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:de.sub.goobi.export.dms.AutomaticDmsExportWithoutHibernate.java

/**
 * Starts copying all directories configured in goobi_config.properties
 * parameter "processDirs" to export folder.
 *
 * @param myProcess//w w w. j  ava 2  s. com
 *            the process object
 * @param zielVerzeichnis
 *            the destination directory
 */
private void directoryDownload(ProcessObject myProcess, String zielVerzeichnis) throws IOException {
    String[] processDirs = ConfigCore.getStringArrayParameter("processDirs");

    for (String processDir : processDirs) {

        SafeFile srcDir = new SafeFile(FilenameUtils.concat(fi.getProcessDataDirectory(),
                processDir.replace("(processtitle)", myProcess.getTitle())));
        SafeFile dstDir = new SafeFile(FilenameUtils.concat(zielVerzeichnis,
                processDir.replace("(processtitle)", myProcess.getTitle())));

        if (srcDir.isDirectory()) {
            srcDir.copyDir(dstDir);
        }
    }
}

From source file:net.sf.jvifm.ui.FileLister.java

public String[] getSelectionFiles() {
    TableItem[] items = table.getSelection();
    String[] result = new String[items.length];

    for (int i = 0; i < items.length; i++) {
        result[i] = FilenameUtils.concat(pwd, items[i].getText(0));
    }/* ww w  .j av a 2  s  .  c  o  m*/
    return result;

}

From source file:edu.cornell.med.icb.goby.readers.sam.TestGobyPaperTop5000s.java

/**
 * Test that SHOULD fail, for local testing, not for server testing.
 * This is designed to be run manually as the 1M doesn't exist on the testing server.
 * Before running this test, run testRoundTrip1M().
 *
 * @throws java.io.IOException error/*w w  w .j a  v  a  2  s  .c  o  m*/
 */
// @Test
public void testRoundTripFail() throws IOException {
    final RoundTripAlignment rtc = new RoundTripAlignment();
    rtc.sourceBamFilename = FilenameUtils.concat(BASE_TEST_INPUT_DIR, "HZFWPTI-5000.sam.gz");
    rtc.destBamFilename = FilenameUtils.concat(BASE_TEST_INPUT_DIR, "JRODTYG-5000.sam.gz");
    rtc.convertBamToGoby = false;
    rtc.convertGobyToBam = false;
    rtc.testRoundTripAny();
}

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

private String getThumbnailFilePath() {
    final long threadId = Thread.currentThread().getId();

    // FFmpeg replaces the "%1d" with a single digit when it creates the output file. This is
    // necessary because FFmpeg requires a unique filename for each output file when outputting
    // multiple images.
    final String thumbnailFileName = String.format("thumbnail-%d-%%1d.png", threadId);

    final String tempDirectoryPath = System.getProperty("java.io.tmpdir");

    return FilenameUtils.concat(tempDirectoryPath, thumbnailFileName);
}

From source file:com.iyonger.apm.web.controller.FileEntryController.java

private void upload(User user, String path, String description, MultipartFile file) throws IOException {
    FileEntry fileEntry = new FileEntry();
    fileEntry.setContentBytes(file.getBytes());
    fileEntry.setDescription(description);
    fileEntry.setPath(FilenameUtils.separatorsToUnix(FilenameUtils.concat(path, file.getOriginalFilename())));
    fileEntryService.save(user, fileEntry);
}

From source file:edu.cornell.med.icb.goby.modes.TestSplicedSamHelper.java

@Test
public void testSamToCompactTrickCase8() throws IOException {

    SAMToCompactMode importer = new SAMToCompactMode();
    importer.setInputFile("test-data/splicedsamhelper/tricky-spliced-8.sam");
    final String outputFilename = FilenameUtils.concat(BASE_TEST_DIR, "spliced-output-alignment-8");
    importer.setOutputFile(outputFilename);
    MutableString seq = new MutableString();
    for (int i = 0; i < 194407 - 7; i++) {
        seq.append('N');
    }/*w w w.j  a va2  s.com*/
    seq.append("NNNNNNTTAGAAAAACAGAGAGAGAAGGAGAGTAAAGGGAGGAGGCGGAGGAGGAGAAAAGAAGAAAGCAGAGANNNNNN");
    String[] refs = { seq.toString() };

