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

Example 1 with SimulationJobStatusPersistent

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

the class VCComprehensiveStatistics method collectMathModelStats.

private void collectMathModelStats(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 = mathModelStats[bInternal ? 0 : 1];
            MathModelInfo[] mathModelInfos = dbServerImpl.getMathModelInfos(user, false);
            for (MathModelInfo mmi : mathModelInfos) {
                Date createDate = mmi.getVersion().getDate();
                long t = createDate.getTime();
                // }
                if (t < startDateInMs || t > endDateInMs) {
                    continue;
                }
                // modelStat.count_model ++;
                try {
                    BigString mathModelXML = dbServerImpl.getMathModelXML(user, mmi.getVersion().getVersionKey());
                    MathModel mathModel = (MathModel) waitForModel(mathModelXML, true);
                    if (mathModel == null) {
                        System.out.println("----------          Skipped MathModel " + mmi.getVersion() + "          ----------");
                        continue;
                    }
                    modelStat.count_model++;
                    boolean bHasCompletedSim = false;
                    for (Simulation sim : mathModel.getSimulations()) {
                        SimulationStatusPersistent ss = dbServerImpl.getSimulationStatus(sim.getKey());
                        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()) {
                                    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 + ". MathModel Statistics ");
    statOutputPW.println("====================================================");
    for (ModelStat modelStat : mathModelStats) {
        statOutputPW.println("\t" + modelStat.title);
        statOutputPW.println("========================================");
        statOutputPW.println("number of mathmodels saved :\t" + modelStat.count_model);
        statOutputPW.println("number of mathmodels that has at least 1 completed simulation :\t" + modelStat.count_model_simcomplete);
        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 2 with SimulationJobStatusPersistent

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

the class VCComprehensiveStatistics method collectBioModelStats.

private void collectBioModelStats(long startDateInMs, long endDateInMs) throws DataAccessException {
    retrieveUsers();
    List<String> internalDeveloper = Arrays.asList(VCComprehensiveStatistics.INTERNAL_DEVELOPERS);
    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 3 with SimulationJobStatusPersistent

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

the class VcmlOmexConverter method vcmlToOmexConversion.

