public Publication createPublicationById( String identifier ) throws ImexCentralException { Publication p = new Publication(); final Identifier i = new Identifier(); i.setAc( identifier ); i.setNs("pmid"); p.getIdentifier().add(i); p.setImexAccession( "N/A" ); allPublications.add( p ); return p; }
public void addPublication( String identifier, String imexAccession, String status, String owner ) { Publication p = new Publication(); final Identifier id = new Identifier(); id.setAc( identifier ); p.getIdentifier().add(id); p.setImexAccession( ( imexAccession == null ? "N/A" : imexAccession ) ); p.setStatus( status ); p.setOwner( owner ); allPublications.add( p ); }
public void addPublication( String identifier, String imexAccession, String status, String owner ) { Publication p = new Publication(); final Identifier id = new Identifier(); id.setAc( identifier ); p.getIdentifier().add(id); p.setImexAccession( ( imexAccession == null ? "N/A" : imexAccession ) ); p.setStatus( status ); p.setOwner( owner ); allPublications.add( new ImexPublication(p)); }
public Publication getPublicationImexAccession( String identifier, boolean create ) throws ImexCentralException { final Publication p = getPublicationById( identifier ); if (p != null){ if( create ) { if( p.getImexAccession() != null && !p.getImexAccession().equals("N/A")) { throw new IllegalStateException( "Publication already has an IMEx id: " + p.getImexAccession() ); } // assigning new IMEx ID p.setImexAccession( "IM-" + imexIdSequence ); imexIdSequence++; } } else { ImexCentralFault imexFault = new ImexCentralFault(); imexFault.setFaultCode(6); IcentralFault fault = new IcentralFault("No publication record found", imexFault); throw new ImexCentralException(fault); } return p; }
Publication pub = new Publication(); pub.setTitle(publication.getTitle()); pub.setImexAccession(publication.getImexId()); for (Xref id : publication.getIdentifiers()){ Identifier identifier = buildIdentifier(id.getId(), id.getDatabase().getShortName());