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

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

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

Introduction

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

Prototype

public static FileInputStream openInputStream(File file) throws IOException

Source Link

Document

Opens a FileInputStream for the specified file, providing better error messages than simply calling new FileInputStream(file).

Usage

From source file:architecture.ee.web.community.struts2.action.ajax.MyAttachmentAction.java

public String updateAttachment() throws Exception {
    if (attachmentId > 0) {
        Attachment attachment = this.getTargetAttachment();
        for (FileInfo f : attachments) {
            attachment.setName(f.getName());
            attachment.setContentType(f.getContentType());
            attachment.setSize((int) FileUtils.sizeOf(f.getFile()));
            try {
                attachment.setInputStream(FileUtils.openInputStream(f.getFile()));
            } catch (IOException e) {
                log.debug(e);/*  ww  w. j  ava2  s  .com*/
            }
            attachmentManager.saveAttachment(attachment);
        }
    }
    return success();
}

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

/**
 * Validates that a file can be reformatted to change the chunk size.
 *
 * @throws IOException if there is a problem reading or writing to the files
 *//*from  w w  w  .  ja v a 2s  .c  o  m*/
@Test
public void reformatChunkSize() throws IOException {
    final ReformatCompactReadsMode reformat = new ReformatCompactReadsMode();

    final String inputFilename = "test-data/compact-reads/s_1_sequence_short.compact-reads";
    reformat.setInputFilenames(inputFilename);
    reformat.setSequencePerChunk(1);
    final String outputFilename = "test-results/reformat-test-chunk-size.compact-reads";
    reformat.setOutputFile(outputFilename);
    reformat.execute();

    final File inputFile = new File(inputFilename);
    final File outputFile = new File(outputFilename);
    assertFalse("The reformatted file should not be the same as the original",
            FileUtils.contentEquals(inputFile, outputFile));

    final ReadsReader inputReader = new ReadsReader(FileUtils.openInputStream(inputFile));
    assertTrue("There should be reads in this file", inputReader.hasNext());

    final List<Reads.ReadEntry> inputEntries = new ArrayList<Reads.ReadEntry>(73);
    for (final Reads.ReadEntry entry : inputReader) {
        inputEntries.add(entry);
    }

    final ReadsReader outputReader = new ReadsReader(FileUtils.openInputStream(outputFile));
    assertTrue("There should be reads in this file", outputReader.hasNext());

    final List<Reads.ReadEntry> outputEntries = new ArrayList<Reads.ReadEntry>(73);
    for (final Reads.ReadEntry entry : outputReader) {
        outputEntries.add(entry);
    }

    assertEquals("The entries of both files should be equal", inputEntries, outputEntries);
}

From source file:com.mirth.connect.util.ArchiveUtils.java

/**
 * Extracts an archive using generic stream factories provided by commons-compress.
 *//*from   w w  w  .j  a va 2  s .c o  m*/
private static void extractGenericArchive(File archiveFile, File destinationFolder) throws CompressException {
    try {
        InputStream inputStream = new BufferedInputStream(FileUtils.openInputStream(archiveFile));

        try {
            inputStream = new CompressorStreamFactory().createCompressorInputStream(inputStream);
        } catch (CompressorException e) {
            // a compressor was not recognized in the stream, in this case we leave the inputStream as-is
        }

        ArchiveInputStream archiveInputStream = new ArchiveStreamFactory()
                .createArchiveInputStream(inputStream);
        ArchiveEntry entry;
        int inputOffset = 0;
        byte[] buffer = new byte[BUFFER_SIZE];

        try {
            while (null != (entry = archiveInputStream.getNextEntry())) {
                File outputFile = new File(
                        destinationFolder.getAbsolutePath() + IOUtils.DIR_SEPARATOR + entry.getName());

                if (entry.isDirectory()) {
                    FileUtils.forceMkdir(outputFile);
                } else {
                    FileOutputStream outputStream = null;

                    try {
                        outputStream = FileUtils.openOutputStream(outputFile);
                        int bytesRead;
                        int outputOffset = 0;

                        while ((bytesRead = archiveInputStream.read(buffer, inputOffset, BUFFER_SIZE)) > 0) {
                            outputStream.write(buffer, outputOffset, bytesRead);
                            inputOffset += bytesRead;
                            outputOffset += bytesRead;
                        }
                    } finally {
                        IOUtils.closeQuietly(outputStream);
                    }
                }
            }
        } finally {
            IOUtils.closeQuietly(archiveInputStream);
        }
    } catch (Exception e) {
        throw new CompressException(e);
    }
}

