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:edu.umn.cs.spatialHadoop.nasa.HDFRasterLayer.java

@Override
public void readFields(DataInput in) throws IOException {
    super.readFields(in);
    this.timestamp = in.readLong();
    int length = in.readInt();
    byte[] serializedData = new byte[length];
    in.readFully(serializedData);/*  ww w . jav a  2 s .  co m*/
    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()) {
        sum = new long[width][height];
        count = new long[width][height];
    }
    buffer = new byte[getHeight() * 2 * 8];
    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++) {
            sum[x][y] = bbuffer.getLong();
            count[x][y] = bbuffer.getLong();
        }
    }
}

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From source file:com.sinelead.car.club.NewsFragment.java

public String getZipString(org.apache.http.HttpResponse response) {

    String resultString = "";
    ByteArrayBuffer bt = new ByteArrayBuffer(4096);
    try {/*w w w.  j  av a  2 s.  c om*/
        // Get
        HttpEntity he = response.getEntity();
        // 
        GZIPInputStream gis = new GZIPInputStream(he.getContent());
        int l;
        byte[] tmp = new byte[4096];
        while ((l = gis.read(tmp)) != -1) {
            bt.append(tmp, 0, l);
        }

        resultString = new String(bt.toByteArray(), "utf-8");
        // UTF-8

    } catch (Exception e) {
        Log.i("ERR", e.toString()); // 
    }

    return resultString;
}

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From source file:com.kkbox.toolkit.internal.api.APIRequest.java

private InputStream getInputStreamFromHttpResponse() throws IOException {
    InputStream inputStream;/* w w  w .  j  a  va2 s. co m*/
    Header contentEncoding = response.getFirstHeader("Content-Encoding");
    if (contentEncoding != null && contentEncoding.getValue().equalsIgnoreCase("gzip")) {
        byte[] inputStreamBuffer = new byte[8192];
        int length;
        ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
        GZIPInputStream gZIPInputStream = new GZIPInputStream(
                new ByteArrayInputStream(EntityUtils.toByteArray(response.getEntity())));
        while ((length = gZIPInputStream.read(inputStreamBuffer)) >= 0) {
            byteArrayOutputStream.write(inputStreamBuffer, 0, length);
        }
        inputStream = new ByteArrayInputStream(byteArrayOutputStream.toByteArray());
        gZIPInputStream.close();
        byteArrayOutputStream.close();
    } else {
        inputStream = response.getEntity().getContent();
    }
    return inputStream;
}

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From source file:it.gnappuraz.netflixsubs.opensubtitles.api.OpenSubtitlesAPIClient.java

private byte[] gunzip(byte[] compressed) throws IOException {
    GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream(compressed));
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    OutputStream out = new BufferedOutputStream(baos);
    byte[] buffer = new byte[1024];
    while (true) {
        synchronized (buffer) {
            int amountRead = gis.read(buffer);
            if (amountRead == -1) {
                break;
            }/*from www .  ja va  2 s . c  o m*/
            out.write(buffer, 0, amountRead);
        }
    }
    out.flush();
    out.close();
    return baos.toByteArray();
}

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From source file:org.owasp.dependencycheck.data.update.nvd.DownloadTask.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/*www.j av a 2  s . c  o m*/
 * @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 {
    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:org.semanticscience.narf.structures.factories.tertiary.ExtractedTertiaryStructureFactory.java

/**
 * Get all nucleic acid tertiary structures produced using information
 * generated by the tertiary structure predictor.
 * /* w w  w  . j a v  a 2 s.  c o  m*/
 * @param aPdbFile
 *            a PDB structure file
 * @param commands
 *            set of commands to modify the execution of the annoator
 * @return a set of annotated nucleic acid tertiary structures
 * @throws FileNotFoundException
 *             if the PDB structure file does not exist
 * @throws IOException
 *             if any IO error occur reading the output of the tertiary
 *             structure annotator or writing the output of the tertiary
 *             structure annotator
 * @throws InvalidResidueException
 *             if any of the residues are invalid
 */
public Set<ExtractedTertiaryStructure> getStructures(File aPdbFile, String[] commands)
        throws FileNotFoundException, IOException, InvalidResidueException {

    if (!aPdbFile.exists() || aPdbFile.isDirectory()) {
        throw new FileNotFoundException("There is no PDB file with the name specified.");
    }

    String extension = PdbHelper.getFileExtension(aPdbFile);
    File directory = new File(FileUtils.getTempDirectoryPath() + "/pdb/");
    File pdbFile = new File(directory.getAbsolutePath() + "/" + aPdbFile.getName());
    FileUtils.copyFile(aPdbFile, pdbFile);
    // check if the file is compressed
    if (extension.equals("gz")) {
        GZIPInputStream gzipInputStream = new GZIPInputStream(new FileInputStream(pdbFile));
        File gunzippedFile = new File(directory.getAbsolutePath() + pdbFile.getName().replace(".gz", ""));
        OutputStream out = new FileOutputStream(gunzippedFile);
        byte[] buf = new byte[1024];
        int len;
        while ((len = gzipInputStream.read(buf)) > 0)
            out.write(buf, 0, len);
        gzipInputStream.close();
        out.close();
        pdbFile.delete();
        pdbFile = gunzippedFile;
    }
    String pdbId = PdbHelper.findPdbId(pdbFile);
    int numberOfModels = PdbHelper.findNumberOfModels(pdbFile);
    Set<ExtractedTertiaryStructure> tertiaryAnnotatedStructures = new HashSet<ExtractedTertiaryStructure>();
    if (numberOfModels == 1) {
        File annotatedStructure = this.execute(pdbFile, commands);
        Map<String, Sequence> sequenceMap = this.parseSequences(pdbFile, annotatedStructure);
        Set<NucleotideInteraction> interactions = this.parseInteractions(sequenceMap, annotatedStructure);
        tertiaryAnnotatedStructures
                .add(new ExtractedTertiaryStructure(this, pdbFile, pdbId, 1, sequenceMap, interactions));
    } else {
        for (int modelNumber = 1; modelNumber <= numberOfModels; modelNumber++) {
            File modelFile = PdbHelper.extractModelFromPDB(pdbFile,
                    new File(FileUtils.getTempDirectoryPath() + "/pdb/"), pdbId, modelNumber);
            File outputFile = this.execute(modelFile, commands);
            Map<String, Sequence> sequenceMap = this.parseSequences(modelFile, outputFile);
            Set<NucleotideInteraction> interactions = this.parseInteractions(sequenceMap, outputFile);
            tertiaryAnnotatedStructures.add(new ExtractedTertiaryStructure(this, pdbFile, pdbId, modelNumber,
                    sequenceMap, interactions));
        }
    }
    return tertiaryAnnotatedStructures;
}

