Example usage for java.util.zip ZipEntry ZipEntry

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

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Introduction

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

Prototype

public ZipEntry(ZipEntry e)

Source Link

Document

Creates a new zip entry with fields taken from the specified zip entry.

Usage

From source file:com.googlecode.dex2jar.v3.Dex2jar.java

private void check(String dir, ZipOutputStream zos) throws IOException {
    if (dirs.contains(dir)) {
        return;/* w  ww . ja  v a  2 s  .c  o  m*/
    }
    dirs.add(dir);
    int i = dir.lastIndexOf('/');
    if (i > 0) {
        check(dir.substring(0, i), zos);
    }
    zos.putNextEntry(new ZipEntry(dir + "/"));
    zos.closeEntry();
}

From source file:com.rover12421.shaka.apktool.lib.AndrolibResourcesAj.java

/**
 * ??//from  ww  w.j  av  a  2s .  co m
 */
private void fuckNotDefinedRes_clearAddRes(File apkFile) throws IOException, ShakaException {
    if (notDefinedRes.size() <= 0) {
        return;
    }

    File tempFile = File.createTempFile(apkFile.getName(), null);
    tempFile.delete();
    tempFile.deleteOnExit();
    boolean renameOk = apkFile.renameTo(tempFile);
    if (!renameOk) {
        throw new ShakaException(
                "could not rename the file " + apkFile.getAbsolutePath() + " to " + tempFile.getAbsolutePath());
    }

    try (ZipInputStream zin = new ZipInputStream(new FileInputStream(tempFile));
            ZipOutputStream zout = new ZipOutputStream(new FileOutputStream(apkFile))) {
        ZipEntry entry = zin.getNextEntry();
        while (entry != null) {
            String name = entry.getName();
            boolean toBeDeleted = false;
            for (String f : notDefinedRes) {
                if (f.equals(name)) {
                    toBeDeleted = true;
                    LogHelper.warning("Delete temp res : " + f);
                    break;
                }
            }
            if (!toBeDeleted) {
                // Add ZIP entry to output stream.
                zout.putNextEntry(new ZipEntry(name));
                // Transfer bytes from the ZIP file to the output file
                IOUtils.copy(zin, zout);
            }
            entry = zin.getNextEntry();
        }
    }

    tempFile.delete();
    notDefinedRes.clear();
}

From source file:com.mgmtp.jfunk.common.util.ExtendedFile.java

private void zip(String prefix, final File file, final ZipOutputStream zipOut) throws IOException {
    if (file.isDirectory()) {
        prefix = prefix + file.getName() + '/';
        for (File child : file.listFiles()) {
            zip(prefix, child, zipOut);/*  www  . ja v  a2s . c  o m*/
        }
    } else {
        FileInputStream in = null;
        try {
            in = new FileInputStream(file);
            zipOut.putNextEntry(new ZipEntry(prefix + file.getName()));
            IOUtils.copy(in, zipOut);
        } finally {
            IOUtils.closeQuietly(in);
            zipOut.flush();
            zipOut.closeEntry();
        }
    }
}

From source file:com.intuit.tank.service.impl.v1.agent.AgentServiceV1.java

private void addFileToZip(String name, InputStream in, ZipOutputStream zip) throws Exception {
    try {/*from   w w w  .  jav  a2  s .c o m*/
        zip.putNextEntry(new ZipEntry(name));
        IOUtils.copy(in, zip);
    } finally {
        IOUtils.closeQuietly(in);
    }
}

From source file:eu.esdihumboldt.hale.io.appschema.writer.AppSchemaMappingUploader.java

