Example usage for org.apache.commons.io FilenameUtils concat

List of usage examples for org.apache.commons.io FilenameUtils concat

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Introduction

In this page you can find the example usage for org.apache.commons.io FilenameUtils concat.

Prototype

public static String concat(String basePath, String fullFilenameToAdd)

Source Link

Document

Concatenates a filename to a base path using normal command line style rules.

Usage

From source file:com.mbrlabs.mundus.assets.FbxConv.java

public FbxConvResult execute() {
    FbxConvResult result = new FbxConvResult();
    if (input == null || output == null) {
        result.setSuccess(false);// ww  w .j a  v  a 2  s  .co m
        result.setResultCode(FbxConvResult.RESULT_CODE_PARAM_ERROR);
        Log.error(TAG, "FbxCov input or output not defined");
        return result;
    }

    if (!input.endsWith("fbx")) {
        result.setSuccess(false);
        result.setResultCode(FbxConvResult.RESULT_CODE_WRONG_INPUT_FORMAT);
        Log.error(TAG, "FbxCov input format not supported");
    }

    // build arguments
    String outputFilename = FilenameUtils.getBaseName(input);
    List<String> args = new ArrayList<String>(6);
    if (flipTexture)
        args.add("-f");
    if (verbose)
        args.add("-v");
    if (outputFormat == OUTPUT_FORMAT_G3DJ) {
        args.add("-o");
        args.add("g3dj");
        outputFilename += ".g3dj";
    } else {
        outputFilename += ".g3db";
    }

    args.add(input);
    String path = FilenameUtils.concat(output, outputFilename);
    args.add(path);
    Log.debug("FbxConv", "Command: " + args);
    pb.command().addAll(args);

    // execute fbx-conv process
    try {
        Process process = pb.start();
        int exitCode = process.waitFor();
        String log = IOUtils.toString(process.getInputStream());

        if (exitCode == 0 && !log.contains("ERROR")) {
            result.setSuccess(true);
            result.setOutputFile(path);
        }
        result.setLog(log);

    } catch (IOException e) {
        e.printStackTrace();
        result.setSuccess(false);
        result.setResultCode(FbxConvResult.RESULT_CODE_IO_ERROR);
    } catch (InterruptedException e) {
        e.printStackTrace();
        result.setSuccess(false);
        result.setResultCode(FbxConvResult.RESULT_CODE_INTERRUPTED);
    }

    return result;
}

From source file:edu.cornell.med.icb.goby.alignments.TestAlignmentIndex.java

@Test
public void test_1_9_5_IndexIssueExtraTests() throws IOException {

    int[] targetLengths = new int[] { 100, 50, 20, 10, 5 };
    final String basename1 = FilenameUtils.concat(BASE_TEST_DIR, "align-index-error-2");
    final AlignmentWriterImpl writer = new AlignmentWriterImpl(basename1);
    writer.setTargetLengths(targetLengths);
    writer.setNumAlignmentEntriesPerChunk(1);
    writer.setSorted(true);/*from  w  w  w.j  a va 2  s.c  om*/
    int queryIndex = 0;

    writer.setAlignmentEntry(queryIndex++, 0, 99, 30, false, constantQueryLength);
    writer.appendEntry();
    writer.setAlignmentEntry(queryIndex++, 1, 0, 30, false, constantQueryLength);
    writer.appendEntry();
    writer.setAlignmentEntry(queryIndex++, 1, 1, 30, false, constantQueryLength);
    writer.appendEntry();
    writer.close();

    AlignmentReaderImpl reader = new AlignmentReaderImpl(basename1);
    reader.reposition(1, 0); // will be (0,99) because reposition goes one chunk before. The previous chunk
    // will have the indexed entry as first entry, plus some other entry, possibly including an entry with
    // position equal to the reposition argument. Repositioning to the chunk before garantees that skipTo will
    // not miss these entries, and appropriately filter the beginning of the chunk with position before (1,0).

