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AISE-TUDelft

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ML4SE23_G4_Small_Clone_Bench

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@Override public void execute () { File currentModelDirectory = new File (this.globalData.getData (String.class, GlobalData.MODEL_INSTALL_DIRECTORY)); File mobileDirectory = new File (currentModelDirectory, "mobile"); mobileDirectory.mkdir (); File mobileModelFile = new File (mobileDirectory, "mobile_model.zip"); FileOutputStream outputStream = null; ZipOutputStream zipStream = null; BusinessModel businessModel = BusinessUnit.getInstance ().getBusinessModel (); try { mobileModelFile.createNewFile (); outputStream = new FileOutputStream (mobileModelFile); zipStream = new ZipOutputStream (outputStream); Dictionary dictionary = businessModel.getDictionary (); for (Definition definition : dictionary.getAllDefinitions ()) { ZipEntry entry = new ZipEntry (definition.getRelativeFileName ()); zipStream.putNextEntry (entry); writeBinary (definition.getAbsoluteFileName (), zipStream); } final String modelFilename = "model.xml"; ZipEntry entry = new ZipEntry (modelFilename); zipStream.putNextEntry (entry); writeBinary (businessModel.getAbsoluteFilename (modelFilename), zipStream); final String logoFilename = dictionary.getModel ().getImageSource (LogoType.mobile); entry = new ZipEntry (logoFilename); zipStream.putNextEntry (entry); writeBinary (businessModel.getAbsoluteFilename (logoFilename), zipStream); } catch (IOException e) { agentLogger.error (e); } finally { StreamHelper.close (zipStream); StreamHelper.close (outputStream); } }

void copyZipToZip (ZipInputStream zis, ZipOutputStream zos) throws Exception { ZipEntry entry; byte [] buffer = new byte [1]; while ((entry = zis.getNextEntry ()) != null) { zos.putNextEntry (new ZipEntry (entry.getName ())); while (zis.available () == 1) { zis.read (buffer, 0, buffer.length); zos.write (buffer, 0, buffer.length); } zis.closeEntry (); zos.closeEntry (); } }

Zip Files

Type-3 (WT3/4)

private static void solve_l1r_l2_svc (Problem prob_col, double [] w, double eps, double Cp, double Cn) { int l = prob_col.l; int w_size = prob_col.n; int j, s, iter = 0; int max_iter = 1000; int active_size = w_size; int max_num_linesearch = 20; double sigma = 0.01; double d, G_loss, G, H; double Gmax_old = Double.POSITIVE_INFINITY; double Gmax_new; double Gmax_init = 0; double d_old, d_diff; double loss_old = 0; double loss_new; double appxcond, cond; int [] index = new int [w_size]; byte [] y = new byte [l]; double [] b = new double [l]; double [] xj_sq = new double [w_size]; double [] C = new double [] {Cn, 0, Cp}; for (j = 0; j < l; j ++) { b [j] = 1; if (prob_col.y [j] > 0) y [j] = 1; else y [j] = - 1; } for (j = 0; j < w_size; j ++) { w [j] = 0; index [j] = j; xj_sq [j] = 0; for (FeatureNode xi : prob_col.x [j]) { int ind = xi.index - 1; double val = xi.value; xi.value *= y [ind]; xj_sq [j] += C [GETI (y, ind)] * val * val; } } while (iter < max_iter) { Gmax_new = 0; for (j = 0; j < active_size; j ++) { int i = j + random.nextInt (active_size - j); swap (index, i, j); } for (s = 0; s < active_size; s ++) { j = index [s]; G_loss = 0; H = 0; for (FeatureNode xi : prob_col.x [j]) { int ind = xi.index - 1; if (b [ind] > 0) { double val = xi.value; double tmp = C [GETI (y, ind)] * val; G_loss -= tmp * b [ind]; H += tmp * val; } } G_loss *= 2; G = G_loss; H *= 2; H = Math.max (H, 1e-12); double Gp = G + 1; double Gn = G - 1; double violation = 0; if (w [j] == 0) { if (Gp < 0) violation = - Gp; else if (Gn > 0) violation = Gn; else if (Gp > Gmax_old / l && Gn < - Gmax_old / l) { active_size --; swap (index, s, active_size); s --; continue; } } else if (w [j] > 0) violation = Math.abs (Gp); else violation = Math.abs (Gn); Gmax_new = Math.max (Gmax_new, violation); if (Gp <= H * w [j]) d = - Gp / H; else if (Gn >= H * w [j]) d = - Gn / H; else d = - w [j]; if (Math.abs (d) < 1.0e-12) continue; double delta = Math.abs (w [j] + d) - Math.abs (w [j]) + G * d; d_old = 0; int num_linesearch; for (num_linesearch = 0; num_linesearch < max_num_linesearch; num_linesearch ++) { d_diff = d_old - d; cond = Math.abs (w [j] + d) - Math.abs (w [j]) - sigma * delta; appxcond = xj_sq [j] * d * d + G_loss * d + cond; if (appxcond <= 0) { for (FeatureNode x : prob_col.x [j]) { b [x.index - 1] += d_diff * x.value; } break; } if (num_linesearch == 0) { loss_old = 0; loss_new = 0; for (FeatureNode x : prob_col.x [j]) { int ind = x.index - 1; if (b [ind] > 0) { loss_old += C [GETI (y, ind)] * b [ind] * b [ind]; } double b_new = b [ind] + d_diff * x.value; b [ind] = b_new; if (b_new > 0) { loss_new += C [GETI (y, ind)] * b_new * b_new; } } } else { loss_new = 0; for (FeatureNode x : prob_col.x [j]) { int ind = x.index - 1; double b_new = b [ind] + d_diff * x.value; b [ind] = b_new; if (b_new > 0) { loss_new += C [GETI (y, ind)] * b_new * b_new; } } } cond = cond + loss_new - loss_old; if (cond <= 0) break; else { d_old = d; d *= 0.5; delta *= 0.5; } } w [j] += d; if (num_linesearch >= max_num_linesearch) { info ("#"); for (int i = 0; i < l; i ++) b [i] = 1; for (int i = 0; i < w_size; i ++) { if (w [i] == 0) continue; for (FeatureNode x : prob_col.x [i]) { b [x.index - 1] -= w [i] * x.value; } } } } if (iter == 0) Gmax_init = Gmax_new; iter ++; if (iter % 10 == 0) info ("."); if (Gmax_new <= eps * Gmax_init) { if (active_size == w_size) break; else { active_size = w_size; info ("*"); Gmax_old = Double.POSITIVE_INFINITY; continue; } } Gmax_old = Gmax_new; } info ("%noptimization finished, #iter = %d%n", iter); if (iter >= max_iter) info ("%nWARNING: reaching max number of iterations%n"); double v = 0; int nnz = 0; for (j = 0; j < w_size; j ++) { for (FeatureNode x : prob_col.x [j]) { x.value *= prob_col.y [x.index - 1]; } if (w [j] != 0) { v += Math.abs (w [j]); nnz ++; } } for (j = 0; j < l; j ++) if (b [j] > 0) v += C [GETI (y, j)] * b [j] * b [j]; info ("Objective value = %f%n", v); info ("#nonzeros/#features = %d/%d%n", nnz, w_size); }

public void shuffle () { Card tempCard = new Card (); for (int i = 0; i < NUM_CARDS; i ++) { int j = i + r.nextInt (NUM_CARDS - i); tempCard = cards [j]; cards [j] = cards [i]; cards [i] = tempCard; } position = 0; }

Shuffle Array in Place

Type-3 (WT3/4)

public synchronized void writeFile (String filename) throws IOException { int amount; byte buffer [] = new byte [4096]; File f = new File (filename); FileInputStream in = new FileInputStream (f); putNextEntry (new ZipEntry (f.getName ())); while ((amount = in.read (buffer)) != - 1) write (buffer, 0, amount); closeEntry (); in.close (); }

private static void zip (File srcDir, File originSrcDir, ZipOutputStream dstStream) throws IOException { byte [] buffer = new byte [ZIP_BUFFER_SIZE]; int bytes = 0; String [] dirList = srcDir.list (); for (int i = 0; i < dirList.length; i ++) { File file = new File (srcDir, dirList [i]); if (file.isDirectory ()) { zip (file, originSrcDir, dstStream); continue; } FileInputStream fis = new FileInputStream (file); ZipEntry entry = new ZipEntry (TFileHandler.removeDirectoryPath (originSrcDir.getAbsolutePath (), file.getAbsolutePath ())); dstStream.putNextEntry (entry); while ((bytes = fis.read (buffer)) != - 1) dstStream.write (buffer, 0, bytes); fis.close (); } }

Zip Files

Type-3 (WT3/4)

void initOut () throws IOException { if (zipped) { zout = new ZipOutputStream (sink); zout.putNextEntry (new ZipEntry ("file.xml")); this.xout = new OutputStreamWriter (zout, "UTF8"); } else { this.xout = new OutputStreamWriter (sink, "UTF8"); } }

public static boolean addZipEntry (String srcZipFile, String newEntryFile, String dstFile) { java.util.zip.ZipOutputStream zout = null; InputStream is = null; try { if (new File (newEntryFile).isDirectory () && ! newEntryFile.substring (newEntryFile.length () - 1).equals (File.separator)) { newEntryFile = newEntryFile + File.separator; } System.err.println ("============"); File fn = new File (dstFile); if (! fn.exists ()) { fn.createNewFile (); } zout = new java.util.zip.ZipOutputStream (new FileOutputStream (dstFile)); ZipFile zipfile = new ZipFile (srcZipFile); ZipEntry entry = null; Enumeration e = zipfile.entries (); byte [] buffer = new byte [1024]; while (e.hasMoreElements ()) { entry = (ZipEntry) e.nextElement (); System.err.println (entry.getName ()); zout.putNextEntry (entry); is = new BufferedInputStream (zipfile.getInputStream (entry)); int count; while ((count = is.read (buffer, 0, 1024)) != - 1) { zout.write (buffer, 0, count); zout.flush (); } is.close (); zout.closeEntry (); } zipFile (null, newEntryFile, "*.*", zout); zout.close (); return true; } catch (java.io.IOException ioex) { LogUtil.getLogger ().error (ioex.getMessage (), ioex); ioex.printStackTrace (); return false; } finally { try { if (zout != null) { zout.close (); } } catch (Exception ex) { } try { if (is != null) { is.close (); } } catch (Exception ex) { } } }

Zip Files

Type-3 (WT3/4)

public void testSavepoint4 () throws Exception { Statement stmt = con.createStatement (); stmt.execute ("CREATE TABLE #savepoint4 (data int)"); stmt.close (); con.setAutoCommit (false); for (int i = 0; i < 3; i ++) { PreparedStatement pstmt = con.prepareStatement ("INSERT INTO #savepoint4 (data) VALUES (?)"); pstmt.setInt (1, 1); assertTrue (pstmt.executeUpdate () == 1); Savepoint savepoint = con.setSavepoint (); assertNotNull (savepoint); assertTrue (savepoint.getSavepointId () == 1); try { savepoint.getSavepointName (); assertTrue (false); } catch (SQLException e) { } pstmt.setInt (1, 2); assertTrue (pstmt.executeUpdate () == 1); pstmt.close (); pstmt = con.prepareStatement ("SELECT SUM(data) FROM #savepoint4"); ResultSet rs = pstmt.executeQuery (); assertTrue (rs.next ()); assertTrue (rs.getInt (1) == 3); assertTrue (! rs.next ()); pstmt.close (); rs.close (); con.rollback (savepoint); pstmt = con.prepareStatement ("SELECT SUM(data) FROM #savepoint4"); rs = pstmt.executeQuery (); assertTrue (rs.next ()); assertTrue (rs.getInt (1) == 1); assertTrue (! rs.next ()); pstmt.close (); rs.close (); con.rollback (); } con.setAutoCommit (true); }

public boolean actualizarIdPartida (int idJugadorDiv, int idRonda, int idPartida) { int intResult = 0; String sql = "UPDATE jugadorxdivxronda " + " SET idPartida = " + idPartida + " WHERE jugadorxDivision_idJugadorxDivision = " + idJugadorDiv + " AND ronda_numeroRonda = " + idRonda; try { connection = conexionBD.getConnection (); connection.setAutoCommit (false); ps = connection.prepareStatement (sql); intResult = ps.executeUpdate (); connection.commit (); } catch (SQLException ex) { ex.printStackTrace (); try { connection.rollback (); } catch (SQLException exe) { exe.printStackTrace (); } } finally { conexionBD.close (ps); conexionBD.close (connection); } return (intResult > 0); }

Execute update and rollback.

Type-3 (WT3/4)

public static String MD5 (String s) { try { MessageDigest m = MessageDigest.getInstance ("MD5"); m.update (s.getBytes (), 0, s.length ()); return new BigInteger (1, m.digest ()).toString (16); } catch (NoSuchAlgorithmException ex) { return ""; } }

private byte [] szyfrujKlucz (byte [] kluczSesyjny) { byte [] zaszyfrowanyKlucz = null; byte [] klucz = null; try { MessageDigest skrot = MessageDigest.getInstance ("SHA-1"); skrot.update (haslo.getBytes ()); byte [] skrotHasla = skrot.digest (); Object kluczDoKlucza = MARS_Algorithm.makeKey (skrotHasla); int resztaKlucza = this.dlugoscKlucza % ROZMIAR_BLOKU; if (resztaKlucza == 0) { klucz = kluczSesyjny; zaszyfrowanyKlucz = new byte [this.dlugoscKlucza]; } else { int liczbaBlokow = this.dlugoscKlucza / ROZMIAR_BLOKU + 1; int nowyRozmiar = liczbaBlokow * ROZMIAR_BLOKU; zaszyfrowanyKlucz = new byte [nowyRozmiar]; klucz = new byte [nowyRozmiar]; byte roznica = (byte) (ROZMIAR_BLOKU - resztaKlucza); System.arraycopy (kluczSesyjny, 0, klucz, 0, kluczSesyjny.length); for (int i = kluczSesyjny.length; i < nowyRozmiar; i ++) klucz [i] = (byte) roznica; } byte [] szyfrogram = null; int liczbaBlokow = klucz.length / ROZMIAR_BLOKU; int offset = 0; for (offset = 0; offset < liczbaBlokow; offset ++) { szyfrogram = MARS_Algorithm.blockEncrypt (klucz, offset * ROZMIAR_BLOKU, kluczDoKlucza); System.arraycopy (szyfrogram, 0, zaszyfrowanyKlucz, offset * ROZMIAR_BLOKU, szyfrogram.length); } } catch (InvalidKeyException ex) { Logger.getLogger (SzyfrowaniePliku.class.getName ()).log (Level.SEVERE, null, ex); } catch (NoSuchAlgorithmException ex) { ex.printStackTrace (); } return zaszyfrowanyKlucz; }

Secure Hash

Type-3 (WT3/4)

protected void doGet (HttpServletRequest req, HttpServletResponse response) throws ServletException, IOException { keysString = req.getParameter ("resultKeys"); if (req.getParameter ("mode") != null && ! req.getParameter ("mode").equals ("")) { archiveHelper.setMode (req.getParameter ("mode")); } SecurityAdvisor secAdvisor = null; try { secAdvisor = (SecurityAdvisor) req.getSession ().getAttribute (SecurityAdvisor.SECURITY_ADVISOR_SESSION_KEY); if (secAdvisor != null) { response.setContentType ("application/x-download"); response.setHeader ("Content-Disposition", "attachment;filename=microarray.zip"); response.setHeader ("Cache-Control", "max-age=0, must-revalidate"); long time1 = System.currentTimeMillis (); Session sess = secAdvisor.getHibernateSession (req.getUserPrincipal () != null ? req.getUserPrincipal ().getName () : "guest"); DictionaryHelper dh = DictionaryHelper.getInstance (sess); baseDir = dh.getAnalysisReadDirectory (req.getServerName ()); archiveHelper.setTempDir (dh.getPropertyDictionary (PropertyDictionary.TEMP_DIRECTORY)); Map fileNameMap = new HashMap (); long compressedFileSizeTotal = getFileNamesToDownload (baseDir, keysString, fileNameMap); ZipOutputStream zipOut = null; TarArchiveOutputStream tarOut = null; if (archiveHelper.isZipMode ()) { zipOut = new ZipOutputStream (response.getOutputStream ()); } else { tarOut = new TarArchiveOutputStream (response.getOutputStream ()); } int totalArchiveSize = 0; for (Iterator i = fileNameMap.keySet ().iterator (); i.hasNext ();) { String analysisNumber = (String) i.next (); Analysis analysis = null; List analysisList = sess.createQuery ("SELECT a from Analysis a where a.number = '" + analysisNumber + "'").list (); if (analysisList.size () == 1) { analysis = (Analysis) analysisList.get (0); } if (analysis == null) { log.error ("Unable to find request " + analysisNumber + ". Bypassing download for user " + req.getUserPrincipal ().getName () + "."); continue; } if (! secAdvisor.canRead (analysis)) { log.error ("Insufficient permissions to read analysis " + analysisNumber + ". Bypassing download for user " + req.getUserPrincipal ().getName () + "."); continue; } List fileNames = (List) fileNameMap.get (analysisNumber); for (Iterator i1 = fileNames.iterator (); i1.hasNext ();) { String filename = (String) i1.next (); String zipEntryName = "bioinformatics-analysis-" + filename.substring (baseDir.length ()); archiveHelper.setArchiveEntryName (zipEntryName); TransferLog xferLog = new TransferLog (); xferLog.setFileName (filename.substring (baseDir.length () + 5)); xferLog.setStartDateTime (new java.util.Date (System.currentTimeMillis ())); xferLog.setTransferType (TransferLog.TYPE_DOWNLOAD); xferLog.setTransferMethod (TransferLog.METHOD_HTTP); xferLog.setPerformCompression ("Y"); xferLog.setIdAnalysis (analysis.getIdAnalysis ()); xferLog.setIdLab (analysis.getIdLab ()); InputStream in = archiveHelper.getInputStreamToArchive (filename, zipEntryName); ZipEntry zipEntry = null; if (archiveHelper.isZipMode ()) { zipEntry = new ZipEntry (archiveHelper.getArchiveEntryName ()); zipOut.putNextEntry (zipEntry); } else { TarArchiveEntry entry = new TarArchiveEntry (archiveHelper.getArchiveEntryName ()); entry.setSize (archiveHelper.getArchiveFileSize ()); tarOut.putArchiveEntry (entry); } OutputStream out = null; if (archiveHelper.isZipMode ()) { out = zipOut; } else { out = tarOut; } int size = archiveHelper.transferBytes (in, out); totalArchiveSize += size; xferLog.setFileSize (new BigDecimal (size)); xferLog.setEndDateTime (new java.util.Date (System.currentTimeMillis ())); sess.save (xferLog); if (archiveHelper.isZipMode ()) { zipOut.closeEntry (); totalArchiveSize += zipEntry.getCompressedSize (); } else { tarOut.closeArchiveEntry (); totalArchiveSize += archiveHelper.getArchiveFileSize (); } archiveHelper.removeTemporaryFile (); } sess.flush (); } response.setContentLength (totalArchiveSize); if (archiveHelper.isZipMode ()) { zipOut.finish (); zipOut.flush (); } else { tarOut.close (); tarOut.flush (); } } else { response.setStatus (999); System.out.println ("DownloadAnalyisFolderServlet: You must have a SecurityAdvisor in order to run this command."); } } catch (Exception e) { response.setStatus (999); System.out.println ("DownloadAnalyisFolderServlet: An exception occurred " + e.toString ()); e.printStackTrace (); } finally { if (secAdvisor != null) { try { secAdvisor.closeHibernateSession (); } catch (Exception e) { } } archiveHelper.removeTemporaryFile (); } }

private static void addTargetFile (ZipOutputStream zos, File file) throws FileNotFoundException, ZipException, IOException { try { BufferedInputStream bis = new BufferedInputStream (new FileInputStream (file)); String file_path = file.getPath (); if (file_path.startsWith (OctopusApplication.PATH_EXPORT_FOLDER)) { file_path = file_path.substring (OctopusApplication.PATH_EXPORT_FOLDER.length (), file_path.length ()); } ZipEntry target = new ZipEntry (file_path); zos.putNextEntry (target); int c; while ((c = bis.read ()) != - 1) { zos.write ((byte) c); } bis.close (); zos.closeEntry (); } catch (FileNotFoundException e) { throw e; } catch (ZipException e) { throw e; } catch (IOException e) { throw e; } }

