Example usage for java.util.concurrent TimeUnit NANOSECONDS

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

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Prototype

TimeUnit NANOSECONDS

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Document

Time unit representing one thousandth of a microsecond.

Usage

From source file:ms1quant.MS1Quant.java

/**
 * @param args the command line arguments MS1Quant parameterfile
 *///from   w ww.  jav a  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:io.netty.handler.timeout.IdleStateHandler.java

/**
 * Return the writerIdleTime that was given when instance this class in milliseconds.
 *
 *///from  w ww .  java 2  s  .  co  m
public long getWriterIdleTimeInMillis() {
    return TimeUnit.NANOSECONDS.toMillis(writerIdleTimeNanos);
}

From source file:org.apache.solr.client.solrj.impl.HttpClusterStateProvider.java

@Override
public Set<String> getLiveNodes() {
    if (liveNodes == null) {
        throw new RuntimeException(
                "We don't know of any live_nodes to fetch the" + " latest live_nodes information from. "
                        + "If you think your Solr cluster is up and is accessible,"
                        + " you could try re-creating a new CloudSolrClient using working"
                        + " solrUrl(s) or zkHost(s).");
    }/*w  w  w  . j  a  v  a 2s.  co  m*/
    if (TimeUnit.SECONDS.convert((System.nanoTime() - liveNodesTimestamp),
            TimeUnit.NANOSECONDS) > getCacheTimeout()) {
        for (String nodeName : liveNodes) {
            try (HttpSolrClient client = new HttpSolrClient.Builder()
                    .withBaseSolrUrl(Utils.getBaseUrlForNodeName(nodeName, urlScheme))
                    .withHttpClient(httpClient).build()) {
                Set<String> liveNodes = fetchLiveNodes(client);
                this.liveNodes = (liveNodes);
                liveNodesTimestamp = System.nanoTime();
                return liveNodes;
            } catch (Exception e) {
                log.warn("Attempt to fetch live_nodes from " + Utils.getBaseUrlForNodeName(nodeName, urlScheme)
                        + " failed.", e);
            }
        }
        throw new RuntimeException("Tried fetching live_nodes using all the node names we knew of, i.e. "
                + liveNodes + ". However, " + "succeeded in obtaining the cluster state from none of them."
                + "If you think your Solr cluster is up and is accessible,"
                + " you could try re-creating a new CloudSolrClient using working"
                + " solrUrl(s) or zkHost(s).");
    } else {
        return liveNodes; // cached copy is fresh enough
    }
}

From source file:com.netflix.genie.web.services.impl.HttpFileTransferImplTest.java

/**
 * Make sure can't get a file if the output location is a directory.
 *
 * @throws GenieException On Error/* w w  w . ja va2 s .com*/
 * @throws IOException    On Error
 */
@Test(expected = ResourceAccessException.class)
public void cantGetWithDirectoryAsOutput() throws GenieException, IOException {
    this.server.expect(MockRestRequestMatchers.requestTo(TEST_URL))
            .andExpect(MockRestRequestMatchers.method(HttpMethod.GET))
            .andRespond(MockRestResponseCreators.withSuccess("junk".getBytes(Charset.forName("UTF-8")),
                    MediaType.APPLICATION_OCTET_STREAM));
    try {
        this.httpFileTransfer.getFile(TEST_URL, this.temporaryFolder.getRoot().getCanonicalPath());
    } finally {
        Mockito.verify(this.downloadTimerId, Mockito.times(1))
                .withTags(MetricsUtils.newFailureTagsMapForException(new ResourceAccessException("test")));
        Mockito.verify(this.downloadTimer, Mockito.times(1)).record(Mockito.anyLong(),
                Mockito.eq(TimeUnit.NANOSECONDS));
    }
}

From source file:com.keedio.nifi.processors.azure.blob.FetchAzureBlobObject.java

@Override
public void onTrigger(final ProcessContext context, final ProcessSession session) throws ProcessException {
    FlowFile flowFile = session.get();/*from w  w w .j av  a  2s. c o  m*/
    if (flowFile == null) {
        return;
    }
    final long startNanos = System.nanoTime();

    final String blobObject = context.getProperty(AZURE_STORAGE_BLOB_OBJECT)
            .evaluateAttributeExpressions(flowFile).getValue();

    final AzureBlobConnectionService connectionService = context.getProperty(AZURE_STORAGE_CONTROLLER_SERVICE)
            .asControllerService(AzureBlobConnectionService.class);

