List of usage examples for java.util.zip ZipEntry setTime
public void setTime(long time)
From source file:org.fuin.utils4j.Utils4J.java
/** * Adds a file to a ZIP output stream./*from ww w. j a v a 2 s . c om*/ * * @param srcFile * File to add - Cannot be <code>null</code>. * @param destPath * Path to use for the file - May be <code>null</code> or empty. * @param out * Destination stream - Cannot be <code>null</code>. * * @throws IOException * Error writing to the output stream. */ private static void zipFile(final File srcFile, final String destPath, final ZipOutputStream out) throws IOException { final byte[] buf = new byte[1024]; final InputStream in = new BufferedInputStream(new FileInputStream(srcFile)); try { final ZipEntry zipEntry = new ZipEntry( concatPathAndFilename(destPath, srcFile.getName(), File.separator)); zipEntry.setTime(srcFile.lastModified()); out.putNextEntry(zipEntry); int len; while ((len = in.read(buf)) > 0) { out.write(buf, 0, len); } out.closeEntry(); } finally { in.close(); } }
From source file:edu.cmu.tetrad.util.TetradSerializableUtils.java
/** * Creates a zip archive of the currently serialized files in * getCurrentDirectory(), placing the archive in getArchiveDirectory(). * * @throws RuntimeException if clazz cannot be serialized. This exception * has an informative message and wraps the * originally thrown exception as root cause. * @see #getCurrentDirectory()//w ww . ja v a 2s. co m * @see #getArchiveDirectory() */ public void archiveCurrentDirectory() throws RuntimeException { System.out.println("Making zip archive of files in " + getCurrentDirectory() + ", putting it in " + getArchiveDirectory() + "."); File current = new File(getCurrentDirectory()); if (!current.exists() || !current.isDirectory()) { throw new IllegalArgumentException("There is no " + current.getAbsolutePath() + " directory. " + "\nThis is where the serialized classes should be. " + "Please run serializeCurrentDirectory() first."); } File archive = new File(getArchiveDirectory()); if (archive.exists() && !archive.isDirectory()) { throw new IllegalArgumentException( "Output directory " + archive.getAbsolutePath() + " is not a directory."); } if (!archive.exists()) { boolean success = archive.mkdirs(); } String[] filenames = current.list(); // Create a buffer for reading the files byte[] buf = new byte[1024]; try { String version = Version.currentRepositoryVersion().toString(); // Create the ZIP file String outFilename = "serializedclasses-" + version + ".zip"; File _file = new File(getArchiveDirectory(), outFilename); FileOutputStream fileOut = new FileOutputStream(_file); ZipOutputStream out = new ZipOutputStream(fileOut); // Compress the files for (String filename : filenames) { File file = new File(current, filename); FileInputStream in = new FileInputStream(file); // Add ZIP entry to output stream. ZipEntry entry = new ZipEntry(filename); entry.setSize(file.length()); entry.setTime(file.lastModified()); out.putNextEntry(entry); // Transfer bytes from the file to the ZIP file int len; while ((len = in.read(buf)) > 0) { out.write(buf, 0, len); } // Complete the entry out.closeEntry(); in.close(); } // Complete the ZIP file out.close(); System.out.println("Finished writing zip file " + outFilename + "."); } catch (IOException e) { throw new RuntimeException("There was an I/O error associated with " + "the process of zipping up files in " + getCurrentDirectory() + ".", e); } }
From source file:edu.cmu.tetradapp.util.TetradSerializableUtils.java
