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bigclonebench-processed

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public void copy(File from, String to) throws SystemException { assert from != null; File dst = new File(folder, to); dst.getParentFile().mkdirs(); FileChannel in = null; FileChannel out = null; try { if (!dst.exists()) dst.createNewFile(); in = new FileInputStream(from).getChannel(); out = new FileOutputStream(dst).getChannel(); in.transferTo(0, in.size(), out); } catch (IOException e) { throw new SystemException(e); } finally { try { if (in != null) in.close(); } catch (Exception e1) { } try { if (out != null) out.close(); } catch (Exception e1) { } } }

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(); }

private void copyFile(File src_file, File dest_file) { InputStream src_stream = null; OutputStream dest_stream = null; try { int b; src_stream = new BufferedInputStream(new FileInputStream(src_file)); dest_stream = new BufferedOutputStream(new FileOutputStream(dest_file)); while ((b = src_stream.read()) != -1) dest_stream.write(b); } catch (Exception e) { XRepository.getLogger().warning(this, "Error on copying the plugin file!"); XRepository.getLogger().warning(this, e); } finally { try { src_stream.close(); dest_stream.close(); } catch (Exception ex2) { } } }

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

public void greatestIncrease(int maxIterations) { double[] increase = new double[numModels]; int[] id = new int[numModels]; Model md = new Model(); double oldPerf = 1; for (int i = 0; i < numModels; i++) { md.addModel(models[i], false); increase[i] = oldPerf - md.getLoss(); id[i] = i; oldPerf = md.getLoss(); } for (int i = 0; i < numModels; i++) { for (int j = 0; j < numModels - 1 - i; j++) { if (increase[j] < increase[j + 1]) { double increasetemp = increase[j]; int temp = id[j]; increase[j] = increase[j + 1]; id[j] = id[j + 1]; increase[j + 1] = increasetemp; id[j + 1] = temp; } } } for (int i = 0; i < maxIterations; i++) { addToEnsemble(models[id[i]]); if (report) ensemble.report(models[id[i]].getName(), allSets); updateBestModel(); } }

public void copyHashAllFilesToDirectory(String baseDirStr, Hashtable newNamesTable, String destDirStr) throws Exception { if (baseDirStr.endsWith(sep)) { baseDirStr = baseDirStr.substring(0, baseDirStr.length() - 1); } if (destDirStr.endsWith(sep)) { destDirStr = destDirStr.substring(0, destDirStr.length() - 1); } FileUtils.getInstance().createDirectory(baseDirStr); if (null == newNamesTable) { newNamesTable = new Hashtable(); } BufferedInputStream in = null; BufferedOutputStream out = null; byte dataBuff[] = new byte[bufferSize]; File baseDir = new File(baseDirStr); baseDir.mkdirs(); if ((baseDir.exists()) && (baseDir.isDirectory())) { if (!newNamesTable.isEmpty()) { Enumeration enumFiles = newNamesTable.keys(); while (enumFiles.hasMoreElements()) { String newName = (String) enumFiles.nextElement(); String oldPathName = (String) newNamesTable.get(newName); if ((newName != null) && (!"".equals(newName)) && (oldPathName != null) && (!"".equals(oldPathName))) { String newPathFileName = destDirStr + sep + newName; String oldPathFileName = baseDirStr + sep + oldPathName; if (oldPathName.startsWith(sep)) { oldPathFileName = baseDirStr + oldPathName; } File f = new File(oldPathFileName); if ((f.exists()) && (f.isFile())) { in = new BufferedInputStream(new FileInputStream(oldPathFileName), bufferSize); out = new BufferedOutputStream(new FileOutputStream(newPathFileName), bufferSize); int readLen; while ((readLen = in.read(dataBuff)) > 0) { out.write(dataBuff, 0, readLen); } out.flush(); in.close(); out.close(); } else { } } } } else { } } else { throw new Exception("Base (baseDirStr) dir not exist !"); } }

public MemoryTextBody(InputStream is, String mimeCharset) throws IOException { this.mimeCharset = mimeCharset; TempPath tempPath = TempStorage.getInstance().getRootTempPath(); ByteArrayOutputStream out = new ByteArrayOutputStream(); IOUtils.copy(is, out); out.close(); tempFile = out.toByteArray(); }

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

private 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(); }

public void submitReport() { String subject = m_Subject.getText(); String description = m_Description.getText(); String email = m_Email.getText(); if (subject.length() == 0) { Util.flashComponent(m_Subject, Color.RED); return; } if (description.length() == 0) { Util.flashComponent(m_Description, Color.RED); return; } DynamicLocalisation loc = m_MainFrame.getLocalisation(); if (email.length() == 0 || email.indexOf("@") == -1 || email.indexOf(".") == -1 || email.startsWith("@")) { email = "anonymous@blaat.com"; } try { String data = URLEncoder.encode("mode", "UTF-8") + "=" + URLEncoder.encode("manual", "UTF-8"); data += "&" + URLEncoder.encode("from", "UTF-8") + "=" + URLEncoder.encode(email, "UTF-8"); data += "&" + URLEncoder.encode("subject", "UTF-8") + "=" + URLEncoder.encode(subject, "UTF-8"); data += "&" + URLEncoder.encode("body", "UTF-8") + "=" + URLEncoder.encode(description, "UTF-8"); data += "&" + URLEncoder.encode("jvm", "UTF-8") + "=" + URLEncoder.encode(System.getProperty("java.version"), "UTF-8"); data += "&" + URLEncoder.encode("ocdsver", "UTF-8") + "=" + URLEncoder.encode(Constants.OPENCDS_VERSION, "UTF-8"); data += "&" + URLEncoder.encode("os", "UTF-8") + "=" + URLEncoder.encode(Constants.OS_NAME + " " + System.getProperty("os.version") + " " + System.getProperty("os.arch"), "UTF-8"); URL url = new URL(Constants.BUGREPORT_SCRIPT); 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) { System.out.println(line); } wr.close(); rd.close(); JOptionPane.showMessageDialog(this, loc.getMessage("ReportBug.SentMessage")); } catch (Exception e) { Logger.getInstance().logException(e); } dispose(); }

public void rename(String virtualWiki, String oldTopicName, String newTopicName) throws Exception { Connection conn = DatabaseConnection.getConnection(); try { boolean commit = false; conn.setAutoCommit(false); try { PreparedStatement pstm = conn.prepareStatement(STATEMENT_RENAME); try { pstm.setString(1, newTopicName); pstm.setString(2, oldTopicName); pstm.setString(3, virtualWiki); if (pstm.executeUpdate() == 0) throw new SQLException("Unable to rename topic " + oldTopicName + " on wiki " + virtualWiki); } finally { pstm.close(); } doUnlockTopic(conn, virtualWiki, oldTopicName); doRenameAllVersions(conn, virtualWiki, oldTopicName, newTopicName); commit = true; } finally { if (commit) conn.commit(); else conn.rollback(); } } finally { conn.close(); } }

@Override protected boolean sendBytes(byte[] data, int offset, int length) { try { String hex = toHex(data, offset, length); URL url = new URL(this.endpoint, "?raw=" + hex); System.out.println("Connecting to " + url); URLConnection conn = url.openConnection(); conn.connect(); Object content = conn.getContent(); return true; } catch (IOException ex) { LOGGER.warning(ex.getMessage()); return false; } }

@Test public void testLargePut() throws Throwable { int size = CommonParameters.BLOCK_SIZE; InputStream is = new FileInputStream(_fileName); RepositoryFileOutputStream ostream = new RepositoryFileOutputStream(_nodeName, _putHandle, CommonParameters.local); int readLen = 0; int writeLen = 0; byte[] buffer = new byte[CommonParameters.BLOCK_SIZE]; while ((readLen = is.read(buffer, 0, size)) != -1) { ostream.write(buffer, 0, readLen); writeLen += readLen; } ostream.close(); CCNStats stats = _putHandle.getNetworkManager().getStats(); Assert.assertEquals(0, stats.getCounter("DeliverInterestFailed")); }

private static void zip(File d) throws FileNotFoundException, IOException { String[] entries = d.list(); byte[] buffer = new byte[4096]; int bytesRead; ZipOutputStream out = new ZipOutputStream(new FileOutputStream(new File(d.getParent() + File.separator + "dist.zip"))); for (int i = 0; i < entries.length; i++) { File f = new File(d, entries[i]); if (f.isDirectory()) continue; FileInputStream in = new FileInputStream(f); int skipl = d.getCanonicalPath().length(); ZipEntry entry = new ZipEntry(f.getPath().substring(skipl)); out.putNextEntry(entry); while ((bytesRead = in.read(buffer)) != -1) out.write(buffer, 0, bytesRead); in.close(); } out.close(); FileUtils.moveFile(new File(d.getParent() + File.separator + "dist.zip"), new File(d + File.separator + "dist.zip")); }

@Override public void connect() throws IOException { URL url = getLocator().getURL(); if (url.getProtocol().equals("file")) { final String newUrlStr = URLUtils.createAbsoluteFileUrl(url.toExternalForm()); if (newUrlStr != null) { if (!newUrlStr.toString().equals(url.toExternalForm())) { logger.warning("Changing file URL to absolute for URL.openConnection, from " + url.toExternalForm() + " to " + newUrlStr); url = new URL(newUrlStr); } } } conn = url.openConnection(); if (!url.getProtocol().equals("ftp") && conn.getURL().getProtocol().equals("ftp")) { logger.warning("URL.openConnection() morphed " + url + " to " + conn.getURL()); throw new IOException("URL.openConnection() returned an FTP connection for a non-ftp url: " + url); } if (conn instanceof HttpURLConnection) { final HttpURLConnection huc = (HttpURLConnection) conn; huc.connect(); final int code = huc.getResponseCode(); if (!(code >= 200 && code < 300)) { huc.disconnect(); throw new IOException("HTTP response code: " + code); } logger.finer("URL: " + url); logger.finer("Response code: " + code); logger.finer("Full content type: " + conn.getContentType()); boolean contentTypeSet = false; if (stripTrailer(conn.getContentType()).equals("text/plain")) { final String ext = PathUtils.extractExtension(url.getPath()); if (ext != null) { final String result = MimeManager.getMimeType(ext); if (result != null) { contentTypeStr = ContentDescriptor.mimeTypeToPackageName(result); contentTypeSet = true; logger.fine("Received content type " + conn.getContentType() + "; overriding based on extension, to: " + result); } } } if (!contentTypeSet) contentTypeStr = ContentDescriptor.mimeTypeToPackageName(stripTrailer(conn.getContentType())); } else { conn.connect(); contentTypeStr = ContentDescriptor.mimeTypeToPackageName(conn.getContentType()); } contentType = new ContentDescriptor(contentTypeStr); sources = new URLSourceStream[1]; sources[0] = new URLSourceStream(); connected = true; }

public static byte[] SHA1(String text) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md; md = MessageDigest.getInstance("SHA-1"); byte[] sha1hash = new byte[40]; md.update(text.getBytes("iso-8859-1"), 0, text.length()); sha1hash = md.digest(); return sha1hash; }

protected static String md5(String s) throws Exception { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(s.getBytes()); byte digest[] = md.digest(); StringBuffer result = new StringBuffer(); for (int i = 0; i < digest.length; i++) { result.append(Integer.toHexString(0xFF & digest[i])); } return result.toString(); }

public void loginMD5() throws Exception { GetMethod get = new GetMethod("http://login.yahoo.com/config/login?.src=www&.done=http://www.yahoo.com"); get.setRequestHeader("user-agent", "Mozilla/5.0 (Macintosh; U; PPC MacOS X; en-us) AppleWebKit/124 (KHTML, like Gecko) Safari/125.1"); client.executeMethod(get); parseResponse(get.getResponseBodyAsStream()); MessageDigest digest = MessageDigest.getInstance("MD5"); digest.update(password.getBytes("US-ASCII")); String hash1 = new String(digest.digest(), "US-ASCII"); String hash2 = hash1 + challenge; digest.update(hash2.getBytes("US-ASCII")); String hash = new String(digest.digest(), "US-ASCII"); NameValuePair[] pairs = { new NameValuePair("login", login), new NameValuePair("password", hash), new NameValuePair(".save", "1"), new NameValuePair(".tries", "1"), new NameValuePair(".src", "www"), new NameValuePair(".md5", "1"), new NameValuePair(".hash", "1"), new NameValuePair(".js", "1"), new NameValuePair(".last", ""), new NameValuePair(".promo", ""), new NameValuePair(".intl", "us"), new NameValuePair(".bypass", ""), new NameValuePair(".u", u), new NameValuePair(".v", "0"), new NameValuePair(".challenge", challenge), new NameValuePair(".yplus", ""), new NameValuePair(".emailCode", ""), new NameValuePair("pkg", ""), new NameValuePair("stepid", ""), new NameValuePair(".ev", ""), new NameValuePair("hasMsgr", "0"), new NameValuePair(".chkP", "Y"), new NameValuePair(".done", "http://www.yahoo.com"), new NameValuePair(".persistent", "y") }; get = new GetMethod("http://login.yahoo.com/config/login"); get.setRequestHeader("user-agent", "Mozilla/5.0 (Macintosh; U; PPC MacOS X; en-us) AppleWebKit/124 (KHTML, like Gecko) Safari/125.1"); get.addRequestHeader("Accept", "*/*"); get.addRequestHeader("Accept-Language", "en-us, ja;q=0.21, de-de;q=0.86, de;q=0.79, fr-fr;q=0.71, fr;q=0.64, nl-nl;q=0.57, nl;q=0.50, it-it;q=0.43, it;q=0.36, ja-jp;q=0.29, en;q=0.93, es-es;q=0.14, es;q=0.07"); get.setQueryString(pairs); client.executeMethod(get); get.getResponseBodyAsString(); }

private void callbackWS(String xmlControl, String ws_results, long docId) { SimpleProvider config; Service service; Object ret; Call call; Object[] parameter; String method; String wsurl; URL url; NodeList delegateNodes; Node actualNode; InputSource xmlcontrolstream; try { xmlcontrolstream = new InputSource(new StringReader(xmlControl)); delegateNodes = SimpleXMLParser.parseDocument(xmlcontrolstream, AgentBehaviour.XML_CALLBACK); actualNode = delegateNodes.item(0); wsurl = SimpleXMLParser.findChildEntry(actualNode, AgentBehaviour.XML_URL); method = SimpleXMLParser.findChildEntry(actualNode, AgentBehaviour.XML_METHOD); if (wsurl == null || method == null) { System.out.println("----- Did not get method or wsurl from the properties! -----"); return; } url = new java.net.URL(wsurl); try { url.openConnection().connect(); } catch (IOException ex) { System.out.println("----- Could not connect to the webservice! -----"); } Vector v_param = new Vector(); v_param.add(ws_results); v_param.add(new Long(docId)); parameter = v_param.toArray(); config = new SimpleProvider(); config.deployTransport("http", new HTTPSender()); service = new Service(config); call = (Call) service.createCall(); call.setTargetEndpointAddress(url); call.setOperationName(new QName("http://schemas.xmlsoap.org/soap/encoding/", method)); try { ret = call.invoke(parameter); if (ret == null) { ret = new String("No response from callback function!"); } System.out.println("Callback function returned: " + ret); } catch (RemoteException ex) { System.out.println("----- Could not invoke the method! -----"); } } catch (Exception ex) { ex.printStackTrace(System.err); } }

ServerInfo getServerInfo(String key, String protocol) throws InvalidKeyException, NoSuchAlgorithmException, InvalidKeySpecException, NoSuchPaddingException, IOException, ClassNotFoundException, IllegalBlockSizeException, BadPaddingException { DESedeKeySpec ks = new DESedeKeySpec(Base64.decode(key)); SecretKeyFactory skf = SecretKeyFactory.getInstance("DESede"); SecretKey sk = skf.generateSecret(ks); Cipher cipher = Cipher.getInstance("DESede"); cipher.init(Cipher.DECRYPT_MODE, sk); ClassLoader cl = this.getClass().getClassLoader(); URL url = cl.getResource(protocol + ".sobj"); JarURLConnection jc = (JarURLConnection) url.openConnection(); ObjectInputStream os = new ObjectInputStream(jc.getInputStream()); SealedObject so = (SealedObject) os.readObject(); return (ServerInfo) so.getObject(cipher); }

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

public static void copyFile(File src, File dest) throws IOException { log.debug("Copying file: '" + src + "' to '" + dest + "'"); FileChannel srcChannel = new FileInputStream(src).getChannel(); FileChannel dstChannel = new FileOutputStream(dest).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); }

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

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

public void getFile(String url, String filepath) throws BggException { System.out.println(url); int retry = retryCount + 1; lastURL = url; for (retriedCount = 0; retriedCount < retry; retriedCount++) { int responseCode = -1; try { HttpURLConnection con = null; BufferedInputStream bis = null; OutputStream osw = null; try { con = (HttpURLConnection) new URL(url).openConnection(); con.setDoInput(true); setHeaders(con); con.setRequestMethod("GET"); responseCode = con.getResponseCode(); bis = new BufferedInputStream(con.getInputStream()); int data; BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(filepath)); while ((data = bis.read()) != -1) bos.write(data); bos.flush(); bos.close(); break; } finally { try { bis.close(); } catch (Exception ignore) { } try { osw.close(); } catch (Exception ignore) { } try { con.disconnect(); } catch (Exception ignore) { } } } catch (IOException ioe) { if (responseCode == UNAUTHORIZED || responseCode == FORBIDDEN) { throw new BggException(ioe.getMessage(), responseCode); } if (retriedCount == retryCount) { throw new BggException(ioe.getMessage(), responseCode); } } try { Thread.sleep(retryIntervalMillis); } catch (InterruptedException ignore) { } } }

private long generateUnixInstallShell(File unixShellFile, String instTemplate, File instClassFile) throws IOException { FileOutputStream byteWriter = new FileOutputStream(unixShellFile); InputStream is = getClass().getResourceAsStream("/" + instTemplate); InputStreamReader isr = new InputStreamReader(is); LineNumberReader reader = new LineNumberReader(isr); String content = ""; String installClassStartStr = "000000000000"; NumberFormat nf = NumberFormat.getInstance(Locale.US); nf.setGroupingUsed(false); nf.setMinimumIntegerDigits(installClassStartStr.length()); int installClassStartPos = 0; long installClassOffset = 0; System.out.println(VAGlobals.i18n("VAArchiver_GenerateInstallShell")); String line = reader.readLine(); while ((line != null) && (!line.startsWith("# InstallClassStart"))) { content += line + "\n"; line = reader.readLine(); } content += "InstallClassStart=" + installClassStartStr + "\n"; installClassStartPos = content.length() - 1 - 1 - installClassStartStr.length(); line = reader.readLine(); while ((line != null) && (!line.startsWith("# InstallClassSize"))) { content += line + "\n"; line = reader.readLine(); } content += new String("InstallClassSize=" + instClassFile.length() + "\n"); line = reader.readLine(); while ((line != null) && (!line.startsWith("# InstallClassName"))) { content += line + "\n"; line = reader.readLine(); } content += new String("InstallClassName=" + instClassName_ + "\n"); line = reader.readLine(); while ((line != null) && (!line.startsWith("# Install class"))) { content += line + "\n"; line = reader.readLine(); } if (line != null) content += line + "\n"; byteWriter.write(content.substring(0, installClassStartPos + 1).getBytes()); byteWriter.write(nf.format(content.length()).getBytes()); byteWriter.write(content.substring(installClassStartPos + 1 + installClassStartStr.length()).getBytes()); installClassOffset = content.length(); content = null; FileInputStream classStream = new FileInputStream(instClassFile); byte[] buf = new byte[2048]; int read = classStream.read(buf); while (read > 0) { byteWriter.write(buf, 0, read); read = classStream.read(buf); } classStream.close(); reader.close(); byteWriter.close(); return installClassOffset; }

private InputStream getSearchInputStream(String name) { URL url = null; try { url = new URL(TheMovieDBXmlPullFeedParser.SEARCH_FEED_URL + URLEncoder.encode(name)); Log.d(Constants.LOG_TAG, "Movie search URL: " + url); } catch (MalformedURLException e) { throw new RuntimeException(e); } try { return url.openConnection().getInputStream(); } catch (IOException e) { throw new RuntimeException(e); } }

private void processBasicContent() { String[] packageNames = sourceCollector.getPackageNames(); for (int i = 0; i < packageNames.length; i++) { XdcSource[] sources = sourceCollector.getXdcSources(packageNames[i]); File dir = new File(outputDir, packageNames[i]); dir.mkdirs(); Set pkgDirs = new HashSet(); for (int j = 0; j < sources.length; j++) { XdcSource source = sources[j]; Properties patterns = source.getPatterns(); if (patterns != null) { tables.put("patterns", patterns); } pkgDirs.add(source.getFile().getParentFile()); DialectHandler dialectHandler = source.getDialectHandler(); Writer out = null; try { String sourceFilePath = source.getFile().getAbsolutePath(); source.setProcessingProperties(baseProperties, j > 0 ? sources[j - 1].getFileName() : null, j < sources.length - 1 ? sources[j + 1].getFileName() : null); String rootComment = XslUtils.transformToString(sourceFilePath, XSL_PKG + "/source-header.xsl", tables); source.setRootComment(rootComment); Document htmlDoc = XslUtils.transform(sourceFilePath, encoding, dialectHandler.getXslResourcePath(), tables); if (LOG.isInfoEnabled()) { LOG.info("Processing source file " + sourceFilePath); } out = IOUtils.getWriter(new File(dir, source.getFile().getName() + ".html"), docencoding); XmlUtils.printHtml(out, htmlDoc); if (sourceProcessor != null) { sourceProcessor.processSource(source, encoding, docencoding); } XdcSource.clearProcessingProperties(baseProperties); } catch (XmlException e) { LOG.error(e.getMessage(), e); } catch (IOException e) { LOG.error(e.getMessage(), e); } finally { if (out != null) { try { out.close(); } catch (IOException e) { LOG.error(e.getMessage(), e); } } } } for (Iterator iter = pkgDirs.iterator(); iter.hasNext(); ) { File docFilesDir = new File((File) iter.next(), "xdc-doc-files"); if (docFilesDir.exists() && docFilesDir.isDirectory()) { File targetDir = new File(dir, "xdc-doc-files"); targetDir.mkdirs(); try { IOUtils.copyTree(docFilesDir, targetDir); } catch (IOException e) { LOG.error(e.getMessage(), e); } } } } }

