Package ubic.gemma.persistence.service.common.description

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 ubic.gemma.persistence.service.AbstractService

log

Constructor Summary

Constructors

Constructor	Description
CharacteristicServiceImpl(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)
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<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>	findExperimentsByUris(Collection<String> uris, Taxon taxon, int limit, boolean loadEEs, boolean rankByLevel)
Map<Characteristic,Identifiable>	getParents(Collection<Characteristic> characteristics, Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents, boolean thawParents)

Methods inherited from class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getIdentifierPropertyName, getSort, load, load, loadAllValueObjects, loadIds, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjects, loadValueObjects, loadValueObjectsByIds

Methods inherited from class ubic.gemma.persistence.service.AbstractService

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

Methods inherited from class java.lang.Object

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

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, 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.common.description.CharacteristicService

create, remove, remove

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

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getIdentifierPropertyName, getSort, load, load, loadIds

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

loadValueObjects, loadValueObjects

Constructor Details

CharacteristicServiceImpl

@Autowired
public CharacteristicServiceImpl(CharacteristicDao characteristicDao,
 StatementDao statementDao)

Method Details

browse

@Transactional(readOnly=true)
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

@Transactional(readOnly=true)
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

@Transactional(readOnly=true)
public Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>> findExperimentsByUris(Collection<String> uris,
 @Nullable
 Taxon taxon,
 int limit,
 boolean loadEEs,
 boolean rankByLevel)

Specified by:

findExperimentsByUris in interface CharacteristicService

See Also:

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

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: CharacteristicService

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

Specified by:

findByParentClasses in interface CharacteristicService

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: 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
@Transactional(readOnly=true)
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

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: 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

@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: CharacteristicService

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

Specified by:

findByValueLike in interface CharacteristicService

findByValueUriOrValueStartingWith

@Transactional(readOnly=true)
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

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

Specified by:

countByValueUri in interface CharacteristicService

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 CharacteristicService

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 CharacteristicService

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 CharacteristicService

findByAnyValue

@Transactional(readOnly=true)
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

@Transactional(readOnly=true)
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

@Transactional(readOnly=true)
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

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

Specified by:

findByPredicate in interface CharacteristicService

findByPredicateUri

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

Specified by:

findByPredicateUri in interface CharacteristicService

findByObject

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

Specified by:

findByObject in interface CharacteristicService

findByObjectUri

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

Specified by:

findByObjectUri in interface CharacteristicService