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nchen909

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bigclonebench-processed

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@Override public void setOntology2Document(URL url2) throws IllegalArgumentException { if (url2 == null) throw new IllegalArgumentException("Input parameter URL for ontology 2 is null."); try { ont2 = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(url2.openStream()); } catch (IOException e) { throw new IllegalArgumentException("Cannot open stream for ontology 2 from given URL."); } catch (OWLOntologyCreationException e) { throw new IllegalArgumentException("Cannot load ontology 2 from given URL."); } }

private void unzipEntry(ZipFile zipfile, ZipEntry entry, File outputDir, BackUpInfoFileGroup fileGroup, LinkedList<String> restoreList) { LinkedList<BackUpInfoFile> fileList = fileGroup.getFileList(); if (entry.isDirectory()) { createDir(new File(outputDir, entry.getName())); return; } for (int i = 0; i < fileList.size(); i++) { if (fileList.get(i).getId().equals(entry.getName())) { for (int j = 0; j < restoreList.size(); j++) { if ((fileList.get(i).getName() + "." + fileList.get(i).getType()).equals(restoreList.get(j))) { counter += 1; File outputFile = new File(outputDir, fileList.get(i).getName() + "." + fileList.get(i).getType()); if (!outputFile.getParentFile().exists()) { createDir(outputFile.getParentFile()); } BufferedInputStream inputStream; BufferedOutputStream outputStream; try { inputStream = new BufferedInputStream(zipfile.getInputStream(entry)); outputStream = new BufferedOutputStream(new FileOutputStream(outputFile)); IOUtils.copy(inputStream, outputStream); outputStream.close(); inputStream.close(); } catch (IOException ex) { throw new BackupException(ex.getMessage()); } } } } } }

protected Document loadDocument() throws MalformedURLException, DocumentException, IOException { if (jiraFilterURL.startsWith("file")) { URL url = getSourceURL(); return parseDocument(url); } else { HttpClient httpClient = new DefaultHttpClient(); List<NameValuePair> formparams = new ArrayList<NameValuePair>(); formparams.add(new BasicNameValuePair("os_username", jiraUser)); formparams.add(new BasicNameValuePair("os_password", jiraPassword)); formparams.add(new BasicNameValuePair("os_cookie", "true")); UrlEncodedFormEntity entity = new UrlEncodedFormEntity(formparams, "UTF-8"); HttpPost post = new HttpPost(getJiraRootUrl() + "/secure/login.jsp"); post.setEntity(entity); HttpResponse response = httpClient.execute(post); response.getEntity().consumeContent(); String url_str = StringEscapeUtils.unescapeXml(jiraFilterURL); HttpGet get = new HttpGet(url_str); response = httpClient.execute(get); return parseDocument(response.getEntity().getContent()); } }

private InputStream callService(String text) { InputStream in = null; try { URL url = new URL(SERVLET_URL); URLConnection conn = url.openConnection(); HttpURLConnection httpConn = (HttpURLConnection) conn; httpConn.setRequestMethod("POST"); httpConn.setDoInput(true); httpConn.setDoOutput(true); httpConn.connect(); DataOutputStream dataStream = new DataOutputStream(conn.getOutputStream()); dataStream.writeBytes(text); dataStream.flush(); dataStream.close(); int responseCode = httpConn.getResponseCode(); if (responseCode == HttpURLConnection.HTTP_OK) { in = httpConn.getInputStream(); } } catch (Exception ex) { ex.printStackTrace(); } return in; }

public static String translate(String s) { try { String result = null; URL url = new URL("http://translate.google.com/translate_t"); URLConnection connection = url.openConnection(); connection.setRequestProperty("User-Agent", "Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1)"); connection.setDoOutput(true); PrintWriter out = new PrintWriter(connection.getOutputStream()); out.print("text=" + URLEncoder.encode(s, "UTF-8") + "&langpair="); if (s.matches("[\\u0000-\\u00ff]+")) { out.print("en|ja"); } else { out.print("ja|en"); } out.print("&hl=en&ie=UTF-8&oe=UTF-8"); out.close(); BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream(), "UTF-8")); String inputLine; while ((inputLine = in.readLine()) != null) { int textPos = inputLine.indexOf("id=result_box"); if (textPos >= 0) { int ltrPos = inputLine.indexOf("dir=ltr", textPos + 9); if (ltrPos >= 0) { int closePos = inputLine.indexOf("<", ltrPos + 8); if (closePos >= 0) { result = inputLine.substring(ltrPos + 8, closePos); } } } } in.close(); return result; } catch (Exception e) { e.printStackTrace(); } return null; }

public static Status checkUpdate() { Status updateStatus = Status.FAILURE; URL url; InputStream is; InputStreamReader isr; BufferedReader r; String line; try { url = new URL(updateURL); is = url.openStream(); isr = new InputStreamReader(is); r = new BufferedReader(isr); String variable, value; while ((line = r.readLine()) != null) { if (!line.equals("") && line.charAt(0) != '/') { variable = line.substring(0, line.indexOf('=')); value = line.substring(line.indexOf('=') + 1); if (variable.equals("Latest Version")) { variable = value; value = variable.substring(0, variable.indexOf(" ")); variable = variable.substring(variable.indexOf(" ") + 1); latestGameVersion = value; latestModifier = variable; if (Float.parseFloat(value) > Float.parseFloat(gameVersion)) updateStatus = Status.NOT_CURRENT; else updateStatus = Status.CURRENT; } else if (variable.equals("Download URL")) downloadURL = value; } } return updateStatus; } catch (MalformedURLException e) { return Status.URL_NOT_FOUND; } catch (IOException e) { return Status.FAILURE; } }

private void copy(String inputPath, String outputPath, String name) { try { FileReader in = new FileReader(inputPath + name); FileWriter out = new FileWriter(outputPath + name); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } }

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

public void xtestURL2() throws Exception { URL url = new URL(IOTest.URL); InputStream inputStream = url.openStream(); OutputStream outputStream = new FileOutputStream("C:/Temp/testURL2.mp4"); IOUtils.copy(inputStream, outputStream); inputStream.close(); outputStream.close(); }

public void send(org.hibernate.Session hsession, Session session, String repositoryName, Vector files, int label, String charset) throws FilesException { ByteArrayInputStream bais = null; FileOutputStream fos = null; try { if ((files == null) || (files.size() <= 0)) { return; } if (charset == null) { charset = MimeUtility.javaCharset(Charset.defaultCharset().displayName()); } Users user = getUser(hsession, repositoryName); Identity identity = getDefaultIdentity(hsession, user); InternetAddress _returnPath = new InternetAddress(identity.getIdeEmail(), identity.getIdeName()); InternetAddress _from = new InternetAddress(identity.getIdeEmail(), identity.getIdeName()); InternetAddress _replyTo = new InternetAddress(identity.getIdeReplyTo(), identity.getIdeName()); InternetAddress _to = new InternetAddress(identity.getIdeEmail(), identity.getIdeName()); for (int i = 0; i < files.size(); i++) { MultiPartEmail email = email = new MultiPartEmail(); email.setCharset(charset); if (_from != null) { email.setFrom(_from.getAddress(), _from.getPersonal()); } if (_returnPath != null) { email.addHeader("Return-Path", _returnPath.getAddress()); email.addHeader("Errors-To", _returnPath.getAddress()); email.addHeader("X-Errors-To", _returnPath.getAddress()); } if (_replyTo != null) { email.addReplyTo(_replyTo.getAddress(), _replyTo.getPersonal()); } if (_to != null) { email.addTo(_to.getAddress(), _to.getPersonal()); } MailPartObj obj = (MailPartObj) files.get(i); email.setSubject("Files-System " + obj.getName()); Date now = new Date(); email.setSentDate(now); File dir = new File(System.getProperty("user.home") + File.separator + "tmp"); if (!dir.exists()) { dir.mkdir(); } File file = new File(dir, obj.getName()); bais = new ByteArrayInputStream(obj.getAttachent()); fos = new FileOutputStream(file); IOUtils.copy(bais, fos); IOUtils.closeQuietly(bais); IOUtils.closeQuietly(fos); EmailAttachment attachment = new EmailAttachment(); attachment.setPath(file.getPath()); attachment.setDisposition(EmailAttachment.ATTACHMENT); attachment.setDescription("File Attachment: " + file.getName()); attachment.setName(file.getName()); email.attach(attachment); String mid = getId(); email.addHeader(RFC2822Headers.IN_REPLY_TO, "<" + mid + ".JavaMail.duroty@duroty" + ">"); email.addHeader(RFC2822Headers.REFERENCES, "<" + mid + ".JavaMail.duroty@duroty" + ">"); email.addHeader("X-DBox", "FILES"); email.addHeader("X-DRecent", "false"); email.setMailSession(session); email.buildMimeMessage(); MimeMessage mime = email.getMimeMessage(); int size = MessageUtilities.getMessageSize(mime); if (!controlQuota(hsession, user, size)) { throw new MailException("ErrorMessages.mail.quota.exceded"); } messageable.storeMessage(mid, mime, user); } } catch (FilesException e) { throw e; } catch (Exception e) { throw new FilesException(e); } catch (java.lang.OutOfMemoryError ex) { System.gc(); throw new FilesException(ex); } catch (Throwable e) { throw new FilesException(e); } finally { GeneralOperations.closeHibernateSession(hsession); IOUtils.closeQuietly(bais); IOUtils.closeQuietly(fos); } }

private static void zipFolder(File folder, ZipOutputStream zipOutputStream, String relativePath) throws IOException { File[] children = folder.listFiles(); for (int i = 0; i < children.length; i++) { File child = children[i]; if (child.isFile()) { String zipEntryName = children[i].getCanonicalPath().replace(relativePath + File.separator, ""); ZipEntry entry = new ZipEntry(zipEntryName); zipOutputStream.putNextEntry(entry); InputStream inputStream = new FileInputStream(child); IOUtils.copy(inputStream, zipOutputStream); inputStream.close(); } else { ZipUtil.zipFolder(child, zipOutputStream, relativePath); } } }

public FlickrObject perform(boolean chkResponse) throws FlickrException { validate(); String data = getRequestData(); OutputStream os = null; InputStream is = null; try { URL url = null; try { url = new URL(m_url); } catch (MalformedURLException mux) { IllegalStateException iax = new IllegalStateException(); iax.initCause(mux); throw iax; } HttpURLConnection con = (HttpURLConnection) url.openConnection(); con.setDoOutput(true); con.setRequestMethod("POST"); os = con.getOutputStream(); OutputStreamWriter osw = new OutputStreamWriter(os); osw.write(data); osw.flush(); is = con.getInputStream(); return processRespons(is, chkResponse); } catch (FlickrException fx) { throw fx; } catch (IOException iox) { throw new FlickrException(iox); } finally { if (os != null) try { os.close(); } catch (IOException _) { } if (is != null) try { is.close(); } catch (IOException _) { } } }

private List<File> ungzipFile(File directory, File compressedFile) throws IOException { List<File> files = new ArrayList<File>(); TarArchiveInputStream in = new TarArchiveInputStream(new GZIPInputStream(new FileInputStream(compressedFile))); try { TarArchiveEntry entry = in.getNextTarEntry(); while (entry != null) { if (entry.isDirectory()) { log.warn("TAR archive contains directories which are being ignored"); entry = in.getNextTarEntry(); continue; } String fn = new File(entry.getName()).getName(); if (fn.startsWith(".")) { log.warn("TAR archive contains a hidden file which is being ignored"); entry = in.getNextTarEntry(); continue; } File targetFile = new File(directory, fn); if (targetFile.exists()) { log.warn("TAR archive contains duplicate filenames, only the first is being extracted"); entry = in.getNextTarEntry(); continue; } files.add(targetFile); log.debug("Extracting file: " + entry.getName() + " to: " + targetFile.getAbsolutePath()); OutputStream fout = new BufferedOutputStream(new FileOutputStream(targetFile)); InputStream entryIn = new FileInputStream(entry.getFile()); IOUtils.copy(entryIn, fout); fout.close(); entryIn.close(); } } finally { in.close(); } return files; }

public static void copy(File src, File dest) throws IOException { if (!src.exists()) { throw new IOException(StaticUtils.format(OStrings.getString("LFC_ERROR_FILE_DOESNT_EXIST"), new Object[] { src.getAbsolutePath() })); } FileInputStream fis = new FileInputStream(src); dest.getParentFile().mkdirs(); FileOutputStream fos = new FileOutputStream(dest); byte[] b = new byte[BUFSIZE]; int readBytes; while ((readBytes = fis.read(b)) > 0) fos.write(b, 0, readBytes); fis.close(); fos.close(); }

public boolean saveVideoXMLOnWebserver() { String text = ""; boolean erg = false; try { URL url = new URL("http://localhost:8080/virtPresenterVerwalter/videofile.jsp?id=" + this.getId()); HttpURLConnection http = (HttpURLConnection) url.openConnection(); BufferedReader in = new BufferedReader(new InputStreamReader(http.getInputStream())); String zeile = ""; while ((zeile = in.readLine()) != null) { text += zeile + "\n"; } in.close(); http.disconnect(); erg = saveVideoXMLOnWebserver(text); System.err.println("Job " + this.getId() + " erfolgreich bearbeitet!"); } catch (MalformedURLException e) { System.err.println("Job " + this.getId() + ": Konnte video.xml nicht erstellen. Verbindung konnte nicht aufgebaut werden."); return false; } catch (IOException e) { System.err.println("Job " + this.getId() + ": Konnte video.xml nicht erstellen. Konnte Daten nicht lesen/schreiben."); return false; } return erg; }

private String getResourceAsString(final String name) throws IOException { final InputStream is = JiBXTestCase.class.getResourceAsStream(name); final ByteArrayOutputStream baos = new ByteArrayOutputStream(); IOUtils.copyAndClose(is, baos); return baos.toString(); }

@Override public void sendContent(OutputStream out, Range range, Map<String, String> params, String contentType) throws IOException, NotAuthorizedException, BadRequestException, NotFoundException { try { resolveFileAttachment(); } catch (NoFileByTheIdException e) { throw new NotFoundException(e.getLocalizedMessage()); } DefinableEntity owningEntity = fa.getOwner().getEntity(); InputStream in = getFileModule().readFile(owningEntity.getParentBinder(), owningEntity, fa); try { if (range != null) { if (logger.isDebugEnabled()) logger.debug("sendContent: ranged content: " + toString(fa)); PartialGetHelper.writeRange(in, range, out); } else { if (logger.isDebugEnabled()) logger.debug("sendContent: send whole file " + toString(fa)); IOUtils.copy(in, out); } out.flush(); } catch (ReadingException e) { throw new IOException(e); } catch (WritingException e) { throw new IOException(e); } finally { IOUtils.closeQuietly(in); } }

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

private CathUtils() throws Exception { super(Ontology.CATH); InputStream is = null; BufferedReader reader = null; try { final String CATH_REGEXP = OntologyFactory.getOntology(Ontology.CATH).getRegularExpression(); final URL url = new URL("http://release.cathdb.info/v3.4.0/CathNames"); is = url.openStream(); reader = new BufferedReader(new InputStreamReader(is, Charset.defaultCharset())); String line = null; while ((line = reader.readLine()) != null) { final String[] tokens = line.split("\\s+"); if (RegularExpressionUtils.getMatches(tokens[0], CATH_REGEXP).size() > 0) { idToName.put(tokens[0], line.substring(line.indexOf(':') + 1, line.length())); } } } finally { try { if (is != null) { is.close(); } } finally { if (reader != null) { reader.close(); } } } }

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 boolean authenticate() { if (empresaFeta == null) empresaFeta = new AltaEmpresaBean(); log.info("authenticating {0}", credentials.getUsername()); boolean bo; try { String passwordEncriptat = credentials.getPassword(); MessageDigest m = MessageDigest.getInstance("MD5"); m.update(passwordEncriptat.getBytes(), 0, passwordEncriptat.length()); passwordEncriptat = new BigInteger(1, m.digest()).toString(16); Query q = entityManager.createQuery("select usuari from Usuaris usuari where usuari.login=? and usuari.password=?"); q.setParameter(1, credentials.getUsername()); q.setParameter(2, passwordEncriptat); Usuaris usuari = (Usuaris) q.getSingleResult(); bo = (usuari != null); if (bo) { if (usuari.isEsAdministrador()) { identity.addRole("admin"); } else { carregaDadesEmpresa(); log.info("nom de l'empresa: " + empresaFeta.getInstance().getNom()); } } } catch (Throwable t) { log.error(t); bo = false; } log.info("L'usuari {0} s'ha identificat bé? : {1} ", credentials.getUsername(), bo ? "si" : "no"); return bo; }

private static byte[] getLoginHashSHA(final char[] password, final int seed) throws GGException { try { final MessageDigest hash = MessageDigest.getInstance("SHA1"); hash.update(new String(password).getBytes()); hash.update(GGUtils.intToByte(seed)); return hash.digest(); } catch (final NoSuchAlgorithmException e) { LOG.error("SHA1 algorithm not usable", e); throw new GGException("SHA1 algorithm not usable!", e); } }

public static NotaFiscal insert(NotaFiscal objNF) { final Connection c = DBConnection.getConnection(); PreparedStatement pst = null; int result; if (c == null) { return null; } if (objNF == null) { return null; } try { c.setAutoCommit(false); String sql = ""; int idNotaFiscal; idNotaFiscal = NotaFiscalDAO.getLastCodigo(); if (idNotaFiscal < 1) { return null; } sql = "INSERT INTO nota_fiscal " + "(id_nota_fiscal, id_fornecedor, total, data_emissao, data_cadastro, numero) " + "VALUES(?, ?, TRUNCATE(?,2), STR_TO_DATE(?,'%d/%m/%Y'), now(), ?) "; pst = c.prepareStatement(sql); pst.setInt(1, idNotaFiscal); pst.setLong(2, objNF.getFornecedor().getCodigo()); pst.setString(3, new DecimalFormat("#0.00").format(objNF.getValor())); pst.setString(4, objNF.getDataEmissaoFormatada()); pst.setString(5, objNF.getNumero()); result = pst.executeUpdate(); pst = null; if (result > 0) { Iterator<ItemNotaFiscal> itINF = (objNF.getItemNotaFiscal()).iterator(); while ((itINF != null) && (itINF.hasNext())) { ItemNotaFiscal objINF = (ItemNotaFiscal) itINF.next(); sql = ""; sql = "INSERT INTO item_nota_fiscal " + "(id_nota_fiscal, id_produto, quantidade, subtotal) " + "VALUES(?, ?, ?, TRUNCATE(?,2))"; pst = c.prepareStatement(sql); pst.setInt(1, idNotaFiscal); pst.setInt(2, objINF.getProduto().getCodigo()); pst.setInt(3, objINF.getQuantidade()); pst.setString(4, new DecimalFormat("#0.00").format(objINF.getSubtotal())); result = pst.executeUpdate(); } } c.commit(); objNF.setCodigo(idNotaFiscal); } catch (final Exception e) { try { c.rollback(); } catch (final Exception e1) { System.out.println("[NotaFiscalDAO.insert.rollback] Erro ao inserir -> " + e1.getMessage()); } System.out.println("[NotaFiscalDAO.insert] Erro ao inserir -> " + e.getMessage()); objNF = null; } finally { DBConnection.closePreparedStatement(pst); DBConnection.closeConnection(c); } return objNF; }

@Override public void doHandler(HttpServletRequest request, HttpServletResponse response) throws IOException, ServletException { String directURL = request.getRequestURL().toString(); response.setCharacterEncoding("gbk"); PrintWriter out = response.getWriter(); try { directURL = urlTools.urlFilter(directURL, true); URL url = new URL(directURL); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream(), "gbk")); String line; while ((line = in.readLine()) != null) { out.println(line); } in.close(); } catch (Exception e) { out.println("file not find"); } out.flush(); }

public void process(String t) { try { MessageDigest md5 = MessageDigest.getInstance(MD5_DIGEST); md5.reset(); md5.update(t.getBytes()); callback.display(null, digestToHexString(md5.digest())); } catch (Exception ex) { callback.display(null, "[failed]"); } }

public static String md5encrypt(String toEncrypt) { if (toEncrypt == null) { throw new IllegalArgumentException("null is not a valid password to encrypt"); } try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(toEncrypt.getBytes()); byte[] hash = md.digest(); return new String(dumpBytes(hash)); } catch (NoSuchAlgorithmException nsae) { return toEncrypt; } }

private void addPNMLFileToLibrary(File selected) { try { FileChannel srcChannel = new FileInputStream(selected.getAbsolutePath()).getChannel(); FileChannel dstChannel = new FileOutputStream(new File(matchingOrderXML).getParent() + "/" + selected.getName()).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); order.add(new ComponentDescription(false, selected.getName().replaceAll(".pnml", ""), 1.0)); updateComponentList(); } catch (IOException ioe) { JOptionPane.showMessageDialog(dialog, "Could not add the PNML file " + selected.getName() + " to the library!"); } }

public void actionPerformed(ActionEvent ev) { if (fileChooser == null) { fileChooser = new JFileChooser(); ExtensionFileFilter fileFilter = new ExtensionFileFilter("Device profile (*.jar, *.zip)"); fileFilter.addExtension("jar"); fileFilter.addExtension("zip"); fileChooser.setFileFilter(fileFilter); } if (fileChooser.showOpenDialog(SwingSelectDevicePanel.this) == JFileChooser.APPROVE_OPTION) { String manifestDeviceName = null; URL[] urls = new URL[1]; ArrayList descriptorEntries = new ArrayList(); JarFile jar = null; try { jar = new JarFile(fileChooser.getSelectedFile()); Manifest manifest = jar.getManifest(); if (manifest != null) { Attributes attrs = manifest.getMainAttributes(); manifestDeviceName = attrs.getValue("Device-Name"); } for (Enumeration en = jar.entries(); en.hasMoreElements(); ) { String entry = ((JarEntry) en.nextElement()).getName(); if ((entry.toLowerCase().endsWith(".xml") || entry.toLowerCase().endsWith("device.txt")) && !entry.toLowerCase().startsWith("meta-inf")) { descriptorEntries.add(entry); } } urls[0] = fileChooser.getSelectedFile().toURL(); } catch (IOException e) { Message.error("Error reading file: " + fileChooser.getSelectedFile().getName() + ", " + Message.getCauseMessage(e), e); return; } finally { if (jar != null) { try { jar.close(); } catch (IOException ignore) { } } } if (descriptorEntries.size() == 0) { Message.error("Cannot find any device profile in file: " + fileChooser.getSelectedFile().getName()); return; } if (descriptorEntries.size() > 1) { manifestDeviceName = null; } ClassLoader classLoader = Common.createExtensionsClassLoader(urls); HashMap devices = new HashMap(); for (Iterator it = descriptorEntries.iterator(); it.hasNext(); ) { String entryName = (String) it.next(); try { devices.put(entryName, DeviceImpl.create(emulatorContext, classLoader, entryName, J2SEDevice.class)); } catch (IOException e) { Message.error("Error parsing device profile, " + Message.getCauseMessage(e), e); return; } } for (Enumeration en = lsDevicesModel.elements(); en.hasMoreElements(); ) { DeviceEntry entry = (DeviceEntry) en.nextElement(); if (devices.containsKey(entry.getDescriptorLocation())) { devices.remove(entry.getDescriptorLocation()); } } if (devices.size() == 0) { Message.info("Device profile already added"); return; } try { File deviceFile = new File(Config.getConfigPath(), fileChooser.getSelectedFile().getName()); if (deviceFile.exists()) { deviceFile = File.createTempFile("device", ".jar", Config.getConfigPath()); } IOUtils.copyFile(fileChooser.getSelectedFile(), deviceFile); DeviceEntry entry = null; for (Iterator it = devices.keySet().iterator(); it.hasNext(); ) { String descriptorLocation = (String) it.next(); Device device = (Device) devices.get(descriptorLocation); if (manifestDeviceName != null) { entry = new DeviceEntry(manifestDeviceName, deviceFile.getName(), descriptorLocation, false); } else { entry = new DeviceEntry(device.getName(), deviceFile.getName(), descriptorLocation, false); } lsDevicesModel.addElement(entry); Config.addDeviceEntry(entry); } lsDevices.setSelectedValue(entry, true); } catch (IOException e) { Message.error("Error adding device profile, " + Message.getCauseMessage(e), e); return; } } }

