Examples with UserLoginInfo org.vcell.util.document.UserLoginInfo used on opensource projects

Example 1 with UserLoginInfo

use of org.vcell.util.document.UserLoginInfo in project vcell by virtualcell.

the class ErrorUtils method sendRemoteLogMessage.

/**
 * send message to Virtual Cell server, if not in debug mode
 * @param userLoginInfo; if null, user previously set info if available
 * @param message
 */
public static void sendRemoteLogMessage(UserLoginInfo argUserLoginInfo, final String message) {
    final UserLoginInfo userLoginInfo = argUserLoginInfo != null ? argUserLoginInfo : ErrorUtils.loginInfo;
    if (!ErrorUtils.bDebugMode && userLoginInfo != null) {
        new Thread(new Runnable() {

            @Override
            public void run() {
                try {
                    final String formattedMessage = new SimpleDateFormat("yyyy/MM/dd HH:mm:ss").format(Calendar.getInstance().getTime()) + "\n" + "vers='" + VCellSoftwareVersion.fromSystemProperty().getSoftwareVersionString() + "' java='" + userLoginInfo.getJava_version() + "' os='" + userLoginInfo.getOs_name() + "' osvers='" + userLoginInfo.getOs_version() + "' arch='" + userLoginInfo.getOs_arch() + "'\n" + message;
                    AmplistorUtils.uploadString(AmplistorUtils.DEFAULT_PROXY_AMPLI_VCELL_LOGS_URL + userLoginInfo.getUserName() + "_" + System.currentTimeMillis(), null, formattedMessage);
                } catch (Exception e) {
                    e.printStackTrace();
                    System.err.println("Failed to upload message to Amplistor " + AmplistorUtils.DEFAULT_PROXY_AMPLI_VCELL_LOGS_URL + " : " + message);
                // ignore
                }
            }
        }).start();
    } else {
        System.err.println("Remote log message: " + message);
    }
}

Example 2 with UserLoginInfo

use of org.vcell.util.document.UserLoginInfo in project vcell by virtualcell.

the class HybridSolverTester method main.

public static void main(java.lang.String[] args) {
    VCMongoMessage.enabled = false;
    boolean bAlternate = false;
    if (args.length == 12) {
        bAlternate = true;
    } else if (args.length != 5) {
        System.out.println("usage: HybridSolverTest userid SimID times(delimited by :) dataIndexes(delimited by :) varNames(delimited by :) numRuns outputFileDirectory bCalclOnly dbPassword useridKey rmiServer rmiPort");
        System.out.println("usage: HybridSolverTest userid SimID all postproc varNames(delimited by :) numRuns outputFileDirectory bCalclOnly dbPassword useridKey rmiServer rmiPort");
        System.out.println("usage: HybridSolverTest mathVCMLFileName startingTrialNo numTrials varNames(delimited by :) bPrintTime vcellSite(rel,beta,...)");
        System.exit(1);
    }
    FileWriter fw = null;
    try {
        if (bAlternate) {
            AltArgsHelper altArgsHelper = new AltArgsHelper(args[0], args[1], args[2], args[3], args[4], Integer.parseInt(args[5]), new File(args[6]), Boolean.parseBoolean(args[7]), args[8], args[9], args[10], args[11]);
            // final String user = args[0];
            // final String simID = args[1];
            // final int numRuns = Integer.parseInt(args[5]);
            // 
            // final String simPrefix  = "SimID_"+simID+"_";
            // File userSimDataDir = new File("\\\\cfs02\\raid\\vcell\\users\\"+user);
            // File outputDir = new File(args[6]);
            // boolean bCalcOnly = Boolean.parseBoolean(args[7]);
            // String dbPassword = args[8];
            // String useridKey = args[9];
            // String rmiServer = args[10];
            // String rmiPort = args[11];
            VCSimulationIdentifier vcSimulationIdentifier = new VCSimulationIdentifier(new KeyValue(altArgsHelper.simID), altArgsHelper.user);
            UserLoginInfo userLoginInfo = new UserLoginInfo(altArgsHelper.user.getName(), new DigestedPassword(altArgsHelper.dbPassword));
            File[] trialList = null;
            VCellConnectionHelper vCellConnectionHelper = null;
            File emptyFile = File.createTempFile("hstempty", null);
            try {
                if (!altArgsHelper.bCalcOnly) {
                    // String rmiUrl = "//" + "rmi-alpha.cam.uchc.edu" + ":" + "40106" + "/"+"VCellBootstrapServer";
                    // String rmiUrl = "//" + "rmi-alpha.cam.uchc.edu" + ":" + "40112" + "/"+"VCellBootstrapServer";
                    String rmiUrl = "//" + altArgsHelper.rmiServer + ".cam.uchc.edu" + ":" + altArgsHelper.rmiPort + "/" + "VCellBootstrapServer";
                    vCellConnectionHelper = new VCellConnectionHelper(userLoginInfo, rmiUrl);
                    for (int runIndex = 0; runIndex < altArgsHelper.numRuns; runIndex++) {
                        System.out.println("-----     Starting run " + (runIndex + 1) + " of " + altArgsHelper.numRuns);
                        runSim(userLoginInfo, vcSimulationIdentifier, vCellConnectionHelper);
                        if (trialList == null) {
                            System.out.println("Sim ran, getting trial list for " + altArgsHelper.simPrefix + " please wait...");
                            trialList = altArgsHelper.userSimDataDir.listFiles(new FileFilter() {

