How to use

getPubmedId

method

in

psidev.psi.mi.jami.model.Publication

public void onPubmedIdUpdate(Publication publication, String oldId) {
  if (oldId == null){
    publicationChangeLogger.log(Level.INFO, "The pubmed id has been initialised for the publication " + publication.toString());
  }
  else if (publication.getPubmedId() == null){
    publicationChangeLogger.log(Level.INFO, "The pubmed id has been reset for the publication " + publication.toString());
  }
  else {
    publicationChangeLogger.log(Level.INFO, "The pubmed id " + oldId + " has been updated with " + publication.getPubmedId() + " in the publication " + publication.toString());
  }
}

public static Xref getPubmedReference(Publication pub){
  if (pub == null){
    return null;
  }
  else if (pub.getPubmedId() == null){
    return null;
  }
  else{
    return XrefUtils.collectFirstIdentifierWithDatabaseAndId(pub.getIdentifiers(), Xref.PUBMED_MI, Xref.PUBMED, pub.getPubmedId());
  }
}

public static String getPubmedId(Experiment exp){
  if (exp == null){
   return null; 
  }
  else if (exp.getPublication() == null){
    return null; 
  }
  else{
    return exp.getPublication().getPubmedId();
  }
}

@Override
public void onImexIdAssigned(Publication intactPublication, String imex) {
  String pubId = intactPublication.getPubmedId() != null ? intactPublication.getPubmedId() : intactPublication.getDoi();
  if (pubId == null && !intactPublication.getIdentifiers().isEmpty()){
    Xref id = intactPublication.getXrefs().iterator().next();
    pubId = id.getId();
  }
  NewAssignedImexEvent evt = new NewAssignedImexEvent(this, pubId, imex, null, null);
  getImexCentralManager().fireOnNewImexAssigned(evt);
}

@Override
public void onMissingImexId(Publication intactPublication) {
  String pubId = intactPublication.getPubmedId() != null ? intactPublication.getPubmedId() : intactPublication.getDoi();
  if (pubId == null && !intactPublication.getIdentifiers().isEmpty()){
    Xref id = intactPublication.getXrefs().iterator().next();
    pubId = id.getId();
  }
  ImexErrorEvent errorEvt = new ImexErrorEvent(this, ImexErrorType.no_IMEX_id, pubId, null, null, null, "Publication "
      + ((IntactPublication)intactPublication).getAc() + " does not have a valid IMEx id and is ignored.");
  imexCentralManager.fireOnImexError(errorEvt);
  // do not update experiments and interactions
  getImexCentralManager().setEnableExperimentsAndInteractionsUpdate(false);
}

@Override
public void onImexIdConflicts(Publication intactPublication, Collection<Xref> conflictingXrefs) {
  String pubId = intactPublication.getPubmedId() != null ? intactPublication.getPubmedId() : intactPublication.getDoi();
  if (pubId == null && !intactPublication.getIdentifiers().isEmpty()){
    Xref id = intactPublication.getXrefs().iterator().next();
    pubId = id.getId();
  }
  ImexErrorEvent errorEvt = new ImexErrorEvent(this, ImexErrorType.publication_imex_conflict, pubId, null, null, null,
      "Publication " + pubId + " cannot be updated because of IMEx identifier conflicts.");
  getImexCentralManager().fireOnImexError(errorEvt);
  // do not update experiments and interactions
  getImexCentralManager().setEnableExperimentsAndInteractionsUpdate(false);
}

@Override
public void onPublicationWhichCannotBeRegistered(Publication intactPublication) {
  String pubId = intactPublication.getPubmedId() != null ? intactPublication.getPubmedId() : intactPublication.getDoi();
  if (pubId == null && !intactPublication.getIdentifiers().isEmpty()){
    Xref id = intactPublication.getXrefs().iterator().next();
    pubId = id.getId();
  }
  // unassigned publication, cannot use the webservice to automatically assign IMEx id for now, ask the curator to manually register and assign IMEx id to this publication
  if (!Pattern.matches(ImexCentralManager.PUBMED_REGEXP.toString(), pubId)){
    log.warn("It is not possible to register an unassigned publication. " +
        "The publication needs to be registered manually by a curator in IMEx central.");
  }
  // the publication is already registered, we just update status and users
  else {
    ImexErrorEvent evt = new ImexErrorEvent(this, ImexErrorType.no_record_created, pubId, null, null, null,
        "It is not possible to register the publication " + pubId + " in IMEx central.");
    getImexCentralManager().fireOnImexError(evt);
  }
  // do not update experiments and interactions
  getImexCentralManager().setEnableExperimentsAndInteractionsUpdate(false);
}

@Override
public void onPublicationAlreadyRegisteredInImexCentral(Publication intactPublication, String imex) {
  String pubId = intactPublication.getPubmedId() != null ? intactPublication.getPubmedId() : intactPublication.getDoi();
  if (pubId == null && !intactPublication.getIdentifiers().isEmpty()){
    Xref id = intactPublication.getXrefs().iterator().next();
    pubId = id.getId();
  }
  // we already have an IMEx id in IMEx central, it is not possible to update the intact publication because we have a conflict
  ImexErrorEvent evt = new ImexErrorEvent(this, ImexErrorType.publication_already_in_imex,
      pubId, imex, null, null, "It is not possible to assign a valid IMEx id to the publication " + pubId
      + " because it already registered in IMEx central with another institution");
  getImexCentralManager().fireOnImexError(evt);
  // do not update experiments and interactions
  getImexCentralManager().setEnableExperimentsAndInteractionsUpdate(false);
}

@Override
public void onImexIdNotRecognized(Publication intactPublication, String imex) {
  String pubId = intactPublication.getPubmedId() != null ? intactPublication.getPubmedId() : intactPublication.getDoi();
  if (pubId == null && !intactPublication.getIdentifiers().isEmpty()){
    Xref id = intactPublication.getXrefs().iterator().next();
    pubId = id.getId();
  }
  ImexErrorEvent errorEvt = new ImexErrorEvent(this, ImexErrorType.imex_not_recognized, pubId, imex, null, null,
      "Publication " + ((IntactPublication)intactPublication).getAc() + " is not matching any record in IMEx central with id " + imex);
  getImexCentralManager().fireOnImexError(errorEvt);
  // do not update experiments and interactions
  getImexCentralManager().setEnableExperimentsAndInteractionsUpdate(false);
}

  hashcode = 31*hashcode + pub.getImexId().hashCode();
else if (pub.getPubmedId() != null){
  hashcode = 31*hashcode + pub.getPubmedId().hashCode();

String pubmed1 = publication1.getPubmedId();
String pubmed2 = publication2.getPubmedId();
String doi1 = publication1.getDoi();
String doi2 = publication2.getDoi();

String pubmed1 = publication1.getPubmedId();
String pubmed2 = publication2.getPubmedId();
boolean hasPubmedId1 = pubmed1 != null;
boolean hasPubmedId2 = pubmed2 != null;

String pubId = publication.getPubmedId() != null ? publication.getPubmedId() : publication.getDoi();
String source = publication.getPubmedId() != null ? Xref.PUBMED : Xref.DOI;
if (pubId == null && !publication.getIdentifiers().isEmpty()){
  Xref id = publication.getXrefs().iterator().next();