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.markeroriented.GFFExportHandler.java

@Override
public void exportData(OutputStream outputStream, String sModule, List<SampleId> sampleIDs,
        ProgressIndicator progress, DBCursor markerCursor, Map<Comparable, Comparable> markerSynonyms,
        int nMinimumGenotypeQuality, int nMinimumReadDepth, Map<String, InputStream> readyToExportFiles)
        throws Exception {
    MongoTemplate mongoTemplate = MongoTemplateManager.get(sModule);
    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);
            }//w ww .ja  v  a 2s  . c  o  m
        }

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

    int markerCount = markerCursor.count();

    List<Individual> individuals = getIndividualsFromSamples(sModule, sampleIDs);
    ArrayList<String> individualList = new ArrayList<String>();
    for (int i = 0; i < sampleIDs.size(); i++) {
        Individual individual = individuals.get(i);
        if (!individualList.contains(individual.getId())) {
            individualList.add(individual.getId());
        }
    }

    String exportName = sModule + "_" + markerCount + "variants_" + individualList.size() + "individuals";
    zos.putNextEntry(new ZipEntry(exportName + ".gff3"));
    String header = "##gff-version 3" + LINE_SEPARATOR;
    zos.write(header.getBytes());

    TreeMap<String, String> typeToOntology = new TreeMap<String, String>();
    typeToOntology.put(Type.SNP.toString(), "SO:0000694");
    typeToOntology.put(Type.INDEL.toString(), "SO:1000032");
    typeToOntology.put(Type.MIXED.toString(), "SO:0001059");
    typeToOntology.put(Type.SYMBOLIC.toString(), "SO:0000109");
    typeToOntology.put(Type.MNP.toString(), "SO:0001059");

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

    while (markerCursor.hasNext()) {
        int nLoadedMarkerCountInLoop = 0;
        Map<Comparable, String> markerChromosomalPositions = new LinkedHashMap<Comparable, String>();
        boolean fStartingNewChunk = true;
        markerCursor.batchSize(nChunkSize);
        while (markerCursor.hasNext() && (fStartingNewChunk || nLoadedMarkerCountInLoop % nChunkSize != 0)) {
            DBObject exportVariant = markerCursor.next();
            DBObject refPos = (DBObject) exportVariant.get(VariantData.FIELDNAME_REFERENCE_POSITION);
            markerChromosomalPositions.put((Comparable) exportVariant.get("_id"),
                    refPos.get(ReferencePosition.FIELDNAME_SEQUENCE) + ":"
                            + refPos.get(ReferencePosition.FIELDNAME_START_SITE));
            nLoadedMarkerCountInLoop++;
            fStartingNewChunk = false;
        }

        List<Comparable> currentMarkers = new ArrayList<Comparable>(markerChromosomalPositions.keySet());
        LinkedHashMap<VariantData, Collection<VariantRunData>> variantsAndRuns = MgdbDao.getSampleGenotypes(
                mongoTemplate, sampleIDs, currentMarkers, true,
                null /*new Sort(VariantData.FIELDNAME_REFERENCE_POSITION + "." + ChromosomalPosition.FIELDNAME_SEQUENCE).and(new Sort(VariantData.FIELDNAME_REFERENCE_POSITION + "." + ChromosomalPosition.FIELDNAME_START_SITE))*/); // query mongo db for matching genotypes
        for (VariantData variant : variantsAndRuns.keySet()) // read data and write results into temporary files (one per sample)
        {
            Comparable variantId = variant.getId();
            List<String> variantDataOrigin = new ArrayList<String>();