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 static boolean copyFile(String source, String destination, boolean replace) { File sourceFile = new File(source); File destinationFile = new File(destination); if (sourceFile.isDirectory() || destinationFile.isDirectory()) return false; if (destinationFile.isFile() && !replace) return false; if (!sourceFile.isFile()) return false; if (replace) destinationFile.delete(); try { File dir = destinationFile.getParentFile(); while (dir != null && !dir.exists()) { dir.mkdir(); } DataOutputStream outStream = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(destinationFile), 10240)); DataInputStream inStream = new DataInputStream(new BufferedInputStream(new FileInputStream(sourceFile), 10240)); try { while (inStream.available() > 0) { outStream.write(inStream.readUnsignedByte()); } } catch (EOFException eof) { } inStream.close(); outStream.close(); } catch (IOException ex) { throw new FailedException("Failed to copy file " + sourceFile.getAbsolutePath() + " to " + destinationFile.getAbsolutePath(), ex).setFile(destinationFile.getAbsolutePath()); } return true; }

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

public static void unZip(String unZipfileName, String outputDirectory) throws IOException, FileNotFoundException { FileOutputStream fileOut; File file; ZipEntry zipEntry; ZipInputStream zipIn = new ZipInputStream(new BufferedInputStream(new FileInputStream(unZipfileName)), encoder); while ((zipEntry = zipIn.getNextEntry()) != null) { file = new File(outputDirectory + File.separator + zipEntry.getName()); if (zipEntry.isDirectory()) { createDirectory(file.getPath(), ""); } else { File parent = file.getParentFile(); if (!parent.exists()) { createDirectory(parent.getPath(), ""); } fileOut = new FileOutputStream(file); int readedBytes; while ((readedBytes = zipIn.read(buf)) > 0) { fileOut.write(buf, 0, readedBytes); } fileOut.close(); } zipIn.closeEntry(); } }

private void copyFile(File dir, File fileToAdd) { try { byte[] readBuffer = new byte[1024]; File file = new File(dir.getCanonicalPath() + File.separatorChar + fileToAdd.getName()); if (file.createNewFile()) { FileInputStream fis = new FileInputStream(fileToAdd); FileOutputStream fos = new FileOutputStream(file); int bytesRead; do { bytesRead = fis.read(readBuffer); fos.write(readBuffer, 0, bytesRead); } while (bytesRead == 0); fos.flush(); fos.close(); fis.close(); } else { logger.severe("unable to create file:" + file.getAbsolutePath()); } } catch (IOException ioe) { logger.severe("unable to create file:" + ioe); } }

private String sha1(String s) { String encrypt = s; try { MessageDigest sha = MessageDigest.getInstance("SHA-1"); sha.update(s.getBytes()); byte[] digest = sha.digest(); final StringBuffer buffer = new StringBuffer(); for (int i = 0; i < digest.length; ++i) { final byte b = digest[i]; final int value = (b & 0x7F) + (b < 0 ? 128 : 0); buffer.append(value < 16 ? "0" : ""); buffer.append(Integer.toHexString(value)); } encrypt = buffer.toString(); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } return encrypt; }

public static void main(String args[]) { org.apache.xml.security.Init.init(); String signatureFileName = args[0]; javax.xml.parsers.DocumentBuilderFactory dbf = javax.xml.parsers.DocumentBuilderFactory.newInstance(); dbf.setNamespaceAware(true); dbf.setAttribute("http://xml.org/sax/features/namespaces", Boolean.TRUE); try { long start = System.currentTimeMillis(); org.apache.xml.security.Init.init(); File f = new File(signatureFileName); System.out.println("Verifying " + signatureFileName); javax.xml.parsers.DocumentBuilder db = dbf.newDocumentBuilder(); org.w3c.dom.Document doc = db.parse(new java.io.FileInputStream(f)); VerifyExampleTest vf = new VerifyExampleTest(); vf.verify(doc); Constants.setSignatureSpecNSprefix("dsig"); Element sigElement = null; NodeList nodes = doc.getElementsByTagNameNS(org.apache.xml.security.utils.Constants.SignatureSpecNS, "Signature"); if (nodes.getLength() != 0) { System.out.println("Found " + nodes.getLength() + " Signature elements."); for (int i = 0; i < nodes.getLength(); i++) { sigElement = (Element) nodes.item(i); XMLSignature signature = new XMLSignature(sigElement, ""); KeyInfo ki = signature.getKeyInfo(); signature.addResourceResolver(new OfflineResolver()); if (ki != null) { if (ki.containsX509Data()) { System.out.println("Could find a X509Data element in the KeyInfo"); } KeyInfo kinfo = signature.getKeyInfo(); X509Certificate cert = null; if (kinfo.containsRetrievalMethod()) { RetrievalMethod m = kinfo.itemRetrievalMethod(0); URL url = new URL(m.getURI()); CertificateFactory cf = CertificateFactory.getInstance("X.509"); cert = (X509Certificate) cf.generateCertificate(url.openStream()); } else { cert = signature.getKeyInfo().getX509Certificate(); } if (cert != null) { System.out.println("The XML signature is " + (signature.checkSignatureValue(cert) ? "valid (good)" : "invalid !!!!! (bad)")); } else { System.out.println("Did not find a Certificate"); PublicKey pk = signature.getKeyInfo().getPublicKey(); if (pk != null) { System.out.println("The XML signatur is " + (signature.checkSignatureValue(pk) ? "valid (good)" : "invalid !!!!! (bad)")); } else { System.out.println("Did not find a public key, so I can't check the signature"); } } } else { System.out.println("Did not find a KeyInfo"); } } } long end = System.currentTimeMillis(); double elapsed = end - start; System.out.println("verified:" + elapsed); } catch (Exception e) { e.printStackTrace(); } }

public boolean chequearMarca(int a, int m, int d) { boolean existe = false; try { cantidadArchivos = obtenerCantidad() + 1; String filenametxt = ""; String filenamezip = ""; int dia = 0; int mes = 0; int ano = 0; for (int i = 1; i < cantidadArchivos; i++) { filenamezip = "recordatorio" + i + ".zip"; filenametxt = "recordatorio" + i + ".txt"; BufferedOutputStream dest = null; BufferedInputStream is = null; ZipEntry entry; ZipFile zipfile = new ZipFile(filenamezip); Enumeration e = zipfile.entries(); while (e.hasMoreElements()) { entry = (ZipEntry) e.nextElement(); is = new BufferedInputStream(zipfile.getInputStream(entry)); int count; byte data[] = new byte[buffer]; FileOutputStream fos = new FileOutputStream(entry.getName()); dest = new BufferedOutputStream(fos, buffer); while ((count = is.read(data, 0, buffer)) != -1) dest.write(data, 0, count); dest.flush(); dest.close(); is.close(); } DataInputStream input = new DataInputStream(new FileInputStream(filenametxt)); dia = Integer.parseInt(input.readLine()); mes = Integer.parseInt(input.readLine()); ano = Integer.parseInt(input.readLine()); if (ano == a && mes == m && dia == d) existe = true; input.close(); } } catch (Exception e) { JOptionPane.showMessageDialog(null, "Error en: " + e.toString(), "Error", JOptionPane.ERROR_MESSAGE); } return (existe); }

private File Gzip(File f) throws IOException { if (f == null || !f.exists()) return null; File dest_dir = f.getParentFile(); String dest_filename = f.getName() + ".gz"; File zipfile = new File(dest_dir, dest_filename); GZIPOutputStream out = new GZIPOutputStream(new FileOutputStream(zipfile)); FileInputStream in = new FileInputStream(f); byte buf[] = new byte[1024]; int len; while ((len = in.read(buf)) > 0) out.write(buf, 0, len); out.finish(); try { in.close(); } catch (Exception e) { } try { out.close(); } catch (Exception e) { } try { f.delete(); } catch (Exception e) { } return zipfile; }

public static void invokeMvnArtifact(final IProject project, final IModuleExtension moduleExtension, final String location) throws CoreException, InterruptedException, IOException { final Properties properties = new Properties(); properties.put("archetypeGroupId", "org.nexopenframework.plugins"); properties.put("archetypeArtifactId", "openfrwk-archetype-webmodule"); final String version = org.maven.ide.eclipse.ext.Maven2Plugin.getArchetypeVersion(); properties.put("archetypeVersion", version); properties.put("artifactId", moduleExtension.getArtifact()); properties.put("groupId", moduleExtension.getGroup()); properties.put("version", moduleExtension.getVersion()); final ILaunchManager launchManager = DebugPlugin.getDefault().getLaunchManager(); final ILaunchConfigurationType launchConfigurationType = launchManager.getLaunchConfigurationType(LAUNCH_CONFIGURATION_TYPE_ID); final ILaunchConfigurationWorkingCopy workingCopy = launchConfigurationType.newInstance(null, "Creating WEB module using Apache Maven archetype"); File archetypePomDirectory = getDefaultArchetypePomDirectory(); try { final String dfPom = getPomFile(moduleExtension.getGroup(), moduleExtension.getArtifact()); final ByteArrayInputStream bais = new ByteArrayInputStream(dfPom.getBytes()); final File f = new File(archetypePomDirectory, "pom.xml"); OutputStream fous = null; try { fous = new FileOutputStream(f); IOUtils.copy(bais, fous); } finally { try { if (fous != null) { fous.close(); } if (bais != null) { bais.close(); } } catch (final IOException e) { } } String goalName = "archetype:create"; boolean offline = false; try { final Class clazz = Thread.currentThread().getContextClassLoader().loadClass("org.maven.ide.eclipse.Maven2Plugin"); final Maven2Plugin plugin = (Maven2Plugin) clazz.getMethod("getDefault", new Class[0]).invoke(null, new Object[0]); offline = plugin.getPreferenceStore().getBoolean("eclipse.m2.offline"); } catch (final ClassNotFoundException e) { Logger.logException("No class [org.maven.ide.eclipse.ext.Maven2Plugin] in classpath", e); } catch (final NoSuchMethodException e) { Logger.logException("No method getDefault", e); } catch (final Throwable e) { Logger.logException(e); } if (offline) { goalName = new StringBuffer(goalName).append(" -o").toString(); } if (!offline) { final IPreferenceStore ps = Maven2Plugin.getDefault().getPreferenceStore(); final String repositories = ps.getString(Maven2PreferenceConstants.P_M2_REPOSITORIES); final String[] repos = repositories.split(org.maven.ide.eclipse.ext.Maven2Plugin.REPO_SEPARATOR); final StringBuffer sbRepos = new StringBuffer(); for (int k = 0; k < repos.length; k++) { sbRepos.append(repos[k]); if (k != repos.length - 1) { sbRepos.append(","); } } properties.put("remoteRepositories", sbRepos.toString()); } workingCopy.setAttribute(ATTR_GOALS, goalName); workingCopy.setAttribute(ATTR_POM_DIR, archetypePomDirectory.getAbsolutePath()); workingCopy.setAttribute(ATTR_PROPERTIES, convertPropertiesToList(properties)); final long timeout = org.maven.ide.eclipse.ext.Maven2Plugin.getTimeout(); TimeoutLaunchConfiguration.launchWithTimeout(new NullProgressMonitor(), workingCopy, project, timeout); FileUtils.copyDirectoryStructure(new File(archetypePomDirectory, project.getName()), new File(location)); FileUtils.deleteDirectory(new File(location + "/src")); FileUtils.forceDelete(new File(location, "pom.xml")); project.refreshLocal(IResource.DEPTH_INFINITE, null); } finally { FileUtils.deleteDirectory(archetypePomDirectory); Logger.log(Logger.INFO, "Invoked removing of archetype POM directory"); } }

public void modify(ModifyInterceptorChain chain, DistinguishedName dn, ArrayList<LDAPModification> mods, LDAPConstraints constraints) throws LDAPException { Connection con = (Connection) chain.getRequest().get(JdbcInsert.MYVD_DB_CON + this.dbInsertName); if (con == null) { throw new LDAPException("Operations Error", LDAPException.OPERATIONS_ERROR, "No Database Connection"); } try { con.setAutoCommit(false); HashMap<String, String> ldap2db = (HashMap<String, String>) chain.getRequest().get(JdbcInsert.MYVD_DB_LDAP2DB + this.dbInsertName); Iterator<LDAPModification> it = mods.iterator(); String sql = "UPDATE " + this.tableName + " SET "; while (it.hasNext()) { LDAPModification mod = it.next(); if (mod.getOp() != LDAPModification.REPLACE) { throw new LDAPException("Only modify replace allowed", LDAPException.OBJECT_CLASS_VIOLATION, ""); } sql += ldap2db.get(mod.getAttribute().getName()) + "=? "; } sql += " WHERE " + this.rdnField + "=?"; PreparedStatement ps = con.prepareStatement(sql); it = mods.iterator(); int i = 1; while (it.hasNext()) { LDAPModification mod = it.next(); ps.setString(i, mod.getAttribute().getStringValue()); i++; } String uid = ((RDN) dn.getDN().getRDNs().get(0)).getValue(); ps.setString(i, uid); ps.executeUpdate(); con.commit(); } catch (SQLException e) { try { con.rollback(); } catch (SQLException e1) { throw new LDAPException("Could not delete entry or rollback transaction", LDAPException.OPERATIONS_ERROR, e.toString(), e); } throw new LDAPException("Could not delete entry", LDAPException.OPERATIONS_ERROR, e.toString(), e); } }

public String getContent(URL url) { Logger.getLogger(this.getClass().getName()).log(Level.INFO, "getting content from " + url.toString()); String content = ""; try { URLConnection httpc; httpc = url.openConnection(); httpc.setDoInput(true); httpc.connect(); BufferedReader in = new BufferedReader(new InputStreamReader(httpc.getInputStream())); String line = ""; while ((line = in.readLine()) != null) { content = content + line; } in.close(); } catch (IOException e) { Logger.getLogger(this.getClass().getName()).log(Level.SEVERE, "Problem writing to " + url, e); } return content; }

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

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

public static void copyFile(File src, File dst) throws IOException { LOGGER.info("Copying file '" + src.getAbsolutePath() + "' to '" + dst.getAbsolutePath() + "'"); FileChannel in = null; FileChannel out = null; try { FileInputStream fis = new FileInputStream(src); in = fis.getChannel(); FileOutputStream fos = new FileOutputStream(dst); out = fos.getChannel(); out.transferFrom(in, 0, in.size()); } finally { try { if (in != null) in.close(); } catch (IOException e) { LOGGER.log(Level.SEVERE, e.getMessage(), e); } if (out != null) { try { out.close(); } catch (IOException e) { LOGGER.log(Level.SEVERE, e.getMessage(), e); } } } }

@Override public RServiceResponse execute(final NexusServiceRequest inData) throws NexusServiceException { final RServiceRequest data = (RServiceRequest) inData; final RServiceResponse retval = new RServiceResponse(); final StringBuilder result = new StringBuilder("R service call results:\n"); RSession session; RConnection connection = null; try { result.append("Session Attachment: \n"); final byte[] sessionBytes = data.getSession(); if (sessionBytes != null && sessionBytes.length > 0) { session = RUtils.getInstance().bytesToSession(sessionBytes); result.append(" attaching to " + session + "\n"); connection = session.attach(); } else { result.append(" creating new session\n"); connection = new RConnection(data.getServerAddress()); } result.append("Input Parameters: \n"); for (String attributeName : data.getInputVariables().keySet()) { final Object parameter = data.getInputVariables().get(attributeName); if (parameter instanceof URI) { final FileObject file = VFS.getManager().resolveFile(((URI) parameter).toString()); final RFileOutputStream ros = connection.createFile(file.getName().getBaseName()); IOUtils.copy(file.getContent().getInputStream(), ros); connection.assign(attributeName, file.getName().getBaseName()); } else { connection.assign(attributeName, RUtils.getInstance().convertToREXP(parameter)); } result.append(" " + parameter.getClass().getSimpleName() + " " + attributeName + "=" + parameter + "\n"); } final REXP rExpression = connection.eval(RUtils.getInstance().wrapCode(data.getCode().replace('\r', '\n'))); result.append("Execution results:\n" + rExpression.asString() + "\n"); if (rExpression.isNull() || rExpression.asString().startsWith("Error")) { retval.setErr(rExpression.asString()); throw new NexusServiceException("R error: " + rExpression.asString()); } result.append("Output Parameters:\n"); final String[] rVariables = connection.eval("ls();").asStrings(); for (String varname : rVariables) { final String[] rVariable = connection.eval("class(" + varname + ")").asStrings(); if (rVariable.length == 2 && "file".equals(rVariable[0]) && "connection".equals(rVariable[1])) { final String rFileName = connection.eval("showConnections(TRUE)[" + varname + "]").asString(); result.append(" R File ").append(varname).append('=').append(rFileName).append('\n'); final RFileInputStream rInputStream = connection.openFile(rFileName); final File file = File.createTempFile("nexus-" + data.getRequestId(), ".dat"); IOUtils.copy(rInputStream, new FileOutputStream(file)); retval.getOutputVariables().put(varname, file.getCanonicalFile().toURI()); } else { final Object varvalue = RUtils.getInstance().convertREXP(connection.eval(varname)); retval.getOutputVariables().put(varname, varvalue); final String printValue = varvalue == null ? "null" : varvalue.getClass().isArray() ? Arrays.asList(varvalue).toString() : varvalue.toString(); result.append(" ").append(varvalue == null ? "" : varvalue.getClass().getSimpleName()).append(' ').append(varname).append('=').append(printValue).append('\n'); } } } catch (ClassNotFoundException cnfe) { retval.setErr(cnfe.getMessage()); LOGGER.error("Rserve Exception", cnfe); } catch (RserveException rse) { retval.setErr(rse.getMessage()); LOGGER.error("Rserve Exception", rse); } catch (REXPMismatchException rme) { retval.setErr(rme.getMessage()); LOGGER.error("REXP Mismatch Exception", rme); } catch (IOException rme) { retval.setErr(rme.getMessage()); LOGGER.error("IO Exception copying file ", rme); } finally { result.append("Session Detachment:\n"); if (connection != null) { RSession outSession; if (retval.isKeepSession()) { try { outSession = connection.detach(); } catch (RserveException e) { LOGGER.debug("Error detaching R session", e); outSession = null; } } else { outSession = null; } final boolean close = outSession == null; if (!close) { retval.setSession(RUtils.getInstance().sessionToBytes(outSession)); result.append(" suspended session for later use\n"); } connection.close(); retval.setSession(null); result.append(" session closed.\n"); } } retval.setOut(result.toString()); return retval; }

public static void copyFile(File source, String target) throws FileNotFoundException, IOException { File fout = new File(target); fout.mkdirs(); fout.delete(); fout = new File(target); FileChannel in = new FileInputStream(source).getChannel(); FileChannel out = new FileOutputStream(target).getChannel(); in.transferTo(0, in.size(), out); in.close(); out.close(); }

protected void createFile(File sourceActionDirectory, File destinationActionDirectory, LinkedList<String> segments) throws DuplicateActionFileException { File currentSrcDir = sourceActionDirectory; File currentDestDir = destinationActionDirectory; String segment = ""; for (int i = 0; i < segments.size() - 1; i++) { segment = segments.get(i); currentSrcDir = new File(currentSrcDir, segment); currentDestDir = new File(currentDestDir, segment); } if (currentSrcDir != null && currentDestDir != null) { File srcFile = new File(currentSrcDir, segments.getLast()); if (srcFile.exists()) { File destFile = new File(currentDestDir, segments.getLast()); if (destFile.exists()) { throw new DuplicateActionFileException(srcFile.toURI().toASCIIString()); } try { FileChannel srcChannel = new FileInputStream(srcFile).getChannel(); FileChannel destChannel = new FileOutputStream(destFile).getChannel(); ByteBuffer buffer = ByteBuffer.allocate((int) srcChannel.size()); while (srcChannel.position() < srcChannel.size()) { srcChannel.read(buffer); } srcChannel.close(); buffer.rewind(); destChannel.write(buffer); destChannel.close(); } catch (Exception ex) { ex.printStackTrace(); } } } }

public void transport(File file) throws TransportException { FTPClient client = new FTPClient(); try { client.connect(getOption("host")); client.login(getOption("username"), getOption("password")); client.changeWorkingDirectory(getOption("remotePath")); transportRecursive(client, file); client.disconnect(); } catch (Exception e) { throw new TransportException(e); } }

public static String hashValue(String password, String salt) throws TeqloException { MessageDigest md = null; try { md = MessageDigest.getInstance("SHA"); md.update(password.getBytes("UTF-8")); md.update(salt.getBytes("UTF-8")); byte raw[] = md.digest(); char[] encoded = (new BASE64Encoder()).encode(raw).toCharArray(); int length = encoded.length; while (length > 0 && encoded[length - 1] == '=') length--; for (int i = 0; i < length; i++) { if (encoded[i] == '+') encoded[i] = '*'; else if (encoded[i] == '/') encoded[i] = '-'; } return new String(encoded, 0, length); } catch (Exception e) { throw new TeqloException("Security", "password", e, "Could not process password"); } }

