Example usage for java.util.zip ZipOutputStream putNextEntry

List of usage examples for java.util.zip ZipOutputStream putNextEntry

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Introduction

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

Prototype

public void putNextEntry(ZipEntry e) throws IOException

Source Link

Document

Begins writing a new ZIP file entry and positions the stream to the start of the entry data.

Usage

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 w w  .j  ava  2s  . c  o 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);
}

From source file:be.neutrinet.ispng.vpn.api.VPNClientConfig.java

protected Representation finalizeZip(List<String> config, ZipOutputStream zip, ByteArrayOutputStream baos)
        throws Exception {
    String file = "";
    for (String s : config) {
        file += s + '\n';
    }/*from  www.  jav  a2  s  .co m*/

    if (caCert == null) {
        caCert = IOUtils.toByteArray(new FileInputStream(VPN.cfg.getProperty("ca.crt")));
    }

    ZipEntry configFile = new ZipEntry("neutrinet.ovpn");
    configFile.setCreationTime(FileTime.from(Instant.now()));
    zip.putNextEntry(configFile);
    zip.write(file.getBytes());
    zip.putNextEntry(new ZipEntry("ca.crt"));
    zip.write(caCert);

    zip.close();

    ByteArrayRepresentation rep = new ByteArrayRepresentation(baos.toByteArray());
    rep.setMediaType(MediaType.APPLICATION_ZIP);
    rep.setSize(baos.size());
    rep.setCharacterSet(CharacterSet.UTF_8);
    rep.setDisposition(new Disposition(Disposition.TYPE_ATTACHMENT));
    return rep;
}

From source file:fr.cirad.mgdb.exporting.individualoriented.DARwinExportHandler.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 {
    MongoTemplate mongoTemplate = MongoTemplateManager.get(sModule);
    GenotypingProject aProject = mongoTemplate.findOne(
            new Query(Criteria.where(GenotypingProject.FIELDNAME_PLOIDY_LEVEL).exists(true)),
            GenotypingProject.class);
    if (aProject == null)
        LOG.warn("Unable to find a project containing ploidy level information! Assuming ploidy level is 2.");

    int ploidy = aProject == null ? 2 : aProject.getPloidyLevel();

    File warningFile = File.createTempFile("export_warnings_", "");
    FileWriter warningFileWriter = new FileWriter(warningFile);

    int markerCount = markerCursor.count();

    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);
            }//  ww w . j a  va 2 s  . com
        }

    String exportName = sModule + "_" + markerCount + "variants_" + individualExportFiles.size()
            + "individuals";

    StringBuffer donFileContents = new StringBuffer(
            "@DARwin 5.0 - DON -" + LINE_SEPARATOR + individualExportFiles.size() + "\t" + 1 + LINE_SEPARATOR
                    + "N" + "\t" + "individual" + LINE_SEPARATOR);

    int count = 0;
    String missingGenotype = "";
    for (int j = 0; j < ploidy; j++)
        missingGenotype += "\tN";

    zos.putNextEntry(new ZipEntry(exportName + ".var"));
    zos.write(("@DARwin 5.0 - ALLELIC - " + ploidy + LINE_SEPARATOR + individualExportFiles.size() + "\t"
            + markerCount * ploidy + LINE_SEPARATOR + "N").getBytes());

    DBCursor markerCursorCopy = markerCursor.copy(); // dunno how expensive this is, but seems safer than keeping all IDs in memory at any time

    short nProgress = 0, nPreviousProgress = 0;
    int avgObjSize = (Integer) mongoTemplate
            .getCollection(mongoTemplate.getCollectionName(VariantRunData.class)).getStats().get("avgObjSize");
    int nChunkSize = nMaxChunkSizeInMb * 1024 * 1024 / avgObjSize;
    markerCursorCopy.batchSize(nChunkSize);

    int nMarkerIndex = 0;
    while (markerCursorCopy.hasNext()) {
        DBObject exportVariant = markerCursorCopy.next();
        Comparable markerId = (Comparable) exportVariant.get("_id");

        if (markerSynonyms != null) {
            Comparable syn = markerSynonyms.get(markerId);
            if (syn != null)
                markerId = syn;
        }
        for (int j = 0; j < ploidy; j++)
            zos.write(("\t" + markerId).getBytes());
    }

