Examples with XMLSource cbit.vcell.xml.XMLSource used on opensource projects

Example 6 with XMLSource

use of cbit.vcell.xml.XMLSource in project vcell by virtualcell.

the class BatchTester method batchScanBioModels.

@SuppressWarnings("static-access")
public void batchScanBioModels(VCMultiBioVisitor databaseVisitor, String statusTable, int chunkSize) throws DataAccessException, XmlParseException, SQLException, IOException {
    PrintStream current = System.out;
    // System.setOut(new PrintStream(new NullStream()));
    try {
        String processHostId = ManagementFactory.getRuntimeMXBean().getName();
        String filename = processHostId + ".txt";
        FileOutputStream fos = new FileOutputStream(filename);
        System.setOut(new PrintStream(fos));
        OutputStreamWriter writer = new OutputStreamWriter(fos);
        // autoflush
        PrintWriter printWriter = new PrintWriter(writer, true);
        Connection conn = connFactory.getConnection(null);
        conn.setAutoCommit(true);
        printWriter.println("reserving slots");
        try (Statement statement = conn.createStatement()) {
            String query = "Update " + statusTable + " set scan_process = '" + processHostId + "', log_file = '" + filename + "' where scanned = 0 and scan_process is null and rownum <= " + chunkSize;
            int uCount = statement.executeUpdate(query);
            if (uCount > chunkSize) {
                throw new Error("logic / SQL bad");
            }
            if (uCount == 0) {
                printWriter.println("No models to scan, exiting");
                System.exit(100);
            }
        }
        printWriter.println("finding  ours");
        ArrayList<BioModelIdent> models = new ArrayList<BatchTester.BioModelIdent>();
        try (Statement statement = conn.createStatement()) {
            String query = "Select id, user_id, model_id from " + statusTable + " where scan_process ='" + processHostId + "' and scanned = 0";
            ResultSet rs = statement.executeQuery(query);
            while (rs.next()) {
                BioModelIdent mi = new BioModelIdent(rs);
                models.add(mi);
                printWriter.println("claiming " + mi.statusId);
            }
        }
        try {
            // start visiting models and writing log
            printWriter.println("Start scanning bio-models......");
            printWriter.println("\n");
            PreparedStatement ps = conn.prepareStatement("Update " + statusTable + " set scanned = 1, good = ? , exception_type = ?, exception = ?, scan_process = null where id = ?");
            for (BioModelIdent modelIdent : models) {
                ScanStatus scanStatus = ScanStatus.PASS;
                String exceptionMessage = null;
                String exceptionClass = null;
                try {
                    User user = new User("", convert(modelIdent.userId));
                    KeyValue modelKey = convert(modelIdent.modelId);
                    BigString bioModelXML = null;
                    // seconds
                    long dbSleepTime = 10;
                    while (bioModelXML == null) {
                        try {
                            bioModelXML = dbServerImpl.getBioModelXML(user, modelKey);
                        } catch (DataAccessException dae) {
                            Throwable cause = dae.getCause();
                            if (cause.getClass().getSimpleName().equals("UniversalConnectionPoolException")) {
                                printWriter.println("No db connection for  " + modelIdent.statusId + ", sleeping " + dbSleepTime + " seconds");
                                Thread.currentThread().sleep(dbSleepTime * 1000);
                                // wait a little longer next time
                                dbSleepTime *= 1.5;
                            } else {
                                // other exception, just rethrow
                                throw dae;
                            }
                        }
                    }
                    BioModel storedModel = cbit.vcell.xml.XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
                    if (databaseVisitor.filterBioModel(storedModel)) {
                        storedModel.refreshDependencies();
                        boolean goodModel = verifyMathDescriptionsUnchanged(storedModel, printWriter);
                        if (goodModel) {
                            printWriter.println("Model for " + modelIdent.statusId + " good");
                            databaseVisitor.setBioModel(storedModel, printWriter);
                            for (BioModel bioModel : databaseVisitor) {
                                SimulationContext[] simContexts = bioModel.getSimulationContexts();
                                for (SimulationContext sc : simContexts) {
                                    // try {
                                    // long start = System.currentTimeMillis();
                                    sc.createNewMathMapping().getMathDescription();
                                // long end = System.currentTimeMillis();
                                // printWriter.println("mapping took " + (end - start)/1000.0 + " sec ");
                                /*
									} catch (Exception e) {
										//printWriter.println("\t " + bioModel.getName() + " :: " + sc.getName() + " ----> math regeneration failed.s");
										// e.printStackTrace();
									}
											 */
                                }
                            }
                        } else {
                            throw new MathRegenFail();
                        }
                    } else {
                        scanStatus = ScanStatus.FILTERED;
                    }
                } catch (Exception e) {
                    lg.error(e.getMessage(), e);
                    scanStatus = ScanStatus.FAIL;
                    exceptionClass = e.getClass().getName();
                    exceptionMessage = e.getMessage();
                    printWriter.println("failed " + modelIdent.statusId);
                    e.printStackTrace(printWriter);
                }
                ps.setInt(1, scanStatus.code);
                ps.setString(2, exceptionClass);
                ps.setString(3, exceptionMessage);
                ps.setLong(4, modelIdent.statusId);
                boolean estat = ps.execute();
                if (estat) {
                    throw new Error("logic");
                }
                int uc = ps.getUpdateCount();
                if (uc != 1) {
                    throw new Error("logic / sql ");
                }
            }
        } catch (Exception e) {
            e.printStackTrace(printWriter);
        }
        printWriter.close();
    } finally {
        System.setOut(current);
    }
}