From source file:com.ariatemplates.attester.maven.ArtifactExtractor.java

public static void unzip(File zipFile, File outputFolder) throws IOException {
    ZipInputStream zipInputStream = null;
    try {/*from  w  ww  . ja v a  2s.  c o m*/
        ZipEntry entry = null;
        zipInputStream = new ZipInputStream(FileUtils.openInputStream(zipFile));
        while ((entry = zipInputStream.getNextEntry()) != null) {
            File outputFile = new File(outputFolder, entry.getName());

            if (entry.isDirectory()) {
                outputFile.mkdirs();
                continue;
            }

            OutputStream outputStream = null;
            try {
                outputStream = FileUtils.openOutputStream(outputFile);
                IOUtils.copy(zipInputStream, outputStream);
                outputStream.close();
            } catch (IOException exception) {
                outputFile.delete();
                throw new IOException(exception);
            } finally {
                IOUtils.closeQuietly(outputStream);
            }
        }
        zipInputStream.close();
    } finally {
        IOUtils.closeQuietly(zipInputStream);
    }
}

From source file:com.book.identification.rest.VolumeResource.java

@GET
@Produces(MediaType.APPLICATION_JSON)/*from w  w w . jav a  2 s . co m*/
@Path("hash/")
public Response hashing() throws IOException {
    VolumeDAO volumeDAO = DAOFactory.getInstance().getVolumeDAO();
    List<Volume> findAll = volumeDAO.findAll();
    Transaction beginTransaction = volumeDAO.getSession().beginTransaction();
    for (Volume volume : findAll) {
        String fileSHA1 = DigestUtils.shaHex(FileUtils.openInputStream(new File(volume.getPath())));
        volume.setHashSH1(fileSHA1);
    }
    beginTransaction.commit();
    return Response.ok("hashed").build();
}

From source file:edu.cornell.med.icb.goby.reads.TestReadsWriter.java

@Test
public void testReadFastBufferedInChunks() throws IOException {
    final String[] sequences = { "ACTGCGCGCG", "AAAAATTTTGGGGGCCCCCCC",
            "AAAAATTTTGGGGGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC" };
    final String[] descriptions = { "hello world", "descr2", "description 3" };
    final String filename = "test-results/reads/written-101.bin";
    final ReadsWriter writer = new ReadsWriterImpl(new FileOutputStream(new File(filename)));

    int expectedCount = 0;
    writer.setNumEntriesPerChunk(9);/*from  w  w  w .  j  a  va  2 s  . co m*/
    final int totalNumSeqs = 13;
    for (int i = 0; i < totalNumSeqs; i++) {
        int j = 0;
        for (final String sequence : sequences) {
            writer.setSequence(sequence);
            writer.setDescription(descriptions[j]);
            writer.appendEntry();
            ++j;
            expectedCount++;
        }
    }
    writer.close();

    FastBufferedInputStream stream = new FastBufferedInputStream(FileUtils.openInputStream(new File(filename)));
    writer.printStats(System.out);

    final MutableString sequence = new MutableString();
    int count = 0;

    ReadsReader reader = new ReadsReader(0, Long.MAX_VALUE, stream);

    while (reader.hasNext()) {
        final Reads.ReadEntry entry = reader.next();
        ReadsReader.decodeSequence(entry, sequence);
        // check that the sequence matches what was encoded:
        assertEquals(sequences[count % sequences.length], sequence.toString());
        assertEquals(descriptions[count % descriptions.length], entry.getDescription());
        assertEquals(count, entry.getReadIndex());
        count++;
    }

    assertEquals(expectedCount, count);

    stream.close();

    // now start at position 10, will skip the first collection.
    stream = new FastBufferedInputStream(FileUtils.openInputStream(new File(filename)));
    reader = new ReadsReader(10, Long.MAX_VALUE, stream);

    count = 0;
    while (reader.hasNext()) {
        final Reads.ReadEntry entry = reader.next();
        ReadsReader.decodeSequence(entry, sequence);
        // check that the sequence matches what was encoded:
        assertEquals(sequences[count % sequences.length], sequence.toString());
        assertEquals(descriptions[count % descriptions.length], entry.getDescription());
        //  assertEquals(count+9, entry.getReadIndex());
        count++;
    }

    assertEquals(expectedCount - 9, count);

