Example usage for java.util.zip GZIPOutputStream GZIPOutputStream

List of usage examples for java.util.zip GZIPOutputStream GZIPOutputStream

  1. HOME
  2. Java
  3. java
  4. java.util.zip.*
  5. GZIPOutputStream
  6. 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:io.aino.agents.core.Sender.java

private byte[] getRequestContent() {
    if (!agentConfig.isGzipEnabled()) {
        return stringToSend.getBytes();
    }/*from w  w  w.j a  v a  2  s .  com*/

    try {
        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        GZIPOutputStream gzipStream = new GZIPOutputStream(baos);
        gzipStream.write(stringToSend.getBytes());

        gzipStream.finish();
        baos.flush();
        byte[] returnBytes = baos.toByteArray();
        baos.close();
        gzipStream.close();

        return returnBytes;
    } catch (IOException e) {
        throw new AgentCoreException("Failed to compress Aino log message using gzip.");
    }
}

From source file:fungus.JungGraphWriter.java

public boolean execute() {
    try {/*from w  w w. java  2  s .c o  m*/
        StringBuffer fn = new StringBuffer();
        Formatter f = new Formatter(fn, Locale.US);
        f.format("%s/graphml-%s-%d-%03d.xml.gz", dir.getPath(), basename, CommonState.seed, CDState.getCycle());
        filename = fn.toString();
        FileOutputStream fos = new FileOutputStream(filename, true);
        GZIPOutputStream gzos = new GZIPOutputStream(fos);

        PrintWriter out = new PrintWriter(new BufferedWriter(new OutputStreamWriter(gzos)));

        writer.save(JungGraphObserver.getGraph(), out);
    } catch (IOException e) {
        log.severe("Couldn't open file " + filename + " for writing");
    }
    return false;
}

From source file:com.ichi2.libanki.sync.BasicHttpSyncer.java

public HttpResponse req(String method, InputStream fobj, int comp, boolean hkey, JSONObject registerData,
        Connection.CancelCallback cancelCallback) {
    File tmpFileBuffer = null;//from   w ww  . j a v a 2 s .c o m
    try {
        String bdry = "--" + BOUNDARY;
        StringWriter buf = new StringWriter();
        // compression flag and session key as post vars
        buf.write(bdry + "\r\n");
        buf.write("Content-Disposition: form-data; name=\"c\"\r\n\r\n" + (comp != 0 ? 1 : 0) + "\r\n");
        if (hkey) {
            buf.write(bdry + "\r\n");
            buf.write("Content-Disposition: form-data; name=\"k\"\r\n\r\n" + mHKey + "\r\n");
        }
        tmpFileBuffer = File.createTempFile("syncer", ".tmp",
                new File(AnkiDroidApp.getCacheStorageDirectory()));
        FileOutputStream fos = new FileOutputStream(tmpFileBuffer);
        BufferedOutputStream bos = new BufferedOutputStream(fos);
        GZIPOutputStream tgt;
        // payload as raw data or json
        if (fobj != null) {
            // header
            buf.write(bdry + "\r\n");
            buf.write(
                    "Content-Disposition: form-data; name=\"data\"; filename=\"data\"\r\nContent-Type: application/octet-stream\r\n\r\n");
            buf.close();
            bos.write(buf.toString().getBytes("UTF-8"));
            // write file into buffer, optionally compressing
            int len;
            BufferedInputStream bfobj = new BufferedInputStream(fobj);
            byte[] chunk = new byte[65536];
            if (comp != 0) {
                tgt = new GZIPOutputStream(bos);
                while ((len = bfobj.read(chunk)) >= 0) {
                    tgt.write(chunk, 0, len);
                }
                tgt.close();
                bos = new BufferedOutputStream(new FileOutputStream(tmpFileBuffer, true));
            } else {
                while ((len = bfobj.read(chunk)) >= 0) {
                    bos.write(chunk, 0, len);
                }
            }
            bos.write(("\r\n" + bdry + "--\r\n").getBytes("UTF-8"));
        } else {
            buf.close();
            bos.write(buf.toString().getBytes("UTF-8"));
        }
        bos.flush();
        bos.close();
        // connection headers
        String url = Collection.SYNC_URL;
        if (method.equals("register")) {
            url = url + "account/signup" + "?username=" + registerData.getString("u") + "&password="
                    + registerData.getString("p");
        } else if (method.startsWith("upgrade")) {
            url = url + method;
        } else {
            url = url + "sync/" + method;
        }
        HttpPost httpPost = new HttpPost(url);
        HttpEntity entity = new ProgressByteEntity(tmpFileBuffer);