            Map<String, Integer> gqValueForSampleId = new LinkedHashMap<String, Integer>();
            Map<String, Integer> dpValueForSampleId = new LinkedHashMap<String, Integer>();
            Map<String, List<String>> individualGenotypes = new LinkedHashMap<String, List<String>>();
            List<String> chromAndPos = Helper.split(markerChromosomalPositions.get(variantId), ":");
            if (chromAndPos.size() == 0)
                LOG.warn("Chromosomal position not found for marker " + variantId);
            // LOG.debug(marker + "\t" + (chromAndPos.length == 0 ? "0" : chromAndPos[0]) + "\t" + 0 + "\t" + (chromAndPos.length == 0 ? 0l : Long.parseLong(chromAndPos[1])) + LINE_SEPARATOR);
            if (markerSynonyms != null) {
                Comparable syn = markerSynonyms.get(variantId);
                if (syn != null)
                    variantId = syn;
            }

            Collection<VariantRunData> runs = variantsAndRuns.get(variant);
            if (runs != null)
                for (VariantRunData run : runs)
                    for (Integer sampleIndex : run.getSampleGenotypes().keySet()) {
                        SampleGenotype sampleGenotype = run.getSampleGenotypes().get(sampleIndex);
                        String individualId = individuals
                                .get(sampleIDs.indexOf(new SampleId(run.getId().getProjectId(), sampleIndex)))
                                .getId();

                        Integer gq = null;
                        try {
                            gq = (Integer) sampleGenotype.getAdditionalInfo().get(VariantData.GT_FIELD_GQ);
                        } catch (Exception ignored) {
                        }
                        if (gq != null && gq < nMinimumGenotypeQuality)
                            continue;

                        Integer dp = null;
                        try {
                            dp = (Integer) sampleGenotype.getAdditionalInfo().get(VariantData.GT_FIELD_DP);
                        } catch (Exception ignored) {
                        }
                        if (dp != null && dp < nMinimumReadDepth)
                            continue;

                        String gtCode = sampleGenotype.getCode();
                        List<String> storedIndividualGenotypes = individualGenotypes.get(individualId);
                        if (storedIndividualGenotypes == null) {
                            storedIndividualGenotypes = new ArrayList<String>();
                            individualGenotypes.put(individualId, storedIndividualGenotypes);
                        }
                        storedIndividualGenotypes.add(gtCode);
                    }

            zos.write((chromAndPos.get(0) + "\t" + StringUtils.join(variantDataOrigin, ";") /*source*/ + "\t"
                    + typeToOntology.get(variant.getType()) + "\t" + Long.parseLong(chromAndPos.get(1)) + "\t"
                    + Long.parseLong(chromAndPos.get(1)) + "\t" + "." + "\t" + "+" + "\t" + "." + "\t")
                            .getBytes());
            Comparable syn = markerSynonyms == null ? null : markerSynonyms.get(variant.getId());
            zos.write(("ID=" + variant.getId() + ";" + (syn != null ? "Name=" + syn + ";" : "") + "alleles="
                    + StringUtils.join(variant.getKnownAlleleList(), "/") + ";" + "refallele="
                    + variant.getKnownAlleleList().get(0) + ";").getBytes());

            for (int j = 0; j < individualList
                    .size(); j++ /* we use this list because it has the proper ordering*/) {

                NumberFormat nf = NumberFormat.getInstance(Locale.US);
                nf.setMaximumFractionDigits(4);
                HashMap<String, Integer> compt1 = new HashMap<String, Integer>();
                int highestGenotypeCount = 0;
                int sum = 0;

                String individualId = individualList.get(j);
                List<String> genotypes = individualGenotypes.get(individualId);
                HashMap<Object, Integer> genotypeCounts = new HashMap<Object, Integer>(); // will help us to keep track of missing genotypes

                String mostFrequentGenotype = null;
                if (genotypes != null)
                    for (String genotype : genotypes) {
                        if (genotype.length() == 0)
                            continue; /* skip missing genotypes */

                        int count = 0;
                        for (String t : variant.getAllelesFromGenotypeCode(genotype)) {
                            for (String t1 : variant.getKnownAlleleList()) {
                                if (t.equals(t1) && !(compt1.containsKey(t1))) {
                                    count++;
                                    compt1.put(t1, count);
                                } else if (t.equals(t1) && compt1.containsKey(t1)) {
                                    if (compt1.get(t1) != 0) {
                                        count++;
                                        compt1.put(t1, count);
                                    } else
                                        compt1.put(t1, count);
                                } else if (!(compt1.containsKey(t1))) {
                                    compt1.put(t1, 0);
                                }
                            }
                        }
                        for (int countValue : compt1.values()) {
                            sum += countValue;
                        }

