Uses of Class
psidev.psi.mi.jami.bridges.exception.BridgeFailedException

Packages that use BridgeFailedException

Package	Description
psidev.psi.mi.jami.bridges.chebi
psidev.psi.mi.jami.bridges.europubmedcentral
psidev.psi.mi.jami.bridges.fetcher
psidev.psi.mi.jami.bridges.fetcher.mock
psidev.psi.mi.jami.bridges.imex
psidev.psi.mi.jami.bridges.imex.mock
psidev.psi.mi.jami.bridges.mapper
psidev.psi.mi.jami.bridges.mapper.mock
psidev.psi.mi.jami.bridges.obo
psidev.psi.mi.jami.bridges.ols
psidev.psi.mi.jami.bridges.ontologymanager.impl
psidev.psi.mi.jami.bridges.uniprot
psidev.psi.mi.jami.bridges.uniprot.taxonomy
psidev.psi.mi.jami.bridges.unisave
psidev.psi.mi.jami.imex.actions
psidev.psi.mi.jami.imex.actions.impl

Uses of BridgeFailedException in psidev.psi.mi.jami.bridges.chebi

Methods in psidev.psi.mi.jami.bridges.chebi that throw BridgeFailedException

Modifier and Type	Method	Description
Collection<BioactiveEntity>	CachedChebiFetcher.fetchByIdentifier(String identifier)	Takes a string identifier and returns the interactors which match.
Collection<BioactiveEntity>	ChebiFetcher.fetchByIdentifier(String identifier)	Searches Chebi for an entry matching the identifier.
Collection<BioactiveEntity>	CachedChebiFetcher.fetchByIdentifiers(Collection<String> identifiers)	Takes a collection of string identifiers and returns the interactors which match.
Collection<BioactiveEntity>	ChebiFetcher.fetchByIdentifiers(Collection<String> identifiers)	Takes a collection of string identifiers and returns the interactors which match.

Uses of BridgeFailedException in psidev.psi.mi.jami.bridges.europubmedcentral

Methods in psidev.psi.mi.jami.bridges.europubmedcentral that throw BridgeFailedException

Modifier and Type	Method	Description
Publication	CachedEuroPubmedCentralFetcher.fetchByIdentifier(String identifier, String source)	Uses the identifier to search for a publication and return a completed record.
Publication	EuroPubmedCentralFetcher.fetchByIdentifier(String id, String source)	Uses the identifier to search for a publication and return a completed record.
Collection<Publication>	CachedEuroPubmedCentralFetcher.fetchByIdentifiers(Map<String,Collection<String>> identifiers)	Uses the identifiers to search for publications and return completed records.
Collection<Publication>	EuroPubmedCentralFetcher.fetchByIdentifiers(Map<String,Collection<String>> identifiers)	Uses the identifiers to search for publications and return completed records.

Constructors in psidev.psi.mi.jami.bridges.europubmedcentral that throw BridgeFailedException

Constructor	Description
CachedEuroPubmedCentralFetcher()	Constructor for CachedEuroPubmedCentralFetcher.
EuroPubmedCentralFetcher()	Initiates the EuroPubmedCentral fetcher

Uses of BridgeFailedException in psidev.psi.mi.jami.bridges.fetcher

Methods in psidev.psi.mi.jami.bridges.fetcher that throw BridgeFailedException

Modifier and Type	Method	Description
C	CvTermFetcher.fetchByIdentifier(String termIdentifier, String miOntologyName)	Uses the identifier and the name of the database to search for a complete form of the cvTerm.
C	CvTermFetcher.fetchByIdentifier(String termIdentifier, CvTerm ontologyDatabase)	Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.
Collection<Gene>	GeneFetcher.fetchByIdentifier(String identifier, int taxID)	fetchByIdentifier.
Collection<I>	InteractorFetcher.fetchByIdentifier(String identifier)	Takes a string identifier and returns the interactors which match.
Publication	PublicationFetcher.fetchByIdentifier(String identifier, String source)	Uses the identifier to search for a publication and return a completed record.
Collection<C>	CvTermFetcher.fetchByIdentifiers(Collection<String> termIdentifiers, String miOntologyName)	Uses the identifier and the name of the database to search for a complete form of the cvTerm.
Collection<C>	CvTermFetcher.fetchByIdentifiers(Collection<String> termIdentifiers, CvTerm ontologyDatabase)	Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.
Collection<Gene>	GeneFetcher.fetchByIdentifiers(Collection<String> identifiers, int taxID)	fetchByIdentifiers.
Collection<I>	InteractorFetcher.fetchByIdentifiers(Collection<String> identifiers)	Takes a collection of string identifiers and returns the interactors which match.
Collection<Publication>	PublicationFetcher.fetchByIdentifiers(Map<String,Collection<String>> identifiers)	Uses the identifiers to search for publications and return completed records.
Collection<C>	CvTermFetcher.fetchByName(String searchName)	Uses the name of the term and the name of the database to search for a complete form of the term.
C	CvTermFetcher.fetchByName(String searchName, String miOntologyName)	Uses the name of the term and the name of the database to search for a complete form of the term.
Collection<C>	CvTermFetcher.fetchByNames(Collection<String> searchNames)	Finds the CvTerms which match the exact names provided.
Collection<C>	CvTermFetcher.fetchByNames(Collection<String> searchNames, String miOntologyName)	Uses the name of the term and the name of the database to search for a complete form of the term.
Organism	OrganismFetcher.fetchByTaxID(int taxID)	Finds the complete organism record matching the provided TaxID number.
Collection<Organism>	OrganismFetcher.fetchByTaxIDs(Collection<Integer> taxIDs)	Finds the complete organism records matching the provided TaxID numbers.
Set<OntologyTerm>	OntologyTermFetcher.fetchRootTerms(String databaseName)	fetchRootTerms.
Set<OntologyTerm>	OntologyTermFetcher.fetchRootTerms(CvTerm database)	fetchRootTerms.
String	SequenceVersionFetcher.fetchSequenceFromVersion(String id, int version)	fetchSequenceFromVersion.
int	SequenceVersionFetcher.fetchVersionFromSequence(String id, String sequence)	fetchVersionFromSequence.

