Example usage for java.util.zip GZIPOutputStream 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:com.ctriposs.r2.filter.compression.GzipCompressor.java

@Override
public byte[] deflate(InputStream data) throws CompressionException {
    ByteArrayOutputStream out;//from  w  w  w.  j a v  a  2s  .  co  m
    GZIPOutputStream gzip = null;

    try {
        out = new ByteArrayOutputStream();
        gzip = new GZIPOutputStream(out);

        IOUtils.copy(data, gzip);
    } catch (IOException e) {
        throw new CompressionException(CompressionConstants.DECODING_ERROR + getContentEncodingName(), e);
    } finally {
        if (gzip != null) {
            IOUtils.closeQuietly(gzip);
        }
    }

    return out.toByteArray();
}

---

From source file:de.undercouch.gradle.tasks.download.CompressionTest.java

@Override
protected Handler[] makeHandlers() throws IOException {
    ContextHandler compressionHandler = new ContextHandler("/" + COMPRESSED) {
        @Override//  w w  w  .  j a v a 2s.  co  m
        public void handle(String target, HttpServletRequest request, HttpServletResponse response,
                int dispatch) throws IOException, ServletException {
            String acceptEncoding = request.getHeader("Accept-Encoding");
            boolean acceptGzip = "gzip".equals(acceptEncoding);

            response.setStatus(200);
            OutputStream os = response.getOutputStream();
            if (acceptGzip) {
                response.setHeader("Content-Encoding", "gzip");
                GZIPOutputStream gos = new GZIPOutputStream(os);
                OutputStreamWriter osw = new OutputStreamWriter(gos);
                osw.write("Compressed");
                osw.close();
                gos.flush();
                gos.close();
            } else {
                OutputStreamWriter osw = new OutputStreamWriter(os);
                osw.write("Uncompressed");
                osw.close();
            }
            os.close();
        }
    };
    return new Handler[] { compressionHandler };
}

---

From source file:ch.ledcom.jpreseed.InitrdRepacker.java

public final void repack(OutputStream out) throws IOException {
    // start new archive
    try (CpioArchiveInputStream cpioIn = new CpioArchiveInputStream(new GZIPInputStream(initrdGz));
            CpioArchiveOutputStream cpioOut = new CpioArchiveOutputStream(new GZIPOutputStream(out))) {
        CpioArchiveEntry cpioEntry;/*from  w w  w.  j  a v  a  2 s. c  om*/

        // add files from base archive
        while ((cpioEntry = cpioIn.getNextCPIOEntry()) != null) {
            if (!additionalFiles.keySet().contains(cpioEntry.getName())) {
                logger.info("Repacking [{}]", cpioEntry.getName());
                cpioOut.putArchiveEntry(cpioEntry);
                long bytesCopied = copy(cpioIn, cpioOut);
                cpioOut.closeArchiveEntry();
                logger.debug("Copied [{}] bytes", bytesCopied);
            }
        }

        // additional files
        for (Map.Entry<String, File> entry : additionalFiles.entrySet()) {
            logger.info("Packing new file [{}]", entry.getKey());
            ArchiveEntry additionalEntry = cpioOut.createArchiveEntry(entry.getValue(), entry.getKey());
            cpioOut.putArchiveEntry(additionalEntry);
            try (InputStream in = new FileInputStream(entry.getValue())) {
                copy(in, cpioOut);
            }
            cpioOut.closeArchiveEntry();
        }
    }
}

---

From source file:mzmatch.ipeak.normalisation.VanDeSompele.java

public static void main(String args[]) {
    try {/*from w w w  .  ja va2s.c o m*/
        Tool.init();

        // parse the commandline options
        Options options = new Options();
        CmdLineParser cmdline = new CmdLineParser(options);

        // check whether we need to show the help
        cmdline.parse(args);
        if (options.help) {
            Tool.printHeader(System.out, application, version);
            cmdline.printUsage(System.out, "");
            return;
        }

        if (options.verbose) {
            Tool.printHeader(System.out, application, version);
            cmdline.printOptions();
        }