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()); } } }

public boolean backupFile(File oldFile, File newFile) { boolean isBkupFileOK = false; FileChannel sourceChannel = null; FileChannel targetChannel = null; try { sourceChannel = new FileInputStream(oldFile).getChannel(); targetChannel = new FileOutputStream(newFile).getChannel(); targetChannel.transferFrom(sourceChannel, 0, sourceChannel.size()); } catch (IOException e) { logger.log(Level.SEVERE, "IO exception occurred while copying config file", e); } finally { if ((newFile != null) && (newFile.exists()) && (newFile.length() > 0)) { isBkupFileOK = true; } try { if (sourceChannel != null) { sourceChannel.close(); } if (targetChannel != null) { targetChannel.close(); } } catch (IOException e) { logger.log(Level.INFO, "closing channels failed"); } } return isBkupFileOK; }

public DoSearch(String searchType, String searchString) { String urlString = dms_url + "/servlet/com.ufnasoft.dms.server.ServerDoSearch"; String rvalue = ""; String filename = dms_home + FS + "temp" + FS + username + "search.xml"; try { String urldata = urlString + "?username=" + URLEncoder.encode(username, "UTF-8") + "&key=" + key + "&search=" + URLEncoder.encode(searchString, "UTF-8") + "&searchtype=" + URLEncoder.encode(searchType, "UTF-8") + "&filename=" + URLEncoder.encode(username, "UTF-8") + "search.xml"; ; DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); DocumentBuilder parser = factory.newDocumentBuilder(); URL u = new URL(urldata); DataInputStream is = new DataInputStream(u.openStream()); FileOutputStream os = new FileOutputStream(filename); int iBufSize = is.available(); byte inBuf[] = new byte[20000 * 1024]; int iNumRead; while ((iNumRead = is.read(inBuf, 0, iBufSize)) > 0) os.write(inBuf, 0, iNumRead); os.close(); is.close(); File f = new File(filename); InputStream inputstream = new FileInputStream(f); Document document = parser.parse(inputstream); NodeList nodelist = document.getElementsByTagName("entry"); int num = nodelist.getLength(); searchDocs = new String[num][3]; searchDocImageName = new String[num]; searchDocsToolTip = new String[num]; for (int i = 0; i < num; i++) { searchDocs[i][0] = DOMUtil.getSimpleElementText((Element) nodelist.item(i), "filename"); searchDocs[i][1] = DOMUtil.getSimpleElementText((Element) nodelist.item(i), "project"); searchDocs[i][2] = DOMUtil.getSimpleElementText((Element) nodelist.item(i), "documentid"); searchDocImageName[i] = DOMUtil.getSimpleElementText((Element) nodelist.item(i), "imagename"); searchDocsToolTip[i] = DOMUtil.getSimpleElementText((Element) nodelist.item(i), "description"); } } catch (MalformedURLException ex) { System.out.println(ex); } catch (ParserConfigurationException ex) { System.out.println(ex); } catch (Exception ex) { System.out.println(ex); } System.out.println(rvalue); if (rvalue.equalsIgnoreCase("yes")) { } }

private void backupFile(ZipOutputStream out, String base, String fn) throws IOException { String f = FileUtils.getAbsolutePath(fn); base = FileUtils.getAbsolutePath(base); if (!f.startsWith(base)) { Message.throwInternalError(f + " does not start with " + base); } f = f.substring(base.length()); f = correctFileName(f); out.putNextEntry(new ZipEntry(f)); InputStream in = FileUtils.openFileInputStream(fn); IOUtils.copyAndCloseInput(in, out); out.closeEntry(); }

private static void insertModuleInEar(File fromEar, File toEar, String moduleType, String moduleName, String contextRoot) throws Exception { ZipInputStream earFile = new ZipInputStream(new FileInputStream(fromEar)); FileOutputStream fos = new FileOutputStream(toEar); ZipOutputStream tempZip = new ZipOutputStream(fos); ZipEntry next = earFile.getNextEntry(); while (next != null) { ByteArrayOutputStream content = new ByteArrayOutputStream(); byte[] data = new byte[30000]; int numberread; while ((numberread = earFile.read(data)) != -1) { content.write(data, 0, numberread); } if (next.getName().equals("META-INF/application.xml")) { content = insertModule(earFile, next, content, moduleType, moduleName, contextRoot); next = new ZipEntry("META-INF/application.xml"); } tempZip.putNextEntry(next); tempZip.write(content.toByteArray()); next = earFile.getNextEntry(); } earFile.close(); tempZip.close(); fos.close(); }

public void zipFile(String baseDir, String fileName, boolean encrypt) throws Exception { List fileList = getSubFiles(new File(baseDir)); ZipOutputStream zos = new ZipOutputStream(new FileOutputStream(fileName + ".temp")); ZipEntry ze = null; byte[] buf = new byte[BUFFER]; byte[] encrypByte = new byte[encrypLength]; int readLen = 0; for (int i = 0; i < fileList.size(); i++) { if (stopZipFile) { zos.close(); File zipFile = new File(fileName + ".temp"); if (zipFile.exists()) zipFile.delete(); break; } File f = (File) fileList.get(i); if (f.getAbsoluteFile().equals(fileName + ".temp")) continue; ze = new ZipEntry(getAbsFileName(baseDir, f)); ze.setSize(f.length()); ze.setTime(f.lastModified()); zos.putNextEntry(ze); InputStream is = new BufferedInputStream(new FileInputStream(f)); readLen = is.read(buf, 0, BUFFER); if (encrypt) { if (readLen >= encrypLength) { System.arraycopy(buf, 0, encrypByte, 0, encrypLength); } else if (readLen > 0) { Arrays.fill(encrypByte, (byte) 0); System.arraycopy(buf, 0, encrypByte, 0, readLen); readLen = encrypLength; } byte[] temp = CryptionControl.getInstance().encryptoECB(encrypByte, rootKey); System.arraycopy(temp, 0, buf, 0, encrypLength); } while (readLen != -1) { zos.write(buf, 0, readLen); readLen = is.read(buf, 0, BUFFER); } is.close(); } zos.close(); File zipFile = new File(fileName + ".temp"); if (zipFile.exists()) zipFile.renameTo(new File(fileName + ".zip")); }

public void run() { if (software == null) return; Jvm.hashtable(HKEY).put(software, this); try { software.setException(null); software.setDownloaded(false); software.setDownloadStartTime(System.currentTimeMillis()); try { software.downloadStarted(); } catch (Exception dsx) { } if (software.getDownloadDir() == null) { software.setException(new Exception("The DownloadDir is null.")); software.setDownloadStartTime(0); software.setDownloaded(false); throw software.getException(); } URL url = new URL(software.getURL()); URLConnection con = url.openConnection(); software.setDownloadLength(con.getContentLength()); inputStream = con.getInputStream(); File file = new File(software.getDownloadDir(), software.getURLFilename()); outputStream = new FileOutputStream(file); int totalBytes = 0; byte[] buffer = new byte[8192]; while (!cancelled) { int bytesRead = Jvm.copyPartialStream(inputStream, outputStream, buffer); if (bytesRead == -1) break; totalBytes += bytesRead; try { software.downloadProgress(totalBytes); } catch (Exception dx) { } } if (!cancelled) software.setDownloaded(true); } catch (Exception x) { software.setException(x); software.setDownloadStartTime(0); software.setDownloaded(false); } try { software.downloadComplete(); } catch (Exception dcx) { } Jvm.hashtable(HKEY).remove(software); closeStreams(); }

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

private static Long getNextPkValueForEntityIncreaseBy(String ename, int count, int increaseBy) { if (increaseBy < 1) increaseBy = 1; String where = "where eoentity_name = '" + ename + "'"; ERXJDBCConnectionBroker broker = ERXJDBCConnectionBroker.connectionBrokerForEntityNamed(ename); Connection con = broker.getConnection(); try { try { con.setAutoCommit(false); con.setReadOnly(false); } catch (SQLException e) { log.error(e, e); } for (int tries = 0; tries < count; tries++) { try { ResultSet resultSet = con.createStatement().executeQuery("select pk_value from pk_table " + where); con.commit(); boolean hasNext = resultSet.next(); long pk = 1; if (hasNext) { pk = resultSet.getLong("pk_value"); con.createStatement().executeUpdate("update pk_table set pk_value = " + (pk + increaseBy) + " " + where); } else { pk = maxIdFromTable(ename); con.createStatement().executeUpdate("insert into pk_table (eoentity_name, pk_value) values ('" + ename + "', " + (pk + increaseBy) + ")"); } con.commit(); return new Long(pk); } catch (SQLException ex) { String s = ex.getMessage().toLowerCase(); boolean creationError = (s.indexOf("error code 116") != -1); creationError |= (s.indexOf("pk_table") != -1 && s.indexOf("does not exist") != -1); creationError |= s.indexOf("ora-00942") != -1; if (creationError) { try { con.rollback(); log.info("creating pk table"); con.createStatement().executeUpdate("create table pk_table (eoentity_name varchar(100) not null, pk_value integer)"); con.createStatement().executeUpdate("alter table pk_table add primary key (eoentity_name)"); con.commit(); } catch (SQLException ee) { throw new NSForwardException(ee, "could not create pk table"); } } else { throw new NSForwardException(ex, "Error fetching PK"); } } } } finally { broker.freeConnection(con); } throw new IllegalStateException("Couldn't get PK"); }

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

public static URLConnection openRemoteDescriptionFile(String urlstr) throws MalformedURLException { URL url = new URL(urlstr); try { URLConnection conn = url.openConnection(); conn.connect(); return conn; } catch (Exception e) { Config conf = Config.loadConfig(); SimpleSocketAddress localServAddr = conf.getLocalProxyServerAddress(); Proxy proxy = new Proxy(Type.HTTP, new InetSocketAddress(localServAddr.host, localServAddr.port)); URLConnection conn; try { conn = url.openConnection(proxy); conn.connect(); return conn; } catch (IOException e1) { logger.error("Failed to retrive desc file:" + url, e1); } } return null; }

public static byte[] generateAuthId(String userName, String password) { byte[] ret = new byte[16]; try { MessageDigest messageDigest = MessageDigest.getInstance("MD5"); String str = userName + password; messageDigest.update(str.getBytes()); ret = messageDigest.digest(); } catch (NoSuchAlgorithmException ex) { ex.printStackTrace(); } return ret; }

public static String hashSHA1(String value) { try { MessageDigest digest = MessageDigest.getInstance("SHA-1"); digest.update(value.getBytes()); BigInteger hash = new BigInteger(1, digest.digest()); return hash.toString(16); } catch (NoSuchAlgorithmException e) { } return null; }

public void importCertFile(File file) throws IOException { File kd; File cd; synchronized (this) { kd = keysDir; cd = certsDir; } if (!cd.isDirectory()) { kd.mkdirs(); cd.mkdirs(); } String newName = file.getName(); File dest = new File(cd, newName); FileChannel sourceChannel = null; FileChannel destinationChannel = null; try { sourceChannel = new FileInputStream(file).getChannel(); destinationChannel = new FileOutputStream(dest).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), destinationChannel); } finally { if (sourceChannel != null) { try { sourceChannel.close(); } catch (IOException e) { } } if (destinationChannel != null) { try { destinationChannel.close(); } catch (IOException e) { } } } }

public void aprovarCandidato(Atividade atividade) throws SQLException { Connection conn = null; String insert = "update Atividade_has_recurso_humano set ativo='true' " + "where atividade_idatividade=" + atividade.getIdAtividade() + " and " + " usuario_idusuario=" + atividade.getRecursoHumano().getIdUsuario(); try { conn = connectionFactory.getConnection(true); conn.setAutoCommit(false); Statement stmt = conn.createStatement(); Integer result = stmt.executeUpdate(insert); conn.commit(); } catch (SQLException e) { conn.rollback(); throw e; } finally { conn.close(); } }

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

public static final String md5(final String s) { try { MessageDigest digest = java.security.MessageDigest.getInstance("MD5"); digest.update(s.getBytes()); byte messageDigest[] = digest.digest(); StringBuffer hexString = new StringBuffer(); for (int i = 0; i < messageDigest.length; i++) { String h = Integer.toHexString(0xFF & messageDigest[i]); while (h.length() < 2) h = "0" + h; hexString.append(h); } return hexString.toString(); } catch (NoSuchAlgorithmException e) { } return ""; }

protected void runTests(URL pBaseURL, String pName, String pHref) throws Exception { URL url = new URL(pBaseURL, pHref); InputSource isource = new InputSource(url.openStream()); isource.setSystemId(url.toString()); Document document = getDocumentBuilder().parse(isource); NodeList schemas = document.getElementsByTagNameNS(null, "Schema"); for (int i = 0; i < schemas.getLength(); i++) { Element schema = (Element) schemas.item(i); runTest(url, schema.getAttribute("name"), schema.getAttribute("href")); } }

private void externalizeFiles(Document doc, File out) throws IOException { File[] files = doc.getImages(); if (files.length > 0) { File dir = new File(out.getParentFile(), out.getName() + ".images"); if (!dir.mkdirs()) throw new IOException("cannot create directory " + dir); if (dir.exists()) { for (int i = 0; i < files.length; i++) { File file = files[i]; File copy = new File(dir, file.getName()); FileChannel from = null, to = null; long count = -1; try { from = new FileInputStream(file).getChannel(); count = from.size(); to = new FileOutputStream(copy).getChannel(); from.transferTo(0, count, to); doc.setImage(file, dir.getName() + "/" + copy.getName()); } catch (Throwable t) { LOG.log(Level.WARNING, "Copying '" + file + "' to '" + copy + "' failed (size=" + count + ")", t); } finally { try { to.close(); } catch (Throwable t) { } try { from.close(); } catch (Throwable t) { } } } } } }

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"))); }

private void copyResources(File oggDecDir, String[] resources, String resPrefix) throws FileNotFoundException, IOException { for (int i = 0; i < resources.length; i++) { String res = resPrefix + resources[i]; InputStream is = this.getClass().getResourceAsStream(res); if (is == null) throw new IllegalArgumentException("cannot find resource '" + res + "'"); File file = new File(oggDecDir, resources[i]); if (!file.exists() || file.length() == 0) { FileOutputStream fos = new FileOutputStream(file); try { IOUtils.copyStreams(is, fos); } finally { fos.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!"); }

private void packageDestZip(File tmpFile) throws FileNotFoundException, IOException { log("Creating launch profile package " + destfile); ZipOutputStream out = new ZipOutputStream(new BufferedOutputStream(new FileOutputStream(destfile))); ZipEntry e = new ZipEntry(RESOURCE_JAR_FILENAME); e.setMethod(ZipEntry.STORED); e.setSize(tmpFile.length()); e.setCompressedSize(tmpFile.length()); e.setCrc(calcChecksum(tmpFile, new CRC32())); out.putNextEntry(e); InputStream in = new BufferedInputStream(new FileInputStream(tmpFile)); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.closeEntry(); out.finish(); out.close(); }

public boolean copyFile(File source, File dest) { try { FileReader in = new FileReader(source); FileWriter out = new FileWriter(dest); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); return true; } catch (Exception e) { return false; } }

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

public static String crypt(String password, String salt) { if (salt.startsWith(magic)) { salt = salt.substring(magic.length()); } int saltEnd = salt.indexOf('$'); if (saltEnd != -1) { salt = salt.substring(0, saltEnd); } if (salt.length() > 8) { salt = salt.substring(0, 8); } MessageDigest md5_1, md5_2; try { md5_1 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); return null; } md5_1.update(password.getBytes()); md5_1.update(magic.getBytes()); md5_1.update(salt.getBytes()); try { md5_2 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); return null; } md5_2.update(password.getBytes()); md5_2.update(salt.getBytes()); md5_2.update(password.getBytes()); byte[] md5_2_digest = md5_2.digest(); int md5Size = md5_2_digest.length; int pwLength = password.length(); for (int i = pwLength; i > 0; i -= md5Size) { md5_1.update(md5_2_digest, 0, i > md5Size ? md5Size : i); } md5_2.reset(); byte[] pwBytes = password.getBytes(); for (int i = pwLength; i > 0; i >>= 1) { if ((i & 1) == 1) { md5_1.update((byte) 0); } else { md5_1.update(pwBytes[0]); } } StringBuffer output = new StringBuffer(magic); output.append(salt); output.append("$"); byte[] md5_1_digest = md5_1.digest(); byte[] saltBytes = salt.getBytes(); for (int i = 0; i < 1000; i++) { md5_2.reset(); if ((i & 1) == 1) { md5_2.update(pwBytes); } else { md5_2.update(md5_1_digest); } if (i % 3 != 0) { md5_2.update(saltBytes); } if (i % 7 != 0) { md5_2.update(pwBytes); } if ((i & 1) != 0) { md5_2.update(md5_1_digest); } else { md5_2.update(pwBytes); } md5_1_digest = md5_2.digest(); } int value; value = ((md5_1_digest[0] & 0xff) << 16) | ((md5_1_digest[6] & 0xff) << 8) | (md5_1_digest[12] & 0xff); output.append(cryptTo64(value, 4)); value = ((md5_1_digest[1] & 0xff) << 16) | ((md5_1_digest[7] & 0xff) << 8) | (md5_1_digest[13] & 0xff); output.append(cryptTo64(value, 4)); value = ((md5_1_digest[2] & 0xff) << 16) | ((md5_1_digest[8] & 0xff) << 8) | (md5_1_digest[14] & 0xff); output.append(cryptTo64(value, 4)); value = ((md5_1_digest[3] & 0xff) << 16) | ((md5_1_digest[9] & 0xff) << 8) | (md5_1_digest[15] & 0xff); output.append(cryptTo64(value, 4)); value = ((md5_1_digest[4] & 0xff) << 16) | ((md5_1_digest[10] & 0xff) << 8) | (md5_1_digest[5] & 0xff); output.append(cryptTo64(value, 4)); value = md5_1_digest[11] & 0xff; output.append(cryptTo64(value, 2)); md5_1 = null; md5_2 = null; md5_1_digest = null; md5_2_digest = null; pwBytes = null; saltBytes = null; password = salt = null; return output.toString(); }

public void put(IMetaCollection aCollection) throws TransducerException { if (null != ioTransducer) { try { URL urlObj = new URL(url); URLConnection urlConn = urlObj.openConnection(); OutputStreamWriter sw = new OutputStreamWriter(urlConn.getOutputStream()); ioTransducer.setWriter(new BufferedWriter(sw)); ioTransducer.put(aCollection); } catch (Exception e) { throw new TransducerException(e); } } else { throw new TransducerException("An IIOTransducer instance must first be set on the URLTransducerAdapter."); } }

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

public void run() { URLConnection con = null; try { con = url.openConnection(); if ("HTTPS".equalsIgnoreCase(url.getProtocol())) { HttpsURLConnection scon = (HttpsURLConnection) con; try { scon.setSSLSocketFactory(SSLUtil.getSSLSocketFactory(clientCertAlias)); HostnameVerifier hv = SSLUtil.getHostnameVerifier(hostCertLevel); if (hv != null) { scon.setHostnameVerifier(hv); } } catch (GeneralSecurityException e) { Debug.logError(e, module); } catch (GenericConfigException e) { Debug.logError(e, module); } } } catch (IOException e) { Debug.logError(e, module); } synchronized (URLConnector.this) { if (timedOut && con != null) { close(con); } else { connection = con; URLConnector.this.notify(); } } }

String fetch_m3u(String m3u) { InputStream pstream = null; if (m3u.startsWith("http://")) { try { URL url = null; if (running_as_applet) url = new URL(getCodeBase(), m3u); else url = new URL(m3u); URLConnection urlc = url.openConnection(); pstream = urlc.getInputStream(); } catch (Exception ee) { System.err.println(ee); return null; } } if (pstream == null && !running_as_applet) { try { pstream = new FileInputStream(System.getProperty("user.dir") + System.getProperty("file.separator") + m3u); } catch (Exception ee) { System.err.println(ee); return null; } } String line = null; while (true) { try { line = readline(pstream); } catch (Exception e) { } if (line == null) break; return line; } return null; }

public void jsFunction_addFile(ScriptableFile infile) throws IOException { if (!infile.jsFunction_exists()) throw new IllegalArgumentException("Cannot add a file that doesn't exists to an archive"); ZipArchiveEntry entry = new ZipArchiveEntry(infile.getName()); entry.setSize(infile.jsFunction_getSize()); out.putArchiveEntry(entry); try { InputStream inStream = infile.jsFunction_createInputStream(); IOUtils.copy(inStream, out); inStream.close(); } finally { out.closeArchiveEntry(); } }

public void run() { LOG.debug(this); String[] parts = createCmdArray(getCommand()); Runtime runtime = Runtime.getRuntime(); try { Process process = runtime.exec(parts); if (isBlocking()) { process.waitFor(); StringWriter out = new StringWriter(); IOUtils.copy(process.getInputStream(), out); String stdout = out.toString().replaceFirst("\\s+$", ""); if (StringUtils.isNotBlank(stdout)) { LOG.info("Process stdout:\n" + stdout); } StringWriter err = new StringWriter(); IOUtils.copy(process.getErrorStream(), err); String stderr = err.toString().replaceFirst("\\s+$", ""); if (StringUtils.isNotBlank(stderr)) { LOG.error("Process stderr:\n" + stderr); } } } catch (IOException ioe) { LOG.error(String.format("Could not exec [%s]", getCommand()), ioe); } catch (InterruptedException ie) { LOG.error(String.format("Interrupted [%s]", getCommand()), ie); } }

private static boolean prepareQualifyingFile(String completePath, String outputFile) { try { File inFile = new File(completePath + fSep + "qualifying.txt"); FileChannel inC = new FileInputStream(inFile).getChannel(); BufferedReader br = new BufferedReader(new FileReader(inFile)); File outFile = new File(completePath + fSep + "SmartGRAPE" + fSep + outputFile); FileChannel outC = new FileOutputStream(outFile, true).getChannel(); boolean endOfFile = true; short movieName = 0; int customer = 0; while (endOfFile) { String line = br.readLine(); if (line != null) { if (line.indexOf(":") >= 0) { movieName = new Short(line.substring(0, line.length() - 1)).shortValue(); } else { customer = new Integer(line.substring(0, line.indexOf(","))).intValue(); ByteBuffer outBuf = ByteBuffer.allocate(6); outBuf.putShort(movieName); outBuf.putInt(customer); outBuf.flip(); outC.write(outBuf); } } else endOfFile = false; } br.close(); outC.close(); return true; } catch (IOException e) { System.err.println(e); return false; } }

public HttpClient(String urlString, String jsonMessage) throws Exception { this.jsonMessage = jsonMessage; connection = (HttpURLConnection) (new URL(urlString)).openConnection(); connection.setDoOutput(true); connection.setDoInput(true); connection.setRequestMethod("POST"); connection.setRequestProperty("Content-type", "text/plain"); }

public void copyFile(File sourceFile, File destFile) throws IOException { Log.level3("Copying " + sourceFile.getPath() + " to " + destFile.getPath()); if (!destFile.exists()) { destFile.createNewFile(); } FileChannel source = null; FileChannel destination = null; try { source = new FileInputStream(sourceFile).getChannel(); destination = new FileOutputStream(destFile).getChannel(); destination.transferFrom(source, 0, source.size()); } finally { if (source != null) { source.close(); } } if (destination != null) { destination.close(); } }

public static void copyFile(String file1, String file2) { File filedata1 = new java.io.File(file1); if (filedata1.exists()) { try { BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(file2)); BufferedInputStream in = new BufferedInputStream(new FileInputStream(file1)); try { int read; while ((read = in.read()) != -1) { out.write(read); } out.flush(); } catch (IOException ex1) { ex1.printStackTrace(); } finally { out.close(); in.close(); } } catch (Exception ex) { ex.printStackTrace(); } } }

protected Collection<BibtexEntry> getBibtexEntries(String ticket, String citations) throws IOException { try { URL url = new URL(URL_BIBTEX); URLConnection conn = url.openConnection(); conn.setRequestProperty("Cookie", ticket + "; " + citations); conn.connect(); BibtexParser parser = new BibtexParser(new BufferedReader(new InputStreamReader(conn.getInputStream()))); return parser.parse().getDatabase().getEntries(); } catch (MalformedURLException e) { throw new RuntimeException(e); } }

public static byte[] generateHash(String strPassword, byte[] salt) { try { MessageDigest md = MessageDigest.getInstance(HASH_ALGORITHM); md.update(strPassword.getBytes(CHAR_ENCODING)); md.update(salt); return md.digest(); } catch (Exception e) { e.printStackTrace(); } return null; }