/** * Creates a zip archive of the currently serialized files in * getCurrentDirectory(), placing the archive in getArchiveDirectory(). * * @throws RuntimeException if clazz cannot be serialized. This exception * has an informative message and wraps the * originally thrown exception as root cause. * @see #getCurrentDirectory()/* w ww .j a v a 2 s . c o m*/ * @see #getArchiveDirectory() */ public void archiveCurrentDirectory() throws RuntimeException { System.out.println("Making zip archive of files in " + getCurrentDirectory() + ", putting it in " + getArchiveDirectory() + "."); File current = new File(getCurrentDirectory()); if (!current.exists() || !current.isDirectory()) { throw new IllegalArgumentException("There is no " + current.getAbsolutePath() + " directory. " + "\nThis is where the serialized classes should be. " + "Please run serializeCurrentDirectory() first."); } File archive = new File(getArchiveDirectory()); if (archive.exists() && !archive.isDirectory()) { throw new IllegalArgumentException( "Output directory " + archive.getAbsolutePath() + " is not a directory."); } if (!archive.exists()) { archive.mkdirs(); } String[] filenames = current.list(); // Create a buffer for reading the files byte[] buf = new byte[1024]; try { String version = Version.currentRepositoryVersion().toString(); // Create the ZIP file String outFilename = "serializedclasses-" + version + ".zip"; File _file = new File(getArchiveDirectory(), outFilename); FileOutputStream fileOut = new FileOutputStream(_file); ZipOutputStream out = new ZipOutputStream(fileOut); // Compress the files for (String filename : filenames) { File file = new File(current, filename); FileInputStream in = new FileInputStream(file); // Add ZIP entry to output stream. ZipEntry entry = new ZipEntry(filename); entry.setSize(file.length()); entry.setTime(file.lastModified()); out.putNextEntry(entry); // Transfer bytes from the file to the ZIP file int len; while ((len = in.read(buf)) > 0) { out.write(buf, 0, len); } // Complete the entry out.closeEntry(); in.close(); } // Complete the ZIP file out.close(); System.out.println("Finished writing zip file " + outFilename + "."); } catch (IOException e) { throw new RuntimeException("There was an I/O error associated with " + "the process of zipping up files in " + getCurrentDirectory() + ".", e); } }
From source file:com.liferay.ide.server.remote.AbstractRemoteServerPublisher.java
protected void addToZip(IPath path, IResource resource, ZipOutputStream zip, boolean adjustGMTOffset) throws IOException, CoreException { switch (resource.getType()) { case IResource.FILE: ZipEntry zipEntry = new ZipEntry(path.toString()); zip.putNextEntry(zipEntry);/*from ww w . j ava 2s . c o m*/ InputStream contents = ((IFile) resource).getContents(); if (adjustGMTOffset) { TimeZone currentTimeZone = TimeZone.getDefault(); Calendar currentDt = new GregorianCalendar(currentTimeZone, Locale.getDefault()); // Get the Offset from GMT taking current TZ into account int gmtOffset = currentTimeZone.getOffset(currentDt.get(Calendar.ERA), currentDt.get(Calendar.YEAR), currentDt.get(Calendar.MONTH), currentDt.get(Calendar.DAY_OF_MONTH), currentDt.get(Calendar.DAY_OF_WEEK), currentDt.get(Calendar.MILLISECOND)); zipEntry.setTime(System.currentTimeMillis() + (gmtOffset * -1)); } try { IOUtils.copy(contents, zip); } finally { contents.close(); } break; case IResource.FOLDER: case IResource.PROJECT: IContainer container = (IContainer) resource; IResource[] members = container.members(); for (IResource res : members) { addToZip(path.append(res.getName()), res, zip, adjustGMTOffset); } } }
From source file:edu.umd.cs.eclipse.courseProjectManager.TurninProjectAction.java
public void run(IAction action) { // TODO Refactor: Should the places where we raise a dialog and return // could throw an exception instead? String timeOfSubmission = "t" + System.currentTimeMillis(); // Make sure we can get the workbench... IWorkbench workbench = PlatformUI.getWorkbench(); if (workbench == null) { Dialogs.errorDialog(null, "Warning: project submission failed", "Could not submit project", "Internal error: Can't get workbench", IStatus.ERROR); return;//from w w w . j a v a2 s. c om } // ...and the workbenchWindow IWorkbenchWindow wwin = workbench.getActiveWorkbenchWindow(); if (wwin == null) { Dialogs.errorDialog(null, "Error submitting project", "Could not submit project", "Internal error: Can't get workbench window", IStatus.ERROR); return; } // Shell to use as parent of dialogs. Shell parent = wwin.getShell(); // Sanity check. if (!