        // check the command-line parameters
        {
            // if the output directories do not exist, create them
            if (options.output != null)
                Tool.createFilePath(options.output, true);
        }

        // load the data
        if (options.verbose)
            System.out.println("Loading data");
        ParseResult result = PeakMLParser.parse(new FileInputStream(options.input), true);

        Header header = result.header;
        IPeakSet<IPeakSet<? extends IPeak>> peaksets = (IPeakSet<IPeakSet<? extends IPeak>>) result.measurement;

        int nrmeasurements = header.getNrMeasurementInfos();

        // remove the stability factor annotation
        for (IPeak peak : peaksets)
            peak.removeAnnotation("stability factor");

        // load the database
        if (options.verbose)
            System.out.println("Loading the molecule database");
        HashMap<String, Molecule> database = MoleculeIO.parseXml(new FileInputStream(options.database));

        // filter the set to include only identifiable metabolites
        if (options.verbose)
            System.out.println("Creating selection");
        Vector<IPeakSet<? extends IPeak>> selection = new Vector<IPeakSet<? extends IPeak>>();
        for (Molecule molecule : database.values()) {
            double mass = molecule.getMass(Mass.MONOISOTOPIC);
            double delta = PeriodicTable.PPM(mass, options.ppm);

            // get the most intense peak containing all the measurements
            Vector<IPeakSet<? extends IPeak>> neighbourhoud = peaksets.getPeaksInMassRange(mass - delta,
                    mass + delta);
            Collections.sort(neighbourhoud, IPeak.sort_intensity_descending);
            for (IPeakSet<? extends IPeak> neighbour : neighbourhoud)
                if (count(neighbour) == nrmeasurements) {
                    selection.add(neighbour);
                    break;
                }
        }

        // calculate the stability factor for each peak in the selection
        if (options.verbose)
            System.out.println("Calculating stability factors");
        for (int peakid1 = 0; peakid1 < selection.size(); ++peakid1) {
            double stddeviations[] = new double[selection.size()];

            IPeakSet<? extends IPeak> peakset1 = selection.get(peakid1);
            for (int peakid2 = 0; peakid2 < selection.size(); ++peakid2) {
                IPeakSet<? extends IPeak> peakset2 = selection.get(peakid2);

                double values[] = new double[nrmeasurements];
                for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid) {
                    int measurementid1 = peakset1.get(measurementid).getMeasurementID();
                    int setid1 = header.indexOfSetInfo(header.getSetInfoForMeasurementID(measurementid1));
                    int measurementid2 = peakset2.get(measurementid).getMeasurementID();
                    int setid2 = header.indexOfSetInfo(header.getSetInfoForMeasurementID(measurementid2));
                    if (setid1 != setid2 || measurementid1 != measurementid2)
                        System.err.println("[WARNING]: differing setid or spectrumid for comparison");

                    values[measurementid] = Math.log(peakset1.get(measurementid).getIntensity()
                            / peakset2.get(measurementid).getIntensity()) / Math.log(2);
                }
                stddeviations[peakid2] = Statistical.stddev(values);
            }

            peakset1.addAnnotation("stability factor", Statistical.mean(stddeviations));
        }

        // sort on the stability factor
        Collections.sort(selection, new IPeak.AnnotationAscending("stability factor"));

        // take the top 10% and calculate the geometric mean
        if (options.verbose)
            System.out.println("Calculating normalisation factors");
        int nrselected = (int) (0.1 * selection.size());
        if (nrselected < 10)
            nrselected = (10 < selection.size() ? 10 : selection.size());
        double normalization_factors[] = new double[nrmeasurements];
        for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid) {
            double values[] = new double[nrselected];
            for (int i = 0; i < nrselected; ++i) {
                IPeak peak = selection.get(i).get(measurementid);
                values[i] = peak.getIntensity();
            }
            normalization_factors[measurementid] = Statistical.geomean(values);
        }

