label int64 0 1 | func1 stringlengths 173 53.1k | func2 stringlengths 173 53.1k | id int64 0 901k |
|---|---|---|---|
0 | protected static void clearTables() throws SQLException { Connection conn = null; Statement stmt = null; try { conn = FidoDataSource.getConnection(); conn.setAutoCommit(false); stmt = conn.createStatement(); ClearData.clearTables(stmt); stmt.executeUpdate("insert into Objects (ObjectId, Description) values (2, '')"); stmt.executeUpdate("insert into Objects (ObjectId, Description) values (3, '')"); stmt.executeUpdate("insert into Objects (ObjectId, Description) values (4, '')"); stmt.executeUpdate("insert into Objects (ObjectId, Description) values (5, '')"); stmt.executeUpdate("insert into Objects (ObjectId, Description) values (6, '')"); stmt.executeUpdate("insert into Objects (ObjectId, Description) values (7, '')"); stmt.executeUpdate("insert into Objects (ObjectId, Description) values (8, '')"); conn.commit(); } catch (SQLException e) { if (conn != null) conn.rollback(); throw e; } finally { if (stmt != null) stmt.close(); if (conn != null) conn.close(); } } | private String md5Digest(String plain) throws Exception { MessageDigest digest = MessageDigest.getInstance("MD5"); digest.update(plain.trim().getBytes()); byte pwdDigest[] = digest.digest(); StringBuilder md5buffer = new StringBuilder(); for (int i = 0; i < pwdDigest.length; i++) { int number = 0xFF & pwdDigest[i]; if (number <= 0xF) { md5buffer.append('0'); } md5buffer.append(Integer.toHexString(number)); } return md5buffer.toString(); } | 15,300 |
1 | public static void copyFile(File sourceFile, File destFile) throws IOException { if (!sourceFile.exists()) { return; } if (!destFile.exists()) { destFile.createNewFile(); } FileChannel source = null; FileChannel destination = null; source = new FileInputStream(sourceFile).getChannel(); destination = new FileOutputStream(destFile).getChannel(); if (destination != null && source != null) { destination.transferFrom(source, 0, source.size()); } if (source != null) { source.close(); } if (destination != null) { destination.close(); } } | public static PortalConfig install(File xml, File dir) throws IOException, ConfigurationException { if (!dir.exists()) { log.info("Creating directory {}", dir); dir.mkdirs(); } if (!xml.exists()) { log.info("Installing default configuration to {}", xml); OutputStream output = new FileOutputStream(xml); try { InputStream input = ResourceLoader.open("res://" + PORTAL_CONFIG_XML); try { IOUtils.copy(input, output); } finally { input.close(); } } finally { output.close(); } } return create(xml, dir); } | 15,301 |
1 | @Test public void testFromFile() throws IOException { File temp = File.createTempFile("fannj_", ".tmp"); temp.deleteOnExit(); IOUtils.copy(this.getClass().getResourceAsStream("xor_float.net"), new FileOutputStream(temp)); Fann fann = new Fann(temp.getPath()); assertEquals(2, fann.getNumInputNeurons()); assertEquals(1, fann.getNumOutputNeurons()); assertEquals(-1f, fann.run(new float[] { -1, -1 })[0], .2f); assertEquals(1f, fann.run(new float[] { -1, 1 })[0], .2f); assertEquals(1f, fann.run(new float[] { 1, -1 })[0], .2f); assertEquals(-1f, fann.run(new float[] { 1, 1 })[0], .2f); fann.close(); } | 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(); } } | 15,302 |
1 | private boolean copy(File in, File out) { try { FileInputStream fis = new FileInputStream(in); FileOutputStream fos = new FileOutputStream(out); FileChannel readableChannel = fis.getChannel(); FileChannel writableChannel = fos.getChannel(); writableChannel.truncate(0); writableChannel.transferFrom(readableChannel, 0, readableChannel.size()); fis.close(); fos.close(); return true; } catch (IOException ioe) { System.out.println("Copy Error: IOException during copy\r\n" + ioe.getMessage()); return false; } } | public static void copyDirs(File sourceDir, File destDir) throws IOException { if (!destDir.exists()) destDir.mkdirs(); for (File file : sourceDir.listFiles()) { if (file.isDirectory()) { copyDirs(file, new File(destDir, file.getName())); } else { FileChannel srcChannel = new FileInputStream(file).getChannel(); File out = new File(destDir, file.getName()); out.createNewFile(); FileChannel dstChannel = new FileOutputStream(out).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } } } | 15,303 |
