Example usage for java.util.zip GZIPInputStream read

Introduction

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

Prototype

public int read(byte b[]) throws IOException 

Source Link

Document

Reads up to b.length bytes of data from this input stream into an array of bytes.

Usage

From source file:org.hupo.psi.mi.psicquic.ws.IndexBasedPsicquicRestServiceTest.java

@Test
public void testGetByQuery_bin() throws Exception {
    ResponseImpl response = (ResponseImpl) service.getByQuery("FANCD1", "tab25-bin", "0",
            String.valueOf(Integer.MAX_VALUE), "n");

    PsicquicStreamingOutput pso = ((GenericEntity<PsicquicStreamingOutput>) response.getEntity()).getEntity();

    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    pso.write(baos);/*from   w  w w.  j a  v a2  s .c  o  m*/

    // gunzip the output
    ByteArrayInputStream bais = new ByteArrayInputStream(baos.toByteArray());
    GZIPInputStream gzipInputStream = new GZIPInputStream(bais);

    ByteArrayOutputStream mitabOut = new ByteArrayOutputStream();

    byte[] buf = new byte[1024];
    int len;
    while ((len = gzipInputStream.read(buf)) > 0)
        mitabOut.write(buf, 0, len);

    gzipInputStream.close();
    mitabOut.close();

    Assert.assertEquals(12, mitabOut.toString().split("\n").length);
}

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From source file:edu.umn.cs.spatialHadoop.visualization.FrequencyMap.java

@Override
public void readFields(DataInput in) throws IOException {
    super.readFields(in);
    int length = in.readInt();
    byte[] serializedData = new byte[length];
    in.readFully(serializedData);//from   w w  w. j av  a  2 s  . c  om
    ByteArrayInputStream bais = new ByteArrayInputStream(serializedData);
    GZIPInputStream gzis = new GZIPInputStream(bais);

    byte[] buffer = new byte[8];
    gzis.read(buffer);
    ByteBuffer bbuffer = ByteBuffer.wrap(buffer);
    int width = bbuffer.getInt();
    int height = bbuffer.getInt();
    // Reallocate memory only if needed
    if (width != this.getWidth() || height != this.getHeight())
        frequencies = new float[width][height];
    buffer = new byte[getHeight() * 4];
    for (int x = 0; x < getWidth(); x++) {
        int size = 0;
        while (size < buffer.length) {
            size += gzis.read(buffer, size, buffer.length - size);
        }
        bbuffer = ByteBuffer.wrap(buffer);
        for (int y = 0; y < getHeight(); y++) {
            frequencies[x][y] = bbuffer.getFloat();
        }
    }
}

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From source file:org.gephi.desktop.importer.DesktopImportControllerUI.java

/**
 * Uncompress a GZIP file.//  w ww.jav  a 2  s.c  om
 */
private static File getGzFile(FileObject in, File out, boolean isTar) throws IOException {

    // Stream buffer
    final int BUFF_SIZE = 8192;
    final byte[] buffer = new byte[BUFF_SIZE];

    GZIPInputStream inputStream = null;
    FileOutputStream outStream = null;

    try {
        inputStream = new GZIPInputStream(new FileInputStream(in.getPath()));
        outStream = new FileOutputStream(out);

        if (isTar) {
            // Read Tar header
            int remainingBytes = readTarHeader(inputStream);

            // Read content
            ByteBuffer bb = ByteBuffer.allocateDirect(4 * BUFF_SIZE);
            byte[] tmpCache = new byte[BUFF_SIZE];
            int nRead, nGet;
            while ((nRead = inputStream.read(tmpCache)) != -1) {
                if (nRead == 0) {
                    continue;
                }
                bb.put(tmpCache);
                bb.position(0);
                bb.limit(nRead);
                while (bb.hasRemaining() && remainingBytes > 0) {
                    nGet = Math.min(bb.remaining(), BUFF_SIZE);
                    nGet = Math.min(nGet, remainingBytes);
                    bb.get(buffer, 0, nGet);
                    outStream.write(buffer, 0, nGet);
                    remainingBytes -= nGet;
                }
                bb.clear();
            }
        } else {
            int len;
            while ((len = inputStream.read(buffer)) > 0) {
                outStream.write(buffer, 0, len);
            }
        }
    } catch (IOException ex) {
        Exceptions.printStackTrace(ex);
    } finally {
        if (inputStream != null) {
            inputStream.close();
        }
        if (outStream != null) {
            outStream.close();
        }
    }