        // scale the found normalization factors
        double maxnf = Statistical.max(normalization_factors);
        for (int sampleid = 0; sampleid < nrmeasurements; ++sampleid)
            normalization_factors[sampleid] /= maxnf;

        // write the selection if needed
        if (options.selection != null) {
            if (options.verbose)
                System.out.println("Writing original selection data");

            PeakMLWriter.write(result.header, selection, null,
                    new GZIPOutputStream(new FileOutputStream(options.selection)), null);
        }

        // normalize all the peaks
        if (options.verbose)
            System.out.println("Normalizing all the entries");
        for (IPeakSet<? extends IPeak> peakset : peaksets) {
            for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid) {
                // TODO why did I do this again ?
                int id = 0;
                int setid = 0;
                int spectrumid = 0;
                for (int i = 0; i < header.getNrSetInfos(); ++i) {
                    SetInfo set = header.getSetInfos().get(i);

                    if (id + set.getNrMeasurementIDs() > measurementid) {
                        setid = i;
                        spectrumid = measurementid - id;
                        break;
                    } else
                        id += set.getNrMeasurementIDs();
                }

                MassChromatogram<Peak> masschromatogram = null;
                for (IPeak p : peakset) {
                    int mymeasurementid = p.getMeasurementID();
                    int mysetid = header.indexOfSetInfo(header.getSetInfoForMeasurementID(mymeasurementid));
                    if (mysetid == setid && mymeasurementid == spectrumid) {
                        masschromatogram = (MassChromatogram<Peak>) p;
                        break;
                    }
                }
                if (masschromatogram == null)
                    continue;

                for (IPeak peak : masschromatogram.getPeaks())
                    peak.setIntensity(peak.getIntensity() / normalization_factors[measurementid]);
            }
        }

        // write the selection if needed
        if (options.selection_normalized != null) {
            if (options.verbose)
                System.out.println("Writing the normalized selection data");

            PeakMLWriter.write(result.header, selection, null,
                    new GZIPOutputStream(new FileOutputStream(options.selection_normalized)), null);
        }

        // write the factors if needed
        if (options.factors != null) {
            if (options.verbose)
                System.out.println("Writing the normalization factors");

            PrintStream out = new PrintStream(options.factors);
            for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid)
                out.println(header.getMeasurementInfo(measurementid).getLabel() + "\t"
                        + normalization_factors[measurementid]);
        }

        // write the plot if needed
        if (options.img != null) {
            if (options.verbose)
                System.out.println("Writing the graph");

            DefaultCategoryDataset dataset = new DefaultCategoryDataset();
            JFreeChart linechart = ChartFactory.createLineChart(null, "measurement", "normalization factor",
                    dataset, PlotOrientation.VERTICAL, false, // legend
                    false, // tooltips
                    false // urls
            );

            CategoryPlot plot = (CategoryPlot) linechart.getPlot();
            CategoryAxis axis = (CategoryAxis) plot.getDomainAxis();
            axis.setCategoryLabelPositions(CategoryLabelPositions.UP_45);
            LineAndShapeRenderer renderer = (LineAndShapeRenderer) plot.getRenderer();

            renderer.setSeriesShapesFilled(0, true);
            renderer.setSeriesShapesVisible(0, true);

            linechart.setBackgroundPaint(Color.WHITE);
            linechart.setBorderVisible(false);
            linechart.setAntiAlias(true);

            plot.setBackgroundPaint(Color.WHITE);
            plot.setDomainGridlinesVisible(true);
            plot.setRangeGridlinesVisible(true);

            // create the datasets
            for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid)
                dataset.addValue(normalization_factors[measurementid], "",
                        header.getMeasurementInfo(measurementid).getLabel());
            JFreeChartTools.writeAsPDF(new FileOutputStream(options.img), linechart, 800, 500);
        }

