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

Example 11 with VCSimulationIdentifier

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

the class ExportMonitorPanelTest method main.

/**
 * main entrypoint - starts the part when it is run as an application
 * @param args java.lang.String[]
 */
public static void main(java.lang.String[] args) {
    try {
        JFrame frame = new javax.swing.JFrame();
        ExportMonitorPanel aExportMonitorPanel;
        aExportMonitorPanel = new ExportMonitorPanel();
        frame.setContentPane(aExportMonitorPanel);
        frame.setSize(aExportMonitorPanel.getSize());
        frame.addWindowListener(new java.awt.event.WindowAdapter() {

            public void windowClosing(java.awt.event.WindowEvent e) {
                System.exit(0);
            }
        });
        frame.show();
        java.awt.Insets insets = frame.getInsets();
        frame.setSize(frame.getWidth() + insets.left + insets.right, frame.getHeight() + insets.top + insets.bottom);
        VCSimulationDataIdentifier vcSimDataId = new VCSimulationDataIdentifier(new VCSimulationIdentifier(new KeyValue("234"), null), 1);
        aExportMonitorPanel.addExportEvent(new ExportEvent(aExportMonitorPanel, 123456789L, null, vcSimDataId.getID(), vcSimDataId.getSimulationKey(), ExportEvent.EXPORT_PROGRESS, "CSV", "", new Double(0.47), null, null), "bogus [application: model]");
        aExportMonitorPanel.addExportEvent(new ExportEvent(aExportMonitorPanel, 987654321L, null, vcSimDataId.getID(), vcSimDataId.getSimulationKey(), ExportEvent.EXPORT_COMPLETE, "GIF", "http://nrcam.uchc.edu/export/987654321.zip", new Double(1), null, null), "simulation [application: model]");
        frame.pack();
        frame.setVisible(true);
    } catch (Throwable exception) {
        System.err.println("Exception occurred in main() of javax.swing.JPanel");
        exception.printStackTrace(System.out);
    }
}

Example 12 with VCSimulationIdentifier

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

the class RunRefSimulationFastOp method runRefSimulation.

