Example usage for java.util.zip GZIPOutputStream GZIPOutputStream

Introduction

In this page you can find the example usage for java.util.zip GZIPOutputStream GZIPOutputStream.

Prototype

public GZIPOutputStream(OutputStream out) throws IOException 

Source Link

Document

Creates a new output stream with a default buffer size.

Usage

From source file:fr.ens.biologie.genomique.eoulsan.io.CompressionType.java

/**
 * Create a GZip output stream./*from www . ja  v  a2s .c  o  m*/
 * @param os the output stream to compress
 * @return a compressed output stream
 * @throws IOException if an error occurs while creating the output stream
 */
public static OutputStream createGZipOutputStream(final OutputStream os) throws IOException {

    return new GZIPOutputStream(os);
}

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From source file:com.pinterest.terrapin.zookeeper.ViewInfo.java

public byte[] toCompressedJson() throws Exception {
    ByteArrayOutputStream out = new ByteArrayOutputStream();
    GZIPOutputStream zipOs = new GZIPOutputStream(out);
    zipOs.write(this.toJson());
    zipOs.close();//from   ww w.j a  va  2s . co  m
    byte[] data = out.toByteArray();
    return data;
}

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From source file:com.asakusafw.runtime.stage.output.BridgeOutputFormat.java

private static void save(Configuration conf, List<OutputSpec> specs) {
    assert conf != null;
    assert specs != null;
    for (OutputSpec spec : specs) {
        if (spec.resolved) {
            throw new IllegalStateException();
        }/*w w w . ja va 2 s .c  om*/
    }
    ByteArrayOutputStream sink = new ByteArrayOutputStream();
    try (DataOutputStream output = new DataOutputStream(new GZIPOutputStream(new Base64OutputStream(sink)))) {
        WritableUtils.writeVLong(output, SERIAL_VERSION);
        WritableUtils.writeVInt(output, specs.size());
        for (OutputSpec spec : specs) {
            WritableUtils.writeString(output, spec.basePath);
            WritableUtils.writeVInt(output, spec.deletePatterns.size());
            for (String pattern : spec.deletePatterns) {
                WritableUtils.writeString(output, pattern);
            }
        }
    } catch (IOException e) {
        throw new IllegalStateException(e);
    }
    conf.set(KEY, new String(sink.toByteArray(), ASCII));
}

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From source file:com.google.cloud.dataflow.sdk.io.CompressedSourceTest.java

private static byte[] compressGzip(byte[] input) throws IOException {
    ByteArrayOutputStream res = new ByteArrayOutputStream();
    try (GZIPOutputStream gzipStream = new GZIPOutputStream(res)) {
        gzipStream.write(input);//from  ww w . j  av a  2  s.c o m
    }
    return res.toByteArray();
}

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From source file:com.microsoft.tfs.core.clients.versioncontrol.engines.internal.workers.BaselineUpdaterWorker.java

/**
 * {@inheritDoc}/*from w  w  w  .j a v a2  s  . c  o m*/
 */
@Override
public WorkerStatus call() throws Exception {
    /*
     * Try not to run any code outside this try block, so our Throwable
     * catch below can report every error (even RuntimeExceptions).
     */
    try {
        boolean completedSuccessfully = false;
        final int token = state.getBaselineFolderCollection().lockForRead();

        try {
            // Present the read lock token that we already hold to prevent
            // it from attempting to acquire another read lock for the call
            // to GetNewBaselineLocation.
            String baselineFilePath = state.getBaselineFolderCollection().getNewBaselineLocation(
                    request.getBaselineFileGUID(), request.getBaselinePartitionLocalItem(), token);

            // Get the uncompressed file size.
            final File fi = new File(baselineFilePath);
            final long uncompressedFileSize = fi.length();

            // Set status message for the monitor.
            monitor.setCurrentWorkDescription(
                    MessageFormat.format(Messages.getString("BaselineUpdaterWorker.UpdatingBaselineFormat"), //$NON-NLS-1$
                            baselineFilePath));

            // Add the .gz extension to this baseline.
            baselineFilePath = baselineFilePath + BaselineFolder.getGzipExtension();

            if (uncompressedFileSize < Worker.MAX_GZIP_INPUT_SIZE) {
                final byte[] buffer = new byte[4096];
                byte[] hashValue = null;

                MessageDigest md5Digest = null;
                if (request.getHashValue() != null) {
                    md5Digest = MessageDigest.getInstance("MD5"); //$NON-NLS-1$
                }

                final GZIPOutputStream outputStream = new GZIPOutputStream(
                        new FileOutputStream(baselineFilePath));
                final String sourceLocalItem = request.getSourceLocalItem();
                final FileSystemUtils util = FileSystemUtils.getInstance();
                final FileSystemAttributes attrs = util.getAttributes(sourceLocalItem);