    Alignments.AlignmentEntry entry = reader.next();
    assertEquals(0, entry.getTargetIndex());
    assertEquals(99, entry.getPosition());
    entry = reader.next();
    assertEquals(1, entry.getTargetIndex());
    assertEquals(0, entry.getPosition());
    entry = reader.next();
    assertEquals(1, entry.getTargetIndex());
    assertEquals(1, entry.getPosition());
    assertFalse(reader.hasNext());
    // Now check that the locations were stored in the index and can be decoded correctly:
    ObjectList<ReferenceLocation> locations = reader.getLocations(1);
    assertEquals(0, locations.get(0).targetIndex);
    assertEquals(99, locations.get(0).position);
    assertEquals(1, locations.get(1).targetIndex);
    assertEquals(0, locations.get(1).position);
    assertEquals(1, locations.get(2).targetIndex);
    assertEquals(1, locations.get(2).position);

    assertEquals("with modulo=1, must recover three locations.", 3, locations.size());

    reader = new AlignmentReaderImpl(basename1);

    entry = reader.skipTo(1, 1);
    assertEquals(1, entry.getTargetIndex());
    assertEquals(1, entry.getPosition());
    assertFalse(reader.hasNext());
}

From source file:edu.cornell.med.icb.goby.stats.TestStatsWriter.java

@Test
public void testVCFFormat2() throws IOException {

    final String file = FilenameUtils.concat(BASE_TEST_DIR, "format-2.vcf");

    VCFWriter writer = new VCFWriter(new PrintWriter(new FileWriter(file)));

    int fieldC = writer.defineField("FORMAT", "GT", 1, ColumnType.String, "Desc GT");
    int fieldD = writer.defineField("FORMAT", "GQ", 1, ColumnType.String, "Desc GQ");
    String samples[] = { "sample-id-1", "sample-id-2", "sample-id-3" };

    writer.defineSamples(samples);/*from  ww w  .  ja v a 2 s  .co m*/
    writer.writeHeader();
    writer.setSampleValue(fieldC, 0, "A");
    writer.setSampleValue(fieldD, 0, "B");
    writer.writeRecord();
    //      writer.setSampleValue(fieldC, 1, "A");
    //       writer.setSampleValue(fieldD, 1, "B");
    // writer.writeRecord();
    writer.setSampleValue(fieldC, 2, "A");
    writer.setSampleValue(fieldD, 2, "B");
    writer.writeRecord();
    writer.close();

    assertEquals(new File("test-data/stats-writer/expected-format-2.vcf"),
            new File("test-results/stats-writer/format-2.vcf"));
}

From source file:ddf.content.plugin.video.VideoThumbnailPlugin.java

public VideoThumbnailPlugin(final BundleContext bundleContext) throws IOException {
    final String bundledFFmpegBinaryPath = getBundledFFmpegBinaryPath();
    final String ffmpegBinaryName = StringUtils.substringAfterLast(bundledFFmpegBinaryPath, "/");
    final String ffmpegFolderPath = FilenameUtils.concat(System.getProperty("ddf.home"),
            "bin_third_party/ffmpeg");
    ffmpegPath = FilenameUtils.concat(ffmpegFolderPath, ffmpegBinaryName);

    try (final InputStream inputStream = bundleContext.getBundle().getEntry(bundledFFmpegBinaryPath)
            .openStream()) {/*from  www .j av  a 2 s  .  co m*/
        copyFFmpegBinary(inputStream);
    }

    limitFFmpegProcessesSemaphore = new Semaphore(MAX_FFMPEG_PROCESSES, true);
}

From source file:edu.kit.dama.ui.repo.staging.DataZipCreator.java

@Override
public void performPostTransferProcessing(TransferTaskContainer pContainer) throws StagingProcessorException {
    LOGGER.debug("Zipping data");
    URL generatedFolder = pContainer.getGeneratedUrl();
    LOGGER.debug("Using target folder: {}", generatedFolder);

    try {//from   ww w . java 2s .co m
        String zipFileName = CryptUtil.stringToSHA1(pContainer.getTransferInformation().getDigitalObjectId())
                + ".zip";
        URL targetZip = URLCreator.appendToURL(generatedFolder, zipFileName);
        LOGGER.debug("Zipping all data to file {}", targetZip);
        File targetFile = new File(targetZip.toURI());

        ITransferInformation info = pContainer.getTransferInformation();
        LOGGER.debug("Obtaining local folder for transfer with id {}", info.getTransferId());