private RowColumnResultSet runRefSimulation(ROI cellROI, ROI[] imageDataROIs, UShortImage psf, FloatImage initRefConc, double experimentalRecoveryTime, LocalWorkspace localWorkspace, ClientTaskStatusSupport progressListener) throws Exception {
    User owner = LocalWorkspace.getDefaultOwner();
    KeyValue simKey = LocalWorkspace.createNewKeyValue();
    // 
    // save first image from normalized time series as the initial concentration field data
    // 
    ExternalDataInfo initialConcentrationExtData = createNewExternalDataInfo(localWorkspace, INITCONC_EXTDATA_NAME);
    Extent extent = initRefConc.getExtent();
    Origin origin = initRefConc.getOrigin();
    ISize isize = new ISize(initRefConc.getNumX(), initRefConc.getNumY(), initRefConc.getNumZ());
    saveExternalData(initRefConc, INITCONC_EXTDATA_VARNAME, initialConcentrationExtData.getExternalDataIdentifier(), localWorkspace);
    FieldFunctionArguments initConditionFFA = new FieldFunctionArguments(INITCONC_EXTDATA_NAME, INITCONC_EXTDATA_VARNAME, new Expression(0.0), VariableType.VOLUME);
    // 
    // save ROIs as a multivariate field data
    // 
    ExternalDataInfo roiExtData = createNewExternalDataInfo(localWorkspace, ROI_EXTDATA_NAME);
    saveROIsAsExternalData(imageDataROIs, localWorkspace, roiExtData.getExternalDataIdentifier());
    ArrayList<FieldFunctionArguments> roiFFAs = new ArrayList<FieldFunctionArguments>();
    for (ROI roi : imageDataROIs) {
        roiFFAs.add(new FieldFunctionArguments(ROI_EXTDATA_NAME, ROI_MASK_NAME_PREFIX + roi.getROIName(), new Expression(0.0), VariableType.VOLUME));
    }
    // 
    // save PSF as a field data
    // 
    ExternalDataInfo psfExtData = createNewExternalDataInfo(localWorkspace, PSF_EXTDATA_NAME);
    savePsfAsExternalData(psf, PSF_EXTDATA_VARNAME, psfExtData.getExternalDataIdentifier(), localWorkspace);
    FieldFunctionArguments psfFFA = new FieldFunctionArguments(PSF_EXTDATA_NAME, PSF_EXTDATA_VARNAME, new Expression(0.0), VariableType.VOLUME);
    TimeBounds timeBounds = getEstimatedRefTimeBound(experimentalRecoveryTime);
    double timeStepVal = REFERENCE_DIFF_DELTAT;
    Expression chirpedDiffusionRate = new Expression(REFERENCE_DIFF_RATE_COEFFICIENT + "*(t+" + REFERENCE_DIFF_DELTAT + ")");
    BioModel bioModel = createRefSimBioModel(simKey, owner, origin, extent, cellROI, timeStepVal, timeBounds, VAR_NAME, new Expression(initConditionFFA.infix()), psfFFA, chirpedDiffusionRate);
    if (progressListener != null) {
        progressListener.setMessage("Running Reference Simulation...");
    }
    // run simulation
    Simulation simulation = bioModel.getSimulation(0);
    ROIDataGenerator roiDataGenerator = getROIDataGenerator(localWorkspace, imageDataROIs);
    simulation.getMathDescription().getPostProcessingBlock().addDataGenerator(roiDataGenerator);
    runFVSolverStandalone(new File(localWorkspace.getDefaultSimDataDirectory()), simulation, initialConcentrationExtData.getExternalDataIdentifier(), roiExtData.getExternalDataIdentifier(), psfExtData.getExternalDataIdentifier(), progressListener, true);
    KeyValue referenceSimKeyValue = simulation.getVersion().getVersionKey();
    VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(referenceSimKeyValue, LocalWorkspace.getDefaultOwner());
    VCSimulationDataIdentifier vcSimDataID = new VCSimulationDataIdentifier(vcSimID, 0);
    File hdf5File = new File(localWorkspace.getDefaultSimDataDirectory(), vcSimDataID.getID() + SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_HDF5);
    // get post processing info (time points, variable sizes)
    DataOperation.DataProcessingOutputInfoOP dataOperationInfo = new DataOperation.DataProcessingOutputInfoOP(null, /*no vcDataIdentifier OK*/
    false, null);
    DataOperationResults.DataProcessingOutputInfo dataProcessingOutputInfo = (DataOperationResults.DataProcessingOutputInfo) DataSetControllerImpl.getDataProcessingOutput(dataOperationInfo, hdf5File);
    // get post processing data
    DataOperation.DataProcessingOutputDataValuesOP dataOperationDataValues = new DataOperation.DataProcessingOutputDataValuesOP(null, /*no vcDataIdentifier OK*/
    ROI_EXTDATA_NAME, TimePointHelper.createAllTimeTimePointHelper(), DataIndexHelper.createSliceDataIndexHelper(0), null, null);
    DataOperationResults.DataProcessingOutputDataValues dataProcessingOutputDataValues = (DataOperationResults.DataProcessingOutputDataValues) DataSetControllerImpl.getDataProcessingOutput(dataOperationDataValues, hdf5File);
    // 
    // delete the simulation files
    // 
    // 
    // remove reference simulation files and field data files
    // 
    File userDir = new File(localWorkspace.getDefaultSimDataDirectory());
    File[] oldSimFilesToDelete = getSimulationFileNames(userDir, referenceSimKeyValue);
    for (int i = 0; oldSimFilesToDelete != null && i < oldSimFilesToDelete.length; i++) {
        oldSimFilesToDelete[i].delete();
    }
    deleteCanonicalExternalData(localWorkspace, initialConcentrationExtData.getExternalDataIdentifier());
    deleteCanonicalExternalData(localWorkspace, roiExtData.getExternalDataIdentifier());
    deleteCanonicalExternalData(localWorkspace, roiExtData.getExternalDataIdentifier());
    // get ref sim time points (distorted by time dilation acceleration)
    double[] rawRefDataTimePoints = dataProcessingOutputInfo.getVariableTimePoints();
    // get shifted time points
    double[] correctedRefDataTimePoints = shiftTimeForBaseDiffRate(rawRefDataTimePoints);
    double[][] refData = dataProcessingOutputDataValues.getDataValues();
    // 
    // for rowColumnResultSet with { "t", "roi1", .... , "roiN" } for reference data
    // 
    int numROIs = imageDataROIs.length;
    String[] columnNames = new String[numROIs + 1];
    columnNames[0] = "t";
    for (int i = 0; i < numROIs; i++) {
        columnNames[i + 1] = imageDataROIs[i].getROIName();
    }
    RowColumnResultSet reducedData = new RowColumnResultSet(columnNames);
    for (int i = 0; i < correctedRefDataTimePoints.length; i++) {
        double[] row = new double[numROIs + 1];
        row[0] = correctedRefDataTimePoints[i];
        double[] roiData = refData[i];
        for (int j = 0; j < numROIs; j++) {
            // roiData[0] is the average over the cell .. postbleach this shouldn't change for pure diffusion
            row[j + 1] = roiData[j + 1];
        }
        reducedData.addRow(row);
    }
    return reducedData;
}

