Example usage for java.util.concurrent TimeUnit MINUTES

List of usage examples for java.util.concurrent TimeUnit MINUTES

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TimeUnit MINUTES

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Document

Time unit representing sixty seconds.

Usage

From source file:io.wcm.caravan.pipeline.impl.JsonPipelineMultipleSubscriptionsTest.java

@Test
public void subscribeConcurrentlyToTransformedPipelineOutputs() throws InterruptedException {

    // this test verifies that pipelines actions are only executed once, even if there are multiple concurrent subscribers
    firstStep = newPipelineWithResponseBody("{id:123}");
    secondStep = firstStep.applyAction(action);
    when(action.execute(any(), any())).thenReturn(firstStep.getOutput());

    // create multiple simultaneous threads that subscribe to the same pipeline output
    // and use a CountDownLatch to delay the subscription until all threads have been started
    CountDownLatch countDown = new CountDownLatch(100);
    ExecutorService executorService = Executors.newCachedThreadPool();
    while (countDown.getCount() > 0) {

        executorService.submit(() -> {

            countDown.await();//from  www  . j  ava2 s. co m
            secondStep.getOutput().subscribe(Subscribers.empty());

            return null; // this is required for the lambda to be considered a Callable<Void> and therefore be allowed to throw exceptions
        });

        countDown.countDown();
    }

    executorService.shutdown();
    executorService.awaitTermination(1, TimeUnit.MINUTES);

    verify(action, times(1)).execute(any(), any());
}

From source file:br.com.semanticwot.cd.conf.AppWebConfiguration.java

@Bean
public CacheManager cacheManager() { // Cache mais avanado, onde  possivel determinar por exemplo o tempo de durao do cache
    CacheBuilder<Object, Object> builder = CacheBuilder.newBuilder().maximumSize(100).expireAfterAccess(5,
            TimeUnit.MINUTES);
    GuavaCacheManager cacheManager = new GuavaCacheManager();
    cacheManager.setCacheBuilder(builder);
    return cacheManager;
}

From source file:com.clearspring.metriccatcher.MetricCatcher.java

/**
 * Create a Metric object from a JSONMetric
 *
 * @param jsonMetric A JSONMetric to make a Metric from
 * @return A Metric equivalent to the given JSONMetric
 *//*from  www.j  a v  a2  s .c  o  m*/
protected Metric createMetric(JSONMetric jsonMetric) {
    // Split the name from the JSON on dots for the metric group/type/name
    MetricName metricName;
    ArrayList<String> parts = new ArrayList<String>(Arrays.asList(jsonMetric.getName().split("\\.")));
    if (parts.size() >= 3) {
        metricName = new MetricName(parts.remove(0), parts.remove(0), StringUtils.join(parts, "."));
    } else {
        metricName = new MetricName(jsonMetric.getName(), "", "");
    }

    Class<?> metricType = jsonMetric.getMetricClass();
    if (metricType == Gauge.class) {
        return Metrics.newGauge(metricName, new GaugeMetricImpl());
    } else if (metricType == Counter.class) {
        return Metrics.newCounter(metricName);
    } else if (metricType == Meter.class) {
        // TODO timeunit
        return Metrics.newMeter(metricName, jsonMetric.getName(), TimeUnit.MINUTES);
    } else if (metricType == Histogram.class) {
        if (jsonMetric.getType().equals("biased")) {
            return Metrics.newHistogram(metricName, true);
        } else {
            return Metrics.newHistogram(metricName, false);
        }
    } else if (metricType == Timer.class) {
        return Metrics.newTimer(metricName, TimeUnit.MILLISECONDS, TimeUnit.SECONDS);
    }