(selection instanceof IStructuredSelection)) { Dialogs.errorDialog(parent, "Warning: Selection is Invalid", "Invalid turnin action: You have selected an object that is not a Project. Please select a Project and try again.", "Object selected is not a Project", IStatus.WARNING); return; } IStructuredSelection structured = (IStructuredSelection) selection; Object obj = structured.getFirstElement(); Debug.print("Selection object is a " + obj.getClass().getName() + " @" + System.identityHashCode(obj)); IProject project; if (obj instanceof IProject) { project = (IProject) obj; } else if (obj instanceof IProjectNature) { project = ((IProjectNature) obj).getProject(); } else { Dialogs.errorDialog(null, "Warning: Selection is Invalid", "Invalid turnin action: You have selected an object that is not a Project. Please select a Project and try again.", "Object selected is not a Project", IStatus.WARNING); return; } Debug.print("Got the IProject for the turnin action @" + System.identityHashCode(project)); // ================================= save dirty editors // ======================================== // save dirty editors try { if (!saveDirtyEditors(project, workbench)) { Dialogs.errorDialog(parent, "Submit not performed", "Projects cannot be submitted unless all open files are saved", "Unsaved files prevent submission", IStatus.WARNING); return; } } catch (CoreException e) { Dialogs.errorDialog(parent, "Submit not performed", "Could not turn on cvs management for all project files", e); return; } // ========================= Add all non-ignored files in the project // ========================= IResource[] files; try { Set<IResource> resourceSet = getProjectResources(project); ArrayList<IFile> addedFiles = new ArrayList<IFile>(); for (Iterator<IResource> iter = resourceSet.iterator(); iter.hasNext();) { IResource resource = iter.next(); if (resource instanceof IFile) { IFile file = (IFile) resource; if (!AutoCVSPlugin.isCVSIgnored(file) && !AutoCVSPlugin.isCVSManaged(file)) { addedFiles.add(file); } } } files = (IResource[]) addedFiles.toArray(new IResource[addedFiles.size()]); } catch (CoreException e) { Dialogs.errorDialog(parent, "Submit not performed", "Could not perform submit; unable to find non-ignored resources", e); return; // TODO what to do here? } // ================================= perform CVS commit // ======================================== // TODO Somehow move this into the previous try block // This forces add/commit operations when AutoSync was shut off // Would it just be easier to enable autoSync and then trigger // a resource changed delta, since this method appears to enable // autoSync anyway? // String cvsStatus = "Not performed"; try { cvsStatus = forceCommit(project, files); } catch (Exception e) { Dialogs.errorDialog(parent, "CVS commit not performed as part of submission due to unexpected exception", e.getClass().getName() + " " + e.getMessage(), e); } // ================================= perform CVS tag // ======================================== try { CVSOperations.tagProject(project, timeOfSubmission, CVSOperations.SYNC); } catch (Exception e) { AutoCVSPlugin.getPlugin().getEventLog() .logError("Error tagging submission; submission via the web unlikely to work", e); } // ================================= find properties // ======================================== // find the .submitProject file IResource submitProjectFile = project.findMember(AutoCVSPlugin.SUBMITPROJECT); if (submitProjectFile == null) { Dialogs.errorDialog(parent, "Warning: Project submission not enabled", "Submission is not enabled", "There is no " + AutoCVSPlugin.SUBMITPROJECT + " file for the project", IStatus.ERROR); return; } // Get the