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

Interface BibliographicReferenceService

All Superinterfaces:

BaseImmutableService<BibliographicReference>, BaseReadOnlyService<BibliographicReference>, BaseService<BibliographicReference>, BaseVoEnabledService<BibliographicReference,BibliographicReferenceValueObject>

All Known Implementing Classes:

BibliographicReferenceServiceImpl

@ParametersAreNonnullByDefault
public interface BibliographicReferenceService
extends BaseService<BibliographicReference>, BaseVoEnabledService<BibliographicReference,BibliographicReferenceValueObject>

Author:

kelsey

Method Summary

Modifier and Type	Method	Description
List<BibliographicReference>	browse(int start, int limit)
List<BibliographicReference>	browse(int start, int limit, String orderField, boolean descending)
long	countDistinctWithRelatedExperiments()
long	countWithRelatedExperiments()
Collection<BibliographicReference>	create(Collection<BibliographicReference> entities)
BibliographicReference	create(BibliographicReference bibliographicReference)
BibliographicReference	find(BibliographicReference bibliographicReference)	check to see if the object already exists
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)
BibliographicReference	findOrCreate(BibliographicReference BibliographicReference)
BibliographicReferenceValueObject	findVOByExternalId(String id)	Get a reference by the unqualified external id.
Map<BibliographicReference,Set<ExpressionExperimentIdAndShortName>>	getRelatedExperiments(int offset, int limit)	Return all the BibRefs that are linked to ExpressionExperiments.
Map<BibliographicReference,Collection<ExpressionExperiment>>	getRelatedExperiments(Collection<BibliographicReference> records)
Collection<Long>	listAll()
BibliographicReference	refresh(String pubMedId)
void	remove(Collection<BibliographicReference> entities)
void	remove(BibliographicReference BibliographicReference)
Collection<BibliographicReference>	save(Collection<BibliographicReference> entities)
BibliographicReference	save(BibliographicReference entity)
List<BibliographicReferenceValueObject>	search(String query)
List<BibliographicReferenceValueObject>	search(String query, boolean searchExperiments, boolean searchBibrefs)
Collection<BibliographicReference>	thaw(Collection<BibliographicReference> bibliographicReferences)
BibliographicReference	thaw(BibliographicReference bibliographicReference)
void	update(Collection<BibliographicReference> entities)
void	update(BibliographicReference entity)

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.BaseVoEnabledService

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Method Details

browse

List<BibliographicReference> browse(int start,
 int limit)

browse

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

find

BibliographicReference find(BibliographicReference bibliographicReference)

check to see if the object already exists

Specified by:

find in interface BaseReadOnlyService<BibliographicReference>

Parameters:

bibliographicReference - reference

Returns:

reference

See Also:

• BaseDao.find(Identifiable)

findOrCreate

@Secured("GROUP_USER")
BibliographicReference findOrCreate(BibliographicReference BibliographicReference)

Specified by:

findOrCreate in interface BaseImmutableService<BibliographicReference>

See Also:

• BaseDao.findOrCreate(Identifiable)

create

@Secured("GROUP_USER")
BibliographicReference create(BibliographicReference bibliographicReference)

Specified by:

create in interface BaseImmutableService<BibliographicReference>

See Also:

• BaseDao.create(Identifiable)

create

@Secured("GROUP_USER")
Collection<BibliographicReference> create(Collection<BibliographicReference> entities)

Specified by:

create in interface BaseImmutableService<BibliographicReference>

See Also:

• BaseDao.create(Collection)

update

@Secured("GROUP_USER")
void update(Collection<BibliographicReference> entities)

Specified by:

update in interface BaseService<BibliographicReference>

See Also:

• BaseDao.update(Collection)

update

@Secured("GROUP_USER")
void update(BibliographicReference entity)

Specified by:

update in interface BaseService<BibliographicReference>

See Also:

• BaseDao.update(Identifiable)

save

@Secured("GROUP_USER")
BibliographicReference save(BibliographicReference entity)

Specified by:

save in interface BaseService<BibliographicReference>

See Also:

• BaseDao.save(Identifiable)

save

@Secured("GROUP_USER")
Collection<BibliographicReference> save(Collection<BibliographicReference> entities)

Specified by:

save in interface BaseService<BibliographicReference>

See Also:

• BaseDao.save(Collection)

remove

@Secured("GROUP_ADMIN")
void remove(BibliographicReference BibliographicReference)

Specified by:

remove in interface BaseImmutableService<BibliographicReference>

See Also:

• BaseDao.remove(Identifiable)

remove

@Secured("GROUP_ADMIN")
void remove(Collection<BibliographicReference> entities)

Specified by:

remove in interface BaseImmutableService<BibliographicReference>

See Also:

• BaseDao.remove(Collection)

findByExternalId

@Nullable
BibliographicReference findByExternalId(DatabaseEntry accession)

findByExternalId

@Nullable
BibliographicReference findByExternalId(String id)

Get a reference by the unqualified external id.

Parameters:

id - id

Returns:

reference

findByExternalId

@Nullable
BibliographicReference findByExternalId(String id,
 String databaseName)

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

Parameters:

id - id

databaseName - db name

Returns:

reference

findVOByExternalId

@Nullable
BibliographicReferenceValueObject findVOByExternalId(String id)

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

Parameters:

id - id

Returns:

reference VO

countDistinctWithRelatedExperiments

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
long countDistinctWithRelatedExperiments()

countWithRelatedExperiments

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
long countWithRelatedExperiments()

getRelatedExperiments

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
Map<BibliographicReference,Set<ExpressionExperimentIdAndShortName>> getRelatedExperiments(int offset,
 int limit)

Return all the BibRefs that are linked to ExpressionExperiments.

Returns:

all references with EEs

getRelatedExperiments

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
Map<BibliographicReference,Collection<ExpressionExperiment>> getRelatedExperiments(Collection<BibliographicReference> records)

listAll

Collection<Long> listAll()

Returns:

all the IDs of bibliographic references in the system.

refresh

@Nullable
@Secured("GROUP_ADMIN")
BibliographicReference refresh(String pubMedId)

search

List<BibliographicReferenceValueObject> search(String query,
 boolean searchExperiments,
 boolean searchBibrefs)
                                        throws SearchException

Throws:

SearchException

search

List<BibliographicReferenceValueObject> search(String query)
                                        throws SearchException

Throws:

SearchException

thaw

BibliographicReference thaw(BibliographicReference bibliographicReference)

thaw

Collection<BibliographicReference> thaw(Collection<BibliographicReference> bibliographicReferences)