Example usage for java.util.concurrent ExecutorService execute

List of usage examples for java.util.concurrent ExecutorService execute

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Introduction

In this page you can find the example usage for java.util.concurrent ExecutorService execute.

Prototype

void execute(Runnable command);

Source Link

Document

Executes the given command at some time in the future.

Usage

From source file:com.tage.calcite.adapter.druid.DruidConnectionImpl.java

/** Executes a request and returns the resulting rows as an
 * {@link Enumerable}, running the parser in a thread provided by
 * {@code service}. *//*  w ww  .j  av a2 s  . co  m*/
public Enumerable<Row> enumerable(final com.tage.calcite.adapter.druid.QueryType queryType,
        final String request, final List<String> fieldNames, final ExecutorService service) throws IOException {
    return new AbstractEnumerable<Row>() {
        public Enumerator<Row> enumerator() {
            final BlockingQueueEnumerator<Row> enumerator = new BlockingQueueEnumerator<>();
            final RunnableQueueSink sink = new RunnableQueueSink() {
                public void send(Row row) throws InterruptedException {
                    enumerator.queue.put(row);
                }

                public void end() {
                    enumerator.done.set(true);
                }

                public void setSourceEnumerable(Enumerable<Row> enumerable) throws InterruptedException {
                    for (Row row : enumerable) {
                        send(row);
                    }
                    end();
                }

                public void run() {
                    try {
                        final Page page = new Page();
                        final List<Primitive> fieldTypes = Collections.nCopies(fieldNames.size(), null);
                        request(queryType, request, this, fieldNames, fieldTypes, page);
                        enumerator.done.set(true);
                    } catch (Throwable e) {
                        enumerator.throwableHolder.set(e);
                        enumerator.done.set(true);
                    }
                }
            };
            service.execute(sink);
            return enumerator;
        }
    };
}

From source file:com.github.cukedoctor.jenkins.CukedoctorPublisher.java

@Override
public void perform(Run<?, ?> build, FilePath workspace, Launcher launcher, TaskListener listener)
        throws IOException, InterruptedException {

    FilePath workspaceJsonSourceDir;//most of the time on slave
    FilePath workspaceJsonTargetDir;//always on master
    if (!hasText(featuresDir)) {
        workspaceJsonSourceDir = workspace;
        workspaceJsonTargetDir = getMasterWorkspaceDir(build);
    } else {/*from  www .j  av a  2s.  com*/
        workspaceJsonSourceDir = new FilePath(workspace, featuresDir);
        workspaceJsonTargetDir = new FilePath(getMasterWorkspaceDir(build), featuresDir);
    }

    logger = listener.getLogger();
    workspaceJsonSourceDir.copyRecursiveTo("**/*.json,**/cukedoctor-intro.adoc,**/cukedoctor.properties",
            workspaceJsonTargetDir);

    System.setProperty("INTRO_CHAPTER_DIR", workspaceJsonTargetDir.getRemote());

    logger.println("");
    logger.println("Generating living documentation for " + build.getFullDisplayName()
            + " with the following arguments: ");
    logger.println("Features dir: " + workspaceJsonSourceDir.getRemote());
    logger.println("Format: " + format.getFormat());
    logger.println("Toc: " + toc.getToc());
    logger.println("Title: " + title);
    logger.println("Numbered: " + Boolean.toString(numbered));
    logger.println("Section anchors: " + Boolean.toString(sectAnchors));
    logger.println("Hide features section: " + Boolean.toString(hideFeaturesSection));
    logger.println("Hide summary: " + Boolean.toString(hideSummary));
    logger.println("Hide scenario keyword: " + Boolean.toString(hideScenarioKeyword));
    logger.println("Hide step time: " + Boolean.toString(hideStepTime));
    logger.println("Hide tags: " + Boolean.toString(hideTags));
    logger.println("");

    Result result = Result.SUCCESS;
    List<Feature> features = FeatureParser.findAndParse(workspaceJsonTargetDir.getRemote());
    if (!features.isEmpty()) {
        if (!hasText(title)) {
            title = "Living Documentation";
        }

        logger.println("Found " + features.size() + " feature(s)...");

        File targetBuildDirectory = new File(build.getRootDir(), CukedoctorBaseAction.BASE_URL);
        if (!targetBuildDirectory.exists()) {
            boolean created = targetBuildDirectory.mkdirs();
            if (!created) {
                listener.error("Could not create file at location: " + targetBuildDirectory.getAbsolutePath());
                result = Result.UNSTABLE;
            }
        }

        GlobalConfig globalConfig = GlobalConfig.getInstance();
        DocumentAttributes documentAttributes = globalConfig.getDocumentAttributes().backend(format.getFormat())
                .toc(toc.getToc()).numbered(numbered).sectAnchors(sectAnchors).docTitle(title);

        globalConfig.getLayoutConfig().setHideFeaturesSection(hideFeaturesSection);

        globalConfig.getLayoutConfig().setHideSummarySection(hideSummary);

        globalConfig.getLayoutConfig().setHideScenarioKeyword(hideScenarioKeyword);

        globalConfig.getLayoutConfig().setHideStepTime(hideStepTime);

        globalConfig.getLayoutConfig().setHideTags(hideTags);