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

                List<String> alleles = mostFrequentGenotype == null ? new ArrayList<String>()
                        : variant.getAllelesFromGenotypeCode(mostFrequentGenotype);

                if (alleles.size() != 0) {
                    zos.write(("acounts=" + individualId + ":").getBytes());

                    for (String knowAllelesCompt : compt1.keySet()) {
                        zos.write(
                                (knowAllelesCompt + " " + nf.format(compt1.get(knowAllelesCompt) / (float) sum)
                                        + " " + compt1.get(knowAllelesCompt) + " ").getBytes());
                    }
                    zos.write((alleles.size() + ";").getBytes());
                }
                if (genotypeCounts.size() > 1) {
                    Comparable sVariantId = markerSynonyms != null ? markerSynonyms.get(variant.getId())
                            : variant.getId();
                    warningFileWriter.write("- Dissimilar genotypes found for variant "
                            + (sVariantId == null ? variant.getId() : sVariantId) + ", individual "
                            + individualId + ". Exporting most frequent: " + StringUtils.join(alleles, ",")
                            + "\n");
                }
            }
            zos.write((LINE_SEPARATOR).getBytes());
        }

        if (progress.hasAborted())
            return;

        nLoadedMarkerCount += nLoadedMarkerCountInLoop;
        nProgress = (short) (nLoadedMarkerCount * 100 / markerCount);
        if (nProgress > nPreviousProgress) {
            //            if (nProgress%5 == 0)
            //               LOG.info("========================= exportData: " + nProgress + "% =========================" + (System.currentTimeMillis() - before)/1000 + "s");
            progress.setCurrentStepProgress(nProgress);
            nPreviousProgress = nProgress;
        }
    }

    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) {
            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:org.pdfgal.pdfgalweb.utils.impl.ZipUtilsImpl.java

/**
 * Adds a new file to the {@link ZipOutputStream}.
 * //  ww w.  jav  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);
}

From source file:org.openremote.beehive.configuration.www.UsersAPI.java

private void writeZipEntry(ZipOutputStream zipOutput, File file, java.nio.file.Path basePath)
        throws IOException {
    ZipEntry entry = new ZipEntry(basePath.relativize(file.toPath()).toString());
    entry.setSize(file.length());//ww w. j  a  v  a 2 s.c o  m
    entry.setTime(file.lastModified());
    zipOutput.putNextEntry(entry);

    IOUtils.copy(new FileInputStream(file), zipOutput);

    zipOutput.flush();
    zipOutput.closeEntry();
}

From source file:com.qwazr.tools.ArchiverTool.java

public void addToZipFile(String entryName, String filePath, ZipOutputStream zos) throws IOException {

    File srcFile = new File(filePath);
    if (!srcFile.exists())
        throw new FileNotFoundException("The file does not exists: " + srcFile.getPath());
    FileInputStream fis = new FileInputStream(srcFile);
    try {//w  w  w. j av a  2 s  .  com
        ZipEntry zipEntry = new ZipEntry(entryName);
        zos.putNextEntry(zipEntry);
        IOUtils.copy(fis, zos);
        zos.closeEntry();
    } finally {
        IOUtils.closeQuietly(fis);
    }
}

From source file:com.asual.summer.bundle.BundleDescriptorMojo.java

private void zip(File directory, File base, ZipOutputStream zos) throws IOException {
    File[] files = directory.listFiles();
    byte[] buffer = new byte[8192];
    int read = 0;
    for (int i = 0, n = files.length; i < n; i++) {
        String name = files[i].getPath().replace(File.separatorChar, '/')
                .substring(base.getPath().length() + 1);
        if (files[i].isDirectory()) {
            if (!name.endsWith("/")) {
                name = name + "/";
            }/* www.j a  v a 2 s .  co  m*/
            ZipEntry entry = new ZipEntry(name);
            zos.putNextEntry(entry);
            zip(files[i], base, zos);
        } else {
            FileInputStream in = new FileInputStream(files[i]);
            ZipEntry entry = new ZipEntry(name);
            zos.putNextEntry(entry);
            while (-1 != (read = in.read(buffer))) {
                zos.write(buffer, 0, read);
            }
            in.close();
        }
    }
}

