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

Example 36 with ObjectNotFoundException

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

the class OptimizationServerResource method getOptRun.

private OptRun getOptRun(User vcellUser) {
    // }else{
    try {
        String optimizationId = (String) getRequestAttributes().get(VCellApiApplication.OPTIMIZATIONID);
        VCellApiApplication application = ((VCellApiApplication) getApplication());
        OptRunContext optRunContext = application.getOptServerImpl().getOptRunContextByOptimizationId(optimizationId);
        if (optRunContext == null) {
            throw new ObjectNotFoundException("optimization id '" + optimizationId + "' not found");
        }
        switch(optRunContext.getStatus()) {
            case Complete:
                {
                    OptRun optRun = CopasiServicePython.readOptRun(optRunContext.getOptRunBinaryFile());
                    return optRun;
                }
            case Queued:
            case Running:
            case Failed:
                {
                    OptProblem optProblem = CopasiServicePython.readOptProblem(optRunContext.getOptProblemBinaryFile());
                    OptRun optRun = new OptRun();
                    optRun.setOptProblem(optProblem);
                    optRun.setStatus(optRunContext.getStatus());
                    optRun.setStatusMessage(optRunContext.getStatus().name());
                    return optRun;
                }
            default:
                {
                    throw new RuntimeException("unexpected optimization status '" + optRunContext.getStatus() + "'");
                }
        }
    } catch (PermissionException e) {
        e.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_UNAUTHORIZED, "permission denied to requested resource");
    } catch (ObjectNotFoundException e) {
        e.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_NOT_FOUND, "optimization not found");
    } catch (Exception e) {
        throw new ResourceException(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }
// }
}

Example 37 with ObjectNotFoundException

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

the class PublicationServerResource method getPublicationRepresentation.

private PublicationRepresentation getPublicationRepresentation(User vcellUser) {
    // if (!application.authenticate(getRequest(), getResponse())){
    // // not authenticated
    // return new SimulationTaskRepresentation[0];
    // }else{
    RestDatabaseService restDatabaseService = ((VCellApiApplication) getApplication()).getRestDatabaseService();
    try {
        PublicationRep publicationRep = restDatabaseService.query(this, vcellUser);
        PublicationRepresentation publicationRepresentation = new PublicationRepresentation(publicationRep);
        return publicationRepresentation;
    } catch (PermissionException e) {
        e.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_UNAUTHORIZED, "permission denied to requested resource");
    } catch (ObjectNotFoundException e) {
        e.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_NOT_FOUND, "publication not found");
    } catch (Exception e) {
        throw new ResourceException(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }
// }
}

Example 38 with ObjectNotFoundException

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

the class RestDatabaseService method getDataSetTimeSeries.

public DataSetTimeSeries getDataSetTimeSeries(SimDataValuesServerResource resource, User vcellUser) throws DataAccessException, ObjectNotFoundException, 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);
    // resource.getRequestAttributes().get(VCellApiApplication.SIMDATAID);
    String jobIndexString = resource.getAttribute(VCellApiApplication.JOBINDEX);
    KeyValue simKey = new KeyValue(simId);
    SimulationRep simRep = getSimulationRep(simKey);
    if (simRep == null) {
        throw new ObjectNotFoundException("Simulation with key " + simKey + " not found");
    }
    int jobIndex = Integer.parseInt(jobIndexString);
    // TODO: pass in variables names from the query parameters.
    String[] variableNames = null;
    User owner = simRep.getOwner();
    VCMessageSession rpcSession = vcMessagingService.createProducerSession();
    try {
        RpcDataServerProxy rpcDataServerProxy = new RpcDataServerProxy(userLoginInfo, rpcSession);
        VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(simKey, owner);
        VCDataIdentifier vcdID = new VCSimulationDataIdentifier(vcSimID, jobIndex);
        DataSetTimeSeries dataSetTimeSeries = rpcDataServerProxy.getDataSetTimeSeries(vcdID, variableNames);
        return dataSetTimeSeries;
    } finally {
        rpcSession.close();
    }
}

Example 39 with ObjectNotFoundException

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

the class RestDatabaseService method startSimulation.

public SimulationRep startSimulation(BiomodelSimulationStartServerResource resource, User vcellUser) throws PermissionException, ObjectNotFoundException, DataAccessException, SQLException {
    // resource.getRequestAttributes().get(VCellApiApplication.SIMDATAID);
    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");
    }
    User owner = simRep.getOwner();
    if (!owner.compareEqual(vcellUser)) {
        throw new PermissionException("not authorized to start simulation");
    }
    VCMessageSession rpcSession = vcMessagingService.createProducerSession();
    try {
        UserLoginInfo userLoginInfo = new UserLoginInfo(vcellUser.getName(), null);
        try {
            userLoginInfo.setUser(vcellUser);
        } catch (Exception e) {
            e.printStackTrace();
            throw new DataAccessException(e.getMessage());
        }
        RpcSimServerProxy rpcSimServerProxy = new RpcSimServerProxy(userLoginInfo, rpcSession);
        VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(simKey, owner);
        rpcSimServerProxy.startSimulation(vcellUser, vcSimID, simRep.getScanCount());
        return simRep;
    } finally {
        rpcSession.close();
    }
}

Example 40 with ObjectNotFoundException

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

the class RestDatabaseService method getBioModelRep.

public BioModelRep getBioModelRep(KeyValue bmKey, User vcellUser) throws SQLException, ObjectNotFoundException, DataAccessException {
    if (vcellUser == null) {
        vcellUser = VCellApiApplication.DUMMY_USER;
    }
    ArrayList<String> conditions = new ArrayList<String>();
    if (bmKey != null) {
        conditions.add("(" + BioModelTable.table.id.getQualifiedColName() + " = " + bmKey.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);
    }
    int startRow = 1;
    int maxRows = 1;
    BioModelRep[] bioModelReps = databaseServerImpl.getBioModelReps(vcellUser, conditionsBuffer.toString(), null, startRow, maxRows);
    for (BioModelRep bioModelRep : bioModelReps) {
        KeyValue[] simContextKeys = bioModelRep.getSimContextKeyList();
        for (KeyValue scKey : simContextKeys) {
            SimContextRep scRep = getSimContextRep(scKey);
            if (scRep != null) {
                bioModelRep.addSimContextRep(scRep);
            }
        }
        KeyValue[] simulationKeys = bioModelRep.getSimKeyList();
        for (KeyValue simKey : simulationKeys) {
            SimulationRep simulationRep = getSimulationRep(simKey);
            if (simulationRep != null) {
                bioModelRep.addSimulationRep(simulationRep);
            }
        }
    }
    if (bioModelReps == null || bioModelReps.length != 1) {
        throw new ObjectNotFoundException("failed to get biomodel");
    }
    return bioModelReps[0];
}