public static boolean vcmlToOmexConversion(String outputBaseDir) throws XmlParseException, IOException, DataAccessException, SQLException {
    // Get VCML file path from -i flag
    int sedmlLevel = 1;
    int sedmlVersion = 2;
    String inputVcmlFile = cliHandler.getInputFilePath();
    // Get directory file path from -o flag
    String outputDir = cliHandler.getOutputDirPath();
    // get VCML name from VCML path
    // String vcmlName = inputVcmlFile.split(File.separator, 10)[inputVcmlFile.split(File.separator, 10).length - 1].split("\\.", 5)[0];
    // platform independent, strips extension too
    String vcmlName = FilenameUtils.getBaseName(inputVcmlFile);
    File vcmlFilePath = new File(inputVcmlFile);
    // Create biomodel
    BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(vcmlFilePath));
    bioModel.refreshDependencies();
    int numSimulations = bioModel.getNumSimulations();
    if (outputBaseDir != null && numSimulations == 0) {
        CLIStandalone.writeSimErrorList(outputBaseDir, vcmlName + " has no simulations.");
        return false;
    }
    // we extract the simulations with field data from the list of simulations since they are not supported
    List<Simulation> simulationsToRemove = new ArrayList<>();
    for (Simulation simulation : bioModel.getSimulations()) {
        boolean bFieldDataFound = false;
        Enumeration<Variable> variables = simulation.getMathDescription().getVariables();
        while (variables.hasMoreElements()) {
            Variable var = variables.nextElement();
            Expression exp = var.getExpression();
            FieldFunctionArguments[] ffas = FieldUtilities.getFieldFunctionArguments(exp);
            if (ffas != null && ffas.length > 0) {
                bFieldDataFound = true;
                // we are done with this simulation if we know it has at least one variable with a field data in its expression
                break;
            }
        }
        if (bFieldDataFound) {
            simulationsToRemove.add(simulation);
            CLIStandalone.writeSimErrorList(outputBaseDir, vcmlName + " excluded: FieldData not supported at this time.");
            SolverDescription solverDescription = simulation.getSolverTaskDescription().getSolverDescription();
            String solverName = solverDescription.getShortDisplayLabel();
            CLIStandalone.writeSimErrorList(outputBaseDir, "   " + solverName);
        }
    }
    for (Simulation simulation : simulationsToRemove) {
        try {
            bioModel.removeSimulation(simulation);
        } catch (PropertyVetoException e) {
            System.out.println("Failed to remove simulation with field data");
            e.printStackTrace();
        }
    }
    // we replace the obsolete solver with the fully supported equivalent
    for (Simulation simulation : bioModel.getSimulations()) {
        if (simulation.getSolverTaskDescription().getSolverDescription().equals(SolverDescription.FiniteVolume)) {
            try {
                simulation.getSolverTaskDescription().setSolverDescription(SolverDescription.SundialsPDE);
            } catch (PropertyVetoException e) {
                System.out.println("Failed to replace obsolete solver");
                e.printStackTrace();
            }
        }
    }
    // NOTE: SEDML exporter exports both SEDML as well as required SBML
    List<Simulation> simsToExport = null;
    Set<String> solverNames = new LinkedHashSet<>();
    if (bHasDataOnly) {
        // make list of simulations to export with only sims that have data on the server
        simsToExport = new ArrayList<Simulation>();
        for (Simulation simulation : bioModel.getSimulations()) {
            SolverDescription solverDescription = simulation.getSolverTaskDescription().getSolverDescription();
            String solverName = solverDescription.getShortDisplayLabel();
            solverNames.add(solverName);
            // check server status
            KeyValue parentKey = simulation.getSimulationVersion().getParentSimulationReference();
            SimulationJobStatusPersistent[] statuses = adminDbTopLevel.getSimulationJobStatusArray(parentKey == null ? simulation.getKey() : parentKey, false);
            if (statuses == null)
                continue;
            if (statuses.length == 0)
                continue;
            for (int i = 0; i < statuses.length; i++) {
                if (statuses[i].hasData()) {
                    simsToExport.add(simulation);
                    continue;
                }
            }
        // String dbDriverName = PropertyLoader.getProperty(PropertyLoader.dbDriverName, null);
        // String dbConnectURL = PropertyLoader.getProperty(PropertyLoader.dbConnectURL, null);
        // String dbSchemaUser = PropertyLoader.getProperty(PropertyLoader.dbUserid, null);
        // String dbPassword = PropertyLoader.getSecretValue(PropertyLoader.dbPasswordValue, PropertyLoader.dbPasswordFile);
        // DataSetControllerImpl dsControllerImpl = new DataSetControllerImpl(null, new File(outputBaseDir), null);
        // 
        // code used to recover field data
        // 
        // HashMap<User, Vector<ExternalDataIdentifier>> allExternalDataIdentifiers = FieldDataDBOperationDriver.getAllExternalDataIdentifiers();
        // Enumeration<Variable> variables = simulation.getMathDescription().getVariables();
        // while(variables.hasMoreElements()) {
        // Variable var = variables.nextElement();
        // Expression exp = var.getExpression();
        // FieldFunctionArguments[] ffas = FieldUtilities.getFieldFunctionArguments( exp);
        // 
        // if(ffas != null && ffas.length > 0) {
        // FieldDataIdentifierSpec[] aaa = DataSetControllerImpl.getFieldDataIdentifierSpecs_private(
        // ffas, simulation.getVersion().getOwner(), true, allExternalDataIdentifiers);
        // 
        // System.out.println((ffas == null) ? "null" : exp.infix() + ", not null:" + ffas.length);
        // }
        // }
        }
    }
    if (outputBaseDir != null && bHasDataOnly == true && simsToExport.size() == 0) {
        CLIStandalone.writeSimErrorList(outputBaseDir, vcmlName + " has no simulations with any results.");
        for (String solverName : solverNames) {
            CLIStandalone.writeSimErrorList(outputBaseDir, "   " + solverName);
        }
        return false;
    }
    String rdfString = getMetadata(vcmlName, bioModel);
    XmlUtil.writeXMLStringToFile(rdfString, String.valueOf(Paths.get(outputDir, "metadata.rdf")), true);
    if (bMakeLogsOnly) {
        return false;
    }
    SEDMLExporter sedmlExporter = new SEDMLExporter(bioModel, sedmlLevel, sedmlVersion, simsToExport);
    String sedmlString = sedmlExporter.getSEDMLFile(outputDir, vcmlName, bForceVCML, bHasDataOnly, true);
    XmlUtil.writeXMLStringToFile(sedmlString, String.valueOf(Paths.get(outputDir, vcmlName + ".sedml")), true);
    // libCombine needs native lib
    ResourceUtil.setNativeLibraryDirectory();
    NativeLoader.load("combinej");
    boolean isDeleted = false;
    boolean isCreated;
    try {
        CombineArchive archive = new CombineArchive();
        String[] files;
        // TODO: try-catch if no files
        File dir = new File(outputDir);
        files = dir.list();
        for (String sd : files) {
            if (sd.endsWith(".sedml")) {
                archive.addFile(Paths.get(outputDir, sd).toString(), // target file name
                "./" + sd, KnownFormats.lookupFormat("sedml"), // mark file as master
                true);
            } else if (sd.endsWith(".sbml") || sd.endsWith(".xml")) {
                archive.addFile(Paths.get(outputDir, sd).toString(), "./" + sd, KnownFormats.lookupFormat("sbml"), // mark file as master
                false);
            } else if (sd.endsWith(".rdf")) {
                archive.addFile(Paths.get(outputDir, sd).toString(), "./" + sd, "http://identifiers.org/combine.specifications/omex-metadata", // KnownFormats.lookupFormat("xml"),
                false);
            }
        }
        archive.addFile(Paths.get(String.valueOf(vcmlFilePath)).toString(), "./" + vcmlName + ".vcml", "http://purl.org/NET/mediatypes/application/vcml+xml", false);
        // writing into combine archive
        String omexPath = Paths.get(outputDir, vcmlName + ".omex").toString();
        File omexFile = new File(omexPath);
        // Deleting file if already exists with same name
        if (omexFile.exists()) {
            omexFile.delete();
        }
        isCreated = archive.writeToFile(omexPath);
        // Removing all other files(like SEDML, XML, SBML) after archiving
        for (String sd : files) {
            // removing
            if (sd.endsWith(".sedml") || sd.endsWith(".sbml") || sd.endsWith("xml") || sd.endsWith("vcml") || sd.endsWith("rdf")) {
                isDeleted = Paths.get(outputDir, sd).toFile().delete();
            }
        }
        if (isDeleted)
            System.out.println("Removed intermediary files");
    } catch (Exception e) {
        throw new RuntimeException("createZipArchive threw exception: " + e.getMessage());
    }
    return isCreated;
}

