Example usage for java.util.zip ZipOutputStream write

Introduction

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

Prototype

public synchronized void write(byte[] b, int off, int len) throws IOException 

Source Link

Document

Writes an array of bytes to the current ZIP entry data.

Usage

From source file:game.com.HandleDownloadFolderServlet.java

private void outputZipStream(ZipOutputStream output, File file) throws FileNotFoundException, IOException {
    for (File currentFile : file.listFiles()) {

        InputStream input = null;
        byte[] buffer = new byte[DEFAULT_BUFFER_SIZE];
        try {//  w  w  w . j av  a 2 s  .com
            if (currentFile.isDirectory()) {
                outputZipStream(output, currentFile);
            } else {
                input = new BufferedInputStream(new FileInputStream(currentFile), DEFAULT_BUFFER_SIZE);
                output.putNextEntry(new ZipEntry(currentFile.getName()));
                for (int length = 0; (length = input.read(buffer)) > 0;) {
                    output.write(buffer, 0, length);
                }
                output.closeEntry();
            }
        } finally {
            if (input != null) {
                try {
                    input.close();
                } catch (Exception logOrIgnore) {
                    logger.error(logOrIgnore.getMessage(), logOrIgnore);
                }
            }
        }
    }
}

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From source file:nl.b3p.viewer.features.ShapeDownloader.java

/**
 * This method zips the directory/*w w  w  . j a  va 2s  . c  o m*/
 *
 * @param dir
 * @param zipDirName
 */
private void zipDirectory(File dir, File zip) throws IOException {
    try {
        List<String> filesListInDir = new ArrayList<String>();
        populateFilesList(dir, filesListInDir);
        //now zip files one by one
        //create ZipOutputStream to write to the zip file
        FileOutputStream fos = new FileOutputStream(zip);
        ZipOutputStream zos = new ZipOutputStream(fos);
        for (String filePath : filesListInDir) {
            //for ZipEntry we need to keep only relative file path, so we used substring on absolute path
            ZipEntry ze = new ZipEntry(
                    filePath.substring(dir.getAbsolutePath().length() + 1, filePath.length()));
            zos.putNextEntry(ze);
            //read the file and write to ZipOutputStream
            FileInputStream fis = new FileInputStream(filePath);
            byte[] buffer = new byte[1024];
            int len;
            while ((len = fis.read(buffer)) > 0) {
                zos.write(buffer, 0, len);
            }
            zos.closeEntry();
            fis.close();
        }
        zos.close();
        fos.close();
    } catch (IOException e) {
        log.error("Could not write zipfile. Exiting.", e);
        throw e;
    }
}

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From source file:ZipSourceCallable.java

public static void zipSource(FilePath workspace, final String directory, final ZipOutputStream out,
        final String prefixToTrim) throws Exception {
    if (!Paths.get(directory).startsWith(Paths.get(prefixToTrim))) {
        throw new Exception(zipSourceError + "prefixToTrim: " + prefixToTrim + ", directory: " + directory);
    }//from w w  w . j  av  a 2 s  .  c o  m

    FilePath dir = new FilePath(workspace, directory);
    List<FilePath> dirFiles = dir.list();
    if (dirFiles == null) {
        throw new Exception("Empty or invalid source directory: " + directory
                + ". Did you download any source as part of your build?");
    }
    byte[] buffer = new byte[1024];
    int bytesRead;

    for (int i = 0; i < dirFiles.size(); i++) {
        FilePath f = new FilePath(workspace, dirFiles.get(i).getRemote());
        if (f.isDirectory()) {
            zipSource(workspace, f.getRemote() + File.separator, out, prefixToTrim);
        } else {
            InputStream inputStream = f.read();
            try {
                String path = trimPrefix(f.getRemote(), prefixToTrim);

                if (path.startsWith(File.separator)) {
                    path = path.substring(1, path.length());
                }