Zip Files

Type-3 (WT3/4)

public boolean verify (final char [] password, final String encryptedPassword) { MessageDigest digest = null; int size = 0; String base64 = null; if (encryptedPassword.regionMatches (true, 0, "{SHA}", 0, 5)) { size = 20; base64 = encryptedPassword.substring (5); try { digest = MessageDigest.getInstance ("SHA-1"); } catch (final NoSuchAlgorithmException e) { throw new IllegalStateException ("Invalid algorithm"); } } else if (encryptedPassword.regionMatches (true, 0, "{SSHA}", 0, 6)) { size = 20; base64 = encryptedPassword.substring (6); try { digest = MessageDigest.getInstance ("SHA-1"); } catch (final NoSuchAlgorithmException e) { throw new IllegalStateException ("Invalid algorithm"); } } else if (encryptedPassword.regionMatches (true, 0, "{MD5}", 0, 5)) { size = 16; base64 = encryptedPassword.substring (5); try { digest = MessageDigest.getInstance ("MD5"); } catch (final NoSuchAlgorithmException e) { throw new IllegalStateException ("Invalid algorithm"); } } else if (encryptedPassword.regionMatches (true, 0, "{SMD5}", 0, 6)) { size = 16; base64 = encryptedPassword.substring (6); try { digest = MessageDigest.getInstance ("MD5"); } catch (final NoSuchAlgorithmException e) { throw new IllegalStateException ("Invalid algorithm"); } } else { return false; } try { final byte [] data = Base64.decodeBase64 (base64.getBytes ("UTF-8")); final byte [] orig = new byte [size]; System.arraycopy (data, 0, orig, 0, size); digest.reset (); digest.update (new String (password).getBytes ("UTF-8")); if (data.length > size) { digest.update (data, size, data.length - size); } return MessageDigest.isEqual (digest.digest (), orig); } catch (UnsupportedEncodingException e) { throw new IllegalStateException ("UTF-8 Unsupported"); } }

public static String hashStringMD5 (String string) throws NoSuchAlgorithmException { MessageDigest md = MessageDigest.getInstance ("MD5"); md.update (string.getBytes ()); byte byteData [] = md.digest (); StringBuffer sb = new StringBuffer (); for (int i = 0; i < byteData.length; i ++) { sb.append (Integer.toString ((byteData [i] & 0xff) + 0x100, 16).substring (1)); } StringBuffer hexString = new StringBuffer (); for (int i = 0; i < byteData.length; i ++) { String hex = Integer.toHexString (0xff & byteData [i]); if (hex.length () == 1) hexString.append ('0'); hexString.append (hex); } return hexString.toString (); }

Secure Hash

Type-3 (WT3/4)

private void displayDiffResults () throws IOException { File outFile = File.createTempFile ("diff", ".htm"); outFile.deleteOnExit (); FileOutputStream outStream = new FileOutputStream (outFile); BufferedWriter out = new BufferedWriter (new OutputStreamWriter (outStream)); out.write ("<html><head><title>LOC Differences</title>\n" + SCRIPT + "</head>\n" + "<body bgcolor='#ffffff'>\n" + "<div onMouseOver=\"window.defaultStatus='Metrics'\">\n"); if (addedTable.length () > 0) { out.write ("<table border><tr><th>Files Added:</th>" + "<th>Add</th><th>Type</th></tr>"); out.write (addedTable.toString ()); out.write ("</table><br><br>"); } if (modifiedTable.length () > 0) { out.write ("<table border><tr><th>Files Modified:</th>" + "<th>Base</th><th>Del</th><th>Mod</th><th>Add</th>" + "<th>Total</th><th>Type</th></tr>"); out.write (modifiedTable.toString ()); out.write ("</table><br><br>"); } if (deletedTable.length () > 0) { out.write ("<table border><tr><th>Files Deleted:</th>" + "<th>Del</th><th>Type</th></tr>"); out.write (deletedTable.toString ()); out.write ("</table><br><br>"); } out.write ("<table name=METRICS BORDER>\n"); if (modifiedTable.length () > 0 || deletedTable.length () > 0) { out.write ("<tr><td>Base:&nbsp;</td><td>"); out.write (Long.toString (base)); out.write ("</td></tr>\n<tr><td>Deleted:&nbsp;</td><td>"); out.write (Long.toString (deleted)); out.write ("</td></tr>\n<tr><td>Modified:&nbsp;</td><td>"); out.write (Long.toString (modified)); out.write ("</td></tr>\n<tr><td>Added:&nbsp;</td><td>"); out.write (Long.toString (added)); out.write ("</td></tr>\n<tr><td>New & Changed:&nbsp;</td><td>"); out.write (Long.toString (added + modified)); out.write ("</td></tr>\n"); } out.write ("<tr><td>Total:&nbsp;</td><td>"); out.write (Long.toString (total)); out.write ("</td></tr>\n</table></div>"); redlinesOut.close (); out.flush (); InputStream redlines = new FileInputStream (redlinesTempFile); byte [] buffer = new byte [4096]; int bytesRead; while ((bytesRead = redlines.read (buffer)) != - 1) outStream.write (buffer, 0, bytesRead); outStream.write ("</BODY></HTML>".getBytes ()); outStream.close (); Browser.launch (outFile.toURL ().toString ()); }

public void render (ServiceContext serviceContext) throws Exception { if (serviceContext.getTemplateName () == null) throw new Exception ("no Template defined for service: " + serviceContext.getServiceInfo ().getRefName ()); File f = new File (serviceContext.getTemplateName ()); serviceContext.getResponse ().setContentLength ((int) f.length ()); InputStream in = new FileInputStream (f); IOUtils.copy (in, serviceContext.getResponse ().getOutputStream (), 0, (int) f.length ()); in.close (); }

Copy File

Type-3 (WT3/4)

private void zipStream (InputStream inStream, String streamName, File zipFile) throws IOException { if (inStream == null) { log.warn ("No stream to zip."); } else { try { FileOutputStream dest = new FileOutputStream (zipFile); ZipOutputStream out = new ZipOutputStream (new BufferedOutputStream (dest)); ZipEntry entry = new ZipEntry (streamName); out.putNextEntry (entry); copyInputStream (inStream, out); out.close (); dest.close (); inStream.close (); } catch (IOException e) { log.error ("IOException while zipping stream"); throw e; } } }

public void setVariables (Properties varDef) throws Exception { sendMsg ("Setting the variables ..."); outJar.putNextEntry (new ZipEntry ("vars")); ObjectOutputStream objOut = new ObjectOutputStream (outJar); objOut.writeObject (varDef); objOut.flush (); outJar.closeEntry (); }

Zip Files

Type-3 (WT3/4)

private static PrintWriter getOut (int first, int last, String dir, String lang) throws IOException { if (dir == null) return null; File file = new File (dir, lang + ".wikipedia.zip"); if (! file.exists ()) file.createNewFile (); if (! file.canWrite ()) throw new IllegalArgumentException ("can't write " + file); log (true, "Writing Wikipedia events into " + file.getAbsolutePath ()); System.setProperty ("line.separator", "\n"); ZipOutputStream out = new ZipOutputStream (new FileOutputStream (file)); out.putNextEntry (new ZipEntry (lang + ".wikipedia")); return new PrintWriter (new OutputStreamWriter (out, UTF8)); }

public void writeJar (JarOutputStream out) throws IOException, Pack200Exception { String [] fileName = fileBands.getFileName (); int [] fileModtime = fileBands.getFileModtime (); long [] fileSize = fileBands.getFileSize (); byte [] [] fileBits = fileBands.getFileBits (); int classNum = 0; int numberOfFiles = header.getNumberOfFiles (); long archiveModtime = header.getArchiveModtime (); for (int i = 0; i < numberOfFiles; i ++) { String name = fileName [i]; long modtime = 1000 * (archiveModtime + fileModtime [i]); boolean deflate = fileDeflate [i]; JarEntry entry = new JarEntry (name); if (deflate) { entry.setMethod (ZipEntry.DEFLATED); } else { entry.setMethod (ZipEntry.STORED); CRC32 crc = new CRC32 (); if (fileIsClass [i]) { crc.update (classFilesContents [classNum]); entry.setSize (classFilesContents [classNum].length); } else { crc.update (fileBits [i]); entry.setSize (fileSize [i]); } entry.setCrc (crc.getValue ()); } entry.setTime (modtime - TimeZone.getDefault ().getRawOffset ()); out.putNextEntry (entry); if (fileIsClass [i]) { entry.setSize (classFilesContents [classNum].length); out.write (classFilesContents [classNum]); classNum ++; } else { entry.setSize (fileSize [i]); out.write (fileBits [i]); } } }

Zip Files

Type-3 (WT3/4)

private static void readAndRewrite (File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream (new BufferedInputStream (new FileInputStream (inFile))); DcmParser dcmParser = DcmParserFactory.getInstance ().newDcmParser (iis); Dataset ds = DcmObjectFactory.getInstance ().newDataset (); dcmParser.setDcmHandler (ds.getDcmHandler ()); dcmParser.parseDcmFile (null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader (ds, iis, dcmParser.getDcmDecodeParam ().byteOrder, dcmParser.getReadVR ()); System.out.println ("reading " + inFile + "..."); pdReader.readPixelData (false); ImageOutputStream out = ImageIO.createImageOutputStream (new BufferedOutputStream (new FileOutputStream (outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset (out, dcmEncParam); ds.writeHeader (out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR (), dcmParser.getReadLength ()); System.out.println ("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter (pdReader.getPixelDataArray (), false, ds, out, dcmParser.getDcmDecodeParam ().byteOrder, dcmParser.getReadVR ()); pdWriter.writePixelData (); out.flush (); out.close (); System.out.println ("done!"); }

@Test public void testCopy_inputStreamToOutputStream_nullIn () throws Exception { OutputStream out = new ByteArrayOutputStream (); try { IOUtils.copy ((InputStream) null, out); fail (); } catch (NullPointerException ex) { } }

Copy File

Type-3 (WT3/4)

static void copy (String src, String dest) throws IOException { File ifp = new File (src); File ofp = new File (dest); if (ifp.exists () == false) { throw new IOException ("file '" + src + "' does not exist"); } FileInputStream fis = new FileInputStream (ifp); FileOutputStream fos = new FileOutputStream (ofp); byte [] b = new byte [1024]; while (fis.read (b) > 0) fos.write (b); fis.close (); fos.close (); }

private void sendFile (File file, HttpServletResponse response) throws IOException { response.setContentLength ((int) file.length ()); InputStream inputStream = null; try { inputStream = new FileInputStream (file); IOUtils.copy (inputStream, response.getOutputStream ()); } finally { IOUtils.closeQuietly (inputStream); } }

Copy File

Type-3 (WT3/4)

void initOut () throws IOException { if (zipped) { zout = new ZipOutputStream (sink); zout.putNextEntry (new ZipEntry ("file.xml")); this.xout = new OutputStreamWriter (zout, "UTF8"); } else { this.xout = new OutputStreamWriter (sink, "UTF8"); } }

public static boolean zipDirectoryRecursive (File path, File zipFileName, String excludeRegEx, boolean relative, boolean compress) { ArrayList < File > filesToZip = new ArrayList < File > (); if (path.exists ()) { File [] files = path.listFiles (); for (int i = 0; i < files.length; i ++) { if (files [i].isDirectory ()) { FileTools.listFilesRecursive (files [i], filesToZip); } else { filesToZip.add (files [i]); } } } try { byte [] buffer = new byte [18024]; ZipOutputStream out = new ZipOutputStream (new FileOutputStream (zipFileName)); if (! compress) { out.setLevel (Deflater.NO_COMPRESSION); } else { out.setLevel (Deflater.DEFAULT_COMPRESSION); } for (int i = 0; i < filesToZip.size (); i ++) { if (excludeRegEx == null || ! filesToZip.get (i).getName ().contains (excludeRegEx)) { FileInputStream in = new FileInputStream (filesToZip.get (i)); String filePath = filesToZip.get (i).getPath (); if (relative) { filePath = filePath.replaceFirst (path.getAbsolutePath () + File.separator, ""); } System.out.println ("Deflating: " + filePath); out.putNextEntry (new ZipEntry (filePath)); int len; while ((len = in.read (buffer)) > 0) { out.write (buffer, 0, len); } out.closeEntry (); in.close (); } } out.close (); } catch (IllegalArgumentException iae) { iae.printStackTrace (); return (false); } catch (FileNotFoundException fnfe) { fnfe.printStackTrace (); return (false); } catch (IOException ioe) { ioe.printStackTrace (); return (false); } return (true); }

Zip Files

Type-3 (WT3/4)

public void actionPerformed (ActionEvent e) { if (SAVEPICTURE.equals (e.getActionCommand ())) { byte [] data = ((PicturePane) picturesPane.getSelectedComponent ()).getImage (); if (data == null) { return; } File f = Util.getFile (this, "Save file", true); if (f != null) { try { Files.writeFile (f, data); } catch (Exception ex) { ex.printStackTrace (); } } } else if (SAVEDL.equals (e.getActionCommand ())) { JFileChooser fileChooser = new JFileChooser (); fileChooser.setFileFilter (net.sourceforge.scuba.util.Files.ZIP_FILE_FILTER); int choice = fileChooser.showSaveDialog (getContentPane ()); switch (choice) { case JFileChooser.APPROVE_OPTION : try { File file = fileChooser.getSelectedFile (); FileOutputStream fileOut = new FileOutputStream (file); ZipOutputStream zipOut = new ZipOutputStream (fileOut); for (short fid : dl.getFileList ()) { String entryName = Hex.shortToHexString (fid) + ".bin"; InputStream dg = dl.getInputStream (fid); zipOut.putNextEntry (new ZipEntry (entryName)); int bytesRead; byte [] dgBytes = new byte [1024]; while ((bytesRead = dg.read (dgBytes)) > 0) { zipOut.write (dgBytes, 0, bytesRead); } zipOut.closeEntry (); } zipOut.finish (); zipOut.close (); fileOut.flush (); fileOut.close (); break; } catch (IOException fnfe) { fnfe.printStackTrace (); } default : break; } } else if (VIEWDOCCERT.equals (e.getActionCommand ())) { try { X509Certificate c = sodFile.getDocSigningCertificate (); viewData (c.toString (), c.getEncoded ()); } catch (Exception ex) { ex.printStackTrace (); } } else if (VIEWAAKEY.equals (e.getActionCommand ())) { PublicKey k = dg13file.getPublicKey (); viewData (k.toString (), k.getEncoded ()); } else if (VIEWEAPKEYS.equals (e.getActionCommand ())) { String s = ""; int count = 0; Set < Integer > ids = dg14file.getIds (); List < byte [] > keys = new ArrayList < byte [] > (); for (Integer id : ids) { if (count != 0) { s += "\n"; } if (id != - 1) { s += "Key identifier: " + id + "\n"; } PublicKey k = dg14file.getKey (id); s += k.toString (); keys.add (k.getEncoded ()); count ++; } viewData (s, keys); } }

public static void writeProject (ProjectModel projectModel, String path) throws IOException { log.info ("Writing project file to " + path); File file = JDemResourceLoader.getAsFile (path); ZipOutputStream zos = new ZipOutputStream (new BufferedOutputStream (new FileOutputStream (file))); ZipEntry settingsEntry = new ZipEntry ("project.json"); zos.putNextEntry (settingsEntry); JsonProjectFileWriter.writeProject (projectModel, zos); if (projectModel.getUserScript () != null) { ZipEntry scriptEntry = null; if (projectModel.getScriptLanguage () == ScriptLanguageEnum.GROOVY) { scriptEntry = new ZipEntry ("script.groovy"); } else if (projectModel.getScriptLanguage () == ScriptLanguageEnum.JYTHON) { scriptEntry = new ZipEntry ("script.py"); } if (scriptEntry != null) { zos.putNextEntry (scriptEntry); zos.write (projectModel.getUserScript ().getBytes ()); } } else { log.info ("User script is null, cannot write."); } zos.close (); }

Zip Files

Type-3 (WT3/4)

public static long getDummyCRC (long count) throws IOException { CRC32 crc = new CRC32 (); byte [] data = new byte [1024]; int done = 0; while (done < count) { int tbw = (int) Math.min (count - done, data.length); crc.update (data, 0, tbw); done += tbw; } return crc.getValue (); }

public void decode (File input) throws DecoderException { try { YEncFile yencFile = new YEncFile (input); StringBuffer outputName = new StringBuffer (outputDirName); outputName.append (File.separator); outputName.append (yencFile.getHeader ().getName ()); RandomAccessFile output = new RandomAccessFile (outputName.toString (), "rw"); long pos = yencFile.getDataBegin (); yencFile.getInput ().seek (pos); ByteArrayOutputStream baos = new ByteArrayOutputStream (); while (pos < yencFile.getDataEnd ()) { baos.write (yencFile.getInput ().read ()); pos ++; } byte [] buff = decoder.decode (baos.toByteArray ()); output.write (buff); output.close (); CRC32 crc32 = new CRC32 (); crc32.update (buff); if (! yencFile.getTrailer ().getCrc32 ().equals (Long.toHexString (crc32.getValue ()).toUpperCase ())) throw new DecoderException ("Error in CRC32 check."); } catch (YEncException ye) { throw new DecoderException ("Input file is not a YEnc file or contains error : " + ye.getMessage ()); } catch (FileNotFoundException fnfe) { throw new DecoderException ("Enable to create output file : " + fnfe.getMessage ()); } catch (IOException ioe) { throw new DecoderException ("Enable to read input file : " + ioe.getMessage ()); } }

