label int64 0 1 | func1 stringlengths 173 53.1k | func2 stringlengths 173 53.1k | id int64 0 901k |
|---|---|---|---|
0 | private List<Token> generateTokens(int tokenCount) throws XSServiceException { final List<Token> tokens = new ArrayList<Token>(tokenCount); final Random r = new Random(); String t = Long.toString(new Date().getTime()) + Integer.toString(r.nextInt()); final MessageDigest m; try { m = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { throw new XSServiceException("Error while creating tokens"); } for (int i = 0; i < tokenCount; ++i) { final Token token = new Token(); token.setValid(true); m.update(t.getBytes(), 0, t.length()); String md5 = new BigInteger(1, m.digest()).toString(16); while (md5.length() < 32) { md5 = String.valueOf(r.nextInt(9)) + md5; } t = md5.substring(0, 8) + "-" + md5.substring(8, 16) + "-" + md5.substring(16, 24) + "-" + md5.substring(24, 32); logger.debug("Generated token #" + (i + 1) + ": " + t); token.setTokenString(t); tokens.add(token); } return tokens; } | public void postData(Reader data, Writer output) { HttpURLConnection urlc = null; try { urlc = (HttpURLConnection) solrUrl.openConnection(); try { urlc.setRequestMethod("POST"); } catch (ProtocolException e) { throw new PostException("Shouldn't happen: HttpURLConnection doesn't support POST??", e); } urlc.setDoOutput(true); urlc.setDoInput(true); urlc.setUseCaches(false); urlc.setAllowUserInteraction(false); urlc.setRequestProperty("Content-type", "text/xml; charset=" + POST_ENCODING); OutputStream out = urlc.getOutputStream(); try { Writer writer = new OutputStreamWriter(out, POST_ENCODING); pipe(data, writer); writer.close(); } catch (IOException e) { throw new PostException("IOException while posting data", e); } finally { if (out != null) out.close(); } InputStream in = urlc.getInputStream(); try { Reader reader = new InputStreamReader(in); pipe(reader, output); reader.close(); } catch (IOException e) { throw new PostException("IOException while reading response", e); } finally { if (in != null) in.close(); } } catch (IOException e) { try { fatal("Solr returned an error: " + urlc.getResponseMessage()); } catch (IOException f) { } fatal("Connection error (is Solr running at " + solrUrl + " ?): " + e); } finally { if (urlc != null) urlc.disconnect(); } } | 16,700 |
0 | public static String MD5Encode(String password) { MessageDigest messageDigest; try { messageDigest = MessageDigest.getInstance("MD5"); messageDigest.update(password.getBytes()); final byte[] digest = messageDigest.digest(); final StringBuilder buf = new StringBuilder(digest.length * 2); final char[] HEX_DIGITS = { '0', '1', '2', '3', '4', '5', '6', '7', '8', '9', 'a', 'b', 'c', 'd', 'e', 'f' }; for (int j = 0; j < digest.length; j++) { buf.append(HEX_DIGITS[(digest[j] >> 4) & 0x0f]); buf.append(HEX_DIGITS[digest[j] & 0x0f]); } return buf.toString(); } catch (NoSuchAlgorithmException e) { return password; } } | public static final void copyFile(File source, File destination) throws IOException { FileChannel sourceChannel = new FileInputStream(source).getChannel(); FileChannel targetChannel = new FileOutputStream(destination).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), targetChannel); sourceChannel.close(); targetChannel.close(); } | 16,701 |
1 | private File uploadFile(InputStream inputStream, File file) { FileOutputStream fileOutputStream = null; try { File dir = file.getParentFile(); if (!dir.exists()) { dir.mkdirs(); } FileUtils.touch(file); fileOutputStream = new FileOutputStream(file); IOUtils.copy(inputStream, fileOutputStream); } catch (IOException e) { throw new FileOperationException("Failed to save uploaded image", e); } finally { try { if (fileOutputStream != null) { fileOutputStream.close(); } } catch (IOException e) { LOGGER.warn("Failed to close resources on uploaded file", e); } } return file; } | private void copyReportFile(ServletRequest req, String reportName, Report report) throws IllegalAccessException, InvocationTargetException, NoSuchMethodException, ClassNotFoundException, FileNotFoundException, IOException { String reportFileName = (String) Class.forName("org.eclipse.birt.report.utility.ParameterAccessor").getMethod("getReport", new Class[] { HttpServletRequest.class, String.class }).invoke(null, new Object[] { req, reportName }); ByteArrayInputStream bais = new ByteArrayInputStream(report.getReportContent()); FileOutputStream fos = new FileOutputStream(new File(reportFileName)); IOUtils.copy(bais, fos); bais.close(); fos.close(); } | 16,702 |
0 | private void createScript(File scriptsLocation, String relativePath, String scriptContent) { Writer fileWriter = null; try { File scriptFile = new File(scriptsLocation.getAbsolutePath() + "/" + relativePath); scriptFile.getParentFile().mkdirs(); fileWriter = new FileWriter(scriptFile); IOUtils.copy(new StringReader(scriptContent), fileWriter); } catch (IOException e) { throw new UnitilsException(e); } finally { IOUtils.closeQuietly(fileWriter); } } | public byte[] download(URL url, OutputStream out) throws IOException { boolean returnByByteArray = (out == null); ByteArrayOutputStream helper = null; if (returnByByteArray) { helper = new ByteArrayOutputStream(); } String s = url.toExternalForm(); URLConnection conn = url.openConnection(); String name = Launcher.getFileName(s); InputStream in = conn.getInputStream(); total = url.openConnection().getContentLength(); setStatusText(String.format("Downloading %s (%.2fMB)...", name, ((float) total / 1024 / 1024))); long justNow = System.currentTimeMillis(); int numRead = -1; byte[] buffer = new byte[2048]; while ((numRead = in.read(buffer)) != -1) { size += numRead; if (returnByByteArray) { helper.write(buffer, 0, numRead); } else { out.write(buffer, 0, numRead); } long now = System.currentTimeMillis(); if ((now - justNow) > 250) { setProgress((int) (((float) size / (float) total) * 100)); justNow = now; } } hideProgress(); if (returnByByteArray) { return helper.toByteArray(); } else { return null; } } | 16,703 |
0 | private void copyFile(String fileName, String messageID, boolean isError) { try { File inputFile = new File(fileName); File outputFile = null; if (isError) { outputFile = new File(provider.getErrorDataLocation(folderName) + messageID + ".xml"); } else { outputFile = new File(provider.getDataProcessedLocation(folderName) + messageID + ".xml"); } FileReader in = new FileReader(inputFile); FileWriter out = new FileWriter(outputFile); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } catch (Exception e) { } } | private void handleNodeDown(long eventID, long nodeID, String eventTime) { Category log = ThreadCategory.getInstance(OutageWriter.class); if (eventID == -1 || nodeID == -1) { log.warn(EventConstants.NODE_DOWN_EVENT_UEI + " ignored - info incomplete - eventid/nodeid: " + eventID + "/" + nodeID); return; } Connection dbConn = null; try { dbConn = DatabaseConnectionFactory.getInstance().getConnection(); try { dbConn.setAutoCommit(false); } catch (SQLException sqle) { log.error("Unable to change database AutoCommit to FALSE", sqle); return; } PreparedStatement activeSvcsStmt = dbConn.prepareStatement(OutageConstants.DB_GET_ACTIVE_SERVICES_FOR_NODE); PreparedStatement openStmt = dbConn.prepareStatement(OutageConstants.DB_OPEN_RECORD); PreparedStatement newOutageWriter = dbConn.prepareStatement(OutageConstants.DB_INS_NEW_OUTAGE); PreparedStatement getNextOutageIdStmt = dbConn.prepareStatement(OutageManagerConfigFactory.getInstance().getGetNextOutageID()); newOutageWriter = dbConn.prepareStatement(OutageConstants.DB_INS_NEW_OUTAGE); if (log.isDebugEnabled()) log.debug("handleNodeDown: creating new outage entries..."); activeSvcsStmt.setLong(1, nodeID); ResultSet activeSvcsRS = activeSvcsStmt.executeQuery(); while (activeSvcsRS.next()) { String ipAddr = activeSvcsRS.getString(1); long serviceID = activeSvcsRS.getLong(2); if (openOutageExists(dbConn, nodeID, ipAddr, serviceID)) { if (log.isDebugEnabled()) log.debug("handleNodeDown: " + nodeID + "/" + ipAddr + "/" + serviceID + " already down"); } else { long outageID = -1; ResultSet seqRS = getNextOutageIdStmt.executeQuery(); if (seqRS.next()) { outageID = seqRS.getLong(1); } seqRS.close(); newOutageWriter.setLong(1, outageID); newOutageWriter.setLong(2, eventID); newOutageWriter.setLong(3, nodeID); newOutageWriter.setString(4, ipAddr); newOutageWriter.setLong(5, serviceID); newOutageWriter.setTimestamp(6, convertEventTimeIntoTimestamp(eventTime)); newOutageWriter.executeUpdate(); if (log.isDebugEnabled()) log.debug("handleNodeDown: Recording outage for " + nodeID + "/" + ipAddr + "/" + serviceID); } } activeSvcsRS.close(); try { dbConn.commit(); if (log.isDebugEnabled()) log.debug("Outage recorded for all active services for " + nodeID); } catch (SQLException se) { log.warn("Rolling back transaction, nodeDown could not be recorded for nodeId: " + nodeID, se); try { dbConn.rollback(); } catch (SQLException sqle) { log.warn("SQL exception during rollback, reason", sqle); } } activeSvcsStmt.close(); openStmt.close(); newOutageWriter.close(); } catch (SQLException sqle) { log.warn("SQL exception while handling \'nodeDown\'", sqle); } finally { try { if (dbConn != null) dbConn.close(); } catch (SQLException e) { log.warn("Exception closing JDBC connection", e); } } } | 16,704 |
1 | @Override protected RequestLogHandler createRequestLogHandler() { try { File logbackConf = File.createTempFile("logback-access", ".xml"); IOUtils.copy(Thread.currentThread().getContextClassLoader().getResourceAsStream("logback-access.xml"), new FileOutputStream(logbackConf)); RequestLogHandler requestLogHandler = new RequestLogHandler(); RequestLogImpl requestLog = new RequestLogImpl(); requestLog.setFileName(logbackConf.getPath()); requestLogHandler.setRequestLog(requestLog); } catch (FileNotFoundException e) { log.error("Could not create request log handler", e); } catch (IOException e) { log.error("Could not create request log handler", e); } return null; } | public void prepareWorkingDirectory() throws Exception { workingDirectory = tempDir + "/profile_" + System.nanoTime(); (new File(workingDirectory)).mkdir(); String monitorCallShellScript = "data/scripts/monitorcall.sh"; URL monitorCallShellScriptUrl = Thread.currentThread().getContextClassLoader().getResource(monitorCallShellScript); File inScriptFile = null; try { inScriptFile = new File(monitorCallShellScriptUrl.toURI()); } catch (URISyntaxException e) { throw e; } monitorShellScript = workingDirectory + "/monitorcall.sh"; File outScriptFile = new File(monitorShellScript); FileChannel inChannel = new FileInputStream(inScriptFile).getChannel(); FileChannel outChannel = new FileOutputStream(outScriptFile).getChannel(); try { inChannel.transferTo(0, inChannel.size(), outChannel); } catch (IOException e) { throw e; } finally { if (inChannel != null) inChannel.close(); if (outChannel != null) outChannel.close(); } try { LinuxCommandExecutor cmdExecutor = new LinuxCommandExecutor(); cmdExecutor.runCommand("chmod 777 " + monitorShellScript); } catch (Exception e) { throw e; } } | 16,705 |
0 | public static void loadFile(final URL url, final StringBuffer buffer) throws IOException { InputStream in = null; BufferedReader dis = null; try { in = url.openStream(); dis = new BufferedReader(new InputStreamReader(in)); int i; while ((i = dis.read()) != -1) { buffer.append((char) i); } } finally { closeStream(in); closeReader(dis); } } | public static byte[] read(URL url) throws IOException { byte[] bytes; InputStream is = null; try { is = url.openStream(); bytes = readAllBytes(is); } finally { if (is != null) { is.close(); } } return bytes; } | 16,706 |
0 | public static String encriptarContrasena(String contrasena) throws NoSuchAlgorithmException, UnsupportedEncodingException { StringBuffer sb = new StringBuffer(); MessageDigest md = MessageDigest.getInstance("SHA-512"); md.update(contrasena.getBytes("UTF-8")); byte[] digestBytes = md.digest(); String hex = null; for (int i = 0; i < digestBytes.length; i++) { hex = Integer.toHexString(0xFF & digestBytes[i]); if (hex.length() < 2) sb.append("0"); sb.append(hex); } return new String(sb); } | public InputStream getDaoConfig(String connectionType) throws IOException { URL url = null; if (connectionType.equals(SQL.ORACLE)) { url = DBCreateConfig.class.getResource("oracle.xml"); } else if (connectionType.equals(SQL.SQL2K)) { url = DBCreateConfig.class.getResource("sql2k.xml"); } return url.openStream(); } | 16,707 |
0 | public static String hash(String plainText) throws Exception { MessageDigest m = MessageDigest.getInstance("MD5"); m.update(plainText.getBytes(), 0, plainText.length()); String hash = new BigInteger(1, m.digest()).toString(16); if (hash.length() == 31) { hash = "0" + hash; } return hash; } | private boolean cacheUrlFile(String filePath, String realUrl, boolean isOnline) { try { URL url = new URL(realUrl); String encoding = "gbk"; BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream(), encoding)); StringBuilder sb = new StringBuilder(); sb.append(configCenter.getWebRoot()).append(getCacheString(isOnline)).append(filePath); fileEditor.createDirectory(sb.toString()); return fileEditor.saveFile(sb.toString(), in); } catch (IOException e) { } return false; } | 16,708 |
1 | private synchronized File gzipTempFile(File tempFile) throws BlogunityException { try { File gzippedFile = new File(BlogunityManager.getSystemConfiguration().getTempDir(), tempFile.getName() + ".gz"); GZIPOutputStream zos = new GZIPOutputStream(new FileOutputStream(gzippedFile)); byte[] readBuffer = new byte[2156]; int bytesIn = 0; FileInputStream fis = new FileInputStream(tempFile); while ((bytesIn = fis.read(readBuffer)) != -1) { zos.write(readBuffer, 0, bytesIn); } fis.close(); zos.close(); return gzippedFile; } catch (Exception e) { throw new BlogunityException(I18NStatusFactory.create(I18N.ERRORS.FEED_GZIP_FAILED, e)); } } | public static void copy(String source, String destination) { FileReader in = null; FileWriter out = null; try { File inputFile = new File(source); File outputFile = new File(destination); in = new FileReader(inputFile); out = new FileWriter(outputFile); int c; while ((c = in.read()) != -1) out.write(c); } catch (IOException e) { e.printStackTrace(); } finally { if (in != null) try { in.close(); } catch (IOException e) { e.printStackTrace(); } if (out != null) try { out.close(); } catch (IOException e) { e.printStackTrace(); } } } | 16,709 |
1 | public long copyFileWithPaths(String userBaseDir, String sourcePath, String destinPath) throws Exception { if (userBaseDir.endsWith(sep)) { userBaseDir = userBaseDir.substring(0, userBaseDir.length() - sep.length()); } String file1FullPath = new String(); if (sourcePath.startsWith(sep)) { file1FullPath = new String(userBaseDir + sourcePath); } else { file1FullPath = new String(userBaseDir + sep + sourcePath); } String file2FullPath = new String(); if (destinPath.startsWith(sep)) { file2FullPath = new String(userBaseDir + destinPath); } else { file2FullPath = new String(userBaseDir + sep + destinPath); } long plussQuotaSize = 0; BufferedInputStream in = null; BufferedOutputStream out = null; byte dataBuff[] = new byte[bufferSize]; File fileordir = new File(file1FullPath); if (fileordir.exists()) { if (fileordir.isFile()) { File file2 = new File(file2FullPath); if (file2.exists()) { plussQuotaSize -= file2.length(); file2.delete(); } FileUtils.getInstance().createDirectory(file2.getParent()); in = new BufferedInputStream(new FileInputStream(file1FullPath), bufferSize); out = new BufferedOutputStream(new FileOutputStream(file2FullPath), bufferSize); int readLen; while ((readLen = in.read(dataBuff)) > 0) { out.write(dataBuff, 0, readLen); plussQuotaSize += readLen; } out.flush(); in.close(); out.close(); } if (fileordir.isDirectory()) { String[] entryList = fileordir.list(); if (entryList.length > 0) { for (int pos = 0; pos < entryList.length; pos++) { String entryName = entryList[pos]; String file1FullPathEntry = new String(file1FullPath.concat(entryList[pos])); String file2FullPathEntry = new String(file2FullPath.concat(entryList[pos])); File file2 = new File(file2FullPathEntry); if (file2.exists()) { plussQuotaSize -= file2.length(); file2.delete(); } FileUtils.getInstance().createDirectory(file2.getParent()); in = new BufferedInputStream(new FileInputStream(file1FullPathEntry), bufferSize); out = new BufferedOutputStream(new FileOutputStream(file2FullPathEntry), bufferSize); int readLen; while ((readLen = in.read(dataBuff)) > 0) { out.write(dataBuff, 0, readLen); plussQuotaSize += readLen; } out.flush(); in.close(); out.close(); } } } } else { throw new Exception("Source file or dir not exist ! file1FullPath = (" + file1FullPath + ")"); } return plussQuotaSize; } | public static void copy(String fromFileName, String toFileName) throws IOException { File fromFile = new File(fromFileName); File toFile = new File(toFileName); if (!fromFile.exists()) throw new IOException("FileCopy: " + "no such source file: " + fromFileName); if (!fromFile.isFile()) throw new IOException("FileCopy: " + "can't copy directory: " + fromFileName); if (!fromFile.canRead()) throw new IOException("FileCopy: " + "source file is unreadable: " + fromFileName); if (toFile.isDirectory()) toFile = new File(toFile, fromFile.getName()); if (toFile.exists()) { if (!toFile.canWrite()) throw new IOException("FileCopy: " + "destination file is unwriteable: " + toFileName); } else { String parent = toFile.getParent(); if (parent == null) parent = System.getProperty("user.dir"); File dir = new File(parent); if (!dir.exists()) 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) { ; } } } | 16,710 |
0 | public final String latestVersion() { String latestVersion = ""; try { URL url = new URL(Constants.officialSite + ":80/LatestVersion"); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); String str; while ((str = in.readLine()) != null) { latestVersion = str; } in.close(); } catch (MalformedURLException e) { } catch (IOException e) { } return latestVersion; } | 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(); } } | 16,711 |
1 | public static Document convertHtmlToXml(final InputStream htmlInputStream, final String classpathXsltResource, final String encoding) { Parser p = new Parser(); javax.xml.parsers.DocumentBuilder db; try { db = javax.xml.parsers.DocumentBuilderFactory.newInstance().newDocumentBuilder(); } catch (ParserConfigurationException e) { log.error("", e); throw new RuntimeException(); } Document document = db.newDocument(); InputStream is = htmlInputStream; if (log.isDebugEnabled()) { ByteArrayOutputStream baos; baos = new ByteArrayOutputStream(); try { IOUtils.copy(is, baos); } catch (IOException e) { log.error("Fail to make input stream copy.", e); } IOUtils.closeQuietly(is); ByteArrayInputStream byteArrayInputStream; byteArrayInputStream = new ByteArrayInputStream(baos.toByteArray()); try { IOUtils.toString(new ByteArrayInputStream(baos.toByteArray()), "UTF-8"); } catch (IOException e) { log.error("", e); } IOUtils.closeQuietly(byteArrayInputStream); is = new ByteArrayInputStream(baos.toByteArray()); } try { InputSource iSource = new InputSource(is); iSource.setEncoding(encoding); Source transformerSource = new SAXSource(p, iSource); Result result = new DOMResult(document); Transformer xslTransformer = getTransformerByName(classpathXsltResource, false); try { xslTransformer.transform(transformerSource, result); } catch (TransformerException e) { throw new RuntimeException(e); } } finally { try { is.close(); } catch (Exception e) { log.warn("", e); } } return document; } | private void copyOutResource(String dstPath, InputStream in) throws FileNotFoundException, IOException { FileOutputStream out = null; try { dstPath = this.outputDir + dstPath; File file = new File(dstPath); file.getParentFile().mkdirs(); out = new FileOutputStream(file); IOUtils.copy(in, out); } finally { if (out != null) { out.close(); } } } | 16,712 |
1 | public byte[] exportCommunityData(String communityId) throws RepositoryException, IOException { Community community; try { community = getCommunityById(communityId); } catch (CommunityNotFoundException e1) { throw new GroupwareRuntimeException("Community to export not found"); } String contentPath = JCRUtil.getNodeById(communityId, community.getWorkspace()).getPath(); try { File zipOutFilename = File.createTempFile("exported-community", ".zip.tmp"); TemporaryFilesHandler.register(null, zipOutFilename); ZipOutputStream out = new ZipOutputStream(new FileOutputStream(zipOutFilename)); File file = File.createTempFile("exported-community", null); TemporaryFilesHandler.register(null, file); FileOutputStream fos = new FileOutputStream(file); exportCommunitySystemView(community, contentPath, fos); fos.close(); File propertiesFile = File.createTempFile("exported-community-properties", null); TemporaryFilesHandler.register(null, propertiesFile); FileOutputStream fosProperties = new FileOutputStream(propertiesFile); fosProperties.write(("communityId=" + communityId).getBytes()); fosProperties.write(";".getBytes()); fosProperties.write(("externalId=" + community.getExternalId()).getBytes()); fosProperties.write(";".getBytes()); fosProperties.write(("title=" + I18NUtils.localize(community.getTitle())).getBytes()); fosProperties.write(";".getBytes()); fosProperties.write(("communityType=" + community.getType()).getBytes()); fosProperties.write(";".getBytes()); fosProperties.write(("communityName=" + community.getName()).getBytes()); fosProperties.close(); FileInputStream finProperties = new FileInputStream(propertiesFile); byte[] bufferProperties = new byte[4096]; out.putNextEntry(new ZipEntry("properties")); int readProperties = 0; while ((readProperties = finProperties.read(bufferProperties)) > 0) { out.write(bufferProperties, 0, readProperties); } finProperties.close(); FileInputStream fin = new FileInputStream(file); byte[] buffer = new byte[4096]; out.putNextEntry(new ZipEntry("xmlData")); int read = 0; while ((read = fin.read(buffer)) > 0) { out.write(buffer, 0, read); } fin.close(); out.close(); ByteArrayOutputStream baos = new ByteArrayOutputStream(); FileInputStream fisZipped = new FileInputStream(zipOutFilename); byte[] bufferOut = new byte[4096]; int readOut = 0; while ((readOut = fisZipped.read(bufferOut)) > 0) { baos.write(bufferOut, 0, readOut); } return baos.toByteArray(); } catch (Exception e) { String errorMessage = "Error exporting backup data, for comunnity with id " + communityId; log.error(errorMessage, e); throw new CMSRuntimeException(errorMessage, e); } } | @Override @Transactional public FileData store(FileData data, InputStream stream) { try { FileData file = save(data); file.setPath(file.getGroup() + File.separator + file.getId()); file = save(file); File folder = new File(PATH, file.getGroup()); if (!folder.exists()) folder.mkdirs(); File filename = new File(folder, file.getId() + ""); IOUtils.copyLarge(stream, new FileOutputStream(filename)); return file; } catch (IOException e) { throw new ServiceException("storage", e); } } | 16,713 |
0 | public static String getSHA1Digest(String inputStr) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md = null; byte[] sha1hash = null; md = MessageDigest.getInstance("SHA"); sha1hash = new byte[40]; md.update(inputStr.getBytes("iso-8859-1"), 0, inputStr.length()); sha1hash = md.digest(); return convertToHex(sha1hash); } | @Test public void usingStream() throws IOException, NameNotFoundException { URL url = new URL("ftp://ftp.ebi.ac.uk/pub/databases/interpro/entry.list"); InterproNameHandler handler = new InterproNameHandler(url.openStream()); String interproName = handler.getNameById("IPR008255"); assertNotNull(interproName); assertEquals("Pyridine nucleotide-disulphide oxidoreductase, class-II, active site", interproName); assertEquals(null, handler.getNameById("Active_site")); } | 16,714 |
0 | private static void init() { try { ClassLoader cl = Thread.currentThread().getContextClassLoader(); Enumeration<URL> enumeration = cl.getResources("extension-services.properties"); do { if (!enumeration.hasMoreElements()) break; URL url = (URL) enumeration.nextElement(); System.out.println(" - " + url); try { props = new Properties(); props.load(url.openStream()); } catch (Exception e) { e.printStackTrace(); } } while (true); } catch (IOException e) { } } | public SSLContext getSSLContext() throws IOException { try { URL url = getClass().getClassLoader().getResource(keyStoreFile); KeyStore keystore = KeyStore.getInstance(type.name()); keystore.load(url.openStream(), keyPassword); KeyManagerFactory kmfactory = KeyManagerFactory.getInstance(KeyManagerFactory.getDefaultAlgorithm()); kmfactory.init(keystore, keyPassword); KeyManager[] keymanagers = kmfactory.getKeyManagers(); SSLContext sslcontext = SSLContext.getInstance(protocol.name()); sslcontext.init(keymanagers, TRUST_MANAGER, null); return sslcontext; } catch (Exception e) { throw new IOException(e); } } | 16,715 |
