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bigclonebench-processed

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public static LicenseKey parseKey(String key) throws InvalidLicenseKeyException { final String f_key = key.trim(); StringTokenizer st = new StringTokenizer(f_key, FIELD_SEPERATOR); int tc = st.countTokens(); int tc_name = tc - 9; try { final String product = st.nextToken(); final String type = st.nextToken(); final String loadStr = st.nextToken(); final int load = Integer.parseInt(loadStr); final String lowMajorVersionStr = st.nextToken(); final int lowMajorVersion = Integer.parseInt(lowMajorVersionStr); final String lowMinorVersionStr = st.nextToken(); final double lowMinorVersion = Double.parseDouble("0." + lowMinorVersionStr); final String highMajorVersionStr = st.nextToken(); final int highMajorVersion = Integer.parseInt(highMajorVersionStr); final String highMinorVersionStr = st.nextToken(); final double highMinorVersion = Double.parseDouble("0." + highMinorVersionStr); String regName = ""; for (int i = 0; i < tc_name; i++) regName += (i == 0 ? st.nextToken() : FIELD_SEPERATOR + st.nextToken()); final String randomHexStr = st.nextToken(); final String md5Str = st.nextToken(); String subKey = f_key.substring(0, f_key.indexOf(md5Str) - 1); byte[] md5; MessageDigest md = null; md = MessageDigest.getInstance("MD5"); md.update(subKey.getBytes()); md.update(FIELD_SEPERATOR.getBytes()); md.update(zuonicsPassword.getBytes()); md5 = md.digest(); String testKey = subKey + FIELD_SEPERATOR; for (int i = 0; i < md5.length; i++) testKey += Integer.toHexString(md5[i]).toUpperCase(); if (!testKey.equals(f_key)) throw new InvalidLicenseKeyException("doesn't hash"); final String f_regName = regName; return new LicenseKey() { public String getProduct() { return product; } public String getType() { return type; } public int getLoad() { return load; } public String getRegName() { return f_regName; } public double getlowVersion() { return lowMajorVersion + lowMinorVersion; } public double getHighVersion() { return highMajorVersion + highMinorVersion; } public String getRandomHexStr() { return randomHexStr; } public String getMD5HexStr() { return md5Str; } public String toString() { return f_key; } public boolean equals(Object obj) { if (obj.toString().equals(toString())) return true; return false; } }; } catch (Exception e) { throw new InvalidLicenseKeyException(e.getMessage()); } }

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; } }

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

protected void copyFile(File sourceFile, File destFile) { FileChannel in = null; FileChannel out = null; try { if (!verifyOrCreateParentPath(destFile.getParentFile())) { throw new IOException("Parent directory path " + destFile.getAbsolutePath() + " did not exist and could not be created"); } if (destFile.exists() || destFile.createNewFile()) { in = new FileInputStream(sourceFile).getChannel(); out = new FileOutputStream(destFile).getChannel(); in.transferTo(0, in.size(), out); } else { throw new IOException("Couldn't create file for " + destFile.getAbsolutePath()); } } catch (IOException ioe) { if (destFile.exists() && destFile.length() < sourceFile.length()) { destFile.delete(); } ioe.printStackTrace(); } finally { try { in.close(); } catch (Throwable t) { } try { out.close(); } catch (Throwable t) { } destFile.setLastModified(sourceFile.lastModified()); } }

private void copyPhoto(final IPhoto photo, final Map.Entry<String, Integer> size) { final File fileIn = new File(storageService.getPhotoPath(photo, storageService.getOriginalDir())); final File fileOut = new File(storageService.getPhotoPath(photo, size.getKey())); InputStream fileInputStream; OutputStream fileOutputStream; try { fileInputStream = new FileInputStream(fileIn); fileOutputStream = new FileOutputStream(fileOut); IOUtils.copy(fileInputStream, fileOutputStream); fileInputStream.close(); fileOutputStream.close(); } catch (final IOException e) { log.error("file io exception", e); return; } }

private void transformFile(File input, File output, Cipher cipher, boolean compress, String progressMessage) throws IOException { FileInputStream fileInputStream = new FileInputStream(input); InputStream inputStream; if (progressMessage != null) { inputStream = new ProgressMonitorInputStream(null, progressMessage, fileInputStream); } else { inputStream = fileInputStream; } FilterInputStream is = new BufferedInputStream(inputStream); FilterOutputStream os = new BufferedOutputStream(new FileOutputStream(output)); FilterInputStream fis; FilterOutputStream fos; if (compress) { fis = is; fos = new GZIPOutputStream(new CipherOutputStream(os, cipher)); } else { fis = new GZIPInputStream(new CipherInputStream(is, cipher)); fos = os; } byte[] buffer = new byte[cipher.getBlockSize() * blocksInBuffer]; int readLength = fis.read(buffer); while (readLength != -1) { fos.write(buffer, 0, readLength); readLength = fis.read(buffer); } if (compress) { GZIPOutputStream gos = (GZIPOutputStream) fos; gos.finish(); } fos.close(); fis.close(); }

private void bokActionPerformed(java.awt.event.ActionEvent evt) { if (this.meetingnamepanel.getEnteredValues().get(0).toString().trim().equals("")) { this.showWarningMessage("Enter Meeting Name"); } else { String[] patlib = newgen.presentation.NewGenMain.getAppletInstance().getPatronLibraryIds(); String xmlreq = newgen.presentation.administration.AdministrationXMLGenerator.getInstance().saveMeetingName("2", meetingnamepanel.getEnteredValues(), patlib); try { java.net.URL url = new java.net.URL(ResourceBundle.getBundle("Administration").getString("ServerURL") + ResourceBundle.getBundle("Administration").getString("ServletSubPath") + "MeetingNameServlet"); java.net.URLConnection urlconn = (java.net.URLConnection) url.openConnection(); urlconn.setDoOutput(true); java.io.OutputStream dos = urlconn.getOutputStream(); dos.write(xmlreq.getBytes()); java.io.InputStream ios = urlconn.getInputStream(); SAXBuilder saxb = new SAXBuilder(); Document retdoc = saxb.build(ios); Element rootelement = retdoc.getRootElement(); if (rootelement.getChild("Error") == null) { this.showInformationMessage(ResourceBundle.getBundle("Administration").getString("DataSavedInDatabase")); } else { this.showErrorMessage(ResourceBundle.getBundle("Administration").getString("ErrorPleaseContactTheVendor")); } } catch (Exception e) { System.out.println(e); } } }

private JButton getButtonImagen() { if (buttonImagen == null) { buttonImagen = new JButton(); buttonImagen.setText("Cargar Imagen"); buttonImagen.setIcon(new ImageIcon(getClass().getResource("/data/icons/view_sidetree.png"))); buttonImagen.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent e) { JFileChooser fc = new JFileChooser(); fc.addChoosableFileFilter(new ImageFilter()); fc.setFileView(new ImageFileView()); fc.setAccessory(new ImagePreview(fc)); int returnVal = fc.showDialog(Resorces.this, "Seleccione una imagen"); if (returnVal == JFileChooser.APPROVE_OPTION) { File file = fc.getSelectedFile(); String rutaGlobal = System.getProperty("user.dir") + file.separator + "data" + file.separator + "imagenes" + file.separator + file.getName(); String rutaRelativa = "data" + file.separator + "imagenes" + file.separator + file.getName(); try { FileInputStream fis = new FileInputStream(file); FileOutputStream fos = new FileOutputStream(rutaGlobal, true); FileChannel canalFuente = fis.getChannel(); FileChannel canalDestino = fos.getChannel(); canalFuente.transferTo(0, canalFuente.size(), canalDestino); fis.close(); fos.close(); } catch (IOException ex) { ex.printStackTrace(); } imagen.setImagenURL(rutaRelativa); System.out.println(rutaGlobal + " " + rutaRelativa); buttonImagen.setIcon(new ImageIcon(getClass().getResource("/data/icons/view_sidetreeOK.png"))); labelImagenPreview.setIcon(gui.procesadorDatos.escalaImageIcon(imagen.getImagenURL())); } else { } } }); } return buttonImagen; }

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 exportDB(String input, String output) { try { Class.forName("org.sqlite.JDBC"); String fileName = input + File.separator + G.databaseName; File dataBase = new File(fileName); if (!dataBase.exists()) { JOptionPane.showMessageDialog(null, "No se encuentra el fichero DB", "Error", JOptionPane.ERROR_MESSAGE); } else { G.conn = DriverManager.getConnection("jdbc:sqlite:" + fileName); HashMap<Integer, String> languageIDs = new HashMap<Integer, String>(); HashMap<Integer, String> typeIDs = new HashMap<Integer, String>(); long tiempoInicio = System.currentTimeMillis(); Element dataBaseXML = new Element("database"); Element languages = new Element("languages"); Statement stat = G.conn.createStatement(); ResultSet rs = stat.executeQuery("select * from language order by id"); while (rs.next()) { int id = rs.getInt("id"); String name = rs.getString("name"); languageIDs.put(id, name); Element language = new Element("language"); language.setText(name); languages.addContent(language); } dataBaseXML.addContent(languages); rs = stat.executeQuery("select * from type order by id"); while (rs.next()) { int id = rs.getInt("id"); String name = rs.getString("name"); typeIDs.put(id, name); } rs = stat.executeQuery("select distinct name from main order by name"); while (rs.next()) { String name = rs.getString("name"); Element image = new Element("image"); image.setAttribute("id", name); Statement stat2 = G.conn.createStatement(); ResultSet rs2 = stat2.executeQuery("select distinct idL from main where name = \"" + name + "\" order by idL"); while (rs2.next()) { int idL = rs2.getInt("idL"); Element language = new Element("language"); language.setAttribute("id", languageIDs.get(idL)); Statement stat3 = G.conn.createStatement(); ResultSet rs3 = stat3.executeQuery("select * from main where name = \"" + name + "\" and idL = " + idL + " order by idT"); while (rs3.next()) { int idT = rs3.getInt("idT"); String word = rs3.getString("word"); Element wordE = new Element("word"); wordE.setAttribute("type", typeIDs.get(idT)); wordE.setText(word); language.addContent(wordE); String pathSrc = input + File.separator + name.substring(0, 1).toUpperCase() + File.separator + name; String pathDst = output + File.separator + name; try { FileChannel srcChannel = new FileInputStream(pathSrc).getChannel(); FileChannel dstChannel = new FileOutputStream(pathDst).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (IOException exc) { System.out.println(exc.getMessage()); System.out.println(exc.toString()); } } rs3.close(); stat3.close(); image.addContent(language); } rs2.close(); stat2.close(); dataBaseXML.addContent(image); } rs.close(); stat.close(); XMLOutputter out = new XMLOutputter(Format.getPrettyFormat()); FileOutputStream f = new FileOutputStream(output + File.separator + G.imagesName); out.output(dataBaseXML, f); f.flush(); f.close(); long totalTiempo = System.currentTimeMillis() - tiempoInicio; System.out.println("El tiempo total es :" + totalTiempo / 1000 + " segundos"); } } catch (Exception e) { e.printStackTrace(); } }

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; }

@SuppressWarnings("unchecked") private void doService(final HttpServletRequest request, final HttpServletResponse response) throws Exception { final String url = request.getRequestURL().toString(); if (url.endsWith("/favicon.ico")) { response.setStatus(HttpServletResponse.SC_NOT_FOUND); return; } if (url.contains("/delay")) { final String delay = StringUtils.substringBetween(url, "/delay", "/"); final int ms = Integer.parseInt(delay); if (LOG.isDebugEnabled()) { LOG.debug("Sleeping for " + ms + " before to deliver " + url); } Thread.sleep(ms); } final URL requestedUrl = new URL(url); final WebRequest webRequest = new WebRequest(requestedUrl); webRequest.setHttpMethod(HttpMethod.valueOf(request.getMethod())); for (final Enumeration<String> en = request.getHeaderNames(); en.hasMoreElements(); ) { final String headerName = en.nextElement(); final String headerValue = request.getHeader(headerName); webRequest.setAdditionalHeader(headerName, headerValue); } final List<NameValuePair> requestParameters = new ArrayList<NameValuePair>(); for (final Enumeration<String> paramNames = request.getParameterNames(); paramNames.hasMoreElements(); ) { final String name = paramNames.nextElement(); final String[] values = request.getParameterValues(name); for (final String value : values) { requestParameters.add(new NameValuePair(name, value)); } } if ("PUT".equals(request.getMethod()) && request.getContentLength() > 0) { final byte[] buffer = new byte[request.getContentLength()]; request.getInputStream().readLine(buffer, 0, buffer.length); webRequest.setRequestBody(new String(buffer)); } else { webRequest.setRequestParameters(requestParameters); } final WebResponse resp = MockConnection_.getResponse(webRequest); response.setStatus(resp.getStatusCode()); for (final NameValuePair responseHeader : resp.getResponseHeaders()) { response.addHeader(responseHeader.getName(), responseHeader.getValue()); } if (WriteContentAsBytes_) { IOUtils.copy(resp.getContentAsStream(), response.getOutputStream()); } else { final String newContent = getModifiedContent(resp.getContentAsString()); final String contentCharset = resp.getContentCharset(); response.setCharacterEncoding(contentCharset); response.getWriter().print(newContent); } response.flushBuffer(); }

public String getString(String arg) throws Exception { URL url = new URL(arg); URLConnection con = url.openConnection(); con.setUseCaches(false); con.connect(); InputStreamReader src = new InputStreamReader(con.getInputStream(), "ISO-8859-1"); StringBuffer stb = new StringBuffer(); char[] buf = new char[1024]; int l; while ((l = src.read(buf, 0, 1024)) >= 0) { stb.append(buf, 0, l); } String res = stb.toString(); if (res.startsWith("<pannenleiter-exception")) { builder.start(new TreeNode((TreeWidget) null, false), false); InputSource xmlInput = new InputSource(new StringReader(res)); parser.setDocumentHandler(builder); parser.parse(xmlInput); } return res; }

String chooseHGVersion(String version) { String line = ""; try { URL connectURL = new URL("http://genome.ucsc.edu/cgi-bin/hgGateway?db=" + version); InputStream urlStream = connectURL.openStream(); BufferedReader reader = new BufferedReader(new InputStreamReader(urlStream)); while ((line = reader.readLine()) != null) { if (line.indexOf("hgsid") != -1) { line = line.substring(line.indexOf("hgsid")); line = line.substring(line.indexOf("VALUE=\"") + 7); line = line.substring(0, line.indexOf("\"")); return line; } } } catch (Exception e) { e.printStackTrace(); } return line; }

public String encode(String plain) { try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(plain.getBytes()); byte b[] = md.digest(); int i; StringBuffer buf = new StringBuffer(""); for (int offset = 0; offset < b.length; offset++) { i = b[offset]; if (i < 0) i += 256; if (i < 16) buf.append("0"); buf.append(Integer.toHexString(i)); } return buf.toString(); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } return null; }

@Test public void testCopy_readerToOutputStream() throws Exception { InputStream in = new ByteArrayInputStream(inData); in = new YellOnCloseInputStreamTest(in); Reader reader = new InputStreamReader(in, "US-ASCII"); ByteArrayOutputStream baout = new ByteArrayOutputStream(); OutputStream out = new YellOnFlushAndCloseOutputStreamTest(baout, false, true); IOUtils.copy(reader, out); assertEquals("Sizes differ", inData.length, baout.size()); assertTrue("Content differs", Arrays.equals(inData, baout.toByteArray())); }

public void check() { statusBar.setStatusText(Labels.getLabel("state.retrievingVersion")); Runnable checkVersionCode = new Runnable() { public void run() { BufferedReader reader = null; String message = null; int messageStyle = SWT.ICON_WARNING; try { URL url = new URL(Version.LATEST_VERSION_URL); URLConnection conn = url.openConnection(); reader = new BufferedReader(new InputStreamReader(conn.getInputStream())); String latestVersion = reader.readLine(); latestVersion = latestVersion.substring(latestVersion.indexOf(' ') + 1); if (!Version.getVersion().equals(latestVersion)) { message = Labels.getLabel("text.version.old"); message = message.replaceFirst("%LATEST", latestVersion); message = message.replaceFirst("%VERSION", Version.getVersion()); messageStyle = SWT.ICON_QUESTION | SWT.YES | SWT.NO; } else { message = Labels.getLabel("text.version.latest"); messageStyle = SWT.ICON_INFORMATION; } } catch (Exception e) { message = Labels.getLabel("exception.UserErrorException.version.latestFailed"); Logger.getLogger(getClass().getName()).log(Level.WARNING, message, e); } finally { try { if (reader != null) reader.close(); } catch (IOException e) { } final String messageToShow = message; final int messageStyleToShow = messageStyle; Display.getDefault().asyncExec(new Runnable() { public void run() { statusBar.setStatusText(null); MessageBox messageBox = new MessageBox(statusBar.getShell(), messageStyleToShow); messageBox.setText(Version.getFullName()); messageBox.setMessage(messageToShow); if (messageBox.open() == SWT.YES) { BrowserLauncher.openURL(Version.DOWNLOAD_URL); } } }); } } }; new Thread(checkVersionCode).start(); }

public static void copyFile(final String inFile, final String outFile) { FileChannel in = null; FileChannel out = null; try { in = new FileInputStream(inFile).getChannel(); out = new FileOutputStream(outFile).getChannel(); in.transferTo(0, in.size(), out); } catch (final Exception e) { } finally { if (in != null) { try { in.close(); } catch (final Exception e) { } } if (out != null) { try { out.close(); } catch (final Exception e) { } } } }

private String loadSchemas() { StringWriter writer = new StringWriter(); try { IOUtils.copy(CoreOdfValidator.class.getResourceAsStream("schema_list.properties"), writer); } catch (IOException e) { e.printStackTrace(); } return writer.toString(); }

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 = 0; 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 < 0x10) sb.append('0'); sb.append(Integer.toHexString(b)); } valueAfterMD5 = sb.toString(); } catch (Exception e) { System.out.println("Error:" + e); } }

@Test public void testXMLDBURLStreamHandler() { System.out.println("testXMLDBURLStreamHandler"); ByteArrayOutputStream baos = new ByteArrayOutputStream(); try { URL url = new URL(XMLDB_URL_1); InputStream is = url.openStream(); copyDocument(is, baos); is.close(); } catch (Exception ex) { ex.printStackTrace(); LOG.error(ex); fail(ex.getMessage()); } }

public void doPost(HttpServletRequest req, HttpServletResponse res) throws ServletException, IOException { PrintWriter out = null; ServletOutputStream outstream = null; try { String action = req.getParameter("nmrshiftdbaction"); String relativepath = ServletUtils.expandRelative(this.getServletConfig(), "/WEB-INF"); TurbineConfig tc = new TurbineConfig(relativepath + "..", relativepath + getServletConfig().getInitParameter("properties")); tc.init(); int spectrumId = -1; DBSpectrum spectrum = null; Export export = null; String format = req.getParameter("format"); if (action.equals("test")) { try { res.setContentType("text/plain"); out = res.getWriter(); List l = DBSpectrumPeer.executeQuery("select SPECTRUM_ID from SPECTRUM limit 1"); if (l.size() > 0) spectrumId = ((Record) l.get(0)).getValue(1).asInt(); out.write("success"); } catch (Exception ex) { out.write("failure"); } } else if (action.equals("rss")) { int numbertoexport = 10; out = res.getWriter(); if (req.getParameter("numbertoexport") != null) { try { numbertoexport = Integer.parseInt(req.getParameter("numbertoexport")); if (numbertoexport < 1 || numbertoexport > 20) throw new NumberFormatException("Number to small/large"); } catch (NumberFormatException ex) { out.println("The parameter <code>numbertoexport</code>must be an integer from 1 to 20"); } } res.setContentType("text/xml"); RssWriter rssWriter = new RssWriter(); rssWriter.setWriter(res.getWriter()); AtomContainerSet soac = new AtomContainerSet(); String query = "select distinct MOLECULE.MOLECULE_ID from MOLECULE, SPECTRUM where SPECTRUM.MOLECULE_ID = MOLECULE.MOLECULE_ID and SPECTRUM.REVIEW_FLAG =\"true\" order by MOLECULE.DATE desc;"; List l = NmrshiftdbUserPeer.executeQuery(query); for (int i = 0; i < numbertoexport; i++) { if (i == l.size()) break; DBMolecule mol = DBMoleculePeer.retrieveByPK(new NumberKey(((Record) l.get(i)).getValue(1).asInt())); IMolecule cdkmol = mol.getAsCDKMoleculeAsEntered(1); soac.addAtomContainer(cdkmol); rssWriter.getLinkmap().put(cdkmol, mol.getEasylink(req)); rssWriter.getDatemap().put(cdkmol, mol.getDate()); rssWriter.getTitlemap().put(cdkmol, mol.getChemicalNamesAsOneStringWithFallback()); rssWriter.getCreatormap().put(cdkmol, mol.getNmrshiftdbUser().getUserName()); rssWriter.setCreator(GeneralUtils.getAdminEmail(getServletConfig())); Vector v = mol.getDBCanonicalNames(); for (int k = 0; k < v.size(); k++) { DBCanonicalName canonName = (DBCanonicalName) v.get(k); if (canonName.getDBCanonicalNameType().getCanonicalNameType() == "INChI") { rssWriter.getInchimap().put(cdkmol, canonName.getName()); break; } } rssWriter.setTitle("NMRShiftDB"); rssWriter.setLink("http://www.nmrshiftdb.org"); rssWriter.setDescription("NMRShiftDB is an open-source, open-access, open-submission, open-content web database for chemical structures and their nuclear magnetic resonance data"); rssWriter.setPublisher("NMRShiftDB.org"); rssWriter.setImagelink("http://www.nmrshiftdb.org/images/nmrshift-logo.gif"); rssWriter.setAbout("http://www.nmrshiftdb.org/NmrshiftdbServlet?nmrshiftdbaction=rss"); Collection coll = new ArrayList(); Vector spectra = mol.selectSpectra(null); for (int k = 0; k < spectra.size(); k++) { Element el = ((DBSpectrum) spectra.get(k)).getCmlSpect(); Element el2 = el.getChildElements().get(0); el.removeChild(el2); coll.add(el2); } rssWriter.getMultiMap().put(cdkmol, coll); } rssWriter.write(soac); } else if (action.equals("getattachment")) { res.setContentType("application/zip"); outstream = res.getOutputStream(); DBSample sample = DBSamplePeer.retrieveByPK(new NumberKey(req.getParameter("sampleid"))); outstream.write(sample.getAttachment()); } else if (action.equals("createreport")) { res.setContentType("application/pdf"); outstream = res.getOutputStream(); boolean yearly = req.getParameter("style").equals("yearly"); int yearstart = Integer.parseInt(req.getParameter("yearstart")); int yearend = Integer.parseInt(req.getParameter("yearend")); int monthstart = 0; int monthend = 0; if (!yearly) { monthstart = Integer.parseInt(req.getParameter("monthstart")); monthend = Integer.parseInt(req.getParameter("monthend")); } int type = Integer.parseInt(req.getParameter("type")); JasperReport jasperReport = (JasperReport) JRLoader.loadObject(relativepath + "/reports/" + (yearly ? "yearly" : "monthly") + "_report_" + type + ".jasper"); Map parameters = new HashMap(); if (yearly) parameters.put("HEADER", "Report for years " + yearstart + " - " + yearend); else parameters.put("HEADER", "Report for " + monthstart + "/" + yearstart + " - " + monthend + "/" + yearend); DBConnection dbconn = TurbineDB.getConnection(); Connection conn = dbconn.getConnection(); Statement stmt = conn.createStatement(); ResultSet rs = null; if (type == 1) { rs = stmt.executeQuery("select YEAR(DATE) as YEAR, " + (yearly ? "" : " MONTH(DATE) as MONTH, ") + "AFFILIATION_1, AFFILIATION_2, MACHINE.NAME as NAME, count(*) as C, sum(WISHED_SPECTRUM like '%13C%' or WISHED_SPECTRUM like '%variable temperature%' or WISHED_SPECTRUM like '%ID sel. NOE%' or WISHED_SPECTRUM like '%solvent suppression%' or WISHED_SPECTRUM like '%standard spectrum%') as 1_D, sum(WISHED_SPECTRUM like '%H,H-COSY%' or WISHED_SPECTRUM like '%NOESY%' or WISHED_SPECTRUM like '%HMQC%' or WISHED_SPECTRUM like '%HMBC%') as 2_D, sum(OTHER_WISHED_SPECTRUM!='') as SPECIAL, sum(OTHER_NUCLEI!='') as HETERO, sum(PROCESS='self') as SELF, sum(PROCESS='robot') as ROBOT, sum(PROCESS='worker') as OPERATOR from (SAMPLE join TURBINE_USER using (USER_ID)) join MACHINE on MACHINE.MACHINE_ID=SAMPLE.MACHINE where YEAR(DATE)>=" + yearstart + " and YEAR(DATE)<=" + yearend + " and LOGIN_NAME<>'testuser' group by YEAR, " + (yearly ? "" : "MONTH, ") + "AFFILIATION_1, AFFILIATION_2, MACHINE.NAME"); } else if (type == 2) { rs = stmt.executeQuery("select YEAR(DATE) as YEAR, " + (yearly ? "" : " MONTH(DATE) as MONTH, ") + "MACHINE.NAME as NAME, count(*) as C, sum(WISHED_SPECTRUM like '%13C%' or WISHED_SPECTRUM like '%variable temperature%' or WISHED_SPECTRUM like '%ID sel. NOE%' or WISHED_SPECTRUM like '%solvent suppression%' or WISHED_SPECTRUM like '%standard spectrum%') as 1_D, sum(WISHED_SPECTRUM like '%H,H-COSY%' or WISHED_SPECTRUM like '%NOESY%' or WISHED_SPECTRUM like '%HMQC%' or WISHED_SPECTRUM like '%HMBC%') as 2_D, sum(OTHER_WISHED_SPECTRUM!='') as SPECIAL, sum(OTHER_NUCLEI!='') as HETERO, sum(PROCESS='self') as SELF, sum(PROCESS='robot') as ROBOT, sum(PROCESS='worker') as OPERATOR from (SAMPLE join TURBINE_USER using (USER_ID)) join MACHINE on MACHINE.MACHINE_ID=SAMPLE.MACHINE group by YEAR, " + (yearly ? "" : "MONTH, ") + "MACHINE.NAME"); } JasperPrint jasperPrint = JasperFillManager.fillReport(jasperReport, parameters, new JRResultSetDataSource(rs)); JasperExportManager.exportReportToPdfStream(jasperPrint, outstream); dbconn.close(); } else if (action.equals("exportcmlbyinchi")) { res.setContentType("text/xml"); out = res.getWriter(); String inchi = req.getParameter("inchi"); String spectrumtype = req.getParameter("spectrumtype"); Criteria crit = new Criteria(); crit.add(DBCanonicalNamePeer.NAME, inchi); crit.addJoin(DBCanonicalNamePeer.MOLECULE_ID, DBSpectrumPeer.MOLECULE_ID); crit.addJoin(DBSpectrumPeer.SPECTRUM_TYPE_ID, DBSpectrumTypePeer.SPECTRUM_TYPE_ID); crit.add(DBSpectrumTypePeer.NAME, spectrumtype); try { GeneralUtils.logToSql(crit.toString(), null); } catch (Exception ex) { } Vector spectra = DBSpectrumPeer.doSelect(crit); if (spectra.size() == 0) { out.write("No such molecule or spectrum"); } else { Element cmlElement = new Element("cml"); cmlElement.addAttribute(new Attribute("convention", "nmrshiftdb-convention")); cmlElement.setNamespaceURI("http://www.xml-cml.org/schema"); Element parent = ((DBSpectrum) spectra.get(0)).getDBMolecule().getCML(1); nu.xom.Node cmldoc = parent.getChild(0); ((Element) cmldoc).setNamespaceURI("http://www.xml-cml.org/schema"); parent.removeChildren(); cmlElement.appendChild(cmldoc); for (int k = 0; k < spectra.size(); k++) { Element parentspec = ((DBSpectrum) spectra.get(k)).getCmlSpect(); Node spectrumel = parentspec.getChild(0); parentspec.removeChildren(); cmlElement.appendChild(spectrumel); ((Element) spectrumel).setNamespaceURI("http://www.xml-cml.org/schema"); } out.write(cmlElement.toXML()); } } else if (action.equals("namelist")) { res.setContentType("application/zip"); outstream = res.getOutputStream(); ByteArrayOutputStream baos = new ByteArrayOutputStream(); ZipOutputStream zipout = new ZipOutputStream(baos); Criteria crit = new Criteria(); crit.addJoin(DBMoleculePeer.MOLECULE_ID, DBSpectrumPeer.MOLECULE_ID); crit.add(DBSpectrumPeer.REVIEW_FLAG, "true"); Vector v = DBMoleculePeer.doSelect(crit); for (int i = 0; i < v.size(); i++) { if (i % 500 == 0) { if (i != 0) { zipout.write(new String("<p>The list is continued <a href=\"nmrshiftdb.names." + i + ".html\">here</a></p></body></html>").getBytes()); zipout.closeEntry(); } zipout.putNextEntry(new ZipEntry("nmrshiftdb.names." + i + ".html")); zipout.write(new String("<html><body><h1>This is a list of strcutures in <a href=\"http://www.nmrshiftdb.org\">NMRShiftDB</a>, starting at " + i + ", Its main purpose is to be found by search engines</h1>").getBytes()); } DBMolecule mol = (DBMolecule) v.get(i); zipout.write(new String("<p><a href=\"" + mol.getEasylink(req) + "\">").getBytes()); Vector cannames = mol.getDBCanonicalNames(); for (int k = 0; k < cannames.size(); k++) { zipout.write(new String(((DBCanonicalName) cannames.get(k)).getName() + " ").getBytes()); } Vector chemnames = mol.getDBChemicalNames(); for (int k = 0; k < chemnames.size(); k++) { zipout.write(new String(((DBChemicalName) chemnames.get(k)).getName() + " ").getBytes()); } zipout.write(new String("</a>. Information we have got: NMR spectra").getBytes()); Vector spectra = mol.selectSpectra(); for (int k = 0; k < spectra.size(); k++) { zipout.write(new String(((DBSpectrum) spectra.get(k)).getDBSpectrumType().getName() + ", ").getBytes()); } if (mol.hasAny3d()) zipout.write(new String("3D coordinates, ").getBytes()); zipout.write(new String("File formats: CML, mol, png, jpeg").getBytes()); zipout.write(new String("</p>").getBytes()); } zipout.write(new String("</body></html>").getBytes()); zipout.closeEntry(); zipout.close(); InputStream is = new ByteArrayInputStream(baos.toByteArray()); byte[] buf = new byte[32 * 1024]; int nRead = 0; while ((nRead = is.read(buf)) != -1) { outstream.write(buf, 0, nRead); } } else if (action.equals("predictor")) { if (req.getParameter("symbol") == null) { res.setContentType("text/plain"); out = res.getWriter(); out.write("please give the symbol to create the predictor for in the request with symbol=X (e. g. symbol=C"); } res.setContentType("application/zip"); outstream = res.getOutputStream(); ByteArrayOutputStream baos = new ByteArrayOutputStream(); ZipOutputStream zipout = new ZipOutputStream(baos); String filename = "org/openscience/nmrshiftdb/PredictionTool.class"; zipout.putNextEntry(new ZipEntry(filename)); JarInputStream jip = new JarInputStream(new FileInputStream(ServletUtils.expandRelative(getServletConfig(), "/WEB-INF/lib/nmrshiftdb-lib.jar"))); JarEntry entry = jip.getNextJarEntry(); while (entry.getName().indexOf("PredictionTool.class") == -1) { entry = jip.getNextJarEntry(); } for (int i = 0; i < entry.getSize(); i++) { zipout.write(jip.read()); } zipout.closeEntry(); zipout.putNextEntry(new ZipEntry("nmrshiftdb.csv")); int i = 0; org.apache.turbine.util.db.pool.DBConnection conn = TurbineDB.getConnection(); HashMap mapsmap = new HashMap(); while (true) { Statement stmt = conn.createStatement(); ResultSet rs = stmt.executeQuery("select HOSE_CODE, VALUE, SYMBOL from HOSE_CODES where CONDITION_TYPE='m' and WITH_RINGS=0 and SYMBOL='" + req.getParameter("symbol") + "' limit " + (i * 1000) + ", 1000"); int m = 0; while (rs.next()) { String code = rs.getString(1); Double value = new Double(rs.getString(2)); String symbol = rs.getString(3); if (mapsmap.get(symbol) == null) { mapsmap.put(symbol, new HashMap()); } for (int spheres = 6; spheres > 0; spheres--) { StringBuffer hoseCodeBuffer = new StringBuffer(); StringTokenizer st = new StringTokenizer(code, "()/"); for (int k = 0; k < spheres; k++) { if (st.hasMoreTokens()) { String partcode = st.nextToken(); hoseCodeBuffer.append(partcode); } if (k == 0) { hoseCodeBuffer.append("("); } else if (k == 3) { hoseCodeBuffer.append(")"); } else { hoseCodeBuffer.append("/"); } } String hoseCode = hoseCodeBuffer.toString(); if (((HashMap) mapsmap.get(symbol)).get(hoseCode) == null) { ((HashMap) mapsmap.get(symbol)).put(hoseCode, new ArrayList()); } ((ArrayList) ((HashMap) mapsmap.get(symbol)).get(hoseCode)).add(value); } m++; } i++; stmt.close(); if (m == 0) break; } Set keySet = mapsmap.keySet(); Iterator it = keySet.iterator(); while (it.hasNext()) { String symbol = (String) it.next(); HashMap hosemap = ((HashMap) mapsmap.get(symbol)); Set keySet2 = hosemap.keySet(); Iterator it2 = keySet2.iterator(); while (it2.hasNext()) { String hoseCode = (String) it2.next(); ArrayList list = ((ArrayList) hosemap.get(hoseCode)); double[] values = new double[list.size()]; for (int k = 0; k < list.size(); k++) { values[k] = ((Double) list.get(k)).doubleValue(); } zipout.write(new String(symbol + "|" + hoseCode + "|" + Statistics.minimum(values) + "|" + Statistics.average(values) + "|" + Statistics.maximum(values) + "\r\n").getBytes()); } } zipout.closeEntry(); zipout.close(); InputStream is = new ByteArrayInputStream(baos.toByteArray()); byte[] buf = new byte[32 * 1024]; int nRead = 0; i = 0; while ((nRead = is.read(buf)) != -1) { outstream.write(buf, 0, nRead); } } else if (action.equals("exportspec") || action.equals("exportmol")) { if (spectrumId > -1) spectrum = DBSpectrumPeer.retrieveByPK(new NumberKey(spectrumId)); else spectrum = DBSpectrumPeer.retrieveByPK(new NumberKey(req.getParameter("spectrumid"))); export = new Export(spectrum); } else if (action.equals("exportmdl")) { res.setContentType("text/plain"); outstream = res.getOutputStream(); DBMolecule mol = DBMoleculePeer.retrieveByPK(new NumberKey(req.getParameter("moleculeid"))); outstream.write(mol.getStructureFile(Integer.parseInt(req.getParameter("coordsetid")), false).getBytes()); } else if (action.equals("exportlastinputs")) { format = action; } else if (action.equals("printpredict")) { res.setContentType("text/html"); out = res.getWriter(); HttpSession session = req.getSession(); VelocityContext context = PredictPortlet.getContext(session, true, true, new StringBuffer(), getServletConfig(), req, true); StringWriter w = new StringWriter(); Velocity.mergeTemplate("predictprint.vm", "ISO-8859-1", context, w); out.println(w.toString()); } else { res.setContentType("text/html"); out = res.getWriter(); out.println("No valid action"); } if (format == null) format = ""; if (format.equals("pdf") || format.equals("rtf")) { res.setContentType("application/" + format); out = res.getWriter(); } if (format.equals("docbook")) { res.setContentType("application/zip"); outstream = res.getOutputStream(); } if (format.equals("svg")) { res.setContentType("image/x-svg"); out = res.getWriter(); } if (format.equals("tiff")) { res.setContentType("image/tiff"); outstream = res.getOutputStream(); } if (format.equals("jpeg")) { res.setContentType("image/jpeg"); outstream = res.getOutputStream(); } if (format.equals("png")) { res.setContentType("image/png"); outstream = res.getOutputStream(); } if (format.equals("mdl") || format.equals("txt") || format.equals("cml") || format.equals("cmlboth") || format.indexOf("exsection") == 0) { res.setContentType("text/plain"); out = res.getWriter(); } if (format.equals("simplehtml") || format.equals("exportlastinputs")) { res.setContentType("text/html"); out = res.getWriter(); } if (action.equals("exportlastinputs")) { int numbertoexport = 4; if (req.getParameter("numbertoexport") != null) { try { numbertoexport = Integer.parseInt(req.getParameter("numbertoexport")); if (numbertoexport < 1 || numbertoexport > 20) throw new NumberFormatException("Number to small/large"); } catch (NumberFormatException ex) { out.println("The parameter <code>numbertoexport</code>must be an integer from 1 to 20"); } } NmrshiftdbUser user = null; try { user = NmrshiftdbUserPeer.getByName(req.getParameter("username")); } catch (NmrshiftdbException ex) { out.println("Seems <code>username</code> is not OK: " + ex.getMessage()); } if (user != null) { List l = NmrshiftdbUserPeer.executeQuery("SELECT LAST_DOWNLOAD_DATE FROM TURBINE_USER where LOGIN_NAME=\"" + user.getUserName() + "\";"); Date lastDownloadDate = ((Record) l.get(0)).getValue(1).asDate(); if (((new Date().getTime() - lastDownloadDate.getTime()) / 3600000) < 24) { out.println("Your last download was at " + lastDownloadDate + ". You may download your last inputs only once a day. Sorry for this, but we need to be carefull with resources. If you want to put your last inputs on your homepage best use some sort of cache (e. g. use wget for downlaod with crond and link to this static resource))!"); } else { NmrshiftdbUserPeer.executeStatement("UPDATE TURBINE_USER SET LAST_DOWNLOAD_DATE=NOW() where LOGIN_NAME=\"" + user.getUserName() + "\";"); Vector<String> parameters = new Vector<String>(); String query = "select distinct MOLECULE.MOLECULE_ID from MOLECULE, SPECTRUM where SPECTRUM.MOLECULE_ID = MOLECULE.MOLECULE_ID and SPECTRUM.REVIEW_FLAG =\"true\" and SPECTRUM.USER_ID=" + user.getUserId() + " order by MOLECULE.DATE desc;"; l = NmrshiftdbUserPeer.executeQuery(query); String url = javax.servlet.http.HttpUtils.getRequestURL(req).toString(); url = url.substring(0, url.length() - 17); for (int i = 0; i < numbertoexport; i++) { if (i == l.size()) break; DBMolecule mol = DBMoleculePeer.retrieveByPK(new NumberKey(((Record) l.get(i)).getValue(1).asInt())); parameters.add(new String("<a href=\"" + url + "/portal/pane0/Results?nmrshiftdbaction=showDetailsFromHome&molNumber=" + mol.getMoleculeId() + "\"><img src=\"" + javax.servlet.http.HttpUtils.getRequestURL(req).toString() + "?nmrshiftdbaction=exportmol&spectrumid=" + ((DBSpectrum) mol.getDBSpectrums().get(0)).getSpectrumId() + "&format=jpeg&size=150x150&backcolor=12632256\"></a>")); } VelocityContext context = new VelocityContext(); context.put("results", parameters); StringWriter w = new StringWriter(); Velocity.mergeTemplate("lateststructures.vm", "ISO-8859-1", context, w); out.println(w.toString()); } } } if (action.equals("exportspec")) { if (format.equals("txt")) { String lastsearchtype = req.getParameter("lastsearchtype"); if (lastsearchtype.equals(NmrshiftdbConstants.TOTALSPECTRUM) || lastsearchtype.equals(NmrshiftdbConstants.SUBSPECTRUM)) { List l = ParseUtils.parseSpectrumFromSpecFile(req.getParameter("lastsearchvalues")); spectrum.initSimilarity(l, lastsearchtype.equals(NmrshiftdbConstants.SUBSPECTRUM)); } Vector v = spectrum.getOptions(); DBMolecule mol = spectrum.getDBMolecule(); out.print(mol.getChemicalNamesAsOneString(false) + mol.getMolecularFormula(false) + "; " + mol.getMolecularWeight() + " Dalton\n\r"); out.print("\n\rAtom\t"); if (spectrum.getDBSpectrumType().getElementSymbol() == ("H")) out.print("Mult.\t"); out.print("Meas."); if (lastsearchtype.equals(NmrshiftdbConstants.TOTALSPECTRUM) || lastsearchtype.equals(NmrshiftdbConstants.SUBSPECTRUM)) { out.print("\tInput\tDiff"); } out.print("\n\r"); out.print("No.\t"); if (spectrum.getDBSpectrumType().getElementSymbol() == ("H")) out.print("\t"); out.print("Shift"); if (lastsearchtype.equals(NmrshiftdbConstants.TOTALSPECTRUM) || lastsearchtype.equals(NmrshiftdbConstants.SUBSPECTRUM)) { out.print("\tShift\tM-I"); } out.print("\n\r"); for (int i = 0; i < v.size(); i++) { out.print(((ValuesForVelocityBean) v.get(i)).getDisplayText() + "\t" + ((ValuesForVelocityBean) v.get(i)).getRange()); if (lastsearchtype.equals(NmrshiftdbConstants.TOTALSPECTRUM) || lastsearchtype.equals(NmrshiftdbConstants.SUBSPECTRUM)) { out.print("\t" + ((ValuesForVelocityBean) v.get(i)).getNameForElements() + "\t" + ((ValuesForVelocityBean) v.get(i)).getDelta()); } out.print("\n\r"); } } if (format.equals("simplehtml")) { String i1 = export.getImage(false, "jpeg", ServletUtils.expandRelative(this.getServletConfig(), "/nmrshiftdbhtml") + "/tmp/" + System.currentTimeMillis(), true); export.pictures[0] = new File(i1).getName(); String i2 = export.getImage(true, "jpeg", ServletUtils.expandRelative(this.getServletConfig(), "/nmrshiftdbhtml") + "/tmp/" + System.currentTimeMillis(), true); export.pictures[1] = new File(i2).getName(); String docbook = export.getHtml(); out.print(docbook); } if (format.equals("pdf") || format.equals("rtf")) { String svgSpec = export.getSpecSvg(400, 200); String svgspecfile = relativepath + "/tmp/" + System.currentTimeMillis() + "s.svg"; new FileOutputStream(svgspecfile).write(svgSpec.getBytes()); export.pictures[1] = svgspecfile; String molSvg = export.getMolSvg(true); String svgmolfile = relativepath + "/tmp/" + System.currentTimeMillis() + "m.svg"; new FileOutputStream(svgmolfile).write(molSvg.getBytes()); export.pictures[0] = svgmolfile; String docbook = export.getDocbook("pdf", "SVG"); TransformerFactory tFactory = TransformerFactory.newInstance(); Transformer transformer = tFactory.newTransformer(new StreamSource("file:" + GeneralUtils.getNmrshiftdbProperty("docbookxslpath", getServletConfig()) + "/fo/docbook.xsl")); ByteArrayOutputStream baos = new ByteArrayOutputStream(); transformer.transform(new StreamSource(new StringReader(docbook)), new StreamResult(baos)); FopFactory fopFactory = FopFactory.newInstance(); FOUserAgent foUserAgent = fopFactory.newFOUserAgent(); OutputStream out2 = new ByteArrayOutputStream(); Fop fop = fopFactory.newFop(format.equals("rtf") ? MimeConstants.MIME_RTF : MimeConstants.MIME_PDF, foUserAgent, out2); TransformerFactory factory = TransformerFactory.newInstance(); transformer = factory.newTransformer(); Source src = new StreamSource(new StringReader(baos.toString())); Result res2 = new SAXResult(fop.getDefaultHandler()); transformer.transform(src, res2); out.print(out2.toString()); } if (format.equals("docbook")) { String i1 = relativepath + "/tmp/" + System.currentTimeMillis() + ".svg"; new FileOutputStream(i1).write(export.getSpecSvg(300, 200).getBytes()); export.pictures[0] = new File(i1).getName(); String i2 = relativepath + "/tmp/" + System.currentTimeMillis() + ".svg"; new FileOutputStream(i2).write(export.getMolSvg(true).getBytes()); export.pictures[1] = new File(i2).getName(); String docbook = export.getDocbook("pdf", "SVG"); String docbookfile = relativepath + "/tmp/" + System.currentTimeMillis() + ".xml"; new FileOutputStream(docbookfile).write(docbook.getBytes()); ByteArrayOutputStream baos = export.makeZip(new String[] { docbookfile, i1, i2 }); outstream.write(baos.toByteArray()); } if (format.equals("svg")) { out.print(export.getSpecSvg(400, 200)); } if (format.equals("tiff") || format.equals("jpeg") || format.equals("png")) { InputStream is = new FileInputStream(export.getImage(false, format, relativepath + "/tmp/" + System.currentTimeMillis(), true)); byte[] buf = new byte[32 * 1024]; int nRead = 0; while ((nRead = is.read(buf)) != -1) { outstream.write(buf, 0, nRead); } } if (format.equals("cml")) { out.print(spectrum.getCmlSpect().toXML()); } if (format.equals("cmlboth")) { Element cmlElement = new Element("cml"); cmlElement.addAttribute(new Attribute("convention", "nmrshiftdb-convention")); cmlElement.setNamespaceURI("http://www.xml-cml.org/schema"); Element parent = spectrum.getDBMolecule().getCML(1, spectrum.getDBSpectrumType().getName().equals("1H")); nu.xom.Node cmldoc = parent.getChild(0); ((Element) cmldoc).setNamespaceURI("http://www.xml-cml.org/schema"); parent.removeChildren(); cmlElement.appendChild(cmldoc); Element parentspec = spectrum.getCmlSpect(); Node spectrumel = parentspec.getChild(0); parentspec.removeChildren(); cmlElement.appendChild(spectrumel); ((Element) spectrumel).setNamespaceURI("http://www.xml-cml.org/schema"); out.write(cmlElement.toXML()); } if (format.indexOf("exsection") == 0) { StringTokenizer st = new StringTokenizer(format, "-"); st.nextToken(); String template = st.nextToken(); Criteria crit = new Criteria(); crit.add(DBSpectrumPeer.USER_ID, spectrum.getUserId()); Vector v = spectrum.getDBMolecule().getDBSpectrums(crit); VelocityContext context = new VelocityContext(); context.put("spectra", v); context.put("molecule", spectrum.getDBMolecule()); StringWriter w = new StringWriter(); Velocity.mergeTemplate("exporttemplates/" + template, "ISO-8859-1", context, w); out.write(w.toString()); } } if (action.equals("exportmol")) { int width = -1; int height = -1; if (req.getParameter("size") != null) { StringTokenizer st = new StringTokenizer(req.getParameter("size"), "x"); width = Integer.parseInt(st.nextToken()); height = Integer.parseInt(st.nextToken()); } boolean shownumbers = true; if (req.getParameter("shownumbers") != null && req.getParameter("shownumbers").equals("false")) { shownumbers = false; } if (req.getParameter("backcolor") != null) { export.backColor = new Color(Integer.parseInt(req.getParameter("backcolor"))); } if (req.getParameter("markatom") != null) { export.selected = Integer.parseInt(req.getParameter("markatom")) - 1; } if (format.equals("svg")) { out.print(export.getMolSvg(true)); } if (format.equals("tiff") || format.equals("jpeg") || format.equals("png")) { InputStream is = new FileInputStream(export.getImage(true, format, relativepath + "/tmp/" + System.currentTimeMillis(), width, height, shownumbers, null)); byte[] buf = new byte[32 * 1024]; int nRead = 0; while ((nRead = is.read(buf)) != -1) { outstream.write(buf, 0, nRead); } } if (format.equals("mdl")) { out.println(spectrum.getDBMolecule().getStructureFile(1, false)); } if (format.equals("cml")) { out.println(spectrum.getDBMolecule().getCMLString(1)); } } if (out != null) out.flush(); else outstream.flush(); } catch (Exception ex) { ex.printStackTrace(); out.print(GeneralUtils.logError(ex, "NmrshiftdbServlet", null, true)); out.flush(); } }