Uses of BridgeFailedException in psidev.psi.mi.jami.bridges.fetcher.mock

Methods in psidev.psi.mi.jami.bridges.fetcher.mock that throw BridgeFailedException

Modifier and Type	Method	Description
T	CvTermCompositeFetcherTemplate.fetchByIdentifier(String termIdentifier, String ontologyDatabaseName)	Uses the identifier and the name of the database to search for a complete form of the cvTerm.
T	CvTermCompositeFetcherTemplate.fetchByIdentifier(String termIdentifier, CvTerm ontologyDatabase)	fetchByIdentifier.
Collection<BioactiveEntity>	FailingBioactiveEntityFetcher.fetchByIdentifier(String identifier)	Takes a string identifier and returns the interactors which match.
CvTerm	FailingCvTermFetcher.fetchByIdentifier(String termIdentifier, String ontologyDatabaseName)	Uses the identifier and the name of the database to search for a complete form of the cvTerm.
CvTerm	FailingCvTermFetcher.fetchByIdentifier(String termIdentifier, CvTerm ontologyDatabase)	fetchByIdentifier.
Collection<Gene>	FailingGeneFetcher.fetchByIdentifier(String identifier)	Takes a string identifier and returns the interactors which match.
Collection<Gene>	FailingGeneFetcher.fetchByIdentifier(String identifier, int taxID)
Collection<Protein>	FailingProteinFetcher.fetchByIdentifier(String identifier)	Takes a string identifier and returns the interactors which match.
Publication	FailingPublicationFetcher.fetchByIdentifier(String pubmedID, String source)	Uses the identifier to search for a publication and return a completed record.
Collection<BioactiveEntity>	MockBioactiveEntityFetcher.fetchByIdentifier(String identifier)	Takes a string identifier and returns the interactors which match.
CvTerm	MockCvTermFetcher.fetchByIdentifier(String termIdentifier, String ontologyDatabaseName)	Uses the identifier and the name of the database to search for a complete form of the cvTerm.
CvTerm	MockCvTermFetcher.fetchByIdentifier(String termIdentifier, CvTerm ontologyDatabase)	fetchByIdentifier.
Collection<Gene>	MockGeneFetcher.fetchByIdentifier(String identifier)	Takes a string identifier and returns the interactors which match.
Collection<Gene>	MockGeneFetcher.fetchByIdentifier(String identifier, int taxID)	fetchByIdentifier.
OntologyTerm	MockOntologyTermFetcher.fetchByIdentifier(String termIdentifier, String ontologyDatabaseName)	Uses the identifier and the name of the database to search for a complete form of the cvTerm.
OntologyTerm	MockOntologyTermFetcher.fetchByIdentifier(String termIdentifier, CvTerm ontologyDatabase)	fetchByIdentifier.
Collection<Protein>	MockProteinFetcher.fetchByIdentifier(String identifier)	Takes a string identifier and returns the interactors which match.
Publication	MockPublicationFetcher.fetchByIdentifier(String pubmedID, String source)	Uses the identifier to search for a publication and return a completed record.
Source	MockSourceFetcher.fetchByIdentifier(String termIdentifier, String ontologyDatabaseName)	Uses the identifier and the name of the database to search for a complete form of the cvTerm.
Source	MockSourceFetcher.fetchByIdentifier(String termIdentifier, CvTerm ontologyDatabase)	fetchByIdentifier.
Collection<T>	CvTermCompositeFetcherTemplate.fetchByIdentifiers(Collection<String> termIdentifiers, String ontologyDatabaseName)	fetchByIdentifiers.
Collection<T>	CvTermCompositeFetcherTemplate.fetchByIdentifiers(Collection<String> termIdentifiers, CvTerm ontologyDatabase)	Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.
Collection<BioactiveEntity>	FailingBioactiveEntityFetcher.fetchByIdentifiers(Collection<String> identifiers)	Takes a collection of string identifiers and returns the interactors which match.
Collection<CvTerm>	FailingCvTermFetcher.fetchByIdentifiers(Collection<String> termIdentifiers, String ontologyDatabaseName)	fetchByIdentifiers.
