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

Class MockSourceFetcher

java.lang.Object

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

All Implemented Interfaces:

CvTermFetcher<Source>, SourceFetcher

public class MockSourceFetcher
extends Object
implements SourceFetcher

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
MockSourceFetcher()	Constructor for MockSourceFetcher.

Method Summary

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

Methods inherited from class java.lang.Object

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

Constructor Detail

MockSourceFetcher

public MockSourceFetcher()

Constructor for MockSourceFetcher.

Method Detail

addOntologyTerm

public void addOntologyTerm(String identifier,
                            Source source)

addOntologyTerm.

Parameters:

identifier - a String object.

source - a Source object.

clear

public void clear()

clear.

fetchByIdentifier

public Source 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<Source>

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 Source fetchByIdentifier(String termIdentifier,
                                CvTerm ontologyDatabase)
                         throws BridgeFailedException

fetchByIdentifier.

Specified by:

fetchByIdentifier in interface CvTermFetcher<Source>

Parameters:

termIdentifier - a String object.

ontologyDatabase - a CvTerm object.

Returns:

a Source object.

Throws:

BridgeFailedException - if any.

fetchByName

public Source 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<Source>

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<Source> 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<Source>

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

fetchByIdentifiers.

Specified by:

fetchByIdentifiers in interface CvTermFetcher<Source>

Parameters:

identifiers - a Collection object.

ontologyDatabaseName - a String object.

Returns:

a Collection object.

Throws:

BridgeFailedException - if any.

fetchByIdentifiers

public Collection<Source> 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<Source>

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<Source> 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<Source>

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<Source> 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<Source>

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.