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)
Collection<Characteristic>	create(Collection<Characteristic> entities)
Characteristic	create(Characteristic c)
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<String,String>	findValueGroupedByValueUri(Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents, boolean includePredicates, boolean includeObjects, int maxResults)
Map<Characteristic,Identifiable>	getParents(Collection<Characteristic> characteristics, Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents, boolean thawParents)
void	remove(Collection<Characteristic> entities)
void	remove(Characteristic c)
Collection<Characteristic>	save(Collection<Characteristic> entities)
Characteristic	save(Characteristic entity)
void	update(Collection<Characteristic> entities)
void	update(Characteristic entity)

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

findOrCreate

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.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)

findValueGroupedByValueUri

Map<String,String> findValueGroupedByValueUri(@Nullable
 Collection<Class<? extends Identifiable>> parentClasses,
 boolean includeNoParents,
 boolean includePredicates,
 boolean includeObjects,
 int maxResults)

See Also:

• CharacteristicDao.findValueGroupedByValueUri(Collection, boolean, boolean, boolean, int)

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)

Specified by:

create in interface BaseImmutableService<Characteristic>

See Also:

• BaseDao.create(Identifiable)

create

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

Specified by:

create in interface BaseImmutableService<Characteristic>

See Also:

• BaseDao.create(Collection)

save

@Secured("GROUP_USER")
Collection<Characteristic> save(Collection<Characteristic> entities)

Specified by:

save in interface BaseService<Characteristic>

See Also:

• BaseDao.save(Collection)

save

@Secured("GROUP_USER")
Characteristic save(Characteristic entity)

Specified by:

save in interface BaseService<Characteristic>

See Also:

• BaseDao.save(Identifiable)

update

@Secured("GROUP_USER")
void update(Characteristic entity)

Specified by:

update in interface BaseService<Characteristic>

See Also:

• BaseDao.update(Identifiable)

update

@Secured("GROUP_USER")
void update(Collection<Characteristic> entities)

Specified by:

update in interface BaseService<Characteristic>

See Also:

• BaseDao.update(Collection)

remove

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

Specified by:

remove in interface BaseImmutableService<Characteristic>

See Also:

• BaseDao.remove(Identifiable)

remove

@Secured("GROUP_USER")
void remove(Collection<Characteristic> entities)

Specified by:

remove in interface BaseImmutableService<Characteristic>

See Also:

• BaseDao.remove(Collection)