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bigclonebench-processed

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public static void DecodeMapFile(String mapFile, String outputFile) throws Exception { byte magicKey = 0; byte[] buffer = new byte[2048]; int nread; InputStream map; OutputStream output; try { map = new FileInputStream(mapFile); } catch (Exception e) { throw new Exception("Map file error", e); } try { output = new FileOutputStream(outputFile); } catch (Exception e) { throw new Exception("Map file error", e); } while ((nread = map.read(buffer, 0, 2048)) != 0) { for (int i = 0; i < nread; ++i) { buffer[i] ^= magicKey; magicKey += 43; } output.write(buffer, 0, nread); } map.close(); output.close(); }

public void createZip(File zipFileName, Vector<File> selected) { try { byte[] buffer = new byte[4096]; ZipOutputStream out = new ZipOutputStream(new BufferedOutputStream(new FileOutputStream(zipFileName), 8096)); out.setLevel(Deflater.BEST_COMPRESSION); out.setMethod(ZipOutputStream.DEFLATED); for (int i = 0; i < selected.size(); i++) { FileInputStream in = new FileInputStream(selected.get(i)); String file = selected.get(i).getPath(); if (file.indexOf("\\") != -1) file = file.substring(file.lastIndexOf(fs) + 1, file.length()); ZipEntry ze = new ZipEntry(file); out.putNextEntry(ze); int len; while ((len = in.read(buffer)) > 0) out.write(buffer, 0, len); out.closeEntry(); in.close(); selected.get(i).delete(); } out.close(); } catch (IllegalArgumentException iae) { iae.printStackTrace(); } catch (FileNotFoundException fnfe) { fnfe.printStackTrace(); } catch (IOException ioe) { ioe.printStackTrace(); } }

public void actionPerformed(ActionEvent e) { if (path.compareTo("") != 0) { imageName = (path.substring(path.lastIndexOf(File.separator) + 1, path.length())); String name = imageName.substring(0, imageName.lastIndexOf('.')); String extension = imageName.substring(imageName.lastIndexOf('.') + 1, imageName.length()); File imageFile = new File(path); directoryPath = "images" + File.separator + imageName.substring(0, 1).toUpperCase(); File directory = new File(directoryPath); directory.mkdirs(); imagePath = "." + File.separator + "images" + File.separator + imageName.substring(0, 1).toUpperCase() + File.separator + imageName; File newFile = new File(imagePath); if (myImagesBehaviour.equals(TLanguage.getString("TIGManageGalleryDialog.REPLACE_IMAGE"))) { Vector<Vector<String>> aux = TIGDataBase.imageSearchByName(name); if (aux.size() != 0) { int idImage = TIGDataBase.imageKeySearchName(name); TIGDataBase.deleteAsociatedOfImage(idImage); } } if (myImagesBehaviour.equals(TLanguage.getString("TIGManageGalleryDialog.ADD_IMAGE"))) { int i = 1; while (newFile.exists()) { imagePath = "." + File.separator + "images" + File.separator + imageName.substring(0, 1).toUpperCase() + File.separator + imageName.substring(0, imageName.lastIndexOf('.')) + "_" + i + imageName.substring(imageName.lastIndexOf('.'), imageName.length()); name = name + "_" + i; newFile = new File(imagePath); i++; } } imagePathThumb = (imagePath.substring(0, imagePath.lastIndexOf("."))).concat("_th.jpg"); imageName = name + "." + extension; try { FileChannel srcChannel = new FileInputStream(path).getChannel(); FileChannel dstChannel = new FileOutputStream(imagePath).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (IOException exc) { System.out.println(exc.getMessage()); System.out.println(exc.toString()); } TIGDataBase.insertDB(theConcepts, imageName, imageName.substring(0, imageName.lastIndexOf('.'))); image = null; if (imageFile != null) { if (TFileUtils.isJAIRequired(imageFile)) { RenderedOp src = JAI.create("fileload", imageFile.getAbsolutePath()); BufferedImage bufferedImage = src.getAsBufferedImage(); image = new ImageIcon(bufferedImage); } else { image = new ImageIcon(imageFile.getAbsolutePath()); } if (image.getImageLoadStatus() == MediaTracker.ERRORED) { int choosenOption = JOptionPane.NO_OPTION; choosenOption = JOptionPane.showConfirmDialog(null, TLanguage.getString("TIGInsertImageAction.MESSAGE"), TLanguage.getString("TIGInsertImageAction.NAME"), JOptionPane.CLOSED_OPTION, JOptionPane.ERROR_MESSAGE); } else { createThumbnail(); } } } }

public void save(InputStream is) throws IOException { File dest = Config.getDataFile(getInternalDate(), getPhysMessageID()); OutputStream os = null; try { os = new FileOutputStream(dest); IOUtils.copyLarge(is, os); } finally { IOUtils.closeQuietly(os); IOUtils.closeQuietly(is); } }

public String loadURLString(java.net.URL url) { try { BufferedReader br = new BufferedReader(new InputStreamReader(url.openStream())); StringBuffer buf = new StringBuffer(); String s = ""; while (br.ready() && s != null) { s = br.readLine(); if (s != null) { buf.append(s); buf.append("\n"); } } return buf.toString(); } catch (IOException ex) { return ""; } catch (NullPointerException npe) { return ""; } }

public File nextEntry() { try { while (hasNext()) { String name = waitingArchEntry.getName(); name = name.substring(name.indexOf("/") + 1); File file = new File(targetDir.getAbsolutePath() + "/" + name); if (waitingArchEntry.isDirectory()) { file.mkdirs(); waitingArchEntry = ais.getNextEntry(); } else { OutputStream os = new FileOutputStream(file); try { IOUtils.copy(ais, os); } finally { IOUtils.closeQuietly(os); } return file; } } } catch (IOException e) { return null; } return null; }

public void copy(File source, File dest) throws IOException { System.out.println("copy " + source + " -> " + dest); FileInputStream in = new FileInputStream(source); try { FileOutputStream out = new FileOutputStream(dest); try { byte[] buf = new byte[1024]; int len = 0; while ((len = in.read(buf)) > 0) out.write(buf, 0, len); } finally { out.close(); } } finally { in.close(); } }

private ArrayList<String> getYearsAndMonths() { String info = ""; ArrayList<String> items = new ArrayList<String>(); try { obtainServerFilesView.setLblProcessText(java.util.ResourceBundle.getBundle("bgpanalyzer/resources/Bundle").getString("ObtainServerFilesView.Label.Progress.Obtaining_Data")); URL url = new URL(URL_ROUTE_VIEWS); URLConnection conn = url.openConnection(); conn.setDoOutput(false); BufferedReader rd = new BufferedReader(new InputStreamReader(conn.getInputStream())); String line; while ((line = rd.readLine()) != null) { if (!line.equals("")) info += line + "%"; } obtainServerFilesView.setLblProcessText(java.util.ResourceBundle.getBundle("bgpanalyzer/resources/Bundle").getString("ObtainServerFilesView.Label.Progress.Processing_Data")); info = Patterns.removeTags(info); StringTokenizer st = new StringTokenizer(info, "%"); info = ""; boolean alternador = false; int index = 1; while (st.hasMoreTokens()) { String token = st.nextToken(); if (!token.trim().equals("")) { int pos = token.indexOf("/"); if (pos != -1) { token = token.substring(1, pos); if (Patterns.hasFormatYYYYdotMM(token)) { items.add(token); } } } } rd.close(); } catch (Exception e) { e.printStackTrace(); } return items; }

protected String getGraphPath(String name) throws ServletException { String hash; try { MessageDigest md = MessageDigest.getInstance(m_messagedigest_algorithm); md.update(name.getBytes()); hash = bytesToHex(md.digest()); } catch (NoSuchAlgorithmException e) { throw new ServletException("NoSuchAlgorithmException while " + "attempting to hash file name: " + e); } File tempDir = (File) getServletContext().getAttribute("javax.servlet.context.tempdir"); return tempDir.getAbsolutePath() + File.separatorChar + hash; }

public String hasheMotDePasse(String mdp) { MessageDigest sha = null; try { sha = MessageDigest.getInstance("SHA-1"); } catch (NoSuchAlgorithmException ex) { } sha.reset(); sha.update(mdp.getBytes()); byte[] digest = sha.digest(); String pass = new String(Base64.encode(digest)); pass = "{SHA}" + pass; return pass; }

public byte[] scramblePassword(String password, String seed) throws NoSuchAlgorithmException { MessageDigest md = MessageDigest.getInstance("SHA-1"); byte[] stage1 = md.digest(password.getBytes()); md.reset(); byte[] stage2 = md.digest(stage1); md.reset(); md.update(seed.getBytes()); md.update(stage2); byte[] result = md.digest(); for (int i = 0; i < result.length; i++) { result[i] ^= stage1[i]; } return result; }

public synchronized String encrypt(String plaintext) { if (plaintext == null) plaintext = ""; MessageDigest md = null; try { md = MessageDigest.getInstance("SHA"); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); return null; } try { md.update(plaintext.getBytes("UTF-8")); } catch (UnsupportedEncodingException e) { e.printStackTrace(); return null; } byte raw[] = md.digest(); String hash = ""; try { hash = Base64Encoder.encode(raw); } catch (IOException e1) { System.err.println("Error encoding password using Jboss Base64Encoder"); e1.printStackTrace(); } return hash; }

@TestTargets({ @TestTargetNew(level = TestLevel.PARTIAL_COMPLETE, notes = "Verifies that the ObjectInputStream constructor calls checkPermission on security manager.", method = "ObjectInputStream", args = { InputStream.class }) }) public void test_ObjectInputStream2() throws IOException { class TestSecurityManager extends SecurityManager { boolean called; Permission permission; void reset() { called = false; permission = null; } @Override public void checkPermission(Permission permission) { if (permission instanceof SerializablePermission) { called = true; this.permission = permission; } } } class TestObjectInputStream extends ObjectInputStream { TestObjectInputStream(InputStream s) throws StreamCorruptedException, IOException { super(s); } } class TestObjectInputStream_readFields extends ObjectInputStream { TestObjectInputStream_readFields(InputStream s) throws StreamCorruptedException, IOException { super(s); } @Override public GetField readFields() throws IOException, ClassNotFoundException, NotActiveException { return super.readFields(); } } class TestObjectInputStream_readUnshared extends ObjectInputStream { TestObjectInputStream_readUnshared(InputStream s) throws StreamCorruptedException, IOException { super(s); } @Override public Object readUnshared() throws IOException, ClassNotFoundException { return super.readUnshared(); } } long id = new java.util.Date().getTime(); String filename = "SecurityPermissionsTest_" + id; File f = File.createTempFile(filename, null); ObjectOutputStream oos = new ObjectOutputStream(new FileOutputStream(f)); oos.writeObject(new Node()); oos.flush(); oos.close(); f.deleteOnExit(); TestSecurityManager s = new TestSecurityManager(); System.setSecurityManager(s); s.reset(); new ObjectInputStream(new FileInputStream(f)); assertTrue("ObjectInputStream(InputStream) ctor must not call checkPermission on security manager on a class which neither overwrites methods readFields nor readUnshared", !s.called); s.reset(); new TestObjectInputStream(new FileInputStream(f)); assertTrue("ObjectInputStream(InputStream) ctor must not call checkPermission on security manager on a class which neither overwrites methods readFields nor readUnshared", !s.called); s.reset(); new TestObjectInputStream_readFields(new FileInputStream(f)); assertTrue("ObjectInputStream(InputStream) ctor must call checkPermission on security manager on a class which overwrites method readFields", s.called); assertEquals("Name of SerializablePermission is not correct", "enableSubclassImplementation", s.permission.getName()); s.reset(); new TestObjectInputStream_readUnshared(new FileInputStream(f)); assertTrue("ObjectInputStream(InputStream) ctor must call checkPermission on security manager on a class which overwrites method readUnshared", s.called); assertEquals("Name of SerializablePermission is not correct", "enableSubclassImplementation", s.permission.getName()); }

public static void copyFile(String sIn, String sOut) throws IOException { File fIn = new File(sIn); File fOut = new File(sOut); FileChannel fcIn = new FileInputStream(fIn).getChannel(); FileChannel fcOut = new FileOutputStream(fOut).getChannel(); try { fcIn.transferTo(0, fcIn.size(), fcOut); } catch (IOException e) { throw e; } finally { if (fcIn != null) fcIn.close(); if (fcOut != null) fcOut.close(); } fOut.setReadable(fIn.canRead()); fOut.setWritable(fIn.canWrite()); fOut.setExecutable(fIn.canExecute()); }

public boolean resolve(String parameters, Reader in, Writer out, DataFieldResolver dataFieldResolver, int[] arrayPositioner) throws IOException { PrintWriter printOut = new PrintWriter(out); URL url = new URL(parameters); Reader urlIn = new InputStreamReader(url.openStream()); int ch = urlIn.read(); while (ch != -1) { out.write(ch); ch = urlIn.read(); } out.flush(); return false; }

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 String email_get_public_hash(String email) { try { if (email != null) { email = email.trim().toLowerCase(); CRC32 crc32 = new CRC32(); crc32.reset(); crc32.update(email.getBytes()); MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.reset(); return crc32.getValue() + " " + new String(md5.digest(email.getBytes())); } } catch (Exception e) { } return ""; }

public void testPreparedStatementRollback1() throws Exception { Connection localCon = getConnection(); Statement stmt = localCon.createStatement(); stmt.execute("CREATE TABLE #psr1 (data BIT)"); localCon.setAutoCommit(false); PreparedStatement pstmt = localCon.prepareStatement("INSERT INTO #psr1 (data) VALUES (?)"); pstmt.setBoolean(1, true); assertEquals(1, pstmt.executeUpdate()); pstmt.close(); localCon.rollback(); ResultSet rs = stmt.executeQuery("SELECT data FROM #psr1"); assertFalse(rs.next()); rs.close(); stmt.close(); localCon.close(); try { localCon.commit(); fail("Expecting commit to fail, connection was closed"); } catch (SQLException ex) { assertEquals("HY010", ex.getSQLState()); } try { localCon.rollback(); fail("Expecting rollback to fail, connection was closed"); } catch (SQLException ex) { assertEquals("HY010", ex.getSQLState()); } }

public static String md5hash(String input) { try { MessageDigest sha1Digest = MessageDigest.getInstance("MD5"); sha1Digest.update(input.getBytes()); return byteArrayToString(sha1Digest.digest()); } catch (Exception e) { logger.error(e.getMessage(), e); } return ""; }

private boolean cacheUrlFile(String filePath, String realUrl, boolean isOnline) { try { URL url = new URL(realUrl); String encoding = "gbk"; BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream(), encoding)); StringBuilder sb = new StringBuilder(); sb.append(configCenter.getWebRoot()).append(getCacheString(isOnline)).append(filePath); fileEditor.createDirectory(sb.toString()); return fileEditor.saveFile(sb.toString(), in); } catch (IOException e) { } return false; }

public static void main(String[] argv) { if (1 < argv.length) { File[] sources = Source(argv[0]); if (null != sources) { for (File src : sources) { File[] targets = Target(src, argv); if (null != targets) { final long srclen = src.length(); try { FileChannel source = new FileInputStream(src).getChannel(); try { for (File tgt : targets) { FileChannel target = new FileOutputStream(tgt).getChannel(); try { source.transferTo(0L, srclen, target); } finally { target.close(); } System.out.printf("Updated %s\n", tgt.getPath()); File[] deletes = Delete(src, tgt); if (null != deletes) { for (File del : deletes) { if (SVN) { if (SvnDelete(del)) System.out.printf("Deleted %s\n", del.getPath()); else System.out.printf("Failed to delete %s\n", del.getPath()); } else if (del.delete()) System.out.printf("Deleted %s\n", del.getPath()); else System.out.printf("Failed to delete %s\n", del.getPath()); } } if (SVN) SvnAdd(tgt); } } finally { source.close(); } } catch (Exception exc) { exc.printStackTrace(); System.exit(1); } } } System.exit(0); } else { System.err.printf("Source file(s) not found in '%s'\n", argv[0]); System.exit(1); } } else { usage(); System.exit(1); } }

void bubbleSort(int[] a) { int i = 0; int j = a.length - 1; int aux = 0; int stop = 0; while (stop == 0) { stop = 1; i = 0; while (i < j) { if (a[i] > a[i + 1]) { aux = a[i]; a[i] = a[i + 1]; a[i + 1] = aux; stop = 0; } i = i + 1; } j = j - 1; } }

protected void copyAndDelete(final URL _src, final long _temp) throws IOException { final File storage = getStorageFile(_src, _temp); final File dest = new File(_src.getFile()); FileChannel in = null; FileChannel out = null; if (storage.equals(dest)) { return; } try { readWriteLock_.lockWrite(); if (dest.exists()) { dest.delete(); } if (storage.exists() && !storage.renameTo(dest)) { in = new FileInputStream(storage).getChannel(); out = new FileOutputStream(dest).getChannel(); final long len = in.size(); final long copied = out.transferFrom(in, 0, in.size()); if (len != copied) { throw new IOException("unable to complete write"); } } } finally { readWriteLock_.unlockWrite(); try { if (in != null) { in.close(); } } catch (final IOException _evt) { FuLog.error(_evt); } try { if (out != null) { out.close(); } } catch (final IOException _evt) { FuLog.error(_evt); } storage.delete(); } }

public static void main(String[] args) throws IOException { String paramFileName = args[0]; BufferedReader inFile_params = new BufferedReader(new FileReader(paramFileName)); String cands_fileName = (inFile_params.readLine().split("\\s+"))[0]; String alignSrcCand_phrasal_fileName = (inFile_params.readLine().split("\\s+"))[0]; String alignSrcCand_word_fileName = (inFile_params.readLine().split("\\s+"))[0]; String source_fileName = (inFile_params.readLine().split("\\s+"))[0]; String trainSrc_fileName = (inFile_params.readLine().split("\\s+"))[0]; String trainTgt_fileName = (inFile_params.readLine().split("\\s+"))[0]; String trainAlign_fileName = (inFile_params.readLine().split("\\s+"))[0]; String alignCache_fileName = (inFile_params.readLine().split("\\s+"))[0]; String alignmentsType = "AlignmentGrids"; int maxCacheSize = 1000; inFile_params.close(); int numSentences = countLines(source_fileName); InputStream inStream_src = new FileInputStream(new File(source_fileName)); BufferedReader srcFile = new BufferedReader(new InputStreamReader(inStream_src, "utf8")); String[] srcSentences = new String[numSentences]; for (int i = 0; i < numSentences; ++i) { srcSentences[i] = srcFile.readLine(); } srcFile.close(); println("Creating src vocabulary @ " + (new Date())); srcVocab = new Vocabulary(); int[] sourceWordsSentences = Vocabulary.initializeVocabulary(trainSrc_fileName, srcVocab, true); int numSourceWords = sourceWordsSentences[0]; int numSourceSentences = sourceWordsSentences[1]; println("Reading src corpus @ " + (new Date())); srcCorpusArray = SuffixArrayFactory.createCorpusArray(trainSrc_fileName, srcVocab, numSourceWords, numSourceSentences); println("Creating src SA @ " + (new Date())); srcSA = SuffixArrayFactory.createSuffixArray(srcCorpusArray, maxCacheSize); println("Creating tgt vocabulary @ " + (new Date())); tgtVocab = new Vocabulary(); int[] targetWordsSentences = Vocabulary.initializeVocabulary(trainTgt_fileName, tgtVocab, true); int numTargetWords = targetWordsSentences[0]; int numTargetSentences = targetWordsSentences[1]; println("Reading tgt corpus @ " + (new Date())); tgtCorpusArray = SuffixArrayFactory.createCorpusArray(trainTgt_fileName, tgtVocab, numTargetWords, numTargetSentences); println("Creating tgt SA @ " + (new Date())); tgtSA = SuffixArrayFactory.createSuffixArray(tgtCorpusArray, maxCacheSize); int trainingSize = srcCorpusArray.getNumSentences(); if (trainingSize != tgtCorpusArray.getNumSentences()) { throw new RuntimeException("Source and target corpora have different number of sentences. This is bad."); } println("Reading alignment data @ " + (new Date())); alignments = null; if ("AlignmentArray".equals(alignmentsType)) { alignments = SuffixArrayFactory.createAlignments(trainAlign_fileName, srcSA, tgtSA); } else if ("AlignmentGrids".equals(alignmentsType) || "AlignmentsGrid".equals(alignmentsType)) { alignments = new AlignmentGrids(new Scanner(new File(trainAlign_fileName)), srcCorpusArray, tgtCorpusArray, trainingSize, true); } else if ("MemoryMappedAlignmentGrids".equals(alignmentsType)) { alignments = new MemoryMappedAlignmentGrids(trainAlign_fileName, srcCorpusArray, tgtCorpusArray); } if (!fileExists(alignCache_fileName)) { alreadyResolved_srcSet = new HashMap<String, TreeSet<Integer>>(); alreadyResolved_tgtSet = new HashMap<String, TreeSet<Integer>>(); } else { try { ObjectInputStream in = new ObjectInputStream(new FileInputStream(alignCache_fileName)); alreadyResolved_srcSet = (HashMap<String, TreeSet<Integer>>) in.readObject(); alreadyResolved_tgtSet = (HashMap<String, TreeSet<Integer>>) in.readObject(); in.close(); } catch (FileNotFoundException e) { System.err.println("FileNotFoundException in AlignCandidates.main(String[]): " + e.getMessage()); System.exit(99901); } catch (IOException e) { System.err.println("IOException in AlignCandidates.main(String[]): " + e.getMessage()); System.exit(99902); } catch (ClassNotFoundException e) { System.err.println("ClassNotFoundException in AlignCandidates.main(String[]): " + e.getMessage()); System.exit(99904); } } println("Processing candidates @ " + (new Date())); PrintWriter outFile_alignSrcCand_phrasal = new PrintWriter(alignSrcCand_phrasal_fileName); PrintWriter outFile_alignSrcCand_word = new PrintWriter(alignSrcCand_word_fileName); InputStream inStream_cands = new FileInputStream(new File(cands_fileName)); BufferedReader candsFile = new BufferedReader(new InputStreamReader(inStream_cands, "utf8")); String line = ""; String cand = ""; line = candsFile.readLine(); int countSatisfied = 0; int countAll = 0; int countSatisfied_sizeOne = 0; int countAll_sizeOne = 0; int prev_i = -1; String srcSent = ""; String[] srcWords = null; int candsRead = 0; int C50count = 0; while (line != null) { ++candsRead; println("Read candidate on line #" + candsRead); int i = toInt((line.substring(0, line.indexOf("|||"))).trim()); if (i != prev_i) { srcSent = srcSentences[i]; srcWords = srcSent.split("\\s+"); prev_i = i; println("New value for i: " + i + " seen @ " + (new Date())); C50count = 0; } else { ++C50count; } line = (line.substring(line.indexOf("|||") + 3)).trim(); cand = (line.substring(0, line.indexOf("|||"))).trim(); cand = cand.substring(cand.indexOf(" ") + 1, cand.length() - 1); JoshuaDerivationTree DT = new JoshuaDerivationTree(cand, 0); String candSent = DT.toSentence(); String[] candWords = candSent.split("\\s+"); String alignSrcCand = DT.alignments(); outFile_alignSrcCand_phrasal.println(alignSrcCand); println(" i = " + i + ", alignSrcCand: " + alignSrcCand); String alignSrcCand_res = ""; String[] linksSrcCand = alignSrcCand.split("\\s+"); for (int k = 0; k < linksSrcCand.length; ++k) { String link = linksSrcCand[k]; if (link.indexOf(',') == -1) { alignSrcCand_res += " " + link.replaceFirst("--", "-"); } else { alignSrcCand_res += " " + resolve(link, srcWords, candWords); } } alignSrcCand_res = alignSrcCand_res.trim(); println(" i = " + i + ", alignSrcCand_res: " + alignSrcCand_res); outFile_alignSrcCand_word.println(alignSrcCand_res); if (C50count == 50) { println("50C @ " + (new Date())); C50count = 0; } line = candsFile.readLine(); } outFile_alignSrcCand_phrasal.close(); outFile_alignSrcCand_word.close(); candsFile.close(); println("Finished processing candidates @ " + (new Date())); try { ObjectOutputStream out = new ObjectOutputStream(new FileOutputStream(alignCache_fileName)); out.writeObject(alreadyResolved_srcSet); out.writeObject(alreadyResolved_tgtSet); out.flush(); out.close(); } catch (IOException e) { System.err.println("IOException in AlignCandidates.main(String[]): " + e.getMessage()); System.exit(99902); } }

private void loadProperties() { if (properties == null) { properties = new Properties(); try { URL url = getClass().getResource(propsFile); properties.load(url.openStream()); } catch (IOException ioe) { ioe.printStackTrace(); } } }

@Override public String encryptPassword(String password) throws JetspeedSecurityException { if (securePasswords == false) { return password; } if (password == null) { return null; } try { if ("SHA-512".equals(passwordsAlgorithm)) { password = password + JetspeedResources.getString("aipo.encrypt_key"); MessageDigest md = MessageDigest.getInstance(passwordsAlgorithm); md.reset(); md.update(password.getBytes()); byte[] hash = md.digest(); StringBuffer sb = new StringBuffer(); for (int i = 0; i < hash.length; i++) { sb.append(Integer.toHexString((hash[i] >> 4) & 0x0F)); sb.append(Integer.toHexString(hash[i] & 0x0F)); } return sb.toString(); } else { MessageDigest md = MessageDigest.getInstance(passwordsAlgorithm); byte[] digest = md.digest(password.getBytes(ALEipConstants.DEF_CONTENT_ENCODING)); ByteArrayOutputStream bas = new ByteArrayOutputStream(digest.length + digest.length / 3 + 1); OutputStream encodedStream = MimeUtility.encode(bas, "base64"); encodedStream.write(digest); encodedStream.flush(); encodedStream.close(); return bas.toString(); } } catch (Exception e) { logger.error("Unable to encrypt password." + e.getMessage(), e); return null; } }

private void publishMap(LWMap map) throws IOException { File savedMap = PublishUtil.saveMap(map); InputStream istream = new BufferedInputStream(new FileInputStream(savedMap)); OutputStream ostream = new BufferedOutputStream(new FileOutputStream(ActionUtil.selectFile("ConceptMap", "vue"))); int fileLength = (int) savedMap.length(); byte bytes[] = new byte[fileLength]; while (istream.read(bytes, 0, fileLength) != -1) ostream.write(bytes, 0, fileLength); istream.close(); ostream.close(); }

private void copyFileToPhotoFolder(File photo, String personId) { try { FileChannel in = new FileInputStream(photo).getChannel(); File dirServer = new File(Constants.PHOTO_DIR); if (!dirServer.exists()) { dirServer.mkdirs(); } File fileServer = new File(Constants.PHOTO_DIR + personId + ".jpg"); if (!fileServer.exists()) { fileServer.createNewFile(); } in.transferTo(0, in.size(), new FileOutputStream(fileServer).getChannel()); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } }

private boolean handlePart(Part p) throws MessagingException, GetterException { String filename = p.getFileName(); if (!p.isMimeType("multipart/*")) { String disp = p.getDisposition(); if (disp == null || disp.equalsIgnoreCase(Part.ATTACHMENT)) { if (checkCriteria(p)) { if (filename == null) filename = "Attachment" + attnum++; if (result == null) { try { File f = File.createTempFile("amorph_pop3-", ".tmp"); f.deleteOnExit(); OutputStream os = new BufferedOutputStream(new FileOutputStream(f)); InputStream is = p.getInputStream(); int c; while ((c = is.read()) != -1) os.write(c); os.close(); result = new FileInputStream(f); System.out.println("saved attachment to file: " + f.getAbsolutePath()); return true; } catch (IOException ex) { throw new GetterException(ex, "Failed to save attachment: " + ex); } } } } } return false; }