        File localFolder = StagingService.getSingleton().getLocalStagingFolder(info,
                StagingService.getSingleton().getContext(info));
        File dataFolder = new File(
                FilenameUtils.concat(localFolder.getAbsolutePath(), Constants.STAGING_DATA_FOLDER_NAME));
        if (!dataFolder.exists()) {
            throw new IOException(
                    "Data folder " + dataFolder.getAbsolutePath() + " does not exist. Aborting zip operation.");
        }

        LOGGER.debug("Start zip operation using data input folder URL {}", dataFolder);
        ZipUtils.zip(new File(dataFolder.toURI()), targetFile);
        LOGGER.debug("Adding zip file {} to container.", targetFile);
        pContainer.addGeneratedFile(targetFile);
        LOGGER.debug("Zip operation successfully finished.");
    } catch (IOException | URISyntaxException ex) {
        throw new StagingProcessorException("Failed to zip data", ex);
    }
}

From source file:edu.kit.dama.staging.handlers.impl.DownloadPreparationHandler.java

@Override
public final void prepareEnvironment(TransferClientProperties pProperties,
        IAuthorizationContext pSecurityContext) throws TransferPreparationException {
    LOGGER.debug("Preparing data download tree");
    LOGGER.debug(" - Obtaining AccessPoint");
    AbstractStagingAccessPoint accessPoint = StagingConfigurationManager.getSingleton()
            .getAccessPointById(pProperties.getStagingAccessPointId());
    LOGGER.debug(" - Getting access URL");
    URL accessUrl = accessPoint.getAccessUrl(getTransferInformation(), pSecurityContext);
    LOGGER.debug(" - Access URL: {}. Getting local staging folder.", accessUrl);
    File localStagingFolder = accessPoint.getLocalPathForUrl(accessUrl, pSecurityContext);
    LOGGER.debug(" - Local staging folder: {}", localStagingFolder);
    File localSettingsFolder = AbstractStagingAccessPoint.getSettingsFolder(localStagingFolder);
    LOGGER.debug(" - Local settings folder: {}. Obtaining file tree destination file.", localSettingsFolder);
    String treeFile = FilenameUtils.concat(localSettingsFolder.getPath(), DATA_FILENAME);

    if (new File(treeFile).exists()
            && !StagingService.getSingleton().isTransferDeleted(getTransferInformation())) {
        throw new TransferPreparationException(
                "Download for this object is still in preparation. Please try again later");
    }//from   w w  w  .j a  va  2 s  .  com
    LOGGER.debug("Writing tree data to {}", treeFile);
    DataOrganizationUtils.writeTreeToFile(treeToDownload, new File(treeFile));

    if (pProperties.isSendMailNotification()) {
        LOGGER.debug("Writing mail notification information to file");
        MailNotificationHelper.storeProperties(localSettingsFolder, pProperties.getReceiverMail());
    }
    LOGGER.debug("Storing access point properties.");
    Properties props = TransferClientPropertiesUtils.propertiesToProperties(pProperties);
    FileOutputStream fout = null;
    try {
        fout = new FileOutputStream(
                new File(localSettingsFolder, pProperties.getStagingAccessPointId() + ".properties"));
        props.store(fout, null);
    } catch (IOException ioe) {
        LOGGER.error("Failed to store access point properies", ioe);
    } finally {
        if (fout != null) {
            try {
                fout.close();
            } catch (IOException ex) {
            }
        }
    }

    LOGGER.debug("Environment preparation successfully finished");
}

From source file:edu.cornell.med.icb.goby.counts.TestReadWriteCounts.java

@Test
@SuppressWarnings("deprecation") // We are intentionally testing a deprecated method here
public void testReadWrite2() throws IOException {
    final String basename = FilenameUtils.concat(BASE_TEST_DIR, "counts-102.bin");
    final CountsWriterI writerI = new CountsWriter(new FileOutputStream(basename), 0);

    final int lengthA = 5;
    final int lengthB = 100000;
    final int lengthC = 10;
    final int lengthD = 1;

    writerI.appendCount(10, lengthA);/*from  w w w . j  ava  2 s . c om*/
    writerI.appendCount(11, lengthB);
    writerI.appendCount(12, lengthC);

    writerI.appendCount(10, lengthD);
    writerI.close();