Collection<CvTerm>	FailingCvTermFetcher.fetchByIdentifiers(Collection<String> termIdentifiers, CvTerm ontologyDatabase)	Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.
Collection<Gene>	FailingGeneFetcher.fetchByIdentifiers(Collection<String> identifiers)	Takes a collection of string identifiers and returns the interactors which match.
Collection<Gene>	FailingGeneFetcher.fetchByIdentifiers(Collection<String> identifiers, int taxID)
Collection<Protein>	FailingProteinFetcher.fetchByIdentifiers(Collection<String> identifiers)	Takes a collection of string identifiers and returns the interactors which match.
Collection<Publication>	FailingPublicationFetcher.fetchByIdentifiers(Map<String,Collection<String>> identifiers)	Uses the identifiers to search for publications and return completed records.
Collection<BioactiveEntity>	MockBioactiveEntityFetcher.fetchByIdentifiers(Collection<String> identifiers)	Takes a collection of string identifiers and returns the interactors which match.
Collection<CvTerm>	MockCvTermFetcher.fetchByIdentifiers(Collection<String> termIdentifiers, String ontologyDatabaseName)	fetchByIdentifiers.
Collection<CvTerm>	MockCvTermFetcher.fetchByIdentifiers(Collection<String> termIdentifiers, CvTerm ontologyDatabase)	Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.
Collection<Gene>	MockGeneFetcher.fetchByIdentifiers(Collection<String> identifiers)	Takes a collection of string identifiers and returns the interactors which match.
Collection<Gene>	MockGeneFetcher.fetchByIdentifiers(Collection<String> identifiers, int taxID)
Collection<OntologyTerm>	MockOntologyTermFetcher.fetchByIdentifiers(Collection<String> identifiers, String ontologyDatabaseName)	fetchByIdentifiers.
Collection<OntologyTerm>	MockOntologyTermFetcher.fetchByIdentifiers(Collection<String> identifiers, CvTerm ontologyDatabase)	Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.
Collection<Protein>	MockProteinFetcher.fetchByIdentifiers(Collection<String> identifiers)	Takes a collection of string identifiers and returns the interactors which match.
Collection<Publication>	MockPublicationFetcher.fetchByIdentifiers(Map<String,Collection<String>> identifiers)	Uses the identifiers to search for publications and return completed records.
Collection<Source>	MockSourceFetcher.fetchByIdentifiers(Collection<String> identifiers, String ontologyDatabaseName)	fetchByIdentifiers.
Collection<Source>	MockSourceFetcher.fetchByIdentifiers(Collection<String> identifiers, CvTerm ontologyDatabase)	Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.
Collection<T>	CvTermCompositeFetcherTemplate.fetchByName(String searchName)	Uses the name of the term and the name of the database to search for a complete form of the term.
T	CvTermCompositeFetcherTemplate.fetchByName(String searchName, String ontologyDatabaseName)	Uses the name of the term and the name of the database to search for a complete form of the term.
Collection<CvTerm>	FailingCvTermFetcher.fetchByName(String searchName)	Uses the name of the term and the name of the database to search for a complete form of the term.
CvTerm	FailingCvTermFetcher.fetchByName(String searchName, String ontologyDatabaseName)	Uses the name of the term and the name of the database to search for a complete form of the term.
Collection<CvTerm>	MockCvTermFetcher.fetchByName(String searchName)	Uses the name of the term and the name of the database to search for a complete form of the term.
CvTerm	MockCvTermFetcher.fetchByName(String searchName, String ontologyDatabaseName)	Uses the name of the term and the name of the database to search for a complete form of the term.
Collection<OntologyTerm>	MockOntologyTermFetcher.fetchByName(String searchName)	Uses the name of the term and the name of the database to search for a complete form of the term.