1 | public void run() { if (getCommand() == null) throw new IllegalArgumentException("Given command is null!"); if (getSocketProvider() == null) throw new IllegalArgumentException("Given connection is not open!"); if (getCommand() instanceof ListCommand) { try { setReply(ReplyWorker.readReply(getSocketProvider(), true)); setStatus(ReplyWorker.FINISHED); } catch (IOException ioe) { setCaughtException(ioe); setStatus(ReplyWorker.ERROR_IO_EXCEPTION); } return; } else if (getCommand() instanceof RetrieveCommand) { RetrieveCommand retrieveCommand = (RetrieveCommand) getCommand(); if (retrieveCommand.getFromFile().getTransferType().intern() == Command.TYPE_I || retrieveCommand.getFromFile().getTransferType().intern() == Command.TYPE_A) { try { log.debug("Download file: " + retrieveCommand.getFromFile().toString()); FileOutputStream out = null; FileChannel channel = null; if (getDownloadMethod() == RetrieveCommand.FILE_BASED) { out = new FileOutputStream(retrieveCommand.getToFile().getFile()); channel = out.getChannel(); if (retrieveCommand.getResumePosition() != -1) { try { channel.position(retrieveCommand.getResumePosition()); } catch (IOException ioe) { setCaughtException(ioe); setStatus(ReplyWorker.ERROR_IO_EXCEPTION); try { channel.close(); } catch (IOException ioe2) { } return; } } } else if (getDownloadMethod() == RetrieveCommand.BYTEBUFFER_BASED) { } int amount; try { while ((amount = getSocketProvider().read(buffer)) != -1) { if (amount == 0) { try { Thread.sleep(4); } catch (InterruptedException e) { } } buffer.flip(); while (buffer.hasRemaining()) { if (getDownloadMethod() == RetrieveCommand.STREAM_BASED) { int rem = buffer.remaining(); byte[] buf = new byte[rem]; buffer.get(buf, 0, rem); this.outputPipe.write(buf, 0, rem); } else if (getDownloadMethod() == RetrieveCommand.BYTEBUFFER_BASED) { } else { channel.write(buffer); } } buffer.clear(); } buffer.flip(); while (buffer.hasRemaining()) { if (getDownloadMethod() == RetrieveCommand.STREAM_BASED) { int rem = buffer.remaining(); byte[] buf = new byte[rem]; buffer.get(buf, 0, rem); this.outputPipe.write(buf, 0, rem); } else if (getDownloadMethod() == RetrieveCommand.BYTEBUFFER_BASED) { } else { channel.write(buffer); } } buffer.clear(); setStatus(ReplyWorker.FINISHED); if (channel != null) channel.close(); if (this.outputPipe != null) this.outputPipe.close(); getSocketProvider().close(); } catch (IOException ioe) { setCaughtException(ioe); setStatus(ReplyWorker.ERROR_IO_EXCEPTION); } finally { try { channel.close(); getSocketProvider().close(); } catch (Exception e) { } } } catch (FileNotFoundException fnfe) { setCaughtException(fnfe); setStatus(ReplyWorker.ERROR_FILE_NOT_FOUND); } } else throw new IllegalArgumentException("Unknown file transfer type for download!"); return; } else if (getCommand() instanceof StoreCommand) { StoreCommand storeCommand = (StoreCommand) getCommand(); if (storeCommand.getToFile().getTransferType().intern() == Command.TYPE_I || storeCommand.getToFile().getTransferType().intern() == Command.TYPE_A) { try { log.debug("Upload file: " + storeCommand.getFromFile()); InputStream in = storeCommand.getStream(); int amount; int socketWrite; int socketAmount = 0; if (in instanceof FileInputStream) { FileChannel channel = ((FileInputStream) in).getChannel(); if (storeCommand.getResumePosition() != -1) { try { channel.position(storeCommand.getResumePosition()); } catch (IOException ioe) { setCaughtException(ioe); setStatus(ReplyWorker.ERROR_IO_EXCEPTION); try { channel.close(); } catch (IOException ioe2) { } return; } } try { while ((amount = channel.read(buffer)) != -1) { buffer.flip(); socketWrite = 0; while ((socketWrite = getSocketProvider().write(buffer)) != -1) { socketAmount += socketWrite; if (amount <= socketAmount) { break; } if (socketWrite == 0) { try { Thread.sleep(4); } catch (InterruptedException e) { } } } if (socketWrite == -1) { break; } socketAmount = 0; buffer.clear(); } setStatus(ReplyWorker.FINISHED); channel.close(); getSocketProvider().close(); } catch (IOException ioe) { setCaughtException(ioe); setStatus(ReplyWorker.ERROR_IO_EXCEPTION); } finally { try { channel.close(); getSocketProvider().close(); } catch (Exception e) { } } } else { try { while ((amount = in.read(buffer.array())) != -1) { buffer.flip(); buffer.limit(amount); socketWrite = 0; while ((socketWrite = getSocketProvider().write(buffer)) != -1) { socketAmount = socketWrite; if (amount <= socketAmount) { break; } if (socketWrite == 0) { try { Thread.sleep(4); } catch (InterruptedException e) { } } } if (socketWrite == -1) { break; } socketAmount = 0; buffer.clear(); } setStatus(ReplyWorker.FINISHED); in.close(); getSocketProvider().close(); } catch (IOException ioe) { setCaughtException(ioe); setStatus(ReplyWorker.ERROR_IO_EXCEPTION); } finally { try { in.close(); getSocketProvider().close(); } catch (Exception e) { } } } } catch (FileNotFoundException fnfe) { setCaughtException(fnfe); setStatus(ReplyWorker.ERROR_FILE_NOT_FOUND); } } else throw new IllegalArgumentException("Unknown file transfer type for upload!"); } else throw new IllegalArgumentException("Given command is not supported!"); } | 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(); } } | 16,716 |
1 | protected static void copyDeleting(File source, File dest) throws ErrorCodeException { byte[] buf = new byte[8 * 1024]; FileInputStream in = null; try { in = new FileInputStream(source); try { FileOutputStream out = new FileOutputStream(dest); try { int count; while ((count = in.read(buf)) >= 0) out.write(buf, 0, count); } finally { out.close(); } } finally { in.close(); } } catch (IOException e) { throw new ErrorCodeException(e); } } | @SuppressWarnings("unchecked") public static void unzip(String input, String output) { try { if (!output.endsWith("/")) output = output + "/"; ZipFile zip = new ZipFile(input); Enumeration entries = zip.entries(); while (entries.hasMoreElements()) { ZipEntry entry = (ZipEntry) entries.nextElement(); if (entry.isDirectory()) { FileUtils.forceMkdir(new File(output + entry.getName())); } else { FileOutputStream out = new FileOutputStream(output + entry.getName()); IOUtils.copy(zip.getInputStream(entry), out); IOUtils.closeQuietly(out); } } } catch (Exception e) { log.error("�����ҵ��ļ�:" + output, e); throw new RuntimeException("�����ҵ��ļ�:" + output, e); } } | 16,717 |
0 | protected void registerClasses() throws PrintException { if (!init) { try { Enumeration<URL> somethingToRegister = this.getClass().getClassLoader().getResources("META-INF/" + getClass().getSimpleName() + ".properties"); while (somethingToRegister.hasMoreElements()) { URL url = (URL) somethingToRegister.nextElement(); InputStream in = url.openStream(); BufferedReader buff = new BufferedReader(new InputStreamReader(in)); String line = buff.readLine(); while (line != null) { log.debug(line); try { Class cls = Class.forName(line); cls.newInstance(); log.debug("class " + line + " registered " + url); } catch (ClassNotFoundException e) { log.error("class " + line + " not found " + url, e); } catch (InstantiationException e) { log.error("class " + line + " not found " + url, e); } catch (IllegalAccessException e) { log.error("class " + line + " not found " + url, e); } line = buff.readLine(); } buff.close(); in.close(); } } catch (IOException e) { throw new PrintException(e.getMessage(), e); } init = true; } } | public InputStream sendCommandRaw(String command, boolean usePost) throws IOException { try { String fullCommand = prefix + command + fixSuffix(command, suffix); long curGap = System.currentTimeMillis() - lastCommandTime; long delayTime = minimumCommandPeriod - curGap; delay(delayTime); URI uri = new URI(fullCommand); URL url = uri.toURL(); if (trace || traceSends) { System.out.println("Sending--> " + url); } if (logFile != null) { logFile.println("Sending--> " + url); } InputStream is = null; for (int i = 0; i < tryCount; i++) { try { URLConnection urc = url.openConnection(); if (usePost) { if (urc instanceof HttpURLConnection) { ((HttpURLConnection) urc).setRequestMethod("POST"); } } if (getTimeout() != -1) { urc.setReadTimeout(getTimeout()); urc.setConnectTimeout(getTimeout()); } is = new BufferedInputStream(urc.getInputStream()); break; } catch (FileNotFoundException e) { throw e; } catch (IOException e) { System.out.println(name + " Error: " + e + " cmd: " + command); } } lastCommandTime = System.currentTimeMillis(); if (is == null) { System.out.println(name + " retry failure cmd: " + url); throw new IOException("Can't send command"); } return is; } catch (URISyntaxException ex) { throw new IOException("bad uri " + ex); } } | 16,718 |
0 | private static synchronized byte[] gerarHash(String frase) { try { MessageDigest md = MessageDigest.getInstance(algoritmo); md.update(frase.getBytes()); return md.digest(); } catch (NoSuchAlgorithmException e) { return null; } } | private String getStreamUrl(String adress) throws MalformedURLException, IOException, ParserConfigurationException, SAXException { URL url = new URL(adress); InputStream is = url.openStream(); DocumentBuilder builder = DocumentBuilderFactory.newInstance().newDocumentBuilder(); org.w3c.dom.Document doc = builder.parse(is); Node linkTag = doc.getElementsByTagName(LINK_TAG_NAME).item(0); String StreamUrl = linkTag.getAttributes().getNamedItem(LINK_ATTR_NAME).getNodeValue(); return StreamUrl; } | 16,719 |
0 | private void downloadFile(File file, String url) { String state = Environment.getExternalStorageState(); if (Environment.MEDIA_MOUNTED.equals(state)) { InputStream in = null; BufferedOutputStream out = null; try { in = new BufferedInputStream(new URL(url).openStream(), IO_BUFFER_SIZE); final FileOutputStream outStream = new FileOutputStream(file); out = new BufferedOutputStream(outStream, IO_BUFFER_SIZE); byte[] bytes = new byte[IO_BUFFER_SIZE]; while (in.read(bytes) > 0) { out.write(bytes); } } catch (IOException e) { e.printStackTrace(); } finally { if (in != null) { try { in.close(); } catch (IOException e) { e.printStackTrace(); } } if (out != null) { try { out.close(); } catch (IOException e) { e.printStackTrace(); } } } } } | public 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; } | 16,720 |
1 | public void objectParserAssesmentItem(int file, int currentquestion, Resource resTemp) { NodeList nl = null; Node n = null; NamedNodeMap nnp = null; Node nsrc = null; URL url = null; String sFilename = ""; String sNewPath = ""; int indexLastSeparator; String sOldPath = ""; try { if (file == 1) { nl = doc.getElementsByTagName("object"); } else { nl = doc_[currentquestion].getElementsByTagName("object"); } for (int i = 0; i < nl.getLength(); i++) { n = nl.item(i); nnp = n.getAttributes(); nsrc = nnp.getNamedItem("data"); String sTemp = nsrc.getTextContent(); url = new URL("file", "localhost", sTemp); sOldPath = url.getFile(); sOldPath = sOldPath.replace('/', File.separatorChar); indexLastSeparator = sOldPath.lastIndexOf(File.separatorChar); String sSourcePath = sOldPath; sFilename = sOldPath.substring(indexLastSeparator + 1); sNewPath = this.sTempLocation + sFilename; FileChannel in = null; FileChannel out = null; try { in = new FileInputStream(sSourcePath).getChannel(); out = new FileOutputStream(sNewPath).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(); } if (file == 1) { sXml = sXml.replace(nsrc.getTextContent(), sFilename); } else { sXml_[currentquestion] = sXml_[currentquestion].replace(nsrc.getTextContent(), sFilename); } lsImages.add(sFilename); resTemp.addFile(sFilename); } } catch (MalformedURLException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } | public static Checksum checksum(File file, Checksum checksum) throws IOException { if (file.isDirectory()) { throw new IllegalArgumentException("Checksums can't be computed on directories"); } InputStream in = null; try { in = new CheckedInputStream(new FileInputStream(file), checksum); IOUtils.copy(in, new NullOutputStream()); } finally { IOUtils.closeQuietly(in); } return checksum; } | 16,721 |
0 | public static void BubbleSortFloat1(float[] num) { boolean flag = true; // set flag to true to begin first pass float temp; // holding variable while (flag) { flag = false; // set flag to false awaiting a possible swap for (int j = 0; j < num.length - 1; j++) { if (num[j] > num[j + 1]) // change to > for ascending sort { temp = num[j]; // swap elements num[j] = num[j + 1]; num[j + 1] = temp; flag = true; // shows a swap occurred } } } } | public void copy(String original, String copy) throws SQLException { try { OutputStream out = openFileOutputStream(copy, false); InputStream in = openFileInputStream(original); IOUtils.copyAndClose(in, out); } catch (IOException e) { throw Message.convertIOException(e, "Can not copy " + original + " to " + copy); } } | 16,722 |
0 | private String fetchCompareContent() throws IOException { URL url = new URL(compareTo); StringWriter sw = new StringWriter(); IOUtils.copy(url.openStream(), sw); return sw.getBuffer().toString(); } | private void request() { try { connection = (HttpURLConnection) new URL(url).openConnection(); if (isCometConnection) { connection.setReadTimeout(0); } else { connection.setReadTimeout(30000); } connection.setInstanceFollowRedirects(false); connection.setDoInput(true); connection.setRequestMethod(method); connection.setRequestProperty("User-Agent", "Mozilla/5.0 (Windows; U; Windows NT 6.0; en-US; rv:1.9.1.5) Gecko/20091102 Firefox/3.5.5 GTB5"); if ("post".equalsIgnoreCase(method)) { connection.setDoOutput(true); connection.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); } if (user != null) { String auth = user + ":" + (password != null ? password : ""); String base64Auth = HttpRequest.Base64.byteArrayToBase64(auth.getBytes()); connection.setRequestProperty("Authorization", "Basic " + base64Auth); } for (Iterator<String> iter = headers.keySet().iterator(); iter.hasNext(); ) { String key = (String) iter.next(); connection.setRequestProperty(key, (String) headers.get(key)); } connection.setUseCaches(false); if (checkAbort()) return; if ("post".equalsIgnoreCase(method)) { DataOutputStream dos = new DataOutputStream(connection.getOutputStream()); activeOS = dos; if (content != null) { dos.writeBytes(content); } if (checkAbort()) return; dos.flush(); dos.close(); activeOS = null; } if (checkAbort()) return; InputStream is = null; try { is = connection.getInputStream(); } catch (IOException e) { if (checkAbort()) return; readyState = 4; if (onreadystatechange != null) { onreadystatechange.onLoaded(); } connection = null; readyState = 0; return; } activeIS = is; if (readyState < 2) { readyState = 2; status = connection.getResponseCode(); statusText = connection.getResponseMessage(); if (onreadystatechange != null) { onreadystatechange.onSent(); } } receiving = initializeReceivingMonitor(); ByteArrayOutputStream baos = new ByteArrayOutputStream(10240); byte[] buffer = new byte[10240]; int read; while (!toAbort && (read = is.read(buffer)) != -1) { if (checkAbort()) return; if (readyState != 3) { readyState = 3; if (onreadystatechange != null) { onreadystatechange.onReceiving(); } } boolean received = false; if (receiving != null) { received = receiving.receiving(baos, buffer, 0, read); } if (!received) { baos.write(buffer, 0, read); } } if (checkAbort()) return; is.close(); activeIS = null; responseText = null; String type = connection.getHeaderField("Content-Type"); if (type != null) { String charset = null; String lowerType = type.toLowerCase(); int idx = lowerType.indexOf("charset="); if (idx != -1) { charset = type.substring(idx + 8); } else { idx = lowerType.indexOf("/xml"); if (idx != -1) { String tmp = baos.toString(); Matcher matcher = Pattern.compile("<\\?.*encoding\\s*=\\s*[\'\"]([^'\"]*)[\'\"].*\\?>", Pattern.MULTILINE).matcher(tmp); if (matcher.find()) { charset = matcher.group(1); } else { responseText = tmp; } } else { idx = lowerType.indexOf("html"); if (idx != -1) { String tmp = baos.toString(); Matcher matcher = Pattern.compile("<meta.*content\\s*=\\s*[\'\"][^'\"]*charset\\s*=\\s*([^'\"]*)\\s*[\'\"].*>", Pattern.MULTILINE | Pattern.CASE_INSENSITIVE).matcher(tmp); if (matcher.find()) { charset = matcher.group(1); } else { responseText = tmp; } } } } if (charset != null) { try { responseText = baos.toString(charset); } catch (UnsupportedEncodingException e) { } } } if (responseText == null) { try { responseText = baos.toString("iso-8859-1"); } catch (UnsupportedEncodingException e) { responseText = baos.toString(); } } readyState = 4; if (onreadystatechange != null) { onreadystatechange.onLoaded(); } connection.disconnect(); readyState = 0; } catch (Exception e) { if (checkAbort()) return; e.printStackTrace(); readyState = 4; if (onreadystatechange != null) { onreadystatechange.onLoaded(); } connection = null; readyState = 0; } } | 16,723 |
0 | private void fileMaker() { try { long allData = 0; double a = 10; int range = 0; int blockLength = 0; File newFile = new File(mfr.getFilename() + ".part"); if (newFile.exists()) { newFile.delete(); } ArrayList<DataRange> rangeList = null; byte[] data = null; newFile.createNewFile(); ByteBuffer buffer = ByteBuffer.allocate(mfr.getBlocksize()); FileChannel rChannel = new FileInputStream(inputFileName).getChannel(); FileChannel wChannel = new FileOutputStream(newFile, true).getChannel(); System.out.println(); System.out.print("File completion: "); System.out.print("|----------|"); openConnection(); http.getResponseHeader(); for (int i = 0; i < fileMap.length; i++) { fileOffset = fileMap[i]; if (fileOffset != -1) { rChannel.read(buffer, fileOffset); buffer.flip(); wChannel.write(buffer); buffer.clear(); } else { if (!rangeQueue) { rangeList = rangeLookUp(i); range = rangeList.size(); openConnection(); http.setRangesRequest(rangeList); http.sendRequest(); http.getResponseHeader(); data = http.getResponseBody(mfr.getBlocksize()); allData += http.getAllTransferedDataLength(); } if ((i * mfr.getBlocksize() + mfr.getBlocksize()) < mfr.getLength()) { blockLength = mfr.getBlocksize(); } else { blockLength = (int) ((int) (mfr.getBlocksize()) + (mfr.getLength() - (i * mfr.getBlocksize() + mfr.getBlocksize()))); } buffer.put(data, (range - rangeList.size()) * mfr.getBlocksize(), blockLength); buffer.flip(); wChannel.write(buffer); buffer.clear(); rangeList.remove(0); if (rangeList.isEmpty()) { rangeQueue = false; } } if ((((double) i / ((double) fileMap.length - 1)) * 100) >= a) { progressBar(((double) i / ((double) fileMap.length - 1)) * 100); a += 10; } } newFile.setLastModified(getMTime()); sha = new SHA1(newFile); if (sha.SHA1sum().equals(mfr.getSha1())) { System.out.println("\nverifying download...checksum matches OK"); System.out.println("used " + (mfr.getLength() - (mfr.getBlocksize() * missing)) + " " + "local, fetched " + (mfr.getBlocksize() * missing)); new File(mfr.getFilename()).renameTo(new File(mfr.getFilename() + ".zs-old")); newFile.renameTo(new File(mfr.getFilename())); allData += mfr.getLengthOfMetafile(); System.out.println("really downloaded " + allData); double overhead = ((double) (allData - (mfr.getBlocksize() * missing)) / ((double) (mfr.getBlocksize() * missing))) * 100; System.out.println("overhead: " + df.format(overhead) + "%"); } else { System.out.println("\nverifying download...checksum don't match"); System.out.println("Deleting temporary file"); newFile.delete(); System.exit(1); } } catch (IOException ex) { System.out.println("Can't read or write, check your permissions."); System.exit(1); } } | public String fetchStockCompanyName(Stock stock) { String companyName = ""; String symbol = StockUtil.getStock(stock); if (isStockCached(symbol)) { return getStockFromCache(symbol); } String url = NbBundle.getMessage(MrSwingDataFeed.class, "MrSwingDataFeed.stockInfo.url", new String[] { symbol, register.get("username", ""), register.get("password", "") }); HttpContext context = new BasicHttpContext(); HttpGet method = new HttpGet(url); try { HttpResponse response = ProxyManager.httpClient.execute(method, context); HttpEntity entity = response.getEntity(); if (entity != null) { companyName = EntityUtils.toString(entity).split("\n")[1]; cacheStock(symbol, companyName); EntityUtils.consume(entity); } } catch (Exception ex) { companyName = ""; } finally { method.abort(); } return companyName; } | 16,724 |
0 | public static String do_checksum(String data) throws NoSuchAlgorithmException { MessageDigest md5 = MessageDigest.getInstance("MD5"); StringBuffer strbuf = new StringBuffer(); md5.update(data.getBytes(), 0, data.length()); byte[] digest = md5.digest(); for (int i = 0; i < digest.length; i++) { strbuf.append(toHexString(digest[i])); } return strbuf.toString(); } | public static boolean start(RootDoc root) { Logger log = Logger.getLogger("DocletGenerator"); if (destination == null) { try { ruleListenerDef = IOUtils.toString(GeneratorOfXmlSchemaForConvertersDoclet.class.getResourceAsStream("/RuleListenersFragment.xsd"), "UTF-8"); String fn = System.getenv("annocultor.xconverter.destination.file.name"); fn = (fn == null) ? "./../../../src/site/resources/schema/XConverterInclude.xsd" : fn; destination = new File(fn); if (destination.exists()) { destination.delete(); } FileOutputStream os; os = new FileOutputStream(new File(destination.getParentFile(), "XConverter.xsd")); IOUtils.copy(new AutoCloseInputStream(GeneratorOfXmlSchemaForConvertersDoclet.class.getResourceAsStream("/XConverterTemplate.xsd")), os); os.close(); os = new FileOutputStream(destination); IOUtils.copy(new AutoCloseInputStream(GeneratorOfXmlSchemaForConvertersDoclet.class.getResourceAsStream("/XConverterInclude.xsd")), os); os.close(); } catch (Exception e) { try { throw new RuntimeException("On destination " + destination.getCanonicalPath(), e); } catch (IOException e1) { throw new RuntimeException(e1); } } } try { String s = Utils.loadFileToString(destination.getCanonicalPath(), "\n"); int breakPoint = s.indexOf(XSD_TEXT_TO_REPLACED_WITH_GENERATED_XML_SIGNATURES); if (breakPoint < 0) { throw new Exception("Signature not found in XSD: " + XSD_TEXT_TO_REPLACED_WITH_GENERATED_XML_SIGNATURES); } String preambula = s.substring(0, breakPoint); String appendix = s.substring(breakPoint); destination.delete(); PrintWriter schemaWriter = new PrintWriter(destination); schemaWriter.print(preambula); ClassDoc[] classes = root.classes(); for (int i = 0; i < classes.length; ++i) { ClassDoc cd = classes[i]; PrintWriter documentationWriter = null; if (getSuperClasses(cd).contains(Rule.class.getName())) { for (ConstructorDoc constructorDoc : cd.constructors()) { if (constructorDoc.isPublic()) { if (isMeantForXMLAccess(constructorDoc)) { if (documentationWriter == null) { File file = new File("./../../../src/site/xdoc/rules." + cd.name() + ".xml"); documentationWriter = new PrintWriter(file); log.info("Generating doc for rule " + file.getCanonicalPath()); printRuleDocStart(cd, documentationWriter); } boolean initFound = false; for (MethodDoc methodDoc : cd.methods()) { if ("init".equals(methodDoc.name())) { if (methodDoc.parameters().length == 0) { initFound = true; break; } } } if (!initFound) { } printConstructorSchema(constructorDoc, schemaWriter); if (documentationWriter != null) { printConstructorDoc(constructorDoc, documentationWriter); } } } } } if (documentationWriter != null) { printRuleDocEnd(documentationWriter); } } schemaWriter.print(appendix); schemaWriter.close(); log.info("Saved to " + destination.getCanonicalPath()); } catch (Exception e) { throw new RuntimeException(e); } return true; } | 16,725 |
1 | public static void main(String[] args) { String host; int port; char[] passphrase; System.out.println("InstallCert - Install CA certificate to Java Keystore"); System.out.println("====================================================="); final BufferedReader reader = new BufferedReader(new InputStreamReader(System.in)); try { if ((args.length == 1) || (args.length == 2)) { String[] c = args[0].split(":"); host = c[0]; port = (c.length == 1) ? 443 : Integer.parseInt(c[1]); String p = (args.length == 1) ? "changeit" : args[1]; passphrase = p.toCharArray(); } else { String tmpStr; do { System.out.print("Enter hostname or IP address: "); tmpStr = StringUtils.defaultIfEmpty(reader.readLine(), null); } while (tmpStr == null); host = tmpStr; System.out.print("Enter port number [443]: "); tmpStr = StringUtils.defaultIfEmpty(reader.readLine(), null); port = tmpStr == null ? 443 : Integer.parseInt(tmpStr); System.out.print("Enter keystore password [changeit]: "); tmpStr = reader.readLine(); String p = "".equals(tmpStr) ? "changeit" : tmpStr; passphrase = p.toCharArray(); } char SEP = File.separatorChar; final File dir = new File(System.getProperty("java.home") + SEP + "lib" + SEP + "security"); final File file = new File(dir, "cacerts"); System.out.println("Loading KeyStore " + file + "..."); InputStream in = new FileInputStream(file); KeyStore ks = KeyStore.getInstance(KeyStore.getDefaultType()); ks.load(in, passphrase); in.close(); SSLContext context = SSLContext.getInstance("TLS"); TrustManagerFactory tmf = TrustManagerFactory.getInstance(TrustManagerFactory.getDefaultAlgorithm()); tmf.init(ks); X509TrustManager defaultTrustManager = (X509TrustManager) tmf.getTrustManagers()[0]; SavingTrustManager tm = new SavingTrustManager(defaultTrustManager); context.init(null, new TrustManager[] { tm }, null); SSLSocketFactory factory = context.getSocketFactory(); System.out.println("Opening connection to " + host + ":" + port + "..."); SSLSocket socket = (SSLSocket) factory.createSocket(host, port); socket.setSoTimeout(10000); try { System.out.println("Starting SSL handshake..."); socket.startHandshake(); socket.close(); System.out.println(); System.out.println("No errors, certificate is already trusted"); } catch (SSLException e) { System.out.println(); e.printStackTrace(System.out); } X509Certificate[] chain = tm.chain; if (chain == null) { System.out.println("Could not obtain server certificate chain"); return; } System.out.println(); System.out.println("Server sent " + chain.length + " certificate(s):"); System.out.println(); MessageDigest sha1 = MessageDigest.getInstance("SHA1"); MessageDigest md5 = MessageDigest.getInstance("MD5"); for (int i = 0; i < chain.length; i++) { X509Certificate cert = chain[i]; System.out.println(" " + (i + 1) + " Subject " + cert.getSubjectDN()); System.out.println(" Issuer " + cert.getIssuerDN()); sha1.update(cert.getEncoded()); System.out.println(" sha1 " + toHexString(sha1.digest())); md5.update(cert.getEncoded()); System.out.println(" md5 " + toHexString(md5.digest())); System.out.println(); } System.out.print("Enter certificate to add to trusted keystore or 'q' to quit [1]: "); String line = reader.readLine().trim(); int k = -1; try { k = (line.length() == 0) ? 0 : Integer.parseInt(line) - 1; } catch (NumberFormatException e) { } if (k < 0 || k >= chain.length) { System.out.println("KeyStore not changed"); } else { try { System.out.println("Creating keystore backup"); final SimpleDateFormat dateFormat = new SimpleDateFormat("yyyyMMddHHmmss"); final File backupFile = new File(dir, CACERTS_KEYSTORE + "." + dateFormat.format(new java.util.Date())); final FileInputStream fis = new FileInputStream(file); final FileOutputStream fos = new FileOutputStream(backupFile); IOUtils.copy(fis, fos); fis.close(); fos.close(); } catch (Exception e) { e.printStackTrace(); } System.out.println("Installing certificate..."); X509Certificate cert = chain[k]; String alias = host + "-" + (k + 1); ks.setCertificateEntry(alias, cert); OutputStream out = new FileOutputStream(file); ks.store(out, passphrase); out.close(); System.out.println(); System.out.println(cert); System.out.println(); System.out.println("Added certificate to keystore '" + file + "' using alias '" + alias + "'"); } } catch (Exception e) { System.out.println(); System.out.println("----------------------------------------------"); System.out.println("Problem occured during installing certificate:"); e.printStackTrace(); System.out.println("----------------------------------------------"); } System.out.println("Press Enter to finish..."); try { reader.readLine(); } catch (IOException e) { e.printStackTrace(); } } | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | 16,726 |