private byte[] writeContent(String mappingFileName, ContentType contentType, ProgressIndicator progress,
        IOReporter reporter) throws IOException {
    try (ByteArrayOutputStream bos = new ByteArrayOutputStream()) {
        if (contentType.equals(DataStoreFile.ZIP_CONTENT_TYPE)) {
            try (ZipOutputStream zos = new ZipOutputStream(bos)) {
                if (includeTargetSchema) {
                    // add target schema to zip
                    addTargetSchemaToZip(zos, null, progress, reporter);
                }//from w w  w  .  j  ava 2 s  .  co  m
                // main mapping configuration file
                zos.putNextEntry(new ZipEntry(mappingFileName + ".appschema"));
                generator.writeMappingConf(zos);
                zos.closeEntry();
                if (generator.getGeneratedMapping().requiresMultipleFiles()) {
                    zos.putNextEntry(new ZipEntry(AppSchemaIO.INCLUDED_TYPES_MAPPING_FILE));
                    generator.writeIncludedTypesMappingConf(zos);
                    zos.closeEntry();
                }
            }
        } else {
            generator.writeMappingConf(bos);
        }

        return bos.toByteArray();
    }
}

From source file:fr.cirad.mgdb.exporting.markeroriented.EigenstratExportHandler.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 {
    // long before = System.currentTimeMillis();

    File warningFile = File.createTempFile("export_warnings_", "");
    FileWriter warningFileWriter = new FileWriter(warningFile);
    File snpFile = null;//from w w  w. ja  v  a  2  s .  co m

    try {
        snpFile = File.createTempFile("snpFile", "");
        FileWriter snpFileWriter = new FileWriter(snpFile);

        ZipOutputStream zos = new ZipOutputStream(outputStream);
        if (ByteArrayOutputStream.class.isAssignableFrom(outputStream.getClass()))
            zos.setLevel(ZipOutputStream.STORED);

        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);
                }
            }

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

        List<Individual> individuals = getIndividualsFromSamples(sModule, sampleIDs);

        ArrayList<String> individualList = new ArrayList<String>();
        StringBuffer indFileContents = new StringBuffer();

        for (int i = 0; i < sampleIDs.size(); i++) {
            Individual individual = individuals.get(i);
            if (!individualList.contains(individual.getId())) {
                individualList.add(individual.getId());
                indFileContents
                        .append(individual.getId() + "\t" + getIndividualGenderCode(sModule, individual.getId())
                                + "\t" + (individual.getPopulation() == null ? "." : individual.getPopulation())
                                + LINE_SEPARATOR);
            }
        }

        String exportName = sModule + "_" + markerCount + "variants_" + individualList.size() + "individuals";
        zos.putNextEntry(new ZipEntry(exportName + ".ind"));
        zos.write(indFileContents.toString().getBytes());

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

        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> 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;
                }
                snpFileWriter.write(variantId + "\t" + (chromAndPos.size() == 0 ? "0" : chromAndPos.get(0))
                        + "\t" + 0 + "\t" + (chromAndPos.size() == 0 ? 0l : Long.parseLong(chromAndPos.get(1)))
                        + LINE_SEPARATOR);

                Map<String, List<String>> individualGenotypes = new LinkedHashMap<String, List<String>>();
                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);
                        }

                for (int j = 0; j < individualList
                        .size(); j++ /* we use this list because it has the proper ordering*/) {
                    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
                    int highestGenotypeCount = 0;
                    String mostFrequentGenotype = null;
                    if (genotypes != 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);
                        }

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

                    int nOutputCode = 0;
                    if (mostFrequentGenotype == null)
                        nOutputCode = 9;
                    else
                        for (String all : Helper.split(mostFrequentGenotype, "/"))
                            if ("0".equals(all))
                                nOutputCode++;
                    if (j == 0 && variant.getKnownAlleleList().size() > 2)
                        warningFileWriter.write("- Variant " + variant.getId()
                                + " is multi-allelic. Make sure Eigenstrat genotype encoding specifications are suitable for you.\n");
                    zos.write(("" + nOutputCode).getBytes());

                    if (genotypeCounts.size() > 1 || alleles.size() > 2) {
                        if (genotypeCounts.size() > 1)
                            warningFileWriter.write("- Dissimilar genotypes found for variant "
                                    + (variantId == null ? variant.getId() : variantId) + ", individual "
                                    + individualId + ". Exporting most frequent: " + nOutputCode + "\n");
                        if (alleles.size() > 2)
                            warningFileWriter.write("- More than 2 alleles found for variant "
                                    + (variantId == null ? variant.getId() : variantId) + ", individual "
                                    + individualId + ". Exporting only the first 2 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;
            }
        }

        snpFileWriter.close();
        zos.putNextEntry(new ZipEntry(exportName + ".snp"));
        BufferedReader in = new BufferedReader(new FileReader(snpFile));
        String sLine;
        while ((sLine = in.readLine()) != null)
            zos.write((sLine + "\n").getBytes());
        in.close();