From source file:dpfmanager.shell.interfaces.console.CommonController.java

private void compressDirectoryToZipfile(String rootDir, String sourceDir, ZipOutputStream out)
        throws IOException, FileNotFoundException {
    for (File file : new File(sourceDir).listFiles()) {
        if (file.isDirectory()) {
            compressDirectoryToZipfile(rootDir, sourceDir + file.getName() + File.separator, out);
        } else {/*from w  w w  . j  a va2s  .co m*/
            ZipEntry entry = new ZipEntry(sourceDir.replace(rootDir, "") + file.getName());
            out.putNextEntry(entry);

            FileInputStream in = new FileInputStream(sourceDir + file.getName());
            IOUtils.copy(in, out);
            IOUtils.closeQuietly(in);
        }
    }
}

From source file:com.wavemaker.tools.project.StageDeploymentManager.java

protected void assembleEar(Map<String, Object> properties, com.wavemaker.tools.io.File warFile) {
    ZipOutputStream out;
    InputStream is;/*from w w w.j a va  2  s .co  m*/
    try {
        com.wavemaker.tools.io.File earFile = (com.wavemaker.tools.io.File) properties
                .get(EAR_FILE_NAME_PROPERTY);
        out = new ZipOutputStream(earFile.getContent().asOutputStream());
        out.putNextEntry(new ZipEntry(warFile.getName()));
        is = warFile.getContent().asInputStream();
        org.apache.commons.io.IOUtils.copy(is, out);
        out.closeEntry();
        is.close();

        Folder webInf = ((Folder) properties.get(BUILD_WEBAPPROOT_PROPERTY)).getFolder("WEB-INF");
        com.wavemaker.tools.io.File appXml = webInf.getFile("application.xml");
        out.putNextEntry(new ZipEntry("META-INF/" + appXml.getName()));
        is = appXml.getContent().asInputStream();
        org.apache.commons.io.IOUtils.copy(is, out);
        out.closeEntry();
        is.close();

        String maniFest = "Manifest-Version: 1.0\n" + "Created-By: WaveMaker Studio (CloudJee Inc.)";
        out.putNextEntry(new ZipEntry("META-INF/MANIFEST.MF"));
        org.apache.commons.io.IOUtils.write(maniFest, out);
        out.closeEntry();
        is.close();
        out.close();
    } catch (IOException ex) {
        throw new WMRuntimeException(ex);
    }
}

From source file:com.liferay.ide.server.remote.AbstractRemoteServerPublisher.java

public IPath publishModuleDelta(String archiveName, IModuleResourceDelta[] deltas, String deletePrefix,
        boolean adjustGMTOffset) throws CoreException {
    IPath path = LiferayServerCore.getTempLocation("partial-war", archiveName); //$NON-NLS-1$

    FileOutputStream outputStream = null;
    ZipOutputStream zip = null;
    File warfile = path.toFile();

    warfile.getParentFile().mkdirs();/*from   w w w.j a  v  a  2s  .c  om*/

    try {
        outputStream = new FileOutputStream(warfile);
        zip = new ZipOutputStream(outputStream);

        Map<ZipEntry, String> deleteEntries = new HashMap<ZipEntry, String>();

        processResourceDeltas(deltas, zip, deleteEntries, deletePrefix, StringPool.EMPTY, adjustGMTOffset);

        for (ZipEntry entry : deleteEntries.keySet()) {
            zip.putNextEntry(entry);
            zip.write(deleteEntries.get(entry).getBytes());
        }