1 | public static String hashJopl(String password, String algorithm, String prefixKey, boolean useDefaultEncoding) { try { MessageDigest digest = MessageDigest.getInstance(algorithm); if (useDefaultEncoding) { digest.update(password.getBytes()); } else { for (char c : password.toCharArray()) { digest.update((byte) (c >> 8)); digest.update((byte) c); } } byte[] digestedPassword = digest.digest(); BASE64Encoder encoder = new BASE64Encoder(); String encodedDigestedStr = encoder.encode(digestedPassword); return prefixKey + encodedDigestedStr; } catch (NoSuchAlgorithmException ne) { return password; } } | public static String getMD5(String password) throws NoSuchAlgorithmException { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(password.getBytes()); byte[] b = md.digest(); StringBuffer sb = new StringBuffer(); for (byte aB : b) { sb.append((Integer.toHexString((aB & 0xFF) | 0x100)).substring(1, 3)); } return sb.toString(); } | 16,727 |
0 | public File getURL(URL url) throws IOException { URLConnection conn = null; File tempFile = null; Logger l = Logger.instance(); String className = getClass().getName(); l.log(Logger.DEBUG, loggerPrefix, className + ".getURL", "GET URL " + url.toString()); try { conn = url.openConnection(); tempFile = readIntoTempFile(conn.getInputStream()); } catch (IOException ioe) { l.log(Logger.ERROR, loggerPrefix, className + ".getURL", ioe); throw ioe; } finally { conn = null; } l.log(Logger.DEBUG, loggerPrefix, className + ".getURL", "received URL"); return tempFile; } | private List<String[]> retrieveData(String query) { List<String[]> data = new Vector<String[]>(); query = query.replaceAll("\\s", "+"); String q = "http://www.uniprot.org/uniprot/?query=" + query + "&format=tab&columns=id,protein%20names,organism"; try { URL url = new URL(q); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String line = ""; reader.readLine(); while ((line = reader.readLine()) != null) { String[] st = line.split("\t"); String[] d = new String[] { st[0], st[1], st[2] }; data.add(d); } reader.close(); if (data.size() == 0) { JOptionPane.showMessageDialog(this, "No data found for query"); } } catch (MalformedURLException e) { System.err.println("Query " + q + " caused exception: "); e.printStackTrace(); } catch (Exception e) { System.err.println("Query " + q + " caused exception: "); e.printStackTrace(); } return data; } | 16,728 |
0 | protected List<? extends SearchResult> searchVideo(String words, int number, int offset, CancelMonitor cancelMonitor) { List<VideoSearchResult> resultsList = new ArrayList<>(); try { // set up the HTTP request factory HttpTransport transport = new NetHttpTransport(); HttpRequestFactory factory = transport.createRequestFactory(new HttpRequestInitializer() { @Override public void initialize(HttpRequest request) { // set the parser JsonCParser parser = new JsonCParser(); parser.jsonFactory = JSON_FACTORY; request.addParser(parser); // set up the Google headers GoogleHeaders headers = new GoogleHeaders(); headers.setApplicationName("OGLExplorer/1.0"); headers.gdataVersion = "2"; request.headers = headers; } }); // build the YouTube URL YouTubeUrl url = new YouTubeUrl("https://gdata.youtube.com/feeds/api/videos"); url.maxResults = number; url.words = words; url.startIndex = offset + 1; // build HttpRequest request = factory.buildGetRequest(url); // execute HttpResponse response = request.execute(); VideoFeed feed = response.parseAs(VideoFeed.class); if (feed.items == null) { return null; } // browse result and convert them to the local generic object model for (int i = 0; i < feed.items.size() && !cancelMonitor.isCanceled(); i++) { Video result = feed.items.get(i); VideoSearchResult modelResult = new VideoSearchResult(offset + i + 1); modelResult.setTitle(result.title); modelResult.setDescription(result.description); modelResult.setThumbnailURL(new URL(result.thumbnail.lowThumbnailURL)); modelResult.setPath(result.player.defaultUrl); resultsList.add(modelResult); } } catch (Exception e) { e.printStackTrace(); } if (cancelMonitor.isCanceled()) { return null; } return resultsList; } | public static String httpUrlConnection_post(String targetURL, String urlParameters) { System.out.println("httpUrlConnection_post"); URL url; HttpURLConnection connection = null; try { url = new URL(targetURL); connection = (HttpURLConnection) url.openConnection(); connection.setRequestMethod("POST"); connection.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); connection.setRequestProperty("Content-Length", "" + Integer.toString(urlParameters.getBytes().length)); connection.setRequestProperty("Content-Language", "en-US"); connection.setUseCaches(false); connection.setConnectTimeout(5000); connection.setReadTimeout(5000); connection.setDoInput(true); connection.setDoOutput(true); DataOutputStream wr = new DataOutputStream(connection.getOutputStream()); wr.writeBytes(urlParameters); wr.flush(); wr.close(); InputStream is = connection.getInputStream(); BufferedReader rd = new BufferedReader(new InputStreamReader(is)); String line; StringBuilder response = new StringBuilder(); while ((line = rd.readLine()) != null) { response.append(line); response.append('\r'); } rd.close(); return response.toString(); } catch (Exception e) { System.out.print(e); return null; } finally { if (connection != null) { connection.disconnect(); } } } | 16,729 |
0 | static List<String> readZipFilesOftypeToFolder(String zipFileLocation, String outputDir, String fileType) { List<String> list = new ArrayList<String>(); ZipFile zipFile = readZipFile(zipFileLocation); FileOutputStream output = null; InputStream inputStream = null; Enumeration<ZipEntry> entries = (Enumeration<ZipEntry>) zipFile.entries(); try { while (entries.hasMoreElements()) { java.util.zip.ZipEntry entry = entries.nextElement(); String entryName = entry.getName(); if (entryName != null && entryName.toLowerCase().endsWith(fileType)) { inputStream = zipFile.getInputStream(entry); String fileName = outputDir + entryName.substring(entryName.lastIndexOf("/")); File file = new File(fileName); output = new FileOutputStream(file); IOUtils.copy(inputStream, output); list.add(fileName); } } } catch (Exception e) { throw new RuntimeException(e); } finally { try { if (output != null) output.close(); if (inputStream != null) inputStream.close(); if (zipFile != null) zipFile.close(); } catch (IOException e) { throw new RuntimeException(e); } } return list; } | public static void bubbleSort(int[] array) { for (int i = 0; i < array.length - 1; i++) { for (int j = 0; j < array.length - i - 1; j++) { if (array[j] > array[j + 1]) { int temp = array[j]; array[j] = array[j + 1]; array[j + 1] = temp; } } System.out.println("��" + (i + 1) + "������"); for (int k = 0; k < array.length; k++) { System.out.print(array[k] + " "); } System.out.println(); } } | 16,730 |
1 | private boolean copyToFile(String folder, String fileName) throws StorageException { InputStream in = Thread.currentThread().getContextClassLoader().getResourceAsStream(folder + "/" + fileName); if (in == null) { return false; } FileOutputStream out = null; try { out = new FileOutputStream(new File(path, fileName)); IOUtils.copy(in, out); in.close(); out.flush(); } catch (Exception e) { throw new StorageException(e); } finally { if (in != null) { IOUtils.closeQuietly(in); } if (out != null) { IOUtils.closeQuietly(out); } } return true; } | public void actionPerformed(ActionEvent e) { final File inputFile = KeyboardHero.midiFile(); try { if (inputFile == null) return; final File dir = (new File(Util.DATA_FOLDER + MidiSong.MIDI_FILES_DIR)); if (dir.exists()) { if (!dir.isDirectory()) { Util.error(Util.getMsg("Err_MidiFilesDirNotDirectory"), dir.getParent()); return; } } else if (!dir.mkdirs()) { Util.error(Util.getMsg("Err_CouldntMkDir"), dir.getParent()); return; } File outputFile = new File(dir.getPath() + File.separator + inputFile.getName()); if (!outputFile.exists() || KeyboardHero.confirm("Que_FileExistsOverwrite")) { final FileChannel inChannel = new FileInputStream(inputFile).getChannel(); inChannel.transferTo(0, inChannel.size(), new FileOutputStream(outputFile).getChannel()); } } catch (Exception ex) { Util.getMsg(Util.getMsg("Err_CouldntImportSong"), ex.toString()); } SongSelector.refresh(); } | 16,731 |
0 | private String fetchHTML(String s) { String str; StringBuffer sb = new StringBuffer(); try { URL url = new URL(s); InputStream is = url.openStream(); InputStreamReader isr = new InputStreamReader(is); BufferedReader br = new BufferedReader(isr); while ((str = br.readLine()) != null) { sb.append(str); } } catch (MalformedURLException e) { } catch (IOException e) { } return sb.toString(); } | public static void createModelZip(String filename, String tempdir, boolean overwrite) throws Exception { FileTools.checkOutput(filename, overwrite); BufferedInputStream origin = null; FileOutputStream dest = new FileOutputStream(filename); ZipOutputStream out = new ZipOutputStream(new BufferedOutputStream(dest)); int BUFFER = 2048; byte data[] = new byte[BUFFER]; File f = new File(tempdir); for (File fs : f.listFiles()) { FileInputStream fi = new FileInputStream(fs.getAbsolutePath()); origin = new BufferedInputStream(fi, BUFFER); ZipEntry entry = new ZipEntry(fs.getName()); out.putNextEntry(entry); int count; while ((count = origin.read(data, 0, BUFFER)) != -1) out.write(data, 0, count); out.closeEntry(); origin.close(); } out.close(); } | 16,732 |
1 | @Override protected int run(CmdLineParser parser) { final List<String> args = parser.getRemainingArgs(); if (args.isEmpty()) { System.err.println("sort :: WORKDIR not given."); return 3; } if (args.size() == 1) { System.err.println("sort :: INPATH not given."); return 3; } final String wrkDir = args.get(0), out = (String) parser.getOptionValue(outputFileOpt); final List<String> strInputs = args.subList(1, args.size()); final List<Path> inputs = new ArrayList<Path>(strInputs.size()); for (final String in : strInputs) inputs.add(new Path(in)); final boolean verbose = parser.getBoolean(verboseOpt); final String intermediateOutName = out == null ? inputs.get(0).getName() : out; final Configuration conf = getConf(); conf.setStrings(INPUT_PATHS_PROP, strInputs.toArray(new String[0])); conf.set(SortOutputFormat.OUTPUT_NAME_PROP, intermediateOutName); final Path wrkDirPath = new Path(wrkDir); final Timer t = new Timer(); try { for (final Path in : inputs) Utils.configureSampling(in, conf); @SuppressWarnings("deprecation") final int maxReduceTasks = new JobClient(new JobConf(conf)).getClusterStatus().getMaxReduceTasks(); conf.setInt("mapred.reduce.tasks", Math.max(1, maxReduceTasks * 9 / 10)); final Job job = new Job(conf); job.setJarByClass(Sort.class); job.setMapperClass(Mapper.class); job.setReducerClass(SortReducer.class); job.setMapOutputKeyClass(LongWritable.class); job.setOutputKeyClass(NullWritable.class); job.setOutputValueClass(SAMRecordWritable.class); job.setInputFormatClass(BAMInputFormat.class); job.setOutputFormatClass(SortOutputFormat.class); for (final Path in : inputs) FileInputFormat.addInputPath(job, in); FileOutputFormat.setOutputPath(job, wrkDirPath); job.setPartitionerClass(TotalOrderPartitioner.class); System.out.println("sort :: Sampling..."); t.start(); InputSampler.<LongWritable, SAMRecordWritable>writePartitionFile(job, new InputSampler.IntervalSampler<LongWritable, SAMRecordWritable>(0.01, 100)); System.out.printf("sort :: Sampling complete in %d.%03d s.\n", t.stopS(), t.fms()); job.submit(); System.out.println("sort :: Waiting for job completion..."); t.start(); if (!job.waitForCompletion(verbose)) { System.err.println("sort :: Job failed."); return 4; } System.out.printf("sort :: Job complete in %d.%03d s.\n", t.stopS(), t.fms()); } catch (IOException e) { System.err.printf("sort :: Hadoop error: %s\n", e); return 4; } catch (ClassNotFoundException e) { throw new RuntimeException(e); } catch (InterruptedException e) { throw new RuntimeException(e); } if (out != null) try { System.out.println("sort :: Merging output..."); t.start(); final Path outPath = new Path(out); final FileSystem srcFS = wrkDirPath.getFileSystem(conf); FileSystem dstFS = outPath.getFileSystem(conf); if (dstFS instanceof LocalFileSystem && dstFS instanceof ChecksumFileSystem) dstFS = ((LocalFileSystem) dstFS).getRaw(); final BAMFileWriter w = new BAMFileWriter(dstFS.create(outPath), new File("")); w.setSortOrder(SAMFileHeader.SortOrder.coordinate, true); w.setHeader(getHeaderMerger(conf).getMergedHeader()); w.close(); final OutputStream outs = dstFS.append(outPath); final FileStatus[] parts = srcFS.globStatus(new Path(wrkDir, conf.get(SortOutputFormat.OUTPUT_NAME_PROP) + "-[0-9][0-9][0-9][0-9][0-9][0-9]*")); { int i = 0; final Timer t2 = new Timer(); for (final FileStatus part : parts) { t2.start(); final InputStream ins = srcFS.open(part.getPath()); IOUtils.copyBytes(ins, outs, conf, false); ins.close(); System.out.printf("sort :: Merged part %d in %d.%03d s.\n", ++i, t2.stopS(), t2.fms()); } } for (final FileStatus part : parts) srcFS.delete(part.getPath(), false); outs.write(BlockCompressedStreamConstants.EMPTY_GZIP_BLOCK); outs.close(); System.out.printf("sort :: Merging complete in %d.%03d s.\n", t.stopS(), t.fms()); } catch (IOException e) { System.err.printf("sort :: Output merging failed: %s\n", e); return 5; } return 0; } | public static void copy(File fromFile, File toFile) throws IOException { if (!fromFile.exists()) throw new IOException("FileCopy: " + "no such source file: " + fromFile.getCanonicalPath()); if (!fromFile.isFile()) throw new IOException("FileCopy: " + "can't copy directory: " + fromFile.getCanonicalPath()); if (!fromFile.canRead()) throw new IOException("FileCopy: " + "source file is unreadable: " + fromFile.getCanonicalPath()); if (toFile.isDirectory()) toFile = new File(toFile, fromFile.getName()); if (toFile.exists()) { if (!toFile.canWrite()) throw new IOException("FileCopy: " + "destination file is unwriteable: " + toFile.getCanonicalPath()); 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[1024 * 1024]; int bytesRead; while ((bytesRead = from.read(buffer)) != -1) to.write(buffer, 0, bytesRead); if (fromFile.isHidden()) { } toFile.setLastModified(fromFile.lastModified()); toFile.setExecutable(fromFile.canExecute()); toFile.setReadable(fromFile.canRead()); toFile.setWritable(toFile.canWrite()); } finally { if (from != null) try { from.close(); } catch (IOException e) { ; } if (to != null) try { to.close(); } catch (IOException e) { ; } } } | 16,733 |
1 | public static String digest(String algorithm, String text) { MessageDigest mDigest = null; try { mDigest = MessageDigest.getInstance(algorithm); mDigest.update(text.getBytes(ENCODING)); } catch (Exception e) { e.printStackTrace(); mDigest = null; } if (mDigest == null) return null; byte[] raw = mDigest.digest(); BASE64Encoder encoder = new BASE64Encoder(); return encoder.encode(raw); } | public static String md5hash(String text) { java.security.MessageDigest md; try { md = java.security.MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { throw new RuntimeException(e); } md.update(text.getBytes()); byte[] md5bytes = md.digest(); return new String(org.apache.commons.codec.binary.Hex.encodeHex(md5bytes)); } | 16,734 |
1 | public int process(ProcessorContext context) throws InterruptedException, ProcessorException { logger.info("JAISaveTask:process"); final RenderedOp im = (RenderedOp) context.get("RenderedOp"); final String path = "s3://s3.amazonaws.com/rssfetch/" + (new Guid()); final PNGEncodeParam.RGB encPar = new PNGEncodeParam.RGB(); encPar.setTransparentRGB(new int[] { 0, 0, 0 }); File tmpFile = null; try { tmpFile = File.createTempFile("thmb", ".png"); OutputStream out = new FileOutputStream(tmpFile); final ParameterBlock pb = (new ParameterBlock()).addSource(im).add(out).add("png").add(encPar); JAI.create("encode", pb, null); out.flush(); out.close(); FileInputStream in = new FileInputStream(tmpFile); final XFile xfile = new XFile(path); final XFileOutputStream xout = new XFileOutputStream(xfile); final com.luzan.common.nfs.s3.XFileExtensionAccessor xfa = ((com.luzan.common.nfs.s3.XFileExtensionAccessor) xfile.getExtensionAccessor()); if (xfa != null) { xfa.setMimeType("image/png"); xfa.setContentLength(tmpFile.length()); } IOUtils.copy(in, xout); xout.flush(); xout.close(); in.close(); context.put("outputPath", path); } catch (IOException e) { logger.error(e); throw new ProcessorException(e); } catch (Throwable e) { logger.error(e); throw new ProcessorException(e); } finally { if (tmpFile != null && tmpFile.exists()) { tmpFile.delete(); } } return TaskState.STATE_MO_START + TaskState.STATE_ENCODE; } | 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 (Exception e) { log.error(e, e); } finally { if (in != null) in.close(); if (out != null) out.close(); } } | 16,735 |
1 | @Override public void start() { try { ftp = new FTPClient(); ftp.connect(this.url.getHost(), this.url.getPort() == -1 ? this.url.getDefaultPort() : this.url.getPort()); String username = "anonymous"; String password = ""; if (this.url.getUserInfo() != null) { username = this.url.getUserInfo().split(":")[0]; password = this.url.getUserInfo().split(":")[1]; } ftp.login(username, password); long startPos = 0; if (getFile().exists()) startPos = getFile().length(); else getFile().createNewFile(); ftp.download(this.url.getPath(), getFile(), startPos, new FTPDTImpl()); ftp.disconnect(true); } catch (Exception ex) { ex.printStackTrace(); speedTimer.cancel(); } } | private static FTPClient getFtpClient(String ftpHost, String ftpUsername, String ftpPassword) throws SocketException, IOException { FTPClient ftp = new FTPClient(); ftp.addProtocolCommandListener(new PrintCommandListener(new PrintWriter(System.out))); ftp.connect(ftpHost); int reply = ftp.getReplyCode(); if (!FTPReply.isPositiveCompletion(reply)) { ftp.disconnect(); return null; } if (!ftp.login(ftpUsername, ftpPassword)) { return null; } ftp.setFileType(FTP.BINARY_FILE_TYPE); ftp.enterLocalPassiveMode(); return ftp; } | 16,736 |
0 | public String doUpload(@ParamName(name = "file") MultipartFile file, @ParamName(name = "uploadDirectory") String _uploadDirectory) throws IOException { String sessionId = (String) RuntimeAccess.getInstance().getSession().getAttribute("SESSION_ID"); String tempUploadDir = MewitProperties.getTemporaryUploadDirectory(); if (!tempUploadDir.endsWith("/") && !tempUploadDir.endsWith("\\")) { tempUploadDir += "\\"; } String fileName = null; int position = file.getOriginalFilename().lastIndexOf("."); if (position <= 0) { fileName = java.util.UUID.randomUUID().toString(); } else { fileName = java.util.UUID.randomUUID().toString() + file.getOriginalFilename().substring(position); } File outputFile = new File(tempUploadDir, fileName); log(INFO, "writing the content of uploaded file to: " + outputFile); FileOutputStream fos = new FileOutputStream(outputFile); IOUtils.copy(file.getInputStream(), fos); file.getInputStream().close(); fos.close(); return doUploadFile(sessionId, outputFile, file.getOriginalFilename()); } | protected void createGraphicalViewer(Composite parent) { final RulerComposite rc = new RulerComposite(parent, SWT.NONE); viewer = new ScrollingGraphicalViewer(); viewer.createControl(rc); editDomain.addViewer(viewer); rc.setGraphicalViewer(viewer); viewer.getControl().setBackground(ColorConstants.white); viewer.setEditPartFactory(new EditPartFactory() { public EditPart createEditPart(EditPart context, Object model) { return new RecorderEditPart(TopLevelModel.getRecorderModel()); } }); viewer.setContents(TopLevelModel.getRecorderModel()); Control control = viewer.getControl(); System.out.println("widget: " + control); DropTarget dt = new DropTarget(control, DND.DROP_MOVE | DND.DROP_COPY | DND.DROP_DEFAULT); dt.setTransfer(new Transfer[] { TextTransfer.getInstance() }); dt.addDropListener(new SensorTransferDropTargetListener(viewer)); } | 16,737 |
1 | 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; } | 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(); } } | 16,738 |
1 | public void downloadFile(OutputStream os, int fileId) throws IOException, SQLException { Connection conn = null; try { conn = ds.getConnection(); Guard.checkConnectionNotNull(conn); PreparedStatement ps = conn.prepareStatement("select * from FILE_BODIES where file_id=?"); ps.setInt(1, fileId); ResultSet rs = ps.executeQuery(); if (!rs.next()) { throw new FileNotFoundException("File with id=" + fileId + " not found!"); } Blob blob = rs.getBlob("data"); InputStream is = blob.getBinaryStream(); IOUtils.copyLarge(is, os); } finally { JdbcDaoHelper.safeClose(conn, log); } } | public void xtestFile1() throws Exception { InputStream inputStream = new FileInputStream(IOTest.FILE); OutputStream outputStream = new FileOutputStream("C:/Temp/testFile1.mp4"); IOUtils.copy(inputStream, outputStream); inputStream.close(); outputStream.close(); } | 16,739 |
0 | public GeocodeResponse getGKCoordinateFromAddress(SearchAddressRequest searchAddressRequest) { GeocodeResponse result = null; String adress = null; if (searchAddressRequest.getAdressTextField() != null) adress = searchAddressRequest.getAdressTextField().getText(); if (adress == null || adress.length() == 0) adress = " "; String postRequest = ""; postRequest = "<?xml version=\"1.0\" encoding=\"UTF-8\"?> \n" + "<xls:XLS xmlns:xls=\"http://www.opengis.net/xls\" xmlns:sch=\"http://www.ascc.net/xml/schematron\" xmlns:gml=\"http://www.opengis.net/gml\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://www.opengis.net/xls \n" + "http://gdi3d.giub.uni-bonn.de:8080/openls-lus/schemas/LocationUtilityService.xsd\" version=\"1.1\"> \n" + " <xls:RequestHeader srsName=\"EPSG:" + Navigator.getEpsg_code() + "\"/> \n" + " <xls:Request methodName=\"GeocodeRequest\" requestID=\"123456789\" version=\"1.1\"> \n" + " <xls:GeocodeRequest> \n" + " <xls:Address countryCode=\"DE\"> \n" + " <xls:freeFormAddress>" + adress + "</xls:freeFormAddress> \n" + " </xls:Address> \n" + " </xls:GeocodeRequest> \n" + " </xls:Request> \n" + "</xls:XLS> \n"; if (Navigator.isVerbose()) { System.out.println("OpenLSGeocoder postRequest " + postRequest); } String errorMessage = ""; try { System.out.println("contacting " + serviceEndPoint); URL u = new URL(serviceEndPoint); HttpURLConnection urlc = (HttpURLConnection) u.openConnection(); urlc.setReadTimeout(Navigator.TIME_OUT); urlc.setAllowUserInteraction(false); urlc.setRequestMethod("POST"); urlc.setRequestProperty("Content-Type", "application/xml"); urlc.setDoOutput(true); urlc.setDoInput(true); urlc.setUseCaches(false); PrintWriter xmlOut = null; xmlOut = new java.io.PrintWriter(urlc.getOutputStream()); xmlOut.write(postRequest); xmlOut.flush(); xmlOut.close(); InputStream is = urlc.getInputStream(); result = new GeocodeResponse(); XLSDocument xlsResponse = XLSDocument.Factory.parse(is); XLSType xlsTypeResponse = xlsResponse.getXLS(); Node node0 = xlsTypeResponse.getDomNode(); NodeList nodes1 = node0.getChildNodes(); for (int i = 0; i < nodes1.getLength(); i++) { Node node1 = nodes1.item(i); NodeList nodes2 = node1.getChildNodes(); for (int j = 0; j < nodes2.getLength(); j++) { Node node2 = nodes2.item(j); NodeList nodes3 = node2.getChildNodes(); for (int k = 0; k < nodes3.getLength(); k++) { Node node3 = nodes3.item(k); String nodeName = node3.getNodeName(); if (nodeName.equalsIgnoreCase("xls:GeocodeResponseList")) { net.opengis.xls.GeocodeResponseListDocument gcrld = net.opengis.xls.GeocodeResponseListDocument.Factory.parse(node3); net.opengis.xls.GeocodeResponseListType geocodeResponseList = gcrld.getGeocodeResponseList(); result.setGeocodeResponseList(geocodeResponseList); } } } } is.close(); } catch (java.net.ConnectException ce) { JOptionPane.showMessageDialog(null, "no connection to geocoder", "Connection Error", JOptionPane.ERROR_MESSAGE); } catch (SocketTimeoutException ste) { ste.printStackTrace(); errorMessage += "<p>Time Out Exception, Server is not responding</p>"; } catch (IOException ioe) { ioe.printStackTrace(); errorMessage += "<p>IO Exception</p>"; } catch (XmlException xmle) { xmle.printStackTrace(); errorMessage += "<p>Error occured during parsing the XML response</p>"; } if (!errorMessage.equals("")) { System.out.println("\nerrorMessage: " + errorMessage + "\n\n"); JLabel label1 = new JLabel("<html><head><style type=\"text/css\"><!--.Stil2 {font-size: 10px;font-weight: bold;}--></style></head><body><span class=\"Stil2\">Geocoder Error</span></body></html>"); JLabel label2 = new JLabel("<html><head><style type=\"text/css\"><!--.Stil2 {font-size: 10px;font-weight: normal;}--></style></head><body><span class=\"Stil2\">" + "<br>" + errorMessage + "<br>" + "<p>please check Java console. If problem persits, please report to system manager</p>" + "</span></body></html>"); Object[] objects = { label1, label2 }; JOptionPane.showMessageDialog(null, objects, "Error Message", JOptionPane.ERROR_MESSAGE); return null; } return result; } | public String MD5(String text) { try { MessageDigest md; md = MessageDigest.getInstance("MD5"); byte[] md5hash = new byte[32]; md.update(text.getBytes("iso-8859-1"), 0, text.length()); md5hash = md.digest(); return convertToHex(md5hash); } catch (Exception e) { System.out.println(e.toString()); } return null; } | 16,740 |