public void decryptFile(String encryptedFile, String decryptedFile, String password) throws Exception { CipherInputStream in; OutputStream out; Cipher cipher; SecretKey key; byte[] byteBuffer; cipher = Cipher.getInstance("DES"); key = new SecretKeySpec(password.getBytes(), "DES"); cipher.init(Cipher.DECRYPT_MODE, key); in = new CipherInputStream(new FileInputStream(encryptedFile), cipher); out = new FileOutputStream(decryptedFile); byteBuffer = new byte[1024]; for (int n; (n = in.read(byteBuffer)) != -1; out.write(byteBuffer, 0, n)) ; in.close(); out.close(); }

private void copyMerge(Path[] sources, OutputStream out) throws IOException { Configuration conf = getConf(); for (int i = 0; i < sources.length; ++i) { FileSystem fs = sources[i].getFileSystem(conf); InputStream in = fs.open(sources[i]); try { IOUtils.copyBytes(in, out, conf, false); } finally { in.close(); } } }

public String MD5(String text) { try { MessageDigest md; md = MessageDigest.getInstance("MD5"); byte[] md5hash = new byte[32]; md.update(text.getBytes("iso-8859-1"), 0, text.length()); md5hash = md.digest(); return convertToHex(md5hash); } catch (Exception e) { System.out.println(e.toString()); } return null; }

public void run() { Vector<Update> updates = new Vector<Update>(); if (dic != null) updates.add(dic); if (gen != null) updates.add(gen); if (res != null) updates.add(res); if (help != null) updates.add(help); for (Iterator iterator = updates.iterator(); iterator.hasNext(); ) { Update update = (Update) iterator.next(); try { File temp = File.createTempFile("fm_" + update.getType(), ".jar"); temp.deleteOnExit(); FileOutputStream out = new FileOutputStream(temp); URL url = new URL(update.getAction()); URLConnection conn = url.openConnection(); com.diccionarioderimas.Utils.setupProxy(conn); InputStream in = conn.getInputStream(); byte[] buffer = new byte[1024]; int read = 0; int total = 0; while ((read = in.read(buffer)) != -1) { out.write(buffer, 0, read); total += read; if (total > 10000) { progressBar.setValue(progressBar.getValue() + total); total = 0; } } out.close(); in.close(); String fileTo = basePath + "diccionariorimas.jar"; if (update.getType() == Update.GENERATOR) fileTo = basePath + "generador.jar"; else if (update.getType() == Update.RESBC) fileTo = basePath + "resbc.me"; else if (update.getType() == Update.HELP) fileTo = basePath + "help.html"; if (update.getType() == Update.RESBC) { Utils.unzip(temp, new File(fileTo)); } else { Utils.copyFile(new FileInputStream(temp), new File(fileTo)); } } catch (Exception e) { e.printStackTrace(); } } setVisible(false); if (gen != null || res != null) { try { new Main(null, basePath, false); } catch (Exception e) { new ErrorDialog(frame, e); } } String restart = ""; if (dic != null) restart += "\nAlgunas de ellas s�lo estar�n disponibles despu�s de reiniciar el diccionario."; JOptionPane.showMessageDialog(frame, "Se han terminado de realizar las actualizaciones." + restart, "Actualizaciones", JOptionPane.INFORMATION_MESSAGE); }

protected String contentString() { String result = null; URL url; String encoding = null; try { url = url(); URLConnection connection = url.openConnection(); connection.setDoInput(true); connection.setDoOutput(false); connection.setUseCaches(false); for (Enumeration e = bindingKeys().objectEnumerator(); e.hasMoreElements(); ) { String key = (String) e.nextElement(); if (key.startsWith("?")) { connection.setRequestProperty(key.substring(1), valueForBinding(key).toString()); } } if (connection.getContentEncoding() != null) { encoding = connection.getContentEncoding(); } if (encoding == null) { encoding = (String) valueForBinding("encoding"); } if (encoding == null) { encoding = "UTF-8"; } InputStream stream = connection.getInputStream(); byte bytes[] = ERXFileUtilities.bytesFromInputStream(stream); stream.close(); result = new String(bytes, encoding); } catch (IOException ex) { throw NSForwardException._runtimeExceptionForThrowable(ex); } return result; }

public static void doVersionCheck(View view) { view.showWaitCursor(); try { URL url = new URL(jEdit.getProperty("version-check.url")); InputStream in = url.openStream(); BufferedReader bin = new BufferedReader(new InputStreamReader(in)); String line; String develBuild = null; String stableBuild = null; while ((line = bin.readLine()) != null) { if (line.startsWith(".build")) develBuild = line.substring(6).trim(); else if (line.startsWith(".stablebuild")) stableBuild = line.substring(12).trim(); } bin.close(); if (develBuild != null && stableBuild != null) { doVersionCheck(view, stableBuild, develBuild); } } catch (IOException e) { String[] args = { jEdit.getProperty("version-check.url"), e.toString() }; GUIUtilities.error(view, "read-error", args); } view.hideWaitCursor(); }

@Override public void executeInterruptible() { encodingTerminated = false; File destinationFile = null; try { Runtime runtime = Runtime.getRuntime(); IconAndFileListElement element; while ((element = getNextFileElement()) != null) { File origFile = element.getFile(); destinationFile = new File(encodeFileCard.getDestinationFolder().getValue(), origFile.getName()); if (!destinationFile.getParentFile().exists()) { destinationFile.getParentFile().mkdirs(); } actualFileLabel.setText(origFile.getName()); actualFileModel.setMaximum((int) origFile.length()); actualFileModel.setValue(0); int bitrate; synchronized (bitratePattern) { Matcher bitrateMatcher = bitratePattern.matcher(encodeFileCard.getBitrate().getValue()); bitrateMatcher.find(); bitrate = Integer.parseInt(bitrateMatcher.group(1)); } List<String> command = new LinkedList<String>(); command.add(encoderFile.getCanonicalPath()); command.add("--mp3input"); command.add("-m"); command.add("j"); String sampleFreq = Settings.getSetting("encode.sample.freq"); if (Util.isNotEmpty(sampleFreq)) { command.add("--resample"); command.add(sampleFreq); } QualityElement quality = (QualityElement) ((JComboBox) encodeFileCard.getQuality().getValueComponent()).getSelectedItem(); command.add("-q"); command.add(Integer.toString(quality.getValue())); command.add("-b"); command.add(Integer.toString(bitrate)); command.add("--cbr"); command.add("-"); command.add(destinationFile.getCanonicalPath()); if (LOG.isDebugEnabled()) { StringBuilder commandLine = new StringBuilder(); boolean first = true; for (String part : command) { if (!first) commandLine.append(" "); commandLine.append(part); first = false; } LOG.debug("Command line: " + commandLine.toString()); } encodingProcess = runtime.exec(command.toArray(new String[0])); lastPosition = 0l; InputStream fileStream = null; try { fileStream = new PositionNotifierInputStream(new FileInputStream(origFile), origFile.length(), 2048, this); IOUtils.copy(fileStream, encodingProcess.getOutputStream()); encodingProcess.getOutputStream().close(); } finally { IOUtils.closeQuietly(fileStream); if (LOG.isDebugEnabled()) { InputStream processOut = null; try { processOut = encodingProcess.getInputStream(); StringWriter sw = new StringWriter(); IOUtils.copy(processOut, sw); LOG.debug("Process output stream:\n" + sw); IOUtils.closeQuietly(processOut); processOut = encodingProcess.getErrorStream(); sw = new StringWriter(); IOUtils.copy(processOut, sw); LOG.debug("Process error stream:\n" + sw); } finally { IOUtils.closeQuietly(processOut); } } } int result = encodingProcess.waitFor(); encodingProcess = null; if (result != 0) { LOG.warn("Encoder process returned error code " + result); } if (Boolean.parseBoolean(encodeFileCard.getCopyTag().getValue())) { MP3File mp3Input = new MP3File(origFile); MP3File mp3Output = new MP3File(destinationFile); boolean write = false; if (mp3Input.hasID3v2tag()) { ID3v2Tag id3v2Tag = new ID3v2Tag(); for (ID3v2Frame frame : mp3Input.getID3v2tag().getAllframes()) { id3v2Tag.addFrame(frame); } mp3Output.setID3v2tag(id3v2Tag); write = true; } if (mp3Input.hasID3v11tag()) { mp3Output.setID3v11tag(mp3Input.getID3v11tag()); write = true; } if (write) mp3Output.write(); } } actualFileLabel.setText(Messages.getString("operations.file.encode.execute.actualfile.terminated")); actualFileModel.setValue(actualFileModel.getMaximum()); } catch (Exception e) { LOG.error("Cannot encode files", e); if (!(e instanceof IOException && encodingTerminated)) MainWindowInterface.showError(e); if (destinationFile != null) destinationFile.delete(); } }

@Test public void testWriteModel() { Model model = new Model(); model.setName("MY_MODEL1"); Stereotype st1 = new Stereotype(); st1.setName("Pirulito1"); PackageObject p1 = new PackageObject("p1"); ClassType type1 = new ClassType("Class1"); type1.setStereotype(st1); type1.addMethod(new Method("doSomething")); p1.add(type1); ClassType type2 = new ClassType("Class2"); Method m2 = new Method("doSomethingElse"); m2.setType(type1); type2.addMethod(m2); p1.add(type2); Generalization g = new Generalization(); g.setSource(type1); g.setTarget(type1); p1.add(g); model.add(p1); ModelWriter writer = new ModelWriter(); try { File modelFile = new File("target", "test.model"); writer.write(model, modelFile); File xmlFile = new File("target", "test.xml"); xmlFile.createNewFile(); IOUtils.copy(new GZIPInputStream(new FileInputStream(modelFile)), new FileOutputStream(xmlFile)); } catch (IOException e) { log.error(e.getMessage(), e); Assert.fail(e.getMessage()); } }

static Object executeMethod(HttpMethod method, int timeout, boolean array) throws HttpRequestFailureException, HttpException, IOException, HttpRequestTimeoutException { try { method.getParams().setSoTimeout(timeout * 1000); int status = -1; Object result = null; System.out.println("Execute method: " + method.getPath() + " " + method.getQueryString()); TwitterclipseConfig config = TwitterclipsePlugin.getDefault().getTwitterclipseConfiguration(); HttpClient httpClient = HttpClientUtils.createHttpClient(TWITTER_BASE_URL, config.getUserId(), config.getPassword()); status = httpClient.executeMethod(method); System.out.println("Received response. status = " + status); if (status == HttpStatus.SC_OK) { InputStream inputStream = method.getResponseBodyAsStream(); ByteArrayOutputStream baos = new ByteArrayOutputStream(); IOUtils.copy(inputStream, baos); String response = new String(baos.toByteArray(), "UTF-8"); System.out.println(response); if (array) result = JSONArray.fromString(response); else result = JSONObject.fromString(response); } else { throw new HttpRequestFailureException(status); } return result; } catch (SocketTimeoutException e) { throw new HttpRequestTimeoutException(e); } finally { method.releaseConnection(); } }

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

public void deleteUser(final List<Integer> userIds) { try { connection.setAutoCommit(false); new ProcessEnvelope().executeNull(new ExecuteProcessAbstractImpl(connection, false, false, true, true) { @Override public void executeProcessReturnNull() throws SQLException { psImpl = connImpl.prepareStatement(sqlCommands.getProperty("user.delete")); Iterator<Integer> iter = userIds.iterator(); int userId; while (iter.hasNext()) { userId = iter.next(); psImpl.setInt(1, userId); psImpl.executeUpdate(); } } }); connection.commit(); cmDB.removeUsers(userIds); } catch (SQLException sqle) { log.error(sqle); if (connection != null) { try { connection.rollback(); } catch (SQLException ex) { } } } finally { if (connection != null) { try { connection.setAutoCommit(true); } catch (SQLException ex) { } } } }

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

public HttpResponse execute(HttpUriRequest request, HttpContext context) throws IOException { URI uri = request.getURI(); String original = uri.toString(); UrlRules rules = UrlRules.getRules(mResolver); UrlRules.Rule rule = rules.matchRule(original); String rewritten = rule.apply(original); if (rewritten == null) { Log.w(TAG, "Blocked by " + rule.mName + ": " + original); throw new BlockedRequestException(rule); } else if (rewritten == original) { return executeWithoutRewriting(request, context); } try { uri = new URI(rewritten); } catch (URISyntaxException e) { throw new RuntimeException("Bad URL from rule: " + rule.mName, e); } RequestWrapper wrapper = wrapRequest(request); wrapper.setURI(uri); request = wrapper; if (LOCAL_LOGV) Log.v(TAG, "Rule " + rule.mName + ": " + original + " -> " + rewritten); return executeWithoutRewriting(request, context); }

private void handleXInclude(final String localName, final Attributes atts) { if ("include".equals(localName)) { this.inXInclude++; String href = atts.getValue("href"); if ((href == null) || "".equals(href.trim())) { href = null; } String parse = atts.getValue("parse"); if ((parse == null) || "".equals(parse.trim())) { parse = "xml"; } String xpointer = atts.getValue("xpointer"); if ((xpointer == null) || "".equals(xpointer.trim())) { xpointer = null; } String encoding = atts.getValue("encoding"); if ((encoding == null) || "".equals(encoding.trim())) { encoding = null; } String accept = atts.getValue("accept"); if ((accept == null) || "".equals(accept.trim())) { accept = null; } String accept_language = atts.getValue("accept-language"); if ((accept_language == null) || "".equals(accept_language.trim())) { accept_language = null; } if (href != null) { if (href.indexOf(":/") == -1) { if (href.startsWith("/")) { href = href.substring(1); } href = this.documentURI + href; } if (this.localParser.get() == null) { this.localParser.set(new CShaniDomParser()); } CShaniDomParser p = (CShaniDomParser) this.localParser.get(); InputStream in = null; try { URL url = new URL(href); URLConnection connection = url.openConnection(); if (accept != null) { connection.addRequestProperty("Accept", accept); } if (accept_language != null) { connection.addRequestProperty("Accept-Language", accept_language); } in = connection.getInputStream(); ADocument doc = null; if (encoding != null) { doc = (ADocument) p.parse(new InputStreamReader(in, encoding)); } else { doc = (ADocument) p.parse(in); } if (xpointer == null) { CDOM2SAX converter = new CDOM2SAX(doc.getDocumentElement()); converter.setProperty("http://xml.org/sax/properties/lexical-handler", this.lHandler); converter.setContentHandler(this.cHandler); converter.setDocumentHandler(this.dHandler); converter.setDTDHandler(this.dtdHandler); converter.serialize(); } else { XPath xpath = new DOMXPath(xpointer); for (Iterator it = doc.getNamespaceList().iterator(); it.hasNext(); ) { CNamespace ns = (CNamespace) it.next(); xpath.addNamespace(ns.getPrefix() == null ? "" : ns.getPrefix(), ns.getNamespaceURI()); } List result = xpath.selectNodes(doc.getDocumentElement()); for (final Iterator it = result.iterator(); it.hasNext(); ) { final Node node = (Node) it.next(); CDOM2SAX converter = new CDOM2SAX(node); converter.setProperty("http://xml.org/sax/properties/lexical-handler", this.lHandler); converter.setContentHandler(this.cHandler); converter.setDocumentHandler(this.dHandler); converter.setDTDHandler(this.dtdHandler); converter.serialize(); } } } catch (final Exception e) { this.xiFallbackFlag++; } finally { try { in.close(); in = null; } catch (final Exception ignore) { } } } } }

protected boolean checkLogin(String username, String password) { log.debug("Called checkLogin with " + username); String urlIn = GeoNetworkContext.url + "/" + GeoNetworkContext.loginService + "?username=" + username + "&password=" + password; Element results = null; String cookieValue = null; try { URL url = new URL(urlIn); URLConnection conn = url.openConnection(); conn.setConnectTimeout(1000); BufferedInputStream in = new BufferedInputStream(conn.getInputStream()); try { results = Xml.loadStream(in); log.debug("CheckLogin to GeoNetwork returned " + Xml.getString(results)); } finally { in.close(); } Map<String, List<String>> headers = conn.getHeaderFields(); List<String> values = headers.get("Set-Cookie"); for (Iterator iter = values.iterator(); iter.hasNext(); ) { String v = (String) iter.next(); if (cookieValue == null) { cookieValue = v; } else { cookieValue = cookieValue + ";" + v; } } } catch (Exception e) { throw new RuntimeException("User login to GeoNetwork failed: ", e); } if (!results.getName().equals("ok")) return false; Session session = getConnection().getSession(); session.removeAttribute("usercookie.object"); session.setAttribute("usercookie.object", cookieValue); log.debug("Cookie set is " + cookieValue); return true; }

@Override public DownloadingItem download(Playlist playlist, String title, File folder, StopDownloadCondition condition, String uuid) throws IOException, StoreStateException { boolean firstIteration = true; Iterator<PlaylistEntry> entries = playlist.getEntries().iterator(); DownloadingItem prevItem = null; File[] previousDownloadedFiles = new File[0]; while (entries.hasNext()) { PlaylistEntry entry = entries.next(); DownloadingItem item = null; LOGGER.info("Downloading from '" + entry.getTitle() + "'"); InputStream is = RESTHelper.inputStream(entry.getUrl()); boolean stopped = false; File nfile = null; try { nfile = createFileStream(folder, entry); item = new DownloadingItem(nfile, uuid.toString(), title, entry, new Date(), getPID(), condition); if (previousDownloadedFiles.length > 0) { item.setPreviousFiles(previousDownloadedFiles); } addItem(item); if (prevItem != null) deletePrevItem(prevItem); prevItem = item; stopped = IOUtils.copyStreams(is, new FileOutputStream(nfile), condition); } catch (IOException e) { LOGGER.log(Level.SEVERE, e.getMessage(), e); radioScheduler.fireException(e); if (!condition.isStopped()) { File[] nfiles = new File[previousDownloadedFiles.length + 1]; System.arraycopy(previousDownloadedFiles, 0, nfiles, 0, previousDownloadedFiles.length); nfiles[nfiles.length - 1] = item.getFile(); previousDownloadedFiles = nfiles; if ((!entries.hasNext()) && (firstIteration)) { firstIteration = false; entries = playlist.getEntries().iterator(); } continue; } } if (stopped) { item.setState(ProcessStates.STOPPED); this.radioScheduler.fireStopDownloading(item); return item; } } return null; }

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

public void save(File selectedFile) throws IOException { if (storeEntriesInFiles) { boolean moved = false; for (int i = 0; i < tempFiles.size(); i++) { File newFile = new File(selectedFile.getAbsolutePath() + "_" + Integer.toString(i) + ".zettmp"); moved = tempFiles.get(i).renameTo(newFile); if (!moved) { BufferedReader read = new BufferedReader(new FileReader(tempFiles.get(i))); PrintWriter write = new PrintWriter(newFile); String s; while ((s = read.readLine()) != null) write.print(s); read.close(); write.flush(); write.close(); tempFiles.get(i).delete(); } tempFiles.set(i, newFile); } } GZIPOutputStream output = new GZIPOutputStream(new BufferedOutputStream(new FileOutputStream(selectedFile))); XStream xml_convert = new XStream(); xml_convert.setMode(XStream.ID_REFERENCES); xml_convert.toXML(this, output); output.flush(); output.close(); }

