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

Class BibliographicReferenceServiceImpl

java.lang.Object

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

ubic.gemma.persistence.service.AbstractVoEnabledService<BibliographicReference,BibliographicReferenceValueObject>

ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl

All Implemented Interfaces:

org.springframework.beans.factory.InitializingBean, BaseImmutableService<BibliographicReference>, BaseReadOnlyService<BibliographicReference>, BaseService<BibliographicReference>, BaseVoEnabledService<BibliographicReference,BibliographicReferenceValueObject>, BibliographicReferenceService

@Service
@ParametersAreNonnullByDefault
public class BibliographicReferenceServiceImpl
extends AbstractVoEnabledService<BibliographicReference,BibliographicReferenceValueObject>
implements BibliographicReferenceService, org.springframework.beans.factory.InitializingBean

Implementation of BibliographicReferenceService. Note: This is only in Core because it uses SearchService, but it could be refactored.

Author:

keshav

See Also:

• BibliographicReferenceService

Field Summary

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

log

Constructor Summary

Constructors

Constructor	Description
BibliographicReferenceServiceImpl(BibliographicReferenceDao bibliographicReferenceDao)

Method Summary

Modifier and Type	Method	Description
void	afterPropertiesSet()
List<BibliographicReference>	browse(int start, int limit)
List<BibliographicReference>	browse(int start, int limit, String orderField, boolean descending)
long	countExperimentLinkedReferences()
BibliographicReference	findByExternalId(String id)	Get a reference by the unqualified external id.
BibliographicReference	findByExternalId(String id, String databaseName)	Retrieve a reference by identifier, qualified by the database name (such as 'pubmed').
BibliographicReference	findByExternalId(DatabaseEntry accession)
BibliographicReferenceValueObject	findVOByExternalId(String id)	Get a reference by the unqualified external id.
Map<BibliographicReference,Set<ExpressionExperiment>>	getAllExperimentLinkedReferences(int offset, int limit)	Return all the BibRefs that are linked to ExpressionExperiments.
Map<BibliographicReference,Collection<ExpressionExperiment>>	getRelatedExperiments(Collection<BibliographicReference> records)
Collection<ExpressionExperiment>	getRelatedExperiments(BibliographicReference bibRef)	Get the ExpressionExperiments, if any, that are linked to the given reference.
Collection<Long>	listAll()
List<BibliographicReferenceValueObject>	loadAllValueObjects()	Loads value objects representing all the entities of specific type.
BibliographicReferenceValueObject	loadValueObject(BibliographicReference entity)
BibliographicReference	refresh(String pubMedId)
List<BibliographicReferenceValueObject>	search(String query)
List<BibliographicReferenceValueObject>	search(SearchSettingsValueObject settings)
Collection<BibliographicReference>	thaw(Collection<BibliographicReference> bibliographicReferences)
BibliographicReference	thaw(BibliographicReference bibliographicReference)

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

loadValueObjectById, 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, 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, remove, remove

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

countAll, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, 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

loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from interface ubic.gemma.persistence.service.common.description.BibliographicReferenceService

create, find, findOrCreate, remove

Constructor Details

BibliographicReferenceServiceImpl

@Autowired
public BibliographicReferenceServiceImpl(BibliographicReferenceDao bibliographicReferenceDao)

Method Details

afterPropertiesSet

public void afterPropertiesSet()
                        throws Exception

Specified by:

afterPropertiesSet in interface org.springframework.beans.factory.InitializingBean

Throws:

Exception

loadValueObject

@Transactional(readOnly=true)
public BibliographicReferenceValueObject loadValueObject(BibliographicReference entity)

Specified by:

loadValueObject in interface BaseVoEnabledService<BibliographicReference,BibliographicReferenceValueObject>

Overrides:

loadValueObject in class AbstractVoEnabledService<BibliographicReference,BibliographicReferenceValueObject>

See Also:

• BaseVoEnabledDao.loadValueObject(Identifiable)

loadAllValueObjects

@Transactional(readOnly=true)
public List<BibliographicReferenceValueObject> loadAllValueObjects()

Description copied from interface: BaseVoEnabledService

Loads value objects representing all the entities of specific type.