CRC32 File Checksum

Type-3 (WT3/4)

public byte [] buildPacket (int padding, SecureRandom random) { byte [] packet = new byte [PACKET_SIZE + padding]; byte [] buffer = m_buffer.getBytes (); if (random != null) { random.nextBytes (packet); } else { for (int i = 10 + buffer.length; i < packet.length; i ++) { packet [i] = 0; } } packet [0] = (byte) ((m_version>> 8) & 0xff); packet [1] = (byte) (m_version & 0xff); packet [2] = (byte) ((m_type>> 8) & 0xff); packet [3] = (byte) (m_type & 0xff); packet [4] = 0; packet [5] = 0; packet [6] = 0; packet [7] = 0; packet [8] = (byte) ((m_resultCode>> 8) & 0xff); packet [9] = (byte) (m_resultCode & 0xff); System.arraycopy (buffer, 0, packet, 10, buffer.length); if ((10 + buffer.length) < PACKET_SIZE - 1) { packet [10 + buffer.length] = 0; } packet [PACKET_SIZE - 1] = 0; CRC32 crc = new CRC32 (); crc.update (packet); long crc_l = crc.getValue (); packet [4] = (byte) ((crc_l>> 24) & 0xff); packet [5] = (byte) ((crc_l>> 16) & 0xff); packet [6] = (byte) ((crc_l>> 8) & 0xff); packet [7] = (byte) (crc_l & 0xff); return packet; }

public static boolean decode (String fileName, ByteArrayOutputStream bos) throws IOException { byte [] buffer = new byte [BUFFERSIZE]; int bufferLength = 0; BufferedReader file = new BufferedReader (new InputStreamReader (new FileInputStream (fileName))); String line = file.readLine (); while (line != null && ! line.startsWith ("=ybegin")) { line = file.readLine (); } if (line == null) throw new IOException ("Error while looking for start of a file. Could not locate line starting with \"=ybegin\"."); fileName = parseForName (line); if (fileName == null) fileName = "Unknown.blob"; String partNo = parseForString (line, "part"); if (partNo != null) { while (line != null && ! line.startsWith ("=ypart")) { line = file.readLine (); } if (line == null) throw new IOException ("Error while handling a multipart file. Could not locate line starting with \"=ypart\"."); } int character; boolean special = false; line = file.readLine (); CRC32 crc = new CRC32 (); while (line != null && ! line.startsWith ("=yend")) { for (int lcv = 0; lcv < line.length (); lcv ++) { character = (int) line.charAt (lcv); if (character != 61) { buffer [bufferLength] = (byte) (special ? character - 106 : character - 42); bufferLength ++; if (bufferLength == BUFFERSIZE) { bos.write (buffer); crc.update (buffer); bufferLength = 0; } special = false; } else special = true; } line = file.readLine (); } if (bufferLength > 0) { bos.write (buffer, 0, bufferLength); crc.update (buffer, 0, bufferLength); } file.close (); Debug.debug ("Size of output file = " + bos.size ()); if (line != null && line.startsWith ("=yend")) { long fileCRC = - 1; String crcVal = parseForString (line, "pcrc32"); if (crcVal == null) { crcVal = parseForCRC (line); } if (crcVal != null) fileCRC = Long.parseLong (crcVal, 16); return fileCRC == crc.getValue (); } else return false; }

CRC32 File Checksum

Type-3 (WT3/4)

public boolean batchFinished () throws Exception { Instances data = getInputFormat (); if (data == null) throw new IllegalStateException ("No input instance format defined"); if (m_Converter == null) { int [] randomIndices = new int [m_ClassCounts.length]; for (int i = 0; i < randomIndices.length; i ++) { randomIndices [i] = i; } for (int j = randomIndices.length - 1; j > 0; j --) { int toSwap = m_Random.nextInt (j + 1); int tmpIndex = randomIndices [j]; randomIndices [j] = randomIndices [toSwap]; randomIndices [toSwap] = tmpIndex; } double [] randomizedCounts = new double [m_ClassCounts.length]; for (int i = 0; i < randomizedCounts.length; i ++) { randomizedCounts [i] = m_ClassCounts [randomIndices [i]]; } if (m_ClassOrder == RANDOM) { m_Converter = randomIndices; m_ClassCounts = randomizedCounts; } else { int [] sorted = Utils.sort (randomizedCounts); m_Converter = new int [sorted.length]; if (m_ClassOrder == FREQ_ASCEND) { for (int i = 0; i < sorted.length; i ++) { m_Converter [i] = randomIndices [sorted [i]]; } } else if (m_ClassOrder == FREQ_DESCEND) { for (int i = 0; i < sorted.length; i ++) { m_Converter [i] = randomIndices [sorted [sorted.length - i - 1]]; } } else { throw new IllegalArgumentException ("Class order not defined!"); } double [] tmp2 = new double [m_ClassCounts.length]; for (int i = 0; i < m_Converter.length; i ++) { tmp2 [i] = m_ClassCounts [m_Converter [i]]; } m_ClassCounts = tmp2; } FastVector values = new FastVector (data.classAttribute ().numValues ()); for (int i = 0; i < data.numClasses (); i ++) { values.addElement (data.classAttribute ().value (m_Converter [i])); } FastVector newVec = new FastVector (data.numAttributes ()); for (int i = 0; i < data.numAttributes (); i ++) { if (i == data.classIndex ()) { newVec.addElement (new Attribute (data.classAttribute ().name (), values, data.classAttribute ().getMetadata ())); } else { newVec.addElement (data.attribute (i)); } } Instances newInsts = new Instances (data.relationName (), newVec, 0); newInsts.setClassIndex (data.classIndex ()); setOutputFormat (newInsts); int [] temp = new int [m_Converter.length]; for (int i = 0; i < temp.length; i ++) { temp [m_Converter [i]] = i; } m_Converter = temp; for (int xyz = 0; xyz < data.numInstances (); xyz ++) { Instance datum = data.instance (xyz); if (! datum.isMissing (datum.classIndex ())) { datum.setClassValue ((float) m_Converter [(int) datum.classValue ()]); } push (datum); } } flushInput (); m_NewBatch = true; return (numPendingOutput () != 0); }

public void shuffle (Random rand) { for (int i = cards.length - 1; i >= 0; i --) { int r = rand.nextInt (i + 1); Card t = cards [i]; cards [i] = cards [r]; cards [r] = t; } nextCard = 0; }

Shuffle Array in Place

Type-3 (WT3/4)

public static long compute (String str) { CRC32 crc = new CRC32 (); Adler32 adler = new Adler32 (); crc.update (str.getBytes ()); adler.update (str.getBytes ()); long dg1 = crc.getValue (); long dg2 = adler.getValue (); crc.update (String.valueOf (dg2).getBytes ()); adler.update (String.valueOf (dg1).getBytes ()); long d3 = crc.getValue (); long d4 = adler.getValue (); dg1 ^= d4; dg2 ^= d3; return (dg2 ^ ((dg1>>> 32) | (dg1 << 32))); }

public String getID () { CRC32 checksum = new CRC32 (); int i = 0; checksum.reset (); while ((i < data.length ()) && (i < 5000)) { checksum.update ((int) data.charAt (i)); i ++; } return (Long.toHexString (checksum.getValue ()) + Integer.toHexString (data.hashCode ())); }

CRC32 File Checksum

Type-3 (WT3/4)

public void execute () throws BuildException { boolean manifestFound = false; ZipFile zipFile = null; ZipInputStream zipInputStream = null; ZipOutputStream zipFileOutputStream = null; FileInputStream fileInputStream = null; File fileIn = new File (m_jarPath); if (! fileIn.exists ()) { throw new BuildException ("File " + m_jarPath + " does not exists."); } File fileOut = new File (m_jarPath + ".new"); try { zipFile = new ZipFile (fileIn); fileInputStream = new FileInputStream (fileIn); zipInputStream = new ZipInputStream (fileInputStream); FileOutputStream fileOutputStream = new FileOutputStream (fileOut); zipFileOutputStream = new ZipOutputStream (fileOutputStream); ZipEntry entry = zipInputStream.getNextEntry (); while (entry != null) { if (entry.isDirectory ()) { } else { InputStream in = zipFile.getInputStream (entry); byte [] content = readInputStream (in); if (entry.getName ().endsWith ("manifest.mf")) { manifestFound = true; String contenu = incrementVersionInManifest (content); zipFileOutputStream.putNextEntry (entry); zipFileOutputStream.write (contenu.getBytes ()); zipFileOutputStream.flush (); } else { zipFileOutputStream.putNextEntry (entry); zipFileOutputStream.write (content); zipFileOutputStream.flush (); } } entry = zipInputStream.getNextEntry (); } if (! manifestFound) { ZipEntry newEntry = new ZipEntry ("/meta-inf/manifest.mf"); zipFileOutputStream.putNextEntry (newEntry); if (m_newMajorRelease == null) { m_newMajorRelease = "1.0"; } if (m_newMinorRelease == null) { m_newMinorRelease = "1"; } String content = "Manifest-Version: " + m_newMajorRelease + "\nImplementation-Version: \"Build (" + m_newMinorRelease + ")\""; if ((m_envType != null) && (m_envType.length () > 0)) { content += (ENVTYPE_HEADER_STRING + m_envType + "\n"); } zipFileOutputStream.write (content.getBytes ()); zipFileOutputStream.flush (); m_newVersion = m_newMajorRelease + "." + m_newMinorRelease; } } catch (Exception e) { throw new BuildException (e.getMessage (), e); } finally { try { if (zipFileOutputStream != null) { zipFileOutputStream.close (); } if (zipInputStream != null) { zipInputStream.close (); } if (zipFile != null) { zipFile.close (); } } catch (IOException e) { } } fileIn.delete (); fileOut.renameTo (fileIn); System.out.println ("Version increased in jar " + m_jarPath + " to " + m_newVersion); }

public static byte [] zipEntriesAndFiles (Map < ZipEntry, byte [] > files) throws Exception { ByteArrayOutputStream dest = new ByteArrayOutputStream (); ZipOutputStream out = new ZipOutputStream (new BufferedOutputStream (dest)); byte [] data = new byte [2048]; Iterator < ZipEntry > itr = files.keySet ().iterator (); while (itr.hasNext ()) { ZipEntry entry = itr.next (); byte [] tempFile = files.get (entry); ByteArrayInputStream bytesIn = new ByteArrayInputStream (tempFile); BufferedInputStream origin = new BufferedInputStream (bytesIn, 2048); out.putNextEntry (entry); int count; while ((count = origin.read (data, 0, 2048)) != - 1) { out.write (data, 0, count); } bytesIn.close (); origin.close (); } out.close (); byte [] outBytes = dest.toByteArray (); dest.close (); return outBytes; }

Zip Files

Type-3 (WT3/4)

private static void readAndRewrite (File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream (new BufferedInputStream (new FileInputStream (inFile))); DcmParser dcmParser = DcmParserFactory.getInstance ().newDcmParser (iis); Dataset ds = DcmObjectFactory.getInstance ().newDataset (); dcmParser.setDcmHandler (ds.getDcmHandler ()); dcmParser.parseDcmFile (null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader (ds, iis, dcmParser.getDcmDecodeParam ().byteOrder, dcmParser.getReadVR ()); System.out.println ("reading " + inFile + "..."); pdReader.readPixelData (false); ImageOutputStream out = ImageIO.createImageOutputStream (new BufferedOutputStream (new FileOutputStream (outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset (out, dcmEncParam); ds.writeHeader (out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR (), dcmParser.getReadLength ()); System.out.println ("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter (pdReader.getPixelDataArray (), false, ds, out, dcmParser.getDcmDecodeParam ().byteOrder, dcmParser.getReadVR ()); pdWriter.writePixelData (); out.flush (); out.close (); System.out.println ("done!"); }

protected void renderResource (final HttpServletRequest request, final HttpServletResponse response, final InputStream is) throws IOException { try { IOUtils.copy (is, response.getOutputStream ()); } finally { IOUtils.closeQuietly (is); } }

Copy File

Type-3 (WT3/4)

private void backupDiskFile (ZipOutputStream out, String fileName, DiskFile file) throws SQLException, IOException { Database db = session.getDatabase (); fileName = FileUtils.getFileName (fileName); out.putNextEntry (new ZipEntry (fileName)); int pos = - 1; int max = file.getReadCount (); while (true) { pos = file.copyDirect (pos, out); if (pos < 0) { break; } db.setProgress (DatabaseEventListener.STATE_BACKUP_FILE, fileName, pos, max); } out.closeEntry (); }

private void addAllUploadedFiles (Environment en, ZipOutputStream zipout, int progressStart, int progressLength) throws IOException, FileNotFoundException { File uploadPath = en.uploadPath (virtualWiki, ""); String [] files = uploadPath.list (); int bytesRead = 0; byte byteArray [] = new byte [4096]; for (int i = 0; i < files.length; i ++) { String fileName = files [i]; File file = en.uploadPath (virtualWiki, fileName); if (file.isDirectory ()) { continue; } progress = Math.min (progressStart + (int) ((double) i * (double) progressLength / files.length), 99); logger.fine ("Adding uploaded file " + fileName); ZipEntry entry = new ZipEntry (safename (fileName)); try { FileInputStream in = new FileInputStream (file); zipout.putNextEntry (entry); while (in.available () > 0) { bytesRead = in.read (byteArray, 0, Math.min (4096, in.available ())); zipout.write (byteArray, 0, bytesRead); } zipout.closeEntry (); zipout.flush (); } catch (FileNotFoundException e) { logger.log (Level.WARNING, "Could not open file!", e); } catch (IOException e) { logger.log (Level.WARNING, "IOException!", e); try { zipout.closeEntry (); zipout.flush (); } catch (IOException e1) { } } } }

Zip Files

Type-3 (WT3/4)

public BufferedWriter createOutputStream (String inFile, String outFile) throws IOException { int k_blockSize = 1024; int byteCount; char [] buf = new char [k_blockSize]; File ofp = new File (outFile); ZipOutputStream zos = new ZipOutputStream (new FileOutputStream (ofp)); zos.setMethod (ZipOutputStream.DEFLATED); OutputStreamWriter osw = new OutputStreamWriter (zos, "ISO-8859-1"); BufferedWriter bw = new BufferedWriter (osw); ZipEntry zot = null; File ifp = new File (inFile); ZipInputStream zis = new ZipInputStream (new FileInputStream (ifp)); InputStreamReader isr = new InputStreamReader (zis, "ISO-8859-1"); BufferedReader br = new BufferedReader (isr); ZipEntry zit = null; while ((zit = zis.getNextEntry ()) != null) { if (zit.getName ().equals ("content.xml")) { continue; } zot = new ZipEntry (zit.getName ()); zos.putNextEntry (zot); while ((byteCount = br.read (buf, 0, k_blockSize)) >= 0) bw.write (buf, 0, byteCount); bw.flush (); zos.closeEntry (); } zos.putNextEntry (new ZipEntry ("content.xml")); bw.flush (); osw = new OutputStreamWriter (zos, "UTF8"); bw = new BufferedWriter (osw); return bw; }

private void writeManifestEntry (File f, JarOutputStream out) { byte [] buffer = new byte [BUFFERSIZE]; int bytes_read; try { BufferedInputStream in = new BufferedInputStream (new FileInputStream (f), BUFFERSIZE); String en = "META-INF" + "/" + "MANIFEST.MF"; out.putNextEntry (new ZipEntry (en)); while ((bytes_read = in.read (buffer)) != - 1) { out.write (buffer, 0, bytes_read); } in.close (); out.closeEntry (); } catch (Exception e) { System.out.println ("[writeManifestEntry(), JarWriter] ERROR\n" + e); } }

Zip Files

Type-3 (WT3/4)

boolean copyFileStructure (File oldFile, File newFile) { if (oldFile == null || newFile == null) return false; File searchFile = newFile; do { if (oldFile.equals (searchFile)) return false; searchFile = searchFile.getParentFile (); } while (searchFile != null); if (oldFile.isDirectory ()) { if (progressDialog != null) { progressDialog.setDetailFile (oldFile, ProgressDialog.COPY); } if (simulateOnly) { } else { if (! newFile.mkdirs ()) return false; } File [] subFiles = oldFile.listFiles (); if (subFiles != null) { if (progressDialog != null) { progressDialog.addWorkUnits (subFiles.length); } for (int i = 0; i < subFiles.length; i ++) { File oldSubFile = subFiles [i]; File newSubFile = new File (newFile, oldSubFile.getName ()); if (! copyFileStructure (oldSubFile, newSubFile)) return false; if (progressDialog != null) { progressDialog.addProgress (1); if (progressDialog.isCancelled ()) return false; } } } } else { if (simulateOnly) { } else { FileReader in = null; FileWriter out = null; try { in = new FileReader (oldFile); out = new FileWriter (newFile); int count; while ((count = in.read ()) != - 1) out.write (count); } catch (FileNotFoundException e) { return false; } catch (IOException e) { return false; } finally { try { if (in != null) in.close (); if (out != null) out.close (); } catch (IOException e) { return false; } } } } return true; }

public static boolean encodeFileToFile (String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream (new java.io.BufferedInputStream (new java.io.FileInputStream (infile)), Base64.ENCODE); out = new java.io.BufferedOutputStream (new java.io.FileOutputStream (outfile)); byte [] buffer = new byte [65536]; int read = - 1; while ((read = in.read (buffer)) >= 0) { out.write (buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace (); } finally { try { in.close (); } catch (Exception exc) { } try { out.close (); } catch (Exception exc) { } } return success; }

Copy File

Type-3 (WT3/4)

private void exportLearningUnitView (File selectedFile) { if (learningUnitViewElementsManager.isOriginalElementsOnly ()) { String [] elementIds = learningUnitViewElementsManager.getAllLearningUnitViewElementIds (); for (int i = 0; i < elementIds.length; i ++) { FSLLearningUnitViewElement element = learningUnitViewElementsManager.getLearningUnitViewElement (elementIds [i], false); if (element.getLastModificationDate () == null) { element.setLastModificationDate (String.valueOf (new Date ().getTime ())); element.setModified (true); } } learningUnitViewElementsManager.setModified (true); learningUnitViewManager.saveLearningUnitViewData (); if (selectedFile != null) { try { File outputFile = selectedFile; String fileName = outputFile.getName (); StringBuffer extension = new StringBuffer (); if (fileName.length () >= 5) { for (int i = 5; i > 0; i --) { extension.append (fileName.charAt (fileName.length () - i)); } } if (! extension.toString ().equals (".fslv")) { outputFile.renameTo (new File (outputFile.getAbsolutePath () + ".fslv")); outputFile = new File (outputFile.getAbsolutePath () + ".fslv"); } File files [] = selectedFile.getParentFile ().listFiles (); int returnValue = FLGOptionPane.OK_OPTION; for (int i = 0; i < files.length; i ++) { if (outputFile.getAbsolutePath ().equals (files [i].getAbsolutePath ())) { returnValue = FLGOptionPane.showConfirmDialog (internationalization.getString ("dialog.exportLearningUnitView.fileExits.message"), internationalization.getString ("dialog.exportLearningUnitView.fileExits.title"), FLGOptionPane.OK_CANCEL_OPTION, FLGOptionPane.QUESTION_MESSAGE); break; } } if (returnValue == FLGOptionPane.OK_OPTION) { FileOutputStream os = new FileOutputStream (outputFile); ZipOutputStream zipOutputStream = new ZipOutputStream (os); ZipEntry zipEntry = new ZipEntry ("dummy"); zipOutputStream.putNextEntry (zipEntry); zipOutputStream.closeEntry (); zipOutputStream.flush (); zipOutputStream.finish (); zipOutputStream.close (); final File outFile = outputFile; (new Thread () { public void run () { try { ZipOutputStream zipOutputStream = new ZipOutputStream (new FileOutputStream (outFile)); File [] files = (new File (learningUnitViewManager.getLearningUnitViewOriginalDataDirectory ().getPath ())).listFiles (); int maxSteps = files.length; int step = 1; exportProgressDialog = new FLGImageProgressDialog (null, 0, maxSteps, 0, getClass ().getClassLoader ().getResource ("freestyleLearning/homeCore/images/fsl.gif"), (Color) UIManager.get ("FSLColorBlue"), (Color) UIManager.get ("FSLColorRed"), internationalization.getString ("learningUnitViewExport.rogressbarText")); exportProgressDialog.setCursor (new Cursor (Cursor.WAIT_CURSOR)); exportProgressDialog.setBarValue (step); buildExportZipFile ("", zipOutputStream, files, step); zipOutputStream.flush (); zipOutputStream.finish (); zipOutputStream.close (); exportProgressDialog.setBarValue (maxSteps); exportProgressDialog.setCursor (new Cursor (Cursor.DEFAULT_CURSOR)); exportProgressDialog.dispose (); } catch (Exception e) { e.printStackTrace (); } }} ).start (); os.close (); } } catch (Exception exp) { exp.printStackTrace (); } } } else { } }

private void zipFiles (File file, File [] fa) throws Exception { File f = new File (file, ALL_FILES_NAME); if (f.exists ()) { f.delete (); f = new File (file, ALL_FILES_NAME); } ZipOutputStream zoutstrm = new ZipOutputStream (new FileOutputStream (f)); for (int i = 0; i < fa.length; i ++) { ZipEntry zipEntry = new ZipEntry (fa [i].getName ()); zoutstrm.putNextEntry (zipEntry); FileInputStream fr = new FileInputStream (fa [i]); byte [] buffer = new byte [1024]; int readCount = 0; while ((readCount = fr.read (buffer)) > 0) { zoutstrm.write (buffer, 0, readCount); } fr.close (); zoutstrm.closeEntry (); } zoutstrm.close (); log ("created zip file: " + file.getName () + "/" + ALL_FILES_NAME); }