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 void updateJava2ScriptProject(String prjFolder, String binRelative) { try { File cpFile = new File(prjFolder, ".classpath"); FileInputStream fis = new FileInputStream(cpFile); String classpath = J2SLaunchingUtil.readAFile(fis); if (classpath != null) { boolean needUpdate = false; if (classpath.indexOf("ECLIPSE_SWT") == -1 && classpath.indexOf("SWT_LIBRARY") == -1 && classpath.indexOf("eclipse.swt") == -1) { int idx = classpath.lastIndexOf("<"); classpath = classpath.substring(0, idx) + "\t<classpathentry kind=\"var\" path=\"ECLIPSE_SWT\"/>\r\n" + classpath.substring(idx); needUpdate = true; } if (classpath.indexOf("AJAX_SWT") == -1 && classpath.indexOf("ajaxswt.jar") == -1) { int idx = classpath.lastIndexOf("<"); classpath = classpath.substring(0, idx) + "\t<classpathentry sourcepath=\"AJAX_SWT_SRC\" kind=\"var\" path=\"AJAX_SWT\"/>\r\n" + classpath.substring(idx); needUpdate = true; } if (classpath.indexOf("AJAX_RPC") == -1 && classpath.indexOf("ajaxrpc.jar") == -1) { int idx = classpath.lastIndexOf("<"); classpath = classpath.substring(0, idx) + "\t<classpathentry sourcepath=\"AJAX_RPC_SRC\" kind=\"var\" path=\"AJAX_RPC\"/>\r\n" + classpath.substring(idx); needUpdate = true; } if (classpath.indexOf("AJAX_PIPE") == -1 && classpath.indexOf("ajaxpipe.jar") == -1) { int idx = classpath.lastIndexOf("<"); classpath = classpath.substring(0, idx) + "\t<classpathentry sourcepath=\"AJAX_PIPE_SRC\" kind=\"var\" path=\"AJAX_PIPE\"/>\r\n" + classpath.substring(idx); needUpdate = true; } if (needUpdate) { try { FileOutputStream fos = new FileOutputStream(cpFile); fos.write(classpath.getBytes("utf-8")); fos.close(); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } } File webinf = new File(prjFolder, "WEB-INF"); webinf.mkdir(); new File(webinf, "classes").mkdir(); File lib = new File(webinf, "lib"); lib.mkdir(); IPath newPath = null; URL starterURL = AjaxPlugin.getDefault().getBundle().getEntry(File.separator); String root = "."; try { root = Platform.asLocalURL(starterURL).getFile(); } catch (IOException e1) { e1.printStackTrace(); } newPath = Path.fromPortableString(root + "/ajaxrpc.jar"); File rpcFile = new File(newPath.toOSString()); try { FileInputStream is = new FileInputStream(rpcFile); FileOutputStream os = new FileOutputStream(new File(lib, "ajaxrpc.jar")); byte[] buf = new byte[1024]; int read = -1; while ((read = is.read(buf)) != -1) { os.write(buf, 0, read); } os.close(); is.close(); } catch (IOException e1) { e1.printStackTrace(); } newPath = Path.fromPortableString(root + "/ajaxpipe.jar"); File pipeFile = new File(newPath.toOSString()); try { FileInputStream is = new FileInputStream(pipeFile); FileOutputStream os = new FileOutputStream(new File(lib, "ajaxpipe.jar")); byte[] buf = new byte[1024]; int read = -1; while ((read = is.read(buf)) != -1) { os.write(buf, 0, read); } os.close(); is.close(); } catch (IOException e1) { e1.printStackTrace(); } StringBuffer buildxml = new StringBuffer(); buildxml.append("<?xml version=\"1.0\"?>\r\n"); buildxml.append("<project name=\"java2script.servlet.pack\" default=\"pack.war\" basedir=\".\">\r\n"); buildxml.append(" <description>Pack Java2Script Servlet Application</description>\r\n"); buildxml.append("\r\n"); String name = new File(prjFolder).getName(); buildxml.append(" <property name=\"java2script.app.name\" value=\"" + name + "\"/>\r\n"); buildxml.append(" <property name=\"bin.folder\" value=\"${basedir}/../" + binRelative + "\"/>\r\n"); buildxml.append("\r\n"); buildxml.append(" <target name=\"pack.war\" depends=\"pack.jar\">\r\n"); buildxml.append(" <tstamp>\r\n"); buildxml.append(" <format property=\"now\" pattern=\"yyyy-MM-dd-HH-mm-ss\"/>\r\n"); buildxml.append(" </tstamp>\r\n"); buildxml.append(" <delete file=\"${basedir}/../${java2script.app.name}.war\" quiet=\"true\"/>\r\n"); buildxml.append(" <zip destfile=\"${basedir}/../${java2script.app.name}.${now}.war\">\r\n"); buildxml.append(" <fileset dir=\"${basedir}/../\">\r\n"); buildxml.append(" <exclude name=\"src/**\"/>\r\n"); buildxml.append(" <exclude name=\"META-INF/**\"/>\r\n"); buildxml.append(" <exclude name=\"WEB-INF/**\"/>\r\n"); buildxml.append(" <exclude name=\"**/*.java\"/>\r\n"); buildxml.append(" <exclude name=\"**/*.class\"/>\r\n"); buildxml.append(" <exclude name=\"**/*.swp\"/>\r\n"); buildxml.append(" <exclude name=\"**/*.swo\"/>\r\n"); buildxml.append(" <exclude name=\"**/*.jar\"/>\r\n"); buildxml.append(" <exclude name=\"**/*.war\"/>\r\n"); buildxml.append(" <exclude name=\".classpath\"/>\r\n"); buildxml.append(" <exclude name=\".project\"/>\r\n"); buildxml.append(" <exclude name=\".j2s\"/>\r\n"); buildxml.append(" <exclude name=\"web.xml\"/>\r\n"); buildxml.append(" <exclude name=\"build.xml\"/>\r\n"); buildxml.append(" <exclude name=\"build.properties\"/>\r\n"); buildxml.append(" <exclude name=\"plugin.xml\"/>\r\n"); buildxml.append(" <exclude name=\"plugin.properties\"/>\r\n"); buildxml.append(" </fileset>\r\n"); buildxml.append(" <fileset dir=\"${basedir}/..\">\r\n"); buildxml.append(" <include name=\"WEB-INF/**\"/>\r\n"); buildxml.append(" <exclude name=\"WEB-INF/build.xml\"/>\r\n"); buildxml.append(" </fileset>\r\n"); buildxml.append(" </zip>\r\n"); buildxml.append(" <copy file=\"${basedir}/../${java2script.app.name}.${now}.war\"\r\n"); buildxml.append(" tofile=\"${basedir}/../${java2script.app.name}.war\"/>\r\n"); buildxml.append(" </target>\r\n"); buildxml.append("\r\n"); buildxml.append(" <target name=\"pack.jar\">\r\n"); buildxml.append(" <delete file=\"${basedir}/lib/${java2script.app.name}.jar\" quiet=\"true\"/>\r\n"); buildxml.append(" <zip destfile=\"${basedir}/lib/${java2script.app.name}.jar\">\r\n"); buildxml.append(" <fileset dir=\"${bin.folder}\">\r\n"); buildxml.append(" <exclude name=\"WEB-INF/**\"/>\r\n"); buildxml.append(" <exclude name=\"**/*.html\"/>\r\n"); buildxml.append(" <exclude name=\"**/*.js\"/>\r\n"); buildxml.append(" <exclude name=\"**/*.css\"/>\r\n"); buildxml.append(" <exclude name=\"**/*.bmp\"/>\r\n"); buildxml.append(" <exclude name=\"**/*.gif\"/>\r\n"); buildxml.append(" <exclude name=\"**/*.png\"/>\r\n"); buildxml.append(" <exclude name=\"**/*.jpg\"/>\r\n"); buildxml.append(" <exclude name=\"**/*.jpeg\"/>\r\n"); buildxml.append(" <exclude name=\"**/*.swp\"/>\r\n"); buildxml.append(" <exclude name=\"**/*.swo\"/>\r\n"); buildxml.append(" <exclude name=\"**/*.jar\"/>\r\n"); buildxml.append(" <exclude name=\"**/*.war\"/>\r\n"); buildxml.append(" <exclude name=\".classpath\"/>\r\n"); buildxml.append(" <exclude name=\".project\"/>\r\n"); buildxml.append(" <exclude name=\".j2s\"/>\r\n"); buildxml.append(" <exclude name=\"web.xml\"/>\r\n"); buildxml.append(" <exclude name=\"build.xml\"/>\r\n"); buildxml.append(" <exclude name=\"build.properties\"/>\r\n"); buildxml.append(" <exclude name=\"plugin.xml\"/>\r\n"); buildxml.append(" <exclude name=\"plugin.properties\"/>\r\n"); buildxml.append(" </fileset>\r\n"); buildxml.append(" </zip>\r\n"); buildxml.append(" </target>\r\n"); buildxml.append("\r\n"); starterURL = AjaxPlugin.getDefault().getBundle().getEntry(File.separator); root = "."; try { root = Platform.asLocalURL(starterURL).getFile(); } catch (IOException e1) { e1.printStackTrace(); } newPath = Path.fromPortableString(root); String ajaxPath = newPath.toOSString(); String key = "net.sf.j2s.ajax"; int idx = ajaxPath.lastIndexOf(key); if (idx != -1) { ajaxPath = ajaxPath.substring(0, idx) + "net.sf.j2s.lib" + ajaxPath.substring(idx + key.length()); } File libFile = new File(ajaxPath); String j2sRelativePath = FileUtil.toRelativePath(libFile.getAbsolutePath(), webinf.getAbsolutePath()); if (j2sRelativePath.length() > 0 && !j2sRelativePath.endsWith("/")) { j2sRelativePath += "/"; } int slashIndex = j2sRelativePath.lastIndexOf('/', j2sRelativePath.length() - 2); String pluginPath = j2sRelativePath.substring(0, slashIndex); String libPluginPath = j2sRelativePath.substring(slashIndex + 1, j2sRelativePath.length() - 1); buildxml.append(" <target name=\"pack.plugins.j2slib.war\">\r\n"); buildxml.append(" <delete file=\"${basedir}/../plugins.war\" quiet=\"true\"/>\r\n"); buildxml.append(" <zip destfile=\"${basedir}/../plugins.war\">\r\n"); buildxml.append(" <fileset dir=\"${basedir}/" + pluginPath + "/\">\r\n"); buildxml.append(" <include name=\"" + libPluginPath + "/**\"/>\r\n"); buildxml.append(" <exclude name=\"" + libPluginPath + "/library.jar\"/>\r\n"); buildxml.append(" <exclude name=\"" + libPluginPath + "/plugin.xml\"/>\r\n"); buildxml.append(" <exclude name=\"" + libPluginPath + "/META-INF/**\"/>\r\n"); buildxml.append(" </fileset>\r\n"); buildxml.append(" </zip>\r\n"); buildxml.append(" </target>\r\n"); buildxml.append("\r\n"); buildxml.append("</project>\r\n"); try { FileOutputStream fos = new FileOutputStream(new File(webinf, "build.xml")); fos.write(buildxml.toString().getBytes()); fos.close(); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } StringBuffer webxml = new StringBuffer(); webxml.append("<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>\r\n"); webxml.append("<!DOCTYPE web-app\r\n"); webxml.append(" PUBLIC \"-//Sun Microsystems, Inc.//DTD Web Application 2.3//EN\"\r\n"); webxml.append(" \"http://java.sun.com/dtd/web-app_2_3.dtd\">\r\n"); webxml.append("<web-app>\r\n"); webxml.append(" <display-name>Java2Script</display-name>\r\n"); webxml.append(" <description>Java2Script application</description>\r\n"); webxml.append(genereateServlet("simplerpc", "net.sf.j2s.ajax.SimpleRPCHttpServlet")); webxml.append(genereateServlet("piperpc", "net.sf.j2s.ajax.CompoundPipeRPCHttpServlet")); webxml.append(" <servlet>\r\n"); webxml.append(" <servlet-name>simplepipe</servlet-name>\r\n"); webxml.append(" <servlet-class>net.sf.j2s.ajax.SimplePipeHttpServlet</servlet-class>\r\n"); webxml.append(" <init-param>\r\n"); webxml.append(" <param-name>simple.pipe.query.timeout</param-name>\r\n"); webxml.append(" <param-value>20000</param-value>\r\n"); webxml.append(" </init-param>\r\n"); webxml.append(" <init-param>\r\n"); webxml.append(" <param-name>simple.pipe.script.breakout</param-name>\r\n"); webxml.append(" <param-value>1200000</param-value>\r\n"); webxml.append(" </init-param>\r\n"); webxml.append(" <init-param>\r\n"); webxml.append(" <param-name>simple.pipe.max.items.per.query</param-name>\r\n"); webxml.append(" <param-value>60</param-value>\r\n"); webxml.append(" </init-param>\r\n"); webxml.append(" </servlet>\r\n"); webxml.append(" <servlet-mapping>\r\n"); webxml.append(" <servlet-name>simplerpc</servlet-name>\r\n"); webxml.append(" <url-pattern>/simplerpc</url-pattern>\r\n"); webxml.append(" </servlet-mapping>\r\n"); webxml.append(" <servlet-mapping>\r\n"); webxml.append(" <servlet-name>piperpc</servlet-name>\r\n"); webxml.append(" <url-pattern>/piperpc</url-pattern>\r\n"); webxml.append(" </servlet-mapping>\r\n"); webxml.append(" <servlet-mapping>\r\n"); webxml.append(" <servlet-name>simplepipe</servlet-name>\r\n"); webxml.append(" <url-pattern>/simplepipe</url-pattern>\r\n"); webxml.append(" </servlet-mapping>\r\n"); webxml.append("</web-app>\r\n"); try { FileOutputStream fos = new FileOutputStream(new File(webinf, "web.xml")); fos.write(webxml.toString().getBytes()); fos.close(); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } catch (FileNotFoundException e1) { e1.printStackTrace(); } }

public String getpage(String leurl) throws Exception { int data; StringBuffer lapage = new StringBuffer(); URL myurl = new URL(leurl); URLConnection conn = myurl.openConnection(); conn.connect(); if (!Pattern.matches("HTTP/... 2.. .*", conn.getHeaderField(0).toString())) { System.out.println(conn.getHeaderField(0).toString()); return lapage.toString(); } InputStream in = conn.getInputStream(); for (data = in.read(); data != -1; data = in.read()) lapage.append((char) data); return lapage.toString(); }

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 boolean verifyPassword(String digest, String password) { String alg = null; int size = 0; if (digest.regionMatches(true, 0, "{SHA}", 0, 5)) { digest = digest.substring(5); alg = "SHA-1"; size = 20; } else if (digest.regionMatches(true, 0, "{SSHA}", 0, 6)) { digest = digest.substring(6); alg = "SHA-1"; size = 20; } else if (digest.regionMatches(true, 0, "{MD5}", 0, 5)) { digest = digest.substring(5); alg = "MD5"; size = 16; } else if (digest.regionMatches(true, 0, "{SMD5}", 0, 6)) { digest = digest.substring(6); alg = "MD5"; size = 16; } try { MessageDigest sha = MessageDigest.getInstance(alg); if (sha == null) { return false; } byte[][] hs = split(Base64.decode(digest), size); byte[] hash = hs[0]; byte[] salt = hs[1]; sha.reset(); sha.update(password.getBytes()); sha.update(salt); byte[] pwhash = sha.digest(); return MessageDigest.isEqual(hash, pwhash); } catch (NoSuchAlgorithmException nsae) { throw new RuntimeException("failed to find " + "algorithm for password hashing.", nsae); } }

public void loadProfilefromConfig(String filename, P xslProfileClass, String profileTag) throws ParserConfigurationException, SAXException, IOException, XPathExpressionException { if (Val.chkStr(profileTag).equals("")) { profileTag = "Profile"; } String configuration_folder_path = this.getConfigurationFolderPath(); if (configuration_folder_path == null || configuration_folder_path.length() == 0) { Properties properties = new Properties(); final URL url = CswProfiles.class.getResource("CswCommon.properties"); properties.load(url.openStream()); configuration_folder_path = properties.getProperty("DEFAULT_CONFIGURATION_FOLDER_PATH"); } DocumentBuilder builder = DocumentBuilderFactory.newInstance().newDocumentBuilder(); ResourcePath rscPath = new ResourcePath(); InputSource configFile = rscPath.makeInputSource(configuration_folder_path + filename); if (configFile == null) { configFile = rscPath.makeInputSource("/" + configuration_folder_path + filename); } Document doc = builder.parse(configFile); NodeList profileNodes = doc.getElementsByTagName(profileTag); for (int i = 0; i < profileNodes.getLength(); i++) { Node currProfile = profileNodes.item(i); XPath xpath = XPathFactory.newInstance().newXPath(); String id = Val.chkStr(xpath.evaluate("ID", currProfile)); String name = Val.chkStr(xpath.evaluate("Name", currProfile)); String description = Val.chkStr(xpath.evaluate("Description", currProfile)); String requestXslt = Val.chkStr(xpath.evaluate("GetRecords/XSLTransformations/Request", currProfile)); String expectedGptXmlOutput = Val.chkStr(xpath.evaluate("GetRecords/XSLTransformations/Request/@expectedGptXmlOutput", currProfile)); if (expectedGptXmlOutput.equals("")) { expectedGptXmlOutput = FORMAT_SEARCH_TO_XSL.MINIMAL_LEGACY_CSWCLIENT.toString(); } String responseXslt = Val.chkStr(xpath.evaluate("GetRecords/XSLTransformations/Response", currProfile)); String requestKVPs = Val.chkStr(xpath.evaluate("GetRecordByID/RequestKVPs", currProfile)); String metadataXslt = Val.chkStr(xpath.evaluate("GetRecordByID/XSLTransformations/Response", currProfile)); boolean extentSearch = Boolean.parseBoolean(Val.chkStr(xpath.evaluate("SupportSpatialQuery", currProfile))); boolean liveDataMaps = Boolean.parseBoolean(Val.chkStr(xpath.evaluate("SupportContentTypeQuery", currProfile))); boolean extentDisplay = Boolean.parseBoolean(Val.chkStr(xpath.evaluate("SupportSpatialBoundary", currProfile))); boolean harvestable = Boolean.parseBoolean(Val.chkStr(xpath.evaluate("Harvestable", currProfile))); requestXslt = configuration_folder_path + requestXslt; responseXslt = configuration_folder_path + responseXslt; metadataXslt = configuration_folder_path + metadataXslt; SearchXslProfile profile = null; try { profile = xslProfileClass.getClass().newInstance(); profile.setId(id); profile.setName(name); profile.setDescription(description); profile.setRequestxslt(requestXslt); profile.setResponsexslt(responseXslt); profile.setMetadataxslt(metadataXslt); profile.setSupportsContentTypeQuery(liveDataMaps); profile.setSupportsSpatialBoundary(extentDisplay); profile.setSupportsSpatialQuery(extentSearch); profile.setKvp(requestKVPs); profile.setHarvestable(harvestable); profile.setFormatRequestToXsl(SearchXslProfile.FORMAT_SEARCH_TO_XSL.valueOf(expectedGptXmlOutput)); profile.setFilter_extentsearch(extentSearch); profile.setFilter_livedatamap(liveDataMaps); addProfile((P) profile); } catch (InstantiationException e) { throw new IOException("Could not instantiate profile class" + e.getMessage()); } catch (IllegalAccessException e) { throw new IOException("Could not instantiate profile class" + e.getMessage()); } } }

protected static String fileName2md5(String input) { try { MessageDigest md = MessageDigest.getInstance("MD5"); md.reset(); md.update(input.getBytes("iso-8859-1")); byte[] byteHash = md.digest(); md.reset(); StringBuffer resultString = new StringBuffer(); for (int i = 0; i < byteHash.length; i++) { resultString.append(Integer.toHexString(0xFF & byteHash[i])); } return (resultString.toString()); } catch (Exception ex) { Logger.error(ex.getClass() + " " + ex.getMessage()); for (int i = 0; i < ex.getStackTrace().length; i++) Logger.error(" " + ex.getStackTrace()[i].toString()); ex.printStackTrace(); } return String.valueOf(Math.random() * Long.MAX_VALUE); }

@Override public CheckAvailabilityResult execute(final CheckAvailabilityAction action, final ExecutionContext context) throws ActionException { if (LOGGER.isDebugEnabled()) { String serverName = null; if (action.getServerId() == CheckAvailability.FEDORA_ID) { serverName = "fedora"; } else if (action.getServerId() == CheckAvailability.KRAMERIUS_ID) { serverName = "kramerius"; } LOGGER.debug("Processing action: CheckAvailability: " + serverName); } ServerUtils.checkExpiredSession(httpSessionProvider); boolean status = true; String url = null; String usr = ""; String pass = ""; if (action.getServerId() == CheckAvailability.FEDORA_ID) { url = configuration.getFedoraHost(); usr = configuration.getFedoraLogin(); pass = configuration.getFedoraPassword(); } else if (action.getServerId() == CheckAvailability.KRAMERIUS_ID) { url = configuration.getKrameriusHost() + SOME_STATIC_KRAMERIUS_PAGE; } else { throw new ActionException("Unknown server id"); } try { URLConnection con = RESTHelper.openConnection(url, usr, pass, false); if (con instanceof HttpURLConnection) { HttpURLConnection httpConnection = (HttpURLConnection) con; int resp = httpConnection.getResponseCode(); if (resp < 200 || resp >= 308) { status = false; LOGGER.info("Server " + url + " answered with HTTP code " + httpConnection.getResponseCode()); } } else { status = false; } } catch (MalformedURLException e) { status = false; e.printStackTrace(); } catch (IOException e) { status = false; e.printStackTrace(); } return new CheckAvailabilityResult(status, url); }

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

public void readPersistentProperties() { try { String file = System.getProperty("user.home") + System.getProperty("file.separator") + ".das2rc"; File f = new File(file); if (f.canRead()) { try { InputStream in = new FileInputStream(f); load(in); in.close(); } catch (IOException e) { e.printStackTrace(); org.das2.util.DasExceptionHandler.handle(e); } } else { if (!f.exists() && f.canWrite()) { try { OutputStream out = new FileOutputStream(f); store(out, ""); out.close(); } catch (IOException e) { e.printStackTrace(); org.das2.util.DasExceptionHandler.handle(e); } } else { System.err.println("Unable to read or write " + file + ". Using defaults."); } } } catch (SecurityException ex) { ex.printStackTrace(); } }

public String preProcessHTML(String uri) { final StringBuffer buf = new StringBuffer(); try { HTMLDocument doc = new HTMLDocument() { public HTMLEditorKit.ParserCallback getReader(int pos) { return new HTMLEditorKit.ParserCallback() { public void handleText(char[] data, int pos) { buf.append(data); buf.append('\n'); } }; } }; URL url = new URI(uri).toURL(); URLConnection conn = url.openConnection(); Reader rd = new InputStreamReader(conn.getInputStream()); new ParserDelegator().parse(rd, doc.getReader(0), Boolean.TRUE); } catch (MalformedURLException e) { System.err.println(e.getMessage()); e.printStackTrace(); } catch (URISyntaxException e) { System.err.println(e.getMessage()); e.printStackTrace(); } catch (IOException e) { System.err.println(e.getMessage()); e.printStackTrace(); } return buf.toString(); }

void startzm() { URL myzzurl; InputStream myzstream; byte zmemimage[]; boolean joined; zmemimage = null; try { System.err.println(zcodefile); myzzurl = new URL(zcodefile); myzstream = myzzurl.openStream(); zmemimage = suckstream(myzstream); } catch (MalformedURLException booga) { try { myzstream = new FileInputStream(zcodefile); zmemimage = suckstream(myzstream); } catch (IOException booga2) { add("North", new Label("Malformed URL")); failed = true; } } catch (IOException booga) { add("North", new Label("I/O Error")); } if (zmemimage != null) { switch(zmemimage[0]) { case 3: zm = new ZMachine3(screen, status_line, zmemimage); break; case 5: remove(status_line); zm = new ZMachine5(screen, zmemimage); break; case 8: remove(status_line); zm = new ZMachine8(screen, zmemimage); break; default: add("North", new Label("Not a valid V3,V5, or V8 story file")); } if (zm != null) zm.start(); } joined = false; if (zmemimage != null) { while (!joined) { try { zm.join(); joined = true; } catch (InterruptedException booga) { } } } System.exit(0); }

public void SendFile(File testfile) { try { SocketChannel sock = SocketChannel.open(new InetSocketAddress("127.0.0.1", 1234)); sock.configureBlocking(true); while (!sock.finishConnect()) { System.out.println("NOT connected!"); } System.out.println("CONNECTED!"); FileInputStream fis = new FileInputStream(testfile); FileChannel fic = fis.getChannel(); long len = fic.size(); Buffer.clear(); Buffer.putLong(len); Buffer.flip(); sock.write(Buffer); long cnt = 0; while (cnt < len) { Buffer.clear(); int add = fic.read(Buffer); cnt += add; Buffer.flip(); while (Buffer.hasRemaining()) { sock.write(Buffer); } } fic.close(); File tmpfile = getTmp().createNewFile("tmp", "tmp"); FileOutputStream fos = new FileOutputStream(tmpfile); FileChannel foc = fos.getChannel(); int mlen = -1; do { Buffer.clear(); mlen = sock.read(Buffer); Buffer.flip(); if (mlen > 0) { foc.write(Buffer); } } while (mlen > 0); foc.close(); } catch (IOException e) { e.printStackTrace(); } }

public static void transfer(File src, File dest, boolean removeSrc) throws FileNotFoundException, IOException { Log.warning("source: " + src); Log.warning("dest: " + dest); if (!src.canRead()) { throw new IOException("can not read src file: " + src); } if (!dest.getParentFile().isDirectory()) { if (!dest.getParentFile().mkdirs()) { throw new IOException("failed to make directories: " + dest.getParent()); } } FileInputStream fis = new FileInputStream(src); FileOutputStream fos = new FileOutputStream(dest); FileChannel fcin = fis.getChannel(); FileChannel fcout = fos.getChannel(); Log.warning("starting transfer from position " + fcin.position() + " to size " + fcin.size()); fcout.transferFrom(fcin, 0, fcin.size()); Log.warning("closing streams and channels"); fcin.close(); fcout.close(); fis.close(); fos.close(); if (removeSrc) { Log.warning("deleting file " + src); src.delete(); } }

public void saveUploadFile(String toFileName, UploadFile uploadFile, SysConfig sysConfig) throws IOException { OutputStream bos = new FileOutputStream(toFileName); IOUtils.copy(uploadFile.getInputStream(), bos); if (sysConfig.isAttachImg(uploadFile.getFileName()) && sysConfig.getReduceAttachImg() == 1) { ImgUtil.reduceImg(toFileName, toFileName + Constant.IMG_SMALL_FILEPREFIX, sysConfig.getReduceAttachImgSize(), sysConfig.getReduceAttachImgSize(), 1); } }

public String buscarArchivos(String nUsuario) { String responce = ""; String request = conf.Conf.buscarArchivo; OutputStreamWriter wr = null; BufferedReader rd = null; try { URL url = new URL(request); URLConnection conn = url.openConnection(); conn.setDoOutput(true); wr = new OutputStreamWriter(conn.getOutputStream()); wr.write("nUsuario=" + nUsuario); wr.flush(); rd = new BufferedReader(new InputStreamReader(conn.getInputStream())); String line; while ((line = rd.readLine()) != null) { responce += line; } } catch (Exception e) { } return responce; }

protected void doDownload(S3Bucket bucket, S3Object s3object) throws Exception { String key = s3object.getKey(); key = trimPrefix(key); String[] path = key.split("/"); String fileName = path[path.length - 1]; String dirPath = ""; for (int i = 0; i < path.length - 1; i++) { dirPath += path[i] + "/"; } File outputDir = new File(downloadFileOutputDir + "/" + dirPath); if (outputDir.exists() == false) { outputDir.mkdirs(); } File outputFile = new File(outputDir, fileName); long size = s3object.getContentLength(); if (outputFile.exists() && outputFile.length() == size) { return; } long startTime = System.currentTimeMillis(); log.info("Download start.S3 file=" + s3object.getKey() + " local file=" + outputFile.getAbsolutePath()); FileOutputStream fout = null; S3Object dataObject = null; try { fout = new FileOutputStream(outputFile); dataObject = s3.getObject(bucket, s3object.getKey()); InputStream is = dataObject.getDataInputStream(); IOUtils.copyStream(is, fout); downloadedFileList.add(key); long downloadTime = System.currentTimeMillis() - startTime; log.info("Download complete.Estimete time=" + downloadTime + "ms " + IOUtils.toBPSText(downloadTime, size)); } catch (Exception e) { log.error("Download fail. s3 file=" + key, e); outputFile.delete(); throw e; } finally { IOUtils.closeNoException(fout); if (dataObject != null) { dataObject.closeDataInputStream(); } } }

public static String getResourceFromURL(URL url, String acceptHeader) throws java.io.IOException { HttpURLConnection urlConnection = (HttpURLConnection) url.openConnection(); urlConnection.setUseCaches(false); urlConnection.setRequestProperty("Accept", acceptHeader); urlConnection.setInstanceFollowRedirects(true); BufferedReader input = new BufferedReader(new InputStreamReader(urlConnection.getInputStream())); String content = ""; String line; while ((line = input.readLine()) != null) { content += line; } input.close(); return content; }