private DataFileType[] getDataFiles(Collection<ContentToSend> contentsToSend) { DataFileType[] files = new DataFileType[contentsToSend.size()]; int fileIndex = 0; for (ContentToSend contentToSend : contentsToSend) { DataFileType dataFile = DataFileType.Factory.newInstance(); dataFile.setFilename(contentToSend.getFileName()); dataFile.setId("D" + fileIndex); dataFile.setMimeType(contentToSend.getMimeType()); dataFile.setContentType(DataFileType.ContentType.EMBEDDED_BASE_64); final StringWriter stringWriter = new StringWriter(); final OutputStream encodeStream = Base64.newEncoder(stringWriter, 0, null); final InputStream is = contentToSend.getInputStream(); try { long sizeCopied = IOUtils.copyLarge(is, encodeStream); dataFile.setSize(BigDecimal.valueOf(sizeCopied)); } catch (IOException e) { throw new RuntimeException("Failed to get input to the file to be sent", e); } finally { IOUtils.closeQuietly(encodeStream); IOUtils.closeQuietly(is); } dataFile.setStringValue(stringWriter.toString()); files[fileIndex++] = dataFile; } return files; }

private void unzipResource(final String resourceName, final File targetDirectory) throws IOException { assertTrue(resourceName.startsWith("/")); final URL resource = this.getClass().getResource(resourceName); assertNotNull("Expected '" + resourceName + "' not found.", resource); assertTrue(targetDirectory.isAbsolute()); FileUtils.deleteDirectory(targetDirectory); assertTrue(targetDirectory.mkdirs()); ZipInputStream in = null; boolean suppressExceptionOnClose = true; try { in = new ZipInputStream(resource.openStream()); ZipEntry e; while ((e = in.getNextEntry()) != null) { if (e.isDirectory()) { continue; } final File dest = new File(targetDirectory, e.getName()); assertTrue(dest.isAbsolute()); OutputStream out = null; try { out = FileUtils.openOutputStream(dest); IOUtils.copy(in, out); suppressExceptionOnClose = false; } finally { try { if (out != null) { out.close(); } suppressExceptionOnClose = true; } catch (final IOException ex) { if (!suppressExceptionOnClose) { throw ex; } } } in.closeEntry(); } suppressExceptionOnClose = false; } finally { try { if (in != null) { in.close(); } } catch (final IOException e) { if (!suppressExceptionOnClose) { throw e; } } } }

private void getRdfResponse(StringBuilder sb, String url) { try { String inputLine = null; BufferedReader reader = new BufferedReader(new InputStreamReader(new URL(url).openStream())); while ((inputLine = reader.readLine()) != null) { sb.append(inputLine); } reader.close(); } catch (MalformedURLException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } }

public static void main(String[] a) { ArrayList<String> allFilesToBeCopied = new ArrayList<String>(); new File(outputDir).mkdirs(); try { FileReader fis = new FileReader(completeFileWithDirToCathFileList); BufferedReader bis = new BufferedReader(fis); String line = ""; String currentCombo = ""; while ((line = bis.readLine()) != null) { String[] allEntries = line.split("\\s+"); String fileName = allEntries[0]; String thisCombo = allEntries[1] + allEntries[2] + allEntries[3] + allEntries[4]; if (currentCombo.equals(thisCombo)) { } else { System.out.println("merke: " + fileName); allFilesToBeCopied.add(fileName); currentCombo = thisCombo; } } System.out.println(allFilesToBeCopied.size()); for (String file : allFilesToBeCopied) { try { FileChannel srcChannel = new FileInputStream(CathDir + file).getChannel(); FileChannel dstChannel = new FileOutputStream(outputDir + file).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (IOException e) { e.printStackTrace(); } } } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } }

private boolean copyFiles(File sourceDir, File destinationDir) { boolean result = false; try { if (sourceDir != null && destinationDir != null && sourceDir.exists() && destinationDir.exists() && sourceDir.isDirectory() && destinationDir.isDirectory()) { File sourceFiles[] = sourceDir.listFiles(); if (sourceFiles != null && sourceFiles.length > 0) { File destFiles[] = destinationDir.listFiles(); if (destFiles != null && destFiles.length > 0) { for (int i = 0; i < destFiles.length; i++) { if (destFiles[i] != null) { destFiles[i].delete(); } } } for (int i = 0; i < sourceFiles.length; i++) { if (sourceFiles[i] != null && sourceFiles[i].exists() && sourceFiles[i].isFile()) { String fileName = destFiles[i].getName(); File destFile = new File(destinationDir.getAbsolutePath() + "/" + fileName); if (!destFile.exists()) destFile.createNewFile(); FileInputStream in = new FileInputStream(sourceFiles[i]); FileOutputStream out = new FileOutputStream(destFile); FileChannel fcIn = in.getChannel(); FileChannel fcOut = out.getChannel(); fcIn.transferTo(0, fcIn.size(), fcOut); } } } } result = true; } catch (Exception e) { System.out.println("Exception in copyFiles Method : " + e); } return result; }

public static boolean decodeFileToFile(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.DECODE); 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; }

void copyFile(File src, File dst) throws IOException { FileInputStream fis = new FileInputStream(src); byte[] buf = new byte[10000]; int n; FileOutputStream fos = new FileOutputStream(dst); while ((n = fis.read(buf)) > 0) fos.write(buf, 0, n); fis.close(); fos.close(); copied++; }

@Override protected void copyContent(String filename) throws IOException { InputStream in = null; try { in = LOADER.getResourceAsStream(RES_PKG + filename); ByteArrayOutputStream out = new ByteArrayOutputStream(); IOUtils.copy(in, out); setResponseData(out.toByteArray()); } finally { if (in != null) { in.close(); } } }

public void copyFile(String source_name, String dest_name) throws IOException { File source_file = new File(source_name); File destination_file = new File(dest_name); Reader source = null; Writer destination = null; char[] buffer; int bytes_read; try { if (!source_file.exists() || !source_file.isFile()) throw new FileCopyException("FileCopy: no such source file: " + source_name); if (!source_file.canRead()) throw new FileCopyException("FileCopy: source file " + "is unreadable: " + source_name); if (destination_file.exists()) { if (destination_file.isFile()) { DataInputStream in = new DataInputStream(System.in); String response; if (!destination_file.canWrite()) throw new FileCopyException("FileCopy: destination " + "file is unwriteable: " + dest_name); } else { throw new FileCopyException("FileCopy: destination " + "is not a file: " + dest_name); } } else { File parentdir = parent(destination_file); if (!parentdir.exists()) throw new FileCopyException("FileCopy: destination " + "directory doesn't exist: " + dest_name); if (!parentdir.canWrite()) throw new FileCopyException("FileCopy: destination " + "directory is unwriteable: " + dest_name); } source = new BufferedReader(new FileReader(source_file)); destination = new BufferedWriter(new FileWriter(destination_file)); buffer = new char[1024]; while (true) { bytes_read = source.read(buffer, 0, 1024); if (bytes_read == -1) break; destination.write(buffer, 0, bytes_read); } } finally { if (source != null) { try { source.close(); } catch (IOException e) { ; } } if (destination != null) { try { destination.close(); } catch (IOException e) { ; } } } }

private FileLog(LOG_LEVEL displayLogLevel, LOG_LEVEL logLevel, String logPath) { this.logLevel = logLevel; this.displayLogLevel = displayLogLevel; if (null != logPath) { logFile = new File(logPath, "current.log"); log(LOG_LEVEL.DEBUG, "FileLog", "Initialising logfile " + logFile.getAbsolutePath() + " ."); try { if (logFile.exists()) { if (!logFile.renameTo(new File(logPath, System.currentTimeMillis() + ".log"))) { File newFile = new File(logPath, System.currentTimeMillis() + ".log"); if (newFile.exists()) { log(LOG_LEVEL.WARN, "FileLog", "The file (" + newFile.getAbsolutePath() + newFile.getName() + ") already exists, will overwrite it."); newFile.delete(); } newFile.createNewFile(); FileInputStream inStream = new FileInputStream(logFile); FileOutputStream outStream = new FileOutputStream(newFile); byte buffer[] = null; int offSet = 0; while (inStream.read(buffer, offSet, 2048) != -1) { outStream.write(buffer); offSet += 2048; } inStream.close(); outStream.close(); logFile.delete(); logFile = new File(logPath, "current.log"); } } logFile.createNewFile(); } catch (IOException e) { logFile = null; } } else { logFile = null; } }

public void init(File file) { InputStream is = null; ByteArrayOutputStream os = null; try { is = new FileInputStream(file); os = new ByteArrayOutputStream(); IOUtils.copy(is, os); } catch (Throwable e) { throw new VisualizerEngineException("Unexcpected exception while reading MDF file", e); } if (simulationEngine != null) simulationEngine.stopSimulation(); simulationEngine = new TrafficAsynchSimulationEngine(); simulationEngine.init(MDFReader.read(os.toByteArray())); simulationEngineThread = null; }

public void run() { for (int i = 0; i < iClNumberOfCycles; i++) { try { long lStartTime = System.currentTimeMillis(); InputStream in = urlClDestinationURL.openStream(); byte buf[] = new byte[1024]; int num; while ((num = in.read(buf)) > 0) ; in.close(); long lStopTime = System.currentTimeMillis(); Node.getLogger().write((lStopTime - lStartTime) + " ms"); avgCalls.update(lStopTime - lStartTime); System.out.print("*"); System.out.flush(); calls.update(); } catch (Exception e) { cntErrors.update(); System.out.print("X"); System.out.flush(); } } }

public static File getFileFromURL(URL url) { File tempFile; BufferedInputStream in = null; BufferedOutputStream out = null; try { String tempDir = System.getProperty("java.io.tmpdir", "."); tempFile = File.createTempFile("xxindex", ".tmp", new File(tempDir)); tempFile.deleteOnExit(); InputStream is = url.openStream(); in = new BufferedInputStream(is); FileOutputStream fos = new FileOutputStream(tempFile); out = new BufferedOutputStream(fos); byte[] b = new byte[1]; while (in.read(b) >= 0) { out.write(b); } logger.debug(url + " written to local file " + tempFile.getAbsolutePath()); } catch (IOException e) { throw new IllegalStateException("Could not create local file for URL: " + url, e); } finally { try { if (in != null) { in.close(); } if (out != null) { out.close(); } } catch (IOException e) { } } return tempFile; }

public void playSIDFromHVSC(String name) { player.reset(); player.setStatus("Loading song: " + name); URL url; try { if (name.startsWith("/")) { name = name.substring(1); } url = getResource(hvscBase + name); if (player.readSID(url.openConnection().getInputStream())) { player.playSID(); } } catch (IOException ioe) { System.out.println("Could not load: "); ioe.printStackTrace(); player.setStatus("Could not load SID: " + ioe.getMessage()); } }

public static void main(String[] args) { LogFrame.getInstance(); for (int i = 0; i < args.length; i++) { String arg = args[i]; if (arg.trim().startsWith(DEBUG_PARAMETER_NAME + "=")) { properties.put(DEBUG_PARAMETER_NAME, arg.trim().substring(DEBUG_PARAMETER_NAME.length() + 1).trim()); if (properties.getProperty(DEBUG_PARAMETER_NAME).toLowerCase().equals(DEBUG_TRUE)) { DEBUG = true; } } else if (arg.trim().startsWith(AUTOCONNECT_PARAMETER_NAME + "=")) { properties.put(AUTOCONNECT_PARAMETER_NAME, arg.trim().substring(AUTOCONNECT_PARAMETER_NAME.length() + 1).trim()); } else if (arg.trim().startsWith(SITE_CONFIG_URL_PARAMETER_NAME + "=")) { properties.put(SITE_CONFIG_URL_PARAMETER_NAME, arg.trim().substring(SITE_CONFIG_URL_PARAMETER_NAME.length() + 1).trim()); } else if (arg.trim().startsWith(DOCSERVICE_URL_PARAMETER_NAME + "=")) { properties.put(DOCSERVICE_URL_PARAMETER_NAME, arg.trim().substring(DOCSERVICE_URL_PARAMETER_NAME.length() + 1).trim()); } else if (arg.trim().startsWith(DOC_ID_PARAMETER_NAME + "=")) { properties.put(DOC_ID_PARAMETER_NAME, arg.trim().substring(DOC_ID_PARAMETER_NAME.length() + 1).trim()); } else if (arg.trim().startsWith(DOCSERVICE_PROXY_FACTORY_PARAMETER_NAME + "=")) { properties.put(DOCSERVICE_PROXY_FACTORY_PARAMETER_NAME, arg.trim().substring(DOCSERVICE_PROXY_FACTORY_PARAMETER_NAME.length() + 1).trim()); RichUIUtils.setDocServiceProxyFactoryClassname(properties.getProperty(DOCSERVICE_PROXY_FACTORY_PARAMETER_NAME)); } else { System.out.println("WARNING! Unknown or undefined parameter: '" + arg.trim() + "'"); } } System.out.println("Annotation Diff GUI startup parameters:"); System.out.println("------------------------------"); for (Object propName : properties.keySet()) { System.out.println(propName.toString() + "=" + properties.getProperty((String) propName)); } System.out.println("------------------------------"); if (properties.getProperty(SITE_CONFIG_URL_PARAMETER_NAME) == null || properties.getProperty(SITE_CONFIG_URL_PARAMETER_NAME).length() == 0) { String err = "Mandatory parameter '" + SITE_CONFIG_URL_PARAMETER_NAME + "' is missing.\n\nApplication will exit."; System.out.println(err); JOptionPane.showMessageDialog(new JFrame(), err, "Error!", JOptionPane.ERROR_MESSAGE); System.exit(-1); } try { String context = System.getProperty(CONTEXT); if (context == null || "".equals(context)) { context = DEFAULT_CONTEXT; } String s = System.getProperty(GateConstants.GATE_HOME_PROPERTY_NAME); if (s == null || s.length() == 0) { File f = File.createTempFile("foo", ""); String gateHome = f.getParent().toString() + context; f.delete(); System.setProperty(GateConstants.GATE_HOME_PROPERTY_NAME, gateHome); f = new File(System.getProperty(GateConstants.GATE_HOME_PROPERTY_NAME)); if (!f.exists()) { f.mkdirs(); } } s = System.getProperty(GateConstants.PLUGINS_HOME_PROPERTY_NAME); if (s == null || s.length() == 0) { System.setProperty(GateConstants.PLUGINS_HOME_PROPERTY_NAME, System.getProperty(GateConstants.GATE_HOME_PROPERTY_NAME) + "/plugins"); File f = new File(System.getProperty(GateConstants.PLUGINS_HOME_PROPERTY_NAME)); if (!f.exists()) { f.mkdirs(); } } s = System.getProperty(GateConstants.GATE_SITE_CONFIG_PROPERTY_NAME); if (s == null || s.length() == 0) { System.setProperty(GateConstants.GATE_SITE_CONFIG_PROPERTY_NAME, System.getProperty(GateConstants.GATE_HOME_PROPERTY_NAME) + "/gate.xml"); } if (properties.getProperty(SITE_CONFIG_URL_PARAMETER_NAME) != null && properties.getProperty(SITE_CONFIG_URL_PARAMETER_NAME).length() > 0) { File f = new File(System.getProperty(GateConstants.GATE_SITE_CONFIG_PROPERTY_NAME)); if (f.exists()) { f.delete(); } f.getParentFile().mkdirs(); f.createNewFile(); URL url = new URL(properties.getProperty(SITE_CONFIG_URL_PARAMETER_NAME)); InputStream is = url.openStream(); FileOutputStream fos = new FileOutputStream(f); int i = is.read(); while (i != -1) { fos.write(i); i = is.read(); } fos.close(); is.close(); } try { Gate.init(); gate.Main.applyUserPreferences(); } catch (Exception e) { e.printStackTrace(); } } catch (Throwable e) { e.printStackTrace(); } MainFrame.getInstance().setVisible(true); MainFrame.getInstance().pack(); if (properties.getProperty(AUTOCONNECT_PARAMETER_NAME, "").toLowerCase().equals(AUTOCONNECT_TRUE)) { if (properties.getProperty(DOC_ID_PARAMETER_NAME) == null || properties.getProperty(DOC_ID_PARAMETER_NAME).length() == 0) { String err = "Can't autoconnect. A parameter '" + DOC_ID_PARAMETER_NAME + "' is missing."; System.out.println(err); JOptionPane.showMessageDialog(new JFrame(), err, "Error!", JOptionPane.ERROR_MESSAGE); ActionShowAnnDiffConnectDialog.getInstance().actionPerformed(null); } else { ActionConnectToAnnDiffGUI.getInstance().actionPerformed(null); } } else { ActionShowAnnDiffConnectDialog.getInstance().actionPerformed(null); } }

public static synchronized String hash(String data) { if (digest == null) { try { digest = MessageDigest.getInstance("SHA-1"); } catch (NoSuchAlgorithmException nsae) { System.err.println("Failed to load the SHA-1 MessageDigest. " + "Jive will be unable to function normally."); } } try { digest.update(data.getBytes("UTF-8")); } catch (UnsupportedEncodingException e) { System.err.println(e); } return encodeHex(digest.digest()); }

public void trimAndWriteNewSff(OutputStream out) throws IOException { TrimParser trimmer = new TrimParser(); SffParser.parseSFF(untrimmedSffFile, trimmer); tempOut.close(); headerBuilder.withNoIndex().numberOfReads(numberOfTrimmedReads); SffWriter.writeCommonHeader(headerBuilder.build(), out); InputStream in = null; try { in = new FileInputStream(tempReadDataFile); IOUtils.copyLarge(in, out); } finally { IOUtil.closeAndIgnoreErrors(in); } }

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 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 static LicenseKey parseKey(String key) throws InvalidLicenseKeyException { final String f_key = key.trim(); StringTokenizer st = new StringTokenizer(f_key, FIELD_SEPERATOR); int tc = st.countTokens(); int tc_name = tc - 9; try { final String product = st.nextToken(); final String type = st.nextToken(); final String loadStr = st.nextToken(); final int load = Integer.parseInt(loadStr); final String lowMajorVersionStr = st.nextToken(); final int lowMajorVersion = Integer.parseInt(lowMajorVersionStr); final String lowMinorVersionStr = st.nextToken(); final double lowMinorVersion = Double.parseDouble("0." + lowMinorVersionStr); final String highMajorVersionStr = st.nextToken(); final int highMajorVersion = Integer.parseInt(highMajorVersionStr); final String highMinorVersionStr = st.nextToken(); final double highMinorVersion = Double.parseDouble("0." + highMinorVersionStr); String regName = ""; for (int i = 0; i < tc_name; i++) regName += (i == 0 ? st.nextToken() : FIELD_SEPERATOR + st.nextToken()); final String randomHexStr = st.nextToken(); final String md5Str = st.nextToken(); String subKey = f_key.substring(0, f_key.indexOf(md5Str) - 1); byte[] md5; MessageDigest md = null; md = MessageDigest.getInstance("MD5"); md.update(subKey.getBytes()); md.update(FIELD_SEPERATOR.getBytes()); md.update(zuonicsPassword.getBytes()); md5 = md.digest(); String testKey = subKey + FIELD_SEPERATOR; for (int i = 0; i < md5.length; i++) testKey += Integer.toHexString(md5[i]).toUpperCase(); if (!testKey.equals(f_key)) throw new InvalidLicenseKeyException("doesn't hash"); final String f_regName = regName; return new LicenseKey() { public String getProduct() { return product; } public String getType() { return type; } public int getLoad() { return load; } public String getRegName() { return f_regName; } public double getlowVersion() { return lowMajorVersion + lowMinorVersion; } public double getHighVersion() { return highMajorVersion + highMinorVersion; } public String getRandomHexStr() { return randomHexStr; } public String getMD5HexStr() { return md5Str; } public String toString() { return f_key; } public boolean equals(Object obj) { if (obj.toString().equals(toString())) return true; return false; } }; } catch (Exception e) { throw new InvalidLicenseKeyException(e.getMessage()); } }

public String encodePassword(String rawPass, Object salt) { MessageDigest sha; try { sha = MessageDigest.getInstance("SHA"); } catch (java.security.NoSuchAlgorithmException e) { throw new LdapDataAccessException("No SHA implementation available!"); } sha.update(rawPass.getBytes()); if (salt != null) { Assert.isInstanceOf(byte[].class, salt, "Salt value must be a byte array"); sha.update((byte[]) salt); } byte[] hash = combineHashAndSalt(sha.digest(), (byte[]) salt); return (salt == null ? SHA_PREFIX : SSHA_PREFIX) + new String(Base64.encodeBase64(hash)); }

public InputStream getExportFile() { URL url = ExportAction.class.getClassLoader().getResource("sysConfig.xml"); if (url != null) try { return url.openStream(); } catch (IOException e) { e.printStackTrace(); } return null; }

public static void transfer(FileInputStream fileInStream, FileOutputStream fileOutStream) throws IOException { FileChannel fileInChannel = fileInStream.getChannel(); FileChannel fileOutChannel = fileOutStream.getChannel(); long fileInSize = fileInChannel.size(); try { long transferred = fileInChannel.transferTo(0, fileInSize, fileOutChannel); if (transferred != fileInSize) { throw new IOException("transfer() did not complete"); } } finally { ensureClose(fileInChannel, fileOutChannel); } }