0 | public String getMD5String(String par1Str) { try { String s = (new StringBuilder()).append(field_27370_a).append(par1Str).toString(); MessageDigest messagedigest = MessageDigest.getInstance("MD5"); messagedigest.update(s.getBytes(), 0, s.length()); return (new BigInteger(1, messagedigest.digest())).toString(16); } catch (NoSuchAlgorithmException nosuchalgorithmexception) { throw new RuntimeException(nosuchalgorithmexception); } } | public static void copieFichier(File fichier1, File fichier2) { FileChannel in = null; FileChannel out = null; try { in = new FileInputStream(fichier1).getChannel(); out = new FileOutputStream(fichier2).getChannel(); in.transferTo(0, in.size(), out); } catch (Exception e) { e.printStackTrace(); } finally { if (in != null) { try { in.close(); } catch (IOException e) { } } if (out != null) { try { out.close(); } catch (IOException e) { } } } } | 15,304 |
1 | 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(); } } | protected ActionForward doExecute(ActionMapping mapping, ActionForm form, HttpServletRequest request, HttpServletResponse response) throws Exception { ActionMessages errors = new ActionMessages(); try { boolean isMultipart = FileUpload.isMultipartContent(request); Store storeInstance = getStoreInstance(request); if (isMultipart) { Map fields = new HashMap(); Vector files = new Vector(); List items = diskFileUpload.parseRequest(request); Iterator iter = items.iterator(); while (iter.hasNext()) { FileItem item = (FileItem) iter.next(); if (item.isFormField()) { fields.put(item.getFieldName(), item.getString()); } else { if (!StringUtils.isBlank(item.getName())) { ByteArrayOutputStream baos = null; try { baos = new ByteArrayOutputStream(); IOUtils.copy(item.getInputStream(), baos); MailPartObj part = new MailPartObj(); part.setAttachent(baos.toByteArray()); part.setContentType(item.getContentType()); part.setName(item.getName()); part.setSize(item.getSize()); files.addElement(part); } catch (Exception ex) { } finally { IOUtils.closeQuietly(baos); } } } } if (files.size() > 0) { storeInstance.send(files, 0, Charset.defaultCharset().displayName()); } } else { errors.add("general", new ActionMessage(ExceptionCode.ERROR_MESSAGES_PREFIX + "mail.send", "The form is null")); request.setAttribute("exception", "The form is null"); request.setAttribute("newLocation", null); doTrace(request, DLog.ERROR, getClass(), "The form is null"); } } catch (Exception ex) { String errorMessage = ExceptionUtilities.parseMessage(ex); if (errorMessage == null) { errorMessage = "NullPointerException"; } errors.add("general", new ActionMessage(ExceptionCode.ERROR_MESSAGES_PREFIX + "general", errorMessage)); request.setAttribute("exception", errorMessage); doTrace(request, DLog.ERROR, getClass(), errorMessage); } finally { } if (errors.isEmpty()) { doTrace(request, DLog.INFO, getClass(), "OK"); return mapping.findForward(Constants.ACTION_SUCCESS_FORWARD); } else { saveErrors(request, errors); return mapping.findForward(Constants.ACTION_FAIL_FORWARD); } } | 15,305 |
1 | public String getWeather(String cityName, String fileAddr) { try { URL url = new URL("http://www.google.com/ig/api?hl=zh_cn&weather=" + cityName); InputStream inputstream = url.openStream(); String s, str; BufferedReader in = new BufferedReader(new InputStreamReader(inputstream)); StringBuffer stringbuffer = new StringBuffer(); Writer out = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(fileAddr), "utf-8")); while ((s = in.readLine()) != null) { stringbuffer.append(s); } str = new String(stringbuffer); out.write(str); out.close(); in.close(); } catch (IOException e) { e.printStackTrace(); } File file = new File(fileAddr); DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); String str = null; try { DocumentBuilder builder = factory.newDocumentBuilder(); Document doc = builder.parse(file); NodeList nodelist1 = (NodeList) doc.getElementsByTagName("forecast_conditions"); NodeList nodelist2 = nodelist1.item(0).getChildNodes(); str = nodelist2.item(4).getAttributes().item(0).getNodeValue() + ",temperature:" + nodelist2.item(1).getAttributes().item(0).getNodeValue() + "℃-" + nodelist2.item(2).getAttributes().item(0).getNodeValue() + "℃"; } catch (Exception e) { e.printStackTrace(); } return str; } | public static GoogleResponse getElevation(String lat, String lon) throws IOException { String url = "http://maps.google.com/maps/api/elevation/xml?locations="; url = url + String.valueOf(lat); url = url + ","; url = url + String.valueOf(lon); url = url + "&sensor=false"; BufferedReader in = new BufferedReader(new InputStreamReader(new URL(url).openStream())); String line; GoogleResponse googleResponse = new GoogleResponse(); googleResponse.lat = Double.valueOf(lat); googleResponse.lon = Double.valueOf(lon); while ((line = in.readLine()) != null) { line = line.trim(); if (line.startsWith("<status>")) { line = line.replace("<status>", ""); line = line.replace("</status>", ""); googleResponse.status = line; if (!line.toLowerCase().equals("ok")) return googleResponse; } else if (line.startsWith("<elevation>")) { line = line.replace("<elevation>", ""); line = line.replace("</elevation>", ""); googleResponse.elevation = Double.valueOf(line); return googleResponse; } } return googleResponse; } | 15,306 |
0 | @Test public final void testImportODS() throws Exception { URL url = ODSTableImporterTest.class.getResource("/Messages.ods"); InputStream in = url.openStream(); ODSTableImporter b = new ODSTableImporter(); b.importODS(in, null); assertMessagesOds(b); } | private int[] Tri(int[] pertinence, int taille) { boolean change = true; int tmp; while (change) { change = false; for (int i = 0; i < taille - 2; i++) { if (pertinence[i] < pertinence[i + 1]) { tmp = pertinence[i]; pertinence[i] = pertinence[i + 1]; pertinence[i + 1] = tmp; change = true; } } } return pertinence; } | 15,307 |
1 | public static void main(String[] args) throws IOException { FileChannel fc = new FileOutputStream("src/com/aaron/nio/data.txt").getChannel(); fc.write(ByteBuffer.wrap("dfsdf ".getBytes())); fc.close(); fc = new RandomAccessFile("src/com/aaron/nio/data.txt", "rw").getChannel(); fc.position(fc.size()); fc.write(ByteBuffer.wrap("中文的 ".getBytes())); fc.close(); fc = new FileInputStream("src/com/aaron/nio/data.txt").getChannel(); ByteBuffer buff = ByteBuffer.allocate(1024); fc.read(buff); buff.flip(); while (buff.hasRemaining()) { System.out.print(buff.getChar()); } fc.close(); } | public void overwriteFileTest() throws Exception { File filefrom = new File("/tmp/from.txt"); File fileto = new File("/tmp/to.txt"); InputStream from = null; OutputStream to = null; try { from = new FileInputStream(filefrom); to = new FileOutputStream(fileto); byte[] buffer = new byte[4096]; int bytes_read; while ((bytes_read = from.read(buffer)) != -1) { to.write(buffer, 0, bytes_read); } } finally { if (from != null) { from.close(); } if (to != null) { to.close(); } } } | 15,308 |
1 | public static String encryptPassword(String password) { String hash = null; try { MessageDigest md = null; md = MessageDigest.getInstance("SHA"); md.update(password.getBytes("UTF-8")); byte raw[] = md.digest(); hash = Base64.encode(raw, false); } catch (Exception e) { } return hash; } | private String getEncryptedPassword() { String encrypted; char[] pwd = password.getPassword(); try { MessageDigest md = MessageDigest.getInstance("SHA-1"); md.update(new String(pwd).getBytes("UTF-8")); byte[] digested = md.digest(); encrypted = new String(Base64Coder.encode(digested)); } catch (Exception e) { encrypted = new String(pwd); } for (int i = 0; i < pwd.length; i++) pwd[i] = 0; return encrypted; } | 15,309 |