        String outputPath = targetBuildDirectory.getAbsolutePath();
        CukedoctorBuildAction action = new CukedoctorBuildAction(build);
        final ExecutorService pool = Executors.newFixedThreadPool(4);
        if ("all".equals(format.getFormat())) {
            File allHtml = new File(
                    outputPath + System.getProperty("file.separator") + CukedoctorBaseAction.ALL_DOCUMENTATION);
            if (!allHtml.exists()) {
                boolean created = allHtml.createNewFile();
                if (!created) {
                    listener.error("Could not create file at location: " + allHtml.getAbsolutePath());
                    result = Result.UNSTABLE;
                }
            }
            InputStream is = null;
            OutputStream os = null;
            try {
                is = getClass().getResourceAsStream("/" + CukedoctorBaseAction.ALL_DOCUMENTATION);
                os = new FileOutputStream(allHtml);

                int copyResult = IOUtils.copy(is, os);
                if (copyResult == -1) {
                    listener.error("File is too big.");//will never reach here but findbugs forced it...
                    result = Result.UNSTABLE;
                }
            } finally {
                if (is != null) {
                    is.close();
                }
                if (os != null) {
                    os.close();
                }
            }

            action.setDocumentationPage(CukedoctorBaseAction.ALL_DOCUMENTATION);
            pool.execute(runAll(features, documentAttributes, outputPath));
        } else {
            action.setDocumentationPage("documentation." + format.getFormat());
            pool.execute(run(features, documentAttributes, outputPath));
        }

        build.addAction(action);
        pool.shutdown();
        try {
            if (format.equals(FormatType.HTML)) {
                pool.awaitTermination(5, TimeUnit.MINUTES);
            } else {
                pool.awaitTermination(15, TimeUnit.MINUTES);
            }
        } catch (final InterruptedException e) {
            Thread.interrupted();
            listener.error(
                    "Your documentation is taking too long to be generated. Halting the generation now to not throttle Jenkins.");
            result = Result.FAILURE;
        }

        if (result.equals(Result.SUCCESS)) {
            listener.hyperlink("../" + CukedoctorBaseAction.BASE_URL, "Documentation generated successfully!");
            logger.println("");
        }

    } else {
        logger.println(String.format("No features Found in %s. %sLiving documentation will not be generated.",
                workspaceJsonTargetDir.getRemote(), "\n"));

    }

    build.setResult(result);
}

From source file:com.clust4j.algo.KMeansTests.java

@Test
public void testSynchronization() {
    /*//from w w  w. ja  v  a  2s  .c o m
     * This is hard to test!
     */
    KMeans km = new KMeans(data_, new KMeansParameters(3).setVerbose(true));

    // create a 2 thread pool with a small buffer for the runnable jobs
    ExecutorService threadPool = Executors.newCachedThreadPool();

    // this job executes the fit after a brief nap
    KMRunnable first = new KMRunnable(km) {
        @Override
        public void run() {
            try {
                Thread.sleep(1000);
                this.model.fit();
                this.hasRun = true;
            } catch (InterruptedException e) {
                System.out.println("First failed!");
            } finally {
                assertNotNull(this.model.getLabels());
            }
        }
    };

    // this tries to get the volatile objs too early...
    KMRunnable second = new KMRunnable(first) {
        @Override
        public void run() {
            boolean was_fit = true;

            try {
                this.labels = model.getLabels();
                this.hasRun = true;
            } catch (ModelNotFitException m) {
                this.labels = null;
                was_fit = false;
            } finally {
                System.out.println("Second");
                assertFalse(was_fit);
                assertNull(this.labels);
            }
        }
    };

    // submit 2 jobs that take a while to run
    threadPool.execute(first);
    threadPool.execute(second);
}

From source file:com.globalsight.everest.webapp.pagehandler.administration.createJobs.CreateJobsMainHandler.java

/**
 * Creates a job//from  ww w .j  a v  a  2 s .co  m
 */
private int createJobs(Map<Object, Object> dataMap) {
    try {
        User user = (User) dataMap.get("user");
        String currentCompanyId = (String) dataMap.get("currentCompanyId");
        String jobName = (String) dataMap.get("jobName");
        String comment = (String) dataMap.get("comment");
        String tmpFolderName = (String) dataMap.get("tmpFolderName");
        String[] filePaths = (String[]) dataMap.get("jobFilePath");
        String[] l10nAndfileProfiles = (String[]) dataMap.get("fileProfile");
        String[] targetLocales = (String[]) dataMap.get("targetLocale");
        String priority = (String) dataMap.get("priority");
        String baseFolder = (String) dataMap.get("baseFolder");
        if (StringUtils.isNotEmpty(baseFolder)) {
            this.saveBaseFolder(user.getUserId(), SELECTED_FOLDER, baseFolder);
        }
        String[] isSwitched = (String[]) dataMap.get("isSwitched");
        String attachmentName = (String) dataMap.get("attachment");
        String baseStorageFolder = (String) dataMap.get("baseStorageFolder");
        String attribute = (String) dataMap.get("attributeString");