OntologyTerm	MockOntologyTermFetcher.fetchByName(String searchName, String ontologyDatabaseName)	Uses the name of the term and the name of the database to search for a complete form of the term.
Collection<Source>	MockSourceFetcher.fetchByName(String searchName)	Uses the name of the term and the name of the database to search for a complete form of the term.
Source	MockSourceFetcher.fetchByName(String searchName, String ontologyDatabaseName)	Uses the name of the term and the name of the database to search for a complete form of the term.
Collection<T>	CvTermCompositeFetcherTemplate.fetchByNames(Collection<String> searchNames)	Finds the CvTerms which match the exact names provided.
Collection<T>	CvTermCompositeFetcherTemplate.fetchByNames(Collection<String> searchNames, String ontologyDatabaseName)	Uses the name of the term and the name of the database to search for a complete form of the term.
Collection<CvTerm>	FailingCvTermFetcher.fetchByNames(Collection<String> searchNames)	Finds the CvTerms which match the exact names provided.
Collection<CvTerm>	FailingCvTermFetcher.fetchByNames(Collection<String> searchNames, String ontologyDatabaseName)	Uses the name of the term and the name of the database to search for a complete form of the term.
Collection<CvTerm>	MockCvTermFetcher.fetchByNames(Collection<String> searchNames)	Finds the CvTerms which match the exact names provided.
Collection<CvTerm>	MockCvTermFetcher.fetchByNames(Collection<String> searchNames, String ontologyDatabaseName)	Uses the name of the term and the name of the database to search for a complete form of the term.
Collection<OntologyTerm>	MockOntologyTermFetcher.fetchByNames(Collection<String> searchNames)	Finds the CvTerms which match the exact names provided.
Collection<OntologyTerm>	MockOntologyTermFetcher.fetchByNames(Collection<String> searchNames, String ontologyDatabaseName)	Uses the name of the term and the name of the database to search for a complete form of the term.
Collection<Source>	MockSourceFetcher.fetchByNames(Collection<String> searchNames)	Finds the CvTerms which match the exact names provided.
Collection<Source>	MockSourceFetcher.fetchByNames(Collection<String> searchNames, String ontologyDatabaseName)	Uses the name of the term and the name of the database to search for a complete form of the term.
Organism	FailingOrganismFetcher.fetchByTaxID(int taxID)	Finds the complete organism record matching the provided TaxID number.
Organism	MockOrganismFetcher.fetchByTaxID(int taxID)	Finds the complete organism record matching the provided TaxID number.
Collection<Organism>	FailingOrganismFetcher.fetchByTaxIDs(Collection<Integer> taxIDs)	Finds the complete organism records matching the provided TaxID numbers.
Collection<Organism>	MockOrganismFetcher.fetchByTaxIDs(Collection<Integer> taxIDs)	Finds the complete organism records matching the provided TaxID numbers.
Set<OntologyTerm>	MockOntologyTermFetcher.fetchRootTerms(String databaseName)	fetchRootTerms.
Set<OntologyTerm>	MockOntologyTermFetcher.fetchRootTerms(CvTerm database)	fetchRootTerms.
Set<OntologyTerm>	OntologyTermCompositeFetcher.fetchRootTerms(String databaseName)	fetchRootTerms.
Set<OntologyTerm>	OntologyTermCompositeFetcher.fetchRootTerms(CvTerm database)	fetchRootTerms.
protected Collection<T>	AbstractFailingFetcher.getEntries(Collection<String> identifier)	getEntries.
protected T	AbstractFailingFetcher.getEntry(String identifier)	getEntry.
protected T	AbstractMockFetcher.getEntry(String identifier)	getEntry.
protected Collection<Gene>	FailingGeneFetcher.getEntry(String identifier)	getEntry.
protected Collection<Protein>	FailingProteinFetcher.getEntry(String identifier)	getEntry.
protected Collection<Gene>	MockGeneFetcher.getEntry(String identifier)	getEntry.
protected Collection<Protein>	MockProteinFetcher.getEntry(String identifier)	getEntry.

