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

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.enderville.enderinstaller.util.InstallerConfig.java

/**
 * The folder of optional mods for this installer.
 *
 * @return//from  w  ww  .  j a va2s. c o m
 */
public static String getExtraModsFolder() {
    return FilenameUtils.concat(getInstallerModsFolder(), "extra/");
}

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From source file:com.enioka.jqm.api.ServiceSimple.java

@GET
@Path("file")
@Produces(MediaType.APPLICATION_OCTET_STREAM)
public InputStream getDeliverableStream(@QueryParam("id") String randomId) {
    if (n == null) {
        throw new ErrorDto("can only retrieve a file when the web app runs on top of JQM", "", 7,
                Status.BAD_REQUEST);//  w ww .java2  s.  c om
    }

    Deliverable d = null;
    EntityManager em = null;
    try {
        em = ((HibernateClient) JqmClientFactory.getClient()).getEm();
        d = em.createQuery("SELECT d from Deliverable d WHERE d.randomId = :ii", Deliverable.class)
                .setParameter("ii", randomId).getSingleResult();
    } catch (NoResultException e) {
        throw new ErrorDto("Deliverable does not exist", 8, e, Status.BAD_REQUEST);
    } catch (Exception e) {
        throw new ErrorDto("Could not retrieve Deliverable metadata from database", 9, e,
                Status.INTERNAL_SERVER_ERROR);
    } finally {
        if (em != null) {
            em.close();
        }
    }

    String ext = FilenameUtils.getExtension(d.getOriginalFileName());
    res.setHeader("Content-Disposition",
            "attachment; filename=" + d.getFileFamily() + "." + d.getId() + "." + ext);
    return getFile(FilenameUtils.concat(n.getDlRepo(), d.getFilePath()));
}

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From source file:com.xiaomi.linden.client.LindenClient.java

private LindenService.ServiceIface buildClient(String parent, String node) {
    String nodePath = FilenameUtils.separatorsToUnix(FilenameUtils.concat(parent, node));
    byte[] bytes = zkClient.readData(nodePath);
    ServiceInstance serviceInstance = JSONObject.parseObject(new String(bytes), ServiceInstance.class);
    String schema = String.format("%s:%s", serviceInstance.getServiceEndpoint().getHost(),
            serviceInstance.getServiceEndpoint().getPort());
    return Thrift.newIface(schema, LindenService.ServiceIface.class);
}

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

@Before
public void setUp() throws IOException {
    {/*from   w  w w  .j  a va  2s. com*/
        outputBasename1 = FilenameUtils.concat(BASE_TEST_DIR, "concat-align-101");
        final AlignmentWriterImpl writer = new AlignmentWriterImpl(outputBasename1);
        writer.setNumAlignmentEntriesPerChunk(1000);
        writer.setAlignerName("first-aligner");
        writer.setAlignerVersion("version-first-aligner");
        final int numQuery = 10;
        int position = 100;
        final int score = 30;

        writer.setPermutation(true);
        for (int targetIndex = 0; targetIndex < numTargets; targetIndex++) {
            for (int queryIndex = 0; queryIndex < numQuery; queryIndex++) {
                Alignments.AlignmentEntry.Builder newEntry = Alignments.AlignmentEntry.newBuilder();
                newEntry.setQueryIndex(2000 + queryIndex);
                newEntry.setTargetIndex(targetIndex);
                newEntry.setScore((float) score);
                newEntry.setPosition(position++);
                newEntry.setMatchingReverseStrand(false);
                newEntry.setMultiplicity(1);
                newEntry.setQueryLength(constantQueryLength);
                newEntry.setQueryIndexOccurrences(numTargets);
                writer.appendEntry(newEntry.build());
                numEntriesIn101++;
                count101++;
            }
        }
        numQueries101 = numQuery;

        writer.close();
        // reads in basename1 hit in 10 different places in the genome. They should be filtered when
        // removing ambiguous reads.
        AlignmentTooManyHitsWriter tmhWriter = new AlignmentTooManyHitsWriter(outputBasename1, 2);
        for (int queryIndex = 0; queryIndex < numQuery; queryIndex++) {
            tmhWriter.append(queryIndex, 10, 30);
        }
        tmhWriter.close();
    }
    {
        outputBasename2 = FilenameUtils.concat(BASE_TEST_DIR, "concat-align-102");
        final AlignmentWriterImpl writer = new AlignmentWriterImpl(outputBasename2);
        writer.setAlignerName("second-aligner");
        writer.setAlignerVersion("version-second-aligner");
        writer.setNumAlignmentEntriesPerChunk(1000);
        writer.setPermutation(true);
        final int numQuery = 13;

        int position = 1;
        final int score = 50;
        for (int targetIndex = 0; targetIndex < numTargets; targetIndex++) {
            for (int queryIndex = 0; queryIndex < numQuery; queryIndex++) {