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

public void run() { try { File outDir = new File(outDirTextField.getText()); if (!outDir.exists()) { SwingUtilities.invokeLater(new Runnable() { public void run() { JOptionPane.showMessageDialog(UnpackWizard.this, "The chosen directory does not exist!", "Directory Not Found Error", JOptionPane.ERROR_MESSAGE); } }); return; } if (!outDir.isDirectory()) { SwingUtilities.invokeLater(new Runnable() { public void run() { JOptionPane.showMessageDialog(UnpackWizard.this, "The chosen file is not a directory!", "Not a Directory Error", JOptionPane.ERROR_MESSAGE); } }); return; } if (!outDir.canWrite()) { SwingUtilities.invokeLater(new Runnable() { public void run() { JOptionPane.showMessageDialog(UnpackWizard.this, "Cannot write to the chosen directory!", "Directory Not Writeable Error", JOptionPane.ERROR_MESSAGE); } }); return; } File archiveDir = new File("foo.bar").getAbsoluteFile().getParentFile(); URL baseUrl = UnpackWizard.class.getClassLoader().getResource(UnpackWizard.class.getName().replaceAll("\\.", "/") + ".class"); if (baseUrl.getProtocol().equals("jar")) { String jarPath = baseUrl.getPath(); jarPath = jarPath.substring(0, jarPath.indexOf('!')); if (jarPath.startsWith("file:")) { try { archiveDir = new File(new URI(jarPath)).getAbsoluteFile().getParentFile(); } catch (URISyntaxException e1) { e1.printStackTrace(System.err); } } } SortedMap<Integer, String> inputFileNames = new TreeMap<Integer, String>(); for (Entry<Object, Object> anEntry : indexProperties.entrySet()) { String key = anEntry.getKey().toString(); if (key.startsWith("archive file ")) { inputFileNames.put(Integer.parseInt(key.substring("archive file ".length())), anEntry.getValue().toString()); } } byte[] buff = new byte[64 * 1024]; try { long bytesToWrite = 0; long bytesReported = 0; long bytesWritten = 0; for (String aFileName : inputFileNames.values()) { File aFile = new File(archiveDir, aFileName); if (aFile.exists()) { if (aFile.isFile()) { bytesToWrite += aFile.length(); } else { final File wrongFile = aFile; SwingUtilities.invokeLater(new Runnable() { public void run() { JOptionPane.showMessageDialog(UnpackWizard.this, "File \"" + wrongFile.getAbsolutePath() + "\" is not a standard file!", "Non Standard File Error", JOptionPane.ERROR_MESSAGE); } }); return; } } else { final File wrongFile = aFile; SwingUtilities.invokeLater(new Runnable() { public void run() { JOptionPane.showMessageDialog(UnpackWizard.this, "File \"" + wrongFile.getAbsolutePath() + "\" does not exist!", "File Not Found Error", JOptionPane.ERROR_MESSAGE); } }); return; } } MultiFileInputStream mfis = new MultiFileInputStream(archiveDir, inputFileNames.values().toArray(new String[inputFileNames.size()])); TarArchiveInputStream tis = new TarArchiveInputStream(new BufferedInputStream(mfis)); TarArchiveEntry tarEntry = tis.getNextTarEntry(); while (tarEntry != null) { File outFile = new File(outDir.getAbsolutePath() + "/" + tarEntry.getName()); if (outFile.exists()) { final File wrongFile = outFile; SwingUtilities.invokeLater(new Runnable() { public void run() { JOptionPane.showMessageDialog(UnpackWizard.this, "Was about to write out file \"" + wrongFile.getAbsolutePath() + "\" but it already " + "exists.\nPlease [re]move existing files out of the way " + "and try again.", "File Not Found Error", JOptionPane.ERROR_MESSAGE); } }); return; } if (tarEntry.isDirectory()) { outFile.getAbsoluteFile().mkdirs(); } else { outFile.getAbsoluteFile().getParentFile().mkdirs(); OutputStream os = new BufferedOutputStream(new FileOutputStream(outFile)); int len = tis.read(buff, 0, buff.length); while (len != -1) { os.write(buff, 0, len); bytesWritten += len; if (bytesWritten - bytesReported > (10 * 1024 * 1024)) { bytesReported = bytesWritten; final int progress = (int) (bytesReported * 100 / bytesToWrite); SwingUtilities.invokeLater(new Runnable() { @Override public void run() { progressBar.setValue(progress); } }); } len = tis.read(buff, 0, buff.length); } os.close(); } tarEntry = tis.getNextTarEntry(); } long expectedCrc = 0; try { expectedCrc = Long.parseLong(indexProperties.getProperty("CRC32", "0")); } catch (NumberFormatException e) { System.err.println("Error while obtaining the expected CRC"); e.printStackTrace(System.err); } if (mfis.getCRC() == expectedCrc) { SwingUtilities.invokeLater(new Runnable() { @Override public void run() { progressBar.setValue(0); JOptionPane.showMessageDialog(UnpackWizard.this, "Extraction completed successfully!", "Done!", JOptionPane.INFORMATION_MESSAGE); } }); return; } else { System.err.println("CRC Error: was expecting " + expectedCrc + " but got " + mfis.getCRC()); SwingUtilities.invokeLater(new Runnable() { public void run() { progressBar.setValue(0); JOptionPane.showMessageDialog(UnpackWizard.this, "CRC Error: the data extracted does not have the expected CRC!\n" + "You should probably delete the extracted files, as they are " + "likely to be invalid.", "CRC Error", JOptionPane.ERROR_MESSAGE); } }); return; } } catch (final IOException e) { e.printStackTrace(System.err); SwingUtilities.invokeLater(new Runnable() { public void run() { progressBar.setValue(0); JOptionPane.showMessageDialog(UnpackWizard.this, "Input/Output Error: " + e.getLocalizedMessage(), "Input/Output Error", JOptionPane.ERROR_MESSAGE); } }); return; } } finally { SwingUtilities.invokeLater(new Runnable() { public void run() { progressBar.setValue(0); setEnabled(true); } }); } }

public void initGet() throws Exception { cl = new DefaultHttpClient(); GetAuthPromter hp = new GetAuthPromter(); cl.setCredentialsProvider(hp); get = new HttpGet(getURL()); get.setHeader("User-Agent", "test"); get.setHeader("Accept", "*/*"); get.setHeader("Range", "bytes=" + getPosition() + "-" + getRangeEnd()); HttpResponse resp = cl.execute(get); ent = resp.getEntity(); setInputStream(ent.getContent()); }

public static String hash(String str) { if (str == null || str.length() == 0) { throw new CaptureSecurityException("String to encript cannot be null or zero length"); } StringBuilder hexString = new StringBuilder(); try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(str.getBytes()); byte[] hash = md.digest(); for (byte element : hash) { if ((0xff & element) < 0x10) { hexString.append('0').append(Integer.toHexString((0xFF & element))); } else { hexString.append(Integer.toHexString(0xFF & element)); } } } catch (NoSuchAlgorithmException e) { throw new CaptureSecurityException(e); } return hexString.toString(); }

public static String toMd5(String s) { String res = ""; try { MessageDigest digest = java.security.MessageDigest.getInstance("MD5"); digest.update(s.getBytes()); byte messageDigest[] = digest.digest(); res = toHexString(messageDigest); } catch (NoSuchAlgorithmException e) { } return res; }

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); } }

public void testCreateNewXMLFile() throws InvalidNodeTypeDefException, ParseException, Exception { JCRNodeSource emptySource = loadTestSource(); assertEquals(false, emptySource.exists()); OutputStream sourceOut = emptySource.getOutputStream(); assertNotNull(sourceOut); InputStream contentIn = getClass().getResourceAsStream(CONTENT_FILE); try { IOUtils.copy(contentIn, sourceOut); sourceOut.flush(); } finally { sourceOut.close(); contentIn.close(); } InputStream contentIn2 = getClass().getResourceAsStream(CONTENT2_FILE); sourceOut = emptySource.getOutputStream(); try { IOUtils.copy(contentIn2, sourceOut); sourceOut.flush(); } finally { sourceOut.close(); contentIn2.close(); } InputStream expected = getClass().getResourceAsStream(CONTENT2_FILE); JCRNodeSource persistentSource = loadTestSource(); assertEquals(true, persistentSource.exists()); InputStream actual = persistentSource.getInputStream(); try { assertTrue(isXmlEqual(expected, actual)); } finally { expected.close(); actual.close(); } JCRNodeSource tmpSrc = (JCRNodeSource) resolveSource(BASE_URL + "users/alexander.saar"); persistentSource.delete(); tmpSrc.delete(); }

public static boolean copy(File from, File to, Override override) throws IOException { FileInputStream in = null; FileOutputStream out = null; FileChannel srcChannel = null; FileChannel destChannel = null; if (override == null) override = Override.NEWER; switch(override) { case NEVER: if (to.isFile()) return false; break; case NEWER: if (to.isFile() && (from.lastModified() - LASTMODIFIED_DIFF_MILLIS) < to.lastModified()) return false; break; } to.getParentFile().mkdirs(); try { in = new FileInputStream(from); out = new FileOutputStream(to); srcChannel = in.getChannel(); destChannel = out.getChannel(); long position = 0L; long count = srcChannel.size(); while (position < count) { long chunk = Math.min(MAX_IO_CHUNK_SIZE, count - position); position += destChannel.transferFrom(srcChannel, position, chunk); } to.setLastModified(from.lastModified()); return true; } finally { CommonUtils.close(srcChannel); CommonUtils.close(destChannel); CommonUtils.close(out); CommonUtils.close(in); } }

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

public static void copyFile(File source, File destination) { if (!source.exists()) { return; } if ((destination.getParentFile() != null) && (!destination.getParentFile().exists())) { destination.getParentFile().mkdirs(); } try { FileChannel srcChannel = new FileInputStream(source).getChannel(); FileChannel dstChannel = new FileOutputStream(destination).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (IOException ioe) { ioe.printStackTrace(); } }

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); } }

public String encodePassword(String password, byte[] salt) throws Exception { if (salt == null) { salt = new byte[12]; secureRandom.nextBytes(salt); } MessageDigest md = MessageDigest.getInstance("MD5"); md.update(salt); md.update(password.getBytes("UTF8")); byte[] digest = md.digest(); byte[] storedPassword = new byte[digest.length + 12]; System.arraycopy(salt, 0, storedPassword, 0, 12); System.arraycopy(digest, 0, storedPassword, 12, digest.length); return new String(Base64.encode(storedPassword)); }

public TreeMap getStrainMap() { TreeMap strainMap = new TreeMap(); String server = ""; try { Datasource[] ds = DatasourceManager.getDatasouce(alias, version, DatasourceManager.ALL_CONTAINS_GROUP); for (int i = 0; i < ds.length; i++) { if (ds[i].getDescription().startsWith(MOUSE_DBSNP)) { if (ds[i].getServer().length() == 0) { Connection con = ds[i].getConnection(); strainMap = Action.lineMode.regularSQL.GenotypeDataSearchAction.getStrainMap(con); break; } else { server = ds[i].getServer(); HashMap serverUrlMap = InitXml.getInstance().getServerMap(); String serverUrl = (String) serverUrlMap.get(server); URL url = new URL(serverUrl + servletName); URLConnection uc = url.openConnection(); uc.setDoOutput(true); OutputStream os = uc.getOutputStream(); StringBuffer buf = new StringBuffer(); buf.append("viewType=getstrains"); buf.append("&hHead=" + hHead); buf.append("&hCheck=" + version); PrintStream ps = new PrintStream(os); ps.print(buf.toString()); ps.close(); ObjectInputStream ois = new ObjectInputStream(uc.getInputStream()); strainMap = (TreeMap) ois.readObject(); ois.close(); } } } } catch (Exception e) { log.error("strain map", e); } return strainMap; }

public static boolean loadTestProperties(Properties props, Class<?> callingClazz, Class<?> hierarchyRootClazz, String resourceBaseName) { if (!hierarchyRootClazz.isAssignableFrom(callingClazz)) { throw new IllegalArgumentException("Class " + callingClazz + " is not derived from " + hierarchyRootClazz); } if (null == resourceBaseName) { throw new NullPointerException("resourceBaseName is null"); } String fqcn = callingClazz.getName(); String uqcn = fqcn.substring(fqcn.lastIndexOf('.') + 1); String callingClassResource = uqcn + ".properties"; String globalCallingClassResource = "/" + callingClassResource; String baseClassResource = resourceBaseName + "-" + uqcn + ".properties"; String globalBaseClassResource = "/" + baseClassResource; String pkgResource = resourceBaseName + ".properties"; String globalResource = "/" + pkgResource; boolean loaded = false; final String[] resources = { baseClassResource, globalBaseClassResource, callingClassResource, globalCallingClassResource, pkgResource, globalResource }; List<URL> urls = new ArrayList<URL>(); Class<?> clazz = callingClazz; do { for (String res : resources) { URL url = clazz.getResource(res); if (null != url && !urls.contains(url)) { urls.add(url); } } if (hierarchyRootClazz.equals(clazz)) { clazz = null; } else { clazz = clazz.getSuperclass(); } } while (null != clazz); ListIterator<URL> it = urls.listIterator(urls.size()); while (it.hasPrevious()) { URL url = it.previous(); InputStream in = null; try { LOG.info("Loading test properties from resource: " + url); in = url.openStream(); props.load(in); loaded = true; } catch (IOException ex) { LOG.warn("Failed to load properties from resource: " + url, ex); } IOUtil.closeSilently(in); } return loaded; }

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

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

@Override public boolean checkConnection() { int status = 0; try { URL url = new URL(TupeloProxy.endpoint); HttpURLConnection conn = (HttpURLConnection) url.openConnection(); status = conn.getResponseCode(); } catch (Exception e) { logger.severe("Connection test failed with code:" + status); e.printStackTrace(); } return status > 199 && status < 400; }

@Test public void testWriteAndReadFirstLevel() throws Exception { JCFSFileServer server = new JCFSFileServer(defaultTcpPort, defaultTcpAddress, defaultUdpPort, defaultUdpAddress, dir, 0, 0); JCFS.configureDiscovery(defaultUdpAddress, defaultUdpPort); try { server.start(); RFile directory1 = new RFile("directory1"); RFile file = new RFile(directory1, "testreadwrite1st.txt"); RFileOutputStream out = new RFileOutputStream(file); out.write("test".getBytes("utf-8")); out.close(); RFileInputStream in = new RFileInputStream(file); byte[] buffer = new byte[4]; int readCount = in.read(buffer); in.close(); assertEquals(4, readCount); String resultRead = new String(buffer, "utf-8"); assertEquals("test", resultRead); } finally { server.stop(); } }

public static String encodePassword(String password) { try { MessageDigest messageDiegest = MessageDigest.getInstance("SHA-1"); messageDiegest.update(password.getBytes("UTF-8")); return Base64.encodeToString(messageDiegest.digest(), false); } catch (NoSuchAlgorithmException e) { log.error("Exception while encoding password"); throw new Error(e); } catch (UnsupportedEncodingException e) { log.error("Exception while encoding password"); throw new Error(e); } }

String digest(final UserAccountEntity account) { try { final MessageDigest digest = MessageDigest.getInstance("SHA-1"); digest.reset(); digest.update(account.getUserId().getBytes("UTF-8")); digest.update(account.getLastLogin().toString().getBytes("UTF-8")); digest.update(account.getPerson().getGivenName().getBytes("UTF-8")); digest.update(account.getPerson().getSurname().getBytes("UTF-8")); digest.update(account.getPerson().getEmail().getBytes("UTF-8")); digest.update(m_random); return new String(Base64.altEncode(digest.digest())); } catch (final Exception e) { LOG.error("Exception", e); throw new RuntimeException(e); } }

public String[] retrieveFasta(String id) throws Exception { URL url = new URL("http://www.ebi.ac.uk/ena/data/view/" + id + "&display=fasta"); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String header = reader.readLine(); StringBuffer seq = new StringBuffer(); String line = ""; while ((line = reader.readLine()) != null) { seq.append(line); } reader.close(); return new String[] { header, seq.toString() }; }

public Constructor run() throws Exception { String path = "META-INF/services/" + ComponentApplicationContext.class.getName(); ClassLoader loader = Thread.currentThread().getContextClassLoader(); final Enumeration<URL> urls; if (loader == null) { urls = ComponentApplicationContext.class.getClassLoader().getResources(path); } else { urls = loader.getResources(path); } while (urls.hasMoreElements()) { URL url = urls.nextElement(); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); try { String className = null; while ((className = reader.readLine()) != null) { final String name = className.trim(); if (!name.startsWith("#") && !name.startsWith(";") && !name.startsWith("//")) { final Class<?> cls; if (loader == null) { cls = Class.forName(name); } else { cls = Class.forName(name, true, loader); } int m = cls.getModifiers(); if (ComponentApplicationContext.class.isAssignableFrom(cls) && !Modifier.isAbstract(m) && !Modifier.isInterface(m)) { Constructor constructor = cls.getDeclaredConstructor(); if (!Modifier.isPublic(constructor.getModifiers())) { constructor.setAccessible(true); } return constructor; } else { throw new ClassCastException(cls.getName()); } } } } finally { reader.close(); } } throw new ComponentApplicationException("No " + "ComponentApplicationContext implementation " + "found."); }

protected void onSubmit() { super.onSubmit(); if (!this.hasError()) { final FileUpload upload = fileUploadField.getFileUpload(); if (upload != null) { try { StringWriter xmlSourceWriter = new StringWriter(); IOUtils.copy(upload.getInputStream(), xmlSourceWriter); processSubmittedDoap(xmlSourceWriter.toString()); } catch (IOException e) { setResponsePage(new ErrorReportPage(new UserReportableException("Unable to add doap using RDF supplied", DoapFormPage.class, e))); } } } }

protected void writeGZippedBytes(byte array[], TupleOutput out) { if (array == null || array.length == 0) { out.writeBoolean(false); writeBytes(array, out); return; } try { ByteArrayOutputStream baos = new ByteArrayOutputStream(array.length); GZIPOutputStream gzout = new GZIPOutputStream(baos); ByteArrayInputStream bais = new ByteArrayInputStream(array); IOUtils.copyTo(bais, gzout); gzout.finish(); gzout.close(); bais.close(); byte compressed[] = baos.toByteArray(); if (compressed.length < array.length) { out.writeBoolean(true); writeBytes(compressed, out); } else { out.writeBoolean(false); writeBytes(array, out); } } catch (IOException err) { throw new RuntimeException(err); } }

@SuppressWarnings("unchecked") public static void unzip(String zipFileName, String folder, boolean isCreate) throws IOException { File file = new File(zipFileName); File folderfile = null; if (file.exists() && file.isFile()) { String mfolder = folder == null ? file.getParent() : folder; String fn = file.getName(); fn = fn.substring(0, fn.lastIndexOf(".")); mfolder = isCreate ? (mfolder + File.separator + fn) : mfolder; folderfile = new File(mfolder); if (!folderfile.exists()) { folderfile.mkdirs(); } } else { throw new FileNotFoundException("不存在 zip 文件"); } ZipFile zipFile = new ZipFile(file); try { Enumeration<ZipArchiveEntry> en = zipFile.getEntries(); ZipArchiveEntry ze = null; while (en.hasMoreElements()) { ze = en.nextElement(); if (ze.isDirectory()) { String dirName = ze.getName(); dirName = dirName.substring(0, dirName.length() - 1); File f = new File(folderfile.getPath() + File.separator + dirName); f.mkdirs(); } else { File f = new File(folderfile.getPath() + File.separator + ze.getName()); if (!f.getParentFile().exists()) { f.getParentFile().mkdirs(); } f.createNewFile(); InputStream in = zipFile.getInputStream(ze); OutputStream out = new FileOutputStream(f); IOUtils.copy(in, out); out.close(); in.close(); } } } finally { zipFile.close(); } }

public static String md5sum(String s, String alg) { try { MessageDigest md = MessageDigest.getInstance(alg); md.update(s.getBytes(), 0, s.length()); StringBuffer sb = new StringBuffer(); synchronized (sb) { for (byte b : md.digest()) sb.append(pad(Integer.toHexString(0xFF & b), ZERO.charAt(0), 2, true)); } return sb.toString(); } catch (Exception ex) { log(ex); } return null; }