Uses of BridgeFailedException in psidev.psi.mi.jami.bridges.imex

Methods in psidev.psi.mi.jami.bridges.imex that throw BridgeFailedException

Modifier and Type	Method	Description
void	DefaultImexCentralClient.createPublication(Publication publication)	Create a new publication record in IMEx central (not implemented yet in production but can be used in test with the MockImexCentralClient)
void	ImexCentralClient.createPublication(Publication publication)	Create a new publication record in IMEx central (not implemented yet in production but can be used in test with the MockImexCentralClient)
Publication	DefaultImexCentralClient.createPublicationById(String identifier, String source)	Creates a publication given a valid pubmed id.
Publication	ImexCentralClient.createPublicationById(String identifier, String source)	Creates a publication given a valid pubmed id.
Publication	DefaultImexCentralClient.fetchByIdentifier(String identifier, String source)	Uses the identifier to search for a publication and return a completed record.
Collection<Publication>	DefaultImexCentralClient.fetchByIdentifiers(Map<String,Collection<String>> identifiers)	Uses the identifiers to search for publications and return completed records.
Publication	DefaultImexCentralClient.fetchPublicationImexAccession(String identifier, String source, boolean aBoolean)	Create a new IMEx id if requested for a given pubmed id
Publication	ImexCentralClient.fetchPublicationImexAccession(String identifier, String source, boolean assign)	Create a new IMEx id if requested for a given pubmed id
List<Publication>	DefaultImexCentralClient.fetchPublicationsByOwner(String owner, int first, int max)	Collect a list of publications associated with a specific owner.
Collection<Publication>	ImexCentralClient.fetchPublicationsByOwner(String owner, int first, int max)	Collect a list of publications associated with a specific owner.
List<Publication>	DefaultImexCentralClient.fetchPublicationsByStatus(String status, int first, int max)	Collect a list of publications having a specific status.
Collection<Publication>	ImexCentralClient.fetchPublicationsByStatus(String status, int first, int max)	Collect a list of publications having a specific status.
Publication	DefaultImexCentralClient.updatePublicationAdminGroup(String identifier, String source, Operation operation, String group)	Update the publication admin group given a valid pubmed identifier and a valid operator.
Publication	ImexCentralClient.updatePublicationAdminGroup(String identifier, String source, Operation operation, String group)	Update the publication admin group given a valid pubmed identifier and a valid operator.
Publication	DefaultImexCentralClient.updatePublicationAdminUser(String identifier, String source, Operation operation, String user)	Update the publication admin user given a valid pubmed identifier and a valid operator.
Publication	ImexCentralClient.updatePublicationAdminUser(String identifier, String source, Operation operation, String user)	Update the publication admin user given a valid pubmed identifier and a valid operator.
Publication	DefaultImexCentralClient.updatePublicationIdentifier(String oldIdentifier, String oldSource, String newIdentifier, String source)	Update publication pubmed identifier, DOI number or internal identifier of an existing record in IMEx central.
Publication	ImexCentralClient.updatePublicationIdentifier(String oldIdentifier, String oldSource, String newIdentifier, String source)	Update publication pubmed identifier, DOI number or internal identifier of an existing record in IMEx central.
Publication	DefaultImexCentralClient.updatePublicationStatus(String identifier, String source, PublicationStatus status)	Update the status of a publication associated with a valid pubmed identifier already registered in IMEx central
Publication	ImexCentralClient.updatePublicationStatus(String identifier, String source, PublicationStatus status)	Update the status of a publication associated with a valid pubmed identifier already registered in IMEx central

Constructors in psidev.psi.mi.jami.bridges.imex that throw BridgeFailedException

Constructor	Description
DefaultImexCentralClient(String username, String password, String endPoint)	Constructor for DefaultImexCentralClient.

Uses of BridgeFailedException in psidev.psi.mi.jami.bridges.imex.mock

Methods in psidev.psi.mi.jami.bridges.imex.mock that throw BridgeFailedException

Modifier and Type	Method	Description
void	MockImexCentralClient.createPublication(Publication publication)	Create a new publication record in IMEx central (not implemented yet in production but can be used in test with the MockImexCentralClient)
Publication	MockImexCentralClient.createPublicationById(String identifier, String source)	Creates a publication given a valid pubmed id.
Publication	MockImexCentralClient.fetchByIdentifier(String identifier, String source)	Uses the identifier to search for a publication and return a completed record.
Collection<Publication>	MockImexCentralClient.fetchByIdentifiers(Map<String,Collection<String>> identifiers)	Uses the identifiers to search for publications and return completed records.
Publication	MockImexCentralClient.fetchPublicationImexAccession(String identifier, String source, boolean create)	Create a new IMEx id if requested for a given pubmed id
List<Publication>	MockImexCentralClient.fetchPublicationsByOwner(String owner, int first, int max)	Collect a list of publications associated with a specific owner.
List<Publication>	MockImexCentralClient.fetchPublicationsByStatus(String status, int first, int max)	Collect a list of publications having a specific status.
Publication	MockImexCentralClient.updatePublicationAdminGroup(String identifier, String source, Operation operation, String group)	Update the publication admin group given a valid pubmed identifier and a valid operator.
Publication	MockImexCentralClient.updatePublicationAdminUser(String identifier, String source, Operation operation, String user)	Update the publication admin user given a valid pubmed identifier and a valid operator.
Publication	MockImexCentralClient.updatePublicationIdentifier(String oldIdentifier, String oldSource, String newIdentifier, String source)	Update publication pubmed identifier, DOI number or internal identifier of an existing record in IMEx central.
Publication	MockImexCentralClient.updatePublicationStatus(String identifier, String source, PublicationStatus status)	Update the status of a publication associated with a valid pubmed identifier already registered in IMEx central

Uses of BridgeFailedException in psidev.psi.mi.jami.bridges.mapper

Methods in psidev.psi.mi.jami.bridges.mapper that throw BridgeFailedException

Modifier and Type	Method	Description
void	ProteinMapper.map(Protein p)	Will remap the protein using the settings provided.