0 | public static void main(String[] args) throws Exception { PatternLayout pl = new PatternLayout("%d{ISO8601} %-5p %c: %m\n"); ConsoleAppender ca = new ConsoleAppender(pl); Logger.getRoot().addAppender(ca); Logger.getRoot().setLevel(Level.INFO); Options options = new Options(); options.addOption("p", "put", false, "put a file in the DHT overlay"); options.addOption("g", "get", false, "get a file from the DHT"); options.addOption("r", "remove", false, "remove a file from the DHT"); options.addOption("u", "update", false, "updates the lease"); options.addOption("j", "join", false, "join the DHT overlay"); options.addOption("c", "config", true, "the configuration file"); options.addOption("k", "key", true, "the key to read a file from"); options.addOption("f", "file", true, "the file to read or write"); options.addOption("a", "app", true, "the application ID"); options.addOption("s", "secret", true, "the secret used to hide data"); options.addOption("t", "ttl", true, "how long in seconds data should persist"); CommandLineParser parser = new PosixParser(); CommandLine cmd = parser.parse(options, args); String configFile = null; String mode = null; String secretStr = null; int ttl = 9999; String keyStr = null; String file = null; int appId = 0; if (cmd.hasOption("j")) { mode = "join"; } if (cmd.hasOption("p")) { mode = "put"; } if (cmd.hasOption("g")) { mode = "get"; } if (cmd.hasOption("r")) { mode = "remove"; } if (cmd.hasOption("u")) { mode = "update"; } if (cmd.hasOption("c")) { configFile = cmd.getOptionValue("c"); } if (cmd.hasOption("k")) { keyStr = cmd.getOptionValue("k"); } if (cmd.hasOption("f")) { file = cmd.getOptionValue("f"); } if (cmd.hasOption("s")) { secretStr = cmd.getOptionValue("s"); } if (cmd.hasOption("t")) { ttl = Integer.parseInt(cmd.getOptionValue("t")); } if (cmd.hasOption("a")) { appId = Integer.parseInt(cmd.getOptionValue("a")); } if (mode == null) { System.err.println("ERROR: --put or --get or --remove or --join or --update is required"); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("DHT", options); System.exit(1); } if (configFile == null) { System.err.println("ERROR: --config is required"); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("DHT", options); System.exit(1); } Properties conf = new Properties(); conf.load(new FileInputStream(configFile)); DHT dht = new DHT(conf); if (mode.equals("join")) { dht.join(); } else if (mode.equals("put")) { if (file == null) { System.err.println("ERROR: --file is required"); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("DHT", options); System.exit(1); } if (keyStr == null) { System.err.println("ERROR: --key is required"); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("DHT", options); System.exit(1); } if (secretStr == null) { System.err.println("ERROR: --secret is required"); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("DHT", options); System.exit(1); } logger.info("putting file " + file); FileInputStream in = new FileInputStream(file); byte[] tmp = new byte[1000000]; int num = in.read(tmp); byte[] value = new byte[num]; System.arraycopy(tmp, 0, value, 0, num); in.close(); if (dht.put((short) appId, keyStr.getBytes(), value, ttl, secretStr.getBytes()) < 0) { logger.info("There was an error while putting a key-value."); System.exit(0); } System.out.println("Ok!"); } else if (mode.equals("get")) { if (file == null) { System.err.println("ERROR: --file is required"); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("DHT", options); System.exit(1); } if (keyStr == null) { System.err.println("ERROR: --key is required"); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("DHT", options); System.exit(1); } logger.info("getting file " + file); ArrayList<byte[]> values = new ArrayList<byte[]>(); if (dht.get((short) appId, keyStr.getBytes(), Integer.MAX_VALUE, values) < 0) { logger.info("There was an error while getting a value."); System.exit(0); } if (values.size() == 0 || values == null) { System.out.println("No values returned."); System.exit(0); } FileOutputStream out = new FileOutputStream(file); System.out.println("Found " + values.size() + " values -- saving the first one only."); out.write(values.get(0)); out.close(); System.out.println("Ok!"); } else if (mode.equals("remove")) { if (keyStr == null) { System.err.println("ERROR: --key