        // body
        httpPost.setEntity(entity);
        httpPost.setHeader("Content-type", "multipart/form-data; boundary=" + BOUNDARY);

        // HttpParams
        HttpParams params = new BasicHttpParams();
        params.setParameter(ConnManagerPNames.MAX_TOTAL_CONNECTIONS, 30);
        params.setParameter(ConnManagerPNames.MAX_CONNECTIONS_PER_ROUTE, new ConnPerRouteBean(30));
        params.setParameter(CoreProtocolPNames.USE_EXPECT_CONTINUE, false);
        params.setParameter(CoreProtocolPNames.USER_AGENT, "AnkiDroid-" + AnkiDroidApp.getPkgVersion());
        HttpProtocolParams.setVersion(params, HttpVersion.HTTP_1_1);
        HttpConnectionParams.setSoTimeout(params, Connection.CONN_TIMEOUT);

        // Registry
        SchemeRegistry registry = new SchemeRegistry();
        registry.register(new Scheme("http", PlainSocketFactory.getSocketFactory(), 80));
        registry.register(new Scheme("https", new EasySSLSocketFactory(), 443));
        ThreadSafeClientConnManager cm = new ThreadSafeClientConnManager(params, registry);
        if (cancelCallback != null) {
            cancelCallback.setConnectionManager(cm);
        }

        try {
            HttpClient httpClient = new DefaultHttpClient(cm, params);
            return httpClient.execute(httpPost);
        } catch (SSLException e) {
            Log.e(AnkiDroidApp.TAG, "SSLException while building HttpClient", e);
            return null;
        }
    } catch (UnsupportedEncodingException e) {
        throw new RuntimeException(e);
    } catch (IOException e) {
        Log.e(AnkiDroidApp.TAG, "BasicHttpSyncer.sync: IOException", e);
        return null;
    } catch (JSONException e) {
        throw new RuntimeException(e);
    } finally {
        if (tmpFileBuffer != null && tmpFileBuffer.exists()) {
            tmpFileBuffer.delete();
        }
    }
}

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

/**
 * Run the map2text mode.//from w w w  .  j  a va2  s .com
 *
 * @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=wiggle_0 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);
        final WiggleWindow wiggleWindow = new WiggleWindow(writer, resolution, 0);

        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;

                CountsReader counts = reader.getCountReader(referenceIndex);
                int lastLength = 0;
                int lastPosition = 0;
                while (counts.hasNextTransition()) {
                    counts.nextTransition();
                    lastPosition = counts.getPosition();
                    lastLength = counts.getLength();
                }
                final int maxWritePosition = (lastPosition + lastLength - 1);
                wiggleWindow.reset();
                wiggleWindow.setMaxDataSize(maxWritePosition);

                writer.printf("variableStep chrom=%s span=%d\n", chromosome, resolution);
                counts = reader.getCountReader(referenceIndex);

                while (counts.hasNextTransition()) {
                    counts.nextTransition();
                    final int length = counts.getLength();

                    final int count = counts.getCount();
                    final int position = counts.getPosition();

                    wiggleWindow.addData(position, length, count);

                    sumCount += count;
                    numCounts++;
                }
                wiggleWindow.finish();
                final double averageCount = sumCount / (double) numCounts;
                System.out.println("average count for sequence " + referenceId + " " + averageCount);
            }
        }
    } finally {
        IOUtils.closeQuietly(writer);
    }
}