Uses of BridgeFailedException in psidev.psi.mi.jami.bridges.mapper.mock

Methods in psidev.psi.mi.jami.bridges.mapper.mock that throw BridgeFailedException

Modifier and Type	Method	Description
void	MockProteinMapper.map(Protein p)	Will remap the protein using the settings provided.

Uses of BridgeFailedException in psidev.psi.mi.jami.bridges.obo

Methods in psidev.psi.mi.jami.bridges.obo that throw BridgeFailedException

Modifier and Type	Method	Description
T	OboFetcherTemplate.fetchByIdentifier(String termIdentifier, String ontologyDatabaseName)	Uses the identifier and the name of the database to search for a complete form of the cvTerm.
T	OboFetcherTemplate.fetchByIdentifier(String termIdentifier, CvTerm ontologyDatabase)	fetchByIdentifier.
Collection<T>	OboFetcherTemplate.fetchByIdentifiers(Collection<String> termIdentifiers, String ontologyDatabaseName)	fetchByIdentifiers.
Collection<T>	OboFetcherTemplate.fetchByIdentifiers(Collection<String> termIdentifiers, CvTerm ontologyDatabase)	Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.
Collection<T>	OboFetcherTemplate.fetchByName(String searchName)	Uses the name of the term and the name of the database to search for a complete form of the term.
T	OboFetcherTemplate.fetchByName(String searchName, String ontologyDatabaseName)	Uses the name of the term and the name of the database to search for a complete form of the term.
Collection<T>	OboFetcherTemplate.fetchByNames(Collection<String> searchNames)	Finds the CvTerms which match the exact names provided.
Collection<T>	OboFetcherTemplate.fetchByNames(Collection<String> searchNames, String ontologyDatabaseName)	Uses the name of the term and the name of the database to search for a complete form of the term.
Set<OntologyTerm>	OboOntologyTermFetcher.fetchRootTerms(String database)	fetchRootTerms.
Set<OntologyTerm>	OboOntologyTermFetcher.fetchRootTerms(CvTerm database)	fetchRootTerms.

Uses of BridgeFailedException in psidev.psi.mi.jami.bridges.ols

Methods in psidev.psi.mi.jami.bridges.ols that throw BridgeFailedException

Modifier and Type	Method	Description
T	AbstractOlsFetcher.fetchByIdentifier(String termIdentifier, String miOntologyName)	Uses the identifier and the name of the database to search for a complete form of the cvTerm.
T	AbstractOlsFetcher.fetchByIdentifier(String termIdentifier, CvTerm ontologyCvTerm)	fetchByIdentifier.
T	CachedOlsFetcher.fetchByIdentifier(String termIdentifier, String miOntologyName)	Uses the identifier and the name of the database to search for a complete form of the cvTerm.
T	CachedOlsFetcher.fetchByIdentifier(String termIdentifier, CvTerm ontologyDatabase)	Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.
Collection<T>	AbstractOlsFetcher.fetchByIdentifiers(Collection<String> termIdentifiers, String miOntologyName)	fetchByIdentifiers.
Collection<T>	AbstractOlsFetcher.fetchByIdentifiers(Collection<String> termIdentifiers, CvTerm ontologyDatabase)	Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.
Collection<T>	CachedOlsFetcher.fetchByIdentifiers(Collection<String> termIdentifiers, String miOntologyName)	fetchByIdentifiers.
Collection<T>	CachedOlsFetcher.fetchByIdentifiers(Collection<String> termIdentifiers, CvTerm ontologyDatabase)	Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.
Collection<T>	AbstractOlsFetcher.fetchByName(String searchName)	Uses the name of the term and the name of the database to search for a complete form of the term.
T	AbstractOlsFetcher.fetchByName(String searchName, String miOntologyName)	Uses the name of the term and the name of the database to search for a complete form of the term.
Collection<T>	CachedOlsFetcher.fetchByName(String searchName)	Uses the name of the term and the name of the database to search for a complete form of the term.
T	CachedOlsFetcher.fetchByName(String searchName, String miOntologyName)	Uses the name of the term and the name of the database to search for a complete form of the term.
Collection<T>	AbstractOlsFetcher.fetchByNames(Collection<String> searchNames)	Finds the CvTerms which match the exact names provided.
Collection<T>	AbstractOlsFetcher.fetchByNames(Collection<String> searchNames, String miOntologyName)	Uses the name of the term and the name of the database to search for a complete form of the term.
Collection<T>	CachedOlsFetcher.fetchByNames(Collection<String> searchNames)	Finds the CvTerms which match the exact names provided.
Collection<T>	CachedOlsFetcher.fetchByNames(Collection<String> searchNames, String miOntologyName)	Uses the name of the term and the name of the database to search for a complete form of the term.
Set<OntologyTerm>	CachedOlsOntologyTermFetcher.fetchRootTerms(String databaseName)	fetchRootTerms.
Set<OntologyTerm>	CachedOlsOntologyTermFetcher.fetchRootTerms(CvTerm database)	fetchRootTerms.
Set<OntologyTerm>	OlsOntologyTermFetcher.fetchRootTerms(String databaseName)	fetchRootTerms.
Set<OntologyTerm>	OlsOntologyTermFetcher.fetchRootTerms(CvTerm database)	fetchRootTerms.

