Example usage for java.util.zip ZipOutputStream ZipOutputStream

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

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Introduction

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

Prototype

public ZipOutputStream(OutputStream out)

Source Link

Document

Creates a new ZIP output stream.

Usage

From source file:be.fedict.eid.applet.service.signer.ooxml.AbstractOOXMLSignatureService.java

private ZipOutputStream copyOOXMLContent(String signatureZipEntryName, OutputStream signedOOXMLOutputStream)
        throws IOException, ParserConfigurationException, SAXException, TransformerConfigurationException,
        TransformerFactoryConfigurationError, TransformerException {
    ZipOutputStream zipOutputStream = new ZipOutputStream(signedOOXMLOutputStream);
    ZipInputStream zipInputStream = new ZipInputStream(this.getOfficeOpenXMLDocumentURL().openStream());
    ZipEntry zipEntry;/*from   w w w. j  a  v a  2s .  c  o  m*/
    boolean hasOriginSigsRels = false;
    while (null != (zipEntry = zipInputStream.getNextEntry())) {
        LOG.debug("copy ZIP entry: " + zipEntry.getName());
        ZipEntry newZipEntry = new ZipEntry(zipEntry.getName());
        zipOutputStream.putNextEntry(newZipEntry);
        if ("[Content_Types].xml".equals(zipEntry.getName())) {
            Document contentTypesDocument = loadDocumentNoClose(zipInputStream);
            Element typesElement = contentTypesDocument.getDocumentElement();

            /*
             * We need to add an Override element.
             */
            Element overrideElement = contentTypesDocument.createElementNS(
                    "http://schemas.openxmlformats.org/package/2006/content-types", "Override");
            overrideElement.setAttribute("PartName", "/" + signatureZipEntryName);
            overrideElement.setAttribute("ContentType",
                    "application/vnd.openxmlformats-package.digital-signature-xmlsignature+xml");
            typesElement.appendChild(overrideElement);

            Element nsElement = contentTypesDocument.createElement("ns");
            nsElement.setAttributeNS(Constants.NamespaceSpecNS, "xmlns:tns",
                    "http://schemas.openxmlformats.org/package/2006/content-types");
            NodeList nodeList = XPathAPI.selectNodeList(contentTypesDocument,
                    "/tns:Types/tns:Default[@Extension='sigs']", nsElement);
            if (0 == nodeList.getLength()) {
                /*
                 * Add Default element for 'sigs' extension.
                 */
                Element defaultElement = contentTypesDocument.createElementNS(
                        "http://schemas.openxmlformats.org/package/2006/content-types", "Default");
                defaultElement.setAttribute("Extension", "sigs");
                defaultElement.setAttribute("ContentType",
                        "application/vnd.openxmlformats-package.digital-signature-origin");
                typesElement.appendChild(defaultElement);
            }

            writeDocumentNoClosing(contentTypesDocument, zipOutputStream, false);
        } else if ("_rels/.rels".equals(zipEntry.getName())) {
            Document relsDocument = loadDocumentNoClose(zipInputStream);

            Element nsElement = relsDocument.createElement("ns");
            nsElement.setAttributeNS(Constants.NamespaceSpecNS, "xmlns:tns",
                    "http://schemas.openxmlformats.org/package/2006/relationships");
            NodeList nodeList = XPathAPI.selectNodeList(relsDocument,
                    "/tns:Relationships/tns:Relationship[@Target='_xmlsignatures/origin.sigs']", nsElement);
            if (0 == nodeList.getLength()) {
                Element relationshipElement = relsDocument.createElementNS(
                        "http://schemas.openxmlformats.org/package/2006/relationships", "Relationship");
                relationshipElement.setAttribute("Id", "rel-id-" + UUID.randomUUID().toString());
                relationshipElement.setAttribute("Type",
                        "http://schemas.openxmlformats.org/package/2006/relationships/digital-signature/origin");
                relationshipElement.setAttribute("Target", "_xmlsignatures/origin.sigs");

                relsDocument.getDocumentElement().appendChild(relationshipElement);
            }

            writeDocumentNoClosing(relsDocument, zipOutputStream, false);
        } else if ("_xmlsignatures/_rels/origin.sigs.rels".equals(zipEntry.getName())) {
            hasOriginSigsRels = true;
            Document originSignRelsDocument = loadDocumentNoClose(zipInputStream);