@Override public void save(String arxivId, InputStream inputStream, String encoding) { String filename = StringUtil.arxivid2filename(arxivId, "tex"); try { Writer writer = new OutputStreamWriter(new FileOutputStream(String.format("%s/%s", LATEX_DOCUMENT_DIR, filename)), encoding); IOUtils.copy(inputStream, writer, encoding); writer.flush(); writer.close(); inputStream.close(); } catch (IOException e) { logger.error("Failed to save the Latex source with id='{}'", arxivId, e); throw new RuntimeException(e); } }

private static void doCopyFile(File srcFile, File destFile, boolean preserveFileDate) throws IOException { if (destFile.exists() && destFile.isDirectory()) throw new IOException("Destination '" + destFile + "' exists but is a directory"); FileInputStream input = new FileInputStream(srcFile); try { FileOutputStream output = new FileOutputStream(destFile); try { IOUtils.copy(input, output); } finally { IOUtils.closeQuietly(output); } } finally { IOUtils.closeQuietly(input); } if (srcFile.length() != destFile.length()) throw new IOException("Failed to copy full contents from '" + srcFile + "' to '" + destFile + "'"); if (preserveFileDate) destFile.setLastModified(srcFile.lastModified()); }

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

public void run() { try { URL read = null; if (_readURL.indexOf("?") >= 0) { read = new URL(_readURL + "&id=" + _id); } else { read = new URL(_readURL + "?id=" + _id); } while (_keepGoing) { String line; while ((line = _in.readLine()) != null) { ConnectionHandlerLocal.DEBUG("< " + line); _linesRead++; _listener.incomingMessage(line); } if (_linesRead == 0) { shutdown(true); return; } if (_keepGoing) { URLConnection urlConn = read.openConnection(); urlConn.setUseCaches(false); _in = new DataInputStream(urlConn.getInputStream()); _linesRead = 0; } } System.err.println("HttpReaderThread: stopping gracefully."); } catch (MalformedURLException e) { e.printStackTrace(); } catch (IOException e) { shutdown(true); } }

protected static byte[] httpConnection(Context context, long token, String url, byte[] pdu, int method, boolean isProxySet, String proxyHost, int proxyPort) throws IOException { if (url == null) { throw new IllegalArgumentException("URL must not be null."); } if (LOCAL_LOGV) { Log.v(TAG, "httpConnection: params list"); Log.v(TAG, "\ttoken\t\t= " + token); Log.v(TAG, "\turl\t\t= " + url); Log.v(TAG, "\tUser-Agent\t\t=" + mUserAgent); Log.v(TAG, "\tmethod\t\t= " + ((method == HTTP_POST_METHOD) ? "POST" : ((method == HTTP_GET_METHOD) ? "GET" : "UNKNOWN"))); Log.v(TAG, "\tisProxySet\t= " + isProxySet); Log.v(TAG, "\tproxyHost\t= " + proxyHost); Log.v(TAG, "\tproxyPort\t= " + proxyPort); } AndroidHttpClient client = null; try { URI hostUrl = new URI(url); HttpHost target = new HttpHost(hostUrl.getHost(), hostUrl.getPort(), HttpHost.DEFAULT_SCHEME_NAME); client = createHttpClient(context); HttpRequest req = null; switch(method) { case HTTP_POST_METHOD: ProgressCallbackEntity entity = new ProgressCallbackEntity(context, token, pdu); entity.setContentType("application/vnd.wap.mms-message"); HttpPost post = new HttpPost(url); post.setEntity(entity); req = post; break; case HTTP_GET_METHOD: req = new HttpGet(url); break; default: Log.e(TAG, "Unknown HTTP method: " + method + ". Must be one of POST[" + HTTP_POST_METHOD + "] or GET[" + HTTP_GET_METHOD + "]."); return null; } HttpParams params = client.getParams(); if (isProxySet) { ConnRouteParams.setDefaultProxy(params, new HttpHost(proxyHost, proxyPort)); } req.setParams(params); req.addHeader(HDR_KEY_ACCEPT, HDR_VALUE_ACCEPT); { String xWapProfileTagName = MmsConfig.getUaProfTagName(); String xWapProfileUrl = MmsConfig.getUaProfUrl(); if (xWapProfileUrl != null) { if (Log.isLoggable(LogTag.TRANSACTION, Log.VERBOSE)) { Log.d(LogTag.TRANSACTION, "[HttpUtils] httpConn: xWapProfUrl=" + xWapProfileUrl); } req.addHeader(xWapProfileTagName, xWapProfileUrl); } } String extraHttpParams = MmsConfig.getHttpParams(); if (extraHttpParams != null) { String line1Number = ((TelephonyManager) context.getSystemService(Context.TELEPHONY_SERVICE)).getLine1Number(); String line1Key = MmsConfig.getHttpParamsLine1Key(); String paramList[] = extraHttpParams.split("\\|"); for (String paramPair : paramList) { String splitPair[] = paramPair.split(":", 2); if (splitPair.length == 2) { String name = splitPair[0].trim(); String value = splitPair[1].trim(); if (line1Key != null) { value = value.replace(line1Key, line1Number); } if (!TextUtils.isEmpty(name) && !TextUtils.isEmpty(value)) { req.addHeader(name, value); } } } } req.addHeader(HDR_KEY_ACCEPT_LANGUAGE, HDR_VALUE_ACCEPT_LANGUAGE); HttpResponse response = client.execute(target, req); StatusLine status = response.getStatusLine(); if (status.getStatusCode() != 200) { throw new IOException("HTTP error: " + status.getReasonPhrase()); } HttpEntity entity = response.getEntity(); byte[] body = null; if (entity != null) { try { if (entity.getContentLength() > 0) { body = new byte[(int) entity.getContentLength()]; DataInputStream dis = new DataInputStream(entity.getContent()); try { dis.readFully(body); } finally { try { dis.close(); } catch (IOException e) { Log.e(TAG, "Error closing input stream: " + e.getMessage()); } } } } finally { if (entity != null) { entity.consumeContent(); } } } return body; } catch (URISyntaxException e) { handleHttpConnectionException(e, url); } catch (IllegalStateException e) { handleHttpConnectionException(e, url); } catch (IllegalArgumentException e) { handleHttpConnectionException(e, url); } catch (SocketException e) { handleHttpConnectionException(e, url); } catch (Exception e) { handleHttpConnectionException(e, url); } finally { if (client != null) { client.close(); } } return null; }

public static void main(String args[]) throws Exception { File file = new File("D:/work/love.txt"); @SuppressWarnings("unused") ZipFile zipFile = new ZipFile("D:/work/test1.zip"); ZipOutputStream zos = new ZipOutputStream(new FileOutputStream("D:/work/test1.zip")); zos.setEncoding("GBK"); ZipEntry entry = null; if (file.isDirectory()) { entry = new ZipEntry(getAbsFileName(source, file) + "/"); } else { entry = new ZipEntry(getAbsFileName(source, file)); } entry.setSize(file.length()); entry.setTime(file.lastModified()); zos.putNextEntry(entry); int readLen = 0; byte[] buf = new byte[2048]; if (file.isFile()) { InputStream in = new BufferedInputStream(new FileInputStream(file)); while ((readLen = in.read(buf, 0, 2048)) != -1) { zos.write(buf, 0, readLen); } in.close(); } zos.close(); }

public static void main(String[] args) throws Exception { HttpClient httpclient = new DefaultHttpClient(); InputStream is = CheckAvailability.class.getResourceAsStream("/isbns.txt"); BufferedReader br = new BufferedReader(new InputStreamReader(is)); String isbn = null; HttpGet get = null; while ((isbn = br.readLine().split(" ")[0]) != null) { System.out.println("Target url: \n\t" + String.format(isbnSearchUrl, isbn)); get = new HttpGet(String.format(isbnSearchUrl, isbn)); HttpResponse resp = httpclient.execute(get); Scanner s = new Scanner(resp.getEntity().getContent()); String pattern = s.findWithinHorizon("((\\d*) hold[s]? on first copy returned of (\\d*) )?[cC]opies", 0); if (pattern != null) { MatchResult match = s.match(); if (match.groupCount() == 3) { if (match.group(2) == null) { System.out.println(isbn + ": copies available"); } else { System.out.println(isbn + ": " + match.group(2) + " holds on " + match.group(3) + " copies"); } } } else { System.out.println(isbn + ": no match"); } get.abort(); } }

public void run() { try { URL url = new URL(UPDATE_URL); URLConnection urlc = url.openConnection(); BufferedReader br = new BufferedReader(new InputStreamReader(urlc.getInputStream())); String versionString = br.readLine(); if (versionString != null && !versionString.equals(PinEmUp.VERSION)) { StringBuilder changelogString = new StringBuilder(); changelogString.append("<html>"); changelogString.append("<p>" + I18N.getInstance().getString("info.updateavailable.part1") + "</p>"); changelogString.append("<p>" + I18N.getInstance().getString("info.updateavailable.part2") + " " + PinEmUp.VERSION + "<br />"); changelogString.append(I18N.getInstance().getString("info.updateavailable.part3") + " " + versionString + "</p>"); changelogString.append("<p>" + I18N.getInstance().getString("info.updateavailable.part4") + " <a href=\"http://pinemup.sourceforge.net\">http://pinemup.sourceforge.net</a></p>"); changelogString.append("<p>&nbsp;</p>"); changelogString.append("<p>Changelog:<br />"); changelogString.append("--------------------------------</p><p>"); boolean firstList = true; String nextLine; do { nextLine = br.readLine(); if (nextLine != null) { if (nextLine.startsWith("-")) { changelogString.append("<li>" + nextLine.substring(2) + "</li>"); } else { if (!firstList) { changelogString.append("</ul>"); } else { firstList = false; } changelogString.append(nextLine + "<ul>"); } } } while (nextLine != null); changelogString.append("</p></html>"); new UpdateDialog(changelogString.toString()); } else if (showUpToDateMessage) { JOptionPane.showMessageDialog(null, I18N.getInstance().getString("info.versionuptodate"), I18N.getInstance().getString("info.title"), JOptionPane.INFORMATION_MESSAGE); } br.close(); } catch (IOException e) { } }

public List<String> loadList(String name) { List<String> ret = new ArrayList<String>(); try { URL url = getClass().getClassLoader().getResource("lists/" + name + ".utf-8"); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream(), "UTF-8")); String line; while ((line = reader.readLine()) != null) { ret.add(line); } reader.close(); } catch (IOException e) { showError("No se puede cargar la lista de valores: " + name, e); } return ret; }

private Metadata readMetadataIndexFileFromNetwork(String mediaMetadataURI) throws IOException { Metadata tempMetadata = new Metadata(); URL url = new URL(mediaMetadataURI); BufferedReader input = new BufferedReader(new InputStreamReader(url.openStream())); String tempLine = null; while ((tempLine = input.readLine()) != null) { Property tempProperty = PropertyList.splitStringIntoKeyAndValue(tempLine); if (tempProperty != null) { tempMetadata.addIfNotNull(tempProperty.getKey(), tempProperty.getValue()); } } input.close(); return tempMetadata; }

public static String getSHA1(String data) throws NoSuchAlgorithmException { String addr; data = data.toLowerCase(Locale.getDefault()); if (data.startsWith("mailto:")) { addr = data.substring(7); } else { addr = data; } MessageDigest md = MessageDigest.getInstance("SHA"); StringBuffer sb = new StringBuffer(); md.update(addr.getBytes()); byte[] digest = md.digest(); for (int i = 0; i < digest.length; i++) { String hex = Integer.toHexString(digest[i]); if (hex.length() == 1) { hex = "0" + hex; } hex = hex.substring(hex.length() - 2); sb.append(hex); } return sb.toString(); }

@Test public void testCopy_inputStreamToOutputStream_IO84() throws Exception { long size = (long) Integer.MAX_VALUE + (long) 1; InputStream in = new NullInputStreamTest(size); OutputStream out = new OutputStream() { @Override public void write(int b) throws IOException { } @Override public void write(byte[] b) throws IOException { } @Override public void write(byte[] b, int off, int len) throws IOException { } }; assertEquals(-1, IOUtils.copy(in, out)); in.close(); assertEquals("copyLarge()", size, IOUtils.copyLarge(in, out)); }

private BoardPattern[] getBoardPatterns() { Resource[] resources = boardManager.getResources("boards"); BoardPattern[] boardPatterns = new BoardPattern[resources.length]; for (int i = 0; i < resources.length; i++) boardPatterns[i] = (BoardPattern) resources[i]; for (int i = 0; i < resources.length; i++) { for (int j = 0; j < resources.length - (i + 1); j++) { String name1 = boardPatterns[j].getName(); String name2 = boardPatterns[j + 1].getName(); if (name1.compareTo(name2) > 0) { BoardPattern tmp = boardPatterns[j]; boardPatterns[j] = boardPatterns[j + 1]; boardPatterns[j + 1] = tmp; } } } return boardPatterns; }

private static void salvarObra(Artista artista, Obra obra) throws Exception { Connection conn = null; PreparedStatement ps = null; int categoria; System.out.println("Migracao.salvarObra() obra: " + obra.toString2()); if (obra.getCategoria() != null) { categoria = getCategoria(obra.getCategoria().getNome()).getCodigo(); } else { categoria = getCategoria("Sem Categoria").getCodigo(); } try { conn = C3P0Pool.getConnection(); String sql = "insert into obra VALUES (?,?,?,?,?,?)"; ps = conn.prepareStatement(sql); ps.setNull(1, Types.INTEGER); ps.setString(2, obra.getTitulo()); ps.setInt(3, obra.getSelec()); ps.setInt(4, categoria); ps.setInt(5, artista.getNumeroInscricao()); ps.setInt(6, obra.getCodigo()); ps.executeUpdate(); conn.commit(); } catch (Exception e) { if (conn != null) conn.rollback(); throw e; } finally { close(conn, ps); } }

public void readContents() throws IOException { fireProgressEvent(new ProgressEvent(this, ProgressEvent.PROGRESS_START, 0.0f, "loading file")); URLConnection conn = url.openConnection(); conn.connect(); filesize = conn.getContentLength(); logger.finest("filesize: " + filesize); InputStreamReader in = new InputStreamReader(conn.getInputStream()); readFirstLine(in); readHeaderLines(in); readData(in); fireProgressEvent(new ProgressEvent(this, ProgressEvent.PROGRESS_FINISH, 1.0f, "loading file")); }

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

public InputStream doRemoteCall(NamedList<String> params) throws IOException { String protocol = "http"; String host = getHost(); int port = Integer.parseInt(getPort()); StringBuilder sb = new StringBuilder(); for (Map.Entry entry : params) { Object key = entry.getKey(); Object value = entry.getValue(); sb.append(key).append("=").append(value).append("&"); } sb.setLength(sb.length() - 1); String file = "/" + getUrl() + "/?" + sb.toString(); URL url = new URL(protocol, host, port, file); logger.debug(url.toString()); InputStream stream; HttpURLConnection conn = (HttpURLConnection) url.openConnection(); try { stream = conn.getInputStream(); } catch (IOException ioe) { InputStream is = conn.getErrorStream(); if (is != null) { String msg = getStringFromInputStream(conn.getErrorStream()); throw new IOException(msg); } else { throw ioe; } } return stream; }

public static int executeUpdate(EOAdaptorChannel channel, String sql, boolean autoCommit) throws SQLException { int rowsUpdated; boolean wasOpen = channel.isOpen(); if (!wasOpen) { channel.openChannel(); } Connection conn = ((JDBCContext) channel.adaptorContext()).connection(); try { Statement stmt = conn.createStatement(); try { rowsUpdated = stmt.executeUpdate(sql); if (autoCommit) { conn.commit(); } } catch (SQLException ex) { if (autoCommit) { conn.rollback(); } throw new RuntimeException("Failed to execute the statement '" + sql + "'.", ex); } finally { stmt.close(); } } finally { if (!wasOpen) { channel.closeChannel(); } } return rowsUpdated; }

private void upgradeSchema() throws IOException { Statement stmt = null; try { int i = getSchema(); if (i < SCHEMA_VERSION) { conn.setAutoCommit(false); stmt = conn.createStatement(); while (i < SCHEMA_VERSION) { String qry; switch(i) { case 1: qry = "CREATE TABLE log (id INTEGER PRIMARY KEY, context VARCHAR(16) NOT NULL, level VARCHAR(16) NOT NULL, time LONG INT NOT NULL, msg LONG VARCHAR NOT NULL, parent INT)"; stmt.executeUpdate(qry); qry = "UPDATE settings SET val = '2' WHERE var = 'schema'"; stmt.executeUpdate(qry); break; case 2: qry = "CREATE TABLE monitor (id INTEGER PRIMARY KEY NOT NULL, status INTEGER NOT NULL)"; stmt.executeUpdate(qry); qry = "UPDATE settings SET val = '3' WHERE var = 'schema'"; stmt.executeUpdate(qry); break; case 3: qry = "CREATE TABLE favs (id INTEGER PRIMARY KEY NOT NULL)"; stmt.executeUpdate(qry); qry = "UPDATE settings SET val = '4' WHERE var = 'schema'"; stmt.executeUpdate(qry); break; case 4: qry = "DROP TABLE log"; stmt.executeUpdate(qry); qry = "UPDATE settings SET val = '5' WHERE var = 'schema'"; stmt.executeUpdate(qry); break; case 5: qry = "UPDATE settings SET val = '120000' WHERE var = 'SleepTime'"; stmt.executeUpdate(qry); qry = "UPDATE settings set val = '6' WHERE var = 'schema'"; stmt.executeUpdate(qry); break; } i++; } conn.commit(); } } catch (SQLException e) { try { conn.rollback(); } catch (SQLException e2) { LOG.trace(SQL_ERROR, e2); LOG.error(e2); } LOG.trace(SQL_ERROR, e); LOG.fatal(e); throw new IOException("Error upgrading data store", e); } finally { try { if (stmt != null) { stmt.close(); } conn.setAutoCommit(true); } catch (SQLException e) { LOG.trace(SQL_ERROR, e); throw new IOException("Unable to cleanup SQL resources", e); } } }

public static final boolean compressToZip(final String sSource, final String sDest, final boolean bDeleteSourceOnSuccess) { ZipOutputStream os = null; InputStream is = null; try { os = new ZipOutputStream(new FileOutputStream(sDest)); is = new FileInputStream(sSource); final byte[] buff = new byte[1024]; int r; String sFileName = sSource; if (sFileName.indexOf('/') >= 0) sFileName = sFileName.substring(sFileName.lastIndexOf('/') + 1); os.putNextEntry(new ZipEntry(sFileName)); while ((r = is.read(buff)) > 0) os.write(buff, 0, r); is.close(); os.flush(); os.closeEntry(); os.close(); } catch (Throwable e) { Log.log(Log.WARNING, "lazyj.Utils", "compressToZip : cannot compress '" + sSource + "' to '" + sDest + "' because", e); return false; } finally { if (is != null) { try { is.close(); } catch (IOException ioe) { } } if (os != null) { try { os.close(); } catch (IOException ioe) { } } } if (bDeleteSourceOnSuccess) try { if (!(new File(sSource)).delete()) Log.log(Log.WARNING, "lazyj.Utils", "compressToZip: could not delete original file (" + sSource + ")"); } catch (SecurityException se) { Log.log(Log.ERROR, "lazyj.Utils", "compressToZip: security constraints prevents file deletion"); } return true; }