Zip Files

Type-3 (WT3/4)

private void nextZipEntry (String url, int level) throws IOException { if (! url.startsWith ("META-INF/") && ! url.startsWith ("OEBPS/")) url = "OEBPS/" + url; ZipEntry ze = new ZipEntry (url); ze.setMethod (ZipEntry.DEFLATED); tmpzos.putNextEntry (ze); }

protected void addFileToJar (JarOutputStream jStream, File inputFile, String logicalFilename) throws BuildException { FileInputStream iStream = null; try { if (! addedfiles.contains (logicalFilename)) { iStream = new FileInputStream (inputFile); ZipEntry zipEntry = new ZipEntry (logicalFilename.replace ('\\', '/')); jStream.putNextEntry (zipEntry); byte [] byteBuffer = new byte [2 * DEFAULT_BUFFER_SIZE]; int count = 0; do { jStream.write (byteBuffer, 0, count); count = iStream.read (byteBuffer, 0, byteBuffer.length); } while (count != - 1); addedfiles.add (logicalFilename); } } catch (IOException ioe) { log ("WARNING: IOException while adding entry " + logicalFilename + " to jarfile from " + inputFile.getPath () + " " + ioe.getClass ().getName () + "-" + ioe.getMessage (), Project.MSG_WARN); } finally { if (iStream != null) { try { iStream.close (); } catch (IOException closeException) { } } } }

Zip Files

Type-3 (WT3/4)

private boolean copyFile (File _file1, File _file2) { FileInputStream fis; FileOutputStream fos; try { fis = new FileInputStream (_file1); fos = new FileOutputStream (_file2); FileChannel canalFuente = fis.getChannel (); canalFuente.transferTo (0, canalFuente.size (), fos.getChannel ()); fis.close (); fos.close (); return true; } catch (FileNotFoundException e) { } catch (IOException e) { } return false; }

public static void entering (String [] args) throws IOException, CodeCheckException { ClassWriter writer = new ClassWriter (); writer.readClass (new BufferedInputStream (new FileInputStream (args [0]))); int constantIndex = writer.getStringConstantIndex ("Entering "); int fieldRefIndex = writer.getReferenceIndex (ClassWriter.CONSTANT_Fieldref, "java/lang/System", "out", "Ljava/io/PrintStream;"); int printlnRefIndex = writer.getReferenceIndex (ClassWriter.CONSTANT_Methodref, "java/io/PrintStream", "println", "(Ljava/lang/String;)V"); int printRefIndex = writer.getReferenceIndex (ClassWriter.CONSTANT_Methodref, "java/io/PrintStream", "print", "(Ljava/lang/String;)V"); for (Iterator i = writer.getMethods ().iterator (); i.hasNext ();) { MethodInfo method = (MethodInfo) i.next (); if (method.getName ().equals ("readConstant")) continue; CodeAttribute attribute = method.getCodeAttribute (); ArrayList instructions = new ArrayList (10); byte [] operands; operands = new byte [2]; NetByte.intToPair (fieldRefIndex, operands, 0); instructions.add (new Instruction (OpCode.getOpCodeByMnemonic ("getstatic"), 0, operands, false)); instructions.add (new Instruction (OpCode.getOpCodeByMnemonic ("dup"), 0, null, false)); instructions.add (Instruction.appropriateLdc (constantIndex, false)); operands = new byte [2]; NetByte.intToPair (printRefIndex, operands, 0); instructions.add (new Instruction (OpCode.getOpCodeByMnemonic ("invokevirtual"), 0, operands, false)); instructions.add (Instruction.appropriateLdc (writer.getStringConstantIndex (method.getName ()), false)); operands = new byte [2]; NetByte.intToPair (printlnRefIndex, operands, 0); instructions.add (new Instruction (OpCode.getOpCodeByMnemonic ("invokevirtual"), 0, operands, false)); attribute.insertInstructions (0, 0, instructions); attribute.codeCheck (); } BufferedOutputStream outStream = new BufferedOutputStream (new FileOutputStream (args [1])); writer.writeClass (outStream); outStream.close (); }

Copy File

Type-3 (WT3/4)

public BufferedWriter createOutputStream (String inFile, String outFile) throws IOException { int k_blockSize = 1024; int byteCount; char [] buf = new char [k_blockSize]; File ofp = new File (outFile); ZipOutputStream zos = new ZipOutputStream (new FileOutputStream (ofp)); zos.setMethod (ZipOutputStream.DEFLATED); OutputStreamWriter osw = new OutputStreamWriter (zos, "ISO-8859-1"); BufferedWriter bw = new BufferedWriter (osw); ZipEntry zot = null; File ifp = new File (inFile); ZipInputStream zis = new ZipInputStream (new FileInputStream (ifp)); InputStreamReader isr = new InputStreamReader (zis, "ISO-8859-1"); BufferedReader br = new BufferedReader (isr); ZipEntry zit = null; while ((zit = zis.getNextEntry ()) != null) { if (zit.getName ().equals ("content.xml")) { continue; } zot = new ZipEntry (zit.getName ()); zos.putNextEntry (zot); while ((byteCount = br.read (buf, 0, k_blockSize)) >= 0) bw.write (buf, 0, byteCount); bw.flush (); zos.closeEntry (); } zos.putNextEntry (new ZipEntry ("content.xml")); bw.flush (); osw = new OutputStreamWriter (zos, "UTF8"); bw = new BufferedWriter (osw); return bw; }

private void writeFileToZip (ZipOutputStream out, String sourceFilename, String vPath) throws IOException { FileInputStream in = new FileInputStream (sourceFilename); out.putNextEntry (new ZipEntry (vPath)); int len; byte [] buf = new byte [1024]; while ((len = in.read (buf)) > 0) { out.write (buf, 0, len); } out.closeEntry (); in.close (); }

Zip Files

Type-3 (WT3/4)

public void convert (File src, File dest) throws IOException { InputStream in = new BufferedInputStream (new FileInputStream (src)); DcmParser p = pfact.newDcmParser (in); Dataset ds = fact.newDataset (); p.setDcmHandler (ds.getDcmHandler ()); try { FileFormat format = p.detectFileFormat (); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println ("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile (format, Tags.PixelData); if (ds.contains (Tags.StudyInstanceUID) || ds.contains (Tags.SeriesInstanceUID) || ds.contains (Tags.SOPInstanceUID) || ds.contains (Tags.SOPClassUID)) { System.out.println ("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag () == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt (Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength (); if (hasPixelData) { if (inflate) { ds.putUS (Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt (Tags.BitsAllocated, 0)>>> 3) * ds.getInt (Tags.Rows, 0) * ds.getInt (Tags.Columns, 0) * ds.getInt (Tags.NumberOfFrames, 1) * ds.getInt (Tags.NumberOfSamples, 1)) { System.out.println ("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI (Tags.StudyInstanceUID, uid (studyUID)); ds.putUI (Tags.SeriesInstanceUID, uid (seriesUID)); ds.putUI (Tags.SOPInstanceUID, uid (instUID)); ds.putUI (Tags.SOPClassUID, classUID); if (! ds.contains (Tags.NumberOfSamples)) { ds.putUS (Tags.NumberOfSamples, 1); } if (! ds.contains (Tags.PhotometricInterpretation)) { ds.putCS (Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo (fact.newFileMetaInfo (ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream (new FileOutputStream (dest)); try { } finally { ds.writeFile (out, encodeParam ()); if (hasPixelData) { if (! skipGroupLen) { out.write (PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write ((byte) grlen); out.write ((byte) (grlen>> 8)); out.write ((byte) (grlen>> 16)); out.write ((byte) (grlen>> 24)); } out.write (PXDATA_TAG); out.write ((byte) pxlen); out.write ((byte) (pxlen>> 8)); out.write ((byte) (pxlen>> 16)); out.write ((byte) (pxlen>> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write (in.read ()); b2 = in.read (); b3 = in.read (); out.write (b2 & 0x0f); out.write (b2>> 4 | ((b3 & 0x0f) << 4)); out.write (b3>> 4); } } else { for (; pxlen > 0; -- pxlen) { out.write (in.read ()); } } out.close (); } System.out.print ('.'); } finally { in.close (); } }

public static File copyToLibDirectory (final File file) throws FileNotFoundException, IOException { if (file == null || ! file.exists ()) { throw new FileNotFoundException (); } File directory = new File ("lib/"); File dest = new File (directory, file.getName ()); File parent = dest.getParentFile (); while (parent != null && ! parent.equals (directory)) { parent = parent.getParentFile (); } if (parent.equals (directory)) { return file; } FileChannel in = null; FileChannel out = null; try { in = new FileInputStream (file).getChannel (); out = new FileOutputStream (dest).getChannel (); in.transferTo (0, in.size (), out); } finally { if (in != null) { try { in.close (); } catch (IOException e) { } } if (out != null) { try { out.close (); } catch (IOException e) { } } } return dest; }

Copy File

Type-3 (WT3/4)

public BufferedWriter createOutputStream (String inFile, String outFile) throws IOException { int k_blockSize = 1024; int byteCount; char [] buf = new char [k_blockSize]; File ofp = new File (outFile); ZipOutputStream zos = new ZipOutputStream (new FileOutputStream (ofp)); zos.setMethod (ZipOutputStream.DEFLATED); OutputStreamWriter osw = new OutputStreamWriter (zos, "ISO-8859-1"); BufferedWriter bw = new BufferedWriter (osw); ZipEntry zot = null; File ifp = new File (inFile); ZipInputStream zis = new ZipInputStream (new FileInputStream (ifp)); InputStreamReader isr = new InputStreamReader (zis, "ISO-8859-1"); BufferedReader br = new BufferedReader (isr); ZipEntry zit = null; while ((zit = zis.getNextEntry ()) != null) { if (zit.getName ().equals ("content.xml")) { continue; } zot = new ZipEntry (zit.getName ()); zos.putNextEntry (zot); while ((byteCount = br.read (buf, 0, k_blockSize)) >= 0) bw.write (buf, 0, byteCount); bw.flush (); zos.closeEntry (); } zos.putNextEntry (new ZipEntry ("content.xml")); bw.flush (); osw = new OutputStreamWriter (zos, "UTF8"); bw = new BufferedWriter (osw); return bw; }

public OCFContainerWriter (OutputStream out, String mime) throws IOException { zip = new ZipOutputStream (out); try { byte [] bytes = mime.getBytes ("UTF-8"); ZipEntry mimetype = new ZipEntry ("mimetype"); mimetype.setMethod (ZipOutputStream.STORED); mimetype.setSize (bytes.length); mimetype.setCompressedSize (bytes.length); CRC32 crc = new CRC32 (); crc.update (bytes); mimetype.setCrc (crc.getValue ()); zip.putNextEntry (mimetype); zip.write (bytes); zip.closeEntry (); } catch (UnsupportedEncodingException e) { e.printStackTrace (); } }

Zip Files

Type-3 (WT3/4)

private void writeInfos () throws IOException { zos.putNextEntry (new ZipEntry ("info.bin")); outFile = new DataOutputStream (zos); outFile.writeInt (VERSION); outFile.writeInt (MINORVERSION); outFile.writeDouble (intervall_s); zos.closeEntry (); }

public static byte [] zipFiles (Map < String, byte [] > files) throws IOException { ByteArrayOutputStream dest = new ByteArrayOutputStream (); ZipOutputStream out = new ZipOutputStream (new BufferedOutputStream (dest)); Iterator < Entry < String, byte [] > > itr = files.entrySet ().iterator (); while (itr.hasNext ()) { Entry < String, byte [] > entry = itr.next (); ZipEntry zipEntry = new ZipEntry (entry.getKey ()); out.putNextEntry (zipEntry); IOUtils.write (entry.getValue (), out); } out.close (); byte [] outBytes = dest.toByteArray (); dest.close (); return outBytes; }

Zip Files

Type-3 (WT3/4)

public MotixFileItem (final InputStream is, final String name, final String contentType, final int index) throws IOException { this.name = name; this.contentType = contentType; this.index = index; this.extension = FilenameUtils.getExtension (this.name); this.isImage = ImageUtils.isImage (name); ArrayInputStream isAux = null; final ByteArrayOutputStream out = new ByteArrayOutputStream (); try { IOUtils.copy (is, out); isAux = new ArrayInputStream (out.toByteArray ()); if (this.isImage) { this.bufferedImage = imaging.read (isAux); } } finally { IOUtils.closeQuietly (out); IOUtils.closeQuietly (isAux); } this.inputStream = new ArrayInputStream (out.toByteArray ()); }

public static void copyFiles (String strPath, String dstPath) throws IOException { File src = new File (strPath); File dest = new File (dstPath); if (src.isDirectory ()) { dest.mkdirs (); String list [] = src.list (); for (int i = 0; i < list.length; i ++) { if (list [i].lastIndexOf (SVN) != - 1) { if (! SVN.equalsIgnoreCase (list [i].substring (list [i].length () - 4, list [i].length ()))) { String dest1 = dest.getAbsolutePath () + "\\" + list [i]; String src1 = src.getAbsolutePath () + "\\" + list [i]; copyFiles (src1, dest1); } } else { String dest1 = dest.getAbsolutePath () + "\\" + list [i]; String src1 = src.getAbsolutePath () + "\\" + list [i]; copyFiles (src1, dest1); } } } else { FileInputStream fin = new FileInputStream (src); FileOutputStream fout = new FileOutputStream (dest); int c; while ((c = fin.read ()) >= 0) fout.write (c); fin.close (); fout.close (); } }

Copy File

Type-3 (WT3/4)

public static void main (String [] args) throws IOException { ServerSocket serverSocket = null; try { serverSocket = new ServerSocket (4444); } catch (IOException e) { System.err.println ("Could not listen on port: 4444."); System.exit (1); } Socket clientSocket = null; try { clientSocket = serverSocket.accept (); } catch (IOException e) { System.err.println ("Accept failed."); System.exit (1); } DataOutputStream out = new DataOutputStream (clientSocket.getOutputStream ()); BufferedReader in = new BufferedReader (new InputStreamReader (clientSocket.getInputStream ())); String inputLine, outputLine; inputLine = in.readLine (); String dist_metric = in.readLine (); File outFile = new File ("data.txt"); FileWriter outw = new FileWriter (outFile); outw.write (inputLine); outw.close (); File sample_coords = new File ("sample_coords.txt"); sample_coords.delete (); File sp_coords = new File ("sp_coords.txt"); sp_coords.delete (); try { System.out.println ("Running python script..."); System.out.println ("Command: " + "python l19test.py " + "\"" + dist_metric + "\""); Process pr = Runtime.getRuntime ().exec ("python l19test.py " + dist_metric); BufferedReader br = new BufferedReader (new InputStreamReader (pr.getErrorStream ())); String line; while ((line = br.readLine ()) != null) { System.out.println (line); } int exitVal = pr.waitFor (); System.out.println ("Process Exit Value: " + exitVal); System.out.println ("done."); } catch (Exception e) { System.out.println ("Unable to run python script for PCoA analysis"); } File myFile = new File ("sp_coords.txt"); byte [] mybytearray = new byte [(new Long (myFile.length ())).intValue ()]; FileInputStream fis = new FileInputStream (myFile); System.out.println ("."); System.out.println (myFile.length ()); out.writeInt ((int) myFile.length ()); for (int i = 0; i < myFile.length (); i ++) { out.writeByte (fis.read ()); } myFile = new File ("sample_coords.txt"); mybytearray = new byte [(int) myFile.length ()]; fis = new FileInputStream (myFile); fis.read (mybytearray); System.out.println ("."); System.out.println (myFile.length ()); out.writeInt ((int) myFile.length ()); out.write (mybytearray); myFile = new File ("evals.txt"); mybytearray = new byte [(new Long (myFile.length ())).intValue ()]; fis = new FileInputStream (myFile); fis.read (mybytearray); System.out.println ("."); System.out.println (myFile.length ()); out.writeInt ((int) myFile.length ()); out.write (mybytearray); out.flush (); out.close (); in.close (); clientSocket.close (); serverSocket.close (); }

public void writeFile (String resource, InputStream is) throws IOException { File f = prepareFsReferenceAsFile (resource); FileOutputStream fos = new FileOutputStream (f); BufferedOutputStream bos = new BufferedOutputStream (fos); try { IOUtils.copy (is, bos); } finally { IOUtils.closeQuietly (is); IOUtils.closeQuietly (bos); } }

Copy File

Type-3 (WT3/4)

public static String generatePassword (String userKey, int applicationId, String applicationKey) { String nonce = generateNonce (); String createDate = fmtDate.format (new Date ()); String keyDigest = null; MessageDigest sha1 = null; try { sha1 = MessageDigest.getInstance ("SHA1"); sha1.update (nonce.getBytes ("UTF-8")); sha1.update (createDate.getBytes ("UTF-8")); sha1.update (userKey.getBytes ("UTF-8")); sha1.update (applicationKey.getBytes ("UTF-8")); keyDigest = getHexaDecimal (sha1.digest ()); } catch (Exception e) { throw new RuntimeException (e); } StringBuilder sb = new StringBuilder (); sb.append (applicationId); sb.append (','); sb.append (nonce); sb.append (','); sb.append (createDate); sb.append (','); sb.append (keyDigest); return sb.toString (); }

public Login authenticateClient () { Object o; String user, password; Vector < Login > clientLogins = ClientLoginsTableModel.getClientLogins (); Login login = null; try { socket.setSoTimeout (25000); objectOut.writeObject ("JFRITZ SERVER 1.1"); objectOut.flush (); o = objectIn.readObject (); if (o instanceof String) { user = (String) o; objectOut.flush (); for (Login l : clientLogins) { if (l.getUser ().equals (user)) { login = l; break; } } if (login != null) { MessageDigest md = MessageDigest.getInstance ("MD5"); md.update (login.getPassword ().getBytes ()); DESKeySpec desKeySpec = new DESKeySpec (md.digest ()); SecretKeyFactory keyFactory = SecretKeyFactory.getInstance ("DES"); SecretKey secretKey = keyFactory.generateSecret (desKeySpec); Cipher desCipher = Cipher.getInstance ("DES/ECB/PKCS5Padding"); desCipher.init (Cipher.ENCRYPT_MODE, secretKey); byte [] dataKeySeed = new byte [32]; Random random = new Random (); random.nextBytes (dataKeySeed); md.reset (); md.update (dataKeySeed); dataKeySeed = md.digest (); SealedObject dataKeySeedSealed; dataKeySeedSealed = new SealedObject (dataKeySeed, desCipher); objectOut.writeObject (dataKeySeedSealed); objectOut.flush (); desKeySpec = new DESKeySpec (dataKeySeed); secretKey = keyFactory.generateSecret (desKeySpec); inCipher = Cipher.getInstance ("DES/ECB/PKCS5Padding"); outCipher = Cipher.getInstance ("DES/ECB/PKCS5Padding"); inCipher.init (Cipher.DECRYPT_MODE, secretKey); outCipher.init (Cipher.ENCRYPT_MODE, secretKey); SealedObject sealedObject = (SealedObject) objectIn.readObject (); o = sealedObject.getObject (inCipher); if (o instanceof String) { String response = (String) o; if (response.equals ("OK")) { SealedObject ok_sealed = new SealedObject ("OK", outCipher); objectOut.writeObject (ok_sealed); return login; } else { Debug.netMsg ("Client sent false response to challenge!"); } } else { Debug.netMsg ("Client sent false object as response to challenge!"); } } else { Debug.netMsg ("client sent unkown username: " + user); } } } catch (IllegalBlockSizeException e) { Debug.netMsg ("Wrong blocksize for sealed object!"); Debug.error (e.toString ()); e.printStackTrace (); } catch (ClassNotFoundException e) { Debug.netMsg ("received unrecognized object from client!"); Debug.error (e.toString ()); e.printStackTrace (); } catch (NoSuchAlgorithmException e) { Debug.netMsg ("MD5 Algorithm not present in this JVM!"); Debug.error (e.toString ()); e.printStackTrace (); } catch (InvalidKeySpecException e) { Debug.netMsg ("Error generating cipher, problems with key spec?"); Debug.error (e.toString ()); e.printStackTrace (); } catch (InvalidKeyException e) { Debug.netMsg ("Error genertating cipher, problems with key?"); Debug.error (e.toString ()); e.printStackTrace (); } catch (NoSuchPaddingException e) { Debug.netMsg ("Error generating cipher, problems with padding?"); Debug.error (e.toString ()); e.printStackTrace (); } catch (IOException e) { Debug.netMsg ("Error authenticating client!"); Debug.error (e.toString ()); e.printStackTrace (); } catch (BadPaddingException e) { Debug.netMsg ("Bad padding exception!"); Debug.error (e.toString ()); e.printStackTrace (); } return null; }