is required"); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("DHT", options); System.exit(1); } if (secretStr == null) { System.err.println("ERROR: --secret is required"); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("DHT", options); System.exit(1); } logger.info("removing <key,value> for key=" + keyStr); if (dht.remove((short) appId, keyStr.getBytes(), secretStr.getBytes()) < 0) { logger.info("There was an error while removing a key."); System.exit(0); } System.out.println("Ok!"); } else if (mode.equals("update")) { if (keyStr == null) { System.err.println("ERROR: --key is required"); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("DHT", options); System.exit(1); } logger.info("updating <key,value> for key=" + keyStr); if (dht.updateLease((short) appId, keyStr.getBytes(), ttl) < 0) { logger.info("There was an error while updating data lease."); System.exit(0); } System.out.println("Ok!"); } DHT.getInstance().stop(); } | private void getRandomGUID(boolean secure) { MessageDigest md5 = null; StringBuffer sbValueBeforeMD5 = new StringBuffer(); try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException 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); } } | 15,310 |
1 | public void handleMessage(Message message) throws Fault { InputStream is = message.getContent(InputStream.class); if (is == null) { return; } CachedOutputStream bos = new CachedOutputStream(); try { IOUtils.copy(is, bos); is.close(); bos.close(); sendMsg("Inbound Message \n" + "--------------" + bos.getOut().toString() + "\n--------------"); message.setContent(InputStream.class, bos.getInputStream()); } catch (IOException e) { throw new Fault(e); } } | 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; } | 15,311 |
1 | private void exportJar(File root, List<File> list, Manifest manifest) throws Exception { JarOutputStream jarOut = null; FileInputStream fin = null; try { jarOut = new JarOutputStream(new FileOutputStream(jarFile), manifest); for (int i = 0; i < list.size(); i++) { String filename = list.get(i).getAbsolutePath(); filename = filename.substring(root.getAbsolutePath().length() + 1); fin = new FileInputStream(list.get(i)); JarEntry entry = new JarEntry(filename.replace('\\', '/')); jarOut.putNextEntry(entry); byte[] buf = new byte[4096]; int read; while ((read = fin.read(buf)) != -1) { jarOut.write(buf, 0, read); } jarOut.closeEntry(); jarOut.flush(); } } finally { if (fin != null) { try { fin.close(); } catch (Exception e) { ExceptionOperation.operate(e); } } if (jarOut != null) { try { jarOut.close(); } catch (Exception e) { } } } } | public void executaAlteracoes() { Album album = Album.getAlbum(); Photo[] fotos = album.getFotos(); Photo f; int ultimoFotoID = -1; int albumID = album.getAlbumID(); sucesso = true; PainelWebFotos.setCursorWait(true); albumID = recordAlbumData(album, albumID); sucesso = recordFotoData(fotos, ultimoFotoID, albumID); String caminhoAlbum = Util.getFolder("albunsRoot").getPath() + File.separator + albumID; File diretorioAlbum = new File(caminhoAlbum); if (!diretorioAlbum.isDirectory()) { if (!diretorioAlbum.mkdir()) { Util.log("[AcaoAlterarAlbum.executaAlteracoes.7]/ERRO: diretorio " + caminhoAlbum + " n�o pode ser criado. abortando"); return; } } for (int i = 0; i < fotos.length; i++) { f = fotos[i]; if (f.getCaminhoArquivo().length() > 0) { try { FileChannel canalOrigem = new FileInputStream(f.getCaminhoArquivo()).getChannel(); FileChannel canalDestino = new FileOutputStream(caminhoAlbum + File.separator + f.getFotoID() + ".jpg").getChannel(); canalDestino.transferFrom(canalOrigem, 0, canalOrigem.size()); canalOrigem = null; canalDestino = null; } catch (Exception e) { Util.log("[AcaoAlterarAlbum.executaAlteracoes.8]/ERRO: " + e); sucesso = false; } } } prepareThumbsAndFTP(fotos, albumID, caminhoAlbum); prepareExtraFiles(album, caminhoAlbum); fireChangesToGUI(fotos); dispatchAlbum(); PainelWebFotos.setCursorWait(false); } | 15,312 |