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 InputSource resolveEntity(String pPublicId, String pSystemId) throws SAXException, IOException { try { URL url = new URL(pSystemId); String fileName = (String) urlMap.get(url); if (fileName != null) { FileInputStream istream = new FileInputStream(new File(schemaDir, fileName)); InputSource isource = new InputSource(istream); isource.setSystemId(url.toString()); return isource; } String file = url.getFile(); if (file == null) { file = ""; } else { int offset = file.lastIndexOf('/'); if (offset >= 0) { file = file.substring(offset + 1); } } if ("".equals(file)) { file = "schema.xsd"; } int offset = file.lastIndexOf('.'); String prefix; String suffix; String numAsStr = ""; if (offset > 0 && offset < file.length()) { prefix = file.substring(0, offset); suffix = file.substring(offset); } else { prefix = file; suffix = ".xsd"; } File f; for (int num = 1; ; ++num) { f = new File(schemaDir, prefix + numAsStr + suffix); if (f.exists()) { numAsStr = "_" + num; } else { break; } } InputStream istream = url.openStream(); schemaDir.mkdirs(); FileOutputStream fos = new FileOutputStream(f); try { byte[] buffer = new byte[1024]; for (; ; ) { int res = istream.read(buffer); if (res == -1) { break; } else if (res > 0) { fos.write(buffer, 0, res); } } istream.close(); fos.close(); fos = null; } finally { if (fos != null) { try { f.delete(); } catch (Throwable ignore) { } } } urlMap.put(url, f.getName()); InputSource isource = new InputSource(new FileInputStream(f)); isource.setSystemId(url.toString()); return isource; } catch (Exception e) { JaxMeServlet.this.log("Failed to resolve URL " + pSystemId, e); } return null; }

private String mkSid() { String temp = toString(); MessageDigest messagedigest = null; try { messagedigest = MessageDigest.getInstance("SHA"); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); return null; } messagedigest.update(temp.getBytes()); byte digest[] = messagedigest.digest(); String chk = ""; for (int i = 0; i < digest.length; i++) { String s = Integer.toHexString(digest[i] & 0xFF); chk += ((s.length() == 1) ? "0" + s : s); } return chk.toString(); }

@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 + ".."); if (remainingsize >= splitsize) { in.transferTo(pos, splitsize, out); pos += splitsize; remainingsize -= splitsize; } else { 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) { } }

public static void main(String[] args) { String logConfiguration = args[2]; DOMConfigurator.configure(logConfiguration); String urlToRun = args[0]; String outputFile = args[1]; InputStream conInput = null; BufferedReader reader = null; BufferedWriter writer = null; if (logger.isDebugEnabled()) { logger.debug("output file is " + outputFile); } try { URL url = new URL(urlToRun); URLConnection urlCon = url.openConnection(); urlCon.connect(); conInput = urlCon.getInputStream(); reader = new BufferedReader(new InputStreamReader(conInput)); File output = new File(outputFile); writer = new BufferedWriter(new FileWriter(output)); String line = null; while ((line = reader.readLine()) != null) { logger.debug(line); writer.write(line); } writer.flush(); } catch (MalformedURLException murle) { logger.error(urlToRun + " is not a valid URL", murle); } catch (IOException ioe) { logger.error("IO Error ocured while opening connection to " + urlToRun, ioe); } finally { try { reader.close(); conInput.close(); writer.close(); } catch (IOException ioe) { throw new RuntimeException("Cannot close readers or streams", ioe); } } }

public synchronized void insertMessage(FrostUnsentMessageObject mo) throws SQLException { AttachmentList files = mo.getAttachmentsOfType(Attachment.FILE); AttachmentList boards = mo.getAttachmentsOfType(Attachment.BOARD); Connection conn = AppLayerDatabase.getInstance().getPooledConnection(); try { conn.setAutoCommit(false); PreparedStatement ps = conn.prepareStatement("INSERT INTO UNSENDMESSAGES (" + "primkey,messageid,inreplyto,board,sendafter,idlinepos,idlinelen,fromname,subject,recipient,msgcontent," + "hasfileattachment,hasboardattachment,timeAdded" + ") VALUES (?,?,?,?,?,?,?,?,?,?,?,?,?,?)"); Long identity = null; Statement stmt = AppLayerDatabase.getInstance().createStatement(); ResultSet rs = stmt.executeQuery("select UNIQUEKEY('UNSENDMESSAGES')"); if (rs.next()) { identity = new Long(rs.getLong(1)); } else { logger.log(Level.SEVERE, "Could not retrieve a new unique key!"); } rs.close(); stmt.close(); mo.setMsgIdentity(identity.longValue()); int i = 1; ps.setLong(i++, mo.getMsgIdentity()); ps.setString(i++, mo.getMessageId()); ps.setString(i++, mo.getInReplyTo()); ps.setInt(i++, mo.getBoard().getPrimaryKey().intValue()); ps.setLong(i++, 0); ps.setInt(i++, mo.getIdLinePos()); ps.setInt(i++, mo.getIdLineLen()); ps.setString(i++, mo.getFromName()); ps.setString(i++, mo.getSubject()); ps.setString(i++, mo.getRecipientName()); ps.setString(i++, mo.getContent()); ps.setBoolean(i++, (files.size() > 0)); ps.setBoolean(i++, (boards.size() > 0)); ps.setLong(i++, mo.getTimeAdded()); int inserted = 0; try { inserted = ps.executeUpdate(); } finally { ps.close(); } if (inserted == 0) { logger.log(Level.SEVERE, "message insert returned 0 !!!"); return; } mo.setMsgIdentity(identity.longValue()); if (files.size() > 0) { PreparedStatement p = conn.prepareStatement("INSERT INTO UNSENDFILEATTACHMENTS" + " (msgref,filename,filesize,filekey)" + " VALUES (?,?,?,?)"); for (Iterator it = files.iterator(); it.hasNext(); ) { FileAttachment fa = (FileAttachment) it.next(); int ix = 1; p.setLong(ix++, mo.getMsgIdentity()); p.setString(ix++, fa.getInternalFile().getPath()); p.setLong(ix++, fa.getFileSize()); p.setString(ix++, fa.getKey()); int ins = p.executeUpdate(); if (ins == 0) { logger.log(Level.SEVERE, "fileattachment insert returned 0 !!!"); } } p.close(); } if (boards.size() > 0) { PreparedStatement p = conn.prepareStatement("INSERT INTO UNSENDBOARDATTACHMENTS" + " (msgref,boardname,boardpublickey,boardprivatekey,boarddescription)" + " VALUES (?,?,?,?,?)"); for (Iterator it = boards.iterator(); it.hasNext(); ) { BoardAttachment ba = (BoardAttachment) it.next(); Board b = ba.getBoardObj(); int ix = 1; p.setLong(ix++, mo.getMsgIdentity()); p.setString(ix++, b.getNameLowerCase()); p.setString(ix++, b.getPublicKey()); p.setString(ix++, b.getPrivateKey()); p.setString(ix++, b.getDescription()); int ins = p.executeUpdate(); if (ins == 0) { logger.log(Level.SEVERE, "boardattachment insert returned 0 !!!"); } } p.close(); } conn.commit(); conn.setAutoCommit(true); } catch (Throwable t) { logger.log(Level.SEVERE, "Exception during insert of unsent message", t); try { conn.rollback(); } catch (Throwable t1) { logger.log(Level.SEVERE, "Exception during rollback", t1); } try { conn.setAutoCommit(true); } catch (Throwable t1) { } } finally { AppLayerDatabase.getInstance().givePooledConnection(conn); } }

public static String generateStringSHA256(String content) { MessageDigest md = null; try { md = MessageDigest.getInstance("SHA-256"); } catch (NoSuchAlgorithmException ex) { Logger.getLogger(ScannerChecksum.class.getName()).log(Level.SEVERE, null, ex); } md.update(content.getBytes()); byte byteData[] = md.digest(); @SuppressWarnings("StringBufferMayBeStringBuilder") StringBuffer sb = new StringBuffer(); for (int i = 0; i < byteData.length; i++) { sb.append(Integer.toString((byteData[i] & 0xff) + 0x100, 16).substring(1)); } @SuppressWarnings("StringBufferMayBeStringBuilder") StringBuffer hexString = new StringBuffer(); for (int i = 0; i < byteData.length; i++) { String hex = Integer.toHexString(0xff & byteData[i]); if (hex.length() == 1) hexString.append('0'); hexString.append(hex); } return hexString.toString(); }

public void testDigest() { try { String myinfo = "我的测试信息"; MessageDigest alga = MessageDigest.getInstance("SHA-1"); alga.update(myinfo.getBytes()); byte[] digesta = alga.digest(); System.out.println("本信息摘要是:" + byte2hex(digesta)); MessageDigest algb = MessageDigest.getInstance("SHA-1"); algb.update(myinfo.getBytes()); if (MessageDigest.isEqual(digesta, algb.digest())) { System.out.println("信息检查正常"); } else { System.out.println("摘要不相同"); } } catch (NoSuchAlgorithmException ex) { System.out.println("非法摘要算法"); } }

private String getStoreName() { try { final MessageDigest digest = MessageDigest.getInstance("MD5"); digest.update(protectionDomain.getBytes()); final byte[] bs = digest.digest(); final StringBuffer sb = new StringBuffer(bs.length * 2); for (int i = 0; i < bs.length; i++) { final String s = Integer.toHexString(bs[i] & 0xff); if (s.length() < 2) sb.append('0'); sb.append(s); } return sb.toString(); } catch (final NoSuchAlgorithmException e) { throw new RuntimeException("Can't save credentials: digest method MD5 unavailable."); } }

public static String encrypt(String password, String algorithm, byte[] salt) { StringBuffer buffer = new StringBuffer(); MessageDigest digest = null; int size = 0; if ("CRYPT".equalsIgnoreCase(algorithm)) { throw new InternalError("Not implemented"); } else if ("SHA".equalsIgnoreCase(algorithm) || "SSHA".equalsIgnoreCase(algorithm)) { size = 20; if (salt != null && salt.length > 0) { buffer.append("{SSHA}"); } else { buffer.append("{SHA}"); } try { digest = MessageDigest.getInstance("SHA-1"); } catch (NoSuchAlgorithmException e) { throw new InternalError("Invalid algorithm"); } } else if ("MD5".equalsIgnoreCase(algorithm) || "SMD5".equalsIgnoreCase(algorithm)) { size = 16; if (salt != null && salt.length > 0) { buffer.append("{SMD5}"); } else { buffer.append("{MD5}"); } try { digest = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { throw new InternalError("Invalid algorithm"); } } int outSize = size; digest.reset(); digest.update(password.getBytes()); if (salt != null && salt.length > 0) { digest.update(salt); outSize += salt.length; } byte[] out = new byte[outSize]; System.arraycopy(digest.digest(), 0, out, 0, size); if (salt != null && salt.length > 0) { System.arraycopy(salt, 0, out, size, salt.length); } buffer.append(Base64.encode(out)); return buffer.toString(); }

void bubbleSort(int ids[]) { boolean flag = true; int temp; while (flag) { flag = false; for (int i = 0; i < ids.length - 1; i++) if (ids[i] < ids[i + 1]) { temp = ids[i]; ids[i] = ids[i + 1]; ids[i + 1] = temp; flag = true; } } }

public static Dimension getJPEGDimension(String urls) throws IOException { URL url; Dimension d = null; try { url = new URL(urls); InputStream fis = url.openStream(); if (fis.read() != 255 || fis.read() != 216) throw new RuntimeException("SOI (Start Of Image) marker 0xff 0xd8 missing"); while (fis.read() == 255) { int marker = fis.read(); int len = fis.read() << 8 | fis.read(); if (marker == 192) { fis.skip(1); int height = fis.read() << 8 | fis.read(); int width = fis.read() << 8 | fis.read(); d = new Dimension(width, height); break; } fis.skip(len - 2); } fis.close(); } catch (MalformedURLException e) { e.printStackTrace(); } return d; }

private static final void copyFile(File srcFile, File destDir, byte[] buffer) { try { File destFile = new File(destDir, srcFile.getName()); InputStream in = new FileInputStream(srcFile); OutputStream out = new FileOutputStream(destFile); int bytesRead; while ((bytesRead = in.read(buffer)) != -1) out.write(buffer, 0, bytesRead); in.close(); out.close(); } catch (IOException ioe) { System.err.println("Couldn't copy file '" + srcFile + "' to directory '" + destDir + "'"); } }

public void guardarCantidad() { try { String can = String.valueOf(cantidadArchivos); File archivo = new File("cantidadArchivos.txt"); FileWriter fw = new FileWriter(archivo); BufferedWriter bw = new BufferedWriter(fw); PrintWriter salida = new PrintWriter(bw); salida.print(can); salida.close(); BufferedInputStream origin = null; FileOutputStream dest = new FileOutputStream("cantidadArchivos.zip"); ZipOutputStream out = new ZipOutputStream(new BufferedOutputStream(dest)); byte data[] = new byte[buffer]; File f = new File("cantidadArchivos.txt"); FileInputStream fi = new FileInputStream(f); origin = new BufferedInputStream(fi, buffer); ZipEntry entry = new ZipEntry("cantidadArchivos.txt"); out.putNextEntry(entry); int count; while ((count = origin.read(data, 0, buffer)) != -1) out.write(data, 0, count); out.close(); } catch (Exception e) { JOptionPane.showMessageDialog(null, "Error en: " + e.toString(), "Error", JOptionPane.ERROR_MESSAGE); } }

public void unzip(String resource) { File f = new File(resource); if (!f.exists()) throw new RuntimeException("The specified resources does not exist (" + resource + ")"); String parent = f.getParent().toString(); try { BufferedOutputStream dest = null; FileInputStream fis = new FileInputStream(resource); ZipInputStream zis = new ZipInputStream(new BufferedInputStream(fis)); ZipEntry entry; while ((entry = zis.getNextEntry()) != null) { log.info("Extracting archive entry: " + entry); String entryPath = new StringBuilder(parent).append(System.getProperty("file.separator")).append(entry.getName()).toString(); if (entry.isDirectory()) { log.info("Creating directory: " + entryPath); (new File(entryPath)).mkdir(); continue; } int count; byte data[] = new byte[BUFFER]; FileOutputStream fos = new FileOutputStream(entryPath); dest = new BufferedOutputStream(fos, BUFFER); while ((count = zis.read(data, 0, BUFFER)) != -1) dest.write(data, 0, count); dest.flush(); dest.close(); } zis.close(); } catch (Exception e) { e.printStackTrace(); } }

private HttpURLConnection getHttpURLConnection(String bizDocToExecute) { StringBuffer servletURL = new StringBuffer(); servletURL.append(getBaseServletURL()); servletURL.append("?_BIZVIEW=").append(bizDocToExecute); Map<String, Object> inputParms = getInputParams(); if (inputParms != null) { Set<Entry<String, Object>> entrySet = inputParms.entrySet(); for (Entry<String, Object> entry : entrySet) { String name = entry.getKey(); String value = entry.getValue().toString(); servletURL.append("&").append(name).append("=").append(value); } } HttpURLConnection connection = null; try { URL url = new URL(servletURL.toString()); connection = (HttpURLConnection) url.openConnection(); } catch (IOException e) { Assert.fail("Failed to connect to the test servlet: " + e); } return connection; }

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!"); }

@Action(value = "ajaxFileUploads", results = { }) public void ajaxFileUploads() throws IOException { String extName = ""; String newFilename = ""; String nowTimeStr = ""; String realpath = ""; if (Validate.StrNotNull(this.getImgdirpath())) { realpath = "Uploads/" + this.getImgdirpath() + "/"; } else { realpath = this.isexistdir(); } SimpleDateFormat sDateFormat; Random r = new Random(); String savePath = ServletActionContext.getServletContext().getRealPath(""); savePath = savePath + realpath; HttpServletResponse response = ServletActionContext.getResponse(); int rannum = (int) (r.nextDouble() * (99999 - 1000 + 1)) + 10000; sDateFormat = new SimpleDateFormat("yyyyMMddHHmmss"); nowTimeStr = sDateFormat.format(new Date()); String filename = request.getHeader("X-File-Name"); if (filename.lastIndexOf(".") >= 0) { extName = filename.substring(filename.lastIndexOf(".")); } newFilename = nowTimeStr + rannum + extName; PrintWriter writer = null; InputStream is = null; FileOutputStream fos = null; try { writer = response.getWriter(); } catch (IOException ex) { log.debug(ImgTAction.class.getName() + "has thrown an exception:" + ex.getMessage()); } try { is = request.getInputStream(); fos = new FileOutputStream(new File(savePath + newFilename)); IOUtils.copy(is, fos); response.setStatus(response.SC_OK); writer.print("{success:'" + realpath + newFilename + "'}"); } catch (FileNotFoundException ex) { response.setStatus(response.SC_INTERNAL_SERVER_ERROR); writer.print("{success: false}"); log.debug(ImgTAction.class.getName() + "has thrown an exception: " + ex.getMessage()); } catch (IOException ex) { response.setStatus(response.SC_INTERNAL_SERVER_ERROR); writer.print("{success: false}"); log.debug(ImgTAction.class.getName() + "has thrown an exception: " + ex.getMessage()); } finally { try { this.setImgdirpath(null); fos.close(); is.close(); } catch (IOException ignored) { } } writer.flush(); writer.close(); }

public static void reconstruct(final List files, final Map properties, final OutputStream fout, final String base_url, final String producer, final PageSize[] size, final List hf) throws CConvertException { OutputStream out = fout; OutputStream out2 = fout; boolean signed = false; OutputStream oldOut = null; File tmp = null; File tmp2 = null; try { tmp = File.createTempFile("yahp", "pdf"); tmp2 = File.createTempFile("yahp", "pdf"); oldOut = out; if ("true".equals(properties.get(IHtmlToPdfTransformer.USE_PDF_SIGNING))) { signed = true; out2 = new FileOutputStream(tmp2); } else { out2 = oldOut; } out = new FileOutputStream(tmp); com.lowagie.text.Document document = null; PdfCopy writer = null; boolean first = true; Map mapSizeDoc = new HashMap(); int totalPage = 0; for (int i = 0; i < files.size(); i++) { final File fPDF = (File) files.get(i); final PdfReader reader = new PdfReader(fPDF.getAbsolutePath()); reader.consolidateNamedDestinations(); final int n = reader.getNumberOfPages(); if (first) { first = false; document = new com.lowagie.text.Document(reader.getPageSizeWithRotation(1)); writer = new PdfCopy(document, out); writer.setPdfVersion(PdfWriter.VERSION_1_3); writer.setFullCompression(); if ("true".equals(properties.get(IHtmlToPdfTransformer.USE_PDF_ENCRYPTION))) { final String password = (String) properties.get(IHtmlToPdfTransformer.PDF_ENCRYPTION_PASSWORD); final int securityType = CDocumentReconstructor.getSecurityFlags(properties); writer.setEncryption(PdfWriter.STRENGTH128BITS, password, null, securityType); } final String title = (String) properties.get(IHtmlToPdfTransformer.PDF_TITLE); if (title != null) { document.addTitle(title); } else if (base_url != null) { document.addTitle(base_url); } final String creator = (String) properties.get(IHtmlToPdfTransformer.PDF_CREATOR); if (creator != null) { document.addCreator(creator); } else { document.addCreator(IHtmlToPdfTransformer.VERSION); } final String author = (String) properties.get(IHtmlToPdfTransformer.PDF_AUTHOR); if (author != null) { document.addAuthor(author); } final String sproducer = (String) properties.get(IHtmlToPdfTransformer.PDF_PRODUCER); if (sproducer != null) { document.addProducer(sproducer); } else { document.addProducer(IHtmlToPdfTransformer.VERSION + " - http://www.allcolor.org/YaHPConverter/ - " + producer); } document.open(); } PdfImportedPage page; for (int j = 0; j < n; ) { ++j; totalPage++; mapSizeDoc.put("" + totalPage, "" + i); page = writer.getImportedPage(reader, j); writer.addPage(page); } } document.close(); out.flush(); out.close(); { final PdfReader reader = new PdfReader(tmp.getAbsolutePath()); ; final int n = reader.getNumberOfPages(); final PdfStamper stp = new PdfStamper(reader, out2); int i = 0; BaseFont.createFont(BaseFont.HELVETICA, BaseFont.WINANSI, BaseFont.EMBEDDED); final CHtmlToPdfFlyingSaucerTransformer trans = new CHtmlToPdfFlyingSaucerTransformer(); while (i < n) { i++; int indexSize = Integer.parseInt((String) mapSizeDoc.get("" + i)); final int[] dsize = size[indexSize].getSize(); final int[] dmargin = size[indexSize].getMargin(); for (final Iterator it = hf.iterator(); it.hasNext(); ) { final CHeaderFooter chf = (CHeaderFooter) it.next(); if (chf.getSfor().equals(CHeaderFooter.ODD_PAGES) && (i % 2 == 0)) { continue; } else if (chf.getSfor().equals(CHeaderFooter.EVEN_PAGES) && (i % 2 != 0)) { continue; } final String text = chf.getContent().replaceAll("<pagenumber>", "" + i).replaceAll("<pagecount>", "" + n); final PdfContentByte over = stp.getOverContent(i); final ByteArrayOutputStream bbout = new ByteArrayOutputStream(); if (chf.getType().equals(CHeaderFooter.HEADER)) { trans.transform(new ByteArrayInputStream(text.getBytes("utf-8")), base_url, new PageSize(dsize[0] - (dmargin[0] + dmargin[1]), dmargin[3]), new ArrayList(), properties, bbout); } else if (chf.getType().equals(CHeaderFooter.FOOTER)) { trans.transform(new ByteArrayInputStream(text.getBytes("utf-8")), base_url, new PageSize(dsize[0] - (dmargin[0] + dmargin[1]), dmargin[2]), new ArrayList(), properties, bbout); } final PdfReader readerHF = new PdfReader(bbout.toByteArray()); if (chf.getType().equals(CHeaderFooter.HEADER)) { over.addTemplate(stp.getImportedPage(readerHF, 1), dmargin[0], dsize[1] - dmargin[3]); } else if (chf.getType().equals(CHeaderFooter.FOOTER)) { over.addTemplate(stp.getImportedPage(readerHF, 1), dmargin[0], 0); } readerHF.close(); } } stp.close(); } try { out2.flush(); } catch (Exception ignore) { } finally { try { out2.close(); } catch (Exception ignore) { } } if (signed) { final String keypassword = (String) properties.get(IHtmlToPdfTransformer.PDF_SIGNING_PRIVATE_KEY_PASSWORD); final String password = (String) properties.get(IHtmlToPdfTransformer.PDF_ENCRYPTION_PASSWORD); final String keyStorepassword = (String) properties.get(IHtmlToPdfTransformer.PDF_SIGNING_KEYSTORE_PASSWORD); final String privateKeyFile = (String) properties.get(IHtmlToPdfTransformer.PDF_SIGNING_PRIVATE_KEY_FILE); final String reason = (String) properties.get(IHtmlToPdfTransformer.PDF_SIGNING_REASON); final String location = (String) properties.get(IHtmlToPdfTransformer.PDF_SIGNING_LOCATION); final boolean selfSigned = !"false".equals(properties.get(IHtmlToPdfTransformer.USE_PDF_SELF_SIGNING)); PdfReader reader = null; if (password != null) { reader = new PdfReader(tmp2.getAbsolutePath(), password.getBytes()); } else { reader = new PdfReader(tmp2.getAbsolutePath()); } final KeyStore ks = selfSigned ? KeyStore.getInstance(KeyStore.getDefaultType()) : KeyStore.getInstance("pkcs12"); ks.load(new FileInputStream(privateKeyFile), keyStorepassword.toCharArray()); final String alias = (String) ks.aliases().nextElement(); final PrivateKey key = (PrivateKey) ks.getKey(alias, keypassword.toCharArray()); final Certificate chain[] = ks.getCertificateChain(alias); final PdfStamper stp = PdfStamper.createSignature(reader, oldOut, '\0'); if ("true".equals(properties.get(IHtmlToPdfTransformer.USE_PDF_ENCRYPTION))) { stp.setEncryption(PdfWriter.STRENGTH128BITS, password, null, CDocumentReconstructor.getSecurityFlags(properties)); } final PdfSignatureAppearance sap = stp.getSignatureAppearance(); if (selfSigned) { sap.setCrypto(key, chain, null, PdfSignatureAppearance.SELF_SIGNED); } else { sap.setCrypto(key, chain, null, PdfSignatureAppearance.WINCER_SIGNED); } if (reason != null) { sap.setReason(reason); } if (location != null) { sap.setLocation(location); } stp.close(); oldOut.flush(); } } catch (final Exception e) { throw new CConvertException("ERROR: An Exception occured while reconstructing the pdf document: " + e.getMessage(), e); } finally { try { tmp.delete(); } catch (final Exception ignore) { } try { tmp2.delete(); } catch (final Exception ignore) { } } }

public static void copy(File src, File dest) throws IOException { OutputStream stream = new FileOutputStream(dest); FileInputStream fis = new FileInputStream(src); byte[] buffer = new byte[16384]; while (fis.available() != 0) { int read = fis.read(buffer); stream.write(buffer, 0, read); } stream.flush(); }

