List of usage examples for java.util.zip ZipEntry ZipEntry
public ZipEntry(ZipEntry e)
From source file:com.esofthead.mycollab.vaadin.resources.StreamDownloadResourceSupportExtDrive.java
private void zipResource(ZipOutputStream zipOutputStream, Collection<Resource> lstRes) { try {//from ww w. j a v a2s .c om List<Resource> recurrResources; for (Resource currentResource : lstRes) { if (currentResource instanceof Folder) { if (!currentResource.isExternalResource()) { recurrResources = resourceService.getResources(currentResource.getPath()); } else { ExternalResourceService service = ResourceUtils .getExternalResourceService(ResourceUtils.getType(currentResource)); recurrResources = service.getResources(ResourceUtils.getExternalDrive(currentResource), currentResource.getPath()); } if (CollectionUtils.isEmpty(recurrResources)) { zipOutputStream.putNextEntry(new ZipEntry(currentResource.getName() + "/")); } else { for (Resource res : recurrResources) { if (res instanceof Content) { addFileToZip(currentResource.getName(), (Content) res, zipOutputStream); } else if (res instanceof Folder) { addFolderToZip(currentResource.getName(), res, zipOutputStream); } } } } else { addFileToZip("", (Content) currentResource, zipOutputStream); } } } catch (Exception e) { LOG.error("Error while save content", e); } }
From source file:ee.ria.xroad.common.messagelog.archive.LogArchiveCache.java
private void addLinkingInfoToArchive(ZipOutputStream zipOut) throws IOException { ZipEntry linkingInfoEntry = new ZipEntry("linkinginfo"); zipOut.putNextEntry(linkingInfoEntry); zipOut.write(linkingInfoBuilder.build()); zipOut.closeEntry();//from w w w .j av a 2 s . c o m linkingInfoBuilder.afterArchiveCreated(); }
From source file:fr.cirad.mgdb.exporting.markeroriented.HapMapExportHandler.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); 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); }//from w w w . j av a2s . c om } 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 + ".hapmap")); String header = "rs#" + "\t" + "alleles" + "\t" + "chrom" + "\t" + "pos" + "\t" + "strand" + "\t" + "assembly#" + "\t" + "center" + "\t" + "protLSID" + "\t" + "assayLSID" + "\t" + "panelLSID" + "\t" + "QCcode"; zos.write(header.getBytes()); for (int i = 0; i < individualList.size(); i++) { zos.write(("\t" + individualList.get(i)).getBytes()); } zos.write((LINE_SEPARATOR).getBytes()); 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 == null || 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(); if (markerSynonyms != null) { Comparable syn = markerSynonyms.get(variantId); if (syn != null) variantId = syn; } boolean fIsSNP = variant.getType().equals(Type.SNP.toString()); byte[] missingGenotype = ("\t" + "NN").getBytes(); String[] chromAndPos = markerChromosomalPositions.get(variant.getId()).split(":"); zos.write(((variantId == null ? variant.getId() : variantId) + "\t" + StringUtils.join(variant.getKnownAlleleList(), "/") + "\t" + chromAndPos[0] + "\t" + Long.parseLong(chromAndPos[1]) + "\t" + "+").getBytes()); for (int j = 0; j < 6; j++) zos.write(("\t" + "NA").getBytes()); 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>>(); 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 gtCode = run.getSampleGenotypes().get(sampleIndex).getCode(); String individualId = individuals .get(sampleIDs.indexOf(new SampleId(run.getId().getProjectId(), sampleIndex))) .getId(); List<String> storedIndividualGenotypes = individualGenotypes.get(individualId); if (storedIndividualGenotypes == null) { storedIndividualGenotypes = new