0 | public File sendPayload(SoapEnvelope payload, URL url) throws IOException { URLConnection conn = null; File tempFile = null; Logger l = Logger.instance(); String className = getClass().getName(); l.log(Logger.DEBUG, loggerPrefix, className + ".sendPayload", "sending payload to " + url.toString()); try { conn = url.openConnection(); conn.setDoOutput(true); payload.writeTo(conn.getOutputStream()); tempFile = readIntoTempFile(conn.getInputStream()); } catch (IOException ioe) { l.log(Logger.ERROR, loggerPrefix, className + ".sendPayload", ioe); throw ioe; } finally { conn = null; } l.log(Logger.DEBUG, loggerPrefix, className + ".sendPayload", "received response"); return tempFile; } | public void testReaderWriterF2() throws Exception { String inFile = "test_data/mri.png"; String outFile = "test_output/mri__smooth_testReaderWriter.mhd"; itkImageFileReaderF2_Pointer reader = itkImageFileReaderF2.itkImageFileReaderF2_New(); itkImageFileWriterF2_Pointer writer = itkImageFileWriterF2.itkImageFileWriterF2_New(); reader.SetFileName(inFile); writer.SetFileName(outFile); writer.SetInput(reader.GetOutput()); writer.Update(); } | 15,313 |
0 | @Override public void update(DisciplinaDTO disciplina) { try { this.criaConexao(false); } catch (ClassNotFoundException ex) { java.util.logging.Logger.getLogger(PostgresqlDisciplinaDAO.class.getName()).log(Level.SEVERE, null, ex); } catch (SQLException ex) { java.util.logging.Logger.getLogger(PostgresqlDisciplinaDAO.class.getName()).log(Level.SEVERE, null, ex); } LOG.debug("Criou a conex�o!"); String sql = "update Disciplina set nome = ? where id = ?"; PreparedStatement stmt = null; try { stmt = this.getConnection().prepareStatement(sql); LOG.debug("PreparedStatement criado com sucesso!"); stmt.setString(1, disciplina.getNome()); stmt.setInt(2, disciplina.getId()); int retorno = stmt.executeUpdate(); if (retorno == 0) { this.getConnection().rollback(); throw new SQLException("Ocorreu um erro inesperado no momento de alterar dados de Revendedor no banco!"); } LOG.debug("Confirmando as altera��es no banco."); this.getConnection().commit(); } catch (SQLException e) { LOG.debug("Desfazendo as altera��es no banco."); try { this.getConnection().rollback(); } catch (SQLException ex) { java.util.logging.Logger.getLogger(PostgresqlDisciplinaDAO.class.getName()).log(Level.SEVERE, null, ex); } LOG.debug("Lan�ando a exce��o da camada de persist�ncia."); try { throw e; } catch (SQLException ex) { java.util.logging.Logger.getLogger(PostgresqlDisciplinaDAO.class.getName()).log(Level.SEVERE, null, ex); } } finally { try { stmt.close(); this.fechaConexao(); } catch (SQLException e) { try { throw e; } catch (SQLException ex) { java.util.logging.Logger.getLogger(PostgresqlDisciplinaDAO.class.getName()).log(Level.SEVERE, null, ex); } } } } | public void SendFile(File testfile) { try { SocketChannel sock = SocketChannel.open(new InetSocketAddress("127.0.0.1", 1234)); sock.configureBlocking(true); while (!sock.finishConnect()) { System.out.println("NOT connected!"); } System.out.println("CONNECTED!"); FileInputStream fis = new FileInputStream(testfile); FileChannel fic = fis.getChannel(); long len = fic.size(); Buffer.clear(); Buffer.putLong(len); Buffer.flip(); sock.write(Buffer); long cnt = 0; while (cnt < len) { Buffer.clear(); int add = fic.read(Buffer); cnt += add; Buffer.flip(); while (Buffer.hasRemaining()) { sock.write(Buffer); } } fic.close(); File tmpfile = getTmp().createNewFile("tmp", "tmp"); FileOutputStream fos = new FileOutputStream(tmpfile); FileChannel foc = fos.getChannel(); int mlen = -1; do { Buffer.clear(); mlen = sock.read(Buffer); Buffer.flip(); if (mlen > 0) { foc.write(Buffer); } } while (mlen > 0); foc.close(); } catch (IOException e) { e.printStackTrace(); } } | 15,314 |
1 | private static void copyFile(File inputFile, File outputFile) throws IOException { FileReader in = new FileReader(inputFile); FileWriter out = new FileWriter(outputFile); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } | public static void copyFile(File destFile, File src) throws IOException { File destDir = destFile.getParentFile(); File tempFile = new File(destFile + "_tmp"); destDir.mkdirs(); InputStream is = new FileInputStream(src); try { FileOutputStream os = new FileOutputStream(tempFile); try { byte[] buf = new byte[8192]; int len; while ((len = is.read(buf)) > 0) os.write(buf, 0, len); } finally { os.close(); } } finally { is.close(); } destFile.delete(); if (!tempFile.renameTo(destFile)) throw new IOException("Unable to rename " + tempFile + " to " + destFile); } | 15,315 |