    // start at 150 is past the start of the second read collection, so this collection is not returned:
    reader = new ReadsReader(150, Long.MAX_VALUE, stream);

    count = 0;
    while (reader.hasNext()) {
        final Reads.ReadEntry entry = reader.next();
        ReadsReader.decodeSequence(entry, sequence);
        // check that the sequence matches what was encoded:
        assertEquals(sequences[count % sequences.length], sequence.toString());
        assertEquals(descriptions[count % descriptions.length], entry.getDescription());
        //  assertEquals(count+9, entry.getReadIndex());
        count++;
    }
    // should have skipped 2:
    assertEquals(expectedCount - 9 * 2, count);

    // start at 0 and end at 150 should return only the second read collection, 9 sequences exactly.
    reader = new ReadsReader(10, 150, stream);

    count = 0;
    while (reader.hasNext()) {
        final Reads.ReadEntry entry = reader.next();
        ReadsReader.decodeSequence(entry, sequence);
        // check that the sequence matches what was encoded:
        assertEquals(sequences[count % sequences.length], sequence.toString());
        assertEquals(descriptions[count % descriptions.length], entry.getDescription());
        //  assertEquals(count+9, entry.getReadIndex());
        count++;
    }

    // should have skipped 2:
    assertEquals(9, count);
}

From source file:com.isomorphic.maven.util.ArchiveUtils.java

/**
 * Steps common to archiving both zip and jar files, which include reading files from disk and using
 * their contents to create {@link ZipEntry ZipEntries} and writing them to a ZipOutputStream.
 * // w  ww. j a v a2 s. c om
 * @param root
 * @param source
 * @param target
 * @throws IOException
 */
private static void zip(File root, File source, ZipOutputStream target) throws IOException {
    String relativePath = root.toURI().relativize(source.toURI()).getPath().replace("\\", "/");

    BufferedInputStream in = null;
    try {
        if (source.isDirectory()) {

            if (!relativePath.endsWith("/")) {
                relativePath += "/";
            }
            ZipEntry entry = ZipEntryFactory.get(target, relativePath);
            entry.setTime(source.lastModified());
            target.putNextEntry(entry);
            target.closeEntry();

            for (File nestedFile : source.listFiles()) {
                zip(root, nestedFile, target);
            }
            return;
        }

        ZipEntry entry = ZipEntryFactory.get(target, relativePath);
        entry.setTime(source.lastModified());
        target.putNextEntry(entry);
        in = new BufferedInputStream(FileUtils.openInputStream(source));
        IOUtils.copy(in, target);
        target.closeEntry();

    } finally {
        IOUtils.closeQuietly(in);
    }
}

From source file:architecture.ee.web.attachment.DefaultAttachmentManager.java

public InputStream getAttachmentInputStream(Attachment attachment) {
    try {/*from  w w  w .j av  a2 s.co m*/
        File file = getAttachmentFromCacheIfExist(attachment);
        return FileUtils.openInputStream(file);
    } catch (IOException e) {
        throw new SystemException(e);
    }
}

From source file:com.github.cherimojava.orchidae.controller.PictureController.java

/**
 * actual method retrieving the picture from disk. Requested picture is only returned if the current user is allowed
 * to view it//from w  w  w  .j  a v a 2s. c  o m
 * 
 * @param id
 *            identification of picture
 * @param type
 *            type of the picture eg _t for thumbnail etc.
 * @return ResponseEntity containing the resource to the picture or NOT_FOUND
 * @throws IOException
 */
private ResponseEntity<Resource> _getPicture(String id, String type) throws IOException {
    File picture = fileUtil.getFileHandle(id + type);
    if (picture.exists()) {
        return new ResponseEntity<Resource>(new InputStreamResource(FileUtils.openInputStream(picture)),
                HttpStatus.OK);
    } else {
        LOG.debug("Could not find picture with id {}", id);
        // picture doesn't exist so return 404
        return new ResponseEntity<>(HttpStatus.NOT_FOUND);
    }
}

From source file:com.comcast.magicwand.spells.web.chrome.ChromePhoenixDriver.java

private void extractZip(File sourceZipFile, String destinationDir) throws IOException {
    LOG.debug("Extracting [{}] to dir [{}]", sourceZipFile, destinationDir);
    ZipInputStream zis = null;//from  www .j a  va2s .  c  om
    ZipEntry entry;

    try {
        zis = new ZipInputStream(FileUtils.openInputStream(sourceZipFile));

        while (null != (entry = zis.getNextEntry())) {
            File dst = Paths.get(destinationDir, entry.getName()).toFile();

            FileOutputStream output = FileUtils.openOutputStream(dst);
            try {
                IOUtils.copy(zis, output);
                output.close();
            } finally {
                IOUtils.closeQuietly(output);
            }
        }
        zis.close();
    } finally {
        IOUtils.closeQuietly(zis);
    }
}