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

public static XMLShowInfo NzbSearch(TVRageShowInfo tvrage, XMLShowInfo xmldata, int latestOrNext) { String newzbin_query = "", csvData = "", hellaQueueDir = "", newzbinUsr = "", newzbinPass = ""; String[] tmp; DateFormat tvRageDateFormat = new SimpleDateFormat("MMM/dd/yyyy"); DateFormat tvRageDateFormatFix = new SimpleDateFormat("yyyy-MM-dd"); newzbin_query = "?q=" + xmldata.showName + "+"; if (latestOrNext == 0) { if (xmldata.searchBy.equals("ShowName Season x Episode")) newzbin_query += tvrage.latestSeasonNum + "x" + tvrage.latestEpisodeNum; else if (xmldata.searchBy.equals("Showname SeriesNum")) newzbin_query += tvrage.latestSeriesNum; else if (xmldata.searchBy.equals("Showname YYYY-MM-DD")) { try { Date airTime = tvRageDateFormat.parse(tvrage.latestAirDate); newzbin_query += tvRageDateFormatFix.format(airTime); } catch (ParseException e) { e.printStackTrace(); } } else if (xmldata.searchBy.equals("Showname EpisodeTitle")) newzbin_query += tvrage.latestTitle; } else { if (xmldata.searchBy.equals("ShowName Season x Episode")) newzbin_query += tvrage.nextSeasonNum + "x" + tvrage.nextEpisodeNum; else if (xmldata.searchBy.equals("Showname SeriesNum")) newzbin_query += tvrage.nextSeriesNum; else if (xmldata.searchBy.equals("Showname YYYY-MM-DD")) { try { Date airTime = tvRageDateFormat.parse(tvrage.nextAirDate); newzbin_query += tvRageDateFormatFix.format(airTime); } catch (ParseException e) { e.printStackTrace(); } } else if (xmldata.searchBy.equals("Showname EpisodeTitle")) newzbin_query += tvrage.nextTitle; } newzbin_query += "&searchaction=Search"; newzbin_query += "&fpn=p"; newzbin_query += "&category=8category=11"; newzbin_query += "&area=-1"; newzbin_query += "&u_nfo_posts_only=0"; newzbin_query += "&u_url_posts_only=0"; newzbin_query += "&u_comment_posts_only=0"; newzbin_query += "&u_v3_retention=1209600"; newzbin_query += "&ps_rb_language=" + xmldata.language; newzbin_query += "&sort=ps_edit_date"; newzbin_query += "&order=desc"; newzbin_query += "&areadone=-1"; newzbin_query += "&feed=csv"; newzbin_query += "&ps_rb_video_format=" + xmldata.format; newzbin_query = newzbin_query.replaceAll(" ", "%20"); System.out.println("http://v3.newzbin.com/search/" + newzbin_query); try { URL url = new URL("http://v3.newzbin.com/search/" + newzbin_query); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); csvData = in.readLine(); if (csvData != null) { JavaNZB.searchCount++; if (searchCount == 6) { searchCount = 0; System.out.println("Sleeping for 60 seconds"); try { Thread.sleep(60000); } catch (InterruptedException e) { e.printStackTrace(); } } tmp = csvData.split(","); tmp[2] = tmp[2].substring(1, tmp[2].length() - 1); tmp[3] = tmp[3].substring(1, tmp[3].length() - 1); Pattern p = Pattern.compile("[\\\\</:>?\\[|\\]\"]"); Matcher matcher = p.matcher(tmp[3]); tmp[3] = matcher.replaceAll(" "); tmp[3] = tmp[3].replaceAll("&", "and"); URLConnection urlConn; DataOutputStream printout; url = new URL("http://v3.newzbin.com/api/dnzb/"); urlConn = url.openConnection(); urlConn.setDoInput(true); urlConn.setDoOutput(true); urlConn.setUseCaches(false); urlConn.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); printout = new DataOutputStream(urlConn.getOutputStream()); String content = "username=" + JavaNZB.newzbinUsr + "&password=" + JavaNZB.newzbinPass + "&reportid=" + tmp[2]; printout.writeBytes(content); printout.flush(); printout.close(); BufferedReader nzbInput = new BufferedReader(new InputStreamReader(urlConn.getInputStream())); String format = ""; if (xmldata.format.equals("17")) format = " Xvid"; if (xmldata.format.equals("131072")) format = " x264"; if (xmldata.format.equals("2")) format = " DVD"; if (xmldata.format.equals("4")) format = " SVCD"; if (xmldata.format.equals("8")) format = " VCD"; if (xmldata.format.equals("32")) format = " HDts"; if (xmldata.format.equals("64")) format = " WMV"; if (xmldata.format.equals("128")) format = " Other"; if (xmldata.format.equals("256")) format = " ratDVD"; if (xmldata.format.equals("512")) format = " iPod"; if (xmldata.format.equals("1024")) format = " PSP"; File f = new File(JavaNZB.hellaQueueDir, tmp[3] + format + ".nzb"); BufferedWriter out = new BufferedWriter(new FileWriter(f)); String str; System.out.println("--Downloading " + tmp[3] + format + ".nzb" + " to queue directory--"); while (null != ((str = nzbInput.readLine()))) out.write(str); nzbInput.close(); out.close(); if (latestOrNext == 0) { xmldata.episode = tvrage.latestEpisodeNum; xmldata.season = tvrage.latestSeasonNum; } else { xmldata.episode = tvrage.nextEpisodeNum; xmldata.season = tvrage.nextSeasonNum; } } else System.out.println("No new episode posted"); System.out.println(); } catch (MalformedURLException e) { } catch (IOException e) { System.out.println("IO Exception from NzbSearch"); } return xmldata; }

@Override public String compute_hash(String plaintext) { MessageDigest d; try { d = MessageDigest.getInstance(get_algorithm_name()); d.update(plaintext.getBytes()); byte[] hash = d.digest(); StringBuffer sb = new StringBuffer(); for (byte b : hash) sb.append(String.format("%02x", b)); return sb.toString(); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } return null; }

static byte[] genDigest(String pad, byte[] passwd) throws NoSuchAlgorithmException { MessageDigest digest = MessageDigest.getInstance(DIGEST_ALGORITHM); digest.update(pad.getBytes()); digest.update(passwd); return digest.digest(); }

private static String md5(String input) { String res = ""; try { MessageDigest cript = MessageDigest.getInstance("MD5"); cript.reset(); cript.update(input.getBytes()); byte[] md5 = cript.digest(); String tmp = ""; for (int i = 0; i < md5.length; i++) { tmp = (Integer.toHexString(0xFF & md5[i])); if (tmp.length() == 1) { res += "0" + tmp; } else { res += tmp; } } } catch (NoSuchAlgorithmException ex) { Log4k.error(pdfPrinter.class.getName(), ex.getMessage()); } return res; }

public void testSystemPropertyConnector() throws Exception { final String rootFolderPath = "test/ConnectorTest/fs/".toLowerCase(); final Connector connector = new SystemPropertyConnector(); final ContentResolver contentResolver = new UnionContentResolver(); final FSContentResolver fsContentResolver = new FSContentResolver(); fsContentResolver.setRootFolderPath(rootFolderPath); contentResolver.addContentResolver(fsContentResolver); contentResolver.addContentResolver(new ClasspathContentResolver()); connector.setContentResolver(contentResolver); String resultString; byte[] resultContent; Object resultObject; resultString = connector.getString("helloWorldPath"); assertNull(resultString); resultContent = connector.getContent("helloWorldPath"); assertNull(resultContent); resultObject = connector.getObject("helloWorldPath"); assertNull(resultObject); System.setProperty("helloWorldPath", "org/settings4j/connector/HelloWorld2.txt"); resultString = connector.getString("helloWorldPath"); assertNotNull(resultString); assertEquals("org/settings4j/connector/HelloWorld2.txt", resultString); resultContent = connector.getContent("helloWorldPath"); assertNotNull(resultContent); assertEquals("Hello World 2", new String(resultContent, "UTF-8")); resultObject = connector.getObject("helloWorldPath"); assertNull(resultObject); System.setProperty("helloWorldPath", "file:org/settings4j/connector/HelloWorld2.txt"); resultString = connector.getString("helloWorldPath"); assertNotNull(resultString); assertEquals("file:org/settings4j/connector/HelloWorld2.txt", resultString); resultContent = connector.getContent("helloWorldPath"); assertNull(resultObject); resultObject = connector.getObject("helloWorldPath"); assertNull(resultObject); System.setProperty("helloWorldPath", "classpath:org/settings4j/connector/HelloWorld2.txt"); resultString = connector.getString("helloWorldPath"); assertNotNull(resultString); assertEquals("classpath:org/settings4j/connector/HelloWorld2.txt", resultString); resultContent = connector.getContent("helloWorldPath"); assertNotNull(resultContent); assertEquals("Hello World 2", new String(resultContent, "UTF-8")); resultObject = connector.getObject("helloWorldPath"); assertNull(resultObject); final InputStream helloWorldIS = new ByteArrayInputStream("Hello World 2 - Test".getBytes("UTF-8")); FileUtils.forceMkdir(new File(rootFolderPath + "/org/settings4j/connector")); final String helloWorldPath = rootFolderPath + "/org/settings4j/connector/HelloWorld2.txt"; final FileOutputStream fileOutputStream = new FileOutputStream(new File(helloWorldPath)); IOUtils.copy(helloWorldIS, fileOutputStream); IOUtils.closeQuietly(helloWorldIS); IOUtils.closeQuietly(fileOutputStream); LOG.info("helloWorld2Path: " + helloWorldPath); System.setProperty("helloWorldPath", "file:org/settings4j/connector/HelloWorld2.txt"); resultString = connector.getString("helloWorldPath"); assertNotNull(resultString); assertEquals("file:org/settings4j/connector/HelloWorld2.txt", resultString); resultContent = connector.getContent("helloWorldPath"); assertNotNull(resultContent); assertEquals("Hello World 2 - Test", new String(resultContent, "UTF-8")); resultObject = connector.getObject("helloWorldPath"); assertNull(resultObject); System.setProperty("helloWorldPath", "org/settings4j/connector/HelloWorld2.txt"); resultString = connector.getString("helloWorldPath"); assertNotNull(resultString); assertEquals("org/settings4j/connector/HelloWorld2.txt", resultString); resultContent = connector.getContent("helloWorldPath"); resultContent = connector.getContent("helloWorldPath"); assertNotNull(resultContent); assertEquals("Hello World 2 - Test", new String(resultContent, "UTF-8")); resultObject = connector.getObject("helloWorldPath"); assertNull(resultObject); System.setProperty("helloWorldPath", "classpath:org/settings4j/connector/HelloWorld2.txt"); resultString = connector.getString("helloWorldPath"); assertNotNull(resultString); assertEquals("classpath:org/settings4j/connector/HelloWorld2.txt", resultString); resultContent = connector.getContent("helloWorldPath"); assertNotNull(resultContent); assertEquals("Hello World 2", new String(resultContent, "UTF-8")); resultObject = connector.getObject("helloWorldPath"); assertNull(resultObject); }

public static String submitURLRequest(String url) throws HttpException, IOException, URISyntaxException { HttpClient httpclient = new DefaultHttpClient(); InputStream stream = null; user_agents = new LinkedList<String>(); user_agents.add("Mozilla/5.0 (Windows; U; Windows NT 6.1; en-US; rv:1.9.2.2) Gecko/20100316 Firefox/3.6.2"); String response_text = ""; URI uri = new URI(url); HttpGet post = new HttpGet(uri); int MAX = user_agents.size() - 1; int index = (int) Math.round(((double) Math.random() * (MAX))); String agent = user_agents.get(index); httpclient.getParams().setParameter(CoreProtocolPNames.USER_AGENT, agent); httpclient.getParams().setParameter("User-Agent", agent); httpclient.getParams().setParameter(ClientPNames.COOKIE_POLICY, CookiePolicy.ACCEPT_NONE); HttpResponse response = httpclient.execute(post); HttpEntity entity = response.getEntity(); if (entity != null) { stream = entity.getContent(); response_text = convertStreamToString(stream); } httpclient.getConnectionManager().shutdown(); if (stream != null) { stream.close(); } return response_text; }

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); }

private void getRandomGUID(boolean secure) { MessageDigest md5 = null; final StringBuilder sbValueBeforeMD5 = new StringBuilder(); try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { logger.fatal("", e); return; } try { final long time = System.currentTimeMillis(); long rand = 0; if (secure) { rand = mySecureRand.nextLong(); } else { rand = myRand.nextLong(); } sbValueBeforeMD5.append(sId); sbValueBeforeMD5.append(":"); sbValueBeforeMD5.append(Long.toString(time)); sbValueBeforeMD5.append(":"); sbValueBeforeMD5.append(Long.toString(rand)); valueBeforeMD5 = sbValueBeforeMD5.toString(); md5.update(valueBeforeMD5.getBytes()); final byte[] array = md5.digest(); final StringBuilder sb = new StringBuilder(); for (int j = 0; j < array.length; ++j) { final int b = array[j] & 0xFF; if (b < 0x10) { sb.append('0'); } sb.append(Integer.toHexString(b)); } valueAfterMD5 = sb.toString(); } catch (Exception e) { logger.fatal("", e); } }

public static void putNextJarEntry(JarOutputStream modelStream, String name, File file) throws IOException { JarEntry entry = new JarEntry(name); entry.setSize(file.length()); modelStream.putNextEntry(entry); InputStream fileStream = new BufferedInputStream(new FileInputStream(file)); IOUtils.copy(fileStream, modelStream); fileStream.close(); }

public static void copyFile(File in, File out) throws IOException { FileChannel sourceChannel = new FileInputStream(in).getChannel(); FileChannel destinationChannel = new FileOutputStream(out).getChannel(); try { sourceChannel.transferTo(0, sourceChannel.size(), destinationChannel); } finally { sourceChannel.close(); destinationChannel.close(); } }

public void add(Site site) throws Exception { DBOperation dbo = null; Connection connection = null; PreparedStatement preparedStatement = null; ResultSet resultSet = null; try { String sqlStr = "insert into t_ip_site (id,name,description,ascii_name,site_path,remark_number,increment_index,use_status,appserver_id) VALUES(?,?,?,?,?,?,?,?,?)"; dbo = createDBOperation(); connection = dbo.getConnection(); connection.setAutoCommit(false); preparedStatement = connection.prepareStatement(sqlStr); preparedStatement.setInt(1, site.getSiteID()); preparedStatement.setString(2, site.getName()); preparedStatement.setString(3, site.getDescription()); preparedStatement.setString(4, site.getAsciiName()); preparedStatement.setString(5, site.getPath()); preparedStatement.setInt(6, site.getRemarkNumber()); preparedStatement.setString(7, site.getIncrementIndex().trim()); preparedStatement.setString(8, String.valueOf(site.getUseStatus())); preparedStatement.setString(9, String.valueOf(site.getAppserverID())); preparedStatement.executeUpdate(); String[] path = new String[1]; path[0] = site.getPath(); selfDefineAdd(path, site, connection, preparedStatement); connection.commit(); int resID = site.getSiteID() + Const.SITE_TYPE_RES; String resName = site.getName(); int resTypeID = Const.RES_TYPE_ID; int operateTypeID = Const.OPERATE_TYPE_ID; String remark = ""; AuthorityManager am = new AuthorityManager(); am.createExtResource(Integer.toString(resID), resName, resTypeID, operateTypeID, remark); site.wirteFile(); } catch (SQLException ex) { connection.rollback(); log.error("����վ��ʧ��!", ex); throw ex; } finally { close(resultSet, null, preparedStatement, connection, dbo); } }

static void test() throws SQLException { Connection conn = null; Statement st = null; ResultSet rs = null; Savepoint sp = null; try { conn = JdbcUtils.getConnection(); conn.setAutoCommit(false); st = conn.createStatement(); String sql = "update user set money=money-10 where id=1"; st.executeUpdate(sql); sp = conn.setSavepoint(); sql = "update user set money=money-10 where id=3"; st.executeUpdate(sql); sql = "select money from user where id=2"; rs = st.executeQuery(sql); float money = 0.0f; if (rs.next()) { money = rs.getFloat("money"); } if (money > 300) throw new RuntimeException("�Ѿ��������ֵ��"); sql = "update user set money=money+10 where id=2"; st.executeUpdate(sql); conn.commit(); } catch (RuntimeException e) { if (conn != null && sp != null) { conn.rollback(sp); conn.commit(); } throw e; } catch (SQLException e) { if (conn != null) conn.rollback(); throw e; } finally { JdbcUtils.free(rs, st, conn); } }

private File prepareFileForUpload(File source, String s3key) throws IOException { File tmp = File.createTempFile("dirsync", ".tmp"); tmp.deleteOnExit(); InputStream in = null; OutputStream out = null; try { in = new FileInputStream(source); out = new DeflaterOutputStream(new CryptOutputStream(new FileOutputStream(tmp), cipher, getDataEncryptionKey())); IOUtils.copy(in, out); in.close(); out.close(); return tmp; } finally { IOUtils.closeQuietly(in); IOUtils.closeQuietly(out); } }

public void copyToCurrentDir(File _copyFile, String _fileName) throws IOException { File outputFile = new File(getCurrentPath() + File.separator + _fileName); FileReader in; FileWriter out; if (!outputFile.exists()) { outputFile.createNewFile(); } in = new FileReader(_copyFile); out = new FileWriter(outputFile); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); reList(); }

public int process(ProcessorContext context) throws InterruptedException, ProcessorException { logger.info("JAISaveTask:process"); final RenderedOp im = (RenderedOp) context.get("RenderedOp"); final String path = "s3://s3.amazonaws.com/rssfetch/" + (new Guid()); final PNGEncodeParam.RGB encPar = new PNGEncodeParam.RGB(); encPar.setTransparentRGB(new int[] { 0, 0, 0 }); File tmpFile = null; try { tmpFile = File.createTempFile("thmb", ".png"); OutputStream out = new FileOutputStream(tmpFile); final ParameterBlock pb = (new ParameterBlock()).addSource(im).add(out).add("png").add(encPar); JAI.create("encode", pb, null); out.flush(); out.close(); FileInputStream in = new FileInputStream(tmpFile); final XFile xfile = new XFile(path); final XFileOutputStream xout = new XFileOutputStream(xfile); final com.luzan.common.nfs.s3.XFileExtensionAccessor xfa = ((com.luzan.common.nfs.s3.XFileExtensionAccessor) xfile.getExtensionAccessor()); if (xfa != null) { xfa.setMimeType("image/png"); xfa.setContentLength(tmpFile.length()); } IOUtils.copy(in, xout); xout.flush(); xout.close(); in.close(); context.put("outputPath", path); } catch (IOException e) { logger.error(e); throw new ProcessorException(e); } catch (Throwable e) { logger.error(e); throw new ProcessorException(e); } finally { if (tmpFile != null && tmpFile.exists()) { tmpFile.delete(); } } return TaskState.STATE_MO_START + TaskState.STATE_ENCODE; }

@Override public void run() { try { FileChannel in = new FileInputStream(inputfile).getChannel(); long pos = 0; for (int i = 1; i <= noofparts; i++) { FileChannel out = new FileOutputStream(outputfile.getAbsolutePath() + "." + "v" + i).getChannel(); status.setText("Rozdělovač: Rozděluji část " + i + ".."); in.transferTo(pos, splitsize, out); pos += splitsize; remainingsize -= splitsize; if (remainingsize < splitsize) in.transferTo(pos, remainingsize, out); pb.setValue(100 * i / noofparts); out.close(); } in.close(); if (deleteOnFinish) new File(inputfile + "").delete(); status.setText("Rozdělovač: Hotovo.."); JOptionPane.showMessageDialog(null, "Rozděleno!", "Rozdělovač", JOptionPane.INFORMATION_MESSAGE); } catch (IOException ex) { } }

private void getRandomGUID(boolean secure) { MessageDigest md5 = null; StringBuffer sbValueBeforeMD5 = new StringBuffer(128); try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { logger.error("Error: " + e); } try { long time = System.currentTimeMillis(); long rand = 0; 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(32); for (int j = 0; j < array.length; ++j) { int b = array[j] & TWO_BYTES; if (b < PAD_BELOW) sb.append('0'); sb.append(Integer.toHexString(b)); } valueAfterMD5 = sb.toString(); } catch (Exception e) { logger.error("Error:" + e); } }

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

public static String encripty(String toEncripty) { if (toEncripty != null) { try { synchronized (toEncripty) { java.security.MessageDigest md = java.security.MessageDigest.getInstance("MD5"); md.update(toEncripty.getBytes()); byte[] hash = md.digest(); StringBuffer hexString = new StringBuffer(); for (int i = 0; i < hash.length; i++) { if ((0xff & hash[i]) < 0x10) hexString.append("0" + Integer.toHexString((0xFF & hash[i]))); else hexString.append(Integer.toHexString(0xFF & hash[i])); } toEncripty = hexString.toString(); } } catch (Exception e) { e.getMessage(); } } return toEncripty; }

private String md5(String txt) { try { MessageDigest m = MessageDigest.getInstance("MD5"); m.update(txt.getBytes(), 0, txt.length()); return new BigInteger(1, m.digest()).toString(16); } catch (Exception e) { return "BAD MD5"; } }

public void init(File file) { InputStream is = null; ByteArrayOutputStream os = null; try { is = new FileInputStream(file); os = new ByteArrayOutputStream(); IOUtils.copy(is, os); } catch (Throwable e) { throw new VisualizerEngineException("Unexcpected exception while reading MDF file", e); } if (simulationEngine != null) simulationEngine.stopSimulation(); simulationEngine = new TrafficAsynchSimulationEngine(); simulationEngine.init(MDFReader.read(os.toByteArray())); simulationEngineThread = null; }

public Vector<String> getVoiceServersNames() { Vector<String> result = new Vector<String>(); boolean serverline = false; String line; String[] splitline; try { URL url = new URL(voiceaddress); URLConnection connection = url.openConnection(); BufferedReader reader = new BufferedReader(new InputStreamReader(connection.getInputStream())); while ((line = reader.readLine()) != null) { if (serverline) { splitline = line.split(":"); result.add(splitline[0]); } if (line.startsWith("!VOICE SERVERS")) { serverline = true; } } } catch (MalformedURLException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } return result; }

private String AddAction(ResultSet node, String modo) throws SQLException { Connection cn = null; Connection cndef = null; String schema = boRepository.getDefaultSchemaName(boApplication.getDefaultApplication()).toLowerCase(); try { cn = this.getRepositoryConnection(p_ctx.getApplication(), p_ctx.getBoSession().getRepository().getName(), 1); cndef = this.getRepositoryConnection(p_ctx.getApplication(), p_ctx.getBoSession().getRepository().getName(), 2); String dml = null; String objecttype = node.getString("OBJECTTYPE"); if (objecttype.equalsIgnoreCase("T")) { boolean exists = existsTable(p_ctx, schema, node.getString("OBJECTNAME").toLowerCase()); String[] sysflds = { "SYS_USER", "SYS_ICN", "SYS_DTCREATE", "SYS_DTSAVE", "SYS_ORIGIN" }; String[] sysfdef = { "VARCHAR(25)", "NUMERIC(7)", "TIMESTAMP DEFAULT now()", "TIMESTAMP", "VARCHAR(30)" }; String[] sysftyp = { "C", "N", "D", "D", "C" }; String[] sysfsiz = { "25", "7", "", "", "30" }; String[] sysfndef = { "", "", "", "", "" }; String[] sysfdes = { "", "", "", "", "" }; if (!exists && !modo.equals("3")) { dml = "CREATE TABLE " + node.getString("OBJECTNAME") + " ("; for (int i = 0; i < sysflds.length; i++) { dml += (sysflds[i] + " " + sysfdef[i] + ((i < (sysflds.length - 1)) ? "," : ")")); } String vt = node.getString("OBJECTNAME"); if (node.getString("SCHEMA").equals("DEF")) { vt = "NGD_" + vt; } else if (node.getString("SCHEMA").equals("SYS")) { vt = "SYS_" + vt; } executeDDL(dml, node.getString("SCHEMA")); } if (modo.equals("3") && exists) { executeDDL("DROP TABLE " + node.getString("OBJECTNAME"), node.getString("SCHEMA")); CallableStatement call = cndef.prepareCall("DELETE FROM NGTDIC WHERE TABLENAME=?"); call.setString(1, node.getString("OBJECTNAME")); call.executeUpdate(); call.close(); } checkDicFields(node.getString("OBJECTNAME"), node.getString("SCHEMA"), sysflds, sysftyp, sysfsiz, sysfndef, sysfdes); } if (objecttype.equalsIgnoreCase("F")) { boolean fldchg = false; boolean fldexi = false; PreparedStatement pstm = cn.prepareStatement("select column_name,udt_name,character_maximum_length,numeric_precision,numeric_scale from information_schema.columns" + " where table_name=? and column_name=? and table_schema=?"); pstm.setString(1, node.getString("TABLENAME").toLowerCase()); pstm.setString(2, node.getString("OBJECTNAME").toLowerCase()); pstm.setString(3, schema); ResultSet rslt = pstm.executeQuery(); if (rslt.next()) { int fieldsiz = rslt.getInt(3); int fielddec = rslt.getInt(5); if (",C,N,".indexOf("," + getNgtFieldTypeFromDDL(rslt.getString(2)) + ",") != -1) { if (getNgtFieldTypeFromDDL(rslt.getString(2)).equals("N")) { fieldsiz = rslt.getInt(4); } if (fielddec != 0) { if (!(fieldsiz + "," + fielddec).equals(node.getString("FIELDSIZE"))) { fldchg = true; } } else { if (!((fieldsiz == 0) && ((node.getString("FIELDSIZE") == null) || (node.getString("FIELDSIZE").length() == 0)))) { if (!("" + fieldsiz).equals(node.getString("FIELDSIZE"))) { fldchg = true; } } } } fldexi = true; } else { fldexi = false; } rslt.close(); pstm.close(); boolean drop = false; if (("20".indexOf(modo) != -1) && !fldexi) { dml = "ALTER TABLE " + node.getString("TABLENAME") + " add \"" + node.getString("OBJECTNAME").toLowerCase() + "\" "; } else if (("20".indexOf(modo) != -1) && fldexi && fldchg) { dml = "ALTER TABLE " + node.getString("TABLENAME") + " ALTER COLUMN \"" + node.getString("OBJECTNAME").toLowerCase() + "\" "; } else if (modo.equals("3") && fldexi) { dml = "ALTER TABLE " + node.getString("TABLENAME") + " drop COLUMN \"" + node.getString("OBJECTNAME").toLowerCase() + "\" "; String sql = "SELECT tc.constraint_name,tc.constraint_type" + " FROM information_schema.table_constraints tc" + " LEFT JOIN information_schema.key_column_usage kcu" + " ON tc.constraint_catalog = kcu.constraint_catalog" + " AND tc.constraint_schema = kcu.constraint_schema" + " AND tc.constraint_name = kcu.constraint_name" + " LEFT JOIN information_schema.referential_constraints rc" + " ON tc.constraint_catalog = rc.constraint_catalog" + " AND tc.constraint_schema = rc.constraint_schema" + " AND tc.constraint_name = rc.constraint_name" + " LEFT JOIN information_schema.constraint_column_usage ccu" + " ON rc.unique_constraint_catalog = ccu.constraint_catalog" + " AND rc.unique_constraint_schema = ccu.constraint_schema" + " AND rc.unique_constraint_name = ccu.constraint_name" + " WHERE tc.table_name = ?" + " AND kcu.column_name = ?" + " and tc.table_schema=?"; PreparedStatement pstmrelc = cn.prepareStatement(sql); pstmrelc.setString(1, node.getString("TABLENAME").toLowerCase()); pstmrelc.setString(2, node.getString("OBJECTNAME").toLowerCase()); pstmrelc.setString(3, schema); ResultSet rsltrelc = pstmrelc.executeQuery(); while (rsltrelc.next()) { String constname = rsltrelc.getString(1); String consttype = rsltrelc.getString(2); PreparedStatement pstmdic = cndef.prepareStatement("DELETE FROM NGTDIC WHERE TABLENAME=? AND OBJECTTYPE=? AND OBJECTNAME=?"); pstmdic.setString(1, node.getString("TABLENAME")); pstmdic.setString(2, consttype.equals("R") ? "FK" : "PK"); pstmdic.setString(3, constname); int nrecs = pstmdic.executeUpdate(); pstm.close(); executeDDL("ALTER TABLE " + node.getString("TABLENAME") + " DROP CONSTRAINT " + constname, node.getString("SCHEMA")); } rsltrelc.close(); pstmrelc.close(); } if ((dml != null) && (dml.length() > 0) && !modo.equals("3")) { String mfield = node.getString("MACROFIELD"); if ((mfield != null) && !(!mfield.equals("TEXTOLIVRE") && !mfield.equals("NUMEROLIVRE") && !mfield.equals("TEXT") && !mfield.equals("BLOB") && !mfield.equals("MDATA"))) { String ngtft = ""; if (mfield.equals("TEXTOLIVRE")) { ngtft = "C"; } else if (mfield.equals("NUMEROLIVRE")) { ngtft = "N"; } else if (mfield.equals("RAW")) { ngtft = "RAW"; } else if (mfield.equals("TIMESTAMP")) { ngtft = "TIMESTAMP"; } else if (mfield.equals("MDATA")) { ngtft = "D"; } else if (mfield.equals("TEXT")) { ngtft = "CL"; } else if (mfield.equals("BLOB")) { ngtft = "BL"; } dml += getDDLFieldFromNGT(ngtft, node.getString("FIELDSIZE")); } else if ((mfield != null) && (mfield.length() > 0)) { dml += getMacrofieldDef(cndef, node.getString("MACROFIELD")); } else { dml += getDDLFieldFromNGT(node.getString("FIELDTYPE"), node.getString("FIELDSIZE")); } } String[] flds = new String[1]; flds[0] = node.getString("OBJECTNAME"); if (dml != null) { executeDDL(dml, node.getString("SCHEMA")); } } if (objecttype.equalsIgnoreCase("V")) { String viewText = null; PreparedStatement pstmrelc = cn.prepareStatement("SELECT view_definition FROM information_schema.views WHERE table_name=? " + "and table_schema=?"); pstmrelc.setString(1, node.getString("OBJECTNAME").toLowerCase()); pstmrelc.setString(2, schema.toLowerCase()); ResultSet rsltrelc = pstmrelc.executeQuery(); boolean exists = false; if (rsltrelc.next()) { exists = true; viewText = rsltrelc.getString(1); viewText = viewText.substring(0, viewText.length() - 1); } rsltrelc.close(); pstmrelc.close(); if (!modo.equals("3")) { String vExpression = node.getString("EXPRESSION"); if (!vExpression.toLowerCase().equals(viewText)) { dml = "CREATE OR REPLACE VIEW \"" + node.getString("OBJECTNAME") + "\" AS \n" + vExpression; executeDDL(dml, node.getString("SCHEMA")); } } else { if (exists) { dml = "DROP VIEW " + node.getString("OBJECTNAME"); executeDDL(dml, node.getString("SCHEMA")); CallableStatement call = cndef.prepareCall("DELETE FROM NGTDIC WHERE TABLENAME=?"); call.setString(1, node.getString("OBJECTNAME")); call.executeUpdate(); call.close(); } } } if (objecttype.startsWith("PCK")) { String templatestr = node.getString("EXPRESSION"); String bstr = "/*begin_package*/"; String estr = "/*end_package*/"; if ("02".indexOf(modo) != -1) { if (templatestr.indexOf(bstr) != -1) { int defpos; dml = templatestr.substring(templatestr.indexOf(bstr), defpos = templatestr.indexOf(estr)); dml = "create or replace package " + node.getString("OBJECTNAME") + " is \n" + dml + "end " + node.getString("OBJECTNAME") + ";\n"; executeDDL(dml, node.getString("SCHEMA")); bstr = "/*begin_package_body*/"; estr = "/*end_package_body*/"; if (templatestr.indexOf(bstr, defpos) != -1) { dml = templatestr.substring(templatestr.indexOf(bstr, defpos), templatestr.indexOf(estr, defpos)); dml = "create or replace package body " + node.getString("OBJECTNAME") + " is \n" + dml + "end " + node.getString("OBJECTNAME") + ";\n"; executeDDL(dml, node.getString("SCHEMA")); } } else { } } } if (objecttype.startsWith("PK") || objecttype.startsWith("UN")) { String sql = "SELECT kcu.column_name" + " FROM information_schema.table_constraints tc" + " LEFT JOIN information_schema.key_column_usage kcu" + " ON tc.constraint_catalog = kcu.constraint_catalog" + " AND tc.constraint_schema = kcu.constraint_schema" + " AND tc.constraint_name = kcu.constraint_name" + " LEFT JOIN information_schema.referential_constraints rc" + " ON tc.constraint_catalog = rc.constraint_catalog" + " AND tc.constraint_schema = rc.constraint_schema" + " AND tc.constraint_name = rc.constraint_name" + " LEFT JOIN information_schema.constraint_column_usage ccu" + " ON rc.unique_constraint_catalog = ccu.constraint_catalog" + " AND rc.unique_constraint_schema = ccu.constraint_schema" + " AND rc.unique_constraint_name = ccu.constraint_name" + " WHERE tc.table_name = ?" + " AND tc.constraint_name = ?" + " and tc.table_schema=? order by ordinal_position"; PreparedStatement pstm = cn.prepareStatement(sql); pstm.setString(1, node.getString("TABLENAME").toLowerCase()); pstm.setString(2, node.getString("OBJECTNAME").toLowerCase()); pstm.setString(3, schema.toLowerCase()); boolean isunique = objecttype.startsWith("UN"); ResultSet rslt = pstm.executeQuery(); boolean exists = false; StringBuffer expression = new StringBuffer(); while (rslt.next()) { if (exists) { expression.append(','); } exists = true; expression.append(rslt.getString(1)); } boolean diff = !expression.toString().toUpperCase().equals(node.getString("EXPRESSION")); rslt.close(); pstm.close(); if ((modo.equals("3") || diff) && exists) { sql = "SELECT tc.constraint_name,tc.table_name" + " FROM information_schema.table_constraints tc" + " LEFT JOIN information_schema.key_column_usage kcu" + " ON tc.constraint_catalog = kcu.constraint_catalog" + " AND tc.constraint_schema = kcu.constraint_schema" + " AND tc.constraint_name = kcu.constraint_name" + " LEFT JOIN information_schema.referential_constraints rc" + " ON tc.constraint_catalog = rc.constraint_catalog" + " AND tc.constraint_schema = rc.constraint_schema" + " AND tc.constraint_name = rc.constraint_name" + " LEFT JOIN information_schema.constraint_column_usage ccu" + " ON rc.unique_constraint_catalog = ccu.constraint_catalog" + " AND rc.unique_constraint_schema = ccu.constraint_schema" + " AND rc.unique_constraint_name = ccu.constraint_name" + " WHERE ccu.constraint_name = ?" + " and tc.table_schema=?"; PreparedStatement pstmrefs = cn.prepareStatement(sql); pstmrefs.setString(1, node.getString("OBJECTNAME").toLowerCase()); pstmrefs.setString(2, schema.toLowerCase()); ResultSet rsltrefs = pstmrefs.executeQuery(); while (rsltrefs.next()) { PreparedStatement pstmdelref = cndef.prepareStatement("DELETE NGTDIC WHERE OBJECTNAME=? AND SCHEMA=? AND TABLENAME=? AND OBJECTTYPE='FK'"); pstmdelref.setString(1, rsltrefs.getString(1)); pstmdelref.setString(2, node.getString("SCHEMA")); pstmdelref.setString(3, rsltrefs.getString(2)); pstmdelref.executeUpdate(); pstmdelref.close(); executeDDL("alter table " + rsltrefs.getString(2) + " drop constraint " + rsltrefs.getString(1), node.getString("SCHEMA")); } rsltrefs.close(); pstmrefs.close(); String insql = "'" + node.getString("EXPRESSION").toLowerCase().replaceAll(",", "\\',\\'") + "'"; sql = "SELECT tc.constraint_name" + " FROM information_schema.table_constraints tc" + " LEFT JOIN information_schema.key_column_usage kcu" + " ON tc.constraint_catalog = kcu.constraint_catalog" + " AND tc.constraint_schema = kcu.constraint_schema" + " AND tc.constraint_name = kcu.constraint_name" + " LEFT JOIN information_schema.referential_constraints rc" + " ON tc.constraint_catalog = rc.constraint_catalog" + " AND tc.constraint_schema = rc.constraint_schema" + " AND tc.constraint_name = rc.constraint_name" + " LEFT JOIN information_schema.constraint_column_usage ccu" + " ON rc.unique_constraint_catalog = ccu.constraint_catalog" + " AND rc.unique_constraint_schema = ccu.constraint_schema" + " AND rc.unique_constraint_name = ccu.constraint_name" + " WHERE tc.table_name=? and " + "kcu.column_name in (" + insql + ")" + " and tc.table_schema=?"; pstmrefs = cn.prepareStatement(sql); pstmrefs.setString(1, node.getString("TABLENAME").toLowerCase()); pstmrefs.setString(2, schema.toLowerCase()); rsltrefs = pstmrefs.executeQuery(); while (rsltrefs.next()) { PreparedStatement pstmdelref = cndef.prepareStatement("DELETE NGTDIC WHERE OBJECTNAME=? AND SCHEMA=? AND TABLENAME=? AND OBJECTTYPE='FK'"); pstmdelref.setString(1, rsltrefs.getString(1)); pstmdelref.setString(2, node.getString("SCHEMA")); pstmdelref.setString(3, node.getString("TABLENAME")); pstmdelref.executeUpdate(); pstmdelref.close(); executeDDL("alter table " + node.getString("TABLENAME") + " drop constraint " + rsltrefs.getString(1), node.getString("SCHEMA")); } rsltrefs.close(); pstmrefs.close(); if (exists && diff) { dml = "alter table " + node.getString("TABLENAME") + " drop constraint " + node.getString("OBJECTNAME"); try { executeDDL(dml, node.getString("SCHEMA")); } catch (Exception e) { logger.warn(LoggerMessageLocalizer.getMessage("ERROR_EXCUTING_DDL") + " (" + dml + ") " + e.getMessage()); } } } if (!modo.equals("3") && (!exists || diff)) { if (isunique) { dml = "alter table " + node.getString("TABLENAME") + " add constraint " + node.getString("OBJECTNAME") + " unique (" + node.getString("EXPRESSION") + ")"; } else { dml = "alter table " + node.getString("TABLENAME") + " add primary key (" + node.getString("EXPRESSION") + ")"; } executeDDL(dml, node.getString("SCHEMA")); } } if (objecttype.startsWith("FK")) { String sql = "SELECT kcu.column_name" + " FROM information_schema.table_constraints tc" + " LEFT JOIN information_schema.key_column_usage kcu" + " ON tc.constraint_catalog = kcu.constraint_catalog" + " AND tc.constraint_schema = kcu.constraint_schema" + " AND tc.constraint_name = kcu.constraint_name" + " LEFT JOIN information_schema.referential_constraints rc" + " ON tc.constraint_catalog = rc.constraint_catalog" + " AND tc.constraint_schema = rc.constraint_schema" + " AND tc.constraint_name = rc.constraint_name" + " LEFT JOIN information_schema.constraint_column_usage ccu" + " ON rc.unique_constraint_catalog = ccu.constraint_catalog" + " AND rc.unique_constraint_schema = ccu.constraint_schema" + " AND rc.unique_constraint_name = ccu.constraint_name" + " WHERE tc.constraint_name=?" + " and tc.table_name=?" + " and tc.table_schema=? order by ordinal_position"; PreparedStatement pstm = cn.prepareStatement(sql); pstm.setString(1, node.getString("OBJECTNAME").toLowerCase()); pstm.setString(2, node.getString("TABLENAME").toLowerCase()); pstm.setString(3, schema.toLowerCase()); ResultSet rslt = pstm.executeQuery(); boolean exists = false; String cExpress = ""; String express = node.getString("EXPRESSION"); if (rslt.next()) { exists = true; if (cExpress.length() > 0) cExpress += ","; cExpress += rslt.getString(1); } rslt.close(); pstm.close(); if (exists && !express.equals(cExpress)) { dml = "alter table " + node.getString("TABLENAME") + " drop constraint " + node.getString("OBJECTNAME"); executeDDL(dml, node.getString("SCHEMA")); } if (!modo.equals("3") && (!exists || !express.equals(cExpress))) { dml = "alter table " + node.getString("TABLENAME") + " add constraint " + node.getString("OBJECTNAME") + " foreign key (" + node.getString("EXPRESSION") + ") references " + node.getString("TABLEREFERENCE") + "(" + node.getString("FIELDREFERENCE") + ")"; executeDDL(dml, node.getString("SCHEMA")); } } if (objecttype.startsWith("IDX")) { boolean unflag = false; String sql = "SELECT n.nspname" + " FROM pg_catalog.pg_class c" + " JOIN pg_catalog.pg_index i ON i.indexrelid = c.oid" + " JOIN pg_catalog.pg_class c2 ON i.indrelid = c2.oid" + " LEFT JOIN pg_catalog.pg_user u ON u.usesysid = c.relowner" + " LEFT JOIN pg_catalog.pg_namespace n ON n.oid = c.relnamespace" + " where c.relname=? and c.relkind='i' and n.nspname=?"; PreparedStatement pstm = cn.prepareStatement(sql); pstm.setString(1, node.getString("OBJECTNAME").toLowerCase()); pstm.setString(2, schema.toLowerCase()); ResultSet rslt = pstm.executeQuery(); boolean drop = false; boolean exists = false; boolean dbunflag = false; String oldexpression = ""; String newexpression = ""; if (rslt.next()) { exists = true; if ((unflag && !(dbunflag = rslt.getString(1).equals("UNIQUE")))) { drop = true; } rslt.close(); pstm.close(); sql = "SELECT kcu.column_name" + " FROM information_schema.table_constraints tc" + " LEFT JOIN information_schema.key_column_usage kcu" + " ON tc.constraint_catalog = kcu.constraint_catalog" + " AND tc.constraint_schema = kcu.constraint_schema" + " AND tc.constraint_name = kcu.constraint_name" + " LEFT JOIN information_schema.referential_constraints rc" + " ON tc.constraint_catalog = rc.constraint_catalog" + " AND tc.constraint_schema = rc.constraint_schema" + " AND tc.constraint_name = rc.constraint_name" + " LEFT JOIN information_schema.constraint_column_usage ccu" + " ON rc.unique_constraint_catalog = ccu.constraint_catalog" + " AND rc.unique_constraint_schema = ccu.constraint_schema" + " AND rc.unique_constraint_name = ccu.constraint_name" + " WHERE tc.constraint_name=?" + " and tc.table_name=?" + " and tc.table_schema=? and tc.constraint_type='UNIQUE'"; pstm = cn.prepareStatement(sql); pstm.setString(1, node.getString("OBJECTNAME").toLowerCase()); pstm.setString(2, node.getString("TABLENAME").toLowerCase()); pstm.setString(3, schema.toLowerCase()); rslt = pstm.executeQuery(); while (rslt.next()) { oldexpression += (((oldexpression.length() > 0) ? "," : "") + rslt.getString(1)); } rslt.close(); pstm.close(); } else { rslt.close(); pstm.close(); } String aux = node.getString("EXPRESSION"); String[] nexo; if (aux != null) { nexo = node.getString("EXPRESSION").split(","); } else { nexo = new String[0]; } for (byte i = 0; i < nexo.length; i++) { newexpression += (((newexpression.length() > 0) ? "," : "") + ((nexo[i]).toUpperCase().trim())); } if (!drop) { drop = (!newexpression.equals(oldexpression)) && !oldexpression.equals(""); } if (exists && (drop || modo.equals("3"))) { if (!dbunflag) { dml = "DROP INDEX " + node.getString("OBJECTNAME"); } else { dml = "ALTER TABLE " + node.getString("TABLENAME") + " DROP CONSTRAINT " + node.getString("OBJECTNAME"); } executeDDL(dml, node.getString("SCHEMA")); exists = false; } if (!exists && !modo.equals("3")) { if (!node.getString("OBJECTNAME").equals("") && !newexpression.equals("")) { if (!unflag) { dml = "CREATE INDEX " + node.getString("OBJECTNAME") + " ON " + node.getString("TABLENAME") + "(" + newexpression + ")"; } else { dml = "ALTER TABLE " + node.getString("TABLENAME") + " ADD CONSTRAINT " + node.getString("OBJECTNAME") + " UNIQUE (" + newexpression + ")"; } executeDDL(dml, node.getString("SCHEMA")); } } } updateDictionaryTable(node, modo); return dml; } catch (SQLException e) { cn.rollback(); cndef.rollback(); throw (e); } finally { } }

