Examples with BigString org.vcell.util.BigString used on opensource projects

Example 51 with BigString

use of org.vcell.util.BigString in project vcell by virtualcell.

the class VCComprehensiveStatistics method collectBioModelStats.

private void collectBioModelStats(long startDateInMs, long endDateInMs) throws DataAccessException {
    retrieveUsers();
    for (User user : userList) {
        if (!userConstraintList.contains(user.getName())) {
            continue;
        }
        if (!internalDeveloper.contains(user.getName())) {
            boolean bInternal = internalUsers.contains(user.getName());
            ModelStat modelStat = bioModelStats[bInternal ? 0 : 1];
            BioModelInfo[] bioModelInfos = dbServerImpl.getBioModelInfos(user, false);
            for (BioModelInfo bmi : bioModelInfos) {
                Date createDate = bmi.getVersion().getDate();
                long t = createDate.getTime();
                // }
                if (t < startDateInMs || t > endDateInMs) {
                    continue;
                }
                // modelStat.count_model ++;
                try {
                    BigString bioModelXML = dbServerImpl.getBioModelXML(user, bmi.getVersion().getVersionKey());
                    BioModel bioModel = (BioModel) waitForModel(bioModelXML, false);
                    if (bioModel == null) {
                        System.out.println("----------          Skipped BioModel " + bmi.getVersion() + "          ----------");
                        continue;
                    }
                    modelStat.count_model++;
                    for (SimulationContext simContext : bioModel.getSimulationContexts()) {
                        modelStat.count_geoDimApplications[simContext.getGeometry().getDimension()]++;
                        if (simContext.isStoch()) {
                            modelStat.count_app_stochastic++;
                        } else {
                            modelStat.count_app_deterministic++;
                        }
                    }
                    boolean bHasCompletedSim = false;
                    for (Simulation sim : bioModel.getSimulations()) {
                        SimulationStatusPersistent ss = dbServerImpl.getSimulationStatus(sim.getKey());
                        if (ss != null) {
                            for (int scan = 0; scan < sim.getScanCount(); scan++) {
                                SimulationJobStatusPersistent jobStatus = ss.getJobStatus(scan);
                                if (jobStatus != null) {
                                    if (jobStatus.getSchedulerStatus() == SchedulerStatus.COMPLETED) {
                                        bHasCompletedSim = true;
                                        long elapsed = jobStatus.getEndDate().getTime() - jobStatus.getStartDate().getTime();
                                        if (elapsed < 2 * MINUTE_IN_MS) {
                                            modelStat.runningTimeHistogram[0]++;
                                        } else if (elapsed < 5 * MINUTE_IN_MS) {
                                            modelStat.runningTimeHistogram[1]++;
                                        } else if (elapsed < 20 * MINUTE_IN_MS) {
                                            modelStat.runningTimeHistogram[2]++;
                                        } else if (elapsed < HOUR_IN_MS) {
                                            modelStat.runningTimeHistogram[3]++;
                                        } else if (elapsed < DAY_IN_MS) {
                                            modelStat.runningTimeHistogram[4]++;
                                        } else {
                                            modelStat.runningTimeHistogram[5]++;
                                        }
                                    }
                                    int dimension = sim.getMathDescription().getGeometry().getDimension();
                                    modelStat.count_geoDimSim[dimension]++;
                                    if (sim.getMathDescription().isNonSpatialStoch() || sim.getMathDescription().isSpatialStoch()) {
                                        modelStat.count_sim_stochastic++;
                                    } else {
                                        modelStat.count_sim_deterministic++;
                                    }
                                    if (dimension > 0) {
                                        if (sim.getSolverTaskDescription().getSolverDescription().isSemiImplicitPdeSolver()) {
                                            modelStat.count_semiSim++;
                                        } else {
                                            modelStat.count_fullySim++;
                                        }
                                    }
                                }
                            }
                        }
                    }
                    if (bHasCompletedSim) {
                        modelStat.count_model_simcomplete++;
                    }
                } catch (Exception e2) {
                    e2.printStackTrace(System.out);
                }
            }
        }
    }
    itemCount++;
    statOutputPW.println(itemCount + ". BioModel Statistics ");
    statOutputPW.println("====================================================");
    for (ModelStat modelStat : bioModelStats) {
        statOutputPW.println("\t" + modelStat.title);
        statOutputPW.println("========================================");
        statOutputPW.println("number of biomodels saved :\t" + modelStat.count_model);
        statOutputPW.println("number of biomodels that has at least 1 completed simulation :\t" + modelStat.count_model_simcomplete);
        statOutputPW.println();
        statOutputPW.println("Application statistics :");
        statOutputPW.println("number of application ODE :\t" + modelStat.count_geoDimApplications[0]);
        statOutputPW.println("number of application 1D :\t" + modelStat.count_geoDimApplications[1]);
        statOutputPW.println("number of application 2D :\t" + modelStat.count_geoDimApplications[2]);
        statOutputPW.println("number of application 3D :\t" + modelStat.count_geoDimApplications[3]);
        statOutputPW.println("number of application stochastic :\t" + modelStat.count_app_stochastic);
        statOutputPW.println("number of application deterministic :\t" + modelStat.count_app_deterministic);
        statOutputPW.println();
        statOutputPW.println("Simulation statistics (including all simulations (stopped, failed, completed) :");
        statOutputPW.println("number of run simulation ODE :\t" + modelStat.count_geoDimSim[0]);
        statOutputPW.println("number of run simulation 1D :\t" + modelStat.count_geoDimSim[1]);
        statOutputPW.println("number of run simulation 2D :\t" + modelStat.count_geoDimSim[2]);
        statOutputPW.println("number of run simulation 3D :\t" + modelStat.count_geoDimSim[3]);
        statOutputPW.println("number of run simulation Semi-Implicit :\t" + modelStat.count_semiSim);
        statOutputPW.println("number of run simulation Fully-Implicit :\t" + modelStat.count_fullySim);
        statOutputPW.println("number of run simulation stochastic :\t" + modelStat.count_sim_stochastic);
        statOutputPW.println("number of run simulation deterministic :\t" + modelStat.count_sim_deterministic);
        statOutputPW.println();
        statOutputPW.println("Running time histogram for completed simulations only:");
        statOutputPW.println("0 ~ 2min:\t" + modelStat.runningTimeHistogram[0]);
        statOutputPW.println("2 ~ 5min:\t" + modelStat.runningTimeHistogram[1]);
        statOutputPW.println("5 ~ 20min:\t" + modelStat.runningTimeHistogram[2]);
        statOutputPW.println("20min ~ 1hr:\t" + modelStat.runningTimeHistogram[3]);
        statOutputPW.println("1hr ~ 1day:\t" + modelStat.runningTimeHistogram[4]);
        statOutputPW.println(">1day:\t" + modelStat.runningTimeHistogram[5]);
        statOutputPW.println();
        statOutputPW.println();
        statOutputPW.flush();
    }
}

