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

Example 6 with VCellBootstrap

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

the class TestMissingSimData method runSim.

private static void runSim(SimIDAndJobID simIDAndJobID) throws Exception {
    if (notCompletedSimIDs.contains(simIDAndJobID.simID.toString())) {
        // System.out.println("--skipping notCompleted");
        return;
    } else if (completedSimIDs.contains(simIDAndJobID.simID.toString())) {
        System.out.println("-----unexpected sim rerun already completed once");
        return;
    }
    VCSimulationIdentifier vcSimulationIdentifier = new VCSimulationIdentifier(simIDAndJobID.simID, simIDAndJobID.user);
    UserLoginInfo userLoginInfo = new UserLoginInfo(simIDAndJobID.user.getName(), new DigestedPassword("xoxoxox"));
    // getVcellClient().getClientServerManager().getConnectionStatus()
    VCellConnection vcellConnection = userConnections.get(simIDAndJobID.user);
    try {
        if (vcellConnection != null) {
            vcellConnection.getMessageEvents();
        }
    } catch (Exception e) {
        e.printStackTrace();
        // assume disconnected
        vcellConnection = null;
    }
    if (vcellConnection == null) {
        VCellBootstrap vCellBootstrap = getVCellBootstrap("rmi-alpha.cam.uchc.edu", 40106, "VCellBootstrapServer", 12, false);
        vcellConnection = vCellBootstrap.getVCellConnection(userLoginInfo);
        userConnections.put(simIDAndJobID.user, vcellConnection);
    }
    SimulationStatusPersistent finalSimStatus = null;
    try {
        SimulationStatusPersistent simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(vcSimulationIdentifier.getSimulationKey());
        System.out.println("initial status=" + simulationStatus);
        BigString simXML = vcellConnection.getUserMetaDbServer().getSimulationXML(vcSimulationIdentifier.getSimulationKey());
        Simulation sim = XmlHelper.XMLToSim(simXML.toString());
        SolverDescription solverDescription = sim.getSolverTaskDescription().getSolverDescription();
        if (solverDescription.equals(SolverDescription.StochGibson) || solverDescription.equals(SolverDescription.FiniteVolume)) {
            // These 2 solvers give too much trouble so skip
            System.out.println("--skipping solver");
            // notCompletedSimIDs.add(simIDAndJobID.simID.toString());
            return;
        }
        int scanCount = sim.getScanCount();
        vcellConnection.getSimulationController().startSimulation(vcSimulationIdentifier, scanCount);
        long startTime = System.currentTimeMillis();
        while (simulationStatus.isStopped() || simulationStatus.isCompleted() || simulationStatus.isFailed()) {
            Thread.sleep(250);
            simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(vcSimulationIdentifier.getSimulationKey());
            MessageEvent[] messageEvents = vcellConnection.getMessageEvents();
            if ((System.currentTimeMillis() - startTime) > 60000) {
                System.out.println("-----Sim finished too fast or took too long to start");
                return;
            }
        // System.out.println(simulationStatus);
        }
        SimulationStatusPersistent lastSimStatus = simulationStatus;
        while (!simulationStatus.isStopped() && !simulationStatus.isCompleted() && !simulationStatus.isFailed()) {
            Thread.sleep(3000);
            simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(vcSimulationIdentifier.getSimulationKey());
            if (!simulationStatus.toString().equals(lastSimStatus.toString())) {
                lastSimStatus = simulationStatus;
                System.out.println("running status=" + simulationStatus);
            }
            // System.out.println(simulationStatus);
            MessageEvent[] messageEvents = vcellConnection.getMessageEvents();
        // for (int i = 0; messageEvents != null && i < messageEvents.length; i++) {
        // System.out.println(messageEvents[i]);
        // }
        }
        finalSimStatus = simulationStatus;
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
        return;
    } finally {
        System.out.println("final status=" + finalSimStatus + "\n");
        if (finalSimStatus == null || !finalSimStatus.isCompleted()) {
            notCompletedSimIDs.add(simIDAndJobID.simID.toString());
        } else {
            completedSimIDs.add(simIDAndJobID.simID.toString());
        }
    }
}

Example 7 with VCellBootstrap

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

the class NagiosVCellCheck method checkVCell.

