Examples with SimulationJobStatus cbit.vcell.server.SimulationJobStatus used on opensource projects

Example 16 with SimulationJobStatus

use of cbit.vcell.server.SimulationJobStatus in project vcell by virtualcell.

the class SimulationControllerImpl method stopSimulation.

/**
 * This method was created by a SmartGuide.
 * @throws JMSException
 * @throws AuthenticationException
 * @throws DataAccessException
 * @throws SQLException
 * @throws FileNotFoundException
 * @exception java.rmi.RemoteException The exception description.
 * @throws VCMessagingException
 */
public void stopSimulation(Simulation simulation) throws FileNotFoundException, SQLException, DataAccessException, AuthenticationException, JMSException, VCMessagingException {
    LocalVCMessageListener localVCMessageListener = new LocalVCMessageListener() {

        public void onLocalVCMessage(VCDestination destination, VCMessage objectMessage) {
            String messageTypeProperty = VCMessagingConstants.MESSAGE_TYPE_PROPERTY;
            String stopSimulationValue = MessageConstants.MESSAGE_TYPE_STOPSIMULATION_VALUE;
            if (destination == VCellTopic.ClientStatusTopic && objectMessage.getObjectContent() instanceof SimulationJobStatus) {
                onClientStatusTopic_SimulationJobStatus(objectMessage);
            } else if (destination == VCellTopic.ServiceControlTopic && objectMessage.getStringProperty(messageTypeProperty).equals(stopSimulationValue)) {
                lg.error("SimulationControllerImpl.stopSimulation() exercising serviceControl topic ... should be removed");
                onServiceControlTopic_StopSimulation(objectMessage);
            } else {
                throw new RuntimeException("SimulationControllerImpl.startSimulation().objectMessageListener:: expecting message with SimulationJobStatus to topic " + VCellTopic.ClientStatusTopic.getName() + ": received \"" + objectMessage.show() + "\" on destination \"" + destination + "\"");
            }
        }
    };
    LocalVCMessageAdapter vcMessageSession = new LocalVCMessageAdapter(localVCMessageListener);
    VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(simulation.getKey(), simulation.getVersion().getOwner());
    simulationDispatcherEngine.onStopRequest(vcSimID, localVCellConnection.getUserLoginInfo().getUser(), simulationDatabase, vcMessageSession);
    vcMessageSession.deliverAll();
}

Example 17 with SimulationJobStatus

use of cbit.vcell.server.SimulationJobStatus in project vcell by virtualcell.

the class SimulationControllerImpl method onSimJobQueue_SimulationTask.

private void onSimJobQueue_SimulationTask(VCMessage vcMessage) {
    SimulationTask simTask = null;
    try {
        SimulationTaskMessage simTaskMessage = new SimulationTaskMessage(vcMessage);
        simTask = simTaskMessage.getSimulationTask();
        LocalSolverController solverController = getOrCreateSolverController(simTask);
        // can only start after updating the database is done
        solverController.startSimulationJob();
    } catch (Exception e) {
        lg.error(e.getMessage(), e);
        KeyValue simKey = simTask.getSimKey();
        VCSimulationIdentifier vcSimID = simTask.getSimulationJob().getVCDataIdentifier().getVcSimID();
        int jobIndex = simTask.getSimulationJob().getJobIndex();
        int taskID = simTask.getTaskID();
        SimulationJobStatus newJobStatus = new SimulationJobStatus(VCellServerID.getSystemServerID(), vcSimID, jobIndex, null, SchedulerStatus.FAILED, taskID, SimulationMessage.jobFailed(e.getMessage()), null, null);
        SimulationJobStatusEvent event = new SimulationJobStatusEvent(this, Simulation.createSimulationID(simKey), newJobStatus, null, null, vcSimID.getOwner().getName());
        fireSimulationJobStatusEvent(event);
    }
}

Example 18 with SimulationJobStatus

use of cbit.vcell.server.SimulationJobStatus in project vcell by virtualcell.

the class AdminService method query.

public SimulationJobStatus[] query(SimpleJobStatusQuerySpec querySpec) throws ObjectNotFoundException, DataAccessException {
    SimulationDatabase simDatabase = new SimulationDatabaseDirect(adminDbTop, dbServerImpl, false);
    SimulationJobStatus[] resultList = simDatabase.queryJobs(querySpec);
    return resultList;
}

Example 19 with SimulationJobStatus

use of cbit.vcell.server.SimulationJobStatus in project vcell by virtualcell.

the class SimulationDatabaseDirectTest method test.

@Test
public void test() {
    try (ConnectionFactory conFactory = DatabaseService.getInstance().createConnectionFactory()) {
        DatabaseServerImpl databaseServerImpl = new DatabaseServerImpl(conFactory, conFactory.getKeyFactory());
        AdminDBTopLevel adminDbTopLevel = new AdminDBTopLevel(conFactory);
        boolean bCache = false;
        SimulationDatabaseDirect simulationDatabaseDirect = new SimulationDatabaseDirect(adminDbTopLevel, databaseServerImpl, bCache);
        SimpleJobStatusQuerySpec querySpec = new SimpleJobStatusQuerySpec();
        querySpec.submitLowMS = null;
        querySpec.submitHighMS = null;
        querySpec.startLowMS = null;
        querySpec.startHighMS = null;
        querySpec.endLowMS = null;
        querySpec.endHighMS = null;
        querySpec.startRow = 0;
        querySpec.maxRows = 100;
        querySpec.serverId = null;
        querySpec.computeHost = null;
        querySpec.userid = null;
        querySpec.simId = null;
        querySpec.jobId = null;
        querySpec.taskId = null;
        querySpec.hasData = null;
        querySpec.waiting = true;
        querySpec.queued = true;
        querySpec.dispatched = true;
        querySpec.running = true;
        querySpec.completed = true;
        querySpec.failed = true;
        querySpec.stopped = true;
        SimulationJobStatus[] resultList = simulationDatabaseDirect.queryJobs(querySpec);
        Gson gson = new Gson();
        for (SimulationJobStatus status : resultList) {
            System.out.println(gson.toJson(status.toRep()));
        }
    // test that there are no repeated jobs
    } catch (Exception e) {
        e.printStackTrace();
        fail("exception: " + e.getMessage());
    }
}

