Example usage for java.util.zip GZIPInputStream GZIPInputStream

Introduction

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

Prototype

public GZIPInputStream(InputStream in) throws IOException 

Source Link

Document

Creates a new input stream with a default buffer size.

Usage

From source file:com.melniqw.instagramsdk.Network.java

private static String sendDummyRequest(String url, String body, Request request) throws IOException {
    HttpURLConnection connection = null;
    try {//from w w  w  . j  a  v a  2s  .c o m
        connection = (HttpURLConnection) new URL(url).openConnection();
        connection.setConnectTimeout(10000);
        connection.setReadTimeout(10000);
        connection.setUseCaches(false);
        connection.setDoInput(true);
        //            connection.setRequestProperty("Content-Type", "text/plain; charset=utf-8");
        if (request == Request.GET) {
            connection.setDoOutput(false);
            connection.setRequestMethod("GET");
        } else if (request == Request.POST) {
            connection.setDoOutput(true);
            connection.setRequestMethod("POST");
        }
        if (REQUEST_ENABLE_COMPRESSION)
            connection.setRequestProperty("Accept-Encoding", "gzip");
        if (request == Request.POST)
            connection.getOutputStream().write(body.getBytes("utf-8"));
        int code = connection.getResponseCode();
        System.out.println(TAG + " responseCode = " + code);
        //It may happen due to keep-alive problem http://stackoverflow.com/questions/1440957/httpurlconnection-getresponsecode-returns-1-on-second-invocation
        if (code == -1)
            throw new WrongResponseCodeException("Network error");
        // ?    200
        //on error can also read error stream from connection.
        InputStream inputStream = new BufferedInputStream(connection.getInputStream(), 8192);
        String encoding = connection.getHeaderField("Content-Encoding");
        if (encoding != null && encoding.equalsIgnoreCase("gzip"))
            inputStream = new GZIPInputStream(inputStream);
        String response = Utils.convertStreamToString(inputStream);
        System.out.println(TAG + " response = " + response);
        return response;
    } finally {
        if (connection != null)
            connection.disconnect();
    }
}

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From source file:HLA.java

private boolean checkHeader(SAMFileHeader header) {
    List<SAMSequenceRecord> sequences = header.getSequenceDictionary().getSequences();
    HashSet<String> map = new HashSet<String>();

    //load kourami panel sequence names
    BufferedReader br;/*from www  .  ja  va2s  .  c o m*/
    try {
        br = new BufferedReader(new InputStreamReader(new GZIPInputStream(
                new FileInputStream(HLA.MSAFILELOC + File.separator + "All_FINAL_with_Decoy.fa.gz"))));
        String curline = "";
        while ((curline = br.readLine()) != null) {
            if (curline.charAt(0) == ('>'))
                map.add(curline.substring(1));
        }
        br.close();
    } catch (IOException ioe) {
        ioe.printStackTrace();
    }

    //check if input bam has sequences to kourami panel
    for (SAMSequenceRecord ssr : sequences) {
        if (!map.contains(ssr.getSequenceName()))
            return false;
    }
    return true;
}

---

From source file:eu.europeana.uim.sugarcrmclient.internal.ExtendedSaajSoapMessageFactory.java

/**
 * Detects if the incoming stream is Gzip encoded
 * /*from w  w  w.  ja v  a  2  s  . c o  m*/
 * @param pb
 * @return an InputStream/GZIPInputStream 
 * @throws IOException
 */
public static InputStream decompressStream(PushbackInputStream pb) throws IOException {
    byte[] signature = new byte[2];
    pb.read(signature);
    pb.unread(signature);

    if (signature[0] == 31 && signature[1] == -117)
        return new GZIPInputStream(pb);
    else
        return pb;
}

---

From source file:uk.ac.ebi.eva.pipeline.jobs.steps.VariantLoaderStepTest.java

@Test
public void loaderStepShouldLoadAllVariants() throws Exception {
    Config.setOpenCGAHome(opencgaHome);/*from   w  ww.  j a  va 2  s .  c  o m*/

    jobOptions.getVariantOptions().put(VariantStorageManager.DB_NAME, dbName);
    jobOptions.getVariantOptions().put(VARIANT_SOURCE, new VariantSource(input, "1", "1", "studyName",
            VariantStudy.StudyType.COLLECTION, VariantSource.Aggregation.NONE));

    //and a variants transform step already executed
    File transformedVcfVariantsFile = new File(
            VariantLoaderStepTest.class.getResource("/small20.vcf.gz.variants.json.gz").getFile());
    File tmpTransformedVcfVariantsFile = new File(outputDir, transformedVcfVariantsFile.getName());
    FileUtils.copyFile(transformedVcfVariantsFile, tmpTransformedVcfVariantsFile);

