Example usage for org.apache.commons.compress.compressors.bzip2 BZip2CompressorInputStream read

Introduction

In this page you can find the example usage for org.apache.commons.compress.compressors.bzip2 BZip2CompressorInputStream read.

Prototype

public int read(byte b[]) throws IOException 

Source Link

Document

Reads some number of bytes from the input stream and stores them into the buffer array b.

Usage

From source file:com.graphhopper.tools.Bzip2.java

public static void main(String[] args) throws IOException {
    if (args.length == 0) {
        throw new IllegalArgumentException("You need to specify the bz2 file!");
    }//from w ww.j a  v  a2s.  com

    String fromFile = args[0];
    if (!fromFile.endsWith(".bz2")) {
        throw new IllegalArgumentException("You need to specify a bz2 file! But was:" + fromFile);
    }
    String toFile = Helper.pruneFileEnd(fromFile);

    FileInputStream in = new FileInputStream(fromFile);
    FileOutputStream out = new FileOutputStream(toFile);
    BZip2CompressorInputStream bzIn = new BZip2CompressorInputStream(in);
    try {
        final byte[] buffer = new byte[1024 * 8];
        int n = 0;
        while (-1 != (n = bzIn.read(buffer))) {
            out.write(buffer, 0, n);
        }
    } finally {
        out.close();
        bzIn.close();
    }
}

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From source file:com.yahoo.ycsb.db.RedisClient.java

public static String decompress(String st) {
    if (compress != null && compress.equals("y")) {
        if (compressAlgo != null && (compressAlgo.equals("lz4") || compressAlgo.equals("lz4hc"))) {
            try {
                int split = st.indexOf('|');
                final int decompressedLength = Integer.parseInt(st.substring(0, split));
                LZ4FastDecompressor decompressor = lz4factory.fastDecompressor();
                byte[] restored = new byte[decompressedLength];
                byte[] compressed = st.substring(split + 1, st.length()).getBytes("ISO-8859-1");
                decompressor.decompress(compressed, 0, restored, 0, decompressedLength);
                String ret = new String(restored, "ISO-8859-1");
                return ret;
            } catch (Exception e) {
                e.printStackTrace();/*from www  .  j  av a2  s  . c  o m*/
            }
        } else if (compressAlgo != null && compressAlgo.equals("bzip2")) {
            try {
                InputStream in = new StringBufferInputStream(st);
                BZip2CompressorInputStream bzIn = new BZip2CompressorInputStream(in);
                byte[] data = st.getBytes("ISO-8859-1");
                ByteArrayOutputStream baos = new ByteArrayOutputStream();
                int n = 0;
                while (-1 != (n = bzIn.read(data))) {
                    baos.write(data, 0, n);
                }
                bzIn.close();
                return baos.toString();
            } catch (Exception e) {
                e.printStackTrace();
            }
        } else if (compressAlgo != null && compressAlgo.equals("snappy")) {
            try {
                byte[] uncompressed = Snappy.uncompress(st.getBytes("ISO-8859-1"));
                String ret = new String(uncompressed, "ISO-8859-1");
                return ret;
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    }
    return st;
}

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From source file:aarddict.Volume.java

static String decompressBz2(byte[] bytes) throws IOException {
    BZip2CompressorInputStream in = new BZip2CompressorInputStream(new ByteArrayInputStream(bytes));

    int n = 0;/*from ww w . jav  a  2 s . co m*/
    ByteArrayOutputStream out = new ByteArrayOutputStream(bytes.length * 5);
    byte[] buf = new byte[1024];
    try {
        while (-1 != (n = in.read(buf))) {
            out.write(buf, 0, n);
        }
    } finally {
        in.close();
        out.close();
    }
    return utf8(out.toByteArray());
}

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From source file:adams.core.io.Bzip2Utils.java

/**
 * Decompresses the specified archive.//from w ww.  ja v a2 s.  com
 * <br><br>
 * See <a href="https://commons.apache.org/compress/examples.html" target="_blank">Apache commons/compress</a>.
 *
 * @param archiveFile   the archive file to decompress
 * @param buffer   the buffer size to use
 * @param outputFile   the destination file
 * @return      the error message, null if everything OK
 */
public static String decompress(File archiveFile, int buffer, File outputFile) {
    String result;
    byte[] buf;
    int len;
    FileInputStream fis;
    BZip2CompressorInputStream in;
    BufferedOutputStream out;
    String msg;

    in = null;
    out = null;
    fis = null;
    result = null;
    try {
        // does file already exist?
        if (outputFile.exists())
            System.err.println("WARNING: overwriting '" + outputFile + "'!");

