How to use

getLifecycleManager

method

in

uk.ac.ebi.intact.core.context.IntactContext

public Publication createPublication(String pmid) {
  Publication pub = new Publication(getInstitution(), pmid);
  IntactContext.getCurrentInstance().getLifecycleManager().getStartStatus().create(pub, "Mock builder");
  return pub;
}

public Publication createPublication(String pmid) {
  Publication pub = new Publication(getInstitution(), pmid);
  IntactContext.getCurrentInstance().getLifecycleManager().getStartStatus().create(pub, "Mock builder");
  return pub;
}

private Publication createPublication(Bibref bibref, DbReference validPrimaryRef) {
  String pubId = validPrimaryRef.getId();
  Publication publication = (Publication) ConversionCache.getElement("pub:"+pubId);
  if (publication != null) {
    return publication;
  }
  publication = new Publication(getInstitution(), pubId);
  IntactConverterUtils.populateXref(bibref.getXref(), publication, this.publicationXrefConverter);
  IntactConverterUtils.populateAnnotations(bibref, publication, getInstitution(), this.annotationConverter);
  IntactContext.getCurrentInstance().getLifecycleManager().getStartStatus().create(publication, "created by xml import");
  ConversionCache.putElement("pub:"+pubId, publication);
  return publication;
}

private Publication createUnassignedPublication(Bibref bibRef, Experiment exp) {
  String pubId = PublicationUtils.nextUnassignedId(IntactContext.getCurrentInstance());
  Publication publication = (Publication) ConversionCache.getElement("pub:"+pubId);
  if (publication != null) {
    return publication;
  }
  publication = new Publication(getInstitution(), pubId);
  CvDatabase pubmed = CvObjectUtils.createCvObject(getInstitution(), CvDatabase.class, CvDatabase.PUBMED_MI_REF, CvDatabase.PUBMED);
  CvXrefQualifier primary = CvObjectUtils.createCvObject(getInstitution(), CvXrefQualifier.class, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF, CvXrefQualifier.PRIMARY_REFERENCE);
  // add unassigned as primary ref
  publication.addXref(new PublicationXref(getInstitution(), pubmed, pubId, primary));
  // add unassigned to exeriment
  exp.addXref(new ExperimentXref(getInstitution(), pubmed, pubId, primary));
  if (bibRef != null){
    IntactConverterUtils.populateXref(bibRef.getXref(), publication, this.publicationXrefConverter);
    IntactConverterUtils.populateAnnotations(bibRef, publication, getInstitution(), this.annotationConverter);
  }
  IntactContext.getCurrentInstance().getLifecycleManager().getStartStatus().create(publication, "created by xml import");
  ConversionCache.putElement("pub:"+pubId, publication);
  return publication;
}