Example usage for org.apache.commons.io FileUtils cleanDirectory

List of usage examples for org.apache.commons.io FileUtils cleanDirectory

  1. HOME
  2. Java
  3. org.apache.commons
  4. org.apache.commons.io.*
  5. FileUtils
  6. cleanDirectory

Introduction

In this page you can find the example usage for org.apache.commons.io FileUtils cleanDirectory.

Prototype

public static void cleanDirectory(File directory) throws IOException

Source Link

Document

Cleans a directory without deleting it.

Usage

From source file:net.technicpack.launchercore.modpacks.ModpackModel.java

public void setInstalledDirectory(File targetDirectory) {
    if (installedDirectory != null && installedDirectory.exists()) {
        try {/*from w ww .j  a va2  s .c om*/
            FileUtils.copyDirectory(installedDirectory, targetDirectory);
            FileUtils.cleanDirectory(installedDirectory);
        } catch (IOException ex) {
            Utils.getLogger().log(Level.SEVERE, ex.getMessage(), ex);
            return;
        }
    }

    installedDirectory = targetDirectory;
    String path = installedDirectory.getAbsolutePath();

    if (path.equals(directories.getModpacksDirectory().getAbsolutePath())) {
        installedPack.setDirectory(InstalledPack.MODPACKS_DIR);
    } else if (path.equals(directories.getLauncherDirectory().getAbsolutePath())) {
        installedPack.setDirectory(InstalledPack.LAUNCHER_DIR);
    } else if (path.startsWith(directories.getModpacksDirectory().getAbsolutePath())) {
        installedPack.setDirectory(InstalledPack.MODPACKS_DIR
                + path.substring(directories.getModpacksDirectory().getAbsolutePath().length() + 1));
    } else if (path.startsWith(directories.getLauncherDirectory().getAbsolutePath())) {
        installedPack.setDirectory(InstalledPack.LAUNCHER_DIR
                + path.substring(directories.getLauncherDirectory().getAbsolutePath().length() + 1));
    } else
        installedPack.setDirectory(path);

    save();
}

From source file:nl.b3p.gis.viewer.services.GisSecurityRealm.java

public static synchronized void flushSPCache() {
    boolean cacheOnDisk = HibernateUtil.cacheOnDisk;

    if (cacheOnDisk) {
        try {/*from ww w  .j  a v  a 2s.c o  m*/
            String dir = HibernateUtil.cacheOnDiskPath;
            File directory = new File(dir);

            FileUtils.cleanDirectory(directory);
        } catch (IOException ex) {
            log.error("Fout tijdens verwijderen disk cache.", ex);
        }

        log.debug("Cache on DISK WMS leeggemaakt.");
    } else {
        perUserNameSPCache.clear();
        //perUserNameSPCache = null;
        //perUserNameSPCache = new HashMap();

        log.debug("Cache in MEMORY WMS leeggemaakt.");
    }
}

From source file:nl.mpi.lamus.filesystem.implementation.LamusWorkspaceDirectoryHandlerTest.java

@Before
public void setUp() throws IOException {
    FileUtils.cleanDirectory(this.workspaceBaseDirectory);
    this.workspaceBaseDirectory.setWritable(true);
}

From source file:nl.mpi.lamus.filesystem.implementation.LamusWorkspaceDirectoryHandlerTest.java

@After
public void tearDown() throws IOException {
    FileUtils.cleanDirectory(this.workspaceBaseDirectory);
}

From source file:nl.mpi.lamus.filesystem.implementation.LamusWorkspaceFileHandlerTest.java

@Before
public void setUp() throws IOException {
    FileUtils.cleanDirectory(workspaceBaseDirectory);

    ReflectionTestUtils.setField(workspaceFileHandler, "archiveFileLocationProvider",
            mockArchiveFileLocationProvider);
    ReflectionTestUtils.setField(workspaceFileHandler, "workspaceAccessChecker", mockWorkspaceAccessChecker);
    ReflectionTestUtils.setField(workspaceFileHandler, "archiveFileHelper", mockArchiveFileHelper);
}

From source file:nl.mpi.lamus.filesystem.implementation.LamusWorkspaceFileHandlerTest.java