    // Uh-oh
    return null;
}

From source file:hudson.plugins.ec2.EC2RetentionStrategy.java

private long internalCheck(EC2Computer computer) {
    /*/*from  ww w  .  ja  v  a  2  s. c o m*/
    * If we've been told never to terminate, or node is null(deleted), no checks to perform
    */
    if (idleTerminationMinutes == 0 || computer.getNode() == null) {
        return 1;
    }

    if (computer.isIdle() && !DISABLED) {
        final long uptime;
        try {
            uptime = computer.getUptime();
        } catch (AmazonClientException | InterruptedException e) {
            // We'll just retry next time we test for idleness.
            LOGGER.fine("Exception while checking host uptime for " + computer.getName()
                    + ", will retry next check. Exception: " + e);
            return 1;
        }
        //on rare occasions, AWS may return fault instance which shows running in AWS console but can not be connected.
        //need terminate such fault instance by {@link #STARTUP_TIMEOUT}
        if (computer.isOffline() && uptime < TimeUnit2.MINUTES.toMillis(STARTUP_TIMEOUT)) {
            return 1;
        }
        final long idleMilliseconds = System.currentTimeMillis() - computer.getIdleStartMilliseconds();
        if (idleTerminationMinutes > 0) {
            // TODO: really think about the right strategy here, see
            // JENKINS-23792
            if (idleMilliseconds > TimeUnit2.MINUTES.toMillis(idleTerminationMinutes)) {
                LOGGER.info("Idle timeout of " + computer.getName() + " after "
                        + TimeUnit2.MILLISECONDS.toMinutes(idleMilliseconds) + " idle minutes");
                computer.getNode().idleTimeout();
            }
        } else {
            final int freeSecondsLeft = (60 * 60)
                    - (int) (TimeUnit2.SECONDS.convert(uptime, TimeUnit2.MILLISECONDS) % (60 * 60));
            // if we have less "free" (aka already paid for) time left than
            // our idle time, stop/terminate the instance
            // See JENKINS-23821
            if (freeSecondsLeft <= TimeUnit.MINUTES.toSeconds(Math.abs(idleTerminationMinutes))) {
                LOGGER.info("Idle timeout of " + computer.getName() + " after "
                        + TimeUnit2.MILLISECONDS.toMinutes(idleMilliseconds) + " idle minutes, with "
                        + TimeUnit2.MILLISECONDS.toMinutes(freeSecondsLeft)
                        + " minutes remaining in billing period");
                computer.getNode().idleTimeout();
            }
        }
    }
    return 1;
}

From source file:com.linkedin.pinot.integration.tests.HybridClusterIntegrationTest.java

@BeforeClass
public void setUp() throws Exception {
    //Clean up/*from  w ww  .j  a v a2 s  . c o m*/
    ensureDirectoryExistsAndIsEmpty(_tmpDir);
    ensureDirectoryExistsAndIsEmpty(_segmentDir);
    ensureDirectoryExistsAndIsEmpty(_tarDir);

    // Start Zk, Kafka and Pinot
    startHybridCluster();

    // Unpack the Avro files
    TarGzCompressionUtils.unTar(new File(TestUtils.getFileFromResourceUrl(OfflineClusterIntegrationTest.class
            .getClassLoader().getResource("On_Time_On_Time_Performance_2014_100k_subset_nonulls.tar.gz"))),
            _tmpDir);

    _tmpDir.mkdirs();

    final List<File> avroFiles = getAllAvroFiles();

    File schemaFile = getSchemaFile();
    schema = Schema.fromFile(schemaFile);
    addSchema(schemaFile, schema.getSchemaName());
    final List<String> invertedIndexColumns = makeInvertedIndexColumns();
    final String sortedColumn = makeSortedColumn();

    // Create Pinot table
    addHybridTable("mytable", "DaysSinceEpoch", "daysSinceEpoch", KafkaStarterUtils.DEFAULT_ZK_STR, KAFKA_TOPIC,
            schema.getSchemaName(), TENANT_NAME, TENANT_NAME, avroFiles.get(0), sortedColumn,
            invertedIndexColumns, null);
    LOGGER.info("Running with Sorted column=" + sortedColumn + " and inverted index columns = "
            + invertedIndexColumns);