Example 13 with VCSimulationIdentifier

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

the class RunSimulation2DOp method runRefSimulation.

public ImageTimeSeries<FloatImage> runRefSimulation(LocalWorkspace localWorkspace, Simulation simulation, String varName, ClientTaskStatusSupport progressListener) throws Exception {
    User owner = LocalWorkspace.getDefaultOwner();
    KeyValue simKey = LocalWorkspace.createNewKeyValue();
    runFVSolverStandalone(new File(localWorkspace.getDefaultSimDataDirectory()), simulation, progressListener);
    Extent extent = simulation.getMathDescription().getGeometry().getExtent();
    Origin origin = simulation.getMathDescription().getGeometry().getOrigin();
    VCDataIdentifier vcDataIdentifier = new VCSimulationDataIdentifier(new VCSimulationIdentifier(simKey, owner), 0);
    CartesianMesh mesh = localWorkspace.getDataSetControllerImpl().getMesh(vcDataIdentifier);
    ISize isize = new ISize(mesh.getSizeX(), mesh.getSizeY(), mesh.getSizeZ());
    double[] dataTimes = localWorkspace.getDataSetControllerImpl().getDataSetTimes(vcDataIdentifier);
    FloatImage[] solutionImages = new FloatImage[dataTimes.length];
    for (int i = 0; i < dataTimes.length; i++) {
        SimDataBlock simDataBlock = localWorkspace.getDataSetControllerImpl().getSimDataBlock(null, vcDataIdentifier, varName, dataTimes[i]);
        double[] doubleData = simDataBlock.getData();
        float[] floatPixels = new float[doubleData.length];
        for (int j = 0; j < doubleData.length; j++) {
            floatPixels[j] = (float) doubleData[j];
        }
        solutionImages[i] = new FloatImage(floatPixels, origin, extent, isize.getX(), isize.getY(), isize.getZ());
    }
    ImageTimeSeries<FloatImage> solution = new ImageTimeSeries<FloatImage>(FloatImage.class, solutionImages, dataTimes, 1);
    return solution;
}

Example 14 with VCSimulationIdentifier

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

the class RunRefSimulationOp method runRefSimulation.

