Package psidev.psi.mi.jami.imex

Class ImexPublicationUpdater

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.imex.ImexPublicationUpdater

All Implemented Interfaces:

MIEnricher<Publication>, PublicationEnricher

public class ImexPublicationUpdater
extends FullPublicationEnricher

This enricher will update a publication having IMEx id and synchronize it with IMEx central

Since:

29/10/14

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields

Modifier and Type	Field	Description
static String	CURATION_DEPTH	Constant CURATION_DEPTH="curation depth"
static String	CURATION_DEPTH_MI	Constant CURATION_DEPTH_MI="MI:0955"
static String	FULL_COVERAGE	Constant FULL_COVERAGE="full coverage"
static String	FULL_COVERAGE_MI	Constant FULL_COVERAGE_MI="MI:0957"
static String	FULL_COVERAGE_TEXT	Constant FULL_COVERAGE_TEXT="Only protein-protein interactions"
static String	IMEX_CURATION	Constant IMEX_CURATION="imex curation"
static String	IMEX_CURATION_MI	Constant IMEX_CURATION_MI="MI:0959"
static String	IMEX_SECONDARY	Constant IMEX_SECONDARY="imex secondary"
static String	IMEX_SECONDARY_MI	Constant IMEX_SECONDARY_MI="MI:0952"

Constructor Summary

Constructors

Constructor	Description
ImexPublicationUpdater(ImexCentralClient fetcher)	Constructor for ImexPublicationUpdater.

Method Summary

Modifier and Type	Method	Description
protected String	collectAndCleanUpImexPrimaryReferenceFrom(Publication publication)	collectAndCleanUpImexPrimaryReferenceFrom.
ImexPublication	find(Publication publicationToEnrich)	find.
PublicationAdminGroupSynchronizer	getAdminGroupSynchronizer()	Getter for the field adminGroupSynchronizer.
PublicationIdentifierSynchronizer	getIdentifierSynchronizer()	Getter for the field identifierSynchronizer.
PublicationStatusSynchronizer	getStatusSynchronizer()	Getter for the field statusSynchronizer.
protected void	onEnrichedVersionNotFound(Publication publicationToEnrich)	onEnrichedVersionNotFound.
protected void	processAnnotations(Publication publicationToEnrich, Publication fetched)	processAnnotations.
protected void	processAuthors(Publication publicationToEnrich, Publication fetched)	processAuthors.
protected void	processCurationDepth(Publication publicationToEnrich, Publication fetched)	processCurationDepth.
protected void	processIdentifiers(Publication publicationToEnrich, Publication fetched)	processIdentifiers.
protected void	processJournal(Publication publicationToEnrich, Publication fetched)	processJournal.
protected void	processPublicationDate(Publication publicationToEnrich, Publication fetched)	processPublicationDate.
protected void	processPublicationTitle(Publication publicationToEnrich, Publication fetched)	processPublicationTitle.
protected void	processReleasedDate(Publication publicationToEnrich, Publication fetched)	processReleasedDate.
protected void	processXrefs(Publication publicationToEnrich, Publication fetched)	processXrefs.
void	setAdminGroupSynchronizer(PublicationAdminGroupSynchronizer adminGroupSynchronizer)	Setter for the field adminGroupSynchronizer.
void	setIdentifierSynchronizer(PublicationIdentifierSynchronizer identifierSynchronizer)	Setter for the field identifierSynchronizer.
void	setStatusSynchronizer(PublicationStatusSynchronizer statusSynchronizer)	Setter for the field statusSynchronizer.

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

processOtherProperties

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

enrich, getPublicationEnricherListener, getPublicationFetcher, getRetryCount, processPublication, setPublicationEnricherListener, 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

Field Detail

IMEX_SECONDARY_MI

public static String IMEX_SECONDARY_MI

Constant IMEX_SECONDARY_MI="MI:0952"

IMEX_SECONDARY

public static String IMEX_SECONDARY

Constant IMEX_SECONDARY="imex secondary"

FULL_COVERAGE_MI

public static String FULL_COVERAGE_MI

Constant FULL_COVERAGE_MI="MI:0957"

FULL_COVERAGE

public static String FULL_COVERAGE

Constant FULL_COVERAGE="full coverage"

IMEX_CURATION_MI

public static String IMEX_CURATION_MI

Constant IMEX_CURATION_MI="MI:0959"

IMEX_CURATION

public static String IMEX_CURATION

Constant IMEX_CURATION="imex curation"

CURATION_DEPTH_MI

public static String CURATION_DEPTH_MI

Constant CURATION_DEPTH_MI="MI:0955"

CURATION_DEPTH

public static String CURATION_DEPTH

Constant CURATION_DEPTH="curation depth"

FULL_COVERAGE_TEXT

public static String FULL_COVERAGE_TEXT

Constant FULL_COVERAGE_TEXT="Only protein-protein interactions"

Constructor Detail

ImexPublicationUpdater

public ImexPublicationUpdater(ImexCentralClient fetcher)

Constructor for ImexPublicationUpdater.