    TreeMap<Integer, Comparable> problematicMarkerIndexToNameMap = new TreeMap<Integer, Comparable>();
    ArrayList<String> distinctAlleles = new ArrayList<String>(); // the index of each allele will be used as its code
    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;
            else
                throw new Exception("Unable to read first line of temp export file " + f.getName());

            donFileContents.append(++count + "\t" + individualId + LINE_SEPARATOR);

            zos.write((LINE_SEPARATOR + count).getBytes());
            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 codedGenotype = "";
                if (mostFrequentGenotype != null)
                    for (String allele : mostFrequentGenotype.split(" ")) {
                        if (!distinctAlleles.contains(allele))
                            distinctAlleles.add(allele);
                        codedGenotype += "\t" + distinctAlleles.indexOf(allele);
                    }
                else
                    codedGenotype = missingGenotype.replaceAll("N", "-1"); // missing data is coded as -1
                zos.write(codedGenotype.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) {
            //            LOG.debug("============= doDARwinExport (" + i + "): " + nProgress + "% =============");
            progress.setCurrentStepProgress(nProgress);
            nPreviousProgress = nProgress;
        }

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

    zos.putNextEntry(new ZipEntry(exportName + ".don"));
    zos.write(donFileContents.toString().getBytes());

    // now read variant names for those that induced warnings
    nMarkerIndex = 0;
    markerCursor.batchSize(nChunkSize);
    while (markerCursor.hasNext()) {
        DBObject exportVariant = markerCursor.next();
        if (problematicMarkerIndexToNameMap.containsKey(nMarkerIndex)) {
            Comparable markerId = (Comparable) exportVariant.get("_id");

            if (markerSynonyms != null) {
                Comparable syn = markerSynonyms.get(markerId);
                if (syn != null)
                    markerId = syn;
            }
            for (int j = 0; j < ploidy; j++)
                zos.write(("\t" + markerId).getBytes());

            problematicMarkerIndexToNameMap.put(nMarkerIndex, markerId);
        }
    }

    warningFileWriter.close();
    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);
}

From source file:nc.noumea.mairie.appock.services.impl.ExportExcelServiceImpl.java

private void addToZipFile(File file, String nomFichier, ZipOutputStream zos) throws IOException {
    FileInputStream fis = new FileInputStream(file);
    ZipEntry zipEntry = new ZipEntry(nomFichier);
    zos.putNextEntry(zipEntry);

    byte[] bytes = new byte[1024];
    int length;// w ww .  ja v a  2  s .  co m
    while ((length = fis.read(bytes)) >= 0) {
        zos.write(bytes, 0, length);
    }

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

From source file:de.mpg.imeji.logic.export.format.ZIPExport.java

/**
 * This method exports all images of the current browse page as a zip file
 * /*from   w  ww .ja  v a2 s. c o m*/
 * @throws Exception
 * @throws URISyntaxException
 */
public void exportAllImages(SearchResult sr, OutputStream out) throws URISyntaxException, Exception {
    List<String> source = sr.getResults();
    ZipOutputStream zip = new ZipOutputStream(out);
    try {
        // Create the ZIP file
        for (int i = 0; i < source.size(); i++) {
            SessionBean session = (SessionBean) BeanHelper.getSessionBean(SessionBean.class);
            ItemController ic = new ItemController(session.getUser());
            Item item = ic.retrieve(new URI(source.get(i)));
            StorageController sc = new StorageController();
            try {
                zip.putNextEntry(new ZipEntry(item.getFilename()));
                sc.read(item.getFullImageUrl().toString(), zip, false);
                // Complete the entry
                zip.closeEntry();
            } catch (ZipException ze) {
                if (ze.getMessage().contains("duplicate entry")) {
                    String name = i + "_" + item.getFilename();
                    zip.putNextEntry(new ZipEntry(name));
                    sc.read(item.getFullImageUrl().toString(), zip, false);
                    // Complete the entry
                    zip.closeEntry();
                }
            }
        }
    } catch (IOException e) {
        e.printStackTrace();
    } finally {
        // Complete the ZIP file
        zip.close();
    }
}

From source file:com.googlecode.clearnlp.component.AbstractStatisticalComponent.java

/** Called by {@link AbstractStatisticalComponent#saveModels(ZipOutputStream)}}. */
protected void saveStatisticalModels(ZipOutputStream zout, String entryName) throws Exception {
    int i, size = s_models.length;
    PrintStream fout;/*from w  ww  .j  a  v a2s  . c om*/

    for (i = 0; i < size; i++) {
        zout.putNextEntry(new ZipEntry(entryName + i));
        fout = UTOutput.createPrintBufferedStream(zout);
        s_models[i].save(fout);
        fout.flush();
        zout.closeEntry();
    }
}

From source file:com.taobao.android.builder.tools.asm.ClazzBasicHandler.java

protected void copyStreamToJar(InputStream zin, ZipOutputStream out, String currentName, long fileTime)
        throws IOException {
    // Create new entry for zip file.