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

public void run() { try { String s = (new StringBuilder()).append("fName=").append(URLEncoder.encode("???", "UTF-8")).append("&lName=").append(URLEncoder.encode("???", "UTF-8")).toString(); URL url = new URL("http://snoop.minecraft.net/"); HttpURLConnection httpurlconnection = (HttpURLConnection) url.openConnection(); httpurlconnection.setRequestMethod("POST"); httpurlconnection.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); httpurlconnection.setRequestProperty("Content-Length", (new StringBuilder()).append("").append(Integer.toString(s.getBytes().length)).toString()); httpurlconnection.setRequestProperty("Content-Language", "en-US"); httpurlconnection.setUseCaches(false); httpurlconnection.setDoInput(true); httpurlconnection.setDoOutput(true); DataOutputStream dataoutputstream = new DataOutputStream(httpurlconnection.getOutputStream()); dataoutputstream.writeBytes(s); dataoutputstream.flush(); dataoutputstream.close(); java.io.InputStream inputstream = httpurlconnection.getInputStream(); BufferedReader bufferedreader = new BufferedReader(new InputStreamReader(inputstream)); StringBuffer stringbuffer = new StringBuffer(); String s1; while ((s1 = bufferedreader.readLine()) != null) { stringbuffer.append(s1); stringbuffer.append('\r'); } bufferedreader.close(); } catch (Exception exception) { } }

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; }

@Test public void testEncryptDecrypt() throws IOException { BlockCipher cipher = new SerpentEngine(); Random rnd = new Random(); byte[] key = new byte[256 / 8]; rnd.nextBytes(key); byte[] iv = new byte[cipher.getBlockSize()]; rnd.nextBytes(iv); byte[] data = new byte[1230000]; new Random().nextBytes(data); ByteArrayOutputStream bout = new ByteArrayOutputStream(); CryptOutputStream eout = new CryptOutputStream(bout, cipher, key); eout.write(data); eout.close(); byte[] eData = bout.toByteArray(); ByteArrayInputStream bin = new ByteArrayInputStream(eData); CryptInputStream din = new CryptInputStream(bin, cipher, key); bout = new ByteArrayOutputStream(); IOUtils.copy(din, bout); eData = bout.toByteArray(); Assert.assertTrue(Arrays.areEqual(data, eData)); }

public static boolean downloadFile(String url, String destination) { BufferedInputStream bi = null; BufferedOutputStream bo = null; File destfile; try { java.net.URL fileurl; try { fileurl = new java.net.URL(url); } catch (MalformedURLException e) { return false; } bi = new BufferedInputStream(fileurl.openStream()); destfile = new File(destination); if (!destfile.createNewFile()) { destfile.delete(); destfile.createNewFile(); } bo = new BufferedOutputStream(new FileOutputStream(destfile)); int readedbyte; while ((readedbyte = bi.read()) != -1) { bo.write(readedbyte); } bo.flush(); } catch (IOException ex) { return false; } finally { try { bi.close(); bo.close(); } catch (Exception ex) { } } 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(); } }

public static InputSource getInputSource(URL url) throws IOException { String proto = url.getProtocol().toLowerCase(); if (!("http".equals(proto) || "https".equals(proto))) throw new IllegalArgumentException("OAI-PMH only allows HTTP(S) as network protocol!"); HttpURLConnection conn = (HttpURLConnection) url.openConnection(); StringBuilder ua = new StringBuilder("Java/"); ua.append(System.getProperty("java.version")); ua.append(" ("); ua.append(OAIHarvester.class.getName()); ua.append(')'); conn.setRequestProperty("User-Agent", ua.toString()); conn.setRequestProperty("Accept-Encoding", "gzip, deflate, identity;q=0.3, *;q=0"); conn.setRequestProperty("Accept-Charset", "utf-8, *;q=0.1"); conn.setRequestProperty("Accept", "text/xml, application/xml, *;q=0.1"); conn.setUseCaches(false); conn.setFollowRedirects(true); log.debug("Opening connection..."); InputStream in = null; try { conn.connect(); in = conn.getInputStream(); } catch (IOException ioe) { int after, code; try { after = conn.getHeaderFieldInt("Retry-After", -1); code = conn.getResponseCode(); } catch (IOException ioe2) { after = -1; code = -1; } if (code == HttpURLConnection.HTTP_UNAVAILABLE && after > 0) throw new RetryAfterIOException(after, ioe); throw ioe; } String encoding = conn.getContentEncoding(); if (encoding == null) encoding = "identity"; encoding = encoding.toLowerCase(); log.debug("HTTP server uses " + encoding + " content encoding."); if ("gzip".equals(encoding)) in = new GZIPInputStream(in); else if ("deflate".equals(encoding)) in = new InflaterInputStream(in); else if (!"identity".equals(encoding)) throw new IOException("Server uses an invalid content encoding: " + encoding); String contentType = conn.getContentType(); String charset = null; if (contentType != null) { contentType = contentType.toLowerCase(); int charsetStart = contentType.indexOf("charset="); if (charsetStart >= 0) { int charsetEnd = contentType.indexOf(";", charsetStart); if (charsetEnd == -1) charsetEnd = contentType.length(); charsetStart += "charset=".length(); charset = contentType.substring(charsetStart, charsetEnd).trim(); } } log.debug("Charset from Content-Type: '" + charset + "'"); InputSource src = new InputSource(in); src.setSystemId(url.toString()); src.setEncoding(charset); return src; }

public boolean refreshRequired() { boolean status = false; Set<String> urls = lastModifiedDates.keySet(); try { for (String urlPath : urls) { Long lastModifiedDate = lastModifiedDates.get(urlPath); URL url = new URL(urlPath); URLConnection connection = url.openConnection(); connection.connect(); long newModDate = connection.getLastModified(); if (newModDate != lastModifiedDate) { status = true; break; } } } catch (Exception e) { LOG.warn("Exception while monitoring update times.", e); return true; } return status; }

private String getData(String requestUrl) throws AuthenticationException, IOException { URL url = new URL(requestUrl); HttpURLConnection conn = (HttpURLConnection) url.openConnection(); String header; try { header = oauthAuthenticator.getHttpAuthorizationHeader(url.toString(), "GET", profile.getOAuthToken(), profile.getOAuthTokenSecret()); } catch (OAuthException e) { throw new AuthenticationException(e); } conn.setRequestProperty("Authorization", header); if (conn.getResponseCode() == HttpURLConnection.HTTP_UNAUTHORIZED) { throw new AuthenticationException(); } InputStreamReader reader = new InputStreamReader(conn.getInputStream()); char[] buffer = new char[1024]; int bytesRead = 0; StringBuilder data = new StringBuilder(); while ((bytesRead = reader.read(buffer)) != -1) { data.append(buffer, 0, bytesRead); } reader.close(); if (conn.getResponseCode() != HttpURLConnection.HTTP_OK) { throw new IOException(conn.getResponseCode() + " " + conn.getResponseMessage() + "\n" + data); } return data.toString(); }

@Override public void onCreate(Bundle savedInstanceState) { super.onCreate(savedInstanceState); setContentView(R.layout.main); final EditText eText = (EditText) findViewById(R.id.address); final Button button = (Button) findViewById(R.id.ButtonGo); button.setOnClickListener(new Button.OnClickListener() { public void onClick(View v) { try { HttpClient httpclient = new DefaultHttpClient(); HttpPost httppost = new HttpPost("https://mt0-app.cloud.cm/rpc/json"); List<NameValuePair> nameValuePairs = new ArrayList<NameValuePair>(2); nameValuePairs.add(new BasicNameValuePair("m", "login")); nameValuePairs.add(new BasicNameValuePair("c", "User")); nameValuePairs.add(new BasicNameValuePair("password", "cloudisgreat")); nameValuePairs.add(new BasicNameValuePair("alias", "cs588")); httppost.setEntity(new UrlEncodedFormEntity(nameValuePairs)); String result = ""; try { HttpResponse response = httpclient.execute(httppost); result = EntityUtils.toString(response.getEntity()); } catch (Exception e) { result = e.getMessage(); } LayoutInflater inflater = (LayoutInflater) WebTest.this.getSystemService(Context.LAYOUT_INFLATER_SERVICE); final View layout = inflater.inflate(R.layout.window1, null); final PopupWindow popup = new PopupWindowTest(layout, 100, 100); Button b = (Button) layout.findViewById(R.id.test_button); b.setOnTouchListener(new OnTouchListener() { @Override public boolean onTouch(View v, MotionEvent event) { Log.d("Debug", "Button activate"); popup.dismiss(); return false; } }); popup.showAtLocation(layout, Gravity.CENTER, 0, 0); View layout2 = inflater.inflate(R.layout.window1, null); final PopupWindow popup2 = new PopupWindowTest(layout2, 100, 100); TextView tview = (TextView) layout2.findViewById(R.id.pagetext); tview.setText(result); popup2.showAtLocation(layout, Gravity.CENTER, 50, -90); } catch (Exception e) { Log.d("Debug", e.toString()); } } }); }

public static void copyFile(String fromFilePath, String toFilePath, boolean overwrite) throws IOException { File fromFile = new File(fromFilePath); File toFile = new File(toFilePath); if (!fromFile.exists()) throw new IOException("FileCopy: " + "no such source file: " + fromFilePath); if (!fromFile.isFile()) throw new IOException("FileCopy: " + "can't copy directory: " + fromFilePath); if (!fromFile.canRead()) throw new IOException("FileCopy: " + "source file is unreadable: " + fromFilePath); if (toFile.isDirectory()) toFile = new File(toFile, fromFile.getName()); if (toFile.exists()) { if (!overwrite) { throw new IOException(toFilePath + " already exists!"); } if (!toFile.canWrite()) { throw new IOException("FileCopy: destination file is unwriteable: " + toFilePath); } String parent = toFile.getParent(); if (parent == null) { parent = System.getProperty("user.dir"); } File dir = new File(parent); if (!dir.exists()) { throw new IOException("FileCopy: destination directory doesn't exist: " + parent); } if (dir.isFile()) { throw new IOException("FileCopy: destination is not a directory: " + parent); } if (!dir.canWrite()) { throw new IOException("FileCopy: destination directory is unwriteable: " + parent); } } FileInputStream from = null; FileOutputStream to = null; try { from = new FileInputStream(fromFile); to = new FileOutputStream(toFile); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = from.read(buffer)) != -1) to.write(buffer, 0, bytesRead); } finally { long lastModified = fromFile.lastModified(); toFile.setLastModified(lastModified); if (from != null) { try { from.close(); } catch (IOException e) { } } if (to != null) { try { to.close(); } catch (IOException e) { } } } }

public static void kopirujSoubor(File vstup, File vystup) throws IOException { FileChannel sourceChannel = new FileInputStream(vstup).getChannel(); FileChannel destinationChannel = new FileOutputStream(vystup).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), destinationChannel); sourceChannel.close(); destinationChannel.close(); }

private final String createMD5(String pwd) throws Exception { MessageDigest md = (MessageDigest) MessageDigest.getInstance("MD5").clone(); md.update(pwd.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); } return app.toString(); }

@Override protected URLConnection openConnection(URL url) throws IOException { try { final HttpServlet servlet; String path = url.getPath(); if (path.matches("reg:.+")) { String registerName = path.replaceAll("reg:([^/]*)/.*", "$1"); servlet = register.get(registerName); if (servlet == null) throw new RuntimeException("No servlet registered with name " + registerName); } else { String servletClassName = path.replaceAll("([^/]*)/.*", "$1"); servlet = (HttpServlet) Class.forName(servletClassName).newInstance(); } final MockHttpServletRequest req = new MockHttpServletRequest().setMethod("GET"); final MockHttpServletResponse resp = new MockHttpServletResponse(); return new HttpURLConnection(url) { @Override public int getResponseCode() throws IOException { serviceIfNeeded(); return resp.status; } @Override public InputStream getInputStream() throws IOException { serviceIfNeeded(); if (resp.status == 500) throw new IOException("Server responded with error 500"); byte[] array = resp.out.toByteArray(); return new ByteArrayInputStream(array); } @Override public InputStream getErrorStream() { try { serviceIfNeeded(); } catch (IOException e) { throw new RuntimeException(e); } if (resp.status != 500) return null; return new ByteArrayInputStream(resp.out.toByteArray()); } @Override public OutputStream getOutputStream() throws IOException { return req.tmp; } @Override public void addRequestProperty(String key, String value) { req.addHeader(key, value); } @Override public void connect() throws IOException { } @Override public boolean usingProxy() { return false; } @Override public void disconnect() { } private boolean called; private void serviceIfNeeded() throws IOException { try { if (!called) { called = true; req.setMethod(getRequestMethod()); servlet.service(req, resp); } } catch (ServletException e) { throw new RuntimeException(e); } } }; } catch (InstantiationException e) { throw new RuntimeException(e); } catch (IllegalAccessException e) { throw new RuntimeException(e); } catch (ClassNotFoundException e) { throw new RuntimeException(e); } }

public static String getMD5(String s) throws Exception { MessageDigest complete = MessageDigest.getInstance("MD5"); complete.update(s.getBytes()); byte[] b = complete.digest(); String result = ""; for (int i = 0; i < b.length; i++) { result += Integer.toString((b[i] & 0xff) + 0x100, 16).substring(1); } return result; }

private void initBanner() { for (int k = 0; k < 3; k++) { if (bannerImg == null) { int i = getRandomId(); imageURL = NbBundle.getMessage(BottomContent.class, "URL_BannerImageLink", Integer.toString(i)); bannerURL = NbBundle.getMessage(BottomContent.class, "URL_BannerLink", Integer.toString(i)); HttpContext context = new BasicHttpContext(); context.setAttribute(ClientContext.COOKIE_STORE, cookieStore); HttpGet method = new HttpGet(imageURL); try { HttpResponse response = ProxyManager.httpClient.execute(method, context); HttpEntity entity = response.getEntity(); if (entity != null) { bannerImg = new ImageIcon(ImageIO.read(entity.getContent())); EntityUtils.consume(entity); } } catch (IOException ex) { bannerImg = null; } finally { method.abort(); } } else { break; } } if (bannerImg == null) { NotifyUtil.error("Banner Error", "Application could not get banner image. Please check your internet connection.", false); } }

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 { } }

private byte[] getBytes(String resource) throws IOException { InputStream is = HttpServletFileDownloadTest.class.getResourceAsStream(resource); ByteArrayOutputStream out = new ByteArrayOutputStream(); IOUtils.copy(is, out); IOUtils.closeQuietly(is); return out.toByteArray(); }

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; }

public String md5sum(String toCompute) throws Exception { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(toCompute.getBytes()); java.math.BigInteger hash = new java.math.BigInteger(1, md.digest()); return hash.toString(16); }

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 Status checkUpdate() { Status updateStatus = Status.FAILURE; URL url; InputStream is; InputStreamReader isr; BufferedReader r; String line; try { url = new URL(updateURL); is = url.openStream(); isr = new InputStreamReader(is); r = new BufferedReader(isr); String variable, value; while ((line = r.readLine()) != null) { if (!line.equals("") && line.charAt(0) != '/') { variable = line.substring(0, line.indexOf('=')); value = line.substring(line.indexOf('=') + 1); if (variable.equals("Latest Version")) { variable = value; value = variable.substring(0, variable.indexOf(" ")); variable = variable.substring(variable.indexOf(" ") + 1); latestGameVersion = value; latestModifier = variable; if (Float.parseFloat(value) > Float.parseFloat(gameVersion)) updateStatus = Status.NOT_CURRENT; else updateStatus = Status.CURRENT; } else if (variable.equals("Download URL")) downloadURL = value; } } return updateStatus; } catch (MalformedURLException e) { return Status.URL_NOT_FOUND; } catch (IOException e) { return Status.FAILURE; } }

protected String loadPage(String url_string) { try { URL url = new URL(url_string); HttpURLConnection connection = null; InputStream is = null; try { connection = (HttpURLConnection) url.openConnection(); int response = connection.getResponseCode(); if (response == HttpURLConnection.HTTP_ACCEPTED || response == HttpURLConnection.HTTP_OK) { is = connection.getInputStream(); String page = ""; while (page.length() < MAX_PAGE_SIZE) { byte[] buffer = new byte[2048]; int len = is.read(buffer); if (len < 0) { break; } page += new String(buffer, 0, len); } return (page); } else { informFailure("httpinvalidresponse", "" + response); return (null); } } finally { try { if (is != null) { is.close(); } if (connection != null) { connection.disconnect(); } } catch (Throwable e) { Debug.printStackTrace(e); } } } catch (Throwable e) { informFailure("httploadfail", e.toString()); return (null); } }

public static void copy(String fromFileName, String toFileName) throws IOException { File fromFile = new File(fromFileName); File toFile = new File(toFileName); if (!fromFile.exists()) throw new IOException("FileCopy: " + "no such source file: " + fromFileName); if (!fromFile.isFile()) throw new IOException("FileCopy: " + "can't copy directory: " + fromFileName); if (!fromFile.canRead()) throw new IOException("FileCopy: " + "source file is unreadable: " + fromFileName); if (toFile.isDirectory()) toFile = new File(toFile, fromFile.getName()); if (toFile.exists()) { if (!toFile.canWrite()) throw new IOException("FileCopy: " + "destination file is unwriteable: " + toFileName); } else { String parent = toFile.getParent(); if (parent == null) parent = System.getProperty("user.dir"); File dir = new File(parent); if (!dir.exists()) dir.mkdir(); if (dir.isFile()) throw new IOException("FileCopy: " + "destination is not a directory: " + parent); if (!dir.canWrite()) throw new IOException("FileCopy: " + "destination directory is unwriteable: " + parent); } FileInputStream from = null; FileOutputStream to = null; try { from = new FileInputStream(fromFile); to = new FileOutputStream(toFile); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = from.read(buffer)) != -1) to.write(buffer, 0, bytesRead); } finally { if (from != null) try { from.close(); } catch (IOException e) { ; } if (to != null) try { to.close(); } catch (IOException e) { ; } } }

private static boolean copyFile(File src, File dest) { FileInputStream fis = null; FileOutputStream fos = null; try { fis = new FileInputStream(src); fos = new FileOutputStream(dest); for (int c = fis.read(); c != -1; c = fis.read()) fos.write(c); return true; } catch (FileNotFoundException e) { e.printStackTrace(); return false; } catch (IOException e) { e.printStackTrace(); return false; } finally { if (fis != null) try { fis.close(); } catch (IOException e) { e.printStackTrace(); } if (fos != null) try { fos.close(); } catch (IOException e) { e.printStackTrace(); } } }

private void copyReportFile(ServletRequest req, String reportName, Report report) throws IllegalAccessException, InvocationTargetException, NoSuchMethodException, ClassNotFoundException, FileNotFoundException, IOException { String reportFileName = (String) Class.forName("org.eclipse.birt.report.utility.ParameterAccessor").getMethod("getReport", new Class[] { HttpServletRequest.class, String.class }).invoke(null, new Object[] { req, reportName }); ByteArrayInputStream bais = new ByteArrayInputStream(report.getReportContent()); FileOutputStream fos = new FileOutputStream(new File(reportFileName)); IOUtils.copy(bais, fos); bais.close(); fos.close(); }

public static boolean copyFile(File source, File dest) { FileChannel srcChannel = null; FileChannel dstChannel = null; try { srcChannel = new FileInputStream(source).getChannel(); dstChannel = new FileOutputStream(dest).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); } catch (IOException e) { return false; } finally { try { if (srcChannel != null) { srcChannel.close(); } } catch (IOException e) { } try { if (dstChannel != null) { dstChannel.close(); } } catch (IOException e) { } } return true; }

public void unpack(File destDirectory, boolean delete) { if (delete) delete(destDirectory); if (destDirectory.exists()) throw new ContentPackageException("Destination directory already exists."); this.destDirectory = destDirectory; this.manifestFile = new File(destDirectory, MANIFEST_FILE_NAME); try { if (zipInputStream == null) zipInputStream = new ZipInputStream(new FileInputStream(zipFile)); ZipEntry zipEntry; while ((zipEntry = zipInputStream.getNextEntry()) != null) { File destFile = new File(destDirectory, zipEntry.getName()); destFile.getParentFile().mkdirs(); if (!zipEntry.isDirectory()) { BufferedOutputStream output = new BufferedOutputStream(new FileOutputStream(destFile), BUFFER_SIZE); byte[] buffer = new byte[BUFFER_SIZE]; int length; while ((length = zipInputStream.read(buffer, 0, BUFFER_SIZE)) != -1) output.write(buffer, 0, length); output.close(); zipInputStream.closeEntry(); } } zipInputStream.close(); } catch (IOException ex) { throw new ContentPackageException(ex); } }