    RandomAccessSequenceTestSupport genomeTestSupport = new RandomAccessSequenceTestSupport(refs);
    importer.setGenome(genomeTestSupport);

    importer.execute();

    AlignmentReader reader = new AlignmentReaderImpl(outputFilename);
    assertTrue(reader.hasNext());
    Alignments.AlignmentEntry first = reader.next();

    assertEquals(0, first.getQueryIndex());
    assertEquals(0, first.getFragmentIndex());
    assertEquals(194301 - 1, first.getPosition());

}

From source file:com.turn.griffin.GriffinLibCacheUtil.java

public boolean finishTempCachePreparation(FileInfo fileInfo) {

    /* Decompress the file */
    decompressFile(getTempCacheCompressedFilePath(fileInfo),
            GriffinCompression.getByName(fileInfo.getCompression()));

    /* Verification */
    String fileHash = computeMD5(getTempCacheFilePath(fileInfo)).get();
    if (!fileInfo.getHash().equals(fileHash)) {
        logger.warn(String.format("File verification for downloaded file failed %s",
                fileInfo.toString().replaceAll(System.getProperty("line.separator"), " ")));
        logger.debug(String.format("Expected hash: %s actual hash: %s", fileInfo.getHash(), fileHash));
        if (logger.isDebugEnabled()) {
            try {
                /* Store file for forensics */
                String tempDir = FilenameUtils.concat(getTempCacheDirectory(), fileInfo.getFilename());
                FileUtils.copyDirectoryToDirectory(new File(tempDir), new File(getForensicCacheDirectory()));
            } catch (IOException e) {
                // Ignore
            }//from  ww  w.  j  a  v a2  s .c  o m
        }
        return false;
    }
    return true;
}

From source file:edu.cornell.med.icb.goby.readers.sam.TestSamRecordParser.java

/**
 * Same test as above, but write the sam to compact and then read the sequence variation form the compact.
 *
 * @throws IOException error reading//from   w  w  w  . j  a  v a 2s .  c  om
 */
@Test
public void testSamToCompactTrickCase17ViaWriter() throws IOException {
    final SAMToCompactMode importer = new SAMToCompactMode();
    importer.setInputFile("test-data/splicedsamhelper/tricky-spliced-17.sam");
    final String outputFilename = FilenameUtils.concat(BASE_TEST_OUTPUT_DIR, "tricky-spliced-17");
    importer.setPreserveSoftClips(true);
    importer.setOutputFile(outputFilename);
    importer.execute();

    final AlignmentReader reader = new AlignmentReaderImpl(outputFilename);
    assertTrue(reader.hasNext());
    final Alignments.AlignmentEntry first = reader.next();

    assertEquals(45881869 - 1, first.getPosition());

    //509.6.68.19057.157284   83   chr1   45881869   29   6S23M1I6M1D16M1I47M   =   45881519   -443   TTACCCGCTTTCCTTGCCCAAATTTTAAGTTTCNGGAAAAGGGGAGGGAAATGGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTGACAGAGTGTCAC   #######################################################ECGGGGGGGGGGGGGGGGGGGGGGGGHHHHHHHHHHHHHHHHHHH   MD:Z:3G4A7C4C1A2T2^T2C4T3A0G5C44   RG:Z:1   XG:i:3   AM:i:29   NM:i:14   SM:i:29   XM:i:10   XO:i:3   XT:A:M

    assertEquals(6, first.getQueryPosition());
    assertEquals("TTACCC", first.getSoftClippedBasesLeft());
    assertEquals("", first.getSoftClippedBasesRight());

    assertEquals(13, first.getSequenceVariationsCount());

    final Alignments.SequenceVariation last = first.getSequenceVariations(12);
    assertEquals("T", last.getTo());
    assertEquals("C", last.getFrom());
    assertArrayEquals(RoundTripAlignment.byteArray(36), last.getToQuality().toByteArray());
}