    CloudBlobContainer blobContainer;
    try {
        blobContainer = connectionService.getCloudBlobContainerReference();
    } catch (URISyntaxException | InvalidKeyException | StorageException e) {
        getLogger().error("Failed to retrieve Azure Object for {}; routing to failure",
                new Object[] { flowFile, e });
        flowFile = session.penalize(flowFile);
        session.transfer(flowFile, REL_FAILURE);
        return;
    }

    CloudBlobWrapper blockBlob = null;
    try {
        blockBlob = new CloudBlobWrapper("overwrite", blobObject, blobContainer);
        //blobContainer.getBlockBlobReference(blobObject);
    } catch (Exception e) {
        getLogger().error("Caught exception while retrieving blob object reference", e);
        flowFile = session.penalize(flowFile);
        session.transfer(flowFile, REL_FAILURE);
        return;
    }

    InputStream blockBlobStream = null;
    ByteArrayOutputStream outputStream = null;
    try {
        outputStream = new ByteArrayOutputStream();
        blockBlob.download(outputStream);
        outputStream.flush();

        blockBlobStream = new ByteArrayInputStream(outputStream.toByteArray());

        flowFile = session.importFrom(blockBlobStream, flowFile);
    } catch (IOException | StorageException e) {
        getLogger().error("Caught exception while retrieving blob object", e);
    } finally {
        IOUtils.closeQuietly(blockBlobStream);
        IOUtils.closeQuietly(outputStream);
    }

    final Map<String, String> attributes = new HashMap<>();

    copyAttributes(connectionService.getContainerName(), blobObject, blockBlob, attributes);

    if (!attributes.isEmpty()) {
        flowFile = session.putAllAttributes(flowFile, attributes);
    }

    session.transfer(flowFile, REL_SUCCESS);

    final long transferMillis = TimeUnit.NANOSECONDS.toMillis(System.nanoTime() - startNanos);
    getLogger().info("Successfully retrieved Blob Object for {} in {} millis; routing to success",
            new Object[] { flowFile, transferMillis });
    session.getProvenanceReporter().fetch(flowFile, blockBlob.toString(), transferMillis);
}

From source file:com.bitplan.mjpegstreamer.MJpegRunnerBase.java

/**
 * get the total elapsedTime//from   w ww . j  a  v  a  2 s .co m
 * @return the total elapsed time in milliseconds
 */
public long elapsedTimeMillisecs() {
    long elapsed = this.now - this.firstFrameNanoTime;
    long result = TimeUnit.MILLISECONDS.convert(elapsed, TimeUnit.NANOSECONDS);
    return result;
}

From source file:org.apache.hadoop.hbase.client.AsyncHBaseAdmin.java

private <T> AdminRequestCallerBuilder<T> newAdminCaller() {
    return this.connection.callerFactory.<T>adminRequest().rpcTimeout(rpcTimeoutNs, TimeUnit.NANOSECONDS)
            .operationTimeout(operationTimeoutNs, TimeUnit.NANOSECONDS).pause(pauseNs, TimeUnit.NANOSECONDS)
            .maxAttempts(maxAttempts).startLogErrorsCnt(startLogErrorsCnt);
}

From source file:org.apache.jackrabbit.oak.plugins.blob.datastore.DataStoreBlobStore.java

@Override
public String writeBlob(InputStream stream) throws IOException {
    boolean threw = true;
    try {/*from  w  w w . j ava  2 s  .  c o  m*/
        long start = System.nanoTime();
        checkNotNull(stream);
        DataRecord dr = writeStream(stream);
        String id = getBlobId(dr);
        threw = false;
        stats.uploaded(System.nanoTime() - start, TimeUnit.NANOSECONDS, dr.getLength());
        stats.uploadCompleted(id);
        return id;
    } catch (DataStoreException e) {
        throw new IOException(e);
    } finally {
        //DataStore does not closes the stream internally
        //So close the stream explicitly
        Closeables.close(stream, threw);
    }
}

From source file:com.netflix.genie.web.jobs.workflow.impl.JobKickoffTask.java

/**
 * {@inheritDoc}//  w ww  . ja va 2  s  .  co m
 */
@Override
public void executeTask(@NotNull final Map<String, Object> context) throws GenieException, IOException {
    final long start = System.nanoTime();
    final Set<Tag> tags = Sets.newHashSet();
    try {
        final JobExecutionEnvironment jobExecEnv = (JobExecutionEnvironment) context
                .get(JobConstants.JOB_EXECUTION_ENV_KEY);
        final String jobWorkingDirectory = jobExecEnv.getJobWorkingDir().getCanonicalPath();
        final JobRequest jobRequest = jobExecEnv.getJobRequest();
        final String user = jobRequest.getUser();
        final Writer writer = (Writer) context.get(JobConstants.WRITER_KEY);
        final String jobId = jobRequest.getId()
                .orElseThrow(() -> new GeniePreconditionException("No job id found. Unable to continue."));
        log.info("Starting Job Kickoff Task for job {}", jobId);

