Interface CharacteristicReadService

All Known Implementing Classes:

CharacteristicReadServiceImpl

public interface CharacteristicReadService

Read-only retrieval service for Characteristic and Statement.

Phase 3 of the CharacteristicService decomposition (strangler fig). This service houses the DAO-bound read cluster previously implemented directly on the CharacteristicServiceImpl facade: browse, findExperimentsByUris, findByParentClasses, findByUri, findBestByUri, findByValueStartingWith, findByValueLike, findByValueUriOrValueStartingWith, countByValueUri, findValueGroupedByValueUri, getParents, findByCategoryStartingWith, findByCategoryUri, findByAnyValue, findByAnyValueStartingWith, findByAnyUri, findByPredicate, findByPredicateUri, findByObject, and findByObjectUri. All methods delegate to CharacteristicDao and StatementDao (with simple aggregation / Hibernate-initialize wrapping where appropriate) and orchestrate no other collaborators.

Write-side methods (create, save, update, remove, plus the inherited BaseService mutators) stay on the CharacteristicService facade.

Callers should generally keep using CharacteristicService as the facade -- the facade delegates to this service. Direct injection is appropriate where a class is logically read-only (REST endpoints, CLIs, browser controllers, intra-core readers).

ACL / @Secured annotations live on CharacteristicService (the caller-facing facade interface); enforcement happens at the facade proxy boundary, so this interface is intentionally unsecured.

See Also:

• CharacteristicService

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)
Map<String,Long>	countExperimentsByUris(Collection<String> uris, boolean includeSubjects, boolean includePredicates, boolean includeObjects, boolean includeCategories, Taxon taxon, Collection<Long> excludedExperimentIds)
Map<String,Long>	countExperimentsByUris(Collection<String> uris, boolean includeSubjects, boolean includePredicates, boolean includeObjects, Taxon taxon, Collection<Long> excludedExperimentIds)
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 given string to a valueUri in the characteristic database.
Collection<Characteristic>	findByUriInAnySlot(String uri)
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<String,String>	findCategoryGroupedByCategoryUri(Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents, int maxResults)
Map<String,Long>	findEeCountsByUriForOriginalValue(Collection<String> uris, String originalValue)
Map<String,Long>	findEeCountsByUriForOriginalValue(Collection<String> uris, String originalValue, Collection<Long> excludedExperimentIds)
Map<String, Map<String,Long>>	findEeCountsByUriGroupedByCategory(Collection<String> uris)
Collection<Long>	findExperimentIdsByUriInAnySlot(String uri)
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)
List<CharacteristicDao.PriorCurationUsage>	findPriorCurationByOriginalValue(String originalValue, int maxResults, Collection<Long> excludedExperimentIds)
Map<String, CharacteristicDao.UsageExample>	findRepresentativeUsageByValueUris(Collection<String> valueUris)	For each value URI, return one representative ACL-visible usage, or omit URIs with no accessible usage.
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)

Method Details

browse

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

Browse through the characteristics, excluding GO annotations.

browse

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

Browse through the characteristics, excluding GO annotations.

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)

countExperimentsByUris

Map<String,Long> countExperimentsByUris(Collection<String> uris,
 boolean includeSubjects,
 boolean includePredicates,
 boolean includeObjects,
 @Nullable
 Taxon taxon,
 Collection<Long> excludedExperimentIds)

See Also:

• CharacteristicDao.countExperimentsByUris(Collection, boolean, boolean, boolean, Taxon, Collection)

countExperimentsByUris

Map<String,Long> countExperimentsByUris(Collection<String> uris,
 boolean includeSubjects,
 boolean includePredicates,
 boolean includeObjects,
 boolean includeCategories,
 @Nullable
 Taxon taxon,
 Collection<Long> excludedExperimentIds)

See Also:

• CharacteristicDao.countExperimentsByUris(Collection, boolean, boolean, boolean, boolean, Taxon, Collection)

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.

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 given string to a valueUri in the characteristic database.

findBestByUri

@Nullable
Characteristic findBestByUri(String uri)

Find the best possible characteristic for a given URI.

findRepresentativeUsageByValueUris

Map<String, CharacteristicDao.UsageExample> findRepresentativeUsageByValueUris(Collection<String> valueUris)

For each value URI, return one representative ACL-visible usage, or omit URIs with no accessible usage.

See Also:

• CharacteristicDao.findRepresentativeUsageByValueUris(Collection)

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.

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.

countByValueUri

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

findEeCountsByUriGroupedByCategory

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

See Also:

• CharacteristicDao.findEeCountsByUriGroupedByCategory(Collection)

findEeCountsByUriForOriginalValue

Map<String,Long> findEeCountsByUriForOriginalValue(Collection<String> uris,
 String originalValue)

See Also:

• CharacteristicDao.findEeCountsByUriForOriginalValue(Collection, String)

findEeCountsByUriForOriginalValue

Map<String,Long> findEeCountsByUriForOriginalValue(Collection<String> uris,
 String originalValue,
 Collection<Long> excludedExperimentIds)

See Also:

• CharacteristicDao.findEeCountsByUriForOriginalValue(Collection, String, Collection)

findPriorCurationByOriginalValue

List<CharacteristicDao.PriorCurationUsage> findPriorCurationByOriginalValue(String originalValue,
 int maxResults,
 Collection<Long> excludedExperimentIds)

See Also:

• CharacteristicDao.findPriorCurationByOriginalValue(String, int, Collection)

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)

findCategoryGroupedByCategoryUri

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

See Also:

• CharacteristicDao.findCategoryGroupedByCategoryUri(Collection, boolean, int)

findByUriInAnySlot

Collection<Characteristic> findByUriInAnySlot(String uri)

See Also:

• CharacteristicDao.findByUriInAnySlot(String)

findExperimentIdsByUriInAnySlot

Collection<Long> findExperimentIdsByUriInAnySlot(String uri)

See Also:

• CharacteristicDao.findExperimentIdsByUriInAnySlot(String)

getParents

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)