    return out;
}

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From source file:com.android.tradefed.util.FileUtil.java

public static void extractGzip(File tarGzipFile, File destDir, String destName)
        throws FileNotFoundException, IOException, ArchiveException {
    GZIPInputStream zipIn = null;
    BufferedOutputStream buffOut = null;
    try {/*w w w. j  a va  2s . c  o  m*/
        File destUnzipFile = new File(destDir.getAbsolutePath(), destName);
        zipIn = new GZIPInputStream(new FileInputStream(tarGzipFile));
        buffOut = new BufferedOutputStream(new FileOutputStream(destUnzipFile));
        int b = 0;
        byte[] buf = new byte[8192];
        while ((b = zipIn.read(buf)) != -1) {
            buffOut.write(buf, 0, b);
        }
    } finally {
        if (zipIn != null)
            zipIn.close();
        if (buffOut != null)
            buffOut.close();
    }
}

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From source file:org.onebusaway.webapp.actions.admin.bundles.SyncBundleAction.java

private void unzipBundle(String tmpDir, String bundleFileName) throws IOException {
    byte[] buffer = new byte[1024];

    GZIPInputStream zipIn = new GZIPInputStream(new FileInputStream(tmpDir + File.separator + bundleFileName));
    FileOutputStream out = new FileOutputStream(tmpDir + File.separator + "unzippedBundle");

    int len;//from   w  w w  .  j  av  a2s  . c  o m
    while ((len = zipIn.read(buffer)) > 0) {
        out.write(buffer, 0, len);
    }

    zipIn.close();
    out.close();

    // Now to untar the unzipped file
    File tarFile = new File(tmpDir + File.separator + "unzippedBundle");
    File untarredFile = new File(tmpDir + File.separator + "untarredBundle");
    //File untarredFile = new File(tmpDir);
    try {
        List<File> fileList = (new FileUtility()).unTar(tarFile, untarredFile);
    } catch (ArchiveException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    return;
}

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From source file:com.iisigroup.cap.utils.CapSerialization.java

/**
 * decompress byte array data with GZIP.
 * // w ww.  j a  v a  2  s. co  m
 * @param input
 *            the input compressed data
 * @return the decompress data
 * @throws java.io.IOException
 */
public byte[] decompress(byte[] input) throws java.io.IOException {

    byte[] buf = new byte[2048];
    byte[] result = null;
    java.io.ByteArrayInputStream bain = null;
    ByteArrayOutputStream baout = null;
    GZIPInputStream gzipin = null;
    try {
        bain = new java.io.ByteArrayInputStream(input);
        gzipin = new GZIPInputStream(bain);
        baout = new ByteArrayOutputStream();
        int size;
        while ((size = gzipin.read(buf)) != -1) {
            baout.write(buf, 0, size);
        }
        result = baout.toByteArray();
        return result;
    } finally {
        IOUtils.closeQuietly(bain);
        IOUtils.closeQuietly(baout);
        IOUtils.closeQuietly(gzipin);
    }

}

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From source file:org.owasp.dependencycheck.data.update.CpeUpdater.java

/**
 * Extracts the file contained in a gzip archive. The extracted file is placed in the exact same path as the file specified.
 *
 * @param file the archive file// w w  w .j  ava 2  s .com
 * @throws FileNotFoundException thrown if the file does not exist
 * @throws IOException thrown if there is an error extracting the file.
 */
private void extractGzip(File file) throws FileNotFoundException, IOException {
    //TODO - move this to a util class as it is duplicative of (copy of) code in the DownloadTask
    final String originalPath = file.getPath();
    final File gzip = new File(originalPath + ".gz");
    if (gzip.isFile() && !gzip.delete()) {
        gzip.deleteOnExit();
    }
    if (!file.renameTo(gzip)) {
        throw new IOException("Unable to rename '" + file.getPath() + "'");
    }
    final File newfile = new File(originalPath);

    final byte[] buffer = new byte[4096];