    ZipEntry newEntry = new ZipEntry(currentName);
    // Make sure there is date and time set.
    if (fileTime != -1) {
        newEntry.setTime(fileTime); // If found set it into output file.
    }/*w w  w .  ja v  a  2 s. c  o  m*/
    out.putNextEntry(newEntry);
    if (zin != null) {
        IOUtils.copy(zin, out);
    }
    IOUtils.closeQuietly(zin);

}

From source file:io.fabric8.maven.generator.springboot.SpringBootGenerator.java

private void copyFilesToFatJar(List<File> libs, List<File> classes, File target) throws IOException {
    File tmpZip = File.createTempFile(target.getName(), null);
    tmpZip.delete();/*from   w w  w .  j a v a  2s  .  com*/

    // Using Apache commons rename, because renameTo has issues across file systems
    FileUtils.moveFile(target, tmpZip);

    byte[] buffer = new byte[8192];
    ZipInputStream zin = new ZipInputStream(new FileInputStream(tmpZip));
    ZipOutputStream out = new ZipOutputStream(new FileOutputStream(target));
    for (ZipEntry ze = zin.getNextEntry(); ze != null; ze = zin.getNextEntry()) {
        if (matchesFatJarEntry(libs, ze.getName(), true) || matchesFatJarEntry(classes, ze.getName(), false)) {
            continue;
        }
        out.putNextEntry(ze);
        for (int read = zin.read(buffer); read > -1; read = zin.read(buffer)) {
            out.write(buffer, 0, read);
        }
        out.closeEntry();
    }

    for (File lib : libs) {
        try (InputStream in = new FileInputStream(lib)) {
            out.putNextEntry(createZipEntry(lib, getFatJarFullPath(lib, true)));
            for (int read = in.read(buffer); read > -1; read = in.read(buffer)) {
                out.write(buffer, 0, read);
            }
            out.closeEntry();
        }
    }

    for (File cls : classes) {
        try (InputStream in = new FileInputStream(cls)) {
            out.putNextEntry(createZipEntry(cls, getFatJarFullPath(cls, false)));
            for (int read = in.read(buffer); read > -1; read = in.read(buffer)) {
                out.write(buffer, 0, read);
            }
            out.closeEntry();
        }
    }

    out.close();
    tmpZip.delete();
}

From source file:com.googlecode.clearnlp.component.AbstractStatisticalComponent.java

protected void saveWeightVector(ZipOutputStream zout, String entryName) throws Exception {
    int i, size = s_models.length;
    ObjectOutputStream oout;/*from   www.j av  a2 s .  c om*/

    for (i = 0; i < size; i++) {
        zout.putNextEntry(new ZipEntry(entryName + i));
        oout = new ObjectOutputStream(new BufferedOutputStream(zout));
        s_models[i].saveWeightVector(oout);
        oout.flush();
        zout.closeEntry();
    }
}

From source file:ZipUtilTest.java

public void testUnpackEntryFromFile() throws IOException {
    final String name = "foo";
    final byte[] contents = "bar".getBytes();

    File file = File.createTempFile("temp", null);
    try {/*from w w w.  j  av  a  2s  .  c o  m*/
        // Create the ZIP file
        ZipOutputStream zos = new ZipOutputStream(new FileOutputStream(file));
        try {
            zos.putNextEntry(new ZipEntry(name));
            zos.write(contents);
            zos.closeEntry();
        } finally {
            IOUtils.closeQuietly(zos);
        }

        // Test the ZipUtil
        byte[] actual = ZipUtil.unpackEntry(file, name);
        assertNotNull(actual);
        assertEquals(new String(contents), new String(actual));
    } finally {
        FileUtils.deleteQuietly(file);
    }
}