        // create GZIP file
        buf = new byte[buffer];
        fis = new FileInputStream(archiveFile.getAbsolutePath());
        in = new BZip2CompressorInputStream(new BufferedInputStream(fis));
        out = new BufferedOutputStream(new FileOutputStream(outputFile), buffer);

        // Transfer bytes from the file to the GZIP file
        while ((len = in.read(buf)) > 0)
            out.write(buf, 0, len);
    } catch (Exception e) {
        msg = "Failed to decompress '" + archiveFile + "': ";
        System.err.println(msg);
        e.printStackTrace();
        result = msg + e;
    } finally {
        FileUtils.closeQuietly(fis);
        FileUtils.closeQuietly(in);
        FileUtils.closeQuietly(out);
    }

    return result;
}

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From source file:example.TestLineRecordReader.java

public String[] readRecordsDirectly(URL testFileUrl, boolean bzip) throws IOException {
    int MAX_DATA_SIZE = 1024 * 1024;
    byte[] data = new byte[MAX_DATA_SIZE];
    FileInputStream fis = new FileInputStream(testFileUrl.getFile());
    int count;/* ww w  . j  av a  2 s .c  om*/
    if (bzip) {
        BZip2CompressorInputStream bzIn = new BZip2CompressorInputStream(fis);
        count = bzIn.read(data);
        bzIn.close();
    } else {
        count = fis.read(data);
    }
    fis.close();
    assertTrue("Test file data too big for buffer", count < data.length);
    return new String(data, 0, count, "UTF-8").split("\n");
}

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From source file:com.github.nethad.clustermeister.integration.JPPFTestNode.java

private File extractBzip2(File bzip2File, File tarFile) throws FileNotFoundException, IOException {
    FileInputStream fin = null;/*from w w  w  .  ja v a2  s. c  o  m*/
    BZip2CompressorInputStream bzIn = null;
    try {
        fin = new FileInputStream(bzip2File);
        BufferedInputStream in = new BufferedInputStream(fin);
        FileOutputStream out = new FileOutputStream(tarFile);
        bzIn = new BZip2CompressorInputStream(in);
        final byte[] buffer = new byte[8192];
        int n = 0;
        while (-1 != (n = bzIn.read(buffer))) {
            out.write(buffer, 0, n);
        }
        out.close();
        bzIn.close();
    } finally {
        try {
            fin.close();
        } catch (IOException ex) {
            //                throw new RuntimeException(ex);
        }
        try {
            bzIn.close();
        } catch (IOException ex) {
            //                throw new RuntimeException(ex);
        }
    }
    return tarFile;
}

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From source file:edu.monash.merc.system.remote.HttpHpaFileGetter.java

public boolean importHPAXMLBZ2(String remoteFile, String localFile) {
    //use httpclient to get the remote file
    HttpClient httpClient = new DefaultHttpClient();
    HttpGet httpGet = new HttpGet(remoteFile);
    BZip2CompressorInputStream bzIn = null;
    FileOutputStream fos = null;//from   w w w  .  ja va 2 s .c o m
    try {
        HttpResponse response = httpClient.execute(httpGet);
        StatusLine status = response.getStatusLine();
        if (status.getStatusCode() == HttpStatus.SC_OK) {
            HttpEntity entity = response.getEntity();
            if (entity != null) {
                InputStream in = entity.getContent();
                bzIn = new BZip2CompressorInputStream(in);
                File aFile = new File(localFile);
                fos = new FileOutputStream(aFile);
                byte[] buffer = new byte[BUFFER_SIZE];
                int len = 0;
                while ((len = bzIn.read(buffer)) != -1) {
                    fos.write(buffer, 0, len);
                }
                fos.flush();
            }
        } else {
            throw new DMRemoteException("can't get the file from " + remoteFile);
        }
    } catch (Exception ex) {
        throw new DMRemoteException(ex);
    } finally {
        try {
            if (fos != null) {
                fos.close();
            }
            if (bzIn != null) {

                bzIn.close();
            }
            httpClient.getConnectionManager().shutdown();
        } catch (Exception e) {
            //ignore whatever caught
        }
    }
    return true;
}

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From source file:org.ala.harvester.WikipediaImageHarvester.java

@Override
public void start(int infosourceId, int timeGap) throws Exception {

    //name index/*from  w w w . j a  va 2 s. c o  m*/
    CBIndexSearch nameIndex = new CBIndexSearch("/data/lucene/namematching");

    //download the images file from DBPedia
    if (!downloaded) {
        System.out.println("Downloading NT triple dump from DBPedia..." + dbpediaImagesFile);
        File bzipFile = new File("/data/images_en.nt.bz2");
        FileUtils.copyURLToFile(new URL(dbpediaImagesFile), bzipFile);
        System.out.println("Downloaded.");