Example 52 with BigString

use of org.vcell.util.BigString in project vcell by virtualcell.

the class VCDatabaseScanner method scanBioModels.

/**
 * Insert the method's description here.
 * Creation date: (2/2/01 3:40:29 PM)
 * @throws DataAccessException
 * @throws XmlParseException
 */
public void scanBioModels(VCDatabaseVisitor databaseVisitor, PrintStream logFilePrintStream, User[] users, KeyValue singleModelKey, HashSet<KeyValue> includeHash, HashSet<KeyValue> excludeHash, boolean bAbortOnDataAccessException) throws DataAccessException, XmlParseException {
    if (users == null) {
        users = getAllUsers();
    }
    try {
        // start visiting models and writing log
        logFilePrintStream.println("Start scanning bio-models......");
        logFilePrintStream.println("\n");
        // adapter for verifyMathDescriptionsUnchanged
        PrintWriter logFilePrintWriter = new PrintWriter(logFilePrintStream);
        for (int i = 0; i < users.length; i++) {
            User user = users[i];
            BioModelInfo[] bioModelInfos = dbServerImpl.getBioModelInfos(user, false);
            for (int j = 0; j < bioModelInfos.length; j++) {
                if (singleModelKey != null && !bioModelInfos[j].getVersion().getVersionKey().compareEqual(singleModelKey)) {
                    System.out.println("skipping biomodel, not the single one that we wanted");
                    continue;
                }
                if (excludeHash != null && excludeHash.contains(bioModelInfos[j].getVersion().getVersionKey())) {
                    System.out.println("skipping bioModel with key '" + bioModelInfos[j].getVersion().getVersionKey() + "'");
                    continue;
                }
                if (includeHash != null && !includeHash.contains(bioModelInfos[j].getVersion().getVersionKey())) {
                    System.out.println("not including bioModel with key '" + bioModelInfos[j].getVersion().getVersionKey() + "'");
                    continue;
                }
                if (!databaseVisitor.filterBioModel(bioModelInfos[j])) {
                    continue;
                }
                try {
                    BigString bioModelXML = dbServerImpl.getBioModelXML(user, bioModelInfos[j].getVersion().getVersionKey());
                    BioModel bioModel = cbit.vcell.xml.XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
                    bioModel.refreshDependencies();
                    // + bioModelInfos[j].getVersion().getName() + " -----> ");
                    logFilePrintStream.println("---- " + (j + 1) + " ----> " + bioModel.getName());
                    databaseVisitor.visitBioModel(bioModel, logFilePrintStream);
                // verifyMathDescriptionsUnchanged(bioModel, logFilePrintWriter);
                } catch (Exception e2) {
                    lg.error(e2.getMessage(), e2);
                    logFilePrintStream.println("======= " + e2.getMessage());
                    if (bAbortOnDataAccessException) {
                        throw e2;
                    }
                }
            }
        }
        logFilePrintStream.close();
    } catch (Exception e) {
        e.printStackTrace();
        System.err.println("error writing to log file.");
    }
}

Example 53 with BigString

use of org.vcell.util.BigString in project vcell by virtualcell.

the class VCDatabaseScanner method multiScanBioModels.