properties from the .submit file, and the .submitUser file, // if it exists // or can be fetched from the server Properties allSubmissionProps = null; try { allSubmissionProps = getAllProperties(timeOfSubmission, parent, project, submitProjectFile); } catch (IOException e) { String message = "IOException finding " + AutoCVSPlugin.SUBMITPROJECT + " and " + AutoCVSPlugin.SUBMITUSER + " files; " + cvsStatus; AutoCVSPlugin.getPlugin().getEventLog().logError(message, e); Dialogs.errorDialog(parent, "Submission failed", message, e.getMessage(), IStatus.ERROR); Debug.print("IOException: " + e); return; } catch (CoreException e) { String message = "IOException finding " + AutoCVSPlugin.SUBMITPROJECT + " and " + AutoCVSPlugin.SUBMITUSER + " files; " + cvsStatus; AutoCVSPlugin.getPlugin().getEventLog().logError(message, e); Dialogs.errorDialog(parent, "Submission failed", message, e.getMessage(), IStatus.ERROR); Debug.print("CoreException: " + e); return; } // // THE ACTUAL SUBMIT HAPPENS HERE // try { // ============================== find files to submit // ==================================== Collection<IFile> cvsFiles = findFilesForSubmission(project); // ========================== assemble zip file in byte array // ============================== ByteArrayOutputStream bytes = new ByteArrayOutputStream(4096); ZipOutputStream zipfile = new ZipOutputStream(bytes); zipfile.setComment("zipfile for submission created by CourseProjectManager version " + AutoCVSPlugin.getPlugin().getVersion()); try { byte[] buf = new byte[4096]; for (IFile file : cvsFiles) { if (!file.exists()) { Debug.print("Resource " + file.getName() + " being ignored because it doesn't exist"); continue; } ZipEntry entry = new ZipEntry(file.getProjectRelativePath().toString()); entry.setTime(file.getModificationStamp()); zipfile.putNextEntry(entry); // Copy file data to zip file InputStream in = file.getContents(); try { while (true) { int n = in.read(buf); if (n < 0) break; zipfile.write(buf, 0, n); } } finally { in.close(); } zipfile.closeEntry(); } } catch (IOException e1) { Dialogs.errorDialog(parent, "Warning: Project submission failed", "Unable to zip files for submission\n" + cvsStatus, e1); return; } finally { if (zipfile != null) zipfile.close(); } // ============================== Post to submit server // ==================================== String version = System.getProperties().getProperty("java.runtime.version"); boolean useEasyHttps = version.startsWith("1.3") || version.startsWith("1.2") || version.startsWith("1.4.0") || version.startsWith("1.4.1") || version.startsWith("1.4.2_0") && version.charAt(7) < '5'; if (useEasyHttps) { String submitURL = allSubmissionProps.getProperty("submitURL"); if (submitURL.startsWith("https")) submitURL = "easy" + submitURL; allSubmissionProps.setProperty("submitURL", submitURL); } // prepare multipart post method MultipartPostMethod filePost = new MultipartPostMethod(allSubmissionProps.getProperty("submitURL")); // add properties addAllPropertiesButSubmitURL(allSubmissionProps, filePost); // add filepart byte[] allInput = bytes.toByteArray(); filePost.addPart(new FilePart("submittedFiles", new ByteArrayPartSource("submit.zip", allInput))); // prepare httpclient HttpClient client = new HttpClient(); client.setConnectionTimeout(5000); int status = client.executeMethod(filePost); // Piggy-back uploading the launch events onto submitting. EclipseLaunchEventLog.postEventLogToServer(project); if (status == HttpStatus.SC_OK) { Dialogs.okDialog(parent, "Project submission successful", "Project " + allSubmissionProps.getProperty("projectNumber") + " was submitted successfully\n" + filePost.getResponseBodyAsString()); } else { Dialogs.errorDialog(parent, "Warning: Project submission failed", "Project submission failed", filePost.getStatusText() + "\n " + cvsStatus, IStatus.CANCEL); AutoCVSPlugin.getPlugin().getEventLog().logMessage(filePost.getResponseBodyAsString()); } } catch (CoreException e) { Dialogs.errorDialog(parent, "Warning: Project submission failed", "Project submissions via https failed\n" + cvsStatus, e); } catch (HttpConnection.ConnectionTimeoutException e) { Dialogs.errorDialog(parent, "Warning: Project submission failed", "Project submissions failed", "Connection timeout while trying to connect to submit server\n " + cvsStatus, IStatus.ERROR); } catch (IOException e) { Dialogs.errorDialog(parent, "Warning: Project submission failed", "Project submissions failed\n " + cvsStatus, e); } }