@After
public void tearDown() throws IOException {
    FileUtils.cleanDirectory(workspaceBaseDirectory);
    if (tempDirectory != null) {
        tempDirectory.setWritable(true);
        FileUtils.cleanDirectory(tempDirectory);
    }/*from   ww  w  .  j  av  a  2s  .  c  o  m*/
    if (anotherTempDirectory != null) {
        anotherTempDirectory.setWritable(true);
        FileUtils.cleanDirectory(anotherTempDirectory);
    }
}

From source file:nl.umcg.westrah.binarymetaanalyzer.BinaryMetaAnalysis.java

public void run() throws IOException {
    initialize();//from   w ww.  java  2  s .com
    loadProbeAnnotation();

    String outdir = settings.getOutput();
    if (usetmp) {
        outdir = tempDir;
    }

    System.out.println("Placing output here: " + outdir);
    outdir = Gpio.formatAsDirectory(outdir);
    Gpio.createDir(outdir);

    System.out.println(
            "Permutations: " + settings.getStartPermutations() + " until " + settings.getNrPermutations());

    String zscoretableheader = null;
    if (settings.isMakezscoretable()) {
        StringBuilder builder = new StringBuilder();
        builder.append("SNP\tAlleles\tAlleleAssessed");
        for (int t = 0; t < traitList.length; t++) {
            builder.append("\t").append(traitList[t].getMetaTraitName()).append("_")
                    .append(traitList[t].getAnnotation());
        }
        zscoretableheader = builder.toString();
    }

    int availableProcessors = Runtime.getRuntime().availableProcessors();
    int cores = settings.getNrThreads();
    if (cores < 1) {
        cores = 1;
    } else if (cores > availableProcessors) {
        cores = availableProcessors;
    }

    System.out.println("Will try to make use of " + cores + " CPU cores");
    System.out.println();

    HashSet<QTLPair> prevSet = null;
    for (int permutation = settings.getStartPermutations(); permutation <= settings
            .getNrPermutations(); permutation++) {
        // load probe annotation and index
        // this particular probe annotation can take multiple probes for a single location into account.

        HashSet<QTLPair> set = new HashSet<>();

        Descriptives.initializeZScoreToPValue();

        // re-intialize for each permutation, just to be sure
        if (permutation > settings.getStartPermutations()) {
            initialize();
            System.out.println("Loading probe annotation from: " + settings.getProbetranslationfile());
            loadProbeAnnotation();
            if (traitList.length == 0) {
                System.err.println("Error: no annotation loaded.");
                System.exit(-1);
            }
        }
        //         clearResultsBuffer();

        // create dataset objects
        System.out.println("Running permutation " + permutation);
        datasets = new BinaryMetaAnalysisDataset[settings.getDatasetlocations().size()];

        System.out.println("Loading datasets");
        for (int d = 0; d < datasets.length; d++) {
            datasets[d] = new BinaryMetaAnalysisDataset(settings.getDatasetlocations().get(d),
                    settings.getDatasetnames().get(d), settings.getDatasetPrefix().get(d), permutation,
                    settings.getDatasetannotations().get(d), probeAnnotation,
                    settings.getFeatureOccuranceScaleMaps().get(d));
        }

        System.out.println("Loaded " + datasets.length + " datasets");

        // create meta-analysis SNP index. have to recreate this every permutation,
        // since the order of SNPs is generated at random.
        System.out.println("Creating SNP index");
        createSNPIndex(outdir);
        System.out.println("Total of " + snpIndex.length + " SNPs");

        System.out.println("Creating probe index");
        createProbeIndex(outdir);
        System.out.println("Total of " + probeIndex.length + " probes");

        // make index of snp/probe combinations, if any specified
        createSNPProbeCombos(outdir);

        // load SNP annotation for SNPs present in dataset
        //         if (snpChr == null) {
        System.out.println("Loading SNP annotation from " + settings.getSNPAnnotationFile());
        loadSNPAnnotation();
        //         }

        // run analysis
        System.out.println("Type of analysis: " + settings.getAnalysisType());
        System.out.println("Cis-window: " + settings.getCisdistance());
        System.out.println("Trans-window: " + settings.getTransdistance());

