public psidev.psi.mi.jami.model.Publication updatePublicationAdminUser( String identifier, String source, Operation operation, String user ) throws BridgeFailedException { psidev.psi.mi.jami.model.Publication p = fetchByIdentifier(identifier, source); if (p != null && p instanceof ImexPublication){ if (user != null && (user.equalsIgnoreCase(intact_user) || user.equalsIgnoreCase(phantom_user))){ ((ImexPublication) p).getCurators().add(user.toLowerCase()); } // user not recognized, throw exception as in the real webservice else { ImexCentralFault imexFault = new ImexCentralFault(); imexFault.setFaultCode(10); IcentralFault fault = new IcentralFault("User not recognized", imexFault); throw new BridgeFailedException(fault); } } else { ImexCentralFault imexFault = new ImexCentralFault(); imexFault.setFaultCode(6); IcentralFault fault = new IcentralFault("No publication record found", imexFault); throw new BridgeFailedException(fault); } return p; }
public Publication updatePublicationStatus( String identifier, PublicationStatus status) throws ImexCentralException { final Publication p = getPublicationById( identifier ); if (!status.toString().equals("NEW") && !status.toString().equals("DISCARDED") && !status.toString().equals("RESERVED") && !status.toString().equals("PROCESSED") && !status.toString().equals("RELEASED") && !status.toString().equals("INPROGRESS") && !status.toString().equals("INCOMPLETE")){ ImexCentralFault imexFault = new ImexCentralFault(); imexFault.setFaultCode(8); IcentralFault fault = new IcentralFault("Status not recognized", imexFault); throw new ImexCentralException(fault); } if( p != null ) { p.setStatus( status.toString() ); } else { ImexCentralFault imexFault = new ImexCentralFault(); imexFault.setFaultCode(6); IcentralFault fault = new IcentralFault("No publication record found", imexFault); throw new ImexCentralException(fault); } return p; }
public Publication updatePublicationAdminGroup( String identifier, Operation operation, String group ) throws ImexCentralException { Publication p = getPublicationById( identifier ); if (p != null){ if (group != null && (group.equalsIgnoreCase(INTACT_GROUP) || group.equalsIgnoreCase(MATRIXDB_GROUP))){ if (p.getAdminGroupList() == null){ p.setAdminGroupList(new Publication.AdminGroupList()); } p.getAdminGroupList().getGroup().add(group.toUpperCase()); } // group not recognized, throw exception as in the real webservice else { ImexCentralFault imexFault = new ImexCentralFault(); imexFault.setFaultCode(11); IcentralFault fault = new IcentralFault("Group not recognized", imexFault); throw new ImexCentralException(fault); } } else { ImexCentralFault imexFault = new ImexCentralFault(); imexFault.setFaultCode(6); IcentralFault fault = new IcentralFault("No publication record found", imexFault); throw new ImexCentralException(fault); } return p; }
public psidev.psi.mi.jami.model.Publication updatePublicationAdminGroup( String identifier, String source, Operation operation, String group ) throws BridgeFailedException { psidev.psi.mi.jami.model.Publication p = fetchByIdentifier(identifier, source); if (p != null && p instanceof ImexPublication){ if (group != null && (group.equalsIgnoreCase(INTACT_GROUP) || group.equalsIgnoreCase(MATRIXDB_GROUP))){ ((ImexPublication) p).getSources().add(new DefaultSource(group)); } // group not recognized, throw exception as in the real webservice else { ImexCentralFault imexFault = new ImexCentralFault(); imexFault.setFaultCode(11); IcentralFault fault = new IcentralFault("Group not recognized", imexFault); throw new BridgeFailedException(fault); } } else if (p != null){ p.setSource(new DefaultSource(group)); } else { ImexCentralFault imexFault = new ImexCentralFault(); imexFault.setFaultCode(6); IcentralFault fault = new IcentralFault("No publication record found", imexFault); throw new BridgeFailedException(fault); } return p; }
