Package psidev.psi.mi.jami.enricher.impl.full

Class FullPublicationUpdater

java.lang.Object

psidev.psi.mi.jami.enricher.impl.AbstractMIEnricher<Publication>

psidev.psi.mi.jami.enricher.impl.minimal.MinimalPublicationEnricher

psidev.psi.mi.jami.enricher.impl.full.FullPublicationEnricher

psidev.psi.mi.jami.enricher.impl.full.FullPublicationUpdater

All Implemented Interfaces:

MIEnricher<Publication>, PublicationEnricher

public class FullPublicationUpdater
extends FullPublicationEnricher

Provides full update of Publication. - update minimal properties as described in MinimalPublicationUpdater - update publication title. If the title of the publication to enrich is different from the title of the fetched publication, it will override the title with the title of the fetched publication - update publication journal. If the journal of the publication to enrich is different from the journal of the fetched publication, it will override the journal with the journal of the fetched publication - update xrefs (imex, etc.) of a publication. It will use DefaultXrefComparator to compare xrefs and add missing xrefs. It will also remove xrefs that are not in the fetched publication - update annotations of a publication. It will use DefaultAnnotationComparator to compare annotations and add missing annotations. It will also remove annotations that are not in the fetched publication

Since:

01/08/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Constructor Summary

Constructors

Modifier	Constructor	Description
	FullPublicationUpdater(PublicationFetcher fetcher)	Constructor for FullPublicationUpdater.
protected	FullPublicationUpdater(MinimalPublicationUpdater minimalPublicationUpdater)	Constructor for FullPublicationUpdater.

Method Summary

Modifier and Type	Method	Description
Publication	find(Publication publicationToEnrich)	find.
protected MinimalPublicationUpdater	getMinimalPublicationUpdater()	Getter for the field minimalPublicationUpdater.
PublicationEnricherListener	getPublicationEnricherListener()	Gets the current publication listener
PublicationFetcher	getPublicationFetcher()	Gets the publication fetcher which is currently being used to retrieve entries
protected void	processAnnotations(Publication publicationToEnrich, Publication fetched)	processAnnotations.
protected void	processJournal(Publication publicationToEnrich, Publication fetched)	processJournal.
void	processPublication(Publication publicationToEnrich, Publication fetchedPublication)	The strategy for the enrichment of the publication.
protected void	processPublicationTitle(Publication publicationToEnrich, Publication fetched)	processPublicationTitle.
protected void	processXrefs(Publication publicationToEnrich, Publication fetched)	processXrefs.
void	setPublicationEnricherListener(PublicationEnricherListener listener)	setPublicationEnricherListener.

Methods inherited from class psidev.psi.mi.jami.enricher.impl.full.FullPublicationEnricher

processCurationDepth, processOtherProperties, processReleasedDate

Methods inherited from class psidev.psi.mi.jami.enricher.impl.minimal.MinimalPublicationEnricher

enrich, getRetryCount, onEnrichedVersionNotFound, processAuthors, processIdentifiers, processPublicationDate, setRetryCount

Methods inherited from class psidev.psi.mi.jami.enricher.impl.AbstractMIEnricher

enrich, enrich

Methods inherited from class java.lang.Object

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

Methods inherited from interface psidev.psi.mi.jami.enricher.MIEnricher

enrich, enrich

Constructor Detail

FullPublicationUpdater

public FullPublicationUpdater(PublicationFetcher fetcher)

Constructor for FullPublicationUpdater.

Parameters:

fetcher - a PublicationFetcher object.

FullPublicationUpdater

protected FullPublicationUpdater(MinimalPublicationUpdater minimalPublicationUpdater)

Constructor for FullPublicationUpdater.

Parameters:

minimalPublicationUpdater - a MinimalPublicationUpdater object.

Method Detail

processPublication

public void processPublication(Publication publicationToEnrich,
                               Publication fetchedPublication)
                        throws EnricherException

The strategy for the enrichment of the publication. This methods can be overwritten to change the behaviour of the enrichment.

Overrides:

processPublication in class MinimalPublicationEnricher

Parameters:

publicationToEnrich - The publication which is being enriched.

fetchedPublication - a Publication object.

Throws:

EnricherException - if any.

processXrefs

protected void processXrefs(Publication publicationToEnrich,
                            Publication fetched)
                     throws EnricherException

processXrefs.

Overrides:

processXrefs in class FullPublicationEnricher

Parameters:

publicationToEnrich - a Publication object.

fetched - a Publication object.

Throws:

EnricherException - if any.

processAnnotations

protected void processAnnotations(Publication publicationToEnrich,
                                  Publication fetched)
                           throws EnricherException

processAnnotations.

Overrides:

processAnnotations in class FullPublicationEnricher

Parameters:

publicationToEnrich - a Publication object.

fetched - a Publication object.

Throws:

EnricherException - if any.

processJournal

protected void processJournal(Publication publicationToEnrich,
                              Publication fetched)
                       throws EnricherException

processJournal.

Overrides:

processJournal in class FullPublicationEnricher

Parameters:

publicationToEnrich - a Publication object.

fetched - a Publication object.

Throws:

EnricherException - if any.

processPublicationTitle

protected void processPublicationTitle(Publication publicationToEnrich,
                                       Publication fetched)
                                throws EnricherException

processPublicationTitle.

Overrides:

processPublicationTitle in class FullPublicationEnricher

Parameters:

publicationToEnrich - a Publication object.

fetched - a Publication object.

Throws:

EnricherException - if any.

setPublicationEnricherListener

public void setPublicationEnricherListener(PublicationEnricherListener listener)

setPublicationEnricherListener.

Sets the listener to report publication changes to. Can be null.

Specified by:

setPublicationEnricherListener in interface PublicationEnricher

Overrides:

setPublicationEnricherListener in class MinimalPublicationEnricher

Parameters:

listener - a PublicationEnricherListener object.

getPublicationFetcher

public PublicationFetcher getPublicationFetcher()

Gets the publication fetcher which is currently being used to retrieve entries

Specified by:

getPublicationFetcher in interface PublicationEnricher

Overrides:

getPublicationFetcher in class MinimalPublicationEnricher

Returns:

the current publication fetcher.

getPublicationEnricherListener

public PublicationEnricherListener getPublicationEnricherListener()

Gets the current publication listener

Specified by:

getPublicationEnricherListener in interface PublicationEnricher

Overrides:

getPublicationEnricherListener in class MinimalPublicationEnricher

Returns:

the current publication listener

find

public Publication find(Publication publicationToEnrich)
                 throws EnricherException

find.

Overrides:

find in class MinimalPublicationEnricher

Parameters:

publicationToEnrich - a T object.

Returns:

a T object.

Throws:

EnricherException - if any.

getMinimalPublicationUpdater

protected MinimalPublicationUpdater getMinimalPublicationUpdater()

Getter for the field minimalPublicationUpdater.

Returns:

a MinimalPublicationUpdater object.