From source file:de.mpg.escidoc.services.dataacquisition.DataHandlerBean.java
/** * fetch data from a given url.//from w w w. j a v a2 s . c o m * * @param url * @return byte[] * @throws SourceNotAvailableException * @throws RuntimeException * @throws AccessException */ public byte[] fetchMetadatafromURL(URL url) throws SourceNotAvailableException, RuntimeException, AccessException { byte[] input = null; URLConnection conn = null; Date retryAfter = null; ByteArrayOutputStream baos = new ByteArrayOutputStream(); ZipOutputStream zos = new ZipOutputStream(baos); try { conn = ProxyHelper.openConnection(url); HttpURLConnection httpConn = (HttpURLConnection) conn; int responseCode = httpConn.getResponseCode(); switch (responseCode) { case 503: String retryAfterHeader = conn.getHeaderField("Retry-After"); if (retryAfterHeader != null) { SimpleDateFormat dateFormat = new SimpleDateFormat("EEE, dd MMM yyyy HH:mm:ss z"); retryAfter = dateFormat.parse(retryAfterHeader); this.logger.debug("Source responded with 503, retry after " + retryAfter + "."); throw new SourceNotAvailableException(retryAfter); } break; case 302: String alternativeLocation = conn.getHeaderField("Location"); return fetchMetadatafromURL(new URL(alternativeLocation)); case 200: this.logger.info("Source responded with 200."); // Fetch file GetMethod method = new GetMethod(url.toString()); HttpClient client = new HttpClient(); ProxyHelper.executeMethod(client, method); input = method.getResponseBody(); httpConn.disconnect(); // Create zip file with fetched file ZipEntry ze = new ZipEntry("unapi"); ze.setSize(input.length); ze.setTime(this.currentDate()); CRC32 crc321 = new CRC32(); crc321.update(input); ze.setCrc(crc321.getValue()); zos.putNextEntry(ze); zos.write(input); zos.flush(); zos.closeEntry(); zos.close(); this.setContentType("application/zip"); this.setFileEnding(".zip"); break; case 403: throw new AccessException("Access to url " + url + " is restricted."); default: throw new RuntimeException("An error occurred during importing from external system: " + responseCode + ": " + httpConn.getResponseMessage() + "."); } } catch (AccessException e) { this.logger.error("Access denied.", e); throw new AccessException(url.toString()); } catch (Exception e) { throw new RuntimeException(e); } return baos.toByteArray(); }
From source file:VASSAL.tools.io.ZipArchive.java
private void writeToDisk() throws IOException { // write all files to a temporary zip archive final File tmpFile = File.createTempFile("tmp", ".zip", archiveFile.getParentFile()); ZipOutputStream out = null;/*www .ja v a 2 s.co m*/ try { out = new ZipOutputStream(new BufferedOutputStream(new FileOutputStream(tmpFile))); out.setLevel(9); final byte[] buf = new byte[8192]; if (zipFile != null) { zipFile.close(); zipFile = null; // copy unmodified file into the temp archive ZipInputStream in = null; try { in = new ZipInputStream(new BufferedInputStream(new FileInputStream(archiveFile))); ZipEntry ze = null; while ((ze = in.getNextEntry()) != null) { // skip modified or removed entries final Entry e = entries.get(ze.getName()); if (e == null || e.file != null) continue; // We can't reuse entries for compressed files because there's // no way to reset all fields to acceptable values. if (ze.getMethod() == ZipEntry.DEFLATED) { ze = new