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

/**
 * Combine tab delimited files and adjusts P-values for multiple testing.
 *
 * @throws java.io.IOException error reading / writing
 *//*from   w  w w.j  av a 2 s .c o  m*/
@Override
public void execute() throws IOException {
    Writer stream = null;
    try {
        stream = outputFilename == null ? new OutputStreamWriter(System.out)
                : outputFilename.endsWith(".gz")
                        ? new OutputStreamWriter(new GZIPOutputStream(new FileOutputStream(outputFilename)))
                        : new FileWriter(outputFilename);
        // start with an array of size 1M. This improves loading time for large datasets.
        DifferentialExpressionResults data = new DifferentialExpressionResults(10000000);

        ObjectList<String> columnIdList = vcf ? getVCFColumns(inputFiles) : getTSVColumns(inputFiles);
        // supplement selectedPValueColumns with the columns that match the selection filters:
        ObjectSet<String> selection = new ObjectOpenHashSet<String>();
        selection.addAll(ObjectArrayList.wrap(selectedPValueColumns));
        for (String col : columnIdList) {
            selection.addAll(ObjectArrayList.wrap(selectedPValueColumns));
            for (String filter : columnSelectionFilter) {
                if (col.contains(filter)) {
                    selection.add(col);
                    System.out.printf("Adding column %s to the selected columns.%n", col);

                }
            }
            System.out.println("column: " + col);
        }

        selectedPValueColumns = selection.toArray(new String[selection.size()]);
        DifferentialExpressionCalculator deCalculator = new DifferentialExpressionCalculator();

        if (vcf) {
            loadVCF(inputFiles, data, deCalculator, columnIdList);
        } else {
            loadTSV(inputFiles, data, deCalculator, columnIdList);
        }
        //    data.write(new PrintWriter(System.out), '\t', deCalculator);
        BenjaminiHochbergAdjustment fdr = new BenjaminiHochbergAdjustment();
        fdr.setNumberAboveThreshold(numIgnoredObservations);
        for (String column : selectedPValueColumns) {
            System.out.println("adjusting column: " + column);
            fdr.adjust(data, column.toLowerCase());
        }
        recordTopHits(data);
        for (int i = 0; i < data.getNumberOfStatistics(); i++) {
            MutableString statisticId = data.getStatisticIdForIndex(i);
            final String statId = statisticId.toString();
            if (!contains(selectedPValueColumns, statId)) {
                adjustedColumnIds.add(statId);
            }
        }

        Collections.sort(data, new ElementIndexComparator());
        if (vcf) {
            combineVCF(inputFiles, data, deCalculator, columnIdList, stream);

        } else {
            combineTSV(inputFiles, data, deCalculator, columnIdList, stream);
        }

    } finally {
        if (outputFilename != null) {
            IOUtils.closeQuietly(stream);
        }
    }
}

From source file:eu.delving.sip.files.StorageHelper.java

public static OutputStream zipOut(File file) throws StorageException {
    try {//w  w  w . j  av a 2s  .  c  o  m
        return new GZIPOutputStream(new FileOutputStream(file));
    } catch (IOException e) {
        throw new StorageException(
                String.format("Unable to create output stream from %s", file.getAbsolutePath()), e);
    }
}

From source file:edu.cornell.med.icb.goby.alignments.AlignmentWriterImpl.java

public AlignmentWriterImpl(final String outputBasename) throws IOException {
    alignmentEntries = new FileOutputStream(outputBasename + ".entries");
    headerOutput = new GZIPOutputStream(new FileOutputStream(outputBasename + ".header"));
    statsWriter = new FileWriter(outputBasename + ".stats");
    this.basename = outputBasename;
    collectionBuilder = Alignments.AlignmentCollection.newBuilder();
    entriesChunkWriter = new MessageChunksWriter(alignmentEntries);
    entriesChunkWriter.setParser(new AlignmentCollectionHandler());
    newEntry = Alignments.AlignmentEntry.newBuilder();
    queryIdentifiers = new IndexedIdentifier();
    targetIdentifiers = new IndexedIdentifier();
    stats = new Properties();
    // we assume stats were written until a client puts stats in this writer.
    statsWritten = true;/*from w w w  . j  a  va  2 s.co m*/
    setPermutation(doc.getBoolean("permutate-query-indices"));