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 static void readFile(FOUserAgent ua, String uri, Writer output, String encoding) throws IOException { InputStream in = getURLInputStream(ua, uri); try { StringWriter writer = new StringWriter(); IOUtils.copy(in, writer, encoding); } finally { IOUtils.closeQuietly(in); } }

public void fileCopy2(File inFile, File outFile) throws Exception { try { FileChannel srcChannel = new FileInputStream(inFile).getChannel(); FileChannel dstChannel = new FileOutputStream(outFile).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (IOException e) { throw new Exception("Could not copy file: " + inFile.getName()); } }

public static String httpUrlConnection_post(String targetURL, String urlParameters) { System.out.println("httpUrlConnection_post"); URL url; HttpURLConnection connection = null; try { url = new URL(targetURL); connection = (HttpURLConnection) url.openConnection(); connection.setRequestMethod("POST"); connection.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); connection.setRequestProperty("Content-Length", "" + Integer.toString(urlParameters.getBytes().length)); connection.setRequestProperty("Content-Language", "en-US"); connection.setUseCaches(false); connection.setConnectTimeout(5000); connection.setReadTimeout(5000); connection.setDoInput(true); connection.setDoOutput(true); DataOutputStream wr = new DataOutputStream(connection.getOutputStream()); wr.writeBytes(urlParameters); wr.flush(); wr.close(); InputStream is = connection.getInputStream(); BufferedReader rd = new BufferedReader(new InputStreamReader(is)); String line; StringBuilder response = new StringBuilder(); while ((line = rd.readLine()) != null) { response.append(line); response.append('\r'); } rd.close(); return response.toString(); } catch (Exception e) { System.out.print(e); return null; } finally { if (connection != null) { connection.disconnect(); } } }

private String getMD5Str(String str) { MessageDigest messageDigest = null; try { messageDigest = MessageDigest.getInstance("MD5"); messageDigest.reset(); messageDigest.update(str.getBytes("UTF-8")); } catch (NoSuchAlgorithmException e) { System.out.println("NoSuchAlgorithmException caught!"); System.exit(-1); } catch (UnsupportedEncodingException e) { e.printStackTrace(); } byte[] byteArray = messageDigest.digest(); StringBuffer md5StrBuff = new StringBuffer(); for (int i = 0; i < byteArray.length; i++) { if (Integer.toHexString(0xFF & byteArray[i]).length() == 1) md5StrBuff.append("0").append(Integer.toHexString(0xFF & byteArray[i])); else md5StrBuff.append(Integer.toHexString(0xFF & byteArray[i])); } return md5StrBuff.toString(); }

@Override @Transactional public FileData store(FileData data, InputStream stream) { try { FileData file = save(data); file.setPath(file.getGroup() + File.separator + file.getId()); file = save(file); File folder = new File(PATH, file.getGroup()); if (!folder.exists()) folder.mkdirs(); File filename = new File(folder, file.getId() + ""); IOUtils.copyLarge(stream, new FileOutputStream(filename)); return file; } catch (IOException e) { throw new ServiceException("storage", e); } }

public static void copyCompletely(InputStream input, OutputStream output) throws IOException { if ((output instanceof FileOutputStream) && (input instanceof FileInputStream)) { try { FileChannel target = ((FileOutputStream) output).getChannel(); FileChannel source = ((FileInputStream) input).getChannel(); source.transferTo(0, Integer.MAX_VALUE, target); source.close(); target.close(); return; } catch (Exception e) { } } byte[] buf = new byte[8192]; while (true) { int length = input.read(buf); if (length < 0) break; output.write(buf, 0, length); } try { input.close(); } catch (IOException ignore) { } try { output.close(); } catch (IOException ignore) { } }

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; }

public static void copy(File sourceFile, File destinationFile) throws IOException { FileChannel sourceChannel = new FileInputStream(sourceFile).getChannel(); FileChannel destinationChannel = new FileOutputStream(destinationFile).getChannel(); destinationChannel.transferFrom(sourceChannel, 0, sourceChannel.size()); sourceChannel.close(); destinationChannel.close(); }

public static void copyFile(File file, File destination) throws Exception { BufferedInputStream in = null; BufferedOutputStream out = null; try { in = new BufferedInputStream(new FileInputStream(file)); out = new BufferedOutputStream(new FileOutputStream(destination)); int c; while ((c = in.read()) != -1) out.write(c); } finally { try { if (out != null) out.close(); } catch (Exception e) { } try { if (in != null) in.close(); } catch (Exception e) { } } }

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(); } }

private void getRandomGUID(boolean secure) { MessageDigest md5 = null; StringBuffer sbValueBeforeMD5 = new StringBuffer(); try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { System.out.println("Error: " + e); } try { long time = System.currentTimeMillis(); long rand = 0L; if (secure) rand = mySecureRand.nextLong(); else rand = myRand.nextLong(); sbValueBeforeMD5.append(s_id); sbValueBeforeMD5.append(":"); sbValueBeforeMD5.append(Long.toString(time)); sbValueBeforeMD5.append(":"); sbValueBeforeMD5.append(Long.toString(rand)); valueBeforeMD5 = sbValueBeforeMD5.toString(); md5.update(valueBeforeMD5.getBytes()); byte array[] = md5.digest(); StringBuffer sb = new StringBuffer(); for (int j = 0; j < array.length; j++) { int b = array[j] & 0xff; if (b < 16) sb.append('0'); sb.append(Integer.toHexString(b)); } valueAfterMD5 = sb.toString(); } catch (Exception e) { System.out.println("Error:" + e); } }

public boolean getFiles(String pRemoteDirectory, String pLocalDirectory) throws IOException { final String methodSignature = "boolean getFiles(String,String): "; FTPClient fc = new FTPClient(); fc.connect(getRemoteHost()); fc.login(getUserName(), getPassword()); fc.changeWorkingDirectory(pRemoteDirectory); FTPFile[] files = fc.listFiles(); boolean retrieved = false; logInfo("Listing Files: "); int retrieveCount = 0; File tmpFile = null; for (int i = 0; i < files.length; i++) { tmpFile = new File(files[i].getName()); if (!tmpFile.isDirectory()) { FileOutputStream fos = new FileOutputStream(pLocalDirectory + "/" + files[i].getName()); retrieved = fc.retrieveFile(files[i].getName(), fos); if (false == retrieved) { logInfo("Unable to retrieve file: " + files[i].getName()); } else { logInfo("Successfully retrieved file: " + files[i].getName()); retrieveCount++; } if (null != fos) { fos.flush(); fos.close(); } } } logInfo("Retrieve count: " + retrieveCount); if (retrieveCount > 0) { return true; } return false; }

public static void main(String args[]) { String midletClass = null; ; File appletInputFile = null; File deviceInputFile = null; File midletInputFile = null; File htmlOutputFile = null; File appletOutputFile = null; File deviceOutputFile = null; File midletOutputFile = null; List params = new ArrayList(); for (int i = 0; i < args.length; i++) { params.add(args[i]); } Iterator argsIterator = params.iterator(); while (argsIterator.hasNext()) { String arg = (String) argsIterator.next(); argsIterator.remove(); if ((arg.equals("--help")) || (arg.equals("-help"))) { System.out.println(usage()); System.exit(0); } else if (arg.equals("--midletClass")) { midletClass = (String) argsIterator.next(); argsIterator.remove(); } else if (arg.equals("--appletInput")) { appletInputFile = new File((String) argsIterator.next()); argsIterator.remove(); } else if (arg.equals("--deviceInput")) { deviceInputFile = new File((String) argsIterator.next()); argsIterator.remove(); } else if (arg.equals("--midletInput")) { midletInputFile = new File((String) argsIterator.next()); argsIterator.remove(); } else if (arg.equals("--htmlOutput")) { htmlOutputFile = new File((String) argsIterator.next()); argsIterator.remove(); } else if (arg.equals("--appletOutput")) { appletOutputFile = new File((String) argsIterator.next()); argsIterator.remove(); } else if (arg.equals("--deviceOutput")) { deviceOutputFile = new File((String) argsIterator.next()); argsIterator.remove(); } else if (arg.equals("--midletOutput")) { midletOutputFile = new File((String) argsIterator.next()); argsIterator.remove(); } } if (midletClass == null || appletInputFile == null || deviceInputFile == null || midletInputFile == null || htmlOutputFile == null || appletOutputFile == null || deviceOutputFile == null || midletOutputFile == null) { System.out.println(usage()); System.exit(0); } try { DeviceImpl device = null; String descriptorLocation = null; JarFile jar = new JarFile(deviceInputFile); for (Enumeration en = jar.entries(); en.hasMoreElements(); ) { String entry = ((JarEntry) en.nextElement()).getName(); if ((entry.toLowerCase().endsWith(".xml") || entry.toLowerCase().endsWith("device.txt")) && !entry.toLowerCase().startsWith("meta-inf")) { descriptorLocation = entry; break; } } if (descriptorLocation != null) { EmulatorContext context = new EmulatorContext() { private DisplayComponent displayComponent = new NoUiDisplayComponent(); private InputMethod inputMethod = new J2SEInputMethod(); private DeviceDisplay deviceDisplay = new J2SEDeviceDisplay(this); private FontManager fontManager = new J2SEFontManager(); private DeviceComponent deviceComponent = new SwingDeviceComponent(true); public DisplayComponent getDisplayComponent() { return displayComponent; } public InputMethod getDeviceInputMethod() { return inputMethod; } public DeviceDisplay getDeviceDisplay() { return deviceDisplay; } public FontManager getDeviceFontManager() { return fontManager; } public InputStream getResourceAsStream(String name) { return MIDletBridge.getCurrentMIDlet().getClass().getResourceAsStream(name); } public DeviceComponent getDeviceComponent() { return deviceComponent; } }; URL[] urls = new URL[1]; urls[0] = deviceInputFile.toURI().toURL(); ClassLoader classLoader = new ExtensionsClassLoader(urls, urls.getClass().getClassLoader()); device = DeviceImpl.create(context, classLoader, descriptorLocation, J2SEDevice.class); } if (device == null) { System.out.println("Error parsing device package: " + descriptorLocation); System.exit(0); } createHtml(htmlOutputFile, device, midletClass, midletOutputFile, appletOutputFile, deviceOutputFile); createMidlet(midletInputFile.toURI().toURL(), midletOutputFile); IOUtils.copyFile(appletInputFile, appletOutputFile); IOUtils.copyFile(deviceInputFile, deviceOutputFile); } catch (IOException ex) { ex.printStackTrace(); } System.exit(0); }

public static final String getUniqueId() { String digest = ""; try { MessageDigest md = MessageDigest.getInstance("MD5"); String timeVal = "" + (System.currentTimeMillis() + 1); String localHost = ""; ; try { localHost = InetAddress.getLocalHost().toString(); } catch (UnknownHostException e) { log.error("Error trying to get localhost" + e.getMessage()); } String randVal = "" + new Random().nextInt(); String val = timeVal + localHost + randVal; md.reset(); md.update(val.getBytes()); digest = toHexString(md.digest()); } catch (NoSuchAlgorithmException e) { log.error("Error trying to generate unique Id" + e.getMessage()); } return digest; }

public void actionPerformed(ActionEvent e) { if (mode == ADD_URL) { String url = JOptionPane.showInputDialog(null, "Enter URL", "Enter URL", JOptionPane.OK_CANCEL_OPTION); if (url == null) return; try { is = new URL(url).openStream(); } catch (Exception ex) { ex.printStackTrace(); } } else if (mode == ADD_FILE) { JFileChooser chooser = new JFileChooser(); chooser.setFileSelectionMode(JFileChooser.FILES_ONLY); chooser.showDialog(null, "Add tab"); File file = chooser.getSelectedFile(); if (file == null) return; try { is = new FileInputStream(file); } catch (FileNotFoundException ex) { ex.printStackTrace(); } } if (repository == null) repository = PersistenceService.getInstance(); List artists = repository.getAllArtists(); EventList artistList = new BasicEventList(); artistList.addAll(artists); addDialog = new AddSongDialog(artistList, JOptionPane.getRootFrame(), true); Song s = addDialog.getSong(); if (is != null) { String tab; try { tab = readTab(is); s.setTablature(tab); addDialog.setSong(s); } catch (Exception ex) { ex.printStackTrace(); } } addDialog.setVisible(true); addDialog.addWindowListener(new WindowAdapter() { public void windowClosed(WindowEvent e) { int ok = addDialog.getReturnStatus(); if (ok == AddSongDialog.RET_CANCEL) return; addSong(); } }); }

public byte[] download(URL url, OutputStream out) throws IOException { boolean returnByByteArray = (out == null); ByteArrayOutputStream helper = null; if (returnByByteArray) { helper = new ByteArrayOutputStream(); } String s = url.toExternalForm(); URLConnection conn = url.openConnection(); String name = Launcher.getFileName(s); InputStream in = conn.getInputStream(); total = url.openConnection().getContentLength(); setStatusText(String.format("Downloading %s (%.2fMB)...", name, ((float) total / 1024 / 1024))); long justNow = System.currentTimeMillis(); int numRead = -1; byte[] buffer = new byte[2048]; while ((numRead = in.read(buffer)) != -1) { size += numRead; if (returnByByteArray) { helper.write(buffer, 0, numRead); } else { out.write(buffer, 0, numRead); } long now = System.currentTimeMillis(); if ((now - justNow) > 250) { setProgress((int) (((float) size / (float) total) * 100)); justNow = now; } } hideProgress(); if (returnByByteArray) { return helper.toByteArray(); } else { return null; } }

public static boolean nioWriteFile(FileInputStream inputStream, FileOutputStream out) { if (inputStream == null && out == null) { return false; } try { FileChannel fci = inputStream.getChannel(); FileChannel fco = out.getChannel(); fco.transferFrom(fci, 0, fci.size()); return true; } catch (Exception e) { e.printStackTrace(); return false; } finally { FileUtil.safeClose(inputStream); FileUtil.safeClose(out); } }

private void execute(File file) throws IOException { if (file == null) throw new RuntimeException("undefined file"); if (!file.exists()) throw new RuntimeException("file not found :" + file); if (!file.isFile()) throw new RuntimeException("not a file :" + file); String login = cfg.getProperty(GC_USERNAME); String password = null; if (cfg.containsKey(GC_PASSWORD)) { password = cfg.getProperty(GC_PASSWORD); } else { password = new String(Base64.decode(cfg.getProperty(GC_PASSWORD64))); } PostMethod post = null; try { HttpClient client = new HttpClient(); post = new PostMethod("https://" + projectName + ".googlecode.com/files"); post.addRequestHeader("User-Agent", getClass().getName()); post.addRequestHeader("Authorization", "Basic " + Base64.encode(login + ":" + password)); List<Part> parts = new ArrayList<Part>(); String s = this.summary; if (StringUtils.isBlank(s)) { s = file.getName() + " (" + TimeUtils.toYYYYMMDD() + ")"; } parts.add(new StringPart("summary", s)); for (String lbl : this.labels) { if (StringUtils.isBlank(lbl)) continue; parts.add(new StringPart("label", lbl.trim())); } parts.add(new FilePart("filename", file)); MultipartRequestEntity requestEntity = new MultipartRequestEntity(parts.toArray(new Part[parts.size()]), post.getParams()); post.setRequestEntity(requestEntity); int status = client.executeMethod(post); if (status != 201) { throw new IOException("http status !=201 : " + post.getResponseBodyAsString()); } else { IOUtils.copyTo(post.getResponseBodyAsStream(), new NullOutputStream()); } } finally { if (post != null) post.releaseConnection(); } }

private ScrollingGraphicalViewer createGraphicalViewer(final Composite parent) { final ScrollingGraphicalViewer viewer = new ScrollingGraphicalViewer(); viewer.createControl(parent); _root = new EditRootEditPart(); viewer.setRootEditPart(_root); getEditDomain().addViewer(viewer); getSite().setSelectionProvider(viewer); viewer.setEditPartFactory(getEditPartFactory()); final KeyHandler keyHandler = new GraphicalViewerKeyHandler(viewer) { @SuppressWarnings("unchecked") @Override public boolean keyPressed(final KeyEvent event) { if (event.stateMask == SWT.MOD1 && event.keyCode == SWT.DEL) { final List<? extends EditorPart> objects = viewer.getSelectedEditParts(); if (objects == null || objects.isEmpty()) return true; final GroupRequest deleteReq = new GroupRequest(RequestConstants.REQ_DELETE); final CompoundCommand compoundCmd = new CompoundCommand("Delete"); for (int i = 0; i < objects.size(); i++) { final EditPart object = (EditPart) objects.get(i); deleteReq.setEditParts(object); final Command cmd = object.getCommand(deleteReq); if (cmd != null) compoundCmd.add(cmd); } getCommandStack().execute(compoundCmd); return true; } if (event.stateMask == SWT.MOD3 && (event.keyCode == SWT.ARROW_DOWN || event.keyCode == SWT.ARROW_LEFT || event.keyCode == SWT.ARROW_RIGHT || event.keyCode == SWT.ARROW_UP)) { final List<? extends EditorPart> objects = viewer.getSelectedEditParts(); if (objects == null || objects.isEmpty()) return true; final GroupRequest moveReq = new ChangeBoundsRequest(RequestConstants.REQ_MOVE); final CompoundCommand compoundCmd = new CompoundCommand("Move"); for (int i = 0; i < objects.size(); i++) { final EditPart object = (EditPart) objects.get(i); moveReq.setEditParts(object); final LocationCommand cmd = (LocationCommand) object.getCommand(moveReq); if (cmd != null) { cmd.setLocation(new Point(event.keyCode == SWT.ARROW_LEFT ? -1 : event.keyCode == SWT.ARROW_RIGHT ? 1 : 0, event.keyCode == SWT.ARROW_DOWN ? 1 : event.keyCode == SWT.ARROW_UP ? -1 : 0)); cmd.setRelative(true); compoundCmd.add(cmd); } } getCommandStack().execute(compoundCmd); return true; } return super.keyPressed(event); } }; keyHandler.put(KeyStroke.getPressed(SWT.F2, 0), getActionRegistry().getAction(GEFActionConstants.DIRECT_EDIT)); viewer.setKeyHandler(keyHandler); viewer.setContents(getEditorInput().getAdapter(NamedUuidEntity.class)); viewer.addDropTargetListener(createTransferDropTargetListener(viewer)); return viewer; }

public void reqservmodif(HttpServletRequest req, HttpServletResponse resp, SessionCommand command) { try { System.err.println(req.getSession().getServletContext().getRealPath("WEB-INF/syncWork")); File tempFile = File.createTempFile("localmodif-", ".medoorequest"); OutputStream fos = new FileOutputStream(tempFile); syncServer.getServerModifications(command.getSession(), fos); InputStream fis = new FileInputStream(tempFile); resp.setContentLength(fis.available()); while (fis.available() > 0) { resp.getOutputStream().write(fis.read()); } resp.getOutputStream().flush(); resp.flushBuffer(); tempFile.delete(); } catch (IOException ioe) { logger.error(ioe.getMessage()); } catch (ImogSerializationException ex) { logger.error(ex.getMessage()); } }

public static void createModelZip(String filename, String tempdir) throws EDITSException { try { BufferedInputStream origin = null; FileOutputStream dest = new FileOutputStream(filename); ZipOutputStream out = new ZipOutputStream(new BufferedOutputStream(dest)); int BUFFER = 2048; byte data[] = new byte[BUFFER]; File f = new File(tempdir); for (File fs : f.listFiles()) { FileInputStream fi = new FileInputStream(fs.getAbsolutePath()); origin = new BufferedInputStream(fi, BUFFER); ZipEntry entry = new ZipEntry(fs.getName()); out.putNextEntry(entry); int count; while ((count = origin.read(data, 0, BUFFER)) != -1) out.write(data, 0, count); out.closeEntry(); origin.close(); } out.close(); } catch (Exception e) { throw new EDITSException("Can not create a model in file " + filename + " from folder " + tempdir); } }

public static void main(String[] argv) { ComboPooledDataSource cpds = null; Connection c = null; try { cpds = new ComboPooledDataSource(); cpds.setDriverClass("org.postgresql.Driver"); cpds.setJdbcUrl("jdbc:postgresql://localhost/c3p0-test"); cpds.setUser("swaldman"); cpds.setPassword("test"); cpds.setMinPoolSize(5); cpds.setAcquireIncrement(5); cpds.setMaxPoolSize(20); c = cpds.getConnection(); c.setAutoCommit(false); Statement stmt = c.createStatement(); stmt.executeUpdate("CREATE TABLE pwtest_table (col1 char(5), col2 char(5))"); ResultSet rs = stmt.executeQuery("SELECT * FROM pwtest_table"); System.err.println("rs: " + rs); System.err.println("rs.getStatement(): " + rs.getStatement()); System.err.println("rs.getStatement().getConnection(): " + rs.getStatement().getConnection()); } catch (Exception e) { e.printStackTrace(); } finally { try { if (c != null) c.rollback(); } catch (Exception e) { e.printStackTrace(); } try { if (cpds != null) cpds.close(); } catch (Exception e) { e.printStackTrace(); } } }

public static Collection<SearchKeyResult> searchKey(String iText, String iKeyServer) throws Exception { Vector<SearchKeyResult> outVec = new Vector<SearchKeyResult>(); String uri = iKeyServer + "/pks/lookup?search=" + URLEncoder.encode(iText, "UTF-8"); URL url = new URL(uri); BufferedReader input = new BufferedReader(new InputStreamReader(url.openStream())); Pattern regex = Pattern.compile("pub.*?<a\\s+href\\s*=\"(.*?)\".*?>\\s*(\\w+)\\s*</a>.*?(\\d+-\\d+-\\d+).*?<a\\s+href\\s*=\".*?\".*?>\\s*(.+?)\\s*</a>", Pattern.CANON_EQ); String line; while ((line = input.readLine()) != null) { Matcher regexMatcher = regex.matcher(line); while (regexMatcher.find()) { String id = regexMatcher.group(2); String downUrl = iKeyServer + regexMatcher.group(1); String downDate = regexMatcher.group(3); String name = HTMLDecoder.decodeHTML(regexMatcher.group(4)); outVec.add(new SearchKeyResult(id, name, downDate, downUrl)); } } input.close(); return outVec; }

private File copyFile(String fileInClassPath, String systemPath) throws Exception { InputStream is = getClass().getResourceAsStream(fileInClassPath); OutputStream os = new FileOutputStream(systemPath); IOUtils.copy(is, os); is.close(); os.close(); return new File(systemPath); }

public static String cryptografar(String senha) { try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(senha.getBytes()); BigInteger hash = new BigInteger(1, md.digest()); senha = hash.toString(16); } catch (NoSuchAlgorithmException ns) { ns.printStackTrace(); } return senha; }

private InputStream getInputStream(final String pUrlStr) throws IOException { URL url; int responseCode; String encoding; url = new URL(pUrlStr); myActiveConnection = (HttpURLConnection) url.openConnection(); myActiveConnection.setRequestProperty("Accept-Encoding", "gzip, deflate"); responseCode = myActiveConnection.getResponseCode(); if (responseCode != RESPONSECODE_OK) { String message; String apiErrorMessage; apiErrorMessage = myActiveConnection.getHeaderField("Error"); if (apiErrorMessage != null) { message = "Received API HTTP response code " + responseCode + " with message \"" + apiErrorMessage + "\" for URL \"" + pUrlStr + "\"."; } else { message = "Received API HTTP response code " + responseCode + " for URL \"" + pUrlStr + "\"."; } throw new OsmosisRuntimeException(message); } myActiveConnection.setConnectTimeout(TIMEOUT); encoding = myActiveConnection.getContentEncoding(); responseStream = myActiveConnection.getInputStream(); if (encoding != null && encoding.equalsIgnoreCase("gzip")) { responseStream = new GZIPInputStream(responseStream); } else if (encoding != null && encoding.equalsIgnoreCase("deflate")) { responseStream = new InflaterInputStream(responseStream, new Inflater(true)); } return responseStream; }

private static void sentRequest() { try { URLConnection urlConn; URL url = new URL(gatewayURL); urlConn = url.openConnection(); urlConn.setRequestProperty("Content-Type", "text/xml"); urlConn.setDoOutput(true); OutputStream ostream = urlConn.getOutputStream(); PrintWriter out = new PrintWriter(ostream); out.print(request); out.close(); ostream.close(); InputStream inStream = urlConn.getInputStream(); File myFile = new File(styleSheetLocation); if (type.equals("A") && myFile.exists()) { TransformerFactory tFactory = TransformerFactory.newInstance(); Transformer transformer = tFactory.newTransformer(new StreamSource(styleSheetLocation)); transformer.transform(new StreamSource(inStream), new StreamResult(System.out)); } else { BufferedReader in = new BufferedReader(new InputStreamReader(inStream)); String inputLine; while ((inputLine = in.readLine()) != null) { System.out.println(inputLine); } in.close(); } } catch (Exception e) { e.printStackTrace(); } }

@Override public void updateItems(List<InputQueueItem> toUpdate) throws DatabaseException { if (toUpdate == null) throw new NullPointerException("toUpdate"); try { getConnection().setAutoCommit(false); } catch (SQLException e) { LOGGER.warn("Unable to set autocommit off", e); } try { PreparedStatement deleteSt = getConnection().prepareStatement(DELETE_ALL_ITEMS_STATEMENT); PreparedStatement selectCount = getConnection().prepareStatement(SELECT_NUMBER_ITEMS_STATEMENT); ResultSet rs = selectCount.executeQuery(); rs.next(); int totalBefore = rs.getInt(1); int deleted = deleteSt.executeUpdate(); int updated = 0; for (InputQueueItem item : toUpdate) { updated += getItemInsertStatement(item).executeUpdate(); } if (totalBefore == deleted && updated == toUpdate.size()) { getConnection().commit(); LOGGER.debug("DB has been updated. Queries: \"" + selectCount + "\" and \"" + deleteSt + "\"."); } else { getConnection().rollback(); LOGGER.error("DB has not been updated -> rollback! Queries: \"" + selectCount + "\" and \"" + deleteSt + "\"."); } } catch (SQLException e) { LOGGER.error(e); } finally { closeConnection(); } }

public void testCreate() throws Exception { File f = File.createTempFile("DiskCacheItemTest", "tmp"); f.deleteOnExit(); try { DiskCacheItem i = new DiskCacheItem(f); i.setLastModified(200005L); i.setTranslationCount(11); i.setEncoding("GB2312"); i.setHeader(new ResponseHeaderImpl("Test2", new String[] { "Value3", "Value4" })); i.setHeader(new ResponseHeaderImpl("Test1", new String[] { "Value1", "Value2" })); byte[] chineseText = new byte[] { -42, -48, -46, -30, 87, 101, 98, 46, 99, 111, 109, 32, -54, -57, -46, -69, -72, -10, -61, -26, -49, -14, -42, -48, -50, -60, -45, -61, -69, -89, -95, -94, -67, -23, -55, -36, -46, -30, -76, -13, -64, -5, -58, -13, -46, -75, -75, -60, -42, -48, -50, -60, -51, -8, -43, -66, -93, -84, -54, -57, -46, -69, -68, -36, -51, -88, -49, -14, -74, -85, -73, -67, -75, -60, -51, -8, -62, -25, -57, -59, -63, -70, -93, -84, -53, -4, -75, -60, -60, -65, -75, -60, -44, -38, -45, -38, -80, -17, -42, -6, -78, -69, -74, -49, -73, -94, -43, -71, -41, -77, -76, -13, -75, -60, -58, -13, -46, -75, -68, -28, -67, -8, -48, -48, -49, -32, -69, -91, -63, -86, -49, -75, -67, -45, -76, -91, -95, -93, -50, -46, -61, -57, -49, -32, -48, -59, -93, -84, -42, -48, -50, -60, -45, -61, -69, -89, -67, -85, -69, -31, -51, -88, -71, -3, -79, -66, -51, -8, -43, -66, -93, -84, -43, -46, -75, -67, -45, -48, -71, -40, -46, -47, -45, -21, -42, -48, -71, -6, -58, -13, -46, -75, -67, -88, -63, -94, -70, -49, -41, -9, -67, -69, -51, -7, -71, -40, -49, -75, -75, -60, -46, -30, -76, -13, -64, -5, -58, -13, -46, -75, -93, -84, -69, -14, -45, -48, -46, -30, -45, -21, -42, -48, -71, -6, 32, -58, -13, -46, -75, -67, -8, -48, -48, -70, -49, -41, -9, -67, -69, -51, -7, -75, -60, -46, -30, -76, -13, -64, -5, -58, -13, -46, -75, -75, -60, -45, -48, -45, -61, -48, -59, -49, -94, -41, -54, -63, -49, -95, -93 }; { InputStream input = new ByteArrayInputStream(chineseText); try { i.setContentAsStream(input); } finally { input.close(); } } assertEquals("GB2312", i.getEncoding()); assertEquals(200005L, i.getLastModified()); assertEquals(11, i.getTranslationCount()); assertFalse(i.isCached()); i.updateAfterAllContentUpdated(null, null); { assertEquals(3, i.getHeaders().size()); int ii = 0; for (ResponseHeader h : i.getHeaders()) { ii++; if (ii == 1) { assertEquals("Content-Length", h.getName()); assertEquals("[279]", Arrays.toString(h.getValues())); } else if (ii == 2) { assertEquals("Test1", h.getName()); assertEquals("[Value1, Value2]", Arrays.toString(h.getValues())); } else if (ii == 3) { assertEquals("Test2", h.getName()); assertEquals("[Value3, Value4]", Arrays.toString(h.getValues())); } } } { FileInputStream input = new FileInputStream(f); StringWriter w = new StringWriter(); try { IOUtils.copy(input, w, "GB2312"); } finally { IOUtils.closeQuietly(input); IOUtils.closeQuietly(w); } assertEquals(new String(chineseText, "GB2312"), w.toString()); } { FileInputStream input = new FileInputStream(f); ByteArrayOutputStream output = new ByteArrayOutputStream(); try { IOUtils.copy(input, output); } finally { IOUtils.closeQuietly(input); IOUtils.closeQuietly(output); } assertTrue(Arrays.equals(chineseText, output.toByteArray())); } } finally { f.delete(); } }

private static void copy(File src, File dst) { try { FileChannel srcChannel = new FileInputStream(src).getChannel(); FileChannel dstChannel = new FileOutputStream(dst).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (IOException e) { e.printStackTrace(); } }