    // Create a subset of the first 8 segments (for offline) and the last 6 segments (for realtime)
    final List<File> offlineAvroFiles = getOfflineAvroFiles(avroFiles);
    final List<File> realtimeAvroFiles = getRealtimeAvroFiles(avroFiles);

    // Load data into H2
    ExecutorService executor = Executors.newCachedThreadPool();
    setupH2AndInsertAvro(avroFiles, executor);

    // Create segments from Avro data
    LOGGER.info("Creating offline segments from avro files " + offlineAvroFiles);
    buildSegmentsFromAvro(offlineAvroFiles, executor, 0, _segmentDir, _tarDir, "mytable", false, null);

    // Initialize query generator
    setupQueryGenerator(avroFiles, executor);

    executor.shutdown();
    executor.awaitTermination(10, TimeUnit.MINUTES);

    // Set up a Helix spectator to count the number of segments that are uploaded and unlock the latch once 12 segments are online
    final CountDownLatch latch = new CountDownLatch(1);
    HelixManager manager = HelixManagerFactory.getZKHelixManager(getHelixClusterName(), "test_instance",
            InstanceType.SPECTATOR, ZkStarter.DEFAULT_ZK_STR);
    manager.connect();
    manager.addExternalViewChangeListener(new ExternalViewChangeListener() {
        @Override
        public void onExternalViewChange(List<ExternalView> externalViewList,
                NotificationContext changeContext) {
            for (ExternalView externalView : externalViewList) {
                if (externalView.getId().contains("mytable")) {

                    Set<String> partitionSet = externalView.getPartitionSet();
                    if (partitionSet.size() == offlineSegmentCount) {
                        int onlinePartitionCount = 0;

                        for (String partitionId : partitionSet) {
                            Map<String, String> partitionStateMap = externalView.getStateMap(partitionId);
                            if (partitionStateMap.containsValue("ONLINE")) {
                                onlinePartitionCount++;
                            }
                        }

                        if (onlinePartitionCount == offlineSegmentCount) {
                            System.out.println("Got " + offlineSegmentCount
                                    + " online tables, unlatching the main thread");
                            latch.countDown();
                        }
                    }
                }
            }
        }
    });

    // Upload the segments
    int i = 0;
    for (String segmentName : _tarDir.list()) {
        System.out.println("Uploading segment " + (i++) + " : " + segmentName);
        File file = new File(_tarDir, segmentName);
        FileUploadUtils.sendSegmentFile("localhost", "8998", segmentName, new FileInputStream(file),
                file.length());
    }

    // Wait for all offline segments to be online
    latch.await();

    // Load realtime data into Kafka
    LOGGER.info("Pushing data from realtime avro files " + realtimeAvroFiles);
    pushAvroIntoKafka(realtimeAvroFiles, KafkaStarterUtils.DEFAULT_KAFKA_BROKER, KAFKA_TOPIC);

    // Wait until the Pinot event count matches with the number of events in the Avro files
    int pinotRecordCount, h2RecordCount;
    long timeInFiveMinutes = System.currentTimeMillis() + 5 * 60 * 1000L;

    Statement statement = _connection.createStatement(ResultSet.TYPE_FORWARD_ONLY, ResultSet.CONCUR_READ_ONLY);
    statement.execute("select count(*) from mytable");
    ResultSet rs = statement.getResultSet();
    rs.first();
    h2RecordCount = rs.getInt(1);
    rs.close();

    waitForRecordCountToStabilizeToExpectedCount(h2RecordCount, timeInFiveMinutes);
}

From source file:com.spotify.helios.ZooKeeperTestingClusterManager.java

@Override
public void start() {
    try {//from  ww w .ja va 2 s . c om
        start0();
    } catch (Exception e) {
        throw Throwables.propagate(e);
    }

    curator = createCurator(connectString(zkAddresses));

    try {
        awaitUp(2, TimeUnit.MINUTES);
    } catch (TimeoutException e) {
        throw Throwables.propagate(e);
    }
}