Parameters:

fetcher - a ImexCentralClient object.

Method Detail

processCurationDepth

protected void processCurationDepth(Publication publicationToEnrich,
                                    Publication fetched)

processCurationDepth.

Overrides:

processCurationDepth in class FullPublicationEnricher

Parameters:

publicationToEnrich - a Publication object.

fetched - a Publication object.

processReleasedDate

protected void processReleasedDate(Publication publicationToEnrich,
                                   Publication fetched)

processReleasedDate.

Overrides:

processReleasedDate in class FullPublicationEnricher

Parameters:

publicationToEnrich - a Publication object.

fetched - a Publication object.

processXrefs

protected void processXrefs(Publication publicationToEnrich,
                            Publication fetched)

processXrefs.

Overrides:

processXrefs in class FullPublicationEnricher

Parameters:

publicationToEnrich - a Publication object.

fetched - a Publication object.

processAnnotations

protected void processAnnotations(Publication publicationToEnrich,
                                  Publication fetched)

processAnnotations.

Overrides:

processAnnotations in class FullPublicationEnricher

Parameters:

publicationToEnrich - a Publication object.

fetched - a Publication object.

processJournal

protected void processJournal(Publication publicationToEnrich,
                              Publication fetched)

processJournal.

Overrides:

processJournal in class FullPublicationEnricher

Parameters:

publicationToEnrich - a Publication object.

fetched - a Publication object.

processPublicationTitle

protected void processPublicationTitle(Publication publicationToEnrich,
                                       Publication fetched)

processPublicationTitle.

Overrides:

processPublicationTitle in class FullPublicationEnricher

Parameters:

publicationToEnrich - a Publication object.

fetched - a Publication object.

processPublicationDate

protected void processPublicationDate(Publication publicationToEnrich,
                                      Publication fetched)

processPublicationDate.

Overrides:

processPublicationDate in class MinimalPublicationEnricher

Parameters:

publicationToEnrich - a Publication object.

fetched - a Publication object.

processAuthors

protected void processAuthors(Publication publicationToEnrich,
                              Publication fetched)

processAuthors.

Overrides:

processAuthors in class MinimalPublicationEnricher

Parameters:

publicationToEnrich - a Publication object.

fetched - a Publication object.

processIdentifiers

protected void processIdentifiers(Publication publicationToEnrich,
                                  Publication fetched)

processIdentifiers.

Overrides:

processIdentifiers in class MinimalPublicationEnricher

Parameters:

publicationToEnrich - a Publication object.

fetched - a Publication object.

find

public ImexPublication find(Publication publicationToEnrich)
                     throws EnricherException

find.

Overrides:

find in class MinimalPublicationEnricher

Parameters:

publicationToEnrich - a T object.

Returns:

a T object.

Throws:

EnricherException - if any.

collectAndCleanUpImexPrimaryReferenceFrom

protected String collectAndCleanUpImexPrimaryReferenceFrom(Publication publication)

collectAndCleanUpImexPrimaryReferenceFrom.

Parameters:

publication - a Publication object.

Returns:

a String object.

getAdminGroupSynchronizer

public PublicationAdminGroupSynchronizer getAdminGroupSynchronizer()

Getter for the field adminGroupSynchronizer.

Returns:

a PublicationAdminGroupSynchronizer object.

setAdminGroupSynchronizer

public void setAdminGroupSynchronizer(PublicationAdminGroupSynchronizer adminGroupSynchronizer)

Setter for the field adminGroupSynchronizer.

Parameters:

adminGroupSynchronizer - a PublicationAdminGroupSynchronizer object.

getStatusSynchronizer

public PublicationStatusSynchronizer getStatusSynchronizer()

Getter for the field statusSynchronizer.

Returns:

a PublicationStatusSynchronizer object.

setStatusSynchronizer

public void setStatusSynchronizer(PublicationStatusSynchronizer statusSynchronizer)

Setter for the field statusSynchronizer.

Parameters:

statusSynchronizer - a PublicationStatusSynchronizer object.

getIdentifierSynchronizer

public PublicationIdentifierSynchronizer getIdentifierSynchronizer()

Getter for the field identifierSynchronizer.

Returns:

a PublicationIdentifierSynchronizer object.

setIdentifierSynchronizer

public void setIdentifierSynchronizer(PublicationIdentifierSynchronizer identifierSynchronizer)

Setter for the field identifierSynchronizer.

Parameters:

identifierSynchronizer - a PublicationIdentifierSynchronizer object.

onEnrichedVersionNotFound

protected void onEnrichedVersionNotFound(Publication publicationToEnrich)
                                  throws EnricherException

onEnrichedVersionNotFound.

Overrides:

onEnrichedVersionNotFound in class MinimalPublicationEnricher

Parameters:

publicationToEnrich - a T object.

Throws:

EnricherException - if any.