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

Class FailingCvTermFetcher

java.lang.Object

psidev.psi.mi.jami.bridges.fetcher.mock.AbstractMockFetcher<T>

psidev.psi.mi.jami.bridges.fetcher.mock.AbstractFailingFetcher<CvTerm>

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

All Implemented Interfaces:

CvTermFetcher<CvTerm>, MockFetcher<CvTerm>

public class FailingCvTermFetcher
extends AbstractFailingFetcher<CvTerm>
implements CvTermFetcher<CvTerm>

A mock fetcher for testing exceptions. It extends the functionality of the mock fetcher but can also throw exceptions. Upon initialisation, an integer is given which sets how many times a query is made before returning the result. If the current query matches the last query and the counter of the number of times is less than the maxQuery set at initialisation, then an exception will be thrown. Additionally, if the maxQuery is set to -1, the fetcher will always throw an exception.

Since:

01/07/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Field Summary

Fields inherited from class psidev.psi.mi.jami.bridges.fetcher.mock.AbstractMockFetcher

localMap

Constructor Summary

Constructors

Constructor	Description
FailingCvTermFetcher(int maxQuery)	Constructor for FailingCvTermFetcher.

Method Summary

Modifier and Type	Method	Description
CvTerm	fetchByIdentifier(String termIdentifier, String ontologyDatabaseName)	Uses the identifier and the name of the database to search for a complete form of the cvTerm.
CvTerm	fetchByIdentifier(String termIdentifier, CvTerm ontologyDatabase)	fetchByIdentifier.
Collection<CvTerm>	fetchByIdentifiers(Collection<String> termIdentifiers, String ontologyDatabaseName)	fetchByIdentifiers.
Collection<CvTerm>	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<CvTerm>	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	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>	fetchByNames(Collection<String> searchNames)	Finds the CvTerms which match the exact names provided.
Collection<CvTerm>	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 psidev.psi.mi.jami.bridges.fetcher.mock.AbstractFailingFetcher

getEntries, getEntry

Methods inherited from class psidev.psi.mi.jami.bridges.fetcher.mock.AbstractMockFetcher

addEntry, clearEntries, removeEntry

Methods inherited from class java.lang.Object

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

Constructor Detail

FailingCvTermFetcher

public FailingCvTermFetcher(int maxQuery)

Constructor for FailingCvTermFetcher.

Parameters:

maxQuery - a int.

Method Detail

fetchByIdentifier

public CvTerm 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<CvTerm>

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 CvTerm fetchByIdentifier(String termIdentifier,
                                CvTerm ontologyDatabase)
                         throws BridgeFailedException

fetchByIdentifier.

Specified by:

fetchByIdentifier in interface CvTermFetcher<CvTerm>

Parameters:

termIdentifier - a String object.

ontologyDatabase - a CvTerm object.

Returns:

a CvTerm object.

Throws:

BridgeFailedException - if any.

fetchByName

public CvTerm 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<CvTerm>

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<CvTerm> 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<CvTerm>

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<CvTerm> fetchByIdentifiers(Collection<String> termIdentifiers,
                                             String ontologyDatabaseName)
                                      throws BridgeFailedException

fetchByIdentifiers.

Specified by:

fetchByIdentifiers in interface CvTermFetcher<CvTerm>

Parameters:

termIdentifiers - a Collection object.

ontologyDatabaseName - a String object.

Returns:

a Collection object.

Throws:

BridgeFailedException - if any.

fetchByIdentifiers

public Collection<CvTerm> fetchByIdentifiers(Collection<String> termIdentifiers,
                                             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<CvTerm>

Parameters:

termIdentifiers - 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<CvTerm> 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<CvTerm>

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<CvTerm> 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<CvTerm>

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.