private static ImageTimeSeries<FloatImage> runRefSimulation(LocalWorkspace localWorkspace, ROI cellROI, double timeStepVal, TimeBounds timeBounds, FloatImage initRefConc, double baseDiffusionRate, ClientTaskStatusSupport progressListener) throws Exception {
    String INITCONC_EXTDATA_NAME = "initConc";
    String INITCONC_EXTDATA_VARNAME = "conc";
    String VAR_NAME = "species";
    User owner = LocalWorkspace.getDefaultOwner();
    KeyValue simKey = LocalWorkspace.createNewKeyValue();
    ExternalDataInfo initialConcentrationExtData = createNewExternalDataInfo(localWorkspace, INITCONC_EXTDATA_NAME);
    Extent extent = initRefConc.getExtent();
    Origin origin = initRefConc.getOrigin();
    ISize isize = new ISize(initRefConc.getNumX(), initRefConc.getNumY(), initRefConc.getNumZ());
    saveExternalData(initRefConc, INITCONC_EXTDATA_VARNAME, initialConcentrationExtData.getExternalDataIdentifier(), localWorkspace);
    FieldFunctionArguments initConditionFFA = new FieldFunctionArguments(INITCONC_EXTDATA_NAME, INITCONC_EXTDATA_VARNAME, new Expression(0.0), VariableType.VOLUME);
    BioModel bioModel = createRefSimBioModel(simKey, owner, origin, extent, cellROI, timeStepVal, timeBounds, VAR_NAME, new Expression(initConditionFFA.infix()), baseDiffusionRate);
    if (progressListener != null) {
        progressListener.setMessage("Running Reference Simulation...");
    }
    // run simulation
    runFVSolverStandalone(new File(localWorkspace.getDefaultSimDataDirectory()), bioModel.getSimulation(0), initialConcentrationExtData.getExternalDataIdentifier(), progressListener, true);
    VCDataIdentifier vcDataIdentifier = new VCSimulationDataIdentifier(new VCSimulationIdentifier(simKey, owner), 0);
    double[] dataTimes = localWorkspace.getDataSetControllerImpl().getDataSetTimes(vcDataIdentifier);
    FloatImage[] solutionImages = new FloatImage[dataTimes.length];
    for (int i = 0; i < dataTimes.length; i++) {
        SimDataBlock simDataBlock = localWorkspace.getDataSetControllerImpl().getSimDataBlock(null, vcDataIdentifier, VAR_NAME, dataTimes[i]);
        double[] doubleData = simDataBlock.getData();
        float[] floatPixels = new float[doubleData.length];
        for (int j = 0; j < doubleData.length; j++) {
            floatPixels[j] = (float) doubleData[j];
        }
        solutionImages[i] = new FloatImage(floatPixels, origin, extent, isize.getX(), isize.getY(), isize.getZ());
    }
    ImageTimeSeries<FloatImage> solution = new ImageTimeSeries<FloatImage>(FloatImage.class, solutionImages, dataTimes, 1);
    return solution;
}

Example 15 with VCSimulationIdentifier

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

the class NagiosVCellMonitor method checkVCell.