Specified by:

loadAllValueObjects in interface BaseVoEnabledService<BibliographicReference,BibliographicReferenceValueObject>

Overrides:

loadAllValueObjects in class AbstractVoEnabledService<BibliographicReference,BibliographicReferenceValueObject>

Returns:

a collection of value objects

browse

@Transactional(readOnly=true)
public List<BibliographicReference> browse(int start,
 int limit)

Specified by:

browse in interface BibliographicReferenceService

browse

@Transactional(readOnly=true)
public List<BibliographicReference> browse(int start,
 int limit,
 String orderField,
 boolean descending)

Specified by:

browse in interface BibliographicReferenceService

findByExternalId

@Transactional(readOnly=true)
public BibliographicReference findByExternalId(DatabaseEntry accession)

Specified by:

findByExternalId in interface BibliographicReferenceService

findByExternalId

@Transactional
public BibliographicReference findByExternalId(String id)

Description copied from interface: BibliographicReferenceService

Get a reference by the unqualified external id.

Specified by:

findByExternalId in interface BibliographicReferenceService

Parameters:

id - id

Returns:

reference

findByExternalId

@Transactional
public BibliographicReference findByExternalId(String id,
 String databaseName)

Description copied from interface: BibliographicReferenceService

Retrieve a reference by identifier, qualified by the database name (such as 'pubmed').

Specified by:

findByExternalId in interface BibliographicReferenceService

Parameters:

id - id

databaseName - db name

Returns:

reference

findVOByExternalId

@Transactional(readOnly=true)
public BibliographicReferenceValueObject findVOByExternalId(String id)

Description copied from interface: BibliographicReferenceService

Get a reference by the unqualified external id. Searches for pubmed by default

Specified by:

findVOByExternalId in interface BibliographicReferenceService

Parameters:

id - id

Returns:

reference VO

See Also:

• BibliographicReferenceService.findVOByExternalId(String)

countExperimentLinkedReferences

@Transactional(readOnly=true)
public long countExperimentLinkedReferences()

Specified by:

countExperimentLinkedReferences in interface BibliographicReferenceService

getAllExperimentLinkedReferences

@Transactional(readOnly=true)
public Map<BibliographicReference,Set<ExpressionExperiment>> getAllExperimentLinkedReferences(int offset,
 int limit)

Description copied from interface: BibliographicReferenceService

Return all the BibRefs that are linked to ExpressionExperiments.

Specified by:

getAllExperimentLinkedReferences in interface BibliographicReferenceService

Returns:

all references with EEs

getRelatedExperiments

@Transactional(readOnly=true)
public Collection<ExpressionExperiment> getRelatedExperiments(BibliographicReference bibRef)

Description copied from interface: BibliographicReferenceService

Get the ExpressionExperiments, if any, that are linked to the given reference.

Specified by:

getRelatedExperiments in interface BibliographicReferenceService

Parameters:

bibRef - reference

Returns:

datasets

getRelatedExperiments

@Transactional(readOnly=true)
public Map<BibliographicReference,Collection<ExpressionExperiment>> getRelatedExperiments(Collection<BibliographicReference> records)

Specified by:

getRelatedExperiments in interface BibliographicReferenceService

listAll

@Transactional(readOnly=true)
public Collection<Long> listAll()

Specified by:

listAll in interface BibliographicReferenceService

Returns:

all the IDs of bibliographic references in the system.

refresh

@Transactional
public BibliographicReference refresh(String pubMedId)

Specified by:

refresh in interface BibliographicReferenceService

search

@Transactional(readOnly=true)
public List<BibliographicReferenceValueObject> search(SearchSettingsValueObject settings)
                                               throws SearchException

Specified by:

search in interface BibliographicReferenceService

Throws:

SearchException

search

@Transactional(readOnly=true)
public List<BibliographicReferenceValueObject> search(String query)
                                               throws SearchException

Specified by:

search in interface BibliographicReferenceService

Throws:

SearchException

thaw

@Transactional(readOnly=true)
public BibliographicReference thaw(BibliographicReference bibliographicReference)

Specified by:

thaw in interface BibliographicReferenceService

thaw

@Transactional(readOnly=true)
public Collection<BibliographicReference> thaw(Collection<BibliographicReference> bibliographicReferences)

Specified by:

thaw in interface BibliographicReferenceService