Package psidev.psi.mi.jami.bridges.fetcher.mock

Class MockOntologyTermFetcher

java.lang.Object

psidev.psi.mi.jami.bridges.fetcher.mock.MockOntologyTermFetcher

All Implemented Interfaces:

CvTermFetcher<OntologyTerm>, OntologyTermFetcher

public class MockOntologyTermFetcher
extends Object
implements OntologyTermFetcher

A mock fetcher for testing. It extends all the methods of the true fetcher, but does not access an external service. Instead, it holds a map which can be loaded with objects and keys. which are then returned. It attempts to replicate the responses of the fetcher in most scenarios.

Since:

08/07/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
MockOntologyTermFetcher()	Constructor for MockOntologyTermFetcher.

Method Summary

Modifier and Type	Method	Description
void	addOntologyTerm(String identifier, OntologyTerm ontologyTerm)	addOntologyTerm.
void	clear()	clear.
OntologyTerm	fetchByIdentifier(String termIdentifier, String ontologyDatabaseName)	Uses the identifier and the name of the database to search for a complete form of the cvTerm.
OntologyTerm	fetchByIdentifier(String termIdentifier, CvTerm ontologyDatabase)	fetchByIdentifier.
Collection<OntologyTerm>	fetchByIdentifiers(Collection<String> identifiers, String ontologyDatabaseName)	fetchByIdentifiers.
Collection<OntologyTerm>	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<OntologyTerm>	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	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>	fetchByNames(Collection<String> searchNames)	Finds the CvTerms which match the exact names provided.
Collection<OntologyTerm>	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>	fetchRootTerms(String databaseName)	fetchRootTerms.
Set<OntologyTerm>	fetchRootTerms(CvTerm database)	fetchRootTerms.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MockOntologyTermFetcher

public MockOntologyTermFetcher()

Constructor for MockOntologyTermFetcher.

Method Detail

addOntologyTerm

public void addOntologyTerm(String identifier,
                            OntologyTerm ontologyTerm)

addOntologyTerm.

Parameters:

identifier - a String object.

ontologyTerm - a OntologyTerm object.

clear

public void clear()

clear.

fetchByIdentifier

public OntologyTerm fetchByIdentifier(String termIdentifier,
                                      String ontologyDatabaseName)
                               throws BridgeFailedException

Uses the identifier and the name of the database to search for a complete form of the cvTerm.

Specified by:

fetchByIdentifier in interface CvTermFetcher<OntologyTerm>

Parameters:

termIdentifier - The identifier for the CvTerm to fetch.

ontologyDatabaseName - The name of the ontology to search for. Eg, psi-mi, psi-mod, go. Must not be Null.

Returns:

A full cvTerm which matches the search term or null if one cannot be found.

Throws:

BridgeFailedException - if any.

fetchByIdentifier

public OntologyTerm fetchByIdentifier(String termIdentifier,
                                      CvTerm ontologyDatabase)
                               throws BridgeFailedException

fetchByIdentifier.

Specified by:

fetchByIdentifier in interface CvTermFetcher<OntologyTerm>

Parameters:

termIdentifier - a String object.

ontologyDatabase - a CvTerm object.

Returns:

a OntologyTerm object.

Throws:

BridgeFailedException - if any.

fetchByName

public OntologyTerm fetchByName(String searchName,
                                String ontologyDatabaseName)
                         throws BridgeFailedException

Uses the name of the term and the name of the database to search for a complete form of the term.

Specified by:

fetchByName in interface CvTermFetcher<OntologyTerm>

Parameters:

searchName - A full or short name for the term to be searched for.

ontologyDatabaseName - The ontology to search for the term in.

Returns:

A fully enriched cvTerm which matches the search term or null if one cannot be found.

Throws:

BridgeFailedException - if any.

fetchByName

public Collection<OntologyTerm> fetchByName(String searchName)
                                     throws BridgeFailedException

Uses the name of the term and the name of the database to search for a complete form of the term.

If the term can not be resolved to a database, then this method may return null.

Specified by:

fetchByName in interface CvTermFetcher<OntologyTerm>

Parameters:

searchName - A full or short name for the term to be searched for.

Returns:

A fully enriched cvTerm which matches the search term or null if one cannot be found.

Throws:

BridgeFailedException - if any.

fetchByIdentifiers

public Collection<OntologyTerm> fetchByIdentifiers(Collection<String> identifiers,
                                                   String ontologyDatabaseName)
                                            throws BridgeFailedException

fetchByIdentifiers.

Specified by:

fetchByIdentifiers in interface CvTermFetcher<OntologyTerm>

Parameters:

identifiers - a Collection object.

ontologyDatabaseName - a String object.

Returns:

a Collection object.

Throws:

BridgeFailedException - if any.

fetchByIdentifiers

public Collection<OntologyTerm> fetchByIdentifiers(Collection<String> identifiers,
                                                   CvTerm ontologyDatabase)
                                            throws BridgeFailedException

Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.

Specified by:

fetchByIdentifiers in interface CvTermFetcher<OntologyTerm>

Parameters:

identifiers - The identifier for the CvTerms to fetch.

ontologyDatabase - The name of the ontology to search for the terms in.

Returns:

A fully enriched cvTerm which matches the search term or null if one cannot be found.

Throws:

BridgeFailedException - if any.

fetchByNames

public Collection<OntologyTerm> fetchByNames(Collection<String> searchNames,
                                             String ontologyDatabaseName)
                                      throws BridgeFailedException

Uses the name of the term and the name of the database to search for a complete form of the term.

Specified by:

fetchByNames in interface CvTermFetcher<OntologyTerm>

Parameters:

searchNames - A full or short name for the term to be searched for.

ontologyDatabaseName - The name of the database to search for the names in.

Returns:

A fully enriched cvTerm which matches the search term or null if one cannot be found.

Throws:

BridgeFailedException - if any.

fetchByNames

public Collection<OntologyTerm> fetchByNames(Collection<String> searchNames)
                                      throws BridgeFailedException

Finds the CvTerms which match the exact names provided.

If the a term found by the search can not be resolved to a database, this method may return null.

Specified by:

fetchByNames in interface CvTermFetcher<OntologyTerm>

Parameters:

searchNames - A collection full or short names for the term to be searched for.

Returns:

A collection of cvTerms which matched a search term.

Throws:

BridgeFailedException - if any.

fetchRootTerms

public Set<OntologyTerm> fetchRootTerms(String databaseName)
                                 throws BridgeFailedException

fetchRootTerms.

Specified by:

fetchRootTerms in interface OntologyTermFetcher

Parameters:

databaseName - : ontology database name

Returns:

a set of root terms for the ontology matching this database name

Throws:

BridgeFailedException - if any.

fetchRootTerms

public Set<OntologyTerm> fetchRootTerms(CvTerm database)
                                 throws BridgeFailedException

fetchRootTerms.

Specified by:

fetchRootTerms in interface OntologyTermFetcher

Parameters:

database - a CvTerm object.

Returns:

a Set object.

Throws:

BridgeFailedException - if any.