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	countExperimentLinkedReferences()
BibliographicReference	create(BibliographicReference bibliographicReference)	Creates the given entity in the persistent storage.
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)	Does a search for the entity in the persistent storage, and if not found, creates it.
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 bibliographicReference)	Get the ExpressionExperiments, if any, that are linked to the given reference.
Collection<Long>	listAll()
BibliographicReference	refresh(String pubMedId)
void	remove(BibliographicReference BibliographicReference)	Removes the given entity from the persistent storage.
List<BibliographicReferenceValueObject>	search(String query)
List<BibliographicReferenceValueObject>	search(SearchSettingsValueObject settings)
Collection<BibliographicReference>	thaw(Collection<BibliographicReference> bibliographicReferences)
BibliographicReference	thaw(BibliographicReference bibliographicReference)

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, streamAll, streamAll

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

save, save, update, update

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

findOrCreate

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

Description copied from interface: BaseImmutableService

Does a search for the entity in the persistent storage, and if not found, creates it.

Specified by:

findOrCreate in interface BaseImmutableService<BibliographicReference>

Parameters:

BibliographicReference - the entity to look for, and create if not found.

Returns:

the entity retrieved from the persistent storage, either found or created.

create

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

Description copied from interface: BaseImmutableService

Creates the given entity in the persistent storage.

Specified by:

create in interface BaseImmutableService<BibliographicReference>

Parameters:

bibliographicReference - the entity to be created.

Returns:

object referencing the persistent instance of the given entity.

remove

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

Description copied from interface: BaseImmutableService

Removes the given entity from the persistent storage.

Specified by:

remove in interface BaseImmutableService<BibliographicReference>

Parameters:

BibliographicReference - the entity to be removed.

findByExternalId

BibliographicReference findByExternalId(DatabaseEntry accession)

findByExternalId

BibliographicReference findByExternalId(String id)

Get a reference by the unqualified external id.

Parameters:

id - id

Returns:

reference

findByExternalId

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

BibliographicReferenceValueObject findVOByExternalId(String id)

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

Parameters:

id - id

Returns:

reference VO

countExperimentLinkedReferences

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
long countExperimentLinkedReferences()

getAllExperimentLinkedReferences

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
Map<BibliographicReference,Set<ExpressionExperiment>> getAllExperimentLinkedReferences(int offset,
 int limit)

Return all the BibRefs that are linked to ExpressionExperiments.

Returns:

all references with EEs

getRelatedExperiments

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperiment> getRelatedExperiments(BibliographicReference bibliographicReference)

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

Parameters:

bibliographicReference - reference

Returns:

datasets

getRelatedExperiments

Map<BibliographicReference,Collection<ExpressionExperiment>> getRelatedExperiments(Collection<BibliographicReference> records)

listAll

Collection<Long> listAll()

Returns:

all the IDs of bibliographic references in the system.

refresh

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

search

List<BibliographicReferenceValueObject> search(SearchSettingsValueObject settings)
                                        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)