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)
BibliographicReference	findOrCreateByDoi(String doi)	Resolve a DOI to a persistent BibliographicReference, fetching it when necessary.
BibliographicReference	findOrCreateByPubMedId(String pubMedId)	Resolve a PubMed id to a persistent BibliographicReference, fetching it from PubMed and persisting it when it is not already in the system.
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 BaseReadOnlyService

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

Methods inherited from interface 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)

findOrCreateByPubMedId

@Secured("GROUP_USER")
BibliographicReference findOrCreateByPubMedId(String pubMedId)

Resolve a PubMed id to a persistent BibliographicReference, fetching it from PubMed and persisting it when it is not already in the system.

Encapsulates the find-or-fetch dance that UpdatePubMedCli and the retired gemma-web ExpressionExperimentController.updatePubMed both open-coded: look up by external id first, otherwise retrieve the record over the wire and findOrCreate(BibliographicReference) it.

Parameters:

pubMedId - a PubMed id (must be non-blank).

Returns:

the persistent reference for pubMedId.

Throws:

IllegalStateException - if no record can be retrieved from PubMed for pubMedId.

findOrCreateByDoi

@Secured("GROUP_USER")
BibliographicReference findOrCreateByDoi(String doi)

Resolve a DOI to a persistent BibliographicReference, fetching it when necessary.

Resolution order: (1) an existing DOI-keyed reference already in Gemma; (2) PubMed-by-DOI (covers DOIs NCBI indexes — yields the richer PubMed record); (3) CrossRef by DOI (covers the rest, notably bioRxiv / medRxiv preprints PubMed does not carry). This is what lets a preprint be attached to an experiment instead of being noted in a free-text comment.

Parameters:

doi - a DOI in any common form (10.x/…, https://doi.org/…, doi:…); normalized internally.

Returns:

the persistent reference for doi.

Throws:

IllegalStateException - if the DOI resolves via neither PubMed nor CrossRef. (Manual entry of such a reference is intentionally not supported here yet.)

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)