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

@Override public ResourceBundle newBundle(String baseName, Locale locale, String format, ClassLoader loader, boolean reload) throws IllegalAccessException, InstantiationException, IOException { if ((baseName == null) || (locale == null) || (format == null) || (loader == null)) { throw new NullPointerException(); } ResourceBundle bundle = null; if (format.equals(XML)) { String bundleName = toBundleName(baseName, locale); String resourceName = toResourceName(bundleName, format); URL url = loader.getResource(resourceName); if (url != null) { URLConnection connection = url.openConnection(); if (connection != null) { if (reload) { connection.setUseCaches(false); } InputStream stream = connection.getInputStream(); if (stream != null) { BufferedInputStream bis = new BufferedInputStream(stream); bundle = new XMLResourceBundle(bis); bis.close(); } } } } return bundle; }

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(); } }

@Override protected void write(InputStream in, OutputStream out, javax.sound.sampled.AudioFormat javaSoundFormat) throws IOException { if (USE_JAVASOUND) { super.write(in, out, javaSoundFormat); } else { try { byte[] header = JavaSoundCodec.createWavHeader(javaSoundFormat); if (header == null) throw new IOException("Unable to create wav header"); out.write(header); IOUtils.copyStream(in, out); } catch (InterruptedIOException e) { logger.log(Level.FINE, "" + e, e); throw e; } catch (IOException e) { logger.log(Level.WARNING, "" + e, e); throw e; } } }

public static void shakeSort(int[] a) { if (a == null) { throw new IllegalArgumentException("Null-pointed array"); } int k = 0; int left = 0; int right = a.length - 1; while (right - left > 0) { k = 0; for (int i = 0; i <= right - 1; i++) { if (a[i] > a[i + 1]) { k = i; int temp = a[i]; a[i] = a[i + 1]; a[i + 1] = temp; } } right = k; k = a.length - 1; for (int i = left; i <= right - 1; i++) { if (a[i] > a[i + 1]) { k = i; int temp = a[i]; a[i] = a[i + 1]; a[i + 1] = temp; } } left = k; } }

public static boolean copyFile(File src, File des) { try { BufferedInputStream in = new BufferedInputStream(new FileInputStream(src)); BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(des)); int b; while ((b = in.read()) != -1) out.write(b); out.flush(); out.close(); in.close(); return true; } catch (IOException ie) { m_logCat.error("Copy file + " + src + " to " + des + " failed!", ie); return false; } }

public static void copyFile(String source, String dest) throws IOException { FileChannel in = null, out = null; try { in = new FileInputStream(new File(source)).getChannel(); out = new FileOutputStream(new File(dest)).getChannel(); in.transferTo(0, in.size(), out); } finally { if (in != null) in.close(); if (out != null) out.close(); } }

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

public void setDefaultMailBox(final int domainId, final int userId) { final EmailAddress defaultMailbox = cmDB.getDefaultMailbox(domainId); try { connection.setAutoCommit(false); new ProcessEnvelope().executeNull(new ExecuteProcessAbstractImpl(connection, false, false, true, true) { @Override public void executeProcessReturnNull() throws SQLException { psImpl = connImpl.prepareStatement(sqlCommands.getProperty(defaultMailbox == null ? "domain.setDefaultMailbox" : "domain.updateDefaultMailbox")); if (defaultMailbox == null) { psImpl.setInt(1, domainId); psImpl.setInt(2, userId); } else { psImpl.setInt(1, userId); psImpl.setInt(2, domainId); } psImpl.executeUpdate(); } }); connection.commit(); cmDB.updateDomains(null, null); } catch (SQLException sqle) { log.error(sqle); if (connection != null) { try { connection.rollback(); } catch (SQLException ex) { } } } finally { if (connection != null) { try { connection.setAutoCommit(true); } catch (SQLException ex) { } } } }

public static int proxy(java.net.URI uri, HttpServletRequest req, HttpServletResponse res) throws IOException { final HostConfiguration hostConfig = new HostConfiguration(); hostConfig.setHost(uri.getHost()); HttpMethodBase httpMethod = null; if (HttpRpcServer.METHOD_GET.equalsIgnoreCase(req.getMethod())) { httpMethod = new GetMethod(uri.toString()); httpMethod.setFollowRedirects(true); } else if (HttpRpcServer.METHOD_POST.equalsIgnoreCase(req.getMethod())) { httpMethod = new PostMethod(uri.toString()); final Enumeration parameterNames = req.getParameterNames(); if (parameterNames != null) while (parameterNames.hasMoreElements()) { final String parameterName = (String) parameterNames.nextElement(); for (String parameterValue : req.getParameterValues(parameterName)) ((PostMethod) httpMethod).addParameter(parameterName, parameterValue); } ((PostMethod) httpMethod).setRequestEntity(new InputStreamRequestEntity(req.getInputStream())); } if (httpMethod == null) throw new IllegalArgumentException("Unsupported http request method"); final int responseCode; final Enumeration headers = req.getHeaderNames(); if (headers != null) while (headers.hasMoreElements()) { final String headerName = (String) headers.nextElement(); final Enumeration headerValues = req.getHeaders(headerName); while (headerValues.hasMoreElements()) { httpMethod.setRequestHeader(headerName, (String) headerValues.nextElement()); } } final HttpState httpState = new HttpState(); if (req.getCookies() != null) for (Cookie cookie : req.getCookies()) { String host = req.getHeader("Host"); if (StringUtils.isEmpty(cookie.getDomain())) cookie.setDomain(StringUtils.isEmpty(host) ? req.getServerName() + ":" + req.getServerPort() : host); if (StringUtils.isEmpty(cookie.getPath())) cookie.setPath("/"); httpState.addCookie(new org.apache.commons.httpclient.Cookie(cookie.getDomain(), cookie.getName(), cookie.getValue(), cookie.getPath(), cookie.getMaxAge(), cookie.getSecure())); } httpMethod.setQueryString(req.getQueryString()); responseCode = (new HttpClient()).executeMethod(hostConfig, httpMethod, httpState); if (responseCode < 0) { httpMethod.releaseConnection(); return responseCode; } if (httpMethod.getResponseHeaders() != null) for (Header header : httpMethod.getResponseHeaders()) res.setHeader(header.getName(), header.getValue()); final InputStream in = httpMethod.getResponseBodyAsStream(); final OutputStream out = res.getOutputStream(); IOUtils.copy(in, out); out.flush(); out.close(); in.close(); httpMethod.releaseConnection(); return responseCode; }

private void publishPage(URL url, String path, File outputFile) throws IOException { if (debug) { System.out.println(" publishing page: " + path); System.out.println(" url == " + url); System.out.println(" file == " + outputFile); } StringBuffer sb = new StringBuffer(); try { InputStream is = url.openStream(); InputStreamReader isr = new InputStreamReader(is); BufferedReader br = new BufferedReader(isr); boolean firstLine = true; String line; do { line = br.readLine(); if (line != null) { if (!firstLine) sb.append("\n"); else firstLine = false; sb.append(line); } } while (line != null); br.close(); } catch (IOException e) { String mess = outputFile.toString() + ": " + e.getMessage(); errors.add(mess); } FileOutputStream fos = new FileOutputStream(outputFile); OutputStreamWriter sw = new OutputStreamWriter(fos); sw.write(sb.toString()); sw.close(); if (prepareArchive) archiveFiles.add(new ArchiveFile(path, outputFile)); }

public void performUpdates(List<PackageDescriptor> downloadList, ProgressListener progressListener) throws IOException, UpdateServiceException_Exception { int i = 0; try { for (PackageDescriptor desc : downloadList) { String urlString = service.getDownloadURL(desc.getPackageId(), desc.getVersion(), desc.getPlatformName()); int minProgress = 20 + 80 * i / downloadList.size(); int maxProgress = 20 + 80 * (i + 1) / downloadList.size(); boolean incremental = UpdateManager.isIncrementalUpdate(); if (desc.getPackageTypeName().equals("RAPIDMINER_PLUGIN")) { ManagedExtension extension = ManagedExtension.getOrCreate(desc.getPackageId(), desc.getName(), desc.getLicenseName()); String baseVersion = extension.getLatestInstalledVersionBefore(desc.getVersion()); incremental &= baseVersion != null; URL url = UpdateManager.getUpdateServerURI(urlString + (incremental ? "?baseVersion=" + URLEncoder.encode(baseVersion, "UTF-8") : "")).toURL(); if (incremental) { LogService.getRoot().info("Updating " + desc.getPackageId() + " incrementally."); try { updatePluginIncrementally(extension, openStream(url, progressListener, minProgress, maxProgress), baseVersion, desc.getVersion()); } catch (IOException e) { LogService.getRoot().warning("Incremental Update failed. Trying to fall back on non incremental Update..."); incremental = false; } } if (!incremental) { LogService.getRoot().info("Updating " + desc.getPackageId() + "."); updatePlugin(extension, openStream(url, progressListener, minProgress, maxProgress), desc.getVersion()); } extension.addAndSelectVersion(desc.getVersion()); } else { URL url = UpdateManager.getUpdateServerURI(urlString + (incremental ? "?baseVersion=" + URLEncoder.encode(RapidMiner.getLongVersion(), "UTF-8") : "")).toURL(); LogService.getRoot().info("Updating RapidMiner core."); updateRapidMiner(openStream(url, progressListener, minProgress, maxProgress), desc.getVersion()); } i++; progressListener.setCompleted(20 + 80 * i / downloadList.size()); } } catch (URISyntaxException e) { throw new IOException(e); } finally { progressListener.complete(); } }

private static void copyFile(File sourceFile, File destFile) { try { 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(); } } } catch (Exception e) { throw new RuntimeException(e); } }

public static void copyFile(File in, File out, boolean read, boolean write, boolean execute) throws FileNotFoundException, IOException { FileChannel inChannel = new FileInputStream(in).getChannel(); File outFile = null; if (out.isDirectory()) { outFile = new File(out.getAbsolutePath() + File.separator + in.getName()); } else { outFile = out; } FileChannel outChannel = new FileOutputStream(outFile).getChannel(); try { int maxCount = (64 * 1024 * 1024) - (32 * 1024); long size = inChannel.size(); long position = 0; while (position < size) { position += inChannel.transferTo(position, maxCount, outChannel); } outFile.setReadable(read); outFile.setWritable(write); outFile.setExecutable(execute); } catch (IOException e) { throw e; } finally { if (inChannel != null) inChannel.close(); if (outChannel != null) outChannel.close(); } }

protected String connectPost(String urlString, String parameter) { String response = null; try { URL url = new URL(urlString); HttpsURLConnection connection = (HttpsURLConnection) url.openConnection(); connection.setDoOutput(true); connection.setUseCaches(false); connection.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); log.fine(connection.getURL().toString()); DataOutputStream out = new DataOutputStream(connection.getOutputStream()); out.write(parameter.getBytes()); out.flush(); out.close(); BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream())); response = in.readLine(); in.close(); log.finest(response); } catch (Exception e) { log.log(Level.SEVERE, urlString, e); } return response; }

@Override public void doExecute(String[] args) { if (args.length != 2) { printUsage(); } else { int fileNo = 0; try { fileNo = Integer.parseInt(args[1]) - 1; } catch (NumberFormatException e) { printUsage(); return; } if (fileNo < 0) { printUsage(); return; } StorageFile[] files = (StorageFile[]) ctx.getRemoteDir().listFiles(); try { StorageFile file = files[fileNo]; File outFile = getOutFile(file); FileOutputStream out = new FileOutputStream(outFile); InputStream in = file.openStream(); IOUtils.copy(in, out); IOUtils.closeQuietly(out); afterSave(outFile); if (outFile.exists()) { print("File written to: " + outFile.getAbsolutePath()); } } catch (IOException e) { printError("Failed to load file. " + e.getMessage()); } catch (Exception e) { printUsage(); return; } } }

public static String encryptPassword(String password) throws NoSuchAlgorithmException, UnsupportedEncodingException { final MessageDigest digester = MessageDigest.getInstance("sha-256"); digester.reset(); digester.update("Carmen Sandiago".getBytes()); return asHex(digester.digest(password.getBytes("UTF-8"))); }

public static String encryptPassword(String password) { try { MessageDigest md = MessageDigest.getInstance("SHA"); md.update(password.getBytes()); byte[] hash = md.digest(); int hashLength = hash.length; StringBuffer hashStringBuf = new StringBuffer(); String byteString; int byteLength; for (int index = 0; index < hashLength; index++) { byteString = String.valueOf(hash[index] + 128); byteLength = byteString.length(); switch(byteLength) { case 1: byteString = "00" + byteString; break; case 2: byteString = "0" + byteString; break; } hashStringBuf.append(byteString); } return hashStringBuf.toString(); } catch (NoSuchAlgorithmException nsae) { log.error("Error getting password hash: " + nsae.getMessage()); return null; } }

private void deleteProject(String uid, String home, HttpServletRequest request, HttpServletResponse response) throws Exception { String project = request.getParameter("project"); String line; response.setContentType("text/html"); PrintWriter out = response.getWriter(); htmlHeader(out, "Project Status", ""); try { synchronized (Class.forName("com.sun.gep.SunTCP")) { Vector list = new Vector(); String directory = home; Runtime.getRuntime().exec("/usr/bin/rm -rf " + directory + project); FilePermission perm = new FilePermission(directory + SUNTCP_LIST, "read,write,execute"); File listfile = new File(directory + SUNTCP_LIST); BufferedReader read = new BufferedReader(new FileReader(listfile)); while ((line = read.readLine()) != null) { if (!((new StringTokenizer(line, "\t")).nextToken().equals(project))) { list.addElement(line); } } read.close(); if (list.size() > 0) { PrintWriter write = new PrintWriter(new BufferedWriter(new FileWriter(listfile))); for (int i = 0; i < list.size(); i++) { write.println((String) list.get(i)); } write.close(); } else { listfile.delete(); } out.println("The project was successfully deleted."); } } catch (Exception e) { out.println("Error accessing this project."); } out.println("<center><form><input type=button value=Continue onClick=\"opener.location.reload(); window.close()\"></form></center>"); htmlFooter(out); }

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

private void publishZip(LWMap map) { try { if (map.getFile() == null) { VueUtil.alert(VueResources.getString("dialog.mapsave.message"), VueResources.getString("dialog.mapsave.title")); return; } File savedCMap = PublishUtil.createZip(map, Publisher.resourceVector); InputStream istream = new BufferedInputStream(new FileInputStream(savedCMap)); OutputStream ostream = new BufferedOutputStream(new FileOutputStream(ActionUtil.selectFile("Export to Zip File", "zip"))); int fileLength = (int) savedCMap.length(); byte bytes[] = new byte[fileLength]; while (istream.read(bytes, 0, fileLength) != -1) ostream.write(bytes, 0, fileLength); istream.close(); ostream.close(); } catch (Exception ex) { System.out.println(ex); VueUtil.alert(VUE.getDialogParent(), VueResources.getString("dialog.export.message") + ex.getMessage(), VueResources.getString("dialog.export.title"), JOptionPane.ERROR_MESSAGE); ex.printStackTrace(); } }

public synchronized void handleRequest(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { CacheEntry entry = null; Tenant tenant = null; if (!tenantInfo.getTenants().isEmpty()) { tenant = tenantInfo.getMatchingTenant(request); if (tenant == null) { tenant = tenantInfo.getTenants().get(0); } entry = tenantToCacheEntry.get(tenant.getName()); } else { entry = cacheEntry; } if (entry == null) { File tempDir = (File) servletContext.getAttribute("javax.servlet.context.tempdir"); tempDir = new File(tempDir, "pustefix-sitemap-cache"); if (!tempDir.exists()) { tempDir.mkdirs(); } entry = new CacheEntry(); entry.file = new File(tempDir, "sitemap" + (tenant == null ? "" : "-" + tenant.getName()) + ".xml"); try { String host = AbstractPustefixRequestHandler.getServerName(request); Document doc = getSearchEngineSitemap(tenant, host); Transformer trf = TransformerFactory.newInstance().newTransformer(); trf.setOutputProperty(OutputKeys.INDENT, "yes"); FileOutputStream out = new FileOutputStream(entry.file); MessageDigest digest; try { digest = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException x) { throw new RuntimeException("Can't create message digest", x); } DigestOutputStream digestOutput = new DigestOutputStream(out, digest); trf.transform(new DOMSource(doc), new StreamResult(digestOutput)); digestOutput.close(); byte[] digestBytes = digest.digest(); entry.etag = MD5Utils.byteToHex(digestBytes); } catch (Exception x) { throw new ServletException("Error creating sitemap", x); } } String reqETag = request.getHeader("If-None-Match"); if (reqETag != null) { if (entry.etag.equals(reqETag)) { response.setStatus(HttpServletResponse.SC_NOT_MODIFIED); response.flushBuffer(); return; } } long reqMod = request.getDateHeader("If-Modified-Since"); if (reqMod != -1) { if (entry.file.lastModified() < reqMod + 1000) { response.setStatus(HttpServletResponse.SC_NOT_MODIFIED); response.flushBuffer(); return; } } response.setContentType("application/xml"); response.setContentLength((int) entry.file.length()); response.setDateHeader("Last-Modified", entry.file.lastModified()); response.setHeader("ETag", entry.etag); OutputStream out = new BufferedOutputStream(response.getOutputStream()); InputStream in = new FileInputStream(entry.file); int bytes_read; byte[] buffer = new byte[8]; while ((bytes_read = in.read(buffer)) != -1) { out.write(buffer, 0, bytes_read); } out.flush(); in.close(); out.close(); }

private static String createBoundary(int number) { MessageDigest digest; try { digest = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { throw new RuntimeException(e); } digest.update(String.valueOf(Math.random()).getBytes()); digest.update(String.valueOf(System.currentTimeMillis()).getBytes()); digest.update(String.valueOf(digest.hashCode()).getBytes()); byte[] bytes = digest.digest(); String paddedNumber = Integer.toString(number); paddedNumber = ("0000000000".substring(0, 10 - paddedNumber.length()) + paddedNumber); StringBuffer buffer = new StringBuffer(); buffer.append("---------------------------------=__"); for (int i = 0; i < 8; i++) { String hex = Integer.toHexString((bytes[i] & 0xff) + 0x100).substring(1); buffer.append(hex); } buffer.append('_'); buffer.append(paddedNumber); return buffer.toString(); }

public static boolean exec_applet(String fname, VarContainer vc, ActionContainer ac, ThingTypeContainer ttc, Output OUT, InputStream IN, boolean AT, Statement state, String[] arggies) { if (!urlpath.endsWith("/")) { urlpath = urlpath + '/'; } if (!urlpath.startsWith("http://")) { urlpath = "http://" + urlpath; } String url = urlpath; if (fname.startsWith("dusty_")) { url = url + "libraries/" + fname; } else { url = url + "users/" + fname; } StringBuffer src = new StringBuffer(2400); try { String s; BufferedReader br = new BufferedReader(new InputStreamReader(new URL(url).openStream())); while ((s = br.readLine()) != null) { src.append(s).append('\n'); } br.close(); } catch (Exception e) { OUT.println(new DSOut(DSOut.ERR_OUT, -1, "Dustyscript failed at reading the file'" + fname + "'\n\t...for 'use' statement"), vc, AT); return false; } fork(src, vc, ac, ttc, OUT, IN, AT, state, arggies); return true; }

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

public static void copiaAnexos(String from, String to, AnexoTO[] anexoTO) { FileChannel in = null, out = null; for (int i = 0; i < anexoTO.length; i++) { try { in = new FileInputStream(new File((uploadDiretorio.concat(from)).concat(File.separator + anexoTO[i].getNome()))).getChannel(); out = new FileOutputStream(new File((uploadDiretorio.concat(to)).concat(File.separator + anexoTO[i].getNome()))).getChannel(); long size = in.size(); MappedByteBuffer buf = in.map(FileChannel.MapMode.READ_ONLY, 0, size); out.write(buf); } catch (Exception e) { e.printStackTrace(); } finally { if (in != null) try { in.close(); } catch (IOException e) { e.printStackTrace(); } if (out != null) try { out.close(); } catch (IOException e) { e.printStackTrace(); } } } }

public synchronized void receive(MessageEvent e) { switch(e.message.getType()) { case MessageTypes.QUIT: activeSessions--; break; case MessageTypes.SHUTDOWN_SERVER: activeSessions--; if (Options.password.trim().equals("")) { System.err.println("No default password set. Shutdown not allowed."); break; } if (e.message.get("pwhash") == null) { System.err.println("Shutdown message without password received. Shutdown not allowed."); break; } try { java.security.MessageDigest hash = java.security.MessageDigest.getInstance("SHA-1"); hash.update(Options.password.getBytes("UTF-8")); if (!java.security.MessageDigest.isEqual(hash.digest(), (byte[]) e.message.get("pwhash"))) { System.err.println("Wrong shutdown password. Shutdown not allowed."); break; } else { System.out.println("Valid shutdown password received."); } } catch (java.security.NoSuchAlgorithmException ex) { System.err.println("Password hash algorithm SHA-1 not supported by runtime."); break; } catch (UnsupportedEncodingException ex) { System.err.println("Password character encoding not supported."); break; } catch (Exception ex) { System.err.println("Unhandled exception occured. Shutdown aborted. Details:"); ex.printStackTrace(System.err); break; } if (activeSessions == 0) tStop(); else System.err.println("there are other active sessions - shutdown failed"); break; default: } }

public static String getMD5(String password) { try { MessageDigest md5 = MessageDigest.getInstance("MD5"); String salt = "UseTheForce4"; password = salt + password; md5.update(password.getBytes(), 0, password.length()); password = new BigInteger(1, md5.digest()).toString(16); } catch (Exception e) { } return password; }

public String getNextObjectId() throws SQLException { long nextserial = 1; String s0 = "lock table serials in exclusive mode"; String s1 = "SELECT nextserial FROM serials WHERE tablename = 'SERVER_OIDS'"; String s2; try { Statement stmt = dbconnect.connection.createStatement(); stmt.executeUpdate(s0); ResultSet rs = stmt.executeQuery(s1); if (!rs.next()) { s2 = "insert into serials (tablename,nextserial) values ('SERVER_OIDS', " + (nextserial) + ")"; } else { nextserial = rs.getLong(1) + 1; s2 = "update serials set nextserial=" + (nextserial) + " where tablename='SERVER_OIDS'"; } stmt.executeUpdate(s2); dbconnect.connection.commit(); rs.close(); stmt.close(); return "" + nextserial; } catch (SQLException e) { dbconnect.connection.rollback(); throw e; } }

private static void readServicesFromUrl(Collection<String> list, URL url) throws IOException { InputStream in = url.openStream(); try { if (in == null) return; BufferedReader r = new BufferedReader(new InputStreamReader(in, "UTF-8")); while (true) { String line = r.readLine(); if (line == null) break; int idx = line.indexOf('#'); if (idx != -1) line = line.substring(0, idx); line = line.trim(); if (line.length() == 0) continue; list.add(line); } } finally { try { if (in != null) in.close(); } catch (Throwable ignore) { } } }

private String MD5(String s) { Log.d("MD5", "Hashing '" + s + "'"); String hash = ""; try { MessageDigest m = MessageDigest.getInstance("MD5"); m.update(s.getBytes(), 0, s.length()); hash = new BigInteger(1, m.digest()).toString(16); Log.d("MD5", "Hash: " + hash); } catch (Exception e) { Log.e("MD5", e.getMessage()); } return hash; }

public static String MD5(String str) { try { MessageDigest md5 = MessageDigest.getInstance("md5"); md5.update(str.getBytes(), 0, str.length()); String sig = new BigInteger(1, md5.digest()).toString(); return sig; } catch (NoSuchAlgorithmException e) { System.err.println("Can not use md5 algorithm"); } return null; }

public void onCreate() { window = ((Window) getFellow("win")); userName = ((Textbox) getFellow("user")); password = ((Textbox) getFellow("password")); session = window.getDesktop().getSession(); if (Executions.getCurrent().getParameter("login") != null) { login = Executions.getCurrent().getParameter("login"); session.setAttribute("login", login); } if (Executions.getCurrent().getParameter("password") != null) { passwordu = Executions.getCurrent().getParameter("password"); } if (Executions.getCurrent().getParameter("option") != null) { option = Executions.getCurrent().getParameter("option"); session.setAttribute("option", option); } if (Executions.getCurrent().getParameter("organization") != null) { organization = Executions.getCurrent().getParameter("organization"); session.setAttribute("organization", organization); } if (Executions.getCurrent().getParameter("project") != null) { project = Executions.getCurrent().getParameter("project"); session.setAttribute("project", project); } if (login != null) { User user = UserDAO.getUserByUserName(login); if (user != null) { String encodedPassword = null; try { MessageDigest digest = MessageDigest.getInstance("MD5"); digest.update(user.getPassword().getBytes()); BASE64Encoder encoder = new BASE64Encoder(); encodedPassword = encoder.encode(digest.digest()); } catch (Exception e) { } if (passwordu.compareTo(encodedPassword) == 0) { session.setAttribute("user", user); session.setAttribute("numero", 5); session.setAttribute("option", option); session.setAttribute("organization", organization); session.setAttribute("project", project); Executions.sendRedirect("menu.zul"); } } } }