ZipEntry(ze.getName()); ze.setTime(ze.getTime()); } out.putNextEntry(ze); IOUtils.copy(in, out, buf); entries.remove(ze.getName()); } in.close(); } finally { IOUtils.closeQuietly(in); } } for (String name : entries.keySet()) { final Entry e = entries.get(name); // write new or modified file into the temp archive FileInputStream in = null; try { in = new FileInputStream(e.file); out.putNextEntry(e.ze); IOUtils.copy(in, out, buf); in.close(); } finally { IOUtils.closeQuietly(in); } } out.close(); } finally { IOUtils.closeQuietly(out); } // Replace old archive with temp archive. if (!tmpFile.renameTo(archiveFile)) { try { FileUtils.forceDelete(archiveFile); FileUtils.moveFile(tmpFile, archiveFile); } catch (IOException e) { String err = "Unable to overwrite " + archiveFile.getAbsolutePath() + ": "; if (!archiveFile.exists()) { err += " file does not exist."; } else if (!archiveFile.canWrite()) { err += " file is not writable."; } else if (!archiveFile.isFile()) { err += " not a normal file."; } err += " Data written to " + tmpFile.getAbsolutePath() + " instead."; throw (IOException) new IOException(err).initCause(e); } } closed = true; modified = false; entries.clear(); }
From source file:de.mpg.escidoc.services.dataacquisition.DataHandlerBean.java
/** * Operation for fetching data of type FILE. * // w ww. j a v a 2 s .c o m * @param importSource * @param identifier * @param listOfFormats * @return byte[] of the fetched file, zip file if more than one record was * fetched * @throws RuntimeException * @throws SourceNotAvailableException */ private byte[] fetchData(String identifier, Format[] formats) throws SourceNotAvailableException, RuntimeException, FormatNotAvailableException { byte[] in = null; FullTextVO fulltext = new FullTextVO(); ByteArrayOutputStream baos = new ByteArrayOutputStream(); ZipOutputStream zos = new ZipOutputStream(baos); try { // Call fetch file for every given format for (int i = 0; i < formats.length; i++) { Format format = formats[i]; fulltext = this.util.getFtObjectToFetch(this.currentSource, format.getName(), format.getType(), format.getEncoding()); // Replace regex with identifier String decoded = java.net.URLDecoder.decode(fulltext.getFtUrl().toString(), this.currentSource.getEncoding()); fulltext.setFtUrl(new URL(decoded)); fulltext.setFtUrl( new URL(fulltext.getFtUrl().toString().replaceAll(this.regex, identifier.trim()))); this.logger.debug("Fetch file from URL: " + fulltext.getFtUrl()); // escidoc file if (this.currentSource.getHarvestProtocol().equalsIgnoreCase("ejb")) { in = this.fetchEjbFile(fulltext, identifier); } // other file else { in = this.fetchFile(fulltext); } this.setFileProperties(fulltext); // If only one file => return it in fetched format if (formats.length == 1) { return in; } // If more than one file => add it to zip else { // If cone service is not available (we do not get a // fileEnding) we have // to make sure that the zip entries differ in name. String fileName = identifier; if (this.getFileEnding().equals("")) { fileName = fileName + "_" + i; } ZipEntry ze = new ZipEntry(fileName + this.getFileEnding()); ze.setSize(in.length); ze.setTime(this.currentDate()); CRC32 crc321 = new CRC32(); crc321.update(in); ze.setCrc(crc321.getValue()); zos.putNextEntry(ze); zos.write(in); zos.flush(); zos.closeEntry(); } } this.setContentType("application/zip"); this.setFileEnding(".zip"); zos.close(); } catch (SourceNotAvailableException e) { this.logger.error("Import Source " + this.currentSource + " not available.", e); throw new SourceNotAvailableException(e); } catch (FormatNotAvailableException e) { throw new FormatNotAvailableException(e.getMessage()); } catch (Exception e) { throw new RuntimeException(e); } return baos.toByteArray(); }
From source file:org.rhq.bundle.ant.AntLauncherTest.java