Constructors in psidev.psi.mi.jami.bridges.ols that throw BridgeFailedException

Constructor	Description
AbstractOlsFetcher()	Constructor for AbstractOlsFetcher.
CachedOlsCvTermFetcher()	Constructor for CachedOlsCvTermFetcher.
CachedOlsFetcher(String cacheName, CvTermFetcher<T> delegateFetcher)	Constructor for CachedOlsFetcher.
CachedOlsOntologyTermFetcher()	Constructor for CachedOlsOntologyTermFetcher.
CachedOlsSourceFetcher()	Constructor for CachedOlsSourceFetcher.
OlsCvTermFetcher()	Constructor for OlsCvTermFetcher.
OlsOntologyTermFetcher()	Constructor for OlsOntologyTermFetcher.
OlsSourceFetcher()	Constructor for OlsSourceFetcher.

Uses of BridgeFailedException in psidev.psi.mi.jami.bridges.ontologymanager.impl

Methods in psidev.psi.mi.jami.bridges.ontologymanager.impl that throw BridgeFailedException

Modifier and Type	Method	Description
protected MIOntologyTermI	AbstractMIOntologyAccess.createNewOntologyTerm(String identifier, String name)	createNewOntologyTerm.

Uses of BridgeFailedException in psidev.psi.mi.jami.bridges.uniprot

Methods in psidev.psi.mi.jami.bridges.uniprot that throw BridgeFailedException

Modifier and Type	Method	Description
Collection<Protein>	CachedUniprotProteinFetcher.fetchByIdentifier(String identifier)	Takes a string identifier and returns the interactors which match.
Collection<Gene>	UniprotGeneFetcher.fetchByIdentifier(String identifier)	Takes a string identifier and returns the interactors which match.
Collection<Gene>	UniprotGeneFetcher.fetchByIdentifier(String identifier, int taxID)	fetchByIdentifier.
Collection<Protein>	UniprotProteinFetcher.fetchByIdentifier(String identifier)	Takes a string identifier and returns the interactors which match.
Collection<Protein>	CachedUniprotProteinFetcher.fetchByIdentifiers(Collection<String> identifiers)	Takes a collection of string identifiers and returns the interactors which match.
Collection<Gene>	UniprotGeneFetcher.fetchByIdentifiers(Collection<String> identifiers)	Takes a collection of string identifiers and returns the interactors which match.
Collection<Gene>	UniprotGeneFetcher.fetchByIdentifiers(Collection<String> identifiers, int taxID)	fetchByIdentifiers.
Collection<Protein>	UniprotProteinFetcher.fetchByIdentifiers(Collection<String> identifiers)	Takes a collection of string identifiers and returns the interactors which match.
Collection<Gene>	CachedUniprotGeneFetcher.getByIdentifier(String identifier)	getByIdentifier.
Collection<Gene>	CachedUniprotGeneFetcher.getByIdentifier(String identifier, int taxID)	getByIdentifier.

Uses of BridgeFailedException in psidev.psi.mi.jami.bridges.uniprot.taxonomy

Methods in psidev.psi.mi.jami.bridges.uniprot.taxonomy that throw BridgeFailedException

Modifier and Type	Method	Description
Organism	CachedUniprotTaxonomyFetcher.fetchByTaxID(int taxID)	Finds the complete organism record matching the provided TaxID number.
Organism	UniprotTaxonomyFetcher.fetchByTaxID(int taxID)	Finds the complete organism record matching the provided TaxID number.
Collection<Organism>	CachedUniprotTaxonomyFetcher.fetchByTaxIDs(Collection<Integer> taxIDs)	Finds the complete organism records matching the provided TaxID numbers.
Collection<Organism>	UniprotTaxonomyFetcher.fetchByTaxIDs(Collection<Integer> taxIDs)	Finds the complete organism records matching the provided TaxID numbers.

