Examples with ObjectNotFoundException org.vcell.util.ObjectNotFoundException used on opensource projects

Example 6 with ObjectNotFoundException

use of org.vcell.util.ObjectNotFoundException in project vcell by virtualcell.

the class RestDatabaseService method saveSimulation.

public SimulationSaveResponse saveSimulation(BiomodelSimulationSaveServerResource resource, User vcellUser, List<OverrideRepresentation> overrideRepresentations) throws PermissionException, ObjectNotFoundException, DataAccessException, SQLException, XmlParseException, PropertyVetoException, MappingException, ExpressionException {
    String simId = resource.getAttribute(VCellApiApplication.SIMULATIONID);
    KeyValue simKey = new KeyValue(simId);
    SimulationRep simRep = getSimulationRep(simKey);
    if (simRep == null) {
        throw new ObjectNotFoundException("Simulation with key " + simKey + " not found");
    }
    boolean myModel = simRep.getOwner().compareEqual(vcellUser);
    // get the bioModel
    String biomodelId = resource.getAttribute(VCellApiApplication.BIOMODELID);
    KeyValue biomodelKey = new KeyValue(biomodelId);
    BigString bioModelXML = this.databaseServerImpl.getBioModelXML(vcellUser, biomodelKey);
    BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
    // copy the simulation as new
    Simulation origSimulation = null;
    for (Simulation sim : bioModel.getSimulations()) {
        if (sim.getKey().equals(simKey)) {
            origSimulation = sim;
        }
    }
    if (origSimulation == null) {
        throw new RuntimeException("cannot find original Simulation");
    }
    SimulationContext simContext = bioModel.getSimulationContext(origSimulation);
    Simulation newUnsavedSimulation = simContext.copySimulation(origSimulation);
    // make appropriate changes
    // MATH OVERRIDES
    MathOverrides mathOverrides = new MathOverrides(newUnsavedSimulation);
    for (OverrideRepresentation overrideRep : overrideRepresentations) {
        overrideRep.applyMathOverrides(mathOverrides);
    }
    newUnsavedSimulation.setMathOverrides(mathOverrides);
    // save bioModel
    String editedBioModelXML = XmlHelper.bioModelToXML(bioModel);
    ServerDocumentManager serverDocumentManager = new ServerDocumentManager(this.databaseServerImpl);
    String modelName = bioModel.getName();
    if (!myModel) {
        modelName = modelName + "_" + Math.abs(new Random().nextInt());
    }
    String newBioModelXML = serverDocumentManager.saveBioModel(new QueryHashtable(), vcellUser, editedBioModelXML, modelName, null);
    BioModel savedBioModel = XmlHelper.XMLToBioModel(new XMLSource(newBioModelXML));
    Simulation savedSimulation = null;
    for (Simulation sim : savedBioModel.getSimulations()) {
        if (sim.getName().equals(newUnsavedSimulation.getName())) {
            savedSimulation = sim;
        }
    }
    if (savedSimulation == null) {
        throw new RuntimeException("cannot find new Simulation");
    }
    return new SimulationSaveResponse(savedBioModel, savedSimulation);
}

Example 7 with ObjectNotFoundException

use of org.vcell.util.ObjectNotFoundException in project vcell by virtualcell.

the class RestDatabaseService method getDataSetMetadata.

public DataSetMetadata getDataSetMetadata(SimDataServerResource resource, User vcellUser) throws ObjectNotFoundException, DataAccessException, SQLException {
    if (vcellUser == null) {
        vcellUser = VCellApiApplication.DUMMY_USER;
    }
    UserLoginInfo userLoginInfo = new UserLoginInfo(vcellUser.getName(), null);
    // resource.getRequestAttributes().get(VCellApiApplication.SIMDATAID);
    String simId = resource.getAttribute(VCellApiApplication.SIMDATAID);
    KeyValue simKey = new KeyValue(simId);
    SimulationRep simRep = getSimulationRep(simKey);
    if (simRep == null) {
        throw new ObjectNotFoundException("Simulation with key " + simKey + " not found");
    }
    User owner = simRep.getOwner();
    int jobIndex = 0;
    VCMessageSession rpcSession = vcMessagingService.createProducerSession();
    try {
        RpcDataServerProxy rpcDataServerProxy = new RpcDataServerProxy(userLoginInfo, rpcSession);
        VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(simKey, owner);
        VCDataIdentifier vcdID = new VCSimulationDataIdentifier(vcSimID, jobIndex);
        DataSetMetadata dataSetMetadata = rpcDataServerProxy.getDataSetMetadata(vcdID);
        return dataSetMetadata;
    } finally {
        rpcSession.close();
    }
}