1 | public static boolean encodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.ENCODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | public static void copyFile(File src, File dst) throws IOException { InputStream in = new FileInputStream(src); OutputStream out = new FileOutputStream(dst); byte[] buf = new byte[1024]; int len; while ((len = in.read(buf)) > 0) out.write(buf, 0, len); in.close(); out.close(); } | 16,741 |
0 | 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; } | private Bitmap downloadBitmap(String url) { final AndroidHttpClient client = AndroidHttpClient.newInstance("Android"); final HttpGet getRequest = new HttpGet(url); try { HttpResponse response = client.execute(getRequest); final int statusCode = response.getStatusLine().getStatusCode(); if (statusCode != HttpStatus.SC_OK) { Log.w(LOG_TAG, "Error " + statusCode + " while retrieving bitmap from " + url); return null; } final HttpEntity entity = response.getEntity(); if (entity != null) { InputStream inputStream = null; try { inputStream = entity.getContent(); final Bitmap bitmap = BitmapFactory.decodeStream(inputStream); return bitmap; } finally { if (inputStream != null) { inputStream.close(); } entity.consumeContent(); } } } catch (Exception e) { getRequest.abort(); Log.w(LOG_TAG, "Error while retrieving bitmap from " + url, e); } finally { if (client != null) { client.close(); } } return null; } | 16,742 |
1 | @Override public String fetchElectronicEdition(Publication pub) { final String url = pub.getEe(); HttpMethod method = null; String responseBody = ""; method = new GetMethod(url); method.setFollowRedirects(true); try { if (StringUtils.isNotBlank(method.getURI().getScheme())) { InputStream is = null; StringWriter writer = new StringWriter(); try { client.executeMethod(method); Header contentType = method.getResponseHeader("Content-Type"); if (contentType != null && StringUtils.isNotBlank(contentType.getValue()) && contentType.getValue().indexOf("text/html") >= 0) { is = method.getResponseBodyAsStream(); IOUtils.copy(is, writer); responseBody = writer.toString(); } else { logger.info("ignoring non-text/html response from page: " + url + " content-type:" + contentType); } } catch (HttpException he) { logger.error("Http error connecting to '" + url + "'"); logger.error(he.getMessage()); } catch (IOException ioe) { logger.error("Unable to connect to '" + url + "'"); } finally { IOUtils.closeQuietly(is); IOUtils.closeQuietly(writer); } } } catch (URIException e) { logger.error(e); } finally { method.releaseConnection(); } return responseBody; } | 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!"); } | 16,743 |
1 | public static File jar(File in, String outArc, File tempDir, PatchConfigXML conf) { FileOutputStream arcFile = null; JarOutputStream jout = null; DirectoryScanner ds = null; ds = new DirectoryScanner(); ds.setCaseSensitive(true); ds.setBasedir(in); ds.scan(); ds.setCaseSensitive(true); String[] names = ds.getIncludedFiles(); ArrayList exName = new ArrayList(); if (names == null || names.length < 1) return null; File tempArc = new File(tempDir, outArc.substring(0, outArc.length())); try { Manifest mf = null; List v = new ArrayList(); for (int i = 0; i < names.length; i++) { if (names[i].toUpperCase().indexOf("MANIFEST.MF") > -1) { FileInputStream fis = new FileInputStream(in.getAbsolutePath() + "/" + names[i].replace('\\', '/')); mf = new Manifest(fis); } else v.add(names[i]); } String[] toJar = new String[v.size()]; v.toArray(toJar); tempArc.createNewFile(); arcFile = new FileOutputStream(tempArc); if (mf == null) jout = new JarOutputStream(arcFile); else jout = new JarOutputStream(arcFile, mf); byte[] buffer = new byte[1024]; for (int i = 0; i < toJar.length; i++) { if (conf != null) { if (!conf.allowFileAction(toJar[i], PatchConfigXML.OP_CREATE)) { exName.add(toJar[i]); continue; } } String currentPath = in.getAbsolutePath() + "/" + toJar[i]; String entryName = toJar[i].replace('\\', '/'); JarEntry currentEntry = new JarEntry(entryName); jout.putNextEntry(currentEntry); FileInputStream fis = new FileInputStream(currentPath); int len; while ((len = fis.read(buffer)) >= 0) jout.write(buffer, 0, len); fis.close(); jout.closeEntry(); } } catch (IOException e) { throw new RuntimeException(e); } finally { try { jout.close(); arcFile.close(); } catch (IOException e1) { throw new RuntimeException(e1); } } return tempArc; } | public static void main(String argv[]) { Matrix A, B, C, Z, O, I, R, S, X, SUB, M, T, SQ, DEF, SOL; int errorCount = 0; int warningCount = 0; double tmp, s; double[] columnwise = { 1., 2., 3., 4., 5., 6., 7., 8., 9., 10., 11., 12. }; double[] rowwise = { 1., 4., 7., 10., 2., 5., 8., 11., 3., 6., 9., 12. }; double[][] avals = { { 1., 4., 7., 10. }, { 2., 5., 8., 11. }, { 3., 6., 9., 12. } }; double[][] rankdef = avals; double[][] tvals = { { 1., 2., 3. }, { 4., 5., 6. }, { 7., 8., 9. }, { 10., 11., 12. } }; double[][] subavals = { { 5., 8., 11. }, { 6., 9., 12. } }; double[][] rvals = { { 1., 4., 7. }, { 2., 5., 8., 11. }, { 3., 6., 9., 12. } }; double[][] pvals = { { 1., 1., 1. }, { 1., 2., 3. }, { 1., 3., 6. } }; double[][] ivals = { { 1., 0., 0., 0. }, { 0., 1., 0., 0. }, { 0., 0., 1., 0. } }; double[][] evals = { { 0., 1., 0., 0. }, { 1., 0., 2.e-7, 0. }, { 0., -2.e-7, 0., 1. }, { 0., 0., 1., 0. } }; double[][] square = { { 166., 188., 210. }, { 188., 214., 240. }, { 210., 240., 270. } }; double[][] sqSolution = { { 13. }, { 15. } }; double[][] condmat = { { 1., 3. }, { 7., 9. } }; int rows = 3, cols = 4; int invalidld = 5; int raggedr = 0; int raggedc = 4; int validld = 3; int nonconformld = 4; int ib = 1, ie = 2, jb = 1, je = 3; int[] rowindexset = { 1, 2 }; int[] badrowindexset = { 1, 3 }; int[] columnindexset = { 1, 2, 3 }; int[] badcolumnindexset = { 1, 2, 4 }; double columnsummax = 33.; double rowsummax = 30.; double sumofdiagonals = 15; double sumofsquares = 650; print("\nTesting constructors and constructor-like methods...\n"); try { A = new Matrix(columnwise, invalidld); errorCount = try_failure(errorCount, "Catch invalid length in packed constructor... ", "exception not thrown for invalid input"); } catch (IllegalArgumentException e) { try_success("Catch invalid length in packed constructor... ", e.getMessage()); } try { A = new Matrix(rvals); tmp = A.get(raggedr, raggedc); } catch (IllegalArgumentException e) { try_success("Catch ragged input to default constructor... ", e.getMessage()); } catch (java.lang.ArrayIndexOutOfBoundsException e) { errorCount = try_failure(errorCount, "Catch ragged input to constructor... ", "exception not thrown in construction...ArrayIndexOutOfBoundsException thrown later"); } try { A = Matrix.constructWithCopy(rvals); tmp = A.get(raggedr, raggedc); } catch (IllegalArgumentException e) { try_success("Catch ragged input to constructWithCopy... ", e.getMessage()); } catch (java.lang.ArrayIndexOutOfBoundsException e) { errorCount = try_failure(errorCount, "Catch ragged input to constructWithCopy... ", "exception not thrown in construction...ArrayIndexOutOfBoundsException thrown later"); } A = new Matrix(columnwise, validld); B = new Matrix(avals); tmp = B.get(0, 0); avals[0][0] = 0.0; C = B.minus(A); avals[0][0] = tmp; B = Matrix.constructWithCopy(avals); tmp = B.get(0, 0); avals[0][0] = 0.0; if ((tmp - B.get(0, 0)) != 0.0) { errorCount = try_failure(errorCount, "constructWithCopy... ", "copy not effected... data visible outside"); } else { try_success("constructWithCopy... ", ""); } avals[0][0] = columnwise[0]; I = new Matrix(ivals); try { check(I, Matrix.identity(3, 4)); try_success("identity... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "identity... ", "identity Matrix not successfully created"); } print("\nTesting access methods...\n"); B = new Matrix(avals); if (B.getRowDimension() != rows) { errorCount = try_failure(errorCount, "getRowDimension... ", ""); } else { try_success("getRowDimension... ", ""); } if (B.getColumnDimension() != cols) { errorCount = try_failure(errorCount, "getColumnDimension... ", ""); } else { try_success("getColumnDimension... ", ""); } B = new Matrix(avals); double[][] barray = B.getArray(); if (barray != avals) { errorCount = try_failure(errorCount, "getArray... ", ""); } else { try_success("getArray... ", ""); } barray = B.getArrayCopy(); if (barray == avals) { errorCount = try_failure(errorCount, "getArrayCopy... ", "data not (deep) copied"); } try { check(barray, avals); try_success("getArrayCopy... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "getArrayCopy... ", "data not successfully (deep) copied"); } double[] bpacked = B.getColumnPackedCopy(); try { check(bpacked, columnwise); try_success("getColumnPackedCopy... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "getColumnPackedCopy... ", "data not successfully (deep) copied by columns"); } bpacked = B.getRowPackedCopy(); try { check(bpacked, rowwise); try_success("getRowPackedCopy... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "getRowPackedCopy... ", "data not successfully (deep) copied by rows"); } try { tmp = B.get(B.getRowDimension(), B.getColumnDimension() - 1); errorCount = try_failure(errorCount, "get(int,int)... ", "OutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { tmp = B.get(B.getRowDimension() - 1, B.getColumnDimension()); errorCount = try_failure(errorCount, "get(int,int)... ", "OutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("get(int,int)... OutofBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "get(int,int)... ", "OutOfBoundsException expected but not thrown"); } try { if (B.get(B.getRowDimension() - 1, B.getColumnDimension() - 1) != avals[B.getRowDimension() - 1][B.getColumnDimension() - 1]) { errorCount = try_failure(errorCount, "get(int,int)... ", "Matrix entry (i,j) not successfully retreived"); } else { try_success("get(int,int)... ", ""); } } catch (java.lang.ArrayIndexOutOfBoundsException e) { errorCount = try_failure(errorCount, "get(int,int)... ", "Unexpected ArrayIndexOutOfBoundsException"); } SUB = new Matrix(subavals); try { M = B.getMatrix(ib, ie + B.getRowDimension() + 1, jb, je); errorCount = try_failure(errorCount, "getMatrix(int,int,int,int)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { M = B.getMatrix(ib, ie, jb, je + B.getColumnDimension() + 1); errorCount = try_failure(errorCount, "getMatrix(int,int,int,int)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("getMatrix(int,int,int,int)... ArrayIndexOutOfBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "getMatrix(int,int,int,int)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } try { M = B.getMatrix(ib, ie, jb, je); try { check(SUB, M); try_success("getMatrix(int,int,int,int)... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "getMatrix(int,int,int,int)... ", "submatrix not successfully retreived"); } } catch (java.lang.ArrayIndexOutOfBoundsException e) { errorCount = try_failure(errorCount, "getMatrix(int,int,int,int)... ", "Unexpected ArrayIndexOutOfBoundsException"); } try { M = B.getMatrix(ib, ie, badcolumnindexset); errorCount = try_failure(errorCount, "getMatrix(int,int,int[])... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { M = B.getMatrix(ib, ie + B.getRowDimension() + 1, columnindexset); errorCount = try_failure(errorCount, "getMatrix(int,int,int[])... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("getMatrix(int,int,int[])... ArrayIndexOutOfBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "getMatrix(int,int,int[])... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } try { M = B.getMatrix(ib, ie, columnindexset); try { check(SUB, M); try_success("getMatrix(int,int,int[])... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "getMatrix(int,int,int[])... ", "submatrix not successfully retreived"); } } catch (java.lang.ArrayIndexOutOfBoundsException e) { errorCount = try_failure(errorCount, "getMatrix(int,int,int[])... ", "Unexpected ArrayIndexOutOfBoundsException"); } try { M = B.getMatrix(badrowindexset, jb, je); errorCount = try_failure(errorCount, "getMatrix(int[],int,int)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { M = B.getMatrix(rowindexset, jb, je + B.getColumnDimension() + 1); errorCount = try_failure(errorCount, "getMatrix(int[],int,int)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("getMatrix(int[],int,int)... ArrayIndexOutOfBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "getMatrix(int[],int,int)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } try { M = B.getMatrix(rowindexset, jb, je); try { check(SUB, M); try_success("getMatrix(int[],int,int)... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "getMatrix(int[],int,int)... ", "submatrix not successfully retreived"); } } catch (java.lang.ArrayIndexOutOfBoundsException e) { errorCount = try_failure(errorCount, "getMatrix(int[],int,int)... ", "Unexpected ArrayIndexOutOfBoundsException"); } try { M = B.getMatrix(badrowindexset, columnindexset); errorCount = try_failure(errorCount, "getMatrix(int[],int[])... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { M = B.getMatrix(rowindexset, badcolumnindexset); errorCount = try_failure(errorCount, "getMatrix(int[],int[])... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("getMatrix(int[],int[])... ArrayIndexOutOfBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "getMatrix(int[],int[])... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } try { M = B.getMatrix(rowindexset, columnindexset); try { check(SUB, M); try_success("getMatrix(int[],int[])... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "getMatrix(int[],int[])... ", "submatrix not successfully retreived"); } } catch (java.lang.ArrayIndexOutOfBoundsException e) { errorCount = try_failure(errorCount, "getMatrix(int[],int[])... ", "Unexpected ArrayIndexOutOfBoundsException"); } try { B.set(B.getRowDimension(), B.getColumnDimension() - 1, 0.); errorCount = try_failure(errorCount, "set(int,int,double)... ", "OutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { B.set(B.getRowDimension() - 1, B.getColumnDimension(), 0.); errorCount = try_failure(errorCount, "set(int,int,double)... ", "OutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("set(int,int,double)... OutofBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "set(int,int,double)... ", "OutOfBoundsException expected but not thrown"); } try { B.set(ib, jb, 0.); tmp = B.get(ib, jb); try { check(tmp, 0.); try_success("set(int,int,double)... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "set(int,int,double)... ", "Matrix element not successfully set"); } } catch (java.lang.ArrayIndexOutOfBoundsException e1) { errorCount = try_failure(errorCount, "set(int,int,double)... ", "Unexpected ArrayIndexOutOfBoundsException"); } M = new Matrix(2, 3, 0.); try { B.setMatrix(ib, ie + B.getRowDimension() + 1, jb, je, M); errorCount = try_failure(errorCount, "setMatrix(int,int,int,int,Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { B.setMatrix(ib, ie, jb, je + B.getColumnDimension() + 1, M); errorCount = try_failure(errorCount, "setMatrix(int,int,int,int,Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("setMatrix(int,int,int,int,Matrix)... ArrayIndexOutOfBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "setMatrix(int,int,int,int,Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } try { B.setMatrix(ib, ie, jb, je, M); try { check(M.minus(B.getMatrix(ib, ie, jb, je)), M); try_success("setMatrix(int,int,int,int,Matrix)... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "setMatrix(int,int,int,int,Matrix)... ", "submatrix not successfully set"); } B.setMatrix(ib, ie, jb, je, SUB); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { errorCount = try_failure(errorCount, "setMatrix(int,int,int,int,Matrix)... ", "Unexpected ArrayIndexOutOfBoundsException"); } try { B.setMatrix(ib, ie + B.getRowDimension() + 1, columnindexset, M); errorCount = try_failure(errorCount, "setMatrix(int,int,int[],Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { B.setMatrix(ib, ie, badcolumnindexset, M); errorCount = try_failure(errorCount, "setMatrix(int,int,int[],Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("setMatrix(int,int,int[],Matrix)... ArrayIndexOutOfBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "setMatrix(int,int,int[],Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } try { B.setMatrix(ib, ie, columnindexset, M); try { check(M.minus(B.getMatrix(ib, ie, columnindexset)), M); try_success("setMatrix(int,int,int[],Matrix)... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "setMatrix(int,int,int[],Matrix)... ", "submatrix not successfully set"); } B.setMatrix(ib, ie, jb, je, SUB); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { errorCount = try_failure(errorCount, "setMatrix(int,int,int[],Matrix)... ", "Unexpected ArrayIndexOutOfBoundsException"); } try { B.setMatrix(rowindexset, jb, je + B.getColumnDimension() + 1, M); errorCount = try_failure(errorCount, "setMatrix(int[],int,int,Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { B.setMatrix(badrowindexset, jb, je, M); errorCount = try_failure(errorCount, "setMatrix(int[],int,int,Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("setMatrix(int[],int,int,Matrix)... ArrayIndexOutOfBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "setMatrix(int[],int,int,Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } try { B.setMatrix(rowindexset, jb, je, M); try { check(M.minus(B.getMatrix(rowindexset, jb, je)), M); try_success("setMatrix(int[],int,int,Matrix)... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "setMatrix(int[],int,int,Matrix)... ", "submatrix not successfully set"); } B.setMatrix(ib, ie, jb, je, SUB); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { errorCount = try_failure(errorCount, "setMatrix(int[],int,int,Matrix)... ", "Unexpected ArrayIndexOutOfBoundsException"); } try { B.setMatrix(rowindexset, badcolumnindexset, M); errorCount = try_failure(errorCount, "setMatrix(int[],int[],Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { B.setMatrix(badrowindexset, columnindexset, M); errorCount = try_failure(errorCount, "setMatrix(int[],int[],Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("setMatrix(int[],int[],Matrix)... ArrayIndexOutOfBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "setMatrix(int[],int[],Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } try { B.setMatrix(rowindexset, columnindexset, M); try { check(M.minus(B.getMatrix(rowindexset, columnindexset)), M); try_success("setMatrix(int[],int[],Matrix)... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "setMatrix(int[],int[],Matrix)... ", "submatrix not successfully set"); } } catch (java.lang.ArrayIndexOutOfBoundsException e1) { errorCount = try_failure(errorCount, "setMatrix(int[],int[],Matrix)... ", "Unexpected ArrayIndexOutOfBoundsException"); } print("\nTesting array-like methods...\n"); S = new Matrix(columnwise, nonconformld); R = Matrix.random(A.getRowDimension(), A.getColumnDimension()); A = R; try { S = A.minus(S); errorCount = try_failure(errorCount, "minus conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("minus conformance check... ", ""); } if (A.minus(R).norm1() != 0.) { errorCount = try_failure(errorCount, "minus... ", "(difference of identical Matrices is nonzero,\nSubsequent use of minus should be suspect)"); } else { try_success("minus... ", ""); } A = R.copy(); A.minusEquals(R); Z = new Matrix(A.getRowDimension(), A.getColumnDimension()); try { A.minusEquals(S); errorCount = try_failure(errorCount, "minusEquals conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("minusEquals conformance check... ", ""); } if (A.minus(Z).norm1() != 0.) { errorCount = try_failure(errorCount, "minusEquals... ", "(difference of identical Matrices is nonzero,\nSubsequent use of minus should be suspect)"); } else { try_success("minusEquals... ", ""); } A = R.copy(); B = Matrix.random(A.getRowDimension(), A.getColumnDimension()); C = A.minus(B); try { S = A.plus(S); errorCount = try_failure(errorCount, "plus conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("plus conformance check... ", ""); } try { check(C.plus(B), A); try_success("plus... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "plus... ", "(C = A - B, but C + B != A)"); } C = A.minus(B); C.plusEquals(B); try { A.plusEquals(S); errorCount = try_failure(errorCount, "plusEquals conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("plusEquals conformance check... ", ""); } try { check(C, A); try_success("plusEquals... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "plusEquals... ", "(C = A - B, but C = C + B != A)"); } A = R.uminus(); try { check(A.plus(R), Z); try_success("uminus... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "uminus... ", "(-A + A != zeros)"); } A = R.copy(); O = new Matrix(A.getRowDimension(), A.getColumnDimension(), 1.0); C = A.arrayLeftDivide(R); try { S = A.arrayLeftDivide(S); errorCount = try_failure(errorCount, "arrayLeftDivide conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("arrayLeftDivide conformance check... ", ""); } try { check(C, O); try_success("arrayLeftDivide... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "arrayLeftDivide... ", "(M.\\M != ones)"); } try { A.arrayLeftDivideEquals(S); errorCount = try_failure(errorCount, "arrayLeftDivideEquals conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("arrayLeftDivideEquals conformance check... ", ""); } A.arrayLeftDivideEquals(R); try { check(A, O); try_success("arrayLeftDivideEquals... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "arrayLeftDivideEquals... ", "(M.\\M != ones)"); } A = R.copy(); try { A.arrayRightDivide(S); errorCount = try_failure(errorCount, "arrayRightDivide conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("arrayRightDivide conformance check... ", ""); } C = A.arrayRightDivide(R); try { check(C, O); try_success("arrayRightDivide... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "arrayRightDivide... ", "(M./M != ones)"); } try { A.arrayRightDivideEquals(S); errorCount = try_failure(errorCount, "arrayRightDivideEquals conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("arrayRightDivideEquals conformance check... ", ""); } A.arrayRightDivideEquals(R); try { check(A, O); try_success("arrayRightDivideEquals... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "arrayRightDivideEquals... ", "(M./M != ones)"); } A = R.copy(); B = Matrix.random(A.getRowDimension(), A.getColumnDimension()); try { S = A.arrayTimes(S); errorCount = try_failure(errorCount, "arrayTimes conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("arrayTimes conformance check... ", ""); } C = A.arrayTimes(B); try { check(C.arrayRightDivideEquals(B), A); try_success("arrayTimes... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "arrayTimes... ", "(A = R, C = A.*B, but C./B != A)"); } try { A.arrayTimesEquals(S); errorCount = try_failure(errorCount, "arrayTimesEquals conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("arrayTimesEquals conformance check... ", ""); } A.arrayTimesEquals(B); try { check(A.arrayRightDivideEquals(B), R); try_success("arrayTimesEquals... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "arrayTimesEquals... ", "(A = R, A = A.*B, but A./B != R)"); } print("\nTesting I/O methods...