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

public static void copyFile(File src, File dst) throws IOException { if (T.t) T.info("Copying " + src + " -> " + dst + "..."); FileInputStream in = new FileInputStream(src); FileOutputStream out = new FileOutputStream(dst); byte buf[] = new byte[40 * KB]; int read; while ((read = in.read(buf)) != -1) { out.write(buf, 0, read); } out.flush(); out.close(); in.close(); if (T.t) T.info("File copied."); }

public CopyAllDataToOtherFolderResponse CopyAllDataToOtherFolder(DPWSContext context, CopyAllDataToOtherFolder CopyAllDataInps) throws DPWSException { CopyAllDataToOtherFolderResponse cpyRp = new CopyAllDataToOtherFolderResponseImpl(); int hany = 0; String errorMsg = null; try { if ((rootDir == null) || (rootDir.length() == (-1))) { errorMsg = LocalStorVerify.ISNT_ROOTFLD; } else { String sourceN = CopyAllDataInps.getSourceName(); String targetN = CopyAllDataInps.getTargetName(); if (LocalStorVerify.isValid(sourceN) && LocalStorVerify.isValid(targetN)) { String srcDir = rootDir + File.separator + sourceN; String trgDir = rootDir + File.separator + targetN; if (LocalStorVerify.isLength(srcDir) && LocalStorVerify.isLength(trgDir)) { for (File fs : new File(srcDir).listFiles()) { File ft = new File(trgDir + '\\' + fs.getName()); FileChannel in = null, out = null; try { in = new FileInputStream(fs).getChannel(); out = new FileOutputStream(ft).getChannel(); long size = in.size(); MappedByteBuffer buf = in.map(FileChannel.MapMode.READ_ONLY, 0, size); out.write(buf); } finally { if (in != null) in.close(); if (out != null) out.close(); hany++; } } } else { errorMsg = LocalStorVerify.FLD_TOOLNG; } } else { errorMsg = LocalStorVerify.ISNT_VALID; } } } catch (Throwable tr) { tr.printStackTrace(); errorMsg = tr.getMessage(); hany = (-1); } if (errorMsg != null) { } cpyRp.setNum(hany); return cpyRp; }

public static void main(String[] args) throws Exception { String linesep = System.getProperty("line.separator"); FileOutputStream fos = new FileOutputStream(new File("lib-licenses.txt")); fos.write(new String("JCP contains the following libraries. Please read this for comments on copyright etc." + linesep + linesep).getBytes()); fos.write(new String("Chemistry Development Kit, master version as of " + new Date().toString() + " (http://cdk.sf.net)" + linesep).getBytes()); fos.write(new String("Copyright 1997-2009 The CDK Development Team" + linesep).getBytes()); fos.write(new String("License: LGPL v2 (http://www.gnu.org/licenses/old-licenses/gpl-2.0.html)" + linesep).getBytes()); fos.write(new String("Download: https://sourceforge.net/projects/cdk/files/" + linesep).getBytes()); fos.write(new String("Source available at: http://sourceforge.net/scm/?type=git&group_id=20024" + linesep + linesep).getBytes()); File[] files = new File(args[0]).listFiles(new JarFileFilter()); for (int i = 0; i < files.length; i++) { if (new File(files[i].getPath() + ".meta").exists()) { Map<String, Map<String, String>> metaprops = readProperties(new File(files[i].getPath() + ".meta")); Iterator<String> itsect = metaprops.keySet().iterator(); while (itsect.hasNext()) { String section = itsect.next(); fos.write(new String(metaprops.get(section).get("Library") + " " + metaprops.get(section).get("Version") + " (" + metaprops.get(section).get("Homepage") + ")" + linesep).getBytes()); fos.write(new String("Copyright " + metaprops.get(section).get("Copyright") + linesep).getBytes()); fos.write(new String("License: " + metaprops.get(section).get("License") + " (" + metaprops.get(section).get("LicenseURL") + ")" + linesep).getBytes()); fos.write(new String("Download: " + metaprops.get(section).get("Download") + linesep).getBytes()); fos.write(new String("Source available at: " + metaprops.get(section).get("SourceCode") + linesep + linesep).getBytes()); } } if (new File(files[i].getPath() + ".extra").exists()) { fos.write(new String("The author says:" + linesep).getBytes()); FileInputStream in = new FileInputStream(new File(files[i].getPath() + ".extra")); int len; byte[] buf = new byte[1024]; while ((len = in.read(buf)) > 0) { fos.write(buf, 0, len); } } fos.write(linesep.getBytes()); } fos.close(); }

@Override public synchronized HttpURLConnection getTileUrlConnection(int zoom, int tilex, int tiley) throws IOException { HttpURLConnection conn = null; try { String url = getTileUrl(zoom, tilex, tiley); conn = (HttpURLConnection) new URL(url).openConnection(); } catch (IOException e) { throw e; } catch (Exception e) { log.error("", e); throw new IOException(e); } try { i.set("conn", conn); i.eval("addHeaders(conn);"); } catch (EvalError e) { String msg = e.getMessage(); if (!AH_ERROR.equals(msg)) { log.error(e.getClass() + ": " + e.getMessage(), e); throw new IOException(e); } } return conn; }

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

@Override public synchronized File download_dictionary(Dictionary dict, String localfpath) { abort = false; try { URL dictionary_location = new URL(dict.getLocation()); InputStream in = dictionary_location.openStream(); FileOutputStream w = new FileOutputStream(local_cache, false); int b = 0; while ((b = in.read()) != -1) { w.write(b); if (abort) throw new Exception("Download Aborted"); } in.close(); w.close(); File lf = new File(localfpath); FileInputStream r = new FileInputStream(local_cache); FileOutputStream fw = new FileOutputStream(lf); int c; while ((c = r.read()) != -1) fw.write(c); r.close(); fw.close(); clearCache(); return lf; } catch (MalformedURLException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } catch (InvalidTupleOperationException e) { e.printStackTrace(); } catch (Exception e) { e.printStackTrace(); } clearCache(); return null; }

public static void copyFile(File src, File dest, boolean force) throws IOException { if (dest.exists()) { if (force) { dest.delete(); } else { throw new IOException("Cannot overwrite existing file: " + dest); } } byte[] buffer = new byte[1]; int read = 0; InputStream in = null; OutputStream out = null; try { in = new FileInputStream(src); out = new FileOutputStream(dest); while (true) { read = in.read(buffer); if (read == -1) { break; } out.write(buffer, 0, read); } } finally { if (in != null) { try { in.close(); } finally { if (out != null) { out.close(); } } } } }

private void saveFile(File destination) { InputStream in = null; OutputStream out = null; try { if (fileScheme) in = new BufferedInputStream(new FileInputStream(source.getPath())); else in = new BufferedInputStream(getContentResolver().openInputStream(source)); out = new BufferedOutputStream(new FileOutputStream(destination)); byte[] buffer = new byte[1024]; while (in.read(buffer) != -1) out.write(buffer); Toast.makeText(this, R.string.saveas_file_saved, Toast.LENGTH_SHORT).show(); } catch (FileNotFoundException e) { Toast.makeText(this, R.string.saveas_error, Toast.LENGTH_SHORT).show(); } catch (IOException e) { Toast.makeText(this, R.string.saveas_error, Toast.LENGTH_SHORT).show(); } finally { if (in != null) { try { in.close(); } catch (IOException e) { } } if (out != null) { try { out.close(); } catch (IOException e) { } } } }

public String sendXml(URL url, String xmlMessage, boolean isResponseExpected) throws IOException { if (url == null) { throw new IllegalArgumentException("url == null"); } if (xmlMessage == null) { throw new IllegalArgumentException("xmlMessage == null"); } LOGGER.finer("url = " + url); LOGGER.finer("xmlMessage = :" + xmlMessage + ":"); LOGGER.finer("isResponseExpected = " + isResponseExpected); String answer = null; try { URLConnection urlConnection = url.openConnection(); urlConnection.setRequestProperty("Content-type", "text/xml"); urlConnection.setDoOutput(true); urlConnection.setUseCaches(false); Writer writer = null; try { writer = new OutputStreamWriter(urlConnection.getOutputStream()); writer.write(xmlMessage); writer.flush(); } finally { if (writer != null) { writer.close(); } } LOGGER.finer("message written"); StringBuilder sb = new StringBuilder(); BufferedReader in = null; try { in = new BufferedReader(new InputStreamReader(urlConnection.getInputStream())); if (isResponseExpected) { String inputLine; while ((inputLine = in.readLine()) != null) { sb.append(inputLine).append("\n"); } answer = sb.toString(); LOGGER.finer("response read"); } } catch (FileNotFoundException e) { LOGGER.log(Level.SEVERE, "No response", e); } finally { if (in != null) { in.close(); } } } catch (ConnectException e) { LOGGER.log(Level.SEVERE, e.getMessage(), e); } LOGGER.finer("answer = :" + answer + ":"); return answer; }

private static boolean genCustomerLocationsFileAndCustomerIndexFile(String completePath, String masterFile, String CustLocationsFileName, String CustIndexFileName) { try { TIntObjectHashMap CustInfoHash = new TIntObjectHashMap(480189, 1); File inFile = new File(completePath + fSep + "SmartGRAPE" + fSep + masterFile); FileChannel inC = new FileInputStream(inFile).getChannel(); File outFile1 = new File(completePath + fSep + "SmartGRAPE" + fSep + CustIndexFileName); FileChannel outC1 = new FileOutputStream(outFile1, true).getChannel(); File outFile2 = new File(completePath + fSep + "SmartGRAPE" + fSep + CustLocationsFileName); FileChannel outC2 = new FileOutputStream(outFile2, true).getChannel(); int fileSize = (int) inC.size(); int totalNoDataRows = fileSize / 7; for (int i = 1; i <= totalNoDataRows; i++) { ByteBuffer mappedBuffer = ByteBuffer.allocate(7); inC.read(mappedBuffer); mappedBuffer.position(0); short movieName = mappedBuffer.getShort(); int customer = mappedBuffer.getInt(); byte rating = mappedBuffer.get(); mappedBuffer.clear(); if (CustInfoHash.containsKey(customer)) { TIntArrayList locations = (TIntArrayList) CustInfoHash.get(customer); locations.add(i); CustInfoHash.put(customer, locations); } else { TIntArrayList locations = new TIntArrayList(); locations.add(i); CustInfoHash.put(customer, locations); } } int[] customers = CustInfoHash.keys(); Arrays.sort(customers); int count = 1; for (int i = 0; i < customers.length; i++) { int customer = customers[i]; TIntArrayList locations = (TIntArrayList) CustInfoHash.get(customer); int noRatingsForCust = locations.size(); ByteBuffer outBuf1 = ByteBuffer.allocate(12); outBuf1.putInt(customer); outBuf1.putInt(count); outBuf1.putInt(count + noRatingsForCust - 1); outBuf1.flip(); outC1.write(outBuf1); count += noRatingsForCust; for (int j = 0; j < locations.size(); j++) { ByteBuffer outBuf2 = ByteBuffer.allocate(4); outBuf2.putInt(locations.get(j)); outBuf2.flip(); outC2.write(outBuf2); } } inC.close(); outC1.close(); outC2.close(); return true; } catch (IOException e) { System.err.println(e); return false; } }

public void copyServer(int id) throws Exception { File in = new File("servers" + File.separatorChar + "server_" + id); File serversDir = new File("servers" + File.separatorChar); int newNumber = serversDir.listFiles().length + 1; System.out.println("New File Number: " + newNumber); File out = new File("servers" + File.separatorChar + "server_" + newNumber); FileChannel inChannel = new FileInputStream(in).getChannel(); FileChannel outChannel = new FileOutputStream(out).getChannel(); try { inChannel.transferTo(0, inChannel.size(), outChannel); } catch (Exception e) { e.printStackTrace(); } finally { if (inChannel != null) inChannel.close(); if (outChannel != null) outChannel.close(); } getServer(newNumber - 1); }

private void preprocessObjects(GeoObject[] objects) throws IOException { System.out.println("objects.length " + objects.length); for (int i = 0; i < objects.length; i++) { String fileName = objects[i].getPath(); int dotindex = fileName.lastIndexOf("."); dotindex = dotindex < 0 ? 0 : dotindex; String tmp = dotindex < 1 ? fileName : fileName.substring(0, dotindex + 3) + "w"; System.out.println("i: " + " world filename " + tmp); File worldFile = new File(tmp); if (worldFile.exists()) { BufferedReader worldFileReader = new BufferedReader(new InputStreamReader(new FileInputStream(worldFile))); if (staticDebugOn) debug("b4nextline: "); line = worldFileReader.readLine(); if (staticDebugOn) debug("line: " + line); if (line != null) { line = worldFileReader.readLine(); if (staticDebugOn) debug("line: " + line); tokenizer = new StringTokenizer(line, " \n\t\r\"", false); objects[i].setLon(Double.valueOf(tokenizer.nextToken()).doubleValue()); line = worldFileReader.readLine(); if (staticDebugOn) debug("line: " + line); tokenizer = new StringTokenizer(line, " \n\t\r\"", false); objects[i].setLat(Double.valueOf(tokenizer.nextToken()).doubleValue()); } } File file = new File(objects[i].getPath()); if (file.exists()) { System.out.println("object src file found "); int slashindex = fileName.lastIndexOf(java.io.File.separator); slashindex = slashindex < 0 ? 0 : slashindex; if (slashindex == 0) { slashindex = fileName.lastIndexOf("/"); slashindex = slashindex < 0 ? 0 : slashindex; } tmp = slashindex < 1 ? fileName : fileName.substring(slashindex + 1, fileName.length()); System.out.println("filename " + destinationDirectory + XPlat.fileSep + tmp); objects[i].setPath(tmp); file = new File(fileName); if (file.exists()) { DataInputStream dataIn = new DataInputStream(new BufferedInputStream(new FileInputStream(fileName))); DataOutputStream dataOut = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(destinationDirectory + XPlat.fileSep + tmp))); System.out.println("copying to " + destinationDirectory + XPlat.fileSep + tmp); for (; ; ) { try { dataOut.writeShort(dataIn.readShort()); } catch (EOFException e) { break; } catch (IOException e) { break; } } dataOut.close(); } } } }

public static void compress(final File zip, final Map<InputStream, String> entries, final IProgressMonitor monitor) throws IOException { if (zip == null || entries == null || CollectionUtils.isEmpty(entries.keySet())) throw new IllegalArgumentException("One ore more parameters are empty!"); if (zip.exists()) zip.delete(); else if (!zip.getParentFile().exists()) zip.getParentFile().mkdirs(); ZipOutputStream out = new ZipOutputStream(new BufferedOutputStream(new FileOutputStream(zip))); out.setLevel(Deflater.BEST_COMPRESSION); try { for (InputStream inputStream : entries.keySet()) { ZipEntry zipEntry = new ZipEntry(skipBeginningSlash(entries.get(inputStream))); out.putNextEntry(zipEntry); IOUtils.copy(inputStream, out); out.closeEntry(); inputStream.close(); if (monitor != null) monitor.worked(1); } } finally { IOUtils.closeQuietly(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(); } }

public void bubbleSort(int[] arr) { boolean swapped = true; int j = 0; int tmp; while (swapped) { swapped = false; j++; for (int i = 0; i < arr.length - j; i++) { if (arr[i] > arr[i + 1]) { tmp = arr[i]; arr[i] = arr[i + 1]; arr[i + 1] = tmp; swapped = true; } } } }

public ArrayList parseFile(File newfile) throws IOException { String s; String firstName; String header; String name = null; Integer PVLoggerID = new Integer(0); String[] tokens; int nvalues = 0; double num1, num2, num3; double xoffset = 1.0; double xdelta = 1.0; double yoffset = 1.0; double ydelta = 1.0; double zoffset = 1.0; double zdelta = 1.0; boolean readfit = false; boolean readraw = false; boolean zerodata = false; boolean baddata = false; boolean harpdata = false; ArrayList fitparams = new ArrayList(); ArrayList xraw = new ArrayList(); ArrayList yraw = new ArrayList(); ArrayList zraw = new ArrayList(); ArrayList sraw = new ArrayList(); ArrayList sxraw = new ArrayList(); ArrayList syraw = new ArrayList(); ArrayList szraw = new ArrayList(); URL url = newfile.toURI().toURL(); InputStream is = url.openStream(); InputStreamReader isr = new InputStreamReader(is); BufferedReader br = new BufferedReader(isr); while ((s = br.readLine()) != null) { tokens = s.split("\\s+"); nvalues = tokens.length; firstName = (String) tokens[0]; if (((String) tokens[0]).length() == 0) { readraw = false; readfit = false; continue; } if ((nvalues == 4) && (!firstName.startsWith("---"))) { if ((Double.parseDouble(tokens[1]) == 0.) && (Double.parseDouble(tokens[2]) == 0.) && (Double.parseDouble(tokens[3]) == 0.)) { zerodata = true; } else { zerodata = false; } if (tokens[1].equals("NaN") || tokens[2].equals("NaN") || tokens[3].equals("NaN")) { baddata = true; } else { baddata = false; } } if (firstName.startsWith("start")) { header = s; } if (firstName.indexOf("WS") > 0) { if (name != null) { dumpData(name, fitparams, sraw, sxraw, syraw, szraw, yraw, zraw, xraw); } name = tokens[0]; readraw = false; readfit = false; zerodata = false; baddata = false; harpdata = false; fitparams.clear(); xraw.clear(); yraw.clear(); zraw.clear(); sraw.clear(); sxraw.clear(); syraw.clear(); szraw.clear(); } if (firstName.startsWith("Area")) ; if (firstName.startsWith("Ampl")) ; if (firstName.startsWith("Mean")) ; if (firstName.startsWith("Sigma")) { fitparams.add(new Double(Double.parseDouble(tokens[3]))); fitparams.add(new Double(Double.parseDouble(tokens[1]))); fitparams.add(new Double(Double.parseDouble(tokens[5]))); } if (firstName.startsWith("Offset")) ; if (firstName.startsWith("Slope")) ; if ((firstName.equals("Position")) && (((String) tokens[2]).equals("Raw"))) { readraw = true; continue; } if ((firstName.equals("Position")) && (((String) tokens[2]).equals("Fit"))) { readfit = true; continue; } if ((firstName.contains("Harp"))) { xraw.clear(); yraw.clear(); zraw.clear(); sraw.clear(); sxraw.clear(); syraw.clear(); szraw.clear(); harpdata = true; readraw = true; name = tokens[0]; continue; } if (firstName.startsWith("---")) continue; if (harpdata == true) { if (((String) tokens[0]).length() != 0) { if (firstName.startsWith("PVLogger")) { try { PVLoggerID = new Integer(Integer.parseInt(tokens[2])); } catch (NumberFormatException e) { } } else { sxraw.add(new Double(Double.parseDouble(tokens[0]))); xraw.add(new Double(Double.parseDouble(tokens[1]))); syraw.add(new Double(Double.parseDouble(tokens[2]))); yraw.add(new Double(Double.parseDouble(tokens[3]))); szraw.add(new Double(Double.parseDouble(tokens[4]))); zraw.add(new Double(Double.parseDouble(tokens[5]))); } } continue; } if (readraw && (!zerodata) && (!baddata)) { sraw.add(new Double(Double.parseDouble(tokens[0]) / Math.sqrt(2.0))); sxraw.add(new Double(Double.parseDouble(tokens[0]) / Math.sqrt(2.0))); syraw.add(new Double(Double.parseDouble(tokens[0]) / Math.sqrt(2.0))); szraw.add(new Double(Double.parseDouble(tokens[0]))); yraw.add(new Double(Double.parseDouble(tokens[1]))); zraw.add(new Double(Double.parseDouble(tokens[2]))); xraw.add(new Double(Double.parseDouble(tokens[3]))); } if (firstName.startsWith("PVLogger")) { try { PVLoggerID = new Integer(Integer.parseInt(tokens[2])); } catch (NumberFormatException e) { } } } dumpData(name, fitparams, sraw, sxraw, syraw, szraw, yraw, zraw, xraw); wiredata.add((Integer) PVLoggerID); return wiredata; }

public static boolean compress(ArrayList sources, File target, Manifest manifest) { try { if (sources == null || sources.size() == 0) return false; if (target.exists()) target.delete(); ZipOutputStream output = null; boolean isJar = target.getName().toLowerCase().endsWith(".jar"); if (isJar) { if (manifest != null) output = new JarOutputStream(new FileOutputStream(target), manifest); else output = new JarOutputStream(new FileOutputStream(target)); } else output = new ZipOutputStream(new FileOutputStream(target)); String baseDir = ((File) sources.get(0)).getParentFile().getAbsolutePath().replace('\\', '/'); if (!baseDir.endsWith("/")) baseDir = baseDir + "/"; int baseDirLength = baseDir.length(); ArrayList list = new ArrayList(); for (Iterator it = sources.iterator(); it.hasNext(); ) { File fileOrDir = (File) it.next(); if (isJar && (manifest != null) && fileOrDir.getName().equals("META-INF")) continue; if (fileOrDir.isDirectory()) list.addAll(getContents(fileOrDir)); else list.add(fileOrDir); } byte[] buffer = new byte[1024]; int bytesRead; for (int i = 0, n = list.size(); i < n; i++) { File file = (File) list.get(i); FileInputStream f_in = new FileInputStream(file); String filename = file.getAbsolutePath().replace('\\', '/'); if (filename.startsWith(baseDir)) filename = filename.substring(baseDirLength); if (isJar) output.putNextEntry(new JarEntry(filename)); else output.putNextEntry(new ZipEntry(filename)); while ((bytesRead = f_in.read(buffer)) != -1) output.write(buffer, 0, bytesRead); f_in.close(); output.closeEntry(); } output.close(); } catch (Exception exc) { exc.printStackTrace(); return false; } return true; }

private static void copy(String fromFileName, String toFileName) throws IOException { File fromFile = new File(fromFileName); File toFile = new File(toFileName); if (!fromFile.exists()) throw new IOException("FileCopy: " + "no such source file: " + fromFileName); if (!fromFile.isFile()) throw new IOException("FileCopy: " + "can't copy directory: " + fromFileName); if (!fromFile.canRead()) throw new IOException("FileCopy: " + "source file is unreadable: " + fromFileName); if (toFile.isDirectory()) toFile = new File(toFile, fromFile.getName()); if (toFile.exists()) { if (!toFile.canWrite()) throw new IOException("FileCopy: " + "destination file is unwriteable: " + toFileName); System.out.print("Overwrite existing file " + toFile.getName() + "? (Y/N): "); System.out.flush(); BufferedReader in = new BufferedReader(new InputStreamReader(System.in)); String response = in.readLine(); if (!response.equals("Y") && !response.equals("y")) throw new IOException("FileCopy: " + "existing file was not overwritten."); } else { String parent = toFile.getParent(); if (parent == null) parent = System.getProperty("user.dir"); File dir = new File(parent); if (!dir.exists()) throw new IOException("FileCopy: " + "destination directory doesn't exist: " + parent); if (dir.isFile()) throw new IOException("FileCopy: " + "destination is not a directory: " + parent); if (!dir.canWrite()) throw new IOException("FileCopy: " + "destination directory is unwriteable: " + parent); } FileInputStream from = null; FileOutputStream to = null; try { from = new FileInputStream(fromFile); to = new FileOutputStream(toFile); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = from.read(buffer)) != -1) to.write(buffer, 0, bytesRead); } finally { if (from != null) try { from.close(); } catch (IOException e) { ; } if (to != null) try { to.close(); } catch (IOException e) { ; } } }