                // Zip files created on the windows file system will not unzip
                // properly on unix systems. Without this change, no directory structure
                // is built when unzipping.
                path = path.replace(File.separator, "/");

                ZipEntry entry = new ZipEntry(path);
                out.putNextEntry(entry);
                while ((bytesRead = inputStream.read(buffer)) != -1) {
                    out.write(buffer, 0, bytesRead);
                }
            } finally {
                inputStream.close();
            }
        }
    }
}

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From source file:org.pdfgal.pdfgalweb.utils.impl.ZipUtilsImpl.java

/**
 * Adds a new file to the {@link ZipOutputStream}.
 * //from ww w.  j av a2s.  c o  m
 * @param fileName
 * @param zos
 * @param originalFileName
 * @throws FileNotFoundException
 * @throws IOException
 */
private void addToZipFile(final String fileName, final ZipOutputStream zos, final String originalFileName)
        throws IOException {

    // File is opened.
    final File file = new File(fileName);

    // File is renamed.
    final String newName = fileName.substring(fileName.indexOf(originalFileName), fileName.length());
    final File renamedFile = new File(newName);
    file.renameTo(renamedFile);

    // File is included into ZIP.
    final FileInputStream fis = new FileInputStream(renamedFile);
    final ZipEntry zipEntry = new ZipEntry(newName);
    zos.putNextEntry(zipEntry);

    final byte[] bytes = new byte[1024];
    int length;
    while ((length = fis.read(bytes)) >= 0) {
        zos.write(bytes, 0, length);
    }

    // Closing elements.
    zos.closeEntry();
    fis.close();

    // File is deleted
    this.fileUtils.delete(newName);
}

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From source file:com.esofthead.mycollab.vaadin.resources.StreamDownloadResourceSupportExtDrive.java

private void addFileToZip(String path, Content res, ZipOutputStream zip) throws Exception {
    byte[] buf = new byte[1024];
    InputStream contentStream;//from  w  w w.  ja v  a2 s  .  co m
    if (!res.isExternalResource()) {
        contentStream = resourceService.getContentStream(res.getPath());
    } else {
        ExternalResourceService service = ResourceUtils.getExternalResourceService(ResourceUtils.getType(res));
        contentStream = service.download(ResourceUtils.getExternalDrive(res), res.getPath());
    }
    if (path.length() == 0)
        path = res.getName();
    else
        path += "/" + res.getName();
    zip.putNextEntry(new ZipEntry(path));
    int byteLength;
    while ((byteLength = contentStream.read(buf)) > 0) {
        zip.write(buf, 0, byteLength);
    }
}

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From source file:com.commonsware.android.backup.BackupService.java

private void zipDir(String basePath, File dir, ZipOutputStream zos) throws IOException {
    byte[] buf = new byte[16384];

    if (dir.listFiles() != null) {
        for (File file : dir.listFiles()) {
            if (file.isDirectory()) {
                String path = basePath + file.getName() + "/";

                zos.putNextEntry(new ZipEntry(path));
                zipDir(path, file, zos);
                zos.closeEntry();//from w  ww. ja  v a2 s  .  com
            } else if (!file.getName().equals(BACKUP_PREFS_FILENAME)) {
                FileInputStream fin = new FileInputStream(file);
                int length;

                zos.putNextEntry(new ZipEntry(basePath + file.getName()));

                while ((length = fin.read(buf)) > 0) {
                    zos.write(buf, 0, length);
                }

                zos.closeEntry();
                fin.close();
            }
        }
    }
}

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From source file:com.polyvi.xface.extension.zip.XZipExt.java