        //decompress
        System.out.println("Decompressing.....");
        FileInputStream in = new FileInputStream(bzipFile);
        FileOutputStream out = new FileOutputStream("/data/images_en.nt");
        BZip2CompressorInputStream bzIn = new BZip2CompressorInputStream(in);
        final byte[] buffer = new byte[1048576];
        int n = 0;
        while (-1 != (n = bzIn.read(buffer))) {
            out.write(buffer, 0, n);
        }
        out.close();
        bzIn.close();
        System.out.println("Decompressed.");
    }

    //iterate through each line
    BufferedReader reader = new BufferedReader(new FileReader("/data/images_en.nt"));
    String line = reader.readLine();
    while (line != null) {
        //            System.out.println("LINE: " + line);

        if (line.contains("depiction")) {
            String[] parts = line.split(" ");

            String dbpediaUrl = parts[0].replaceAll(">", "").replaceAll("<", "");
            String resourceName = parts[0].substring(parts[0].lastIndexOf('/') + 1);
            String nameToMatch = resourceName.replace(">", "").replaceAll("_", " ").trim();
            // println(nameToMatch)

            try {

                //name must be a bionomial or trinomial
                if (nameToMatch.contains("-") || nameToMatch.contains(" ")) {

                    //only match things that look like binomials or trinomials
                    NameSearchResult nsr = null;

                    try {
                        nameIndex.searchForRecord(nameToMatch, null);
                    } catch (HomonymException he) {

                    }
                    if (nsr == null) {
                        //search for common name
                        nsr = nameIndex.searchForCommonName(nameToMatch);
                    }

                    if (nsr != null
                            && (RankType.SPECIES.equals(nsr.getRank())
                                    || RankType.SUBSPECIES.equals(nsr.getRank()))
                            && nsr.getLsid() != null && nsr.getLsid().contains("biodiversity.org.au")
                            && nsr.getRankClassification().getScientificName() != null
                            && nsr.getRankClassification().getScientificName().contains(" ")) {

                        //validate the match
                        String dbpediaPage = WebUtils.getUrlContentAsString(dbpediaUrl);
                        if (dbpediaPage.contains("http://dbpedia.org/ontology/genus")
                                || dbpediaPage.contains("http://dbpedia.org/ontology/species")
                                || dbpediaPage.contains("http://dbpedia.org/property/genus")
                                || dbpediaPage.contains("http://dbpedia.org/property/species")
                                || dbpediaPage.contains("http://dbpedia.org/property/binomial")
                                || dbpediaPage.contains("http://dbpedia.org/ontology/phylum")) {
                            System.out.println("URL: " + dbpediaUrl + ", matched string: " + nameToMatch
                                    + ", to " + nsr.getRank().toString() + ": "
                                    + nsr.getRankClassification().getScientificName());

                            //TODO
                            //download image full res image
                            //download wikipedia page for image e.g. http://en.wikipedia.org/wiki/File:Kangur.rudy.drs.jpg
                            //retrieve creator, rights, licence, date
                            //save to repository
                            String wikiPageUrl = getWikiPageUrl(dbpediaPage);

                            if (wikiPageUrl != null && !"".equals(wikiPageUrl)) {
                                List<String> imagePageUrlList = getImagePageUrlList(wikiPageUrl);
                                harvestImagePages(imagePageUrlList, nsr, infosourceId);
                            }

                        } else {
                            System.out.println(
                                    "False positive for " + "http://en.wikipedia.org/wiki/" + resourceName);
                        }
                    }
                }
            } catch (Exception e) {
                e.printStackTrace();
            }
        }

        line = reader.readLine();
    }

    System.out.println("Finished.");
}

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

/**
 * Uncompress a Bzip2 file.//ww w  . ja  va  2 s.c  om
 */
private static File getBzipFile(FileObject in, File out, boolean isTar) throws IOException {

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

    BZip2CompressorInputStream inputStream = null;
    FileOutputStream outStream = null;

    try {
        FileInputStream is = new FileInputStream(in.getPath());
        inputStream = new BZip2CompressorInputStream(is);
        outStream = new FileOutputStream(out.getAbsolutePath());

        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:org.gephi.io.importer.api.ImportUtils.java

/**
 * Uncompress a Bzip2 file.//from  w w w.j  a v a 2s  .  c  o m
 */
public static File getBzipFile(FileObject in, File out, boolean isTar) throws IOException {

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

    BZip2CompressorInputStream inputStream = null;
    FileOutputStream outStream = null;

    try {
        FileInputStream is = new FileInputStream(in.getPath());
        inputStream = new BZip2CompressorInputStream(is);
        outStream = new FileOutputStream(out.getAbsolutePath());

        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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