Example 4 with SimulationJobStatusPersistent

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

the class AdminDBTopLevel method getSimulationStatus.

/**
 * Insert the method's description here.
 * Creation date: (1/31/2003 2:35:44 PM)
 * @return cbit.vcell.solvers.SimulationJobStatus[]
 * @param bActiveOnly boolean
 * @param owner cbit.vcell.server.User
 */
SimulationStatusPersistent getSimulationStatus(KeyValue simKey, boolean bEnableRetry) throws java.sql.SQLException, DataAccessException {
    Object lock = new Object();
    Connection con = conFactory.getConnection(lock);
    try {
        SimulationJobStatusPersistent[] jobStatuses = jobDB.getSimulationJobStatus(con, simKey);
        if (jobStatuses.length > 0) {
            return new SimulationStatusPersistent(jobStatuses);
        } else {
            return null;
        }
    } catch (Throwable e) {
        lg.error("failure in getSimulationStatus()", e);
        if (bEnableRetry && isBadConnection(con)) {
            conFactory.failed(con, lock);
            return getSimulationStatus(simKey, false);
        } else {
            handle_DataAccessException_SQLException(e);
            // never gets here;
            return null;
        }
    } finally {
        conFactory.release(con, lock);
    }
}

Example 5 with SimulationJobStatusPersistent

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

the class AdminDBTopLevel method getSimulationJobStatus.

/**
 * Insert the method's description here.
 * Creation date: (1/31/2003 2:35:44 PM)
 * @return cbit.vcell.solvers.SimulationJobStatus[]
 * @param bActiveOnly boolean
 * @param owner cbit.vcell.server.User
 */
public SimulationJobStatusPersistent getSimulationJobStatus(KeyValue simKey, int jobIndex, int taskID, boolean bEnableRetry) throws java.sql.SQLException, DataAccessException {
    Object lock = new Object();
    Connection con = conFactory.getConnection(lock);
    try {
        SimulationJobStatusPersistent jobStatus = getSimulationJobStatus(con, simKey, jobIndex, taskID);
        return jobStatus;
    } catch (Throwable e) {
        lg.error("failure in getSimulationJobStatus()", e);
        if (bEnableRetry && isBadConnection(con)) {
            conFactory.failed(con, lock);
            return getSimulationJobStatus(simKey, jobIndex, taskID, false);
        } else {
            handle_DataAccessException_SQLException(e);
            // never gets here;
            return null;
        }
    } finally {
        conFactory.release(con, lock);
    }
}