\n"); try { DecimalFormat fmt = new DecimalFormat("0.0000E00"); fmt.setDecimalFormatSymbols(new DecimalFormatSymbols(Locale.US)); PrintWriter FILE = new PrintWriter(new FileOutputStream("JamaTestMatrix.out")); A.print(FILE, fmt, 10); FILE.close(); R = Matrix.read(new BufferedReader(new FileReader("JamaTestMatrix.out"))); if (A.minus(R).norm1() < .001) { try_success("print()/read()...", ""); } else { errorCount = try_failure(errorCount, "print()/read()...", "Matrix read from file does not match Matrix printed to file"); } } catch (java.io.IOException ioe) { warningCount = try_warning(warningCount, "print()/read()...", "unexpected I/O error, unable to run print/read test; check write permission in current directory and retry"); } catch (Exception e) { try { e.printStackTrace(System.out); warningCount = try_warning(warningCount, "print()/read()...", "Formatting error... will try JDK1.1 reformulation..."); DecimalFormat fmt = new DecimalFormat("0.0000"); PrintWriter FILE = new PrintWriter(new FileOutputStream("JamaTestMatrix.out")); A.print(FILE, fmt, 10); FILE.close(); R = Matrix.read(new BufferedReader(new FileReader("JamaTestMatrix.out"))); if (A.minus(R).norm1() < .001) { try_success("print()/read()...", ""); } else { errorCount = try_failure(errorCount, "print()/read() (2nd attempt) ...", "Matrix read from file does not match Matrix printed to file"); } } catch (java.io.IOException ioe) { warningCount = try_warning(warningCount, "print()/read()...", "unexpected I/O error, unable to run print/read test; check write permission in current directory and retry"); } } R = Matrix.random(A.getRowDimension(), A.getColumnDimension()); String tmpname = "TMPMATRIX.serial"; try { ObjectOutputStream out = new ObjectOutputStream(new FileOutputStream(tmpname)); out.writeObject(R); ObjectInputStream sin = new ObjectInputStream(new FileInputStream(tmpname)); A = (Matrix) sin.readObject(); try { check(A, R); try_success("writeObject(Matrix)/readObject(Matrix)...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "writeObject(Matrix)/readObject(Matrix)...", "Matrix not serialized correctly"); } } catch (java.io.IOException ioe) { warningCount = try_warning(warningCount, "writeObject()/readObject()...", "unexpected I/O error, unable to run serialization test; check write permission in current directory and retry"); } catch (Exception e) { errorCount = try_failure(errorCount, "writeObject(Matrix)/readObject(Matrix)...", "unexpected error in serialization test"); } print("\nTesting linear algebra methods...\n"); A = new Matrix(columnwise, 3); T = new Matrix(tvals); T = A.transpose(); try { check(A.transpose(), T); try_success("transpose...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "transpose()...", "transpose unsuccessful"); } A.transpose(); try { check(A.norm1(), columnsummax); try_success("norm1...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "norm1()...", "incorrect norm calculation"); } try { check(A.normInf(), rowsummax); try_success("normInf()...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "normInf()...", "incorrect norm calculation"); } try { check(A.normF(), Math.sqrt(sumofsquares)); try_success("normF...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "normF()...", "incorrect norm calculation"); } try { check(A.trace(), sumofdiagonals); try_success("trace()...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "trace()...", "incorrect trace calculation"); } try { check(A.getMatrix(0, A.getRowDimension() - 1, 0, A.getRowDimension() - 1).det(), 0.); try_success("det()...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "det()...", "incorrect determinant calculation"); } SQ = new Matrix(square); try { check(A.times(A.transpose()), SQ); try_success("times(Matrix)...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "times(Matrix)...", "incorrect Matrix-Matrix product calculation"); } try { check(A.times(0.), Z); try_success("times(double)...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "times(double)...", "incorrect Matrix-scalar product calculation"); } A = new Matrix(columnwise, 4); QRDecomposition QR = A.qr(); R = QR.getR(); try { check(A, QR.getQ().times(R)); try_success("QRDecomposition...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "QRDecomposition...", "incorrect QR decomposition calculation"); } SingularValueDecomposition SVD = A.svd(); try { check(A, SVD.getU().times(SVD.getS().times(SVD.getV().transpose()))); try_success("SingularValueDecomposition...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "SingularValueDecomposition...", "incorrect singular value decomposition calculation"); } DEF = new Matrix(rankdef); try { check(DEF.rank(), Math.min(DEF.getRowDimension(), DEF.getColumnDimension()) - 1); try_success("rank()...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "rank()...", "incorrect rank calculation"); } B = new Matrix(condmat); SVD = B.svd(); double[] singularvalues = SVD.getSingularValues(); try { check(B.cond(), singularvalues[0] / singularvalues[Math.min(B.getRowDimension(), B.getColumnDimension()) - 1]); try_success("cond()...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "cond()...", "incorrect condition number calculation"); } int n = A.getColumnDimension(); A = A.getMatrix(0, n - 1, 0, n - 1); A.set(0, 0, 0.); LUDecomposition LU = A.lu(); try { check(A.getMatrix(LU.getPivot(), 0, n - 1), LU.getL().times(LU.getU())); try_success("LUDecomposition...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "LUDecomposition...", "incorrect LU decomposition calculation"); } X = A.inverse(); try { check(A.times(X), Matrix.identity(3, 3)); try_success("inverse()...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "inverse()...", "incorrect inverse calculation"); } O = new Matrix(SUB.getRowDimension(), 1, 1.0); SOL = new Matrix(sqSolution); SQ = SUB.getMatrix(0, SUB.getRowDimension() - 1, 0, SUB.getRowDimension() - 1); try { check(SQ.solve(SOL), O); try_success("solve()...", ""); } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "solve()...", e1.getMessage()); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "solve()...", e.getMessage()); } A = new Matrix(pvals); CholeskyDecomposition Chol = A.chol(); Matrix L = Chol.getL(); try { check(A, L.times(L.transpose())); try_success("CholeskyDecomposition...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "CholeskyDecomposition...", "incorrect Cholesky decomposition calculation"); } X = Chol.solve(Matrix.identity(3, 3)); try { check(A.times(X), Matrix.identity(3, 3)); try_success("CholeskyDecomposition solve()...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "CholeskyDecomposition solve()...", "incorrect Choleskydecomposition solve calculation"); } EigenvalueDecomposition Eig = A.eig(); Matrix D = Eig.getD(); Matrix V = Eig.getV(); try { check(A.times(V), V.times(D)); try_success("EigenvalueDecomposition (symmetric)...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "EigenvalueDecomposition (symmetric)...", "incorrect symmetric Eigenvalue decomposition calculation"); } A = new Matrix(evals); Eig = A.eig(); D = Eig.getD(); V = Eig.getV(); try { check(A.times(V), V.times(D)); try_success("EigenvalueDecomposition (nonsymmetric)...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "EigenvalueDecomposition (nonsymmetric)...", "incorrect nonsymmetric Eigenvalue decomposition calculation"); } print("\nTestMatrix completed.\n"); print("Total errors reported: " + Integer.toString(errorCount) + "\n"); print("Total warnings reported: " + Integer.toString(warningCount) + "\n"); } | 16,744 |
1 | static void copyFile(File file, File destDir) { File destFile = new File(destDir, file.getName()); if (destFile.exists() && (!destFile.canWrite())) { throw new SyncException("Cannot overwrite " + destFile + " because " + "it is read-only"); } try { FileInputStream in = new FileInputStream(file); try { FileOutputStream out = new FileOutputStream(destFile); try { byte[] buffer = new byte[BUFFER_SIZE]; int read; while ((read = in.read(buffer)) != -1) { out.write(buffer, 0, read); } } finally { out.close(); } } finally { in.close(); } } catch (IOException e) { throw new SyncException("I/O error copying " + file + " to " + destDir + " (message: " + e.getMessage() + ")", e); } if (!destFile.setLastModified(file.lastModified())) { throw new SyncException("Could not set last modified timestamp " + "of " + destFile); } } | 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(); } } | 16,745 |
0 | public static String loadWebsiteHtmlCode(String url, String useragent) { HttpClient httpClient = new DefaultHttpClient(); HttpGet getMethod = new HttpGet(url); String htmlCode = ""; if (useragent != null) { getMethod.setHeader("user-agent", useragent); } try { HttpResponse resp = httpClient.execute(getMethod); int statusCode = resp.getStatusLine().getStatusCode(); if (statusCode != HttpStatus.SC_OK) { logger.debug("Method failed!" + statusCode); } htmlCode = EntityUtils.toString(resp.getEntity()); } catch (Exception e) { logger.debug("Fatal protocol violation: " + e.getMessage()); logger.trace(e); } return htmlCode; } | @Override public void render(Output output) throws IOException { output.setStatus(headersFile.getStatusCode(), headersFile.getStatusMessage()); for (Entry<String, Set<String>> header : headersFile.getHeadersMap().entrySet()) { Set<String> values = header.getValue(); for (String value : values) { output.addHeader(header.getKey(), value); } } if (file != null) { InputStream inputStream = new FileInputStream(file); try { output.open(); OutputStream out = output.getOutputStream(); IOUtils.copy(inputStream, out); } finally { inputStream.close(); output.close(); } } } | 16,746 |
0 | @Override public InputStream getInputStream() { String url = resourceURL_; try { return new URL(url).openStream(); } catch (Exception e) { } try { return new FileInputStream("/" + url); } catch (Exception e) { e.printStackTrace(); } return null; } | public static void copyFile(File in, File out) throws IOException { if (in.getCanonicalPath().equals(out.getCanonicalPath())) { return; } 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(); } } } | 16,747 |
0 | public void run() { try { HttpURLConnection con = (HttpURLConnection) url.openConnection(); Osm2Model osm = new Osm2Model(pedestrian, filterCyclic); osm.progress.connect(this, "progress(int)"); osm.parseFile(con.getInputStream(), con.getContentLength()); if (osm.somethingImported()) { done.emit(); } else { nothing.emit(); } } catch (Exception e) { failed.emit(); } } | private void criarQuestaoMultiplaEscolha(QuestaoMultiplaEscolha q) throws SQLException { PreparedStatement stmt = null; String sql = "INSERT INTO multipla_escolha (id_questao, texto, gabarito) VALUES (?,?,?)"; try { for (Alternativa alternativa : q.getAlternativa()) { stmt = conexao.prepareStatement(sql); stmt.setInt(1, q.getIdQuestao()); stmt.setString(2, alternativa.getTexto()); stmt.setBoolean(3, alternativa.getGabarito()); stmt.executeUpdate(); conexao.commit(); } } catch (SQLException e) { conexao.rollback(); throw e; } } | 16,748 |
1 | public String jsFunction_send(String postData) { URL url = null; try { if (_uri.startsWith("http")) { url = new URL(_uri); } else { url = new URL("file://./" + _uri); } } catch (MalformedURLException e) { IdeLog.logError(ScriptingPlugin.getDefault(), Messages.WebRequest_Error, e); return StringUtils.EMPTY; } try { URLConnection conn = url.openConnection(); OutputStreamWriter wr = null; if (this._method.equals("post")) { conn.setDoOutput(true); wr = new OutputStreamWriter(conn.getOutputStream()); wr.write(postData); wr.flush(); } BufferedReader rd = new BufferedReader(new InputStreamReader(conn.getInputStream())); StringBuffer sb = new StringBuffer(); String line; while ((line = rd.readLine()) != null) { sb.append(line + "\r\n"); } if (wr != null) { wr.close(); } rd.close(); String result = sb.toString(); return result; } catch (Exception e) { IdeLog.logError(ScriptingPlugin.getDefault(), Messages.WebRequest_Error, e); return StringUtils.EMPTY; } } | public void sendMessage(Message msg) { if (!blackList.contains(msg.getTo())) { Hashtable<String, String> content = msg.getContent(); Enumeration<String> keys = content.keys(); String key; String data = "to=" + msg.getTo() + "&from=" + msg.getFrom() + "&"; while (keys.hasMoreElements()) { key = (String) keys.nextElement(); data += key + "=" + content.get(key) + "&"; } URL url = null; try { logger.log(this, Level.FINER, "sending " + data + " to " + msg.getTo()); url = new URL("http://" + msg.getTo() + ":8080/webmsgservice?" + data); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); in.readLine(); in.close(); logger.log(this, Level.FINER, "message sent to " + msg.getTo()); } catch (MalformedURLException e) { blackList.add(msg.getTo()); logger.log(this, Level.WARNING, "an error occured during message sending (" + msg.getTo() + ") : " + e.getMessage()); e.printStackTrace(); } catch (IOException e) { logger.log(this, Level.WARNING, "an error occured during message sending (" + msg.getTo() + ") : " + e.getMessage()); blackList.add(msg.getTo()); } } else { logger.log(this, Level.FINE, "will not send message to " + msg.getTo() + " because black listed IP"); } } | 16,749 |
0 | 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); } } | @Override public void run() { try { status = UploadStatus.INITIALISING; DefaultHttpClient httpclient = new DefaultHttpClient(); HttpGet httpget = new HttpGet("http://www.filedropper.com"); httpget.setHeader("User-Agent", "Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.9.2.2) Gecko/20100316 Firefox/3.6.2 GTBDFff GTB7.0"); HttpResponse httpresponse = httpclient.execute(httpget); httpresponse.getEntity().consumeContent(); httppost = new HttpPost("http://www.filedropper.com/index.php?xml=true"); httppost.setHeader("User-Agent", "Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.9.2.2) Gecko/20100316 Firefox/3.6.2 GTBDFff GTB7.0"); MultipartEntity requestEntity = new MultipartEntity(HttpMultipartMode.BROWSER_COMPATIBLE); requestEntity.addPart("file", new MonitoredFileBody(file, uploadProgress)); requestEntity.addPart("Upload", new StringBody("Submit Query")); httppost.setEntity(requestEntity); status = UploadStatus.UPLOADING; httpresponse = httpclient.execute(httppost); String strResponse = EntityUtils.toString(httpresponse.getEntity()); status = UploadStatus.GETTINGLINK; downURL = "http://www.filedropper.com/" + strResponse.substring(strResponse.lastIndexOf("=") + 1); NULogger.getLogger().info(downURL); uploadFinished(); } catch (Exception ex) { ex.printStackTrace(); NULogger.getLogger().severe(ex.toString()); uploadFailed(); } } | 16,750 |
0 | public BufferedImage processUsingTemp(InputStream input, DjatokaDecodeParam params) throws DjatokaException { File in; try { in = File.createTempFile("tmp", ".jp2"); FileOutputStream fos = new FileOutputStream(in); in.deleteOnExit(); IOUtils.copyStream(input, fos); } catch (IOException e) { logger.error(e, e); throw new DjatokaException(e); } BufferedImage bi = process(in.getAbsolutePath(), params); if (in != null) in.delete(); return bi; } | public static boolean isMatchingAsPassword(final String password, final String amd5Password) { boolean response = false; try { final MessageDigest algorithm = MessageDigest.getInstance("MD5"); algorithm.reset(); algorithm.update(password.getBytes()); final byte[] md5Byte = algorithm.digest(); final StringBuffer buffer = new StringBuffer(); for (final byte b : md5Byte) { if ((b <= 15) && (b >= 0)) { buffer.append("0"); } buffer.append(Integer.toHexString(0xFF & b)); } response = (amd5Password != null) && amd5Password.equals(buffer.toString()); } catch (final NoSuchAlgorithmException e) { ProjektUtil.LOG.error("No digester MD5 found in classpath!", e); } return response; } | 16,751 |
0 | public HashMap parseFile(File newfile) throws IOException { String s; String[] tokens; int nvalues = 0; double num1, num2, num3; boolean baddata = false; URL url = newfile.toURL(); InputStream is = url.openStream(); InputStreamReader isr = new InputStreamReader(is); BufferedReader br = new BufferedReader(isr); HashMap data = new HashMap(); while ((s = br.readLine()) != null) { tokens = s.split("\\s+"); nvalues = tokens.length; if (nvalues == 2) { data.put(new String(tokens[0]), new Double(Double.parseDouble(tokens[1]))); } else { System.out.println("Sorry, trouble reading reference file."); } } return data; } | public void removerTopicos(Topicos topicos) throws ClassNotFoundException, SQLException { this.criaConexao(false); String sql = "DELETE FROM \"Topicos\" " + " WHERE \"id_Topicos\" = ?"; PreparedStatement stmt = null; try { stmt = connection.prepareStatement(sql); stmt.setString(1, topicos.getIdTopicos()); stmt.executeUpdate(); connection.commit(); } catch (SQLException e) { connection.rollback(); throw e; } finally { try { stmt.close(); this.fechaConexao(); } catch (SQLException e) { throw e; } } } | 16,752 |
0 | public HttpURLConnection getURLConnection() throws IOException { String url_str = getServerURL(); URL url = new URL(url_str); HttpURLConnection urlConnection; if (url_str.toLowerCase().startsWith("https")) { HttpsURLConnection urlSConnection = (HttpsURLConnection) url.openConnection(); urlSConnection.setHostnameVerifier(new HostnameVerifier() { public boolean verify(String hostname, SSLSession session) { return true; } }); urlConnection = urlSConnection; } else urlConnection = (HttpURLConnection) url.openConnection(); urlConnection.setRequestMethod("POST"); if (useHTTPProxy && getProxyLogin() != null) { String authString = getProxyLogin() + ":" + getProxyPassword(); String auth = "Basic " + new sun.misc.BASE64Encoder().encode(authString.getBytes()); urlConnection.setRequestProperty("Proxy-Authorization", auth); } urlConnection.setDoOutput(true); if (useHTTPProxy) { System.getProperties().put("proxySet", "true"); System.getProperties().put("proxyHost", proxyHost); System.getProperties().put("proxyPort", String.valueOf(proxyPort)); } return urlConnection; } | public void serviceDocument(final TranslationRequest request, final TranslationResponse response, final Document document) throws Exception { response.addHeaders(document.getResponseHeaders()); try { IOUtils.copy(document.getInputStream(), response.getOutputStream()); response.setEndState(ResponseStateOk.getInstance()); } catch (Exception e) { response.setEndState(new ResponseStateException(e)); log.warn("Error parsing XML of " + document, e); } } | 16,753 |
1 | @org.junit.Test public void simpleRead() throws Exception { final InputStream istream = StatsInputStreamTest.class.getResourceAsStream("/testFile.txt"); final StatsInputStream ris = new StatsInputStream(istream); assertEquals("read size", 0, ris.getSize()); IOUtils.copy(ris, new NullOutputStream()); assertEquals("in the end", 30, ris.getSize()); } | public void sendContent(OutputStream out, Range range, Map<String, String> params, String contentType) throws IOException { LOGGER.debug("GET REQUEST OR RESPONSE - Send content: " + file.getAbsolutePath()); FileInputStream in = null; try { in = new FileInputStream(file); int bytes = IOUtils.copy(in, out); LOGGER.debug("wrote bytes: " + bytes); out.flush(); } finally { IOUtils.closeQuietly(in); } } | 16,754 |
0 | public void appendFetch(IProgress progress, PrintWriter pw, String list, int from, int to) throws IOException { progress.start(); try { File storage = new File(cacheDirectory.getValue(), "mboxes"); storage.mkdirs(); File mbox = new File(storage, list + "-" + from + "-" + to + ".mbox"); if (mbox.exists()) { BufferedReader in = new BufferedReader(new InputStreamReader(new ProgressInputStream(new FileInputStream(mbox), progress, 10000))); String line; while ((line = in.readLine()) != null) { pw.write(line); pw.write('\n'); } in.close(); return; } progress.setScale(100); IProgress subProgress1 = progress.getSub(75); URL url = getGmaneURL(list, from, to); BufferedReader in = new BufferedReader(new InputStreamReader(new ProgressInputStream(url.openStream(), subProgress1, 10000))); PrintWriter writeToMbox = new PrintWriter(mbox); int lines = 0; String line; while ((line = in.readLine()) != null) { lines++; if (line.matches("^From .*$") && !line.matches("^From .*? .*[0-9][0-9]:[0-9][0-9]:[0-9][0-9].*$")) { line = ">" + line; } writeToMbox.write(line); writeToMbox.write('\n'); } in.close(); writeToMbox.close(); appendFetch(progress.getSub(25), pw, list, from, to); } finally { progress.done(); } } | 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); } } | 16,755 |
0 | private void getLines(PackageManager pm) throws PackageManagerException { final Pattern p = Pattern.compile("\\s*deb\\s+(ftp://|http://)(\\S+)\\s+((\\S+\\s*)*)(./){0,1}"); Matcher m; if (updateUrlAndFile == null) updateUrlAndFile = new ArrayList<UrlAndFile>(); BufferedReader f; String protocol; String host; String shares; String adress; try { f = new BufferedReader(new FileReader(sourcesList)); while ((protocol = f.readLine()) != null) { m = p.matcher(protocol); if (m.matches()) { protocol = m.group(1); host = m.group(2); if (m.group(3).trim().equalsIgnoreCase("./")) shares = ""; else shares = m.group(3).trim(); if (shares == null) adress = protocol + host; else { shares = shares.replace(" ", "/"); if (!host.endsWith("/") && !shares.startsWith("/")) host = host + "/"; adress = host + shares; while (adress.contains("//")) adress = adress.replace("//", "/"); adress = protocol + adress; } if (!adress.endsWith("/")) adress = adress + "/"; String changelogdir = adress; changelogdir = changelogdir.substring(changelogdir.indexOf("//") + 2); if (changelogdir.endsWith("/")) changelogdir = changelogdir.substring(0, changelogdir.lastIndexOf("/")); changelogdir = changelogdir.replace('/', '_'); changelogdir = changelogdir.replaceAll("\\.", "_"); changelogdir = changelogdir.replaceAll("-", "_"); changelogdir = changelogdir.replaceAll(":", "_COLON_"); adress = adress + "Packages.gz"; final String serverFileLocation = adress.replaceAll(":", "_COLON_"); final NameFileLocation nfl = new NameFileLocation(); try { final GZIPInputStream in = new GZIPInputStream(new ConnectToServer(pm).getInputStream(adress)); final String rename = new File(nfl.rename(serverFileLocation, listsDir)).getCanonicalPath(); final FileOutputStream out = new FileOutputStream(rename); final byte[] buf = new byte[4096]; int len; while ((len = in.read(buf)) > 0) out.write(buf, 0, len); out.close(); in.close(); final File file = new File(rename); final UrlAndFile uaf = new UrlAndFile(protocol + host, file, changelogdir); updateUrlAndFile.add(uaf); } catch (final Exception e) { final String message = "URL: " + adress + " caused exception"; if (null != pm) { logger.warn(message, e); pm.addWarning(message + "\n" + e.toString()); } else logger.warn(message, e); e.printStackTrace(); } } } f.close(); } catch (final FileNotFoundException e) { final String message = PreferenceStoreHolder.getPreferenceStoreByName("Screen").getPreferenceAsString("sourcesList.corrupt", "Entry not found sourcesList.corrupt"); if (null != pm) { logger.warn(message, e); pm.addWarning(message + "\n" + e.toString()); } else logger.warn(message, e); e.printStackTrace(); } catch (final IOException e) { final String message = PreferenceStoreHolder.getPreferenceStoreByName("Screen").getPreferenceAsString("SearchForServerFile.getLines.IOException", "Entry not found SearchForServerFile.getLines.IOException"); if (null != pm) { logger.warn(message, e); pm.addWarning(message + "\n" + e.toString()); } else logger.warn(message, e); e.printStackTrace(); } } | public Attributes getAttributes() throws SchemaViolationException, NoSuchAlgorithmException, UnsupportedEncodingException { BasicAttributes outAttrs = new BasicAttributes(true); BasicAttribute oc = new BasicAttribute("objectclass", "inetOrgPerson"); oc.add("organizationalPerson"); oc.add("person"); outAttrs.put(oc); if (lastName != null && firstName != null) { outAttrs.put("sn", lastName); outAttrs.put("givenName", firstName); outAttrs.put("cn", firstName + " " + lastName); } else { throw new SchemaViolationException("user must have surname"); } if (password != null) { MessageDigest sha = MessageDigest.getInstance("md5"); sha.reset(); sha.update(password.getBytes("utf-8")); byte[] digest = sha.digest(); String hash = Base64.encodeBase64String(digest); outAttrs.put("userPassword", "{MD5}" + hash); } if (email != null) { outAttrs.put("mail", email); } return (Attributes) outAttrs; } | 16,756 |
1 | @SuppressWarnings("unchecked") @Override public synchronized void drop(DropTargetDropEvent arg0) { Helper.log().debug("Dropped"); Transferable t = arg0.getTransferable(); try { arg0.acceptDrop(arg0.getDropAction()); List<File> filelist = (List<File>) t.getTransferData(t.getTransferDataFlavors()[0]); for (File file : filelist) { Helper.log().debug(file.getAbsolutePath()); if (file.getName().toLowerCase().contains(".lnk")) { Helper.log().debug(file.getName() + " is a link"); File target = new File(rp.getRoot().getFullPath() + "/" + file.getName()); Helper.log().debug("I have opened the mayor at " + target.getAbsolutePath()); FileOutputStream fo = new FileOutputStream(target); FileInputStream fi = new FileInputStream(file); int i = 0; while (fi.available() > 0) { fo.write(fi.read()); System.out.print("."); i++; } Helper.log().debug(i + " bytes have been written to " + target.getAbsolutePath()); fo.close(); fi.close(); } } rp.redraw(); } catch (Throwable tr) { tr.printStackTrace(); } Helper.log().debug(arg0.getSource().toString()); } | private void copy(File sourceFile, File destinationFile) { try { FileChannel in = new FileInputStream(sourceFile).getChannel(); FileChannel out = new FileOutputStream(destinationFile).getChannel(); try { in.transferTo(0, in.size(), out); in.close(); out.close(); } catch (IOException e) { } } catch (FileNotFoundException e) { } } | 16,757 |