public psidev.psi.mi.jami.model.Publication updatePublicationStatus(String identifier, String source, PublicationStatus status) throws BridgeFailedException { psidev.psi.mi.jami.model.Publication p = fetchByIdentifier(identifier, source); if (p != null && p instanceof ImexPublication){ ((ImexPublication) p).setStatus(status); } else { ImexCentralFault imexFault = new ImexCentralFault(); imexFault.setFaultCode(6); IcentralFault fault = new IcentralFault("No publication record found", imexFault); throw new BridgeFailedException(fault); } return p; }
public Publication updatePublicationAdminUser( String identifier, Operation operation, String user ) throws ImexCentralException { Publication p = getPublicationById( identifier ); if (p != null){ if (user != null && (user.equalsIgnoreCase(intact_user) || user.equalsIgnoreCase(phantom_user))){ if (p.getAdminUserList() == null){ p.setAdminUserList(new Publication.AdminUserList()); } p.getAdminUserList().getUser().add(user.toLowerCase()); } // user not recognized, throw exception as in the real webservice else { ImexCentralFault imexFault = new ImexCentralFault(); imexFault.setFaultCode(10); IcentralFault fault = new IcentralFault("User not recognized", imexFault); throw new ImexCentralException(fault); } } else { ImexCentralFault imexFault = new ImexCentralFault(); imexFault.setFaultCode(6); IcentralFault fault = new IcentralFault("No publication record found", imexFault); throw new ImexCentralException(fault); } return 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; }
public psidev.psi.mi.jami.model.Publication fetchPublicationImexAccession( String identifier, String source, boolean create ) throws BridgeFailedException { final psidev.psi.mi.jami.model.Publication p = fetchByIdentifier(identifier, source); if (p != null){ if( create ) { if( p.getImexId() != null) { throw new IllegalStateException( "Publication already has an IMEx id: " + p.getImexId() ); } // assigning new IMEx ID p.assignImexId("IM-" + imexIdSequence); imexIdSequence++; } } else { ImexCentralFault imexFault = new ImexCentralFault(); imexFault.setFaultCode(6); IcentralFault fault = new IcentralFault("No publication record found", imexFault); throw new BridgeFailedException(fault); } return p; } }
imexFault.setFaultCode(3); imexFault.setFaultCode(6);
imexFault.setFaultCode(3); imexFault.setFaultCode(6);
@Override public Publication updatePublicationIdentifier(String oldIdentifier, String newIdentifier) throws ImexCentralException { Publication existingPub = getPublicationById(newIdentifier); // if the new identifier is already in IMEx central, we don't update anything if (existingPub != null){ ImexCentralFault imexFault = new ImexCentralFault(); imexFault.setFaultCode(3); IcentralFault fault = new IcentralFault("New publication identifier " + newIdentifier + "already used in IMEx central.", imexFault); throw new ImexCentralException( "Impossible to update the identifier of " + oldIdentifier, fault ); } try { return port.updatePublicationIdentifier( buildIdentifier(oldIdentifier ), buildIdentifier(newIdentifier) ); } catch ( IcentralFault f ) { throw new ImexCentralException( "Error while attempting to upate the identifier to '"+ newIdentifier +"' for publication " + oldIdentifier, f ); } }
public psidev.psi.mi.jami.model.Publication updatePublicationIdentifier(String oldIdentifier, String oldSource, String newIdentifier, String source) throws BridgeFailedException { psidev.psi.mi.jami.model.Publication existingPub = fetchByIdentifier(newIdentifier, source); // if the new identifier is already in IMEx central, we don't update anything if (existingPub != null){ ImexCentralFault imexFault = new ImexCentralFault(); imexFault.setFaultCode(3); IcentralFault fault = new IcentralFault("New publication identifier " + newIdentifier + "already used in IMEx central.", imexFault); throw new BridgeFailedException( "Impossible to update the identifier of " + oldIdentifier, fault ); } try { Publication pub = port.updatePublicationIdentifier( buildIdentifier(oldIdentifier, oldSource ), buildIdentifier(newIdentifier, source) ); if (pub != null){ return new ImexPublication(pub); } } catch ( IcentralFault f ) { throw new BridgeFailedException( "Error while attempting to upate the identifier to '"+ newIdentifier +"' for publication " + oldIdentifier, f ); } return null; }