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

Class CharacteristicDaoImpl

java.lang.Object

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

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

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

ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl

All Implemented Interfaces:

BaseDao<Characteristic>, BaseVoEnabledDao<Characteristic,CharacteristicValueObject>, BrowsingDao<Characteristic>, CharacteristicDao, FilteringDao<Characteristic>, FilteringVoEnabledDao<Characteristic,CharacteristicValueObject>

@Repository
public class CharacteristicDaoImpl
extends AbstractNoopFilteringVoEnabledDao<Characteristic,CharacteristicValueObject>
implements CharacteristicDao

Author:

Luke, Paul

See Also:

• Characteristic

Field Summary

Fields inherited from class ubic.gemma.persistence.service.AbstractVoEnabledDao

REPORT_SLOW_QUERY_AFTER_MS

Fields inherited from class ubic.gemma.persistence.service.AbstractDao

log

Constructor Summary

Constructors

Constructor	Description
CharacteristicDaoImpl(SessionFactory sessionFactory)

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 orderField, boolean descending)	Browse through the characteristics, excluding GO annotations, with sorting.
Map<String,Long>	countByValueUriGroupedByNormalizedValue(Collection<String> uris, Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents)	Count characteristics matching the provided value URIs.
protected CharacteristicValueObject	doLoadValueObject(Characteristic entity)	Load a value object for a given entity.
Characteristic	findBestByUri(String uri)	Return the characteristic with the most frequently used non-null value by URI.
Collection<Characteristic>	findByCategory(String value)
Collection<Characteristic>	findByCategoryLike(String query, Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents, int maxResults)
Collection<Characteristic>	findByCategoryUri(String uri, Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents, int maxResults)
Collection<Characteristic>	findByParentClasses(Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents, String category, int maxResults)
Collection<Characteristic>	findByUri(String uri, String category, Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents, int maxResults)	Find characteristics with the given URI.
Collection<Characteristic>	findByValue(String value)
Collection<Characteristic>	findByValueLike(String search, String category, Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents, int maxResults)	Finds all Characteristics whose value match the given search term
Map<String,Characteristic>	findByValueLikeGroupedByNormalizedValue(String valueLike, Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents)	Find characteristics by value matching the provided LIKE pattern.
Map<String,Characteristic>	findByValueUriGroupedByNormalizedValue(String valueUri, Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents)	Find characteristics by URI.
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>	findExperimentReferencesByUris(Collection<String> uris, boolean includeSubjects, boolean includePredicates, boolean includeObjects, Taxon taxon, int limit, boolean rankByLevel)	Since proxies are returned, they cannot be collected in a HashSet which would otherwise cause their initialization by accessing Object.hashCode().
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>	findExperimentsByUris(Collection<String> uris, boolean includeSubjects, boolean includePredicates, boolean includeObjects, Taxon taxon, int limit, boolean rankByLevel)	This search looks at direct annotations, factor values and biomaterials in that order.
Collection<Class<? extends Identifiable>>	getParentClasses()	Obtain the classes of entities can can own a Characteristic.
Map<Characteristic,Identifiable>	getParents(Collection<Characteristic> characteristics, Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents)	Obtain the parents (i.e.

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

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

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

doLoadValueObjects, loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds, postProcessValueObjects

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

countAll, create, create, find, findByProperty, findByPropertyIn, findOneByProperty, findOrCreate, getBatchSize, getElementClass, getEntityName, getIdentifierPropertyName, getSessionFactory, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, remove, save, save, streamAll, streamAll, streamQuery, 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.BaseDao

countAll, create, create, find, findOrCreate, getElementClass, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, remove, save, save, streamAll, streamAll, update, update

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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

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

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

loadValueObjects, loadValueObjects

Constructor Details

CharacteristicDaoImpl

@Autowired
public CharacteristicDaoImpl(SessionFactory sessionFactory)

Method Details

browse

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

Description copied from interface: CharacteristicDao

Browse through the characteristics, excluding GO annotations.

Specified by:

browse in interface BrowsingDao<Characteristic>

Specified by:

browse in interface CharacteristicDao

Parameters:

start - How far into the list to start

limit - Maximum records to retrieve (might be subject to security filtering)

Returns:

characteristics

browse

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

Description copied from interface: CharacteristicDao

Browse through the characteristics, excluding GO annotations, with sorting.

Specified by:

browse in interface BrowsingDao<Characteristic>

Specified by:

browse in interface CharacteristicDao

Parameters:

start - query offset

limit - maximum amount of entries

orderField - order field

descending - order direction

Returns:

characteristics

findByParentClasses

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

Specified by:

findByParentClasses in interface CharacteristicDao

findByCategory

public Collection<Characteristic> findByCategory(String value)

Specified by:

findByCategory in interface CharacteristicDao

findByCategoryLike

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

Specified by:

findByCategoryLike in interface CharacteristicDao

findByCategoryUri

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

Specified by:

findByCategoryUri in interface CharacteristicDao

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 rankByLevel)

Description copied from interface: CharacteristicDao

This search looks at direct annotations, factor values and biomaterials in that order.

