List of usage examples for java.util.zip ZipOutputStream STORED
int STORED
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From source file:JarUtil.java
/** * Writes all given files to the specified jar-file. * //w ww.j av a2 s .c o m * @param files * all files that should be added to the JAR file * @param sourceDir * The parent directory containing the given files. * @param target * The jar file which should be created * @param compress * True when the jar file should be compressed * @throws FileNotFoundException * when a file could not be found * @throws IOException * when a file could not be read or the jar file could not be * written to. */ public static void jar(File sourceDir, OutputStream target, boolean compress) throws IOException { File[] files = sourceDir.listFiles(); // creates target-jar-file: JarOutputStream out = new JarOutputStream(target); if (compress) { out.setLevel(ZipOutputStream.DEFLATED); } else { out.setLevel(ZipOutputStream.STORED); } // create a CRC32 object: CRC32 crc = new CRC32(); byte[] buffer = new byte[1024 * 1024]; // add all files: int sourceDirLength = sourceDir.getAbsolutePath().length() + 1; for (File file : files) { addFile(file, out, crc, sourceDirLength, buffer); } out.close(); }
From source file:com.joliciel.talismane.machineLearning.linearsvm.LinearSVMOneVsRestModel.java
@Override public void writeModelToStream(OutputStream outputStream) { try {// w w w .j a v a 2 s. c om ZipOutputStream zos = new ZipOutputStream(outputStream); zos.setLevel(ZipOutputStream.STORED); int i = 0; for (Model model : models) { LOG.debug("Writing model " + i + " for outcome " + outcomes.get(i)); ZipEntry zipEntry = new ZipEntry("model" + i); i++; zos.putNextEntry(zipEntry); Writer writer = new OutputStreamWriter(zos, "UTF-8"); Writer unclosableWriter = new UnclosableWriter(writer); model.save(unclosableWriter); zos.closeEntry(); zos.flush(); } } catch (UnsupportedEncodingException e) { LogUtils.logError(LOG, e); throw new RuntimeException(e); } catch (IOException e) { LogUtils.logError(LOG, e); throw new RuntimeException(e); } }
From source file:JarUtil.java
/** * Adds the given file to the specified JAR file. * //from w ww. j ava2s . c o m * @param file * the file that should be added * @param jarFile * The JAR to which the file should be added * @param parentDir * the parent directory of the file, this is used to calculate * the path witin the JAR file. When null is given, the file will * be added into the root of the JAR. * @param compress * True when the jar file should be compressed * @throws FileNotFoundException * when the jarFile does not exist * @throws IOException * when a file could not be written or the jar-file could not * read. */ public static void addToJar(File file, File jarFile, File parentDir, boolean compress) throws FileNotFoundException, IOException { File tmpJarFile = File.createTempFile("tmp", ".jar", jarFile.getParentFile()); JarOutputStream out = new JarOutputStream(new FileOutputStream(tmpJarFile)); if (compress) { out.setLevel(ZipOutputStream.DEFLATED); } else { out.setLevel(ZipOutputStream.STORED); } // copy contents of old jar to new jar: JarFile inputFile = new JarFile(jarFile); JarInputStream in = new JarInputStream(new FileInputStream(jarFile)); CRC32 crc = new CRC32(); byte[] buffer = new byte[512 * 1024]; JarEntry entry = (JarEntry) in.getNextEntry(); while (entry != null) { InputStream entryIn = inputFile.getInputStream(entry); add(entry, entryIn, out, crc, buffer); entryIn.close(); entry = (JarEntry) in.getNextEntry(); } in.close(); inputFile.close(); int sourceDirLength; if (parentDir == null) { sourceDirLength = file.getAbsolutePath().lastIndexOf(File.separatorChar) + 1; } else { sourceDirLength = file.getAbsolutePath().lastIndexOf(File.separatorChar) + 1 - parentDir.getAbsolutePath().length(); } addFile(file, out, crc, sourceDirLength, buffer); out.close(); // remove old jar file and rename temp file to old one: if (jarFile.delete()) { if (!tmpJarFile.renameTo(jarFile)) { throw new IOException( "Unable to rename temporary JAR file to [" + jarFile.getAbsolutePath() + "]."); } } else { throw new IOException("Unable to delete old JAR file [" + jarFile.getAbsolutePath() + "]."); } }
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 www.j a v a 2s.com*/ 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.jhash.oimadmin.Utils.java
