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<? extends Identifiable>> parentClasses, boolean includeNoParents)
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<Class<? extends Identifiable>> parentClasses, boolean includeNoParents, int maxResults)
Collection<Characteristic>	findByCategoryUri(String query, Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents, int maxResults)
Collection<Statement>	findByObject(String value)
Collection<Statement>	findByObjectUri(String uri)
Collection<Characteristic>	findByParentClasses(Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents, String category, int maxResults)	Find characteristics that have a particular parent class or lack thereof.
Collection<Statement>	findByPredicate(String value)
Collection<Statement>	findByPredicateUri(String uri)
Collection<Characteristic>	findByUri(String uri, String category, Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents, int maxResults)	Looks for an exact match of the give string to a valueUri in the characteristic database
Collection<Characteristic>	findByValueLike(String search, String category, Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents, int maxResults)	Returns a collection of characteristics that have a value matching the given SQL LIKE pattern.
Collection<Characteristic>	findByValueStartingWith(String search, String category, Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents, int maxResults)	Returns a collection of characteristics that have a value starting with the given string.
Map<String,Characteristic>	findByValueUriOrValueStartingWith(String search, Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents)	Find characteristics that have a value (prefix) or value URI (exact match) matching the given string.
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>	findExperimentsByUris(Collection<String> uris, boolean includeSubjects, boolean includePredicates, boolean includeObjects, Taxon taxon, int limit, boolean loadEEs, boolean rankByLevel)
Map<Characteristic,Identifiable>	getParents(Collection<Characteristic> characteristics, Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents, boolean thawParents)
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, loadOrFail, loadOrFail, streamAll, streamAll

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, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery, load, load, loadIds

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

loadValueObjects, loadValueObjects

Method Details

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,
 boolean includeSubjects,
 boolean includePredicates,
 boolean includeObjects,
 @Nullable
 Taxon taxon,
 int limit,
 boolean loadEEs,
 boolean rankByLevel)

See Also:

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

findByParentClasses

Collection<Characteristic> findByParentClasses(@Nullable
 Collection<Class<? extends Identifiable>> parentClasses,
 boolean includeNoParents,
 @Nullable
 String category,
 int maxResults)

Find characteristics that have a particular parent class or lack thereof.

Throws:

IllegalArgumentException - if parentClasses is

findByUri

Collection<Characteristic> findByUri(String uri,
 @Nullable
 String category,
 @Nullable
 Collection<Class<? extends Identifiable>> parentClasses,
 boolean includeNoParents,
 int maxResults)

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

findBestByUri

@Nullable
Characteristic findBestByUri(String uri)

Find the best possible characteristic for a given URI.

findByValueStartingWith

Collection<Characteristic> findByValueStartingWith(String search,
 @Nullable
 String category,
 @Nullable
 Collection<Class<? extends Identifiable>> parentClasses,
 boolean includeNoParents,
 int maxResults)

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, String, Collection, boolean, int) to do wildcard searches instead.

findByValueLike

Collection<Characteristic> findByValueLike(String search,
 @Nullable
 String category,
 @Nullable
 Collection<Class<? extends Identifiable>> parentClasses,
 boolean includeNoParents,
 int maxResults)

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

findByValueUriOrValueStartingWith

Map<String,Characteristic> findByValueUriOrValueStartingWith(String search,
 @Nullable
 Collection<Class<? extends Identifiable>> parentClasses,
 boolean includeNoParents)

Find characteristics that have a value (prefix) or value URI (exact match) matching the given string.

Parameters:

parentClasses - if not null, restrict to characteristics that have parents of the given classes.

includeNoParents - if true, include characteristics that have no parents.

See Also:

• CharacteristicDao.findByValueLikeGroupedByNormalizedValue(String, Collection, boolean)
• CharacteristicDao.findByValueUriGroupedByNormalizedValue(String, Collection, boolean)

countByValueUri

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

getParents

@Secured("GROUP_ADMIN")
Map<Characteristic,Identifiable> getParents(Collection<Characteristic> characteristics,
 @Nullable
 Collection<Class<? extends Identifiable>> parentClasses,
 boolean includeNoParents,
 boolean thawParents)

Parameters:

thawParents - if true, the parents will be initialized if they are proxies

See Also:

• CharacteristicDao.getParents(Collection, Collection, boolean)

findByCategoryStartingWith

Collection<Characteristic> findByCategoryStartingWith(String queryPrefix,
 @Nullable
 Collection<Class<? extends Identifiable>> parentClasses,
 boolean includeNoParents,
 int maxResults)

findByCategoryUri

Collection<Characteristic> findByCategoryUri(String query,
 @Nullable
 Collection<Class<? extends Identifiable>> parentClasses,
 boolean includeNoParents,
 int maxResults)

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.