            Element relationshipElement = originSignRelsDocument.createElementNS(
                    "http://schemas.openxmlformats.org/package/2006/relationships", "Relationship");
            String relationshipId = "rel-" + UUID.randomUUID().toString();
            relationshipElement.setAttribute("Id", relationshipId);
            relationshipElement.setAttribute("Type",
                    "http://schemas.openxmlformats.org/package/2006/relationships/digital-signature/signature");
            String target = FilenameUtils.getName(signatureZipEntryName);
            LOG.debug("target: " + target);
            relationshipElement.setAttribute("Target", target);
            originSignRelsDocument.getDocumentElement().appendChild(relationshipElement);

            writeDocumentNoClosing(originSignRelsDocument, zipOutputStream, false);
        } else {
            IOUtils.copy(zipInputStream, zipOutputStream);
        }
    }

    if (false == hasOriginSigsRels) {
        /*
         * Add signature relationships document.
         */
        addOriginSigsRels(signatureZipEntryName, zipOutputStream);
        addOriginSigs(zipOutputStream);
    }

    /*
     * Return.
     */
    zipInputStream.close();
    return zipOutputStream;
}

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;/* w  w w.j  a v  a2s  .c  om*/
    File warfile = path.toFile();

    warfile.getParentFile().mkdirs();

    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:org.elasticsearch.plugins.PluginManagerIT.java

/** creates a plugin .zip and returns the url for testing */
private String createPlugin(final Path structure, String... properties) throws IOException {
    writeProperties(structure, properties);
    Path zip = createTempDir().resolve(structure.getFileName() + ".zip");
    try (ZipOutputStream stream = new ZipOutputStream(Files.newOutputStream(zip))) {
        Files.walkFileTree(structure, new SimpleFileVisitor<Path>() {
            @Override/*  ww w.ja v a  2 s.  co m*/
            public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
                stream.putNextEntry(new ZipEntry(structure.relativize(file).toString()));
                Files.copy(file, stream);
                return FileVisitResult.CONTINUE;
            }
        });
    }
    if (randomBoolean()) {
        writeSha1(zip, false);
    } else if (randomBoolean()) {
        writeMd5(zip, false);
    }
    return zip.toUri().toURL().toString();
}

From source file:msearch.filmlisten.MSFilmlisteSchreiben.java

private void xmlSchreibenStart(String datei) throws IOException, XMLStreamException {
    File file = new File(datei);
    File dir = new File(file.getParent());
    if (!dir.exists()) {
        if (!dir.mkdirs()) {
            MSLog.fehlerMeldung(947623049, MSLog.FEHLER_ART_PROG,
                    "MSearchIoXmlFilmlisteSchreiben.xmlSchreibenStart",
                    "Kann den Pfad nicht anlegen: " + dir.toString());
        }/* ww w .  ja  v  a2 s.c om*/
    }
    MSLog.systemMeldung("   --> Start Schreiben nach: " + datei);
    XMLOutputFactory outFactory = XMLOutputFactory.newInstance();
    if (datei.endsWith(MSConst.FORMAT_BZ2)) {
        bZip2CompressorOutputStream = new BZip2CompressorOutputStream(new FileOutputStream(file),
                9 /*Blocksize: 1 - 9*/);
        out = new OutputStreamWriter(bZip2CompressorOutputStream, MSConst.KODIERUNG_UTF);
    } else if (datei.endsWith(MSConst.FORMAT_ZIP)) {
        zipOutputStream = new ZipOutputStream(new FileOutputStream(file));
        ZipEntry entry = new ZipEntry(MSConst.XML_DATEI_FILME);
        zipOutputStream.putNextEntry(entry);
        out = new OutputStreamWriter(zipOutputStream, MSConst.KODIERUNG_UTF);
    } else {
        out = new OutputStreamWriter(new FileOutputStream(file), MSConst.KODIERUNG_UTF);
    }
    writer = outFactory.createXMLStreamWriter(out);
    writer.writeStartDocument("UTF-8", "1.0");
    writer.writeCharacters("\n");//neue Zeile
    writer.writeStartElement(MSConst.XML_START);
    writer.writeCharacters("\n");//neue Zeile
}