@MediumTest public void testUrlRewriteRules() throws Exception { ContentResolver resolver = getContext().getContentResolver(); GoogleHttpClient client = new GoogleHttpClient(resolver, "Test", false); Settings.Gservices.putString(resolver, "url:test", "http://foo.bar/ rewrite " + mServerUrl + "new/"); Settings.Gservices.putString(resolver, "digest", mServerUrl); try { HttpGet method = new HttpGet("http://foo.bar/path"); HttpResponse response = client.execute(method); String body = EntityUtils.toString(response.getEntity()); assertEquals("/new/path", body); } finally { client.close(); } }

public static String getHash(String text) { try { MessageDigest md = MessageDigest.getInstance("SHA-1"); md.update(text.getBytes()); byte[] array = md.digest(); StringBuffer sb = new StringBuffer(); for (int i = 0; i < array.length; i++) { sb.append(Integer.toHexString((array[i] & 0xFF) | 0x100)); } return sb.toString(); } catch (NoSuchAlgorithmException ex) { Logger.getLogger(User.class.getName()).log(Level.SEVERE, null, ex); return null; } }

public static String MD5(String text) { byte[] md5hash = new byte[32]; try { MessageDigest md; md = MessageDigest.getInstance("MD5"); md.update(text.getBytes("iso-8859-1"), 0, text.length()); md5hash = md.digest(); } catch (Exception e) { e.printStackTrace(); } return convertToHex(md5hash); }

public static final String convertPassword(final String srcPwd) { StringBuilder out; MessageDigest md; byte[] byteValues; byte singleChar = 0; try { md = MessageDigest.getInstance("MD5"); md.update(srcPwd.getBytes()); byteValues = md.digest(); if ((byteValues == null) || (byteValues.length <= 0)) { return null; } out = new StringBuilder(byteValues.length * 2); for (byte element : byteValues) { singleChar = (byte) (element & 0xF0); singleChar = (byte) (singleChar >>> 4); singleChar = (byte) (singleChar & 0x0F); out.append(PasswordConverter.ENTRIES[singleChar]); singleChar = (byte) (element & 0x0F); out.append(PasswordConverter.ENTRIES[singleChar]); } return out.toString(); } catch (final NoSuchAlgorithmException e) { e.printStackTrace(); return null; } }

void write() throws IOException { if (!allowUnlimitedArgs && args != null && args.length > 1) throw new IllegalArgumentException("Only one argument allowed unless allowUnlimitedArgs is enabled"); String shebang = "#!" + interpretter; for (int i = 0; i < args.length; i++) { shebang += " " + args[i]; } shebang += '\n'; IOUtils.copy(new StringReader(shebang), outputStream); }

public InputStream openFileInputStream(String fileName) throws IOException { if (fileName.indexOf(':') > 1) { URL url = new URL(fileName); InputStream in = url.openStream(); return in; } fileName = translateFileName(fileName); FileInputStream in = new FileInputStream(fileName); trace("openFileInputStream", fileName, in); return in; }

public void getZipFiles(String filename) { try { String destinationname = "c:\\mods\\peu\\"; byte[] buf = new byte[1024]; ZipInputStream zipinputstream = null; ZipEntry zipentry; zipinputstream = new ZipInputStream(new FileInputStream(filename)); zipentry = zipinputstream.getNextEntry(); while (zipentry != null) { String entryName = zipentry.getName(); System.out.println("entryname " + entryName); int n; FileOutputStream fileoutputstream; File newFile = new File(entryName); String directory = newFile.getParent(); if (directory == null) { if (newFile.isDirectory()) break; } fileoutputstream = new FileOutputStream(destinationname + entryName); while ((n = zipinputstream.read(buf, 0, 1024)) > -1) fileoutputstream.write(buf, 0, n); fileoutputstream.close(); zipinputstream.closeEntry(); zipentry = zipinputstream.getNextEntry(); } zipinputstream.close(); } catch (Exception e) { e.printStackTrace(); } }

public synchronized String encrypt(String plaintext) { MessageDigest md = null; try { md = MessageDigest.getInstance("SHA"); md.update(plaintext.getBytes("UTF-8")); } catch (NoSuchAlgorithmException e) { log().error("failed to encrypt the password.", e); throw new RuntimeException("failed to encrypt the password.", e); } catch (UnsupportedEncodingException e) { log().error("failed to encrypt the password.", e); throw new RuntimeException("failed to encrypt the password.", e); } byte raw[] = md.digest(); String hash = (new BASE64Encoder()).encode(raw); return hash; }

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

private String grabInformationFromWeb(String query, String infoName) throws Exception { String result = ""; URL url = new URL(query); HttpURLConnection request = null; request = (HttpURLConnection) url.openConnection(); if (request != null) { InputStream in = url.openStream(); int c = 0; StringBuilder sb = new StringBuilder(); while ((c = in.read()) != -1) { sb = sb.append((char) c); } String s = sb.toString(); result = Utils.getTagValue(s, "<" + infoName + ">", "</" + infoName + ">"); in.close(); } return result; }

public String useService(HashMap<String, String> input) { String output = ""; if (input.size() < 1) { return ""; } String data = ""; try { for (String key : input.keySet()) { data += "&" + URLEncoder.encode(key, "UTF-8") + "=" + URLEncoder.encode(input.get(key), "UTF-8"); } data = data.substring(1); URL url = new URL(serviceUrl); URLConnection conn = url.openConnection(); conn.setDoOutput(true); OutputStreamWriter wr = new OutputStreamWriter(conn.getOutputStream()); wr.write(data); wr.flush(); BufferedReader rd = new BufferedReader(new InputStreamReader(conn.getInputStream())); String line; while ((line = rd.readLine()) != null) { output += line; } wr.close(); rd.close(); } catch (Exception e) { e.printStackTrace(); } return output; }

protected List webservice(URL url, List locations, boolean followRedirect) throws GeoServiceException { long start = System.currentTimeMillis(); int rowCount = 0, hitCount = 0; try { HttpURLConnection con; try { con = (HttpURLConnection) url.openConnection(); try { con.getClass().getMethod("setConnectTimeout", new Class[] { Integer.TYPE }).invoke(con, new Object[] { TIMEOUT }); } catch (Throwable t) { LOG.info("can't set connection timeout"); } con.setRequestMethod("POST"); con.setDoOutput(true); con.setDoInput(true); Writer out = new OutputStreamWriter(con.getOutputStream(), UTF8); out.write(HEADER + "\n"); for (int i = 0; i < locations.size(); i++) { if (i > 0) out.write("\n"); out.write(encode((GeoLocation) locations.get(i))); } out.close(); } catch (IOException e) { throw new GeoServiceException("Accessing GEO Webservice failed", e); } List rows = new ArrayList(); try { BufferedReader in = new BufferedReader(new InputStreamReader(con.getInputStream(), UTF8)); for (int l = 0; l < locations.size(); l++) { String line = in.readLine(); LOG.finer(line); if (line == null) break; if (l == 0 && followRedirect) { try { return webservice(new URL(line), locations, false); } catch (MalformedURLException e) { } } rowCount++; List row = new ArrayList(); if (!line.startsWith("?")) { StringTokenizer hits = new StringTokenizer(line, ";"); while (hits.hasMoreTokens()) { GeoLocation hit = decode(hits.nextToken()); if (hit != null) { row.add(hit); hitCount++; } } } rows.add(row); } in.close(); } catch (IOException e) { throw new GeoServiceException("Reading from GEO Webservice failed", e); } if (rows.size() < locations.size()) throw new GeoServiceException("GEO Webservice returned " + rows.size() + " rows for " + locations.size() + " locations"); return rows; } finally { long secs = (System.currentTimeMillis() - start) / 1000; LOG.fine("query for " + locations.size() + " locations in " + secs + "s resulted in " + rowCount + " rows and " + hitCount + " total hits"); } }

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 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 void initializeFromURL(URL url, AVList params) throws IOException { URLConnection connection = url.openConnection(); String message = this.validateURLConnection(connection, SHAPE_CONTENT_TYPES); if (message != null) { throw new IOException(message); } this.shpChannel = Channels.newChannel(WWIO.getBufferedInputStream(connection.getInputStream())); URLConnection shxConnection = this.getURLConnection(WWIO.replaceSuffix(url.toString(), INDEX_FILE_SUFFIX)); if (shxConnection != null) { message = this.validateURLConnection(shxConnection, INDEX_CONTENT_TYPES); if (message != null) Logging.logger().warning(message); else { InputStream shxStream = this.getURLStream(shxConnection); if (shxStream != null) this.shxChannel = Channels.newChannel(WWIO.getBufferedInputStream(shxStream)); } } URLConnection prjConnection = this.getURLConnection(WWIO.replaceSuffix(url.toString(), PROJECTION_FILE_SUFFIX)); if (prjConnection != null) { message = this.validateURLConnection(prjConnection, PROJECTION_CONTENT_TYPES); if (message != null) Logging.logger().warning(message); else { InputStream prjStream = this.getURLStream(prjConnection); if (prjStream != null) this.prjChannel = Channels.newChannel(WWIO.getBufferedInputStream(prjStream)); } } this.setValue(AVKey.DISPLAY_NAME, url.toString()); this.initialize(params); URL dbfURL = WWIO.makeURL(WWIO.replaceSuffix(url.toString(), ATTRIBUTE_FILE_SUFFIX)); if (dbfURL != null) { try { this.attributeFile = new DBaseFile(dbfURL); } catch (Exception e) { } } }

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

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

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

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 boolean writeResource(PluginProxy eclipseInstallPlugin, ResourceProxy translation, LocaleProxy locale) throws Exception { String translationResourceName = determineTranslatedResourceName(translation, locale); String pluginNameInDirFormat = eclipseInstallPlugin.getName().replace(Messages.getString("Characters_period"), File.separator); if (translation.getRelativePath().contains(pluginNameInDirFormat)) { return writeResourceToBundleClasspath(translation, locale); } else if (translationResourceName.contains(File.separator)) { String resourcePath = translationResourceName.substring(0, translationResourceName.lastIndexOf(File.separatorChar)); File resourcePathDirectory = new File(directory.getPath() + File.separatorChar + resourcePath); resourcePathDirectory.mkdirs(); } File fragmentResource = new File(directory.getPath() + File.separatorChar + translationResourceName); File translatedResource = new File(translation.getFileResource().getAbsolutePath()); FileChannel inputChannel = new FileInputStream(translatedResource).getChannel(); FileChannel outputChannel = new FileOutputStream(fragmentResource).getChannel(); inputChannel.transferTo(0, inputChannel.size(), outputChannel); inputChannel.close(); outputChannel.close(); return true; }

public static PortalConfig install(File xml, File dir) throws IOException, ConfigurationException { if (!dir.exists()) { log.info("Creating directory {}", dir); dir.mkdirs(); } if (!xml.exists()) { log.info("Installing default configuration to {}", xml); OutputStream output = new FileOutputStream(xml); try { InputStream input = ResourceLoader.open("res://" + PORTAL_CONFIG_XML); try { IOUtils.copy(input, output); } finally { input.close(); } } finally { output.close(); } } return create(xml, dir); }

public static boolean copyFile(File soureFile, File destFile) { boolean copySuccess = false; if (soureFile != null && destFile != null && soureFile.exists()) { try { new File(destFile.getParent()).mkdirs(); BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(destFile)); BufferedInputStream in = new BufferedInputStream(new FileInputStream(soureFile)); for (int currentByte = in.read(); currentByte != -1; currentByte = in.read()) out.write(currentByte); in.close(); out.close(); copySuccess = true; } catch (Exception e) { copySuccess = false; } } return copySuccess; }

protected IStatus run(IProgressMonitor monitor) { try { updateRunning = true; distributor = getFromFile("[SERVER]", "csz", getAppPath() + "/server.ini"); MAC = getFromFile("[SPECIFICINFO]", "MAC", getAppPath() + "/register.ini"); serial = getFromFile("[SPECIFICINFO]", "serial", getAppPath() + "/register.ini"); if (MAC.equals("not_found") || serial.equals("not_found") || !serial.startsWith(distributor)) { try { MAC = getFromFile("[SPECIFICINFO]", "MAC", getAppPath() + "/register.ini"); serial = getFromFile("[SPECIFICINFO]", "serial", getAppPath() + "/register.ini"); } catch (Exception e) { System.out.println(e); } } else { try { url = new URL("http://" + getFromFile("[SERVER]", "url", getAppPath() + "/server.ini")); } catch (MalformedURLException e) { System.out.println(e); } download = "/download2.php?distributor=" + distributor + "&&mac=" + MAC + "&&serial=" + serial; readXML(); if (htmlMessage.contains("error")) { try { PrintWriter pw = new PrintWriter(getAppPath() + "/register.ini"); pw.write(""); pw.close(); } catch (IOException e) { System.out.println(e); } setProperty(IProgressConstants.ICON_PROPERTY, IconImg.liveUpIco); if (isModal(this)) { showResults2(); } else { setProperty(IProgressConstants.KEEP_PROPERTY, Boolean.TRUE); setProperty(IProgressConstants.ACTION_PROPERTY, getUpdateCompletedAction2()); } } else { if (!getDBVersion().equals(latestVersion)) { try { OutputStream out = null; HttpURLConnection conn = null; InputStream in = null; int size; try { URL url = new URL(fileLoc); String outFile = getAppPath() + "/temp/" + getFileName(url); File oFile = new File(outFile); oFile.delete(); out = new BufferedOutputStream(new FileOutputStream(outFile)); monitor.beginTask("Connecting to NWD Server", 100); conn = (HttpURLConnection) url.openConnection(); conn.setConnectTimeout(20000); conn.connect(); if (conn.getResponseCode() / 100 != 2) { System.out.println("Error: " + conn.getResponseCode()); return null; } monitor.worked(100); monitor.done(); size = conn.getContentLength(); monitor.beginTask("Download Worm Definition", size); in = conn.getInputStream(); byte[] buffer; String downloadedSize; long numWritten = 0; boolean status = true; while (status) { if (size - numWritten > 1024) { buffer = new byte[1024]; } else { buffer = new byte[(int) (size - numWritten)]; } int read = in.read(buffer); if (read == -1) { break; } out.write(buffer, 0, read); numWritten += read; downloadedSize = Long.toString(numWritten / 1024) + " KB"; monitor.worked(read); monitor.subTask(downloadedSize + " of " + Integer.toString(size / 1024) + " KB"); if (size == numWritten) { status = false; } if (monitor.isCanceled()) return Status.CANCEL_STATUS; } if (in != null) { in.close(); } if (out != null) { out.close(); } try { ZipFile zFile = new ZipFile(outFile); Enumeration all = zFile.entries(); while (all.hasMoreElements()) { ZipEntry zEntry = (ZipEntry) all.nextElement(); long zSize = zEntry.getSize(); if (zSize > 0) { if (zEntry.getName().endsWith("script")) { InputStream instream = zFile.getInputStream(zEntry); FileOutputStream fos = new FileOutputStream(oldLoc[0]); int ch; while ((ch = instream.read()) != -1) { fos.write(ch); } instream.close(); fos.close(); } else if (zEntry.getName().endsWith("data")) { InputStream instream = zFile.getInputStream(zEntry); FileOutputStream fos = new FileOutputStream(oldLoc[1]); int ch; while ((ch = instream.read()) != -1) { fos.write(ch); } instream.close(); fos.close(); } } } File xFile = new File(outFile); xFile.deleteOnExit(); } catch (Exception e) { e.printStackTrace(); } try { monitor.done(); monitor.beginTask("Install Worm Definition", 10000); monitor.worked(2500); CorePlugin.getDefault().getRawPacketHandler().removeRawPacketListener(p); p = null; if (!wormDB.getConn().isClosed()) { shutdownDB(); } System.out.println(wormDB.getConn().isClosed()); for (int i = 0; i < 2; i++) { try { Process pid = Runtime.getRuntime().exec("cmd /c copy \"" + oldLoc[i].replace("/", "\\") + "\" \"" + newLoc[i].replace("/", "\\") + "\"/y"); } catch (Exception e) { e.printStackTrace(); } new File(oldLoc[i]).deleteOnExit(); } monitor.worked(2500); initialArray(); p = new PacketPrinter(); CorePlugin.getDefault().getRawPacketHandler().addRawPacketListener(p); monitor.worked(2500); monitor.done(); setProperty(IProgressConstants.ICON_PROPERTY, IconImg.liveUpIco); if (isModal(this)) { showResults(); } else { setProperty(IProgressConstants.KEEP_PROPERTY, Boolean.TRUE); setProperty(IProgressConstants.ACTION_PROPERTY, getUpdateCompletedAction()); } } catch (Exception e) { setProperty(IProgressConstants.ICON_PROPERTY, IconImg.liveUpIco); if (isModal(this)) { showResults2(); } else { setProperty(IProgressConstants.KEEP_PROPERTY, Boolean.TRUE); setProperty(IProgressConstants.ACTION_PROPERTY, getUpdateCompletedAction2()); } System.out.println(e); } finally { } } catch (Exception e) { e.printStackTrace(); } } catch (Exception e) { setProperty(IProgressConstants.ICON_PROPERTY, IconImg.liveUpIco); if (isModal(this)) { showResults2(); } else { setProperty(IProgressConstants.KEEP_PROPERTY, Boolean.TRUE); setProperty(IProgressConstants.ACTION_PROPERTY, getUpdateCompletedAction2()); } e.printStackTrace(); } } else { cancel(); setProperty(IProgressConstants.ICON_PROPERTY, IconImg.liveUpIco); if (isModal(this)) { showResults1(); } else { setProperty(IProgressConstants.KEEP_PROPERTY, Boolean.TRUE); setProperty(IProgressConstants.ACTION_PROPERTY, getUpdateCompletedAction1()); } } } } return Status.OK_STATUS; } catch (Exception e) { showResults2(); return Status.OK_STATUS; } finally { lock.release(); updateRunning = false; if (getValue("AUTO_UPDATE")) schedule(10800000); } }

private static int ejecutaUpdate(String database, String SQL) throws Exception { int i = 0; DBConnectionManager dbm = null; Connection bd = null; try { dbm = DBConnectionManager.getInstance(); bd = dbm.getConnection(database); Statement st = bd.createStatement(); i = st.executeUpdate(SQL); bd.commit(); st.close(); dbm.freeConnection(database, bd); } catch (Exception e) { log.error("SQL error: " + SQL, e); Exception excep; if (dbm == null) excep = new Exception("Could not obtain pool object DbConnectionManager"); else if (bd == null) excep = new Exception("The Db connection pool could not obtain a database connection"); else { bd.rollback(); excep = new Exception("SQL Error: " + SQL + " error: " + e); dbm.freeConnection(database, bd); } throw excep; } return i; }

public boolean save(Object obj) { boolean bool = false; this.result = null; if (obj == null) return bool; Connection conn = null; try { conn = ConnectUtil.getConnect(); conn.setAutoCommit(false); String sql = SqlUtil.getInsertSql(this.getCls()); PreparedStatement ps = conn.prepareStatement(sql); setPsParams(ps, obj); ps.executeUpdate(); ps.close(); conn.commit(); bool = true; } catch (Exception e) { try { conn.rollback(); } catch (SQLException e1) { } this.result = e.getMessage(); } finally { this.closeConnectWithTransaction(conn); } return bool; }

public static void main(String[] args) { FileInputStream in; DeflaterOutputStream out; FileOutputStream fos; FileDialog fd; fd = new FileDialog(new Frame(), "Find a file to deflate", FileDialog.LOAD); fd.show(); if (fd.getFile() != null) { try { in = new FileInputStream(new File(fd.getDirectory(), fd.getFile())); fos = new FileOutputStream(new File("Deflated.out")); out = new DeflaterOutputStream(fos, new Deflater(Deflater.DEFLATED, true)); int bytes_read = 0; byte[] buffer = new byte[1024]; while ((bytes_read = in.read(buffer)) != -1) { out.write(buffer, 0, bytes_read); } fos.flush(); fos.close(); out.flush(); out.close(); in.close(); } catch (Exception e) { e.printStackTrace(); } System.out.println("Done"); } }

private void saveFile(InputStream in, String fullPath) { try { File sysfile = new File(fullPath); if (!sysfile.exists()) { sysfile.createNewFile(); } java.io.OutputStream out = new FileOutputStream(sysfile); org.apache.commons.io.IOUtils.copy(in, out); out.close(); } catch (Exception e) { e.printStackTrace(); } }

public static List<String> unTar(File tarFile, File directory) throws IOException { List<String> result = new ArrayList<String>(); InputStream inputStream = new FileInputStream(tarFile); TarArchiveInputStream in = new TarArchiveInputStream(inputStream); TarArchiveEntry entry = in.getNextTarEntry(); while (entry != null) { OutputStream out = new FileOutputStream(new File(directory, entry.getName())); IOUtils.copy(in, out); out.close(); result.add(entry.getName()); entry = in.getNextTarEntry(); } in.close(); return result; }

public static String md5(String input) { String res = ""; try { MessageDigest algorithm = MessageDigest.getInstance("MD5"); algorithm.reset(); algorithm.update(input.getBytes()); byte[] md5 = algorithm.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) { if (globali.jcVariabili.DEBUG) globali.jcFunzioni.erroreSQL(ex.toString()); } return res; }