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

Interface ImexAssigner

All Known Implementing Classes:

ImexAssignerImpl

public interface ImexAssigner

Interface for assigning IMEx id to a publication and updating intact publications, experiments and interactions

Since:

29/03/12

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

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.
ImexCentralClient	getImexCentralClient()	getImexCentralClient.
int	getNextImexChunkNumberAndFilterValidImexIdsFrom(Publication publication)	getNextImexChunkNumberAndFilterValidImexIdsFrom.
boolean	isEntitledToImex(InteractionEvidence interaction)	isEntitledToImex.
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

Method Detail

assignImexIdentifier

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)

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

boolean updateImexIdentifierForExperiment(Experiment experiment,
                                          String imexId)
                                   throws EnricherException

Add a IMEx primary reference to the experiment

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

boolean updateImexIdentifierForInteraction(InteractionEvidence interaction,
                                           String imexId)
                                    throws EnricherException

Add a IMEx primary reference to the interaction

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.

isEntitledToImex

boolean isEntitledToImex(InteractionEvidence interaction)

isEntitledToImex.

Parameters:

interaction - a InteractionEvidence object.

Returns:

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

clearInteractionImexContext

void clearInteractionImexContext()

clearInteractionImexContext.

getNextImexChunkNumberAndFilterValidImexIdsFrom

int getNextImexChunkNumberAndFilterValidImexIdsFrom(Publication publication)

getNextImexChunkNumberAndFilterValidImexIdsFrom.

Parameters:

publication - a Publication object.

Returns:

a int.

getImexCentralClient

ImexCentralClient getImexCentralClient()

getImexCentralClient.

Returns:

a ImexCentralClient object.