public static void insert(Connection c, MLPApprox net, int azioneId, String descrizione, int[] indiciID, int output, Date from, Date to) throws SQLException { try { PreparedStatement ps = c.prepareStatement(insertNet, PreparedStatement.RETURN_GENERATED_KEYS); ArrayList<Integer> indexes = new ArrayList<Integer>(indiciID.length); for (int i = 0; i < indiciID.length; i++) indexes.add(indiciID[i]); ps.setObject(1, net); ps.setInt(2, azioneId); ps.setObject(3, indexes); ps.setInt(4, output); ps.setDate(5, from); ps.setDate(6, to); ps.setString(7, descrizione); ps.executeUpdate(); ResultSet key = ps.getGeneratedKeys(); if (key.next()) { int id = key.getInt(1); for (int i = 0; i < indiciID.length; i++) { PreparedStatement psIndex = c.prepareStatement(insertNetIndex); psIndex.setInt(1, indiciID[i]); psIndex.setInt(2, id); psIndex.executeUpdate(); } } } catch (SQLException e) { e.printStackTrace(); try { c.rollback(); } catch (SQLException e1) { e1.printStackTrace(); throw e1; } throw e; } }

private void addMaintainerScripts(TarOutputStream tar, PackageInfo info) throws IOException, ScriptDataTooLargeException { for (final MaintainerScript script : info.getMaintainerScripts().values()) { if (script.getSize() > Integer.MAX_VALUE) { throw new ScriptDataTooLargeException("The script data is too large for the tar file. script=[" + script.getType().getFilename() + "]."); } final TarEntry entry = standardEntry(script.getType().getFilename(), UnixStandardPermissions.EXECUTABLE_FILE_MODE, (int) script.getSize()); tar.putNextEntry(entry); IOUtils.copy(script.getStream(), tar); tar.closeEntry(); } }

public static File copyFile(File file, String dirName) { File destDir = new File(dirName); if (!destDir.exists() || !destDir.isDirectory()) { destDir.mkdirs(); } File src = file; File dest = new File(dirName, src.getName()); try { if (!dest.exists()) { dest.createNewFile(); } FileChannel source = new FileInputStream(src).getChannel(); FileChannel destination = new FileOutputStream(dest).getChannel(); destination.transferFrom(source, 0, source.size()); source.close(); destination.close(); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } return dest; }

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 long copy(File src, File dest) throws UtilException { FileChannel srcFc = null; FileChannel destFc = null; try { srcFc = new FileInputStream(src).getChannel(); destFc = new FileOutputStream(dest).getChannel(); long srcLength = srcFc.size(); srcFc.transferTo(0, srcLength, destFc); return srcLength; } catch (IOException e) { throw new UtilException(e); } finally { try { if (srcFc != null) srcFc.close(); srcFc = null; } catch (IOException e) { } try { if (destFc != null) destFc.close(); destFc = null; } catch (IOException e) { } } }

@TestTargetNew(level = TestLevel.COMPLETE, notes = "", method = "getServerCertificates", args = { }) public final void test_getServerCertificates() throws Exception { try { URL url = new URL("https://localhost:55555"); HttpsURLConnection connection = (HttpsURLConnection) url.openConnection(); try { connection.getServerCertificates(); fail("IllegalStateException wasn't thrown"); } catch (IllegalStateException ise) { } } catch (Exception e) { fail("Unexpected exception " + e + " for exception case"); } HttpsURLConnection con = new MyHttpsURLConnection(new URL("https://www.fortify.net/"), "X.508"); try { Certificate[] cert = con.getServerCertificates(); fail("SSLPeerUnverifiedException wasn't thrown"); } catch (SSLPeerUnverifiedException e) { } con = new MyHttpsURLConnection(new URL("https://www.fortify.net/"), "X.509"); try { Certificate[] cert = con.getServerCertificates(); assertNotNull(cert); assertEquals(1, cert.length); } catch (Exception e) { fail("Unexpected exception " + e); } }

public static boolean doPost(String urlString, Map<String, String> nameValuePairs) throws IOException { URL url = new URL(urlString); URLConnection conn = url.openConnection(); conn.setDoOutput(true); PrintWriter out = new PrintWriter(conn.getOutputStream()); boolean first = true; for (Map.Entry<String, String> pair : nameValuePairs.entrySet()) { if (first) first = false; else out.print('&'); String name = pair.getKey(); String value = pair.getValue(); out.print(name); out.print('='); out.print(URLEncoder.encode(value, "UTF-8")); } out.close(); Scanner in; StringBuilder response = new StringBuilder(); try { in = new Scanner(conn.getInputStream()); } catch (IOException ex) { if (!(conn instanceof HttpURLConnection)) throw ex; InputStream err = ((HttpURLConnection) conn).getErrorStream(); in = new Scanner(err); } while (in.hasNextLine()) { response.append(in.nextLine()); response.append("\n"); } in.close(); return true; }

public static String cryptSha(String target) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md = MessageDigest.getInstance("SHA"); md.update(target.getBytes("UTF-16")); BigInteger res = new BigInteger(1, md.digest(key.getBytes())); return res.toString(16); }

private static boolean insereTutorial(final Connection con, final Tutorial tut, final Autor aut, final Descricao desc) { try { con.setAutoCommit(false); Statement smt = con.createStatement(); if (aut.getCodAutor() == 0) { GeraID.gerarCodAutor(con, aut); smt.executeUpdate("INSERT INTO autor VALUES(" + aut.getCodAutor() + ",'" + aut.getNome() + "','" + aut.getEmail() + "')"); } GeraID.gerarCodDescricao(con, desc); GeraID.gerarCodTutorial(con, tut); String titulo = tut.getTitulo().replaceAll("['\"]", ""); String coment = tut.getComentario().replaceAll("[']", "\""); String texto = desc.getTexto().replaceAll("[']", "\""); smt.executeUpdate("INSERT INTO descricao VALUES(" + desc.getCodDesc() + ",'" + texto + "')"); smt.executeUpdate("INSERT INTO tutorial VALUES(" + tut.getCodigo() + ",'" + titulo + "','" + coment + "'," + desc.getCodDesc() + ")"); smt.executeUpdate("INSERT INTO tut_aut VALUES(" + tut.getCodigo() + "," + aut.getCodAutor() + ")"); con.commit(); return (true); } catch (SQLException e) { try { JOptionPane.showMessageDialog(null, "Rolling back transaction", "TUTORIAL: Database error", JOptionPane.ERROR_MESSAGE); System.out.print(e.getMessage()); con.rollback(); } catch (SQLException e1) { System.err.print(e1.getSQLState()); } return (false); } finally { try { con.setAutoCommit(true); } catch (SQLException e2) { System.err.print(e2.getSQLState()); } } }

public BufferedImage extract() throws DjatokaException { boolean useRegion = false; int left = 0; int top = 0; int width = 50; int height = 50; boolean useleftDouble = false; Double leftDouble = 0.0; boolean usetopDouble = false; Double topDouble = 0.0; boolean usewidthDouble = false; Double widthDouble = 0.0; boolean useheightDouble = false; Double heightDouble = 0.0; if (params.getRegion() != null) { StringTokenizer st = new StringTokenizer(params.getRegion(), "{},"); String token; if ((token = st.nextToken()).contains(".")) { topDouble = Double.parseDouble(token); usetopDouble = true; } else top = Integer.parseInt(token); if ((token = st.nextToken()).contains(".")) { leftDouble = Double.parseDouble(token); useleftDouble = true; } else left = Integer.parseInt(token); if ((token = st.nextToken()).contains(".")) { heightDouble = Double.parseDouble(token); useheightDouble = true; } else height = Integer.parseInt(token); if ((token = st.nextToken()).contains(".")) { widthDouble = Double.parseDouble(token); usewidthDouble = true; } else width = Integer.parseInt(token); useRegion = true; } try { if (is != null) { File f = File.createTempFile("tmp", ".jp2"); f.deleteOnExit(); FileOutputStream fos = new FileOutputStream(f); sourceFile = f.getAbsolutePath(); IOUtils.copyStream(is, fos); is.close(); fos.close(); } } catch (IOException e) { throw new DjatokaException(e); } try { Jp2_source inputSource = new Jp2_source(); Kdu_compressed_source input = null; Jp2_family_src jp2_family_in = new Jp2_family_src(); Jp2_locator loc = new Jp2_locator(); jp2_family_in.Open(sourceFile, true); inputSource.Open(jp2_family_in, loc); inputSource.Read_header(); input = inputSource; Kdu_codestream codestream = new Kdu_codestream(); codestream.Create(input); Kdu_channel_mapping channels = new Kdu_channel_mapping(); if (inputSource.Exists()) channels.Configure(inputSource, false); else channels.Configure(codestream); int ref_component = channels.Get_source_component(0); Kdu_coords ref_expansion = getReferenceExpansion(ref_component, channels, codestream); Kdu_dims image_dims = new Kdu_dims(); codestream.Get_dims(ref_component, image_dims); Kdu_coords imageSize = image_dims.Access_size(); Kdu_coords imagePosition = image_dims.Access_pos(); if (useleftDouble) left = imagePosition.Get_x() + (int) Math.round(leftDouble * imageSize.Get_x()); if (usetopDouble) top = imagePosition.Get_y() + (int) Math.round(topDouble * imageSize.Get_y()); if (useheightDouble) height = (int) Math.round(heightDouble * imageSize.Get_y()); if (usewidthDouble) width = (int) Math.round(widthDouble * imageSize.Get_x()); if (useRegion) { imageSize.Set_x(width); imageSize.Set_y(height); imagePosition.Set_x(left); imagePosition.Set_y(top); } int reduce = 1 << params.getLevelReductionFactor(); imageSize.Set_x(imageSize.Get_x() * ref_expansion.Get_x()); imageSize.Set_y(imageSize.Get_y() * ref_expansion.Get_y()); imagePosition.Set_x(imagePosition.Get_x() * ref_expansion.Get_x() / reduce - ((ref_expansion.Get_x() / reduce - 1) / 2)); imagePosition.Set_y(imagePosition.Get_y() * ref_expansion.Get_y() / reduce - ((ref_expansion.Get_y() / reduce - 1) / 2)); Kdu_dims view_dims = new Kdu_dims(); view_dims.Assign(image_dims); view_dims.Access_size().Set_x(imageSize.Get_x()); view_dims.Access_size().Set_y(imageSize.Get_y()); int region_buf_size = imageSize.Get_x() * imageSize.Get_y(); int[] region_buf = new int[region_buf_size]; Kdu_region_decompressor decompressor = new Kdu_region_decompressor(); decompressor.Start(codestream, channels, -1, params.getLevelReductionFactor(), 16384, image_dims, ref_expansion, new Kdu_coords(1, 1), false, Kdu_global.KDU_WANT_OUTPUT_COMPONENTS); Kdu_dims new_region = new Kdu_dims(); Kdu_dims incomplete_region = new Kdu_dims(); Kdu_coords viewSize = view_dims.Access_size(); incomplete_region.Assign(image_dims); int[] imgBuffer = new int[viewSize.Get_x() * viewSize.Get_y()]; int[] kduBuffer = null; while (decompressor.Process(region_buf, image_dims.Access_pos(), 0, 0, region_buf_size, incomplete_region, new_region)) { Kdu_coords newOffset = new_region.Access_pos(); Kdu_coords newSize = new_region.Access_size(); newOffset.Subtract(view_dims.Access_pos()); kduBuffer = region_buf; int imgBuffereIdx = newOffset.Get_x() + newOffset.Get_y() * viewSize.Get_x(); int kduBufferIdx = 0; int xDiff = viewSize.Get_x() - newSize.Get_x(); for (int j = 0; j < newSize.Get_y(); j++, imgBuffereIdx += xDiff) { for (int i = 0; i < newSize.Get_x(); i++) { imgBuffer[imgBuffereIdx++] = kduBuffer[kduBufferIdx++]; } } } BufferedImage image = new BufferedImage(imageSize.Get_x(), imageSize.Get_y(), BufferedImage.TYPE_INT_RGB); image.setRGB(0, 0, viewSize.Get_x(), viewSize.Get_y(), imgBuffer, 0, viewSize.Get_x()); if (params.getRotationDegree() > 0) { image = ImageProcessingUtils.rotate(image, params.getRotationDegree()); } decompressor.Native_destroy(); channels.Native_destroy(); if (codestream.Exists()) codestream.Destroy(); inputSource.Native_destroy(); input.Native_destroy(); jp2_family_in.Native_destroy(); return image; } catch (KduException e) { e.printStackTrace(); throw new DjatokaException(e); } catch (Exception e) { e.printStackTrace(); throw new DjatokaException(e); } }

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 boolean verifySignature() { try { byte[] data = readFile(name + ".tmp1.bin"); if (data == null) return false; if (data[data.length - 0x104] != 'N' || data[data.length - 0x103] != 'G' || data[data.length - 0x102] != 'I' || data[data.length - 0x101] != 'S') return false; byte[] signature = new byte[0x100]; byte[] module = new byte[data.length - 0x104]; System.arraycopy(data, data.length - 0x100, signature, 0, 0x100); System.arraycopy(data, 0, module, 0, data.length - 0x104); BigIntegerEx power = new BigIntegerEx(BigIntegerEx.LITTLE_ENDIAN, new byte[] { 0x01, 0x00, 0x01, 0x00 }); BigIntegerEx mod = new BigIntegerEx(BigIntegerEx.LITTLE_ENDIAN, new byte[] { (byte) 0x6B, (byte) 0xCE, (byte) 0xF5, (byte) 0x2D, (byte) 0x2A, (byte) 0x7D, (byte) 0x7A, (byte) 0x67, (byte) 0x21, (byte) 0x21, (byte) 0x84, (byte) 0xC9, (byte) 0xBC, (byte) 0x25, (byte) 0xC7, (byte) 0xBC, (byte) 0xDF, (byte) 0x3D, (byte) 0x8F, (byte) 0xD9, (byte) 0x47, (byte) 0xBC, (byte) 0x45, (byte) 0x48, (byte) 0x8B, (byte) 0x22, (byte) 0x85, (byte) 0x3B, (byte) 0xC5, (byte) 0xC1, (byte) 0xF4, (byte) 0xF5, (byte) 0x3C, (byte) 0x0C, (byte) 0x49, (byte) 0xBB, (byte) 0x56, (byte) 0xE0, (byte) 0x3D, (byte) 0xBC, (byte) 0xA2, (byte) 0xD2, (byte) 0x35, (byte) 0xC1, (byte) 0xF0, (byte) 0x74, (byte) 0x2E, (byte) 0x15, (byte) 0x5A, (byte) 0x06, (byte) 0x8A, (byte) 0x68, (byte) 0x01, (byte) 0x9E, (byte) 0x60, (byte) 0x17, (byte) 0x70, (byte) 0x8B, (byte) 0xBD, (byte) 0xF8, (byte) 0xD5, (byte) 0xF9, (byte) 0x3A, (byte) 0xD3, (byte) 0x25, (byte) 0xB2, (byte) 0x66, (byte) 0x92, (byte) 0xBA, (byte) 0x43, (byte) 0x8A, (byte) 0x81, (byte) 0x52, (byte) 0x0F, (byte) 0x64, (byte) 0x98, (byte) 0xFF, (byte) 0x60, (byte) 0x37, (byte) 0xAF, (byte) 0xB4, (byte) 0x11, (byte) 0x8C, (byte) 0xF9, (byte) 0x2E, (byte) 0xC5, (byte) 0xEE, (byte) 0xCA, (byte) 0xB4, (byte) 0x41, (byte) 0x60, (byte) 0x3C, (byte) 0x7D, (byte) 0x02, (byte) 0xAF, (byte) 0xA1, (byte) 0x2B, (byte) 0x9B, (byte) 0x22, (byte) 0x4B, (byte) 0x3B, (byte) 0xFC, (byte) 0xD2, (byte) 0x5D, (byte) 0x73, (byte) 0xE9, (byte) 0x29, (byte) 0x34, (byte) 0x91, (byte) 0x85, (byte) 0x93, (byte) 0x4C, (byte) 0xBE, (byte) 0xBE, (byte) 0x73, (byte) 0xA9, (byte) 0xD2, (byte) 0x3B, (byte) 0x27, (byte) 0x7A, (byte) 0x47, (byte) 0x76, (byte) 0xEC, (byte) 0xB0, (byte) 0x28, (byte) 0xC9, (byte) 0xC1, (byte) 0xDA, (byte) 0xEE, (byte) 0xAA, (byte) 0xB3, (byte) 0x96, (byte) 0x9C, (byte) 0x1E, (byte) 0xF5, (byte) 0x6B, (byte) 0xF6, (byte) 0x64, (byte) 0xD8, (byte) 0x94, (byte) 0x2E, (byte) 0xF1, (byte) 0xF7, (byte) 0x14, (byte) 0x5F, (byte) 0xA0, (byte) 0xF1, (byte) 0xA3, (byte) 0xB9, (byte) 0xB1, (byte) 0xAA, (byte) 0x58, (byte) 0x97, (byte) 0xDC, (byte) 0x09, (byte) 0x17, (byte) 0x0C, (byte) 0x04, (byte) 0xD3, (byte) 0x8E, (byte) 0x02, (byte) 0x2C, (byte) 0x83, (byte) 0x8A, (byte) 0xD6, (byte) 0xAF, (byte) 0x7C, (byte) 0xFE, (byte) 0x83, (byte) 0x33, (byte) 0xC6, (byte) 0xA8, (byte) 0xC3, (byte) 0x84, (byte) 0xEF, (byte) 0x29, (byte) 0x06, (byte) 0xA9, (byte) 0xB7, (byte) 0x2D, (byte) 0x06, (byte) 0x0B, (byte) 0x0D, (byte) 0x6F, (byte) 0x70, (byte) 0x9E, (byte) 0x34, (byte) 0xA6, (byte) 0xC7, (byte) 0x31, (byte) 0xBE, (byte) 0x56, (byte) 0xDE, (byte) 0xDD, (byte) 0x02, (byte) 0x92, (byte) 0xF8, (byte) 0xA0, (byte) 0x58, (byte) 0x0B, (byte) 0xFC, (byte) 0xFA, (byte) 0xBA, (byte) 0x49, (byte) 0xB4, (byte) 0x48, (byte) 0xDB, (byte) 0xEC, (byte) 0x25, (byte) 0xF3, (byte) 0x18, (byte) 0x8F, (byte) 0x2D, (byte) 0xB3, (byte) 0xC0, (byte) 0xB8, (byte) 0xDD, (byte) 0xBC, (byte) 0xD6, (byte) 0xAA, (byte) 0xA6, (byte) 0xDB, (byte) 0x6F, (byte) 0x7D, (byte) 0x7D, (byte) 0x25, (byte) 0xA6, (byte) 0xCD, (byte) 0x39, (byte) 0x6D, (byte) 0xDA, (byte) 0x76, (byte) 0x0C, (byte) 0x79, (byte) 0xBF, (byte) 0x48, (byte) 0x25, (byte) 0xFC, (byte) 0x2D, (byte) 0xC5, (byte) 0xFA, (byte) 0x53, (byte) 0x9B, (byte) 0x4D, (byte) 0x60, (byte) 0xF4, (byte) 0xEF, (byte) 0xC7, (byte) 0xEA, (byte) 0xAC, (byte) 0xA1, (byte) 0x7B, (byte) 0x03, (byte) 0xF4, (byte) 0xAF, (byte) 0xC7 }); byte[] result = new BigIntegerEx(BigIntegerEx.LITTLE_ENDIAN, signature).modPow(power, mod).toByteArray(); byte[] digest; byte[] properResult = new byte[0x100]; for (int i = 0; i < properResult.length; i++) properResult[i] = (byte) 0xBB; MessageDigest md = MessageDigest.getInstance("SHA1"); md.update(module); md.update("MAIEV.MOD".getBytes()); digest = md.digest(); System.arraycopy(digest, 0, properResult, 0, digest.length); for (int i = 0; i < result.length; i++) if (result[i] != properResult[i]) return false; return true; } catch (Exception e) { System.out.println("Failed to verify signature: " + e.toString()); } return false; }

protected void copyFile(String inputFilePath, String outputFilePath) throws GenerationException { String from = getTemplateDir() + inputFilePath; try { logger.debug("Copying from " + from + " to " + outputFilePath); InputStream inputStream = Thread.currentThread().getContextClassLoader().getResourceAsStream(from); if (inputStream == null) { throw new GenerationException("Source file not found: " + from); } FileOutputStream outputStream = new FileOutputStream(new File(outputFilePath)); IOUtils.copy(inputStream, outputStream); inputStream.close(); outputStream.close(); } catch (Exception e) { throw new GenerationException("Error while copying file: " + from, e); } }

private void chooseGame(DefaultHttpClient httpclient) throws IOException, ClientProtocolException { HttpGet httpget = new HttpGet(Constants.STRATEGICDOMINATION_URL + "/gameboard.cgi?gameid=" + 1687); HttpResponse response = httpclient.execute(httpget); HttpEntity entity = response.getEntity(); System.out.println("cg form get: " + response.getStatusLine()); if (entity != null) { InputStream inStream = entity.getContent(); IOUtils.copy(inStream, System.out); } System.out.println("cg set of cookies:"); List<Cookie> cookies = httpclient.getCookieStore().getCookies(); if (cookies.isEmpty()) { System.out.println("None"); } else { for (int i = 0; i < cookies.size(); i++) { System.out.println("- " + cookies.get(i).toString()); } } }

public static final void copyFile(String srcFilename, String dstFilename) throws IOException { FileInputStream fis = null; FileOutputStream fos = null; FileChannel ifc = null; FileChannel ofc = null; Util.copyBuffer.clear(); try { fis = new FileInputStream(srcFilename); ifc = fis.getChannel(); fos = new FileOutputStream(dstFilename); ofc = fos.getChannel(); int sz = (int) ifc.size(); int n = 0; while (n < sz) { if (ifc.read(Util.copyBuffer) < 0) { break; } Util.copyBuffer.flip(); n += ofc.write(Util.copyBuffer); Util.copyBuffer.compact(); } } finally { try { if (ifc != null) { ifc.close(); } else if (fis != null) { fis.close(); } } catch (IOException exc) { } try { if (ofc != null) { ofc.close(); } else if (fos != null) { fos.close(); } } catch (IOException exc) { } } }

public void sendContent(OutputStream out, Range range, Map map, String string) throws IOException, NotAuthorizedException, BadRequestException { System.out.println("sendContent " + file); RFileInputStream in = new RFileInputStream(file); try { IOUtils.copyLarge(in, out); } finally { in.close(); } }

private void copy(File fin, File fout) throws IOException { FileOutputStream out = new FileOutputStream(fout); FileInputStream 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); } in.close(); out.close(); }