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; }

public TestReport runImpl() throws Exception { DocumentFactory df = new SAXDocumentFactory(GenericDOMImplementation.getDOMImplementation(), parserClassName); File f = (new File(testFileName)); URL url = f.toURL(); Document doc = df.createDocument(null, rootTag, url.toString(), url.openStream()); File ser1 = File.createTempFile("doc1", "ser"); File ser2 = File.createTempFile("doc2", "ser"); try { ObjectOutputStream oos; oos = new ObjectOutputStream(new FileOutputStream(ser1)); oos.writeObject(doc); oos.close(); ObjectInputStream ois; ois = new ObjectInputStream(new FileInputStream(ser1)); doc = (Document) ois.readObject(); ois.close(); oos = new ObjectOutputStream(new FileOutputStream(ser2)); oos.writeObject(doc); oos.close(); } catch (IOException e) { DefaultTestReport report = new DefaultTestReport(this); report.setErrorCode("io.error"); report.addDescriptionEntry("message", e.getClass().getName() + ": " + e.getMessage()); report.addDescriptionEntry("file.name", testFileName); report.setPassed(false); return report; } InputStream is1 = new FileInputStream(ser1); InputStream is2 = new FileInputStream(ser2); for (; ; ) { int i1 = is1.read(); int i2 = is2.read(); if (i1 == -1 && i2 == -1) { return reportSuccess(); } if (i1 != i2) { DefaultTestReport report = new DefaultTestReport(this); report.setErrorCode("difference.found"); report.addDescriptionEntry("file.name", testFileName); report.setPassed(false); return report; } } }

private String writeInputStreamToString(InputStream stream) { StringWriter stringWriter = new StringWriter(); try { IOUtils.copy(stream, stringWriter); } catch (IOException e) { e.printStackTrace(); } String namespaces = stringWriter.toString().trim(); return namespaces; }

private void copy(File fin, File fout) throws IOException { FileOutputStream out = null; FileInputStream in = null; try { out = new FileOutputStream(fout); in = new FileInputStream(fin); byte[] buf = new byte[2048]; int read = in.read(buf); while (read > 0) { out.write(buf, 0, read); read = in.read(buf); } } catch (IOException _e) { throw _e; } finally { if (in != null) in.close(); if (out != null) out.close(); } }

public static JSONObject doJSONQuery(String urlstr) throws IOException, MalformedURLException, JSONException, SolrException { URL url = new URL(urlstr); HttpURLConnection con = null; try { con = (HttpURLConnection) url.openConnection(); BufferedReader in = new BufferedReader(new InputStreamReader(con.getInputStream())); StringBuffer buffer = new StringBuffer(); String str; while ((str = in.readLine()) != null) { buffer.append(str + "\n"); } in.close(); JSONObject response = new JSONObject(buffer.toString()); return response; } catch (IOException e) { if (con != null) { try { int statusCode = con.getResponseCode(); if (statusCode >= 400) { throw (new SolrSelectUtils()).new SolrException(statusCode); } } catch (IOException exc) { } } throw (e); } }

public static byte[] hash(String identifier) { if (function.equals("SHA-1")) { try { MessageDigest md = MessageDigest.getInstance(function); md.reset(); byte[] code = md.digest(identifier.getBytes()); byte[] value = new byte[KEY_LENGTH / 8]; int shrink = code.length / value.length; int bitCount = 1; for (int j = 0; j < code.length * 8; j++) { int currBit = ((code[j / 8] & (1 << (j % 8))) >> j % 8); if (currBit == 1) bitCount++; if (((j + 1) % shrink) == 0) { int shrinkBit = (bitCount % 2 == 0) ? 0 : 1; value[j / shrink / 8] |= (shrinkBit << ((j / shrink) % 8)); bitCount = 1; } } return value; } catch (Exception e) { e.printStackTrace(); } } if (function.equals("CRC32")) { CRC32 crc32 = new CRC32(); crc32.reset(); crc32.update(identifier.getBytes()); long code = crc32.getValue(); code &= (0xffffffffffffffffL >>> (64 - KEY_LENGTH)); byte[] value = new byte[KEY_LENGTH / 8]; for (int i = 0; i < value.length; i++) { value[value.length - i - 1] = (byte) ((code >> 8 * i) & 0xff); } return value; } if (function.equals("Java")) { int code = identifier.hashCode(); code &= (0xffffffff >>> (32 - KEY_LENGTH)); byte[] value = new byte[KEY_LENGTH / 8]; for (int i = 0; i < value.length; i++) { value[value.length - i - 1] = (byte) ((code >> 8 * i) & 0xff); } return value; } return null; }

public static final String MD5(String value) { try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(value.getBytes()); BigInteger hash = new BigInteger(1, md.digest()); String newValue = hash.toString(16); return newValue; } catch (NoSuchAlgorithmException ns) { ns.printStackTrace(); return null; } }

public boolean check(String password) throws UnsupportedEncodingException, NoSuchAlgorithmException { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(username.getBytes("ISO-8859-1")); md.update((byte) ':'); md.update(realm.getBytes("ISO-8859-1")); md.update((byte) ':'); md.update(password.getBytes("ISO-8859-1")); byte[] ha1 = md.digest(); String hexHa1 = new String(Hex.encodeHex(ha1)); md.reset(); md.update(method.getBytes("ISO-8859-1")); md.update((byte) ':'); md.update(uri.getBytes("ISO-8859-1")); byte[] ha2 = md.digest(); String hexHa2 = new String(Hex.encodeHex(ha2)); md.reset(); md.update(hexHa1.getBytes("ISO-8859-1")); md.update((byte) ':'); md.update(nonce.getBytes("ISO-8859-1")); md.update((byte) ':'); md.update(nc.getBytes("ISO-8859-1")); md.update((byte) ':'); md.update(cnonce.getBytes("ISO-8859-1")); md.update((byte) ':'); md.update(qop.getBytes("ISO-8859-1")); md.update((byte) ':'); md.update(hexHa2.getBytes("ISO-8859-1")); byte[] digest = md.digest(); String hexDigest = new String(Hex.encodeHex(digest)); return (hexDigest.equalsIgnoreCase(response)); }

public static byte[] clearPassToUserPassword(String clearpass, HashAlg alg, byte[] salt) { if (alg == null) { throw new IllegalArgumentException("Invalid hash argorithm."); } try { MessageDigest digester = null; StringBuilder resultInText = new StringBuilder(); switch(alg) { case MD5: resultInText.append("{MD5}"); digester = MessageDigest.getInstance("MD5"); break; case SMD5: resultInText.append("{SMD5}"); digester = MessageDigest.getInstance("MD5"); break; case SHA: resultInText.append("{SHA}"); digester = MessageDigest.getInstance("SHA"); break; case SSHA: resultInText.append("{SSHA}"); digester = MessageDigest.getInstance("SHA"); break; default: break; } digester.reset(); digester.update(clearpass.getBytes(DEFAULT_ENCODING)); byte[] hash = null; if (salt != null && (alg == HashAlg.SMD5 || alg == HashAlg.SSHA)) { digester.update(salt); hash = ArrayUtils.addAll(digester.digest(), salt); } else { hash = digester.digest(); } resultInText.append(new String(Base64.encodeBase64(hash), DEFAULT_ENCODING)); return resultInText.toString().getBytes(DEFAULT_ENCODING); } catch (UnsupportedEncodingException uee) { log.warn("Error occurred while hashing password ", uee); return new byte[0]; } catch (java.security.NoSuchAlgorithmException nse) { log.warn("Error occurred while hashing password ", nse); return new byte[0]; } }

public synchronized String encrypt(String plaintext) throws Exception { MessageDigest md = null; try { md = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { throw e; } try { md.update(plaintext.getBytes("UTF-8")); } catch (UnsupportedEncodingException e) { throw e; } byte raw[] = md.digest(); String hash = (new BASE64Encoder()).encode(raw); return hash; }

private void doPOST(HttpURLConnection connection, InputStream inputXML) throws MessageServiceException { try { OutputStream requestStream = new BufferedOutputStream(connection.getOutputStream()); IOUtils.copyAndClose(inputXML, requestStream); connection.connect(); } catch (IOException e) { throw new MessageServiceException(e.getMessage(), e); } }

public void run() { try { File inf = new File(dest); if (!inf.exists()) { inf.getParentFile().mkdirs(); } FileChannel in = new FileInputStream(src).getChannel(); FileChannel out = new FileOutputStream(dest).getChannel(); out.transferFrom(in, 0, in.size()); in.close(); out.close(); } catch (IOException e) { e.printStackTrace(); System.err.println("Error copying file \n" + src + "\n" + dest); } }

public static void copyFile(File sourceFile, File destFile) throws IOException { if (!destFile.exists()) { destFile.createNewFile(); } FileChannel source = null; FileChannel destination = null; try { source = new FileInputStream(sourceFile).getChannel(); destination = new FileOutputStream(destFile).getChannel(); destination.transferFrom(source, 0, source.size()); } finally { if (source != null) { source.close(); } if (destination != null) { destination.close(); } } }

public static void copyFile(File destFile, File src) throws IOException { File destDir = destFile.getParentFile(); File tempFile = new File(destFile + "_tmp"); destDir.mkdirs(); InputStream is = new FileInputStream(src); try { FileOutputStream os = new FileOutputStream(tempFile); try { byte[] buf = new byte[8192]; int len; while ((len = is.read(buf)) > 0) os.write(buf, 0, len); } finally { os.close(); } } finally { is.close(); } destFile.delete(); if (!tempFile.renameTo(destFile)) throw new IOException("Unable to rename " + tempFile + " to " + destFile); }

public static synchronized String encrypt(String plaintext) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md = null; md = MessageDigest.getInstance("SHA"); md.update(plaintext.getBytes("UTF-8")); byte raw[] = md.digest(); String hash = (new BASE64Encoder()).encode(raw); return hash; }

public String hash(String senha) { String result = ""; try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(senha.getBytes()); byte[] hashMd5 = md.digest(); for (int i = 0; i < hashMd5.length; i++) result += Integer.toHexString((((hashMd5[i] >> 4) & 0xf) << 4) | (hashMd5[i] & 0xf)); } catch (NoSuchAlgorithmException ex) { Logger.getInstancia().log(TipoLog.ERRO, ex); } return result; }

private void load() throws SQLException { Connection conn = null; Statement stmt = null; try { conn = FidoDataSource.getConnection(); conn.setAutoCommit(false); stmt = conn.createStatement(); ClearData.clearTables(stmt); stmt.executeUpdate("insert into Objects (ObjectId, Description) values (100, 'Person')"); stmt.executeUpdate("insert into Objects (ObjectId, Description) values (101, 'john')"); stmt.executeUpdate("insert into Objects (ObjectId, Description) values (200, 'Dog')"); stmt.executeQuery("select setval('objects_objectid_seq', 1000)"); stmt.executeUpdate("insert into ClassLinkTypes (LinkName, LinkType) values ('hasa', 2)"); stmt.executeUpdate("insert into ObjectLinks (ObjectId, LinkName, LinkToObject) values (100, 'isa', 1)"); stmt.executeUpdate("insert into ObjectLinks (ObjectId, LinkName, LinkToObject) values (101, 'instance', 100)"); stmt.executeUpdate("insert into ObjectLinks (ObjectId, LinkName, LinkToObject) values (200, 'isa', 1)"); stmt.executeUpdate("insert into Dictionary (Word, SenseNumber, GrammarString, ObjectId) values ('LEFT-WALL', '1', 'AV+', 1)"); stmt.executeUpdate("insert into Dictionary (Word, SenseNumber, GrammarString, ObjectId) values ('john', '1', 'S+ | DO-', 1)"); stmt.executeUpdate("insert into Dictionary (Word, SenseNumber, GrammarString, ObjectId) values ('a', '1', 'D+', 1)"); stmt.executeUpdate("insert into Dictionary (Word, SenseNumber, GrammarString, ObjectId) values ('dog', '1', '[D-] & (S+ | DO-)', 200)"); stmt.executeUpdate("insert into Dictionary (Word, SenseNumber, GrammarString, ObjectId) values ('have', '1', 'S- & AV- & DO+', 1)"); stmt.executeUpdate("insert into LanguageMorphologies (LanguageName, MorphologyTag, Rank, Root, Surface, Used) values " + " ('English', 'third singular', 1, 'have', 'has', TRUE)"); stmt.executeUpdate("insert into GrammarLinks (LinkName, LinkType) values ('S', 1)"); stmt.executeUpdate("insert into GrammarLinks (LinkName, LinkType) values ('DO', 3)"); stmt.executeUpdate("insert into GrammarLinks (LinkName, LinkType) values ('AV', 7)"); stmt.executeUpdate("insert into GrammarLinks (LinkName, LinkType) values ('D', 10)"); stmt.executeUpdate("insert into Articles (ArticleName, Dereference) values ('a', 2)"); stmt.executeUpdate("insert into FrameSlots (SlotName) values ('actor')"); stmt.executeUpdate("insert into FrameSlots (SlotName) values ('object')"); stmt.executeUpdate("insert into Verbs (VerbName, Type, SubjectSlot, IndirectObjectSlot, PredicateNounSlot) values ('have', 1, 'actor', '', 'object')"); stmt.executeQuery("select setval('instructions_instructionid_seq', 1)"); stmt.executeUpdate("insert into Instructions (Type, ExecuteString, FrameSlot, Operator, LinkName, ObjectId, AttributeName) " + "values (3, 'link %actor hasa %object', null, 0, null, null, null)"); stmt.executeQuery("select setval('transactions_transactionid_seq', 1)"); stmt.executeUpdate("insert into Transactions (InstructionId, Description) values (2, 'have - link')"); stmt.executeQuery("select setval('verbtransactions_verbid_seq', 1)"); stmt.executeUpdate("insert into VerbTransactions (VerbString, MoodType, TransactionId) values ('have', 1, 2)"); stmt.executeUpdate("insert into VerbConstraints (VerbId, FrameSlot, ObjectId) values (2, 'actor', 1)"); stmt.executeUpdate("insert into VerbConstraints (VerbId, FrameSlot, ObjectId) values (2, 'object', 1)"); stmt.executeUpdate("insert into ProperNouns (Noun, SenseNumber, ObjectId) values ('john', 1, 101)"); stmt.executeUpdate("update SystemProperties set value = 'Tutorial 1 Data' where name = 'DB Data Version'"); conn.commit(); } catch (SQLException e) { if (conn != null) conn.rollback(); throw e; } finally { if (stmt != null) stmt.close(); if (conn != null) conn.close(); } }

public static URL getIconURLForUser(String id) { try { URL url = new URL("http://profiles.yahoo.com/" + id); BufferedReader r = new BufferedReader(new InputStreamReader(url.openStream())); String input = null; while ((input = r.readLine()) != null) { if (input.indexOf("<a href=\"") < 0) continue; if (input.indexOf("<img src=\"") < 0) continue; if (input.indexOf("<a href=\"") > input.indexOf("<img src=\"")) continue; String href = input.substring(input.indexOf("<a href=\"") + 9); String src = input.substring(input.indexOf("<img src=\"") + 10); if (href.indexOf("\"") < 0) continue; if (src.indexOf("\"") < 0) continue; href = href.substring(0, href.indexOf("\"")); src = src.substring(0, src.indexOf("\"")); if (href.equals(src)) { return new URL(href); } } } catch (IOException e) { } URL toReturn = null; try { toReturn = new URL("http://us.i1.yimg.com/us.yimg.com/i/ppl/no_photo.gif"); } catch (MalformedURLException e) { Debug.assrt(false); } return toReturn; }

@Before public void BeforeTheTest() throws Exception { URL url = ProfileParserTest.class.getClassLoader().getResource("ca/uhn/hl7v2/conf/parser/tests/example_ack.xml"); URLConnection conn = url.openConnection(); InputStream instream = conn.getInputStream(); if (instream == null) throw new Exception("can't find the xml file"); BufferedReader in = new BufferedReader(new InputStreamReader(instream)); int tmp = 0; StringBuffer buf = new StringBuffer(); while ((tmp = in.read()) != -1) { buf.append((char) tmp); } profileString = buf.toString(); }

public void load() throws ResourceInstantiationException { if (null == url) { throw new ResourceInstantiationException("URL not set (null)."); } try { BufferedReader defReader = new BomStrippingInputStreamReader((url).openStream(), ENCODING); String line; LinearNode node; while (null != (line = defReader.readLine())) { node = new LinearNode(line); try { this.add(node); } catch (GateRuntimeException ex) { throw new ResourceInstantiationException(ex); } } defReader.close(); isModified = false; } catch (Exception x) { throw new ResourceInstantiationException(x); } }

private boolean copyFile(File inFile, File outFile) { BufferedReader reader = null; BufferedWriter writer = null; try { reader = new BufferedReader(new FileReader(inFile)); writer = new BufferedWriter(new FileWriter(outFile)); while (reader.ready()) { writer.write(reader.read()); } writer.flush(); } catch (IOException ex) { ex.printStackTrace(); } finally { if (reader != null) { try { reader.close(); } catch (IOException ex) { ex.printStackTrace(); return false; } } if (writer != null) { try { writer.close(); } catch (IOException ex) { 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; }

public InputStream getStream(Hashtable<String, String> pValue) throws IOException { List<NameValuePair> nvps = new ArrayList<NameValuePair>(); Enumeration<String> enm = pValue.keys(); String key; while (enm.hasMoreElements()) { key = enm.nextElement(); nvps.add(new BasicNameValuePair(key, pValue.get(key))); } httpPost.setEntity(new UrlEncodedFormEntity(nvps, HTTP.UTF_8)); HttpResponse response = httpclient.execute(httpPost); HttpEntity entity = response.getEntity(); return entity.getContent(); }

public static void copyFile(File input, File output) throws Exception { FileReader in = new FileReader(input); FileWriter out = new FileWriter(output); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); }

@Override public Class<?> loadClass(final String name) throws ClassNotFoundException { final String baseName = StringUtils.substringBefore(name, "$"); if (baseName.startsWith("java") && !whitelist.contains(baseName) && !additionalWhitelist.contains(baseName)) { throw new NoClassDefFoundError(name + " is a restricted class for GAE"); } if (!name.startsWith("com.gargoylesoftware")) { return super.loadClass(name); } super.loadClass(name); final InputStream is = getResourceAsStream(name.replaceAll("\\.", "/") + ".class"); final ByteArrayOutputStream bos = new ByteArrayOutputStream(); try { IOUtils.copy(is, bos); final byte[] bytes = bos.toByteArray(); return defineClass(name, bytes, 0, bytes.length); } catch (final IOException e) { throw new RuntimeException(e); } }

private void handleInclude(Element elem) throws Exception { String source = getTextContent(elem); URL url = null; try { url = new URL(source); } catch (MalformedURLException e) { url = XmlConfig.class.getResource(source); } Document doc = db.parse(url.openStream()); handleDocument(doc); }

public static void resize(File originalFile, File resizedFile, int width, String format) throws IOException { if (format != null && "gif".equals(format.toLowerCase())) { resize(originalFile, resizedFile, width, 1); return; } FileInputStream fis = new FileInputStream(originalFile); ByteArrayOutputStream byteStream = new ByteArrayOutputStream(); int readLength = -1; int bufferSize = 1024; byte bytes[] = new byte[bufferSize]; while ((readLength = fis.read(bytes, 0, bufferSize)) != -1) { byteStream.write(bytes, 0, readLength); } byte[] in = byteStream.toByteArray(); fis.close(); byteStream.close(); Image inputImage = Toolkit.getDefaultToolkit().createImage(in); waitForImage(inputImage); int imageWidth = inputImage.getWidth(null); if (imageWidth < 1) throw new IllegalArgumentException("image width " + imageWidth + " is out of range"); int imageHeight = inputImage.getHeight(null); if (imageHeight < 1) throw new IllegalArgumentException("image height " + imageHeight + " is out of range"); int height = -1; double scaleW = (double) imageWidth / (double) width; double scaleY = (double) imageHeight / (double) height; if (scaleW >= 0 && scaleY >= 0) { if (scaleW > scaleY) { height = -1; } else { width = -1; } } Image outputImage = inputImage.getScaledInstance(width, height, java.awt.Image.SCALE_DEFAULT); checkImage(outputImage); encode(new FileOutputStream(resizedFile), outputImage, format); }

public void removeGames(List<Game> games) throws SQLException { Connection conn = ConnectionManager.getManager().getConnection(); PreparedStatement stm = null; conn.setAutoCommit(false); try { for (Game game : games) { stm = conn.prepareStatement(Statements.DELETE_GAME); stm.setInt(1, game.getGameID()); stm.executeUpdate(); } } catch (SQLException e) { conn.rollback(); throw e; } finally { if (stm != null) stm.close(); } conn.commit(); conn.setAutoCommit(true); }

public String getWebPage(String url) { String content = ""; URL urlObj = null; try { urlObj = new URL(url); } catch (MalformedURLException urlEx) { urlEx.printStackTrace(); throw new Error("URL creation failed."); } try { BufferedReader reader = new BufferedReader(new InputStreamReader(urlObj.openStream())); String line; while ((line = reader.readLine()) != null) { content += line; } } catch (IOException e) { e.printStackTrace(); throw new Error("Page retrieval failed."); } return content; }

public static void copyFile(File from, File to) throws IOException { FileInputStream in = new FileInputStream(from); FileOutputStream out = new FileOutputStream(to); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); }

@Override protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException { PrintWriter writer = null; InputStream is = null; FileOutputStream fos = null; try { writer = response.getWriter(); } catch (IOException ex) { log(OctetStreamReader.class.getName() + "has thrown an exception: " + ex.getMessage()); } String filename = request.getHeader("X-File-Name"); try { is = request.getInputStream(); fos = new FileOutputStream(new File(targetPath + filename)); IOUtils.copy(is, fos); response.setStatus(HttpServletResponse.SC_OK); writer.print("{success: true}"); } catch (FileNotFoundException ex) { response.setStatus(HttpServletResponse.SC_INTERNAL_SERVER_ERROR); writer.print("{success: false}"); log(OctetStreamReader.class.getName() + "has thrown an exception: " + ex.getMessage()); } catch (IOException ex) { response.setStatus(HttpServletResponse.SC_INTERNAL_SERVER_ERROR); writer.print("{success: false}"); log(OctetStreamReader.class.getName() + "has thrown an exception: " + ex.getMessage()); } finally { try { fos.close(); is.close(); } catch (IOException ignored) { } } writer.flush(); writer.close(); }

private void dumpFile(File repository, File copy) { try { if (copy.exists() && !copy.delete()) { throw new RuntimeException("can't delete copy: " + copy); } printFile("Real Archive File", repository); new ZipArchive(repository.getPath()); IOUtils.copyFiles(repository, copy); printFile("Copy Archive File", copy); new ZipArchive(copy.getPath()); } catch (IOException e) { e.printStackTrace(); } }

@Test public void testCopy_readerToWriter_nullOut() throws Exception { InputStream in = new ByteArrayInputStream(inData); in = new YellOnCloseInputStreamTest(in); Reader reader = new InputStreamReader(in, "US-ASCII"); try { IOUtils.copy(reader, (Writer) null); fail(); } catch (NullPointerException ex) { } }

public SimpleParser(String filepath) throws Exception { this.path = filepath; InputStream is = null; try { if (this.path.indexOf("http") == 0) { URL url = new URL(this.path); is = url.openStream(); } else if (this.path.indexOf("<?xml") == 0) { is = new ByteArrayInputStream(filepath.getBytes(encoding)); } else { File f = new File(this.path); if (!f.exists()) { setError("File not found : " + this.path); } else { is = new FileInputStream(f); } } if (is != null) { DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance(); DocumentBuilder dBuilder = dbFactory.newDocumentBuilder(); doc = dBuilder.parse(is); doc.getDocumentElement().normalize(); } } catch (Exception ex) { Malgn.errorLog("{SimpleParser.constructor} Path:" + filepath + " " + ex.getMessage()); setError("Parser Error : " + ex.getMessage()); } finally { if (is != null) is.close(); } }

private String readHtmlFile(String htmlFileName) { StringBuffer buffer = new StringBuffer(); java.net.URL url = getClass().getClassLoader().getResource("freestyleLearning/homeCore/help/" + htmlFileName); try { BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String string = " "; while (string != null) { string = reader.readLine(); if (string != null) buffer.append(string); } } catch (Exception exc) { System.out.println(exc); } return new String(buffer); }

@Override protected ModelAndView handleRequestInternal(final HttpServletRequest request, final HttpServletResponse response) throws Exception { final String filename = ServletRequestUtils.getRequiredStringParameter(request, "id"); final File file = new File(path, filename + ".html"); logger.debug("Getting static content from: " + file.getPath()); final InputStream is = getServletContext().getResourceAsStream(file.getPath()); OutputStream out = null; if (is != null) { try { out = response.getOutputStream(); IOUtils.copy(is, out); } catch (IOException ioex) { logger.error(ioex); } finally { is.close(); if (out != null) { out.close(); } } } return null; }

public static boolean start(RootDoc root) { Logger log = Logger.getLogger("DocletGenerator"); if (destination == null) { try { ruleListenerDef = IOUtils.toString(GeneratorOfXmlSchemaForConvertersDoclet.class.getResourceAsStream("/RuleListenersFragment.xsd"), "UTF-8"); String fn = System.getenv("annocultor.xconverter.destination.file.name"); fn = (fn == null) ? "./../../../src/site/resources/schema/XConverterInclude.xsd" : fn; destination = new File(fn); if (destination.exists()) { destination.delete(); } FileOutputStream os; os = new FileOutputStream(new File(destination.getParentFile(), "XConverter.xsd")); IOUtils.copy(new AutoCloseInputStream(GeneratorOfXmlSchemaForConvertersDoclet.class.getResourceAsStream("/XConverterTemplate.xsd")), os); os.close(); os = new FileOutputStream(destination); IOUtils.copy(new AutoCloseInputStream(GeneratorOfXmlSchemaForConvertersDoclet.class.getResourceAsStream("/XConverterInclude.xsd")), os); os.close(); } catch (Exception e) { try { throw new RuntimeException("On destination " + destination.getCanonicalPath(), e); } catch (IOException e1) { throw new RuntimeException(e1); } } } try { String s = Utils.loadFileToString(destination.getCanonicalPath(), "\n"); int breakPoint = s.indexOf(XSD_TEXT_TO_REPLACED_WITH_GENERATED_XML_SIGNATURES); if (breakPoint < 0) { throw new Exception("Signature not found in XSD: " + XSD_TEXT_TO_REPLACED_WITH_GENERATED_XML_SIGNATURES); } String preambula = s.substring(0, breakPoint); String appendix = s.substring(breakPoint); destination.delete(); PrintWriter schemaWriter = new PrintWriter(destination); schemaWriter.print(preambula); ClassDoc[] classes = root.classes(); for (int i = 0; i < classes.length; ++i) { ClassDoc cd = classes[i]; PrintWriter documentationWriter = null; if (getSuperClasses(cd).contains(Rule.class.getName())) { for (ConstructorDoc constructorDoc : cd.constructors()) { if (constructorDoc.isPublic()) { if (isMeantForXMLAccess(constructorDoc)) { if (documentationWriter == null) { File file = new File("./../../../src/site/xdoc/rules." + cd.name() + ".xml"); documentationWriter = new PrintWriter(file); log.info("Generating doc for rule " + file.getCanonicalPath()); printRuleDocStart(cd, documentationWriter); } boolean initFound = false; for (MethodDoc methodDoc : cd.methods()) { if ("init".equals(methodDoc.name())) { if (methodDoc.parameters().length == 0) { initFound = true; break; } } } if (!initFound) { } printConstructorSchema(constructorDoc, schemaWriter); if (documentationWriter != null) { printConstructorDoc(constructorDoc, documentationWriter); } } } } } if (documentationWriter != null) { printRuleDocEnd(documentationWriter); } } schemaWriter.print(appendix); schemaWriter.close(); log.info("Saved to " + destination.getCanonicalPath()); } catch (Exception e) { throw new RuntimeException(e); } return true; }

private boolean get(String surl, File dst, Get get) throws IOException { boolean ret = false; InputStream is = null; OutputStream os = null; try { try { if (surl.startsWith("file://")) { is = new FileInputStream(surl.substring(7)); } else { URL url = new URL(surl); is = url.openStream(); } if (is != null) { os = new FileOutputStream(dst); int read; byte[] buffer = new byte[4096]; while ((read = is.read(buffer)) > 0) { os.write(buffer, 0, read); } ret = true; } } catch (ConnectException ex) { log("Connect exception " + ex.getMessage(), ex, 3); if (dst.exists()) dst.delete(); } catch (UnknownHostException ex) { log("Unknown host " + ex.getMessage(), ex, 3); } catch (FileNotFoundException ex) { log("File not found: " + ex.getMessage(), 3); } } finally { if (is != null) is.close(); if (os != null) os.close(); is = null; os = null; } if (ret) { try { is = new FileInputStream(dst); os = new FileOutputStream(getCachedFile(get)); int read; byte[] buffer = new byte[4096]; while ((read = is.read(buffer)) > 0) { os.write(buffer, 0, read); } } finally { if (is != null) is.close(); if (os != null) os.close(); is = null; os = null; } } return ret; }