Example 7 with XMLSource

use of cbit.vcell.xml.XMLSource in project vcell by virtualcell.

the class BatchTester method batchScanMathModels.

@SuppressWarnings("static-access")
public void batchScanMathModels(BadMathVisitor databaseVisitor, String statusTable, int chunkSize) throws DataAccessException, XmlParseException, SQLException, IOException {
    PrintStream current = System.out;
    // System.setOut(new PrintStream(new NullStream()));
    try {
        String processHostId = ManagementFactory.getRuntimeMXBean().getName();
        String filename = processHostId + ".txt";
        FileOutputStream fos = new FileOutputStream(filename);
        System.setOut(new PrintStream(fos));
        OutputStreamWriter writer = new OutputStreamWriter(fos);
        // autoflush
        PrintWriter printWriter = new PrintWriter(writer, true);
        Connection conn = connFactory.getConnection(null);
        conn.setAutoCommit(true);
        printWriter.println("reserving slots");
        try (Statement statement = conn.createStatement()) {
            String query = "Update " + statusTable + " set scan_process = '" + processHostId + "', log_file = '" + filename + "' where scanned = 0 and scan_process is null and rownum <= " + chunkSize;
            int uCount = statement.executeUpdate(query);
            if (uCount > chunkSize) {
                throw new Error("logic / SQL bad");
            }
            if (uCount == 0) {
                printWriter.println("No models to scan, exiting");
                System.exit(100);
            }
        }
        printWriter.println("finding  ours");
        ArrayList<MathModelIdent> models = new ArrayList<BatchTester.MathModelIdent>();
        try (Statement statement = conn.createStatement()) {
            String query = "Select model_id from " + statusTable + " where scan_process ='" + processHostId + "' and scanned = 0";
            ResultSet rs = statement.executeQuery(query);
            while (rs.next()) {
                MathModelIdent mmi = new MathModelIdent(rs);
                models.add(mmi);
                printWriter.println("claiming " + mmi.id);
            }
        }
        try {
            // start visiting models and writing log
            printWriter.println("Start scanning math-models......");
            printWriter.println("\n");
            PreparedStatement ps = conn.prepareStatement("Update " + statusTable + " set scanned = 1, good = ? , exception_type = ?, exception = ?, scan_process = null where model_id = ?");
            for (MathModelIdent modelIdent : models) {
                ScanStatus scanStatus = ScanStatus.PASS;
                String exceptionMessage = null;
                String exceptionClass = null;
                try {
                    KeyValue modelKey = convert(modelIdent.id);
                    BigString mathModelXML = null;
                    // seconds
                    long dbSleepTime = 10;
                    while (mathModelXML == null) {
                        try {
                            mathModelXML = dbServerImpl.getMathModelXML(BatchTester.ADMINISTRATOR, modelKey);
                        } catch (DataAccessException dae) {
                            Throwable cause = dae.getCause();
                            if (cause.getClass().getSimpleName().equals("UniversalConnectionPoolException")) {
                                printWriter.println("No db connection for  " + modelIdent.id + ", sleeping " + dbSleepTime + " seconds");
                                Thread.currentThread().sleep(dbSleepTime * 1000);
                                // wait a little longer next time
                                dbSleepTime *= 1.5;
                            } else {
                                // other exception, just rethrow
                                throw dae;
                            }
                        }
                    }
                    MathModel storedModel = cbit.vcell.xml.XmlHelper.XMLToMathModel(new XMLSource(mathModelXML.toString()));
                    databaseVisitor.visitMathModel(storedModel, System.out);
                } catch (Exception e) {
                    lg.error(e.getMessage(), e);
                    scanStatus = ScanStatus.FAIL;
                    exceptionClass = e.getClass().getName();
                    exceptionMessage = e.getMessage();
                    printWriter.println("failed " + modelIdent.id);
                    e.printStackTrace(printWriter);
                }
                ps.setInt(1, scanStatus.code);
                ps.setString(2, exceptionClass);
                ps.setString(3, exceptionMessage);
                ps.setLong(4, modelIdent.id);
                boolean estat = ps.execute();
                if (estat) {
                    throw new Error("logic");
                }
                int uc = ps.getUpdateCount();
                if (uc != 1) {
                    throw new Error("logic / sql ");
                }
                printWriter.println("model " + modelIdent.id + " " + scanStatus);
            }
            printWriter.close();
        } finally {
            System.setOut(current);
        }
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 8 with XMLSource

use of cbit.vcell.xml.XMLSource in project vcell by virtualcell.