ArrayList<String>(); individualGenotypes.put(individualId, storedIndividualGenotypes); } storedIndividualGenotypes.add(gtCode); gqValueForSampleId.put(individualId, (Integer) sampleGenotype.getAdditionalInfo().get(VariantData.GT_FIELD_GQ)); dpValueForSampleId.put(individualId, (Integer) sampleGenotype.getAdditionalInfo().get(VariantData.GT_FIELD_DP)); } int writtenGenotypeCount = 0; for (String individualId : individualList /* we use this list because it has the proper ordering */) { int individualIndex = individualList.indexOf(individualId); while (writtenGenotypeCount < individualIndex - 1) { zos.write(missingGenotype); writtenGenotypeCount++; } 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 */ Integer gqValue = gqValueForSampleId.get(individualId); if (gqValue != null && gqValue < nMinimumGenotypeQuality) continue; /* skip this sample because its GQ is under the threshold */ Integer dpValue = dpValueForSampleId.get(individualId); if (dpValue != null && dpValue < nMinimumReadDepth) continue; /* skip this sample because its DP is under the threshold */ int gtCount = 1 + MgdbDao.getCountForKey(genotypeCounts, genotype); if (gtCount > highestGenotypeCount) { highestGenotypeCount = gtCount; mostFrequentGenotype = genotype; } genotypeCounts.put(genotype, gtCount); } byte[] exportedGT = mostFrequentGenotype == null ? missingGenotype : ("\t" + StringUtils.join(variant.getAllelesFromGenotypeCode(mostFrequentGenotype), fIsSNP ? "" : "/")).getBytes(); zos.write(exportedGT); writtenGenotypeCount++; if (genotypeCounts.size() > 1) warningFileWriter.write("- Dissimilar genotypes found for variant " + (variantId == null ? variant.getId() : variantId) + ", individual " + individualId + ". Exporting most frequent: " + new String(exportedGT) + "\n"); } while (writtenGenotypeCount < individualList.size()) { zos.write(missingGenotype); writtenGenotypeCount++; } 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:com.joliciel.lefff.LefffMemoryLoader.java
public void serializeMemoryBase(LefffMemoryBase memoryBase, File memoryBaseFile) { LOG.debug("serializeMemoryBase"); boolean isZip = false; if (memoryBaseFile.getName().endsWith(".zip")) isZip = true;//from w w w. java 2s.c om FileOutputStream fos = null; ObjectOutputStream out = null; ZipOutputStream zos = null; try { fos = new FileOutputStream(memoryBaseFile); if (isZip) { zos = new ZipOutputStream(fos); zos.putNextEntry(new ZipEntry("lefff.obj")); out = new ObjectOutputStream(zos); } else { out = new ObjectOutputStream(fos); } try { out.writeObject(memoryBase); } finally { out.flush(); out.close(); } } catch (IOException ioe) { throw new RuntimeException(ioe); } }
From source file:com.joliciel.jochre.lexicon.TextFileLexicon.java
public void serialize(File memoryBaseFile) { LOG.debug("serialize"); boolean isZip = false; if (memoryBaseFile.getName().endsWith(".zip")) isZip = true;/*from www.jav a 2 s . com*/ FileOutputStream fos = null; ObjectOutputStream out = null; ZipOutputStream zos = null; try { fos = new FileOutputStream(memoryBaseFile); if (isZip) { zos = new ZipOutputStream(fos); zos.putNextEntry(new ZipEntry("lexicon.obj")); out = new ObjectOutputStream(zos); } else { out = new ObjectOutputStream(fos); } try { out.writeObject(this); } finally { out.flush(); out.close(); } } catch (IOException ioe) { throw new RuntimeException(ioe); } }
From source file:fedora.server.storage.translation.AtomDOSerializer.java