/**
 * ??zip// www . j av  a 2  s.c  o  m
 *
 * @param srcIs
 * @param zos
 * @throws IOException
 * @throws IllegalArgumentException
 */
private void writeToZip(InputStream srcIs, ZipOutputStream zos) throws IOException, IllegalArgumentException {
    if (null == srcIs || null == zos) {
        XLog.e(CLASS_NAME, "Method writeToZip: param is null!");
        throw new IllegalArgumentException();
    }
    try {
        byte[] readBuffer = new byte[XConstant.BUFFER_LEN];
        int bytesIn = 0;
        bytesIn = srcIs.read(readBuffer);
        while (bytesIn != -1) {
            zos.write(readBuffer, 0, bytesIn);
            bytesIn = srcIs.read(readBuffer);
        }
    } catch (IOException e) {
        XLog.e(CLASS_NAME, "Zip file failed!");
        throw new IOException();
    } finally {
        srcIs.close();
        zos.closeEntry();
    }
}

---

From source file:fr.gael.dhus.datastore.FileSystemDataStore.java

/**
 * Generates a zip file./* www.  j a v  a  2 s. c  o  m*/
 *
 * @param source      source file or directory to compress.
 * @param destination destination of zipped file.
 * @return the zipped file.
 */
private void generateZip(File source, File destination) throws IOException {
    if (source == null || !source.exists()) {
        throw new IllegalArgumentException("source file should exist");
    }
    if (destination == null) {
        throw new IllegalArgumentException("destination file should be not null");
    }

    FileOutputStream output = new FileOutputStream(destination);
    ZipOutputStream zip_out = new ZipOutputStream(output);
    zip_out.setLevel(cfgManager.getDownloadConfiguration().getCompressionLevel());

    List<QualifiedFile> file_list = getFileList(source);
    byte[] buffer = new byte[BUFFER_SIZE];
    for (QualifiedFile qualified_file : file_list) {
        ZipEntry entry = new ZipEntry(qualified_file.getQualifier());
        InputStream input = new FileInputStream(qualified_file.getFile());

        int read;
        zip_out.putNextEntry(entry);
        while ((read = input.read(buffer)) != -1) {
            zip_out.write(buffer, 0, read);
        }
        input.close();
        zip_out.closeEntry();
    }
    zip_out.close();
    output.close();
}

---

From source file:com.yifanlu.PSXperiaTool.ZpakCreate.java

public void create(boolean noCompress) throws IOException {
    Logger.info("Generating zpak file from directory %s with compression = %b", mDirectory.getPath(),
            !noCompress);//from w  w w . j a  v  a2 s. c  om
    IOFileFilter filter = new IOFileFilter() {
        public boolean accept(File file) {
            if (file.getName().startsWith(".")) {
                Logger.debug("Skipping file %s", file.getPath());
                return false;
            }
            return true;
        }

        public boolean accept(File file, String s) {
            if (s.startsWith(".")) {
                Logger.debug("Skipping file %s", file.getPath());
                return false;
            }
            return true;
        }
    };
    Iterator<File> it = FileUtils.iterateFiles(mDirectory, filter, TrueFileFilter.INSTANCE);
    ZipOutputStream out = new ZipOutputStream(mOut);
    out.setMethod(noCompress ? ZipEntry.STORED : ZipEntry.DEFLATED);
    while (it.hasNext()) {
        File current = it.next();
        FileInputStream in = new FileInputStream(current);
        ZipEntry zEntry = new ZipEntry(
                current.getPath().replace(mDirectory.getPath(), "").substring(1).replace("\\", "/"));
        if (noCompress) {
            zEntry.setSize(in.getChannel().size());
            zEntry.setCompressedSize(in.getChannel().size());
            zEntry.setCrc(getCRC32(current));
        }
        out.putNextEntry(zEntry);
        Logger.verbose("Adding file %s", current.getPath());
        int n;
        while ((n = in.read(mBuffer)) != -1) {
            out.write(mBuffer, 0, n);
        }
        in.close();
        out.closeEntry();
    }
    out.close();
    Logger.debug("Done with ZPAK creation.");
}

---

From source file:fr.cirad.mgdb.exporting.individualoriented.PLinkExportHandler.java