Example 8 with ObjectNotFoundException

use of org.vcell.util.ObjectNotFoundException in project vcell by virtualcell.

the class SimDataValuesServerResource method getSimDataValuesRepresentation.

private SimDataValuesRepresentation getSimDataValuesRepresentation(User vcellUser) {
    // if (!application.authenticate(getRequest(), getResponse())){
    // // not authenticated
    // return new SimulationTaskRepresentation[0];
    // }else{
    RestDatabaseService restDatabaseService = ((VCellApiApplication) getApplication()).getRestDatabaseService();
    try {
        DataSetTimeSeries dataSetTimeSeries = restDatabaseService.getDataSetTimeSeries(this, vcellUser);
        SimDataValuesRepresentation simDataRepresentation = new SimDataValuesRepresentation(dataSetTimeSeries);
        return simDataRepresentation;
    } catch (PermissionException e) {
        e.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_UNAUTHORIZED, "not authorized to stop simulation");
    } catch (ObjectNotFoundException e) {
        e.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_NOT_FOUND, "simulation not found");
    } catch (Exception e) {
        throw new ResourceException(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }
// }
}

Example 9 with ObjectNotFoundException

use of org.vcell.util.ObjectNotFoundException in project vcell by virtualcell.

the class UserVerifier method authenticateUser.

public User authenticateUser(String userid, char[] secret) {
    DigestedPassword digestedPassword = UserLoginInfo.DigestedPassword.createAlreadyDigested(new String(secret));
    AuthenticationInfo authInfo = useridMap.get(userid);
    if (authInfo != null) {
        if (authInfo.digestedPassword.equals(digestedPassword)) {
            return authInfo.user;
        }
    }
    if ((System.currentTimeMillis() - lastQueryTimestampMS) > MIN_QUERY_TIME_MS) {
        synchronized (adminDbTopLevel) {
            User user = null;
            try {
                user = adminDbTopLevel.getUser(userid, digestedPassword, true, false);
            } catch (ObjectNotFoundException e) {
                e.printStackTrace();
            } catch (DataAccessException e) {
                e.printStackTrace();
            } catch (SQLException e) {
                e.printStackTrace();
            }
            // refresh stored list of user infos (for authentication)
            if (user != null) {
                useridMap.put(userid, new AuthenticationInfo(user, digestedPassword));
            }
            lastQueryTimestampMS = System.currentTimeMillis();
            return user;
        }
    } else {
        return null;
    }
}

Example 10 with ObjectNotFoundException

use of org.vcell.util.ObjectNotFoundException in project vcell by virtualcell.

the class RestDatabaseService method getPublicationRep.

public PublicationRep getPublicationRep(KeyValue pubKey, User vcellUser) throws SQLException, ObjectNotFoundException, DataAccessException {
    if (vcellUser == null) {
        vcellUser = VCellApiApplication.DUMMY_USER;
    }
    ArrayList<String> conditions = new ArrayList<String>();
    if (pubKey != null) {
        conditions.add("(" + PublicationTable.table.id.getQualifiedColName() + " = " + pubKey.toString() + ")");
    } else {
        throw new RuntimeException("bioModelID not specified");
    }
    StringBuffer conditionsBuffer = new StringBuffer();
    for (String condition : conditions) {
        if (conditionsBuffer.length() > 0) {
            conditionsBuffer.append(" AND ");
        }
        conditionsBuffer.append(condition);
    }
    PublicationRep[] publicationReps = databaseServerImpl.getPublicationReps(vcellUser, conditionsBuffer.toString(), null);
    if (publicationReps == null || publicationReps.length != 1) {
        throw new ObjectNotFoundException("failed to get publication");
    }
    return publicationReps[0];
}