public void setNewPassword(String password) { try { final MessageDigest digest = MessageDigest.getInstance("MD5"); digest.update(password.getBytes()); final String encrypted = "{MD5}" + new String(Base64Encoder.encode(digest.digest())); setUserPassword(encrypted.getBytes()); this.newPassword = password; firePropertyChange("newPassword", "", password); firePropertyChange("password", new byte[0], getUserPassword()); } catch (final NoSuchAlgorithmException e) { throw new RuntimeException("Can't encrypt user's password", e); } }

public boolean WriteFile(java.io.Serializable inObj, String fileName) throws Exception { FileOutputStream out; try { SecretKey skey = null; AlgorithmParameterSpec aps; out = new FileOutputStream(fileName); cipher = Cipher.getInstance(algorithm); KeySpec kspec = new PBEKeySpec(filePasswd.toCharArray()); SecretKeyFactory skf = SecretKeyFactory.getInstance(algorithm); skey = skf.generateSecret(kspec); MessageDigest md = MessageDigest.getInstance(res.getString("MD5")); md.update(filePasswd.getBytes()); byte[] digest = md.digest(); System.arraycopy(digest, 0, salt, 0, 8); aps = new PBEParameterSpec(salt, iterations); out.write(salt); ObjectOutputStream s = new ObjectOutputStream(out); cipher.init(Cipher.ENCRYPT_MODE, skey, aps); SealedObject so = new SealedObject(inObj, cipher); s.writeObject(so); s.flush(); out.close(); } catch (Exception e) { Log.out("fileName=" + fileName); Log.out("algorithm=" + algorithm); Log.out(e); throw e; } return true; }

public static Photo createPhoto(String title, String userLogin, String pathToPhoto, String basePathImage) throws NoSuchAlgorithmException, IOException { String id = CryptSHA1.genPhotoID(userLogin, title); String extension = pathToPhoto.substring(pathToPhoto.lastIndexOf(".")); String destination = basePathImage + id + extension; FileInputStream fis = new FileInputStream(pathToPhoto); FileOutputStream fos = new FileOutputStream(destination); FileChannel fci = fis.getChannel(); FileChannel fco = fos.getChannel(); ByteBuffer buffer = ByteBuffer.allocate(1024); while (true) { int read = fci.read(buffer); if (read == -1) break; buffer.flip(); fco.write(buffer); buffer.clear(); } fci.close(); fco.close(); fos.close(); fis.close(); ImageIcon image; ImageIcon thumb; String destinationThumb = basePathImage + "thumb/" + id + extension; image = new ImageIcon(destination); int maxSize = 150; int origWidth = image.getIconWidth(); int origHeight = image.getIconHeight(); if (origWidth > origHeight) { thumb = new ImageIcon(image.getImage().getScaledInstance(maxSize, -1, Image.SCALE_SMOOTH)); } else { thumb = new ImageIcon(image.getImage().getScaledInstance(-1, maxSize, Image.SCALE_SMOOTH)); } BufferedImage bi = new BufferedImage(thumb.getIconWidth(), thumb.getIconHeight(), BufferedImage.TYPE_INT_RGB); Graphics g = bi.getGraphics(); g.drawImage(thumb.getImage(), 0, 0, null); try { ImageIO.write(bi, "JPG", new File(destinationThumb)); } catch (IOException ioe) { System.out.println("Error occured saving thumbnail"); } Photo photo = new Photo(id); photo.setTitle(title); photo.basePathImage = basePathImage; return photo; }

public static void copyToFileAndCloseStreams(InputStream istr, File destFile) throws IOException { OutputStream ostr = null; try { ostr = new FileOutputStream(destFile); IOUtils.copy(istr, ostr); } finally { if (ostr != null) ostr.close(); if (istr != null) istr.close(); } }

public ISOMsg filter(ISOChannel channel, ISOMsg m, LogEvent evt) throws VetoException { if (key == null || fields == null) throw new VetoException("MD5Filter not configured"); try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(getKey()); int[] f = getFields(m); for (int i = 0; i < f.length; i++) { int fld = f[i]; if (m.hasField(fld)) { ISOComponent c = m.getComponent(fld); if (c instanceof ISOBinaryField) md.update((byte[]) c.getValue()); else md.update(((String) c.getValue()).getBytes()); } } byte[] digest = md.digest(); if (m.getDirection() == ISOMsg.OUTGOING) { m.set(new ISOBinaryField(64, digest, 0, 8)); m.set(new ISOBinaryField(128, digest, 8, 8)); } else { byte[] rxDigest = new byte[16]; if (m.hasField(64)) System.arraycopy((byte[]) m.getValue(64), 0, rxDigest, 0, 8); if (m.hasField(128)) System.arraycopy((byte[]) m.getValue(128), 0, rxDigest, 8, 8); if (!Arrays.equals(digest, rxDigest)) { evt.addMessage(m); evt.addMessage("MAC expected: " + ISOUtil.hexString(digest)); evt.addMessage("MAC received: " + ISOUtil.hexString(rxDigest)); throw new VetoException("invalid MAC"); } m.unset(64); m.unset(128); } } catch (NoSuchAlgorithmException e) { throw new VetoException(e); } catch (ISOException e) { throw new VetoException(e); } return m; }

public void init(String password) { try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(password.getBytes("UTF-8"), 0, password.length()); byte[] rawKey = md.digest(); skeySpec = new SecretKeySpec(rawKey, "AES"); ivSpec = new IvParameterSpec(rawKey); cipher = Cipher.getInstance("AES/CBC/PKCS5Padding"); } catch (UnsupportedEncodingException ex) { Logger.getLogger(AES.class.getName()).log(Level.SEVERE, null, ex); } catch (NoSuchPaddingException ex) { Logger.getLogger(AES.class.getName()).log(Level.SEVERE, null, ex); } catch (NoSuchAlgorithmException ex) { Logger.getLogger(AES.class.getName()).log(Level.SEVERE, null, ex); } }

public static void copyFile(File src, File dst) throws IOException { if (T.t) T.info("Copying " + src + " -> " + dst + "..."); FileInputStream in = new FileInputStream(src); FileOutputStream out = new FileOutputStream(dst); byte buf[] = new byte[40 * KB]; int read; while ((read = in.read(buf)) != -1) { out.write(buf, 0, read); } out.flush(); out.close(); in.close(); if (T.t) T.info("File copied."); }

public static void perform(ChangeSet changes, ArchiveInputStream in, ArchiveOutputStream out) throws IOException { ArchiveEntry entry = null; while ((entry = in.getNextEntry()) != null) { System.out.println(entry.getName()); boolean copy = true; for (Iterator it = changes.asSet().iterator(); it.hasNext(); ) { Change change = (Change) it.next(); if (change.type() == ChangeSet.CHANGE_TYPE_DELETE) { DeleteChange delete = ((DeleteChange) change); if (entry.getName() != null && entry.getName().equals(delete.targetFile())) { copy = false; } } } if (copy) { System.out.println("Copy: " + entry.getName()); long size = entry.getSize(); out.putArchiveEntry(entry); IOUtils.copy((InputStream) in, out, (int) size); out.closeArchiveEntry(); } System.out.println("---"); } out.close(); }

private void _connect() throws SocketException, IOException { try { ftpClient.disconnect(); } catch (Exception ex) { } ftpClient.connect(host, port); ftpClient.login("anonymous", ""); ftpClient.enterLocalActiveMode(); }

public TextureData newTextureData(URL url, int internalFormat, int pixelFormat, boolean mipmap, String fileSuffix) throws IOException { InputStream stream = new BufferedInputStream(url.openStream()); try { return newTextureData(stream, internalFormat, pixelFormat, mipmap, fileSuffix); } finally { stream.close(); } }

public boolean delMail(MailObject mail) throws NetworkException, ContentException { HttpClient client = HttpConfig.newInstance(); HttpGet get = new HttpGet(HttpConfig.bbsURL() + HttpConfig.BBS_MAIL_DEL + mail.getId()); try { HttpResponse response = client.execute(get); HttpEntity entity = response.getEntity(); if (HTTPUtil.isXmlContentType(response)) { HTTPUtil.consume(response.getEntity()); return true; } else { String msg = BBSBodyParseHelper.parseFailMsg(entity); throw new ContentException(msg); } } catch (ClientProtocolException e) { e.printStackTrace(); throw new NetworkException(e); } catch (IOException e) { e.printStackTrace(); throw new NetworkException(e); } }

public static void find(String pckgname, Class<?> tosubclass) { String name = new String(pckgname); if (!name.startsWith("/")) { name = "/" + name; } name = name.replace('.', '/'); URL url = tosubclass.getResource(name); System.out.println(name + "->" + url); if (url == null) return; File directory = new File(url.getFile()); if (directory.exists()) { String[] files = directory.list(); for (int i = 0; i < files.length; i++) { if (files[i].endsWith(".class")) { String classname = files[i].substring(0, files[i].length() - 6); try { Object o = Class.forName(pckgname + "." + classname).newInstance(); if (tosubclass.isInstance(o)) { System.out.println(classname); } } catch (ClassNotFoundException cnfex) { System.err.println(cnfex); } catch (InstantiationException iex) { } catch (IllegalAccessException iaex) { } } } } else { try { JarURLConnection conn = (JarURLConnection) url.openConnection(); String starts = conn.getEntryName(); JarFile jfile = conn.getJarFile(); Enumeration<JarEntry> e = jfile.entries(); while (e.hasMoreElements()) { ZipEntry entry = e.nextElement(); String entryname = entry.getName(); if (entryname.startsWith(starts) && (entryname.lastIndexOf('/') <= starts.length()) && entryname.endsWith(".class")) { String classname = entryname.substring(0, entryname.length() - 6); if (classname.startsWith("/")) classname = classname.substring(1); classname = classname.replace('/', '.'); try { Object o = Class.forName(classname).newInstance(); if (tosubclass.isInstance(o)) { System.out.println(classname.substring(classname.lastIndexOf('.') + 1)); } } catch (ClassNotFoundException cnfex) { System.err.println(cnfex); } catch (InstantiationException iex) { } catch (IllegalAccessException iaex) { } } } } catch (IOException ioex) { System.err.println(ioex); } } }

private MimeTypesProvider() { File mimeTypesFile = new File(XPontusConstantsIF.XPONTUS_HOME_DIR, "mimes.properties"); try { if (!mimeTypesFile.exists()) { OutputStream os = null; InputStream is = getClass().getResourceAsStream("/net/sf/xpontus/configuration/mimetypes.properties"); os = FileUtils.openOutputStream(mimeTypesFile); IOUtils.copy(is, os); IOUtils.closeQuietly(is); IOUtils.closeQuietly(os); } provider = new XPontusMimetypesFileTypeMap(mimeTypesFile.getAbsolutePath()); MimetypesFileTypeMap.setDefaultFileTypeMap(provider); } catch (Exception err) { err.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 sortPlayersTurn() { Token tempT = new Token(); Player tempP = new Player("test name", tempT); int tempN = 0; boolean exchangeMade = true; for (int i = 0; i < playerNum - 1 && exchangeMade; i++) { exchangeMade = false; for (int j = 0; j < playerNum - 1 - i; j++) { if (diceSum[j] < diceSum[j + 1]) { tempP = players[j]; tempN = diceSum[j]; players[j] = players[j + 1]; diceSum[j] = diceSum[j + 1]; players[j + 1] = tempP; diceSum[j + 1] = tempN; exchangeMade = true; } } } }

@Override public String entryToObject(TupleInput input) { boolean zipped = input.readBoolean(); if (!zipped) { return input.readString(); } int len = input.readInt(); try { byte array[] = new byte[len]; input.read(array); GZIPInputStream in = new GZIPInputStream(new ByteArrayInputStream(array)); ByteArrayOutputStream out = new ByteArrayOutputStream(); IOUtils.copyTo(in, out); in.close(); out.close(); return new String(out.toByteArray()); } catch (IOException err) { throw new RuntimeException(err); } }

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(IPath fromFileName, IPath toFileName) throws IOException { File fromFile = fromFileName.toFile(); File toFile = toFileName.toFile(); 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()) 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); } InputStream from = null; OutputStream to = null; try { from = new BufferedInputStream(new FileInputStream(fromFile)); to = new BufferedOutputStream(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) { } } }

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

public void run() { try { Socket socket = getSocket(); System.out.println("opening socket to " + address + " on " + port); InputStream in = socket.getInputStream(); for (; ; ) { FileTransferHeader header = FileTransferHeader.readHeader(in); if (header == null) break; System.out.println("header: " + header); List<String> parts = header.getFilename().getSegments(); String filename; if (parts.size() > 0) filename = "dl-" + parts.get(parts.size() - 1); else filename = "dl-" + session.getScreenname(); System.out.println("writing to file " + filename); long sum = 0; if (new File(filename).exists()) { FileInputStream fis = new FileInputStream(filename); byte[] block = new byte[10]; for (int i = 0; i < block.length; ) { int count = fis.read(block); if (count == -1) break; i += count; } FileTransferChecksum summer = new FileTransferChecksum(); summer.update(block, 0, 10); sum = summer.getValue(); } FileChannel fileChannel = new FileOutputStream(filename).getChannel(); FileTransferHeader outHeader = new FileTransferHeader(header); outHeader.setHeaderType(FileTransferHeader.HEADERTYPE_ACK); outHeader.setIcbmMessageId(cookie); outHeader.setBytesReceived(0); outHeader.setReceivedChecksum(sum); OutputStream socketOut = socket.getOutputStream(); System.out.println("sending header: " + outHeader); outHeader.write(socketOut); for (int i = 0; i < header.getFileSize(); ) { long transferred = fileChannel.transferFrom(Channels.newChannel(in), 0, header.getFileSize() - i); System.out.println("transferred " + transferred); if (transferred == -1) return; i += transferred; } System.out.println("finished transfer!"); fileChannel.close(); FileTransferHeader doneHeader = new FileTransferHeader(header); doneHeader.setHeaderType(FileTransferHeader.HEADERTYPE_RECEIVED); doneHeader.setFlags(doneHeader.getFlags() | FileTransferHeader.FLAG_DONE); doneHeader.setBytesReceived(doneHeader.getBytesReceived() + 1); doneHeader.setIcbmMessageId(cookie); doneHeader.setFilesLeft(doneHeader.getFilesLeft() - 1); doneHeader.write(socketOut); if (doneHeader.getFilesLeft() - 1 <= 0) { socket.close(); break; } } } catch (IOException e) { e.printStackTrace(); return; } }

public static void fileCopy(final File src, final File dest, final boolean overwrite) throws IOException { if (!dest.exists() || (dest.exists() && overwrite)) { final FileChannel srcChannel = new FileInputStream(src).getChannel(); final FileChannel dstChannel = new FileOutputStream(dest).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } }

void copyFile(String sInput, String sOutput) throws IOException { File inputFile = new File(sInput); File outputFile = new File(sOutput); FileReader in = new FileReader(inputFile); FileWriter out = new FileWriter(outputFile); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); }

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

private void copyFileToDir(MyFile file, MyFile to, wlPanel panel) throws IOException { Utilities.print("started copying " + file.getAbsolutePath() + "\n"); FileOutputStream fos = new FileOutputStream(new File(to.getAbsolutePath())); FileChannel foc = fos.getChannel(); FileInputStream fis = new FileInputStream(new File(file.getAbsolutePath())); FileChannel fic = fis.getChannel(); Date d1 = new Date(); long amount = foc.transferFrom(fic, rest, fic.size() - rest); fic.close(); foc.force(false); foc.close(); Date d2 = new Date(); long time = d2.getTime() - d1.getTime(); double secs = time / 1000.0; double rate = amount / secs; frame.getStatusArea().append(secs + "s " + "amount: " + Utilities.humanReadable(amount) + " rate: " + Utilities.humanReadable(rate) + "/s\n", "black"); panel.updateView(); }

public void testConvert() throws IOException, ConverterException { InputStreamReader reader = new InputStreamReader(new FileInputStream("test" + File.separator + "input" + File.separator + "A0851ohneex.dat"), CharsetUtil.forName("x-PICA")); FileWriter writer = new FileWriter("test" + File.separator + "output" + File.separator + "ddbInterToMarcxmlTest.out"); Converter c = context.getConverter("ddb-intern", "MARC21-xml", "x-PICA", "UTF-8"); ConversionParameters params = new ConversionParameters(); params.setSourceCharset("x-PICA"); params.setTargetCharset("UTF-8"); params.setAddCollectionHeader(true); params.setAddCollectionFooter(true); c.convert(reader, writer, params); }

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(); } } }

@Override public void render(Output output) throws IOException { output.setStatus(statusCode, statusMessage); if (headersMap != null) { Iterator<Entry<String, String>> iterator = headersMap.entrySet().iterator(); while (iterator.hasNext()) { Entry<String, String> header = iterator.next(); output.addHeader(header.getKey(), header.getValue()); } } if (file != null) { InputStream inputStream = new FileInputStream(file); try { output.open(); OutputStream out = output.getOutputStream(); IOUtils.copy(inputStream, out); } finally { inputStream.close(); output.close(); } } }

private void addAllSpecialPages(Environment env, ZipOutputStream zipout, int progressStart, int progressLength) throws Exception, IOException { ResourceBundle messages = ResourceBundle.getBundle("ApplicationResources", locale); String tpl; int count = 0; int numberOfSpecialPages = 7; progress = Math.min(progressStart + (int) ((double) count * (double) progressLength / numberOfSpecialPages), 99); count++; String cssContent = wb.readRaw(virtualWiki, "StyleSheet"); addZipEntry(zipout, "css/vqwiki.css", cssContent); progress = Math.min(progressStart + (int) ((double) count * (double) progressLength / numberOfSpecialPages), 99); count++; tpl = getTemplateFilledWithContent("search"); addTopicEntry(zipout, tpl, "WikiSearch", "WikiSearch.html"); progress = Math.min(progressStart + (int) ((double) count * (double) progressLength / numberOfSpecialPages), 99); count++; zipout.putNextEntry(new ZipEntry("applets/export2html-applet.jar")); IOUtils.copy(new FileInputStream(ctx.getRealPath("/WEB-INF/classes/export2html/export2html-applet.jar")), zipout); zipout.closeEntry(); zipout.flush(); try { ByteArrayOutputStream bos = new ByteArrayOutputStream(); JarOutputStream indexjar = new JarOutputStream(bos); JarEntry jarEntry; File searchDir = new File(wb.getSearchEngine().getSearchIndexPath(virtualWiki)); String files[] = searchDir.list(); StringBuffer listOfAllFiles = new StringBuffer(); for (int i = 0; i < files.length; i++) { if (listOfAllFiles.length() > 0) { listOfAllFiles.append(","); } listOfAllFiles.append(files[i]); jarEntry = new JarEntry("lucene/index/" + files[i]); indexjar.putNextEntry(jarEntry); IOUtils.copy(new FileInputStream(new File(searchDir, files[i])), indexjar); indexjar.closeEntry(); } indexjar.flush(); indexjar.putNextEntry(new JarEntry("lucene/index.dir")); IOUtils.copy(new StringReader(listOfAllFiles.toString()), indexjar); indexjar.closeEntry(); indexjar.flush(); indexjar.close(); zipout.putNextEntry(new ZipEntry("applets/index.jar")); zipout.write(bos.toByteArray()); zipout.closeEntry(); zipout.flush(); bos.reset(); } catch (Exception e) { logger.log(Level.FINE, "Exception while adding lucene index: ", e); } progress = Math.min(progressStart + (int) ((double) count * (double) progressLength / numberOfSpecialPages), 99); count++; StringBuffer content = new StringBuffer(); content.append("<table><tr><th>" + messages.getString("common.date") + "</th><th>" + messages.getString("common.topic") + "</th><th>" + messages.getString("common.user") + "</th></tr>" + IOUtils.LINE_SEPARATOR); Collection all = null; try { Calendar cal = Calendar.getInstance(); ChangeLog cl = wb.getChangeLog(); int n = env.getIntSetting(Environment.PROPERTY_RECENT_CHANGES_DAYS); if (n == 0) { n = 5; } all = new ArrayList(); for (int i = 0; i < n; i++) { Collection col = cl.getChanges(virtualWiki, cal.getTime()); if (col != null) { all.addAll(col); } cal.add(Calendar.DATE, -1); } } catch (Exception e) { } DateFormat df = DateFormat.getDateTimeInstance(DateFormat.SHORT, DateFormat.SHORT, locale); for (Iterator iter = all.iterator(); iter.hasNext(); ) { Change change = (Change) iter.next(); content.append("<tr><td class=\"recent\">" + df.format(change.getTime()) + "</td><td class=\"recent\"><a href=\"" + safename(change.getTopic()) + ".html\">" + change.getTopic() + "</a></td><td class=\"recent\">" + change.getUser() + "</td></tr>"); } content.append("</table>" + IOUtils.LINE_SEPARATOR); tpl = getTemplateFilledWithContent(null); tpl = tpl.replaceAll("@@CONTENTS@@", content.toString()); addTopicEntry(zipout, tpl, "RecentChanges", "RecentChanges.html"); logger.fine("Done adding all special topics."); }