    File transformedVariantsFile = new File(
            VariantLoaderStepTest.class.getResource("/small20.vcf.gz.file.json.gz").getFile());
    File tmpTransformedVariantsFile = new File(outputDir, transformedVariantsFile.getName());
    FileUtils.copyFile(transformedVariantsFile, tmpTransformedVariantsFile);

    // When the execute method in variantsLoad is executed
    JobExecution jobExecution = jobLauncherTestUtils.launchStep(GenotypedVcfJob.LOAD_VARIANTS);

    //Then variantsLoad step should complete correctly
    assertEquals(ExitStatus.COMPLETED, jobExecution.getExitStatus());
    assertEquals(BatchStatus.COMPLETED, jobExecution.getStatus());

    // And the number of documents in db should be the same number of line of the vcf transformed file
    VariantStorageManager variantStorageManager = StorageManagerFactory.getVariantStorageManager();
    VariantDBAdaptor variantDBAdaptor = variantStorageManager.getDBAdaptor(dbName, null);
    VariantDBIterator iterator = variantDBAdaptor.iterator(new QueryOptions());
    long lines = getLines(new GZIPInputStream(new FileInputStream(transformedVcfVariantsFile)));

    assertEquals(count(iterator), lines);

    tmpTransformedVcfVariantsFile.delete();
    tmpTransformedVariantsFile.delete();
}

---

From source file:com.sshtools.common.vomanagementtool.common.VOHelper.java

public static void checkUpdateVOMSConfigFiles() throws IOException {
    refreshVOMSConfig();//  w w w. ja  v  a 2 s  .  c  o m
    if (!(new File(vomslocation).exists())) {
        boolean success = (new File(vomslocation).mkdir());
        if (!success) {
            throw new IOException("Couldn't create directory for VOMS support: " + vomslocation);
        }
    }
    if (!new File(vomslocation).isDirectory()) {
        throw new IOException("Location: " + vomslocation + " is not a directory");
    } else {

        URL vomsURL = new URL(vomsConfigURL);
        InputStream in;
        try {
            in = new GZIPInputStream(vomsURL.openStream());

        } catch (FileNotFoundException fnf) {
            throw new IOException("URL: " + vomslocation + " does not exists.");
        } catch (IOException ioe) {
            throw new IOException(
                    "Failed to download VOMS config '" + vomsConfigURL + "'.\n" + ioe.getMessage());
        }

        try {
            untar(in, vomslocation);
        } catch (IOException ioe) {
            throw new IOException("Untarring VOMS config into '" + vomslocation + "'.\n" + ioe.getMessage());
        }
    }

    //Favourites
    if (!(new File(favouritesFile).exists())) {
        boolean success = (new File(favouritesFile).createNewFile());
        if (!success) {
            throw new IOException(
                    "Couldn't create 'Favourites' directory to allow you to store your VOs: " + favouritesFile);
        }
    }
    try {
        Chmod(true, "755", vomslocation);
    } catch (IOException ioe) {
        throw new IOException("Cannot change directory permission of " + vomslocation + ".");
    }

}

---

From source file:com.twentyn.patentExtractor.Util.java

public static Document decompressXMLDocument(byte[] bytes) throws IOException, ParserConfigurationException,
        SAXException, TransformerConfigurationException, TransformerException {
    // With help from http://stackoverflow.com/questions/309424/read-convert-an-inputstream-to-a-string
    ByteArrayInputStream bais = new ByteArrayInputStream(bytes);
    InputStream s = new GZIPInputStream(new Base64InputStream(bais));
    DocumentBuilder documentBuilder = mkDocBuilderFactory().newDocumentBuilder();
    Document doc = documentBuilder.parse(s);
    s.close();//from w  ww. ja v  a2s . c o m
    return doc;
}

---

From source file:de.unidue.ltl.pos.trainmodel.misc.SharedTaskReader.java

@Override
public void initialize(UimaContext context) throws ResourceInitializationException {
    super.initialize(context);

    posMappingProvider = new MappingProvider();
    posMappingProvider.setDefault(MappingProvider.LOCATION, "classpath:/de/tudarmstadt/ukp/dkpro/"
            + "core/api/lexmorph/tagset/${language}-${tagger.tagset}-pos.map");
    posMappingProvider.setDefault(MappingProvider.BASE_TYPE, POS.class.getName());
    posMappingProvider.setDefault("tagger.tagset", "default");
    posMappingProvider.setOverride(MappingProvider.LOCATION, mappingPosLocation);
    posMappingProvider.setOverride(MappingProvider.LANGUAGE, language);
    posMappingProvider.setOverride("tagger.tagset", posTagset);

    try {/*  ww  w.j  a  v  a  2 s  . c o m*/
        for (Resource r : getResources()) {
            String name = r.getResource().getFile().getName();
            InputStreamReader is = null;
            if (name.endsWith(".gz")) {
                is = new InputStreamReader(new GZIPInputStream(r.getInputStream()), encoding);
            } else {
                is = new InputStreamReader(r.getInputStream(), encoding);
            }
            br = new BufferedReader(is);
            bfs.add(br);
        }
    } catch (Exception e) {
        throw new IllegalStateException(e);
    }
}