    final CountsReader reader = new CountsReader(new FileInputStream(basename));

    for (int index = 0; index < lengthA; index++) {
        assertTrue(reader.hasNextPosition());
        assertEquals(10, reader.nextCountAtPosition());
    }
    for (int index = 0; index < lengthB; index++) {
        assertTrue(reader.hasNextPosition());
        assertEquals(11, reader.nextCountAtPosition());
    }
    for (int index = 0; index < lengthC; index++) {
        assertTrue(reader.hasNextPosition());
        assertEquals(12, reader.nextCountAtPosition());
    }
    for (int index = 0; index < lengthD; index++) {
        assertTrue(reader.hasNextPosition());
        assertEquals(10, reader.nextCountAtPosition());
    }
    assertFalse(reader.hasNextPosition());
}

From source file:edu.cornell.med.icb.goby.alignments.TestPositionSlices.java

@Test
public void testThreeSlice() throws IOException {
    final String basename = "align-position-slices-3";
    buildAlignment(basename);//w w  w  .j  a va2s  . c  om

    {// check that we can read everything only between 1 13 and 2 123:
        final AlignmentReader reader = new AlignmentReaderImpl(FilenameUtils.concat(BASE_TEST_DIR, basename), 1,
                13, 2, 123);

        check(reader, 1, 13);
        check(reader, 1, 13);
        check(reader, 1, 13);
        check(reader, 2, 123);
        assertFalse(reader.hasNext());
        reader.close();
    }
}

From source file:edu.cornell.med.icb.goby.counts.TestCountsArchive.java

@Test
public void testIndices() throws IOException {
    final String basename = FilenameUtils.concat(BASE_TEST_DIR, "102.bin");
    final CountsArchiveWriter writer = new CountsArchiveWriter(basename);
    CountsWriterI cw = writer.newCountWriter(0);
    writer.returnWriter(cw);//w  ww.j  a va  2  s.  c  o  m

    cw = writer.newCountWriter(1);

    writer.returnWriter(cw);
    writer.close();
    final CountsArchiveReader reader = new CountsArchiveReader(basename);
    assertEquals(2, reader.getNumberOfIndices());
    assertEquals(2, reader.getIndices().size());
    assertNotNull(reader.getCountReader(0));
    assertNotNull(reader.getCountReader(1));
}

From source file:edu.kit.dama.staging.util.StagingUtils.java

/**
 * Get the temporary directory of the transfer associated with the provided
 * transfer container. This directory is located in the user home directory
 * under ~/.lsdf/&lt;TID&gt;, where &lt;TID&gt; stands for the transfer ID of this
 * transfer. To avoid problems with invalid pathnames, the TID gets UTF-8
 * URL-encoded. Within the temporary directory the transfer can store status
 * information or checkpoint data to be able to resume failed transfers.
 *
 * @param pContainer The transfer container for which the temp dir should be
 * returned./*from  ww  w.  j  a  va 2s . c  o m*/
 *
 * @return The transfer's temporary directory
 *
 * @throws IOException If there was not set any TID for this transfer or if
 * there are problems getting the users home directory
 */
public static String getTempDir(TransferTaskContainer pContainer) throws IOException {
    if (pContainer != null) {
        LOGGER.debug("Determining transfer tmp directory.");
        File userHome = SystemUtils.getUserHome();
        if (!isAccessibleDirectory(userHome)) {
            //user home not usable (maybe no home directory available). Try system temp dir...
            userHome = SystemUtils.getJavaIoTmpDir();
            if (!isAccessibleDirectory(userHome)) {
                throw new IOException("Failed to obtain valid temp directory. UserHome ("
                        + SystemUtils.getUserHome() + ") and TmpDir (" + userHome + ") are not usable.");
            } else {
                LOGGER.debug("Using tmp directory.");
            }
        } else {
            LOGGER.debug("Using user home directory.");
        }

        return FilenameUtils.concat(FilenameUtils.concat(userHome.getCanonicalPath(), ".lsdf"),
                URLEncoder.encode(pContainer.getUniqueTransferIdentifier(), "UTF-8"));
    } else {
        throw new IOException(
                "Failed to obtain temporary transfer directory. Transfer container must not be 'null'");
    }
}