Examples with SimulationRep cbit.vcell.modeldb.SimulationRep used on opensource projects

Example 6 with SimulationRep

use of cbit.vcell.modeldb.SimulationRep in project vcell by virtualcell.

the class RestDatabaseService method getSimulationRep.

public SimulationRep getSimulationRep(KeyValue key) throws DataAccessException, SQLException {
    SimulationRep simulationRep = simMap.get(key);
    if (simulationRep != null) {
        return simulationRep;
    } else {
        System.out.println("getting simulation rep for simKey = " + key);
        simulationRep = databaseServerImpl.getSimulationRep(key);
        if (simulationRep != null) {
            System.out.println("found simulation key = " + key + " number of cached simulations is " + simMap.size());
            simMap.put(key, simulationRep);
        } else {
            System.out.println("couldn't find simulation key = " + key);
        }
        return simulationRep;
    }
}

Example 7 with SimulationRep

use of cbit.vcell.modeldb.SimulationRep in project vcell by virtualcell.

the class BiomodelSimulationStartServerResource method start.

@Override
public Representation start() {
    VCellApiApplication application = ((VCellApiApplication) getApplication());
    User vcellUser = application.getVCellUser(getChallengeResponse(), AuthenticationPolicy.prohibitInvalidCredentials);
    RestDatabaseService restDatabaseService = application.getRestDatabaseService();
    try {
        SimulationRep simRep = restDatabaseService.startSimulation(this, vcellUser);
        Representation representation = new StringRepresentation("simulation started", MediaType.TEXT_PLAIN);
        redirectSeeOther("/" + VCellApiApplication.SIMTASK + "?" + SimulationTasksServerResource.PARAM_SIM_ID + "=" + simRep.getKey().toString() + "&" + SimulationTasksServerResource.PARAM_STATUS_COMPLETED + "=on" + "&" + SimulationTasksServerResource.PARAM_STATUS_DISPATCHED + "=on" + "&" + SimulationTasksServerResource.PARAM_STATUS_FAILED + "=on" + "&" + SimulationTasksServerResource.PARAM_STATUS_QUEUED + "=on" + "&" + SimulationTasksServerResource.PARAM_STATUS_RUNNING + "=on" + "&" + SimulationTasksServerResource.PARAM_STATUS_STOPPED + "=on" + "&" + SimulationTasksServerResource.PARAM_STATUS_WAITING + "=on" + "&" + SimulationTasksServerResource.PARAM_START_ROW + "=1" + "&" + SimulationTasksServerResource.PARAM_MAX_ROWS + "=" + Integer.toString(simRep.getScanCount() * 4));
        return representation;
    } catch (PermissionException e) {
        e.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_UNAUTHORIZED, "not authorized to start 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 8 with SimulationRep

use of cbit.vcell.modeldb.SimulationRep in project vcell by virtualcell.

the class BiomodelSimulationStopServerResource method stop.

@Override
public Representation stop() {
    VCellApiApplication application = ((VCellApiApplication) getApplication());
    User vcellUser = application.getVCellUser(getChallengeResponse(), AuthenticationPolicy.prohibitInvalidCredentials);
    RestDatabaseService restDatabaseService = application.getRestDatabaseService();
    try {
        SimulationRep simRep = restDatabaseService.stopSimulation(this, vcellUser);
        Representation representation = new StringRepresentation("simulation stopped", MediaType.TEXT_PLAIN);
        redirectSeeOther("/" + VCellApiApplication.SIMTASK + "?" + SimulationTasksServerResource.PARAM_SIM_ID + "=" + simRep.getKey().toString() + "&" + SimulationTasksServerResource.PARAM_STATUS_COMPLETED + "=on" + "&" + SimulationTasksServerResource.PARAM_STATUS_DISPATCHED + "=on" + "&" + SimulationTasksServerResource.PARAM_STATUS_FAILED + "=on" + "&" + SimulationTasksServerResource.PARAM_STATUS_QUEUED + "=on" + "&" + SimulationTasksServerResource.PARAM_STATUS_RUNNING + "=on" + "&" + SimulationTasksServerResource.PARAM_STATUS_STOPPED + "=on" + "&" + SimulationTasksServerResource.PARAM_STATUS_WAITING + "=on" + "&" + SimulationTasksServerResource.PARAM_START_ROW + "=1" + "&" + SimulationTasksServerResource.PARAM_MAX_ROWS + "=" + Integer.toString(simRep.getScanCount() * 4));
        return representation;
    } 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 SimulationRep

use of cbit.vcell.modeldb.SimulationRep 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 10 with SimulationRep

use of cbit.vcell.modeldb.SimulationRep 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();
    }
}