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

Interface CharacteristicService

All Superinterfaces:

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

All Known Implementing Classes:

CharacteristicServiceImpl

public interface CharacteristicService
extends BaseService<Characteristic>, BaseVoEnabledService<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>	countCharacteristicsByValueUri(Collection<String> uris)
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>	findByCategory(String queryPrefix)
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>	findCharacteristicsByValueUriOrValueLike(String search)
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>	findExperimentsByUris(Collection<String> uris, Taxon taxon, int limit, boolean loadEEs, boolean rankByLevel)
Filter	getFilter(String property, Filter.Operator operator, String value)
Filter	getFilter(String property, Filter.Operator operator, Collection<String> values)
Set<String>	getFilterableProperties()
String	getFilterablePropertyDescription(String property)
Class<?>	getFilterablePropertyType(String property)
Map<Characteristic,Identifiable>	getParents(Collection<Characteristic> characteristics, Collection<Class<?>> parentClasses, int maxResults)
Sort	getSort(String property, Sort.Direction direction)
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

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.

findCharacteristicsByValueUriOrValueLike

Map<String,Characteristic> findCharacteristicsByValueUriOrValueLike(String search)

See Also:

CharacteristicDao.findCharacteristicsByValueUriOrValueLikeGroupedByNormalizedValue(String)

countCharacteristicsByValueUri

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

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.

findByCategory

Collection<? extends Characteristic> findByCategory(String queryPrefix)

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.

getFilterableProperties

Set<String> getFilterableProperties()

See Also:

FilteringDao.getFilterableProperties()

getFilterablePropertyType

Class<?> getFilterablePropertyType(String property)

See Also:

FilteringDao.getFilterablePropertyType(String)

getFilterablePropertyDescription

@Nullable
String getFilterablePropertyDescription(String property)

See Also:

FilteringDao.getFilterablePropertyDescription(String)

getFilter

Filter getFilter(String property,
                 Filter.Operator operator,
                 String value)
          throws IllegalArgumentException

Throws:

IllegalArgumentException

See Also:

FilteringDao.getFilterableProperties()

getFilter

Filter getFilter(String property,
                 Filter.Operator operator,
                 Collection<String> values)
          throws IllegalArgumentException

Throws:

IllegalArgumentException

See Also:

FilteringDao.getFilter(String, Filter.Operator, Collection)

getSort

Sort getSort(String property,
             @Nullable
             Sort.Direction direction)
      throws IllegalArgumentException

Throws:

IllegalArgumentException

See Also:

FilteringDao.getSort(String, Sort.Direction)