/**
 * Insert the method's description here.
 * Creation date: (2/2/01 3:40:29 PM)
 * @throws DataAccessException
 * @throws XmlParseException
 */
public void multiScanBioModels(VCMultiBioVisitor databaseVisitor, Writer writer, User[] users, boolean bAbortOnDataAccessException) throws DataAccessException, XmlParseException {
    assert users != null;
    try {
        PrintWriter printWriter = new PrintWriter(writer);
        // start visiting models and writing log
        printWriter.println("Start scanning bio-models......");
        printWriter.println("\n");
        for (int i = 0; i < users.length; i++) {
            User user = users[i];
            BioModelInfo[] bioModelInfos = dbServerImpl.getBioModelInfos(user, false);
            for (int j = 0; j < bioModelInfos.length; j++) {
                BioModelInfo bmi = bioModelInfos[j];
                if (!databaseVisitor.filterBioModel(bmi)) {
                    continue;
                }
                try {
                    BigString bioModelXML = dbServerImpl.getBioModelXML(user, bmi.getVersion().getVersionKey());
                    BioModel storedModel = cbit.vcell.xml.XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
                    System.out.println(storedModel.getName());
                    if (databaseVisitor.filterBioModel(storedModel)) {
                        storedModel.refreshDependencies();
                        verifyMathDescriptionsUnchanged(storedModel, printWriter);
                        databaseVisitor.setBioModel(storedModel, printWriter);
                        // + bioModelInfos[j].getVersion().getName() + " -----> ");
                        printWriter.println("---- " + (j + 1) + " ----> " + storedModel.getName());
                        for (BioModel bioModel : databaseVisitor) {
                            SimulationContext[] simContexts = bioModel.getSimulationContexts();
                            for (SimulationContext sc : simContexts) {
                                try {
                                    sc.createNewMathMapping().getMathDescription();
                                } catch (Exception e) {
                                    printWriter.println("\t " + bioModel.getName() + " :: " + sc.getName() + " ----> math regeneration failed.s");
                                // e.printStackTrace();
                                }
                            }
                        }
                    }
                } catch (Exception e2) {
                    lg.error(e2.getMessage(), e2);
                    printWriter.println("======= " + e2.getMessage());
                    if (bAbortOnDataAccessException) {
                        throw e2;
                    }
                }
            }
        }
        printWriter.close();
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 54 with BigString

use of org.vcell.util.BigString in project vcell by virtualcell.

the class VCDatabaseScanner method scanGeometries.

/**
 * Insert the method's description here.
 * Creation date: (2/2/01 3:40:29 PM)
 * @throws DataAccessException
 * @throws XmlParseException
 */
public void scanGeometries(VCDatabaseVisitor databaseVisitor, PrintStream logFilePrintStream, User[] users, KeyValue singleGeometryKey, HashSet<KeyValue> includeHash, HashSet<KeyValue> excludeHash, boolean bAbortOnDataAccessException) throws DataAccessException, XmlParseException {
    if (users == null) {
        users = getAllUsers();
    }
    try {
        // start visiting models and writing log
        logFilePrintStream.println("Start scanning geometries......");
        logFilePrintStream.println("\n");
        for (int i = 0; i < users.length; i++) {
            User user = users[i];
            GeometryInfo[] geoInfos = dbServerImpl.getGeometryInfos(user, false);
            for (int j = 0; j < geoInfos.length; j++) {
                if (singleGeometryKey != null && !geoInfos[j].getVersion().getVersionKey().compareEqual(singleGeometryKey)) {
                    System.out.println("skipping geometry, not the single one that we wanted");
                    continue;
                }
                if (excludeHash != null && excludeHash.contains(geoInfos[j].getVersion().getVersionKey())) {
                    System.out.println("skipping geometry with key '" + geoInfos[j].getVersion().getVersionKey() + "'");
                    continue;
                }
                if (includeHash != null && !includeHash.contains(geoInfos[j].getVersion().getVersionKey())) {
                    System.out.println("not including geometry with key '" + geoInfos[j].getVersion().getVersionKey() + "'");
                    continue;
                }
                if (!databaseVisitor.filterGeometry(geoInfos[j])) {
                    continue;
                }
                try {
                    BigString geometryXML = dbServerImpl.getGeometryXML(user, geoInfos[j].getVersion().getVersionKey());
                    Geometry geometry = cbit.vcell.xml.XmlHelper.XMLToGeometry(new XMLSource(geometryXML.toString()));
                    geometry.refreshDependencies();
                    databaseVisitor.visitGeometry(geometry, logFilePrintStream);
                } catch (Exception e2) {
                    lg.error(e2.getMessage(), e2);
                    if (bAbortOnDataAccessException) {
                        throw e2;
                    }
                }
            }
        }
        logFilePrintStream.close();
    } catch (Exception e) {
        System.err.println("error writing to log file.");
    }
}

Example 55 with BigString

use of org.vcell.util.BigString 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();
}