        BasicL10nProfile l10Profile = getBasicL10Profile(l10nAndfileProfiles);
        // init files and file profiles infomation
        List<File> sourceFilesList = new ArrayList<File>();
        List<String> descList = new ArrayList<String>();
        List<String> fpIdList = new ArrayList<String>();
        List<FileProfile> fileProfileList = new ArrayList<FileProfile>();
        // init target locale infomation
        String locs = this.initTargetLocale(targetLocales);
        // for GBS-2137, initialize the job with "IN_QUEUE" state
        SessionManager sessionMgr = (SessionManager) dataMap.get(SESSION_MANAGER);
        String uuid = sessionMgr.getAttribute("uuid") == null ? null : (String) sessionMgr.getAttribute("uuid");
        sessionMgr.removeElement("uuid");

        Job job = JobCreationMonitor.initializeJob(jobName, uuid, user.getUserId(), l10Profile.getId(),
                priority, Job.IN_QUEUE);
        this.initDescAndFileProfile(descList, fpIdList, filePaths, l10nAndfileProfiles, l10Profile,
                tmpFolderName, job, isSwitched, sourceFilesList, fileProfileList);
        Map<String, long[]> filesToFpId = FileProfileUtil.excuteScriptOfFileProfile(descList, fileProfileList,
                job);
        Set<String> fileNames = filesToFpId.keySet();
        Integer pageCount = new Integer(fileNames.size());
        String jobUuid = uuid == null ? ((JobImpl) job).getUuid() : uuid;
        List<JobAttribute> jobAttribtues = getJobAttributes(attribute, l10Profile);
        // cache job attributes if there are any
        if (jobAttribtues != null && jobAttribtues.size() != 0) {
            RuntimeCache.addJobAtttibutesCache(jobUuid, jobAttribtues);
        }

        int count = 0;
        List<CxeMessage> cxeMsgs = new ArrayList<CxeMessage>();
        for (Iterator<String> i = fileNames.iterator(); i.hasNext();) {
            String fileName = i.next();
            long[] tmp = filesToFpId.get(fileName);
            String fileProfileId = String.valueOf(tmp[0]);
            int exitValue = (int) tmp[1];

            String key = jobName + fileName + ++count;
            CxeProxy.setTargetLocales(key, locs);
            // If use JMS
            if (FileImportUtil.USE_JMS) {
                CxeProxy.importFromFileSystem(fileName, String.valueOf(job.getId()), jobName, fileProfileId,
                        pageCount, count, 1, 1, Boolean.TRUE, Boolean.FALSE, CxeProxy.IMPORT_TYPE_L10N,
                        exitValue, priority);
            }
            // If not use JMS, we control the concurrent threads number
            else {
                CxeMessage cxeMessage = CxeProxy.formCxeMessageType(fileName, String.valueOf(job.getId()),
                        jobName, fileProfileId, pageCount, count, 1, 1, Boolean.TRUE, Boolean.FALSE,
                        CxeProxy.IMPORT_TYPE_L10N, exitValue, priority, String.valueOf(job.getCompanyId()));
                cxeMsgs.add(cxeMessage);
            }
        }

        // If not use JMS
        if (cxeMsgs.size() > 0) {
            ExecutorService pool = Executors.newFixedThreadPool(100);
            for (CxeMessage msg : cxeMsgs) {
                FileImportRunnable runnable = new FileImportRunnable(msg);
                Thread t = new MultiCompanySupportedThread(runnable);
                pool.execute(t);
            }
            pool.shutdown();
        }

        // save job attributes if there are any
        if (jobAttribtues != null) {
            saveAttributes(jobAttribtues, currentCompanyId, job);
        }

        // save job comment
        if (!StringUtils.isEmpty(comment) || !StringUtils.isEmpty(attachmentName)) {
            String dir = convertFilePath(AmbFileStoragePathUtils.getFileStorageDirPath(job.getCompanyId()))
                    + File.separator + "GlobalSight" + File.separator + "CommentReference" + File.separator
                    + "tmp" + File.separator + baseStorageFolder.split(",")[0];
            SaveCommentThread sct = new SaveCommentThread(jobName, comment, attachmentName, user.getUserId(),
                    dir);
            sct.start();
        }
        // Send email at the end.
        Project project = l10Profile.getProject();
        if (comment == null || comment.equals("null")) {
            comment = "";
        }
        sendUploadCompletedEmail(filePaths, fpIdList, jobName, comment, new Date(), user, currentCompanyId,
                project);

        // after all steps, delete files that are used to create job
        for (File source : sourceFilesList) {
            FileUtil.deleteFile(source);
        }
        // delete the upload directory
        File uploads = new File(AmbFileStoragePathUtils.getCxeDocDir() + File.separator + TMP_FOLDER_NAME
                + File.separator + tmpFolderName);
        if (uploads != null && uploads.exists()) {
            FileUtil.deleteFile(uploads);
        }
        return SUCCEED;
    } catch (FileNotFoundException ex) {
        logger.error("Cannot find the tmp uploaded files.", ex);
        return FAIL;
    } catch (Exception e) {
        logger.error("Create job failed.", e);
        return FAIL;
    }
}

From source file:ubic.BAMSandAllen.optimize.GreedyMultiThreaded.java

/**
 * Iteratively remove rows from the B data matrix of the matrix pair, each
 * time increasing the correlation the maximum possible
 * //from   w w  w.j a va2  s.c o  m
 * @param iterations
 *            number of iterations to perform
 * @param slow
 *            indicates whether to re-compute regressions for every gene
 *            removal test
 * @throws Exception
 */
public void run(int iterations, boolean slow, boolean keepSign) throws Exception {
    StopWatch watch = new StopWatch();
    watch.start();
    StopWatch smallWatch = new StopWatch();
    long startTime = System.currentTimeMillis();

    double firstBaseLine = pair.getCorrelation(true);
    // make it more negative if it starts below zero
    boolean increase = firstBaseLine > 0;
    // force the increase on random runs with low correlation
    if (Math.abs(firstBaseLine) < 0.1)
        increase = true;

