents

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_MAP_VALUES_READ"})
Map<Characteristic,Identifiable> getParents(Collection<Characteristic> characteristics,
                                                  @Nullable
                                                  Collection<Class<?>> parentClasses,
                                                  int maxResults)

Parameters:

characteristics - characteristics

Returns:

a map of the specified characteristics to their annotated objects.

findByCategoryStartingWith

Collection<Characteristic> findByCategoryStartingWith(String queryPrefix)

findByCategoryUri

Collection<Characteristic> findByCategoryUri(String query)

findByAnyValue

Collection<? extends Characteristic> findByAnyValue(String value)

Find a characteristic by any value it contains including its category, value, predicates and objects.

findByAnyValueStartingWith

Collection<? extends Characteristic> findByAnyValueStartingWith(String value)

Find a characteristic by any value it contains including its category, value, predicates and objects that starts with the given query.

findByAnyUri

Collection<? extends Characteristic> findByAnyUri(String uri)

Find a characteristic or statement by any URI it contains including its category, value, predicates and objects.

findByPredicate

Collection<Statement> findByPredicate(String value)

findByPredicateUri

Collection<Statement> findByPredicateUri(String uri)

findByObject

Collection<Statement> findByObject(String value)

findByObjectUri

Collection<Statement> findByObjectUri(String uri)

create

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

Description copied from interface: BaseImmutableService

Creates the given entity in the persistent storage.

Specified by:

create in interface BaseImmutableService<Characteristic>

Parameters:

c - the entity to be created.

Returns:

object referencing the persistent instance of the given entity.

remove

@Secured("GROUP_ADMIN")
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<Characteristic>

Parameters:

id - the ID of entity to be removed.

remove

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

Description copied from interface: BaseImmutableService

Removes the given entity from the persistent storage.

Specified by:

remove in interface BaseImmutableService<Characteristic>

Parameters:

c - the entity to be removed.