From source file:io.fabric8.apiman.rest.Kubernetes2ApimanFilter.java

/**
 * @see javax.servlet.Filter#init(javax.servlet.FilterConfig)
 *//*from  ww w  .j a v  a 2 s  .co m*/
@Override
public void init(FilterConfig config) throws ServletException {
    // maximum 10000 tokens in the cache
    Number nsCacheMaxsize = Systems.getEnvVarOrSystemProperty(NS_CACHE_MAXSIZE, 10000);
    // cache for 60  min
    Number nsTTL = Systems.getEnvVarOrSystemProperty(NS_TTL, 10);
    if (nsCache == null) {
        nsCache = CacheBuilder.newBuilder().concurrencyLevel(4) // allowed concurrency among update operations
                .maximumSize(nsCacheMaxsize.longValue()).expireAfterWrite(nsTTL.longValue(), TimeUnit.MINUTES)
                .build(new CacheLoader<String, ApimanInfo>() {
                    public ApimanInfo load(String authToken) throws Exception {
                        return syncKubernetesToApiman(authToken);
                    }
                });
    }
    boolean isTestMode = getSystemPropertyOrEnvVar(ApimanStarter.APIMAN_TESTMODE, false);
    if (!isTestMode && !isWatching) {
        watchNamespaces();
    }

}

From source file:ms1quant.MS1Quant.java

/**
 * @param args the command line arguments MS1Quant parameterfile
 *///from   w  ww .j a va  2  s .  c o m
public static void main(String[] args) throws Exception {

    BufferedReader reader = null;
    try {
        System.out.println(
                "=================================================================================================");
        System.out.println("Umpire MS1 quantification and feature detection analysis (version: "
                + UmpireInfo.GetInstance().Version + ")");
        if (args.length < 3 || !args[1].startsWith("-mode")) {
            System.out
                    .println("command : java -jar -Xmx10G MS1Quant.jar ms1quant.params -mode[1 or 2] [Option]");
            System.out.println("\n-mode");
            System.out.println("\t1:Single file mode--> mzXML_file PepXML_file");
            System.out.println("\t\tEx: -mode1 file1.mzXML file1.pep.xml");
            System.out.println(
                    "\t2:Folder mode--> mzXML_Folder PepXML_Folder, all generated csv tables will be merged into a single csv file");
            System.out.println("\t\tEx: -mode2 /data/mzxml/ /data/pepxml/");
            System.out.println("\nOptions");
            System.out.println(
                    "\t-C\tNo of concurrent files to be processed (only for folder mode), Ex. -C5, default:1");
            System.out.println("\t-p\tMinimum probability, Ex. -p0.9, default:0.9");
            System.out.println("\t-ID\tDetect identified feature only");
            System.out.println("\t-O\toutput folder, Ex. -O/data/");
            return;
        }
        ConsoleLogger consoleLogger = new ConsoleLogger();
        consoleLogger.SetConsoleLogger(Level.DEBUG);
        consoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "ms1quant_debug.log");
        Logger logger = Logger.getRootLogger();
        logger.debug("Command: " + Arrays.toString(args));
        logger.info("MS1Quant version: " + UmpireInfo.GetInstance().Version);

        String parameterfile = args[0];
        logger.info("Parameter file: " + parameterfile);
        File paramfile = new File(parameterfile);
        if (!paramfile.exists()) {
            logger.error("Parameter file " + paramfile.getAbsolutePath()
                    + " cannot be found. The program will exit.");
        }

        reader = new BufferedReader(new FileReader(paramfile.getAbsolutePath()));
        String line = "";
        InstrumentParameter param = new InstrumentParameter(InstrumentParameter.InstrumentType.TOF5600);
        int NoCPUs = 2;
        int NoFile = 1;
        param.DetermineBGByID = false;
        param.EstimateBG = true;