public boolean performFinish() { try { IJavaProject javaProject = JavaCore.create(getProject()); final IProjectDescription projectDescription = ResourcesPlugin.getWorkspace().newProjectDescription(projectPage.getProjectName()); projectDescription.setLocation(null); getProject().create(projectDescription, null); List<IClasspathEntry> classpathEntries = new ArrayList<IClasspathEntry>(); projectDescription.setNatureIds(getNatures()); List<String> builderIDs = new ArrayList<String>(); addBuilders(builderIDs); ICommand[] buildCMDS = new ICommand[builderIDs.size()]; int i = 0; for (String builderID : builderIDs) { ICommand build = projectDescription.newCommand(); build.setBuilderName(builderID); buildCMDS[i++] = build; } projectDescription.setBuildSpec(buildCMDS); getProject().open(null); getProject().setDescription(projectDescription, null); addClasspaths(classpathEntries, getProject()); javaProject.setRawClasspath(classpathEntries.toArray(new IClasspathEntry[classpathEntries.size()]), null); javaProject.setOutputLocation(new Path("/" + projectPage.getProjectName() + "/bin"), null); createFiles(); return true; } catch (Exception exception) { StatusManager.getManager().handle(new Status(IStatus.ERROR, getPluginID(), "Problem creating " + getProjectTypeName() + " project. Ignoring.", exception)); try { getProject().delete(true, null); } catch (Exception e) { } return false; } }

public static Document getSkeleton() { Document doc = null; String filesep = System.getProperty("file.separator"); try { java.net.URL url = Skeleton.class.getResource(filesep + "simplemassimeditor" + filesep + "resources" + filesep + "configskeleton.xml"); InputStream input = url.openStream(); DocumentBuilder parser = DocumentBuilderFactory.newInstance().newDocumentBuilder(); try { doc = parser.parse(input); } catch (SAXException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } catch (ParserConfigurationException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } return doc; }

public static void copy(File toCopy, File dest) throws IOException { FileInputStream src = new FileInputStream(toCopy); FileOutputStream out = new FileOutputStream(dest); try { while (src.available() > 0) { out.write(src.read()); } } finally { src.close(); out.close(); } }

public static void copy(String fromFileName, String toFileName) throws IOException { File fromFile = new File(fromFileName); File toFile = new File(toFileName); if (!fromFile.exists()) throw new IOException("FileCopy: " + "no such source file: " + fromFileName); if (!fromFile.isFile()) throw new IOException("FileCopy: " + "can't copy directory: " + fromFileName); if (!fromFile.canRead()) throw new IOException("FileCopy: " + "source file is unreadable: " + fromFileName); if (toFile.isDirectory()) toFile = new File(toFile, fromFile.getName()); if (toFile.exists()) { if (!toFile.canWrite()) throw new IOException("FileCopy: " + "destination file is unwriteable: " + toFileName); System.out.print("Overwrite existing file " + toFile.getName() + "? (Y/N): "); System.out.flush(); BufferedReader in = new BufferedReader(new InputStreamReader(System.in)); String response = in.readLine(); if (!response.equals("Y") && !response.equals("y")) throw new IOException("FileCopy: " + "existing file was not overwritten."); } else { String parent = toFile.getParent(); if (parent == null) parent = System.getProperty("user.dir"); File dir = new File(parent); if (!dir.exists()) throw new IOException("FileCopy: " + "destination directory doesn't exist: " + parent); if (dir.isFile()) throw new IOException("FileCopy: " + "destination is not a directory: " + parent); if (!dir.canWrite()) throw new IOException("FileCopy: " + "destination directory is unwriteable: " + parent); } FileInputStream from = null; FileOutputStream to = null; try { from = new FileInputStream(fromFile); to = new FileOutputStream(toFile); 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) { ; } } }

private Drawable fetchImage(String iconUrl, Context ctx) { URL url; HttpClient httpClient = new DefaultHttpClient(); try { if (PreferenceManager.getDefaultSharedPreferences(ctx).getBoolean("use.urlimg.com", true)) { iconUrl = iconUrl.substring(iconUrl.indexOf("//") + 2); iconUrl = "http://urlimg.com/width/100/" + iconUrl; } Log.d(ImageCache.class.getName(), "Loading image from: " + iconUrl); HttpGet httpGet = new HttpGet(iconUrl); HttpResponse response = httpClient.execute(httpGet); InputStream content = response.getEntity().getContent(); Drawable d = Drawable.createFromStream(content, "src"); content.close(); httpGet.abort(); return d; } catch (IOException e) { Log.e(ImageCache.class.getName(), "IOException while fetching: " + iconUrl); return TELKA; } finally { } }

public static void openFile(PublicHubList hublist, String url) { BufferedReader fichAl; String linha; try { if (url.startsWith("http://")) fichAl = new BufferedReader(new InputStreamReader((new java.net.URL(url)).openStream())); else fichAl = new BufferedReader(new FileReader(url)); while ((linha = fichAl.readLine()) != null) { try { hublist.addDCHub(new DCHub(linha, DCHub.hublistFormater)); } catch (Exception e) { e.printStackTrace(); } } } catch (IOException e) { e.printStackTrace(); } }

public static StringBuffer readURLText(URL url, StringBuffer errorText) { StringBuffer page = new StringBuffer(""); String thisLine; try { BufferedReader source = new BufferedReader(new InputStreamReader(url.openStream())); while ((thisLine = source.readLine()) != null) { page.append(thisLine + "\n"); } return page; } catch (Exception e) { return errorText; } }

public void write(HttpServletRequest req, HttpServletResponse res, Object bean) throws IntrospectionException, IllegalAccessException, NoSuchMethodException, InvocationTargetException, IOException { res.setContentType(contentType); final Object r; if (HttpRpcServer.HttpRpcOutput.class.isAssignableFrom(bean.getClass())) { HttpRpcServer.HttpRpcOutput output = (HttpRpcServer.HttpRpcOutput) bean; r = output.getResult(); } else r = bean; if (r != null) { final ServletOutputStream outputStream = res.getOutputStream(); if (File.class.isAssignableFrom(r.getClass())) { File file = (File) r; InputStream in = null; try { in = new FileInputStream(file); IOUtils.copy(in, outputStream); } finally { if (in != null) in.close(); } } else if (InputStream.class.isAssignableFrom(r.getClass())) { InputStream in = null; try { in = (InputStream) r; if (ByteArrayInputStream.class.isAssignableFrom(r.getClass())) res.addHeader("Content-Length", Integer.toString(in.available())); IOUtils.copy(in, outputStream); } finally { if (in != null) in.close(); } } outputStream.flush(); } }

public static void main(String argv[]) { Matrix A, B, C, Z, O, I, R, S, X, SUB, M, T, SQ, DEF, SOL; int errorCount = 0; int warningCount = 0; double tmp, s; double[] columnwise = { 1., 2., 3., 4., 5., 6., 7., 8., 9., 10., 11., 12. }; double[] rowwise = { 1., 4., 7., 10., 2., 5., 8., 11., 3., 6., 9., 12. }; double[][] avals = { { 1., 4., 7., 10. }, { 2., 5., 8., 11. }, { 3., 6., 9., 12. } }; double[][] rankdef = avals; double[][] tvals = { { 1., 2., 3. }, { 4., 5., 6. }, { 7., 8., 9. }, { 10., 11., 12. } }; double[][] subavals = { { 5., 8., 11. }, { 6., 9., 12. } }; double[][] rvals = { { 1., 4., 7. }, { 2., 5., 8., 11. }, { 3., 6., 9., 12. } }; double[][] pvals = { { 1., 1., 1. }, { 1., 2., 3. }, { 1., 3., 6. } }; double[][] ivals = { { 1., 0., 0., 0. }, { 0., 1., 0., 0. }, { 0., 0., 1., 0. } }; double[][] evals = { { 0., 1., 0., 0. }, { 1., 0., 2.e-7, 0. }, { 0., -2.e-7, 0., 1. }, { 0., 0., 1., 0. } }; double[][] square = { { 166., 188., 210. }, { 188., 214., 240. }, { 210., 240., 270. } }; double[][] sqSolution = { { 13. }, { 15. } }; double[][] condmat = { { 1., 3. }, { 7., 9. } }; int rows = 3, cols = 4; int invalidld = 5; int raggedr = 0; int raggedc = 4; int validld = 3; int nonconformld = 4; int ib = 1, ie = 2, jb = 1, je = 3; int[] rowindexset = { 1, 2 }; int[] badrowindexset = { 1, 3 }; int[] columnindexset = { 1, 2, 3 }; int[] badcolumnindexset = { 1, 2, 4 }; double columnsummax = 33.; double rowsummax = 30.; double sumofdiagonals = 15; double sumofsquares = 650; print("\nTesting constructors and constructor-like methods...\n"); try { A = new Matrix(columnwise, invalidld); errorCount = try_failure(errorCount, "Catch invalid length in packed constructor... ", "exception not thrown for invalid input"); } catch (IllegalArgumentException e) { try_success("Catch invalid length in packed constructor... ", e.getMessage()); } try { A = new Matrix(rvals); tmp = A.get(raggedr, raggedc); } catch (IllegalArgumentException e) { try_success("Catch ragged input to default constructor... ", e.getMessage()); } catch (java.lang.ArrayIndexOutOfBoundsException e) { errorCount = try_failure(errorCount, "Catch ragged input to constructor... ", "exception not thrown in construction...ArrayIndexOutOfBoundsException thrown later"); } try { A = Matrix.constructWithCopy(rvals); tmp = A.get(raggedr, raggedc); } catch (IllegalArgumentException e) { try_success("Catch ragged input to constructWithCopy... ", e.getMessage()); } catch (java.lang.ArrayIndexOutOfBoundsException e) { errorCount = try_failure(errorCount, "Catch ragged input to constructWithCopy... ", "exception not thrown in construction...ArrayIndexOutOfBoundsException thrown later"); } A = new Matrix(columnwise, validld); B = new Matrix(avals); tmp = B.get(0, 0); avals[0][0] = 0.0; C = B.minus(A); avals[0][0] = tmp; B = Matrix.constructWithCopy(avals); tmp = B.get(0, 0); avals[0][0] = 0.0; if ((tmp - B.get(0, 0)) != 0.0) { errorCount = try_failure(errorCount, "constructWithCopy... ", "copy not effected... data visible outside"); } else { try_success("constructWithCopy... ", ""); } avals[0][0] = columnwise[0]; I = new Matrix(ivals); try { check(I, Matrix.identity(3, 4)); try_success("identity... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "identity... ", "identity Matrix not successfully created"); } print("\nTesting access methods...\n"); B = new Matrix(avals); if (B.getRowDimension() != rows) { errorCount = try_failure(errorCount, "getRowDimension... ", ""); } else { try_success("getRowDimension... ", ""); } if (B.getColumnDimension() != cols) { errorCount = try_failure(errorCount, "getColumnDimension... ", ""); } else { try_success("getColumnDimension... ", ""); } B = new Matrix(avals); double[][] barray = B.getArray(); if (barray != avals) { errorCount = try_failure(errorCount, "getArray... ", ""); } else { try_success("getArray... ", ""); } barray = B.getArrayCopy(); if (barray == avals) { errorCount = try_failure(errorCount, "getArrayCopy... ", "data not (deep) copied"); } try { check(barray, avals); try_success("getArrayCopy... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "getArrayCopy... ", "data not successfully (deep) copied"); } double[] bpacked = B.getColumnPackedCopy(); try { check(bpacked, columnwise); try_success("getColumnPackedCopy... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "getColumnPackedCopy... ", "data not successfully (deep) copied by columns"); } bpacked = B.getRowPackedCopy(); try { check(bpacked, rowwise); try_success("getRowPackedCopy... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "getRowPackedCopy... ", "data not successfully (deep) copied by rows"); } try { tmp = B.get(B.getRowDimension(), B.getColumnDimension() - 1); errorCount = try_failure(errorCount, "get(int,int)... ", "OutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { tmp = B.get(B.getRowDimension() - 1, B.getColumnDimension()); errorCount = try_failure(errorCount, "get(int,int)... ", "OutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("get(int,int)... OutofBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "get(int,int)... ", "OutOfBoundsException expected but not thrown"); } try { if (B.get(B.getRowDimension() - 1, B.getColumnDimension() - 1) != avals[B.getRowDimension() - 1][B.getColumnDimension() - 1]) { errorCount = try_failure(errorCount, "get(int,int)... ", "Matrix entry (i,j) not successfully retreived"); } else { try_success("get(int,int)... ", ""); } } catch (java.lang.ArrayIndexOutOfBoundsException e) { errorCount = try_failure(errorCount, "get(int,int)... ", "Unexpected ArrayIndexOutOfBoundsException"); } SUB = new Matrix(subavals); try { M = B.getMatrix(ib, ie + B.getRowDimension() + 1, jb, je); errorCount = try_failure(errorCount, "getMatrix(int,int,int,int)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { M = B.getMatrix(ib, ie, jb, je + B.getColumnDimension() + 1); errorCount = try_failure(errorCount, "getMatrix(int,int,int,int)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("getMatrix(int,int,int,int)... ArrayIndexOutOfBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "getMatrix(int,int,int,int)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } try { M = B.getMatrix(ib, ie, jb, je); try { check(SUB, M); try_success("getMatrix(int,int,int,int)... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "getMatrix(int,int,int,int)... ", "submatrix not successfully retreived"); } } catch (java.lang.ArrayIndexOutOfBoundsException e) { errorCount = try_failure(errorCount, "getMatrix(int,int,int,int)... ", "Unexpected ArrayIndexOutOfBoundsException"); } try { M = B.getMatrix(ib, ie, badcolumnindexset); errorCount = try_failure(errorCount, "getMatrix(int,int,int[])... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { M = B.getMatrix(ib, ie + B.getRowDimension() + 1, columnindexset); errorCount = try_failure(errorCount, "getMatrix(int,int,int[])... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("getMatrix(int,int,int[])... ArrayIndexOutOfBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "getMatrix(int,int,int[])... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } try { M = B.getMatrix(ib, ie, columnindexset); try { check(SUB, M); try_success("getMatrix(int,int,int[])... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "getMatrix(int,int,int[])... ", "submatrix not successfully retreived"); } } catch (java.lang.ArrayIndexOutOfBoundsException e) { errorCount = try_failure(errorCount, "getMatrix(int,int,int[])... ", "Unexpected ArrayIndexOutOfBoundsException"); } try { M = B.getMatrix(badrowindexset, jb, je); errorCount = try_failure(errorCount, "getMatrix(int[],int,int)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { M = B.getMatrix(rowindexset, jb, je + B.getColumnDimension() + 1); errorCount = try_failure(errorCount, "getMatrix(int[],int,int)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("getMatrix(int[],int,int)... ArrayIndexOutOfBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "getMatrix(int[],int,int)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } try { M = B.getMatrix(rowindexset, jb, je); try { check(SUB, M); try_success("getMatrix(int[],int,int)... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "getMatrix(int[],int,int)... ", "submatrix not successfully retreived"); } } catch (java.lang.ArrayIndexOutOfBoundsException e) { errorCount = try_failure(errorCount, "getMatrix(int[],int,int)... ", "Unexpected ArrayIndexOutOfBoundsException"); } try { M = B.getMatrix(badrowindexset, columnindexset); errorCount = try_failure(errorCount, "getMatrix(int[],int[])... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { M = B.getMatrix(rowindexset, badcolumnindexset); errorCount = try_failure(errorCount, "getMatrix(int[],int[])... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("getMatrix(int[],int[])... ArrayIndexOutOfBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "getMatrix(int[],int[])... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } try { M = B.getMatrix(rowindexset, columnindexset); try { check(SUB, M); try_success("getMatrix(int[],int[])... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "getMatrix(int[],int[])... ", "submatrix not successfully retreived"); } } catch (java.lang.ArrayIndexOutOfBoundsException e) { errorCount = try_failure(errorCount, "getMatrix(int[],int[])... ", "Unexpected ArrayIndexOutOfBoundsException"); } try { B.set(B.getRowDimension(), B.getColumnDimension() - 1, 0.); errorCount = try_failure(errorCount, "set(int,int,double)... ", "OutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { B.set(B.getRowDimension() - 1, B.getColumnDimension(), 0.); errorCount = try_failure(errorCount, "set(int,int,double)... ", "OutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("set(int,int,double)... OutofBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "set(int,int,double)... ", "OutOfBoundsException expected but not thrown"); } try { B.set(ib, jb, 0.); tmp = B.get(ib, jb); try { check(tmp, 0.); try_success("set(int,int,double)... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "set(int,int,double)... ", "Matrix element not successfully set"); } } catch (java.lang.ArrayIndexOutOfBoundsException e1) { errorCount = try_failure(errorCount, "set(int,int,double)... ", "Unexpected ArrayIndexOutOfBoundsException"); } M = new Matrix(2, 3, 0.); try { B.setMatrix(ib, ie + B.getRowDimension() + 1, jb, je, M); errorCount = try_failure(errorCount, "setMatrix(int,int,int,int,Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { B.setMatrix(ib, ie, jb, je + B.getColumnDimension() + 1, M); errorCount = try_failure(errorCount, "setMatrix(int,int,int,int,Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("setMatrix(int,int,int,int,Matrix)... ArrayIndexOutOfBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "setMatrix(int,int,int,int,Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } try { B.setMatrix(ib, ie, jb, je, M); try { check(M.minus(B.getMatrix(ib, ie, jb, je)), M); try_success("setMatrix(int,int,int,int,Matrix)... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "setMatrix(int,int,int,int,Matrix)... ", "submatrix not successfully set"); } B.setMatrix(ib, ie, jb, je, SUB); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { errorCount = try_failure(errorCount, "setMatrix(int,int,int,int,Matrix)... ", "Unexpected ArrayIndexOutOfBoundsException"); } try { B.setMatrix(ib, ie + B.getRowDimension() + 1, columnindexset, M); errorCount = try_failure(errorCount, "setMatrix(int,int,int[],Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { B.setMatrix(ib, ie, badcolumnindexset, M); errorCount = try_failure(errorCount, "setMatrix(int,int,int[],Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("setMatrix(int,int,int[],Matrix)... ArrayIndexOutOfBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "setMatrix(int,int,int[],Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } try { B.setMatrix(ib, ie, columnindexset, M); try { check(M.minus(B.getMatrix(ib, ie, columnindexset)), M); try_success("setMatrix(int,int,int[],Matrix)... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "setMatrix(int,int,int[],Matrix)... ", "submatrix not successfully set"); } B.setMatrix(ib, ie, jb, je, SUB); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { errorCount = try_failure(errorCount, "setMatrix(int,int,int[],Matrix)... ", "Unexpected ArrayIndexOutOfBoundsException"); } try { B.setMatrix(rowindexset, jb, je + B.getColumnDimension() + 1, M); errorCount = try_failure(errorCount, "setMatrix(int[],int,int,Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { B.setMatrix(badrowindexset, jb, je, M); errorCount = try_failure(errorCount, "setMatrix(int[],int,int,Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("setMatrix(int[],int,int,Matrix)... ArrayIndexOutOfBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "setMatrix(int[],int,int,Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } try { B.setMatrix(rowindexset, jb, je, M); try { check(M.minus(B.getMatrix(rowindexset, jb, je)), M); try_success("setMatrix(int[],int,int,Matrix)... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "setMatrix(int[],int,int,Matrix)... ", "submatrix not successfully set"); } B.setMatrix(ib, ie, jb, je, SUB); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { errorCount = try_failure(errorCount, "setMatrix(int[],int,int,Matrix)... ", "Unexpected ArrayIndexOutOfBoundsException"); } try { B.setMatrix(rowindexset, badcolumnindexset, M); errorCount = try_failure(errorCount, "setMatrix(int[],int[],Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { B.setMatrix(badrowindexset, columnindexset, M); errorCount = try_failure(errorCount, "setMatrix(int[],int[],Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("setMatrix(int[],int[],Matrix)... ArrayIndexOutOfBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "setMatrix(int[],int[],Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } try { B.setMatrix(rowindexset, columnindexset, M); try { check(M.minus(B.getMatrix(rowindexset, columnindexset)), M); try_success("setMatrix(int[],int[],Matrix)... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "setMatrix(int[],int[],Matrix)... ", "submatrix not successfully set"); } } catch (java.lang.ArrayIndexOutOfBoundsException e1) { errorCount = try_failure(errorCount, "setMatrix(int[],int[],Matrix)... ", "Unexpected ArrayIndexOutOfBoundsException"); } print("\nTesting array-like methods...\n"); S = new Matrix(columnwise, nonconformld); R = Matrix.random(A.getRowDimension(), A.getColumnDimension()); A = R; try { S = A.minus(S); errorCount = try_failure(errorCount, "minus conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("minus conformance check... ", ""); } if (A.minus(R).norm1() != 0.) { errorCount = try_failure(errorCount, "minus... ", "(difference of identical Matrices is nonzero,\nSubsequent use of minus should be suspect)"); } else { try_success("minus... ", ""); } A = R.copy(); A.minusEquals(R); Z = new Matrix(A.getRowDimension(), A.getColumnDimension()); try { A.minusEquals(S); errorCount = try_failure(errorCount, "minusEquals conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("minusEquals conformance check... ", ""); } if (A.minus(Z).norm1() != 0.) { errorCount = try_failure(errorCount, "minusEquals... ", "(difference of identical Matrices is nonzero,\nSubsequent use of minus should be suspect)"); } else { try_success("minusEquals... ", ""); } A = R.copy(); B = Matrix.random(A.getRowDimension(), A.getColumnDimension()); C = A.minus(B); try { S = A.plus(S); errorCount = try_failure(errorCount, "plus conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("plus conformance check... ", ""); } try { check(C.plus(B), A); try_success("plus... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "plus... ", "(C = A - B, but C + B != A)"); } C = A.minus(B); C.plusEquals(B); try { A.plusEquals(S); errorCount = try_failure(errorCount, "plusEquals conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("plusEquals conformance check... ", ""); } try { check(C, A); try_success("plusEquals... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "plusEquals... ", "(C = A - B, but C = C + B != A)"); } A = R.uminus(); try { check(A.plus(R), Z); try_success("uminus... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "uminus... ", "(-A + A != zeros)"); } A = R.copy(); O = new Matrix(A.getRowDimension(), A.getColumnDimension(), 1.0); C = A.arrayLeftDivide(R); try { S = A.arrayLeftDivide(S); errorCount = try_failure(errorCount, "arrayLeftDivide conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("arrayLeftDivide conformance check... ", ""); } try { check(C, O); try_success("arrayLeftDivide... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "arrayLeftDivide... ", "(M.\\M != ones)"); } try { A.arrayLeftDivideEquals(S); errorCount = try_failure(errorCount, "arrayLeftDivideEquals conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("arrayLeftDivideEquals conformance check... ", ""); } A.arrayLeftDivideEquals(R); try { check(A, O); try_success("arrayLeftDivideEquals... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "arrayLeftDivideEquals... ", "(M.\\M != ones)"); } A = R.copy(); try { A.arrayRightDivide(S); errorCount = try_failure(errorCount, "arrayRightDivide conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("arrayRightDivide conformance check... ", ""); } C = A.arrayRightDivide(R); try { check(C, O); try_success("arrayRightDivide... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "arrayRightDivide... ", "(M./M != ones)"); } try { A.arrayRightDivideEquals(S); errorCount = try_failure(errorCount, "arrayRightDivideEquals conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("arrayRightDivideEquals conformance check... ", ""); } A.arrayRightDivideEquals(R); try { check(A, O); try_success("arrayRightDivideEquals... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "arrayRightDivideEquals... ", "(M./M != ones)"); } A = R.copy(); B = Matrix.random(A.getRowDimension(), A.getColumnDimension()); try { S = A.arrayTimes(S); errorCount = try_failure(errorCount, "arrayTimes conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("arrayTimes conformance check... ", ""); } C = A.arrayTimes(B); try { check(C.arrayRightDivideEquals(B), A); try_success("arrayTimes... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "arrayTimes... ", "(A = R, C = A.*B, but C./B != A)"); } try { A.arrayTimesEquals(S); errorCount = try_failure(errorCount, "arrayTimesEquals conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("arrayTimesEquals conformance check... ", ""); } A.arrayTimesEquals(B); try { check(A.arrayRightDivideEquals(B), R); try_success("arrayTimesEquals... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "arrayTimesEquals... ", "(A = R, A = A.*B, but A./B != R)"); } print("\nTesting I/O methods...\n"); try { DecimalFormat fmt = new DecimalFormat("0.0000E00"); fmt.setDecimalFormatSymbols(new DecimalFormatSymbols(Locale.US)); PrintWriter FILE = new PrintWriter(new FileOutputStream("JamaTestMatrix.out")); A.print(FILE, fmt, 10); FILE.close(); R = Matrix.read(new BufferedReader(new FileReader("JamaTestMatrix.out"))); if (A.minus(R).norm1() < .001) { try_success("print()/read()...", ""); } else { errorCount = try_failure(errorCount, "print()/read()...", "Matrix read from file does not match Matrix printed to file"); } } catch (java.io.IOException ioe) { warningCount = try_warning(warningCount, "print()/read()...", "unexpected I/O error, unable to run print/read test; check write permission in current directory and retry"); } catch (Exception e) { try { e.printStackTrace(System.out); warningCount = try_warning(warningCount, "print()/read()...", "Formatting error... will try JDK1.1 reformulation..."); DecimalFormat fmt = new DecimalFormat("0.0000"); PrintWriter FILE = new PrintWriter(new FileOutputStream("JamaTestMatrix.out")); A.print(FILE, fmt, 10); FILE.close(); R = Matrix.read(new BufferedReader(new FileReader("JamaTestMatrix.out"))); if (A.minus(R).norm1() < .001) { try_success("print()/read()...", ""); } else { errorCount = try_failure(errorCount, "print()/read() (2nd attempt) ...", "Matrix read from file does not match Matrix printed to file"); } } catch (java.io.IOException ioe) { warningCount = try_warning(warningCount, "print()/read()...", "unexpected I/O error, unable to run print/read test; check write permission in current directory and retry"); } } R = Matrix.random(A.getRowDimension(), A.getColumnDimension()); String tmpname = "TMPMATRIX.serial"; try { ObjectOutputStream out = new ObjectOutputStream(new FileOutputStream(tmpname)); out.writeObject(R); ObjectInputStream sin = new ObjectInputStream(new FileInputStream(tmpname)); A = (Matrix) sin.readObject(); try { check(A, R); try_success("writeObject(Matrix)/readObject(Matrix)...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "writeObject(Matrix)/readObject(Matrix)...", "Matrix not serialized correctly"); } } catch (java.io.IOException ioe) { warningCount = try_warning(warningCount, "writeObject()/readObject()...", "unexpected I/O error, unable to run serialization test; check write permission in current directory and retry"); } catch (Exception e) { errorCount = try_failure(errorCount, "writeObject(Matrix)/readObject(Matrix)...", "unexpected error in serialization test"); } print("\nTesting linear algebra methods...\n"); A = new Matrix(columnwise, 3); T = new Matrix(tvals); T = A.transpose(); try { check(A.transpose(), T); try_success("transpose...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "transpose()...", "transpose unsuccessful"); } A.transpose(); try { check(A.norm1(), columnsummax); try_success("norm1...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "norm1()...", "incorrect norm calculation"); } try { check(A.normInf(), rowsummax); try_success("normInf()...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "normInf()...", "incorrect norm calculation"); } try { check(A.normF(), Math.sqrt(sumofsquares)); try_success("normF...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "normF()...", "incorrect norm calculation"); } try { check(A.trace(), sumofdiagonals); try_success("trace()...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "trace()...", "incorrect trace calculation"); } try { check(A.getMatrix(0, A.getRowDimension() - 1, 0, A.getRowDimension() - 1).det(), 0.); try_success("det()...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "det()...", "incorrect determinant calculation"); } SQ = new Matrix(square); try { check(A.times(A.transpose()), SQ); try_success("times(Matrix)...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "times(Matrix)...", "incorrect Matrix-Matrix product calculation"); } try { check(A.times(0.), Z); try_success("times(double)...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "times(double)...", "incorrect Matrix-scalar product calculation"); } A = new Matrix(columnwise, 4); QRDecomposition QR = A.qr(); R = QR.getR(); try { check(A, QR.getQ().times(R)); try_success("QRDecomposition...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "QRDecomposition...", "incorrect QR decomposition calculation"); } SingularValueDecomposition SVD = A.svd(); try { check(A, SVD.getU().times(SVD.getS().times(SVD.getV().transpose()))); try_success("SingularValueDecomposition...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "SingularValueDecomposition...", "incorrect singular value decomposition calculation"); } DEF = new Matrix(rankdef); try { check(DEF.rank(), Math.min(DEF.getRowDimension(), DEF.getColumnDimension()) - 1); try_success("rank()...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "rank()...", "incorrect rank calculation"); } B = new Matrix(condmat); SVD = B.svd(); double[] singularvalues = SVD.getSingularValues(); try { check(B.cond(), singularvalues[0] / singularvalues[Math.min(B.getRowDimension(), B.getColumnDimension()) - 1]); try_success("cond()...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "cond()...", "incorrect condition number calculation"); } int n = A.getColumnDimension(); A = A.getMatrix(0, n - 1, 0, n - 1); A.set(0, 0, 0.); LUDecomposition LU = A.lu(); try { check(A.getMatrix(LU.getPivot(), 0, n - 1), LU.getL().times(LU.getU())); try_success("LUDecomposition...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "LUDecomposition...", "incorrect LU decomposition calculation"); } X = A.inverse(); try { check(A.times(X), Matrix.identity(3, 3)); try_success("inverse()...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "inverse()...", "incorrect inverse calculation"); } O = new Matrix(SUB.getRowDimension(), 1, 1.0); SOL = new Matrix(sqSolution); SQ = SUB.getMatrix(0, SUB.getRowDimension() - 1, 0, SUB.getRowDimension() - 1); try { check(SQ.solve(SOL), O); try_success("solve()...", ""); } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "solve()...", e1.getMessage()); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "solve()...", e.getMessage()); } A = new Matrix(pvals); CholeskyDecomposition Chol = A.chol(); Matrix L = Chol.getL(); try { check(A, L.times(L.transpose())); try_success("CholeskyDecomposition...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "CholeskyDecomposition...", "incorrect Cholesky decomposition calculation"); } X = Chol.solve(Matrix.identity(3, 3)); try { check(A.times(X), Matrix.identity(3, 3)); try_success("CholeskyDecomposition solve()...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "CholeskyDecomposition solve()...", "incorrect Choleskydecomposition solve calculation"); } EigenvalueDecomposition Eig = A.eig(); Matrix D = Eig.getD(); Matrix V = Eig.getV(); try { check(A.times(V), V.times(D)); try_success("EigenvalueDecomposition (symmetric)...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "EigenvalueDecomposition (symmetric)...", "incorrect symmetric Eigenvalue decomposition calculation"); } A = new Matrix(evals); Eig = A.eig(); D = Eig.getD(); V = Eig.getV(); try { check(A.times(V), V.times(D)); try_success("EigenvalueDecomposition (nonsymmetric)...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "EigenvalueDecomposition (nonsymmetric)...", "incorrect nonsymmetric Eigenvalue decomposition calculation"); } print("\nTestMatrix completed.\n"); print("Total errors reported: " + Integer.toString(errorCount) + "\n"); print("Total warnings reported: " + Integer.toString(warningCount) + "\n"); }