    // if we are going against the current correlation sign - eg go from
    // positive correlation to negative
    if (!keepSign) {
        increase = !increase;
    }

    List<GreedyThreadRunner> runners = new LinkedList<GreedyThreadRunner>();

    // create the runners
    for (int threadInd = 0; threadInd < threads; threadInd++) {
        MatrixPair pairCopy = (MatrixPair) deepCopy(pair);
        runners.add(new GreedyThreadRunner(pairCopy, slow, increase));
    }

    for (int i = 0; i < iterations; i++) {
        smallWatch.reset();
        smallWatch.start();

        ExecutorService pool;
        pool = Executors.newFixedThreadPool(threads);
        // divide up the rows
        List<String> rows = pair.getMatrixBDataRows();
        List<Collection<String>> splits = split(rows, threads);

        double baseLine = pair.getCorrelation(true);

        log.info("Base correlation:" + baseLine + " size:" + pair.getMatrixBDataRows().size());

        // set the baseline and call the runners
        for (int threadInd = 0; threadInd < threads; threadInd++) {
            GreedyThreadRunner runner = runners.get(threadInd);
            runner.setBaseline(baseLine);

            // set residual calculation triangles to match accross all
            // threads, if we are doing partial regression
            if (pair instanceof ConnectivityAndAllenPartialExpressionMatrixPair) {
                ConnectivityAndAllenPartialExpressionMatrixPair partialPair = ((ConnectivityAndAllenPartialExpressionMatrixPair) pair);
                // only do it if we are regressing on expression
                if (partialPair
                        .getRegressType() == ConnectivityAndAllenPartialExpressionMatrixPair.RegressMatrix.BOTH
                        && partialPair
                                .getRegressType() == ConnectivityAndAllenPartialExpressionMatrixPair.RegressMatrix.EXPRESSION) {
                    RegressionVector triangles = partialPair.getTrianglesMatrixB();
                    runner.setTrianglesMatrixB(triangles);
                }
            }

            runner.setRowsToTest(splits.get(threadInd));
            // log.info( "Split size:" + splits.get( threadInd ).size() );
            pool.execute(runner);
        }

        // log.info( "Waiting for threads to finish" );
        pool.shutdown();
        pool.awaitTermination(15, TimeUnit.MINUTES);

        // go through all the runners and get results
        double bestIncrease = Double.MAX_VALUE * -1;
        String bestRow = null;
        for (GreedyThreadRunner runner : runners) {
            double diff = runner.getBestIncrease();
            if (!increase) {
                diff *= -1;
            }
            if (diff > bestIncrease) {
                bestRow = runner.getBestRow();
                bestIncrease = diff;
            }
        }

        if (bestRow == null) {
            log.info("No best row found " + pair.getCorrelation(true));
            log.info("Putting remaining " + rows.size() + " genes at end of file");
            for (String row : rows) {
                outputRowToFile(startTime, row);
                FileTools.stringToFile(i + "," + baseLine + "," + row + "\n",
                        new File(SetupParameters.getDataFolder() + "LOOResults." + startTime + ".txt"), true);
            }
            break;
        }

        pair.removeMatrixBDataRowFast(bestRow);
        for (GreedyThreadRunner runner : runners) {
            runner.removeRow(bestRow);
        }

        outputRowToFile(startTime, bestRow);
        // write correlation

        FileTools.stringToFile(i + "," + baseLine + "," + bestRow + "\n",
                new File(SetupParameters.getDataFolder() + "LOOResults." + startTime + ".txt"), true);

        int eta = (int) (smallWatch.getTime() / 1000) / 2 * pair.getMatrixBDataRows().size() / 3600;
        log.info(bestRow + " changes correlation by " + bestIncrease + " time:" + (smallWatch.getTime() / 1000)
                + "s total:" + (watch.getTime() / 1000) + "s estimated hours remaining:" + eta);
    }
    log.info("Start time:" + startTime);
    FileTools.stringToFile(startTime + "\n",
            new File(SetupParameters.getDataFolder() + "Link." + startTime + ".txt"), true);

    // make a link between it's output files and starttime - akward hack
    File jarFile = new File(this.getClass().getProtectionDomain().getCodeSource().getLocation().toURI());
    FileTools.stringToFile(jarFile.toString() + "\n",
            new File(SetupParameters.getDataFolder() + "Link." + startTime + ".txt"), true);

}

From source file:org.apache.maven.plugin.invoker.AbstractInvokerMojo.java

/**
 * Runs the specified build jobs.//from   w  w w .  j ava 2  s .c o  m
 *
 * @param projectsDir The base directory of all projects, must not be <code>null</code>.
 * @param buildJobs   The build jobs to run must not be <code>null</code> nor contain <code>null</code> elements.
 * @throws org.apache.maven.plugin.MojoExecutionException
 *          If any build could not be launched.
 */
private void runBuilds(final File projectsDir, BuildJob[] buildJobs) throws MojoExecutionException {
    if (!localRepositoryPath.exists()) {
        localRepositoryPath.mkdirs();
    }