        //<editor-fold defaultstate="collapsed" desc="Read parameter file">
        while ((line = reader.readLine()) != null) {
            if (!"".equals(line) && !line.startsWith("#")) {
                logger.info(line);
                //System.out.println(line);
                if (line.split("=").length < 2) {
                    continue;
                }
                if (line.split("=").length < 2) {
                    continue;
                }
                String type = line.split("=")[0].trim();
                if (type.startsWith("para.")) {
                    type = type.replace("para.", "SE.");
                }
                String value = line.split("=")[1].trim();
                switch (type) {
                case "Thread": {
                    NoCPUs = Integer.parseInt(value);
                    break;
                }
                //<editor-fold defaultstate="collapsed" desc="instrument parameters">

                case "SE.MS1PPM": {
                    param.MS1PPM = Float.parseFloat(value);
                    break;
                }
                case "SE.MS2PPM": {
                    param.MS2PPM = Float.parseFloat(value);
                    break;
                }
                case "SE.SN": {
                    param.SNThreshold = Float.parseFloat(value);
                    break;
                }
                case "SE.MS2SN": {
                    param.MS2SNThreshold = Float.parseFloat(value);
                    break;
                }
                case "SE.MinMSIntensity": {
                    param.MinMSIntensity = Float.parseFloat(value);
                    break;
                }
                case "SE.MinMSMSIntensity": {
                    param.MinMSMSIntensity = Float.parseFloat(value);
                    break;
                }
                case "SE.MinRTRange": {
                    param.MinRTRange = Float.parseFloat(value);
                    break;
                }
                case "SE.MaxNoPeakCluster": {
                    param.MaxNoPeakCluster = Integer.parseInt(value);
                    param.MaxMS2NoPeakCluster = Integer.parseInt(value);
                    break;
                }
                case "SE.MinNoPeakCluster": {
                    param.MinNoPeakCluster = Integer.parseInt(value);
                    param.MinMS2NoPeakCluster = Integer.parseInt(value);
                    break;
                }
                case "SE.MinMS2NoPeakCluster": {
                    param.MinMS2NoPeakCluster = Integer.parseInt(value);
                    break;
                }
                case "SE.MaxCurveRTRange": {
                    param.MaxCurveRTRange = Float.parseFloat(value);
                    break;
                }
                case "SE.Resolution": {
                    param.Resolution = Integer.parseInt(value);
                    break;
                }
                case "SE.RTtol": {
                    param.RTtol = Float.parseFloat(value);
                    break;
                }
                case "SE.NoPeakPerMin": {
                    param.NoPeakPerMin = Integer.parseInt(value);
                    break;
                }
                case "SE.StartCharge": {
                    param.StartCharge = Integer.parseInt(value);
                    break;
                }
                case "SE.EndCharge": {
                    param.EndCharge = Integer.parseInt(value);
                    break;
                }
                case "SE.MS2StartCharge": {
                    param.MS2StartCharge = Integer.parseInt(value);
                    break;
                }
                case "SE.MS2EndCharge": {
                    param.MS2EndCharge = Integer.parseInt(value);
                    break;
                }
                case "SE.NoMissedScan": {
                    param.NoMissedScan = Integer.parseInt(value);
                    break;
                }
                case "SE.Denoise": {
                    param.Denoise = Boolean.valueOf(value);
                    break;
                }
                case "SE.EstimateBG": {
                    param.EstimateBG = Boolean.valueOf(value);
                    break;
                }
                case "SE.RemoveGroupedPeaks": {
                    param.RemoveGroupedPeaks = Boolean.valueOf(value);
                    break;
                }
                case "SE.MinFrag": {
                    param.MinFrag = Integer.parseInt(value);
                    break;
                }
                case "SE.IsoPattern": {
                    param.IsoPattern = Float.valueOf(value);
                    break;
                }
                case "SE.StartRT": {
                    param.startRT = Float.valueOf(value);
                }
                case "SE.EndRT": {
                    param.endRT = Float.valueOf(value);
                }