private CheckResults checkVCell(VCELL_CHECK_LEVEL checkLevel, String rmiHostName, int rmiPort, String rmiBootstrapStubName, String vcellNagiosPassword, int criticalTimeout, int monitorPort) throws Exception {
    SimulationStatusPersistent lastSimStatus = null;
    String vcellVersion = null;
    TreeMap<VCELL_CHECK_LEVEL, Long> levelTimesMillisec = new TreeMap<NagiosVCellMonitor.VCELL_CHECK_LEVEL, Long>();
    long startTime = System.currentTimeMillis();
    VCellConnection vcellConnection = null;
    try {
        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());
        }
        vcellVersion = vcellBootstrap.getVCellSoftwareVersion();
        levelTimesMillisec.put(VCELL_CHECK_LEVEL.RMI_ONLY_0, System.currentTimeMillis() - startTime);
        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");
            }
            UserLoginInfo userLoginInfo = new UserLoginInfo(VCELL_NAGIOS_USER, new DigestedPassword(vcellNagiosPassword));
            vcellConnection = vcellBootstrap.getVCellConnection(userLoginInfo);
            levelTimesMillisec.put(VCELL_CHECK_LEVEL.CONNECT_1, System.currentTimeMillis() - startTime - levelTimesMillisec.get(VCELL_CHECK_LEVEL.RMI_ONLY_0));
            if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.INFOS_2.ordinal()) {
                VCInfoContainer vcInfoContainer = vcellConnection.getUserMetaDbServer().getVCInfoContainer();
                levelTimesMillisec.put(VCELL_CHECK_LEVEL.INFOS_2, System.currentTimeMillis() - startTime - levelTimesMillisec.get(VCELL_CHECK_LEVEL.CONNECT_1));
                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 (userLoginInfo.getUserName().equals(bioModelInfo.getVersion().getOwner().getName()) && 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();
                    levelTimesMillisec.put(VCELL_CHECK_LEVEL.LOAD_3, System.currentTimeMillis() - startTime - levelTimesMillisec.get(VCELL_CHECK_LEVEL.INFOS_2));
                    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);
                        levelTimesMillisec.put(VCELL_CHECK_LEVEL.DATA_4, System.currentTimeMillis() - startTime - levelTimesMillisec.get(VCELL_CHECK_LEVEL.LOAD_3));
                        if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.RUN_5.ordinal()) {
                            KeyValue copy1Key = null;
                            KeyValue copy2Key = null;
                            VCSimulationIdentifier testRunSimID = 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 + "_rmi" + rmiPort + "_siteprt" + monitorPort;
                                boolean bForceCleanup = true;
                                while (true) {
                                    boolean bMessy = false;
                                    for (BioModelInfo bioModelInfo : vcInfoContainer.getBioModelInfos()) {
                                        if (userLoginInfo.getUserName().equals(bioModelInfo.getVersion().getOwner().getName()) && bioModelInfo.getVersion().getName().equals(copyModelName)) {
                                            bMessy = true;
                                            if (bForceCleanup) {
                                                try {
                                                    vcellConnection.getUserMetaDbServer().deleteBioModel(bioModelInfo.getVersion().getVersionKey());
                                                } catch (Exception e) {
                                                    e.printStackTrace();
                                                }
                                            } else {
                                                throw new MessyTestEnvironmentException("Messy test environment, not expecting " + copyModelName + " and couldn't cleanup");
                                            }
                                        }
                                    }
                                    if (!bMessy) {
                                        break;
                                    }
                                    // get new vcInfoContainer without cleaned-up model
                                    vcInfoContainer = vcellConnection.getUserMetaDbServer().getVCInfoContainer();
                                    bForceCleanup = false;
                                }
                                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());
                                }
                                testRunSimID = new VCSimulationIdentifier(newSimulation.getVersion().getVersionKey(), copyBioModel.getVersion().getOwner());
                                vcellConnection.getSimulationController().startSimulation(testRunSimID, 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(testRunSimID);
                                        vcellConnection.getMessageEvents();
                                        break;
                                    }
                                    simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(newSimulation.getVersion().getVersionKey());
                                    if (simulationStatus != null && !simulationStatus.toString().equals((lastSimStatus == null ? null : lastSimStatus.toString()))) {
                                        lastSimStatus = simulationStatus;
                                    }
                                    if (simulationStatus != null && simulationStatus.isFailed()) {
                                        throw new Exception("time " + ((System.currentTimeMillis() - startTime) / 1000) + ", Sim execution failed key:" + testRunSimID.getSimulationKey() + " sim " + newSimulation.getName() + " model " + copyBioModel.getVersion().getName() + " messg " + simulationStatus.getFailedMessage());
                                    }
                                    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();
                                }
                                if (testRunSimID != null) {
                                    deleteSimData(testRunSimID);
                                }
                            }
                            levelTimesMillisec.put(VCELL_CHECK_LEVEL.RUN_5, System.currentTimeMillis() - startTime - levelTimesMillisec.get(VCELL_CHECK_LEVEL.DATA_4));
                        }
                    }
                }
            }
        }
        return new CheckResults(vcellVersion, levelTimesMillisec, lastSimStatus, System.currentTimeMillis() - startTime, null);
    } catch (Exception e) {
        return new CheckResults(vcellVersion, levelTimesMillisec, lastSimStatus, System.currentTimeMillis() - startTime, e);
    } finally {
        vcellConnection = null;
    }
}