Secure Hash

Type-3 (WT3/4)

public Thread transmitThread (final Socket s, final CountDownLatch abortLatch) { final Thread theThread = new Thread () { @Override public void run () { final Random r = new Random (); final Counter counter = new Counter ("TRANSMIT", plotter); counter.start (); try { final DataOutputStream dos = new DataOutputStream (new BufferedOutputStream (s.getOutputStream ())); while (! Thread.interrupted ()) { if (! running.get ()) { Thread.sleep (1000); continue; } final int packetSize = r.nextInt (8192) + 2048; final byte [] packet = new byte [packetSize]; r.nextBytes (packet); final CRC32 crc = new CRC32 (); crc.update (packet); dos.writeInt (packetSize); counter.addBytes (INTEGER_BYTES); dos.write (packet); counter.addBytes (packetSize); dos.writeLong (crc.getValue ()); counter.addBytes (CRC_BYTES); dos.flush (); } } catch (InterruptedException e) { System.out.println ("Transmitter thread interrupted!"); } catch (Exception e) { System.err.println ("Unexpected error in transmitter thread: " + e.getMessage ()); } finally { abortLatch.countDown (); counter.interrupt (); } }} ; return theThread; }

private static String getUnicodeStringIfOriginalMatches (AbstractUnicodeExtraField f, byte [] orig) { if (f != null) { CRC32 crc32 = new CRC32 (); crc32.update (orig); long origCRC32 = crc32.getValue (); if (origCRC32 == f.getNameCRC32 ()) { try { return ZipEncodingHelper.UTF8_ZIP_ENCODING.decode (f.getUnicodeName ()); } catch (IOException ex) { return null; } } } return null; }

CRC32 File Checksum

Type-3 (WT3/4)

@Override public List < SectionFinderResult > lookForSections (String text, Section < ? > father, Type type) { ArrayList < SectionFinderResult > result = new ArrayList < SectionFinderResult > (); Pattern TABLE_LINE = Pattern.compile (TABLE_LINE_REGEXP, Pattern.MULTILINE); Matcher m = TABLE_LINE.matcher (text); int end = 0; int tableStart = - 1; int tableEnd = - 1; while (m.find (end)) { int start = m.start (); end = m.end (); if (tableEnd == start) { tableEnd = end; } else { addResultIfAvailable (result, tableStart, tableEnd); tableStart = start; tableEnd = end; } if (end >= text.length ()) break; } addResultIfAvailable (result, tableStart, tableEnd); return result; }

public LinkedList < SearchResult > search (String strRequest) { LinkedList < SearchResult > ret = new LinkedList < SearchResult > (); HttpClient h = new HttpClient (); try { String strRequestUrl = "http://www.youporn.com/search"; if (strRequest.toLowerCase ().contains ("straight!")) { strRequestUrl += "?type=straight"; strRequest = strRequest.replaceAll ("straight!", ""); } if (strRequest.toLowerCase ().contains ("gay!")) { strRequestUrl += "?type=gay"; strRequest = strRequest.replaceAll ("gay!", ""); } if (strRequest.toLowerCase ().contains ("cocks!")) { strRequestUrl += "?type=cocks"; strRequest = strRequest.replaceAll ("cocks!", ""); } if (! strRequestUrl.endsWith ("search")) strRequestUrl += "&"; else strRequestUrl += "?"; strRequestUrl += "query=" + URLEncoder.encode (strRequest, "UTF-8"); if (NoMuleRuntime.DEBUG) System.out.println (strRequestUrl); GetMethod get = new GetMethod (strRequestUrl); Date d = new Date ((new Date ()).getTime () + (1 * 24 * 3600 * 1000)); h.getState ().addCookie (new Cookie (".youporn.com", "age_check", "1", "/", d, false)); h.executeMethod (get); BufferedReader in = new BufferedReader (new InputStreamReader (get.getResponseBodyAsStream ())); String s = ""; String res = ""; while ((s = in.readLine ()) != null) { res += s; } get.releaseConnection (); if (NoMuleRuntime.DEBUG) System.out.println (res); String regexp = "\\<a href\\=\"\\/watch\\/[^\"]+\"\\>[^\\<]+"; Pattern p = Pattern.compile (regexp); Matcher m = p.matcher (res); while (m.find ()) { int startPos = m.start () + "<a href=\"".length (); String strUrl = "http://www.youporn.com"; int pos = 0; for (pos = startPos; pos < m.end () && (res.charAt (pos) != '\"'); pos ++) { strUrl += res.charAt (pos); } String strTitle = res.substring (pos + 2, m.end ()); if (strTitle.trim ().length () > 0) ret.add (new SearchResult (strTitle + " at YouPorn", strUrl)); } return ret; } catch (UnsupportedEncodingException e) { e.printStackTrace (); } catch (HttpException e) { e.printStackTrace (); } catch (IOException e) { e.printStackTrace (); } return null; }

Extract Matches Using Regex

Type-3 (WT3/4)

public static InputStream gunzip (final InputStream inputStream) throws IOException { Assert.notNull (inputStream, "inputStream"); GZIPInputStream gzipInputStream = new GZIPInputStream (inputStream); InputOutputStream inputOutputStream = new InputOutputStream (); IOUtils.copy (gzipInputStream, inputOutputStream); return inputOutputStream.getInputStream (); }

public void writeConfigurationFile () throws IOException, ComponentException { SystemConfig config = parent.getParentSystem ().getConfiguration (); File original = config.getLocation (); File backup = new File (original.getParentFile (), original.getName () + "." + System.currentTimeMillis ()); FileInputStream in = new FileInputStream (original); FileOutputStream out = new FileOutputStream (backup); byte [] buffer = new byte [2048]; try { int bytesread = 0; while ((bytesread = in.read (buffer)) > 0) { out.write (buffer, 0, bytesread); } } catch (IOException e) { logger.warn ("Failed to copy backup of configuration file"); throw e; } finally { in.close (); out.close (); } FileWriter replace = new FileWriter (original); replace.write (config.toFileFormat ()); replace.close (); logger.info ("Re-wrote configuration file " + original.getPath ()); }

Copy File

Type-3 (WT3/4)

public void streamDataToZip (VolumeTimeSeries vol, ZipOutputStream zout) throws Exception { ZipEntry entry = new ZipEntry (vol.getId () + ".dat"); zout.putNextEntry (entry); if (vol instanceof FloatVolumeTimeSeries) { streamData (((FloatVolumeTimeSeries) vol).getData (), zout); } else if (vol instanceof RGBVolumeTimeSeries) { streamData (((RGBVolumeTimeSeries) vol).getARGBData (), zout); } else if (vol instanceof BinaryVolumeTimeSeries) { streamData (((BinaryVolumeTimeSeries) vol).getBinaryData (), zout); } }

private void zipLog (InfoRolling info) { boolean zipped = false; File [] logFiles = info.getFiles (); try { GregorianCalendar gc = (GregorianCalendar) GregorianCalendar.getInstance (); gc.roll (Calendar.DAY_OF_MONTH, info.getBackRolling ()); final String prefixFileName = logFileName.substring (0, logFileName.indexOf (".")); final String date = sdf.format (gc.getTime ()); String tarName = new StringBuffer (prefixFileName).append (date).append (".tar").toString (); String gzipFileName = new StringBuffer (tarName).append (".zip").toString (); String tarPath = new StringBuffer (logDir).append (File.separator).append (tarName).toString (); TarArchive ta = new TarArchive (new FileOutputStream (tarPath)); for (int i = 0; i < logFiles.length; i ++) { File file = logFiles [i]; TarEntry te = new TarEntry (file); ta.writeEntry (te, true); } ta.closeArchive (); ZipEntry zipEntry = new ZipEntry (tarName); zipEntry.setMethod (ZipEntry.DEFLATED); ZipOutputStream zout = new ZipOutputStream (new FileOutputStream (new StringBuffer (logDir).append (File.separator).append (gzipFileName).toString ())); zout.putNextEntry (zipEntry); InputStream in = new FileInputStream (tarPath); byte [] buffer = new byte [2048]; int ch = 0; while ((ch = in.read (buffer)) >= 0) { zout.write (buffer, 0, ch); } zout.flush (); zout.close (); in.close (); logFiles = new File (getFile ().substring (0, getFile ().lastIndexOf (File.separator))).listFiles (new FileFilter () { public boolean accept (File file) { return file.getName ().endsWith (".tar"); }} ); for (int i = 0; i < logFiles.length; i ++) { File file = logFiles [i]; System.out.println ("cancello : " + file.getAbsolutePath () + " : " + file.delete ()); } logFiles = new File (getFile ().substring (0, getFile ().lastIndexOf (File.separator))).listFiles (new FileFilter () { public boolean accept (File file) { return file.getName ().indexOf (prefixFileName + ".log" + date) != - 1 && ! file.getName ().endsWith (".zip"); }} ); for (int i = 0; i < logFiles.length; i ++) { File file = logFiles [i]; System.out.println ("cancello : " + file.getAbsolutePath () + " : " + file.delete ()); } zipped = true; } catch (FileNotFoundException ex) { LogLog.error ("Filenotfound: " + ex.getMessage (), ex); } catch (IOException ex) { LogLog.error ("IOException: " + ex.getMessage (), ex); } finally { if (zipped) { for (int i = 0; i < logFiles.length; i ++) { File file = logFiles [i]; file.delete (); } } } }

Zip Files

Type-3 (WT3/4)

public SWORDEntry ingestDepost (final DepositCollection pDeposit, final ServiceDocument pServiceDocument) throws SWORDException { try { ZipFileAccess tZipFile = new ZipFileAccess (super.getTempDir ()); LOG.debug ("copying file"); String tZipTempFileName = super.getTempDir () + "uploaded-file.tmp"; IOUtils.copy (pDeposit.getFile (), new FileOutputStream (tZipTempFileName)); Datastream tDatastream = new LocalDatastream (super.getGenericFileName (pDeposit), this.getContentType (), tZipTempFileName); _datastreamList.add (tDatastream); _datastreamList.addAll (tZipFile.getFiles (tZipTempFileName)); int i = 0; boolean found = false; for (i = 0; i < _datastreamList.size (); i ++) { if (_datastreamList.get (i).getId ().equalsIgnoreCase ("mets")) { found = true; break; } } if (found) { SAXBuilder tBuilder = new SAXBuilder (); _mets = new METSObject (tBuilder.build (((LocalDatastream) _datastreamList.get (i)).getPath ())); LocalDatastream tLocalMETSDS = (LocalDatastream) _datastreamList.remove (i); new File (tLocalMETSDS.getPath ()).delete (); _datastreamList.add (_mets.getMETSDs ()); _datastreamList.addAll (_mets.getMetadataDatastreams ()); } else { throw new SWORDException ("Couldn't find a METS document in the zip file, ensure it is named mets.xml or METS.xml"); } SWORDEntry tEntry = super.ingestDepost (pDeposit, pServiceDocument); tZipFile.removeLocalFiles (); return tEntry; } catch (IOException tIOExcpt) { String tMessage = "Couldn't retrieve METS from deposit: " + tIOExcpt.toString (); LOG.error (tMessage); tIOExcpt.printStackTrace (); throw new SWORDException (tMessage, tIOExcpt); } catch (JDOMException tJDOMExcpt) { String tMessage = "Couldn't build METS from deposit: " + tJDOMExcpt.toString (); LOG.error (tMessage); tJDOMExcpt.printStackTrace (); throw new SWORDException (tMessage, tJDOMExcpt); } }

public void testReadPerMemberSixSmall () throws IOException { GZIPMembersInputStream gzin = new GZIPMembersInputStream (new ByteArrayInputStream (sixsmall_gz)); gzin.setEofEachMember (true); for (int i = 0; i < 3; i ++) { int count2 = IOUtils.copy (gzin, new NullOutputStream ()); assertEquals ("wrong 1-byte member count", 1, count2); gzin.nextMember (); int count3 = IOUtils.copy (gzin, new NullOutputStream ()); assertEquals ("wrong 5-byte member count", 5, count3); gzin.nextMember (); } int countEnd = IOUtils.copy (gzin, new NullOutputStream ()); assertEquals ("wrong eof count", 0, countEnd); }

Copy File

Type-3 (WT3/4)

private void nextZipEntry (String url, int level) throws IOException { if (! url.startsWith ("META-INF/") && ! url.startsWith ("OEBPS/")) url = "OEBPS/" + url; ZipEntry ze = new ZipEntry (url); ze.setMethod (ZipEntry.DEFLATED); tmpzos.putNextEntry (ze); }

private void writeEntry (File file, ZipOutputStream output, File oya) throws IOException { BufferedInputStream input = new BufferedInputStream (new FileInputStream (file)); String fn = extractRelativeZipPath (file.getAbsolutePath (), oya.getAbsolutePath ()); ZipEntry entry = new ZipEntry (this.convertZipEntrySeparator (fn)); output.putNextEntry (entry); int b; while ((b = input.read ()) != - 1) { output.write (b); } input.close (); output.closeEntry (); }

Zip Files

Type-3 (WT3/4)

private static void readAndRewrite (File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream (new BufferedInputStream (new FileInputStream (inFile))); DcmParser dcmParser = DcmParserFactory.getInstance ().newDcmParser (iis); Dataset ds = DcmObjectFactory.getInstance ().newDataset (); dcmParser.setDcmHandler (ds.getDcmHandler ()); dcmParser.parseDcmFile (null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader (ds, iis, dcmParser.getDcmDecodeParam ().byteOrder, dcmParser.getReadVR ()); System.out.println ("reading " + inFile + "..."); pdReader.readPixelData (false); ImageOutputStream out = ImageIO.createImageOutputStream (new BufferedOutputStream (new FileOutputStream (outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset (out, dcmEncParam); ds.writeHeader (out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR (), dcmParser.getReadLength ()); System.out.println ("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter (pdReader.getPixelDataArray (), false, ds, out, dcmParser.getDcmDecodeParam ().byteOrder, dcmParser.getReadVR ()); pdWriter.writePixelData (); out.flush (); out.close (); System.out.println ("done!"); }

public void putFile (CompoundName file, FileInputStream fileInput) throws IOException { File fullDir = new File (REMOTE_BASE_DIR.getCanonicalPath ()); for (int i = 0; i < file.size () - 1; i ++) fullDir = new File (fullDir, file.get (i)); fullDir.mkdirs (); File outputFile = new File (fullDir, file.get (file.size () - 1)); FileOutputStream outStream = new FileOutputStream (outputFile); for (int byteIn = fileInput.read (); byteIn != - 1; byteIn = fileInput.read ()) outStream.write (byteIn); fileInput.close (); outStream.close (); }

Copy File

Type-3 (WT3/4)

public static int getCrc32asInt (byte [] in) { if (in == null || in.length == 0) return - 1; CRC32 crc = new CRC32 (); crc.update (in); return (int) crc.getValue (); }

private void readHeader () throws IOException { CRC32 headCRC = new CRC32 (); int magic = in.read (); if (magic < 0) { eos = true; return; } headCRC.update (magic); if (magic != (GZIP_MAGIC>> 8)) throw new IOException ("Error in GZIP header, first byte doesn't match"); magic = in.read (); if (magic != (GZIP_MAGIC & 0xff)) throw new IOException ("Error in GZIP header, second byte doesn't match"); headCRC.update (magic); int CM = in.read (); if (CM != 8) throw new IOException ("Error in GZIP header, data not in deflate format"); headCRC.update (CM); int flags = in.read (); if (flags < 0) throw new EOFException ("Early EOF in GZIP header"); headCRC.update (flags); if ((flags & 0xd0) != 0) throw new IOException ("Reserved flag bits in GZIP header != 0"); for (int i = 0; i < 6; i ++) { int readByte = in.read (); if (readByte < 0) throw new EOFException ("Early EOF in GZIP header"); headCRC.update (readByte); } if ((flags & FEXTRA) != 0) { for (int i = 0; i < 2; i ++) { int readByte = in.read (); if (readByte < 0) throw new EOFException ("Early EOF in GZIP header"); headCRC.update (readByte); } if (in.read () < 0 || in.read () < 0) throw new EOFException ("Early EOF in GZIP header"); int len1, len2, extraLen; len1 = in.read (); len2 = in.read (); if ((len1 < 0) || (len2 < 0)) throw new EOFException ("Early EOF in GZIP header"); headCRC.update (len1); headCRC.update (len2); extraLen = (len1 << 8) | len2; for (int i = 0; i < extraLen; i ++) { int readByte = in.read (); if (readByte < 0) throw new EOFException ("Early EOF in GZIP header"); headCRC.update (readByte); } } if ((flags & FNAME) != 0) { int readByte; while ((readByte = in.read ()) > 0) headCRC.update (readByte); if (readByte < 0) throw new EOFException ("Early EOF in GZIP file name"); headCRC.update (readByte); } if ((flags & FCOMMENT) != 0) { int readByte; while ((readByte = in.read ()) > 0) headCRC.update (readByte); if (readByte < 0) throw new EOFException ("Early EOF in GZIP comment"); headCRC.update (readByte); } if ((flags & FHCRC) != 0) { int tempByte; int crcval = in.read (); if (crcval < 0) throw new EOFException ("Early EOF in GZIP header"); tempByte = in.read (); if (tempByte < 0) throw new EOFException ("Early EOF in GZIP header"); crcval = (crcval << 8) | tempByte; if (crcval != ((int) headCRC.getValue () & 0xffff)) throw new IOException ("Header CRC value mismatch"); } readGZIPHeader = true; }