                //</editor-fold>
                }
            }
        }
        //</editor-fold>

        int mode = 1;
        if (args[1].equals("-mode2")) {
            mode = 2;
        } else if (args[1].equals("-mode1")) {
            mode = 1;
        } else {
            logger.error("-mode number not recongized. The program will exit.");
        }

        String mzXML = "";
        String pepXML = "";
        String mzXMLPath = "";
        String pepXMLPath = "";
        File mzXMLfile = null;
        File pepXMLfile = null;
        File mzXMLfolder = null;
        File pepXMLfolder = null;
        int idx = 0;
        if (mode == 1) {
            mzXML = args[2];
            logger.info("Mode1 mzXML file: " + mzXML);
            mzXMLfile = new File(mzXML);
            if (!mzXMLfile.exists()) {
                logger.error("Mode1 mzXML file " + mzXMLfile.getAbsolutePath()
                        + " cannot be found. The program will exit.");
                return;
            }
            pepXML = args[3];
            logger.info("Mode1 pepXML file: " + pepXML);
            pepXMLfile = new File(pepXML);
            if (!pepXMLfile.exists()) {
                logger.error("Mode1 pepXML file " + pepXMLfile.getAbsolutePath()
                        + " cannot be found. The program will exit.");
                return;
            }
            idx = 4;
        } else if (mode == 2) {
            mzXMLPath = args[2];
            logger.info("Mode2 mzXML folder: " + mzXMLPath);
            mzXMLfolder = new File(mzXMLPath);
            if (!mzXMLfolder.exists()) {
                logger.error("Mode2 mzXML folder " + mzXMLfolder.getAbsolutePath()
                        + " does not exist. The program will exit.");
                return;
            }
            pepXMLPath = args[3];
            logger.info("Mode2 pepXML folder: " + pepXMLPath);
            pepXMLfolder = new File(pepXMLPath);
            if (!pepXMLfolder.exists()) {
                logger.error("Mode2 pepXML folder " + pepXMLfolder.getAbsolutePath()
                        + " does not exist. The program will exit.");
                return;
            }
            idx = 4;
        }

        String outputfolder = "";
        float MinProb = 0f;
        for (int i = idx; i < args.length; i++) {
            if (args[i].startsWith("-")) {
                if (args[i].equals("-ID")) {
                    param.TargetIDOnly = true;
                    logger.info("Detect ID feature only: true");
                }
                if (args[i].startsWith("-O")) {
                    outputfolder = args[i].substring(2);
                    logger.info("Output folder: " + outputfolder);

                    File outputfile = new File(outputfolder);
                    if (!outputfolder.endsWith("\\") | outputfolder.endsWith("/")) {
                        outputfolder += "/";
                    }
                    if (!outputfile.exists()) {
                        outputfile.mkdir();
                    }
                }
                if (args[i].startsWith("-C")) {
                    try {
                        NoFile = Integer.parseInt(args[i].substring(2));
                        logger.info("No of concurrent files: " + NoFile);
                    } catch (Exception ex) {
                        logger.error(args[i]
                                + " is not a correct integer format, will process only one file at a time.");
                    }
                }
                if (args[i].startsWith("-p")) {
                    try {
                        MinProb = Float.parseFloat(args[i].substring(2));
                        logger.info("probability threshold: " + MinProb);
                    } catch (Exception ex) {
                        logger.error(args[i] + " is not a correct format, will use 0 as threshold instead.");
                    }
                }
            }
        }

        reader.close();
        TandemParam tandemparam = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600);
        PTMManager.GetInstance();

        if (param.TargetIDOnly) {
            param.EstimateBG = false;
            param.ApexDelta = 1.5f;
            param.NoMissedScan = 10;
            param.MiniOverlapP = 0.2f;
            param.RemoveGroupedPeaks = false;
            param.CheckMonoIsotopicApex = false;
            param.DetectByCWT = false;
            param.FillGapByBK = false;
            param.IsoCorrThreshold = -1f;
            param.SmoothFactor = 3;
        }

        if (mode == 1) {
            logger.info("Processing " + mzXMLfile.getAbsolutePath() + "....");
            long time = System.currentTimeMillis();
            LCMSPeakMS1 LCMS1 = new LCMSPeakMS1(mzXMLfile.getAbsolutePath(), NoCPUs);
            LCMS1.SetParameter(param);

