Package psidev.psi.mi.jami.imex.actions.impl

Class ImexAssignerImpl

java.lang.Object

psidev.psi.mi.jami.imex.actions.impl.ImexAssignerImpl

All Implemented Interfaces:

ImexAssigner

public class ImexAssignerImpl
extends Object
implements ImexAssigner

This class will assign an IMEx id to a publication using imex central webservice and update experiments and interactions

Since:

02/03/12

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
ImexAssignerImpl(ImexCentralClient client)	Constructor for ImexAssignerImpl.

Method Summary

Modifier and Type	Method	Description
Publication	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	clearInteractionImexContext()	clearInteractionImexContext.
protected int	getCurrentIndex()	Getter for the field currentIndex.
ImexCentralClient	getImexCentralClient()	getImexCentralClient.
protected Pattern	getInteraction_imex_regexp()	Getter for the field interaction_imex_regexp.
int	getNextImexChunkNumberAndFilterValidImexIdsFrom(Publication publication)	getNextImexChunkNumberAndFilterValidImexIdsFrom.
boolean	isEntitledToImex(InteractionEvidence interaction)	isEntitledToImex.
protected void	setCurrentIndex(int currentIndex)	Setter for the field currentIndex.
boolean	updateImexIdentifierForExperiment(Experiment experiment, String imexId)	Add a IMEx primary reference to the experiment
boolean	updateImexIdentifierForInteraction(InteractionEvidence interaction, String imexId)	Add a IMEx primary reference to the interaction

Methods inherited from class java.lang.Object

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

Constructor Detail

ImexAssignerImpl

public ImexAssignerImpl(ImexCentralClient client)

Constructor for ImexAssignerImpl.

Parameters:

client - a ImexCentralClient object.

Method Detail

assignImexIdentifier

public Publication assignImexIdentifier(Publication publication,
                                        Publication imexPublication)
                                 throws BridgeFailedException

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). It adds an IMEx primary reference to the intact publication. It is only possible to assign a new IMEx id to publications having valid pubmed ids (no unassigned and no DOI number)

Specified by:

assignImexIdentifier in interface ImexAssigner

Parameters:

publication - : the publication in IntAct

imexPublication - : the publication in IMEx

Returns:

the imex id if the IMEx assigner was successful, null otherwise

Throws:

BridgeFailedException - if no record found or no IMEx id

updateImexIdentifierForExperiment

public boolean updateImexIdentifierForExperiment(Experiment experiment,
                                                 String imexId)
                                          throws EnricherException

Add a IMEx primary reference to the experiment

Specified by:

updateImexIdentifierForExperiment in interface ImexAssigner

Parameters:

experiment - a Experiment object.

imexId - a String object.

Returns:

true if the IMEx assigner did an update of the experiment, false otherwise

Throws:

EnricherException - if any.

updateImexIdentifierForInteraction

public boolean updateImexIdentifierForInteraction(InteractionEvidence interaction,
                                                  String imexId)
                                           throws EnricherException

Add a IMEx primary reference to the interaction

Specified by:

updateImexIdentifierForInteraction in interface ImexAssigner

Parameters:

interaction - a InteractionEvidence object.

imexId - a String object.

Returns:

true if the IMEx assigner did an update of the interaction, false otherwise

Throws:

EnricherException - if any.

getImexCentralClient

public ImexCentralClient getImexCentralClient()

getImexCentralClient.

Specified by:

getImexCentralClient in interface ImexAssigner

Returns:

a ImexCentralClient object.

isEntitledToImex

public boolean isEntitledToImex(InteractionEvidence interaction)

isEntitledToImex.

Specified by:

isEntitledToImex in interface ImexAssigner

Parameters:

interaction - a InteractionEvidence object.

Returns:

true if the interaction can have an IMEx id, false otherwise

clearInteractionImexContext

public void clearInteractionImexContext()

clearInteractionImexContext.

Specified by:

clearInteractionImexContext in interface ImexAssigner

getNextImexChunkNumberAndFilterValidImexIdsFrom

public int getNextImexChunkNumberAndFilterValidImexIdsFrom(Publication publication)

getNextImexChunkNumberAndFilterValidImexIdsFrom.

Specified by:

getNextImexChunkNumberAndFilterValidImexIdsFrom in interface ImexAssigner

Parameters:

publication - a Publication object.

Returns:

a int.

getCurrentIndex

protected int getCurrentIndex()

Getter for the field currentIndex.

Returns:

a int.

getInteraction_imex_regexp

protected Pattern getInteraction_imex_regexp()

Getter for the field interaction_imex_regexp.

Returns:

a Pattern object.

setCurrentIndex

protected void setCurrentIndex(int currentIndex)

Setter for the field currentIndex.

Parameters:

currentIndex - a int.