public static String[] putFECSplitFile(String uri, File file, int htl, boolean mode) { FcpFECUtils fecutils = null; Vector segmentHeaders = null; Vector segmentFileMaps = new Vector(); Vector checkFileMaps = new Vector(); Vector segmentKeyMaps = new Vector(); Vector checkKeyMaps = new Vector(); int fileLength = (int) file.length(); String output = new String(); int maxThreads = frame1.frostSettings.getIntValue("splitfileUploadThreads"); Thread[] chunkThreads = null; String[][] chunkResults = null; Thread[] checkThreads = null; String[][] checkResults = null; int threadCount = 0; String board = getBoard(file); { fecutils = new FcpFECUtils(frame1.frostSettings.getValue("nodeAddress"), frame1.frostSettings.getIntValue("nodePort")); synchronized (fecutils.getClass()) { try { segmentHeaders = fecutils.FECSegmentFile("OnionFEC_a_1_2", fileLength); } catch (Exception e) { } } int chunkCnt = 0; int checkCnt = 0; synchronized (fecutils.getClass()) { try { Socket fcpSock; BufferedInputStream fcpIn; PrintStream fcpOut; for (int i = 0; i < segmentHeaders.size(); i++) { int blockCount = (int) ((FcpFECUtilsSegmentHeader) segmentHeaders.get(i)).BlockCount; int blockNo = 0; fcpSock = new Socket(InetAddress.getByName(frame1.frostSettings.getValue("nodeAddress")), frame1.frostSettings.getIntValue("nodePort")); fcpSock.setSoTimeout(1800000); fcpOut = new PrintStream(fcpSock.getOutputStream()); fcpIn = new BufferedInputStream(fcpSock.getInputStream()); FileInputStream fileIn = new FileInputStream(file); File[] chunkFiles = new File[blockCount]; { System.out.println("Processing segment " + i); fileIn.skip(((FcpFECUtilsSegmentHeader) segmentHeaders.get(i)).Offset); long segLength = ((FcpFECUtilsSegmentHeader) segmentHeaders.get(i)).BlockCount * ((FcpFECUtilsSegmentHeader) segmentHeaders.get(i)).BlockSize; System.out.println("segLength = " + Long.toHexString(segLength)); String headerString = "SegmentHeader\n" + ((FcpFECUtilsSegmentHeader) segmentHeaders.get(i)).reconstruct() + "EndMessage\n"; String dataHeaderString = "\0\0\0\2FECEncodeSegment\nMetadataLength=" + Long.toHexString(headerString.length()) + "\nDataLength=" + Long.toHexString(headerString.length() + segLength) + "\nData\n" + headerString; System.out.print(dataHeaderString); fcpOut.print(dataHeaderString); long count = 0; while (count < segLength) { byte[] buffer = new byte[(int) ((FcpFECUtilsSegmentHeader) segmentHeaders.get(i)).BlockSize]; System.out.println(Long.toHexString(((FcpFECUtilsSegmentHeader) segmentHeaders.get(i)).Offset + count)); int inbytes = fileIn.read(buffer); if (inbytes < 0) { System.out.println("End of input file - no data"); for (int j = 0; j < buffer.length; j++) buffer[j] = 0; inbytes = buffer.length; } if (inbytes < buffer.length) { System.out.println("End of input file - not enough data"); for (int j = inbytes; j < buffer.length; j++) buffer[j] = 0; inbytes = buffer.length; } if (inbytes > segLength - count) inbytes = (int) (segLength - count); fcpOut.write(buffer); File uploadMe = new File(frame1.keypool + String.valueOf(System.currentTimeMillis()) + "-" + chunkCnt + ".tmp"); chunkFiles[blockNo] = uploadMe; uploadMe.deleteOnExit(); FileOutputStream fileOut = new FileOutputStream(uploadMe); fileOut.write(buffer, 0, (int) inbytes); fileOut.close(); count += inbytes; chunkCnt++; ; blockNo++; if (blockNo >= blockCount) break; } segmentFileMaps.add(chunkFiles); fcpOut.flush(); fileIn.close(); } int checkNo = 0; int checkBlockCount = (int) ((FcpFECUtilsSegmentHeader) segmentHeaders.get(i)).CheckBlockCount; File[] checkFiles = new File[checkBlockCount]; File uploadMe = null; FileOutputStream outFile = null; { String currentLine; long checkBlockSize = ((FcpFECUtilsSegmentHeader) segmentHeaders.get(i)).CheckBlockSize; int checkPtr = 0; int length = 0; do { boolean started = false; currentLine = fecutils.getLine(fcpIn).trim(); if (currentLine.equals("DataChunk")) { started = true; } if (currentLine.startsWith("Length=")) { length = Integer.parseInt((currentLine.split("="))[1], 16); } if (currentLine.equals("Data")) { int currentRead; byte[] buffer = new byte[(int) length]; if (uploadMe == null) { uploadMe = new File(frame1.keypool + String.valueOf(System.currentTimeMillis()) + "-chk-" + checkCnt + ".tmp"); uploadMe.deleteOnExit(); outFile = new FileOutputStream(uploadMe); } currentRead = fcpIn.read(buffer); while (currentRead < length) { currentRead += fcpIn.read(buffer, currentRead, length - currentRead); } outFile.write(buffer); checkPtr += currentRead; if (checkPtr == checkBlockSize) { outFile.close(); checkFiles[checkNo] = uploadMe; uploadMe = null; checkNo++; checkCnt++; checkPtr = 0; } } } while (currentLine.length() > 0); checkFileMaps.add(checkFiles); } fcpOut.close(); fcpIn.close(); fcpSock.close(); } } catch (Exception e) { System.out.println("putFECSplitFile NOT GOOD " + e.toString()); } } int chunkNo = 0; int uploadedBytes = 0; for (int i = 0; i < segmentFileMaps.size(); i++) { File[] currentFileMap = (File[]) segmentFileMaps.get(i); chunkThreads = new Thread[currentFileMap.length]; chunkResults = new String[currentFileMap.length][2]; threadCount = 0; for (int j = 0; j < currentFileMap.length; j++) { if (DEBUG) System.out.println("Chunk: " + chunkNo); while (getActiveThreads(chunkThreads) >= maxThreads) mixed.wait(5000); chunkThreads[threadCount] = new putKeyThread("CHK@", currentFileMap[j], htl, chunkResults, threadCount, mode); chunkThreads[threadCount].start(); threadCount++; uploadedBytes += currentFileMap[j].length(); updateUploadTable(file, uploadedBytes, mode); mixed.wait(1000); chunkNo++; } while (getActiveThreads(chunkThreads) > 0) { if (DEBUG) System.out.println("Active Splitfile inserts remaining: " + getActiveThreads(chunkThreads)); mixed.wait(3000); } segmentKeyMaps.add(chunkResults); } int checkNo = 0; for (int i = 0; i < checkFileMaps.size(); i++) { File[] currentFileMap = (File[]) checkFileMaps.get(i); checkThreads = new Thread[currentFileMap.length]; checkResults = new String[currentFileMap.length][2]; threadCount = 0; for (int j = 0; j < currentFileMap.length; j++) { if (DEBUG) System.out.println("Check: " + checkNo); while (getActiveThreads(checkThreads) >= maxThreads) mixed.wait(5000); checkThreads[threadCount] = new putKeyThread("CHK@", currentFileMap[j], htl, checkResults, threadCount, mode); checkThreads[threadCount].start(); threadCount++; uploadedBytes += currentFileMap[j].length(); updateUploadTable(file, uploadedBytes, mode); mixed.wait(1000); checkNo++; } while (getActiveThreads(checkThreads) > 0) { if (DEBUG) System.out.println("Active Checkblock inserts remaining: " + getActiveThreads(checkThreads)); mixed.wait(3000); } checkKeyMaps.add(checkResults); } checkThreads = null; } String redirect = null; { synchronized (fecutils.getClass()) { try { redirect = fecutils.FECMakeMetadata(segmentHeaders, segmentKeyMaps, checkKeyMaps, "Frost"); } catch (Exception e) { System.out.println("putFECSplitFile NOT GOOD " + e.toString()); } } String[] sortedRedirect = redirect.split("\n"); for (int z = 0; z < sortedRedirect.length; z++) System.out.println(sortedRedirect[z]); int sortStart = -1; int sortEnd = -1; for (int line = 0; line < sortedRedirect.length; line++) { if (sortedRedirect[line].equals("Document")) { sortStart = line + 1; break; } } for (int line = sortStart; line < sortedRedirect.length; line++) { if (sortedRedirect[line].equals("End")) { sortEnd = line; break; } } System.out.println("sortStart " + sortStart + " sortEnd " + sortEnd); if (sortStart < sortEnd) Arrays.sort(sortedRedirect, sortStart, sortEnd); redirect = new String(); for (int line = 0; line < sortedRedirect.length; line++) redirect += sortedRedirect[line] + "\n"; System.out.println(redirect); } int tries = 0; String[] result = { "Error", "Error" }; while (!result[0].equals("Success") && !result[0].equals("KeyCollision") && tries < 8) { tries++; try { FcpConnection connection = new FcpConnection(frame1.frostSettings.getValue("nodeAddress"), frame1.frostSettings.getValue("nodePort")); output = connection.putKeyFromFile(uri, null, redirect.getBytes(), htl, mode); } catch (FcpToolsException e) { if (DEBUG) System.out.println("FcpToolsException " + e); frame1.displayWarning(e.toString()); } catch (UnknownHostException e) { if (DEBUG) System.out.println("UnknownHostException"); frame1.displayWarning(e.toString()); } catch (IOException e) { if (DEBUG) System.out.println("IOException"); frame1.displayWarning(e.toString()); } result = result(output); mixed.wait(3000); if (DEBUG) System.out.println("*****" + result[0] + " " + result[1] + " "); } if ((result[0].equals("Success") || result[0].equals("KeyCollision")) && mode) { try { GregorianCalendar cal = new GregorianCalendar(); cal.setTimeZone(TimeZone.getTimeZone("GMT")); String dirdate = cal.get(Calendar.YEAR) + "."; dirdate += cal.get(Calendar.MONTH) + 1 + "."; dirdate += cal.get(Calendar.DATE); String fileSeparator = System.getProperty("file.separator"); String destination = frame1.keypool + board + fileSeparator + dirdate + fileSeparator; FcpConnection connection = new FcpConnection(frame1.frostSettings.getValue("nodeAddress"), frame1.frostSettings.getValue("nodePort")); String contentKey = result(connection.putKeyFromFile(uri, null, redirect.getBytes(), htl, false))[1]; String prefix = new String("freenet:"); if (contentKey.startsWith(prefix)) contentKey = contentKey.substring(prefix.length()); FileAccess.writeFile("Already uploaded today", destination + contentKey + ".lck"); } catch (Exception e) { } } return result; }

public static final String crypt(String password, String salt) throws NoSuchAlgorithmException { String magic = "$1$"; byte finalState[]; MessageDigest ctx, ctx1; long l; if (salt.startsWith(magic)) { salt = salt.substring(magic.length()); } if (salt.indexOf('$') != -1) { salt = salt.substring(0, salt.indexOf('$')); } if (salt.length() > 8) { salt = salt.substring(0, 8); } ctx = MessageDigest.getInstance("MD5"); ctx.update(password.getBytes()); ctx.update(magic.getBytes()); ctx.update(salt.getBytes()); ctx1 = MessageDigest.getInstance("MD5"); ctx1.update(password.getBytes()); ctx1.update(salt.getBytes()); ctx1.update(password.getBytes()); finalState = ctx1.digest(); for (int pl = password.length(); pl > 0; pl -= 16) { for (int i = 0; i < (pl > 16 ? 16 : pl); i++) ctx.update(finalState[i]); } clearbits(finalState); for (int i = password.length(); i != 0; i >>>= 1) { if ((i & 1) != 0) { ctx.update(finalState[0]); } else { ctx.update(password.getBytes()[0]); } } finalState = ctx.digest(); for (int i = 0; i < 1000; i++) { ctx1 = MessageDigest.getInstance("MD5"); if ((i & 1) != 0) { ctx1.update(password.getBytes()); } else { for (int c = 0; c < 16; c++) ctx1.update(finalState[c]); } if ((i % 3) != 0) { ctx1.update(salt.getBytes()); } if ((i % 7) != 0) { ctx1.update(password.getBytes()); } if ((i & 1) != 0) { for (int c = 0; c < 16; c++) ctx1.update(finalState[c]); } else { ctx1.update(password.getBytes()); } finalState = ctx1.digest(); } StringBuffer result = new StringBuffer(); result.append(magic); result.append(salt); result.append("$"); l = (bytes2u(finalState[0]) << 16) | (bytes2u(finalState[6]) << 8) | bytes2u(finalState[12]); result.append(to64(l, 4)); l = (bytes2u(finalState[1]) << 16) | (bytes2u(finalState[7]) << 8) | bytes2u(finalState[13]); result.append(to64(l, 4)); l = (bytes2u(finalState[2]) << 16) | (bytes2u(finalState[8]) << 8) | bytes2u(finalState[14]); result.append(to64(l, 4)); l = (bytes2u(finalState[3]) << 16) | (bytes2u(finalState[9]) << 8) | bytes2u(finalState[15]); result.append(to64(l, 4)); l = (bytes2u(finalState[4]) << 16) | (bytes2u(finalState[10]) << 8) | bytes2u(finalState[5]); result.append(to64(l, 4)); l = bytes2u(finalState[11]); result.append(to64(l, 2)); clearbits(finalState); return result.toString(); }

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

protected void configureGraphicalViewer() { super.configureGraphicalViewer(); GraphicalViewer viewer = getGraphicalViewer(); viewer.setEditPartFactory(createEditPartFactory()); ScalableRootEditPart rootEditPart = new ScalableRootEditPart(); viewer.setRootEditPart(rootEditPart); ZoomManager manager = rootEditPart.getZoomManager(); double[] zoomLevels = new double[] { 0.25, 0.5, 0.75, 1.0, 1.5, 2.0, 2.5, 3.0, 4.0, 5.0, 10.0, 20.0 }; manager.setZoomLevels(zoomLevels); ArrayList zoomContributions = new ArrayList(); zoomContributions.add(ZoomManager.FIT_ALL); zoomContributions.add(ZoomManager.FIT_HEIGHT); zoomContributions.add(ZoomManager.FIT_WIDTH); manager.setZoomLevelContributions(zoomContributions); getActionRegistry().registerAction(new ZoomInAction(manager)); getActionRegistry().registerAction(new ZoomOutAction(manager)); getGraphicalViewer().setKeyHandler(new GraphicalViewerKeyHandler(getGraphicalViewer())); String menuId = this.getClass().getName() + ".EditorContext"; MenuManager menuMgr = new MenuManager(menuId, menuId); openPropertyAction = new OpenPropertyViewAction(viewer); openOutlineAction = new OpenOutlineViewAction(viewer); saveAsImageAction = new SaveAsImageAction(viewer); createDiagramAction(viewer); getSite().registerContextMenu(menuId, menuMgr, viewer); PrintAction printAction = new PrintAction(this); printAction.setImageDescriptor(UMLPlugin.getImageDescriptor("icons/print.gif")); getActionRegistry().registerAction(printAction); final DeleteAction deleteAction = new DeleteAction((IWorkbenchPart) this); deleteAction.setSelectionProvider(getGraphicalViewer()); getActionRegistry().registerAction(deleteAction); viewer.addSelectionChangedListener(new ISelectionChangedListener() { public void selectionChanged(SelectionChangedEvent event) { deleteAction.update(); } }); menuMgr.add(new Separator("edit")); menuMgr.add(getActionRegistry().getAction(ActionFactory.DELETE.getId())); menuMgr.add(getActionRegistry().getAction(ActionFactory.UNDO.getId())); menuMgr.add(getActionRegistry().getAction(ActionFactory.REDO.getId())); menuMgr.add(new Separator("zoom")); menuMgr.add(getActionRegistry().getAction(GEFActionConstants.ZOOM_IN)); menuMgr.add(getActionRegistry().getAction(GEFActionConstants.ZOOM_OUT)); fillDiagramPopupMenu(menuMgr); menuMgr.add(new Separator("print")); menuMgr.add(saveAsImageAction); menuMgr.add(printAction); menuMgr.add(new Separator("views")); menuMgr.add(openPropertyAction); menuMgr.add(openOutlineAction); menuMgr.add(new Separator("generate")); menuMgr.add(new Separator("additions")); viewer.setContextMenu(menuMgr); viewer.setKeyHandler(new GraphicalViewerKeyHandler(viewer).setParent(getCommonKeyHandler())); }

public static String getUserToken(String userName) { if (userName != null && userName.trim().length() > 0) try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update((userName + seed).getBytes("ISO-8859-1")); return BaseController.bytesToHex(md.digest()); } catch (NullPointerException npe) { } catch (NoSuchAlgorithmException e) { } catch (UnsupportedEncodingException e) { } return null; }

public static byte[] md5raw(String data) { try { MessageDigest md = MessageDigest.getInstance(MD); md.update(data.getBytes(UTF8)); return md.digest(); } catch (Exception e) { throw new RuntimeException(e); } }

@Override public void execute() throws BuildException { final String GC_USERNAME = "google-code-username"; final String GC_PASSWORD = "google-code-password"; if (StringUtils.isBlank(this.projectName)) throw new BuildException("undefined project"); if (this.file == null) throw new BuildException("undefined file"); if (!this.file.exists()) throw new BuildException("file not found :" + file); if (!this.file.isFile()) throw new BuildException("not a file :" + file); if (this.config == null) throw new BuildException("undefined config"); if (!this.config.exists()) throw new BuildException("file not found :" + config); if (!this.config.isFile()) throw new BuildException("not a file :" + config); PostMethod post = null; try { Properties cfg = new Properties(); FileInputStream fin = new FileInputStream(this.config); cfg.loadFromXML(fin); fin.close(); if (!cfg.containsKey(GC_USERNAME)) throw new BuildException("undefined " + GC_USERNAME + " in " + this.config); if (!cfg.containsKey(GC_PASSWORD)) throw new BuildException("undefined " + GC_PASSWORD + " in " + this.config); HttpClient client = new HttpClient(); post = new PostMethod("https://" + projectName + ".googlecode.com/files"); post.addRequestHeader("User-Agent", getClass().getName()); post.addRequestHeader("Authorization", "Basic " + Base64.encode(cfg.getProperty(GC_USERNAME) + ":" + cfg.getProperty(GC_PASSWORD))); List<Part> parts = new ArrayList<Part>(); String s = this.summary; if (StringUtils.isBlank(s)) { s = this.file.getName() + " (" + TimeUtils.toYYYYMMDD() + ")"; } parts.add(new StringPart("summary", s)); for (String lbl : this.labels.split("[, \t\n]+")) { if (StringUtils.isBlank(lbl)) continue; parts.add(new StringPart("label", lbl.trim())); } parts.add(new FilePart("filename", this.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 BuildException("http status !=201 : " + post.getResponseBodyAsString()); } else { IOUtils.copyTo(post.getResponseBodyAsStream(), new NullOutputStream()); } } catch (BuildException e) { throw e; } catch (Exception e) { throw new BuildException(e); } finally { if (post != null) post.releaseConnection(); } }

public void executaAlteracoes() { Album album = Album.getAlbum(); Photo[] fotos = album.getFotos(); Photo f; int ultimoFotoID = -1; int albumID = album.getAlbumID(); sucesso = true; PainelWebFotos.setCursorWait(true); albumID = recordAlbumData(album, albumID); sucesso = recordFotoData(fotos, ultimoFotoID, albumID); String caminhoAlbum = Util.getFolder("albunsRoot").getPath() + File.separator + albumID; File diretorioAlbum = new File(caminhoAlbum); if (!diretorioAlbum.isDirectory()) { if (!diretorioAlbum.mkdir()) { Util.log("[AcaoAlterarAlbum.executaAlteracoes.7]/ERRO: diretorio " + caminhoAlbum + " n�o pode ser criado. abortando"); return; } } for (int i = 0; i < fotos.length; i++) { f = fotos[i]; if (f.getCaminhoArquivo().length() > 0) { try { FileChannel canalOrigem = new FileInputStream(f.getCaminhoArquivo()).getChannel(); FileChannel canalDestino = new FileOutputStream(caminhoAlbum + File.separator + f.getFotoID() + ".jpg").getChannel(); canalDestino.transferFrom(canalOrigem, 0, canalOrigem.size()); canalOrigem = null; canalDestino = null; } catch (Exception e) { Util.log("[AcaoAlterarAlbum.executaAlteracoes.8]/ERRO: " + e); sucesso = false; } } } prepareThumbsAndFTP(fotos, albumID, caminhoAlbum); prepareExtraFiles(album, caminhoAlbum); fireChangesToGUI(fotos); dispatchAlbum(); PainelWebFotos.setCursorWait(false); }

public static void copyFile(final File sourceFile, final 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(); } }

@Override protected svm_model loadModel(InputStream inputStream) throws IOException { File tmpFile = File.createTempFile("tmp", ".mdl"); FileOutputStream output = new FileOutputStream(tmpFile); try { IOUtils.copy(inputStream, output); return libsvm.svm.svm_load_model(tmpFile.getPath()); } finally { output.close(); tmpFile.delete(); } }

private static String deviceIdFromCombined_Device_ID(Context context) { StringBuilder builder = new StringBuilder(); builder.append(deviceIdFromIMEI(context)); builder.append(deviceIdFromPseudo_Unique_Id()); builder.append(deviceIdFromAndroidId(context)); builder.append(deviceIdFromWLAN_MAC_Address(context)); builder.append(deviceIdFromBT_MAC_Address(context)); String m_szLongID = builder.toString(); MessageDigest m = null; try { m = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } m.update(m_szLongID.getBytes(), 0, m_szLongID.length()); byte p_md5Data[] = m.digest(); String m_szUniqueID = new String(); for (int i = 0; i < p_md5Data.length; i++) { int b = (0xFF & p_md5Data[i]); if (b <= 0xF) m_szUniqueID += "0"; m_szUniqueID += Integer.toHexString(b); } return m_szUniqueID; }

@SuppressWarnings("finally") private void compress(File src) throws IOException { if (this.switches.contains(Switch.test)) return; checkSourceFile(src); if (src.getPath().endsWith(".bz2")) { this.log.println("WARNING: skipping file because it already has .bz2 suffix:").println(src); return; } final File dst = new File(src.getPath() + ".bz2").getAbsoluteFile(); if (!checkDestFile(dst)) return; FileChannel inChannel = null; FileChannel outChannel = null; FileOutputStream fileOut = null; BZip2OutputStream bzOut = null; FileLock inLock = null; FileLock outLock = null; try { inChannel = new FileInputStream(src).getChannel(); final long inSize = inChannel.size(); inLock = inChannel.tryLock(0, inSize, true); if (inLock == null) throw error("source file locked by another process: " + src); fileOut = new FileOutputStream(dst); outChannel = fileOut.getChannel(); bzOut = new BZip2OutputStream( new BufferedXOutputStream(fileOut, 8192), Math.min( (this.blockSize == -1) ? BZip2OutputStream.MAX_BLOCK_SIZE : this.blockSize, BZip2OutputStream.chooseBlockSize(inSize) ) ); outLock = outChannel.tryLock(); if (outLock == null) throw error("destination file locked by another process: " + dst); final boolean showProgress = this.switches.contains(Switch.showProgress); long pos = 0; int progress = 0; if (showProgress || this.verbose) { this.log.print("source: " + src).print(": size=").println(inSize); this.log.println("target: " + dst); } while (true) { final long maxStep = showProgress ? Math.max(8192, (inSize - pos) / MAX_PROGRESS) : (inSize - pos); if (maxStep <= 0) { if (showProgress) { for (int i = progress; i < MAX_PROGRESS; i++) this.log.print('#'); this.log.println(" done"); } break; } else { final long step = inChannel.transferTo(pos, maxStep, bzOut); if ((step == 0) && (inChannel.size() != inSize)) throw error("file " + src + " has been modified concurrently by another process"); pos += step; if (showProgress) { final double p = (double) pos / (double) inSize; final int newProgress = (int) (MAX_PROGRESS * p); for (int i = progress; i < newProgress; i++) this.log.print('#'); progress = newProgress; } } } inLock.release(); inChannel.close(); bzOut.closeInstance(); final long outSize = outChannel.position(); outChannel.truncate(outSize); outLock.release(); fileOut.close(); if (this.verbose) { final double ratio = (inSize == 0) ? (outSize * 100) : ((double) outSize / (double) inSize); this.log.print("raw size: ").print(inSize) .print("; compressed size: ").print(outSize) .print("; compression ratio: ").print(ratio).println('%'); } if (!this.switches.contains(Switch.keep)) { if (!src.delete()) throw error("unable to delete sourcefile: " + src); } } catch (final IOException ex) { IO.tryClose(inChannel); IO.tryClose(bzOut); IO.tryClose(fileOut); IO.tryRelease(inLock); IO.tryRelease(outLock); try { this.log.println(); } finally { throw ex; } } }

private static void copy(String srcFilename, String dstFilename, boolean override) throws IOException, XPathFactoryConfigurationException, SAXException, ParserConfigurationException, XPathExpressionException { File fileToCopy = new File(rootDir + "test-output/" + srcFilename); if (fileToCopy.exists()) { File newFile = new File(rootDir + "test-output/" + dstFilename); if (!newFile.exists() || override) { try { FileChannel srcChannel = new FileInputStream(rootDir + "test-output/" + srcFilename).getChannel(); FileChannel dstChannel = new FileOutputStream(rootDir + "test-output/" + dstFilename).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (IOException e) { } } } }

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(); } }

private void refreshCacheFile(RepositoryFile file, File cacheFile) throws FileNotFoundException, IOException { FileOutputStream fos = new FileOutputStream(cacheFile); InputStream is = file.getInputStream(); int count = IOUtils.copy(is, fos); logger.debug("===========================================================> wrote bytes to cache " + count); fos.flush(); IOUtils.closeQuietly(fos); IOUtils.closeQuietly(file.getInputStream()); }

private static boolean moveFiles(String sourceDir, String targetDir) { boolean isFinished = false; boolean fileMoved = false; File stagingDir = new File(sourceDir); if (!stagingDir.exists()) { System.out.println(getTimeStamp() + "ERROR - source directory does not exist."); return true; } if (stagingDir.listFiles() == null) { System.out.println(getTimeStamp() + "ERROR - Empty file list. Possible permission error on source directory " + sourceDir); return true; } File[] fileList = stagingDir.listFiles(); for (int x = 0; x < fileList.length; x++) { File f = fileList[x]; if (f.getName().startsWith(".")) { continue; } String targetFileName = targetDir + File.separator + f.getName(); String operation = "move"; boolean success = f.renameTo(new File(targetFileName)); if (success) { fileMoved = true; } else { operation = "mv"; try { Process process = Runtime.getRuntime().exec(new String[] { "mv", f.getCanonicalPath(), targetFileName }); process.waitFor(); process.destroy(); if (!new File(targetFileName).exists()) { success = false; } else { success = true; fileMoved = true; } } catch (Exception e) { success = false; } if (!success) { operation = "copy"; FileChannel in = null; FileChannel out = null; try { in = new FileInputStream(f).getChannel(); File outFile = new File(targetFileName); out = new FileOutputStream(outFile).getChannel(); in.transferTo(0, in.size(), out); in.close(); in = null; out.close(); out = null; f.delete(); success = true; } catch (Exception e) { success = false; } finally { if (in != null) { try { in.close(); } catch (Exception e) { } } if (out != null) { try { out.close(); } catch (Exception e) { } } } } } if (success) { System.out.println(getTimeStamp() + operation + " " + f.getAbsolutePath() + " to " + targetDir); fileMoved = true; } else { System.out.println(getTimeStamp() + "ERROR - " + operation + " " + f.getName() + " to " + targetFileName + " failed."); isFinished = true; } } if (fileMoved && !isFinished) { try { currentLastActivity = System.currentTimeMillis(); updateLastActivity(currentLastActivity); } catch (NumberFormatException e) { System.out.println(getTimeStamp() + "ERROR: NumberFormatException when trying to update lastActivity."); isFinished = true; } catch (IOException e) { System.out.println(getTimeStamp() + "ERROR: IOException when trying to update lastActivity. " + e.toString()); isFinished = true; } } return isFinished; }

protected static void copyFile(File in, File out) throws IOException { java.io.FileWriter filewriter = null; java.io.FileReader filereader = null; try { filewriter = new java.io.FileWriter(out); filereader = new java.io.FileReader(in); char[] buf = new char[4096]; int nread = filereader.read(buf, 0, 4096); while (nread >= 0) { filewriter.write(buf, 0, nread); nread = filereader.read(buf, 0, 4096); } buf = null; } finally { try { filereader.close(); } catch (Throwable t) { } try { filewriter.close(); } catch (Throwable t) { } } }

public void loadXML(URL flux, int status, File file) { try { SAXBuilder sbx = new SAXBuilder(); try { if (file.exists()) { file.delete(); } if (!file.exists()) { URLConnection conn = flux.openConnection(); conn.setConnectTimeout(5000); conn.setReadTimeout(10000); InputStream is = conn.getInputStream(); OutputStream out = new FileOutputStream(file); byte buf[] = new byte[1024]; int len; while ((len = is.read(buf)) > 0) out.write(buf, 0, len); out.close(); is.close(); } } catch (Exception e) { Log.e(Constants.PROJECT_TAG, "Exeption retrieving XML", e); } try { document = sbx.build(new FileInputStream(file)); } catch (Exception e) { Log.e(Constants.PROJECT_TAG, "xml error ", e); } } catch (Exception e) { Log.e(Constants.PROJECT_TAG, "TsukiQueryError", e); } if (document != null) { root = document.getRootElement(); PopulateDatabase(root, status); } }

public static Drawable fetchCachedDrawable(String url) throws MalformedURLException, IOException { Log.d(LOG_TAG, "Fetching cached : " + url); String cacheName = md5(url); checkAndCreateDirectoryIfNeeded(); File r = new File(CACHELOCATION + cacheName); if (!r.exists()) { InputStream is = (InputStream) fetch(url); FileOutputStream fos = new FileOutputStream(CACHELOCATION + cacheName); int nextChar; while ((nextChar = is.read()) != -1) fos.write((char) nextChar); fos.flush(); } FileInputStream fis = new FileInputStream(CACHELOCATION + cacheName); Drawable d = Drawable.createFromStream(fis, "src"); return d; }

private void _save(ActionRequest req, ActionResponse res, PortletConfig config, ActionForm form) throws Exception { List list = (List) req.getAttribute(WebKeys.LANGUAGE_MANAGER_LIST); for (int i = 0; i < list.size(); i++) { long langId = ((Language) list.get(i)).getId(); try { String filePath = getGlobalVariablesPath() + "cms_language_" + langId + ".properties"; String tmpFilePath = getTemporyDirPath() + "cms_language_" + langId + "_properties.tmp"; File from = new java.io.File(tmpFilePath); from.createNewFile(); File to = new java.io.File(filePath); to.createNewFile(); FileChannel srcChannel = new FileInputStream(from).getChannel(); FileChannel dstChannel = new FileOutputStream(to).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (NonWritableChannelException we) { } catch (IOException e) { Logger.error(this, "Property File save Failed " + e, e); } } SessionMessages.add(req, "message", "message.languagemanager.save"); }

public int read(String name) { status = STATUS_OK; try { name = name.trim(); if (name.indexOf("://") > 0) { URL url = new URL(name); in = new BufferedInputStream(url.openStream()); } else { in = new BufferedInputStream(new FileInputStream(name)); } status = read(in); } catch (IOException e) { status = STATUS_OPEN_ERROR; } return status; }