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From source file:org.mitre.xtext.converters.ArchiveNavigator.java

private File gunzip(File theFile, String fname) throws IOException {

    GZIPInputStream gzipInputStream = new GZIPInputStream(new FileInputStream(theFile));
    String outFilename = tempDir.toString() + File.separator + fname + ".tar";
    File outFile = new File(outFilename);
    OutputStream out = new BufferedOutputStream(new FileOutputStream(outFilename));

    byte[] buf = new byte[1024];
    int len;//from   w ww .  j av  a2s  .c  o  m
    while ((len = gzipInputStream.read(buf)) > 0) {
        out.write(buf, 0, len);
    }

    gzipInputStream.close();
    out.close();
    return outFile;
}

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From source file:eu.stratuslab.storage.disk.resources.DisksResource.java

private long inflateFile(InputStream gzippedContents, File inflatedFile) {

    GZIPInputStream in = null;
    OutputStream out = null;/*  w  ww.  ja va  2s . c  o m*/

    try {

        in = new GZIPInputStream(gzippedContents);
        out = new FileOutputStream(inflatedFile);

        byte[] buf = new byte[1024];
        int len;
        while ((len = in.read(buf)) > 0) {
            out.write(buf, 0, len);
        }

    } catch (IOException e) {
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, e.getMessage());
    } finally {
        FileUtils.closeIgnoringError(in);
        FileUtils.closeIgnoringError(out);
    }
    return DiskUtils.convertBytesToGibiBytes(inflatedFile.length());
}

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From source file:autoupdater.FileDAO.java

/**
 * Untars and ungzips a .tar.gz file./*from   w  w  w .j a va 2s .co m*/
 *
 * @param in a {@code GZIPInputStream} of the file that needs to be
 * ungzipped and untarred
 * @param fileLocationOnDiskToDownloadTo the file to ungzip and untar to
 * @return true if successful
 * @throws IOException
 */
public boolean unGzipAndUntarFile(GZIPInputStream in, File fileLocationOnDiskToDownloadTo) throws IOException {

    try {
        FileOutputStream fos = new FileOutputStream(fileLocationOnDiskToDownloadTo);
        byte[] buffer = new byte[1024];
        int len;
        while ((len = in.read(buffer)) != -1) {
            fos.write(buffer, 0, len);
        }
        //close resources
        fos.close();
        in.close();

        untar(fileLocationOnDiskToDownloadTo);
    } catch (IOException e) {
        e.printStackTrace();
    }
    return true;
}

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From source file:com.l2jfree.security.Base64.java

/**
 * Decodes data from Base64 notation, automatically detecting
 * gzip-compressed data and decompressing it.
 * /*from   www.ja  va2 s.  co  m*/
 * @param s
 *            the string to decode
 * @return the decoded data
 * @since 1.4
 */
public static byte[] decode(String s) {
    byte[] bytes;
    try {
        bytes = s.getBytes(PREFERRED_ENCODING);
    } // end try
    catch (java.io.UnsupportedEncodingException uee) {
        bytes = s.getBytes();
    } // end catch
      // </change>

    // Decode
    bytes = decode(bytes, 0, bytes.length);

    // Check to see if it's gzip-compressed
    // GZIP Magic Two-Byte Number: 0x8b1f (35615)
    if (bytes.length >= 2) {

        int head = (bytes[0] & 0xff) | ((bytes[1] << 8) & 0xff00);
        if (bytes.length >= 4 && // Don't want to get ArrayIndexOutOfBounds exception
                java.util.zip.GZIPInputStream.GZIP_MAGIC == head) {
            java.io.ByteArrayInputStream bais = null;
            java.util.zip.GZIPInputStream gzis = null;
            java.io.ByteArrayOutputStream baos = null;
            byte[] buffer = new byte[2048];
            int length = 0;

            try {
                baos = new java.io.ByteArrayOutputStream();
                bais = new java.io.ByteArrayInputStream(bytes);
                gzis = new java.util.zip.GZIPInputStream(bais);

                while ((length = gzis.read(buffer)) >= 0) {
                    baos.write(buffer, 0, length);
                } // end while: reading input

                // No error? Get new bytes.
                bytes = baos.toByteArray();

            } // end try
            catch (java.io.IOException e) {
                // Just return originally-decoded bytes
            } // end catch
            finally {
                IOUtils.closeQuietly(baos);
                IOUtils.closeQuietly(gzis);
                IOUtils.closeQuietly(bais);
            } // end finally

        } // end if: gzipped
    } // end if: bytes.length >= 2

    return bytes;
}

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