    //-----------------------------------------------
    // interpolate settings file
    //-----------------------------------------------

    File interpolatedSettingsFile = null;
    if (settingsFile != null) {
        if (cloneProjectsTo != null) {
            interpolatedSettingsFile = new File(cloneProjectsTo, "interpolated-" + settingsFile.getName());
        } else {
            interpolatedSettingsFile = new File(settingsFile.getParentFile(),
                    "interpolated-" + settingsFile.getName());
        }
        buildInterpolatedFile(settingsFile, interpolatedSettingsFile);
    }

    //-----------------------------------------------
    // merge settings file
    //-----------------------------------------------

    SettingsXpp3Writer settingsWriter = new SettingsXpp3Writer();

    File mergedSettingsFile;
    Settings mergedSettings = this.settings;
    if (mergeUserSettings) {
        if (interpolatedSettingsFile != null) {
            // Have to merge the specified settings file (dominant) and the one of the invoking Maven process
            Reader reader = null;
            try {
                reader = new XmlStreamReader(interpolatedSettingsFile);
                SettingsXpp3Reader settingsReader = new SettingsXpp3Reader();
                Settings dominantSettings = settingsReader.read(reader);

                // MINVOKER-137: NPE on dominantSettings.getRuntimeInfo()
                // DefaultMavenSettingsBuilder does the same trick
                if (dominantSettings.getRuntimeInfo() == null) {
                    RuntimeInfo rtInfo = new RuntimeInfo(dominantSettings);
                    rtInfo.setFile(interpolatedSettingsFile);
                    dominantSettings.setRuntimeInfo(rtInfo);
                }

                Settings recessiveSettings = cloneSettings();

                SettingsUtils.merge(dominantSettings, recessiveSettings, TrackableBase.USER_LEVEL);

                mergedSettings = dominantSettings;
                getLog().debug("Merged specified settings file with settings of invoking process");
            } catch (XmlPullParserException e) {
                throw new MojoExecutionException("Could not read specified settings file", e);
            } catch (IOException e) {
                throw new MojoExecutionException("Could not read specified settings file", e);
            } finally {
                IOUtil.close(reader);
            }
        }
    }
    if (this.settingsFile != null && !mergeUserSettings) {
        mergedSettingsFile = interpolatedSettingsFile;
    } else {
        try {
            mergedSettingsFile = File.createTempFile("invoker-settings", ".xml");

            FileWriter fileWriter = null;
            try {
                fileWriter = new FileWriter(mergedSettingsFile);
                settingsWriter.write(fileWriter, mergedSettings);
            } finally {
                IOUtil.close(fileWriter);
            }

            if (getLog().isDebugEnabled()) {
                getLog().debug("Created temporary file for invoker settings.xml: "
                        + mergedSettingsFile.getAbsolutePath());
            }
        } catch (IOException e) {
            throw new MojoExecutionException("Could not create temporary file for invoker settings.xml", e);
        }
    }
    final File finalSettingsFile = mergedSettingsFile;

    if (mavenHome != null) {
        actualMavenVersion = SelectorUtils.getMavenVersion(mavenHome);
    } else {
        actualMavenVersion = SelectorUtils.getMavenVersion();
    }
    scriptRunner.setGlobalVariable("mavenVersion", actualMavenVersion);

    if (javaHome != null) {
        resolveExternalJreVersion();
    } else {
        actualJreVersion = SelectorUtils.getJreVersion();
    }

    try {
        if (isParallelRun()) {
            getLog().info("use parallelThreads " + parallelThreads);

            ExecutorService executorService = Executors.newFixedThreadPool(parallelThreads);
            for (final BuildJob job : buildJobs) {
                executorService.execute(new Runnable() {
                    public void run() {
                        try {
                            runBuild(projectsDir, job, finalSettingsFile);
                        } catch (MojoExecutionException e) {
                            throw new RuntimeException(e.getMessage(), e);
                        }
                    }
                });
            }

            try {
                executorService.shutdown();
                // TODO add a configurable time out
                executorService.awaitTermination(Long.MAX_VALUE, TimeUnit.MILLISECONDS);
            } catch (InterruptedException e) {
                throw new MojoExecutionException(e.getMessage(), e);
            }
        } else {
            for (BuildJob job : buildJobs) {
                runBuild(projectsDir, job, finalSettingsFile);
            }
        }
    } finally {
        if (interpolatedSettingsFile != null && cloneProjectsTo == null) {
            interpolatedSettingsFile.delete();
        }
        if (mergedSettingsFile != null && mergedSettingsFile.exists()) {
            mergedSettingsFile.delete();
        }
    }
}

From source file:MSUmpire.DIA.DIAPack.java

public void AssignQuant(boolean export) throws IOException, SQLException {
    Logger.getRootLogger().info("Assign peak cluster to identified peptides");
    GenerateClusterScanNomapping();//from www. j a v  a  2  s .  c  o  m

    ExecutorService executorPool = null;
    for (PeakCluster cluster : MS1FeatureMap.PeakClusters) {
        cluster.Identified = false;
    }

    for (PepIonID pepIonID : IDsummary.GetPepIonList().values()) {
        pepIonID.MS1PeakClusters = new ArrayList<>();
        pepIonID.MS2UnfragPeakClusters = new ArrayList<>();
    }