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(); } } }

protected static void copyDeleting(File source, File dest) throws ErrorCodeException { byte[] buf = new byte[8 * 1024]; FileInputStream in = null; try { in = new FileInputStream(source); try { FileOutputStream out = new FileOutputStream(dest); try { int count; while ((count = in.read(buf)) >= 0) out.write(buf, 0, count); } finally { out.close(); } } finally { in.close(); } } catch (IOException e) { throw new ErrorCodeException(e); } }

private String sendMessage(HttpURLConnection connection, String reqMessage) throws IOException, XMLStreamException { 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(); byte[] byteArray = baos.toByteArray(); String resMessage = new String(byteArray, "UTF-8"); if (msgLog.isTraceEnabled()) msgLog.trace("Incoming Response SOAPMessage\n" + resMessage); return resMessage; }

public static double[][] getCurrency() throws IOException { URL url = new URL("http://hk.finance.yahoo.com/currency"); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream(), "big5")); double currency[][] = new double[11][11]; while (true) { String line = in.readLine(); String reg = "<td\\s((align=\"right\"\\sclass=\"yfnc_tabledata1\")" + "|(class=\"yfnc_tabledata1\"\\salign=\"right\"))>" + "([\\d|\\.]+)</td>"; Matcher m = Pattern.compile(reg).matcher(line); int i = 0, j = 0; boolean isfound = false; while (m.find()) { isfound = true; currency[i][j] = Double.parseDouble(m.group(4)); if (j == 10) { j = 0; i++; } else j++; } if (isfound) break; } return currency; }

private void onDhReply(final SshDhReply msg) throws GeneralSecurityException, IOException { if ((this.keyPair == null) || this.connection.isServer()) throw new SshException("%s: unexpected %s", this.connection.uri, msg.getType()); final BigInteger k; { final DHPublicKeySpec remoteKeySpec = new DHPublicKeySpec(new BigInteger(msg.f), P1, G); final KeyFactory dhKeyFact = KeyFactory.getInstance("DH"); final DHPublicKey remotePubKey = (DHPublicKey) dhKeyFact.generatePublic(remoteKeySpec); final KeyAgreement dhKex = KeyAgreement.getInstance("DH"); dhKex.init(this.keyPair.getPrivate()); dhKex.doPhase(remotePubKey, true); k = new BigInteger(dhKex.generateSecret()); } final MessageDigest md = createMessageDigest(); final byte[] h; { updateByteArray(md, SshVersion.LOCAL.toString().getBytes()); updateByteArray(md, this.connection.getRemoteSshVersion().toString().getBytes()); updateByteArray(md, this.keyExchangeInitLocal.getPayload()); updateByteArray(md, this.keyExchangeInitRemote.getPayload()); updateByteArray(md, msg.hostKey); updateByteArray(md, ((DHPublicKey) this.keyPair.getPublic()).getY().toByteArray()); updateByteArray(md, msg.f); updateBigInt(md, k); h = md.digest(); } if (this.sessionId == null) this.sessionId = h; this.keyExchangeInitLocal = null; this.keyExchangeInitRemote = null; this.h = h; this.k = k; this.connection.send(new SshKeyExchangeNewKeys()); }

public DefaultMainControl(@NotNull final FileFilter scriptFileFilter, @NotNull final String scriptExtension, @NotNull final String scriptName, final int spellType, @Nullable final String spellFile, @NotNull final String scriptsDir, final ErrorView errorView, @NotNull final EditorFactory<G, A, R> editorFactory, final boolean forceReadFromFiles, @NotNull final GlobalSettings globalSettings, @NotNull final ConfigSourceFactory configSourceFactory, @NotNull final PathManager pathManager, @NotNull final GameObjectMatchers gameObjectMatchers, @NotNull final GameObjectFactory<G, A, R> gameObjectFactory, @NotNull final ArchetypeTypeSet archetypeTypeSet, @NotNull final ArchetypeSet<G, A, R> archetypeSet, @NotNull final ArchetypeChooserModel<G, A, R> archetypeChooserModel, @NotNull final AutojoinLists<G, A, R> autojoinLists, @NotNull final AbstractMapManager<G, A, R> mapManager, @NotNull final PluginModel<G, A, R> pluginModel, @NotNull final DelegatingMapValidator<G, A, R> validators, @NotNull final ScriptedEventEditor<G, A, R> scriptedEventEditor, @NotNull final AbstractResources<G, A, R> resources, @NotNull final Spells<NumberSpell> numberSpells, @NotNull final Spells<GameObjectSpell<G, A, R>> gameObjectSpells, @NotNull final PluginParameterFactory<G, A, R> pluginParameterFactory, @NotNull final ValidatorPreferences validatorPreferences, @NotNull final MapWriter<G, A, R> mapWriter) { final XmlHelper xmlHelper; try { xmlHelper = new XmlHelper(); } catch (final ParserConfigurationException ex) { log.fatal("Cannot create XML parser: " + ex.getMessage()); throw new MissingResourceException("Cannot create XML parser: " + ex.getMessage(), null, null); } final AttributeRangeChecker<G, A, R> attributeRangeChecker = new AttributeRangeChecker<G, A, R>(validatorPreferences); final EnvironmentChecker<G, A, R> environmentChecker = new EnvironmentChecker<G, A, R>(validatorPreferences); final DocumentBuilder documentBuilder = xmlHelper.getDocumentBuilder(); try { final URL url = IOUtils.getResource(globalSettings.getConfigurationDirectory(), "GameObjectMatchers.xml"); final ErrorViewCollector gameObjectMatchersErrorViewCollector = new ErrorViewCollector(errorView, url); try { documentBuilder.setErrorHandler(new ErrorViewCollectorErrorHandler(gameObjectMatchersErrorViewCollector, ErrorViewCategory.GAMEOBJECTMATCHERS_FILE_INVALID)); try { final GameObjectMatchersParser gameObjectMatchersParser = new GameObjectMatchersParser(documentBuilder, xmlHelper.getXPath()); gameObjectMatchersParser.readGameObjectMatchers(url, gameObjectMatchers, gameObjectMatchersErrorViewCollector); } finally { documentBuilder.setErrorHandler(null); } } catch (final IOException ex) { gameObjectMatchersErrorViewCollector.addWarning(ErrorViewCategory.GAMEOBJECTMATCHERS_FILE_INVALID, ex.getMessage()); } final ValidatorFactory<G, A, R> validatorFactory = new ValidatorFactory<G, A, R>(validatorPreferences, gameObjectMatchers, globalSettings, mapWriter); loadValidators(validators, validatorFactory, errorView); editorFactory.initMapValidators(validators, gameObjectMatchersErrorViewCollector, globalSettings, gameObjectMatchers, attributeRangeChecker, validatorPreferences); validators.addValidator(attributeRangeChecker); validators.addValidator(environmentChecker); } catch (final FileNotFoundException ex) { errorView.addWarning(ErrorViewCategory.GAMEOBJECTMATCHERS_FILE_INVALID, "GameObjectMatchers.xml: " + ex.getMessage()); } final GameObjectMatcher shopSquareMatcher = gameObjectMatchers.getMatcher("system_shop_square", "shop_square"); if (shopSquareMatcher != null) { final GameObjectMatcher noSpellsMatcher = gameObjectMatchers.getMatcher("system_no_spells", "no_spells"); if (noSpellsMatcher != null) { final GameObjectMatcher blockedMatcher = gameObjectMatchers.getMatcher("system_blocked", "blocked"); validators.addValidator(new ShopSquareChecker<G, A, R>(validatorPreferences, shopSquareMatcher, noSpellsMatcher, blockedMatcher)); } final GameObjectMatcher paidItemMatcher = gameObjectMatchers.getMatcher("system_paid_item"); if (paidItemMatcher != null) { validators.addValidator(new PaidItemShopSquareChecker<G, A, R>(validatorPreferences, shopSquareMatcher, paidItemMatcher)); } } Map<String, TreasureTreeNode> specialTreasureLists; try { final URL url = IOUtils.getResource(globalSettings.getConfigurationDirectory(), "TreasureLists.xml"); final ErrorViewCollector treasureListsErrorViewCollector = new ErrorViewCollector(errorView, url); try { final InputStream inputStream = url.openStream(); try { documentBuilder.setErrorHandler(new ErrorViewCollectorErrorHandler(treasureListsErrorViewCollector, ErrorViewCategory.TREASURES_FILE_INVALID)); try { final Document specialTreasureListsDocument = documentBuilder.parse(new InputSource(inputStream)); specialTreasureLists = TreasureListsParser.parseTreasureLists(specialTreasureListsDocument); } finally { documentBuilder.setErrorHandler(null); } } finally { inputStream.close(); } } catch (final IOException ex) { treasureListsErrorViewCollector.addWarning(ErrorViewCategory.TREASURES_FILE_INVALID, ex.getMessage()); specialTreasureLists = Collections.emptyMap(); } catch (final SAXException ex) { treasureListsErrorViewCollector.addWarning(ErrorViewCategory.TREASURES_FILE_INVALID, ex.getMessage()); specialTreasureLists = Collections.emptyMap(); } } catch (final FileNotFoundException ex) { errorView.addWarning(ErrorViewCategory.TREASURES_FILE_INVALID, "TreasureLists.xml: " + ex.getMessage()); specialTreasureLists = Collections.emptyMap(); } final ConfigSource configSource = forceReadFromFiles ? configSourceFactory.getFilesConfigSource() : configSourceFactory.getConfigSource(globalSettings.getConfigSourceName()); treasureTree = TreasureLoader.parseTreasures(errorView, specialTreasureLists, configSource, globalSettings); final ArchetypeAttributeFactory archetypeAttributeFactory = new DefaultArchetypeAttributeFactory(); final ArchetypeAttributeParser archetypeAttributeParser = new ArchetypeAttributeParser(archetypeAttributeFactory); final ArchetypeTypeParser archetypeTypeParser = new ArchetypeTypeParser(archetypeAttributeParser); ArchetypeTypeList eventTypeSet = null; try { final URL url = IOUtils.getResource(globalSettings.getConfigurationDirectory(), CommonConstants.TYPEDEF_FILE); final ErrorViewCollector typesErrorViewCollector = new ErrorViewCollector(errorView, url); documentBuilder.setErrorHandler(new ErrorViewCollectorErrorHandler(typesErrorViewCollector, ErrorViewCategory.GAMEOBJECTMATCHERS_FILE_INVALID)); try { final ArchetypeTypeSetParser archetypeTypeSetParser = new ArchetypeTypeSetParser(documentBuilder, archetypeTypeSet, archetypeTypeParser); archetypeTypeSetParser.loadTypesFromXML(typesErrorViewCollector, new InputSource(url.toString())); } finally { documentBuilder.setErrorHandler(null); } final ArchetypeTypeList eventTypeSetTmp = archetypeTypeSet.getList("event"); if (eventTypeSetTmp == null) { typesErrorViewCollector.addWarning(ErrorViewCategory.TYPES_ENTRY_INVALID, "list 'list_event' does not exist"); } else { eventTypeSet = eventTypeSetTmp; } } catch (final FileNotFoundException ex) { errorView.addWarning(ErrorViewCategory.TYPES_FILE_INVALID, CommonConstants.TYPEDEF_FILE + ": " + ex.getMessage()); } if (eventTypeSet == null) { eventTypeSet = new ArchetypeTypeList(); } scriptArchUtils = editorFactory.newScriptArchUtils(eventTypeSet); final ScriptedEventFactory<G, A, R> scriptedEventFactory = editorFactory.newScriptedEventFactory(scriptArchUtils, gameObjectFactory, scriptedEventEditor, archetypeSet); scriptArchEditor = new DefaultScriptArchEditor<G, A, R>(scriptedEventFactory, scriptExtension, scriptName, scriptArchUtils, scriptFileFilter, globalSettings, mapManager, pathManager); scriptedEventEditor.setScriptArchEditor(scriptArchEditor); scriptArchData = editorFactory.newScriptArchData(); scriptArchDataUtils = editorFactory.newScriptArchDataUtils(scriptArchUtils, scriptedEventFactory, scriptedEventEditor); final long timeStart = System.currentTimeMillis(); if (log.isInfoEnabled()) { log.info("Start to load archetypes..."); } configSource.read(globalSettings, resources, errorView); for (final R archetype : archetypeSet.getArchetypes()) { final CharSequence editorFolder = archetype.getEditorFolder(); if (editorFolder != null && !editorFolder.equals(GameObject.EDITOR_FOLDER_INTERN)) { final String[] tmp = StringUtils.PATTERN_SLASH.split(editorFolder, 2); if (tmp.length == 2) { final String panelName = tmp[0]; final String folderName = tmp[1]; archetypeChooserModel.addArchetype(panelName, folderName, archetype); } } } if (log.isInfoEnabled()) { log.info("Archetype loading took " + (double) (System.currentTimeMillis() - timeStart) / 1000.0 + " seconds."); } if (spellType != 0) { new ArchetypeSetSpellLoader<G, A, R>(gameObjectFactory).load(archetypeSet, spellType, gameObjectSpells); gameObjectSpells.sort(); } if (spellFile != null) { try { final URL url = IOUtils.getResource(globalSettings.getConfigurationDirectory(), spellFile); final ErrorViewCollector errorViewCollector = new ErrorViewCollector(errorView, url); documentBuilder.setErrorHandler(new ErrorViewCollectorErrorHandler(errorViewCollector, ErrorViewCategory.SPELLS_FILE_INVALID)); try { XMLSpellLoader.load(errorViewCollector, url, xmlHelper.getDocumentBuilder(), numberSpells); } finally { documentBuilder.setErrorHandler(null); } } catch (final FileNotFoundException ex) { errorView.addWarning(ErrorViewCategory.SPELLS_FILE_INVALID, spellFile + ": " + ex.getMessage()); } numberSpells.sort(); } final File scriptsFile = new File(globalSettings.getMapsDirectory(), scriptsDir); final PluginModelParser<G, A, R> pluginModelParser = new PluginModelParser<G, A, R>(pluginParameterFactory); new PluginModelLoader<G, A, R>(pluginModelParser).loadPlugins(errorView, scriptsFile, pluginModel); new AutojoinListsParser<G, A, R>(errorView, archetypeSet, autojoinLists).loadList(globalSettings.getConfigurationDirectory()); ArchetypeTypeChecks.addChecks(archetypeTypeSet, attributeRangeChecker, environmentChecker); }

public void print(PrintWriter out) { out.println("<?xml version=\"1.0\"?>\n" + "<?xml-stylesheet type=\"text/xsl\" href=\"http://www.urbigene.com/foaf/foaf2html.xsl\" ?>\n" + "<rdf:RDF \n" + "xml:lang=\"en\" \n" + "xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" \n" + "xmlns:rdfs=\"http://www.w3.org/2000/01/rdf-schema#\" \n" + "xmlns=\"http://xmlns.com/foaf/0.1/\" \n" + "xmlns:foaf=\"http://xmlns.com/foaf/0.1/\" \n" + "xmlns:dc=\"http://purl.org/dc/elements/1.1/\">\n"); out.println("<!-- generated with SciFoaf http://www.urbigene.com/foaf -->"); if (this.mainAuthor == null && this.authors.getAuthorCount() > 0) { this.mainAuthor = this.authors.getAuthorAt(0); } if (this.mainAuthor != null) { out.println("<foaf:PersonalProfileDocument rdf:about=\"\">\n" + "\t<foaf:primaryTopic rdf:nodeID=\"" + this.mainAuthor.getID() + "\"/>\n" + "\t<foaf:maker rdf:resource=\"mailto:plindenbaum@yahoo.fr\"/>\n" + "\t<dc:title>FOAF for " + XMLUtilities.escape(this.mainAuthor.getName()) + "</dc:title>\n" + "\t<dc:description>\n" + "\tFriend-of-a-Friend description for " + XMLUtilities.escape(this.mainAuthor.getName()) + "\n" + "\t</dc:description>\n" + "</foaf:PersonalProfileDocument>\n\n"); } for (int i = 0; i < this.laboratories.size(); ++i) { Laboratory lab = this.laboratories.getLabAt(i); out.println("<foaf:Group rdf:ID=\"laboratory_ID" + i + "\" >"); out.println("\t<foaf:name>" + XMLUtilities.escape(lab.toString()) + "</foaf:name>"); for (int j = 0; j < lab.getAuthorCount(); ++j) { out.println("\t<foaf:member rdf:resource=\"#" + lab.getAuthorAt(j).getID() + "\" />"); } out.println("</foaf:Group>\n\n"); } for (int i = 0; i < this.authors.size(); ++i) { Author author = authors.getAuthorAt(i); out.println("<foaf:Person rdf:ID=\"" + xmlName(author.getID()) + "\" >"); out.println("\t<foaf:name>" + xmlName(author.getName()) + "</foaf:name>"); out.println("\t<foaf:title>Dr</foaf:title>"); out.println("\t<foaf:family_name>" + xmlName(author.getLastName()) + "</foaf:family_name>"); if (author.getForeName() != null && author.getForeName().length() > 2) { out.println("\t<foaf:firstName>" + xmlName(author.getForeName()) + "</foaf:firstName>"); } String prop = author.getProperty("foaf:mbox"); if (prop != null) { String tokens[] = prop.split("[\t ]+"); for (int j = 0; j < tokens.length; ++j) { if (tokens[j].trim().length() == 0) continue; if (tokens[j].equals("mailto:")) continue; if (!tokens[j].startsWith("mailto:")) tokens[j] = "mailto:" + tokens[j]; try { MessageDigest md = MessageDigest.getInstance("SHA"); md.update(tokens[j].getBytes()); byte[] digest = md.digest(); out.print("\t<foaf:mbox_sha1sum>"); for (int k = 0; k < digest.length; k++) { String hex = Integer.toHexString(digest[k]); if (hex.length() == 1) hex = "0" + hex; hex = hex.substring(hex.length() - 2); out.print(hex); } out.println("</foaf:mbox_sha1sum>"); } catch (Exception err) { out.println("\t<foaf:mbox rdf:resource=\"" + tokens[j] + "\" />"); } } } prop = author.getProperty("foaf:nick"); if (prop != null) { String tokens[] = prop.split("[\t ]+"); for (int j = 0; j < tokens.length; ++j) { if (tokens[j].trim().length() == 0) continue; out.println("\t<foaf:surname>" + XMLUtilities.escape(tokens[j]) + "</foaf:surname>"); } } prop = author.getProperty("foaf:homepage"); if (prop != null) { String tokens[] = prop.split("[\t ]+"); for (int j = 0; j < tokens.length; ++j) { if (!tokens[j].trim().startsWith("http://")) continue; if (tokens[j].trim().equals("http://")) continue; out.println("\t<foaf:homepage rdf:resource=\"" + XMLUtilities.escape(tokens[j].trim()) + "\"/>"); } } out.println("\t<foaf:publications rdf:resource=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Search&amp;itool=pubmed_Abstract&amp;term=" + author.getTerm() + "\"/>"); prop = author.getProperty("foaf:img"); if (prop != null) { String tokens[] = prop.split("[\t ]+"); for (int j = 0; j < tokens.length; ++j) { if (!tokens[j].trim().startsWith("http://")) continue; if (tokens[j].trim().equals("http://")) continue; out.println("\t<foaf:depiction rdf:resource=\"" + XMLUtilities.escape(tokens[j].trim()) + "\"/>"); } } AuthorList knows = this.whoknowwho.getKnown(author); for (int j = 0; j < knows.size(); ++j) { out.println("\t<foaf:knows rdf:resource=\"#" + xmlName(knows.getAuthorAt(j).getID()) + "\" />"); } Paper publications[] = this.papers.getAuthorPublications(author).toArray(); if (!(publications.length == 0)) { HashSet meshes = new HashSet(); for (int j = 0; j < publications.length; ++j) { meshes.addAll(publications[j].meshTerms); } for (Iterator itermesh = meshes.iterator(); itermesh.hasNext(); ) { MeshTerm meshterm = (MeshTerm) itermesh.next(); out.println("\t<foaf:interest>\n" + "\t\t<rdf:Description rdf:about=\"" + meshterm.getURL() + "\">\n" + "\t\t\t<dc:title>" + XMLUtilities.escape(meshterm.toString()) + "</dc:title>\n" + "\t\t</rdf:Description>\n" + "\t</foaf:interest>"); } } out.println("</foaf:Person>\n\n"); } Paper paperarray[] = this.papers.toArray(); for (int i = 0; i < paperarray.length; ++i) { out.println("<foaf:Document rdf:about=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=" + paperarray[i].getPMID() + "\">"); out.println("<dc:title>" + XMLUtilities.escape(paperarray[i].getTitle()) + "</dc:title>"); for (Iterator iter = paperarray[i].authors.iterator(); iter.hasNext(); ) { Author author = (Author) iter.next(); out.println("<dc:author rdf:resource=\"#" + XMLUtilities.escape(author.getID()) + "\"/>"); } out.println("</foaf:Document>"); } out.println("</rdf:RDF>"); }

public void save(UploadedFile file, Long student, Long activity) { File destiny = new File(fileFolder, student + "_" + activity + "_" + file.getFileName()); try { IOUtils.copy(file.getFile(), new FileOutputStream(destiny)); } catch (IOException e) { throw new RuntimeException("Erro ao copiar o arquivo.", e); } }

public Configuration(URL url) { InputStream in = null; try { load(in = url.openStream()); } catch (Exception e) { throw new RuntimeException("Could not load configuration from " + url, e); } finally { if (in != null) { try { in.close(); } catch (IOException ignore) { } } } }

public static synchronized String hash(String data) { if (digest == null) { try { digest = MessageDigest.getInstance("SHA-1"); } catch (NoSuchAlgorithmException nsae) { nsae.printStackTrace(); } } try { digest.update(data.getBytes("UTF-8")); } catch (UnsupportedEncodingException e) { System.err.println(e); } return encodeHex(digest.digest()); }

public static String MD5_hex(String p) { MessageDigest md; try { md = MessageDigest.getInstance("MD5"); md.update(p.getBytes()); BigInteger hash = new BigInteger(1, md.digest()); String ret = hash.toString(16); return ret; } catch (NoSuchAlgorithmException e) { logger.error("can not create confirmation key", e); throw new TechException(e); } }

public static void copyFile(String original, String destination) throws Exception { File original_file = new File(original); File destination_file = new File(destination); if (!original_file.exists()) throw new Exception("File with path " + original + " does not exist."); if (destination_file.exists()) throw new Exception("File with path " + destination + " already exists."); FileReader in = new FileReader(original_file); FileWriter out = new FileWriter(destination_file); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); }

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 void loadProperties() { try { java.util.Properties props = new java.util.Properties(); java.net.URL url = ClassLoader.getSystemResource("env.properties"); props.load(url.openStream()); this.proxyCertificatePath = props.getProperty("proxy.certificate.path"); this.dummyFileDirName = props.getProperty("delete.dummyFileDirName"); this.idleTimeTestDelay = new Integer(props.getProperty("idleTimeTestDelaySeconds")); if (props.getProperty("gridftp.timeoutMilliSecs") != null) { this.gridftpTimeoutMilliSecs = new Integer(props.getProperty("gridftp.timeoutMilliSecs").trim()); } this.assertContentInWriteTests = new Boolean(props.getProperty("assertContentInWriteTests")); this.gridftpHost1 = props.getProperty("gridftp.host1"); this.gridftpPort1 = new Integer(props.getProperty("gridftp.port1")); this.gridftpHost2 = props.getProperty("gridftp.host2"); this.gridftpPort2 = new Integer(props.getProperty("gridftp.port2")); this.srbGsiHost = props.getProperty("srb.gsi.host"); this.srbGsiPort = new Integer(props.getProperty("srb.gsi.port")); this.srbGsiPortMin = new Integer(props.getProperty("srb.gsi.port.min")); this.srbGsiPortMax = new Integer(props.getProperty("srb.gsi.port.max")); this.srbGsiDefaultResource = props.getProperty("srb.gsi.defaultResource"); this.srbEncryptHost = props.getProperty("srb.encrypt.host"); this.srbEncryptPort = new Integer(props.getProperty("srb.encrypt.port")); this.srbEncryptPortMin = new Integer(props.getProperty("srb.encrypt.port.min")); this.srbEncryptPortMax = new Integer(props.getProperty("srb.encrypt.port.max")); this.srbEncryptDefaultResource = props.getProperty("srb.encrypt.defaultResource"); this.srbEncryptHomeDirectory = props.getProperty("srb.encrypt.homeDirectory"); this.srbEncryptMcatZone = props.getProperty("srb.encrypt.mcatZone"); this.srbEncryptMdasDomainName = props.getProperty("srb.encrypt.mdasDomainName"); this.srbEncryptUsername = props.getProperty("srb.encrypt.username"); this.srbEncryptPassword = props.getProperty("srb.encrypt.password"); this.sftpHost = props.getProperty("sftp.host"); this.sftpPort = new Integer(props.getProperty("sftp.port")); this.sftpPath = props.getProperty("sftp.path"); this.sftpUsername = props.getProperty("sftp.username"); this.sftpPassword = props.getProperty("sftp.password"); if (props.getProperty("sftp.timeoutMilliSecs") != null) { this.sftpTimeoutMilliSecs = new Integer(props.getProperty("sftp.timeoutMilliSecs").trim()); } irodsEncryptHost = props.getProperty("irods.encrypt.host"); irodsEncryptPort = new Integer(props.getProperty("irods.encrypt.port")); irodsEncryptResource = props.getProperty("irods.encrypt.defaultResource"); irodsEncryptHomeDirectory = props.getProperty("irods.encrypt.homeDirectory"); irodsEncryptZone = props.getProperty("irods.encrypt.zone"); irodsEncryptUsername = props.getProperty("irods.encrypt.username"); irodsEncryptPassword = props.getProperty("irods.encrypt.password"); irodsGsiHost = props.getProperty("irods.gsi.host"); irodsGsiPort = new Integer(props.getProperty("irods.gsi.port")); irodsGsiZone = props.getProperty("irods.gsi.zone"); srbQueryTimeout = new Integer(props.getProperty("srb.query.timeout")); this.ftpUri = props.getProperty("ftp.uri"); this.httpUri = props.getProperty("http.uri"); this.httpProxy = props.getProperty("http.proxy"); this.httpPort = new Integer(props.getProperty("http.port")); this.fileUri = props.getProperty("file.uri"); java.net.URI tempUri = new java.net.URI(this.fileUri); File f = new File(tempUri); if (!f.exists()) { String temp = System.getProperty("java.io.tmpdir"); System.out.println("Cannot list [" + fileUri + "] listing java.io.tmpdir instead [" + temp + "]"); this.fileUri = temp; } useSrbGsiInFsCopyTest = new Boolean(props.getProperty("srb.gsi.use.in.fs.copy.test")); useSrbEncryptInFsCopyTest = new Boolean(props.getProperty("srb.encrypt.use.in.fs.copy.test")); useGridftpHost1InFsCopyTest = new Boolean(props.getProperty("gridftp.host1.use.in.fs.copy.test")); useGridftpHost2InFsCopyTest = new Boolean(props.getProperty("gridftp.host2.use.in.fs.copy.test")); useSftpInFsCopyTest = new Boolean(props.getProperty("sftp.use.in.fs.copy.test")); useLocalFileInFsCopyTest = new Boolean(props.getProperty("file.use.in.fs.copy.test")); useIrodsGsiCopyTest = new Boolean(props.getProperty("irods.gsi.use.in.fs.copy.test")); useIrodsEncryptCopyTest = new Boolean(props.getProperty("irods.encrypt.use.in.fs.copy.test")); assertNotNull(this.proxyCertificatePath); assertNotNull(this.dummyFileDirName); assertNotNull(this.idleTimeTestDelay); assertNotNull(this.ftpUri); assertNotNull(this.httpUri); } catch (Exception ex) { Logger.getLogger(AbstractTestClass.class.getName()).log(Level.SEVERE, null, ex); fail("Unable to locate and load 'testsettings.properties' file in source " + ex); } }

public void process() { try { update("Shutdown knowledge base ...", 0); DBHelper.shutdownDB(); update("Shutdown knowledge base ...", 9); String zipDir = P.DIR.getPKBDataPath(); update("Backup in progress ...", 10); List<String> fileList = getFilesToZip(zipDir); File file = new File(fileName); ZipOutputStream zout = new ZipOutputStream(new FileOutputStream(file)); byte[] readBuffer = new byte[2156]; int bytesIn = 0; for (int i = 0; i < fileList.size(); i++) { String filePath = fileList.get(i); File f = new File(filePath); FileInputStream fis = new FileInputStream(f); String zipEntryName = f.getPath().substring(zipDir.length() + 1); ZipEntry anEntry = new ZipEntry(zipEntryName); zout.putNextEntry(anEntry); while ((bytesIn = fis.read(readBuffer)) != -1) { zout.write(readBuffer, 0, bytesIn); } fis.close(); int percentage = (int) Math.round((i + 1) * 80.0 / fileList.size()); update("Backup in progress ...", 10 + percentage); } zout.close(); update("Restart knowledge base ...", 91); DBHelper.startDB(); update("Backup is done!", 100); } catch (Exception ex) { ex.printStackTrace(); update("Error occurs during backup!", 100); } }

private static void main(String[] args) { try { File f = new File("test.txt"); if (f.exists()) { throw new IOException(f + " already exists. I don't want to overwrite it."); } StraightStreamReader in; char[] cbuf = new char[0x1000]; int read; int totRead; FileOutputStream out = new FileOutputStream(f); for (int i = 0x00; i < 0x100; i++) { out.write(i); } out.close(); in = new StraightStreamReader(new FileInputStream(f)); for (int i = 0x00; i < 0x100; i++) { read = in.read(); if (read != i) { System.err.println("Error: " + i + " read as " + read); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = in.read(cbuf); if (totRead != 0x100) { System.err.println("Simple buffered read did not read the full amount: 0x" + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i]); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = 0; while (totRead <= 0x100 && (read = in.read(cbuf, totRead, 0x100 - totRead)) > 0) { totRead += read; } if (totRead != 0x100) { System.err.println("Not enough read. Bytes read: " + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i]); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = 0; while (totRead <= 0x100 && (read = in.read(cbuf, totRead + 0x123, 0x100 - totRead)) > 0) { totRead += read; } if (totRead != 0x100) { System.err.println("Not enough read. Bytes read: " + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i + 0x123] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i + 0x123]); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = 0; while (totRead <= 0x100 && (read = in.read(cbuf, totRead + 0x123, 7)) > 0) { totRead += read; } if (totRead != 0x100) { System.err.println("Not enough read. Bytes read: " + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i + 0x123] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i + 0x123]); } } in.close(); f.delete(); } catch (IOException x) { System.err.println(x.getMessage()); } }

private String sendMessage(HttpURLConnection connection, String reqMessage) throws IOException, XMLStreamException { 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(); byte[] byteArray = baos.toByteArray(); String resMessage = new String(byteArray, "UTF-8"); if (msgLog.isTraceEnabled()) msgLog.trace("Incoming Response SOAPMessage\n" + resMessage); return resMessage; }

public void writeTo(OutputStream out) throws IOException { if (!closed) { throw new IOException("Stream not closed"); } if (isInMemory()) { memoryOutputStream.writeTo(out); } else { FileInputStream fis = new FileInputStream(outputFile); try { IOUtils.copy(fis, out); } finally { IOUtils.closeQuietly(fis); } } }

private void _PostParser(Document document, AnnotationManager annoMan, Document htmldoc, String baseurl) { xformer = annoMan.getTransformer(); builder = annoMan.getBuilder(); String annohash = ""; if (document == null) return; NodeList ndlist = document.getElementsByTagNameNS(annoNS, "body"); if (ndlist.getLength() != 1) { System.out.println("Sorry Annotation Body was found " + ndlist.getLength() + " times"); return; } Element bodynode = (Element) ndlist.item(0); Node htmlNode = bodynode.getElementsByTagName("html").item(0); if (htmlNode == null) htmlNode = bodynode.getElementsByTagName("HTML").item(0); Document newdoc = builder.newDocument(); Element rootelem = newdoc.createElementNS(rdfNS, "r:RDF"); rootelem.setAttribute("xmlns:r", rdfNS); rootelem.setAttribute("xmlns:a", annoNS); rootelem.setAttribute("xmlns:d", dubNS); rootelem.setAttribute("xmlns:t", threadNS); newdoc.appendChild(rootelem); Element tmpelem; NodeList tmpndlist; Element annoElem = newdoc.createElementNS(annoNS, "a:Annotation"); rootelem.appendChild(annoElem); tmpelem = (Element) document.getElementsByTagNameNS(annoNS, "context").item(0); String context = tmpelem.getChildNodes().item(0).getNodeValue(); annoElem.setAttributeNS(annoNS, "a:context", context); NodeList elemcontl = tmpelem.getElementsByTagNameNS(alNS, "context-element"); Node ncontext_element = null; if (elemcontl.getLength() > 0) { Node old_context_element = elemcontl.item(0); ncontext_element = newdoc.importNode(old_context_element, true); } tmpndlist = document.getElementsByTagNameNS(dubNS, "title"); annoElem.setAttributeNS(dubNS, "d:title", tmpndlist.getLength() > 0 ? tmpndlist.item(0).getChildNodes().item(0).getNodeValue() : "Default"); tmpelem = (Element) document.getElementsByTagNameNS(dubNS, "creator").item(0); annoElem.setAttributeNS(dubNS, "d:creator", tmpelem.getChildNodes().item(0).getNodeValue()); tmpelem = (Element) document.getElementsByTagNameNS(annoNS, "created").item(0); annoElem.setAttributeNS(annoNS, "a:created", tmpelem.getChildNodes().item(0).getNodeValue()); tmpelem = (Element) document.getElementsByTagNameNS(dubNS, "date").item(0); annoElem.setAttributeNS(dubNS, "d:date", tmpelem.getChildNodes().item(0).getNodeValue()); tmpndlist = document.getElementsByTagNameNS(dubNS, "language"); String language = (tmpndlist.getLength() > 0 ? tmpndlist.item(0).getChildNodes().item(0).getNodeValue() : "en"); annoElem.setAttributeNS(dubNS, "d:language", language); Node typen = newdoc.importNode(document.getElementsByTagNameNS(rdfNS, "type").item(0), true); annoElem.appendChild(typen); Element contextn = newdoc.createElementNS(annoNS, "a:context"); contextn.setAttributeNS(rdfNS, "r:resource", context); annoElem.appendChild(contextn); Node annotatesn = newdoc.importNode(document.getElementsByTagNameNS(annoNS, "annotates").item(0), true); annoElem.appendChild(annotatesn); Element newbodynode = newdoc.createElementNS(annoNS, "a:body"); annoElem.appendChild(newbodynode); if (ncontext_element != null) { contextn.appendChild(ncontext_element); } else { System.out.println("No context element found, we create one..."); try { XPointer xptr = new XPointer(htmldoc); NodeRange xprange = xptr.getRange(context, htmldoc); Element context_elem = newdoc.createElementNS(alNS, "al:context-element"); context_elem.setAttributeNS(alNS, "al:text", xprange.getContentString()); context_elem.appendChild(newdoc.createTextNode(annoMan.generateContextString(xprange))); contextn.appendChild(context_elem); } catch (XPointerRangeException e2) { e2.printStackTrace(); } } WordFreq wf = new WordFreq(annoMan.extractTextFromNode(htmldoc)); Element docident = newdoc.createElementNS(alNS, "al:document-identifier"); annotatesn.appendChild(docident); docident.setAttributeNS(alNS, "al:orig-url", ((Element) annotatesn).getAttributeNS(rdfNS, "resource")); docident.setAttributeNS(alNS, "al:version", "1"); Iterator it = null; it = wf.getSortedWordlist(); Map.Entry ent; String word; int count; int i = 0; while (it.hasNext()) { ent = (Map.Entry) it.next(); word = ((String) ent.getKey()); count = ((Counter) ent.getValue()).count; if ((word.length() > 4) && (i < 10)) { Element wordelem = newdoc.createElementNS(alNS, "al:word"); wordelem.setAttributeNS(alNS, "al:freq", Integer.toString(count)); wordelem.appendChild(newdoc.createTextNode(word)); docident.appendChild(wordelem); i++; } } try { StringWriter strw = new StringWriter(); MessageDigest messagedigest = MessageDigest.getInstance("MD5"); xformer.transform(new DOMSource(newdoc), new StreamResult(strw)); messagedigest.update(strw.toString().getBytes()); byte[] md5bytes = messagedigest.digest(); annohash = ""; for (int b = 0; b < md5bytes.length; b++) { String s = Integer.toHexString(md5bytes[b] & 0xFF); annohash = annohash + ((s.length() == 1) ? "0" + s : s); } this.annohash = annohash; annoElem.setAttribute("xmlns:al", alNS); annoElem.setAttributeNS(alNS, "al:id", getAnnohash()); Location = (baseurl + "/annotation/" + getAnnohash()); annoElem.setAttributeNS(rdfNS, "r:about", Location); newbodynode.setAttributeNS(rdfNS, "r:resource", baseurl + "/annotation/body/" + getAnnohash()); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } catch (TransformerException e) { e.printStackTrace(); } annoMan.store(newdoc.getDocumentElement()); annoMan.createAnnoResource(newdoc.getDocumentElement(), getAnnohash()); if (htmlNode != null) annoMan.createAnnoBody(htmlNode, getAnnohash()); Location = (this.baseurl + "/annotation/" + getAnnohash()); annoElem.setAttributeNS(rdfNS, "r:about", Location); this.responseDoc = newdoc; }

public void fileCopy(File inFile, File outFile) { try { FileInputStream in = new FileInputStream(inFile); FileOutputStream out = new FileOutputStream(outFile); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } catch (IOException e) { System.err.println("Hubo un error de entrada/salida!!!"); } }

public void processAction(DatabaseAdapter db_, DataDefinitionActionDataListType parameters) throws Exception { PreparedStatement ps = null; try { if (log.isDebugEnabled()) log.debug("db connect - " + db_.getClass().getName()); String seqName = DefinitionService.getString(parameters, "sequence_name", null); if (seqName == null) { String errorString = "Name of sequnce not found"; log.error(errorString); throw new Exception(errorString); } String tableName = DefinitionService.getString(parameters, "name_table", null); if (tableName == null) { String errorString = "Name of table not found"; log.error(errorString); throw new Exception(errorString); } String columnName = DefinitionService.getString(parameters, "name_pk_field", null); if (columnName == null) { String errorString = "Name of column not found"; log.error(errorString); throw new Exception(errorString); } CustomSequenceType seqSite = new CustomSequenceType(); seqSite.setSequenceName(seqName); seqSite.setTableName(tableName); seqSite.setColumnName(columnName); long seqValue = db_.getSequenceNextValue(seqSite); String valueColumnName = DefinitionService.getString(parameters, "name_value_field", null); if (columnName == null) { String errorString = "Name of valueColumnName not found"; log.error(errorString); throw new Exception(errorString); } String insertValue = DefinitionService.getString(parameters, "insert_value", null); if (columnName == null) { String errorString = "Name of insertValue not found"; log.error(errorString); throw new Exception(errorString); } String sql = "insert into " + tableName + " " + "(" + columnName + "," + valueColumnName + ")" + "values" + "(?,?)"; if (log.isDebugEnabled()) { log.debug(sql); log.debug("pk " + seqValue); log.debug("value " + insertValue); } ps = db_.prepareStatement(sql); ps.setLong(1, seqValue); ps.setString(2, insertValue); ps.executeUpdate(); db_.commit(); } catch (Exception e) { try { db_.rollback(); } catch (Exception e1) { } log.error("Error insert value", e); throw e; } finally { org.riverock.generic.db.DatabaseManager.close(ps); ps = null; } }

private static List retrieveQuotes(Report report, Symbol symbol, TradingDate startDate, TradingDate endDate) throws ImportExportException { List quotes = new ArrayList(); String URLString = constructURL(symbol, startDate, endDate); EODQuoteFilter filter = new YahooEODQuoteFilter(symbol); PreferencesManager.ProxyPreferences proxyPreferences = PreferencesManager.loadProxySettings(); try { URL url = new URL(URLString); InputStreamReader input = new InputStreamReader(url.openStream()); BufferedReader bufferedInput = new BufferedReader(input); String line = bufferedInput.readLine(); while (line != null) { line = bufferedInput.readLine(); if (line != null) { try { EODQuote quote = filter.toEODQuote(line); quotes.add(quote); verify(report, quote); } catch (QuoteFormatException e) { report.addError(Locale.getString("YAHOO") + ":" + symbol + ":" + Locale.getString("ERROR") + ": " + e.getMessage()); } } } bufferedInput.close(); } catch (BindException e) { throw new ImportExportException(Locale.getString("UNABLE_TO_CONNECT_ERROR", e.getMessage())); } catch (ConnectException e) { throw new ImportExportException(Locale.getString("UNABLE_TO_CONNECT_ERROR", e.getMessage())); } catch (UnknownHostException e) { throw new ImportExportException(Locale.getString("UNKNOWN_HOST_ERROR", e.getMessage())); } catch (NoRouteToHostException e) { throw new ImportExportException(Locale.getString("DESTINATION_UNREACHABLE_ERROR", e.getMessage())); } catch (MalformedURLException e) { throw new ImportExportException(Locale.getString("INVALID_PROXY_ERROR", proxyPreferences.host, proxyPreferences.port)); } catch (FileNotFoundException e) { } catch (IOException e) { throw new ImportExportException(Locale.getString("ERROR_DOWNLOADING_QUOTES")); } return quotes; }