private static String checkVCell(VCELL_CHECK_LEVEL checkLevel, String rmiHostName, int rmiPort, String rmiBootstrapStubName, String vcellNagiosPassword, int warningTimeout, int criticalTimeout) throws Exception {
    long startTime = System.currentTimeMillis();
    SimulationStatusPersistent lastSimStatus = null;
    if (rmiHostName == null || rmiPort == -1) {
        throw new UnexpectedTestStateException("Host name/ip and rmiPort required for testing, rmihostname=" + rmiHostName + " rmiport=" + rmiPort);
    }
    String rmiUrl = "//" + rmiHostName + ":" + rmiPort + "/" + rmiBootstrapStubName;
    VCellBootstrap vcellBootstrap = null;
    try {
        vcellBootstrap = (VCellBootstrap) Naming.lookup(rmiUrl);
    } catch (Exception e) {
        throw new UnexpectedTestStateException("Error during bootstrap lookup, " + e.getClass().getSimpleName() + " " + e.getMessage());
    }
    if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.CONNECT_1.ordinal()) {
        if (vcellNagiosPassword == null) {
            throw new UnexpectedTestStateException("vcellNagios Password required for " + VCELL_CHECK_LEVEL.CONNECT_1.toString() + " and above");
        }
        VCellConnection vcellConnection = vcellBootstrap.getVCellConnection(new UserLoginInfo("vcellNagios", new DigestedPassword(vcellNagiosPassword)));
        if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.INFOS_2.ordinal()) {
            VCInfoContainer vcInfoContainer = vcellConnection.getUserMetaDbServer().getVCInfoContainer();
            if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.LOAD_3.ordinal()) {
                KeyValue bioModelKey = null;
                final String testModelName = "Solver Suite 5.1 (BETA only ode)";
                for (BioModelInfo bioModelInfo : vcInfoContainer.getBioModelInfos()) {
                    if (bioModelInfo.getVersion().getName().equals(testModelName)) {
                        bioModelKey = bioModelInfo.getVersion().getVersionKey();
                        break;
                    }
                }
                BigString bioModelXML = vcellConnection.getUserMetaDbServer().getBioModelXML(bioModelKey);
                BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
                bioModel.refreshDependencies();
                if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.DATA_4.ordinal()) {
                    final String testSimContextName = "non-spatial ODE";
                    SimulationContext simulationContext = bioModel.getSimulationContext(testSimContextName);
                    final String testSimName = "Copy of combined ida/cvode";
                    Simulation simulation = simulationContext.getSimulation(testSimName);
                    if (simulation == null) {
                        throw new UnexpectedTestStateException("Couldn't find sim '" + testSimName + "' for " + checkLevel.toString());
                    }
                    VCSimulationDataIdentifier vcSimulationDataIdentifier = new VCSimulationDataIdentifier(simulation.getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), 0);
                    ArrayList<AnnotatedFunction> outputFunctionsList = simulationContext.getOutputFunctionContext().getOutputFunctionsList();
                    OutputContext outputContext = new OutputContext(outputFunctionsList.toArray(new AnnotatedFunction[outputFunctionsList.size()]));
                    double[] times = vcellConnection.getDataSetController().getDataSetTimes(vcSimulationDataIdentifier);
                    ODESimData odeSimData = vcellConnection.getDataSetController().getODEData(vcSimulationDataIdentifier);
                    // SimDataBlock simDataBlock = vcellConnection.getDataSetController().getSimDataBlock(outputContext, vcSimulationDataIdentifier, "RanC_cyt",times[times.length-1]);
                    if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.RUN_5.ordinal()) {
                        KeyValue copy1Key = null;
                        KeyValue copy2Key = null;
                        try {
                            if (simulationContext.getSimulations().length != 1) {
                                throw new UnexpectedTestStateException("Expecting only 1 sim to be copied for " + checkLevel.toString());
                            }
                            SimulationStatusPersistent simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(simulation.getVersion().getVersionKey());
                            if (!simulationStatus.isCompleted()) {
                                throw new UnexpectedTestStateException("Expecting completed sim to copy for " + checkLevel.toString());
                            }
                            String copyModelName = testModelName + "_" + rmiHostName + "_" + rmiPort;
                            for (BioModelInfo bioModelInfo : vcInfoContainer.getBioModelInfos()) {
                                if (bioModelInfo.getVersion().getName().equals(copyModelName)) {
