Class CharacteristicServiceImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractService<Characteristic>

ubic.gemma.persistence.service.AbstractFilteringVoEnabledService<Characteristic, CharacteristicValueObject>

ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl

All Implemented Interfaces:

BaseImmutableService<Characteristic>, BaseReadOnlyService<Characteristic>, BaseService<Characteristic>, BaseVoEnabledService<Characteristic, CharacteristicValueObject>, CharacteristicService, FilteringService<Characteristic>, FilteringVoEnabledService<Characteristic, CharacteristicValueObject>

@Service
public class CharacteristicServiceImpl
extends AbstractFilteringVoEnabledService<Characteristic, CharacteristicValueObject>
implements CharacteristicService

Author:

Luke

See Also:

• CharacteristicService

Field Summary

Fields inherited from class AbstractService

log

Constructor Summary

Constructors

Constructor	Description
CharacteristicServiceImpl(CharacteristicDao characteristicDao)

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, 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 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<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)
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 it when none is accessible), so a search hit can be shown in the context it has actually been applied.
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 AbstractFilteringVoEnabledService

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery, load, load, loadAllValueObjects, loadIds, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjects, loadValueObjects, loadValueObjectsByCursor, loadValueObjectsByIds

Methods inherited from class AbstractService

countAll, create, create, ensureInSession, ensureInSession, find, findOrCreate, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, remove, remove, save, save, streamAll, streamAll, update, update

Methods inherited from class Object

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

Methods inherited from interface BaseImmutableService

findOrCreate

Methods inherited from interface BaseReadOnlyService

countAll, find, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, streamAll, streamAll

Methods inherited from interface BaseVoEnabledService

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from interface CharacteristicService

create, create, remove, remove, save, save, update, update

Methods inherited from interface FilteringService

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery, load, load, loadIds

Methods inherited from interface FilteringVoEnabledService

loadValueObjects, loadValueObjects, loadValueObjectsByCursor

Constructor Details

CharacteristicServiceImpl

@Autowired
public CharacteristicServiceImpl(CharacteristicDao characteristicDao)

Method Details

browse

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

Description copied from interface: CharacteristicService

Browse through the characteristics, excluding GO annotations.

Specified by:

browse in interface CharacteristicService

Parameters:

start - How far into the list to start

limit - Maximum records to retrieve

Returns:

characteristics

browse

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

Description copied from interface: CharacteristicService

Browse through the characteristics, excluding GO annotations.

Specified by:

browse in interface CharacteristicService

Parameters:

start - How far into the list to start

limit - Maximum records to retrieve

sortField - sort field

descending - sor order

Returns:

characteristics

findExperimentsByUris

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 CharacteristicService

See Also:

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

countExperimentsByUris

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 CharacteristicService

See Also:

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

findByParentClasses

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

Description copied from interface: CharacteristicService

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

Specified by:

findByParentClasses in interface CharacteristicService

findByUri

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

Description copied from interface: CharacteristicService

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

Specified by:

findByUri in interface CharacteristicService

findBestByUri

@Nullable
public Characteristic findBestByUri(String uri)

Description copied from interface: CharacteristicService

Find the best possible characteristic for a given URI.

Specified by:

findBestByUri in interface CharacteristicService

findRepresentativeUsageByValueUris

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

Description copied from interface: CharacteristicService

For each value URI, return one representative ACL-visible usage (or omit it when none is accessible), so a search hit can be shown in the context it has actually been applied.

Specified by:

findRepresentativeUsageByValueUris in interface CharacteristicService

See Also:

• CharacteristicDao.findRepresentativeUsageByValueUris(Collection)

findByValueStartingWith

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

Description copied from interface: CharacteristicService

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

Specified by:

findByValueStartingWith in interface CharacteristicService

findByValueLike

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

Description copied from interface: CharacteristicService

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

Specified by:

findByValueLike in interface CharacteristicService

findByValueUriOrValueStartingWith

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

Description copied from interface: CharacteristicService

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

Specified by:

findByValueUriOrValueStartingWith in interface CharacteristicService

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

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

Specified by:

countByValueUri in interface CharacteristicService

findEeCountsByUriGroupedByCategory

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

Specified by:

findEeCountsByUriGroupedByCategory in interface CharacteristicService

See Also:

• CharacteristicDao.findEeCountsByUriGroupedByCategory(Collection)

findEeCountsByUriForOriginalValue

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

Specified by:

findEeCountsByUriForOriginalValue in interface CharacteristicService

See Also:

• CharacteristicDao.findEeCountsByUriForOriginalValue(Collection, String)

findEeCountsByUriForOriginalValue

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

Specified by:

findEeCountsByUriForOriginalValue in interface CharacteristicService

See Also:

• CharacteristicDao.findEeCountsByUriForOriginalValue(Collection, String, Collection)

findPriorCurationByOriginalValue

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

Specified by:

findPriorCurationByOriginalValue in interface CharacteristicService

See Also:

• CharacteristicDao.findPriorCurationByOriginalValue(String, int, Collection)

findValueGroupedByValueUri

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

Specified by:

findValueGroupedByValueUri in interface CharacteristicService

See Also:

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

getParents

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

Specified by:

getParents in interface CharacteristicService

Parameters:

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

See Also:

• CharacteristicDao.getParents(Collection, Collection, boolean)

findByCategoryStartingWith

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

Specified by:

findByCategoryStartingWith in interface CharacteristicService

findByCategoryUri

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

Specified by:

findByCategoryUri in interface CharacteristicService

findByAnyValue

public Collection<? extends Characteristic> findByAnyValue(String value)

Description copied from interface: CharacteristicService

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

Specified by:

findByAnyValue in interface CharacteristicService

findByAnyValueStartingWith

public Collection<? extends Characteristic> findByAnyValueStartingWith(String value)

Description copied from interface: CharacteristicService

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 CharacteristicService

findByAnyUri

public Collection<? extends Characteristic> findByAnyUri(String uri)

Description copied from interface: CharacteristicService

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

Specified by:

findByAnyUri in interface CharacteristicService

findByPredicate

public Collection<Statement> findByPredicate(String value)

Specified by:

findByPredicate in interface CharacteristicService

findByPredicateUri

public Collection<Statement> findByPredicateUri(String uri)

Specified by:

findByPredicateUri in interface CharacteristicService

findByObject

public Collection<Statement> findByObject(String value)

Specified by:

findByObject in interface CharacteristicService

findByObjectUri

public Collection<Statement> findByObjectUri(String uri)

Specified by:

findByObjectUri in interface CharacteristicService