Uses of BridgeFailedException in psidev.psi.mi.jami.bridges.unisave

Methods in psidev.psi.mi.jami.bridges.unisave that throw BridgeFailedException

Modifier and Type	Method	Description
String	CachedUnisaveClient.fetchSequenceFromVersion(String id, int version)	fetchSequenceFromVersion.
String	UnisaveClient.fetchSequenceFromVersion(String id, int version)	fetchSequenceFromVersion.
int	CachedUnisaveClient.fetchVersionFromSequence(String id, String sequence)	fetchVersionFromSequence.
int	UnisaveClient.fetchVersionFromSequence(String id, String sequence)	fetchVersionFromSequence.
Map<Integer,String>	UnisaveClient.getAllSequencesBeforeDate(String identifier, Date date)	Get the map of sequences (and their sequence version in uniprot) existing in unisave before this date
List<SequenceVersion>	UnisaveClient.getAvailableSequenceUpdate(String identifier, String sequence)	Collects all available sequence update fro mUniSave.
FastaSequence	UnisaveClient.getFastaSequence(String identifier, int version)	Retrieve a fasta sequence corresponding to a given EntryVersion.
String	UnisaveClient.getLastSequenceAtTheDate(String identifier, Date date)	getLastSequenceAtTheDate.
String	UnisaveClient.getSequenceFor(String identifier, int sequence_version)	getSequenceFor.
int	UnisaveClient.getSequenceVersion(String identifier, String sequence)	Returns the sequence version of a sequence for a certain uniprot ac.
List<Integer>	UnisaveClient.getVersions(String identifier)	Searches for all entry version given its identifier.

Constructors in psidev.psi.mi.jami.bridges.unisave that throw BridgeFailedException

Constructor	Description
CachedUnisaveClient()	Constructor for CachedUnisaveClient.

Uses of BridgeFailedException in psidev.psi.mi.jami.imex.actions

Methods in psidev.psi.mi.jami.imex.actions that throw BridgeFailedException

Modifier and Type	Method	Description
Publication	ImexAssigner.assignImexIdentifier(Publication publication, Publication imexPublication)	Assign a new IMEx id to a publication that has not been assigned yet and update/clean up the annotations of the publication (full coverage and imex curation).
void	PublicationStatusSynchronizer.discardPublicationInImexCentral(Publication publication, ImexPublication imexPublication)	Synchronize publication status with IMEx central and update the IMEx central record if necessary.
Publication	ImexCentralPublicationRegister.getExistingPublicationInImexCentral(String publicationId, String source)	Retrieve an existing record in IMEx central matching the publication identifier (pubmed, doi, jint or imex).
boolean	PublicationIdentifierSynchronizer.isPublicationIdentifierInSyncWithImexCentral(String pubId, String source, ImexPublication imexPublication)	It will look at all identifiers attached to the record in IMEx central and see if the publication identifier is also attached to the IMEx record
Publication	ImexCentralPublicationRegister.registerPublicationInImexCentral(Publication publication)	Register a publication in IMEx central which is not existing in IMEx central.
void	PublicationAdminGroupSynchronizer.synchronizePublicationAdminGroup(Publication publication, ImexPublication imexPublication)	Update IMEx central and synchronize the publication ADMIN group.
void	PublicationIdentifierSynchronizer.synchronizePublicationIdentifier(Publication publication, Publication imexPublication)	Update the IMEx record in case intact publication has a valid pubmed, unassigned or doi identifier that is not in IMEx central.
void	PublicationStatusSynchronizer.synchronizePublicationStatusWithImexCentral(Publication intactPublication, ImexPublication imexPublication)	Synchronize publication status with IMEx central and update the IMEx central record if necessary.

Uses of BridgeFailedException in psidev.psi.mi.jami.imex.actions.impl

Methods in psidev.psi.mi.jami.imex.actions.impl that throw BridgeFailedException

Modifier and Type	Method	Description
Publication	ImexAssignerImpl.assignImexIdentifier(Publication publication, Publication imexPublication)	Assign a new IMEx id to a publication that has not been assigned yet and update/clean up the annotations of the publication (full coverage and imex curation).
void	PublicationStatusSynchronizerImpl.discardPublicationInImexCentral(Publication publication, ImexPublication imexPublication)	Synchronize publication status with IMEx central and update the IMEx central record if necessary.
Publication	ImexCentralPublicationRegisterImpl.getExistingPublicationInImexCentral(String publicationId, String source)	Retrieve an existing record in IMEx central matching the publication identifier (pubmed, doi, jint or imex).
boolean	PublicationIdentifierSynchronizerImpl.isPublicationIdentifierInSyncWithImexCentral(String pubId, String source, ImexPublication imexPublication)	It will look at all identifiers attached to the record in IMEx central and see if the publication identifier is also attached to the IMEx record
Publication	ImexCentralPublicationRegisterImpl.registerPublicationInImexCentral(Publication publication)	Register a publication in IMEx central which is not existing in IMEx central.
void	PublicationAdminGroupSynchronizerImpl.synchronizePublicationAdminGroup(Publication publication, ImexPublication imexPublication)	Update IMEx central and synchronize the publication ADMIN group.
void	PublicationIdentifierSynchronizerImpl.synchronizePublicationIdentifier(Publication publication, Publication imexPublication)	Update the IMEx record in case intact publication has a valid pubmed, unassigned or doi identifier that is not in IMEx central.
void	PublicationStatusSynchronizerImpl.synchronizePublicationStatusWithImexCentral(Publication publication, ImexPublication imexPublication)	Synchronize publication status with IMEx central and update the IMEx central record if necessary.