        // write the normalized values
        if (options.verbose)
            System.out.println("Writing the normalized data");
        PeakMLWriter.write(result.header, peaksets.getPeaks(), null,
                new GZIPOutputStream(new FileOutputStream(options.output)), null);
    } catch (Exception e) {
        Tool.unexpectedError(e, application);
    }
}

---

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

/**
 * compress byte array data with GZIP./*from  www  . jav a  2  s  .  com*/
 * 
 * @param input
 *            the input data
 * @return the compressed data
 * @throws java.io.IOException
 */
public byte[] compress(byte[] input) throws java.io.IOException {
    byte[] result = null;
    java.io.ByteArrayOutputStream baout = null;
    GZIPOutputStream gzipout = null;
    try {
        baout = new java.io.ByteArrayOutputStream();
        gzipout = new GZIPOutputStream(baout);
        gzipout.write(input);
        gzipout.finish();
        result = baout.toByteArray();
        return result;
    } finally {
        IOUtils.closeQuietly(baout);
        IOUtils.closeQuietly(gzipout);
    }
}

---

From source file:com.streamsets.datacollector.cluster.TarFileCreator.java

public static void createTarGz(File dir, File outputFile) throws IOException {
    Utils.checkState(dir.isDirectory(), Utils.formatL("Path {} is not a directory", dir));
    Utils.checkState(dir.canRead(), Utils.formatL("Directory {} cannot be read", dir));
    FileOutputStream dest = new FileOutputStream(outputFile);
    TarOutputStream out = new TarOutputStream(new BufferedOutputStream(new GZIPOutputStream(dest), 65536));
    File[] files = dir.listFiles();
    Utils.checkState(files != null, Utils.formatL("Directory {} could not be read", dir));
    Utils.checkState(files.length > 0, Utils.formatL("Directory {} is empty", dir));
    tarFolder(null, dir.getAbsolutePath(), out);
    out.close();/*from   w w w.  j a va  2s .c  o  m*/
}

---

From source file:com.useekm.types.AbstractGeo.java

public static byte[] gzip(byte[] bytes) {
    try {/*  www.j a v a2  s . c o  m*/
        ByteArrayOutputStream bos = new ByteArrayOutputStream();
        BufferedOutputStream bufos = new BufferedOutputStream(new GZIPOutputStream(bos));
        bufos.write(bytes);
        bufos.close();
        byte[] retval = bos.toByteArray();
        bos.close();
        return retval;
    } catch (IOException e) {
        throw new IllegalStateException("Unexpected IOException on inmemory gzip", e);
    }
}

---

From source file:com.wattzap.model.social.SelfLoopsAPI.java

public static int uploadActivity(String email, String passWord, String fileName, String note)
        throws IOException {
    JSONObject jsonObj = null;//w w  w .j a  va 2s .c  o m

    FileInputStream in = null;
    GZIPOutputStream out = null;
    CloseableHttpClient httpClient = HttpClients.createDefault();
    try {
        HttpPost httpPost = new HttpPost(url);
        httpPost.setHeader("enctype", "multipart/mixed");

        in = new FileInputStream(fileName);
        // Create stream to compress data and write it to the to file.
        ByteArrayOutputStream obj = new ByteArrayOutputStream();
        out = new GZIPOutputStream(obj);

        // Copy bytes from one stream to the other
        byte[] buffer = new byte[4096];
        int bytes_read;
        while ((bytes_read = in.read(buffer)) != -1) {
            out.write(buffer, 0, bytes_read);
        }
        out.close();
        in.close();

        ByteArrayBody bin = new ByteArrayBody(obj.toByteArray(), ContentType.create("application/x-gzip"),
                fileName);
        HttpEntity reqEntity = MultipartEntityBuilder.create()
                .addPart("email", new StringBody(email, ContentType.TEXT_PLAIN))
                .addPart("pw", new StringBody(passWord, ContentType.TEXT_PLAIN)).addPart("tcxfile", bin)
                .addPart("note", new StringBody(note, ContentType.TEXT_PLAIN)).build();

        httpPost.setEntity(reqEntity);