---

From source file:com.evilisn.DAO.CertMapper.java

public static byte[] httpGetBin(URI uri, boolean bActiveCheckUnknownHost) throws Exception

{

    InputStream is = null;/*from   www. j a v  a 2 s. co  m*/

    InputStream is_temp = null;

    try {

        if (uri == null)
            return null;

        URL url = uri.toURL();

        if (bActiveCheckUnknownHost) {

            url.getProtocol();

            String host = url.getHost();

            int port = url.getPort();

            if (port == -1)

                port = url.getDefaultPort();

            InetSocketAddress isa = new InetSocketAddress(host, port);

            if (isa.isUnresolved()) {

                //fix JNLP popup error issue

                throw new UnknownHostException("Host Unknown:" + isa.toString());

            }

        }

        HttpURLConnection uc = (HttpURLConnection) url.openConnection();

        uc.setDoInput(true);

        uc.setAllowUserInteraction(false);

        uc.setInstanceFollowRedirects(true);

        setTimeout(uc);

        String contentEncoding = uc.getContentEncoding();

        int len = uc.getContentLength();

        // is = uc.getInputStream();

        if (contentEncoding != null && contentEncoding.toLowerCase().indexOf("gzip") != -1)

        {

            is_temp = uc.getInputStream();

            is = new GZIPInputStream(is_temp);

        }

        else if (contentEncoding != null && contentEncoding.toLowerCase().indexOf("deflate") != -1)

        {

            is_temp = uc.getInputStream();

            is = new InflaterInputStream(is_temp);

        }

        else

        {

            is = uc.getInputStream();

        }

        if (len != -1) {

            int ch = 0, i = 0;

            byte[] res = new byte[len];

            while ((ch = is.read()) != -1) {

                res[i++] = (byte) (ch & 0xff);

            }

            return res;

        } else {

            ArrayList<byte[]> buffer = new ArrayList<byte[]>();

            int buf_len = 1024;

            byte[] res = new byte[buf_len];

            int ch = 0, i = 0;

            while ((ch = is.read()) != -1) {

                res[i++] = (byte) (ch & 0xff);

                if (i == buf_len) {

                    //rotate

                    buffer.add(res);

                    i = 0;

                    res = new byte[buf_len];

                }

            }

            int total_len = buffer.size() * buf_len + i;

            byte[] buf = new byte[total_len];

            for (int j = 0; j < buffer.size(); j++) {

                System.arraycopy(buffer.get(j), 0, buf, j * buf_len, buf_len);

            }

            if (i > 0) {

                System.arraycopy(res, 0, buf, buffer.size() * buf_len, i);

            }

            return buf;

        }

    } catch (Exception e) {

        e.printStackTrace();

        return null;

    } finally {

        closeInputStream(is_temp);

        closeInputStream(is);

    }

}

---

From source file:ezbake.deployer.publishers.ezcentos.EzCentosThriftRunnerPublisher.java

/**
 * Copies files from the artifact .tar file
 * that end in the suffix to the specified destination.
 *
 * @param artifact// w w  w .ja  v a 2  s .c om
 * @param destination
 * @param suffix
 * @return Paths that the files were copied to
 * @throws IOException
 */
private List<String> copyFiles(DeploymentArtifact artifact, File destination, String suffix)
        throws IOException {
    TarArchiveInputStream tarIn = new TarArchiveInputStream(
            new GZIPInputStream(new ByteArrayInputStream(artifact.getArtifact())));
    List<String> filePaths = new ArrayList<>();
    try {
        TarArchiveEntry entry = tarIn.getNextTarEntry();

        while (entry != null) {
            if (entry.getName().endsWith(suffix)) {
                String newFilePath = destination + File.separator + entry.getName();
                FileOutputStream fos = new FileOutputStream(newFilePath);
                try {
                    IOUtils.copy(tarIn, fos);
                } finally {
                    IOUtils.closeQuietly(fos);
                }
                filePaths.add(newFilePath);
            }
            entry = tarIn.getNextTarEntry();
        }
    } finally {
        IOUtils.closeQuietly(tarIn);
    }

    return filePaths;
}

---

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