        TextFile zscoreTableTf = null;
        TextFile zscoreTableTfNrSamples = null;

        if (settings.isMakezscoretable()) {

            String tableoutfile = outdir + "ZScoreMatrix-Permutation" + permutation + ".txt.gz";
            String tableoutfileNrSamples = outdir + "ZScoreMatrixNrSamples-Permutation" + permutation
                    + ".txt.gz";
            if (permutation == 0) {
                tableoutfile = outdir + "ZScoreMatrix.txt.gz";
                tableoutfileNrSamples = outdir + "ZScoreMatrixNrSamples.txt.gz";
            }
            System.out.println("Writing z-score table: " + tableoutfile);
            zscoreTableTf = new TextFile(tableoutfile, TextFile.W, 10 * 1048576);
            zscoreTableTfNrSamples = new TextFile(tableoutfileNrSamples, TextFile.W, 10 * 1048576);

            // write header
            zscoreTableTf.writeln(zscoretableheader);
            zscoreTableTfNrSamples.writeln(zscoretableheader);
        }

        ExecutorService threadPool = Executors.newFixedThreadPool(cores);
        CompletionService<Triple<ArrayList<QTL>, String, String>> pool = new ExecutorCompletionService<Triple<ArrayList<QTL>, String, String>>(
                threadPool);

        maxSavedPvalue = -Double.MAX_VALUE;
        locationToStoreResult = 0;
        bufferHasOverFlown = false;
        System.out.println("Max P: " + maxSavedPvalue + "\tLocationToStoreResult: " + locationToStoreResult);

        System.out.println("Starting meta-analysis");
        ProgressBar pb = new ProgressBar(snpList.length);
        int returned = 0;
        ArrayList<Future> futures = new ArrayList<>();
        for (int snp = 0; snp < snpList.length; snp++) {
            // this can go in different threads..
            boolean outputallzscores = true;
            if (permutation > 0) {
                outputallzscores = fullpermutationoutput;
            }
            BinaryMetaAnalysisTask t = new BinaryMetaAnalysisTask(settings, probeAnnotation, datasets, snpIndex,
                    snpList, snpChr, snpPositions, probeIndex, snpprobeCombos, traitMap, traitList, snp, DEBUG,
                    outputallzscores);
            futures.add(pool.submit(t));
        }

        // give the threadpool the signal to shutdown
        threadPool.shutdown();

        int addcalled = 0;
        while (returned < snpList.length) {
            try {
                Future<Triple<ArrayList<QTL>, String, String>> threadfuture = pool.take();
                if (threadfuture != null) {
                    Triple<ArrayList<QTL>, String, String> result = threadfuture.get();

                    for (QTL q : result.getLeft()) {
                        if (!DEBUG) {
                            addEQTL(q);
                        } else {

                            //                        int snpid = q.getSNPId();
                            //                        MetaQTL4MetaTrait trait = q.getMetaTrait();

                            //                        QTLPair combo = new QTLPair();
                            //                        combo.snpid = snpid;
                            //                        combo.trait = trait;
                            //                        set.add(combo);

                        }

                        addcalled++;
                    }
                    if (settings.isMakezscoretable()) {
                        zscoreTableTf.writeln(result.getMiddle());

                        zscoreTableTfNrSamples.writeln(result.getRight());
                    }
                    result = null;
                    returned++;
                    pb.iterate();
                }
                threadfuture = null;
            } catch (InterruptedException e) {
                e.printStackTrace();
            } catch (ExecutionException e) {
                e.printStackTrace();
            }
        }
        pb.close();

        if (DEBUG) {
            if (prevSet != null) {
                // compare sets
                TextFile tf = new TextFile(outdir + "debug-p" + permutation + ".txt", TextFile.W);
                for (QTLPair p : prevSet) {
                    if (!set.contains(p)) {
                        tf.writeln(snpList[p.snpid] + "\t" + p.trait.getMetaTraitName());
                    }
                }
                tf.close();
            }
            prevSet = set;
        }

        System.out.println("Snps returned: " + returned + "\tNr of snps submitted: " + snpList.length
                + "\tNr of eQTLs evaluated: " + addcalled);
        System.out.println("Max P: " + maxSavedPvalue + "\tLocationToStoreResult: " + locationToStoreResult);

        if (settings.isMakezscoretable()) {
            zscoreTableTf.close();
            zscoreTableTfNrSamples.close();

            if (usetmp) {

                String filename = "ZScoreMatrix-Permutation" + permutation + ".txt.gz";
                if (permutation == 0) {
                    filename = "ZScoreMatrix.txt.gz";
                }
                File source = new File(tempDir + filename);
                File dest = new File(settings.getOutput() + filename);
                if (dest.exists()) {
                    System.out.println(
                            "Destination file: " + dest.getAbsolutePath() + " exists already.. Deleting!");
                    dest.delete();
                }
                System.out.println(
                        "Moving file: " + tempDir + filename + " --> " + settings.getOutput() + filename);
                FileUtils.moveFile(source, dest);