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(); } }

@Override public void actionPerformed(ActionEvent e) { if (copiedFiles_ != null) { File[] tmpFiles = new File[copiedFiles_.length]; File tmpDir = new File(Settings.getPropertyString(ConstantKeys.project_dir), "tmp/"); tmpDir.mkdirs(); for (int i = copiedFiles_.length - 1; i >= 0; i--) { Frame f = FrameManager.getInstance().getFrameAtIndex(i); try { File in = f.getFile(); File out = new File(tmpDir, f.getFile().getName()); FileChannel inChannel = new FileInputStream(in).getChannel(); FileChannel outChannel = new FileOutputStream(out).getChannel(); inChannel.transferTo(0, inChannel.size(), outChannel); if (inChannel != null) inChannel.close(); if (outChannel != null) outChannel.close(); tmpFiles[i] = out; } catch (IOException e1) { e1.printStackTrace(); } } try { FrameManager.getInstance().insertFrames(getTable().getSelectedRow(), FrameManager.INSERT_TYPE.MOVE, tmpFiles); } catch (IOException e1) { e1.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 store(String path, InputStream stream) throws IOException { toIgnore.add(normalizePath(path)); ZipEntry entry = new ZipEntry(path); zipOutput.putNextEntry(entry); IOUtils.copy(stream, zipOutput); zipOutput.closeEntry(); }

public int addPermissionsForUserAndAgenda(Integer userId, Integer agendaId, String permissions) throws TechnicalException { if (permissions == null) { throw new TechnicalException(new Exception(new Exception("Column 'permissions' cannot be null"))); } Session session = null; Transaction transaction = null; try { session = HibernateUtil.getCurrentSession(); transaction = session.beginTransaction(); String query = "INSERT INTO j_user_agenda (userId, agendaId, permissions) VALUES(" + userId + "," + agendaId + ",\"" + permissions + "\")"; Statement statement = session.connection().createStatement(); int rowsUpdated = statement.executeUpdate(query); transaction.commit(); return rowsUpdated; } catch (HibernateException ex) { if (transaction != null) transaction.rollback(); throw new TechnicalException(ex); } catch (SQLException e) { if (transaction != null) transaction.rollback(); throw new TechnicalException(e); } }

public int update(BusinessObject o) throws DAOException { int update = 0; Currency curr = (Currency) o; try { PreparedStatement pst = connection.prepareStatement(XMLGetQuery.getQuery("UPDATE_CURRENCY")); pst.setString(1, curr.getName()); pst.setInt(2, curr.getIdBase()); pst.setDouble(3, curr.getValue()); pst.setInt(4, curr.getId()); update = pst.executeUpdate(); if (update <= 0) { connection.rollback(); throw new DAOException("Number of rows <= 0"); } else if (update > 1) { connection.rollback(); throw new DAOException("Number of rows > 1"); } connection.commit(); } catch (SQLException e) { Log.write(e.getMessage()); throw new DAOException("A SQLException has occured"); } catch (NullPointerException npe) { Log.write(npe.getMessage()); throw new DAOException("Connection null"); } return update; }

private static String getRegistrationClasses() { CentralRegistrationClass c = new CentralRegistrationClass(); String name = c.getClass().getCanonicalName().replace('.', '/').concat(".class"); try { Enumeration<URL> urlEnum = c.getClass().getClassLoader().getResources("META-INF/MANIFEST.MF"); while (urlEnum.hasMoreElements()) { URL url = urlEnum.nextElement(); String file = url.getFile(); JarURLConnection jarConnection = (JarURLConnection) url.openConnection(); Manifest mf = jarConnection.getManifest(); Attributes attrs = (Attributes) mf.getAttributes(name); if (attrs != null) { String classes = attrs.getValue("RegistrationClasses"); return classes; } } } catch (IOException ex) { ex.printStackTrace(); } return ""; }

@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 FileChannel getFileChannel(Object o) throws IOException { Class c = o.getClass(); try { Method m = c.getMethod("getChannel", null); return (FileChannel) m.invoke(o, null); } catch (IllegalAccessException x) { } catch (NoSuchMethodException x) { } catch (InvocationTargetException x) { if (x.getTargetException() instanceof IOException) throw (IOException) x.getTargetException(); } if (o instanceof FileInputStream) return new MyFileChannelImpl((FileInputStream) o); if (o instanceof FileOutputStream) return new MyFileChannelImpl((FileOutputStream) o); if (o instanceof RandomAccessFile) return new MyFileChannelImpl((RandomAccessFile) o); Assert.UNREACHABLE(o.getClass().toString()); return null; }

@Test public void shouldDownloadFileUsingPublicLink() throws Exception { String bucketName = "test-" + UUID.randomUUID(); Service service = new WebClientService(credentials); service.createBucket(bucketName); File file = folder.newFile("foo.txt"); FileUtils.writeStringToFile(file, UUID.randomUUID().toString()); service.createObject(bucketName, file.getName(), file, new NullProgressListener()); String publicUrl = service.getPublicUrl(bucketName, file.getName(), new DateTime().plusDays(5)); File saved = folder.newFile("saved.txt"); InputStream input = new URL(publicUrl).openConnection().getInputStream(); FileOutputStream output = new FileOutputStream(saved); IOUtils.copy(input, output); output.close(); assertThat("Corrupted download", Files.computeMD5(saved), equalTo(Files.computeMD5(file))); service.deleteObject(bucketName, file.getName()); service.deleteBucket(bucketName); }

public static String getTextFromPart(Part part) { try { if (part != null && part.getBody() != null) { InputStream in = part.getBody().getInputStream(); String mimeType = part.getMimeType(); if (mimeType != null && MimeUtility.mimeTypeMatches(mimeType, "text/*")) { ByteArrayOutputStream out = new ByteArrayOutputStream(); IOUtils.copy(in, out); in.close(); in = null; String charset = getHeaderParameter(part.getContentType(), "charset"); if (charset != null) { charset = CharsetUtil.toJavaCharset(charset); } if (charset == null) { charset = "ASCII"; } String result = out.toString(charset); out.close(); return result; } } } catch (OutOfMemoryError oom) { Log.e(Email.LOG_TAG, "Unable to getTextFromPart " + oom.toString()); } catch (Exception e) { Log.e(Email.LOG_TAG, "Unable to getTextFromPart " + e.toString()); } return null; }

public void run() { try { Socket socket = getSocket(); System.out.println("opening socket to " + address + " on " + port); InputStream in = socket.getInputStream(); for (; ; ) { FileTransferHeader header = FileTransferHeader.readHeader(in); if (header == null) break; System.out.println("header: " + header); String[] parts = header.getFilename().getSegments(); String filename; if (parts.length > 0) filename = "dl-" + parts[parts.length - 1]; else filename = "dl-" + session.getScreenname(); System.out.println("writing to file " + filename); long sum = 0; if (new File(filename).exists()) { FileInputStream fis = new FileInputStream(filename); byte[] block = new byte[10]; for (int i = 0; i < block.length; ) { int count = fis.read(block); if (count == -1) break; i += count; } FileTransferChecksum summer = new FileTransferChecksum(); summer.update(block, 0, 10); sum = summer.getValue(); } FileChannel fileChannel = new FileOutputStream(filename).getChannel(); FileTransferHeader outHeader = new FileTransferHeader(header); outHeader.setHeaderType(FileTransferHeader.HEADERTYPE_ACK); outHeader.setIcbmMessageId(cookie); outHeader.setBytesReceived(0); outHeader.setReceivedChecksum(sum); OutputStream socketOut = socket.getOutputStream(); System.out.println("sending header: " + outHeader); outHeader.write(socketOut); for (int i = 0; i < header.getFileSize(); ) { long transferred = fileChannel.transferFrom(Channels.newChannel(in), 0, header.getFileSize() - i); System.out.println("transferred " + transferred); if (transferred == -1) return; i += transferred; } System.out.println("finished transfer!"); fileChannel.close(); FileTransferHeader doneHeader = new FileTransferHeader(header); doneHeader.setHeaderType(FileTransferHeader.HEADERTYPE_RECEIVED); doneHeader.setFlags(doneHeader.getFlags() | FileTransferHeader.FLAG_DONE); doneHeader.setBytesReceived(doneHeader.getBytesReceived() + 1); doneHeader.setIcbmMessageId(cookie); doneHeader.setFilesLeft(doneHeader.getFilesLeft() - 1); doneHeader.write(socketOut); if (doneHeader.getFilesLeft() - 1 <= 0) { socket.close(); break; } } } catch (IOException e) { e.printStackTrace(); return; } }

protected void setUp() throws Exception { testOutputDirectory = new File(getClass().getResource("/").getPath()); zipFile = new File(this.testOutputDirectory, "/plugin.zip"); zipOutputDirectory = new File(this.testOutputDirectory, "zip"); zipOutputDirectory.mkdir(); logger.fine("zip dir created"); ZipOutputStream zos = new ZipOutputStream(new FileOutputStream(zipFile)); zos.putNextEntry(new ZipEntry("css/")); zos.putNextEntry(new ZipEntry("css/system.properties")); System.getProperties().store(zos, null); zos.closeEntry(); zos.putNextEntry(new ZipEntry("js/")); zos.putNextEntry(new ZipEntry("js/system.properties")); System.getProperties().store(zos, null); zos.closeEntry(); zos.putNextEntry(new ZipEntry("WEB-INF/")); zos.putNextEntry(new ZipEntry("WEB-INF/classes/")); zos.putNextEntry(new ZipEntry("WEB-INF/classes/system.properties")); System.getProperties().store(zos, null); zos.closeEntry(); zos.putNextEntry(new ZipEntry("WEB-INF/lib/")); zos.putNextEntry(new ZipEntry("WEB-INF/lib/mylib.jar")); File jarFile = new File(this.testOutputDirectory.getPath() + "/mylib.jar"); JarOutputStream jos = new JarOutputStream(new FileOutputStream(jarFile)); jos.putNextEntry(new ZipEntry("vqwiki/")); jos.putNextEntry(new ZipEntry("vqwiki/plugins/")); jos.putNextEntry(new ZipEntry("vqwiki/plugins/system.properties")); System.getProperties().store(jos, null); jos.closeEntry(); jos.close(); IOUtils.copy(new FileInputStream(jarFile), zos); zos.closeEntry(); zos.close(); jarFile.delete(); }

private static KeyStore createKeyStore(final URL url, final String password) throws KeyStoreException, NoSuchAlgorithmException, CertificateException, IOException { if (url == null) { throw new IllegalArgumentException("Keystore url may not be null"); } LOG.debug("Initializing key store"); KeyStore keystore = KeyStore.getInstance("jks"); InputStream is = null; try { is = url.openStream(); keystore.load(is, password != null ? password.toCharArray() : null); } finally { if (is != null) is.close(); } return keystore; }

@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; }

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

@Override public byte[] getAvatar() throws IOException { HttpUriRequest request; try { request = new HttpGet(mUrl); } catch (IllegalArgumentException e) { IOException ioe = new IOException("Invalid url " + mUrl); ioe.initCause(e); throw ioe; } HttpResponse response = mClient.execute(request); HttpEntity entity = response.getEntity(); InputStream in = entity.getContent(); ByteArrayOutputStream os = new ByteArrayOutputStream(); try { byte[] data = new byte[1024]; int nbread; while ((nbread = in.read(data)) != -1) { os.write(data, 0, nbread); } } finally { in.close(); os.close(); } return os.toByteArray(); }

public int commit() throws TransactionException, SQLException, ConnectionFactoryException { Connection conn = ConnectionFactoryProxy.getInstance().getConnection(_poolName); conn.setAutoCommit(false); int numRowsUpdated = 0; try { Iterator statements = _statements.iterator(); while (statements.hasNext()) { StatementData sd = (StatementData) statements.next(); PreparedStatement ps = conn.prepareStatement(sd.statement); Iterator params = sd.params.iterator(); int index = 1; while (params.hasNext()) { ps.setString(index++, (String) params.next()); } numRowsUpdated += ps.executeUpdate(); } conn.commit(); } catch (SQLException ex) { System.err.println("com.zenark.zsql.TransactionImpl.commit() failed: Queued Statements follow"); Iterator statements = _statements.iterator(); while (statements.hasNext()) { StatementData sd = (StatementData) statements.next(); System.err.println("+--Statement: " + sd.statement + " with " + sd.params.size() + " parameters"); for (int loop = 0; loop < sd.params.size(); loop++) { System.err.println("+--Param : " + (String) sd.params.get(loop)); } } throw ex; } finally { _statements.clear(); conn.rollback(); conn.clearWarnings(); ConnectionFactoryProxy.getInstance().releaseConnection(conn); } return numRowsUpdated; }

public static InputStream retrievePricesHTML(String username, String password) throws IOException, SAXException { List<String> cookies = new ArrayList<String>(); URL url = new URL("http://motormouth.com.au/default_fl.aspx"); HttpURLConnection loginConnection = (HttpURLConnection) url.openConnection(); String viewStateValue = HTMLParser.parseHTMLInputTagValue(new InputStreamReader(loginConnection.getInputStream()), "__VIEWSTATE"); setCookies(cookies, loginConnection); HttpURLConnection postCredsConnection = (HttpURLConnection) url.openConnection(); postCredsConnection.setDoOutput(true); postCredsConnection.setRequestMethod("POST"); postCredsConnection.setInstanceFollowRedirects(false); postCredsConnection.setRequestProperty("Cookie", buildCookieString(cookies)); OutputStreamWriter postCredsWriter = new OutputStreamWriter(postCredsConnection.getOutputStream()); postCredsWriter.append("__VIEWSTATE=").append(URLEncoder.encode(viewStateValue, "UTF-8")).append('&'); postCredsWriter.append("Login_Module1%3Ausername=").append(URLEncoder.encode(username, "UTF-8")).append('&'); postCredsWriter.append("Login_Module1%3Apassword=").append(URLEncoder.encode(password, "UTF-8")).append('&'); postCredsWriter.append("Login_Module1%3AButtonLogin.x=0").append('&'); postCredsWriter.append("Login_Module1%3AButtonLogin.y=0"); postCredsWriter.flush(); postCredsWriter.close(); int postResponseCode = postCredsConnection.getResponseCode(); if (postResponseCode == 302) { setCookies(cookies, postCredsConnection); URL dataUrl = new URL(url, postCredsConnection.getHeaderField("Location")); HttpURLConnection dataConnection = (HttpURLConnection) dataUrl.openConnection(); dataConnection.setRequestProperty("Cookie", buildCookieString(cookies)); InputStream dataInputStream = dataConnection.getInputStream(); return dataInputStream; } else if (postResponseCode == 200) { URL dataUrl = new URL(url, "/secure/mymotormouth.aspx"); HttpURLConnection dataConnection = (HttpURLConnection) dataUrl.openConnection(); dataConnection.setRequestProperty("Cookie", buildCookieString(cookies)); InputStream dataInputStream = dataConnection.getInputStream(); return dataInputStream; } else { return null; } }

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) { } } } } }

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

public void 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 Channel getChannelFromSite(String siteURL) throws LinkNotFoundException, MalformedURLException, SAXException, IOException { String channelURL = ""; siteURL = siteURL.trim(); if (!siteURL.startsWith("http://")) { siteURL = "http://" + siteURL; } URL url = new URL(siteURL); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); String[] lines = new String[3]; for (int i = 0; i < lines.length; i++) { if ((lines[i] = in.readLine()) == null) { lines[i] = ""; break; } } if (lines[0].contains("xml version")) { if (lines[0].contains("rss") || lines[1].contains("rss")) { channelURL = siteURL; } if (lines[0].contains("Atom") || lines[1].contains("Atom") || lines[2].contains("Atom")) { channelURL = siteURL; } } in.close(); in = new BufferedReader(new InputStreamReader(url.openStream())); String iconURL = null; String inputLine; if ("".equals(channelURL)) { boolean isIconURLFound = false; boolean isChannelURLFound = false; while ((inputLine = in.readLine()) != null) { if (inputLine.contains("type=\"image/x-icon\"") || inputLine.toLowerCase().contains("rel=\"shortcut icon\"")) { String tmp = new String(inputLine); String[] smallLines = inputLine.replace(">", ">\n").split("\n"); for (String smallLine : smallLines) { if (smallLine.contains("type=\"image/x-icon\"") || smallLine.toLowerCase().contains("rel=\"shortcut icon\"")) { tmp = smallLine; break; } } isIconURLFound = true; iconURL = tmp.replaceAll("^.*href=\"", ""); iconURL = iconURL.replaceAll("\".*", ""); tmp = null; String originalSiteURL = new String(siteURL); siteURL = getHome(siteURL); if (iconURL.charAt(0) == '/') { if (siteURL.charAt(siteURL.length() - 1) == '/') { iconURL = siteURL + iconURL.substring(1); } else { iconURL = siteURL + iconURL; } } else if (!iconURL.startsWith("http://")) { if (siteURL.charAt(siteURL.length() - 1) == '/') { iconURL = siteURL + iconURL; } else { iconURL = siteURL + "/" + iconURL; } } siteURL = originalSiteURL; if (isChannelURLFound && isIconURLFound) { break; } } if ((inputLine.contains("type=\"application/rss+xml\"") || inputLine.contains("type=\"application/atom+xml\"")) && !isChannelURLFound) { if (!inputLine.contains("href=")) { while ((inputLine = in.readLine()) != null) { if (inputLine.contains("href=")) { break; } } } inputLine = inputLine.replace(">", ">\n"); String[] smallLines = inputLine.split("\n"); for (String smallLine : smallLines) { if (smallLine.contains("type=\"application/rss+xml\"") || smallLine.contains("type=\"application/atom+xml\"")) { inputLine = smallLine; break; } } channelURL = inputLine.replaceAll("^.*href=\"", ""); channelURL = channelURL.replaceAll("\".*", ""); if (channelURL.charAt(0) == '/') { if (siteURL.charAt(siteURL.length() - 1) == '/') { channelURL = siteURL + channelURL.substring(1); } else { channelURL = siteURL + channelURL; } } else if (!channelURL.startsWith("http://")) { if (siteURL.charAt(siteURL.length() - 1) == '/') { channelURL = siteURL + channelURL; } else { channelURL = siteURL + "/" + channelURL; } } isChannelURLFound = true; if (isChannelURLFound && isIconURLFound) { break; } } if (inputLine.contains("</head>".toLowerCase())) { break; } } in.close(); if ("".equals(channelURL)) { throw new LinkNotFoundException(); } } channel = getChannelFromXML(channelURL.trim()); if (iconURL == null || "".equals(iconURL.trim())) { iconURL = "favicon.ico"; if (siteURL.equalsIgnoreCase(channel.getChannelURL())) { siteURL = channel.getLink(); } siteURL = getHome(siteURL); if (siteURL.charAt(siteURL.length() - 1) == '/') { iconURL = siteURL + iconURL; } else { iconURL = siteURL + "/" + iconURL; } } try { String iconFileName = getHome(channel.getLink()); if (iconFileName.startsWith("http://")) { iconFileName = iconFileName.substring(7); } iconFileName = iconFileName.replaceAll("\\W", " ").trim().replace(" ", "_").concat(".ico"); String iconPath = JReader.getConfig().getShortcutIconsDir() + File.separator + iconFileName; InputStream inIcon = new URL(iconURL).openStream(); OutputStream outIcon = new FileOutputStream(iconPath); byte[] buf = new byte[1024]; int len; while ((len = inIcon.read(buf)) > 0) { outIcon.write(buf, 0, len); } inIcon.close(); outIcon.close(); channel.setIconPath(iconPath); } catch (Exception e) { } return channel; }

protected void discoverRegistryEntries() { DataSourceRegistry registry = this; try { ClassLoader loader = DataSetURI.class.getClassLoader(); Enumeration<URL> urls; if (loader == null) { urls = ClassLoader.getSystemResources("META-INF/org.virbo.datasource.DataSourceFactory.extensions"); } else { urls = loader.getResources("META-INF/org.virbo.datasource.DataSourceFactory.extensions"); } while (urls.hasMoreElements()) { URL url = urls.nextElement(); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String s = reader.readLine(); while (s != null) { s = s.trim(); if (s.length() > 0) { String[] ss = s.split("\\s"); for (int i = 1; i < ss.length; i++) { if (ss[i].contains(".")) { System.err.println("META-INF/org.virbo.datasource.DataSourceFactory.extensions contains extension that contains period: "); System.err.println(ss[0] + " " + ss[i] + " in " + url); System.err.println("This sometimes happens when extension files are concatenated, so check that all are terminated by end-of-line"); System.err.println(""); throw new IllegalArgumentException("DataSourceFactory.extensions contains extension that contains period: " + url); } registry.registerExtension(ss[0], ss[i], null); } } s = reader.readLine(); } reader.close(); } if (loader == null) { urls = ClassLoader.getSystemResources("META-INF/org.virbo.datasource.DataSourceFactory.mimeTypes"); } else { urls = loader.getResources("META-INF/org.virbo.datasource.DataSourceFactory.mimeTypes"); } while (urls.hasMoreElements()) { URL url = urls.nextElement(); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String s = reader.readLine(); while (s != null) { s = s.trim(); if (s.length() > 0) { String[] ss = s.split("\\s"); for (int i = 1; i < ss.length; i++) { registry.registerMimeType(ss[0], ss[i]); } } s = reader.readLine(); } reader.close(); } if (loader == null) { urls = ClassLoader.getSystemResources("META-INF/org.virbo.datasource.DataSourceFormat.extensions"); } else { urls = loader.getResources("META-INF/org.virbo.datasource.DataSourceFormat.extensions"); } while (urls.hasMoreElements()) { URL url = urls.nextElement(); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String s = reader.readLine(); while (s != null) { s = s.trim(); if (s.length() > 0) { String[] ss = s.split("\\s"); for (int i = 1; i < ss.length; i++) { if (ss[i].contains(".")) { System.err.println("META-INF/org.virbo.datasource.DataSourceFormat.extensions contains extension that contains period: "); System.err.println(ss[0] + " " + ss[i] + " in " + url); System.err.println("This sometimes happens when extension files are concatenated, so check that all are terminated by end-of-line"); System.err.println(""); throw new IllegalArgumentException("DataSourceFactory.extensions contains extension that contains period: " + url); } registry.registerFormatter(ss[0], ss[i]); } } s = reader.readLine(); } reader.close(); } if (loader == null) { urls = ClassLoader.getSystemResources("META-INF/org.virbo.datasource.DataSourceEditorPanel.extensions"); } else { urls = loader.getResources("META-INF/org.virbo.datasource.DataSourceEditorPanel.extensions"); } while (urls.hasMoreElements()) { URL url = urls.nextElement(); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String s = reader.readLine(); while (s != null) { s = s.trim(); if (s.length() > 0) { String[] ss = s.split("\\s"); for (int i = 1; i < ss.length; i++) { if (ss[i].contains(".")) { System.err.println("META-INF/org.virbo.datasource.DataSourceEditorPanel.extensions contains extension that contains period: "); System.err.println(ss[0] + " " + ss[i] + " in " + url); System.err.println("This sometimes happens when extension files are concatenated, so check that all are terminated by end-of-line"); System.err.println(""); throw new IllegalArgumentException("DataSourceFactory.extensions contains extension that contains period: " + url); } registry.registerEditor(ss[0], ss[i]); } } s = reader.readLine(); } reader.close(); } if (loader == null) { urls = ClassLoader.getSystemResources("META-INF/org.virbo.datasource.DataSourceFormatEditorPanel.extensions"); } else { urls = loader.getResources("META-INF/org.virbo.datasource.DataSourceFormatEditorPanel.extensions"); } while (urls.hasMoreElements()) { URL url = urls.nextElement(); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String s = reader.readLine(); while (s != null) { s = s.trim(); if (s.length() > 0) { String[] ss = s.split("\\s"); for (int i = 1; i < ss.length; i++) { if (ss[i].contains(".")) { System.err.println("META-INF/org.virbo.datasource.DataSourceFormatEditorPanel.extensions contains extension that contains period: "); System.err.println(ss[0] + " " + ss[i] + " in " + url); System.err.println("This sometimes happens when extension files are concatenated, so check that all are terminated by end-of-line"); System.err.println(""); throw new IllegalArgumentException("DataSourceFactory.extensions contains extension that contains period: " + url); } registry.registerFormatEditor(ss[0], ss[i]); } } s = reader.readLine(); } reader.close(); } } catch (IOException e) { e.printStackTrace(); } }