private static void prepare() { System.err.println("PREPARING-----------------------------------------"); deleteHome(); InputStream configStream = null; FileOutputStream tempStream = null; try { configStream = AllTests.class.getClassLoader().getResourceAsStream("net/sf/archimede/test/resources/repository.xml"); new File("temp").mkdir(); tempStream = new FileOutputStream(new File("temp/repository.xml")); IOUtils.copy(configStream, tempStream); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } finally { try { if (configStream != null) { configStream.close(); } } catch (IOException e) { e.printStackTrace(); } finally { if (tempStream != null) { try { tempStream.close(); } catch (IOException e) { e.printStackTrace(); } } } } String repositoryName = "jackrabbit.repository"; Properties jndiProperties = new Properties(); jndiProperties.put("java.naming.provider.url", "http://sf.net/projects/archimede#1"); jndiProperties.put("java.naming.factory.initial", "org.apache.jackrabbit.core.jndi.provider.DummyInitialContextFactory"); startupUtil = new StartupJcrUtil(REPOSITORY_HOME, "temp/repository.xml", repositoryName, jndiProperties); startupUtil.init(); }

public void test3() throws FileNotFoundException, IOException { Decoder decoder1 = new MP3Decoder(new FileInputStream("/home/marc/tmp/test1.mp3")); Decoder decoder2 = new OggDecoder(new FileInputStream("/home/marc/tmp/test1.ogg")); FileOutputStream out = new FileOutputStream("/home/marc/tmp/test.pipe"); IOUtils.copy(decoder1, out); IOUtils.copy(decoder2, out); }

@Override public void updateItems(List<InputQueueItem> toUpdate) throws DatabaseException { if (toUpdate == null) throw new NullPointerException("toUpdate"); try { getConnection().setAutoCommit(false); } catch (SQLException e) { LOGGER.warn("Unable to set autocommit off", e); } try { PreparedStatement deleteSt = getConnection().prepareStatement(DELETE_ALL_ITEMS_STATEMENT); PreparedStatement selectCount = getConnection().prepareStatement(SELECT_NUMBER_ITEMS_STATEMENT); ResultSet rs = selectCount.executeQuery(); rs.next(); int totalBefore = rs.getInt(1); int deleted = deleteSt.executeUpdate(); int updated = 0; for (InputQueueItem item : toUpdate) { updated += getItemInsertStatement(item).executeUpdate(); } if (totalBefore == deleted && updated == toUpdate.size()) { getConnection().commit(); LOGGER.debug("DB has been updated. Queries: \"" + selectCount + "\" and \"" + deleteSt + "\"."); } else { getConnection().rollback(); LOGGER.error("DB has not been updated -> rollback! Queries: \"" + selectCount + "\" and \"" + deleteSt + "\"."); } } catch (SQLException e) { LOGGER.error(e); } finally { closeConnection(); } }

void copyFile(File src, File dst) throws IOException { InputStream in = new FileInputStream(src); OutputStream out = new FileOutputStream(dst); byte[] buf = new byte[1024]; int len; while ((len = in.read(buf)) > 0) out.write(buf, 0, len); in.close(); out.close(); }

public byte[] read(IFile input) { InputStream contents = null; try { ByteArrayOutputStream baos = new ByteArrayOutputStream(); contents = input.getContents(); IOUtils.copy(contents, baos); return baos.toByteArray(); } catch (IOException e) { Activator.logUnexpected(null, e); } catch (CoreException e) { Activator.logUnexpected(null, e); } finally { IOUtils.closeQuietly(contents); } return null; }

@Test public void testCopy_readerToOutputStream_nullOut() throws Exception { InputStream in = new ByteArrayInputStream(inData); in = new YellOnCloseInputStreamTest(in); Reader reader = new InputStreamReader(in, "US-ASCII"); try { IOUtils.copy(reader, (OutputStream) null); fail(); } catch (NullPointerException ex) { } }

public static void copyFile(File in, File out) throws IOException { 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(); } }

public int procesar() { int mas = 0; String uriOntologia = "", source = "", uri = ""; String fichOrigenHTML = "", fichOrigenLN = ""; String ficheroOutOWL = ""; md5 firma = null; StringTokenV2 entra = null, entra2 = null, entra3 = null; FileInputStream lengNat = null; BufferedInputStream lengNat2 = null; DataInputStream entradaLenguajeNatural = null; FileWriter salOWL = null; BufferedWriter salOWL2 = null; PrintWriter salidaOWL = null; String sujeto = "", verbo = "", CD = "", CI = "", fraseOrigen = ""; StringTokenV2 token2; boolean bandera = false; OntClass c = null; OntClass cBak = null; String claseTrabajo = ""; String nombreClase = "", nombrePropiedad = "", variasPalabras = ""; int incre = 0, emergencia = 0; String lineaSalida = ""; String[] ontologia = new String[5]; ontologia[0] = "http://www.criado.info/owl/vertebrados_es.owl#"; ontologia[1] = "http://www.w3.org/2001/sw/WebOnt/guide-src/wine#"; ontologia[2] = "http://www.co-ode.org/ontologies/pizza/2005/10/18/pizza.owl#"; ontologia[3] = "http://www.w3.org/2001/sw/WebOnt/guide-src/food#"; ontologia[4] = "http://www.daml.org/2001/01/gedcom/gedcom#"; String[] ontologiaSource = new String[5]; ontologiaSource[0] = this.directorioMapeo + "\\" + "mapeo_vertebrados_es.xml"; ontologiaSource[1] = this.directorioMapeo + "\\" + "mapeo_wine_es.xml"; ontologiaSource[2] = this.directorioMapeo + "\\" + "mapeo_pizza_es.xml"; ontologiaSource[3] = this.directorioMapeo + "\\" + "mapeo_food_es.xml"; ontologiaSource[4] = this.directorioMapeo + "\\" + "mapeo_parentesco_es.xml"; mapeoIdiomas clasesOntologias; try { if ((entrada = entradaFichero.readLine()) != null) { if (entrada.trim().length() > 10) { entrada2 = new StringTokenV2(entrada.trim(), "\""); if (entrada2.isIncluidaSubcadena("<fichero ontologia=")) { ontologiaOrigen = entrada2.getToken(2); fichOrigenHTML = entrada2.getToken(4); fichOrigenLN = entrada2.getToken(6); if (ontologiaOrigen.equals("VERTEBRADOS")) { source = ontologiaSource[0]; uriOntologia = ontologia[0]; } if (ontologiaOrigen.equals("WINE")) { source = ontologiaSource[1]; uriOntologia = ontologia[1]; } if (ontologiaOrigen.equals("PIZZA")) { source = ontologiaSource[2]; uriOntologia = ontologia[2]; } if (ontologiaOrigen.equals("FOOD")) { source = ontologiaSource[3]; uriOntologia = ontologia[3]; } if (ontologiaOrigen.equals("PARENTESCOS")) { source = ontologiaSource[4]; uriOntologia = ontologia[4]; } firma = new md5(uriOntologia, false); clasesOntologias = new mapeoIdiomas(source); uri = ""; ficheroOutOWL = ""; entra2 = new StringTokenV2(fichOrigenHTML, "\\"); int numToken = entra2.getNumeroTokenTotales(); entra = new StringTokenV2(fichOrigenHTML, " "); if (entra.isIncluidaSubcadena(directorioLocal)) { entra = new StringTokenV2(entra.getQuitar(directorioLocal) + "", " "); uri = entra.getCambiar("\\", "/"); uri = entra.getQuitar(entra2.getToken(numToken)) + ""; entra3 = new StringTokenV2(entra2.getToken(numToken), "."); ficheroOutOWL = entra3.getToken(1) + "_" + firma.toString() + ".owl"; uri = urlPatron + uri + ficheroOutOWL; } entra3 = new StringTokenV2(fichOrigenHTML, "."); ficheroOutOWL = entra3.getToken(1) + "_" + firma.toString() + ".owl"; lineaSalida = "<vistasemantica origen=\"" + fichOrigenLN + "\" destino=\"" + uri + "\" />"; lengNat = new FileInputStream(fichOrigenLN); lengNat2 = new BufferedInputStream(lengNat); entradaLenguajeNatural = new DataInputStream(lengNat2); salOWL = new FileWriter(ficheroOutOWL); salOWL2 = new BufferedWriter(salOWL); salidaOWL = new PrintWriter(salOWL2); while ((entradaInstancias = entradaLenguajeNatural.readLine()) != null) { sujeto = ""; verbo = ""; CD = ""; CI = ""; fraseOrigen = ""; if (entradaInstancias.trim().length() > 10) { entrada2 = new StringTokenV2(entradaInstancias.trim(), "\""); if (entrada2.isIncluidaSubcadena("<oracion sujeto=")) { sujeto = entrada2.getToken(2).trim(); verbo = entrada2.getToken(4).trim(); CD = entrada2.getToken(6).trim(); CI = entrada2.getToken(8).trim(); fraseOrigen = entrada2.getToken(10).trim(); if (sujeto.length() > 0 & verbo.length() > 0 & CD.length() > 0) { bandera = false; c = null; cBak = null; nombreClase = clasesOntologias.getClaseInstancia(CD); if (nombreClase.length() > 0) { bandera = true; } if (bandera) { if (incre == 0) { salidaOWL.write(" <rdf:RDF " + "\n"); salidaOWL.write(" xmlns:j.0=\"" + uriOntologia + "\"" + "\n"); salidaOWL.write(" xmlns:protege=\"http://protege.stanford.edu/plugins/owl/protege#\"" + "\n"); salidaOWL.write(" xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\"" + "\n"); salidaOWL.write(" xmlns:xsd=\"http://www.w3.org/2001/XMLSchema#\"" + "\n"); salidaOWL.write(" xmlns:rdfs=\"http://www.w3.org/2000/01/rdf-schema#\"" + "\n"); salidaOWL.write(" xmlns:owl=\"http://www.w3.org/2002/07/owl#\" " + "\n"); salidaOWL.write(" xmlns=\"" + uri + "#\"" + "\n"); salidaOWL.write(" xml:base=\"" + uri + "\">" + "\n"); salidaOWL.write(" <owl:Ontology rdf:about=\"\">" + "\n"); salidaOWL.write(" <owl:imports rdf:resource=\"" + uriOntologia + "\"/>" + "\n"); salidaOWL.write(" </owl:Ontology>" + "\n"); salidaOWL.flush(); salida.write(lineaSalida + "\n"); salida.flush(); incre = 1; } salidaOWL.write(" <j.0:" + nombreClase + " rdf:ID=\"" + sujeto.toUpperCase() + "\"/>" + "\n"); salidaOWL.write(" <owl:AllDifferent>" + "\n"); salidaOWL.write(" <owl:distinctMembers rdf:parseType=\"Collection\">" + "\n"); salidaOWL.write(" <" + nombreClase + " rdf:about=\"#" + sujeto.toUpperCase() + "\"/>" + "\n"); salidaOWL.write(" </owl:distinctMembers>" + "\n"); salidaOWL.write(" </owl:AllDifferent>" + "\n"); salidaOWL.flush(); bandera = false; } } } } } salidaOWL.write(" </rdf:RDF>" + "\n" + "\n"); salidaOWL.write("<!-- Creado por [html2ws] http://www.luis.criado.org -->" + "\n"); salidaOWL.flush(); } } mas = 1; } else { salida.write("</listaVistasSemanticas>\n"); salida.flush(); salida.close(); bw2.close(); fw2.close(); salidaOWL.close(); entradaFichero.close(); ent2.close(); ent1.close(); mas = -1; } } catch (Exception e) { mas = -2; salida.write("No se encuentra: " + fichOrigen + "\n"); salida.flush(); } return mas; }

public ResourceMigratorBuilder createResourceMigratorBuilder(NotificationReporter reporter) { return new ResourceMigratorBuilder() { public ResourceMigrator getCompletedResourceMigrator() { return new ResourceMigrator() { public void migrate(InputMetadata meta, InputStream inputStream, OutputCreator outputCreator) throws IOException, ResourceMigrationException { OutputStream outputStream = outputCreator.createOutputStream(); IOUtils.copy(inputStream, outputStream); } }; } public void setTarget(Version version) { } public void startType(String typeName) { } public void setRegexpPathRecogniser(String re) { } public void setCustomPathRecogniser(PathRecogniser pathRecogniser) { } public void addRegexpContentRecogniser(Version version, String re) { } public void addCustomContentRecogniser(Version version, ContentRecogniser contentRecogniser) { } public XSLStreamMigratorBuilder createXSLStreamMigratorBuilder() { return null; } public void addStep(Version inputVersion, Version outputVersion, StreamMigrator streamMigrator) { } public void endType() { } }; }

private static File[] getWsdls(File dirfile) throws Exception { File[] allfiles = dirfile.listFiles(); List<File> files = new ArrayList<File>(); if (allfiles != null) { MessageDigest md = MessageDigest.getInstance("MD5"); String outputDir = argMap.get(OUTPUT_DIR); for (File file : allfiles) { if (file.getName().endsWith(WSDL_SUFFIX)) { files.add(file); } if (file.getName().endsWith(WSDL_SUFFIX) || file.getName().endsWith(XSD_SUFFIX)) { md.update(FileUtil.getBytes(file)); } } computedHash = md.digest(); hashFile = new File(outputDir + File.separator + argMap.get(BASE_PACKAGE).replace('.', File.separatorChar) + File.separator + "hash.md5"); if (hashFile.exists()) { byte[] readHash = FileUtil.getBytes(hashFile); if (Arrays.equals(readHash, computedHash)) { System.out.println("Skipping generation, files not changed."); files.clear(); } } } File[] filesarr = new File[files.size()]; files.toArray(filesarr); return filesarr; }

public static String encrypt(String text) { char[] toEncrypt = text.toCharArray(); StringBuffer hexString = new StringBuffer(); try { MessageDigest dig = MessageDigest.getInstance("MD5"); dig.reset(); String pw = ""; for (int i = 0; i < toEncrypt.length; i++) { pw += toEncrypt[i]; } dig.update(pw.getBytes()); byte[] digest = dig.digest(); int digestLength = digest.length; for (int i = 0; i < digestLength; i++) { hexString.append(hexDigit(digest[i])); } } catch (java.security.NoSuchAlgorithmException ae) { ae.printStackTrace(); } return hexString.toString(); }

public static void refreshSession(int C_ID) { Connection con = null; try { con = getConnection(); PreparedStatement updateLogin = con.prepareStatement("UPDATE customer SET c_login = NOW(), c_expiration = DATE_ADD(NOW(), INTERVAL 2 HOUR) WHERE c_id = ?"); updateLogin.setInt(1, C_ID); updateLogin.executeUpdate(); con.commit(); updateLogin.close(); returnConnection(con); } catch (java.lang.Exception ex) { try { con.rollback(); ex.printStackTrace(); } catch (Exception se) { System.err.println("Transaction rollback failed."); } } }

private synchronized Map load() { if (!mustReloadConfigurationFiles()) { return groups; } SAXParser saxParser = null; JSODefaultHandler saxHandler = new JSODefaultHandler(); try { final Collection resourcesByOrigin = getConfigResources(); final LinkedList resourcesList = new LinkedList(); Iterator iOrigin = resourcesByOrigin.iterator(); while (iOrigin.hasNext()) { Resource resource = (Resource) iOrigin.next(); String origin = resource.getSource(); if (origin.startsWith(LOCAL_CLASSPATH) || JarRestrictionManager.getInstance().isJarAllowed(origin)) { LOG.debug("Adding " + CONFIGURATION_FILE_NAME + " from " + origin + "."); resourcesList.addFirst(resource.getUrl()); } else { LOG.debug("Jar " + origin + " refused. See jso.allowedJar property in jso.properties file."); } } URL external = getExternalResource(); if (external != null) { resourcesList.addFirst(external); } saxParser = SAXParserFactory.newInstance().newSAXParser(); Iterator ite = resourcesList.iterator(); while (ite.hasNext()) { final URL url = (URL) ite.next(); LOG.debug("Parsing of file " + url.toString() + "."); InputStream input = null; try { input = url.openStream(); saxParser.parse(input, saxHandler); } catch (SAXException e) { LOG.error("Parsing of file " + url.toString() + " failed! Parsing still continues.", e); } catch (IOException e) { LOG.error("Reading of file " + url.toString() + " failed! Parsing still continues.", e); } finally { if (input != null) { try { input.close(); } catch (IOException e) { LOG.error("Closing inputstream of file " + url.toString() + " failed! Parsing still continues.", e); } } } } } catch (SAXException e) { throw new RuntimeException(e); } catch (IOException e) { throw new RuntimeException(e); } catch (ParserConfigurationException e) { throw new RuntimeException(e); } this.defaultLocation = (String) saxHandler.getDefaultValues().get("location"); this.defaultTimestampPolicy = (String) saxHandler.getDefaultValues().get("timeStampPolicy"); if (this.defaultTimestampPolicy == null) this.defaultTimestampPolicy = Group.TIMESTAMP_LOCAL; this.groups = saxHandler.getListGroups(); return this.groups; }

public static String hash(String text) { try { MessageDigest md = MessageDigest.getInstance("SHA-256"); md.update(text.getBytes()); byte[] digest = md.digest(); StringBuffer sb = new StringBuffer(digest.length * 2); for (int i = 0; i < digest.length; ++i) { byte b = digest[i]; int high = (b & 0xF0) >> 4; int low = b & 0xF; sb.append(DECIMAL_HEX[high]); sb.append(DECIMAL_HEX[low]); } return sb.toString(); } catch (NoSuchAlgorithmException e) { throw new NonBusinessException("Error hashing string", e); } }

private static boolean unzipWithWarning(File source, File targetDirectory, OverwriteValue policy) { try { if (!source.exists()) return false; ZipInputStream input = new ZipInputStream(new FileInputStream(source)); ZipEntry zipEntry = null; byte[] buffer = new byte[1024]; while ((zipEntry = input.getNextEntry()) != null) { if (zipEntry.isDirectory()) continue; File newFile = new File(targetDirectory, zipEntry.getName()); if (newFile.exists()) { switch(policy.value) { case NO_TO_ALL: continue; case YES_TO_ALL: break; default: switch(policy.value = confirmOverwrite(zipEntry.getName())) { case NO_TO_ALL: case NO: continue; default: } } } newFile.getParentFile().mkdirs(); int bytesRead; FileOutputStream output = new FileOutputStream(newFile); while ((bytesRead = input.read(buffer)) != -1) output.write(buffer, 0, bytesRead); output.close(); input.closeEntry(); } input.close(); } catch (Exception exc) { exc.printStackTrace(); return false; } return true; }

public String getResourceAsString(String name) throws IOException { String content = null; InputStream stream = aClass.getResourceAsStream(name); if (stream != null) { ByteArrayOutputStream buffer = new ByteArrayOutputStream(); IOUtils.copyAndClose(stream, buffer); content = buffer.toString(); } else { Assert.fail("Resource not available: " + name); } return content; }

public static String crypt(String senha) { String md5 = null; MessageDigest md; try { md = MessageDigest.getInstance(CRYPT_ALGORITHM); md.update(senha.getBytes()); Hex hex = new Hex(); md5 = new String(hex.encode(md.digest())); } catch (NoSuchAlgorithmException e) { logger.error(ResourceUtil.getLOGMessage("_nls.mensagem.geral.log.crypt.no.such.algorithm", CRYPT_ALGORITHM)); } return md5; }

public boolean GetExternalLanguage() { String thisURL, newURL, TheLine; boolean ReadOK = true; int SlashPos = -1; thisURL = getDocumentBase().toString(); SlashPos = thisURL.lastIndexOf("/"); newURL = thisURL.substring(0, (SlashPos + 1)) + "language.txt"; try { URL url = new URL(newURL); try { InputStream TheFile = url.openStream(); try { DataInputStream MyData = new DataInputStream(TheFile); try { while ((TheLine = MyData.readLine()) != null) { if (TheLine.substring(0, 1).compareTo("*") == 0) { if (!ExternalLanguageVariable(TheLine)) { ReadOK = false; break; } } } } catch (Exception e) { System.out.println("Error " + e.toString()); ReadOK = false; } } catch (Exception e) { System.out.println("Error " + e.toString()); ReadOK = false; } } catch (Exception f) { System.out.println("Error " + f.toString()); ReadOK = false; } } catch (Exception g) { System.out.println("Error " + g.toString()); ReadOK = false; } return ReadOK; }

public void run() { iStream = null; try { tryProxy = false; URLConnection connection = url.openConnection(); if (connection instanceof HttpURLConnection) { HttpURLConnection htc = (HttpURLConnection) connection; contentLength = htc.getContentLength(); } InputStream i = connection.getInputStream(); iStream = new LoggedInputStream(i, wa); } catch (ConnectException x) { tryProxy = true; exception = x; } catch (Exception x) { exception = x; } finally { if (dialog != null) { Thread.yield(); dialog.setVisible(false); } } }

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; }

private void createWar() throws IOException, XMLStreamException { String appName = this.fileout.getName(); int i = appName.indexOf("."); if (i != -1) appName = appName.substring(0, i); ZipOutputStream zout = new ZipOutputStream(new FileOutputStream(this.fileout)); { ZipEntry entry = new ZipEntry("WEB-INF/web.xml"); zout.putNextEntry(entry); XMLOutputFactory factory = XMLOutputFactory.newInstance(); XMLStreamWriter w = factory.createXMLStreamWriter(zout, "ASCII"); w.writeStartDocument("ASCII", "1.0"); w.writeStartElement("web-app"); w.writeAttribute("xsi", XSI, "schemaLocation", "http://java.sun.com/xml/ns/javaee http://java.sun.com/xml /ns/javaee/web-app_2_5.xsd"); w.writeAttribute("version", "2.5"); w.writeAttribute("xmlns", J2EE); w.writeAttribute("xmlns:xsi", XSI); w.writeStartElement("description"); w.writeCharacters("Site maintenance for " + appName); w.writeEndElement(); w.writeStartElement("display-name"); w.writeCharacters(appName); w.writeEndElement(); w.writeStartElement("servlet"); w.writeStartElement("servlet-name"); w.writeCharacters("down"); w.writeEndElement(); w.writeStartElement("jsp-file"); w.writeCharacters("/WEB-INF/jsp/down.jsp"); w.writeEndElement(); w.writeEndElement(); w.writeStartElement("servlet-mapping"); w.writeStartElement("servlet-name"); w.writeCharacters("down"); w.writeEndElement(); w.writeStartElement("url-pattern"); w.writeCharacters("/*"); w.writeEndElement(); w.writeEndElement(); w.writeEndElement(); w.writeEndDocument(); w.flush(); zout.closeEntry(); } { ZipEntry entry = new ZipEntry("WEB-INF/jsp/down.jsp"); zout.putNextEntry(entry); PrintWriter w = new PrintWriter(zout); if (this.messageFile != null) { IOUtils.copyTo(new FileReader(this.messageFile), w); } else if (this.messageString != null) { w.print("<html><body>" + this.messageString + "</body></html>"); } else { w.print("<html><body><div style='text-align:center;font-size:500%;'>Oh No !<br/><b>" + appName + "</b><br/>is down for maintenance!</div></body></html>"); } w.flush(); zout.closeEntry(); } zout.finish(); zout.flush(); zout.close(); }

private String sendMessage(HttpURLConnection connection, String reqMessage) throws IOException { if (msgLog.isTraceEnabled()) msgLog.trace("Outgoing SOAPMessage\n" + reqMessage); BufferedOutputStream out = new BufferedOutputStream(connection.getOutputStream()); out.write(reqMessage.getBytes("UTF-8")); out.close(); InputStream inputStream = null; if (connection.getResponseCode() < 400) inputStream = connection.getInputStream(); else inputStream = connection.getErrorStream(); ByteArrayOutputStream baos = new ByteArrayOutputStream(1024); IOUtils.copyStream(baos, inputStream); inputStream.close(); String response = new String(baos.toByteArray(), "UTF-8"); if (msgLog.isTraceEnabled()) msgLog.trace("Incoming Response SOAPMessage\n" + response); return response; }