Resulting EEs are filtered by ACLs.

The returned collection of EEs is effectively a Set, but since we cannot use since this should be interchangable with CharacteristicDao.findExperimentReferencesByUris(Collection, boolean, boolean, boolean, Taxon, int, boolean).

Ranking results by level guarantees correctness if a limit is used as datasets matched by direct annotation will be considered before those matched by factor values or biomaterials. It is however expensive.

Specified by:

findExperimentsByUris in interface CharacteristicDao

Parameters:

uris - collection of URIs used for matching characteristics (via Characteristic.getValueUri())

includeSubjects - lookup subjects (or values for regular characteristics)

includePredicates - lookup predicates (only applicable to Statements)

includeObjects - lookup objects (only applicable to Statements)

taxon - taxon to restrict EEs to, or null to ignore

limit - limit how many results to return. Set to -1 for no limit.

rankByLevel - rank results by level before limiting, has no effect if limit is -1

Returns:

map of classes (ExpressionExperiment, FactorValue, BioMaterial) to the matching URI to EEs which have an associated characteristic using the given URI. The class lets us track where the annotation was.

findExperimentReferencesByUris

public Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>> findExperimentReferencesByUris(Collection<String> uris,
 boolean includeSubjects,
 boolean includePredicates,
 boolean includeObjects,
 @Nullable
 Taxon taxon,
 int limit,
 boolean rankByLevel)

Since proxies are returned, they cannot be collected in a HashSet which would otherwise cause their initialization by accessing Object.hashCode(). Thus we need to create a TreeSet over the EE IDs.

Specified by:

findExperimentReferencesByUris in interface CharacteristicDao

See Also:

• Session.load(Object, Serializable)

findByUri

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

Description copied from interface: CharacteristicDao

Find characteristics with the given URI.

Specified by:

findByUri in interface CharacteristicDao

Parameters:

category - restrict the category of the characteristic, or null to ignore

parentClasses - only return characteristics that have parents of these classes, or null to ignore

includeNoParents - include characteristics that have no parents

maxResults - maximum number of results to return, or -1 for no limit

findBestByUri

public Characteristic findBestByUri(String uri)

Description copied from interface: CharacteristicDao

Return the characteristic with the most frequently used non-null value by URI.

Specified by:

findBestByUri in interface CharacteristicDao

findByValueUriGroupedByNormalizedValue

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

Description copied from interface: CharacteristicDao

Find characteristics by URI.

The mapping key is the normalized value of the characteristics as per CharacteristicUtils.getNormalizedValue(Characteristic).

Specified by:

findByValueUriGroupedByNormalizedValue in interface CharacteristicDao

findByValueLikeGroupedByNormalizedValue

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

Description copied from interface: CharacteristicDao

Find characteristics by value matching the provided LIKE pattern.

The mapping key is the normalized value of the characteristics as per CharacteristicUtils.getNormalizedValue(Characteristic).

Specified by:

findByValueLikeGroupedByNormalizedValue in interface CharacteristicDao

countByValueUriGroupedByNormalizedValue

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

Description copied from interface: CharacteristicDao

Count characteristics matching the provided value URIs.

The mapping key is the normalized value of the characteristics as per CharacteristicUtils.getNormalizedValue(Characteristic).

Specified by:

countByValueUriGroupedByNormalizedValue in interface CharacteristicDao

findByValue

public Collection<Characteristic> findByValue(String value)

Specified by:

findByValue in interface CharacteristicDao

findByValueLike

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

Description copied from interface: CharacteristicDao

Finds all Characteristics whose value match the given search term

Specified by:

findByValueLike in interface CharacteristicDao

Parameters:

category - constraint the category of the characteristic, or null to ignore

getParentClasses

public Collection<Class<? extends Identifiable>> getParentClasses()

Description copied from interface: CharacteristicDao

Obtain the classes of entities can can own a Characteristic.

Specified by:

getParentClasses in interface CharacteristicDao

getParents

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

Description copied from interface: CharacteristicDao

Obtain the parents (i.e. owners) of the given characteristics.

Specified by:

getParents in interface CharacteristicDao

Parameters:

characteristics - characteristics to find parents for

parentClasses - restrict the parents to these classes, all parents are returned if null. If supplied, at least one parent must be provided unless includeNoParents is true.

includeNoParents - include characteristics that have no parents, those will be mapped explicitly to null.

Returns:

the supplied characteristics mapped to their parents, or null if the characteristic has no parent and includeNoParents is true. A characteristic may not have multiple parents.

doLoadValueObject

protected CharacteristicValueObject doLoadValueObject(Characteristic entity)

Description copied from class: AbstractVoEnabledDao

Load a value object for a given entity.

This should be fast and efficient, and avoid any database query or post-processing. If you need to perform additional queries, implement AbstractVoEnabledDao.postProcessValueObjects(List) instead.

Specified by:

doLoadValueObject in class AbstractVoEnabledDao<Characteristic,CharacteristicValueObject>