From source file:com.nridge.core.base.std.FilUtl.java

/**
 * Compresses the input file into a ZIP file container.
 *
 * @param aInFileName The file name to be compressed.
 * @param aZipFileName The file name of the ZIP container.
 * @throws IOException Related to opening the file streams and
 * related read/write operations.//w w w.j  a  v a  2s .  c om
 */
static public void zipFile(String aInFileName, String aZipFileName) throws IOException {
    File inFile;
    int byteCount;
    byte[] ioBuf;
    FileInputStream fileIn;
    ZipOutputStream zipOut;
    FileOutputStream fileOut;

    inFile = new File(aInFileName);
    if (inFile.isDirectory())
        return;

    ioBuf = new byte[FILE_IO_BUFFER_SIZE];
    fileIn = new FileInputStream(inFile);
    fileOut = new FileOutputStream(aZipFileName);
    zipOut = new ZipOutputStream(fileOut);
    zipOut.putNextEntry(new ZipEntry(inFile.getName()));
    byteCount = fileIn.read(ioBuf);
    while (byteCount > 0) {
        zipOut.write(ioBuf, 0, byteCount);
        byteCount = fileIn.read(ioBuf);
    }
    fileIn.close();
    zipOut.closeEntry();
    zipOut.close();
}

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

/**
 * ?/*  ww w.  jav a  2 s  .  c  o  m*/
 *
 * @param srcFileURL
 *            URL
 * @param zipFileURL
 *            ?zip??URL
 * @throws FileNotFoundException
 * @throws IOException
 * @throws IllegalArgumentException
 */
private void zipDir(String srcFileURL, String zipFileURL)
        throws FileNotFoundException, IOException, IllegalArgumentException {
    Uri srcFileUri = getFileUri(srcFileURL);
    Uri dstFileUri = getFileUri(zipFileURL);

    if (areFilesSame(srcFileUri, dstFileUri)) {
        throw new IllegalArgumentException();
    }
    prepareForZipDir(dstFileUri);

    ZipOutputStream zos = new ZipOutputStream(mResourceApi.openOutputStream(dstFileUri));
    compressDir(srcFileUri, zos, "");
    zos.close();
}

From source file:com.evolveum.midpoint.cli.ninja.action.ExportAction.java

private Writer createWriter() throws IOException {
    File file = getParams().getFile();
    if (file != null) {
        if (file.exists()) {
            file.delete();// www.j a  va2  s.c  o m
        }
        file.createNewFile();

        OutputStream os = new FileOutputStream(file);
        if (getParams().isZip()) {
            os = new ZipOutputStream(os);
        }
        Writer writer = new OutputStreamWriter(os, StandardCharsets.UTF_8);
        return new BufferedWriter(writer);
    }

    return new LogWriter(STD_OUT);
}

From source file:ZipTransformTest.java

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

    File file1 = File.createTempFile("temp", null);
    File file2 = File.createTempFile("temp", null);
    try {//w w  w .j  a va2s .  c  o  m
        // Create the ZIP file
        ZipOutputStream zos = new ZipOutputStream(new FileOutputStream(file1));
        try {
            zos.putNextEntry(new ZipEntry(name));
            zos.write(contents);
            zos.closeEntry();
        } finally {
            IOUtils.closeQuietly(zos);
        }

        // Transform the ZIP file
        FileInputStream in = null;
        FileOutputStream out = null;
        try {
            in = new FileInputStream(file1);
            out = new FileOutputStream(file2);

            ZipUtil.transformEntry(in, name, new FileZipEntryTransformer() {
                protected void transform(ZipEntry zipEntry, File in, File out) throws IOException {
                    FileWriter fw = new FileWriter(out);
                    fw.write("CAFEBABE");
                    fw.close();
                }
            }, out);
        } finally {
            IOUtils.closeQuietly(in);
            IOUtils.closeQuietly(out);
        }