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 String getHtml(String path) throws Exception { URL url = new URL(path); URLConnection conn = url.openConnection(); conn.setDoOutput(true); InputStream inputStream = conn.getInputStream(); InputStreamReader isr = new InputStreamReader(inputStream, "UTF-8"); StringBuilder sb = new StringBuilder(); BufferedReader in = new BufferedReader(isr); String inputLine; while ((inputLine = in.readLine()) != null) { sb.append(inputLine); } String result = sb.toString(); return result; }

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 md5(String value) throws NoSuchAlgorithmException { MessageDigest messageDigest = MessageDigest.getInstance("MD5"); try { messageDigest.update(value.getBytes("UTF-8")); } catch (UnsupportedEncodingException e) { messageDigest.update(value.getBytes()); } byte[] bytes = messageDigest.digest(); return byteArrayToHexString(bytes); }

public String hash(String plainTextPassword) { try { MessageDigest digest = MessageDigest.getInstance(digestAlgorithm); digest.update(plainTextPassword.getBytes(charset)); byte[] rawHash = digest.digest(); return new String(Hex.encodeHex(rawHash)); } catch (Exception ex) { throw new RuntimeException(ex); } }

private static long saveAndClosePDFDocument(PDDocument document, OutputStreamProvider outProvider) throws IOException, COSVisitorException { File tempFile = null; InputStream in = null; OutputStream out = null; try { tempFile = File.createTempFile("temp", "pdf"); OutputStream tempFileOut = new FileOutputStream(tempFile); tempFileOut = new BufferedOutputStream(tempFileOut); document.save(tempFileOut); document.close(); tempFileOut.close(); long length = tempFile.length(); in = new BufferedInputStream(new FileInputStream(tempFile)); out = new BufferedOutputStream(outProvider.getOutputStream()); IOUtils.copy(in, out); return length; } finally { if (in != null) { IOUtils.closeQuietly(in); } if (out != null) { IOUtils.closeQuietly(out); } if (tempFile != null && !FileUtils.deleteQuietly(tempFile)) { tempFile.deleteOnExit(); } } }

private void copyFile(File sourceFile, File targetFile) { beNice(); dispatchEvent(SynchronizationEventType.FileCopy, sourceFile, targetFile); File temporaryFile = new File(targetFile.getPath().concat(".jnstemp")); while (temporaryFile.exists()) { try { beNice(); temporaryFile.delete(); beNice(); } catch (Exception ex) { } } try { if (targetFile.exists()) { targetFile.delete(); } FileInputStream fis = new FileInputStream(sourceFile); FileOutputStream fos = new FileOutputStream(temporaryFile); byte[] buffer = new byte[204800]; int readBytes = 0; int counter = 0; while ((readBytes = fis.read(buffer)) != -1) { counter++; updateStatus("... processing fragment " + String.valueOf(counter)); fos.write(buffer, 0, readBytes); } fis.close(); fos.close(); temporaryFile.renameTo(targetFile); temporaryFile.setLastModified(sourceFile.lastModified()); targetFile.setLastModified(sourceFile.lastModified()); } catch (IOException e) { Exception dispatchedException = new Exception("ERROR: Copy File( " + sourceFile.getPath() + ", " + targetFile.getPath() + " )"); dispatchEvent(dispatchedException, sourceFile, targetFile); } dispatchEvent(SynchronizationEventType.FileCopyDone, sourceFile, targetFile); }

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

private void downloadPhoto(File photo, String url) { try { HttpClient httpClient = new DefaultHttpClient(); Log.v(TAG, "Dowloading photo from " + Server.URL + url); HttpGet request = new HttpGet(Server.URL + url); HttpResponse response = httpClient.execute(request); HttpEntity entity = response.getEntity(); InputStream serverPhoto = entity.getContent(); photo.createNewFile(); FileOutputStream photoStream = new FileOutputStream(photo); byte[] buf = new byte[1024]; int len; while ((len = serverPhoto.read(buf)) > 0) { photoStream.write(buf, 0, len); } photoStream.flush(); photoStream.close(); } catch (Exception e) { Log.e(TAG, e.getMessage()); } }

public boolean createUser(String username, String password, String name) throws Exception { boolean user_created = false; try { statement = connect.prepareStatement("SELECT COUNT(*) from toepen.users WHERE username = ? LIMIT 1"); statement.setString(1, username); resultSet = statement.executeQuery(); resultSet.next(); if (resultSet.getInt(1) == 0) { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.update(password.getBytes()); BigInteger hash = new BigInteger(1, md5.digest()); String password_hash = hash.toString(16); long ctime = System.currentTimeMillis() / 1000; statement = connect.prepareStatement("INSERT INTO toepen.users " + "(username, password, name, ctime) " + "VALUES (?, ?, ?, ?)"); statement.setString(1, username); statement.setString(2, password_hash); statement.setString(3, name); statement.setLong(4, ctime); if (statement.executeUpdate() > 0) { user_created = true; } } } catch (Exception ex) { System.out.println(ex); } finally { close(); return user_created; } }

@Override protected void doPost(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException { long startTime = System.currentTimeMillis(); boolean validClient = true; boolean validSession = false; String sessionKey = req.getParameter("sid"); String storedKey = CLIENT_SESSION_KEYS.get(req.getRemoteAddr()); if (sessionKey != null && storedKey != null && sessionKey.equals(storedKey)) validSession = true; DataStore ds = DataStore.getConnection(); if (IPV6_DETECTED) { boolean doneWarning; synchronized (SJQServlet.class) { doneWarning = IPV6_WARNED; if (!IPV6_WARNED) IPV6_WARNED = true; } if (!doneWarning) LOG.warn("IPv6 interface detected; client restriction settings ignored [restrictions do not support IPv6 addresses]"); } else { String[] clntRestrictions = ds.getSetting("ValidClients", "").split(";"); List<IPMatcher> matchers = new ArrayList<IPMatcher>(); if (clntRestrictions.length == 1 && clntRestrictions[0].trim().length() == 0) { LOG.warn("All client connections are being accepted and processed, please consider setting up client restrictions in SJQ settings"); } else { for (String s : clntRestrictions) { s = s.trim(); try { matchers.add(new IPMatcher(s)); } catch (IPMatcherException e) { LOG.error("Invalid client restriction settings; client restrictions ignored!", e); matchers.clear(); break; } } validClient = matchers.size() > 0 ? false : true; for (IPMatcher m : matchers) { try { if (m.match(req.getRemoteAddr())) { validClient = true; break; } } catch (IPMatcherException e) { LOG.error("IPMatcherException", e); } } } } String clntProto = req.getParameter("proto"); if (clntProto == null || Integer.parseInt(clntProto) != SJQ_PROTO) throw new RuntimeException("Server is speaking protocol '" + SJQ_PROTO + "', but client is speaking protocol '" + clntProto + "'; install a client version that matches the server protocol version!"); resp.setHeader("Content-Type", "text/plain"); resp.setDateHeader("Expires", 0); resp.setDateHeader("Last-Modified", System.currentTimeMillis()); resp.setHeader("Cache-Control", "no-store, no-cache, must-revalidate"); resp.setHeader("Pragma", "no-cache"); String cmd = req.getParameter("cmd"); if (cmd == null) { DataStore.returnConnection(ds); return; } ActiveClientList list = ActiveClientList.getInstance(); BufferedWriter bw = new BufferedWriter(resp.getWriter()); if (cmd.equals("pop")) { if (!validClient) { LOG.warn("Client IP rejected: " + req.getRemoteAddr()); notAuthorized(resp, bw); } else { list.add(req.getRemoteHost()); ClientParser clnt = new ClientParser(new StringReader(ds.getClientConf(req.getRemoteHost()))); String offDay = clnt.getGlobalOption("OFFDAY"); String offHour = clnt.getGlobalOption("OFFHOUR"); Calendar now = Calendar.getInstance(); if (RangeInterpreter.inRange(now.get(Calendar.DAY_OF_WEEK), 1, 7, offDay) || RangeInterpreter.inRange(now.get(Calendar.HOUR_OF_DAY), 0, 23, offHour)) { LOG.warn("Client '" + req.getRemoteAddr() + "' currently disabled via OFFDAY/OFFHOUR settings."); bw.write("null"); } else { Task t = TaskQueue.getInstance().pop(req.getRemoteHost(), getPopCandidates(req.getRemoteHost(), clnt)); if (t == null) bw.write("null"); else { t.setResourcesUsed(Integer.parseInt(clnt.getTask(t.getTaskId()).getOption("RESOURCES"))); Object obj = null; if (t.getObjType().equals("media")) obj = Butler.SageApi.mediaFileAPI.GetMediaFileForID(Integer.parseInt(t.getObjId())); else if (t.getObjType().equals("sysmsg")) obj = SystemMessageUtils.getSysMsg(t.getObjId()); ClientTask cTask = clnt.getTask(t.getTaskId()); JSONObject jobj = cTask.toJSONObject(obj); String objType = null; try { if (jobj != null) objType = jobj.getString(Task.JSON_OBJ_TYPE); } catch (JSONException e) { throw new RuntimeException("Invalid ClienTask JSON object conversion!"); } if (obj == null || jobj == null) { LOG.error("Source object has disappeared! [" + t.getObjType() + "/" + t.getObjId() + "]"); TaskQueue.getInstance().updateTask(t.getObjId(), t.getTaskId(), Task.State.FAILED, t.getObjType()); bw.write("null"); } else if (objType.equals("media")) { try { long ratio = calcRatio(jobj.getString(Task.JSON_OBJ_ID), jobj.getString(Task.JSON_NORECORDING)); if (ratio > 0 && new FieldTimeUntilNextRecording(null, "<=", ratio + "S").run()) { LOG.info("Client '" + req.getRemoteAddr() + "' cannot pop task '" + t.getObjType() + "/" + t.getTaskId() + "/" + t.getObjId() + "'; :NORECORDING option prevents running of this task"); TaskQueue.getInstance().pushBack(t); bw.write("null"); } else bw.write(jobj.toString()); } catch (JSONException e) { throw new RuntimeException(e); } } else bw.write(jobj.toString()); } } } } else if (cmd.equals("update")) { if (!validClient) { LOG.warn("Client IP rejected: " + req.getRemoteAddr()); notAuthorized(resp, bw); } else { list.add(req.getRemoteHost()); try { Task t = new Task(new JSONObject(req.getParameter("data"))); TaskQueue.getInstance().updateTask(t); } catch (JSONException e) { throw new RuntimeException("Input error; client '" + req.getRemoteHost() + "', CMD: update", e); } } } else if (cmd.equals("showQ")) { if (validSession) bw.write(TaskQueue.getInstance().toJSONArray().toString()); else notAuthorized(resp, bw); } else if (cmd.equals("log")) { if (validSession) { String mediaId = req.getParameter("m"); String taskId = req.getParameter("t"); String objType = req.getParameter("o"); if ((mediaId != null && !mediaId.equals("0")) && (taskId != null && !taskId.equals("0"))) bw.write(ds.readLog(mediaId, taskId, objType)); else { BufferedReader r = new BufferedReader(new FileReader("sjq.log")); String line; while ((line = r.readLine()) != null) bw.write(line + "\n"); r.close(); } } else notAuthorized(resp, bw); } else if (cmd.equals("appState")) { if (validSession) bw.write(Butler.dumpAppTrace()); else notAuthorized(resp, bw); } else if (cmd.equals("writeLog")) { if (!validClient) { LOG.warn("Client IP reject: " + req.getRemoteAddr()); notAuthorized(resp, bw); } else { String mediaId = req.getParameter("m"); String taskId; if (!mediaId.equals("-1")) taskId = req.getParameter("t"); else taskId = req.getRemoteHost(); String objType = req.getParameter("o"); if (!mediaId.equals("0") && Boolean.parseBoolean(ds.getSetting("IgnoreTaskOutput", "false"))) { LOG.info("Dropping task output as per settings"); DataStore.returnConnection(ds); return; } String data = req.getParameter("data"); String[] msg = StringUtils.splitByWholeSeparator(data, "\r\n"); if (msg == null || msg.length == 1) msg = StringUtils.split(data, '\r'); if (msg == null || msg.length == 1) msg = StringUtils.split(data, '\n'); long now = System.currentTimeMillis(); for (String line : msg) ds.logForTaskClient(mediaId, taskId, line, now, objType); if (msg.length > 0) ds.flushLogs(); } } else if (cmd.equals("ruleset")) { if (validSession) bw.write(ds.getSetting("ruleset", "")); else notAuthorized(resp, bw); } else if (cmd.equals("saveRuleset")) { if (validSession) { ds.setSetting("ruleset", req.getParameter("data")); bw.write("Success"); } else notAuthorized(resp, bw); } else if (cmd.equals("getClients")) { if (validSession) bw.write(ActiveClientList.getInstance().toJSONArray().toString()); else notAuthorized(resp, bw); } else if (cmd.equals("loadClnt")) { if (validSession) bw.write(ds.getClientConf(req.getParameter("id"))); else notAuthorized(resp, bw); } else if (cmd.equals("saveClnt")) { if (validSession) { if (ds.saveClientConf(req.getParameter("id"), req.getParameter("data"))) bw.write("Success"); else bw.write("Failed"); } else notAuthorized(resp, bw); } else if (cmd.equals("history")) { if (validSession) { int start, limit; try { start = Integer.parseInt(req.getParameter("start")); limit = Integer.parseInt(req.getParameter("limit")); } catch (NumberFormatException e) { start = 0; limit = -1; } bw.write(ds.getJobHistory(Integer.parseInt(req.getParameter("t")), start, limit, req.getParameter("sort")).toString()); } else notAuthorized(resp, bw); } else if (cmd.equals("getSrvSetting")) { if (validSession) bw.write(ds.getSetting(req.getParameter("var"), "")); else notAuthorized(resp, bw); } else if (cmd.equals("setSrvSetting")) { if (validSession) { ds.setSetting(req.getParameter("var"), req.getParameter("val")); bw.write("Success"); } else notAuthorized(resp, bw); } else if (cmd.equals("setFileCleaner")) { if (validSession) { ds.setSetting("DelRegex", req.getParameter("orphan")); ds.setSetting("IfRegex", req.getParameter("parent")); ds.setSetting("IgnoreRegex", req.getParameter("ignore")); new Thread(new FileCleaner()).start(); bw.write("Success"); } else notAuthorized(resp, bw); } else if (cmd.equals("getFileCleanerSettings")) { if (validSession) { bw.write(ds.getSetting("DelRegex", "") + "\n"); bw.write(ds.getSetting("IfRegex", "") + "\n"); bw.write(ds.getSetting("IgnoreRegex", "")); } else notAuthorized(resp, bw); } else if (cmd.equals("writeSrvSettings")) { if (validSession) { try { ds.setSettings(new JSONObject(req.getParameter("data"))); } catch (JSONException e) { throw new RuntimeException(e); } bw.write("Success"); } else notAuthorized(resp, bw); } else if (cmd.equals("readSrvSettings")) { if (validSession) bw.write(ds.readSettings().toString()); else notAuthorized(resp, bw); } else if (cmd.equals("login")) { String pwd = ds.getSetting("password", ""); try { MessageDigest msg = MessageDigest.getInstance("MD5"); msg.update(req.getParameter("password").getBytes()); String userPwd = new String(msg.digest()); if (pwd.length() > 0 && pwd.equals(userPwd)) { bw.write("Success"); int key = new java.util.Random().nextInt(); resp.addHeader("SJQ-Session-Token", Integer.toString(key)); CLIENT_SESSION_KEYS.put(req.getRemoteAddr(), Integer.toString(key)); } else bw.write("BadPassword"); } catch (NoSuchAlgorithmException e) { bw.write(e.getLocalizedMessage()); } } else if (cmd.equals("editPwd")) { try { MessageDigest msg = MessageDigest.getInstance("MD5"); String curPwd = ds.getSetting("password", ""); String oldPwd = req.getParameter("old"); msg.update(oldPwd.getBytes()); oldPwd = new String(msg.digest()); msg.reset(); String newPwd = req.getParameter("new"); String confPwd = req.getParameter("conf"); if (!curPwd.equals(oldPwd)) bw.write("BadOld"); else if (!newPwd.equals(confPwd) || newPwd.length() == 0) bw.write("BadNew"); else { msg.update(newPwd.getBytes()); newPwd = new String(msg.digest()); ds.setSetting("password", newPwd); bw.write("Success"); } } catch (NoSuchAlgorithmException e) { bw.write(e.getLocalizedMessage()); } } else if (cmd.equals("runStats")) { if (validSession) { JSONObject o = new JSONObject(); try { o.put("last", Long.parseLong(ds.getSetting("LastRun", "0"))); o.put("next", Long.parseLong(ds.getSetting("NextRun", "0"))); bw.write(o.toString()); } catch (JSONException e) { bw.write(e.getLocalizedMessage()); } } else notAuthorized(resp, bw); } else if (cmd.equals("runQLoader")) { if (validSession) { Butler.wakeQueueLoader(); bw.write("Success"); } else notAuthorized(resp, bw); } else if (cmd.equals("delActiveQ")) { if (validSession) { if (TaskQueue.getInstance().delete(req.getParameter("m"), req.getParameter("t"))) bw.write("Success"); else bw.write("Failed"); } else notAuthorized(resp, bw); } else if (cmd.equals("clearActiveQ")) { if (validSession) { if (TaskQueue.getInstance().clear()) bw.write("Success"); else bw.write("Failed"); } else notAuthorized(resp, bw); } else if (cmd.equals("editPri")) { if (validSession) { try { int priority = Integer.parseInt(req.getParameter("p")); if (TaskQueue.getInstance().editPriority(req.getParameter("m"), req.getParameter("t"), priority)) bw.write("Success"); else bw.write("Failed"); } catch (NumberFormatException e) { bw.write("Failed"); } } else notAuthorized(resp, bw); } else if (cmd.equals("clearHistory")) { if (validSession) { if (ds.clear(Integer.parseInt(req.getParameter("t")))) bw.write("Success"); else bw.write("Failed"); } else notAuthorized(resp, bw); } else if (cmd.equals("delHistRow")) { if (validSession) { if (ds.delTask(req.getParameter("m"), req.getParameter("t"), Integer.parseInt(req.getParameter("y")), req.getParameter("o"))) bw.write("Success"); else bw.write("Failed"); } else notAuthorized(resp, bw); } else if (cmd.equals("rmLog")) { if (validSession) { String mid = req.getParameter("m"); String tid = req.getParameter("t"); String oid = req.getParameter("o"); if (mid.equals("0") && tid.equals("0") && oid.equals("null")) { bw.write("Failed: Can't delete server log file (sjq.log) while SageTV is running!"); } else if (ds.clearLog(mid, tid, oid)) bw.write("Success"); else bw.write("Failed"); } else notAuthorized(resp, bw); } else if (cmd.equals("qryMediaFile")) { if (validSession) { JSONArray jarr = new JSONArray(); MediaFileAPI.List mediaList = Butler.SageApi.mediaFileAPI.GetMediaFiles(ds.getMediaMask()); String qry = req.getParameter("q"); int max = Integer.parseInt(req.getParameter("m")); for (MediaFileAPI.MediaFile mf : mediaList) { if ((qry.matches("\\d+") && Integer.toString(mf.GetMediaFileID()).startsWith(qry)) || mf.GetMediaTitle().matches(".*" + Pattern.quote(qry) + ".*") || fileSegmentMatches(mf, qry)) { JSONObject o = new JSONObject(); try { o.put("value", mf.GetFileForSegment(0).getAbsolutePath()); String subtitle = null; if (mf.GetMediaFileAiring() != null && mf.GetMediaFileAiring().GetShow() != null) subtitle = mf.GetMediaFileAiring().GetShow().GetShowEpisode(); String display; if (subtitle != null && subtitle.length() > 0) display = mf.GetMediaTitle() + ": " + subtitle; else display = mf.GetMediaTitle(); o.put("display", mf.GetMediaFileID() + " - " + display); jarr.put(o); if (jarr.length() >= max) break; } catch (JSONException e) { e.printStackTrace(System.out); } } } bw.write(jarr.toString()); } else notAuthorized(resp, bw); } else if (cmd.equals("debugMediaFile")) { if (validSession) { if (Butler.debugQueueLoader(req.getParameter("f"))) bw.write("Success"); else bw.write("Failed"); } else notAuthorized(resp, bw); } else if (cmd.equals("killTask")) { if (validSession) { if (TaskQueue.getInstance().killTask(req.getParameter("m"), req.getParameter("t"), req.getParameter("o"))) bw.write("Success"); else bw.write("Failed"); } else notAuthorized(resp, bw); } else if (cmd.equals("keepAlive")) { bw.write(Boolean.toString(!TaskQueue.getInstance().isTaskKilled(req.getParameter("m"), req.getParameter("t"), req.getParameter("o")))); } bw.close(); DataStore.returnConnection(ds); LOG.info("Servlet POST request completed [" + (System.currentTimeMillis() - startTime) + "ms]"); return; }

public static boolean copy(File source, File dest) { FileChannel in = null, out = null; try { in = new FileInputStream(source).getChannel(); out = new FileOutputStream(dest).getChannel(); long size = in.size(); MappedByteBuffer buf = in.map(FileChannel.MapMode.READ_ONLY, 0, size); out.write(buf); if (in != null) in.close(); if (out != null) out.close(); } catch (IOException e) { e.printStackTrace(); return false; } return true; }

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(); } }

static Object read(String path, String encoding, boolean return_string) throws IOException { InputStream in; if (path.startsWith("classpath:")) { path = path.substring("classpath:".length()); URL url = Estimate.class.getClassLoader().getResource(path); if (url == null) { throw new IllegalArgumentException("Not found " + path + " in classpath."); } System.out.println("read content from:" + url.getFile()); in = url.openStream(); } else { File f = new File(path); if (!f.exists()) { throw new IllegalArgumentException("Not found " + path + " in system."); } System.out.println("read content from:" + f.getAbsolutePath()); in = new FileInputStream(f); } Reader re; if (encoding != null) { re = new InputStreamReader(in, encoding); } else { re = new InputStreamReader(in); } if (!return_string) { return re; } char[] chs = new char[1024]; int count; StringBuffer content = new StringBuffer(); while ((count = re.read(chs)) != -1) { content.append(chs, 0, count); } re.close(); return content.toString(); }

int[] slowSort() { int[] values = getValues(); int n = values.length; for (int pass = 1; pass < n; pass++) { for (int i = 0; i < n - pass; i++) { if (values[i] > values[i + 1]) { int temp = values[i]; values[i] = values[i + 1]; values[i + 1] = temp; } } } return values; }

public void elimina(Cliente cli) throws errorSQL, errorConexionBD { System.out.println("GestorCliente.elimina()"); int id = cli.getId(); String sql; Statement stmt = null; try { gd.begin(); sql = "DELETE FROM cliente WHERE cod_cliente =" + id; System.out.println("Ejecutando: " + sql); stmt = gd.getConexion().createStatement(); stmt.executeUpdate(sql); System.out.println("executeUpdate"); sql = "DELETE FROM persona WHERE id =" + id; System.out.println("Ejecutando: " + sql); stmt.executeUpdate(sql); gd.commit(); System.out.println("commit"); stmt.close(); } catch (SQLException e) { gd.rollback(); throw new errorSQL(e.toString()); } catch (errorConexionBD e) { System.err.println("Error en GestorCliente.elimina(): " + e); } catch (errorSQL e) { System.err.println("Error en GestorCliente.elimina(): " + e); } }

public static BufferedReader getReader(int license) { URL url = getResource(license); if (url == null) return null; InputStream inStream; try { inStream = url.openStream(); } catch (IOException e) { return null; } return new BufferedReader(new InputStreamReader(inStream)); }

public static void main(String[] args) throws ParseException, FileNotFoundException, IOException { InputStream input = new BufferedInputStream(UpdateLanguages.class.getResourceAsStream("definition_template")); Translator t = new Translator(input, "UTF8"); Node template = Translator.Start(); File langs = new File("support/support/translate/languages"); for (File f : langs.listFiles()) { if (f.getName().endsWith(".lng")) { input = new BufferedInputStream(new FileInputStream(f)); try { Translator.ReInit(input, "UTF8"); } catch (java.lang.NullPointerException e) { new Translator(input, "UTF8"); } Node newFile = Translator.Start(); ArrayList<Addition> additions = new ArrayList<Addition>(); syncKeys(template, newFile, additions); ArrayList<String> fileLines = new ArrayList<String>(); Scanner scanner = new Scanner(new BufferedReader(new FileReader(f))); while (scanner.hasNextLine()) { fileLines.add(scanner.nextLine()); } int offset = 0; for (Addition a : additions) { System.out.println("Key added " + a + " to " + f.getName()); if (a.afterLine < 0 || a.afterLine >= fileLines.size()) { fileLines.add(a.getAddition(0)); } else { fileLines.add(a.afterLine + (offset++) + 1, a.getAddition(0)); } } f.delete(); Writer writer = new BufferedWriter(new FileWriter(f)); for (String s : fileLines) writer.write(s + "\n"); writer.close(); System.out.println("Language " + f.getName() + " had " + additions.size() + " additions"); } } File defFile = new File(langs, "language.lng"); defFile.delete(); defFile.createNewFile(); InputStream copyStream = new BufferedInputStream(UpdateLanguages.class.getResourceAsStream("definition_template")); OutputStream out = new BufferedOutputStream(new FileOutputStream(defFile)); int c = 0; while ((c = copyStream.read()) >= 0) out.write(c); out.close(); System.out.println("Languages updated."); }

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 void testJPEGBuffImage() throws MalformedURLException, IOException { System.out.println("JPEGCodec BufferedImage:"); long start = Calendar.getInstance().getTimeInMillis(); for (int i = 0; i < images.length; i++) { String url = Constants.getDefaultURIMediaConnectorBasePath() + "albums/hund/" + images[i]; InputStream istream = (new URL(url)).openStream(); JPEGImageDecoder dec = JPEGCodec.createJPEGDecoder(istream); BufferedImage image = dec.decodeAsBufferedImage(); int width = image.getWidth(); int height = image.getHeight(); istream.close(); System.out.println("w: " + width + " - h: " + height); } long stop = Calendar.getInstance().getTimeInMillis(); System.out.println("zeit: " + (stop - start)); }

public void openFtpConnection(String workingDirectory) throws RQLException { try { ftpClient = new FTPClient(); ftpClient.connect(server); ftpClient.login(user, password); ftpClient.changeWorkingDirectory(workingDirectory); } catch (IOException ioex) { throw new RQLException("FTP client could not be created. Please check attributes given in constructor.", ioex); } }

private static String loadUrlToString(String a_url) throws IOException { URL l_url1 = new URL(a_url); BufferedReader br = new BufferedReader(new InputStreamReader(l_url1.openStream())); String l_content = ""; String l_ligne = null; l_content = br.readLine(); while ((l_ligne = br.readLine()) != null) { l_content += AA.SL + l_ligne; } return l_content; }

private void addEMInformation() { try { long emDate = System.currentTimeMillis(); if (_local == true) { File emFile = new File("emprotz.dat"); if (!emFile.exists()) { return; } emDate = emFile.lastModified(); } if (emDate > this._emFileDate) { this._emFileDate = emDate; this._emDate = emDate; for (int ii = 0; ii < this._projectInfo.size(); ii++) { Information info = getInfo(ii); if (info != null) { info._emDeadline = null; info._emFrames = null; info._emValue = null; } } Reader reader = null; if (_local == true) { reader = new FileReader("emprotz.dat"); } else { StringBuffer urlName = new StringBuffer(); urlName.append("http://home.comcast.net/"); urlName.append("~wxdude1/emsite/download/"); urlName.append("emprotz.zip"); try { URL url = new URL(urlName.toString()); InputStream stream = url.openStream(); ZipInputStream zip = new ZipInputStream(stream); zip.getNextEntry(); reader = new InputStreamReader(zip); } catch (MalformedURLException mue) { mue.printStackTrace(); } } BufferedReader file = new BufferedReader(reader); try { String line1 = null; int count = 0; while ((line1 = file.readLine()) != null) { String line2 = (line1 != null) ? file.readLine() : null; String line3 = (line2 != null) ? file.readLine() : null; String line4 = (line3 != null) ? file.readLine() : null; count++; if ((count > 1) && (line1 != null) && (line2 != null) && (line3 != null) && (line4 != null)) { if (line1.length() > 2) { int posBegin = line1.indexOf("\"", 0); int posEnd = line1.indexOf("\"", posBegin + 1); if ((posBegin >= 0) && (posEnd >= 0)) { String project = line1.substring(posBegin + 1, posEnd - posBegin); int projectNum = Integer.parseInt(project); Integer deadline = Integer.valueOf(line2.trim()); Double value = Double.valueOf(line3.trim()); Integer frames = Integer.valueOf(line4.trim()); Information info = getInfo(projectNum); if (info == null) { info = createInfo(projectNum); } if (info._emValue == null) { info._emDeadline = deadline; info._emFrames = frames; info._emValue = value; } } } } } } catch (Exception e) { e.printStackTrace(); } finally { file.close(); } } } catch (FileNotFoundException e) { } catch (IOException e) { } }