    //Assign precursor features and grouped fragments for all identified peptide ions for a isolation window
    for (LCMSPeakDIAMS2 DIAWindow : DIAWindows) {
        DIA_window_Quant dia_w = new DIA_window_Quant(GetQ1Name(), GetQ2Name(), GetQ3Name(), ScanClusterMap_Q1,
                ScanClusterMap_Q2, ScanClusterMap_Q3, MS1FeatureMap, DIAWindow, IDsummary, NoCPUs);
        dia_w.run();
    }

    executorPool = Executors.newFixedThreadPool(NoCPUs);

    //Match fragments and calculate quantification for each peptide ion
    for (PepIonID pepIonID : IDsummary.GetPepIonList().values()) {
        DIAAssignQuantUnit quantunit = new DIAAssignQuantUnit(pepIonID, MS1FeatureMap, parameter);
        executorPool.execute(quantunit);
    }
    executorPool.shutdown();

    try {
        executorPool.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS);
    } catch (InterruptedException e) {
        Logger.getRootLogger().info("interrupted..");
    }

    if (export) {
        ExportID();
    }
}

From source file:MSUmpire.DIA.DIAPack.java

public void GenerateRawMGF() throws IOException, Exception {

    if (RawMGFExist()) {
        return;//from ww  w .  j a va  2s .co m
    }
    Logger.getRootLogger().info("Extracting pseudo MS/MS spectra with raw intensity");
    HashMap<Integer, ArrayList<PseudoMSMSProcessing>> ScanList = new HashMap<>();
    HashMap<String, PseudoMSMSProcessing> UnfragScanList = new HashMap<>();
    parameter.BoostComplementaryIon = false;
    ExecutorService executorPool = Executors.newFixedThreadPool(NoCPUs);
    for (LCMSPeakDIAMS2 DIAwindow : DIAWindows) {
        DIAwindow.ReadPeakCluster();
        DIAwindow.ReadPrecursorFragmentClu2Cur();
        DIAwindow.BuildFragmentMS1ranking();
        DIAwindow.FilterByCriteria();
        DIAwindow.BuildFragmentUnfragranking();
        DIAwindow.FilterByCriteriaUnfrag();
        for (PeakCluster ms1cluster : MS1FeatureMap.PeakClusters) {
            if (DIAwindow.DIA_MZ_Range.getX() <= ms1cluster.GetMaxMz()
                    && DIAwindow.DIA_MZ_Range.getY() >= ms1cluster.TargetMz()
                    && DIAwindow.FragmentsClu2Cur.containsKey(ms1cluster.Index)) {
                DIAwindow.ExtractFragmentForPeakCluser(ms1cluster);
                if (DIAwindow.Last_MZ_Range == null || DIAwindow.Last_MZ_Range.getY() < ms1cluster.TargetMz()) {
                    PseudoMSMSProcessing mSMSProcessing = new PseudoMSMSProcessing(ms1cluster, parameter);
                    executorPool.execute(mSMSProcessing);
                    if (!ScanList.containsKey(ms1cluster.Index)) {
                        ScanList.put(ms1cluster.Index, new ArrayList<PseudoMSMSProcessing>());
                    }
                    ScanList.get(ms1cluster.Index).add(mSMSProcessing);
                }
            }
        }

        for (PeakCluster ms2cluster : DIAwindow.PeakClusters) {
            if (DIAwindow.DIA_MZ_Range.getX() <= ms2cluster.TargetMz()
                    && DIAwindow.DIA_MZ_Range.getY() >= ms2cluster.TargetMz()
                    && DIAwindow.UnFragIonClu2Cur.containsKey(ms2cluster.Index)) {
                DIAwindow.ExtractFragmentForUnfragPeakCluser(ms2cluster);
                PseudoMSMSProcessing mSMSProcessing = new PseudoMSMSProcessing(ms2cluster, parameter);
                executorPool.execute(mSMSProcessing);
                UnfragScanList.put(DIAwindow.WindowID + ";" + ms2cluster.Index, mSMSProcessing);
            }
        }
        DIAwindow.ClearAllPeaks();
        System.gc();
        Logger.getRootLogger()
                .info("(Memory usage:" + Math.round(
                        (Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory()) / 1048576)
                        + "MB)");
    }
    executorPool.shutdown();

    try {
        executorPool.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS);
    } catch (InterruptedException e) {
        Logger.getRootLogger().info("interrupted..");
    }
    ReadScanNoMapping();
    String mgffile = GetSkylineFolder() + GetForLibQ1Name() + ".mgf";
    FileWriter mgfWriter = new FileWriter(mgffile, false);