        // if ((removedResources != null) && (removedResources.size() > 0)) {
        // writeRemovedResources(removedResources, zip);
        // }
    } catch (Exception ex) {
        ex.printStackTrace();
    } finally {
        if (zip != null) {
            try {
                zip.close();
            } catch (IOException localIOException1) {

            }
        }
    }

    return new Path(warfile.getAbsolutePath());
}

From source file:com.metamx.druid.loading.S3SegmentPusher.java

@Override
public DataSegment push(File file, DataSegment segment) throws IOException {
    log.info("Uploading [%s] to S3", file);
    String outputKey = JOINER.join(config.getBaseKey().isEmpty() ? null : config.getBaseKey(),
            segment.getDataSource(),/*from   ww  w  . ja v  a  2 s.c  o  m*/
            String.format("%s_%s", segment.getInterval().getStart(), segment.getInterval().getEnd()),
            segment.getVersion(), segment.getShardSpec().getPartitionNum());

    File indexFilesDir = file;

    long indexSize = 0;
    final File zipOutFile = File.createTempFile("druid", "index.zip");
    ZipOutputStream zipOut = null;
    try {
        zipOut = new ZipOutputStream(new FileOutputStream(zipOutFile));
        File[] indexFiles = indexFilesDir.listFiles();
        for (File indexFile : indexFiles) {
            log.info("Adding indexFile[%s] with size[%,d].  Total size[%,d]", indexFile, indexFile.length(),
                    indexSize);
            if (indexFile.length() >= Integer.MAX_VALUE) {
                throw new ISE("indexFile[%s] too large [%,d]", indexFile, indexFile.length());
            }
            zipOut.putNextEntry(new ZipEntry(indexFile.getName()));
            IOUtils.copy(new FileInputStream(indexFile), zipOut);
            indexSize += indexFile.length();
        }
    } finally {
        Closeables.closeQuietly(zipOut);
    }

    try {
        S3Object toPush = new S3Object(zipOutFile);

        final String outputBucket = config.getBucket();
        toPush.setBucketName(outputBucket);
        toPush.setKey(outputKey + "/index.zip");

        log.info("Pushing %s.", toPush);
        s3Client.putObject(outputBucket, toPush);

        DataSegment outputSegment = segment.withSize(indexSize).withLoadSpec(ImmutableMap
                .<String, Object>of("type", "s3_zip", "bucket", outputBucket, "key", toPush.getKey()));

        File descriptorFile = File.createTempFile("druid", "descriptor.json");
        StreamUtils.copyToFileAndClose(new ByteArrayInputStream(jsonMapper.writeValueAsBytes(segment)),
                descriptorFile);
        S3Object descriptorObject = new S3Object(descriptorFile);
        descriptorObject.setBucketName(outputBucket);
        descriptorObject.setKey(outputKey + "/descriptor.json");

        log.info("Pushing %s", descriptorObject);
        s3Client.putObject(outputBucket, descriptorObject);

        log.info("Deleting Index File[%s]", indexFilesDir);
        FileUtils.deleteDirectory(indexFilesDir);

        log.info("Deleting zipped index File[%s]", zipOutFile);
        zipOutFile.delete();

        log.info("Deleting descriptor file[%s]", descriptorFile);
        descriptorFile.delete();

        return outputSegment;
    } catch (NoSuchAlgorithmException e) {
        throw new IOException(e);
    } catch (S3ServiceException e) {
        throw new IOException(e);
    }
}

From source file:com.cisco.ca.cstg.pdi.services.ConfigurationServiceImpl.java

private void addToZipOutputStream(String filePath, ZipOutputStream zip) throws IOException {
    byte[] buf = new byte[1024];
    int len;//from  www .jav a 2s.c  o m
    File input = new File(filePath);
    try (FileInputStream in = new FileInputStream(input)) {
        zip.putNextEntry(new ZipEntry(input.getName()));
        while ((len = in.read(buf)) > 0) {
            zip.write(buf, 0, len);
        }
        zip.flush();
    }
}