0 | public String useService(HashMap<String, String> input) { String output = ""; if (input.size() < 1) { return ""; } String data = ""; try { for (String key : input.keySet()) { data += "&" + URLEncoder.encode(key, "UTF-8") + "=" + URLEncoder.encode(input.get(key), "UTF-8"); } data = data.substring(1); URL url = new URL(serviceUrl); URLConnection conn = url.openConnection(); conn.setDoOutput(true); OutputStreamWriter wr = new OutputStreamWriter(conn.getOutputStream()); wr.write(data); wr.flush(); BufferedReader rd = new BufferedReader(new InputStreamReader(conn.getInputStream())); String line; while ((line = rd.readLine()) != null) { output += line; } wr.close(); rd.close(); } catch (Exception e) { e.printStackTrace(); } return output; } | public ViewedCandidatesIndex getAllViewedCandidates() throws BookKeeprCommunicationException { try { synchronized (httpClient) { HttpGet req = new HttpGet(remoteHost.getUrl() + "/cand/viewed"); req.setHeader("Accept-Encoding", "gzip"); HttpResponse resp = httpClient.execute(req); if (resp.getStatusLine().getStatusCode() == HttpStatus.SC_OK) { try { InputStream in = resp.getEntity().getContent(); Header hdr = resp.getFirstHeader("Content-Encoding"); String enc = ""; if (hdr != null) { enc = resp.getFirstHeader("Content-Encoding").getValue(); } if (enc.equals("gzip")) { in = new GZIPInputStream(in); } XMLAble xmlable = XMLReader.read(in); in.close(); if (xmlable instanceof ViewedCandidatesIndex) { ViewedCandidatesIndex p = (ViewedCandidatesIndex) xmlable; return p; } else { resp.getEntity().consumeContent(); throw new BookKeeprCommunicationException("BookKeepr returned the wrong thing for ViewedCandidatesIndex"); } } catch (SAXException ex) { Logger.getLogger(BookKeeprConnection.class.getName()).log(Level.WARNING, "Got a malformed message from the bookkeepr", ex); throw new BookKeeprCommunicationException(ex); } } else { throw new BookKeeprCommunicationException("Got a " + resp.getStatusLine().getStatusCode() + " from the BookKeepr"); } } } catch (HttpException ex) { throw new BookKeeprCommunicationException(ex); } catch (IOException ex) { throw new BookKeeprCommunicationException(ex); } catch (URISyntaxException ex) { throw new BookKeeprCommunicationException(ex); } } | 16,758 |
0 | void loadImage(Frame frame, URL url) throws Exception { URLConnection conn = url.openConnection(); String mimeType = conn.getContentType(); long length = conn.getContentLength(); InputStream is = conn.getInputStream(); loadImage(frame, is, length, mimeType); } | public static String login() throws Exception { if (sid == null) { String login = ROLAPClientAux.loadProperties().getProperty("user"); String password = ROLAPClientAux.loadProperties().getProperty("password"); MessageDigest md = MessageDigest.getInstance("MD5"); md.update(password.getBytes()); String password2 = asHexString(md.digest()); String query = "/server/login?user=" + login + "&extern_password=" + password + "&password=" + password2; Vector<String> res = ROLAPClientAux.sendRequest(query); String vals[] = res.get(0).split(";"); sid = vals[0]; } return sid; } | 16,759 |
0 | public static void copy(File in, File out) throws Exception { FileChannel sourceChannel = new FileInputStream(in).getChannel(); FileChannel destinationChannel = new FileOutputStream(out).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), destinationChannel); sourceChannel.close(); destinationChannel.close(); } | private static String md5(String digest, String data) throws IOException { MessageDigest messagedigest; try { messagedigest = MessageDigest.getInstance(digest); } catch (NoSuchAlgorithmException e) { throw new RuntimeException(e); } messagedigest.update(data.getBytes("ISO-8859-1")); byte[] bytes = messagedigest.digest(); StringBuilder stringbuffer = new StringBuilder(bytes.length * 2); for (int j = 0; j < bytes.length; j++) { int k = bytes[j] >>> 4 & 0x0f; stringbuffer.append(hexChars[k]); k = bytes[j] & 0x0f; stringbuffer.append(hexChars[k]); } return stringbuffer.toString(); } | 16,760 |
1 | private void processData(InputStream raw) { String fileName = remoteName; if (localName != null) { fileName = localName; } try { FileOutputStream fos = new FileOutputStream(new File(fileName), true); IOUtils.copy(raw, fos); LOG.info("ok"); } catch (IOException e) { LOG.error("error writing file", e); } } | public static boolean copyFileCover(String srcFileName, String descFileName, boolean coverlay) { File srcFile = new File(srcFileName); if (!srcFile.exists()) { System.out.println("�����ļ�ʧ�ܣ�Դ�ļ�" + srcFileName + "������!"); return false; } else if (!srcFile.isFile()) { System.out.println("�����ļ�ʧ�ܣ�" + srcFileName + "����һ���ļ�!"); return false; } File descFile = new File(descFileName); if (descFile.exists()) { if (coverlay) { System.out.println("Ŀ���ļ��Ѵ��ڣ���ɾ��!"); if (!FileOperateUtils.delFile(descFileName)) { System.out.println("ɾ��Ŀ���ļ�" + descFileName + "ʧ��!"); return false; } } else { System.out.println("�����ļ�ʧ�ܣ�Ŀ���ļ�" + descFileName + "�Ѵ���!"); return false; } } else { if (!descFile.getParentFile().exists()) { System.out.println("Ŀ���ļ����ڵ�Ŀ¼�����ڣ�����Ŀ¼!"); if (!descFile.getParentFile().mkdirs()) { System.out.println("����Ŀ���ļ����ڵ�Ŀ¼ʧ��!"); return false; } } } int readByte = 0; InputStream ins = null; OutputStream outs = null; try { ins = new FileInputStream(srcFile); outs = new FileOutputStream(descFile); byte[] buf = new byte[1024]; while ((readByte = ins.read(buf)) != -1) { outs.write(buf, 0, readByte); } System.out.println("���Ƶ����ļ�" + srcFileName + "��" + descFileName + "�ɹ�!"); return true; } catch (Exception e) { System.out.println("�����ļ�ʧ�ܣ�" + e.getMessage()); return false; } finally { if (outs != null) { try { outs.close(); } catch (IOException oute) { oute.printStackTrace(); } } if (ins != null) { try { ins.close(); } catch (IOException ine) { ine.printStackTrace(); } } } } | 16,761 |
1 | 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); } } | private String digestPassword(String password) { StringBuffer hexString = new StringBuffer(); try { MessageDigest algorithm = MessageDigest.getInstance("MD5"); algorithm.reset(); algorithm.update(password.getBytes()); byte[] messageDigest = algorithm.digest(); for (byte b : messageDigest) { hexString.append(Integer.toHexString(0xFF & b)); } } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } return hexString.toString(); } | 16,762 |
0 | public static String getHash(String text) { if (text == null) return null; try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(text.getBytes()); byte[] hashedTextBytes = md.digest(); BigInteger hashedTextBigInteger = new BigInteger(1, hashedTextBytes); String hashedTextString = hashedTextBigInteger.toString(16); return hashedTextString; } catch (NoSuchAlgorithmException e) { LOG.warning(e.toString()); return null; } } | public MpegPresentation(URL url) throws IOException { File file = new File(url.getPath()); InputStream input = url.openStream(); DataInputStream ds = new DataInputStream(input); try { parseFile(ds); prepareTracks(); if (audioTrackBox != null && audioHintTrackBox != null) { audioTrack = new AudioTrack(audioTrackBox, audioHintTrackBox, file); } if (videoTrackBox != null && videoHintTrackBox != null) { videoTrack = new VideoTrack(videoTrackBox, videoHintTrackBox, file); } } finally { ds.close(); input.close(); } } | 16,763 |
0 | public void elimina(Cliente cli) throws errorSQL, errorConexionBD { System.out.println("GestorCliente.elimina()"); int id = cli.getId(); String sql; Statement stmt = null; try { gd.begin(); sql = "DELETE FROM cliente WHERE cod_cliente = '" + id + "'"; System.out.println("Ejecutando: " + sql); stmt = gd.getConexion().createStatement(); stmt.executeUpdate(sql); System.out.println("executeUpdate"); gd.commit(); System.out.println("commit"); stmt.close(); } catch (SQLException e) { gd.rollback(); throw new errorSQL(e.toString()); } catch (errorConexionBD e) { System.err.println("Error en GestorCliente.elimina(): " + e); } catch (errorSQL e) { System.err.println("Error en GestorCliente.elimina(): " + e); } } | 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; } | 16,764 |
0 | 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(); } } | 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"); } FileChannel input = new FileInputStream(srcFile).getChannel(); try { FileChannel output = new FileOutputStream(destFile).getChannel(); try { output.transferFrom(input, 0, input.size()); } 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()); } } | 16,765 |
1 | public void onMessage(Message message) { LOG.debug("onMessage"); DownloadMessage downloadMessage; try { downloadMessage = new DownloadMessage(message); } catch (JMSException e) { LOG.error("JMS error: " + e.getMessage(), e); return; } String caName = downloadMessage.getCaName(); boolean update = downloadMessage.isUpdate(); LOG.debug("issuer: " + caName); CertificateAuthorityEntity certificateAuthority = this.certificateAuthorityDAO.findCertificateAuthority(caName); if (null == certificateAuthority) { LOG.error("unknown certificate authority: " + caName); return; } if (!update && Status.PROCESSING != certificateAuthority.getStatus()) { LOG.debug("CA status not marked for processing"); return; } String crlUrl = certificateAuthority.getCrlUrl(); if (null == crlUrl) { LOG.warn("No CRL url for CA " + certificateAuthority.getName()); certificateAuthority.setStatus(Status.NONE); return; } NetworkConfig networkConfig = this.configurationDAO.getNetworkConfig(); HttpClient httpClient = new HttpClient(); if (null != networkConfig) { httpClient.getHostConfiguration().setProxy(networkConfig.getProxyHost(), networkConfig.getProxyPort()); } HttpClientParams httpClientParams = httpClient.getParams(); httpClientParams.setParameter("http.socket.timeout", new Integer(1000 * 20)); LOG.debug("downloading CRL from: " + crlUrl); GetMethod getMethod = new GetMethod(crlUrl); getMethod.addRequestHeader("User-Agent", "jTrust CRL Client"); int statusCode; try { statusCode = httpClient.executeMethod(getMethod); } catch (Exception e) { downloadFailed(caName, crlUrl); throw new RuntimeException(); } if (HttpURLConnection.HTTP_OK != statusCode) { LOG.debug("HTTP status code: " + statusCode); downloadFailed(caName, crlUrl); throw new RuntimeException(); } String crlFilePath; File crlFile = null; try { crlFile = File.createTempFile("crl-", ".der"); InputStream crlInputStream = getMethod.getResponseBodyAsStream(); OutputStream crlOutputStream = new FileOutputStream(crlFile); IOUtils.copy(crlInputStream, crlOutputStream); IOUtils.closeQuietly(crlInputStream); IOUtils.closeQuietly(crlOutputStream); crlFilePath = crlFile.getAbsolutePath(); LOG.debug("temp CRL file: " + crlFilePath); } catch (IOException e) { downloadFailed(caName, crlUrl); if (null != crlFile) { crlFile.delete(); } throw new RuntimeException(e); } try { this.notificationService.notifyHarvester(caName, crlFilePath, update); } catch (JMSException e) { crlFile.delete(); throw new RuntimeException(e); } } | public ActualTask(TEditor editor, TIGDataBase dataBase, String directoryPath) { File myDirectory = new File(directoryPath); int i; Vector images = new Vector(); images = dataBase.allImageSearch(); lengthOfTask = images.size() * 2; String directory = directoryPath + "Images" + myDirectory.separator; File newDirectoryFolder = new File(directory); newDirectoryFolder.mkdirs(); try { DocumentBuilderFactory domFactory = DocumentBuilderFactory.newInstance(); DocumentBuilder domBuilder = domFactory.newDocumentBuilder(); doc = domBuilder.newDocument(); } catch (Exception exc) { System.out.println(exc.getMessage()); System.out.println(exc.toString()); } Element dbElement = doc.createElement("dataBase"); for (i = 0; ((i < images.size()) && !stop); i++) { current = i; String element = (String) images.elementAt(i); String pathSrc = "Images" + File.separator + element.substring(0, 1).toUpperCase() + File.separator + element; String name = pathSrc.substring(pathSrc.lastIndexOf(myDirectory.separator) + 1, pathSrc.length()); String pathDst = directory + name; try { FileChannel srcChannel = new FileInputStream(pathSrc).getChannel(); FileChannel dstChannel = new FileOutputStream(pathDst).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (IOException exc) { System.out.println(exc.getMessage()); System.out.println(exc.toString()); } Vector keyWords = new Vector(); keyWords = dataBase.asociatedConceptSearch((String) images.elementAt(i)); Element imageElement = doc.createElement("image"); Element imageNameElement = doc.createElement("name"); imageNameElement.appendChild(doc.createTextNode(name)); imageElement.appendChild(imageNameElement); for (int j = 0; j < keyWords.size(); j++) { Element keyWordElement = doc.createElement("keyWord"); keyWordElement.appendChild(doc.createTextNode((String) keyWords.elementAt(j))); imageElement.appendChild(keyWordElement); } dbElement.appendChild(imageElement); } try { doc.appendChild(dbElement); File dst = new File(directory.concat("Images")); BufferedWriter bufferWriter = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(dst), "UTF-8")); TransformerFactory transformerFactory = TransformerFactory.newInstance(); Transformer transformer = transformerFactory.newTransformer(); DOMSource source = new DOMSource(doc); StreamResult result = new StreamResult(bufferWriter); transformer.transform(source, result); bufferWriter.close(); } catch (Exception exc) { System.out.println(exc.getMessage()); System.out.println(exc.toString()); } current = lengthOfTask; } | 16,766 |
0 | @Override public void exec() { if (fileURI == null) return; InputStream is = null; try { if (fileURI.toLowerCase().startsWith("dbgp://")) { String uri = fileURI.substring(7); if (uri.toLowerCase().startsWith("file/")) { uri = fileURI.substring(5); is = new FileInputStream(new File(uri)); } else { XmldbURI pathUri = XmldbURI.create(URLDecoder.decode(fileURI.substring(15), "UTF-8")); Database db = getJoint().getContext().getDatabase(); DBBroker broker = null; try { broker = db.getBroker(); DocumentImpl resource = broker.getXMLResource(pathUri, Lock.READ_LOCK); if (resource.getResourceType() == DocumentImpl.BINARY_FILE) { is = broker.getBinaryResource((BinaryDocument) resource); } else { return; } } catch (EXistException e) { exception = e; } finally { db.release(broker); } } } else { URL url = new URL(fileURI); URLConnection conn = url.openConnection(); is = conn.getInputStream(); } ByteArrayOutputStream baos = new ByteArrayOutputStream(); byte[] buf = new byte[256]; int c; while ((c = is.read(buf)) > -1) { baos.write(buf, 0, c); } source = baos.toByteArray(); success = true; } catch (MalformedURLException e) { exception = e; } catch (IOException e) { exception = e; } catch (PermissionDeniedException e) { exception = e; } finally { if (is != null) try { is.close(); } catch (IOException e) { if (exception == null) exception = e; } } } | public void run() { String s; s = ""; try { URL url = new URL("http://www.m-w.com/dictionary/" + word); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); String str; while (((str = in.readLine()) != null) && (!stopped)) { s = s + str; } in.close(); } catch (MalformedURLException e) { } catch (IOException e) { } Pattern pattern = Pattern.compile("Main Entry:.+?<br>(.+?)</td>", Pattern.CASE_INSENSITIVE | Pattern.DOTALL); Matcher matcher = pattern.matcher(s); java.io.StringWriter wr = new java.io.StringWriter(); HTMLDocument doc = null; HTMLEditorKit kit = (HTMLEditorKit) editor.getEditorKit(); try { doc = (HTMLDocument) editor.getDocument(); } catch (Exception e) { } System.out.println(wr); editor.setContentType("text/html"); if (matcher.find()) try { kit.insertHTML(doc, editor.getCaretPosition(), "<HR>" + matcher.group(1) + "<HR>", 0, 0, null); } catch (Exception e) { JOptionPane.showMessageDialog(null, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } else try { kit.insertHTML(doc, editor.getCaretPosition(), "<HR><FONT COLOR='RED'>NOT FOUND!!</FONT><HR>", 0, 0, null); } catch (Exception e) { JOptionPane.showMessageDialog(null, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } button.setEnabled(true); } | 16,767 |
0 | @Test public void test_lookupType_NonExistingName() throws Exception { URL url = new URL(baseUrl + "/lookupType/blah-blah"); HttpURLConnection connection = (HttpURLConnection) url.openConnection(); connection.setRequestMethod("GET"); connection.setRequestProperty("Accept", "application/json"); assertThat(connection.getResponseCode(), equalTo(200)); assertThat(getResponse(connection), equalTo("[]")); assertThat(connection.getHeaderField("Content-Type"), equalTo("application/json; charset=utf-8")); connection = (HttpURLConnection) url.openConnection(); connection.setRequestMethod("GET"); connection.setRequestProperty("Accept", "application/xml"); assertThat(connection.getResponseCode(), equalTo(200)); assertThat(getResponse(connection), equalTo("<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?><rowset/>")); assertThat(connection.getHeaderField("Content-Type"), equalTo("application/xml; charset=utf-8")); } | public static void postData(Reader data, URL endpoint, Writer output) throws Exception { HttpURLConnection urlc = null; try { urlc = (HttpURLConnection) endpoint.openConnection(); try { urlc.setRequestMethod("POST"); } catch (ProtocolException e) { throw new Exception("Shouldn't happen: HttpURLConnection doesn't support POST??", e); } urlc.setDoOutput(true); urlc.setDoInput(true); urlc.setUseCaches(false); urlc.setAllowUserInteraction(false); urlc.setRequestProperty("Content-type", "text/xml; charset=" + "UTF-8"); OutputStream out = urlc.getOutputStream(); try { Writer writer = new OutputStreamWriter(out, "UTF-8"); pipe(data, writer); writer.close(); } catch (IOException e) { throw new Exception("IOException while posting data", e); } finally { if (out != null) { out.close(); } } InputStream in = urlc.getInputStream(); try { Reader reader = new InputStreamReader(in); pipe(reader, output); reader.close(); } catch (IOException e) { throw new Exception("IOException while reading response", e); } finally { if (in != null) { in.close(); } } } catch (IOException e) { throw new Exception("Connection error (is server running at " + endpoint + " ?): " + e); } finally { if (urlc != null) { urlc.disconnect(); } } } | 16,768 |
1 | 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); } | public int procesar() { int mas = 0; String uriOntologia = "", source = "", uri = ""; String fichOrigenHTML = "", fichOrigenLN = ""; String ficheroOutOWL = ""; md5 firma = null; StringTokenV2 entra = null, entra2 = null, entra3 = null; FileInputStream lengNat = null; BufferedInputStream lengNat2 = null; DataInputStream entradaLenguajeNatural = null; FileWriter salOWL = null; BufferedWriter salOWL2 = null; PrintWriter salidaOWL = null; String sujeto = "", verbo = "", CD = "", CI = "", fraseOrigen = ""; StringTokenV2 token2; boolean bandera = false; OntClass c = null; OntClass cBak = null; String claseTrabajo = ""; String nombreClase = "", nombrePropiedad = "", variasPalabras = ""; int incre = 0, emergencia = 0; String lineaSalida = ""; String[] ontologia = new String[5]; ontologia[0] = "http://www.criado.info/owl/vertebrados_es.owl#"; ontologia[1] = "http://www.w3.org/2001/sw/WebOnt/guide-src/wine#"; ontologia[2] = "http://www.co-ode.org/ontologies/pizza/2005/10/18/pizza.owl#"; ontologia[3] = "http://www.w3.org/2001/sw/WebOnt/guide-src/food#"; ontologia[4] = "http://www.daml.org/2001/01/gedcom/gedcom#"; String[] ontologiaSource = new String[5]; ontologiaSource[0] = this.directorioMapeo + "\\" + "mapeo_vertebrados_es.xml"; ontologiaSource[1] = this.directorioMapeo + "\\" + "mapeo_wine_es.xml"; ontologiaSource[2] = this.directorioMapeo + "\\" + "mapeo_pizza_es.xml"; ontologiaSource[3] = this.directorioMapeo + "\\" + "mapeo_food_es.xml"; ontologiaSource[4] = this.directorioMapeo + "\\" + "mapeo_parentesco_es.xml"; mapeoIdiomas clasesOntologias; try { if ((entrada = entradaFichero.readLine()) != null) { if (entrada.trim().length() > 10) { entrada2 = new StringTokenV2(entrada.trim(), "\""); if (entrada2.isIncluidaSubcadena("<fichero ontologia=")) { ontologiaOrigen = entrada2.getToken(2); fichOrigenHTML = entrada2.getToken(4); fichOrigenLN = entrada2.getToken(6); if (ontologiaOrigen.equals("VERTEBRADOS")) { source = ontologiaSource[0]; uriOntologia = ontologia[0]; } if (ontologiaOrigen.equals("WINE")) { source = ontologiaSource[1]; uriOntologia = ontologia[1]; } if (ontologiaOrigen.equals("PIZZA")) { source = ontologiaSource[2]; uriOntologia = ontologia[2]; } if (ontologiaOrigen.equals("FOOD")) { source = ontologiaSource[3]; uriOntologia = ontologia[3]; } if (ontologiaOrigen.equals("PARENTESCOS")) { source = ontologiaSource[4]; uriOntologia = ontologia[4]; } firma = new md5(uriOntologia, false); clasesOntologias = new mapeoIdiomas(source); uri = ""; ficheroOutOWL = ""; entra2 = new StringTokenV2(fichOrigenHTML, "\\"); int numToken = entra2.getNumeroTokenTotales(); entra = new StringTokenV2(fichOrigenHTML, " "); if (entra.isIncluidaSubcadena(directorioLocal)) { entra = new StringTokenV2(entra.getQuitar(directorioLocal) + "", " "); uri = entra.getCambiar("\\", "/"); uri = entra.getQuitar(entra2.getToken(numToken)) + ""; entra3 = new StringTokenV2(entra2.getToken(numToken), "."); ficheroOutOWL = entra3.getToken(1) + "_" + firma.toString() + ".owl"; uri = urlPatron + uri + ficheroOutOWL; } entra3 = new StringTokenV2(fichOrigenHTML, "."); ficheroOutOWL = entra3.getToken(1) + "_" + firma.toString() + ".owl"; lineaSalida = "<vistasemantica origen=\"" + fichOrigenLN + "\" destino=\"" + uri + "\" />"; lengNat = new FileInputStream(fichOrigenLN); lengNat2 = new BufferedInputStream(lengNat); entradaLenguajeNatural = new DataInputStream(lengNat2); salOWL = new FileWriter(ficheroOutOWL); salOWL2 = new BufferedWriter(salOWL); salidaOWL = new PrintWriter(salOWL2); while ((entradaInstancias = entradaLenguajeNatural.readLine()) != null) { sujeto = ""; verbo = ""; CD = ""; CI = ""; fraseOrigen = ""; if (entradaInstancias.trim().length() > 10) { entrada2 = new StringTokenV2(entradaInstancias.trim(), "\""); if (entrada2.isIncluidaSubcadena("<oracion sujeto=")) { sujeto = entrada2.getToken(2).trim(); verbo = entrada2.getToken(4).trim(); CD = entrada2.getToken(6).trim(); CI = entrada2.getToken(8).trim(); fraseOrigen = entrada2.getToken(10).trim(); if (sujeto.length() > 0 & verbo.length() > 0 & CD.length() > 0) { bandera = false; c = null; cBak = null; nombreClase = clasesOntologias.getClaseInstancia(CD); if (nombreClase.length() > 0) { bandera = true; } if (bandera) { if (incre == 0) { salidaOWL.write(" <rdf:RDF " + "\n"); salidaOWL.write(" xmlns:j.0=\"" + uriOntologia + "\"" + "\n"); salidaOWL.write(" xmlns:protege=\"http://protege.stanford.edu/plugins/owl/protege#\"" + "\n"); salidaOWL.write(" xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\"" + "\n"); salidaOWL.write(" xmlns:xsd=\"http://www.w3.org/2001/XMLSchema#\"" + "\n"); salidaOWL.write(" xmlns:rdfs=\"http://www.w3.org/2000/01/rdf-schema#\"" + "\n"); salidaOWL.write(" xmlns:owl=\"http://www.w3.org/2002/07/owl#\" " + "\n"); salidaOWL.write(" xmlns=\"" + uri + "#\"" + "\n"); salidaOWL.write(" xml:base=\"" + uri + "\">" + "\n"); salidaOWL.write(" <owl:Ontology rdf:about=\"\">" + "\n"); salidaOWL.write(" <owl:imports rdf:resource=\"" + uriOntologia + "\"/>" + "\n"); salidaOWL.write(" </owl:Ontology>" + "\n"); salidaOWL.flush(); salida.write(lineaSalida + "\n"); salida.flush(); incre = 1; } salidaOWL.write(" <j.0:" + nombreClase + " rdf:ID=\"" + sujeto.toUpperCase() + "\"/>" + "\n"); salidaOWL.write(" <owl:AllDifferent>" + "\n"); salidaOWL.write(" <owl:distinctMembers rdf:parseType=\"Collection\">" + "\n"); salidaOWL.write(" <" + nombreClase + " rdf:about=\"#" + sujeto.toUpperCase() + "\"/>" + "\n"); salidaOWL.write(" </owl:distinctMembers>" + "\n"); salidaOWL.write(" </owl:AllDifferent>" + "\n"); salidaOWL.flush(); bandera = false; } } } } } salidaOWL.write(" </rdf:RDF>" + "\n" + "\n"); salidaOWL.write("<!-- Creado por [html2ws] http://www.luis.criado.org -->" + "\n"); salidaOWL.flush(); } } mas = 1; } else { salida.write("</listaVistasSemanticas>\n"); salida.flush(); salida.close(); bw2.close(); fw2.close(); salidaOWL.close(); entradaFichero.close(); ent2.close(); ent1.close(); mas = -1; } } catch (Exception e) { mas = -2; salida.write("No se encuentra: " + fichOrigen + "\n"); salida.flush(); } return mas; } | 16,769 |