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

        zos.close();
        progress.setCurrentStepProgress((short) 100);
    } finally {
        if (snpFile != null && snpFile.exists())
            snpFile.delete();
    }
}

From source file:com.aurel.track.exchange.track.exporter.TrackExportBL.java

public static ZipOutputStream exportWorkItemsWithAttachments(List<ReportBean> reportBeanList, Integer personID,
        OutputStream outputStream) {

    ZipOutputStream zipOutputStream = new ZipOutputStream(outputStream);

    Document document = exportWorkItems(reportBeanList, personID);
    ZipEntry dataEntry = new ZipEntry(ExchangeFieldNames.EXCHANGE_ZIP_ENTRY);
    try {//from w w w .j ava  2s  . co m
        zipOutputStream.putNextEntry(dataEntry);
    } catch (IOException e) {
        LOGGER.error("Adding the XML data to the zip failed with " + e.getMessage());
        LOGGER.debug(ExceptionUtils.getStackTrace(e));
    }
    ReportBeansToXML.convertToXml(zipOutputStream, document);
    //zipOutputStream.closeEntry();
    //get the attachments for each workItem (if exist)
    if (reportBeanList != null) {
        for (ReportBean reportBean : reportBeanList) {
            TWorkItemBean workItemBean = reportBean.getWorkItemBean();
            Integer workItemID = workItemBean.getObjectID();
            String workItemAttachmentsDirectory = AttachBL.getFullDirName(null, workItemID);
            File file = new File(workItemAttachmentsDirectory);
            if (file.exists() && file.isDirectory()) {
                ReportBL.zipFiles(file, zipOutputStream, file.getAbsolutePath());
            }
        }
    }
    try {
        zipOutputStream.close();
    } catch (IOException e) {
        LOGGER.warn("Closing the zip failed with " + e.getMessage());
        LOGGER.debug(ExceptionUtils.getStackTrace(e));
    }
    return zipOutputStream;
}

From source file:com.genericworkflownodes.knime.nodes.io.outputfile.OutputFileNodeModel.java

/**
 * {@inheritDoc}/*  w w w  . j ava  2 s  .  c o  m*/
 */
@Override
protected void saveInternals(final File internDir, final ExecutionMonitor exec)
        throws IOException, CanceledExecutionException {
    ZipOutputStream out = new ZipOutputStream(new FileOutputStream(new File(internDir, "loadeddata")));
    ZipEntry entry = new ZipEntry("rawdata.bin");
    out.putNextEntry(entry);
    out.write(data.getBytes());
    out.close();
}

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 {//from w w  w. j  a v  a2s. co  m
            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);
                }
            }
        }
    }
}

From source file:com.anritsu.mcrepositorymanager.utils.Packing.java

public boolean addPackageToArchive(McPackage p) {
    boolean result = false;
    for (String link : p.getDownloadLinks()) {
        try {//  w w  w  . j av  a2s .c  om
            String dowloadLink[] = link.split("/");
            String fileName = dowloadLink[dowloadLink.length - 1];
            System.out.println("Archiving " + fileName + ": " + link);
            status.getArchivedPackages().add(fileName);

            byte[] buf = new byte[1024];
            int len;
            FileInputStream in = new FileInputStream(FOLDER_PATH + fileName);
            ZipEntry e = new ZipEntry(fileName);
            out.putNextEntry(e);
            while ((len = in.read(buf)) > 0) {
                out.write(buf, 0, len);
            }
            out.closeEntry();
            in.close();
            LOGGER.log(Level.INFO, link + " succesfully archived!");
            result = true;
        } catch (Exception ex) {
            Logger.getLogger(Packing.class.getName()).log(Level.SEVERE, null, ex);
            result = false;
        }
    }
    return result;
}