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Example 11 with BigString

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

the class ClientDocumentManager method save.

/**
 * Insert the method's description here.
 * Creation date: (10/28/00 12:08:30 AM)
 */
public Geometry save(Geometry geometry) throws DataAccessException {
    try {
        String geometryXML = null;
        try {
            geometryXML = XmlHelper.geometryToXML(geometry);
        } catch (XmlParseException e) {
            e.printStackTrace(System.out);
            throw new DataAccessException(e.getMessage());
        }
        String savedGeometryXML = sessionManager.getUserMetaDbServer().saveGeometry(new BigString(geometryXML)).toString();
        Geometry savedGeometry = getGeometryFromDatabaseXML(savedGeometryXML);
        KeyValue savedKey = savedGeometry.getVersion().getVersionKey();
        if (xmlHash.get(savedKey) == null) {
            xmlHash.put(savedKey, savedGeometryXML);
        }
        updateGeometryRelatedHashes(savedGeometry);
        return savedGeometry;
    } catch (RemoteProxyException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException(VCellErrorMessages.FAIL_SAVE_MESSAGE + "\n\n" + e.getMessage());
    }
}
Also used : Geometry(cbit.vcell.geometry.Geometry) KeyValue(org.vcell.util.document.KeyValue) BigString(org.vcell.util.BigString) XmlParseException(cbit.vcell.xml.XmlParseException) BigString(org.vcell.util.BigString) DataAccessException(org.vcell.util.DataAccessException) RemoteProxyException(cbit.vcell.message.server.bootstrap.client.RemoteProxyVCellConnectionFactory.RemoteProxyException)

Example 12 with BigString

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

the class HybridSolverTester method runSim.

private static void runSim(UserLoginInfo userLoginInfo, VCSimulationIdentifier vcSimulationIdentifier, VCellConnectionHelper vcellConnectionHelper) throws Exception {
    SimulationStatusPersistent simulationStatus = vcellConnectionHelper.getSimulationStatus(vcSimulationIdentifier.getSimulationKey());
    System.out.println("initial status=" + simulationStatus);
    if (simulationStatus != null && simulationStatus.isRunning()) /*!simulationStatus.isNeverRan() && !simulationStatus.isCompleted()*/
    {
        throw new Exception("Sim in unexpected state " + simulationStatus);
    }
    int intialMaxTaskID = vcellConnectionHelper.getMaxTaskID(simulationStatus);
    BigString simXML = vcellConnectionHelper.getSimulationXML(vcSimulationIdentifier.getSimulationKey());
    Simulation sim = XmlHelper.XMLToSim(simXML.toString());
    int scanCount = sim.getScanCount();
    vcellConnectionHelper.startSimulation(vcSimulationIdentifier, scanCount);
    long startTime = System.currentTimeMillis();
    // wait until sim has stopped running
    while ((simulationStatus = vcellConnectionHelper.getSimulationStatus(vcSimulationIdentifier.getSimulationKey())) == null || (simulationStatus.isStopped() || simulationStatus.isCompleted() || simulationStatus.isFailed())) {
        MessageEvent[] messageEvents = vcellConnectionHelper.getMessageEvents();
        if (vcellConnectionHelper.getMaxTaskID(simulationStatus) > intialMaxTaskID) {
            // new sim must have started
            break;
        }
        Thread.sleep(250);
        // }
        if ((System.currentTimeMillis() - startTime) > 120000) {
            throw new Exception("Sim finished too fast or took too long to start");
        }
    }
    SimulationStatusPersistent lastSimStatus = simulationStatus;
    while (!simulationStatus.isStopped() && !simulationStatus.isCompleted() && !simulationStatus.isFailed()) {
        Thread.sleep(3000);
        simulationStatus = vcellConnectionHelper.getSimulationStatus(vcSimulationIdentifier.getSimulationKey());
        if (simulationStatus != null && !simulationStatus.toString().equals(lastSimStatus.toString())) {
            lastSimStatus = simulationStatus;
            System.out.println("running status=" + simulationStatus);
        }
        MessageEvent[] messageEvents = vcellConnectionHelper.getMessageEvents();
    // for(int i = 0;i<(messageEvents==null?0:messageEvents.length);i++){
    // System.out.println(messageEvents[i].toString());
    // }
    }
    System.out.println("last run simStatus=" + simulationStatus);
}
Also used : Simulation(cbit.vcell.solver.Simulation) MessageEvent(cbit.rmi.event.MessageEvent) SimulationStatusPersistent(cbit.vcell.server.SimulationStatusPersistent) BigString(org.vcell.util.BigString) IOException(java.io.IOException) FileNotFoundException(java.io.FileNotFoundException)