/** * {@inheritDoc}//from ww w.j a v a2 s .c o m */ public void serialize(DigitalObject obj, OutputStream out, String encoding, int transContext) throws ObjectIntegrityException, StreamIOException, UnsupportedEncodingException { m_obj = obj; m_encoding = (encoding == null || encoding == "") ? "UTF-8" : encoding; m_transContext = transContext; m_pid = PID.getInstance(m_obj.getPid()); m_feed = abdera.newFeed(); if (m_format.equals(ATOM_ZIP1_1)) { m_zout = new ZipOutputStream(out); } addObjectProperties(); m_feed.setIcon("http://www.fedora-commons.org/images/logo_vertical_transparent_200_251.png"); addDatastreams(); if (m_format.equals(ATOM_ZIP1_1)) { try { m_zout.putNextEntry(new ZipEntry("atommanifest.xml")); m_feed.writeTo("prettyxml", m_zout); m_zout.closeEntry(); m_zout.close(); } catch (IOException e) { throw new StreamIOException(e.getMessage(), e); } } else { try { m_feed.writeTo("prettyxml", out); } catch (IOException e) { throw new StreamIOException(e.getMessage(), e); } } }
From source file:com.diffplug.gradle.ZipMisc.java
/** * Creates a single-entry zip file.// w w w . ja v a 2s . c o m * * @param input an uncompressed file * @param pathWithinArchive the path within the archive * @param output the new zip file it will be compressed into */ public static void zip(File input, String pathWithinArchive, File output) throws IOException { try (ZipOutputStream zipStream = new ZipOutputStream( new BufferedOutputStream(new FileOutputStream(output)))) { zipStream.setMethod(ZipOutputStream.DEFLATED); zipStream.setLevel(9); zipStream.putNextEntry(new ZipEntry(pathWithinArchive)); try (BufferedInputStream inputStream = new BufferedInputStream(new FileInputStream(input))) { copy(inputStream, zipStream); } } }
From source file:edu.umd.cs.submitServer.servlets.UploadSubmission.java
@Override public void doPost(HttpServletRequest request, HttpServletResponse response) throws IOException, ServletException { long now = System.currentTimeMillis(); Timestamp submissionTimestamp = new Timestamp(now); // these are set by filters or previous servlets Project project = (Project) request.getAttribute(PROJECT); StudentRegistration studentRegistration = (StudentRegistration) request.getAttribute(STUDENT_REGISTRATION); MultipartRequest multipartRequest = (MultipartRequest) request.getAttribute(MULTIPART_REQUEST); boolean webBasedUpload = ((Boolean) request.getAttribute("webBasedUpload")).booleanValue(); String clientTool = multipartRequest.getCheckedParameter("submitClientTool"); String clientVersion = multipartRequest.getOptionalCheckedParameter("submitClientVersion"); String cvsTimestamp = multipartRequest.getOptionalCheckedParameter("cvstagTimestamp"); Collection<FileItem> files = multipartRequest.getFileItems(); Kind kind;// ww w . j a v a 2 s.c o m byte[] zipOutput = null; // zipped version of bytesForUpload boolean fixedZip = false; try { if (files.size() > 1) { ByteArrayOutputStream bos = new ByteArrayOutputStream(); ZipOutputStream zos = new ZipOutputStream(bos); for (FileItem item : files) { String name = item.getName(); if (name == null || name.length() == 0) continue; byte[] bytes = item.get(); ZipEntry zentry = new ZipEntry(name); zentry.setSize(bytes.length); zentry.setTime(now); zos.putNextEntry(zentry); zos.write(bytes); zos.closeEntry(); } zos.flush(); zos.close(); zipOutput = bos.toByteArray(); kind = Kind.MULTIFILE_UPLOAD; } else { FileItem fileItem = multipartRequest.getFileItem(); if (fileItem == null) { response.sendError(HttpServletResponse.SC_BAD_REQUEST, "There was a problem processing your submission. " + "No files were found in your submission"); return; } // get size in bytes long sizeInBytes = fileItem.getSize(); if (sizeInBytes == 0 || sizeInBytes > Integer.MAX_VALUE) { response.sendError(HttpServletResponse.SC_BAD_REQUEST, "Trying upload file of size " + sizeInBytes); return; } // copy the fileItem into a byte array byte[] bytesForUpload = fileItem.get(); String fileName = fileItem.getName(); boolean