            LCMS1.Resume = false;
            if (!param.TargetIDOnly) {
                LCMS1.CreatePeakFolder();
            }
            LCMS1.ExportPeakClusterTable = true;

            if (pepXMLfile.exists()) {
                tandemparam.InteractPepXMLPath = pepXMLfile.getAbsolutePath();
                LCMS1.ParsePepXML(tandemparam, MinProb);
                logger.info("No. of PSMs included: " + LCMS1.IDsummary.PSMList.size());
                logger.info("No. of Peptide ions included: " + LCMS1.IDsummary.GetPepIonList().size());
            }

            if (param.TargetIDOnly) {
                LCMS1.SaveSerializationFile = false;
            }

            if (param.TargetIDOnly || !LCMS1.ReadPeakCluster()) {
                LCMS1.PeakClusterDetection();
            }

            if (pepXMLfile.exists()) {
                LCMS1.AssignQuant(false);
                LCMS1.IDsummary.ExportPepID(outputfolder);
            }
            time = System.currentTimeMillis() - time;
            logger.info(LCMS1.ParentmzXMLName + " processed time:"
                    + String.format("%d hour, %d min, %d sec", TimeUnit.MILLISECONDS.toHours(time),
                            TimeUnit.MILLISECONDS.toMinutes(time)
                                    - TimeUnit.HOURS.toMinutes(TimeUnit.MILLISECONDS.toHours(time)),
                            TimeUnit.MILLISECONDS.toSeconds(time)
                                    - TimeUnit.MINUTES.toSeconds(TimeUnit.MILLISECONDS.toMinutes(time))));
            LCMS1.BaseClearAllPeaks();
            LCMS1.SetSpectrumParser(null);
            LCMS1.IDsummary = null;
            LCMS1 = null;
            System.gc();
        } else if (mode == 2) {

            LCMSID IDsummary = new LCMSID("", "", "");
            logger.info("Parsing all pepXML files in " + pepXMLPath + "....");
            for (File file : pepXMLfolder.listFiles()) {
                if (file.getName().toLowerCase().endsWith("pep.xml")
                        || file.getName().toLowerCase().endsWith("pepxml")) {
                    PepXMLParser pepXMLParser = new PepXMLParser(IDsummary, file.getAbsolutePath(), MinProb);
                }
            }
            HashMap<String, LCMSID> LCMSIDMap = IDsummary.GetLCMSIDFileMap();

            ExecutorService executorPool = null;
            executorPool = Executors.newFixedThreadPool(NoFile);

            logger.info("Processing all mzXML files in " + mzXMLPath + "....");
            for (File file : mzXMLfolder.listFiles()) {
                if (file.getName().toLowerCase().endsWith("mzxml")) {
                    LCMSID id = LCMSIDMap.get(FilenameUtils.getBaseName(file.getName()));
                    if (id == null || id.PSMList == null) {
                        logger.warn("No IDs found in :" + FilenameUtils.getBaseName(file.getName())
                                + ". Quantification for this file is skipped");
                        continue;
                    }
                    if (!id.PSMList.isEmpty()) {
                        MS1TargetQuantThread thread = new MS1TargetQuantThread(file, id, NoCPUs, outputfolder,
                                param);
                        executorPool.execute(thread);
                    }
                }
            }
            LCMSIDMap.clear();
            LCMSIDMap = null;
            IDsummary = null;
            executorPool.shutdown();
            try {
                executorPool.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS);
            } catch (InterruptedException e) {
                logger.info("interrupted..");
            }