                InputStream inputStream;
                if (attrs.isSymbolicLink()) {
                    final String linkTarget = util.getSymbolicLink(sourceLocalItem);
                    inputStream = new ByteArrayInputStream(linkTarget.getBytes("UTF-8")); //$NON-NLS-1$
                } else {
                    inputStream = new FileInputStream(request.getSourceLocalItem());
                }

                try {
                    int bytesRead;

                    while (true) {
                        bytesRead = inputStream.read(buffer, 0, buffer.length);

                        if (bytesRead <= 0) {
                            break;
                        }

                        if (null != md5Digest) {
                            md5Digest.update(buffer, 0, bytesRead);
                        }

                        outputStream.write(buffer, 0, bytesRead);
                    }

                    if (null != md5Digest) {
                        hashValue = md5Digest.digest();
                    }
                } finally {
                    if (outputStream != null) {
                        IOUtils.closeSafely(outputStream);
                    }
                    if (inputStream != null) {
                        IOUtils.closeSafely(inputStream);
                    }
                }

                if (null != hashValue && 16 == hashValue.length && null != request.getHashValue()
                        && 16 == request.getHashValue().length
                        && !Arrays.equals(request.getHashValue(), hashValue)) {
                    // The hash value didn't match the provided hash value.
                    // Delete the baseline from disk.
                    FileHelpers.deleteFileWithoutException(baselineFilePath);
                } else {
                    completedSuccessfully = true;
                }
            } else {
                // TODO: We didn't attempt to gzip.
            }
        } catch (final Exception ex) {
            log.trace("BaselineUpdater", ex); //$NON-NLS-1$
        } finally {
            state.getBaselineFolderCollection().unlockForRead(token);

            if (!completedSuccessfully) {
                state.addFailedRequest(request);
            }
        }
    } catch (final Throwable t) {
        /*
         * An actual error happened. We have to communicate this problem to
         * the thread submitting tasks so it can take the correct action
         * (shut down other workers).
         */
        state.setFatalError(t);
        return new WorkerStatus(this, FinalState.ERROR);
    }

    return new WorkerStatus(this, FinalState.NORMAL);
}

---

From source file:com.flurry.proguard.UploadProGuardMapping.java

/**
 * Create a gzipped tar archive containing the ProGuard mapping file
 *
 * @param file the mapping.txt file/*from  w  w  w .j  a  v a2s  .  com*/
 * @param uuid the build uuid
 * @return the tar-gzipped archive
 */
private static File createArchive(File file, String uuid) {
    try {
        File tarZippedFile = File.createTempFile("tar-zipped-file", ".tgz");
        TarArchiveOutputStream taos = new TarArchiveOutputStream(
                new GZIPOutputStream(new BufferedOutputStream(new FileOutputStream(tarZippedFile))));
        taos.putArchiveEntry(new TarArchiveEntry(file, uuid + ".txt"));
        IOUtils.copy(new FileInputStream(file), taos);
        taos.closeArchiveEntry();
        taos.finish();
        taos.close();
        return tarZippedFile;
    } catch (IOException e) {
        failWithError("IO Exception while trying to tar and zip the file.", e);
        return null;
    }
}

---

From source file:com.moss.simpledeb.core.DebWriter.java

private byte[] buildGzipTar(List<ArchivePath> paths) throws Exception {

    byte[] tarData;
    {/*from  w ww .j av  a 2  s .co m*/
        ByteArrayOutputStream tarOut = new ByteArrayOutputStream();
        TarArchiveOutputStream tar = new TarArchiveOutputStream(tarOut);

        Set<String> writtenPaths = new HashSet<String>();
        for (ArchivePath path : paths) {
            String name = path.entry().getName();

            if (writtenPaths.contains(name)) {
                throw new RuntimeException("Duplicate archive entry: " + name);
            }

            writtenPaths.add(name);

            tar.putArchiveEntry(path.entry());

            if (!path.entry().isDirectory()) {
                InputStream in = path.read();
                byte[] buffer = new byte[1024 * 10];
                for (int numRead = in.read(buffer); numRead != -1; numRead = in.read(buffer)) {
                    tar.write(buffer, 0, numRead);
                }
                in.close();
            }

            tar.closeArchiveEntry();
        }

        tar.close();
        tarData = tarOut.toByteArray();
    }

    byte[] gzipData;
    {
        ByteArrayOutputStream gzipOut = new ByteArrayOutputStream();
        GZIPOutputStream gzip = new GZIPOutputStream(gzipOut);
        gzip.write(tarData);
        gzip.close();

        gzipData = gzipOut.toByteArray();
    }

    return gzipData;
}

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From source file:de.mpg.escidoc.services.fledgeddata.webservice.oaiServlet.java