isSpecialSingleFile = OfficeFileName.matcher(fileName).matches(); FormatDescription desc = FormatIdentification.identify(bytesForUpload); if (!isSpecialSingleFile && desc != null && desc.getMimeType().equals("application/zip")) { fixedZip = FixZip.hasProblem(bytesForUpload); kind = Kind.ZIP_UPLOAD; if (fixedZip) { bytesForUpload = FixZip.fixProblem(bytesForUpload, studentRegistration.getStudentRegistrationPK()); kind = Kind.FIXED_ZIP_UPLOAD; } zipOutput = bytesForUpload; } else { // ========================================================================================== // [NAT] [Buffer to ZIP Part] // Check the type of the upload and convert to zip format if // possible // NOTE: I use both MagicMatch and FormatDescription (above) // because MagicMatch was having // some trouble identifying all zips String mime = URLConnection.getFileNameMap().getContentTypeFor(fileName); if (!isSpecialSingleFile && mime == null) try { MagicMatch match = Magic.getMagicMatch(bytesForUpload, true); if (match != null) mime = match.getMimeType(); } catch (Exception e) { // leave mime as null } if (!isSpecialSingleFile && "application/zip".equalsIgnoreCase(mime)) { zipOutput = bytesForUpload; kind = Kind.ZIP_UPLOAD2; } else { InputStream ins = new ByteArrayInputStream(bytesForUpload); if ("application/x-gzip".equalsIgnoreCase(mime)) { ins = new GZIPInputStream(ins); } ByteArrayOutputStream bos = new ByteArrayOutputStream(); ZipOutputStream zos = new ZipOutputStream(bos); if (!isSpecialSingleFile && ("application/x-gzip".equalsIgnoreCase(mime) || "application/x-tar".equalsIgnoreCase(mime))) { kind = Kind.TAR_UPLOAD; TarInputStream tins = new TarInputStream(ins); TarEntry tarEntry = null; while ((tarEntry = tins.getNextEntry()) != null) { zos.putNextEntry(new ZipEntry(tarEntry.getName())); tins.copyEntryContents(zos); zos.closeEntry(); } tins.close(); } else { // Non-archive file type if (isSpecialSingleFile) kind = Kind.SPECIAL_ZIP_FILE; else kind = Kind.SINGLE_FILE; // Write bytes to a zip file ZipEntry zentry = new ZipEntry(fileName); zos.putNextEntry(zentry); zos.write(bytesForUpload); zos.closeEntry(); } zos.flush(); zos.close(); zipOutput = bos.toByteArray(); } // [END Buffer to ZIP Part] // ========================================================================================== } } } catch (NullPointerException e) { response.sendError(HttpServletResponse.SC_BAD_REQUEST, "There was a problem processing your submission. " + "You should submit files that are either zipped or jarred"); return; } finally { for (FileItem fItem : files) fItem.delete(); } if (webBasedUpload) { clientTool = "web"; clientVersion = kind.toString(); } Submission submission = uploadSubmission(project, studentRegistration, zipOutput, request, submissionTimestamp, clientTool, clientVersion, cvsTimestamp, getDatabaseProps(), getSubmitServerServletLog()); request.setAttribute("submission", submission); if (!webBasedUpload) { response.setContentType("text/plain"); PrintWriter out = response.getWriter(); out.println("Successful submission #" + submission.getSubmissionNumber() + " received for project " + project.getProjectNumber()); out.flush(); out.close(); return; } boolean instructorUpload = ((Boolean) request.getAttribute("instructorViewOfStudent")).booleanValue(); // boolean // isCanonicalSubmission="true".equals(request.getParameter("isCanonicalSubmission")); // set the successful submission as a request attribute String redirectUrl; if (fixedZip) { redirectUrl = request.getContextPath() + "/view/fixedSubmissionUpload.jsp?submissionPK=" + submission.getSubmissionPK(); } if (project.getCanonicalStudentRegistrationPK() == studentRegistration.getStudentRegistrationPK()) { redirectUrl = request.getContextPath() + "/view/instructor/projectUtilities.jsp?projectPK=" + project.getProjectPK(); } else if (instructorUpload) { redirectUrl = request.getContextPath() + "/view/instructor/project.jsp?projectPK=" + project.getProjectPK(); } else { redirectUrl = request.getContextPath() + "/view/project.jsp?projectPK=" + project.getProjectPK(); } response.sendRedirect(redirectUrl); }