        // At this point all contents are written to the run script and we call an explicit flush and close to write
        // the contents to the file before we execute it.
        try {
            writer.flush();
            writer.close();
        } catch (IOException e) {
            throw new GenieServerException("Failed to execute job", e);
        }
        // Create user, if enabled
        if (isUserCreationEnabled) {
            createUser(user, jobRequest.getGroup().orElse(null));
        }
        final List<String> command = new ArrayList<>();

        // If the OS is linux use setsid to launch the process so that the entire process tree
        // is launched in process group id which is the same as the pid of the parent process
        if (SystemUtils.IS_OS_LINUX) {
            command.add("setsid");
        }

        // Set the ownership to the user and run as the user, if enabled
        if (isRunAsUserEnabled) {
            changeOwnershipOfDirectory(jobWorkingDirectory, user);

            // This is needed because the genie.log file is still generated as the user running Genie system.
            makeDirGroupWritable(jobWorkingDirectory + "/genie/logs");
            command.add("sudo");
            command.add("-u");
            command.add(user);
        }

        final String runScript = jobWorkingDirectory + JobConstants.FILE_PATH_DELIMITER
                + JobConstants.GENIE_JOB_LAUNCHER_SCRIPT;
        command.add(runScript);

        // Cannot convert to executor because it does not provide an api to get process id.
        final ProcessBuilder pb = new ProcessBuilder(command).directory(jobExecEnv.getJobWorkingDir())
                .redirectOutput(new File(jobExecEnv.getJobWorkingDir() + JobConstants.GENIE_LOG_PATH))
                .redirectError(new File(jobExecEnv.getJobWorkingDir() + JobConstants.GENIE_LOG_PATH));

        //
        // Check if file can be executed. This is to fix issue where execution of the run script fails because
        // the file may be used by some other program
        //
        canExecute(runScript);
        try {
            final Process process = pb.start();
            final int processId = this.getProcessId(process);
            final Instant timeout = Instant.now().plus(
                    jobRequest.getTimeout().orElse(JobRequest.DEFAULT_TIMEOUT_DURATION), ChronoUnit.SECONDS);
            final JobExecution jobExecution = new JobExecution.Builder(this.hostname).withId(jobId)
                    .withProcessId(processId).withCheckDelay(jobExecEnv.getCommand().getCheckDelay())
                    .withTimeout(timeout).withMemory(jobExecEnv.getMemory()).build();
            context.put(JobConstants.JOB_EXECUTION_DTO_KEY, jobExecution);
        } catch (final IOException ie) {
            throw new GenieServerException("Unable to start command " + String.valueOf(command), ie);
        }
        log.info("Finished Job Kickoff Task for job {}", jobId);
        MetricsUtils.addSuccessTags(tags);
    } catch (final Throwable t) {
        MetricsUtils.addFailureTagsWithException(tags, t);
        throw t;
    } finally {
        this.getRegistry().timer(JOB_KICKOFF_TASK_TIMER_NAME, tags).record(System.nanoTime() - start,
                TimeUnit.NANOSECONDS);
    }
}

From source file:com.netflix.genie.web.services.impl.S3FileTransferImpl.java

/**
 * {@inheritDoc}/*from   ww  w.  ja v  a 2  s  .  c  om*/
 */
@Override
public long getLastModifiedTime(final String path) throws GenieException {
    final long start = System.nanoTime();
    final long lastModTime;
    final Set<Tag> tags = Sets.newHashSet();
    try {
        final AmazonS3URI s3Uri = this.getS3Uri(path);
        try {
            final ObjectMetadata o = this.s3ClientFactory.getClient(s3Uri).getObjectMetadata(s3Uri.getBucket(),
                    s3Uri.getKey());
            lastModTime = o.getLastModified().getTime();
        } catch (final Exception ase) {
            final String message = String.format("Failed getting the metadata of the s3 file %s", path);
            log.error(message);
            throw new GenieServerException(message, ase);
        }
        MetricsUtils.addSuccessTags(tags);
    } catch (Throwable t) {
        MetricsUtils.addFailureTagsWithException(tags, t);
        throw t;
    } finally {
        this.registry.timer(GET_METADATA_TIMER_NAME, tags).record(System.nanoTime() - start,
                TimeUnit.NANOSECONDS);
    }
    return lastModTime;
}