Examples with ODESimData cbit.vcell.solver.ode.ODESimData used on opensource projects

Example 11 with ODESimData

use of cbit.vcell.solver.ode.ODESimData in project vcell by virtualcell.

the class SimulationData method getDataTimes.

/**
 * This method was created in VisualAge.
 * @return double[]
 */
public synchronized double[] getDataTimes() throws DataAccessException {
    if (getIsODEData()) {
        // for ODE's we need to rebuild
        try {
            ODESimData odeSimData = null;
            if (odeIdentifier.equals(ODE_DATA_IDENTIFIER)) {
                odeSimData = ODESimData.readODEDataFile(getODEDataFile());
            } else if (odeIdentifier.equals(IDA_DATA_IDENTIFIER)) {
                odeSimData = ODESimData.readIDADataFile(vcDataId, getODEDataFile(), odeKeepMost, getJobFunctionsFile());
            } else if (odeIdentifier.equals(NETCDF_DATA_IDENTIFIER)) {
                odeSimData = ODESimData.readNCDataFile(vcDataId, getODEDataFile(), getJobFunctionsFile());
            } else {
                throw new DataAccessException("Unexpected data format:" + odeIdentifier);
            }
            if (odeSimData == null) {
                return null;
            }
            int timeIndex = odeSimData.findColumn("t");
            if (timeIndex < 0) {
                // ok, time probably doesn't exist like for a histogram dataset ... just use first index.
                timeIndex = 0;
                LG.warn("cannot find time ('t') column in ODESimData, assuming first column holds the independent variable (maybe not time)");
            }
            dataTimes = odeSimData.extractColumn(timeIndex);
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
            throw new DataAccessException("error getting dataset times: " + e.getMessage());
        } catch (FileNotFoundException e) {
            e.printStackTrace();
            throw new DataAccessException("error getting dataset times: " + e.getMessage());
        }
    }
    return dataTimes;
}

Example 12 with ODESimData

use of cbit.vcell.solver.ode.ODESimData 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();
}