1 | public void deleteInstance(int instanceId) throws FidoDatabaseException, ObjectNotFoundException { try { Connection conn = null; Statement stmt = null; try { conn = fido.util.FidoDataSource.getConnection(); conn.setAutoCommit(false); stmt = conn.createStatement(); if (contains(stmt, instanceId) == false) throw new ObjectNotFoundException(instanceId); ObjectLinkTable objectLinkList = new ObjectLinkTable(); ObjectAttributeTable objectAttributeList = new ObjectAttributeTable(); objectLinkList.deleteObject(stmt, instanceId); objectAttributeList.deleteObject(stmt, instanceId); stmt.executeUpdate("delete from Objects where ObjectId = " + instanceId); conn.commit(); } catch (SQLException e) { if (conn != null) conn.rollback(); throw e; } finally { if (stmt != null) stmt.close(); if (conn != null) conn.close(); } } catch (SQLException e) { throw new FidoDatabaseException(e); } } | private void insertService(String table, int type) { Connection con = null; log.info(""); log.info("正在生成" + table + "的服务。。。。。。。"); try { con = DODataSource.getDefaultCon(); con.setAutoCommit(false); Statement stmt = con.createStatement(); Statement stmt2 = con.createStatement(); String serviceUid = UUIDHex.getInstance().generate(); DOBO bo = DOBO.getDOBOByName(StringUtil.getDotName(table)); List props = new ArrayList(); StringBuffer mainSql = null; String name = ""; String l10n = ""; String prefix = StringUtil.getDotName(table); Boolean isNew = null; switch(type) { case 1: name = prefix + ".insert"; l10n = name; props = bo.retrieveProperties(); mainSql = getInsertSql(props, table); isNew = Boolean.TRUE; break; case 2: name = prefix + ".update"; l10n = name; props = bo.retrieveProperties(); mainSql = this.getModiSql(props, table); isNew = Boolean.FALSE; break; case 3: DOBOProperty property = DOBOProperty.getDOBOPropertyByName(bo.getName(), "objuid"); System.out.println("BOBOBO::::::" + bo); System.out.println("Property::::::" + property); if (property == null) { return; } name = prefix + ".delete"; l10n = name; props.add(property); mainSql = new StringBuffer("delete from ").append(table).append(" where objuid = ?"); break; case 4: property = DOBOProperty.getDOBOPropertyByName(bo.getName(), "objuid"); if (property == null) { return; } name = prefix + ".browse"; l10n = name; props.add(property); mainSql = new StringBuffer("select * from ").append(table).append(" where objuid = ?"); break; case 5: name = prefix + ".list"; l10n = name; mainSql = new StringBuffer("select * from ").append(table); } this.setParaLinkBatch(props, stmt2, serviceUid, isNew); StringBuffer aSql = new StringBuffer("insert into DO_Service(objuid,l10n,name,bouid,mainSql) values(").append("'").append(serviceUid).append("','").append(l10n).append("','").append(name).append("','").append(this.getDOBOUid(table)).append("','").append(mainSql).append("')"); log.info("Servcice's Sql:" + aSql.toString()); stmt.executeUpdate(aSql.toString()); stmt2.executeBatch(); con.commit(); } catch (SQLException ex) { try { con.rollback(); } catch (SQLException ex2) { ex2.printStackTrace(); } ex.printStackTrace(); } finally { try { if (!con.isClosed()) { con.close(); } } catch (SQLException ex1) { ex1.printStackTrace(); } } } | 16,770 |
1 | 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 void compressFile(String filePath) { String outPut = filePath + ".zip"; try { FileInputStream in = new FileInputStream(filePath); GZIPOutputStream out = new GZIPOutputStream(new FileOutputStream(outPut)); byte[] buffer = new byte[4096]; int bytes_read; while ((bytes_read = in.read(buffer)) != -1) out.write(buffer, 0, bytes_read); in.close(); out.close(); } catch (Exception c) { c.printStackTrace(); } } | 16,771 |
1 | public static String generateMD5(String clear) { byte hash[] = null; try { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.update(clear.getBytes()); hash = md5.digest(); } catch (NoSuchAlgorithmException e) { } if (hash != null) { StringBuffer hexString = new StringBuffer(); for (int i = 0; i < hash.length; i++) { String tmp = Integer.toHexString(0xFF & hash[i]); if (tmp.length() == 1) { tmp = "0" + tmp; } hexString.append(tmp); } return hexString.toString(); } else { return null; } } | public RandomGUID() { MessageDigest md5 = null; try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { throw new RuntimeException(e.getClass().getName() + ": " + e.getMessage()); } try { long time = System.currentTimeMillis(); long rand = 0; rand = myRand.nextLong(); StringBuffer sb = new StringBuffer(); sb.append(s_id); sb.append(":"); sb.append(Long.toString(time)); sb.append(":"); sb.append(Long.toString(rand)); md5.update(sb.toString().getBytes()); byte[] array = md5.digest(); sb.setLength(0); 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) { throw new RuntimeException(e.getClass().getName() + ": " + e.getMessage()); } } | 16,772 |
0 | public Configuration(URL url) { InputStream in = null; try { load(in = url.openStream()); } catch (Exception e) { throw new RuntimeException("Could not load configuration from " + url, e); } finally { if (in != null) { try { in.close(); } catch (IOException ignore) { } } } } | 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!"); } | 16,773 |
1 | public static String calculate(String message, String algorithm, boolean base64) throws IllegalArgumentException { MessageDigest md = null; try { md = MessageDigest.getInstance(algorithm); } catch (NoSuchAlgorithmException e) { String error = "'" + algorithm + "' is not a supported MessageDigest algorithm."; LOG.error(error, e); throw new IllegalArgumentException(error); } md.update(message.getBytes()); byte[] digestData = md.digest(); String digest = null; if (base64) { Base64Encoder enc = new Base64Encoder(); enc.translate(digestData); digest = new String(enc.getCharArray()); } else { digest = byteArrayToHex(digestData); } return digest; } | public synchronized String decrypt(String plaintext) throws Exception { MessageDigest md = null; String strhash = new String((new BASE64Decoder()).decodeBuffer(plaintext)); System.out.println("strhash1122 " + strhash); try { md = MessageDigest.getInstance("MD5"); } catch (Exception e) { e.printStackTrace(); } byte raw[] = md.digest(); try { md.update(new String(raw).getBytes("UTF-8")); } catch (Exception e) { e.printStackTrace(); } System.out.println("plain text " + strhash); String strcode = new String(raw); System.out.println("strcode.." + strcode); return strcode; } | 16,774 |
0 | static String fetchURLComposeExternPackageList(String urlpath, String pkglisturlpath) { String link = pkglisturlpath + "package-list"; try { boolean relative = isRelativePath(urlpath); readPackageList((new URL(link)).openStream(), urlpath, relative); } catch (MalformedURLException exc) { return getText("doclet.MalformedURL", link); } catch (IOException exc) { return getText("doclet.URL_error", link); } return null; } | private void createProperty(String objectID, String value, String propertyID, Long userID) throws JspTagException { ClassProperty classProperty = new ClassProperty(new Long(propertyID)); String newValue = value; if (classProperty.getName().equals("Password")) { try { MessageDigest crypt = MessageDigest.getInstance("MD5"); crypt.update(value.getBytes()); byte digest[] = crypt.digest(); StringBuffer hexString = new StringBuffer(); for (int i = 0; i < digest.length; i++) { hexString.append(hexDigit(digest[i])); } newValue = hexString.toString(); crypt.reset(); } catch (NoSuchAlgorithmException e) { System.err.println("jspShop: Could not get instance of MD5 algorithm. Please fix this!" + e.getMessage()); e.printStackTrace(); throw new JspTagException("Error crypting password!: " + e.getMessage()); } } Properties properties = new Properties(new Long(objectID), userID); try { Property property = properties.create(new Long(propertyID), newValue); pageContext.setAttribute(getId(), property); } catch (CreateException e) { throw new JspTagException("Could not create PropertyValue, CreateException: " + e.getMessage()); } } | 16,775 |
0 | public static String getFileText(URL _url) { try { InputStream input = _url.openStream(); String content = IOUtils.toString(input); IOUtils.closeQuietly(input); return content; } catch (Exception err) { LOG.error(_url.toString(), err); return ""; } } | @Override public void execute(IAlert alert, IReport report, Rule rule, Row row) { try { URL url = new URL(getUrl()); URLConnection con = url.openConnection(); con.setConnectTimeout(getTimeout()); con.setDoOutput(true); OutputStream out = con.getOutputStream(); out.write(formatOutput(report, alert, rule, row).getBytes()); BufferedReader in = new BufferedReader(new InputStreamReader(con.getInputStream())); StringBuilder input = new StringBuilder(); String line = null; while ((line = in.readLine()) != null) { input.append(line); input.append('\n'); } in.close(); this.lastResult = input.toString(); } catch (Throwable e) { logError("Error sending alert", e); if (!isHeadless()) { alert.setEnabled(false); JOptionPane.showMessageDialog(null, "Can't send alert " + e + "\n" + alert.getName() + " alert disabled.", "Action Error", JOptionPane.ERROR_MESSAGE); } } } | 16,776 |
1 | 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; } | @Override public void setDocumentSpace(DocumentSpace space) { for (Document doc : space) { File result = new File(parent, doc.getName()); if (doc instanceof XMLDOMDocument) { new PlainXMLDocumentWriter(result).writeDocument(doc); } else if (doc instanceof BinaryDocument) { BinaryDocument bin = (BinaryDocument) doc; try { IOUtils.copy(bin.getContent().getInputStream(), new FileOutputStream(result)); } catch (IOException e) { throw ManagedIOException.manage(e); } } else { System.err.println("Unkown Document type"); } } } | 16,777 |
1 | public void createZip(File zipFileName, Vector<File> selected) { try { byte[] buffer = new byte[4096]; ZipOutputStream out = new ZipOutputStream(new BufferedOutputStream(new FileOutputStream(zipFileName), 8096)); out.setLevel(Deflater.BEST_COMPRESSION); out.setMethod(ZipOutputStream.DEFLATED); for (int i = 0; i < selected.size(); i++) { FileInputStream in = new FileInputStream(selected.get(i)); String file = selected.get(i).getPath(); if (file.indexOf("\\") != -1) file = file.substring(file.lastIndexOf(fs) + 1, file.length()); ZipEntry ze = new ZipEntry(file); out.putNextEntry(ze); int len; while ((len = in.read(buffer)) > 0) out.write(buffer, 0, len); out.closeEntry(); in.close(); selected.get(i).delete(); } out.close(); } catch (IllegalArgumentException iae) { iae.printStackTrace(); } catch (FileNotFoundException fnfe) { fnfe.printStackTrace(); } catch (IOException ioe) { ioe.printStackTrace(); } } | public 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; } | 16,778 |
0 | private boolean authenticate(String reply) { String user = reply.substring(0, reply.indexOf(" ")); String resp = reply.substring(reply.indexOf(" ") + 1); if (!module.users.contains(user)) { error = "so such user " + user; return false; } try { LineNumberReader secrets = new LineNumberReader(new FileReader(module.secretsFile)); String line; while ((line = secrets.readLine()) != null) { if (line.startsWith(user + ":")) { MessageDigest md4 = MessageDigest.getInstance("BrokenMD4"); md4.update(new byte[4]); md4.update(line.substring(line.indexOf(":") + 1).getBytes("US-ASCII")); md4.update(challenge.getBytes("US-ASCII")); String hash = Util.base64(md4.digest()); if (hash.equals(resp)) { secrets.close(); return true; } } } secrets.close(); } catch (Exception e) { logger.fatal(e.toString()); error = "server configuration error"; return false; } error = "authentication failure for module " + module.name; return false; } | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | 16,779 |
0 | private static byte[] get256RandomBits() throws IOException { URL url = null; try { url = new URL(SRV_URL); } catch (MalformedURLException e) { e.printStackTrace(); } HttpsURLConnection hu = (HttpsURLConnection) url.openConnection(); hu.setConnectTimeout(2500); InputStream is = hu.getInputStream(); byte[] content = new byte[is.available()]; is.read(content); is.close(); hu.disconnect(); byte[] randomBits = new byte[32]; String line = new String(content); Matcher m = DETAIL.matcher(line); if (m.find()) { for (int i = 0; i < 32; i++) randomBits[i] = (byte) (Integer.parseInt(m.group(1).substring(i * 2, i * 2 + 2), 16) & 0xFF); } return randomBits; } | private void fileUpload() throws IOException { HttpClient httpclient = new DefaultHttpClient(); HttpPost httppost = new HttpPost(postURL); MultipartEntity mpEntity = new MultipartEntity(HttpMultipartMode.BROWSER_COMPATIBLE); mpEntity.addPart("Filename", new StringBody(file.getName())); mpEntity.addPart("Filedata", new MonitoredFileBody(file, uploadProgress)); httppost.setEntity(mpEntity); NULogger.getLogger().log(Level.INFO, "executing request {0}", httppost.getRequestLine()); NULogger.getLogger().info("Now uploading your file into sharesend.com"); status = UploadStatus.UPLOADING; HttpResponse response = httpclient.execute(httppost); status = UploadStatus.GETTINGLINK; HttpEntity resEntity = response.getEntity(); NULogger.getLogger().info(response.getStatusLine().toString()); if (resEntity != null) { uploadresponse = EntityUtils.toString(resEntity); } NULogger.getLogger().log(Level.INFO, "Upload Response : {0}", uploadresponse); NULogger.getLogger().log(Level.INFO, "Download Link : http://sharesend.com/{0}", uploadresponse); downloadlink = "http://sharesend.com/" + uploadresponse; downURL = downloadlink; httpclient.getConnectionManager().shutdown(); uploadFinished(); } | 16,780 |
1 | @Override public void doMove(File from, File to) throws IOException { int res = showConfirmation("File will be moved in p4, are you sure to move ", from.getAbsolutePath()); if (res == JOptionPane.NO_OPTION) { return; } Status status = fileStatusProvider.getFileStatusForce(from); if (status == null) { return; } if (status.isLocal()) { logWarning(this, from.getName() + " is not revisioned. Should not be deleted by p4nb"); return; } to.getParentFile().mkdirs(); BufferedInputStream in = new BufferedInputStream(new FileInputStream(from)); BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(to)); byte[] buffer = new byte[8192]; int read = 0; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } in.close(); out.flush(); out.close(); if (status != Status.NONE) { revert(from); } if (status != Status.ADD) { delete(from); } else { from.delete(); } add(to); } | private static File createTempWebXml(Class portletClass, File portletDir, String appName, String portletName) throws IOException, FileNotFoundException { File pathToWebInf = new File(portletDir, "WEB-INF"); File tempWebXml = File.createTempFile("web", ".xml", pathToWebInf); tempWebXml.deleteOnExit(); OutputStream webOutputStream = new FileOutputStream(tempWebXml); PortletUnitWebXmlStream streamSource = WEB_XML_STREAM_FACTORY; IOUtils.copy(streamSource.createStream(portletClass, appName, portletName), webOutputStream); webOutputStream.close(); return tempWebXml; } | 16,781 |
1 | public String getTemplateString(String templateFilename) { InputStream is = servletContext.getResourceAsStream("/resources/" + templateFilename); StringWriter writer = new StringWriter(); try { IOUtils.copy(is, writer); } catch (IOException e) { e.printStackTrace(); } return writer.toString(); } | public static void main(String[] args) throws Exception { DES des = new DES(); StreamBlockReader reader = new StreamBlockReader(new FileInputStream("D:\\test.txt")); StreamBlockWriter writer = new StreamBlockWriter(new FileOutputStream("D:\\test1.txt")); SingleKey key = new SingleKey(new Block(64), ""); key = new SingleKey(new Block("1111111100000000111111110000000011111111000000001111111100000000"), ""); Mode mode = new ECBDESMode(des); des.encrypt(reader, writer, key, mode); } | 16,782 |
0 | public static void copy(Object arg1, Object arg2) { Writer writer = null; Reader reader = null; InputStream inStream = null; OutputStream outStream = null; try { if (arg2 instanceof Writer) { writer = (Writer) arg2; if (arg1 instanceof Reader) { reader = (Reader) arg1; copy(reader, writer); } else if (arg1 instanceof String) { reader = new FileReader(new File((String) arg1)); copy(reader, writer); } else if (arg1 instanceof File) { reader = new FileReader((File) arg1); copy(reader, writer); } else if (arg1 instanceof URL) { copy(((URL) arg1).openStream(), writer); } else if (arg1 instanceof InputStream) { reader = new InputStreamReader((InputStream) arg1); copy(reader, writer); } else if (arg1 instanceof RandomAccessFile) { copy((RandomAccessFile) arg1, writer); } else { throw new TypeError("Invalid first argument to copy()"); } } else if (arg2 instanceof OutputStream) { outStream = (OutputStream) arg2; if (arg1 instanceof Reader) { copy((Reader) arg1, new OutputStreamWriter(outStream)); } else if (arg1 instanceof String) { inStream = new FileInputStream(new File((String) arg1)); copy(inStream, outStream); } else if (arg1 instanceof File) { inStream = new FileInputStream((File) arg1); copy(inStream, outStream); } else if (arg1 instanceof URL) { copy(((URL) arg1).openStream(), outStream); } else if (arg1 instanceof InputStream) { copy((InputStream) arg1, outStream); } else if (arg1 instanceof RandomAccessFile) { copy((RandomAccessFile) arg1, outStream); } else { throw new TypeError("Invalid first argument to copy()"); } } else if (arg2 instanceof RandomAccessFile) { RandomAccessFile out = (RandomAccessFile) arg2; if (arg1 instanceof Reader) { copy((Reader) arg1, out); } else if (arg1 instanceof String) { inStream = new FileInputStream(new File((String) arg1)); copy(inStream, out); } else if (arg1 instanceof File) { inStream = new FileInputStream((File) arg1); copy(inStream, out); } else if (arg1 instanceof URL) { copy(((URL) arg1).openStream(), out); } else if (arg1 instanceof InputStream) { copy((InputStream) arg1, out); } else if (arg1 instanceof RandomAccessFile) { copy((RandomAccessFile) arg1, out); } else { throw new TypeError("Invalid first argument to copy()"); } } else if (arg2 instanceof File || arg2 instanceof String) { File outFile = null; if (arg2 instanceof File) { outFile = (File) arg2; } else { outFile = new File((String) arg2); } outStream = new FileOutputStream(outFile); if (arg1 instanceof Reader) { copy((Reader) arg1, new OutputStreamWriter(outStream)); } else if (arg1 instanceof String) { inStream = new FileInputStream(new File((String) arg1)); copy(inStream, outStream); } else if (arg1 instanceof File) { inStream = new FileInputStream((File) arg1); copy(inStream, outStream); } else if (arg1 instanceof URL) { copy(((URL) arg1).openStream(), outStream); } else if (arg1 instanceof InputStream) { copy((InputStream) arg1, outStream); } else if (arg1 instanceof RandomAccessFile) { copy((RandomAccessFile) arg1, outStream); } else { throw new TypeError("Invalid first argument to copy()"); } } else { throw new TypeError("Invalid second argument to copy()"); } } catch (IOException e) { throw new IOError(e.getMessage(), e); } } | private static Long statusSWGCraftTime() { long current = System.currentTimeMillis() / 1000L; if (current < (previousStatusCheck + SWGCraft.STATUS_CHECK_DELAY)) return previousStatusTime; URL url = null; try { synchronized (previousStatusTime) { if (current >= previousStatusCheck + SWGCraft.STATUS_CHECK_DELAY) { url = SWGCraft.getStatusTextURL(); String statusTime = ZReader.read(url.openStream()); previousStatusTime = Long.valueOf(statusTime); previousStatusCheck = current; } return previousStatusTime; } } catch (UnknownHostException e) { SWGCraft.showUnknownHostDialog(url, e); } catch (Throwable e) { SWGAide.printDebug("cmgr", 1, "SWGResourceManager:statusSWGCraftTime:", e.toString()); } return Long.valueOf(0); } | 16,783 |
1 | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | public static boolean copy(File from, File to, Override override) throws IOException { FileInputStream in = null; FileOutputStream out = null; FileChannel srcChannel = null; FileChannel destChannel = null; if (override == null) override = Override.NEWER; switch(override) { case NEVER: if (to.isFile()) return false; break; case NEWER: if (to.isFile() && (from.lastModified() - LASTMODIFIED_DIFF_MILLIS) < to.lastModified()) return false; break; } to.getParentFile().mkdirs(); try { in = new FileInputStream(from); out = new FileOutputStream(to); srcChannel = in.getChannel(); destChannel = out.getChannel(); long position = 0L; long count = srcChannel.size(); while (position < count) { long chunk = Math.min(MAX_IO_CHUNK_SIZE, count - position); position += destChannel.transferFrom(srcChannel, position, chunk); } to.setLastModified(from.lastModified()); return true; } finally { CommonUtils.close(srcChannel); CommonUtils.close(destChannel); CommonUtils.close(out); CommonUtils.close(in); } } | 16,784 |
0 | public void run(IAction action) { int style = PlatformUI.getWorkbench().getActiveWorkbenchWindow().getShell().getStyle(); Shell shell = new Shell((style & SWT.MIRRORED) != 0 ? SWT.RIGHT_TO_LEFT : SWT.NONE); GraphicalViewer viewer = new ScrollingGraphicalViewer(); viewer.createControl(shell); viewer.setEditDomain(new DefaultEditDomain(null)); viewer.setRootEditPart(new ScalableFreeformRootEditPart()); viewer.setEditPartFactory(new ProjectEditPartFactory()); viewer.setContents(getContents()); viewer.flush(); int printMode = new PrintModeDialog(shell).open(); if (printMode == -1) return; PrintDialog dialog = new PrintDialog(shell, SWT.NULL); PrinterData data = dialog.open(); if (data != null) { PrintGraphicalViewerOperation op = new PrintGraphicalViewerOperation(new Printer(data), viewer); op.setPrintMode(printMode); op.run(selectedFile.getName()); } } | public static void compressFile(File f) throws IOException { File target = new File(f.toString() + ".gz"); System.out.print("Compressing: " + f.getName() + ".. "); long initialSize = f.length(); FileInputStream fis = new FileInputStream(f); GZIPOutputStream out = new GZIPOutputStream(new FileOutputStream(target)); byte[] buf = new byte[1024]; int read; while ((read = fis.read(buf)) != -1) { out.write(buf, 0, read); } System.out.println("Done."); fis.close(); out.close(); long endSize = target.length(); System.out.println("Initial size: " + initialSize + "; Compressed size: " + endSize); } | 16,785 |
0 | public static byte[] readUrl(URL url) { BufferedInputStream in = null; try { class Part { byte[] partData; int len; } in = new BufferedInputStream(url.openStream()); LinkedList<Part> parts = new LinkedList<Part>(); int len = 1; while (len > 0) { byte[] data = new byte[1024]; len = in.read(data); if (len > 0) { Part part = new Part(); part.partData = data; part.len = len; parts.add(part); } } int length = 0; for (Part part : parts) length += part.len; byte[] result = new byte[length]; int pos = 0; for (Part part : parts) { System.arraycopy(part.partData, 0, result, pos, part.len); pos += part.len; } return result; } catch (IOException e) { return null; } finally { if (in != null) { try { in.close(); } catch (IOException e) { } } } } | private void loadDateFormats() { String fileToLocate = "/" + FILENAME_DATE_FMT; URL url = getClass().getClassLoader().getResource(fileToLocate); if (url == null) { return; } List<String> lines; try { lines = IOUtils.readLines(url.openStream()); } catch (IOException e) { throw new ConfigurationException("Problem loading file " + fileToLocate, e); } for (String line : lines) { if (line.startsWith("#") || StringUtils.isBlank(line)) { continue; } String[] parts = StringUtils.split(line, "="); addFormat(parts[0], new SimpleDateFormat(parts[1])); } } | 16,786 |
0 | public void fileUpload() throws Exception { DefaultHttpClient httpclient = new DefaultHttpClient(); HttpPost httppost = new HttpPost(postURL); MultipartEntity reqEntity = new MultipartEntity(HttpMultipartMode.BROWSER_COMPATIBLE); reqEntity.addPart("fff", new MonitoredFileBody(file, uploadProgress)); httppost.setEntity(reqEntity); NULogger.getLogger().info("Now uploading your file into 2shared.com. Please wait......................"); status = UploadStatus.UPLOADING; HttpResponse response = httpclient.execute(httppost); status = UploadStatus.GETTINGLINK; HttpEntity resEntity = response.getEntity(); if (resEntity != null) { String page = EntityUtils.toString(resEntity); NULogger.getLogger().log(Level.INFO, "PAGE :{0}", page); } } | public static void main(String argv[]) { System.out.println("Starting URL tests"); System.out.println("Test 1: Simple URL test"); try { URL url = new URL("http", "www.fsf.org", 80, "/"); if (!url.getProtocol().equals("http") || !url.getHost().equals("www.fsf.org") || url.getPort() != 80 || !url.getFile().equals("/")) System.out.println("FAILED: Simple URL test"); System.out.println("URL is: " + url.toString()); URLConnection uc = url.openConnection(); if (uc instanceof HttpURLConnection) System.out.println("Got the expected connection type"); HttpURLConnection hc = (HttpURLConnection) uc; hc.connect(); System.out.flush(); System.out.println("Dumping response headers"); for (int i = 0; ; i++) { String key = hc.getHeaderFieldKey(i); if (key == null) break; System.out.println(key + ": " + hc.getHeaderField(i)); } System.out.flush(); System.out.println("Dumping contents"); BufferedReader br = new BufferedReader(new InputStreamReader(hc.getInputStream())); for (String str = br.readLine(); str != null; str = br.readLine()) { System.out.println(str); } System.out.flush(); hc.disconnect(); System.out.println("Content Type: " + hc.getContentType()); System.out.println("Content Encoding: " + hc.getContentEncoding()); System.out.println("Content Length: " + hc.getContentLength()); System.out.println("Date: " + hc.getDate()); System.out.println("Expiration: " + hc.getExpiration()); System.out.println("Last Modified: " + hc.getLastModified()); System.out.println("PASSED: Simple URL test"); } catch (IOException e) { System.out.println("FAILED: Simple URL test: " + e); } System.out.println("Test 2: URL parsing test"); try { URL url = new URL("http://www.urbanophile.com/arenn/trans/trans.html#mis"); if (!url.toString().equals("http://www.urbanophile.com/arenn/trans/trans.html#mis")) System.out.println("FAILED: Parse URL test: " + url.toString()); else { System.out.println("Parsed ok: " + url.toString()); url = new URL("http://www.foo.com:8080/#"); if (!url.toString().equals("http://www.foo.com:8080/#")) System.out.println("FAILED: Parse URL test: " + url.toString()); else { System.out.println("Parsed ok: " + url.toString()); url = new URL("http://www.bar.com/test:file/"); if (!url.toString().equals("http://www.bar.com/test:file/")) System.out.println("FAILED: Parse URL test: " + url.toString()); else { System.out.println("Parsed ok: " + url.toString()); url = new URL("http://www.gnu.org"); if (!url.toString().equals("http://www.gnu.org/")) System.out.println("FAILED: Parse URL test: " + url.toString()); else { System.out.println("Parsed ok: " + url.toString()); url = new URL("HTTP://www.fsf.org/"); if (!url.toString().equals("http://www.fsf.org/")) System.out.println("FAILED: Parse URL test: " + url.toString()); else { System.out.println("Parsed ok: " + url.toString()); System.out.println("PASSED: URL parse test"); } } } } } } catch (IOException e) { System.out.println("FAILED: URL parsing test: " + e); } System.out.println("Test 3: getContent test"); try { URL url = new URL("http://localhost/~arenn/services.txt"); Object obj = url.getContent(); System.out.println("Object type is: " + obj.getClass().getName()); if (obj instanceof InputStream) { System.out.println("Got InputStream, so dumping contents"); BufferedReader br = new BufferedReader(new InputStreamReader((InputStream) obj)); for (String str = br.readLine(); str != null; str = br.readLine()) System.out.println(str); br.close(); } else { System.out.println("FAILED: Object is not an InputStream"); } System.out.println("PASSED: getContent test"); } catch (IOException e) { System.out.println("FAILED: getContent test: " + e); } System.out.println("URL test complete"); } | 16,787 |