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 static void copyFile(File src, String srcEncoding, File dest, String destEncoding) throws IOException { InputStreamReader in = new InputStreamReader(new FileInputStream(src), srcEncoding); OutputStreamWriter out = new OutputStreamWriter(new RobustFileOutputStream(dest), destEncoding); int c; while ((c = in.read()) != -1) out.write(c); out.flush(); in.close(); out.close(); }

protected InputStream createIconType(HttpServletRequest req, HttpServletResponse res) throws ServletException, IOException { JavaliController.debug(JavaliController.LG_VERBOSE, "Creating iconType"); String cHash = PRM_TYPE + "=" + TP_ICON; String iconName = req.getParameter("iconName"); if (iconName == null) { res.sendError(res.SC_NOT_FOUND); return null; } Locale loc = null; HttpSession sess = req.getSession(false); JavaliSession jsess = null; int menuType = -1; String menuTypeString = req.getParameter(PRM_MENU_TYPE); try { menuType = new Integer(menuTypeString).intValue(); } catch (Exception e) { } if (sess != null) jsess = (JavaliSession) sess.getAttribute(FormConstants.SESSION_BINDING); if (jsess != null && jsess.getUser() != null) loc = jsess.getUser().getLocale(); else if (sess != null) loc = (Locale) sess.getAttribute(FormConstants.LOCALE_BINDING); if (loc == null) loc = Locale.getDefault(); if (menuType == -1) menuType = MENU_TYPE_TEXTICON; String iconText = JavaliResource.getString("icon." + iconName, loc); if (iconText == null) { iconText = req.getParameter(PRM_MENU_NAME); if (iconText == null) iconText = ""; } cHash += ", " + PRM_ICON_NAME + "=" + iconName + ", text=" + iconText + ", menuType=" + menuType; String iconFileName = null; String fontName = req.getParameter(PRM_FONT_NAME); if (fontName == null) { fontName = "Helvetica"; } cHash += "," + PRM_FONT_NAME + "=" + fontName; String fontSizeString = req.getParameter(PRM_FONT_SIZE); int fontSize; try { fontSize = Integer.parseInt(fontSizeString); } catch (NumberFormatException nfe) { fontSize = 12; } cHash += "," + PRM_FONT_SIZE + "=" + fontSize; String fontTypeString = req.getParameter(PRM_FONT_TYPE); int fontType = Font.BOLD; if ("PLAIN".equalsIgnoreCase(fontTypeString)) fontType = Font.PLAIN; if ("BOLD".equalsIgnoreCase(fontTypeString)) fontType = Font.BOLD; if ("ITALIC".equalsIgnoreCase(fontTypeString)) fontType = Font.ITALIC; if ("ITALICBOLD".equalsIgnoreCase(fontTypeString) || "BOLDITALIC".equalsIgnoreCase(fontTypeString) || "BOLD_ITALIC".equalsIgnoreCase(fontTypeString) || "ITALIC_BOLD".equalsIgnoreCase(fontTypeString)) { fontType = Font.ITALIC | Font.BOLD; } cHash += "," + PRM_FONT_TYPE + "=" + fontType; String fontColor = req.getParameter(PRM_FONT_COLOR); if (fontColor == null || fontColor.equals("")) fontColor = "0x000000"; cHash += "," + PRM_FONT_COLOR + "=" + fontColor; String fName = cacheInfo.file(cHash); JavaliController.debug(JavaliController.LG_VERBOSE, "Called for: " + fName); if (fName == null) { JavaliController.debug(JavaliController.LG_VERBOSE, "No cache found for: " + cHash); if (getServletConfig() != null && getServletConfig().getServletContext() != null) { if (iconName != null && iconName.startsWith("/")) iconFileName = getServletConfig().getServletContext().getRealPath(iconName + ".gif"); else iconFileName = getServletConfig().getServletContext().getRealPath("/icons/" + iconName + ".gif"); File iconFile = new File(iconFileName); if (!iconFile.exists()) { JavaliController.debug(JavaliController.LG_VERBOSE, "Could not find: " + iconFileName); res.sendError(res.SC_NOT_FOUND); return null; } iconFileName = iconFile.getAbsolutePath(); JavaliController.debug(JavaliController.LG_VERBOSE, "file: " + iconFileName + " and cHash=" + cHash); } else { JavaliController.debug(JavaliController.LG_VERBOSE, "No ServletConfig=" + getServletConfig() + " or servletContext"); res.sendError(res.SC_NOT_FOUND); return null; } File tmp = File.createTempFile(PREFIX, SUFIX, cacheDir); OutputStream out = new FileOutputStream(tmp); if (menuType == MENU_TYPE_ICON) { FileInputStream in = new FileInputStream(iconFileName); byte buf[] = new byte[2048]; int read = -1; while ((read = in.read(buf)) != -1) out.write(buf, 0, read); } else if (menuType == MENU_TYPE_TEXT) MessageImage.sendAsGIF(MessageImage.makeMessageImage(iconText, fontName, fontSize, fontType, fontColor, false, "0x000000", true), out); else MessageImage.sendAsGIF(MessageImage.makeIconImage(iconFileName, iconText, fontName, fontColor, fontSize, fontType), out); out.close(); cacheInfo.putFile(cHash, tmp); fName = cacheInfo.file(cHash); } return new FileInputStream(new File(cacheDir, fName)); }

public static String compute(String text) { try { MessageDigest md; md = MessageDigest.getInstance("MD5"); byte[] md5hash = new byte[32]; md.update(text.getBytes("UTF-8"), 0, text.length()); md5hash = md.digest(); return convertToHex(md5hash); } catch (NoSuchAlgorithmException nax) { RuntimeException rx = new IllegalStateException(); rx.initCause(rx); throw rx; } catch (UnsupportedEncodingException uex) { RuntimeException rx = new IllegalStateException(); rx.initCause(uex); throw rx; } }

public void service(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { long time = System.currentTimeMillis(); String text = request.getParameter("text"); String parsedQueryString = request.getQueryString(); if (text == null) { String[] fonts = new File(ctx.getRealPath("/WEB-INF/fonts/")).list(); text = "accepted params: text,font,size,color,background,nocache,aa,break"; response.setContentType("text/html"); PrintWriter out = response.getWriter(); out.println("<html>"); out.println("<body>"); out.println("<p>"); out.println("Usage: " + request.getServletPath() + "?params[]<BR>"); out.println("Acceptable Params are: <UL>"); out.println("<LI><B>text</B><BR>"); out.println("The body of the image"); out.println("<LI><B>font</B><BR>"); out.println("Available Fonts (in folder '/WEB-INF/fonts/') <UL>"); for (int i = 0; i < fonts.length; i++) { if (!"CVS".equals(fonts[i])) { out.println("<LI>" + fonts[i]); } } out.println("</UL>"); out.println("<LI><B>size</B><BR>"); out.println("An integer, i.e. size=100"); out.println("<LI><B>color</B><BR>"); out.println("in rgb, i.e. color=255,0,0"); out.println("<LI><B>background</B><BR>"); out.println("in rgb, i.e. background=0,0,255"); out.println("transparent, i.e. background=''"); out.println("<LI><B>aa</B><BR>"); out.println("antialias (does not seem to work), aa=true"); out.println("<LI><B>nocache</B><BR>"); out.println("if nocache is set, we will write out the image file every hit. Otherwise, will write it the first time and then read the file"); out.println("<LI><B>break</B><BR>"); out.println("An integer greater than 0 (zero), i.e. break=20"); out.println("</UL>"); out.println("</UL>"); out.println("Example:<BR>"); out.println("&lt;img border=1 src=\"" + request.getServletPath() + "?font=arial.ttf&text=testing&color=255,0,0&size=100\"&gt;<BR>"); out.println("<img border=1 src='" + request.getServletPath() + "?font=arial.ttf&text=testing&color=255,0,0&size=100'><BR>"); out.println("</body>"); out.println("</html>"); return; } String myFile = (request.getQueryString() == null) ? "empty" : PublicEncryptionFactory.digestString(parsedQueryString).replace('\\', '_').replace('/', '_'); myFile = Config.getStringProperty("PATH_TO_TITLE_IMAGES") + myFile + ".png"; File file = new File(ctx.getRealPath(myFile)); if (!file.exists() || (request.getParameter("nocache") != null)) { StringTokenizer st = null; Iterator i = hm.entrySet().iterator(); while (i.hasNext()) { Map.Entry entry = (Map.Entry) i.next(); String key = (String) entry.getKey(); if (parsedQueryString.indexOf(key) > -1) { String val = (String) entry.getValue(); parsedQueryString = UtilMethods.replace(parsedQueryString, key, val); } } st = new StringTokenizer(parsedQueryString, "&"); while (st.hasMoreTokens()) { try { String x = st.nextToken(); String key = x.split("=")[0]; String val = x.split("=")[1]; if ("text".equals(key)) { text = val; } } catch (Exception e) { } } text = URLDecoder.decode(text, "UTF-8"); Logger.debug(this.getClass(), "building title image:" + file.getAbsolutePath()); file.createNewFile(); try { String font_file = "/WEB-INF/fonts/arial.ttf"; if (request.getParameter("font") != null) { font_file = "/WEB-INF/fonts/" + request.getParameter("font"); } font_file = ctx.getRealPath(font_file); float size = 20.0f; if (request.getParameter("size") != null) { size = Float.parseFloat(request.getParameter("size")); } Color background = Color.white; if (request.getParameter("background") != null) { if (request.getParameter("background").equals("transparent")) try { background = new Color(Color.TRANSLUCENT); } catch (Exception e) { } else try { st = new StringTokenizer(request.getParameter("background"), ","); int x = Integer.parseInt(st.nextToken()); int y = Integer.parseInt(st.nextToken()); int z = Integer.parseInt(st.nextToken()); background = new Color(x, y, z); } catch (Exception e) { } } Color color = Color.black; if (request.getParameter("color") != null) { try { st = new StringTokenizer(request.getParameter("color"), ","); int x = Integer.parseInt(st.nextToken()); int y = Integer.parseInt(st.nextToken()); int z = Integer.parseInt(st.nextToken()); color = new Color(x, y, z); } catch (Exception e) { Logger.info(this, e.getMessage()); } } int intBreak = 0; if (request.getParameter("break") != null) { try { intBreak = Integer.parseInt(request.getParameter("break")); } catch (Exception e) { } } java.util.ArrayList<String> lines = null; if (intBreak > 0) { lines = new java.util.ArrayList<String>(10); lines.ensureCapacity(10); int start = 0; String line = null; int offSet; for (; ; ) { try { for (; isWhitespace(text.charAt(start)); ++start) ; if (isWhitespace(text.charAt(start + intBreak - 1))) { lines.add(text.substring(start, start + intBreak)); start += intBreak; } else { for (offSet = -1; !isWhitespace(text.charAt(start + intBreak + offSet)); ++offSet) ; lines.add(text.substring(start, start + intBreak + offSet)); start += intBreak + offSet; } } catch (Exception e) { if (text.length() > start) lines.add(leftTrim(text.substring(start))); break; } } } else { java.util.StringTokenizer tokens = new java.util.StringTokenizer(text, "|"); if (tokens.hasMoreTokens()) { lines = new java.util.ArrayList<String>(10); lines.ensureCapacity(10); for (; tokens.hasMoreTokens(); ) lines.add(leftTrim(tokens.nextToken())); } } Font font = Font.createFont(Font.TRUETYPE_FONT, new FileInputStream(font_file)); font = font.deriveFont(size); BufferedImage buffer = new BufferedImage(1, 1, BufferedImage.TYPE_INT_RGB); Graphics2D g2 = buffer.createGraphics(); if (request.getParameter("aa") != null) { g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); } else { g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF); } FontRenderContext fc = g2.getFontRenderContext(); Rectangle2D fontBounds = null; Rectangle2D textLayoutBounds = null; TextLayout tl = null; boolean useTextLayout = false; useTextLayout = Boolean.parseBoolean(request.getParameter("textLayout")); int width = 0; int height = 0; int offSet = 0; if (1 < lines.size()) { int heightMultiplier = 0; int maxWidth = 0; for (; heightMultiplier < lines.size(); ++heightMultiplier) { fontBounds = font.getStringBounds(lines.get(heightMultiplier), fc); tl = new TextLayout(lines.get(heightMultiplier), font, fc); textLayoutBounds = tl.getBounds(); if (maxWidth < Math.ceil(fontBounds.getWidth())) maxWidth = (int) Math.ceil(fontBounds.getWidth()); } width = maxWidth; int boundHeigh = (int) Math.ceil((!useTextLayout ? fontBounds.getHeight() : textLayoutBounds.getHeight())); height = boundHeigh * lines.size(); offSet = ((int) (boundHeigh * 0.2)) * (lines.size() - 1); } else { fontBounds = font.getStringBounds(text, fc); tl = new TextLayout(text, font, fc); textLayoutBounds = tl.getBounds(); width = (int) fontBounds.getWidth(); height = (int) Math.ceil((!useTextLayout ? fontBounds.getHeight() : textLayoutBounds.getHeight())); } buffer = new BufferedImage(width, height - offSet, BufferedImage.TYPE_INT_ARGB); g2 = buffer.createGraphics(); g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); g2.setFont(font); g2.setColor(background); if (!background.equals(new Color(Color.TRANSLUCENT))) g2.fillRect(0, 0, width, height); g2.setColor(color); if (1 < lines.size()) { for (int numLine = 0; numLine < lines.size(); ++numLine) { int y = (int) Math.ceil((!useTextLayout ? fontBounds.getY() : textLayoutBounds.getY())); g2.drawString(lines.get(numLine), 0, -y * (numLine + 1)); } } else { int y = (int) Math.ceil((!useTextLayout ? fontBounds.getY() : textLayoutBounds.getY())); g2.drawString(text, 0, -y); } BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(file)); ImageIO.write(buffer, "png", out); out.close(); } catch (Exception ex) { Logger.info(this, ex.toString()); } } response.setContentType("image/png"); BufferedInputStream bis = new BufferedInputStream(new FileInputStream(file)); OutputStream os = response.getOutputStream(); byte[] buf = new byte[4096]; int i = 0; while ((i = bis.read(buf)) != -1) { os.write(buf, 0, i); } os.close(); bis.close(); Logger.debug(this.getClass(), "time to build title: " + (System.currentTimeMillis() - time) + "ms"); return; }

public String buscaSAIKU() { URL url; Properties prop = new CargaProperties().Carga(); BufferedReader in; String inputLine; String miLinea = null; try { url = new URL(prop.getProperty("SAIKU")); in = new BufferedReader(new InputStreamReader(url.openStream())); while ((inputLine = in.readLine()) != null) { if (inputLine.contains("lastSuccessfulBuild/artifact/saiku-bi-platform-plugin/target")) { miLinea = inputLine; log.debug(miLinea); miLinea = miLinea.substring(miLinea.indexOf("lastSuccessfulBuild/artifact/saiku-bi-platform-plugin/target")); miLinea = miLinea.substring(0, miLinea.indexOf("\">")); miLinea = url + miLinea; } } } catch (Throwable t) { } log.debug("Detetectado last build SAIKU: " + miLinea); return miLinea; }

public IOCacheArray(final File file, int capacity, final IIOCacheArrayObjectMaker iomaker, int chunkSize, String name) { super(capacity, null, chunkSize, name); generator = new ICacheArrayObjectMaker() { FileOutputStream outStream; FileInputStream inStream; FileChannel outChannel; FileChannel inChannel; boolean inited = false; private synchronized void init() { if (!inited) { try { outStream = new FileOutputStream(file); inStream = new FileInputStream(file); outChannel = outStream.getChannel(); inChannel = inStream.getChannel(); } catch (FileNotFoundException foe) { Logging.errorln("IOCacheArray constuctor error: Could not open file " + file + ". Exception " + foe); Logging.errorln("outStream " + outStream + " inStream " + inStream + " outchan " + outChannel + " inchannel " + inChannel); } } inited = true; } public Object make(int itemIndex, int baseIndex, Object[] data) { init(); return iomaker.read(inChannel, itemIndex, baseIndex, data); } public boolean flush(int baseIndex, Object[] data) { init(); return iomaker.write(outChannel, baseIndex, data); } public CacheArrayBlockSummary summarize(int baseIndex, Object[] data) { init(); return iomaker.summarize(baseIndex, data); } }; }

public static void copy(String fromFileName, String toFileName) throws IOException { File fromFile = new File(fromFileName); File toFile = new File(toFileName); if (!fromFile.exists()) throw new IOException("FileCopy: " + "no such source file: " + fromFileName); if (!fromFile.isFile()) throw new IOException("FileCopy: " + "can't copy directory: " + fromFileName); if (!fromFile.canRead()) throw new IOException("FileCopy: " + "source file is unreadable: " + fromFileName); if (toFile.isDirectory()) toFile = new File(toFile, fromFile.getName()); if (toFile.exists()) { if (!toFile.canWrite()) throw new IOException("FileCopy: " + "destination file is unwriteable: " + toFileName); System.out.print("Overwrite existing file " + toFile.getName() + "? (Y/N): "); System.out.flush(); BufferedReader in = new BufferedReader(new InputStreamReader(System.in)); String response = in.readLine(); if (!response.equals("Y") && !response.equals("y")) throw new IOException("FileCopy: " + "existing file was not overwritten."); } else { String parent = toFile.getParent(); if (parent == null) parent = System.getProperty("user.dir"); File dir = new File(parent); if (!dir.exists()) throw new IOException("FileCopy: " + "destination directory doesn't exist: " + parent); if (dir.isFile()) throw new IOException("FileCopy: " + "destination is not a directory: " + parent); if (!dir.canWrite()) throw new IOException("FileCopy: " + "destination directory is unwriteable: " + parent); } FileInputStream from = null; FileOutputStream to = null; try { from = new FileInputStream(fromFile); to = new FileOutputStream(toFile); 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) { ; } } }

private String writeInputStreamToString(InputStream stream) { StringWriter stringWriter = new StringWriter(); try { IOUtils.copy(stream, stringWriter); } catch (IOException e) { e.printStackTrace(); } String namespaces = stringWriter.toString().trim(); return namespaces; }

public void copyFile(File a_fileSrc, File a_fileDest, boolean a_append) throws IOException { a_fileDest.getParentFile().mkdirs(); FileInputStream in = null; FileOutputStream out = null; FileChannel fcin = null; FileChannel fcout = null; try { in = new FileInputStream(a_fileSrc); out = new FileOutputStream(a_fileDest, a_append); fcin = in.getChannel(); fcout = out.getChannel(); ByteBuffer buffer = ByteBuffer.allocate(16 * 1024); while (true) { buffer.clear(); int r = fcin.read(buffer); if (r == -1) { break; } buffer.flip(); fcout.write(buffer); } } catch (IOException ex) { throw ex; } finally { if (in != null) { in.close(); } if (out != null) { out.close(); } if (fcin != null) { fcin.close(); } if (fcout != null) { fcout.close(); } } }

private void stripOneFilex(File inFile, File outFile) throws IOException { StreamTokenizer reader = new StreamTokenizer(new FileReader(inFile)); BufferedWriter writer = new BufferedWriter(new FileWriter(outFile)); reader.slashSlashComments(false); reader.slashStarComments(false); reader.eolIsSignificant(true); int token; while ((token = reader.nextToken()) != StreamTokenizer.TT_EOF) { switch(token) { case StreamTokenizer.TT_NUMBER: throw new IllegalStateException("didn't expect TT_NUMBER: " + reader.nval); case StreamTokenizer.TT_WORD: System.out.print(reader.sval); writer.write("WORD:" + reader.sval, 0, reader.sval.length()); default: char outChar = (char) reader.ttype; System.out.print(outChar); writer.write(outChar); } } }

public static void main(String[] args) throws IOException { long start = System.currentTimeMillis(); FileResourceManager frm = CommonsTransactionContext.configure(new File("C:/tmp")); try { frm.start(); } catch (ResourceManagerSystemException e) { throw new RuntimeException(e); } FileInputStream is = new FileInputStream("C:/Alfresco/WCM_Eval_Guide2.0.pdf"); CommonsTransactionOutputStream os = new CommonsTransactionOutputStream(new Ownerr()); IOUtils.copy(is, os); IOUtils.closeQuietly(is); IOUtils.closeQuietly(os); try { frm.stop(FileResourceManager.SHUTDOWN_MODE_NORMAL); } catch (ResourceManagerSystemException e) { throw new RuntimeException(e); } System.out.println(System.currentTimeMillis() - start); }

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 static String getRolesString(HttpServletRequest hrequest, HttpServletResponse hresponse, String username, String servicekey) { String registerapp = SSOFilter.getRegisterapp(); String u = SSOUtil.addParameter(registerapp + "/api/getroles", "username", username); u = SSOUtil.addParameter(u, "servicekey", servicekey); String roles = ""; try { URL url = new URL(u); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String line; while ((line = reader.readLine()) != null) { roles = line.trim(); } reader.close(); } catch (MalformedURLException e) { return null; } catch (IOException e) { return null; } if ("error".equals(roles)) { return ""; } return roles.trim(); }

public static String loadUrl(URL url, String charset) throws MyException { try { URLConnection conn = url.openConnection(); InputStream urlin = conn.getInputStream(); BufferedReader in = new BufferedReader(new InputStreamReader(urlin, charset)); StringBuffer buff = new StringBuffer(); char[] cbuf = new char[1028]; int count; while ((count = in.read(cbuf)) != -1) { buff.append(new String(cbuf, 0, count)); } return buff.toString(); } catch (FileNotFoundException e) { e.printStackTrace(); throw new MyException(MyException.ERROR_FILENOTFOUND, e.getMessage()); } catch (IOException e) { e.printStackTrace(); throw new MyException(MyException.ERROR_IO, e.getMessage()); } }

private void inject(int x, int y) throws IOException { Tag source = data.getTag(); Log.event(Log.DEBUG_INFO, "source: " + source.getString()); if (source == Tag.ORGANISM) { String seed = data.readString(); data.readTag(Tag.STREAM); injectCodeTape(data.getIn(), seed, x, y); } else if (source == Tag.URL) { String url = data.readString(); String seed = url.substring(url.lastIndexOf('.') + 1); BufferedReader urlIn = null; try { urlIn = new BufferedReader(new InputStreamReader(new URL(url).openStream())); injectCodeTape(urlIn, seed, x, y); } finally { if (urlIn != null) urlIn.close(); } } else data.writeString("unknown organism source: " + source.getString()); }

private void httpDo(HttpUriRequest hr, String url, Map<String, String> headers, AjaxStatus status) throws ClientProtocolException, IOException { if (AGENT != null) { hr.addHeader("User-Agent", AGENT); } if (headers != null) { for (String name : headers.keySet()) { hr.addHeader(name, headers.get(name)); } } if (GZIP && headers == null || !headers.containsKey("Accept-Encoding")) { hr.addHeader("Accept-Encoding", "gzip"); } String cookie = makeCookie(); if (cookie != null) { hr.addHeader("Cookie", cookie); } if (ah != null) { ah.applyToken(this, hr); } DefaultHttpClient client = getClient(); HttpContext context = new BasicHttpContext(); CookieStore cookieStore = new BasicCookieStore(); context.setAttribute(ClientContext.COOKIE_STORE, cookieStore); HttpResponse response = client.execute(hr, context); byte[] data = null; String redirect = url; int code = response.getStatusLine().getStatusCode(); String message = response.getStatusLine().getReasonPhrase(); String error = null; if (code < 200 || code >= 300) { try { HttpEntity entity = response.getEntity(); byte[] s = AQUtility.toBytes(entity.getContent()); error = new String(s, "UTF-8"); AQUtility.debug("error", error); } catch (Exception e) { AQUtility.debug(e); } } else { HttpEntity entity = response.getEntity(); HttpHost currentHost = (HttpHost) context.getAttribute(ExecutionContext.HTTP_TARGET_HOST); HttpUriRequest currentReq = (HttpUriRequest) context.getAttribute(ExecutionContext.HTTP_REQUEST); redirect = currentHost.toURI() + currentReq.getURI(); int size = Math.max(32, Math.min(1024 * 64, (int) entity.getContentLength())); PredefinedBAOS baos = new PredefinedBAOS(size); Header encoding = entity.getContentEncoding(); if (encoding != null && encoding.getValue().equalsIgnoreCase("gzip")) { InputStream is = new GZIPInputStream(entity.getContent()); AQUtility.copy(is, baos); } else { entity.writeTo(baos); } data = baos.toByteArray(); } AQUtility.debug("response", code); if (data != null) { AQUtility.debug(data.length, url); } status.code(code).message(message).error(error).redirect(redirect).time(new Date()).data(data).client(client).context(context).headers(response.getAllHeaders()); }

public void execute() throws BuildException { Project proj = getProject(); if (templateFile == null) throw new BuildException("Template file not set"); if (targetFile == null) throw new BuildException("Target file not set"); try { File template = new File(templateFile); File target = new File(targetFile); if (!template.exists()) throw new BuildException("Template file does not exist " + template.toString()); if (!template.canRead()) throw new BuildException("Cannot read template file: " + template.toString()); if (((!append) && (!overwrite)) && (!target.exists())) throw new BuildException("Target file already exists and append and overwrite are false " + target.toString()); if (VERBOSE) { System.out.println("ProcessTemplate: tmpl in " + template.toString()); System.out.println("ProcessTemplate: file out " + target.toString()); } BufferedReader reader = new BufferedReader(new FileReader(template)); BufferedWriter writer = new BufferedWriter(new FileWriter(targetFile, append)); parse(reader, writer); writer.flush(); writer.close(); } catch (Exception e) { if (VERBOSE) e.printStackTrace(); throw new BuildException(e); } }

private File writeResourceToFile(String resource) throws IOException { File tmp = File.createTempFile("zfppt" + resource, null); InputStream res = Thread.currentThread().getContextClassLoader().getResourceAsStream(resource); OutputStream out = new FileOutputStream(tmp); IOUtils.copy(res, out); out.close(); return tmp; }

public static long writePropertiesInOpenXMLDocument(String ext, InputStream in, OutputStreamProvider outProvider, Map<String, String> properties) { in = new BufferedInputStream(in); try { File tempPptx = null; POIXMLDocument doc; if (ext.toLowerCase().equals("docx")) { doc = new XWPFDocument(in); } else if (ext.toLowerCase().equals("xlsx")) { doc = new XSSFWorkbook(in); } else if (ext.toLowerCase().equals("pptx")) { tempPptx = File.createTempFile("temp", "pptx"); OutputStream tempPptxOut = new FileOutputStream(tempPptx); tempPptxOut = new BufferedOutputStream(tempPptxOut); IOUtils.copy(in, tempPptxOut); tempPptxOut.close(); doc = new XSLFSlideShow(tempPptx.getAbsolutePath()); } else { throw new IllegalArgumentException("Writing properties for a " + ext + " file is not supported"); } for (Map.Entry<String, String> property : properties.entrySet()) { CoreProperties coreProperties = doc.getProperties().getCoreProperties(); if (property.getKey().equals(Metadata.TITLE)) { coreProperties.setTitle(property.getValue()); } else if (property.getKey().equals(Metadata.AUTHOR)) { coreProperties.setCreator(property.getValue()); } else if (property.getKey().equals(Metadata.KEYWORDS)) { coreProperties.getUnderlyingProperties().setKeywordsProperty(property.getValue()); } else if (property.getKey().equals(Metadata.COMMENTS)) { coreProperties.setDescription(property.getValue()); } else if (property.getKey().equals(Metadata.SUBJECT)) { coreProperties.setSubjectProperty(property.getValue()); } else if (property.getKey().equals(Metadata.COMPANY)) { doc.getProperties().getExtendedProperties().getUnderlyingProperties().setCompany(property.getValue()); } else { org.apache.poi.POIXMLProperties.CustomProperties customProperties = doc.getProperties().getCustomProperties(); if (customProperties.contains(property.getKey())) { int index = 0; for (CTProperty prop : customProperties.getUnderlyingProperties().getPropertyArray()) { if (prop.getName().equals(property.getKey())) { customProperties.getUnderlyingProperties().removeProperty(index); break; } index++; } } customProperties.addProperty(property.getKey(), property.getValue()); } } in.close(); File tempOpenXMLDocumentFile = File.createTempFile("temp", "tmp"); OutputStream tempOpenXMLDocumentOut = new FileOutputStream(tempOpenXMLDocumentFile); tempOpenXMLDocumentOut = new BufferedOutputStream(tempOpenXMLDocumentOut); doc.write(tempOpenXMLDocumentOut); tempOpenXMLDocumentOut.close(); long length = tempOpenXMLDocumentFile.length(); InputStream tempOpenXMLDocumentIn = new FileInputStream(tempOpenXMLDocumentFile); tempOpenXMLDocumentIn = new BufferedInputStream(tempOpenXMLDocumentIn); OutputStream out = null; try { out = outProvider.getOutputStream(); out = new BufferedOutputStream(out); IOUtils.copy(tempOpenXMLDocumentIn, out); out.flush(); } finally { IOUtils.closeQuietly(out); } if (!FileUtils.deleteQuietly(tempOpenXMLDocumentFile)) { tempOpenXMLDocumentFile.deleteOnExit(); } if (tempPptx != null && !FileUtils.deleteQuietly(tempPptx)) { tempPptx.deleteOnExit(); } return length; } catch (IOException e) { throw new RuntimeException(e); } catch (InvalidFormatException e) { throw new RuntimeException(e); } catch (OpenXML4JException e) { throw new RuntimeException(e); } catch (XmlException e) { throw new RuntimeException(e); } finally { IOUtils.closeQuietly(in); } }

private Date fetchLastModifiedDate(String archName) { Date modifdate = null; URL url = null; try { url = new URL(jEdit.getProperty(OOO_DICTS_PROP) + archName + ".zip"); } catch (MalformedURLException mfue) { Log.log(Log.ERROR, HunspellDictsManager.class, "Invalid archive name : " + archName); GUIUtilities.error(null, "spell-check-hunspell-error-fetch", new String[] { mfue.getMessage() }); } if (url != null) { try { URLConnection connect = url.openConnection(); connect.connect(); if (connect.getLastModified() == 0) { Log.log(Log.ERROR, HunspellDictsManager.class, "no lastModifiedDate for " + archName); } else { modifdate = new Date(connect.getLastModified()); System.out.println("Modif date :" + DateFormat.getInstance().format(modifdate)); return modifdate; } } catch (IOException ioe) { GUIUtilities.error(null, "spell-check-hunspell-error-fetch", new String[] { ioe.getMessage() }); ioe.printStackTrace(); } } return modifdate; }

public void delete(String fileToDelete) throws IOException { FTPClient ftp = new FTPClient(); try { int reply = 0; ftp.connect(this.endpointURL, this.endpointPort); reply = ftp.getReplyCode(); if (!FTPReply.isPositiveCompletion(reply)) { ftp.disconnect(); throw new IOException("Ftp delete server refused connection."); } if (!ftp.login("anonymous", "")) { ftp.logout(); throw new IOException("FTP: server wrong passwd"); } ftp.enterLocalPassiveMode(); log.debug("Deleted: " + ftp.deleteFile(fileToDelete)); ftp.logout(); } catch (Exception e) { throw new IOException(e.getMessage()); } }

