/** * * @param xref the xref to check * @return */ private boolean xrefPointsToOwnAc(Xref xref) { if (xref.getPrimaryId().startsWith(config.getAcPrefix())) { return true; } else { for (InstitutionXref institutionXref : IntactContext.getCurrentInstance().getInstitution().getXrefs()) { if (institutionXref.getPrimaryId().equals(xref.getCvDatabase().getIdentifier())) { return true; } } return false; } }
/** * * @param xref the xref to check * @return */ private boolean xrefPointsToOwnAc(Xref xref) { if (xref.getPrimaryId().startsWith(config.getAcPrefix())) { return true; } else { for (InstitutionXref institutionXref : IntactContext.getCurrentInstance().getInstitution().getXrefs()) { if (institutionXref.getPrimaryId().equals(xref.getCvDatabase().getIdentifier())) { return true; } } return false; } }
@Override protected Institution fetchFromDataSource(Institution intactObject) { InstitutionXref idXref = null; for (InstitutionXref xref : intactObject.getXrefs()) { if (CvObjectUtils.getPsiMiIdentityXref(xref.getCvDatabase()).getPrimaryId() .equals(CvDatabase.PSI_MI_MI_REF)) { idXref = xref; } } if (idXref != null) { return IntactContext.getCurrentInstance().getDataContext().getDaoFactory() .getInstitutionDao().getByXref(idXref.getPrimaryId()); } return IntactContext.getCurrentInstance().getDataContext().getDaoFactory() .getInstitutionDao().getByShortLabel(intactObject.getShortLabel()); }
if (!intactObject.getXrefs().isEmpty()){ Collection<uk.ac.ebi.intact.model.Xref> primaryRefs = searchXrefs(intactObject, CvDatabase.PUBMED_MI_REF, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF, isCheckInitializedCollections());
Collection<InstitutionXref> ownerRefs = institution.getXrefs();
PersisterContext.getInstance().addToPersist(intactObject); for (InstitutionXref xref : intactObject.getXrefs()) { if (log.isDebugEnabled()) log.debug("\tSaving database: "+xref.getCvDatabase().getShortLabel()); try {