CRC32 File Checksum

Type-3 (WT3/4)

private void zipStream (InputStream inStream, String streamName, File zipFile) throws IOException { if (inStream == null) { log.warn ("No stream to zip."); } else { try { FileOutputStream dest = new FileOutputStream (zipFile); ZipOutputStream out = new ZipOutputStream (new BufferedOutputStream (dest)); ZipEntry entry = new ZipEntry (streamName); out.putNextEntry (entry); copyInputStream (inStream, out); out.close (); dest.close (); inStream.close (); } catch (IOException e) { log.error ("IOException while zipping stream"); throw e; } } }

public void close () { logger.debug ("Closing output file."); outfile.close (); tempFile.renameTo (new File (fileName)); if (toZIP) { logger.debug ("ZIPping output file."); try { ZipOutputStream zipout = new ZipOutputStream (new FileOutputStream (fileName + ".zip")); zipout.setLevel (9); String outfilezipname = fileName.substring (fileName.lastIndexOf (System.getProperty ("file.separator")) + 1); zipout.putNextEntry (new ZipEntry (outfilezipname)); FileInputStream fis = new FileInputStream (fileName); byte [] buffer = new byte [65536]; int len; while ((len = fis.read (buffer)) > 0) { zipout.write (buffer, 0, len); } zipout.close (); fis.close (); logger.debug ("ZIPping output file ok."); logger.debug ("Removing " + fileName); (new File (fileName)).delete (); } catch (IOException ex) { logger.debug ("Error when zipping file", ex); } } }

Zip Files

Type-3 (WT3/4)

@BeforeClass public static void createProblem () throws IOException, ParserConfigurationException, TransformerException { problem = File.createTempFile ("___prb___", ".problem"); System.out.println ("created temporary problem " + problem); ZipOutputStream zos = new ZipOutputStream (new FileOutputStream (problem)); PrintStream ps = new PrintStream (zos); zos.putNextEntry (new ZipEntry ("MANIFEST")); DocumentBuilderFactory builderFactory = DocumentBuilderFactory.newInstance (); DocumentBuilder builder = builderFactory.newDocumentBuilder (); Document doc = builder.newDocument (); Element root = doc.createElement ("resources"); doc.appendChild (root); Element alias = doc.createElement ("alias"); alias.setAttribute ("path", "STATEMENT"); alias.setAttribute ("target", "statement.txt"); root.appendChild (alias); Element contents1 = doc.createElement ("contents"); contents1.setAttribute ("path", "ANSWER"); contents1.setTextContent ("42"); root.appendChild (contents1); Element contents2 = doc.createElement ("contents"); contents2.setAttribute ("path", "STATEMENT EXT"); contents2.setTextContent ("TXT"); root.appendChild (contents2); Element teacher = doc.createElement ("teacher"); teacher.setAttribute ("path", "ANSWER"); root.appendChild (teacher); Source source = new DOMSource (doc); Result result = new StreamResult (zos); Transformer xformer = TransformerFactory.newInstance ().newTransformer (); xformer.transform (source, result); zos.putNextEntry (new ZipEntry ("statement.txt")); ps.println ("���� ����� ������������ ����� � ����?"); zos.closeEntry (); zos.close (); }

public static boolean exportStandalone (String projectDirectory, String destinyJARPath) { boolean exported = true; try { File destinyJarFile = new File (destinyJARPath); FileOutputStream mergedFile = new FileOutputStream (destinyJarFile); ZipOutputStream os = new ZipOutputStream (mergedFile); String manifest = Writer.defaultManifestFile ("es.eucm.eadventure.engine.EAdventureStandalone"); ZipEntry manifestEntry = new ZipEntry ("META-INF/MANIFEST.MF"); os.putNextEntry (manifestEntry); os.write (manifest.getBytes ()); os.closeEntry (); os.flush (); File.mergeZipAndDirToJar ("web/eAdventure_temp.jar", projectDirectory, os); addNeededLibrariesToJar (os, Controller.getInstance ()); os.close (); } catch (FileNotFoundException e) { exported = false; ReportDialog.GenerateErrorReport (e, true, "UNKNOWNERROR"); } catch (IOException e) { exported = false; ReportDialog.GenerateErrorReport (e, true, "UNKNOWNERROR"); } return exported; }

Zip Files

Type-3 (WT3/4)

@Override public boolean copy (Document document, Folder folder) throws Exception { boolean isCopied = false; if (document.getId () != null && folder.getId () != null) { Document copiedDoc = new DocumentModel (); copiedDoc.setValues (document.getValues ()); copiedDoc.setFolder (folder); copiedDoc.setId (null); em.persist (copiedDoc); resourceAuthorityService.applyAuthority (copiedDoc); List < Preference > preferences = prefService.findAll (); Preference preference = new PreferenceModel (); if (preferences != null && ! preferences.isEmpty ()) { preference = preferences.get (0); } String repo = preference.getRepository (); SimpleDateFormat sdf = new SimpleDateFormat (Constants.DATEFORMAT_YYYYMMDD); Calendar calendar = Calendar.getInstance (); StringBuffer sbRepo = new StringBuffer (repo); sbRepo.append (File.separator); StringBuffer sbFolder = new StringBuffer (sdf.format (calendar.getTime ())); sbFolder.append (File.separator).append (calendar.get (Calendar.HOUR_OF_DAY)); File fFolder = new File (sbRepo.append (sbFolder).toString ()); if (! fFolder.exists ()) { fFolder.mkdirs (); } copiedDoc.setLocation (sbFolder.toString ()); em.merge (copiedDoc); File in = new File (repo + File.separator + document.getLocation () + File.separator + document.getId () + "." + document.getExt ()); File out = new File (fFolder.getAbsolutePath () + File.separator + copiedDoc.getId () + "." + copiedDoc.getExt ()); FileChannel inChannel = new FileInputStream (in).getChannel (); FileChannel outChannel = new FileOutputStream (out).getChannel (); try { inChannel.transferTo (0, inChannel.size (), outChannel); } catch (IOException e) { throw e; } finally { if (inChannel != null) inChannel.close (); if (outChannel != null) outChannel.close (); } } return isCopied; }

private static void copy (File source, File target) throws IOException { FileInputStream from = null; FileOutputStream to = null; try { from = new FileInputStream (source); to = new FileOutputStream (target); byte [] buffer = new byte [4096]; int bytesRead; while ((bytesRead = from.read (buffer)) != - 1) to.write (buffer, 0, bytesRead); } finally { if (from != null) try { from.close (); } catch (IOException e) { } if (to != null) try { to.close (); } catch (IOException e) { } } }

Copy File

Type-3 (WT3/4)

File createJar (File jar, String...entries) throws IOException { OutputStream out = new FileOutputStream (jar); try { JarOutputStream jos = new JarOutputStream (out); for (String e : entries) { jos.putNextEntry (new JarEntry (getPathForZipEntry (e))); jos.write (getBodyForEntry (e).getBytes ()); } jos.close (); } finally { out.close (); } return jar; }

public void run (IProgressMonitor runnerMonitor) throws CoreException { try { Map < String, File > projectFiles = new HashMap < String, File > (); IPath basePath = new Path ("/"); for (File nextLocation : filesToZip) { projectFiles.putAll (getFilesToZip (nextLocation, basePath, fileFilter)); } if (projectFiles.isEmpty ()) { PlatformActivator.logDebug ("Zip file (" + zipFileName + ") not created because there were no files to zip"); return; } IPath resultsPath = PlatformActivator.getDefault ().getResultsPath (); File copyRoot = resultsPath.toFile (); copyRoot.mkdirs (); IPath zipFilePath = resultsPath.append (new Path (finalZip)); String zipFileName = zipFilePath.toPortableString (); ZipOutputStream out = new ZipOutputStream (new FileOutputStream (zipFileName)); try { out.setLevel (Deflater.DEFAULT_COMPRESSION); for (String filePath : projectFiles.keySet ()) { File nextFile = projectFiles.get (filePath); FileInputStream fin = new FileInputStream (nextFile); try { out.putNextEntry (new ZipEntry (filePath)); try { byte [] bin = new byte [4096]; int bread = fin.read (bin, 0, 4096); while (bread != - 1) { out.write (bin, 0, bread); bread = fin.read (bin, 0, 4096); } } finally { out.closeEntry (); } } finally { fin.close (); } } } finally { out.close (); } } catch (FileNotFoundException e) { Status error = new Status (Status.ERROR, PlatformActivator.PLUGIN_ID, Status.ERROR, e.getLocalizedMessage (), e); throw new CoreException (error); } catch (IOException e) { Status error = new Status (Status.ERROR, PlatformActivator.PLUGIN_ID, Status.ERROR, e.getLocalizedMessage (), e); throw new CoreException (error); } }

Zip Files

Type-3 (WT3/4)

public static long getCRC (String content) { if (content.length () == 0) return 0; final java.util.zip.CRC32 crc = new java.util.zip.CRC32 (); java.io.OutputStream crcOut = new java.io.OutputStream () { @Override public void write (int b) throws java.io.IOException { crc.update (b); }} ; try { new java.io.OutputStreamWriter (crcOut).write (content); } catch (java.io.IOException e) { throw new IllegalStateException ("Could not check CRC of message"); } return crc.getValue (); }

public static long checksum1 (File file) throws IOException { CRC32 crc = new CRC32 (); FileReader fr = new FileReader (file); int data; while ((data = fr.read ()) != - 1) { crc.update (data); } fr.close (); return crc.getValue (); }

CRC32 File Checksum

Type-3 (WT3/4)

public BufferedWriter createOutputStream (String inFile, String outFile) throws IOException { int k_blockSize = 1024; int byteCount; char [] buf = new char [k_blockSize]; File ofp = new File (outFile); ZipOutputStream zos = new ZipOutputStream (new FileOutputStream (ofp)); zos.setMethod (ZipOutputStream.DEFLATED); OutputStreamWriter osw = new OutputStreamWriter (zos, "ISO-8859-1"); BufferedWriter bw = new BufferedWriter (osw); ZipEntry zot = null; File ifp = new File (inFile); ZipInputStream zis = new ZipInputStream (new FileInputStream (ifp)); InputStreamReader isr = new InputStreamReader (zis, "ISO-8859-1"); BufferedReader br = new BufferedReader (isr); ZipEntry zit = null; while ((zit = zis.getNextEntry ()) != null) { if (zit.getName ().equals ("content.xml")) { continue; } zot = new ZipEntry (zit.getName ()); zos.putNextEntry (zot); while ((byteCount = br.read (buf, 0, k_blockSize)) >= 0) bw.write (buf, 0, byteCount); bw.flush (); zos.closeEntry (); } zos.putNextEntry (new ZipEntry ("content.xml")); bw.flush (); osw = new OutputStreamWriter (zos, "UTF8"); bw = new BufferedWriter (osw); return bw; }

public static < T extends ZipNode > void saveAll (OutputStream outputstream, Collection < T > list, ZipStreamFilter filter) throws Exception { ZipOutputStream zip_out = new ZipOutputStream (outputstream); try { ZipEntry entry = new ZipEntry (".info/info.properties"); entry.setTime (0); zip_out.putNextEntry (entry); String info = "filter = " + filter.getClass ().getName () + "\n" + "count = " + list.size () + "\n"; zip_out.write (info.getBytes ()); for (T object : list) { save (zip_out, object, filter); } } catch (Throwable ex) { ex.printStackTrace (); } finally { try { zip_out.close (); } catch (IOException e) { } } }

Zip Files

Type-3 (WT3/4)

public void preparaEscrita (DadosSeriais dados, String dir) throws BasicException { String idArquivo = dados.getIdColeta ().toString (); if (dados.getIdResumo () != null) { idArquivo += "_" + dados.getIdResumo ().toString (); } if (dir == null || dir.trim ().equals ("")) { throw BasicException.errorHandling ("Diret�rio Imagem de Dados n�o foi definido.", "msgErroNaoExisteDiretorioImagem", new String [] {}, log); } try { fos = new FileOutputStream (new File (dir.trim (), "pdump." + idArquivo + ".data.xml.zip")); } catch (FileNotFoundException e) { throw BasicException.errorHandling ("Erro ao abrir arquivo de dados xml para escrita", "msgErroCriarArquivoDadosXML", e, log); } zipOutputStream = new ZipOutputStream (fos); zipOutputStream.setLevel (Deflater.DEFAULT_COMPRESSION); try { zipOutputStream.putNextEntry (new ZipEntry ("pdump." + idArquivo + ".data.xml")); xmlWriter = XMLOutputFactory.newInstance ().createXMLStreamWriter (zipOutputStream, ENCODING); } catch (Exception e) { throw BasicException.errorHandling ("Erro ao criar entrada em arquivo compactado", "msgErroCriarEntradaZipArquivoDadosXML", e, log); } XMLStreamWriter osw = null; try { xmlWriter = XMLOutputFactory.newInstance ().createXMLStreamWriter (zipOutputStream, ENCODING); } catch (Exception e) { throw BasicException.errorHandling ("Erro ao criar entrada em arquivo compactado", "msgErroCriarEntradaZipArquivoDadosXML", e, log); } SimpleDateFormat dateFormat = new SimpleDateFormat ("yyyy-MM-dd'T'HH:mm:ss"); if (dados.getTipos ().size () > 0) { tipos = new int [dados.getTipos ().size ()]; for (int c = 0; c < dados.getTipos ().size (); c ++) { String tipo = dados.getTipos ().get (c); if (tipo.equals (LIT_INTEIRO)) { tipos [c] = INTEIRO; } else if (tipo.equals (LIT_DECIMAL)) { tipos [c] = DECIMAL; } else if (tipo.equals (LIT_DATA)) { tipos [c] = DATA; } else { tipos [c] = TEXTO; } } } try { xmlWriter.writeStartDocument (ENCODING, "1.0"); xmlWriter.writeStartElement ("coleta"); xmlWriter.writeAttribute ("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance"); xmlWriter.writeAttribute ("xsi:noNamespaceSchemaLocation", "http://www.pingifes.lcc.ufmg.br/dtd/pingifes_dados_seriais.xsd"); xmlWriter.writeStartElement ("id"); xmlWriter.writeCharacters (idArquivo); xmlWriter.writeEndElement (); xmlWriter.writeStartElement ("data"); xmlWriter.writeCharacters (dateFormat.format (dados.getDataColeta ())); xmlWriter.writeEndElement (); xmlWriter.writeStartElement ("sql"); xmlWriter.writeCData (dados.getSql ()); xmlWriter.writeEndElement (); xmlWriter.writeStartElement ("cabecalho"); for (int c = 0; c < dados.getCabecalho ().size (); c ++) { xmlWriter.writeStartElement ("nome"); xmlWriter.writeAttribute ("tipo", dados.getTipos ().get (c)); xmlWriter.writeCharacters (dados.getCabecalho ().get (c)); xmlWriter.writeEndElement (); } xmlWriter.writeEndElement (); xmlWriter.writeStartElement ("quantidade"); xmlWriter.writeCharacters ("" + dados.getQuantidade ()); xmlWriter.writeEndElement (); xmlWriter.writeStartElement ("dados"); } catch (XMLStreamException e) { throw BasicException.errorHandling ("Erro ao escrever dados em arquivo compactado", "msgErroEscreverArquivoDadosXML", e, log); } calculadorHash = new CalculaHash (); }

private void zipDir (File dir, String jarEntry, JarOutputStream jos) throws IOException { String [] dirList = dir.list (); for (int i = 0; i < dirList.length; i ++) { File f = new File (dir, dirList [i]); if (f.isDirectory ()) { zipDir (f, jarEntry + dirList [i] + File.separatorChar, jos); continue; } FileInputStream fis = new FileInputStream (f); ZipEntry anEntry = new ZipEntry (jarEntry + dirList [i]); jos.putNextEntry (anEntry); byte [] readBuffer = new byte [2156]; int bytesIn = 0; while ((bytesIn = fis.read (readBuffer)) != - 1) { jos.write (readBuffer, 0, bytesIn); } fis.close (); } }

Zip Files

Type-3 (WT3/4)

private void exportLearningUnitView (File selectedFile) { if (learningUnitViewElementsManager.isOriginalElementsOnly ()) { String [] elementIds = learningUnitViewElementsManager.getAllLearningUnitViewElementIds (); for (int i = 0; i < elementIds.length; i ++) { FSLLearningUnitViewElement element = learningUnitViewElementsManager.getLearningUnitViewElement (elementIds [i], false); if (element.getLastModificationDate () == null) { element.setLastModificationDate (String.valueOf (new Date ().getTime ())); element.setModified (true); } } learningUnitViewElementsManager.setModified (true); learningUnitViewManager.saveLearningUnitViewData (); if (selectedFile != null) { try { File outputFile = selectedFile; String fileName = outputFile.getName (); StringBuffer extension = new StringBuffer (); if (fileName.length () >= 5) { for (int i = 5; i > 0; i --) { extension.append (fileName.charAt (fileName.length () - i)); } } if (! extension.toString ().equals (".fslv")) { outputFile.renameTo (new File (outputFile.getAbsolutePath () + ".fslv")); outputFile = new File (outputFile.getAbsolutePath () + ".fslv"); } File files [] = selectedFile.getParentFile ().listFiles (); int returnValue = FLGOptionPane.OK_OPTION; for (int i = 0; i < files.length; i ++) { if (outputFile.getAbsolutePath ().equals (files [i].getAbsolutePath ())) { returnValue = FLGOptionPane.showConfirmDialog (internationalization.getString ("dialog.exportLearningUnitView.fileExits.message"), internationalization.getString ("dialog.exportLearningUnitView.fileExits.title"), FLGOptionPane.OK_CANCEL_OPTION, FLGOptionPane.QUESTION_MESSAGE); break; } } if (returnValue == FLGOptionPane.OK_OPTION) { FileOutputStream os = new FileOutputStream (outputFile); ZipOutputStream zipOutputStream = new ZipOutputStream (os); ZipEntry zipEntry = new ZipEntry ("dummy"); zipOutputStream.putNextEntry (zipEntry); zipOutputStream.closeEntry (); zipOutputStream.flush (); zipOutputStream.finish (); zipOutputStream.close (); final File outFile = outputFile; (new Thread () { public void run () { try { ZipOutputStream zipOutputStream = new ZipOutputStream (new FileOutputStream (outFile)); File [] files = (new File (learningUnitViewManager.getLearningUnitViewOriginalDataDirectory ().getPath ())).listFiles (); int maxSteps = files.length; int step = 1; exportProgressDialog = new FLGImageProgressDialog (null, 0, maxSteps, 0, getClass ().getClassLoader ().getResource ("freestyleLearning/homeCore/images/fsl.gif"), (Color) UIManager.get ("FSLColorBlue"), (Color) UIManager.get ("FSLColorRed"), internationalization.getString ("learningUnitViewExport.rogressbarText")); exportProgressDialog.setCursor (new Cursor (Cursor.WAIT_CURSOR)); exportProgressDialog.setBarValue (step); buildExportZipFile ("", zipOutputStream, files, step); zipOutputStream.flush (); zipOutputStream.finish (); zipOutputStream.close (); exportProgressDialog.setBarValue (maxSteps); exportProgressDialog.setCursor (new Cursor (Cursor.DEFAULT_CURSOR)); exportProgressDialog.dispose (); } catch (Exception e) { e.printStackTrace (); } }} ).start (); os.close (); } } catch (Exception exp) { exp.printStackTrace (); } } } else { } }

public static void addToJar (JarOutputStream jos, JarFile jf) throws IOException { Enumeration e = jf.entries (); while (e.hasMoreElements ()) { ZipEntry je = (ZipEntry) e.nextElement (); InputStream io = jf.getInputStream (je); byte b [] = new byte [4096]; int read = 0; try { jos.putNextEntry (je); while ((read = io.read (b, 0, 4096)) != - 1) { jos.write (b, 0, read); } } catch (ZipException ze) { throw ze; } } }