public static String getUserPass(String user) throws NoSuchAlgorithmException { MessageDigest digest = MessageDigest.getInstance("MD5"); digest.update(user.getBytes()); byte[] hash = digest.digest(); System.out.println("Returning user pass:" + hash); return hash.toString(); }

private static BufferedReader createReaderConnection(String urlString) throws SiteNotFoundException { BufferedReader reader = null; try { URL url = new URL(urlString); HttpURLConnection conn = (HttpURLConnection) url.openConnection(); conn.setRequestProperty("User-agent", "Mozilla/4.5"); if (conn.getResponseCode() != HttpURLConnection.HTTP_OK) { Logger.logln("Response code for url [" + urlString + "] was " + conn.getResponseCode() + " [" + conn.getResponseMessage() + "]"); throw new SiteNotFoundException(urlString); } reader = new BufferedReader(new InputStreamReader(conn.getInputStream())); } catch (IOException ex) { Logger.logln("" + ex); } return reader; }

public void copyFile2(String src, String dest) throws IOException { FileWriter fw = null; FileReader fr = null; BufferedReader br = null; BufferedWriter bw = null; File source = null; try { fr = new FileReader(src); fw = new FileWriter(dest); br = new BufferedReader(fr); bw = new BufferedWriter(fw); source = new File(src); int fileLength = (int) source.length(); char charBuff[] = new char[fileLength]; while (br.read(charBuff, 0, fileLength) != -1) bw.write(charBuff, 0, fileLength); } catch (FileNotFoundException fnfe) { throw new FileCopyException(src + " " + MM.PHRASES.getPhrase("35")); } catch (IOException ioe) { throw new FileCopyException(MM.PHRASES.getPhrase("36")); } finally { try { if (br != null) br.close(); if (bw != null) bw.close(); } catch (IOException ioe) { } } }

public static void main(String[] args) throws Exception { File rootDir = new File("C:\\dev\\workspace_fgd\\gouvqc_crggid\\WebContent\\WEB-INF\\upload"); File storeDir = new File(rootDir, "storeDir"); File workDir = new File(rootDir, "workDir"); LoggerFacade loggerFacade = new CommonsLoggingLogger(logger); final FileResourceManager frm = new SmbFileResourceManager(storeDir.getPath(), workDir.getPath(), true, loggerFacade); frm.start(); final String resourceId = "811375c8-7cae-4429-9a0e-9222f47dab45"; { if (!frm.resourceExists(resourceId)) { String txId = frm.generatedUniqueTxId(); frm.startTransaction(txId); FileInputStream inputStream = new FileInputStream(resourceId); frm.createResource(txId, resourceId); OutputStream outputStream = frm.writeResource(txId, resourceId); IOUtils.copy(inputStream, outputStream); IOUtils.closeQuietly(inputStream); IOUtils.closeQuietly(outputStream); frm.prepareTransaction(txId); frm.commitTransaction(txId); } } for (int i = 0; i < 30; i++) { final int index = i; new Thread() { @Override public void run() { try { String txId = frm.generatedUniqueTxId(); frm.startTransaction(txId); InputStream inputStream = frm.readResource(resourceId); frm.prepareTransaction(txId); frm.commitTransaction(txId); synchronized (System.out) { System.out.println(index + " ***********************" + txId + " (début)"); } String contenu = TikaUtils.getParsedContent(inputStream, "file.pdf"); synchronized (System.out) { System.out.println(index + " ***********************" + txId + " (fin)"); } } catch (ResourceManagerSystemException e) { throw new RuntimeException(e); } catch (ResourceManagerException e) { throw new RuntimeException(e); } catch (TikaException e) { throw new RuntimeException(e); } catch (IOException e) { throw new RuntimeException(e); } } }.start(); } Thread.sleep(60000); frm.stop(FileResourceManager.SHUTDOWN_MODE_NORMAL); }

public void create_list() { try { String data = URLEncoder.encode("PHPSESSID", "UTF-8") + "=" + URLEncoder.encode(this.get_session(), "UTF-8"); URL url = new URL(URL_LOLA + FILE_CREATE_LIST); 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; line = rd.readLine(); wr.close(); rd.close(); System.out.println("Gene list saved in LOLA"); } catch (Exception e) { System.out.println("error in createList()"); e.printStackTrace(); } }

public LinkedList<NameValuePair> getQuestion() { InputStream is = null; String result = ""; LinkedList<NameValuePair> question = new LinkedList<NameValuePair>(); try { HttpClient httpclient = new DefaultHttpClient(); HttpPost httppost = new HttpPost(domain); httppost.setEntity(new UrlEncodedFormEntity(library)); HttpResponse response = httpclient.execute(httppost); HttpEntity entity = response.getEntity(); is = entity.getContent(); } catch (Exception e) { Log.e("log_tag", "Error in http connection " + e.toString()); } try { BufferedReader reader = new BufferedReader(new InputStreamReader(is, "iso-8859-1"), 8); StringBuilder sb = new StringBuilder(); String line = null; while ((line = reader.readLine()) != null) { sb.append(line); } is.close(); result = sb.toString(); if (result.equals("null,")) { return null; } } catch (Exception e) { Log.e("log_tag", "Error converting result " + e.toString()); } try { JSONObject json = new JSONObject(result); JSONArray data = json.getJSONArray("data"); JSONObject quest = data.getJSONObject(0); question.add(new BasicNameValuePair("q", quest.getString("q"))); question.add(new BasicNameValuePair("a", quest.getString("a"))); question.add(new BasicNameValuePair("b", quest.getString("b"))); question.add(new BasicNameValuePair("c", quest.getString("c"))); question.add(new BasicNameValuePair("d", quest.getString("d"))); question.add(new BasicNameValuePair("correct", quest.getString("correct"))); return question; } catch (JSONException e) { Log.e("log_tag", "Error parsing data " + e.toString()); } return null; }

public static boolean copyFile(File src, File target) throws IOException { if (src == null || target == null || !src.exists()) return false; if (!target.exists()) if (!createNewFile(target)) return false; InputStream ins = new BufferedInputStream(new FileInputStream(src)); OutputStream ops = new BufferedOutputStream(new FileOutputStream(target)); int b; while (-1 != (b = ins.read())) ops.write(b); Streams.safeClose(ins); Streams.safeFlush(ops); Streams.safeClose(ops); return target.setLastModified(src.lastModified()); }

private void copy(File inputFile, File outputFile) { BufferedReader reader = null; BufferedWriter writer = null; try { reader = new BufferedReader(new InputStreamReader(new FileInputStream(inputFile), "UTF-8")); writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(outputFile), "UTF-8")); while (reader.ready()) { writer.write(reader.readLine()); writer.write(System.getProperty("line.separator")); } } catch (IOException e) { } finally { try { if (reader != null) reader.close(); if (writer != null) writer.close(); } catch (IOException e1) { } } }

private void unzipEntry(ZipFile zipfile, ZipEntry entry, File outputDir) throws IOException { if (entry.isDirectory()) { createDir(new File(outputDir, entry.getName())); return; } File outputFile = new File(outputDir, entry.getName()); if (!outputFile.getParentFile().exists()) { createDir(outputFile.getParentFile()); } BufferedInputStream inputStream = new BufferedInputStream(zipfile.getInputStream(entry)); BufferedOutputStream outputStream = new BufferedOutputStream(new FileOutputStream(outputFile)); IOUtils.copy(inputStream, outputStream); outputStream.close(); inputStream.close(); }

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

private static void copyContent(final File srcFile, final File dstFile, final boolean gzipContent) throws IOException { final File dstFolder = dstFile.getParentFile(); dstFolder.mkdirs(); if (!dstFolder.exists()) { throw new RuntimeException("Unable to create the folder " + dstFolder.getAbsolutePath()); } final InputStream in = new FileInputStream(srcFile); OutputStream out = new FileOutputStream(dstFile); if (gzipContent) { out = new GZIPOutputStream(out); } try { final byte[] buffer = new byte[1024]; int read; while ((read = in.read(buffer)) != -1) { out.write(buffer, 0, read); } } finally { in.close(); out.close(); } }

public void run() { try { Socket socket = getSocket(); System.out.println("opening socket to " + address + " on " + port); InputStream in = socket.getInputStream(); for (; ; ) { FileTransferHeader header = FileTransferHeader.readHeader(in); if (header == null) break; System.out.println("header: " + header); String[] parts = header.getFilename().getSegments(); String filename; if (parts.length > 0) filename = "dl-" + parts[parts.length - 1]; else filename = "dl-" + session.getScreenname(); System.out.println("writing to file " + filename); long sum = 0; if (new File(filename).exists()) { FileInputStream fis = new FileInputStream(filename); byte[] block = new byte[10]; for (int i = 0; i < block.length; ) { int count = fis.read(block); if (count == -1) break; i += count; } FileTransferChecksum summer = new FileTransferChecksum(); summer.update(block, 0, 10); sum = summer.getValue(); } FileChannel fileChannel = new FileOutputStream(filename).getChannel(); FileTransferHeader outHeader = new FileTransferHeader(header); outHeader.setHeaderType(FileTransferHeader.HEADERTYPE_ACK); outHeader.setIcbmMessageId(cookie); outHeader.setBytesReceived(0); outHeader.setReceivedChecksum(sum); OutputStream socketOut = socket.getOutputStream(); System.out.println("sending header: " + outHeader); outHeader.write(socketOut); for (int i = 0; i < header.getFileSize(); ) { long transferred = fileChannel.transferFrom(Channels.newChannel(in), 0, header.getFileSize() - i); System.out.println("transferred " + transferred); if (transferred == -1) return; i += transferred; } System.out.println("finished transfer!"); fileChannel.close(); FileTransferHeader doneHeader = new FileTransferHeader(header); doneHeader.setHeaderType(FileTransferHeader.HEADERTYPE_RECEIVED); doneHeader.setFlags(doneHeader.getFlags() | FileTransferHeader.FLAG_DONE); doneHeader.setBytesReceived(doneHeader.getBytesReceived() + 1); doneHeader.setIcbmMessageId(cookie); doneHeader.setFilesLeft(doneHeader.getFilesLeft() - 1); doneHeader.write(socketOut); if (doneHeader.getFilesLeft() - 1 <= 0) { socket.close(); break; } } } catch (IOException e) { e.printStackTrace(); return; } }

public static void testAutoIncrement() { final int count = 3; final Object lock = new Object(); for (int i = 0; i < count; i++) { new Thread(new Runnable() { @Override public void run() { while (true) { StringBuilder buffer = new StringBuilder(128); buffer.append("insert into DOMAIN ( ").append(LS); buffer.append(" DOMAIN_ID, TOP_DOMAIN_ID, DOMAIN_HREF, ").append(LS); buffer.append(" DOMAIN_RANK, DOMAIN_TYPE, DOMAIN_STATUS, ").append(LS); buffer.append(" DOMAIN_ICO_CREATED, DOMAIN_CDATE ").append(LS); buffer.append(") values ( ").append(LS); buffer.append(" null ,null, ?,").append(LS); buffer.append(" 1, 2, 1, ").append(LS); buffer.append(" 0, now() ").append(LS); buffer.append(") ").append(LS); String sqlInsert = buffer.toString(); boolean isAutoCommit = false; int i = 0; Connection conn = null; PreparedStatement pstmt = null; ResultSet rs = null; try { conn = ConnHelper.getConnection(); conn.setAutoCommit(isAutoCommit); pstmt = conn.prepareStatement(sqlInsert); for (i = 0; i < 10; i++) { String lock = "" + ((int) (Math.random() * 100000000)) % 100; pstmt.setString(1, lock); pstmt.executeUpdate(); } if (!isAutoCommit) conn.commit(); rs = pstmt.executeQuery("select max(DOMAIN_ID) from DOMAIN"); if (rs.next()) { String str = System.currentTimeMillis() + " " + rs.getLong(1); } } catch (Exception e) { try { if (!isAutoCommit) conn.rollback(); } catch (SQLException ex) { ex.printStackTrace(System.out); } String msg = System.currentTimeMillis() + " " + Thread.currentThread().getName() + " - " + i + " " + e.getMessage() + LS; FileIO.writeToFile("D:/DEAD_LOCK.txt", msg, true, "GBK"); } finally { ConnHelper.close(conn, pstmt, rs); } } } }).start(); } }

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 Logging() throws Exception { File home = new File(System.getProperty("user.home"), ".jorgan"); if (!home.exists()) { home.mkdirs(); } File logging = new File(home, "logging.properties"); if (!logging.exists()) { InputStream input = getClass().getResourceAsStream("logging.properties"); OutputStream output = null; try { output = new FileOutputStream(logging); IOUtils.copy(input, output); } finally { IOUtils.closeQuietly(input); IOUtils.closeQuietly(output); } } FileInputStream input = null; try { input = new FileInputStream(logging); LogManager.getLogManager().readConfiguration(input); } finally { IOUtils.closeQuietly(input); } }

@Override public void save(File folder) { actInstance = instance; this.setProperty(EsomMapper.PROPERTY_INSTANCE, String.valueOf(actInstance)); log.debug("instance: " + this.getProperty(EsomMapper.PROPERTY_INSTANCE)); if (this.getProperty(EsomMapper.PROPERTY_LRN_RADIO_SELECTED) == EsomMapper.RADIO_LOAD_SELECTED) { File src = new File(this.getProperty(EsomMapper.PROPERTY_LRN_FILE)); if (src.getParent() != folder.getPath()) { log.debug("saving lrn file in save folder " + folder.getPath()); File dst = new File(folder.getAbsolutePath() + File.separator + src.getName() + String.valueOf(actInstance)); try { FileReader fr = new FileReader(src); BufferedReader br = new BufferedReader(fr); dst.createNewFile(); FileWriter fw = new FileWriter(dst); BufferedWriter bw = new BufferedWriter(fw); int i = 0; while ((i = br.read()) != -1) bw.write(i); bw.flush(); bw.close(); br.close(); fr.close(); } catch (FileNotFoundException e) { log.error("Error while opening lrn sourcefile! Saving wasn't possible!!!"); e.printStackTrace(); } catch (IOException e) { log.error("Error while creating lrn destfile! Creating wasn't possible!!!"); e.printStackTrace(); } this.setProperty(EsomMapper.PROPERTY_LRN_FILE, dst.getName()); log.debug("done saving lrn file"); } } if (this.getProperty(EsomMapper.PROPERTY_WTS_RADIO_SELECTED) == EsomMapper.RADIO_LOAD_SELECTED) { File src = new File(this.getProperty(EsomMapper.PROPERTY_WTS_FILE)); if (src.getParent() != folder.getPath()) { log.debug("saving wts file in save folder " + folder.getPath()); File dst = new File(folder.getAbsolutePath() + File.separator + src.getName() + String.valueOf(actInstance)); try { FileReader fr = new FileReader(src); BufferedReader br = new BufferedReader(fr); dst.createNewFile(); FileWriter fw = new FileWriter(dst); BufferedWriter bw = new BufferedWriter(fw); int i = 0; while ((i = br.read()) != -1) bw.write(i); bw.flush(); bw.close(); br.close(); fr.close(); } catch (FileNotFoundException e) { log.error("Error while opening wts sourcefile! Saving wasn't possible!!!"); e.printStackTrace(); } catch (IOException e) { log.error("Error while creating wts destfile! Creating wasn't possible!!!"); e.printStackTrace(); } this.setProperty(EsomMapper.PROPERTY_WTS_FILE, dst.getName()); log.debug("done saving wts file"); } } if (this.getProperty(EsomMapper.PROPERTY_LRN_RADIO_SELECTED) == EsomMapper.RADIO_SELECT_FROM_DATANAV_SELECTED) { this.setProperty(EsomMapper.PROPERTY_LRN_FILE, "EsomMapper" + this.actInstance + ".lrn"); File dst = new File(folder + File.separator + this.getProperty(EsomMapper.PROPERTY_LRN_FILE)); try { FileWriter fw = new FileWriter(dst); BufferedWriter bw = new BufferedWriter(fw); bw.write("# EsomMapper LRN save file\n"); bw.write("% " + this.inputVectors.getNumRows() + "\n"); bw.write("% " + this.inputVectors.getNumCols() + "\n"); bw.write("% 9"); for (IColumn col : this.inputVectors.getColumns()) { if (col.getType() == IClusterNumber.class) bw.write("\t2"); else if (col.getType() == String.class) bw.write("\t8"); else bw.write("\t1"); } bw.write("\n% Key"); for (IColumn col : this.inputVectors.getColumns()) { bw.write("\t" + col.getLabel()); } bw.write("\n"); int keyIterator = 0; for (Vector<Object> row : this.inputVectors.getGrid()) { bw.write(this.inputVectors.getKey(keyIterator++).toString()); for (Object point : row) bw.write("\t" + point.toString()); bw.write("\n"); } bw.flush(); fw.flush(); bw.close(); fw.close(); } catch (IOException e) { e.printStackTrace(); } this.setProperty(EsomMapper.PROPERTY_LRN_RADIO_SELECTED, EsomMapper.RADIO_LOAD_SELECTED); } if (this.getProperty(EsomMapper.PROPERTY_WTS_RADIO_SELECTED) == EsomMapper.RADIO_SELECT_FROM_DATANAV_SELECTED) { this.setProperty(EsomMapper.PROPERTY_WTS_FILE, "EsomMapper" + this.actInstance + ".wts"); MyRetina tempRetina = new MyRetina(this.outputRetina.getNumRows(), this.outputRetina.getNumCols(), this.outputRetina.getDim(), this.outputRetina.getDistanceFunction(), this.outputRetina.isToroid()); for (int row = 0; row < this.outputRetina.getNumRows(); row++) { for (int col = 0; col < this.outputRetina.getNumCols(); col++) { for (int dim = 0; dim < this.outputRetina.getDim(); dim++) { tempRetina.setNeuron(row, col, dim, this.outputRetina.getPointasDoubleArray(row, col)[dim]); } } } EsomIO.writeWTSFile(folder + File.separator + this.getProperty(EsomMapper.PROPERTY_WTS_FILE), tempRetina); this.setProperty(EsomMapper.PROPERTY_WTS_RADIO_SELECTED, EsomMapper.RADIO_LOAD_SELECTED); } EsomMapper.instance++; }

public void testSetRequestProperty() throws Exception { MockHTTPServer httpServer = new MockHTTPServer("HTTP Server for User-Specified Request Property", 2); httpServer.start(); synchronized (bound) { if (!httpServer.started) { bound.wait(5000); } } HttpURLConnection urlConnection = (HttpURLConnection) new URL("http://localhost:" + httpServer.port()).openConnection(); assertEquals(0, urlConnection.getRequestProperties().size()); final String PROPERTY1 = "Accept"; final String PROPERTY2 = "Connection"; urlConnection.setRequestProperty(PROPERTY1, null); urlConnection.setRequestProperty(PROPERTY1, null); urlConnection.setRequestProperty(PROPERTY2, "keep-alive"); assertEquals(2, urlConnection.getRequestProperties().size()); assertNull(urlConnection.getRequestProperty(PROPERTY1)); assertEquals("keep-alive", urlConnection.getRequestProperty(PROPERTY2)); urlConnection.setRequestProperty(PROPERTY1, "/"); urlConnection.setRequestProperty(PROPERTY2, null); assertEquals("/", urlConnection.getRequestProperty(PROPERTY1)); assertNull(urlConnection.getRequestProperty(PROPERTY2)); }

public void setUrl(URL url) throws PDFException, PDFSecurityException, IOException { InputStream in = null; try { URLConnection urlConnection = url.openConnection(); in = urlConnection.getInputStream(); String pathOrURL = url.toString(); setInputStream(in, pathOrURL); } finally { if (in != null) { in.close(); } } }

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

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

public static String hash(String in, String algorithm) { if (StringUtils.isBlank(algorithm)) algorithm = DEFAULT_ALGORITHM; try { md = MessageDigest.getInstance(algorithm); } catch (NoSuchAlgorithmException nsae) { logger.error("No such algorithm exception", nsae); } md.reset(); md.update(in.getBytes()); String out = null; try { out = Base64Encoder.encode(md.digest()); } catch (IOException e) { logger.error("Error converting to Base64 ", e); } if (out.endsWith("\n")) out = out.substring(0, out.length() - 1); return out; }

public static String md5(String text) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md; md = MessageDigest.getInstance("MD5"); byte[] md5hash; md.update(text.getBytes("iso-8859-1"), 0, text.length()); md5hash = md.digest(); return convertToHex(md5hash); }