Example 20 with SimulationJobStatus

use of cbit.vcell.server.SimulationJobStatus in project vcell by virtualcell.

the class HealthService method runsimLoop.

private void runsimLoop() {
    try {
        Thread.sleep(SIMULATION_LOOP_START_DELAY);
    } catch (InterruptedException e1) {
    }
    UserLoginInfo userLoginInfo = new UserLoginInfo(testUserid, testPassword);
    while (true) {
        long id = simStartEvent();
        KeyValue savedBioModelKey = null;
        VCSimulationIdentifier runningSimId = null;
        try {
            RemoteProxyVCellConnectionFactory vcellConnectionFactory = new RemoteProxyVCellConnectionFactory(host, port, userLoginInfo);
            VCellConnection vcellConnection = vcellConnectionFactory.createVCellConnection();
            String vcmlString = IOUtils.toString(getClass().getResourceAsStream("/TestTemplate.vcml"));
            BioModel templateBioModel = XmlHelper.XMLToBioModel(new XMLSource(vcmlString));
            templateBioModel.clearVersion();
            String newBiomodelName = "test_" + System.currentTimeMillis();
            templateBioModel.setName(newBiomodelName);
            // remove all existing simulations from stored template model, and add new one
            while (templateBioModel.getNumSimulations() > 0) {
                templateBioModel.removeSimulation(templateBioModel.getSimulation(0));
            }
            MathMappingCallback callback = new MathMappingCallback() {

                @Override
                public void setProgressFraction(float fractionDone) {
                }

                @Override
                public void setMessage(String message) {
                }

                @Override
                public boolean isInterrupted() {
                    return false;
                }
            };
            templateBioModel.getSimulationContext(0).addNewSimulation("sim", callback, NetworkGenerationRequirements.ComputeFullStandardTimeout);
            BigString vcml = new BigString(XmlHelper.bioModelToXML(templateBioModel));
            String[] independentSims = new String[0];
            BigString savedBioModelVCML = vcellConnection.getUserMetaDbServer().saveBioModelAs(vcml, newBiomodelName, independentSims);
            BioModel savedBioModel = XmlHelper.XMLToBioModel(new XMLSource(savedBioModelVCML.toString()));
            savedBioModelKey = savedBioModel.getVersion().getVersionKey();
            Simulation sim = savedBioModel.getSimulation(0);
            VCSimulationIdentifier vcSimId = new VCSimulationIdentifier(sim.getKey(), sim.getVersion().getOwner());
            long eventTimestamp = System.currentTimeMillis();
            SimulationStatus simStatus = vcellConnection.getSimulationController().startSimulation(vcSimId, 1);
            simSubmitEvent(id, vcSimId);
            runningSimId = vcSimId;
            long startTime_MS = System.currentTimeMillis();
            while (simStatus.isActive()) {
                if ((System.currentTimeMillis() - startTime_MS) > SIMULATION_TIMEOUT) {
                    throw new RuntimeException("simulation took longer than " + SIMULATION_TIMEOUT + " to complete");
                }
                Thread.sleep(1000);
                MessageEvent[] messageEvents = vcellConnection.getMessageEvents();
                if (messageEvents != null) {
                    for (MessageEvent event : messageEvents) {
                        if (event instanceof SimulationJobStatusEvent) {
                            SimulationJobStatusEvent jobEvent = (SimulationJobStatusEvent) event;
                            SimulationJobStatus jobStatus = jobEvent.getJobStatus();
                            VCSimulationIdentifier eventSimId = jobStatus.getVCSimulationIdentifier();
                            if (eventSimId.getOwner().equals(userLoginInfo.getUser()) && eventSimId.getSimulationKey().equals(sim.getKey())) {
                                simStatus = SimulationStatus.updateFromJobEvent(simStatus, jobEvent);
                            }
                        }
                    }
                }
            }
            runningSimId = null;
            if (!simStatus.isCompleted()) {
                throw new RuntimeException("failed: " + simStatus.getDetails());
            }
            simSuccess(id);
        } catch (Throwable e) {
            simFailed(id, e.getMessage());
        } finally {
            // cleanup
            try {
                RemoteProxyVCellConnectionFactory vcellConnectionFactory = new RemoteProxyVCellConnectionFactory(host, port, userLoginInfo);
                VCellConnection vcellConnection = vcellConnectionFactory.createVCellConnection();
                if (runningSimId != null) {
                    try {
                        vcellConnection.getSimulationController().stopSimulation(runningSimId);
                    } catch (Exception e) {
                        e.printStackTrace(System.out);
                    }
                }
                if (savedBioModelKey != null) {
                    vcellConnection.getUserMetaDbServer().deleteBioModel(savedBioModelKey);
                }
            } catch (Exception e) {
                e.printStackTrace(System.out);
            }
        }
        try {
            Thread.sleep(SIMULATION_LOOP_SLEEP);
        } catch (InterruptedException e) {
            e.printStackTrace();
        }
    }
}