                filename = "ZScoreMatrixNrSamples-Permutation" + permutation + ".txt.gz";
                if (permutation == 0) {
                    filename = "ZScoreMatrixNrSamples.txt.gz";
                }
                source = new File(tempDir + filename);
                dest = new File(settings.getOutput() + filename);
                if (dest.exists()) {
                    System.out.println(
                            "Destination file: " + dest.getAbsolutePath() + " exists already.. Deleting!");
                    dest.delete();
                }
                System.out.println(
                        "Moving file: " + tempDir + filename + " --> " + settings.getOutput() + filename);
                FileUtils.moveFile(source, dest);
            }
        }

        for (BinaryMetaAnalysisDataset dataset : datasets) {
            dataset.close();
        }

        if (!DEBUG) {
            writeBuffer(outdir, permutation);

        }
    }
    if (usetmp) {
        // move remaining contents of tmp dir to final directory
        File source = new File(tempDir);
        File dest = new File(settings.getOutput());
        FileUtils.copyDirectory(source, dest);
        FileUtils.cleanDirectory(source);
    }
}

From source file:nz.co.testamation.core.mock.sftp.SFTPMockServer.java

@Reset
public void reset() {
    try {/*from  w ww.  j a  va2 s .c o  m*/
        FileUtils.cleanDirectory(rootDir);
        for (String directory : defaultDirectories) {
            createDirOrFile(directory, true);
        }
    } catch (IOException e) {
        throw new RuntimeException(e);
    }
}

From source file:opennlp.tools.parse_thicket.kernel_interface.style_classif.TSNE_ImporterProcessor.java

public void importFileCreatClassifDirs() {
    Map<Integer, String> id_Text = new HashMap<Integer, String>();
    Map<Integer, String> id_Label = new HashMap<Integer, String>();

    try {/*  ww  w .j  a  v a  2 s  .  c  o m*/
        FileUtils.cleanDirectory(new File(resourceWorkDir + "/txt"));
    } catch (IOException e2) {
        e2.printStackTrace();
    }

    String text = null;
    try {
        text = FileUtils.readFileToString(new File(resourceWorkDir + importFilePath),
                Charset.defaultCharset().toString());
    } catch (IOException e) {

        e.printStackTrace();
    }

    String[] portions = StringUtils.substringsBetween(text, "<text ", "/text>");
    for (int i = 0; i < portions.length; i++) {
        String label = StringUtils.substringBetween(portions[i], "id=\"", "\">");
        String po = StringUtils.substringBetween(portions[i], "\">", "<");
        id_Text.put(i, po);
        id_Label.put(i, label);
        if (true) {
            String localDirName = label.substring(0, 4);
            if (!new File(resourceWorkDir + "txt/" + localDirName).exists())
                try {
                    FileUtils.forceMkdir(new File(resourceWorkDir + "txt/" + localDirName));
                } catch (IOException e1) {
                    e1.printStackTrace();
                }
            try {
                label = label.replace('/', '_');
                String fullPath = resourceWorkDir + "txt/" + localDirName + "/" + i + label + ".txt";
                FileUtils.writeStringToFile(new File(fullPath), po);
            } catch (IOException e) {
                e.printStackTrace();
            }
        }
    }

}

From source file:org.abs_models.backend.erlang.ErlApp.java

public ErlApp(File destDir, File http_index_file, File http_static_dir)
        throws IOException, InternalBackendException {
    // FIXME this should probably be a method; strange to have a
    // class which does all its work in the constructor
    super();//from  w  w  w  .java  2  s  . c  om
    this.destDir = destDir;
    this.destCodeDir = new File(destDir, "absmodel/src/");
    this.destIncludeDir = new File(destDir, "absmodel/include/");
    destDir.mkdirs();
    FileUtils.cleanDirectory(destDir);
    destDir.mkdirs();
    new File(destDir, "absmodel/ebin").mkdir();
    index_file = http_index_file;
    static_dir = http_static_dir;
    if (static_dir != null && !static_dir.isDirectory()) {
        throw new InternalBackendException("Please provide a directory with static files");
    }
    copyRuntime();
}