Class CharacteristicReadServiceImpl

java.lang.Object

ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl

All Implemented Interfaces:

CharacteristicReadService

@Service("characteristicReadService")
public class CharacteristicReadServiceImpl
extends Object
implements CharacteristicReadService

Implementation of CharacteristicReadService.

All public methods are @Transactional(readOnly = true). ACL enforcement is the responsibility of the facade CharacteristicService interface -- this class is unsecured at the AOP boundary on purpose, so intra-gemma-core callers can bypass duplicate ACL checks once authenticated.

See Also:

• CharacteristicService

Constructor Summary

Constructors

Constructor	Description
CharacteristicReadServiceImpl(CharacteristicDao characteristicDao, StatementDao statementDao)

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 query, 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)

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

CharacteristicReadServiceImpl

@Autowired
public CharacteristicReadServiceImpl(CharacteristicDao characteristicDao,
 StatementDao statementDao)

Method Details

browse

@Transactional(readOnly=true)
public List<Characteristic> browse(int start,
 int limit)

Description copied from interface: CharacteristicReadService

Browse through the characteristics, excluding GO annotations.

Specified by:

browse in interface CharacteristicReadService

browse

@Transactional(readOnly=true)
public List<Characteristic> browse(int start,
 int limit,
 String sortField,
 boolean descending)

Description copied from interface: CharacteristicReadService

Browse through the characteristics, excluding GO annotations.

Specified by:

browse in interface CharacteristicReadService

findExperimentsByUris

@Transactional(readOnly=true)
public 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)

Specified by:

findExperimentsByUris in interface CharacteristicReadService

See Also:

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

countExperimentsByUris

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

Specified by:

countExperimentsByUris in interface CharacteristicReadService

See Also:

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

countExperimentsByUris

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

Specified by:

countExperimentsByUris in interface CharacteristicReadService

See Also:

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

findByParentClasses

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

Description copied from interface: CharacteristicReadService

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

Specified by:

findByParentClasses in interface CharacteristicReadService

findByUri

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

Description copied from interface: CharacteristicReadService

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

Specified by:

findByUri in interface CharacteristicReadService

findBestByUri

@Nullable
@Transactional(readOnly=true)
public Characteristic findBestByUri(String uri)

Description copied from interface: CharacteristicReadService

Find the best possible characteristic for a given URI.

Specified by:

findBestByUri in interface CharacteristicReadService

findRepresentativeUsageByValueUris

@Transactional(readOnly=true)
public Map<String, CharacteristicDao.UsageExample> findRepresentativeUsageByValueUris(Collection<String> valueUris)

Description copied from interface: CharacteristicReadService

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

Specified by:

findRepresentativeUsageByValueUris in interface CharacteristicReadService

See Also:

• CharacteristicDao.findRepresentativeUsageByValueUris(Collection)

findByValueStartingWith

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

Description copied from interface: CharacteristicReadService

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

Specified by:

findByValueStartingWith in interface CharacteristicReadService

findByValueLike

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

Description copied from interface: CharacteristicReadService

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

Specified by:

findByValueLike in interface CharacteristicReadService

findByValueUriOrValueStartingWith

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

Description copied from interface: CharacteristicReadService

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

Specified by:

findByValueUriOrValueStartingWith in interface CharacteristicReadService

countByValueUri

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

Specified by:

countByValueUri in interface CharacteristicReadService

findEeCountsByUriGroupedByCategory

@Transactional(readOnly=true)
public Map<String, Map<String,Long>> findEeCountsByUriGroupedByCategory(Collection<String> uris)

Specified by:

findEeCountsByUriGroupedByCategory in interface CharacteristicReadService

See Also:

• CharacteristicDao.findEeCountsByUriGroupedByCategory(Collection)

findEeCountsByUriForOriginalValue

@Transactional(readOnly=true)
public Map<String,Long> findEeCountsByUriForOriginalValue(Collection<String> uris,
 String originalValue)

Specified by:

findEeCountsByUriForOriginalValue in interface CharacteristicReadService

See Also:

• CharacteristicDao.findEeCountsByUriForOriginalValue(Collection, String)

findEeCountsByUriForOriginalValue

@Transactional(readOnly=true)
public Map<String,Long> findEeCountsByUriForOriginalValue(Collection<String> uris,
 String originalValue,
 Collection<Long> excludedExperimentIds)

Specified by:

findEeCountsByUriForOriginalValue in interface CharacteristicReadService

See Also:

• CharacteristicDao.findEeCountsByUriForOriginalValue(Collection, String, Collection)

findPriorCurationByOriginalValue

@Transactional(readOnly=true)
public List<CharacteristicDao.PriorCurationUsage> findPriorCurationByOriginalValue(String originalValue,
 int maxResults,
 Collection<Long> excludedExperimentIds)

Specified by:

findPriorCurationByOriginalValue in interface CharacteristicReadService

See Also:

• CharacteristicDao.findPriorCurationByOriginalValue(String, int, Collection)

findValueGroupedByValueUri

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

Specified by:

findValueGroupedByValueUri in interface CharacteristicReadService

See Also:

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

findCategoryGroupedByCategoryUri

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

Specified by:

findCategoryGroupedByCategoryUri in interface CharacteristicReadService

See Also:

• CharacteristicDao.findCategoryGroupedByCategoryUri(Collection, boolean, int)

findByUriInAnySlot

@Transactional(readOnly=true)
public Collection<Characteristic> findByUriInAnySlot(String uri)

Specified by:

findByUriInAnySlot in interface CharacteristicReadService

See Also:

• CharacteristicDao.findByUriInAnySlot(String)

findExperimentIdsByUriInAnySlot

@Transactional(readOnly=true)
public Collection<Long> findExperimentIdsByUriInAnySlot(String uri)

Specified by:

findExperimentIdsByUriInAnySlot in interface CharacteristicReadService

See Also:

• CharacteristicDao.findExperimentIdsByUriInAnySlot(String)

getParents

@Transactional(readOnly=true)
public Map<Characteristic, Identifiable> getParents(Collection<Characteristic> characteristics,
 @Nullable
 Collection<Class<? extends Identifiable>> parentClasses,
 boolean includeNoParents,
 boolean thawParents)

Specified by:

getParents in interface CharacteristicReadService

Parameters:

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

See Also:

• CharacteristicDao.getParents(Collection, Collection, boolean)

findByCategoryStartingWith

@Transactional(readOnly=true)
public Collection<Characteristic> findByCategoryStartingWith(String query,
 @Nullable
 Collection<Class<? extends Identifiable>> parentClasses,
 boolean includeNoParents,
 int maxResults)

Specified by:

findByCategoryStartingWith in interface CharacteristicReadService

findByCategoryUri

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

Specified by:

findByCategoryUri in interface CharacteristicReadService

findByAnyValue

@Transactional(readOnly=true)
public Collection<? extends Characteristic> findByAnyValue(String value)

Description copied from interface: CharacteristicReadService

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

Specified by:

findByAnyValue in interface CharacteristicReadService

findByAnyValueStartingWith

@Transactional(readOnly=true)
public Collection<? extends Characteristic> findByAnyValueStartingWith(String value)

Description copied from interface: CharacteristicReadService

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

Specified by:

findByAnyValueStartingWith in interface CharacteristicReadService

findByAnyUri

@Transactional(readOnly=true)
public Collection<? extends Characteristic> findByAnyUri(String uri)

Description copied from interface: CharacteristicReadService

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

Specified by:

findByAnyUri in interface CharacteristicReadService

findByPredicate

@Transactional(readOnly=true)
public Collection<Statement> findByPredicate(String value)

Specified by:

findByPredicate in interface CharacteristicReadService

findByPredicateUri

@Transactional(readOnly=true)
public Collection<Statement> findByPredicateUri(String uri)

Specified by:

findByPredicateUri in interface CharacteristicReadService

findByObject

@Transactional(readOnly=true)
public Collection<Statement> findByObject(String value)

Specified by:

findByObject in interface CharacteristicReadService

findByObjectUri

@Transactional(readOnly=true)
public Collection<Statement> findByObjectUri(String uri)

Specified by:

findByObjectUri in interface CharacteristicReadService