                                @Override
                                public boolean accept(File pathname) {
                                    // }
                                    return pathname.getName().startsWith(altArgsHelper.simPrefix) && !pathname.getName().endsWith(".simtask.xml");
                                }
                            });
                        }
                        System.out.println("-----     Copying run " + (runIndex + 1) + " of " + altArgsHelper.numRuns);
                        File outputRunDir = makeOutputRunDir(altArgsHelper.outputDir, runIndex);
                        for (int j = 0; j < trialList.length; j++) {
                            File localCopyFile = new File(outputRunDir, trialList[j].getName());
                            try {
                                // copy remote sim data file to local
                                FileUtils.copyFile(trialList[j], localCopyFile);
                                // delete remote
                                trialList[j].delete();
                            } catch (Exception e) {
                                System.out.println("failed to copy '" + trialList[j].getAbsolutePath() + "', error=" + e.getMessage() + ".  Putting empty file as placeholder");
                                try {
                                    // copy empty file to local in place of problematic remote sim data file, later analysis will skip it
                                    FileUtils.copyFile(emptyFile, localCopyFile);
                                } catch (Exception e2) {
                                    System.out.println("Faild to copy file and failed to copy empty, " + e2.getMessage());
                                }
                            }
                        }
                    }
                }
                // calc stats
                String dateStr = dateFormat.format(new Date());
                String outPrefix = altArgsHelper.simID + "_" + dateStr + "_0";
                File outputFile = new File(altArgsHelper.outputDir, outPrefix + ".csv");
                while (outputFile.exists()) {
                    outPrefix = TokenMangler.getNextEnumeratedToken(outPrefix);
                    outputFile = new File(altArgsHelper.outputDir, outPrefix + ".csv");
                }
                fw = new FileWriter(outputFile);
                fw.write("\"" + altArgsHelper.toString() + "\"\n");
                for (int runIndex = 0; runIndex < altArgsHelper.numRuns; runIndex++) {
                    makeAltCSV(altArgsHelper, fw, runIndex, makeOutputRunDir(altArgsHelper.outputDir, runIndex));
                }
                fw.close();
            } finally {
                if (!altArgsHelper.bCalcOnly) {
                    File[] straglers = altArgsHelper.userSimDataDir.listFiles(new FileFilter() {

                        @Override
                        public boolean accept(File pathname) {
                            return pathname.getName().startsWith(altArgsHelper.simPrefix);
                        }
                    });
                    if (straglers != null) {
                        for (int i = 0; i < straglers.length; i++) {
                            straglers[i].delete();
                        }
                    }
                }
            }
        } else {
            String site = args[5];
            HybridSolverTester hst = new HybridSolverTester(args[0], Integer.parseInt(args[1]), Integer.parseInt(args[2]), args[3], Boolean.parseBoolean(args[4]));
            hst.runHybridTest(site);
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        System.exit(1);
    } finally {
        if (fw != null) {
            try {
                fw.close();
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    }
}

Example 3 with UserLoginInfo

use of org.vcell.util.document.UserLoginInfo 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;
    }
}

Example 4 with UserLoginInfo

use of org.vcell.util.document.UserLoginInfo in project vcell by virtualcell.

the class ClientFactory method createRemoteVCellConnectionFactory.

public static VCellConnectionFactory createRemoteVCellConnectionFactory(String host, int port, String userid, String password) throws Exception {
    DigestedPassword digestedPassword = new DigestedPassword(password);
    org.vcell.util.document.UserLoginInfo userLoginInfo = new org.vcell.util.document.UserLoginInfo(userid, digestedPassword);
    VCellConnectionFactory vcConnFactory = new RemoteProxyVCellConnectionFactory(host, port, userLoginInfo);
    return vcConnFactory;
}

Example 5 with UserLoginInfo

use of org.vcell.util.document.UserLoginInfo in project vcell by virtualcell.

the class ClientTester method VCellConnectionFactoryInit.

/**
 * This method was created in VisualAge.
 * @return VCellConnection
 * @param args java.lang.String[]
 */
protected static cbit.vcell.server.VCellConnectionFactory VCellConnectionFactoryInit(String[] args, String programName) throws Exception {
    if (args.length != 3 && args.length != 4 && args.length != 7) {
        System.err.println("usage: " + programName + " -local userid password [driverName connectionURL userid password]");
        System.err.println("usage: " + programName + " -jms userid password");
        System.err.println("usage: " + programName + " host port userid password");
        throw new Exception("cannot connect");
    }
    cbit.vcell.server.VCellConnectionFactory vcConnFactory = null;
    new cbit.vcell.resource.PropertyLoader();
    if (args[0].startsWith("-")) {
        UserLoginInfo userLoginInfo = new UserLoginInfo(args[1], new UserLoginInfo.DigestedPassword(args[2]));
        if (args[0].equalsIgnoreCase("-jms")) {
            vcConnFactory = new cbit.vcell.message.server.bootstrap.LocalVCellConnectionFactory(userLoginInfo);
        } else if (args[0].equalsIgnoreCase("-local")) {
            vcConnFactory = new cbit.vcell.message.server.bootstrap.LocalVCellConnectionFactory(userLoginInfo);
            if (args.length == 7) {
                ConnectionFactory conFactory = DatabaseService.getInstance().createConnectionFactory(args[3], args[4], args[5], args[6]);
                ((cbit.vcell.message.server.bootstrap.LocalVCellConnectionFactory) vcConnFactory).setConnectionFactory(conFactory);
            }
        }
    } else {
        String apihost = args[0];
        Integer apiport = Integer.parseInt(args[1]);
        UserLoginInfo userLoginInfo = new UserLoginInfo(args[2], new UserLoginInfo.DigestedPassword(args[3]));
        vcConnFactory = new RemoteProxyVCellConnectionFactory(apihost, apiport, userLoginInfo);
    }
    return vcConnFactory;
}