@SuppressWarnings("finally") private void decompress(final File src) throws IOException { final String srcPath = src.getPath(); checkSourceFile(src); final boolean test = this.switches.contains(Switch.test); final File dst; if (test) dst = File.createTempFile("jaxlib-bzip", null); else { if (srcPath.endsWith(".bz2")) dst = new File(srcPath.substring(0, srcPath.length() - 4)); else { this.log.println("WARNING: Can't guess original name, using extension \".out\":").println(srcPath); dst = new File(srcPath + ".out"); } } if (!checkDestFile(dst)) return; final boolean showProgress = this.switches.contains(Switch.showProgress); BZip2InputStream in = null; FileOutputStream out = null; FileChannel outChannel = null; FileLock inLock = null; FileLock outLock = null; try { final FileInputStream in0 = new FileInputStream(src); final FileChannel inChannel = in0.getChannel(); final long inSize = inChannel.size(); inLock = inChannel.tryLock(0, inSize, true); if (inLock == null) throw error("source file locked by another process: " + src); in = new BZip2InputStream(new BufferedXInputStream(in0, 8192)); out = new FileOutputStream(dst); outChannel = out.getChannel(); outLock = outChannel.tryLock(); if (outLock == null) throw error("destination file locked by another process: " + dst); if (showProgress || this.verbose) { this.log.print("source: " + src).print(": size=").println(inSize); this.log.println("target: " + dst); } long pos = 0; int progress = 0; final long maxStep = showProgress ? Math.max(8192, inSize / MAX_PROGRESS) : Integer.MAX_VALUE; while (true) { final long step = outChannel.transferFrom(in, pos, maxStep); if (step <= 0) { final long a = inChannel.size(); if (a != inSize) throw error("file " + src + " has been modified concurrently by another process"); if (inChannel.position() >= inSize) { if (showProgress) { for (int i = progress; i < MAX_PROGRESS; i++) this.log.print('#'); this.log.println(" done"); } break; } } else { pos += step; if (showProgress) { final double p = (double) inChannel.position() / (double) inSize; final int newProgress = (int) (MAX_PROGRESS * p); for (int i = progress; i < newProgress; i++) this.log.print('#'); progress = newProgress; } } } final long outSize = outChannel.size(); in.close(); out.close(); if (this.verbose) { final double ratio = (outSize == 0) ? (inSize * 100) : ((double) inSize / (double) outSize); this.log.print("compressed size: ").print(inSize) .print("; decompressed size: ").print(outSize) .print("; compression ratio: ").print(ratio).println('%'); } if (!test && !this.switches.contains(Switch.keep)) { if (!src.delete()) throw error("unable to delete sourcefile: " + src); } if (test && !dst.delete()) throw error("unable to delete testfile: " + dst); } catch (final IOException ex) { IO.tryClose(in); IO.tryClose(out); IO.tryRelease(inLock); IO.tryRelease(outLock); try { this.log.println(); } finally { throw ex; } } }

public static int[] bubbleSort2(int[] source) { if (null != source && source.length > 0) { boolean flag = false; while (!flag) { for (int i = 0; i < source.length - 1; i++) { if (source[i] > source[i + 1]) { int temp = source[i]; source[i] = source[i + 1]; source[i + 1] = temp; break; } else if (i == source.length - 2) { flag = true; } } } } return source; }

public static void test(String args[]) { int trace; int bytes_read = 0; int last_contentLenght = 0; try { BufferedReader reader; URL url; url = new URL(args[0]); URLConnection istream = url.openConnection(); last_contentLenght = istream.getContentLength(); reader = new BufferedReader(new InputStreamReader(istream.getInputStream())); System.out.println(url.toString()); String line; trace = t2pNewTrace(); while ((line = reader.readLine()) != null) { bytes_read = bytes_read + line.length() + 1; t2pProcessLine(trace, line); } t2pHandleEventPairs(trace); t2pSort(trace, 0); t2pExportTrace(trace, new String("pngtest2.png"), 1000, 700, (float) 0, (float) 33); t2pExportTrace(trace, new String("pngtest3.png"), 1000, 700, (float) 2.3, (float) 2.44); System.out.println("Press any key to contiune read from stream !!!"); System.out.println(t2pGetProcessName(trace, 0)); System.in.read(); istream = url.openConnection(); if (last_contentLenght != istream.getContentLength()) { istream = url.openConnection(); istream.setRequestProperty("Range", "bytes=" + Integer.toString(bytes_read) + "-"); System.out.println(Integer.toString(istream.getContentLength())); reader = new BufferedReader(new InputStreamReader(istream.getInputStream())); while ((line = reader.readLine()) != null) { System.out.println(line); t2pProcessLine(trace, line); } } else System.out.println("File not changed !"); t2pDeleteTrace(trace); } catch (MalformedURLException e) { System.out.println("MalformedURLException !!!"); } catch (IOException e) { System.out.println("File not found " + args[0]); } ; }

public static void bubbleSort(int[] array) { for (int i = 0; i < array.length - 1; i++) { for (int j = 0; j < array.length - i - 1; j++) { if (array[j] > array[j + 1]) { int temp = array[j]; array[j] = array[j + 1]; array[j + 1] = temp; } } System.out.println("��" + (i + 1) + "������"); for (int k = 0; k < array.length; k++) { System.out.print(array[k] + " "); } System.out.println(); } }

public static String md5EncodeString(String s) throws UnsupportedEncodingException, NoSuchAlgorithmException { if (s == null) return null; if (StringUtils.isBlank(s)) return ""; MessageDigest algorithm = MessageDigest.getInstance("MD5"); algorithm.reset(); algorithm.update(s.getBytes("UTF-8")); byte messageDigest[] = algorithm.digest(); StringBuffer hexString = new StringBuffer(); for (int i = 0; i < messageDigest.length; i++) { String hex = Integer.toHexString(0xFF & messageDigest[i]); if (hex.length() == 1) { hexString.append('0'); } hexString.append(hex); } return hexString.toString(); }

public static void copyFile(File from, File to) { try { FileInputStream in = new FileInputStream(from); FileOutputStream out = new FileOutputStream(to); byte[] buffer = new byte[1024 * 16]; int read = 0; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } in.close(); } catch (IOException e) { e.printStackTrace(); } }

private BibtexDatabase importInspireEntries(String key, OutputPrinter frame) { String url = constructUrl(key); try { HttpURLConnection conn = (HttpURLConnection) (new URL(url)).openConnection(); conn.setRequestProperty("User-Agent", "Jabref"); InputStream inputStream = conn.getInputStream(); INSPIREBibtexFilterReader reader = new INSPIREBibtexFilterReader(new InputStreamReader(inputStream)); ParserResult pr = BibtexParser.parse(reader); return pr.getDatabase(); } catch (IOException e) { frame.showMessage(Globals.lang("An Exception ocurred while accessing '%0'", url) + "\n\n" + e.toString(), Globals.lang(getKeyName()), JOptionPane.ERROR_MESSAGE); } catch (RuntimeException e) { frame.showMessage(Globals.lang("An Error occurred while fetching from INSPIRE source (%0):", new String[] { url }) + "\n\n" + e.getMessage(), Globals.lang(getKeyName()), JOptionPane.ERROR_MESSAGE); } return null; }

public final void propertyChange(final PropertyChangeEvent event) { if (fChecker != null && event.getProperty().equals(ISpellCheckPreferenceKeys.SPELLING_USER_DICTIONARY)) { if (fUserDictionary != null) { fChecker.removeDictionary(fUserDictionary); fUserDictionary = null; } final String file = (String) event.getNewValue(); if (file.length() > 0) { try { final URL url = new URL("file", null, file); InputStream stream = url.openStream(); if (stream != null) { try { fUserDictionary = new PersistentSpellDictionary(url); fChecker.addDictionary(fUserDictionary); } finally { stream.close(); } } } catch (MalformedURLException exception) { } catch (IOException exception) { } } } }

@Override public User login(String username, String password) { User user = null; try { user = (User) em.createQuery("Select o from User o where o.username = :username").setParameter("username", username).getSingleResult(); } catch (NoResultException e) { throw new NestedException(e.getMessage(), e); } try { MessageDigest digest = java.security.MessageDigest.getInstance("MD5"); digest.update(password.getBytes("UTF-8")); byte[] hash = digest.digest(); BigInteger bigInt = new BigInteger(1, hash); String hashtext = bigInt.toString(16); while (hashtext.length() < 32) { hashtext = "0" + hashtext; } if (hashtext.equals(user.getPassword())) return user; } catch (Exception e) { throw new NestedException(e.getMessage(), e); } return null; }

private void createUser(AddEditUserForm addform, HttpServletRequest request, ActionMapping mapping) throws Exception { MessageDigest md = (MessageDigest) MessageDigest.getInstance("MD5").clone(); md.update(addform.getPassword().getBytes("UTF-8")); byte[] pd = md.digest(); StringBuffer app = new StringBuffer(); for (int i = 0; i < pd.length; i++) { String s2 = Integer.toHexString(pd[i] & 0xFF); app.append((s2.length() == 1) ? "0" + s2 : s2); } Session hbsession = HibernateUtil.currentSession(); try { Transaction tx = hbsession.beginTransaction(); NvUsers user = new NvUsers(); user.setLogin(addform.getLogin()); user.setPassword(app.toString()); hbsession.save(user); hbsession.flush(); if (!hbsession.connection().getAutoCommit()) { tx.commit(); } } finally { HibernateUtil.closeSession(); } }

private void doUpload(UploadKind uploadKind, WriteKind writeKind) throws Exception { int n = 512 * 1024; AtomicInteger total = new AtomicInteger(0); ServerSocket ss = startSinkServer(total); URL url = new URL("http://localhost:" + ss.getLocalPort() + "/test1"); HttpURLConnection conn = (HttpURLConnection) url.openConnection(); conn.setDoOutput(true); conn.setRequestMethod("POST"); if (uploadKind == UploadKind.CHUNKED) { conn.setChunkedStreamingMode(-1); } else { conn.setFixedLengthStreamingMode(n); } OutputStream out = conn.getOutputStream(); if (writeKind == WriteKind.BYTE_BY_BYTE) { for (int i = 0; i < n; ++i) { out.write('x'); } } else { byte[] buf = new byte[writeKind == WriteKind.SMALL_BUFFERS ? 256 : 64 * 1024]; Arrays.fill(buf, (byte) 'x'); for (int i = 0; i < n; i += buf.length) { out.write(buf, 0, Math.min(buf.length, n - i)); } } out.close(); assertTrue(conn.getResponseCode() > 0); assertEquals(uploadKind == UploadKind.CHUNKED ? -1 : n, total.get()); }

private void alterarArtista(Artista artista) throws Exception { Connection conn = null; PreparedStatement ps = null; try { conn = C3P0Pool.getConnection(); String sql = "UPDATE artista SET nome = ?,sexo = ?,email = ?,obs = ?,telefone = ? where numeroinscricao = ?"; ps = conn.prepareStatement(sql); ps.setString(1, artista.getNome()); ps.setBoolean(2, artista.isSexo()); ps.setString(3, artista.getEmail()); ps.setString(4, artista.getObs()); ps.setString(5, artista.getTelefone()); ps.setInt(6, artista.getNumeroInscricao()); ps.executeUpdate(); alterarEndereco(conn, ps, artista); delObras(conn, ps, artista.getNumeroInscricao()); sql = "insert into obra VALUES (?,?,?,?,?,?)"; ps = conn.prepareStatement(sql); for (Obra obra : artista.getListaObras()) { salvarObra(conn, ps, obra, artista.getNumeroInscricao()); } conn.commit(); } catch (Exception e) { if (conn != null) conn.rollback(); throw e; } finally { close(conn, ps); } }

public int instantiate(int objectId, String description) throws FidoDatabaseException, ObjectNotFoundException, ClassLinkTypeNotFoundException { try { Connection conn = null; Statement stmt = null; ResultSet rs = null; try { String sql = "insert into Objects (Description) " + "values ('" + description + "')"; conn = fido.util.FidoDataSource.getConnection(); conn.setAutoCommit(false); stmt = conn.createStatement(); if (contains(stmt, objectId) == false) throw new ObjectNotFoundException(objectId); stmt.executeUpdate(sql); int id; sql = "select currval('objects_objectid_seq')"; rs = stmt.executeQuery(sql); if (rs.next() == false) throw new SQLException("No rows returned from select currval() query"); else id = rs.getInt(1); ObjectLinkTable objectLinkList = new ObjectLinkTable(); objectLinkList.linkObjects(stmt, id, "instance", objectId); conn.commit(); return id; } catch (SQLException e) { if (conn != null) conn.rollback(); throw e; } finally { if (rs != null) rs.close(); if (stmt != null) stmt.close(); if (conn != null) conn.close(); } } catch (SQLException e) { throw new FidoDatabaseException(e); } }

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

public void copyContent(long mailId1, long mailId2) throws Exception { File file1 = new File(this.getMailDir(mailId1) + "/"); File file2 = new File(this.getMailDir(mailId2) + "/"); this.recursiveDir(file2); if (file1.isDirectory()) { File[] files = file1.listFiles(); if (files != null) { for (int i = 0; i < files.length; i++) { if (files[i].isFile()) { File file2s = new File(file2.getAbsolutePath() + "/" + files[i].getName()); if (!file2s.exists()) { file2s.createNewFile(); BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(file2s)); BufferedInputStream in = new BufferedInputStream(new FileInputStream(files[i])); int read; while ((read = in.read()) != -1) { out.write(read); } out.flush(); if (in != null) { try { in.close(); } catch (IOException ex1) { ex1.printStackTrace(); } } if (out != null) { try { out.close(); } catch (IOException ex) { ex.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(); } }

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

public void processExplicitSchemaAndWSDL(HttpServletRequest req, HttpServletResponse res) throws IOException, ServletException { HashMap services = configContext.getAxisConfiguration().getServices(); String filePart = req.getRequestURL().toString(); String schema = filePart.substring(filePart.lastIndexOf("/") + 1, filePart.length()); if ((services != null) && !services.isEmpty()) { Iterator i = services.values().iterator(); while (i.hasNext()) { AxisService service = (AxisService) i.next(); InputStream stream = service.getClassLoader().getResourceAsStream("META-INF/" + schema); if (stream != null) { OutputStream out = res.getOutputStream(); res.setContentType("text/xml"); IOUtils.copy(stream, out, true); return; } } } }

public static void main(String[] a) { ArrayList<String> allFilesToBeCopied = new ArrayList<String>(); new File(outputDir).mkdirs(); try { FileReader fis = new FileReader(completeFileWithDirToCathFileList); BufferedReader bis = new BufferedReader(fis); String line = ""; String currentCombo = ""; while ((line = bis.readLine()) != null) { String[] allEntries = line.split("\\s+"); String fileName = allEntries[0]; String thisCombo = allEntries[1] + allEntries[2] + allEntries[3] + allEntries[4]; if (currentCombo.equals(thisCombo)) { } else { System.out.println("merke: " + fileName); allFilesToBeCopied.add(fileName); currentCombo = thisCombo; } } System.out.println(allFilesToBeCopied.size()); for (String file : allFilesToBeCopied) { try { FileChannel srcChannel = new FileInputStream(CathDir + file).getChannel(); FileChannel dstChannel = new FileOutputStream(outputDir + file).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (IOException e) { e.printStackTrace(); } } } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } }

public void includeJs(Group group, Writer out, PageContext pageContext) throws IOException { includeResource(pageContext, out, RetentionHelper.buildRootRetentionFilePath(group, ".js"), JS_BEGIN_TAG, JS_END_TAG); ByteArrayOutputStream outtmp = new ByteArrayOutputStream(); if (AbstractGroupBuilder.getInstance().buildGroupJsIfNeeded(group, outtmp, pageContext.getServletContext())) { FileOutputStream fileStream = new FileOutputStream(new File(RetentionHelper.buildFullRetentionFilePath(group, ".js"))); IOUtils.copy(new ByteArrayInputStream(outtmp.toByteArray()), fileStream); fileStream.close(); } }

private void documentFileChooserActionPerformed(java.awt.event.ActionEvent evt) { if (evt.getActionCommand().equals(JFileChooser.APPROVE_SELECTION)) { File selectedFile = documentFileChooser.getSelectedFile(); File collectionCopyFile; String newDocumentName = selectedFile.getName(); Document newDocument = new Document(newDocumentName); if (activeCollection.containsDocument(newDocument)) { int matchingFilenameDistinguisher = 1; StringBuilder distinguisherReplacer = new StringBuilder(); newDocumentName = newDocumentName.concat("(" + matchingFilenameDistinguisher + ")"); newDocument.setDocumentName(newDocumentName); while (activeCollection.containsDocument(newDocument)) { matchingFilenameDistinguisher++; newDocumentName = distinguisherReplacer.replace(newDocumentName.length() - 2, newDocumentName.length() - 1, new Integer(matchingFilenameDistinguisher).toString()).toString(); newDocument.setDocumentName(newDocumentName); } } Scanner tokenizer = null; FileChannel fileSource = null; FileChannel collectionDestination = null; HashMap<String, Integer> termHashMap = new HashMap<String, Integer>(); Index collectionIndex = activeCollection.getIndex(); int documentTermMaxFrequency = 0; int currentTermFrequency; try { tokenizer = new Scanner(new BufferedReader(new FileReader(selectedFile))); tokenizer.useDelimiter(Pattern.compile("\\p{Space}|\\p{Punct}|\\p{Cntrl}")); String nextToken; while (tokenizer.hasNext()) { nextToken = tokenizer.next().toLowerCase(); if (!nextToken.isEmpty()) if (termHashMap.containsKey(nextToken)) termHashMap.put(nextToken, termHashMap.get(nextToken) + 1); else termHashMap.put(nextToken, 1); } Term newTerm; for (String term : termHashMap.keySet()) { newTerm = new Term(term); if (!collectionIndex.termExists(newTerm)) collectionIndex.addTerm(newTerm); currentTermFrequency = termHashMap.get(term); if (currentTermFrequency > documentTermMaxFrequency) documentTermMaxFrequency = currentTermFrequency; collectionIndex.addOccurence(newTerm, newDocument, currentTermFrequency); } activeCollection.addDocument(newDocument); String userHome = System.getProperty("user.home"); String fileSeparator = System.getProperty("file.separator"); collectionCopyFile = new File(userHome + fileSeparator + "Infrared" + fileSeparator + activeCollection.getDocumentCollectionName() + fileSeparator + newDocumentName); collectionCopyFile.createNewFile(); fileSource = new FileInputStream(selectedFile).getChannel(); collectionDestination = new FileOutputStream(collectionCopyFile).getChannel(); collectionDestination.transferFrom(fileSource, 0, fileSource.size()); } catch (FileNotFoundException e) { System.err.println(e.getMessage() + " This error should never occur! The file was just selected!"); return; } catch (IOException e) { JOptionPane.showMessageDialog(this, "An I/O error occured during file transfer!", "File transfer I/O error", JOptionPane.WARNING_MESSAGE); return; } finally { try { if (tokenizer != null) tokenizer.close(); if (fileSource != null) fileSource.close(); if (collectionDestination != null) collectionDestination.close(); } catch (IOException e) { System.err.println(e.getMessage()); } } processWindowEvent(new WindowEvent(this, WindowEvent.WINDOW_CLOSING)); } else if (evt.getActionCommand().equalsIgnoreCase(JFileChooser.CANCEL_SELECTION)) processWindowEvent(new WindowEvent(this, WindowEvent.WINDOW_CLOSING)); }

public void execute() { File sourceFile = new File(oarfilePath); File destinationFile = new File(deploymentDirectory + File.separator + sourceFile.getName()); try { FileInputStream fis = new FileInputStream(sourceFile); FileOutputStream fos = new FileOutputStream(destinationFile); byte[] readArray = new byte[2048]; while (fis.read(readArray) != -1) { fos.write(readArray); } fis.close(); fos.flush(); fos.close(); } catch (IOException ioe) { logger.severe("failed to copy the file:" + ioe); } }

public void movePrior(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[moveCount - 1] + " and organize_id= '" + orgID[moveCount - 1] + "'"; try { con = dbo.getConnection(); con.setAutoCommit(false); ps = con.prepareStatement(strQuery); result = ps.executeQuery(); int maxOrderNo = 0; if (result.next()) { maxOrderNo = result.getInt(1); } String[] sqls = new String[moveCount + 1]; sqls[0] = "update " + Common.ORGANIZE_TABLE + " set show_order=" + maxOrderNo + " 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.movePrior(): ERROR Inserting data " + "in T_SYS_ORGANIZE update !! resultCount = " + resultCount); } } con.commit(); } catch (SQLException se) { if (con != null) { con.rollback(); } throw new CesSystemException("Organize.movePrior(): SQLException while mov organize order " + " :\n\t" + se); } finally { con.setAutoCommit(true); close(dbo, ps, result); } }

@Deprecated public void test() { try { String query = "* <http://xmlns.com/foaf/0.1/workplaceHomepage> <http://www.deri.ie/>" + "* <http://xmlns.com/foaf/0.1/knows> *"; String url = "http://sindice.com/api/v2/search?qt=advanced&q=" + URLEncoder.encode(query, "utf-8") + "&qt=advanced"; URL urlObj = new URL(url); URLConnection con = urlObj.openConnection(); if (con != null) { Model model = ModelFactory.createDefaultModel(); model.read(con.getInputStream(), null); } System.out.println(url); } catch (MalformedURLException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } }

public static String getSHA1Digest(String inputStr) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md = null; byte[] sha1hash = null; md = MessageDigest.getInstance("SHA"); sha1hash = new byte[40]; md.update(inputStr.getBytes("iso-8859-1"), 0, inputStr.length()); sha1hash = md.digest(); return convertToHex(sha1hash); }

public Source resolve(String href, String base) throws TransformerException { if (href.endsWith(".txt")) { try { URL url = new URL(new URL(base), href); java.io.InputStream in = url.openConnection().getInputStream(); java.io.InputStreamReader reader = new java.io.InputStreamReader(in, "iso-8859-1"); StringBuffer sb = new StringBuffer(); while (true) { int c = reader.read(); if (c < 0) break; sb.append((char) c); } com.icl.saxon.expr.TextFragmentValue tree = new com.icl.saxon.expr.TextFragmentValue(sb.toString(), url.toString(), (com.icl.saxon.Controller) transformer); return tree.getFirst(); } catch (Exception err) { throw new TransformerException(err); } } else { return null; } }

public static boolean decodeFileToFile(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.DECODE); 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 String getETag(final String uri, final long lastModified) { try { final MessageDigest dg = MessageDigest.getInstance("MD5"); dg.update(uri.getBytes("utf-8")); dg.update(new byte[] { (byte) ((lastModified >> 24) & 0xFF), (byte) ((lastModified >> 16) & 0xFF), (byte) ((lastModified >> 8) & 0xFF), (byte) (lastModified & 0xFF) }); return CBASE64Codec.encode(dg.digest()); } catch (final Exception ignore) { return uri + lastModified; } }

public void filter(File source, File destination, MNamespace mNamespace) throws Exception { BufferedReader reader = new BufferedReader(new FileReader(source)); BufferedWriter writer = new BufferedWriter(new FileWriter(destination)); int line = 0; int column = 0; Stack parseStateStack = new Stack(); parseStateStack.push(new ParseState(mNamespace)); for (Iterator i = codePieces.iterator(); i.hasNext(); ) { NamedCodePiece cp = (NamedCodePiece) i.next(); while (line < cp.getStartLine()) { line++; column = 0; writer.write(reader.readLine()); writer.newLine(); } while (column < cp.getStartPosition()) { writer.write(reader.read()); column++; } cp.write(writer, parseStateStack, column); while (line < cp.getEndLine()) { line++; column = 0; reader.readLine(); } while (column < cp.getEndPosition()) { column++; reader.read(); } } String data; while ((data = reader.readLine()) != null) { writer.write(data); writer.newLine(); } reader.close(); writer.close(); }

public static Map<String, List<String>> getResponseHeader(String address) { System.out.println(address); URLConnection conn = null; Map<String, List<String>> responseHeader = null; try { URL url = new URL(address); conn = url.openConnection(); responseHeader = conn.getHeaderFields(); } catch (Exception e) { e.printStackTrace(); } return responseHeader; }

public static void copyFile(File sourceFile, File destFile) throws IOException { FileChannel inputFileChannel = new FileInputStream(sourceFile).getChannel(); FileChannel outputFileChannel = new FileOutputStream(destFile).getChannel(); long offset = 0L; long length = inputFileChannel.size(); final long MAXTRANSFERBUFFERLENGTH = 1024 * 1024; try { for (; offset < length; ) { offset += inputFileChannel.transferTo(offset, MAXTRANSFERBUFFERLENGTH, outputFileChannel); inputFileChannel.position(offset); } } finally { try { outputFileChannel.close(); } catch (Exception ignore) { } try { inputFileChannel.close(); } catch (IOException ignore) { } } }

private String createDefaultRepoConf() throws IOException { InputStream confIn = getClass().getResourceAsStream(REPO_CONF_PATH); File tempConfFile = File.createTempFile("repository", "xml"); tempConfFile.deleteOnExit(); IOUtils.copy(confIn, new FileOutputStream(tempConfFile)); return tempConfFile.getAbsolutePath(); }

public void exportFile() { String expfolder = PropertyHandler.getInstance().getProperty(PropertyHandler.KINDLE_EXPORT_FOLDER_KEY); File out = new File(expfolder + File.separator + previewInfo.getTitle() + ".prc"); File f = new File(absPath); try { FileOutputStream fout = new FileOutputStream(out); FileInputStream fin = new FileInputStream(f); int read = 0; byte[] buffer = new byte[1024 * 1024]; while ((read = fin.read(buffer)) > 0) { fout.write(buffer, 0, read); } fin.close(); fout.close(); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } }

private void resourceDirectoryCopy(String resource, IProject project, String target, IProgressMonitor monitor) throws URISyntaxException, IOException, CoreException { if (!target.endsWith("/")) { target += "/"; } String res = resource; if (!res.endsWith("/")) ; { res += "/"; } Enumeration<URL> it = bundle.findEntries(resource, "*", false); while (it.hasMoreElements()) { URL url = it.nextElement(); File f = new File(FileLocator.toFileURL(url).toURI()); String fName = f.getName(); boolean skip = false; for (String skiper : skipList) { if (fName.equals(skiper)) { skip = true; break; } } if (skip) { continue; } String targetName = target + fName; if (f.isDirectory()) { IFolder folder = project.getFolder(targetName); if (!folder.exists()) { folder.create(true, true, monitor); } resourceDirectoryCopy(res + f.getName(), project, targetName, monitor); } else if (f.isFile()) { IFile targetFile = project.getFile(targetName); InputStream is = null; try { is = url.openStream(); if (targetFile.exists()) { targetFile.setContents(is, true, false, monitor); } else { targetFile.create(is, true, monitor); } } catch (Exception e) { throw new IOException(e); } finally { if (is != null) { is.close(); } } } } }

public void copyFile(String oldPath, String newPath) { try { int bytesum = 0; int byteread = 0; File oldfile = new File(oldPath); if (oldfile.exists()) { InputStream inStream = new FileInputStream(oldPath); FileOutputStream fs = new FileOutputStream(newPath); byte[] buffer = new byte[1444]; while ((byteread = inStream.read(buffer)) != -1) { bytesum += byteread; System.out.println(bytesum); fs.write(buffer, 0, byteread); } inStream.close(); } } catch (Exception e) { System.out.println("复制单个文件操作出错"); e.printStackTrace(); } }

public static void main(String[] args) { for (int i = 0; i < args.length - 2; i++) { if (!CommonArguments.parseArguments(args, i, u)) { u.usage(); System.exit(1); } if (CommonParameters.startArg > (i + 1)) i = CommonParameters.startArg - 1; } if (args.length < CommonParameters.startArg + 2) { u.usage(); System.exit(1); } try { int readsize = 1024; ContentName argName = ContentName.fromURI(args[CommonParameters.startArg]); CCNHandle handle = CCNHandle.open(); File theFile = new File(args[CommonParameters.startArg + 1]); if (theFile.exists()) { System.out.println("Overwriting file: " + args[CommonParameters.startArg + 1]); } FileOutputStream output = new FileOutputStream(theFile); long starttime = System.currentTimeMillis(); CCNInputStream input; if (CommonParameters.unversioned) input = new CCNInputStream(argName, handle); else input = new CCNFileInputStream(argName, handle); if (CommonParameters.timeout != null) { input.setTimeout(CommonParameters.timeout); } byte[] buffer = new byte[readsize]; int readcount = 0; long readtotal = 0; while ((readcount = input.read(buffer)) != -1) { readtotal += readcount; output.write(buffer, 0, readcount); output.flush(); } if (CommonParameters.verbose) System.out.println("ccngetfile took: " + (System.currentTimeMillis() - starttime) + "ms"); System.out.println("Retrieved content " + args[CommonParameters.startArg + 1] + " got " + readtotal + " bytes."); System.exit(0); } catch (ConfigurationException e) { System.out.println("Configuration exception in ccngetfile: " + e.getMessage()); e.printStackTrace(); } catch (MalformedContentNameStringException e) { System.out.println("Malformed name: " + args[CommonParameters.startArg] + " " + e.getMessage()); e.printStackTrace(); } catch (IOException e) { System.out.println("Cannot write file or read content. " + e.getMessage()); e.printStackTrace(); } System.exit(1); }

public static final void copyFile(File source, File destination) throws IOException { FileChannel sourceChannel = new FileInputStream(source).getChannel(); FileChannel targetChannel = new FileOutputStream(destination).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), targetChannel); sourceChannel.close(); targetChannel.close(); }

public static boolean decodeFileToFile(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.DECODE); 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; }

@Override public void run() { try { if (!Util.isSufficienDataForUpload(recordedGeoPoints)) return; final InputStream gpxInputStream = new ByteArrayInputStream(RecordedRouteGPXFormatter.create(recordedGeoPoints).getBytes()); final HttpClient httpClient = new DefaultHttpClient(); final HttpPost request = new HttpPost(UPLOADSCRIPT_URL); final MultipartEntity requestEntity = new MultipartEntity(); requestEntity.addPart("gpxfile", new InputStreamBody(gpxInputStream, "" + System.currentTimeMillis() + ".gpx")); httpClient.getParams().setBooleanParameter("http.protocol.expect-continue", false); request.setEntity(requestEntity); final HttpResponse response = httpClient.execute(request); final int status = response.getStatusLine().getStatusCode(); if (status != HttpStatus.SC_OK) { logger.error("GPXUploader", "status != HttpStatus.SC_OK"); } else { final Reader r = new InputStreamReader(new BufferedInputStream(response.getEntity().getContent())); final char[] buf = new char[8 * 1024]; int read; final StringBuilder sb = new StringBuilder(); while ((read = r.read(buf)) != -1) sb.append(buf, 0, read); logger.debug("GPXUploader", "Response: " + sb.toString()); } } catch (final Exception e) { } }

public void deleteInstance(int instanceId) throws FidoDatabaseException, ObjectNotFoundException { try { Connection conn = null; Statement stmt = null; try { conn = fido.util.FidoDataSource.getConnection(); conn.setAutoCommit(false); stmt = conn.createStatement(); if (contains(stmt, instanceId) == false) throw new ObjectNotFoundException(instanceId); ObjectLinkTable objectLinkList = new ObjectLinkTable(); ObjectAttributeTable objectAttributeList = new ObjectAttributeTable(); objectLinkList.deleteObject(stmt, instanceId); objectAttributeList.deleteObject(stmt, instanceId); stmt.executeUpdate("delete from Objects where ObjectId = " + instanceId); conn.commit(); } catch (SQLException e) { if (conn != null) conn.rollback(); throw e; } finally { if (stmt != null) stmt.close(); if (conn != null) conn.close(); } } catch (SQLException e) { throw new FidoDatabaseException(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 static void copy(File source, File target) throws IOException { FileInputStream from = null; FileOutputStream to = null; try { from = new FileInputStream(source); to = new FileOutputStream(target); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = from.read(buffer)) != -1) to.write(buffer, 0, bytesRead); } finally { if (from != null) try { from.close(); } catch (IOException e) { } if (to != null) try { to.close(); } catch (IOException e) { } } }

public final void copyFile(final File fromFile, final File toFile) throws IOException { this.createParentPathIfNeeded(toFile); final FileChannel sourceChannel = new FileInputStream(fromFile).getChannel(); final FileChannel targetChannel = new FileOutputStream(toFile).getChannel(); final long sourceFileSize = sourceChannel.size(); sourceChannel.transferTo(0, sourceFileSize, targetChannel); }

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 static void copy(File source, File target) throws IOException { FileInputStream in = new FileInputStream(source); FileOutputStream out = new FileOutputStream(target); byte[] buffer = new byte[4096]; int no = 0; try { while ((no = in.read(buffer)) != -1) out.write(buffer, 0, no); } finally { in.close(); out.close(); } }

private static void createNonCompoundData(String dir, String type) { try { Set s = new HashSet(); File nouns = new File(dir + "index." + type); FileInputStream fis = new FileInputStream(nouns); InputStreamReader reader = new InputStreamReader(fis); StringBuffer sb = new StringBuffer(); int chr = reader.read(); while (chr >= 0) { if (chr == '\n' || chr == '\r') { String line = sb.toString(); if (line.length() > 0) { if (line.charAt(0) != ' ') { String[] spaceSplit = PerlHelp.split(line); if (spaceSplit[0].indexOf('_') < 0) { s.add(spaceSplit[0]); } } } sb.setLength(0); } else { sb.append((char) chr); } chr = reader.read(); } System.out.println(type + " size=" + s.size()); File output = new File(dir + "nonCompound." + type + "s.gz"); FileOutputStream fos = new FileOutputStream(output); GZIPOutputStream gzos = new GZIPOutputStream(new BufferedOutputStream(fos)); PrintWriter writer = new PrintWriter(gzos); writer.println("# This file was extracted from WordNet data, the following copyright notice"); writer.println("# from WordNet is attached."); writer.println("#"); writer.println("# This software and database is being provided to you, the LICENSEE, by "); writer.println("# Princeton University under the following license. By obtaining, using "); writer.println("# and/or copying this software and database, you agree that you have "); writer.println("# read, understood, and will comply with these terms and conditions.: "); writer.println("# "); writer.println("# Permission to use, copy, modify and distribute this software and "); writer.println("# database and its documentation for any purpose and without fee or "); writer.println("# royalty is hereby granted, provided that you agree to comply with "); writer.println("# the following copyright notice and statements, including the disclaimer, "); writer.println("# and that the same appear on ALL copies of the software, database and "); writer.println("# documentation, including modifications that you make for internal "); writer.println("# use or for distribution. "); writer.println("# "); writer.println("# WordNet 1.7 Copyright 2001 by Princeton University. All rights reserved. "); writer.println("# "); writer.println("# THIS SOFTWARE AND DATABASE IS PROVIDED \"AS IS\" AND PRINCETON "); writer.println("# UNIVERSITY MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR "); writer.println("# IMPLIED. BY WAY OF EXAMPLE, BUT NOT LIMITATION, PRINCETON "); writer.println("# UNIVERSITY MAKES NO REPRESENTATIONS OR WARRANTIES OF MERCHANT- "); writer.println("# ABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE OR THAT THE USE "); writer.println("# OF THE LICENSED SOFTWARE, DATABASE OR DOCUMENTATION WILL NOT "); writer.println("# INFRINGE ANY THIRD PARTY PATENTS, COPYRIGHTS, TRADEMARKS OR "); writer.println("# OTHER RIGHTS. "); writer.println("# "); writer.println("# The name of Princeton University or Princeton may not be used in"); writer.println("# advertising or publicity pertaining to distribution of the software"); writer.println("# and/or database. Title to copyright in this software, database and"); writer.println("# any associated documentation shall at all times remain with"); writer.println("# Princeton University and LICENSEE agrees to preserve same. "); for (Iterator i = s.iterator(); i.hasNext(); ) { String mwe = (String) i.next(); writer.println(mwe); } writer.close(); } catch (Exception e) { e.printStackTrace(); } }

public void testCodingFromFileSmaller() throws Exception { ByteArrayOutputStream baos = new ByteArrayOutputStream(); WritableByteChannel channel = newChannel(baos); HttpParams params = new BasicHttpParams(); SessionOutputBuffer outbuf = new SessionOutputBufferImpl(1024, 128, params); HttpTransportMetricsImpl metrics = new HttpTransportMetricsImpl(); LengthDelimitedEncoder encoder = new LengthDelimitedEncoder(channel, outbuf, metrics, 16); File tmpFile = File.createTempFile("testFile", "txt"); FileOutputStream fout = new FileOutputStream(tmpFile); OutputStreamWriter wrtout = new OutputStreamWriter(fout); wrtout.write("stuff;"); wrtout.write("more stuff;"); wrtout.flush(); wrtout.close(); FileChannel fchannel = new FileInputStream(tmpFile).getChannel(); encoder.transfer(fchannel, 0, 20); String s = baos.toString("US-ASCII"); assertTrue(encoder.isCompleted()); assertEquals("stuff;more stuff", s); tmpFile.delete(); }

@Override public void writeTo(final TrackRepresentation t, final Class<?> type, final Type genericType, final Annotation[] annotations, final MediaType mediaType, final MultivaluedMap<String, Object> httpHeaders, final OutputStream entityStream) throws WebApplicationException { if (mediaType.isCompatible(MediaType.APPLICATION_OCTET_STREAM_TYPE)) { InputStream is = null; try { httpHeaders.add("Content-Type", "audio/mp3"); IOUtils.copy(is = t.getInputStream(mediaType), entityStream); } catch (final IOException e) { LOG.warn("IOException : maybe remote client has disconnected"); } finally { IOUtils.closeQuietly(is); } } }