1 | public static byte[] computeMD5(String s) { try { MessageDigest md = MessageDigest.getInstance("MD5"); md.reset(); md.update(s.getBytes()); return md.digest(); } catch (NoSuchAlgorithmException ex) { throw new RuntimeException(ex); } } | public static String digest(String value, String algorithm) throws Exception { MessageDigest algo = MessageDigest.getInstance(algorithm); algo.reset(); algo.update(value.getBytes("UTF-8")); return StringTool.byteArrayToString(algo.digest()); } | 16,788 |
0 | static boolean writeProperties(Map<String, String> customProps, File destination) throws IOException { synchronized (PropertiesIO.class) { L.info(Msg.msg("PropertiesIO.writeProperties.start")); File tempFile = null; BufferedInputStream existingCfgInStream = null; FileInputStream in = null; FileOutputStream out = null; PrintStream ps = null; FileChannel fromChannel = null, toChannel = null; String line = null; try { existingCfgInStream = new BufferedInputStream(destination.exists() ? new FileInputStream(destination) : defaultPropertiesStream()); tempFile = File.createTempFile("properties-", ".tmp", null); ps = new PrintStream(tempFile); while ((line = Utils.readLine(existingCfgInStream)) != null) { String lineReady2write = setupLine(line, customProps); ps.println(lineReady2write); } destination.getParentFile().mkdirs(); in = new FileInputStream(tempFile); out = new FileOutputStream(destination, false); fromChannel = in.getChannel(); toChannel = out.getChannel(); fromChannel.transferTo(0, fromChannel.size(), toChannel); L.info(Msg.msg("PropertiesIO.writeProperties.done").replace("#file#", destination.getAbsolutePath())); return true; } finally { if (existingCfgInStream != null) existingCfgInStream.close(); if (ps != null) ps.close(); if (fromChannel != null) fromChannel.close(); if (toChannel != null) toChannel.close(); if (out != null) out.close(); if (in != null) in.close(); if (tempFile != null && tempFile.exists()) tempFile.delete(); } } } | public static final String getContent(String address) { String content = ""; OutputStream out = null; URLConnection conn = null; InputStream in = null; try { URL url = new URL(address); out = new ByteArrayOutputStream(); conn = url.openConnection(); in = conn.getInputStream(); byte[] buffer = new byte[1024]; int numRead; while ((numRead = in.read(buffer)) != -1) { out.write(buffer, 0, numRead); } content = out.toString(); } catch (Exception exception) { exception.printStackTrace(); } finally { try { if (in != null) { in.close(); } if (out != null) { out.close(); } } catch (IOException ioe) { } } return content; } | 16,789 |
0 | public Manifest(URL url) throws IOException { if (!url.getProtocol().equals("jar")) { url = new URL("jar:" + url.toExternalForm() + "!/"); } JarURLConnection uc = (JarURLConnection) url.openConnection(); setManifest(uc.getManifest()); } | @Test public void usingStream() throws IOException, NameNotFoundException { URL url = new URL("ftp://ftp.ebi.ac.uk/pub/databases/interpro/entry.list"); InterproNameHandler handler = new InterproNameHandler(url.openStream()); String interproName = handler.getNameById("IPR008255"); assertNotNull(interproName); assertEquals("Pyridine nucleotide-disulphide oxidoreductase, class-II, active site", interproName); assertEquals(null, handler.getNameById("Active_site")); } | 16,790 |
1 | private void displayDiffResults() throws IOException { File outFile = File.createTempFile("diff", ".htm"); outFile.deleteOnExit(); FileOutputStream outStream = new FileOutputStream(outFile); BufferedWriter out = new BufferedWriter(new OutputStreamWriter(outStream)); out.write("<html><head><title>LOC Differences</title>\n" + SCRIPT + "</head>\n" + "<body bgcolor='#ffffff'>\n" + "<div onMouseOver=\"window.defaultStatus='Metrics'\">\n"); if (addedTable.length() > 0) { out.write("<table border><tr><th>Files Added:</th>" + "<th>Add</th><th>Type</th></tr>"); out.write(addedTable.toString()); out.write("</table><br><br>"); } if (modifiedTable.length() > 0) { out.write("<table border><tr><th>Files Modified:</th>" + "<th>Base</th><th>Del</th><th>Mod</th><th>Add</th>" + "<th>Total</th><th>Type</th></tr>"); out.write(modifiedTable.toString()); out.write("</table><br><br>"); } if (deletedTable.length() > 0) { out.write("<table border><tr><th>Files Deleted:</th>" + "<th>Del</th><th>Type</th></tr>"); out.write(deletedTable.toString()); out.write("</table><br><br>"); } out.write("<table name=METRICS BORDER>\n"); if (modifiedTable.length() > 0 || deletedTable.length() > 0) { out.write("<tr><td>Base: </td><td>"); out.write(Long.toString(base)); out.write("</td></tr>\n<tr><td>Deleted: </td><td>"); out.write(Long.toString(deleted)); out.write("</td></tr>\n<tr><td>Modified: </td><td>"); out.write(Long.toString(modified)); out.write("</td></tr>\n<tr><td>Added: </td><td>"); out.write(Long.toString(added)); out.write("</td></tr>\n<tr><td>New & Changed: </td><td>"); out.write(Long.toString(added + modified)); out.write("</td></tr>\n"); } out.write("<tr><td>Total: </td><td>"); out.write(Long.toString(total)); out.write("</td></tr>\n</table></div>"); redlinesOut.close(); out.flush(); InputStream redlines = new FileInputStream(redlinesTempFile); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = redlines.read(buffer)) != -1) outStream.write(buffer, 0, bytesRead); outStream.write("</BODY></HTML>".getBytes()); outStream.close(); Browser.launch(outFile.toURL().toString()); } | void execute(HttpClient client, MonitoredService svc) { try { URI uri = getURI(svc); PageSequenceHttpMethod method = getMethod(); method.setURI(uri); if (getVirtualHost() != null) { method.getParams().setVirtualHost(getVirtualHost()); } if (getUserAgent() != null) { method.addRequestHeader("User-Agent", getUserAgent()); } if (m_parms.length > 0) { method.setParameters(m_parms); } if (m_page.getUserInfo() != null) { String userInfo = m_page.getUserInfo(); String[] streetCred = userInfo.split(":", 2); if (streetCred.length == 2) { client.getState().setCredentials(new AuthScope(AuthScope.ANY), new UsernamePasswordCredentials(streetCred[0], streetCred[1])); method.setDoAuthentication(true); } } int code = client.executeMethod(method); if (!getRange().contains(code)) { throw new PageSequenceMonitorException("response code out of range for uri:" + uri + ". Expected " + getRange() + " but received " + code); } InputStream inputStream = method.getResponseBodyAsStream(); ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); try { IOUtils.copy(inputStream, outputStream); } finally { IOUtils.closeQuietly(inputStream); IOUtils.closeQuietly(outputStream); } String responseString = outputStream.toString(); if (getFailurePattern() != null) { Matcher matcher = getFailurePattern().matcher(responseString); if (matcher.find()) { throw new PageSequenceMonitorException(getResolvedFailureMessage(matcher)); } } if (getSuccessPattern() != null) { Matcher matcher = getSuccessPattern().matcher(responseString); if (!matcher.find()) { throw new PageSequenceMonitorException("failed to find '" + getSuccessPattern() + "' in page content at " + uri); } } } catch (URIException e) { throw new IllegalArgumentException("unable to construct URL for page: " + e, e); } catch (HttpException e) { throw new PageSequenceMonitorException("HTTP Error " + e, e); } catch (IOException e) { throw new PageSequenceMonitorException("I/O Error " + e, e); } } | 16,791 |
0 | public static String encodePassword(String password) { try { MessageDigest messageDiegest = MessageDigest.getInstance("SHA-1"); messageDiegest.update(password.getBytes("UTF-8")); return Base64.encodeToString(messageDiegest.digest(), false); } catch (NoSuchAlgorithmException e) { log.error("Exception while encoding password"); throw new Error(e); } catch (UnsupportedEncodingException e) { log.error("Exception while encoding password"); throw new Error(e); } } | @Test public void testExactCopySize() throws IOException { final int size = Byte.SIZE + RANDOMIZER.nextInt(TEST_DATA.length - Long.SIZE); final InputStream in = new ByteArrayInputStream(TEST_DATA); final ByteArrayOutputStream out = new ByteArrayOutputStream(size); final int cpySize = ExtraIOUtils.copy(in, out, size); assertEquals("Mismatched copy size", size, cpySize); final byte[] subArray = ArrayUtils.subarray(TEST_DATA, 0, size), outArray = out.toByteArray(); assertArrayEquals("Mismatched data", subArray, outArray); } | 16,792 |
0 | private String encryptUserPassword(int userId, String password) { password = password.trim(); if (password.length() == 0) { return ""; } else { MessageDigest md; try { md = MessageDigest.getInstance("SHA"); } catch (NoSuchAlgorithmException ex) { throw new BoardRuntimeException(ex); } md.update(String.valueOf(userId).getBytes()); md.update(password.getBytes()); byte b[] = md.digest(); StringBuffer sb = new StringBuffer(1 + b.length * 2); for (int i = 0; i < b.length; i++) { int ii = b[i]; if (ii < 0) { ii = 256 + ii; } sb.append(getHexadecimalValue2(ii)); } return sb.toString(); } } | public byte[] downloadAttachmentContent(Attachment issueAttachment) throws IOException { byte[] result = null; URL url = new URL(issueAttachment.getContentURL()); BufferedReader inputReader = null; try { inputReader = new BufferedReader(new InputStreamReader(url.openStream())); StringBuilder contentBuilder = new StringBuilder(); String line; while ((line = inputReader.readLine()) != null) { contentBuilder.append(line); } result = contentBuilder.toString().getBytes(); } finally { if (inputReader != null) { inputReader.close(); } } return result; } | 16,793 |
1 | public static File copyToLibDirectory(final File file) throws FileNotFoundException, IOException { if (file == null || !file.exists()) { throw new FileNotFoundException(); } File directory = new File("lib/"); File dest = new File(directory, file.getName()); File parent = dest.getParentFile(); while (parent != null && !parent.equals(directory)) { parent = parent.getParentFile(); } if (parent.equals(directory)) { return file; } FileChannel in = null; FileChannel out = null; try { in = new FileInputStream(file).getChannel(); out = new FileOutputStream(dest).getChannel(); in.transferTo(0, in.size(), out); } finally { if (in != null) { try { in.close(); } catch (IOException e) { } } if (out != null) { try { out.close(); } catch (IOException e) { } } } return dest; } | public static void main(String[] args) throws IOException { ReadableByteChannel in = Channels.newChannel((new FileInputStream("/home/sannies/suckerpunch-distantplanet_h1080p/suckerpunch-distantplanet_h1080p.mov"))); Movie movie = MovieCreator.build(in); in.close(); List<Track> tracks = movie.getTracks(); movie.setTracks(new LinkedList<Track>()); double startTime = 35.000; double endTime = 145.000; boolean timeCorrected = false; for (Track track : tracks) { if (track.getSyncSamples() != null && track.getSyncSamples().length > 0) { if (timeCorrected) { throw new RuntimeException("The startTime has already been corrected by another track with SyncSample. Not Supported."); } startTime = correctTimeToNextSyncSample(track, startTime); endTime = correctTimeToNextSyncSample(track, endTime); timeCorrected = true; } } for (Track track : tracks) { long currentSample = 0; double currentTime = 0; long startSample = -1; long endSample = -1; for (int i = 0; i < track.getDecodingTimeEntries().size(); i++) { TimeToSampleBox.Entry entry = track.getDecodingTimeEntries().get(i); for (int j = 0; j < entry.getCount(); j++) { if (currentTime <= startTime) { startSample = currentSample; } if (currentTime <= endTime) { endSample = currentSample; } else { break; } currentTime += (double) entry.getDelta() / (double) track.getTrackMetaData().getTimescale(); currentSample++; } } movie.addTrack(new CroppedTrack(track, startSample, endSample)); } long start1 = System.currentTimeMillis(); IsoFile out = new DefaultMp4Builder().build(movie); long start2 = System.currentTimeMillis(); FileOutputStream fos = new FileOutputStream(String.format("output-%f-%f.mp4", startTime, endTime)); FileChannel fc = fos.getChannel(); out.getBox(fc); fc.close(); fos.close(); long start3 = System.currentTimeMillis(); System.err.println("Building IsoFile took : " + (start2 - start1) + "ms"); System.err.println("Writing IsoFile took : " + (start3 - start2) + "ms"); System.err.println("Writing IsoFile speed : " + (new File(String.format("output-%f-%f.mp4", startTime, endTime)).length() / (start3 - start2) / 1000) + "MB/s"); } | 16,794 |
0 | public static String md5(String word) { MessageDigest alg = null; try { alg = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException ex) { Logger.getLogger(ServletUtils.class.getName()).log(Level.SEVERE, null, ex); } alg.reset(); alg.update(word.getBytes()); byte[] digest = alg.digest(); StringBuilder hashedWord = new StringBuilder(); String hx; for (int i = 0; i < digest.length; i++) { hx = Integer.toHexString(0xFF & digest[i]); if (hx.length() == 1) { hx = "0" + hx; } hashedWord.append(hx); } return hashedWord.toString(); } | public static File copyFile(File file, String dirName) { File destDir = new File(dirName); if (!destDir.exists() || !destDir.isDirectory()) { destDir.mkdirs(); } File src = file; File dest = new File(dirName, src.getName()); try { if (!dest.exists()) { dest.createNewFile(); } FileChannel source = new FileInputStream(src).getChannel(); FileChannel destination = new FileOutputStream(dest).getChannel(); destination.transferFrom(source, 0, source.size()); source.close(); destination.close(); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } return dest; } | 16,795 |
0 | 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 String addEqError(EquivalencyException e, int namespaceId) throws SQLException { List l = Arrays.asList(e.getListOfEqErrors()); int size = l.size(); String sql = getClassifyDAO().getStatement(TABLE_KEY, "ADD_CLASSIFY_EQ_ERROR"); PreparedStatement ps = null; conn.setAutoCommit(false); try { deleteCycleError(namespaceId); deleteEqError(namespaceId); long conceptGID1 = -1; long conceptGID2 = -1; ps = conn.prepareStatement(sql); for (int i = 0; i < l.size(); i++) { EqError error = (EqError) l.get(i); ConceptRef ref1 = error.getConcept1(); ConceptRef ref2 = error.getConcept2(); conceptGID1 = getConceptGID(ref1, namespaceId); conceptGID2 = getConceptGID(ref2, namespaceId); ps.setLong(1, conceptGID1); ps.setLong(2, conceptGID2); ps.setInt(3, namespaceId); int result = ps.executeUpdate(); if (result == 0) { throw new SQLException("unable to add eq error: " + sql); } } conn.commit(); return "EquivalencyException: Concept: " + conceptGID1 + " namespaceId: " + namespaceId + " conceptGID2: " + conceptGID2 + ((size > 1) ? "...... more" : ""); } catch (SQLException sqle) { conn.rollback(); throw sqle; } catch (Exception ex) { conn.rollback(); throw toSQLException(ex, "cannot add eq errors"); } finally { conn.setAutoCommit(true); if (ps != null) { ps.close(); } } } | 16,796 |
1 | 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 void importDB(String input, String output) { try { Class.forName("org.sqlite.JDBC"); String fileName = output + File.separator + G.databaseName; File dataBase = new File(fileName); if (!dataBase.exists()) { G.conn = DriverManager.getConnection("jdbc:sqlite:" + fileName); createTablesDB(); } else G.conn = DriverManager.getConnection("jdbc:sqlite:" + fileName); long tiempoInicio = System.currentTimeMillis(); String directoryPath = input + File.separator; File myDirectory = new File(directoryPath); String[] list = myDirectory.list(); File fileXML = new File(input + File.separator + G.imagesName); if (!fileXML.exists()) { JOptionPane.showMessageDialog(null, "No se encuentra el fichero XML", "Error", JOptionPane.ERROR_MESSAGE); } else { SAXBuilder builder = new SAXBuilder(false); Document docXML = builder.build(fileXML); Element root = docXML.getRootElement(); List images = root.getChildren("image"); Iterator j = images.iterator(); List<Element> globalLanguages = root.getChild("languages").getChildren("language"); Iterator<Element> langsI = globalLanguages.iterator(); HashMap<String, Integer> languageIDs = new HashMap<String, Integer>(); HashMap<String, Integer> typeIDs = new HashMap<String, Integer>(); Element e; int i = 0; int contTypes = 0; int contImages = 0; while (langsI.hasNext()) { e = langsI.next(); languageIDs.put(e.getText(), i); PreparedStatement stmt = G.conn.prepareStatement("INSERT OR IGNORE INTO language (id,name) VALUES (?,?)"); stmt.setInt(1, i); stmt.setString(2, e.getText()); stmt.executeUpdate(); stmt.close(); i++; } G.conn.setAutoCommit(false); while (j.hasNext()) { Element image = (Element) j.next(); String id = image.getAttributeValue("id"); List languages = image.getChildren("language"); Iterator k = languages.iterator(); if (exists(list, id)) { String pathSrc = directoryPath.concat(id); String pathDst = output + File.separator + id.substring(0, 1).toUpperCase() + File.separator; String folder = output + File.separator + id.substring(0, 1).toUpperCase(); String pathDstTmp = pathDst.concat(id); String idTmp = id; File testFile = new File(pathDstTmp); int cont = 1; while (testFile.exists()) { idTmp = id.substring(0, id.lastIndexOf('.')) + '_' + cont + id.substring(id.lastIndexOf('.'), id.length()); pathDstTmp = pathDst + idTmp; testFile = new File(pathDstTmp); cont++; } pathDst = pathDstTmp; id = idTmp; File newDirectoryFolder = new File(folder); if (!newDirectoryFolder.exists()) { newDirectoryFolder.mkdirs(); } try { FileChannel srcChannel = new FileInputStream(pathSrc).getChannel(); FileChannel dstChannel = new FileOutputStream(pathDst).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (IOException exc) { System.out.println(exc.toString()); } while (k.hasNext()) { Element languageElement = (Element) k.next(); String language = languageElement.getAttributeValue("id"); List words = languageElement.getChildren("word"); Iterator l = words.iterator(); while (l.hasNext()) { Element wordElement = (Element) l.next(); String type = wordElement.getAttributeValue("type"); if (!typeIDs.containsKey(type)) { typeIDs.put(type, contTypes); PreparedStatement stmt = G.conn.prepareStatement("INSERT OR IGNORE INTO type (id,name) VALUES (?,?)"); stmt.setInt(1, contTypes); stmt.setString(2, type); stmt.executeUpdate(); stmt.close(); contTypes++; } PreparedStatement stmt = G.conn.prepareStatement("INSERT OR IGNORE INTO main (word, idL, idT, name, nameNN) VALUES (?,?,?,?,?)"); stmt.setString(1, wordElement.getText().toLowerCase()); stmt.setInt(2, languageIDs.get(language)); stmt.setInt(3, typeIDs.get(type)); stmt.setString(4, id); stmt.setString(5, id); stmt.executeUpdate(); stmt.close(); if (contImages == 5000) { G.conn.commit(); contImages = 0; } else contImages++; } } } else { } } G.conn.setAutoCommit(true); G.conn.close(); long totalTiempo = System.currentTimeMillis() - tiempoInicio; System.out.println("El tiempo total es :" + totalTiempo / 1000 + " segundos"); } } catch (Exception e) { e.printStackTrace(); } } | 16,797 |
0 | public void doStatementQueryAndUpdate(Connection conn, String id) throws SQLException { try { int key = getNextKey(); Statement s1 = conn.createStatement(); String bValue = "doStatementQueryAndUpdate:" + id + testId; if (key >= MAX_KEY_VALUE) { key = key % MAX_KEY_VALUE; s1.executeUpdate("delete from many_threads where a = " + key); } int count = s1.executeUpdate("insert into many_threads values (" + key + ", '" + bValue + "', 0)"); assertEquals(1, count); assertEquals(key, executeQuery(s1, "select a from many_threads where a = " + key)); s1.executeUpdate("update many_threads set value = a * a, b = b || '&" + bValue + "' where a = " + (key + 1)); s1.close(); if (!conn.getAutoCommit()) { conn.commit(); } } catch (SQLException e) { if (!conn.getAutoCommit()) { try { conn.rollback(); } catch (SQLException e2) { } } } } | public DataRecord addRecord(InputStream input) throws DataStoreException { File temporary = null; try { temporary = newTemporaryFile(); DataIdentifier tempId = new DataIdentifier(temporary.getName()); usesIdentifier(tempId); long length = 0; MessageDigest digest = MessageDigest.getInstance(DIGEST); OutputStream output = new DigestOutputStream(new FileOutputStream(temporary), digest); try { length = IOUtils.copyLarge(input, output); } finally { output.close(); } DataIdentifier identifier = new DataIdentifier(digest.digest()); File file; synchronized (this) { usesIdentifier(identifier); file = getFile(identifier); System.out.println("new file name: " + file.getName()); File parent = file.getParentFile(); System.out.println("parent file: " + file.getParentFile().getName()); if (!parent.isDirectory()) { parent.mkdirs(); } if (!file.exists()) { temporary.renameTo(file); if (!file.exists()) { throw new IOException("Can not rename " + temporary.getAbsolutePath() + " to " + file.getAbsolutePath() + " (media read only?)"); } } else { long now = System.currentTimeMillis(); if (file.lastModified() < now) { file.setLastModified(now); } } if (!file.isFile()) { throw new IOException("Not a file: " + file); } if (file.length() != length) { throw new IOException(DIGEST + " collision: " + file); } } inUse.remove(tempId); return new FileDataRecord(identifier, file); } catch (NoSuchAlgorithmException e) { throw new DataStoreException(DIGEST + " not available", e); } catch (IOException e) { throw new DataStoreException("Could not add record", e); } finally { if (temporary != null) { temporary.delete(); } } } | 16,798 |
0 | public void testJTLM_publish100_blockSize() throws Exception { EXISchema corpus = EXISchemaFactoryTestUtil.getEXISchema("/JTLM/schemas/TLMComposite.xsd", getClass(), m_compilerErrors); Assert.assertEquals(0, m_compilerErrors.getTotalCount()); GrammarCache grammarCache = new GrammarCache(corpus, GrammarOptions.STRICT_OPTIONS); AlignmentType[] alignments = new AlignmentType[] { AlignmentType.preCompress, AlignmentType.compress }; int[] blockSizes = { 1, 100, 101 }; Transmogrifier encoder = new Transmogrifier(); EXIDecoder decoder = new EXIDecoder(999); encoder.setOutputOptions(HeaderOptionsOutputType.lessSchemaId); encoder.setEXISchema(grammarCache); decoder.setEXISchema(grammarCache); for (AlignmentType alignment : alignments) { for (int i = 0; i < blockSizes.length; i++) { Scanner scanner; InputSource inputSource; encoder.setAlignmentType(alignment); encoder.setBlockSize(blockSizes[i]); ByteArrayOutputStream baos = new ByteArrayOutputStream(); encoder.setOutputStream(baos); URL url = resolveSystemIdAsURL("/JTLM/publish100.xml"); inputSource = new InputSource(url.toString()); inputSource.setByteStream(url.openStream()); byte[] bts; int n_events, n_texts; encoder.encode(inputSource); bts = baos.toByteArray(); decoder.setInputStream(new ByteArrayInputStream(bts)); scanner = decoder.processHeader(); ArrayList<EXIEvent> exiEventList = new ArrayList<EXIEvent>(); EXIEvent exiEvent; n_events = 0; n_texts = 0; while ((exiEvent = scanner.nextEvent()) != null) { ++n_events; if (exiEvent.getEventVariety() == EXIEvent.EVENT_CH) { if (exiEvent.getCharacters().length() == 0) { --n_events; continue; } if (n_texts % 100 == 0) { final int n = n_texts / 100; Assert.assertEquals(JTLMTest.publish100_centennials[n], exiEvent.getCharacters().makeString()); } ++n_texts; } exiEventList.add(exiEvent); } Assert.assertEquals(10610, n_events); } } } | 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(); } } | 16,799 |
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