}

From source file:com.hbs.common.josn.JSONUtil.java

public static void writeJSONToResponse(HttpServletResponse response, String encoding, boolean wrapWithComments,
        String serializedJSON, boolean smd, boolean gzip, String contentType) throws IOException {
    String json = serializedJSON == null ? "" : serializedJSON;
    if (wrapWithComments) {
        StringBuilder sb = new StringBuilder("/* ");
        sb.append(json);//  w  w  w  .ja  v  a  2  s. c  om
        sb.append(" */");
        json = sb.toString();
    }
    if (log.isDebugEnabled()) {
        log.debug("[JSON]" + json);
    }

    if (contentType == null) {
        contentType = "application/json";
    }
    response.setContentType((smd ? "application/json-rpc;charset=" : contentType + ";charset=") + encoding);
    if (gzip) {
        response.addHeader("Content-Encoding", "gzip");
        GZIPOutputStream out = null;
        InputStream in = null;
        try {
            out = new GZIPOutputStream(response.getOutputStream());
            in = new ByteArrayInputStream(json.getBytes());
            byte[] buf = new byte[1024];
            int len;
            while ((len = in.read(buf)) > 0) {
                out.write(buf, 0, len);
            }
        } finally {
            if (in != null)
                in.close();
            if (out != null) {
                out.finish();
                out.close();
            }
        }

    } else {
        response.setContentLength(json.getBytes(encoding).length);
        PrintWriter out = response.getWriter();
        out.print(json);
    }
}

From source file:com.codemarvels.ant.aptrepotask.AptRepoTask.java

public void execute() {
    if (repoDir == null) {
        log("repoDir attribute is empty !", LogLevel.ERR.getLevel());
        throw new RuntimeException("Bad attributes for apt-repo task");
    }/*from   www.j  a v  a 2  s . co m*/
    log("repo dir: " + repoDir);
    File repoFolder = new File(repoDir);
    if (!repoFolder.exists()) {
        repoFolder.mkdirs();
    }
    File[] files = repoFolder.listFiles(new FileFilter() {
        public boolean accept(File pathname) {
            if (pathname.getName().endsWith(FILE_DEB_EXT)) {
                return true;
            }
            return false;
        }
    });
    Packages packages = new Packages();
    for (int i = 0; i < files.length; i++) {
        File file = files[i];
        PackageEntry packageEntry = new PackageEntry();
        packageEntry.setSize(file.length());
        packageEntry.setSha1(Utils.getDigest("SHA-1", file));
        packageEntry.setSha256(Utils.getDigest("SHA-256", file));
        packageEntry.setMd5sum(Utils.getDigest("MD5", file));
        String fileName = file.getName();
        packageEntry.setFilename(fileName);
        log("found deb: " + fileName);
        try {
            ArchiveInputStream control_tgz;
            ArArchiveEntry entry;
            TarArchiveEntry control_entry;
            ArchiveInputStream debStream = new ArchiveStreamFactory().createArchiveInputStream("ar",
                    new FileInputStream(file));
            while ((entry = (ArArchiveEntry) debStream.getNextEntry()) != null) {
                if (entry.getName().equals("control.tar.gz")) {
                    ControlHandler controlHandler = new ControlHandler();
                    GZIPInputStream gzipInputStream = new GZIPInputStream(debStream);
                    control_tgz = new ArchiveStreamFactory().createArchiveInputStream("tar", gzipInputStream);
                    while ((control_entry = (TarArchiveEntry) control_tgz.getNextEntry()) != null) {
                        log("control entry: " + control_entry.getName(), LogLevel.DEBUG.getLevel());
                        if (control_entry.getName().trim().equals(CONTROL_FILE_NAME)) {
                            ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
                            IOUtils.copy(control_tgz, outputStream);
                            String content_string = outputStream.toString("UTF-8");
                            outputStream.close();
                            controlHandler.setControlContent(content_string);
                            log("control cont: " + outputStream.toString("utf-8"), LogLevel.DEBUG.getLevel());
                            break;
                        }
                    }
                    control_tgz.close();
                    if (controlHandler.hasControlContent()) {
                        controlHandler.handle(packageEntry);
                    } else {
                        throw new RuntimeException("no control content found for: " + file.getName());
                    }
                    break;
                }
            }
            debStream.close();
            packages.addPackageEntry(packageEntry);
        } catch (Exception e) {
            String msg = FAILED_TO_CREATE_APT_REPO + " " + file.getName();
            log(msg, e, LogLevel.ERR.getLevel());
            throw new RuntimeException(msg, e);
        }
    }
    try {
        File packagesFile = new File(repoDir, PACKAGES_GZ);
        packagesWriter = new BufferedWriter(
                new OutputStreamWriter(new GZIPOutputStream(new FileOutputStream(packagesFile))));
        packagesWriter.write(packages.toString());
        DefaultHashes hashes = Utils.getDefaultDigests(packagesFile);
        ReleaseInfo pinfo = new ReleaseInfo(PACKAGES_GZ, packagesFile.length(), hashes);
        Release release = new Release();
        release.addInfo(pinfo);
        final File releaseFile = new File(repoDir, RELEASE);
        FileUtils.fileWrite(releaseFile, release.toString());
    } catch (IOException e) {
        throw new RuntimeException("writing files failed", e);
    } finally {
        if (packagesWriter != null) {
            try {
                packagesWriter.close();
            } catch (IOException e) {
                throw new RuntimeException("writing files failed", e);
            }
        }
    }
}