        // Test the ZipUtil
        byte[] actual = ZipUtil.unpackEntry(file2, name);
        assertNotNull(actual);
        assertEquals("CAFEBABE", new String(actual));
    } finally {
        FileUtils.deleteQuietly(file1);
        FileUtils.deleteQuietly(file2);
    }
}

From source file:fr.cirad.mgdb.exporting.markeroriented.VcfExportHandler.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 {
    Integer projectId = null;/*from   w  ww.  ja v  a 2  s  .  co  m*/
    for (SampleId spId : sampleIDs) {
        if (projectId == null)
            projectId = spId.getProject();
        else if (projectId != spId.getProject()) {
            projectId = 0;
            break; // more than one project are involved: no header will be written
        }
    }

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

    MongoTemplate mongoTemplate = MongoTemplateManager.get(sModule);
    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);
            }
        }

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

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

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

    VariantContextWriter writer = null;
    try {
        List<String> distinctSequenceNames = new ArrayList<String>();

        String sequenceSeqCollName = MongoTemplateManager.getMongoCollectionName(Sequence.class);
        if (mongoTemplate.collectionExists(sequenceSeqCollName)) {
            DBCursor markerCursorCopy = markerCursor.copy();
            markerCursorCopy.batchSize(nQueryChunkSize);
            while (markerCursorCopy.hasNext()) {
                int nLoadedMarkerCountInLoop = 0;
                boolean fStartingNewChunk = true;
                while (markerCursorCopy.hasNext()
                        && (fStartingNewChunk || nLoadedMarkerCountInLoop % nQueryChunkSize != 0)) {
                    DBObject exportVariant = markerCursorCopy.next();
                    String chr = (String) ((DBObject) exportVariant
                            .get(VariantData.FIELDNAME_REFERENCE_POSITION))
                                    .get(ReferencePosition.FIELDNAME_SEQUENCE);
                    if (!distinctSequenceNames.contains(chr))
                        distinctSequenceNames.add(chr);
                }
            }
            markerCursorCopy.close();
        }

        Collections.sort(distinctSequenceNames, new AlphaNumericStringComparator());
        SAMSequenceDictionary dict = createSAMSequenceDictionary(sModule, distinctSequenceNames);
        writer = new CustomVCFWriter(null, zos, dict, false, false, true);
        //         VariantContextWriterBuilder vcwb = new VariantContextWriterBuilder();
        //         vcwb.unsetOption(Options.INDEX_ON_THE_FLY);
        //         vcwb.unsetOption(Options.DO_NOT_WRITE_GENOTYPES);
        //         vcwb.setOption(Options.USE_ASYNC_IOINDEX_ON_THE_FLY);
        //         vcwb.setOption(Options.ALLOW_MISSING_FIELDS_IN_HEADER);
        //         vcwb.setReferenceDictionary(dict);
        //         writer = vcwb.build();
        //         writer = new AsyncVariantContextWriter(writer, 3000);

        progress.moveToNextStep(); // done with dictionary
        DBCursor headerCursor = mongoTemplate
                .getCollection(MongoTemplateManager.getMongoCollectionName(DBVCFHeader.class))
                .find(new BasicDBObject("_id." + VcfHeaderId.FIELDNAME_PROJECT, projectId));
        Set<VCFHeaderLine> headerLines = new HashSet<VCFHeaderLine>();
        boolean fWriteCommandLine = true, fWriteEngineHeaders = true; // default values

        while (headerCursor.hasNext()) {
            DBVCFHeader dbVcfHeader = DBVCFHeader.fromDBObject(headerCursor.next());
            headerLines.addAll(dbVcfHeader.getHeaderLines());

            // Add sequence header lines (not stored in our vcf header collection)
            BasicDBObject projection = new BasicDBObject(SequenceStats.FIELDNAME_SEQUENCE_LENGTH, true);
            int nSequenceIndex = 0;
            for (String sequenceName : distinctSequenceNames) {
                String sequenceInfoCollName = MongoTemplateManager.getMongoCollectionName(SequenceStats.class);
                boolean fCollectionExists = mongoTemplate.collectionExists(sequenceInfoCollName);
                if (fCollectionExists) {
                    DBObject record = mongoTemplate.getCollection(sequenceInfoCollName).findOne(
                            new Query(Criteria.where("_id").is(sequenceName)).getQueryObject(), projection);
                    if (record == null) {
                        LOG.warn("Sequence '" + sequenceName + "' not found in collection "
                                + sequenceInfoCollName);
                        continue;
                    }