public static Checksum checksum(File file, Checksum checksum) throws IOException { if (file.isDirectory()) { throw new IllegalArgumentException("Checksums can't be computed on directories"); } InputStream in = null; try { in = new CheckedInputStream(new FileInputStream(file), checksum); IOUtils.copy(in, new NullOutputStream()); } finally { IOUtils.closeQuietly(in); } return checksum; }

public static void proxyRequest(IPageContext context, Writer writer, String proxyPath) throws IOException { URLConnection connection = new URL(proxyPath).openConnection(); connection.setDoInput(true); connection.setDoOutput(false); connection.setUseCaches(false); connection.setRequestProperty("Content-Type", "text/html; charset=UTF-8"); connection.setReadTimeout(30000); connection.setConnectTimeout(5000); Enumeration<String> e = context.httpRequest().getHeaderNames(); while (e.hasMoreElements()) { String name = e.nextElement(); if (name.equalsIgnoreCase("HOST") || name.equalsIgnoreCase("Accept-Encoding") || name.equalsIgnoreCase("Authorization")) continue; Enumeration<String> headers = context.httpRequest().getHeaders(name); while (headers.hasMoreElements()) { String header = headers.nextElement(); connection.setRequestProperty(name, header); } } if (connection instanceof HttpURLConnection) { HttpURLConnection httpConnection = (HttpURLConnection) connection; httpConnection.setRequestMethod(context.httpRequest().getMethod()); if ("POST".equalsIgnoreCase(context.httpRequest().getMethod()) || "PUT".equalsIgnoreCase(context.httpRequest().getMethod())) { Enumeration<String> names = context.httpRequest().getParameterNames(); StringBuilder body = new StringBuilder(); while (names.hasMoreElements()) { String key = names.nextElement(); for (String value : context.parameters(key)) { if (body.length() > 0) { body.append('&'); } try { body.append(key).append("=").append(URLEncoder.encode(value, "UTF-8")); } catch (UnsupportedEncodingException ex) { } } } if (body.length() > 0) { connection.setDoOutput(true); OutputStreamWriter out = new OutputStreamWriter(connection.getOutputStream()); out.write(body.toString()); out.close(); } } } try { IOUtils.copy(connection.getInputStream(), writer); } catch (IOException ex) { writer.write("<span>SSI Error: " + ex.getMessage() + "</span>"); } }

public EncodedScript(PackageScript source, DpkgData data) throws IOException { _source = source; final ByteArrayOutputStream bytes = new ByteArrayOutputStream(); OutputStream output = null; try { output = MimeUtility.encode(bytes, BASE64); } catch (final MessagingException e) { throw new IOException("Failed to uuencode script. name=[" + _source.getFriendlyName() + "], reason=[" + e.getMessage() + "]."); } IOUtils.write(HEADER, bytes, Dpkg.CHAR_ENCODING); bytes.flush(); IOUtils.copy(_source.getSource(data), output); output.flush(); IOUtils.write(FOOTER, bytes, Dpkg.CHAR_ENCODING); bytes.flush(); output.close(); bytes.close(); _encoded = bytes.toString(Dpkg.CHAR_ENCODING); }

public void setInput(String input, Component caller, FFMpegProgressReceiver recv) throws IOException { inputMedium = null; if (input.contains("youtube")) { URL url = new URL(input); InputStreamReader read = new InputStreamReader(url.openStream()); BufferedReader in = new BufferedReader(read); String inputLine; String line = null; String vid = input.substring(input.indexOf("?v=") + 3); if (vid.indexOf("&") != -1) vid = vid.substring(0, vid.indexOf("&")); while ((inputLine = in.readLine()) != null) { if (inputLine.contains("\"t\": \"")) { line = inputLine.substring(inputLine.indexOf("\"t\": \"") + 6); line = line.substring(0, line.indexOf("\"")); break; } } in.close(); if (line == null) throw new IOException("Could not find flv-Video"); Downloader dl = new Downloader("http://www.youtube.com/get_video?video_id=" + vid + "&t=" + line, recv, lang); dl.start(); return; } Runtime rt = Runtime.getRuntime(); Process p = rt.exec(new String[] { path, "-i", input }); BufferedReader br = new BufferedReader(new InputStreamReader(p.getErrorStream())); String line; Codec videoCodec = null; Codec audioCodec = null; double duration = -1; String aspectRatio = null; String scala = null; String colorSpace = null; String rate = null; String mrate = null; String aRate = null; String aFreq = null; String aChannel = null; try { while ((line = br.readLine()) != null) { if (Constants.debug) System.out.println(line); if (line.contains("Duration:")) { int hours = Integer.parseInt(line.substring(12, 14)); int mins = Integer.parseInt(line.substring(15, 17)); double secs = Double.parseDouble(line.substring(18, line.indexOf(','))); duration = secs + 60 * mins + hours * 60 * 60; Pattern pat = Pattern.compile("[0-9]+ kb/s"); Matcher m = pat.matcher(line); if (m.find()) mrate = line.substring(m.start(), m.end()); } if (line.contains("Video:")) { String info = line.substring(24); String parts[] = info.split(", "); Pattern pat = Pattern.compile("Video: [a-zA-Z0-9]+,"); Matcher m = pat.matcher(line); String codec = ""; if (m.find()) codec = line.substring(m.start(), m.end()); videoCodec = supportedCodecs.getCodecByName(codec.replace("Video: ", "").replace(",", "")); colorSpace = parts[1]; pat = Pattern.compile("[0-9]+x[0-9]+"); m = pat.matcher(info); if (m.find()) scala = info.substring(m.start(), m.end()); pat = Pattern.compile("DAR [0-9]+:[0-9]+"); m = pat.matcher(info); if (m.find()) aspectRatio = info.substring(m.start(), m.end()).replace("DAR ", ""); else if (scala != null) aspectRatio = String.valueOf((double) (Math.round(((double) ConvertUtils.getWidthFromScala(scala) / (double) ConvertUtils.getHeightFromScala(scala)) * 100)) / 100); pat = Pattern.compile("[0-9]+ kb/s"); m = pat.matcher(info); if (m.find()) rate = info.substring(m.start(), m.end()); } else if (line.contains("Audio:")) { String info = line.substring(24); Pattern pat = Pattern.compile("Audio: [a-zA-Z0-9]+,"); Matcher m = pat.matcher(line); String codec = ""; if (m.find()) codec = line.substring(m.start(), m.end()).replace("Audio: ", "").replace(",", ""); if (codec.equals("mp3")) codec = "libmp3lame"; audioCodec = supportedCodecs.getCodecByName(codec); pat = Pattern.compile("[0-9]+ kb/s"); m = pat.matcher(info); if (m.find()) aRate = info.substring(m.start(), m.end()); pat = Pattern.compile("[0-9]+ Hz"); m = pat.matcher(info); if (m.find()) aFreq = info.substring(m.start(), m.end()); if (line.contains("5.1")) aChannel = "5.1"; else if (line.contains("2.1")) aChannel = "2.1"; else if (line.contains("stereo")) aChannel = "Stereo"; else if (line.contains("mono")) aChannel = "Mono"; } if (videoCodec != null && audioCodec != null && duration != -1) { if (rate == null && mrate != null && aRate != null) rate = String.valueOf(ConvertUtils.getRateFromRateString(mrate) - ConvertUtils.getRateFromRateString(aRate)) + " kb/s"; inputMedium = new InputMedium(audioCodec, videoCodec, input, duration, colorSpace, aspectRatio, scala, rate, mrate, aRate, aFreq, aChannel); break; } } if ((videoCodec != null || audioCodec != null) && duration != -1) inputMedium = new InputMedium(audioCodec, videoCodec, input, duration, colorSpace, aspectRatio, scala, rate, mrate, aRate, aFreq, aChannel); } catch (Exception exc) { if (caller != null) JOptionPane.showMessageDialog(caller, lang.inputerror + " Audiocodec? " + (audioCodec != null) + " Videocodec? " + (videoCodec != null), lang.error, JOptionPane.ERROR_MESSAGE); if (Constants.debug) System.out.println("Audiocodec: " + audioCodec + "\nVideocodec: " + videoCodec); if (Constants.debug) exc.printStackTrace(); throw new IOException("Input file error"); } if (inputMedium == null) { if (caller != null) JOptionPane.showMessageDialog(caller, lang.inputerror + " Audiocodec? " + (audioCodec != null) + " Videocodec? " + (videoCodec != null), lang.error, JOptionPane.ERROR_MESSAGE); if (Constants.debug) System.out.println("Audiocodec: " + audioCodec + "\nVideocodec: " + videoCodec); throw new IOException("Input file error"); } }

public static String[] parseM3U(String strURL, Context c) { URL url; URLConnection urlConn = null; String TAG = "parseM3U"; Vector<String> radio = new Vector<String>(); final String filetoken = "http"; try { url = new URL(strURL); urlConn = url.openConnection(); Log.d(TAG, "Got data"); } catch (IOException ioe) { Log.e(TAG, "Could not connect to " + strURL); } try { DataInputStream in = new DataInputStream(urlConn.getInputStream()); BufferedReader br = new BufferedReader(new InputStreamReader(in)); String strLine; while ((strLine = br.readLine()) != null) { String temp = strLine.toLowerCase(); Log.d(TAG, strLine); if (temp.startsWith(filetoken)) { radio.add(temp); Log.d(TAG, "Found audio " + temp); } } br.close(); in.close(); } catch (Exception e) { Log.e(TAG, "Trouble reading file: " + e.getMessage()); } String[] t = new String[0]; String[] r = null; if (radio.size() != 0) { r = (String[]) radio.toArray(t); Log.d(TAG, "Found total: " + String.valueOf(r.length)); } return r; }

private void createHomeTab() { Tabpanel homeTab = new Tabpanel(); windowContainer.addWindow(homeTab, Msg.getMsg(EnvWeb.getCtx(), "Home").replaceAll("&", ""), false); Portallayout portalLayout = new Portallayout(); portalLayout.setWidth("100%"); portalLayout.setHeight("100%"); portalLayout.setStyle("position: absolute; overflow: auto"); homeTab.appendChild(portalLayout); Portalchildren portalchildren = null; int currentColumnNo = 0; String sql = "SELECT COUNT(DISTINCT COLUMNNO) " + "FROM PA_DASHBOARDCONTENT " + "WHERE (AD_CLIENT_ID=0 OR AD_CLIENT_ID=?) AND ISACTIVE='Y'"; int noOfCols = DB.getSQLValue(null, sql, EnvWeb.getCtx().getAD_Client_ID()); int width = noOfCols <= 0 ? 100 : 100 / noOfCols; sql = "SELECT x.*, m.AD_MENU_ID " + "FROM PA_DASHBOARDCONTENT x " + "LEFT OUTER JOIN AD_MENU m ON x.AD_WINDOW_ID=m.AD_WINDOW_ID " + "WHERE (x.AD_CLIENT_ID=0 OR x.AD_CLIENT_ID=?) AND x.ISACTIVE='Y' " + "AND x.zulfilepath not in (?, ?, ?) " + "ORDER BY x.COLUMNNO, x.AD_CLIENT_ID, x.LINE "; PreparedStatement pstmt = null; ResultSet rs = null; try { pstmt = DB.prepareStatement(sql, null); pstmt.setInt(1, EnvWeb.getCtx().getAD_Client_ID()); pstmt.setString(2, ACTIVITIES_PATH); pstmt.setString(3, FAVOURITES_PATH); pstmt.setString(4, VIEWS_PATH); rs = pstmt.executeQuery(); while (rs.next()) { int columnNo = rs.getInt("ColumnNo"); if (portalchildren == null || currentColumnNo != columnNo) { portalchildren = new Portalchildren(); portalLayout.appendChild(portalchildren); portalchildren.setWidth(width + "%"); portalchildren.setStyle("padding: 5px"); currentColumnNo = columnNo; } Panel panel = new Panel(); panel.setStyle("margin-bottom:10px"); panel.setTitle(rs.getString("Name")); String description = rs.getString("Description"); if (description != null) panel.setTooltiptext(description); String collapsible = rs.getString("IsCollapsible"); panel.setCollapsible(collapsible.equals("Y")); panel.setBorder("normal"); portalchildren.appendChild(panel); Panelchildren content = new Panelchildren(); panel.appendChild(content); boolean panelEmpty = true; String htmlContent = rs.getString("HTML"); if (htmlContent != null) { StringBuffer result = new StringBuffer("<html><head>"); URL url = getClass().getClassLoader().getResource("org/compiere/images/PAPanel.css"); InputStreamReader ins; try { ins = new InputStreamReader(url.openStream()); BufferedReader bufferedReader = new BufferedReader(ins); String cssLine; while ((cssLine = bufferedReader.readLine()) != null) result.append(cssLine + "\n"); } catch (IOException e1) { logger.log(Level.SEVERE, e1.getLocalizedMessage(), e1); } result.append("</head><body><div class=\"content\">\n"); result.append(stripHtml(htmlContent, false) + "<br>\n"); result.append("</div>\n</body>\n</html>\n</html>"); Html html = new Html(); html.setContent(result.toString()); content.appendChild(html); panelEmpty = false; } int AD_Window_ID = rs.getInt("AD_Window_ID"); if (AD_Window_ID > 0) { int AD_Menu_ID = rs.getInt("AD_Menu_ID"); ToolBarButton btn = new ToolBarButton(String.valueOf(AD_Menu_ID)); MMenu menu = new MMenu(EnvWeb.getCtx(), AD_Menu_ID, null); btn.setLabel(menu.getName()); btn.addEventListener(Events.ON_CLICK, this); content.appendChild(btn); panelEmpty = false; } int PA_Goal_ID = rs.getInt("PA_Goal_ID"); if (PA_Goal_ID > 0) { StringBuffer result = new StringBuffer("<html><head>"); URL url = getClass().getClassLoader().getResource("org/compiere/images/PAPanel.css"); InputStreamReader ins; try { ins = new InputStreamReader(url.openStream()); BufferedReader bufferedReader = new BufferedReader(ins); String cssLine; while ((cssLine = bufferedReader.readLine()) != null) result.append(cssLine + "\n"); } catch (IOException e1) { logger.log(Level.SEVERE, e1.getLocalizedMessage(), e1); } result.append("</head><body><div class=\"content\">\n"); result.append(renderGoals(PA_Goal_ID, content)); result.append("</div>\n</body>\n</html>\n</html>"); Html html = new Html(); html.setContent(result.toString()); content.appendChild(html); panelEmpty = false; } String url = rs.getString("ZulFilePath"); if (url != null) { try { Component component = Executions.createComponents(url, content, null); if (component != null) { if (component instanceof DashboardPanel) { DashboardPanel dashboardPanel = (DashboardPanel) component; if (!dashboardPanel.getChildren().isEmpty()) { content.appendChild(dashboardPanel); dashboardRunnable.add(dashboardPanel); panelEmpty = false; } } else { content.appendChild(component); panelEmpty = false; } } } catch (Exception e) { logger.log(Level.WARNING, "Failed to create components. zul=" + url, e); } } if (panelEmpty) panel.detach(); } } catch (Exception e) { logger.log(Level.WARNING, "Failed to create dashboard content", e); } finally { Util.closeCursor(pstmt, rs); } registerWindow(homeTab); if (!portalLayout.getDesktop().isServerPushEnabled()) portalLayout.getDesktop().enableServerPush(true); dashboardRunnable.refreshDashboard(); dashboardThread = new Thread(dashboardRunnable, "UpdateInfo"); dashboardThread.setDaemon(true); dashboardThread.start(); }

private String fetchURL(String url) { StringBuilder content = new StringBuilder(); String line; BufferedReader input = null; try { URL urlToFetch = new URL(url); input = new BufferedReader(new InputStreamReader(urlToFetch.openStream())); while ((line = input.readLine()) != null) { content.append(line); } input.close(); return content.toString(); } catch (java.io.IOException ex) { return null; } }

public void sorter() { String inputLine1, inputLine2; String epiNames[] = new String[1000]; String epiEpisodes[] = new String[1000]; int lineCounter = 0; try { String pluginDir = pluginInterface.getPluginDirectoryName(); String eplist_file = pluginDir + System.getProperty("file.separator") + "EpisodeList.txt"; File episodeList = new File(eplist_file); if (!episodeList.isFile()) { episodeList.createNewFile(); } final BufferedReader in = new BufferedReader(new FileReader(episodeList)); while ((inputLine1 = in.readLine()) != null) { if ((inputLine2 = in.readLine()) != null) { epiNames[lineCounter] = inputLine1; epiEpisodes[lineCounter] = inputLine2; lineCounter++; } } in.close(); int epiLength = epiNames.length; for (int i = 0; i < (lineCounter); i++) { for (int j = 0; j < (lineCounter - 1); j++) { if (epiNames[j].compareToIgnoreCase(epiNames[j + 1]) > 0) { String temp = epiNames[j]; epiNames[j] = epiNames[j + 1]; epiNames[j + 1] = temp; String temp2 = epiEpisodes[j]; epiEpisodes[j] = epiEpisodes[j + 1]; epiEpisodes[j + 1] = temp2; } } } File episodeList2 = new File(eplist_file); BufferedWriter bufWriter = new BufferedWriter(new FileWriter(episodeList2)); for (int i = 0; i <= lineCounter; i++) { if (epiNames[i] == null) { break; } bufWriter.write(epiNames[i] + "\n"); bufWriter.write(epiEpisodes[i] + "\n"); } bufWriter.close(); } catch (IOException e) { e.printStackTrace(); } }

public void reset(int currentPilot) { try { PreparedStatement psta = jdbc.prepareStatement("DELETE FROM component_prop " + "WHERE pilot_id = ? "); psta.setInt(1, currentPilot); psta.executeUpdate(); jdbc.commit(); } catch (SQLException e) { jdbc.rollback(); log.debug(e); } }

public static void copyFile(File src, File dst) { try { FileInputStream fis = new FileInputStream(src); FileOutputStream fos = new FileOutputStream(dst); try { byte[] buf = new byte[1024]; int i = 0; while ((i = fis.read(buf)) != -1) fos.write(buf, 0, i); } catch (IOException e) { throw e; } finally { if (fis != null) fis.close(); if (fos != null) fos.close(); } } catch (IOException e) { logger.error("Error coping file from " + src + " to " + dst, e); } }

public static void doVersionCheck(View view) { view.showWaitCursor(); try { URL url = new URL(jEdit.getProperty("version-check.url")); InputStream in = url.openStream(); BufferedReader bin = new BufferedReader(new InputStreamReader(in)); String line; String version = null; String build = null; while ((line = bin.readLine()) != null) { if (line.startsWith(".version")) version = line.substring(8).trim(); else if (line.startsWith(".build")) build = line.substring(6).trim(); } bin.close(); if (version != null && build != null) { if (jEdit.getBuild().compareTo(build) < 0) newVersionAvailable(view, version, url); else { GUIUtilities.message(view, "version-check" + ".up-to-date", new String[0]); } } } catch (IOException e) { String[] args = { jEdit.getProperty("version-check.url"), e.toString() }; GUIUtilities.error(view, "read-error", args); } view.hideWaitCursor(); }

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 static boolean start(RootDoc root) { Logger log = Logger.getLogger("DocletGenerator"); if (destination == null) { try { ruleListenerDef = IOUtils.toString(GeneratorOfXmlSchemaForConvertersDoclet.class.getResourceAsStream("/RuleListenersFragment.xsd"), "UTF-8"); String fn = System.getenv("annocultor.xconverter.destination.file.name"); fn = (fn == null) ? "./../../../src/site/resources/schema/XConverterInclude.xsd" : fn; destination = new File(fn); if (destination.exists()) { destination.delete(); } FileOutputStream os; os = new FileOutputStream(new File(destination.getParentFile(), "XConverter.xsd")); IOUtils.copy(new AutoCloseInputStream(GeneratorOfXmlSchemaForConvertersDoclet.class.getResourceAsStream("/XConverterTemplate.xsd")), os); os.close(); os = new FileOutputStream(destination); IOUtils.copy(new AutoCloseInputStream(GeneratorOfXmlSchemaForConvertersDoclet.class.getResourceAsStream("/XConverterInclude.xsd")), os); os.close(); } catch (Exception e) { try { throw new RuntimeException("On destination " + destination.getCanonicalPath(), e); } catch (IOException e1) { throw new RuntimeException(e1); } } } try { String s = Utils.loadFileToString(destination.getCanonicalPath(), "\n"); int breakPoint = s.indexOf(XSD_TEXT_TO_REPLACED_WITH_GENERATED_XML_SIGNATURES); if (breakPoint < 0) { throw new Exception("Signature not found in XSD: " + XSD_TEXT_TO_REPLACED_WITH_GENERATED_XML_SIGNATURES); } String preambula = s.substring(0, breakPoint); String appendix = s.substring(breakPoint); destination.delete(); PrintWriter schemaWriter = new PrintWriter(destination); schemaWriter.print(preambula); ClassDoc[] classes = root.classes(); for (int i = 0; i < classes.length; ++i) { ClassDoc cd = classes[i]; PrintWriter documentationWriter = null; if (getSuperClasses(cd).contains(Rule.class.getName())) { for (ConstructorDoc constructorDoc : cd.constructors()) { if (constructorDoc.isPublic()) { if (isMeantForXMLAccess(constructorDoc)) { if (documentationWriter == null) { File file = new File("./../../../src/site/xdoc/rules." + cd.name() + ".xml"); documentationWriter = new PrintWriter(file); log.info("Generating doc for rule " + file.getCanonicalPath()); printRuleDocStart(cd, documentationWriter); } boolean initFound = false; for (MethodDoc methodDoc : cd.methods()) { if ("init".equals(methodDoc.name())) { if (methodDoc.parameters().length == 0) { initFound = true; break; } } } if (!initFound) { } printConstructorSchema(constructorDoc, schemaWriter); if (documentationWriter != null) { printConstructorDoc(constructorDoc, documentationWriter); } } } } } if (documentationWriter != null) { printRuleDocEnd(documentationWriter); } } schemaWriter.print(appendix); schemaWriter.close(); log.info("Saved to " + destination.getCanonicalPath()); } catch (Exception e) { throw new RuntimeException(e); } return true; }

protected void copyAndDelete(final URL _src, final long _temp) throws IOException { final File storage = getStorageFile(_src, _temp); final File dest = new File(_src.getFile()); FileChannel in = null; FileChannel out = null; if (storage.equals(dest)) { return; } try { readWriteLock_.lockWrite(); if (dest.exists()) { dest.delete(); } if (storage.exists() && !storage.renameTo(dest)) { in = new FileInputStream(storage).getChannel(); out = new FileOutputStream(dest).getChannel(); final long len = in.size(); final long copied = out.transferFrom(in, 0, in.size()); if (len != copied) { throw new IOException("unable to complete write"); } } } finally { readWriteLock_.unlockWrite(); try { if (in != null) { in.close(); } } catch (final IOException _evt) { FuLog.error(_evt); } try { if (out != null) { out.close(); } } catch (final IOException _evt) { FuLog.error(_evt); } storage.delete(); } }

public String stringOfUrl(String addr) throws IOException { ByteArrayOutputStream output = new ByteArrayOutputStream(); URL url = new URL(addr); IOUtils.copy(url.openStream(), output); return output.toString(); }

public String loadURLString(java.net.URL url) { try { BufferedReader br = new BufferedReader(new InputStreamReader(url.openStream())); StringBuffer buf = new StringBuffer(); String s = ""; while (br.ready() && s != null) { s = br.readLine(); if (s != null) { buf.append(s); buf.append("\n"); } } return buf.toString(); } catch (IOException ex) { return ""; } catch (NullPointerException npe) { return ""; } }

private void getServiceReponse(String service, NameSpaceDefinition nsDefinition) throws Exception { Pattern pattern = Pattern.compile("(?i)(?:.*(xmlns(?:\\:\\w+)?=\\\"http\\:\\/\\/www\\.ivoa\\.net\\/.*" + service + "[^\\\"]*\\\").*)"); pattern = Pattern.compile(".*xmlns(?::\\w+)?=(\"[^\"]*(?i)(?:" + service + ")[^\"]*\").*"); logger.debug("read " + this.url + service); BufferedReader in = new BufferedReader(new InputStreamReader((new URL(this.url + service)).openStream())); String inputLine; BufferedWriter bfw = new BufferedWriter(new FileWriter(this.baseDirectory + service + ".xml")); boolean found = false; while ((inputLine = in.readLine()) != null) { if (!found) { Matcher m = pattern.matcher(inputLine); if (m.matches()) { nsDefinition.init("xmlns:vosi=" + m.group(1)); found = true; } } bfw.write(inputLine + "\n"); } in.close(); bfw.close(); }

public void myCheckCredHandler(View v) { Log.d("login_section", "entered handler"); EditText Username = (EditText) findViewById(R.id.Username); EditText Password = (EditText) findViewById(R.id.user_pass); String username_S = Username.getText().toString(); String pass_S = Password.getText().toString(); TextView ltv = (TextView) findViewById(R.id.LoginPagetv); HttpClient httpclient = createHttpClient(); HttpPost httppost = new HttpPost(authenticationURL); try { List<NameValuePair> nameValuePairs = new ArrayList<NameValuePair>(2); nameValuePairs.add(new BasicNameValuePair("login", username_S)); nameValuePairs.add(new BasicNameValuePair("password", pass_S)); httppost.setEntity(new UrlEncodedFormEntity(nameValuePairs)); HttpResponse response = httpclient.execute(httppost); int status = response.getStatusLine().getStatusCode(); String responseBody = EntityUtils.toString(response.getEntity()); Log.d("login_section", responseBody); JSONObject jsonObject = new JSONObject(responseBody); if (status == this.statusOK && jsonObject.getBoolean("logged_in")) { ltv.setText("You have been logged in. :D"); etracks.setLogged(true); etracks.setUserToken(jsonObject.getString("user_token")); Intent it = new Intent(Intent.ACTION_VIEW); it.setClassName(this, etracks.class.getName()); this.finish(); startActivity(it); } else if (status == this.statusUnprocessable && !jsonObject.getBoolean("logged_in")) { if (!jsonObject.isNull("errors")) ltv.setText(jsonObject.getString("errors")); else ltv.setText("login unsuccessful"); } else Log.d("login_section", "what just happened?"); } catch (ClientProtocolException e) { } catch (IOException e) { } catch (JSONException e) { e.printStackTrace(); } }