@Override
public void exportData(OutputStream outputStream, String sModule, Collection<File> individualExportFiles,
        boolean fDeleteSampleExportFilesOnExit, ProgressIndicator progress, DBCursor markerCursor,
        Map<Comparable, Comparable> markerSynonyms, Map<String, InputStream> readyToExportFiles)
        throws Exception {
    File warningFile = File.createTempFile("export_warnings_", "");
    FileWriter warningFileWriter = new FileWriter(warningFile);

    ZipOutputStream zos = new ZipOutputStream(outputStream);

    if (readyToExportFiles != null)
        for (String readyToExportFile : readyToExportFiles.keySet()) {
            zos.putNextEntry(new ZipEntry(readyToExportFile));
            InputStream inputStream = readyToExportFiles.get(readyToExportFile);
            byte[] dataBlock = new byte[1024];
            int count = inputStream.read(dataBlock, 0, 1024);
            while (count != -1) {
                zos.write(dataBlock, 0, count);
                count = inputStream.read(dataBlock, 0, 1024);
            }/*from  w  ww  .jav a 2 s  .co  m*/
        }

    MongoTemplate mongoTemplate = MongoTemplateManager.get(sModule);
    int markerCount = markerCursor.count();

    String exportName = sModule + "_" + markerCount + "variants_" + individualExportFiles.size()
            + "individuals";
    zos.putNextEntry(new ZipEntry(exportName + ".ped"));

    TreeMap<Integer, Comparable> problematicMarkerIndexToNameMap = new TreeMap<Integer, Comparable>();
    short nProgress = 0, nPreviousProgress = 0;
    int i = 0;
    for (File f : individualExportFiles) {
        BufferedReader in = new BufferedReader(new FileReader(f));
        try {
            String individualId, line = in.readLine(); // read sample id
            if (line != null) {
                individualId = line;
                String population = getIndividualPopulation(sModule, line);
                String individualInfo = (population == null ? "." : population) + " " + individualId;
                zos.write((individualInfo + " 0 0 0 " + getIndividualGenderCode(sModule, individualId))
                        .getBytes());
            } else
                throw new Exception("Unable to read first line of temp export file " + f.getName());

            int nMarkerIndex = 0;
            while ((line = in.readLine()) != null) {
                List<String> genotypes = MgdbDao.split(line, "|");
                HashMap<Object, Integer> genotypeCounts = new HashMap<Object, Integer>(); // will help us to keep track of missing genotypes
                int highestGenotypeCount = 0;
                String mostFrequentGenotype = null;
                for (String genotype : genotypes) {
                    if (genotype.length() == 0)
                        continue; /* skip missing genotypes */

                    int gtCount = 1 + MgdbDao.getCountForKey(genotypeCounts, genotype);
                    if (gtCount > highestGenotypeCount) {
                        highestGenotypeCount = gtCount;
                        mostFrequentGenotype = genotype;
                    }
                    genotypeCounts.put(genotype, gtCount);
                }

                if (genotypeCounts.size() > 1) {
                    warningFileWriter.write("- Dissimilar genotypes found for variant " + nMarkerIndex
                            + ", individual " + individualId + ". Exporting most frequent: "
                            + mostFrequentGenotype + "\n");
                    problematicMarkerIndexToNameMap.put(nMarkerIndex, "");
                }

                String[] alleles = mostFrequentGenotype == null ? new String[0]
                        : mostFrequentGenotype.split(" ");
                if (alleles.length > 2) {
                    warningFileWriter.write("- More than 2 alleles found for variant " + nMarkerIndex
                            + ", individual " + individualId + ". Exporting only the first 2 alleles.\n");
                    problematicMarkerIndexToNameMap.put(nMarkerIndex, "");
                }