                Alignments.AlignmentEntry.Builder newEntry = Alignments.AlignmentEntry.newBuilder();
                newEntry.setQueryIndex(1000 + queryIndex);
                newEntry.setTargetIndex(targetIndex);
                newEntry.setScore((float) score);
                newEntry.setPosition(position++);
                newEntry.setMatchingReverseStrand(false);
                newEntry.setMultiplicity(1);
                newEntry.setQueryLength(constantQueryLength);
                newEntry.setQueryIndexOccurrences(numTargets);
                writer.appendEntry(newEntry.build());
                numEntriesIn102++;
                count102++;
            }
        }
        numQueries102 = numQuery;

        writer.close();
        // reads in basename 2 have just one hit, they are never ambiguous
        AlignmentTooManyHitsWriter tmhWriter = new AlignmentTooManyHitsWriter(outputBasename2, 2);
        for (int queryIndex = 0; queryIndex < numQuery; queryIndex++) {
            tmhWriter.append(queryIndex, 1, 30);
        }
        tmhWriter.close();
    }

}

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From source file:es.urjc.mctwp.image.management.ImageCollectionManager.java

/**
 * It parses and stores temporarily, a list of files.
 * /*from   w w w. j  a v a2 s .  c  om*/
 * @param colName
 * @param files
 * @throws ImageCollectionException
 * @throws ImageException
 * @throws IOException
 */
public void storeTemporalImages(String colName, List<File> files)
        throws ImageCollectionException, ImageException, IOException {

    for (File file : files) {
        Image image = impm.createImage(file);

        if (image != null) {
            if (image instanceof SingleImage) {
                SingleImage simg = (SingleImage) image;

                String ext = ImageUtils.getFileExtension(simg.getContent());
                File tmpFile = new File(FilenameUtils.concat(sysTempDir.getAbsolutePath(),
                        image.getId() + FilenameUtils.EXTENSION_SEPARATOR_STR + ext));
                if (tmpFile.exists())
                    tmpFile.delete();
                FileUtils.copyFile(simg.getContent(), tmpFile);

                imcc.storeContent(colName, tmpFile, true);
                tmpFile.delete();
            } else {

                //Create temp directory where put all file content of Image
                File tmpDir = new File(FilenameUtils.concat(sysTempDir.getAbsolutePath(),
                        image.getId() + FilenameUtils.EXTENSION_SEPARATOR_STR + image.getType()));
                if (tmpDir.exists())
                    FileUtils.deleteDirectory(tmpDir);
                tmpDir.mkdir();

                if (image instanceof SeriesImage) {

                    List<Image> images = ((SeriesImage) image).getImages();
                    if (images != null && !images.isEmpty()) {

                        for (Image img : images)
                            copyToDirectory(tmpDir, img);

                    }
                } else if (image instanceof ComplexImage) {

                    List<File> auxFiles = ((ComplexImage) image).getContent();
                    if (auxFiles != null && !auxFiles.isEmpty()) {

                        for (File auxFile : auxFiles)
                            copyToDirectory(tmpDir, auxFile);
                    }
                }

                //Store content and delete temporal directory
                imcc.storeContent(colName, tmpDir, true);
                FileUtils.deleteDirectory(tmpDir);
            }
        }
    }
}

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

@Test
public void testBeforeSlice() throws IOException {
    final String basename = "align-position-slices-5";
    buildAlignment(basename);//from  w ww.j av  a2s  .com

    {// check that we can read skipTo before the start of the slice and only get entries that are within the slice
     // boundaries.
        final AlignmentReader reader = new AlignmentReaderImpl(FilenameUtils.concat(BASE_TEST_DIR, basename), 2,
                300, 2, 300);

        final Alignments.AlignmentEntry alignmentEntry = reader.skipTo(2, 0);

        assertNotNull(alignmentEntry);
        assertEquals(2, alignmentEntry.getTargetIndex());
        assertEquals(300, alignmentEntry.getPosition());
        check(reader, 2, 300);

        assertFalse(reader.hasNext());
        reader.close();
    }
}

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

@Test
public void testIterateSortedTwoMutations() throws IOException {

    final String basename = "align-skip-to-1-concat-two-mutations";
    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 a2 s . c  o  m
    writer.setTargetLengths(targetLengths);
    // we write this alignment sorted:

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

    newEntry = prepareAlignmentEntry(0, 1, 100, 3, true, new int[] { 2, 31, 34 }, 35);
    writer.appendEntry(newEntry.build());

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

    final IntSet variantReadIndices = new IntOpenHashSet();
    final IntSet variantPositionOnRef = new IntOpenHashSet();
    IterateSortedAlignmentsListImpl iterator = new IterateSortedAlignmentsListImpl() {

        public void processPositions(int referenceIndex, int intermediatePosition,
                DiscoverVariantPositionData positionBaseInfos) {

        }

        @Override
        public void observeVariantBase(ConcatSortedAlignmentReader sortedReaders,
                Alignments.AlignmentEntry alignmentEntry,
                Int2ObjectMap<DiscoverVariantPositionData> positionToBases, Alignments.SequenceVariation var,
                char toChar, char fromChar, byte toQual, int currentReferenceIndex, int currentRefPosition,
                int currentReadIndex) {
            variantReadIndices.add(currentReadIndex);
            variantPositionOnRef.add(currentRefPosition);
        }

    };
    iterator.iterate(basenamePath);

    assertTrue(variantReadIndices.contains(34));
    assertTrue(variantReadIndices.contains(2));
    assertTrue(variantReadIndices.contains(5));
    assertTrue(variantPositionOnRef.contains(101));
    assertTrue(variantPositionOnRef.contains(130));
    assertTrue(variantPositionOnRef.contains(133));

}

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From source file:cop.maven.plugins.AbstractRestToRamlMojoTest.java

@Test(groups = "checkOutputDirectoryExists")
public void shouldUpdateOutOnceWhenMultipleCheckOutput() throws Exception {
    File dir = TestUtils.createTempDir();

    Build build = new Build();
    build.setDirectory(dir.getAbsolutePath());
    mojo.project.setBuild(build);/*from w w w  . ja  v  a 2s.  c  o m*/

    mojo.out = "sub";
    checkOutputDirectoryExists(mojo);
    assertThat(mojo.out).isEqualTo(FilenameUtils.concat(dir.getAbsolutePath(), "sub"));

    checkOutputDirectoryExists(mojo);
    assertThat(mojo.out).isEqualTo(FilenameUtils.concat(dir.getAbsolutePath(), "sub"));
}

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From source file:edu.ku.brc.af.core.db.BackupServiceFactory.java

/**
 * @param restoreName/*from   w  w  w  .j a v  a  2s  .c  om*/
 * @return
 */
protected String getStatsName(final String restoreName) {
    String baseFileName = FilenameUtils.getBaseName(restoreName);
    String path = FilenameUtils.getFullPath(restoreName);
    return FilenameUtils.concat(path, baseFileName + ".stats");
}

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

public TerrainAsset createTerrainAsset(int vertexResolution, int size) throws IOException {
    String terraFilename = "terrain_" + UUID.randomUUID().toString() + ".terra";
    String metaFilename = terraFilename + ".meta";

    // create meta file
    String metaPath = FilenameUtils.concat(rootFolder.path(), metaFilename);
    MetaFile meta = createNewMetaFile(new FileHandle(metaPath), AssetType.TERRAIN);
    meta.setTerrainSize(size);//  ww w . ja v  a2  s  .  c  om
    meta.save();

    // create terra file
    String terraPath = FilenameUtils.concat(rootFolder.path(), terraFilename);
    File terraFile = new File(terraPath);
    FileUtils.touch(terraFile);

    // create initial height data
    float[] data = new float[vertexResolution * vertexResolution];
    for (int i = 0; i < data.length; i++) {
        data[i] = 0;
    }

    // write terra file
    DataOutputStream outputStream = new DataOutputStream(
            new BufferedOutputStream(new GZIPOutputStream(new FileOutputStream(terraFile))));
    for (float f : data) {
        outputStream.writeFloat(f);
    }
    outputStream.flush();
    outputStream.close();

    // load & apply standard chessboard texture
    TerrainAsset asset = new TerrainAsset(meta, new FileHandle(terraFile));
    asset.load();

    TextureAsset chessboard = (TextureAsset) findAssetByID(STANDARD_ASSET_TEXTURE_CHESSBOARD);
    if (chessboard != null) {
        // create splatmap
        PixmapTextureAsset splatmap = createPixmapTextureAsset(SplatMap.DEFAULT_SIZE);
        asset.setSplatmap(splatmap);
        asset.setSplatBase(chessboard);
        asset.applyDependencies();
    }

    addAsset(asset);
    return asset;
}

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