/**
 * Get a response Writer depending on acceptable encodings
 * @param request the servlet's request information
 * @param response the servlet's response information
 * @exception IOException an I/O error occurred
 *///from  w w  w . j a  va  2s. c  o m
public static Writer getWriter(HttpServletRequest request, HttpServletResponse response) throws IOException {
    Writer out;
    String encodings = request.getHeader("Accept-Encoding");

    if (encodings != null && encodings.indexOf("gzip") != -1) {
        response.setHeader("Content-Encoding", "gzip");
        out = new OutputStreamWriter(new GZIPOutputStream(response.getOutputStream()), "UTF-8");
    } else if (encodings != null && encodings.indexOf("deflate") != -1) {
        response.setHeader("Content-Encoding", "deflate");
        out = new OutputStreamWriter(new DeflaterOutputStream(response.getOutputStream()), "UTF-8");
    } else {
        out = response.getWriter();
    }
    return out;
}

---

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

/**
 * Run the map2text mode.//  ww w . j av  a2 s  .c  om
 *
 * @throws java.io.IOException error reading / writing
 */
@Override
public void execute() throws IOException {
    PrintWriter writer = null;
    try {
        writer = new PrintWriter(
                new GZIPOutputStream(new FastBufferedOutputStream(new FileOutputStream(outputFile + ".gz"))));
        writer.write("track type=bedGraph name=" + label + " visibility=full viewLimits=1:200\n");
        final AlignmentReaderImpl alignment = new AlignmentReaderImpl(inputBasename);
        alignment.readHeader();
        alignment.close();
        final IndexedIdentifier referenceIds = alignment.getTargetIdentifiers();
        final DoubleIndexedIdentifier backwards = new DoubleIndexedIdentifier(referenceIds);
        final CountsArchiveReader reader = new CountsArchiveReader(inputBasename,
                alternativeCountArchiveExtension);

        for (int referenceIndex = 0; referenceIndex < reader.getNumberOfIndices(); referenceIndex++) {
            String referenceId = backwards.getId(referenceIndex).toString();
            boolean processThisSequence = true;
            // prepare reference ID for UCSC genome browser.
            if ("MT".equalsIgnoreCase(referenceId)) {
                // patch chromosome name for UCSC genome browser:
                referenceId = "M";
            }

            // ignore c22_H2, c5_H2, and other contigs but not things like chr1 (mm9)
            if (referenceId.startsWith("c") && !referenceId.startsWith("chr")) {
                processThisSequence = false;
            }

            // ignore NT_*
            if (referenceId.startsWith("NT_")) {
                processThisSequence = false;
            }

            if (filterByReferenceNames && !includeReferenceNames.contains(referenceId)) {
                processThisSequence = false;
            }

            if (processThisSequence) {
                // prepend the reference id with "chr" if it doesn't use that already
                final String chromosome;
                if (referenceId.startsWith("chr")) {
                    chromosome = referenceId;
                } else {
                    chromosome = "chr" + referenceId;
                }

                long sumCount = 0;
                int numCounts = 0;

                final CountsReader counts = reader.getCountReader(referenceIndex);
                int writePosition;
                while (counts.hasNextTransition()) {
                    counts.nextTransition();
                    final int length = counts.getLength();

                    final int count = counts.getCount();
                    final int position = counts.getPosition();
                    writePosition = position + 1;
                    if (count != 0) {
                        writer.printf("%s %d %d %d\n", chromosome, writePosition, writePosition + length,
                                count);
                    }
                    sumCount += count;
                    numCounts++;
                }
                final double averageCount = sumCount / (double) numCounts;
                System.out.println("average count for sequence " + referenceId + " " + averageCount);
            }
        }
    } finally {
        IOUtils.closeQuietly(writer);
    }
}

---

From source file:uk.ac.bbsrc.tgac.miso.integration.util.IntegrationUtils.java

public static byte[] compress(byte[] content) throws IOException {
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    Base64OutputStream b64os = new Base64OutputStream(baos);
    GZIPOutputStream gzip = new GZIPOutputStream(b64os);
    gzip.write(content);/*ww w .j a v  a2s . c o  m*/
    gzip.close();
    return baos.toByteArray();
}

---

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