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(); } }

private void write(File src, File dst, byte id3v1Tag[], byte id3v2HeadTag[], byte id3v2TailTag[]) throws IOException { if (src == null || !src.exists()) throw new IOException(Debug.getDebug("missing src", src)); if (!src.getName().toLowerCase().endsWith(".mp3")) throw new IOException(Debug.getDebug("src not mp3", src)); if (dst == null) throw new IOException(Debug.getDebug("missing dst", dst)); if (dst.exists()) { dst.delete(); if (dst.exists()) throw new IOException(Debug.getDebug("could not delete dst", dst)); } boolean hasId3v1 = new MyID3v1().hasID3v1(src); long id3v1Length = hasId3v1 ? ID3_V1_TAG_LENGTH : 0; long id3v2HeadLength = new MyID3v2().findID3v2HeadLength(src); long id3v2TailLength = new MyID3v2().findID3v2TailLength(src, hasId3v1); OutputStream os = null; InputStream is = null; try { dst.getParentFile().mkdirs(); os = new FileOutputStream(dst); os = new BufferedOutputStream(os); if (!skipId3v2Head && !skipId3v2 && id3v2HeadTag != null) os.write(id3v2HeadTag); is = new FileInputStream(src); is = new BufferedInputStream(is); is.skip(id3v2HeadLength); long total_to_read = src.length(); total_to_read -= id3v1Length; total_to_read -= id3v2HeadLength; total_to_read -= id3v2TailLength; byte buffer[] = new byte[1024]; long total_read = 0; while (total_read < total_to_read) { int remainder = (int) (total_to_read - total_read); int readSize = Math.min(buffer.length, remainder); int read = is.read(buffer, 0, readSize); if (read <= 0) throw new IOException("unexpected EOF"); os.write(buffer, 0, read); total_read += read; } if (!skipId3v2Tail && !skipId3v2 && id3v2TailTag != null) os.write(id3v2TailTag); if (!skipId3v1 && id3v1Tag != null) os.write(id3v1Tag); } finally { try { if (is != null) is.close(); } catch (Throwable e) { Debug.debug(e); } try { if (os != null) os.close(); } catch (Throwable e) { Debug.debug(e); } } }

public static void unzip2(File zipfile, File outputdir) throws IOException { //Buffer for extracting files byte[] buffer = new byte[1024]; //Zip file ZipFile zip = new ZipFile(zipfile); //Get entries Enumeration<ZipArchiveEntry> files = zip.getEntries(); //Iterate through the entries while(files.hasMoreElements()) { //Get entry ZipArchiveEntry ze = files.nextElement(); //Resolve entry file File newFile = new File(outputdir + File.separator + ze.getName()); //Make parent directories newFile.getParentFile().mkdirs(); if(ze.isDirectory()) { //If directory, create it newFile.mkdir(); } else { //If file, extract it InputStream is = zip.getInputStream(ze); FileOutputStream fos = new FileOutputStream(newFile); int len; while((len = is.read(buffer)) > 0) { fos.write(buffer, 0, len); } fos.close(); is.close(); } } //Cleanup zip.close(); }

public static String generateSHA1Digest(String text) { try { MessageDigest md; md = MessageDigest.getInstance("SHA-1"); byte[] sha1hash = new byte[40]; md.update(text.getBytes("UTF-8"), 0, text.length()); sha1hash = md.digest(); return convertToHex(sha1hash); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } catch (UnsupportedEncodingException e) { e.printStackTrace(); } return null; }

public void update() { try { String passwordMD5 = new String(); if (this.password != null && this.password.length() > 0) { MessageDigest md = MessageDigest.getInstance("md5"); md.update(this.password.getBytes()); byte[] digest = md.digest(); for (int i = 0; i < digest.length; i++) { passwordMD5 += Integer.toHexString((digest[i] >> 4) & 0xf); passwordMD5 += Integer.toHexString((digest[i] & 0xf)); } } this.authCode = new String(Base64Encoder.encode(new String(this.username + ";" + passwordMD5).getBytes())); } catch (Throwable throwable) { throwable.printStackTrace(); } }

public MapInfo loadLocalMapData(String fileName) { MapInfo info = mapCacheLocal.get(fileName); if (info != null && info.getContent() == null) { try { BufferedReader bufferedreader; URL fetchUrl = new URL(localMapContextUrl, fileName); URLConnection urlconnection = fetchUrl.openConnection(); if (urlconnection.getContentEncoding() != null) { bufferedreader = new BufferedReader(new InputStreamReader(urlconnection.getInputStream(), urlconnection.getContentEncoding())); } else { bufferedreader = new BufferedReader(new InputStreamReader(urlconnection.getInputStream(), "utf-8")); } String line; StringBuilder mapContent = new StringBuilder(); while ((line = bufferedreader.readLine()) != null) { mapContent.append(line); mapContent.append("\n"); } info.setContent(mapContent.toString()); GameMapImplementation gameMap = GameMapImplementation.createFromMapInfo(info); } catch (IOException _ex) { System.err.println("HexTD::readFile:: Can't read from " + fileName); } } return info; }

public static boolean sendPostRequest(String path, Map<String, String> params, String encoding) throws Exception { StringBuilder sb = new StringBuilder(""); if (params != null && !params.isEmpty()) { for (Map.Entry<String, String> entry : params.entrySet()) { sb.append(entry.getKey()).append('=').append(URLEncoder.encode(entry.getValue(), encoding)).append('&'); } sb.deleteCharAt(sb.length() - 1); } byte[] data = sb.toString().getBytes(); URL url = new URL(path); HttpURLConnection conn = (HttpURLConnection) url.openConnection(); conn.setRequestMethod("POST"); conn.setConnectTimeout(5 * 1000); conn.setDoOutput(true); conn.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); conn.setRequestProperty("Content-Length", String.valueOf(data.length)); OutputStream outStream = conn.getOutputStream(); outStream.write(data); outStream.flush(); outStream.close(); if (conn.getResponseCode() == 200) { InputStream inputStream = conn.getInputStream(); return ResponseResult.parseXML(inputStream); } return false; }

public boolean copyDirectoryTree(File srcPath, File dstPath) { try { if (srcPath.isDirectory()) { if (!dstPath.exists()) dstPath.mkdir(); String files[] = srcPath.list(); for (int i = 0; i < files.length; i++) copyDirectoryTree(new File(srcPath, files[i]), new File(dstPath, files[i])); } else { if (!srcPath.exists()) { errMsgLog += "copyDirectoryTree I/O error from '" + srcPath + "' does not exist.\n"; lastErrMsgLog = errMsgLog; return (false); } else { InputStream in = new FileInputStream(srcPath); OutputStream out = new FileOutputStream(dstPath); byte[] buf = new byte[10240]; int len; while ((len = in.read(buf)) > 0) out.write(buf, 0, len); in.close(); out.close(); } } return (true); } catch (Exception e) { errMsgLog += "copyDirectoryTree I/O error from '" + srcPath.getName() + "' to '" + dstPath.getName() + "\n " + e + "\n"; lastErrMsgLog = errMsgLog; return (false); } }

protected void validate(long googcmId, long reservePrice, String description, String category, int days, String status, String title, byte[] imgBytes) throws PortalException, SystemException { if (Validator.isNull(description)) throw new AuctionDescriptionException(); else if (Validator.isNull(title)) throw new AuctionTitleException(); else if (Validator.isNull(category)) throw new CategoryIdException(); if (googcmId < 1000000000l | googcmId > 999999999999999l) throw new AuctionGoogCMIdException(); long imgMaxSize = 1048576l; if ((imgBytes == null) || (imgBytes.length > ((int) imgMaxSize))) throw new AuctionImageSizeException(); if (days != 3 & days != 7 & days != 10) throw new AuctionEndeDateException(); if ((reservePrice < 0) || (reservePrice > 10000)) throw new AuctionReservePriceException(); try { URL url = new URL("https://checkout.google.com/api/checkout/v2/checkoutForm/Merchant/" + googcmId); URLConnection conn = url.openConnection(); BufferedReader rd = new BufferedReader(new InputStreamReader(conn.getInputStream())); boolean sellerExists = true; String line; while ((line = rd.readLine()) != null) { if (line.contains("" + googcmId)) { throw new AuctionGoogCMAccountException(); } } rd.close(); } catch (IOException e) { e.printStackTrace(); } }

private void transform(CommandLine commandLine) throws IOException { Reader reader; if (commandLine.hasOption('i')) { reader = createFileReader(commandLine.getOptionValue('i')); } else { reader = createStandardInputReader(); } Writer writer; if (commandLine.hasOption('o')) { writer = createFileWriter(commandLine.getOptionValue('o')); } else { writer = createStandardOutputWriter(); } String mapRule = commandLine.getOptionValue("m"); try { SrxTransformer transformer = new SrxAnyTransformer(); Map<String, Object> parameterMap = new HashMap<String, Object>(); if (mapRule != null) { parameterMap.put(Srx1Transformer.MAP_RULE_NAME, mapRule); } transformer.transform(reader, writer, parameterMap); } finally { cleanupReader(reader); cleanupWriter(writer); } }

public boolean downloadFile(String sourceFilename, String targetFilename) throws RQLException { checkFtpClient(); InputStream in = null; try { in = ftpClient.retrieveFileStream(sourceFilename); if (in == null) { return false; } FileOutputStream target = new FileOutputStream(targetFilename); IOUtils.copy(in, target); in.close(); target.close(); return ftpClient.completePendingCommand(); } catch (IOException ex) { throw new RQLException("Download of file with name " + sourceFilename + " via FTP from server " + server + " failed.", ex); } }

public XmldbURI createFile(String newName, InputStream is, Long length, String contentType) throws IOException, PermissionDeniedException, CollectionDoesNotExistException { if (LOG.isDebugEnabled()) LOG.debug("Create '" + newName + "' in '" + xmldbUri + "'"); XmldbURI newNameUri = XmldbURI.create(newName); MimeType mime = MimeTable.getInstance().getContentTypeFor(newName); if (mime == null) { mime = MimeType.BINARY_TYPE; } DBBroker broker = null; Collection collection = null; BufferedInputStream bis = new BufferedInputStream(is); VirtualTempFile vtf = new VirtualTempFile(); BufferedOutputStream bos = new BufferedOutputStream(vtf); IOUtils.copy(bis, bos); bis.close(); bos.close(); vtf.close(); if (mime.isXMLType() && vtf.length() == 0L) { if (LOG.isDebugEnabled()) LOG.debug("Creating dummy XML file for null resource lock '" + newNameUri + "'"); vtf = new VirtualTempFile(); IOUtils.write("<null_resource/>", vtf); vtf.close(); } TransactionManager transact = brokerPool.getTransactionManager(); Txn txn = transact.beginTransaction(); try { broker = brokerPool.get(subject); collection = broker.openCollection(xmldbUri, Lock.WRITE_LOCK); if (collection == null) { LOG.debug("Collection " + xmldbUri + " does not exist"); transact.abort(txn); throw new CollectionDoesNotExistException(xmldbUri + ""); } if (mime.isXMLType()) { if (LOG.isDebugEnabled()) LOG.debug("Inserting XML document '" + mime.getName() + "'"); VirtualTempFileInputSource vtfis = new VirtualTempFileInputSource(vtf); IndexInfo info = collection.validateXMLResource(txn, broker, newNameUri, vtfis); DocumentImpl doc = info.getDocument(); doc.getMetadata().setMimeType(mime.getName()); collection.store(txn, broker, info, vtfis, false); } else { if (LOG.isDebugEnabled()) LOG.debug("Inserting BINARY document '" + mime.getName() + "'"); InputStream fis = vtf.getByteStream(); bis = new BufferedInputStream(fis); DocumentImpl doc = collection.addBinaryResource(txn, broker, newNameUri, bis, mime.getName(), length.longValue()); bis.close(); } transact.commit(txn); if (LOG.isDebugEnabled()) LOG.debug("Document created sucessfully"); } catch (EXistException e) { LOG.error(e); transact.abort(txn); throw new IOException(e); } catch (TriggerException e) { LOG.error(e); transact.abort(txn); throw new IOException(e); } catch (SAXException e) { LOG.error(e); transact.abort(txn); throw new IOException(e); } catch (LockException e) { LOG.error(e); transact.abort(txn); throw new PermissionDeniedException(xmldbUri + ""); } catch (IOException e) { LOG.error(e); transact.abort(txn); throw e; } catch (PermissionDeniedException e) { LOG.error(e); transact.abort(txn); throw e; } finally { if (vtf != null) { vtf.delete(); } if (collection != null) { collection.release(Lock.WRITE_LOCK); } brokerPool.release(broker); if (LOG.isDebugEnabled()) LOG.debug("Finished creation"); } XmldbURI newResource = xmldbUri.append(newName); return newResource; }

public void moveNext(String[] showOrder, String[] orgID, String targetShowOrder, String targetOrgID) throws Exception { Connection con = null; PreparedStatement ps = null; ResultSet result = null; int moveCount = showOrder.length; DBOperation dbo = factory.createDBOperation(POOL_NAME); String strQuery = "select show_order from " + Common.ORGANIZE_TABLE + " where show_order=" + showOrder[0] + " and organize_id= '" + orgID[0] + "'"; try { con = dbo.getConnection(); con.setAutoCommit(false); ps = con.prepareStatement(strQuery); result = ps.executeQuery(); int minOrderNo = 0; if (result.next()) { minOrderNo = result.getInt(1); } String[] sqls = new String[moveCount + 1]; sqls[0] = "update " + Common.ORGANIZE_TABLE + " set show_order=" + minOrderNo + " where show_order=" + targetShowOrder + " and organize_id= '" + targetOrgID + "'"; for (int i = 0; i < showOrder.length; i++) { sqls[i + 1] = "update " + Common.ORGANIZE_TABLE + " set show_order=show_order+1" + " where show_order=" + showOrder[i] + " and organize_id= '" + orgID[i] + "'"; } for (int j = 0; j < sqls.length; j++) { ps = con.prepareStatement(sqls[j]); int resultCount = ps.executeUpdate(); if (resultCount != 1) { throw new CesSystemException("Organize.moveNext(): ERROR Inserting data " + "in T_SYS_ORGANIZE update !! resultCount = " + resultCount); } } con.commit(); } catch (SQLException se) { if (con != null) { con.rollback(); } throw new CesSystemException("Organize.moveNext(): SQLException while mov organize order " + " :\n\t" + se); } finally { con.setAutoCommit(true); close(dbo, ps, result); } }

@Override public void dispatchContent(InputStream is) throws IOException { if (LOG.isDebugEnabled()) { LOG.debug("Sending content message over JMS"); } final ByteArrayOutputStream bos = new ByteArrayOutputStream(); IOUtils.copy(is, bos); this.send(new MessageCreator() { @Override public Message createMessage(Session session) throws JMSException { BytesMessage message = session.createBytesMessage(); message.writeBytes(bos.toByteArray()); return message; } }); }

private void sendActionPerformed(java.awt.event.ActionEvent evt) { if (name.getText().length() < 3) { JOptionPane.showMessageDialog(comment, "Too short name (at least 3)"); return; } if (comment.getText().length() < 10) { JOptionPane.showMessageDialog(comment, "Too short comment (at least 10)"); return; } Thread t = new Thread(new Runnable() { public void run() { try { String data = URLEncoder.encode("send_id", "UTF-8") + "=" + URLEncoder.encode("1", "UTF-8"); data += "&" + URLEncoder.encode("author", "UTF-8") + "=" + URLEncoder.encode(name.getText(), "UTF-8"); data += "&" + URLEncoder.encode("location", "UTF-8") + "=" + URLEncoder.encode(System.getProperty("user.language"), "UTF-8"); data += "&" + URLEncoder.encode("contact", "UTF-8") + "=" + URLEncoder.encode(email.getText(), "UTF-8"); data += "&" + URLEncoder.encode("content", "UTF-8") + "=" + URLEncoder.encode(comment.getText(), "UTF-8"); data += "&" + URLEncoder.encode("rate", "UTF-8") + "=" + URLEncoder.encode(rate.getSelectedItem().toString(), "UTF-8"); System.out.println(data); URL url = new URL("http://javablock.sourceforge.net/book/index.php"); URLConnection conn = url.openConnection(); conn.setDoOutput(true); OutputStreamWriter wr = new OutputStreamWriter(conn.getOutputStream()); wr.write(data); wr.flush(); BufferedReader rd = new BufferedReader(new InputStreamReader(conn.getInputStream())); String address = rd.readLine(); JPanel panel = new JPanel(); panel.add(new JLabel("Comment added")); panel.add(new JTextArea("visit: http://javablock.sourceforge.net/")); JOptionPane.showMessageDialog(null, new JLabel("Comment sended correctly!")); wr.close(); rd.close(); hide(); } catch (IOException ex) { Logger.getLogger(guestBook.class.getName()).log(Level.SEVERE, null, ex); } } }); t.start(); }

@Override public JSONObject runCommand(JSONObject payload, HttpSession session) throws DefinedException { String sessionId = session.getId(); log.debug("Login -> runCommand SID: " + sessionId); JSONObject toReturn = new JSONObject(); boolean isOK = true; String username = null; try { username = payload.getString(ComConstants.LogIn.Request.USERNAME); } catch (JSONException e) { log.error("SessionId=" + sessionId + ", Missing username parameter", e); throw new DefinedException(StatusCodesV2.PARAMETER_ERROR); } String password = null; if (isOK) { try { password = payload.getString(ComConstants.LogIn.Request.PASSWORD); } catch (JSONException e) { log.error("SessionId=" + sessionId + ", Missing password parameter", e); throw new DefinedException(StatusCodesV2.PARAMETER_ERROR); } } if (isOK) { MessageDigest m = null; try { m = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { log.error("SessionId=" + sessionId + ", MD5 algorithm does not exist", e); e.printStackTrace(); throw new DefinedException(StatusCodesV2.INTERNAL_SYSTEM_FAILURE); } m.update(password.getBytes(), 0, password.length()); password = new BigInteger(1, m.digest()).toString(16); UserSession userSession = pli.login(username, password); try { if (userSession != null) { session.setAttribute("user", userSession); toReturn.put(ComConstants.Response.STATUS_CODE, StatusCodesV2.LOGIN_OK.getStatusCode()); toReturn.put(ComConstants.Response.STATUS_MESSAGE, StatusCodesV2.LOGIN_OK.getStatusMessage()); } else { log.error("SessionId=" + sessionId + ", Login failed: username=" + username + " not found"); toReturn.put(ComConstants.Response.STATUS_CODE, StatusCodesV2.LOGIN_USER_OR_PASSWORD_INCORRECT.getStatusCode()); toReturn.put(ComConstants.Response.STATUS_MESSAGE, StatusCodesV2.LOGIN_USER_OR_PASSWORD_INCORRECT.getStatusMessage()); } } catch (JSONException e) { log.error("SessionId=" + sessionId + ", JSON exception occured in response", e); e.printStackTrace(); throw new DefinedException(StatusCodesV2.INTERNAL_SYSTEM_FAILURE); } } log.debug("Login <- runCommand SID: " + sessionId); return toReturn; }

private String hash(String clearPassword) { if (salt == 0) return null; MessageDigest md = null; try { md = MessageDigest.getInstance("SHA1"); } catch (NoSuchAlgorithmException e) { throw new AssertionError("Can't find the SHA1 algorithm in the java.security package"); } String saltString = String.valueOf(salt); md.update(saltString.getBytes()); md.update(clearPassword.getBytes()); byte[] digestBytes = md.digest(); StringBuffer digestSB = new StringBuffer(); for (int i = 0; i < digestBytes.length; i++) { int lowNibble = digestBytes[i] & 0x0f; int highNibble = (digestBytes[i] >> 4) & 0x0f; digestSB.append(Integer.toHexString(highNibble)); digestSB.append(Integer.toHexString(lowNibble)); } String digestStr = digestSB.toString(); return digestStr; }

private boolean enregistreToi() { PrintWriter lEcrivain; String laDest = "./img_types/" + sonImage; if (!new File("./img_types").exists()) { new File("./img_types").mkdirs(); } try { FileChannel leFicSource = new FileInputStream(sonFichier).getChannel(); FileChannel leFicDest = new FileOutputStream(laDest).getChannel(); leFicSource.transferTo(0, leFicSource.size(), leFicDest); leFicSource.close(); leFicDest.close(); lEcrivain = new PrintWriter(new FileWriter(new File("bundll/types.jay"), true)); lEcrivain.println(sonNom); lEcrivain.println(sonImage); if (sonOptionRadio1.isSelected()) { lEcrivain.println("0:?"); } if (sonOptionRadio2.isSelected()) { lEcrivain.println("1:" + JOptionPane.showInputDialog(null, "Vous avez choisis de rendre ce terrain difficile � franchir.\nVeuillez en indiquer la raison.", "Demande de pr�cision", JOptionPane.INFORMATION_MESSAGE)); } if (sonOptionRadio3.isSelected()) { lEcrivain.println("2:?"); } lEcrivain.close(); return true; } catch (Exception lException) { return false; } }

public static String doGet(String http_url, String get_data) { URL url; try { if ((get_data != "") && (get_data != null)) { url = new URL(http_url + "?" + get_data); } else { url = new URL(http_url); } URLConnection conn = url.openConnection(); InputStream stream = new BufferedInputStream(conn.getInputStream()); try { StringBuffer b = new StringBuffer(); int ch; while ((ch = stream.read()) != -1) b.append((char) ch); return b.toString(); } finally { stream.close(); } } catch (IOException e) { ; } catch (ClassCastException e) { e.printStackTrace(); } return null; }

private static String retrieveVersion(InputStream is) throws RepositoryException { ByteArrayOutputStream buffer = new ByteArrayOutputStream(); try { IOUtils.copy(is, buffer); } catch (IOException e) { throw new RepositoryException(exceptionLocalizer.format("device-repository-file-missing", DeviceRepositoryConstants.VERSION_FILENAME), e); } return buffer.toString().trim(); }

protected void copyDependents() { for (File source : dependentFiles.keySet()) { try { if (!dependentFiles.get(source).exists()) { if (dependentFiles.get(source).isDirectory()) dependentFiles.get(source).mkdirs(); else dependentFiles.get(source).getParentFile().mkdirs(); } IOUtils.copyEverything(source, dependentFiles.get(source)); } catch (IOException e) { e.printStackTrace(); } } }

private void copy(File sourceFile, File destinationFile) { try { FileChannel in = new FileInputStream(sourceFile).getChannel(); FileChannel out = new FileOutputStream(destinationFile).getChannel(); try { in.transferTo(0, in.size(), out); in.close(); out.close(); } catch (IOException e) { GTLogger.getInstance().error(e); } } catch (FileNotFoundException e) { GTLogger.getInstance().error(e); } }

static String doHttp(String postURL, String text) { String returnValue = null; StringBuffer sb = new StringBuffer(); sb.append("bsh.client=Remote"); sb.append("&bsh.script="); sb.append(URLEncoder.encode(text)); String formData = sb.toString(); try { URL url = new URL(postURL); HttpURLConnection urlcon = (HttpURLConnection) url.openConnection(); urlcon.setRequestMethod("POST"); urlcon.setRequestProperty("Content-type", "application/x-www-form-urlencoded"); urlcon.setDoOutput(true); urlcon.setDoInput(true); PrintWriter pout = new PrintWriter(new OutputStreamWriter(urlcon.getOutputStream(), "8859_1"), true); pout.print(formData); pout.flush(); int rc = urlcon.getResponseCode(); if (rc != HttpURLConnection.HTTP_OK) System.out.println("Error, HTTP response: " + rc); returnValue = urlcon.getHeaderField("Bsh-Return"); BufferedReader bin = new BufferedReader(new InputStreamReader(urlcon.getInputStream())); String line; while ((line = bin.readLine()) != null) System.out.println(line); System.out.println("Return Value: " + returnValue); } catch (MalformedURLException e) { System.out.println(e); } catch (IOException e2) { System.out.println(e2); } return returnValue; }

private void readCard() { try { final String urlString = createURLStringExistRESTGetXQuery("//scheda[cata = \"" + cata + "\"]"); InputStream inputStream = new URL(urlString).openStream(); uiSchedaXml.read(inputStream); inputStream.close(); } catch (MalformedURLException e) { System.out.println(e); } catch (IOException e) { System.out.println(e); } }

private void getImage(String filename) throws MalformedURLException, IOException, SAXException, FileNotFoundException { String url = Constants.STRATEGICDOMINATION_URL + "/images/gameimages/" + filename; WebRequest req = new GetMethodWebRequest(url); WebResponse response = wc.getResponse(req); File file = new File("etc/images/" + filename); FileOutputStream outputStream = new FileOutputStream(file); IOUtils.copy(response.getInputStream(), outputStream); }

protected static String getBiopaxId(Reaction reaction) { String id = null; if (reaction.getId() > Reaction.NO_ID_ASSIGNED) { id = reaction.getId().toString(); } else { try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(reaction.getTextualRepresentation().getBytes()); byte[] digestBytes = md.digest(); StringBuilder digesterSb = new StringBuilder(32); for (int i = 0; i < digestBytes.length; i++) { int intValue = digestBytes[i] & 0xFF; if (intValue < 0x10) digesterSb.append('0'); digesterSb.append(Integer.toHexString(intValue)); } id = digesterSb.toString(); } catch (NoSuchAlgorithmException e) { } } return id; }

private String httpGet(String urlString, boolean postStatus) throws Exception { URL url; URLConnection conn; String answer = ""; try { if (username.equals("") || password.equals("")) throw new AuthNotProvidedException(); url = new URL(urlString); conn = url.openConnection(); conn.setRequestProperty("Authorization", "Basic " + getAuthentificationString()); if (postStatus) { conn.setDoOutput(true); conn.setUseCaches(false); conn.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); DataOutputStream das = new DataOutputStream(conn.getOutputStream()); String content = "status=" + URLEncoder.encode(statusMessage, "UTF-8") + "&source=" + URLEncoder.encode("sametimetwitterclient", "UTF-8"); das.writeBytes(content); das.flush(); das.close(); } InputStream is = (InputStream) conn.getInputStream(); BufferedReader br = new BufferedReader(new InputStreamReader(is)); String line; while ((line = br.readLine()) != null) { answer += line + "\n"; } br.close(); } catch (FileNotFoundException ex) { System.out.println(ex.toString()); throw new RuntimeException("Page not Found. Maybe Twitter-API has changed."); } catch (UnknownHostException ex) { System.out.println(ex.toString()); throw new RuntimeException("Network connection problems. Could not find twitter.com"); } catch (IOException ex) { System.out.println("IO-Exception"); if (ex.getMessage().indexOf("401") > -1) { authenthicated = AUTH_BAD; throw new AuthNotAcceptedException(); } System.out.println(ex.toString()); } if (checkForError(answer) != null) { throw new RuntimeException(checkForError(answer)); } authenthicated = AUTH_OK; return answer; }

@Override public void render(Output output) throws IOException { output.setStatus(headersFile.getStatusCode(), headersFile.getStatusMessage()); for (Entry<String, Set<String>> header : headersFile.getHeadersMap().entrySet()) { Set<String> values = header.getValue(); for (String value : values) { output.addHeader(header.getKey(), value); } } if (file != null) { InputStream inputStream = new FileInputStream(file); try { output.open(); OutputStream out = output.getOutputStream(); IOUtils.copy(inputStream, out); } finally { inputStream.close(); output.close(); } } }

public static InputStream getRequest(String path) throws Exception { HttpGet httpGet = new HttpGet(path); HttpResponse httpResponse = sClient.execute(httpGet); if (httpResponse.getStatusLine().getStatusCode() == HttpStatus.SC_OK) { BufferedHttpEntity bufHttpEntity = new BufferedHttpEntity(httpResponse.getEntity()); return bufHttpEntity.getContent(); } else { return null; } }

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!"); }

@Override public void backup() { Connection connection = null; PreparedStatement prestm = null; try { if (logger.isInfoEnabled()) logger.info("backup table " + getOrigin() + " start..."); Class.forName(driver); connection = DriverManager.getConnection(url, username, password); String tableExistsResult = ""; prestm = connection.prepareStatement("show tables from " + schema + " like '" + getDestination() + "';"); ResultSet rs = prestm.executeQuery(); if (rs.next()) tableExistsResult = rs.getString(1); rs.close(); prestm.close(); if (StringUtils.isBlank(tableExistsResult)) { String createTableSql = ""; prestm = connection.prepareStatement("show create table " + getOrigin() + ";"); rs = prestm.executeQuery(); if (rs.next()) createTableSql = rs.getString(2); rs.close(); prestm.close(); createTableSql = createTableSql.replaceAll("`" + getOrigin() + "`", "`" + getDestination() + "`"); createTableSql = createTableSql.replaceAll("auto_increment", ""); createTableSql = createTableSql.replaceAll("AUTO_INCREMENT", ""); Matcher matcher = stripRelationTablePattern.matcher(createTableSql); if (matcher.find()) createTableSql = matcher.replaceAll(""); matcher = normalizePattern.matcher(createTableSql); if (matcher.find()) createTableSql = matcher.replaceAll("\n )"); Statement stm = connection.createStatement(); stm.execute(createTableSql); if (logger.isDebugEnabled()) logger.debug("table '" + getDestination() + "' created!"); } else if (logger.isDebugEnabled()) logger.debug("table '" + getDestination() + "' already exists"); Date date = new Date(); date.setTime(TimeUtil.addHours(date, -getHours()).getTimeInMillis()); date.setTime(TimeUtil.getTodayAtMidnight().getTimeInMillis()); if (logger.isInfoEnabled()) logger.info("backuping records before: " + date); long currentRows = 0L; prestm = connection.prepareStatement("select count(*) from " + getOrigin() + " where " + getCondition() + ""); java.sql.Date sqlDate = new java.sql.Date(date.getTime()); prestm.setDate(1, sqlDate); rs = prestm.executeQuery(); if (rs.next()) currentRows = rs.getLong(1); rs.close(); prestm.close(); if (currentRows > 0) { connection.setAutoCommit(false); prestm = connection.prepareStatement("INSERT INTO " + getDestination() + " SELECT * FROM " + getOrigin() + " WHERE " + getCondition()); prestm.setDate(1, sqlDate); int rows = prestm.executeUpdate(); prestm.close(); if (logger.isInfoEnabled()) logger.info(rows + " rows backupped"); prestm = connection.prepareStatement("DELETE FROM " + getOrigin() + " WHERE " + getCondition()); prestm.setDate(1, sqlDate); rows = prestm.executeUpdate(); prestm.close(); connection.commit(); if (logger.isInfoEnabled()) logger.info(rows + " rows deleted"); } else if (logger.isInfoEnabled()) logger.info("no backup need"); if (logger.isInfoEnabled()) logger.info("backup table " + getOrigin() + " end"); } catch (SQLException e) { logger.error(e, e); if (applicationContext != null) applicationContext.publishEvent(new TrapEvent(this, "dbcon", "Errore SQL durante il backup dei dati della tabella " + getOrigin(), e)); try { connection.rollback(); } catch (SQLException e1) { } } catch (Throwable e) { logger.error(e, e); if (applicationContext != null) applicationContext.publishEvent(new TrapEvent(this, "generic", "Errore generico durante il backup dei dati della tabella " + getOrigin(), e)); try { connection.rollback(); } catch (SQLException e1) { } } finally { try { if (prestm != null) prestm.close(); } catch (SQLException e) { } try { if (connection != null) connection.close(); } catch (SQLException e) { } } }