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

Class CharacteristicDaoImpl

java.lang.Object

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

ubic.gemma.persistence.service.AbstractVoEnabledDao<O,VO>

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

Nested Class Summary

Nested classes/interfaces inherited from interface ubic.gemma.persistence.service.common.description.CharacteristicDao

CharacteristicDao.CharacteristicUsageFrequency

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

elementClass, log

Fields inherited from interface ubic.gemma.persistence.service.common.description.CharacteristicDao

OBJECT_ALIAS

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>	countCharacteristicsByValueUriGroupedByNormalizedValue(Collection<String> uris)	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<? extends Characteristic>	findByCategory(String query)
Collection<Characteristic>	findByUri(String uri)
Collection<Characteristic>	findByUri(Collection<String> uris)
Collection<Characteristic>	findByValue(String search)	Finds all Characteristics whose value match the given search term
Map<String,Characteristic>	findCharacteristicsByValueUriOrValueLikeGroupedByNormalizedValue(String value)	Find characteristics by value matching the provided LIKE pattern.
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>	findExperimentReferencesByUris(Collection<String> uris, 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, Taxon taxon, int limit, boolean rankByLevel)	This search looks at direct annotations, factor values and biomaterials in that order.
Map<Characteristic,Identifiable>	getParents(Collection<Characteristic> characteristics, Collection<Class<?>> parentClasses, int maxResults)	Obtain the parents (i.e.
String	normalizeByValue(Characteristic characteristic)	Normalize a characteristic by value.

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

count, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyType, getSort, 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, getIdentifierPropertyName, getSessionFactory, load, load, loadAll, loadReference, loadReference, 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.BaseDao

countAll, create, create, find, findOrCreate, getElementClass, getIdentifierPropertyName, load, load, loadAll, loadReference, loadReference, remove, remove, remove, save, save, 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, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyType, getSort, load, load, loadIds

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

loadValueObjects, loadValueObjects

Constructor Detail

CharacteristicDaoImpl

@Autowired
public CharacteristicDaoImpl(SessionFactory sessionFactory)

Method Detail

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

findByCategory

public Collection<? extends Characteristic> findByCategory(String query)

Specified by:

findByCategory in interface CharacteristicDao

findExperimentsByUris

public Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>> findExperimentsByUris(Collection<String> uris,
                                                                                                                  @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, 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())

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,
                                                                                                                           @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(Collection<String> uris)

Specified by:

findByUri in interface CharacteristicDao

findByUri

public Collection<Characteristic> findByUri(String uri)

Specified by:

findByUri in interface CharacteristicDao

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

countCharacteristicsByValueUriGroupedByNormalizedValue

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

Description copied from interface: CharacteristicDao

Count characteristics matching the provided value URIs.

The mapping key is the normalized value of the characteristics as per CharacteristicDao.normalizeByValue(Characteristic).

Specified by:

countCharacteristicsByValueUriGroupedByNormalizedValue in interface CharacteristicDao

findCharacteristicsByValueUriOrValueLikeGroupedByNormalizedValue

public Map<String,Characteristic> findCharacteristicsByValueUriOrValueLikeGroupedByNormalizedValue(String value)

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 CharacteristicDao.normalizeByValue(Characteristic).

Specified by:

findCharacteristicsByValueUriOrValueLikeGroupedByNormalizedValue in interface CharacteristicDao

normalizeByValue

public String normalizeByValue(Characteristic characteristic)

Description copied from interface: CharacteristicDao

Normalize a characteristic by value.

This is obtained by taking the value URI or value if the former is null and converting it to lowercase.

Specified by:

normalizeByValue in interface CharacteristicDao

findByValue

public Collection<Characteristic> findByValue(String search)

Description copied from interface: CharacteristicDao

Finds all Characteristics whose value match the given search term

Specified by:

findByValue in interface CharacteristicDao

Parameters:

search - search

Returns:

characteristics

getParents

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

Description copied from interface: CharacteristicDao

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

If a characteristic lacks a parent, its entry will be missing from the returned map.

Specified by:

getParents in interface CharacteristicDao

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>