the class StandaloneRuleBasedTest method checkNonspatialStochasticSimContext.

private static void checkNonspatialStochasticSimContext(SimulationContext srcSimContext, File baseDirectory, int numTrials, long bngTimeoutDuration) throws Exception {
    if (!srcSimContext.getApplicationType().equals(Application.NETWORK_STOCHASTIC) || srcSimContext.getGeometry().getDimension() != 0) {
        throw new RuntimeException("simContext is of type " + srcSimContext.getApplicationType() + " and geometry dimension of " + srcSimContext.getGeometry().getDimension() + ", expecting nonspatial stochastic");
    }
    BioModel origBioModel = srcSimContext.getBioModel();
    BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(XmlHelper.bioModelToXML(origBioModel)));
    bioModel.refreshDependencies();
    // create ODE and RuleBased
    SimulationContext newODEApp = SimulationContext.copySimulationContext(srcSimContext, "aUniqueNewODEApp", false, Application.NETWORK_DETERMINISTIC);
    SimulationContext newRuleBasedApp = SimulationContext.copySimulationContext(srcSimContext, "aUniqueNewRuleBasedApp", false, Application.RULE_BASED_STOCHASTIC);
    newODEApp.setBioModel(bioModel);
    newRuleBasedApp.setBioModel(bioModel);
    ArrayList<AnnotatedFunction> outputFunctionsList = srcSimContext.getOutputFunctionContext().getOutputFunctionsList();
    // OutputContext outputContext = new OutputContext(outputFunctionsList.toArray(new AnnotatedFunction[outputFunctionsList.size()]));
    newODEApp.getOutputFunctionContext().setOutputFunctions(outputFunctionsList);
    newRuleBasedApp.getOutputFunctionContext().setOutputFunctions(outputFunctionsList);
    NetworkGenerationRequirements networkGenRequirements = NetworkGenerationRequirements.getComputeFull(bngTimeoutDuration);
    bioModel.addSimulationContext(newODEApp);
    newODEApp.refreshMathDescription(new MathMappingCallbackTaskAdapter(null), networkGenRequirements);
    bioModel.addSimulationContext(newRuleBasedApp);
    newRuleBasedApp.refreshMathDescription(new MathMappingCallbackTaskAdapter(null), networkGenRequirements);
    srcSimContext.refreshMathDescription(new MathMappingCallbackTaskAdapter(null), networkGenRequirements);
    // Create non-spatialStoch, ODE and RuleBased sims
    Simulation nonspatialStochAppNewSim = srcSimContext.addNewSimulation(STOCH_SIM_NAME, /*SimulationOwner.DEFAULT_SIM_NAME_PREFIX*/
    new MathMappingCallbackTaskAdapter(null), networkGenRequirements);
    Simulation newODEAppNewSim = newODEApp.addNewSimulation(ODE_SIM_NAME, new MathMappingCallbackTaskAdapter(null), networkGenRequirements);
    Simulation newRuleBasedAppNewSim = newRuleBasedApp.addNewSimulation(NFS_SIM_NAME, new MathMappingCallbackTaskAdapter(null), networkGenRequirements);
    nonspatialStochAppNewSim.setSimulationOwner(srcSimContext);
    newODEAppNewSim.setSimulationOwner(newODEApp);
    newRuleBasedAppNewSim.setSimulationOwner(newRuleBasedApp);
    try {
        bioModel.getModel().getSpeciesContexts();
        ArrayList<String> varNameList = new ArrayList<String>();
        for (SpeciesContextSpec scs : srcSimContext.getReactionContext().getSpeciesContextSpecs()) {
            varNameList.add(scs.getSpeciesContext().getName());
        }
        String[] varNames = varNameList.toArray(new String[0]);
        OutputTimeSpec outputTimeSpec = nonspatialStochAppNewSim.getSolverTaskDescription().getOutputTimeSpec();
        ArrayList<Double> sampleTimeList = new ArrayList<Double>();
        if (outputTimeSpec instanceof UniformOutputTimeSpec) {
            double endingTime = nonspatialStochAppNewSim.getSolverTaskDescription().getTimeBounds().getEndingTime();
            double dT = ((UniformOutputTimeSpec) outputTimeSpec).getOutputTimeStep();
            int currTimeIndex = 0;
            while (currTimeIndex * dT <= (endingTime + 1e-8)) {
                sampleTimeList.add(currTimeIndex * dT);
                currTimeIndex++;
            }
        }
        double[] sampleTimes = new double[sampleTimeList.size()];
        for (int i = 0; i < sampleTimes.length; i++) {
            sampleTimes[i] = sampleTimeList.get(i);
        }
        TimeSeriesMultitrialData sampleDataStoch1 = new TimeSeriesMultitrialData("stochastic1", varNames, sampleTimes, numTrials);
        TimeSeriesMultitrialData sampleDataStoch2 = new TimeSeriesMultitrialData("stochastic2", varNames, sampleTimes, numTrials);
        TimeSeriesMultitrialData sampleDataDeterministic = new TimeSeriesMultitrialData("determinstic", varNames, sampleTimes, 1);
        runsolver(nonspatialStochAppNewSim, baseDirectory, numTrials, sampleDataStoch1);
        runsolver(newODEAppNewSim, baseDirectory, 1, sampleDataDeterministic);
        runsolver(newRuleBasedAppNewSim, baseDirectory, numTrials, sampleDataStoch2);
        StochtestFileUtils.writeVarDiffData(new File(baseDirectory, VARDIFF_FILE), sampleDataStoch1, sampleDataStoch2);
        StochtestFileUtils.writeKolmogorovSmirnovTest(new File(baseDirectory, KS_TEST_FILE), sampleDataStoch1, sampleDataStoch2);
        StochtestFileUtils.writeChiSquareTest(new File(baseDirectory, ChiSquared_TEST_FILE), sampleDataStoch1, sampleDataStoch2);
        StochtestFileUtils.writeData(sampleDataStoch1, new File(baseDirectory, "data." + sampleDataStoch1.datasetName + ".json"));
        StochtestFileUtils.writeData(sampleDataStoch2, new File(baseDirectory, "data." + sampleDataStoch2.datasetName + ".json"));
        StochtestFileUtils.writeData(sampleDataDeterministic, new File(baseDirectory, "data." + sampleDataDeterministic.datasetName + ".json"));
    } finally {
        srcSimContext.removeSimulation(nonspatialStochAppNewSim);
        newODEApp.removeSimulation(newODEAppNewSim);
        newRuleBasedApp.removeSimulation(newRuleBasedAppNewSim);
    }
}