public static void createJarFileFromContent(Map<String, byte[]> content, String[] fileSequence, String jarFileName) {//from ww w . ja v a2 s . c o m logger.trace("createJarFileFromContent({},{})", content, jarFileName); logger.trace("Trying to create a new jar file"); try (ZipOutputStream jarFileOutputStream = new ZipOutputStream(new FileOutputStream(jarFileName))) { jarFileOutputStream.setMethod(ZipOutputStream.STORED); for (String jarItem : fileSequence) { logger.trace("Processing item {}", jarItem); byte[] fileContent = content.get(jarItem); if (fileContent == null) throw new NullPointerException("Failed to locate content for file " + jarItem); JarEntry pluginXMLFileEntry = new JarEntry(jarItem); pluginXMLFileEntry.setTime(System.currentTimeMillis()); pluginXMLFileEntry.setSize(fileContent.length); pluginXMLFileEntry.setCompressedSize(fileContent.length); CRC32 crc = new CRC32(); crc.update(fileContent); pluginXMLFileEntry.setCrc(crc.getValue()); jarFileOutputStream.putNextEntry(pluginXMLFileEntry); jarFileOutputStream.write(fileContent); jarFileOutputStream.closeEntry(); } } catch (Exception exception) { throw new OIMAdminException("Failed to create the Jar file " + jarFileName, exception); } }
From source file:it.cnr.icar.eric.common.Utility.java
public static ZipOutputStream createZipOutputStream(String baseDir, String[] relativeFilePaths, OutputStream os) throws FileNotFoundException, IOException { if (baseDir.startsWith("file:/")) { baseDir = baseDir.substring(5);/*from www.j a v a 2 s.co m*/ } ZipOutputStream zipoutputstream = new ZipOutputStream(os); zipoutputstream.setMethod(ZipOutputStream.STORED); for (int i = 0; i < relativeFilePaths.length; i++) { File file = new File(baseDir + FILE_SEPARATOR + relativeFilePaths[i]); byte[] buffer = new byte[1000]; int n; FileInputStream fis; // Calculate the CRC-32 value. This isn't strictly necessary // for deflated entries, but it doesn't hurt. CRC32 crc32 = new CRC32(); fis = new FileInputStream(file); while ((n = fis.read(buffer)) > -1) { crc32.update(buffer, 0, n); } fis.close(); // Create a zip entry. ZipEntry zipEntry = new ZipEntry(relativeFilePaths[i]); zipEntry.setSize(file.length()); zipEntry.setTime(file.lastModified()); zipEntry.setCrc(crc32.getValue()); // Add the zip entry and associated data. zipoutputstream.putNextEntry(zipEntry); fis = new FileInputStream(file); while ((n = fis.read(buffer)) > -1) { zipoutputstream.write(buffer, 0, n); } fis.close(); zipoutputstream.closeEntry(); } return zipoutputstream; }
From source file:brut.androlib.res.AndrolibResources.java
public void installFramework(File frameFile, String tag) throws AndrolibException { InputStream in = null;/* w ww .ja va2 s. c om*/ ZipOutputStream out = null; try { ZipFile zip = new ZipFile(frameFile); ZipEntry entry = zip.getEntry("resources.arsc"); if (entry == null) { throw new AndrolibException("Can't find resources.arsc file"); } in = zip.getInputStream(entry); byte[] data = IOUtils.toByteArray(in); ARSCData arsc = ARSCDecoder.decode(new ByteArrayInputStream(data), true, true); publicizeResources(data, arsc.getFlagsOffsets()); File outFile = new File(getFrameworkDir(), String.valueOf(arsc.getOnePackage().getId()) + (tag == null ? "" : '-' + tag) + ".apk"); out = new ZipOutputStream(new FileOutputStream(outFile)); out.setMethod(ZipOutputStream.STORED); CRC32 crc = new CRC32(); crc.update(data); entry = new ZipEntry("resources.arsc"); entry.setSize(data.length); entry.setCrc(crc.getValue()); out.putNextEntry(entry); out.write(data); zip.close(); LOGGER.info("Framework installed to: " + outFile); } catch (IOException ex) { throw new AndrolibException(ex); } finally { IOUtils.closeQuietly(in); IOUtils.closeQuietly(out); } }
From source file:nl.mpi.tg.eg.frinex.rest.CsvController.java
@RequestMapping(value = "/audio_{yearString}-{monthString}-{dayString}.zip", method = RequestMethod.GET) @ResponseBody//from w w w. j av a 2 s .c om public void getAudioZip(HttpServletResponse response, @PathVariable(value = "yearString", required = true) int selectedYear, @PathVariable(value = "monthString", required = true) int selectedMonth, @PathVariable(value = "dayString", required = true) int selectedDay) throws IOException { response.setContentType("application/zip"); Calendar calendar = Calendar.getInstance(); calendar.set(Calendar.YEAR, selectedYear); calendar.set(Calendar.MONTH, selectedMonth - 1); calendar.set(Calendar.DAY_OF_MONTH, selectedDay); calendar.set(Calendar.HOUR_OF_DAY, 0); calendar.set(Calendar.MINUTE, 0); calendar.set(Calendar.SECOND, 0); Date selectedDate = calendar.getTime(); calendar.set(Calendar.DAY_OF_MONTH, selectedDay + 1); Date selectedEndDate = calendar.getTime(); String selectedDateString = new SimpleDateFormat("yyyy-MM-dd").format(selectedDate); response.addHeader("Content-Disposition", "attachment; filename=\"audio_" + selectedDateString + ".zip\""); response.addHeader("Content-Transfer-Encoding", "binary"); try (ByteArrayOutputStream outputStream = new ByteArrayOutputStream()) { try (ZipOutputStream zipOutputStream = new ZipOutputStream(outputStream)) { zipOutputStream.setLevel(ZipOutputStream.STORED); for (AudioData audioData : audioDataRepository.findAllBySubmitDateBetween(selectedDate, selectedEndDate)) { addToZipArchive(zipOutputStream, audioData.getUserId() + "_" + audioData.getScreenName() + "_" + audioData.getStimulusId() + "_" + audioData.getId() + ".ogg", audioData.getDataBlob()); } } response.getOutputStream().write(outputStream.toByteArray()); response.getOutputStream().flush(); } }