    for (final int ScanNo : new java.util.TreeSet<>(ScanClusterMap_Q1.keySet())) {
        int ClusterIndex = ScanClusterMap_Q1.get(ScanNo);
        XYPointCollection Scan = new XYPointCollection();
        PseudoMSMSProcessing mSMSProcessing = null;
        for (PseudoMSMSProcessing MS2Processing : ScanList.get(ClusterIndex)) {
            mSMSProcessing = MS2Processing;
            for (PrecursorFragmentPairEdge fragmentClusterUnit : MS2Processing.fragments) {
                Scan.AddPointKeepMaxIfValueExisted(fragmentClusterUnit.FragmentMz,
                        fragmentClusterUnit.Intensity);
            }
        }
        StringBuilder mgfString = new StringBuilder();
        mgfString.append("BEGIN IONS\n");
        mgfString.append("PEPMASS=" + mSMSProcessing.Precursorcluster.TargetMz() + "\n");
        mgfString.append("CHARGE=" + mSMSProcessing.Precursorcluster.Charge + "+\n");
        mgfString.append("RTINSECONDS=" + mSMSProcessing.Precursorcluster.PeakHeightRT[0] * 60f + "\n");
        mgfString.append("TITLE=ClusterIndex:" + mSMSProcessing.Precursorcluster.Index + "\n");
        for (int i = 0; i < Scan.PointCount(); i++) {
            mgfString.append(Scan.Data.get(i).getX()).append(" ").append(Scan.Data.get(i).getY()).append("\n");
        }
        mgfString.append("END IONS\n\n");
        mgfWriter.write(mgfString.toString());
    }
    mgfWriter.close();

    ////////////////////////////////////////////////////////////////////////////////
    String mgffile2 = GetSkylineFolder() + GetForLibQ2Name() + ".mgf";
    FileWriter mgfWriter2 = new FileWriter(mgffile2, false);

    for (final int ScanNo : new java.util.TreeSet<>(ScanClusterMap_Q2.keySet())) {
        int ClusterIndex = ScanClusterMap_Q2.get(ScanNo);
        XYPointCollection Scan = new XYPointCollection();
        PseudoMSMSProcessing mSMSProcessing = null;
        for (PseudoMSMSProcessing MS2Processing : ScanList.get(ClusterIndex)) {
            mSMSProcessing = MS2Processing;
            for (PrecursorFragmentPairEdge fragmentClusterUnit : MS2Processing.fragments) {
                Scan.AddPointKeepMaxIfValueExisted(fragmentClusterUnit.FragmentMz,
                        fragmentClusterUnit.Intensity);
            }
        }
        StringBuilder mgfString = new StringBuilder();
        mgfString.append("BEGIN IONS\n");
        mgfString.append("PEPMASS=" + mSMSProcessing.Precursorcluster.TargetMz() + "\n");
        mgfString.append("CHARGE=" + mSMSProcessing.Precursorcluster.Charge + "+\n");
        mgfString.append("RTINSECONDS=" + mSMSProcessing.Precursorcluster.PeakHeightRT[0] * 60f + "\n");
        mgfString.append("TITLE=ClusterIndex:" + mSMSProcessing.Precursorcluster.Index + "\n");
        for (int i = 0; i < Scan.PointCount(); i++) {
            mgfString.append(Scan.Data.get(i).getX()).append(" ").append(Scan.Data.get(i).getY()).append("\n");
        }
        mgfString.append("END IONS\n\n");
        mgfWriter2.write(mgfString.toString());
    }

    mgfWriter2.close();

    ////////////////////////////////
    String mgffile3 = GetSkylineFolder() + GetForLibQ3Name() + ".mgf";
    FileWriter mgfWriter3 = new FileWriter(mgffile3, false);
    mzXMLParser Q3mzxml = new mzXMLParser(FilenameUtils.getFullPath(Filename) + GetQ3Name() + ".mzXML",
            parameter, SpectralDataType.DataType.DDA, null, NoCPUs);
    Q3mzxml.GetAllScanCollectionByMSLabel(false, true, false, false);
    for (final int ScanNo : new java.util.TreeSet<>(ScanClusterMap_Q3.keySet())) {
        String key = ScanClusterMap_Q3.get(ScanNo);
        XYPointCollection Scan = new XYPointCollection();
        PseudoMSMSProcessing mSMSProcessing = UnfragScanList.get(key);

        for (PrecursorFragmentPairEdge fragmentClusterUnit : mSMSProcessing.fragments) {
            Scan.AddPointKeepMaxIfValueExisted(fragmentClusterUnit.FragmentMz, fragmentClusterUnit.Intensity);
        }

        StringBuilder mgfString = new StringBuilder();
        mgfString.append("BEGIN IONS\n");
        mgfString.append("PEPMASS=" + mSMSProcessing.Precursorcluster.TargetMz() + "\n");
        mgfString.append("CHARGE=" + mSMSProcessing.Precursorcluster.Charge + "+\n");
        mgfString.append("RTINSECONDS=" + mSMSProcessing.Precursorcluster.PeakHeightRT[0] * 60f + "\n");
        mgfString.append("TITLE=ClusterIndex:" + mSMSProcessing.Precursorcluster.Index + "\n");
        for (int i = 0; i < Scan.PointCount(); i++) {
            mgfString.append(Scan.Data.get(i).getX()).append(" ").append(Scan.Data.get(i).getY()).append("\n");
        }
        mgfString.append("END IONS\n\n");
        mgfWriter3.write(mgfString.toString());
    }
    mgfWriter3.close();
}

