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

Class CharacteristicServiceImpl

java.lang.Object

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

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<?>> parentClasses)
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<Characteristic>	findByCategoryUri(String query)
Collection<Statement>	findByObject(String value)
Collection<Statement>	findByObjectUri(String uri)
Collection<Statement>	findByPredicate(String value)
Collection<Statement>	findByPredicateUri(String uri)
Collection<Characteristic>	findByUri(String searchString)	Looks for an exact match of the give string to a valueUri in the characteristic database
Collection<Characteristic>	findByUri(Collection<String> uris)	given a collection of strings that represent URI's will find all the characteristics that are used in the system with URI's matching anyone in the given collection
Collection<Characteristic>	findByValueLike(String search)	Returns a collection of characteristics that have a value matching the given SQL LIKE pattern.
Collection<Characteristic>	findByValueStartingWith(String search)	Returns a collection of characteristics that have a value starting with the given string.
Map<String,Characteristic>	findByValueUriOrValueLike(String search, Collection<Class<?>> parentClasses)
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<?>> parentClasses, int maxResults)

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, 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

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 Detail

CharacteristicServiceImpl

@Autowired
public CharacteristicServiceImpl(CharacteristicDao characteristicDao,
                                 StatementDao statementDao)

Method Detail

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)

findByUri

@Transactional(readOnly=true)
public Collection<Characteristic> findByUri(Collection<String> uris)

Description copied from interface: CharacteristicService

given a collection of strings that represent URI's will find all the characteristics that are used in the system with URI's matching anyone in the given collection

Specified by:

findByUri in interface CharacteristicService

Parameters:

uris - uris

Returns:

characteristics

findByUri

@Transactional(readOnly=true)
public Collection<Characteristic> findByUri(String searchString)

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

Parameters:

searchString - search string

Returns:

characteristics

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)

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) to do wildcard searches instead.

Specified by:

findByValueStartingWith in interface CharacteristicService

findByValueLike

@Transactional(readOnly=true)
public Collection<Characteristic> findByValueLike(String search)

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

findByValueUriOrValueLike

@Transactional(readOnly=true)
public Map<String,Characteristic> findByValueUriOrValueLike(String search,
                                                                  @Nullable
                                                                  Collection<Class<?>> parentClasses)

Specified by:

findByValueUriOrValueLike in interface CharacteristicService

See Also:

CharacteristicDao#findCharacteristicsByValueUriOrValueLikeGroupedByNormalizedValue(String, String, Collection)

countByValueUri

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

Specified by:

countByValueUri in interface CharacteristicService

getParents

@Transactional(readOnly=true)
public Map<Characteristic,Identifiable> getParents(Collection<Characteristic> characteristics,
                                                         @Nullable
                                                         Collection<Class<?>> parentClasses,
                                                         int maxResults)

Specified by:

getParents in interface CharacteristicService

Parameters:

characteristics - characteristics

Returns:

a map of the specified characteristics to their annotated objects.

findByCategoryStartingWith

@Transactional(readOnly=true)
public Collection<Characteristic> findByCategoryStartingWith(String query)

Specified by:

findByCategoryStartingWith in interface CharacteristicService

findByCategoryUri

@Transactional(readOnly=true)
public Collection<Characteristic> findByCategoryUri(String query)

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