                String all1 = alleles.length == 0 ? "0" : alleles[0];
                String all2 = alleles.length == 0 ? "0" : alleles[alleles.length == 1 ? 0 : 1];
                if (all1.length() != 1 || all2.length() != 1) {
                    warningFileWriter
                            .write("- SNP expected, but alleles are not coded on a single char for variant "
                                    + nMarkerIndex + ", individual " + individualId
                                    + ". Ignoring this genotype.\n");
                    problematicMarkerIndexToNameMap.put(nMarkerIndex, "");
                } else
                    zos.write((" " + all1 + " " + all2).getBytes());

                nMarkerIndex++;
            }
        } catch (Exception e) {
            LOG.error("Error exporting data", e);
            progress.setError("Error exporting data: " + e.getClass().getSimpleName()
                    + (e.getMessage() != null ? " - " + e.getMessage() : ""));
            return;
        } finally {
            in.close();
        }

        if (progress.hasAborted())
            return;

        nProgress = (short) (++i * 100 / individualExportFiles.size());
        if (nProgress > nPreviousProgress) {
            progress.setCurrentStepProgress(nProgress);
            nPreviousProgress = nProgress;
        }
        zos.write('\n');

        if (!f.delete()) {
            f.deleteOnExit();
            LOG.info("Unable to delete tmp export file " + f.getAbsolutePath());
        }
    }
    warningFileWriter.close();

    zos.putNextEntry(new ZipEntry(exportName + ".map"));

    int avgObjSize = (Integer) mongoTemplate
            .getCollection(mongoTemplate.getCollectionName(VariantRunData.class)).getStats().get("avgObjSize");
    int nChunkSize = nMaxChunkSizeInMb * 1024 * 1024 / avgObjSize;

    markerCursor.batchSize(nChunkSize);
    int nMarkerIndex = 0;
    while (markerCursor.hasNext()) {
        DBObject exportVariant = markerCursor.next();
        DBObject refPos = (DBObject) exportVariant.get(VariantData.FIELDNAME_REFERENCE_POSITION);
        Comparable markerId = (Comparable) exportVariant.get("_id");
        String chrom = (String) refPos.get(ReferencePosition.FIELDNAME_SEQUENCE);
        Long pos = ((Number) refPos.get(ReferencePosition.FIELDNAME_START_SITE)).longValue();

        if (chrom == null)
            LOG.warn("Chromosomal position not found for marker " + markerId);
        Comparable exportedId = markerSynonyms == null ? markerId : markerSynonyms.get(markerId);
        zos.write(((chrom == null ? "0" : chrom) + " " + exportedId + " " + 0 + " " + (pos == null ? 0 : pos)
                + LINE_SEPARATOR).getBytes());

        if (problematicMarkerIndexToNameMap.containsKey(nMarkerIndex)) { // we are going to need this marker's name for the warning file
            Comparable variantName = markerId;
            if (markerSynonyms != null) {
                Comparable syn = markerSynonyms.get(markerId);
                if (syn != null)
                    variantName = syn;
            }
            problematicMarkerIndexToNameMap.put(nMarkerIndex, variantName);
        }
        nMarkerIndex++;
    }

    if (warningFile.length() > 0) {
        zos.putNextEntry(new ZipEntry(exportName + "-REMARKS.txt"));
        int nWarningCount = 0;
        BufferedReader in = new BufferedReader(new FileReader(warningFile));
        String sLine;
        while ((sLine = in.readLine()) != null) {
            for (Integer aMarkerIndex : problematicMarkerIndexToNameMap.keySet())
                sLine = sLine.replaceAll("__" + aMarkerIndex + "__",
                        problematicMarkerIndexToNameMap.get(aMarkerIndex).toString());
            zos.write((sLine + "\n").getBytes());
            in.readLine();
            nWarningCount++;
        }
        LOG.info("Number of Warnings for export (" + exportName + "): " + nWarningCount);
        in.close();
    }
    warningFile.delete();

    zos.close();
    progress.setCurrentStepProgress((short) 100);
}

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