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

@Test
public void testIterateSortedWithReadInsertions() throws IOException {

    final String basename = "align-skip-to-1-concat";
    final String basenamePath = FilenameUtils.concat(BASE_TEST_DIR, basename);
    final AlignmentWriterImpl writer = new AlignmentWriterImpl(basenamePath);
    writer.setNumAlignmentEntriesPerChunk(1);

    final int numTargets = 3;
    final int[] targetLengths = new int[numTargets];

    for (int referenceIndex = 0; referenceIndex < numTargets; referenceIndex++) {
        targetLengths[referenceIndex] = 1000;
    }//from  w  w  w  .j av a  2 s .c o  m
    writer.setTargetLengths(targetLengths);
    // we write this alignment sorted:

    writer.setSorted(true);
    Alignments.AlignmentEntry.Builder newEntry;

    newEntry = prepareAlignmentEntryWithReadInsertion(0, 1, 100, 30, false, new int[] { 4, 3 });
    writer.appendEntry(newEntry.build());

    writer.close();
    writer.printStats(System.out);

    final Int2IntMap positionMap = new Int2IntOpenHashMap();
    final Int2IntMap readIndexMap = new Int2IntOpenHashMap();

    IterateSortedAlignmentsListImpl iterator = new IterateSortedAlignmentsListImpl() {

        @Override
        public void processPositions(int referenceIndex, int intermediatePosition,
                DiscoverVariantPositionData positionBaseInfos) {
            int coverage = 0;
            for (PositionBaseInfo info : positionBaseInfos) {
                coverage += info.from != '-' ? 1 : 0;
                readIndexMap.put(info.readIndex, readIndexMap.get(info.readIndex) + 1);
            }
            // store one-based positions
            positionMap.put(intermediatePosition + 1, coverage);
            //    System.out.printf("position: %d listSize: %d%n", position, coverage);
        }
    };
    iterator.iterate(basenamePath);
    // check coverage on ref:
    for (int i = 0; i < 100; i++) {
        assertEquals("position " + i, 0, positionMap.get(i));
    }
    for (int i = 100; i < 132; i++) {

        assertEquals("position " + i, 1, positionMap.get(i));
    }
    //check read index:
    for (int i = 1; i < 35; i++) {
        assertEquals("read-index " + i, 1, readIndexMap.get(i));

    }

}

From source file:edu.cornell.med.icb.goby.modes.TestSplicedSamHelper.java

@Test
public void testSamToCompactTrickCase9() throws IOException {

    SAMToCompactMode importer = new SAMToCompactMode();
    importer.setInputFile("test-data/splicedsamhelper/tricky-spliced-9.sam");
    final String outputFilename = FilenameUtils.concat(BASE_TEST_DIR, "spliced-output-alignment-9");
    importer.setOutputFile(outputFilename);
    MutableString seq = new MutableString();

    seq.append("NNNTTAGAAAAACAGAGAGAGAAGGAGAGTAAAGGGAGGAGGCGGAGGAGGAGAAAAGAAGAAAGCAGAGANNNNNN");
    for (int i = 0; i < 573; i++) {
        seq.insert(25, '-');
    }/*from   w  w  w  . ja  v a  2s . c  o  m*/
    String[] refs = { seq.toString() };

    RandomAccessSequenceTestSupport genomeTestSupport = new RandomAccessSequenceTestSupport(refs);
    importer.setGenome(genomeTestSupport);

    importer.execute();

    AlignmentReader reader = new AlignmentReaderImpl(outputFilename);
    assertTrue(reader.hasNext());
    Alignments.AlignmentEntry first = reader.next();

    assertEquals(0, first.getQueryIndex());
    assertEquals(0, first.getFragmentIndex());
    assertEquals(3 - 1, first.getPosition());

}