private File createZip(String[] content, File destDir, String zipName, String[] entryName) throws Exception { FileOutputStream stream = null; ZipOutputStream out = null;// ww w .j a va 2s . co m try { destDir.mkdirs(); File zipFile = new File(destDir, zipName); stream = new FileOutputStream(zipFile); out = new ZipOutputStream(stream); assertEquals(content.length, entryName.length); for (int i = 0; i < content.length; i++) { ZipEntry zipAdd = new ZipEntry(entryName[i]); zipAdd.setTime(System.currentTimeMillis()); out.putNextEntry(zipAdd); out.write(content[i].getBytes()); } return zipFile; } finally { if (out != null) { out.close(); } if (stream != null) { stream.close(); } } }
From source file:org.broad.igv.feature.genome.GenomeManager.java
/** * Rewrite the {@link Globals#GENOME_ARCHIVE_SEQUENCE_FILE_LOCATION_KEY} property to equal * the specified {@code newSequencePath}. Works by creating a temp file and renaming * * @param targetFile A .genome file, in zip format * @param newSequencePath/*from www . j a va2s. com*/ * @return boolean indicating success or failure. * @throws IOException */ static boolean rewriteSequenceLocation(File targetFile, String newSequencePath) throws IOException { ZipFile targetZipFile = new ZipFile(targetFile); boolean success = false; File tmpZipFile = File.createTempFile("tmpGenome", ".zip"); ZipEntry propEntry = targetZipFile.getEntry(Globals.GENOME_ARCHIVE_PROPERTY_FILE_NAME); InputStream propertyInputStream = null; ZipOutputStream zipOutputStream = null; Properties inputProperties = new Properties(); try { propertyInputStream = targetZipFile.getInputStream(propEntry); BufferedReader reader = new BufferedReader(new InputStreamReader(propertyInputStream)); //Copy over property.txt, only replacing a few properties inputProperties.load(reader); inputProperties.put(Globals.GENOME_ARCHIVE_SEQUENCE_FILE_LOCATION_KEY, newSequencePath); inputProperties.put(Globals.GENOME_ARCHIVE_CUSTOM_SEQUENCE_LOCATION_KEY, Boolean.TRUE.toString()); ByteArrayOutputStream propertyBytes = new ByteArrayOutputStream(); PrintWriter propertyFileWriter = new PrintWriter(new OutputStreamWriter(propertyBytes)); inputProperties.store(propertyFileWriter, null); propertyFileWriter.flush(); byte[] newPropertyBytes = propertyBytes.toByteArray(); Enumeration<? extends ZipEntry> entries = targetZipFile.entries(); zipOutputStream = new ZipOutputStream(new FileOutputStream(tmpZipFile)); while (entries.hasMoreElements()) { ZipEntry curEntry = entries.nextElement(); ZipEntry writeEntry = null; if (curEntry.getName().equals(Globals.GENOME_ARCHIVE_PROPERTY_FILE_NAME)) { writeEntry = new ZipEntry(Globals.GENOME_ARCHIVE_PROPERTY_FILE_NAME); writeEntry.setSize(newPropertyBytes.length); zipOutputStream.putNextEntry(writeEntry); zipOutputStream.write(newPropertyBytes); continue; } else { //Because the compressed size can vary, //we generate a new ZipEntry and copy some attributes writeEntry = new ZipEntry(curEntry.getName()); writeEntry.setSize(curEntry.getSize()); writeEntry.setComment(curEntry.getComment()); writeEntry.setTime(curEntry.getTime()); } zipOutputStream.putNextEntry(writeEntry); InputStream tmpIS = null; try { tmpIS = targetZipFile.getInputStream(writeEntry); int bytes = IOUtils.copy(tmpIS, zipOutputStream); log.debug(bytes + " bytes written to " + targetFile); } finally { if (tmpIS != null) tmpIS.close(); } } } catch (Exception e) { tmpZipFile.delete(); throw new RuntimeException(e.getMessage(), e); } finally { if (propertyInputStream != null) propertyInputStream.close(); if (zipOutputStream != null) { zipOutputStream.flush(); zipOutputStream.finish(); zipOutputStream.close(); } zipOutputStream = null; System.gc(); success = true; } //This is a hack. I don't know why it's necessary, //but for some reason the output zip file seems to be corrupt //at least when called from GenomeManager.refreshArchive try { Thread.sleep(1500); } catch (InterruptedException e) { // } //Rename tmp file if (success) { targetFile.delete(); FileUtils.copyFile(tmpZipFile, targetFile); success = targetFile.exists(); tmpZipFile.delete(); } return success; }