                                    throw new UnexpectedTestStateException("Messy test environment, not expecting " + copyModelName + " to exist at this point");
                                }
                            }
                            BigString copyBioModelXMLStr = vcellConnection.getUserMetaDbServer().saveBioModelAs(bioModelXML, copyModelName, null);
                            BioModel copyBioModel = XmlHelper.XMLToBioModel(new XMLSource(copyBioModelXMLStr.toString()));
                            copy1Key = copyBioModel.getVersion().getVersionKey();
                            copyBioModel.refreshDependencies();
                            Simulation copySim = copyBioModel.getSimulationContext(testSimContextName).copySimulation(copyBioModel.getSimulationContext(testSimContextName).getSimulation(testSimName));
                            final String copyTestSimName = "test";
                            copySim.setName(copyTestSimName);
                            copyBioModel.refreshDependencies();
                            copyBioModelXMLStr = new BigString(XmlHelper.bioModelToXML(copyBioModel));
                            copyBioModelXMLStr = vcellConnection.getUserMetaDbServer().saveBioModel(copyBioModelXMLStr, null);
                            copyBioModel = XmlHelper.XMLToBioModel(new XMLSource(copyBioModelXMLStr.toString()));
                            copy2Key = copyBioModel.getVersion().getVersionKey();
                            copyBioModel.refreshDependencies();
                            Simulation newSimulation = copyBioModel.getSimulationContext(testSimContextName).getSimulation(copyTestSimName);
                            simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(newSimulation.getVersion().getVersionKey());
                            if (simulationStatus != null && !simulationStatus.isNeverRan()) {
                                throw new UnexpectedTestStateException("Expecting new sim to have 'never ran' status for " + checkLevel.toString());
                            }
                            VCSimulationIdentifier newSimID = new VCSimulationIdentifier(newSimulation.getVersion().getVersionKey(), copyBioModel.getVersion().getOwner());
                            vcellConnection.getSimulationController().startSimulation(newSimID, 1);
                            lastSimStatus = simulationStatus;
                            MessageEvent[] messageEvents = null;
                            while (simulationStatus == null || (!simulationStatus.isStopped() && !simulationStatus.isCompleted() && !simulationStatus.isFailed())) {
                                Thread.sleep(200);
                                if (((System.currentTimeMillis() - startTime) / 1000) > criticalTimeout) {
                                    vcellConnection.getSimulationController().stopSimulation(newSimID);
                                    vcellConnection.getMessageEvents();
                                    break;
                                }
                                simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(newSimulation.getVersion().getVersionKey());
                                if (simulationStatus != null && !simulationStatus.toString().equals((lastSimStatus == null ? null : lastSimStatus.toString()))) {
                                    lastSimStatus = simulationStatus;
                                }
                                messageEvents = vcellConnection.getMessageEvents();
                            }
                        } finally {
                            try {
                                if (copy1Key != null) {
                                    vcellConnection.getUserMetaDbServer().deleteBioModel(copy1Key);
                                }
                            } catch (Exception e) {
                                e.printStackTrace();
                            }
                            try {
                                if (copy2Key != null) {
                                    vcellConnection.getUserMetaDbServer().deleteBioModel(copy2Key);
                                }
                            } catch (Exception e) {
                                e.printStackTrace();
                            }
                        }
                    }
                }
            }
        }
    }
    long endTime = System.currentTimeMillis();
    if (criticalTimeout != -1 && ((endTime - startTime) / 1000) > criticalTimeout) {
        throw new Exception(checkLevel.toString() + " test exceeded criticalTimeout=" + criticalTimeout + " seconds lastSimStatus=" + lastSimStatus);
    }
    if (warningTimeout != -1 && ((endTime - startTime) / 1000) > warningTimeout) {
        throw new WarningTestConditionException(checkLevel.toString() + " test exceeded warningTimeout=" + warningTimeout + " seconds lastSimStatus=" + lastSimStatus);
    }
    return vcellBootstrap.getVCellSoftwareVersion();
}