            if (outputfolder == null | outputfolder.equals("")) {
                outputfolder = mzXMLPath;
            }

            logger.info("Merging PSM files..");
            File output = new File(outputfolder);
            FileWriter writer = new FileWriter(output.getAbsolutePath() + "/PSM_merge.csv");
            boolean header = false;
            for (File csvfile : output.listFiles()) {
                if (csvfile.getName().toLowerCase().endsWith("_psms.csv")) {
                    BufferedReader outreader = new BufferedReader(new FileReader(csvfile));
                    String outline = outreader.readLine();
                    if (!header) {
                        writer.write(outline + "\n");
                        header = true;
                    }
                    while ((outline = outreader.readLine()) != null) {
                        writer.write(outline + "\n");
                    }
                    outreader.close();
                    csvfile.delete();
                }
            }
            writer.close();
        }
        logger.info("MS1 quant module is complete.");
    } catch (Exception e) {
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e));
        throw e;
    }
}

From source file:gov.llnl.lc.smt.command.gui.SmtGui.java

@Override
public boolean doCommand(SmtConfig config) throws Exception {
    boolean exit = false;

    MessageManager.getInstance()//from  w  w  w . j av a  2 s  .  co  m
            .postMessage(new SmtMessage(SmtMessageType.SMT_MSG_INIT, "** Initializing the ServiceUpdater"));
    initServiceUpdater(config);
    MessageManager.getInstance().postMessage(
            new SmtMessage(SmtMessageType.SMT_MSG_INIT, "** Finished ServiceUpdater initialization"));

    if (OMService == null) {
        System.err.println("The service is null");
    } else {
        // this is the GUI command, and it can take a subcommand and an argument
        String subCommand = null;
        String subCommandArg = null;

        if (config != null) {
            Map<String, String> map = config.getConfigMap();
            subCommand = map.get(SmtProperty.SMT_SUBCOMMAND.getName());
            subCommandArg = map.get(subCommand);
        }

        // start all managers
        /* refer to SmtConsole, may need a manager to do this more cleanly */
        exit = (UpdateService == null) || (OMService == null);
        if (!exit) {
            logger.severe("Starting the SMT GUI Application Now");
            MessageManager.getInstance().postMessage(
                    new SmtMessage(SmtMessageType.SMT_MSG_INIT, "ready to start the graphical interface"));
            SmtGuiApplication.go(UpdateService, OMService, this);
        } else
            logger.severe("Could not start the SMT GUI Application, check service updater");

        // infinite wait loop
        while (!exit)
            TimeUnit.MINUTES.sleep(5);
    }
    return true;
}

From source file:it.anyplace.sync.bep.IndexBrowser.java

private IndexBrowser(IndexRepository indexRepository, IndexHandler indexHandler, String folder,
        boolean includeParentInList, boolean allowParentInRoot, Comparator<FileInfo> ordering) {
    checkNotNull(indexRepository);/*from   w w  w .ja  va  2s  . c o m*/
    checkNotNull(indexHandler);
    checkNotNull(emptyToNull(folder));
    this.indexRepository = indexRepository;
    this.indexHandler = indexHandler;
    this.indexHandler.getEventBus().register(indexHandlerEventListener);
    this.folder = folder;
    this.includeParentInList = includeParentInList;
    this.allowParentInRoot = allowParentInRoot;
    this.ordering = ordering;
    PARENT_FILE_INFO = FileInfo.newBuilder().setFolder(folder).setTypeDir().setPath(PARENT_PATH).build();
    ROOT_FILE_INFO = FileInfo.newBuilder().setFolder(folder).setTypeDir().setPath(ROOT_PATH).build();
    this.currentPath = ROOT_PATH;
    executorService.scheduleWithFixedDelay(new Runnable() {
        @Override
        public void run() {
            logger.debug("folder cache cleanup");
            listFolderCache.cleanUp();
            fileInfoCache.cleanUp();
        }

    }, 1, 1, TimeUnit.MINUTES);
}