Zip Files

Type-3 (WT3/4)

private void ZipCode (NpsContext ctxt, ZipOutputStream out) throws Exception { String filename = "JOB" + GetId () + ".data"; out.putNextEntry (new ZipEntry (filename)); try { ZipWriter writer = new ZipWriter (out); writer.print (code); } finally { out.closeEntry (); } }

private byte [] injectModifiedText () { byte [] buffer = new byte [BUFFER_SIZE]; boolean contentFound = false; boolean stylesFound = false; ByteArrayOutputStream out = new ByteArrayOutputStream (2 * fileData.length); ZipOutputStream zipOutputStream = new ZipOutputStream (out); ZipInputStream zipInputStream = new ZipInputStream (new ByteArrayInputStream (fileData)); try { ZipEntry zipEntry = zipInputStream.getNextEntry (); while (zipEntry != null) { zipOutputStream.putNextEntry (new ZipEntry (zipEntry.getName ())); if (content != null && zipEntry.getName ().equals ("content.xml")) { contentFound = true; if (log.isTraceEnabled ()) { log.trace ("Write content.xml to fileData\n" + content); } else if (log.isDebugEnabled ()) { log.trace ("Write content.xml to fileData, length = " + content.length ()); } zipOutputStream.write (content.getBytes ("UTF-8")); } else if (styles != null && zipEntry.getName ().equals ("styles.xml")) { stylesFound = true; if (log.isTraceEnabled ()) { log.trace ("Write styles.xml to fileData\n" + styles); } else if (log.isDebugEnabled ()) { log.debug ("Write styles.xml to fileData, length = " + styles.length ()); } zipOutputStream.write (styles.getBytes ("UTF-8")); } else { int read = zipInputStream.read (buffer); while (read > - 1) { zipOutputStream.write (buffer, 0, read); read = zipInputStream.read (buffer); } } zipEntry = zipInputStream.getNextEntry (); } } catch (IOException ex) { log.error ("Exception while injecting content and styles into odt", ex); throw new IllegalArgumentException ("fileData is probably not an odt file: " + ex); } finally { IOUtils.closeQuietly (zipInputStream); IOUtils.closeQuietly (zipOutputStream); } if (content != null && ! contentFound) { log.error ("fileData is not an odt file, no content.xml found, throwing exception."); throw new IllegalArgumentException ("fileData is not an odt file, no content.xml found"); } if (styles != null && ! stylesFound) { log.error ("fileData is not an odt file, no styles.xml found, throwing exception."); throw new IllegalArgumentException ("fileData is not an odt file, no styles.xml found"); } byte [] result = out.toByteArray (); if (log.isDebugEnabled ()) { log.debug ("Injected content. File data changed from " + fileData.length + " bytes to " + result.length + " bytes."); } return result; }

Zip Files

Type-3 (WT3/4)

private void backupDiskFile (ZipOutputStream out, String fileName, DiskFile file) throws SQLException, IOException { Database db = session.getDatabase (); fileName = FileUtils.getFileName (fileName); out.putNextEntry (new ZipEntry (fileName)); int pos = - 1; int max = file.getReadCount (); while (true) { pos = file.copyDirect (pos, out); if (pos < 0) { break; } db.setProgress (DatabaseEventListener.STATE_BACKUP_FILE, fileName, pos, max); } out.closeEntry (); }

private void zipFiles () throws ZipException, IOException { ZipOutputStream zipOuputStream = new ZipOutputStream (new FileOutputStream (zipFile)); for (File sourceDir : sourceDirs) { File [] sourceFiles = sourceDir.listFiles (new SourceFileFilter ()); if (sourceFiles != null) { for (File sourceFile : sourceFiles) { ZipEntry zipEntry = new ZipEntry (sourceFile.getName ()); zipOuputStream.putNextEntry (zipEntry); if (logger.isInfoEnabled ()) { logger.info ("Adding zip entry " + sourceFile.getAbsolutePath () + " to " + zipFile.getAbsolutePath ()); } if (sourceFile.length () > BYTE_ARRAY_BUFF_SIZE) { BufferedInputStream bis = new BufferedInputStream (new FileInputStream (sourceFile), BYTE_ARRAY_BUFF_SIZE); byte [] buf = new byte [BYTE_ARRAY_BUFF_SIZE]; int b; while ((b = bis.read (buf, 0, BYTE_ARRAY_BUFF_SIZE)) != - 1) { zipOuputStream.write (buf, 0, b); } bis.close (); } else { byte [] fileContents = FileUtil.getFileContentsAsByteArray (sourceFile); zipOuputStream.write (fileContents); } zipOuputStream.closeEntry (); } } } zipOuputStream.close (); }

Zip Files

Type-3 (WT3/4)

static void writeZipEntry (final byte [] data, final ZipOutputStream out, final ZipEntry entry, final boolean isCopy) throws IOException { if (isCopy) { out.putNextEntry (entry); try { out.write (data); } finally { out.closeEntry (); } } else { final ZipEntry entryCopy = new ZipEntry (entry.getName ()); entryCopy.setTime (entry.getTime ()); entryCopy.setMethod (ZipOutputStream.STORED); entryCopy.setSize (data.length); entryCopy.setCompressedSize (data.length); final CRC32 crc = new CRC32 (); crc.update (data); entryCopy.setCrc (crc.getValue ()); out.putNextEntry (entryCopy); try { out.write (data); } finally { out.closeEntry (); } } }

public int calculateCRC () { CRC32 crc = new CRC32 (); crc.reset (); crc.update (getData (), 2, getData ().length - 2); return (short) (crc.getValue ()); }

CRC32 File Checksum

Type-3 (WT3/4)

@Override public void write (DataOutput dataOutput, byte [] object) throws IOException { ZipOutputStream zos = new ZipOutputStream (new DataOutputOutputStream (dataOutput)); zos.setMethod (ZipOutputStream.DEFLATED); zos.putNextEntry (new ZipEntry ("a")); zos.write (object, 0, object.length); zos.finish (); zos.close (); }

private void archiveDirectory (ZipOutputStream out, File dir, String path) throws IOException { byte [] buf = new byte [16384]; File [] files = dir.listFiles (); if (files.length > 0) { for (int x = 0; x < files.length; x ++) { if (files [x].isFile ()) { FileInputStream in = new FileInputStream (files [x]); out.putNextEntry (new ZipEntry (path + files [x].getName ())); int len; while ((len = in.read (buf)) > 0) { out.write (buf, 0, len); } out.closeEntry (); in.close (); } else { archiveDirectory (out, files [x], path + files [x].getName () + File.separator); } } } else { out.putNextEntry (new ZipEntry (path)); out.closeEntry (); } }

Zip Files

Type-3 (WT3/4)

private void ZipCode (NpsContext ctxt, ZipOutputStream out) throws Exception { String filename = "JOB" + GetId () + ".data"; out.putNextEntry (new ZipEntry (filename)); try { ZipWriter writer = new ZipWriter (out); writer.print (code); } finally { out.closeEntry (); } }

@Override protected void doGet (HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException { ZipOutputStream zipout = new ZipOutputStream (resp.getOutputStream ()); ZipOutputStream zipout2 = new ZipOutputStream (new FileOutputStream (new File ("c:/t.zip"))); for (int i = 0; i < 200; i ++) { BufferedImage img = new BufferedImage (800 + i, 600 + i, BufferedImage.TYPE_INT_RGB); Graphics2D g = (Graphics2D) img.getGraphics (); g.setPaint (new GradientPaint (0, 0, Color.YELLOW, img.getWidth () - 1, img.getHeight () - 1, Color.BLUE, true)); g.fillRect (0, 0, img.getWidth (), img.getHeight ()); for (int t = 0; t < img.getHeight (); t += 10) { g.setColor (new Color (t + 1 * 100 + 1 * 10000)); g.drawLine (0, t, img.getWidth (), t); } g.dispose (); ZipEntry entry = new ZipEntry ("hoge" + i + ".bmp"); zipout.putNextEntry (entry); ImageIO.write (img, "bmp", zipout); ZipEntry entry2 = new ZipEntry ("hoge" + i + ".bmp"); zipout2.putNextEntry (entry2); ImageIO.write (img, "bmp", zipout2); } zipout.close (); zipout2.close (); }

Zip Files

Type-3 (WT3/4)

protected boolean doRequest (HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { String path = request.getPathInfo (); if (! path.startsWith (alias)) { throw new ServletException ("Path '" + path + "' does not start with registered alias '" + alias + "'"); } String internal; if (alias.equals ("/")) { internal = name + path; } else { internal = name + path.substring (alias.length (), path.length ()); } URL resource = httpContext.getResource (internal); if (resource == null) { return false; } String mimeType = servletContext.getMimeType (internal); if (mimeType != null) { response.setContentType (mimeType); } InputStream is = resource.openStream (); OutputStream os = response.getOutputStream (); IOUtils.copyAndClose (is, os); return true; }

public CmsSetupTestResult execute (CmsSetupBean setupBean) { CmsSetupTestResult testResult = new CmsSetupTestResult (this); String basePath = setupBean.getWebAppRfsPath (); if (! basePath.endsWith (File.separator)) { basePath += File.separator; } File file1; Random rnd = new Random (); do { file1 = new File (basePath + "test" + rnd.nextInt (1000)); } while (file1.exists ()); boolean success = false; try { file1.createNewFile (); FileWriter fw = new FileWriter (file1); fw.write ("aA1"); fw.close (); success = true; FileReader fr = new FileReader (file1); success = success && (fr.read () == 'a'); success = success && (fr.read () == 'A'); success = success && (fr.read () == '1'); success = success && (fr.read () == - 1); fr.close (); success = file1.delete (); success = ! file1.exists (); } catch (Exception e) { success = false; } if (! success) { testResult.setRed (); testResult.setInfo ("OpenCms cannot be installed without read and write privileges for path " + basePath + "! Please check you are running your servlet container with the right user and privileges."); testResult.setHelp ("Not enough permissions to create/read/write a file"); testResult.setResult (RESULT_FAILED); } else { testResult.setGreen (); testResult.setResult (RESULT_PASSED); } return testResult; }

Copy File

Type-3 (WT3/4)

private void backupPageStore (ZipOutputStream out, String fileName, PageStore store) throws SQLException, IOException { Database db = session.getDatabase (); fileName = FileUtils.getFileName (fileName); out.putNextEntry (new ZipEntry (fileName)); int max = store.getPageCount (); int pos = 0; while (true) { pos = store.copyDirect (pos, out); if (pos < 0) { break; } db.setProgress (DatabaseEventListener.STATE_BACKUP_FILE, fileName, pos, max); } out.closeEntry (); }

void writeRawDataFile (RawDataFileImpl rawDataFile, int number) throws IOException, TransformerConfigurationException, SAXException { numOfScans = rawDataFile.getNumOfScans (); dataPointsOffsets = rawDataFile.getDataPointsOffsets (); dataPointsLengths = rawDataFile.getDataPointsLengths (); consolidatedDataPointsOffsets = new TreeMap < Integer, Long > (); logger.info ("Saving data points of: " + rawDataFile.getName ()); String rawDataSavedName = "Raw data file #" + number + " " + rawDataFile.getName (); zipOutputStream.putNextEntry (new ZipEntry (rawDataSavedName + ".scans")); long newOffset = 0; byte buffer [] = new byte [1 << 20]; RandomAccessFile dataPointsFile = rawDataFile.getDataPointsFile (); for (Integer storageID : dataPointsOffsets.keySet ()) { if (canceled) return; final long offset = dataPointsOffsets.get (storageID); dataPointsFile.seek (offset); final int bytes = dataPointsLengths.get (storageID) * 4 * 2; consolidatedDataPointsOffsets.put (storageID, newOffset); if (buffer.length < bytes) { buffer = new byte [bytes * 2]; } dataPointsFile.read (buffer, 0, bytes); zipOutputStream.write (buffer, 0, bytes); newOffset += bytes; progress = 0.9 * ((double) offset / dataPointsFile.length ()); } if (canceled) return; logger.info ("Saving raw data description of: " + rawDataFile.getName ()); zipOutputStream.putNextEntry (new ZipEntry (rawDataSavedName + ".xml")); OutputStream finalStream = zipOutputStream; StreamResult streamResult = new StreamResult (finalStream); SAXTransformerFactory tf = (SAXTransformerFactory) SAXTransformerFactory.newInstance (); TransformerHandler hd = tf.newTransformerHandler (); Transformer serializer = hd.getTransformer (); serializer.setOutputProperty (OutputKeys.INDENT, "yes"); serializer.setOutputProperty (OutputKeys.ENCODING, "UTF-8"); hd.setResult (streamResult); hd.startDocument (); saveRawDataInformation (rawDataFile, hd); hd.endDocument (); }

Zip Files

Type-3 (WT3/4)

private void loadMap () { final String wordList = "vietwordlist.txt"; try { File dataFile = new File (supportDir, wordList); if (! dataFile.exists ()) { final ReadableByteChannel input = Channels.newChannel (ClassLoader.getSystemResourceAsStream ("dict/" + dataFile.getName ())); final FileChannel output = new FileOutputStream (dataFile).getChannel (); output.transferFrom (input, 0, 1000000L); input.close (); output.close (); } long fileLastModified = dataFile.lastModified (); if (map == null) { map = new HashMap (); } else { if (fileLastModified <= mapLastModified) { return; } map.clear (); } mapLastModified = fileLastModified; BufferedReader bs = new BufferedReader (new InputStreamReader (new FileInputStream (dataFile), "UTF-8")); String accented; while ((accented = bs.readLine ()) != null) { String plain = VietUtilities.stripDiacritics (accented); map.put (plain.toLowerCase (), accented); } bs.close (); } catch (IOException e) { map = null; e.printStackTrace (); JOptionPane.showMessageDialog (this, myResources.getString ("Cannot_find_\"") + wordList + myResources.getString ("\"_in\n") + supportDir.toString (), VietPad.APP_NAME, JOptionPane.ERROR_MESSAGE); } }

private void copyFile (File sourcefile, File targetfile) { BufferedInputStream in = null; BufferedOutputStream out = null; try { in = new BufferedInputStream (new FileInputStream (sourcefile)); out = new BufferedOutputStream (new FileOutputStream (targetfile)); byte [] buffer = new byte [4096]; int bytesread = 0; while ((bytesread = in.read (buffer)) >= 0) { out.write (buffer, 0, bytesread); } } catch (IOException e) { e.printStackTrace (); } finally { try { if (in != null) { in.close (); } if (out != null) { out.close (); } } catch (IOException e) { e.printStackTrace (); } } }

Copy File

Type-3 (WT3/4)

public BufferedWriter createOutputStream (String inFile, String outFile) throws IOException { int k_blockSize = 1024; int byteCount; char [] buf = new char [k_blockSize]; File ofp = new File (outFile); ZipOutputStream zos = new ZipOutputStream (new FileOutputStream (ofp)); zos.setMethod (ZipOutputStream.DEFLATED); OutputStreamWriter osw = new OutputStreamWriter (zos, "ISO-8859-1"); BufferedWriter bw = new BufferedWriter (osw); ZipEntry zot = null; File ifp = new File (inFile); ZipInputStream zis = new ZipInputStream (new FileInputStream (ifp)); InputStreamReader isr = new InputStreamReader (zis, "ISO-8859-1"); BufferedReader br = new BufferedReader (isr); ZipEntry zit = null; while ((zit = zis.getNextEntry ()) != null) { if (zit.getName ().equals ("content.xml")) { continue; } zot = new ZipEntry (zit.getName ()); zos.putNextEntry (zot); while ((byteCount = br.read (buf, 0, k_blockSize)) >= 0) bw.write (buf, 0, byteCount); bw.flush (); zos.closeEntry (); } zos.putNextEntry (new ZipEntry ("content.xml")); bw.flush (); osw = new OutputStreamWriter (zos, "UTF8"); bw = new BufferedWriter (osw); return bw; }

private void writeDynData (final int time_s) throws IOException { this.zos.putNextEntry (new ZipEntry ("step." + time_s + ".bin")); this.outFile = new DataOutputStream (this.zos); this.buf.position (0); this.outFile.writeDouble (time_s); this.quad.writeDynData (null, this.buf); this.outFile.writeInt (this.buf.position ()); this.outFile.write (this.buf.array (), 0, this.buf.position ()); this.zos.closeEntry (); }

Zip Files

Type-3 (WT3/4)

public static int save () { try { String filename = "tyrant.sav"; FileDialog fd = new FileDialog (new Frame (), "Save Game", FileDialog.SAVE); fd.setFile (filename); fd.setVisible (true); if (fd.getFile () != null) { filename = fd.getDirectory () + fd.getFile (); } else { return 0; } FileOutputStream f = new FileOutputStream (filename); ZipOutputStream z = new ZipOutputStream (f); z.putNextEntry (new ZipEntry ("data.xml")); if (! save (new ObjectOutputStream (z))) { throw new Error ("Save game failed"); } Game.message ("Game saved - " + filename); z.closeEntry (); z.close (); if (saveHasBeenCalledAlready) Game.message ("Please note that you can only restore the game with the same version of Tyrant (v" + VERSION + ")."); saveHasBeenCalledAlready = false; } catch (Exception e) { Game.message ("Error while saving: " + e.toString ()); if (QuestApp.isapplet) { Game.message ("This may be due to your browser security restrictions"); Game.message ("If so, run the web start or downloaded application version instead"); } System.out.println (e); return - 1; } return 1; }

private void writeEntry (byte [] data, String name, ZipOutputStream outStream) throws IOException { ZipEntry entry = new ZipEntry (name); entry.setSize (data.length); entry.setTime (System.currentTimeMillis ()); if (outStream != null) { outStream.putNextEntry (entry); outStream.write (data); outStream.closeEntry (); } }

Zip Files

Type-3 (WT3/4)

private void cleanupStagingEnvironment (File stagingDir) throws FileUpdateException { if (stagingDir != null && stagingDir.exists () && stagingDir.isDirectory ()) { File [] files = stagingDir.listFiles (); for (int i = 0; i < files.length; i ++) { File f = files [i]; if (! f.delete ()) { logger.error ("Could not delete: " + f.getAbsolutePath ()); throw new SessionEnvironmentException ("Could not delete: " + f.getAbsolutePath ()); } } if (stagingDir.exists ()) { if (stagingDir.delete ()) { logger.debug (stagingDir + " was successfully deleted"); } else { logger.error ("Could not clean up staging directory: " + stagingDir.getAbsolutePath ()); throw new SessionEnvironmentException ("Could not remove directory: " + stagingDir.getAbsolutePath ()); } } } else { throw new SessionEnvironmentException ("Staging directory undefined, does not exist, or is not a directory"); } }

public static boolean deleteDir (File dir) { if (dir.exists ()) { File [] files = dir.listFiles (); for (int i = 0; i < files.length; i ++) { if (files [i].isDirectory ()) { deleteDir (files [i]); } else { files [i].delete (); } } } return (dir.delete ()); }