From source file:com.paniclauncher.data.Settings.java

/**
 * This checks the servers hashes.xml file and downloads and new/updated files that differ from what the user has
 *///from   w  ww.j  av a2 s .co m
private void checkForUpdatedFiles() {
    String hashes = null;
    while (hashes == null) {
        hashes = Utils.urlToString(getFileURL("launcher/hashes.xml"));
        if (hashes == null) {
            boolean changed = disableServerGetNext(); // Disable the server and get the next one
            if (!changed) {
                this.offlineMode = true;
                return;
            }
        }
    }
    ArrayList<PanicLauncherDownloadable> downloads = new ArrayList<PanicLauncherDownloadable>();
    try {
        DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
        DocumentBuilder builder = factory.newDocumentBuilder();
        Document document = builder.parse(new InputSource(new StringReader(hashes)));
        document.getDocumentElement().normalize();
        NodeList nodeList = document.getElementsByTagName("hash");
        for (int i = 0; i < nodeList.getLength(); i++) {
            Node node = nodeList.item(i);
            if (node.getNodeType() == Node.ELEMENT_NODE) {
                Element element = (Element) node;
                String name = element.getAttribute("name");
                String type = element.getAttribute("type");
                String md5 = element.getAttribute("md5");
                File file = null;
                if (type.equalsIgnoreCase("Root")) {
                    file = new File(configsDir, name);
                } else if (type.equalsIgnoreCase("Images")) {
                    file = new File(imagesDir, name);
                    name = "images/" + name;
                } else if (type.equalsIgnoreCase("Skins")) {
                    file = new File(skinsDir, name);
                    name = "skins/" + name;
                } else if (type.equalsIgnoreCase("Languages")) {
                    file = new File(languagesDir, name);
                    name = "languages/" + name;
                } else if (type.equalsIgnoreCase("Libraries")) {
                    file = new File(librariesDir, name);
                    name = "libraries/" + name;
                } else if (type.equalsIgnoreCase("Launcher")) {
                    String version = element.getAttribute("version");
                    if (!getVersion().equalsIgnoreCase(version)) {
                        if (getVersion().equalsIgnoreCase("%VERSION%")) {
                            continue;
                        } else {
                            log("Update to Launcher found. Current version: " + this.version + ", New version: "
                                    + version);
                            downloadUpdate();
                        }
                    } else {
                        continue;
                    }
                } else {
                    continue; // Don't know what to do with this file so ignore it
                }
                boolean download = false; // If we have to download the file or not
                if (!file.exists()) {
                    download = true; // File doesn't exist so download it
                } else {
                    if (!Utils.getMD5(file).equalsIgnoreCase(md5)) {
                        download = true; // MD5 hashes don't match so download it
                    }
                }

                if (download) {
                    if (!file.canWrite()) {
                        file.delete();
                    }
                    downloads.add(new PanicLauncherDownloadable("launcher/" + name, file, md5));
                    log("Downloading: " + name);
                }
            }
        }
    } catch (SAXException e) {
        this.console.logStackTrace(e);
    } catch (ParserConfigurationException e) {
        this.console.logStackTrace(e);
    } catch (IOException e) {
        this.console.logStackTrace(e);
    }
    ExecutorService executor = Executors.newFixedThreadPool(8);
    for (PanicLauncherDownloadable download : downloads) {
        executor.execute(download);
    }
    executor.shutdown();
    while (!executor.isTerminated()) {
    }
}

From source file:org.deegree.tools.coverage.converter.RasterConverter.java

/**
 * @param numThreads/*  w  w  w.  j  a v  a2  s  .com*/
 * @param outLoc
 * @throws InterruptedException
 * @throws IOException
 * 
 */
private int convert(AbstractCoverage source, String outLoc, int numThreads, String outputFormat,
        final boolean verbose) throws InterruptedException, IOException {
    List<SimpleRaster> tiles = new LinkedList<SimpleRaster>();
    getTiles(source, tiles);
    if (tiles.isEmpty()) {
        System.err.println("Found no raster tiles in source: " + source + ", hence nothing to convert.");
        return 1;
    }
    ExecutorService executor = Executors.newFixedThreadPool(numThreads);
    SimpleRaster simpleRaster = tiles.get(0);
    RasterReader rasterReader = ((ByteBufferRasterData) simpleRaster.getRasterData()).getReader();
    File file = rasterReader.file();
    File outputLocation = getOutputLocation(file, outLoc, outputFormat, tiles.size() == 1);

    for (final SimpleRaster tile : tiles) {
        File outFile = null;
        ByteBufferRasterData data = (ByteBufferRasterData) tile.getRasterData();
        RasterReader origReader = data.getReader();
        final String tileName = origReader.getDataLocationId();
        if (tiles.size() == 1) {
            if (outputLocation.isFile()) {
                outFile = outputLocation.getAbsoluteFile();
            } else {
                outFile = createNewFile(outputLocation, tileName, outputFormat);
            }
        } else {
            outFile = createNewFile(outputLocation, tileName, outputFormat);
        }
        final File absTileFilename = outFile;
        System.out.println("Converting: " + tileName + " -> file: " + absTileFilename);

        Runnable command = new Runnable() {
            public void run() {
                try {
                    String thread = Thread.currentThread().getName();
                    System.out.println(thread + " saving... " + tileName);
                    RasterFactory.saveRasterToFile(tile, absTileFilename);
                    tile.dispose();
                    System.out.println(thread + " done... " + tileName);
                } catch (Exception e) {
                    System.err.println("Ar error occurred while processing tile: " + tileName + ": "
                            + e.getLocalizedMessage());
                    if (verbose) {
                        e.printStackTrace();
                    }
                }
            }
        };
        executor.execute(command);

    }
    shutdownExecutorAndWaitForFinish(executor);
    return 0;
}