From source file:hudson.model.UsageStatistics.java

/**
 * Gets the encrypted usage stat data to be sent to the Hudson server.
 *///from w  ww.  ja  v  a2 s .  com
public String getStatData() throws IOException {
    Hudson h = Hudson.getInstance();

    JSONObject o = new JSONObject();
    o.put("stat", 1);
    o.put("install", Util.getDigestOf(h.getSecretKey()));
    o.put("version", Hudson.VERSION);

    List<JSONObject> nodes = new ArrayList<JSONObject>();
    for (Computer c : h.getComputers()) {
        JSONObject n = new JSONObject();
        if (c.getNode() == h) {
            n.put("master", true);
            n.put("jvm-vendor", System.getProperty("java.vm.vendor"));
            n.put("jvm-version", System.getProperty("java.version"));
        }
        n.put("executors", c.getNumExecutors());
        DescriptorImpl descriptor = h.getDescriptorByType(DescriptorImpl.class);
        n.put("os", descriptor.get(c));
        nodes.add(n);
    }
    o.put("nodes", nodes);

    List<JSONObject> plugins = new ArrayList<JSONObject>();
    for (PluginWrapper pw : h.getPluginManager().getPlugins()) {
        if (!pw.isActive())
            continue; // treat disabled plugins as if they are uninstalled
        JSONObject p = new JSONObject();
        p.put("name", pw.getShortName());
        p.put("version", pw.getVersion());
        plugins.add(p);
    }
    o.put("plugins", plugins);

    JSONObject jobs = new JSONObject();
    List<TopLevelItem> items = h.getItems();
    for (TopLevelItemDescriptor d : Items.all()) {
        int cnt = 0;
        for (TopLevelItem item : items) {
            if (item.getDescriptor() == d)
                cnt++;
        }
        jobs.put(d.getJsonSafeClassName(), cnt);
    }
    o.put("jobs", jobs);

    try {
        ByteArrayOutputStream baos = new ByteArrayOutputStream();

        // json -> UTF-8 encode -> gzip -> encrypt -> base64 -> string
        OutputStreamWriter w = new OutputStreamWriter(
                new GZIPOutputStream(new CombinedCipherOutputStream(baos, getCipher(), "AES")), "UTF-8");
        o.write(w);
        w.close();

        return new String(Base64.encode(baos.toByteArray()));
    } catch (GeneralSecurityException e) {
        throw new Error(e); // impossible
    }
}