Delete Folder and Contents

Type-3 (WT3/4)

private void exportAllSettings (HTTPurl urlData, OutputStream outStream) throws Exception { CaptureDeviceList devList = CaptureDeviceList.getInstance (); if (devList.getActiveDeviceCount () > 0) { PageTemplate template = new PageTemplate (store.getProperty ("path.template") + File.separator + "SettingsLoad.html"); StringBuffer buff = new StringBuffer (); buff.append ("<tr><td><img border=0 src='/images/stop.png' align='absmiddle' width='24' height='24'></td><td>Can not save settings while a capture is in progress.</td></tr>"); template.replaceAll ("$result", buff.toString ()); outStream.write (template.getPageBytes ()); return; } boolean matchList = "true".equalsIgnoreCase (urlData.getParameter ("MatchList")); boolean autoAdd = "true".equalsIgnoreCase (urlData.getParameter ("AutoAdd")); boolean channelMapping = "true".equalsIgnoreCase (urlData.getParameter ("ChannelMapping")); boolean deviceSelection = "true".equalsIgnoreCase (urlData.getParameter ("DeviceSelection")); boolean agentMapping = "true".equalsIgnoreCase (urlData.getParameter ("AgentMapping")); boolean channels = "true".equalsIgnoreCase (urlData.getParameter ("Channels")); boolean tasks = "true".equalsIgnoreCase (urlData.getParameter ("Tasks")); boolean systemProp = "true".equalsIgnoreCase (urlData.getParameter ("SystemProp")); boolean schedules = "true".equalsIgnoreCase (urlData.getParameter ("Schedules")); boolean authSettings = "true".equalsIgnoreCase (urlData.getParameter ("AuthSettings")); ByteArrayOutputStream bytesOut = new ByteArrayOutputStream (); ZipOutputStream out = new ZipOutputStream (bytesOut); out.setComment ("TV Scheduler Pro Settings file (Version: 1.0)"); if (channels) { out.putNextEntry (new ZipEntry ("Channels.xml")); StringBuffer channelData = new StringBuffer (); store.saveChannels (channelData); byte [] channelBytes = channelData.toString ().getBytes ("UTF-8"); out.write (channelBytes); out.closeEntry (); } if (matchList) { out.putNextEntry (new ZipEntry ("MatchList.xml")); StringBuffer matchData = new StringBuffer (); store.saveMatchList (matchData); byte [] matchBytes = matchData.toString ().getBytes ("UTF-8"); out.write (matchBytes); out.closeEntry (); } if (autoAdd) { out.putNextEntry (new ZipEntry ("EpgAutoAdd.xml")); StringBuffer addData = new StringBuffer (); store.saveEpgAutoList (addData); byte [] addBytes = addData.toString ().getBytes ("UTF-8"); out.write (addBytes); out.closeEntry (); } if (tasks) { out.putNextEntry (new ZipEntry ("Tasks.xml")); StringBuffer taskData = new StringBuffer (); store.saveTaskList (taskData); byte [] taskBytes = taskData.toString ().getBytes ("UTF-8"); out.write (taskBytes); out.closeEntry (); } if (channelMapping) { GuideStore guideStore = GuideStore.getInstance (); out.putNextEntry (new ZipEntry ("ChannelMap.sof")); ByteArrayOutputStream chanMapBytes = new ByteArrayOutputStream (); guideStore.saveChannelMap (chanMapBytes); out.write (chanMapBytes.toByteArray ()); out.closeEntry (); } if (deviceSelection) { out.putNextEntry (new ZipEntry ("CaptureDevices.sof")); ByteArrayOutputStream deviceBytes = new ByteArrayOutputStream (); devList.saveDeviceList (deviceBytes); out.write (deviceBytes.toByteArray ()); out.closeEntry (); } if (agentMapping) { out.putNextEntry (new ZipEntry ("AgentMap.sof")); ByteArrayOutputStream agentMapBytes = new ByteArrayOutputStream (); store.saveAgentToThemeMap (agentMapBytes); out.write (agentMapBytes.toByteArray ()); out.closeEntry (); } if (schedules) { out.putNextEntry (new ZipEntry ("Times.sof")); ByteArrayOutputStream timesBytes = new ByteArrayOutputStream (); store.saveSchedule (timesBytes); out.write (timesBytes.toByteArray ()); out.closeEntry (); } if (systemProp) { HashMap < String, String > serverProp = new HashMap < String, String > (); serverProp.put ("epg.showunlinked", store.getProperty ("epg.showunlinked")); serverProp.put ("path.theme", store.getProperty ("path.theme")); serverProp.put ("path.theme.epg", store.getProperty ("path.theme.epg")); serverProp.put ("capture.path", store.getProperty ("capture.path")); serverProp.put ("capture.averagedatarate", store.getProperty ("capture.averagedatarate")); serverProp.put ("capture.autoselectmethod", store.getProperty ("capture.autoselectmethod")); serverProp.put ("capture.minspacesoft", store.getProperty ("capture.minspacesoft")); serverProp.put ("capture.includecalculatedusage", store.getProperty ("capture.includecalculatedusage")); serverProp.put ("capture.deftype", store.getProperty ("capture.deftype")); serverProp.put ("capture.filename.patterns", store.getProperty ("capture.filename.patterns")); serverProp.put ("capture.path.details", store.getProperty ("capture.path.details")); serverProp.put ("capture.capturefailedtimeout", store.getProperty ("capture.capturefailedtimeout")); serverProp.put ("schedule.buffer.start", store.getProperty ("schedule.buffer.start")); serverProp.put ("schedule.buffer.end", store.getProperty ("schedule.buffer.end")); serverProp.put ("schedule.buffer.end.epg", store.getProperty ("schedule.buffer.end.epg")); serverProp.put ("schedule.wake.system", store.getProperty ("schedule.wake.system")); serverProp.put ("schedule.overlap", store.getProperty ("schedule.overlap")); serverProp.put ("sch.autodel.action", store.getProperty ("sch.autodel.action")); serverProp.put ("sch.autodel.time", store.getProperty ("sch.autodel.time")); serverProp.put ("guide.source.http.pwd", store.getProperty ("guide.source.http.pwd")); serverProp.put ("guide.source.xml.channelList", store.getProperty ("guide.source.xml.channelList")); serverProp.put ("guide.source.type", store.getProperty ("guide.source.type")); serverProp.put ("guide.source.http", store.getProperty ("guide.source.http")); serverProp.put ("guide.source.file", store.getProperty ("guide.source.file")); serverProp.put ("guide.action.name", store.getProperty ("guide.action.name")); serverProp.put ("guide.source.http.usr", store.getProperty ("guide.source.http.usr")); serverProp.put ("guide.source.schedule", store.getProperty ("guide.source.schedule")); serverProp.put ("guide.warn.overlap", store.getProperty ("guide.warn.overlap")); serverProp.put ("proxy.server", store.getProperty ("proxy.server")); serverProp.put ("proxy.port", store.getProperty ("proxy.port")); serverProp.put ("proxy.server.usr", store.getProperty ("proxy.server.usr")); serverProp.put ("proxy.server.pwd", store.getProperty ("proxy.server.pwd")); serverProp.put ("email.server", store.getProperty ("email.server")); serverProp.put ("email.from.name", store.getProperty ("email.from.name")); serverProp.put ("email.to", store.getProperty ("email.to")); serverProp.put ("email.from", store.getProperty ("email.from")); serverProp.put ("email.send.weeklyreport", store.getProperty ("email.send.weeklyreport")); serverProp.put ("email.send.capfinished", store.getProperty ("email.send.capfinished")); serverProp.put ("email.send.epgloaded", store.getProperty ("email.send.epgloaded")); serverProp.put ("email.send.onwarning", store.getProperty ("email.send.onwarning")); serverProp.put ("email.send.freespacelow", store.getProperty ("email.send.freespacelow")); serverProp.put ("email.send.serverstarted", store.getProperty ("email.send.serverstarted")); serverProp.put ("tasks.deftask", store.getProperty ("tasks.deftask")); serverProp.put ("tasks.pretask", store.getProperty ("tasks.pretask")); serverProp.put ("tasks.nodataerrortask", store.getProperty ("tasks.nodataerrortask")); serverProp.put ("tasks.starterrortask", store.getProperty ("tasks.starterrortask")); serverProp.put ("filebrowser.dirsattop", store.getProperty ("filebrowser.dirsattop")); serverProp.put ("filebrowser.masks", store.getProperty ("filebrowser.masks")); serverProp.put ("server.kbled", store.getProperty ("server.kbled")); ByteArrayOutputStream serverpropBytes = new ByteArrayOutputStream (); ObjectOutputStream oos = new ObjectOutputStream (serverpropBytes); oos.writeObject (serverProp); oos.close (); out.putNextEntry (new ZipEntry ("ServerProperties.sof")); out.write (serverpropBytes.toByteArray ()); out.closeEntry (); } if (authSettings) { File authFile = new File (store.getProperty ("path.data") + File.separator + "authentication.prop"); if (authFile.exists ()) { out.putNextEntry (new ZipEntry ("authentication.prop")); FileInputStream is = new FileInputStream (authFile); byte [] buff = new byte [1024]; int read = is.read (buff); while (read != - 1) { out.write (buff, 0, read); read = is.read (buff); } out.closeEntry (); is.close (); } } out.flush (); out.close (); StringBuffer header = new StringBuffer (); header.append ("HTTP/1.1 200 OK\n"); header.append ("Content-Type: application/zip\n"); header.append ("Content-Length: " + bytesOut.size () + "\n"); header.append ("Content-Disposition: attachment; filename=\"TV Scheduler Pro Settings.zip\"\n"); DateFormat df = new SimpleDateFormat ("EEE, dd MMM yyyy hh:mm:ss 'GMT'", new Locale ("En", "Us", "Unix")); header.append ("Last-Modified: " + df.format (new Date ()) + "\n"); header.append ("\n"); outStream.write (header.toString ().getBytes ()); ByteArrayInputStream zipStream = new ByteArrayInputStream (bytesOut.toByteArray ()); byte [] bytes = new byte [4096]; int read = zipStream.read (bytes); while (read > - 1) { outStream.write (bytes, 0, read); outStream.flush (); read = zipStream.read (bytes); } }

public void testImport () throws Exception { Init.importEverything (); String filename = Framework.onlyInstance ().getAppHomeDir () + "sts-sql/example.stz"; ZipOutputStream zo = new ZipOutputStream (new FileOutputStream (filename)); StringWriter swt; byte [] data; swt = new StringWriter (); ExportCSVRegattaWizard erw = new ExportCSVRegattaWizard (new JFrame ()); erw.doExport (swt); data = swt.toString ().getBytes (); zo.putNextEntry (new ZipEntry ("regatta.csv")); zo.write (data); swt = new StringWriter (); ExportCSVEntriesWizard eew = new ExportCSVEntriesWizard (new JFrame ()); eew.doExport (swt); data = swt.toString ().getBytes (); zo.putNextEntry (new ZipEntry ("entries.csv")); zo.write (data); swt = new StringWriter (); ExportCSVRaceDataWizard edw = new ExportCSVRaceDataWizard (new JFrame ()); edw.doExport (swt); data = swt.toString ().getBytes (); zo.putNextEntry (new ZipEntry ("race-data.csv")); zo.write (data); zo.close (); }

Zip Files

Type-3 (WT3/4)

public void service (HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { ServletContext context = getServletContext (); String forw = null; try { int maxUploadSize = 50000000; MultipartRequest multi = new MultipartRequest (request, ".", maxUploadSize); String descrizione = multi.getParameter ("text"); File myFile = multi.getFile ("uploadfile"); String filePath = multi.getOriginalFileName ("uploadfile"); String path = "C:\\files\\"; try { FileInputStream inStream = new FileInputStream (myFile); FileOutputStream outStream = new FileOutputStream (path + myFile.getName ()); while (inStream.available () > 0) { outStream.write (inStream.read ()); } inStream.close (); outStream.close (); } catch (FileNotFoundException fnfe) { fnfe.printStackTrace (); } catch (IOException ioe) { ioe.printStackTrace (); } forw = "../sendDoc.jsp"; request.setAttribute ("contentType", context.getMimeType (path + myFile.getName ())); request.setAttribute ("text", descrizione); request.setAttribute ("path", path + myFile.getName ()); request.setAttribute ("size", Long.toString (myFile.length ()) + " Bytes"); RequestDispatcher rd = request.getRequestDispatcher (forw); rd.forward (request, response); } catch (Exception e) { e.printStackTrace (); } }

public static void writeToPetrify (TransitionSystem ts, Writer bw) throws IOException { File temp = new File ("_temp"); BufferedWriter tw = new BufferedWriter (new FileWriter (temp)); BufferedReader tr = new BufferedReader (new FileReader (temp)); HashSet < ModelGraphVertex > sources = new HashSet < ModelGraphVertex > (); HashSet < ModelGraphVertex > dests = new HashSet < ModelGraphVertex > (); ArrayList transitions = ts.getEdges (); HashSet < String > events = new HashSet < String > (); for (int i = 0; i < transitions.size (); i ++) { TransitionSystemEdge transition = (TransitionSystemEdge) transitions.get (i); events.add (replaceBadSymbols (transition.getIdentifier ())); sources.add (transition.getSource ()); dests.add (transition.getDest ()); if (ts.getStateNameFlag () == TransitionSystem.ID) { tw.write ("s" + transition.getSource ().getId () + " "); tw.write (replaceBadSymbols (transition.getIdentifier ()) + " "); tw.write ("s" + transition.getDest ().getId () + "\n"); } else { tw.write (replaceBadSymbols (transition.getSource ().getIdentifier ()) + " "); tw.write (replaceBadSymbols (transition.getIdentifier ()) + " "); tw.write (replaceBadSymbols (transition.getDest ().getIdentifier ()) + "\n"); } } tw.close (); bw.write (".model " + ts.getName ().replaceAll (" ", "_") + "\n"); bw.write (".dummy "); Iterator it = events.iterator (); while (it.hasNext ()) bw.write (it.next () + " "); bw.write ("\n"); bw.write (".state graph" + "\n"); int c; while ((c = tr.read ()) != - 1) bw.write (c); tr.close (); temp.delete (); for (ModelGraphVertex dest : dests) { if (sources.contains (dest)) { sources.remove (dest); } } ModelGraphVertex source = sources.isEmpty () ? null : sources.iterator ().next (); if (ts.getStateNameFlag () == TransitionSystem.ID) { if (! ts.hasExplicitEnd ()) bw.write (".marking {s0}" + "\n"); else bw.write (".marking {s" + source.getId () + "}\n"); } else if (source != null) { bw.write (".marking {" + replaceBadSymbols (source.getIdentifier ()) + "}\n"); } bw.write (".end"); }

Copy File

Type-3 (WT3/4)

private void writeInfos () throws IOException { zos.putNextEntry (new ZipEntry ("info.bin")); outFile = new DataOutputStream (zos); outFile.writeInt (VERSION); outFile.writeInt (MINORVERSION); outFile.writeDouble (intervall_s); zos.closeEntry (); }

private void addToZip (String path, String srcFile, ZipOutputStream zip) { File folder = new File (srcFile); if (folder.isDirectory ()) { this.addFolderToZip (path, srcFile, zip); } else { try { boolean includeFile = false; if (this.excludePattern == null) { includeFile = true; } else { if (srcFile.contains (this.excludePattern)) { includeFile = false; } else { includeFile = true; } } if (includeFile == true) { this.zipMonitor.setNumberNextFile (); this.zipMonitor.setCurrentJobFile (srcFile); if (zipMonitor.isCanceled ()) { return; } FileInputStream in = new FileInputStream (srcFile); zip.putNextEntry (new ZipEntry (path + File.separator + folder.getName ())); byte [] buf = new byte [1024]; int len; while ((len = in.read (buf)) > 0) { zip.write (buf, 0, len); } } } catch (Exception ex) { ex.printStackTrace (); } } }

Zip Files

Type-3 (WT3/4)

private Service getServiceInstance (String className) { try { Class clazz = Class.forName (className); return (Service) clazz.getConstructor (new Class [] {}).newInstance (new Object [] {}); } catch (ClassNotFoundException e) { this.logger.error (className, e); return null; } catch (SecurityException e) { this.logger.error (className, e); return null; } catch (NoSuchMethodException e) { this.logger.error (className, e); return null; } catch (IllegalArgumentException e) { this.logger.error (className, e); return null; } catch (InstantiationException e) { this.logger.error (className, e); return null; } catch (IllegalAccessException e) { this.logger.error (className, e); return null; } catch (InvocationTargetException e) { this.logger.error (className, e); return null; } }

private void setCommandInput () { mCommandInput = null; try { Class < ? > consoleReaderClass = Class.forName ("jline.ConsoleReader"); if (consoleReaderClass != null) { Class < ? > consoleInputClass = Class.forName ("jline.ConsoleReaderInputStream"); if (consoleInputClass != null) { Object jline = consoleReaderClass.newInstance (); Constructor < ? > constructor = consoleInputClass.getConstructor (consoleReaderClass); if (constructor != null) { mCommandInput = (InputStream) constructor.newInstance (jline); } } } } catch (Exception e1) { mLogger.info ("Exception loading jline"); } if (mCommandInput == null) mCommandInput = System.in; }

Instantiate Using Reflection

Type-3 (WT3/4)

public static String CreateZip (String [] filesToZip, String zipFileName) { byte [] buffer = new byte [18024]; try { ZipOutputStream out = new ZipOutputStream (new FileOutputStream (zipFileName)); out.setLevel (Deflater.BEST_COMPRESSION); for (int i = 0; i < filesToZip.length; i ++) { FileInputStream in = new FileInputStream (filesToZip [i]); String fileName = null; for (int X = filesToZip [i].length () - 1; X >= 0; X --) { if (filesToZip [i].charAt (X) == '\\' || filesToZip [i].charAt (X) == '/') { fileName = filesToZip [i].substring (X + 1); break; } else if (X == 0) fileName = filesToZip [i]; } out.putNextEntry (new ZipEntry (fileName)); int len; while ((len = in.read (buffer)) > 0) out.write (buffer, 0, len); out.closeEntry (); in.close (); } out.close (); } catch (IllegalArgumentException e) { return "Failed to create zip: " + e.toString (); } catch (FileNotFoundException e) { return "Failed to create zip: " + e.toString (); } catch (IOException e) { return "Failed to create zip: " + e.toString (); } return "Success"; }

private void createButtonCopyToClipboard () { buttonCopyToClipboard = new Button (shell, SWT.PUSH); buttonCopyToClipboard.setText ("Co&py to Clipboard"); buttonCopyToClipboard.setLayoutData (SharedStyle.relativeToBottomRight (buttonClose)); buttonCopyToClipboard.addSelectionListener (new SelectionAdapter () { @Override public void widgetSelected (final SelectionEvent event) { IOUtils.copyToClipboard (Version.getEnvironmentReport ()); }} ); }

Copy File

Type-3 (WT3/4)

public void transform (File inputMatrixFile, MatrixIO.Format inputFormat, File outputMatrixFile) throws IOException { FileChannel original = new FileInputStream (inputMatrixFile).getChannel (); FileChannel copy = new FileOutputStream (outputMatrixFile).getChannel (); copy.transferFrom (original, 0, original.size ()); original.close (); copy.close (); }

public static void main (String [] args) throws IOException { if (args.length == 0) { System.out.println ("Usage: \nGZIPcompress file\n" + "\tUses GZIP compression to compress " + "the file to test.gz"); System.exit (1); } BufferedReader in = new BufferedReader (new FileReader (args [0])); BufferedOutputStream out = new BufferedOutputStream (new GZIPOutputStream (new FileOutputStream ("test.gz"))); System.out.println ("Writing file"); int c; while ((c = in.read ()) != - 1) out.write (c); in.close (); out.close (); System.out.println ("Reading file"); BufferedReader in2 = new BufferedReader (new InputStreamReader (new GZIPInputStream (new FileInputStream ("test.gz")))); String s; while ((s = in2.readLine ()) != null) System.out.println (s); }

Copy File

Type-3 (WT3/4)