Examples with VCSimulationIdentifier cbit.vcell.solver.VCSimulationIdentifier used on opensource projects

Example 41 with VCSimulationIdentifier

use of cbit.vcell.solver.VCSimulationIdentifier 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 42 with VCSimulationIdentifier

use of cbit.vcell.solver.VCSimulationIdentifier 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 43 with VCSimulationIdentifier

use of cbit.vcell.solver.VCSimulationIdentifier in project vcell by virtualcell.

the class RestDatabaseService method stopSimulation.

public SimulationRep stopSimulation(BiomodelSimulationStopServerResource 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 stop 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.stopSimulation(vcellUser, vcSimID);
        return simRep;
    } finally {
        rpcSession.close();
    }
}

Example 44 with VCSimulationIdentifier

use of cbit.vcell.solver.VCSimulationIdentifier in project vcell by virtualcell.

the class BioModelWindowManager method updateSimulationDataViewers.

/**
 * Insert the method's description here.
 * Creation date: (7/20/2004 1:13:06 PM)
 */
private void updateSimulationDataViewers(ApplicationComponents appComponents, SimulationContext found) {
    SimulationWindow[] simWindows = appComponents.getSimulationWindows();
    Simulation[] sims = found.getSimulations();
    Hashtable<VCSimulationIdentifier, Simulation> hash = new Hashtable<VCSimulationIdentifier, Simulation>();
    for (int i = 0; i < sims.length; i++) {
        SimulationInfo simInfo = sims[i].getSimulationInfo();
        if (simInfo != null) {
            VCSimulationIdentifier vcSimulationIdentifier = simInfo.getAuthoritativeVCSimulationIdentifier();
            hash.put(vcSimulationIdentifier, sims[i]);
        }
    }
    for (int i = 0; i < simWindows.length; i++) {
        SimulationWindow sw = simWindows[i];
        if (hash.containsKey(simWindows[i].getVcSimulationIdentifier())) {
            sw.resetSimulation((Simulation) hash.get(sw.getVcSimulationIdentifier()));
        } else if (sw.isShowingLocalSimulation()) {
            sw.setLocalState(LocalState.LOCAL_SIMMODFIED);
        } else {
            ChildWindowManager childWindowManager = ChildWindowManager.findChildWindowManager(getJPanel());
            ChildWindow childWindow = childWindowManager.getChildWindowFromContext(sw);
            if (childWindow != null) {
                childWindowManager.closeChildWindow(childWindow);
            }
        }
    }
}

Example 45 with VCSimulationIdentifier

use of cbit.vcell.solver.VCSimulationIdentifier in project vcell by virtualcell.

the class ClientRequestManager method getServerSimulationStatus.

/**
 * Insert the method's description here.
 * Creation date: (6/7/2004 1:27:25 PM)
 * @return cbit.vcell.solver.ode.gui.SimulationStatus
 * @param simulation cbit.vcell.solver.Simulation
 */
public SimulationStatus getServerSimulationStatus(SimulationInfo simInfo) {
    SimulationStatus simStatus = null;
    if (simInfo == null) {
        // unsaved simulation ... won't have simulation status
        return null;
    }
    try {
        VCSimulationIdentifier vcSimulationIdentifier = simInfo.getAuthoritativeVCSimulationIdentifier();
        simStatus = getClientServerManager().getJobManager().getServerSimulationStatus(vcSimulationIdentifier);
    } catch (Throwable exc) {
        exc.printStackTrace(System.out);
    }
    return simStatus;
}