From source file:com.migo.utils.GenUtils.java
/** * ??/* ww w . j a v a 2s . c o m*/ */ public static void generatorCode(Map<String, String> table, List<Map<String, String>> columns, ZipOutputStream zip) { //?? Configuration config = getConfig(); //? TableEntity tableEntity = new TableEntity(); tableEntity.setTableName(table.get("tableName")); tableEntity.setComments(table.get("tableComment")); //????Java?? String className = tableToJava(tableEntity.getTableName(), config.getString("tablePrefix")); tableEntity.setClassName(className); tableEntity.setClassname(StringUtils.uncapitalize(className)); //? List<ColumnEntity> columsList = new ArrayList<>(); for (Map<String, String> column : columns) { ColumnEntity columnEntity = new ColumnEntity(); columnEntity.setColumnName(column.get("columnName")); columnEntity.setDataType(column.get("dataType")); columnEntity.setComments(column.get("columnComment")); columnEntity.setExtra(column.get("extra")); //????Java?? String attrName = columnToJava(columnEntity.getColumnName()); columnEntity.setAttrName(attrName); columnEntity.setAttrname(StringUtils.uncapitalize(attrName)); //???Java String attrType = config.getString(columnEntity.getDataType(), "unknowType"); columnEntity.setAttrType(attrType); //? if ("PRI".equalsIgnoreCase(column.get("columnKey")) && tableEntity.getPk() == null) { tableEntity.setPk(columnEntity); } columsList.add(columnEntity); } tableEntity.setColumns(columsList); // if (tableEntity.getPk() == null) { tableEntity.setPk(tableEntity.getColumns().get(0)); } //velocity? Properties prop = new Properties(); prop.put("file.resource.loader.class", "org.apache.velocity.runtime.resource.loader.ClasspathResourceLoader"); Velocity.init(prop); //??? Map<String, Object> map = new HashMap<>(); map.put("tableName", tableEntity.getTableName()); map.put("comments", tableEntity.getComments()); map.put("pk", tableEntity.getPk()); map.put("className", tableEntity.getClassName()); map.put("classname", tableEntity.getClassname()); map.put("pathName", tableEntity.getClassname().toLowerCase()); map.put("columns", tableEntity.getColumns()); map.put("package", config.getString("package")); map.put("author", config.getString("author")); map.put("email", config.getString("email")); map.put("datetime", DateUtils.format(new Date(), DateUtils.DATE_TIME_PATTERN)); VelocityContext context = new VelocityContext(map); //?? List<String> templates = getTemplates(); for (String template : templates) { //? StringWriter sw = new StringWriter(); Template tpl = Velocity.getTemplate(template, "UTF-8"); tpl.merge(context, sw); try { //zip zip.putNextEntry(new ZipEntry( getFileName(template, tableEntity.getClassName(), config.getString("package")))); IOUtils.write(sw.toString(), zip, "UTF-8"); IOUtils.closeQuietly(sw); zip.closeEntry(); } catch (IOException e) { throw new RRException("???" + tableEntity.getTableName(), e); } } }
From source file:com.replaymod.sponge.recording.AbstractRecorder.java
@Override public void addOutput(OutputStream out) throws IOException { ZipOutputStream zipOut = new ZipOutputStream(out); zipOut.putNextEntry(new ZipEntry("recording.tmcpr")); outputs.put(out, zipOut);/*from w w w . ja v a2 s . c om*/ }