Example 13 with BigString

use of org.vcell.util.BigString 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;
    }
}
Also used : VCSimulationIdentifier(cbit.vcell.solver.VCSimulationIdentifier) KeyValue(org.vcell.util.document.KeyValue) MessageEvent(cbit.rmi.event.MessageEvent) VCellBootstrap(cbit.vcell.server.VCellBootstrap) BigString(org.vcell.util.BigString) ODESimData(cbit.vcell.solver.ode.ODESimData) DigestedPassword(org.vcell.util.document.UserLoginInfo.DigestedPassword) BigString(org.vcell.util.BigString) VCInfoContainer(org.vcell.util.document.VCInfoContainer) AnnotatedFunction(cbit.vcell.solver.AnnotatedFunction) VCellConnection(cbit.vcell.server.VCellConnection) BioModelInfo(org.vcell.util.document.BioModelInfo) SimulationStatusPersistent(cbit.vcell.server.SimulationStatusPersistent) TreeMap(java.util.TreeMap) SimulationContext(cbit.vcell.mapping.SimulationContext) VCSimulationDataIdentifier(cbit.vcell.solver.VCSimulationDataIdentifier) IOException(java.io.IOException) OutputContext(cbit.vcell.simdata.OutputContext) Simulation(cbit.vcell.solver.Simulation) BioModel(cbit.vcell.biomodel.BioModel) UserLoginInfo(org.vcell.util.document.UserLoginInfo) XMLSource(cbit.vcell.xml.XMLSource)

Example 14 with BigString

use of org.vcell.util.BigString 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);
    }
}
Also used : User(org.vcell.util.document.User) KeyValue(org.vcell.util.document.KeyValue) ArrayList(java.util.ArrayList) BigString(org.vcell.util.BigString) BigString(org.vcell.util.BigString) ResultSet(java.sql.ResultSet) DataAccessException(org.vcell.util.DataAccessException) PrintWriter(java.io.PrintWriter) PrintStream(java.io.PrintStream) PreparedStatement(java.sql.PreparedStatement) Statement(java.sql.Statement) Connection(java.sql.Connection) PreparedStatement(java.sql.PreparedStatement) SimulationContext(cbit.vcell.mapping.SimulationContext) SQLException(java.sql.SQLException) XmlParseException(cbit.vcell.xml.XmlParseException) IOException(java.io.IOException) DataAccessException(org.vcell.util.DataAccessException) FileOutputStream(java.io.FileOutputStream) BioModel(cbit.vcell.biomodel.BioModel) OutputStreamWriter(java.io.OutputStreamWriter) XMLSource(cbit.vcell.xml.XMLSource)

Example 15 with BigString

use of org.vcell.util.BigString 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();
    }
}
Also used : MathModel(cbit.vcell.mathmodel.MathModel) KeyValue(org.vcell.util.document.KeyValue) ArrayList(java.util.ArrayList) BigString(org.vcell.util.BigString) BigString(org.vcell.util.BigString) ResultSet(java.sql.ResultSet) DataAccessException(org.vcell.util.DataAccessException) PrintWriter(java.io.PrintWriter) PrintStream(java.io.PrintStream) PreparedStatement(java.sql.PreparedStatement) Statement(java.sql.Statement) Connection(java.sql.Connection) PreparedStatement(java.sql.PreparedStatement) SQLException(java.sql.SQLException) XmlParseException(cbit.vcell.xml.XmlParseException) IOException(java.io.IOException) DataAccessException(org.vcell.util.DataAccessException) FileOutputStream(java.io.FileOutputStream) OutputStreamWriter(java.io.OutputStreamWriter) XMLSource(cbit.vcell.xml.XMLSource)

Aggregations

BigString (org.vcell.util.BigString)55 DataAccessException (org.vcell.util.DataAccessException)39 KeyValue (org.vcell.util.document.KeyValue)24 XmlParseException (cbit.vcell.xml.XmlParseException)22 BioModel (cbit.vcell.biomodel.BioModel)19 XMLSource (cbit.vcell.xml.XMLSource)19 SQLException (java.sql.SQLException)16 Simulation (cbit.vcell.solver.Simulation)15 User (org.vcell.util.document.User)15 BioModelInfo (org.vcell.util.document.BioModelInfo)13 SimulationContext (cbit.vcell.mapping.SimulationContext)12 SimulationStatusPersistent (cbit.vcell.server.SimulationStatusPersistent)10 ObjectNotFoundException (org.vcell.util.ObjectNotFoundException)10 RemoteProxyException (cbit.vcell.message.server.bootstrap.client.RemoteProxyVCellConnectionFactory.RemoteProxyException)9 MathException (cbit.vcell.math.MathException)8 ExpressionException (cbit.vcell.parser.ExpressionException)8 VCSimulationIdentifier (cbit.vcell.solver.VCSimulationIdentifier)6 Connection (java.sql.Connection)6 MessageEvent (cbit.rmi.event.MessageEvent)5 MappingException (cbit.vcell.mapping.MappingException)5