        CloseableHttpResponse response = null;
        try {
            response = httpClient.execute(httpPost);
            int code = response.getStatusLine().getStatusCode();
            switch (code) {
            case 200:

                HttpEntity respEntity = response.getEntity();

                if (respEntity != null) {
                    // EntityUtils to get the response content
                    String content = EntityUtils.toString(respEntity);
                    //System.out.println(content);
                    JSONParser jsonParser = new JSONParser();
                    jsonObj = (JSONObject) jsonParser.parse(content);
                }

                break;
            case 403:
                throw new RuntimeException(
                        "Authentification failure " + email + " " + response.getStatusLine());
            default:
                throw new RuntimeException("Error " + code + " " + response.getStatusLine());
            }
        } catch (ParseException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        } finally {
            if (response != null) {
                response.close();
            }
        }

        int activityId = ((Long) jsonObj.get("activity_id")).intValue();

        // parse error code
        int error = ((Long) jsonObj.get("error_code")).intValue();
        if (activityId == -1) {
            String message = (String) jsonObj.get("message");
            switch (error) {
            case 102:
                throw new RuntimeException("Empty TCX file " + fileName);
            case 103:
                throw new RuntimeException("Invalide TCX Format " + fileName);
            case 104:
                throw new RuntimeException("TCX Already Present " + fileName);
            case 105:
                throw new RuntimeException("Invalid XML " + fileName);
            case 106:
                throw new RuntimeException("invalid compression algorithm");
            case 107:
                throw new RuntimeException("Invalid file mime types");
            default:
                throw new RuntimeException(message + " " + error);
            }
        }

        return activityId;
    } finally {
        if (in != null) {
            in.close();
        }
        if (out != null) {
            out.close();
        }
        httpClient.close();
    }
}

---

From source file:net.sf.ehcache.constructs.web.PageInfoTest.java

/**
 * Create gzip file in tmp//w ww.  j  a va 2 s . c o  m
 *
 * @throws Exception
 */
protected void setUp() throws Exception {
    String testGzipFile = System.getProperty("java.io.tmpdir") + File.separator + "test.gzip";
    testFile = new File(testGzipFile);
    FileOutputStream fout = new FileOutputStream(testFile);
    GZIPOutputStream gzipOutputStream = new GZIPOutputStream(fout);
    for (int j = 0; j < 100; j++) {
        for (int i = 0; i < 1000; i++) {
            gzipOutputStream.write(i);
        }
    }
    gzipOutputStream.close();
}

---

From source file:ca.uhn.fhir.rest.client.apache.GZipContentInterceptor.java

@Override
public void interceptRequest(IHttpRequest theRequestInterface) {
    HttpRequestBase theRequest = ((ApacheHttpRequest) theRequestInterface).getApacheRequest();
    if (theRequest instanceof HttpEntityEnclosingRequest) {
        Header[] encodingHeaders = theRequest.getHeaders(Constants.HEADER_CONTENT_ENCODING);
        if (encodingHeaders == null || encodingHeaders.length == 0) {
            HttpEntityEnclosingRequest req = (HttpEntityEnclosingRequest) theRequest;

            ByteArrayOutputStream bos = new ByteArrayOutputStream();
            GZIPOutputStream gos;
            try {
                gos = new GZIPOutputStream(bos);
                req.getEntity().writeTo(gos);
                gos.finish();//  www. j  a v  a2  s . c om
            } catch (IOException e) {
                ourLog.warn("Failed to GZip outgoing content", e);
                return;
            }

            byte[] byteArray = bos.toByteArray();
            ByteArrayEntity newEntity = new ByteArrayEntity(byteArray);
            req.setEntity(newEntity);
            req.addHeader(Constants.HEADER_CONTENT_ENCODING, "gzip");
        }
    }

}

---

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