    GZIPInputStream cin = null;
    FileOutputStream out = null;
    try {
        cin = new GZIPInputStream(new FileInputStream(gzip));
        out = new FileOutputStream(newfile);

        int len;
        while ((len = cin.read(buffer)) > 0) {
            out.write(buffer, 0, len);
        }
    } finally {
        if (cin != null) {
            try {
                cin.close();
            } catch (IOException ex) {
                LOGGER.trace("ignore", ex);
            }
        }
        if (out != null) {
            try {
                out.close();
            } catch (IOException ex) {
                LOGGER.trace("ignore", ex);
            }
        }
        if (gzip.isFile()) {
            FileUtils.deleteQuietly(gzip);
        }
    }
}

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From source file:com.edgenius.wiki.service.impl.SitemapServiceImpl.java

public boolean removePage(String pageUuid) throws IOException {
    boolean removed = false;
    String sitemapIndex = metadata.getSitemapIndex(pageUuid);
    if (sitemapIndex == null) {
        log.warn("Page {} does not exist in sitemap", pageUuid);
        return removed;
    }//from  ww w  .  ja  v a 2  s.c  o  m

    String sitemapZip = SITEMAP_NAME_PREFIX + sitemapIndex + ".xml.gz";
    File sizemapZipFile = new File(mapResourcesRoot.getFile(), sitemapZip);
    if (!sizemapZipFile.exists()) {
        throw new IOException("Remove pageUuid " + pageUuid + " from sitemap failed becuase sitemap not found");
    }

    PipedInputStream bis = new PipedInputStream();
    PipedOutputStream bos = new PipedOutputStream(bis);
    InputStream zipfile = new FileInputStream(sizemapZipFile);
    GZIPInputStream gzipstream = new GZIPInputStream(zipfile);
    byte[] bytes = new byte[1024 * 1000];
    int len = 0;
    while ((len = gzipstream.read(bytes)) > 0) {
        bos.write(bytes, 0, len);
    }

    IOUtils.closeQuietly(zipfile);
    IOUtils.closeQuietly(gzipstream);

    String pageUrl = metadata.getPageUrl(pageUuid);
    String body = IOUtils.toString(bis);
    int loc = body.indexOf("<loc>" + pageUrl + "</loc>");
    if (loc != -1) {
        int start = StringUtils.lastIndexOf(body, "<url>", loc);
        int end = StringUtils.indexOf(body, "</url>", loc);
        if (start != -1 && end != -1) {
            //remove this URL
            body = StringUtils.substring(body, start, end + 6);
            zipToFile(sizemapZipFile, body.getBytes());
            removed = true;
        }
    }

    metadata.removePageMap(pageUuid);

    return removed;
}

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From source file:eu.domibus.ebms3.common.CompressionService.java

/**
 * Decompress given GZIP Stream. Separated from {@link eu.domibus.ebms3.common.CompressionService#compress(java.io.InputStream, java.util.zip.GZIPOutputStream)}
 * just for a better overview even though they share the same logic (except finish() ).
 *
 * @param sourceStream Stream of compressed data
 * @param targetStream Stream of uncompressed data
 * @throws IOException//w w w .j a v  a 2s . c  om
 */
private void decompress(final GZIPInputStream sourceStream, final OutputStream targetStream)
        throws IOException {

    final byte[] buffer = new byte[1024];

    try {
        int i;
        while ((i = sourceStream.read(buffer)) > 0) {
            targetStream.write(buffer, 0, i);
        }

        sourceStream.close();
        targetStream.close();

    } catch (IOException e) {
        CompressionService.LOG.error(
                "I/O exception during gzip compression. method: doDecompress(GZIPInputStream, OutputStream");
        throw e;
    }
}

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From source file:TextFileHandler.java

/**
 * Retrieve a String from a .gz file/* w w w.  j  a v a2 s  .  com*/
 * @param fileName e.g. bar.xml.gz
 * @return
 */
public String openGZipFile(String fileName) {
    try {
        GZIPInputStream in = new GZIPInputStream(new FileInputStream(fileName));
        StringBuffer buf = new StringBuffer();
        byte[] b = new byte[1024];
        int length;
        while ((length = in.read(b)) > 0) {
            String s = new String(b);
            buf.append(s);
        }
        return buf.toString().trim();
    } catch (Exception e) {
        System.out.println(e.getMessage());
    }
    return null;
}

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