Example 9 with XMLSource

use of cbit.vcell.xml.XMLSource in project vcell by virtualcell.

the class ClientRobot method run.

/**
 * Insert the method's description here.
 * Creation date: (3/8/01 3:04:15 PM)
 */
public void run() {
    try {
        String[] args = { host, userid, password };
        setManagerManager(cbit.vcell.client.test.ClientTester.mainInit(args, "ClientRobot", null));
        for (int i = 0; i < 10; i++) {
            log.print("Robot " + getName() + "starting loop : " + i);
            BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(bioModelFile));
            String newName = "bioModel_" + getName() + "_" + Math.random();
            log.print("Saving bioModel \"" + newName + "\"");
            getManagerManager().getDocumentManager().saveAsNew(bioModel, newName, null);
            BioModelInfo[] bioModelInfos = getManagerManager().getDocumentManager().getBioModelInfos();
            if (bioModelInfos != null && bioModelInfos.length > 0) {
                for (int j = 0; j < bioModelInfos.length; j++) {
                    log.print("bioModelInfo[" + j + "] = " + bioModelInfos[j]);
                }
            }
        }
    } catch (Throwable e) {
        log.exception(e);
    } finally {
        log.alert("Robot " + getName() + " exiting");
    }
}

Example 10 with XMLSource

use of cbit.vcell.xml.XMLSource in project vcell by virtualcell.

the class SBMLExportTest method getBiomodelByName.

static BioModel getBiomodelByName(VCellConnection vcn, String name) throws RemoteProxyException, DataAccessException, XmlParseException {
    EscapedName eName = new EscapedName(name);
    UserMetaDbServer dataServer = vcn.getUserMetaDbServer();
    for (BioModelInfo bmi : dataServer.getBioModelInfos(false)) {
        String mName = bmi.getVersion().getName();
        if (eName.matches(mName)) {
            KeyValue bioModelKey = bmi.getVersion().getVersionKey();
            BigString bioModelXML = dataServer.getBioModelXML(bioModelKey);
            BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
            return bioModel;
        }
    }
    // if not found, list what's available
    for (BioModelInfo bmi : dataServer.getBioModelInfos(false)) {
        String mName = bmi.getVersion().getName();
        System.out.println(mName);
    }
    return null;
}