Package ubic.gemma.persistence.service.genome.taxon

Class TaxonDaoImpl

java.lang.Object

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

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

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

ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao<Taxon,TaxonValueObject>

ubic.gemma.persistence.service.genome.taxon.TaxonDaoImpl

All Implemented Interfaces:

org.springframework.beans.factory.InitializingBean, BaseDao<Taxon>, BaseVoEnabledDao<Taxon,TaxonValueObject>, CachedFilteringDao<Taxon>, CachedFilteringVoEnabledDao<Taxon,TaxonValueObject>, FilteringDao<Taxon>, FilteringVoEnabledDao<Taxon,TaxonValueObject>, TaxonDao

@Repository
public class TaxonDaoImpl
extends AbstractQueryFilteringVoEnabledDao<Taxon,TaxonValueObject>
implements TaxonDao

Author:

pavlidis

See Also:

Taxon

Nested Class Summary

Nested classes/interfaces inherited from class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao

AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer, AbstractFilteringVoEnabledDao.FilterablePropertyMeta

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.genome.taxon.TaxonDao

OBJECT_ALIAS

Constructor Summary

Constructors

Constructor	Description
TaxonDaoImpl(SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
protected void	configureFilterableProperties(AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer configurer)	Register filterable properties.
Taxon	create(Taxon taxon)	Create an object.
protected TaxonValueObject	doLoadValueObject(Taxon entity)	Load a value object for a given entity.
Taxon	find(Taxon taxon)	Does a look up for the given entity in the persistent storage, usually looking for a specific identifier ( either id or a string property).
Taxon	findByCommonName(String commonName)
Taxon	findByNcbiId(Integer ncbiId)
Taxon	findByScientificName(String scientificName)	Searches for a taxon by its scientific name, case insensitive.
Collection<Taxon>	findTaxonUsedInEvidence()
protected Query	getFilteringCountQuery(Filters filters)	Produce a query that will be used to retrieve the size of AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).
protected Query	getFilteringQuery(Filters filters, Sort sort)	Produce a query for retrieving value objects after applying a set of filters and a given ordering.
protected void	initializeCachedFilteringResult(Taxon cachedEntity)	Initialize a result from AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort) retrieved from the Hibernate StandardQueryCache.

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

count, countWithCache, getEntityTransformer, getFilteringIdQuery, getValueObjectTransformer, load, load, loadIds, loadIdsWithCache, loadValueObjects, loadValueObjects, loadValueObjectsWithCache, loadValueObjectsWithCache, loadWithCache, loadWithCache

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

afterPropertiesSet, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyMeta, getFilterablePropertyMeta, getFilterablePropertyType, getSort

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, 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, 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, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyType, getSort, load, load, loadIds

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

loadValueObjects, loadValueObjects

Constructor Detail

TaxonDaoImpl

@Autowired
public TaxonDaoImpl(SessionFactory sessionFactory)

Method Detail

create

public Taxon create(Taxon taxon)

Description copied from interface: BaseDao

Create an object. If the entity type is immutable, this may also remove any existing entities identified by an appropriate 'find' method.

Specified by:

create in interface BaseDao<Taxon>

Overrides:

create in class AbstractDao<Taxon>

Parameters:

taxon - the entity to create

Returns:

the persistent version of the entity

find

public Taxon find(Taxon taxon)

Description copied from interface: BaseDao

Does a look up for the given entity in the persistent storage, usually looking for a specific identifier ( either id or a string property).

Specified by:

find in interface BaseDao<Taxon>

Overrides:

find in class AbstractDao<Taxon>

Parameters:

taxon - the entity to look for.

Returns:

an entity that was found in the persistent storage, or null if no such entity was found.

findByCommonName

public Taxon findByCommonName(String commonName)

Specified by:

findByCommonName in interface TaxonDao

findByScientificName

public Taxon findByScientificName(String scientificName)

Description copied from interface: TaxonDao

Searches for a taxon by its scientific name, case insensitive.

Specified by:

findByScientificName in interface TaxonDao

Parameters:

scientificName - the scientific name to be matched

Returns:

a Taxon whose scientific name matches the given string.

findTaxonUsedInEvidence

public Collection<Taxon> findTaxonUsedInEvidence()

Specified by:

findTaxonUsedInEvidence in interface TaxonDao

findByNcbiId

public Taxon findByNcbiId(Integer ncbiId)

Specified by:

findByNcbiId in interface TaxonDao

doLoadValueObject

protected TaxonValueObject doLoadValueObject(Taxon 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<Taxon,TaxonValueObject>

configureFilterableProperties

protected void configureFilterableProperties(AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer configurer)

Description copied from class: AbstractFilteringVoEnabledDao

Register filterable properties.

Overrides:

configureFilterableProperties in class AbstractFilteringVoEnabledDao<Taxon,TaxonValueObject>

getFilteringQuery

protected Query getFilteringQuery(@Nullable
                                  Filters filters,
                                  @Nullable
                                  Sort sort)

Description copied from class: AbstractQueryFilteringVoEnabledDao

Produce a query for retrieving value objects after applying a set of filters and a given ordering.

Note that if your implementation does not produce a List of AbstractQueryFilteringVoEnabledDao when Query.list() is invoked, you must override AbstractQueryFilteringVoEnabledDao.getValueObjectTransformer().

The make the cached query (i.e. AbstractQueryFilteringVoEnabledDao.loadWithCache(Filters, Sort) behave the same, you also have to explicitly initialize any lazy relations in AbstractVoEnabledDao.doLoadValueObject(Identifiable) because the VO constructor will not initialize them.

Specified by:

getFilteringQuery in class AbstractQueryFilteringVoEnabledDao<Taxon,TaxonValueObject>

Returns:

a Query that produce a list of AbstractQueryFilteringVoEnabledDao

initializeCachedFilteringResult

protected void initializeCachedFilteringResult(Taxon cachedEntity)

Description copied from class: AbstractQueryFilteringVoEnabledDao

Initialize a result from AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort) retrieved from the Hibernate StandardQueryCache.

Lazy-loaded relations that are fetched in AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort) must be initialized manually in this method to ensure that the entity has all the expected fields if they are retrieved from the second-level cache.

Specified by:

initializeCachedFilteringResult in class AbstractQueryFilteringVoEnabledDao<Taxon,TaxonValueObject>

getFilteringCountQuery

protected Query getFilteringCountQuery(@Nullable
                                       Filters filters)

Description copied from class: AbstractQueryFilteringVoEnabledDao

Produce a query that will be used to retrieve the size of AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).

Overrides:

getFilteringCountQuery in class AbstractQueryFilteringVoEnabledDao<Taxon,TaxonValueObject>

Returns:

a Query which must return a single Long value