                    Map<String, String> sequenceLineData = new LinkedHashMap<String, String>();
                    sequenceLineData.put("ID", (String) record.get("_id"));
                    sequenceLineData.put("length",
                            ((Number) record.get(SequenceStats.FIELDNAME_SEQUENCE_LENGTH)).toString());
                    headerLines.add(new VCFContigHeaderLine(sequenceLineData, nSequenceIndex++));
                }
            }
            fWriteCommandLine = headerCursor.size() == 1 && dbVcfHeader.getWriteCommandLine(); // wouldn't make sense to include command lines for several runs
            if (!dbVcfHeader.getWriteEngineHeaders())
                fWriteEngineHeaders = false;
        }
        headerCursor.close();

        VCFHeader header = new VCFHeader(headerLines, individualList);
        header.setWriteCommandLine(fWriteCommandLine);
        header.setWriteEngineHeaders(fWriteEngineHeaders);
        writer.writeHeader(header);

        short nProgress = 0, nPreviousProgress = 0;
        long nLoadedMarkerCount = 0;
        HashMap<SampleId, Comparable /*phID*/> phasingIDsBySample = new HashMap<SampleId, Comparable>();

        while (markerCursor.hasNext()) {
            if (progress.hasAborted())
                return;

            int nLoadedMarkerCountInLoop = 0;
            boolean fStartingNewChunk = true;
            markerCursor.batchSize(nQueryChunkSize);
            List<Comparable> currentMarkers = new ArrayList<Comparable>();
            while (markerCursor.hasNext()
                    && (fStartingNewChunk || nLoadedMarkerCountInLoop % nQueryChunkSize != 0)) {
                DBObject exportVariant = markerCursor.next();
                currentMarkers.add((Comparable) exportVariant.get("_id"));
                nLoadedMarkerCountInLoop++;
                fStartingNewChunk = false;
            }

            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()) {
                VariantContext vc = variant.toVariantContext(variantsAndRuns.get(variant),
                        !ObjectId.isValid(variant.getId().toString()), sampleIDToIndividualIdMap,
                        phasingIDsBySample, nMinimumGenotypeQuality, nMinimumReadDepth, warningFileWriter,
                        markerSynonyms == null ? variant.getId() : markerSynonyms.get(variant.getId()));
                try {
                    writer.add(vc);
                } catch (Throwable t) {
                    Exception e = new Exception("Unable to convert to VariantContext: " + variant.getId(), t);
                    LOG.debug("error", e);
                    throw e;
                }

                if (nLoadedMarkerCountInLoop > currentMarkers.size())
                    LOG.error("Bug: writing variant number " + nLoadedMarkerCountInLoop + " (only "
                            + currentMarkers.size() + " variants expected)");
            }

            nLoadedMarkerCount += nLoadedMarkerCountInLoop;
            nProgress = (short) (nLoadedMarkerCount * 100 / markerCount);
            if (nProgress > nPreviousProgress) {
                progress.setCurrentStepProgress(nProgress);
                nPreviousProgress = nProgress;
            }
        }
        progress.setCurrentStepProgress((short) 100);

    } catch (Exception e) {
        LOG.error("Error exporting", e);
        progress.setError(e.getMessage());
        return;
    } finally {
        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());
                nWarningCount++;
            }
            LOG.info("Number of Warnings for export (" + exportName + "): " + nWarningCount);
            in.close();
        }
        warningFile.delete();
        if (writer != null)
            try {
                writer.close();
            } catch (Throwable ignored) {
            }
    }
}

From source file:ee.ria.xroad.common.asic.AsicContainer.java

/**
 * Write this container to the given output stream in ZIP format.
 * @param out the stream for writing container
 * @throws Exception if errors occurred when writing ZIP entries
 */// w ww .  j a  v a2s. c o m
public void write(OutputStream out) throws Exception {
    try (ZipOutputStream zip = new ZipOutputStream(out)) {
        AsicHelper.write(this, zip);
    }
}