1 | public static void copyFile(File in, File out, boolean append) throws IOException { FileChannel inChannel = new FileInputStream(in).getChannel(); FileChannel outChannel = new FileOutputStream(out, append).getChannel(); try { inChannel.transferTo(0, inChannel.size(), outChannel); } catch (IOException e) { throw e; } finally { if (inChannel != null) inChannel.close(); if (outChannel != null) outChannel.close(); } } | public void doPost(HttpServletRequest req, HttpServletResponse res) throws ServletException, IOException { PrintWriter out = null; ServletOutputStream outstream = null; try { String action = req.getParameter("nmrshiftdbaction"); String relativepath = ServletUtils.expandRelative(this.getServletConfig(), "/WEB-INF"); TurbineConfig tc = new TurbineConfig(relativepath + "..", relativepath + getServletConfig().getInitParameter("properties")); tc.init(); int spectrumId = -1; DBSpectrum spectrum = null; Export export = null; String format = req.getParameter("format"); if (action.equals("test")) { try { res.setContentType("text/plain"); out = res.getWriter(); List l = DBSpectrumPeer.executeQuery("select SPECTRUM_ID from SPECTRUM limit 1"); if (l.size() > 0) spectrumId = ((Record) l.get(0)).getValue(1).asInt(); out.write("success"); } catch (Exception ex) { out.write("failure"); } } else if (action.equals("rss")) { int numbertoexport = 10; out = res.getWriter(); if (req.getParameter("numbertoexport") != null) { try { numbertoexport = Integer.parseInt(req.getParameter("numbertoexport")); if (numbertoexport < 1 || numbertoexport > 20) throw new NumberFormatException("Number to small/large"); } catch (NumberFormatException ex) { out.println("The parameter <code>numbertoexport</code>must be an integer from 1 to 20"); } } res.setContentType("text/xml"); RssWriter rssWriter = new RssWriter(); rssWriter.setWriter(res.getWriter()); AtomContainerSet soac = new AtomContainerSet(); String query = "select distinct MOLECULE.MOLECULE_ID from MOLECULE, SPECTRUM where SPECTRUM.MOLECULE_ID = MOLECULE.MOLECULE_ID and SPECTRUM.REVIEW_FLAG =\"true\" order by MOLECULE.DATE desc;"; List l = NmrshiftdbUserPeer.executeQuery(query); for (int i = 0; i < numbertoexport; i++) { if (i == l.size()) break; DBMolecule mol = DBMoleculePeer.retrieveByPK(new NumberKey(((Record) l.get(i)).getValue(1).asInt())); IMolecule cdkmol = mol.getAsCDKMoleculeAsEntered(1); soac.addAtomContainer(cdkmol); rssWriter.getLinkmap().put(cdkmol, mol.getEasylink(req)); rssWriter.getDatemap().put(cdkmol, mol.getDate()); rssWriter.getTitlemap().put(cdkmol, mol.getChemicalNamesAsOneStringWithFallback()); rssWriter.getCreatormap().put(cdkmol, mol.getNmrshiftdbUser().getUserName()); rssWriter.setCreator(GeneralUtils.getAdminEmail(getServletConfig())); Vector v = mol.getDBCanonicalNames(); for (int k = 0; k < v.size(); k++) { DBCanonicalName canonName = (DBCanonicalName) v.get(k); if (canonName.getDBCanonicalNameType().getCanonicalNameType() == "INChI") { rssWriter.getInchimap().put(cdkmol, canonName.getName()); break; } } rssWriter.setTitle("NMRShiftDB"); rssWriter.setLink("http://www.nmrshiftdb.org"); rssWriter.setDescription("NMRShiftDB is an open-source, open-access, open-submission, open-content web database for chemical structures and their nuclear magnetic resonance data"); rssWriter.setPublisher("NMRShiftDB.org"); rssWriter.setImagelink("http://www.nmrshiftdb.org/images/nmrshift-logo.gif"); rssWriter.setAbout("http://www.nmrshiftdb.org/NmrshiftdbServlet?nmrshiftdbaction=rss"); Collection coll = new ArrayList(); Vector spectra = mol.selectSpectra(null); for (int k = 0; k < spectra.size(); k++) { Element el = ((DBSpectrum) spectra.get(k)).getCmlSpect(); Element el2 = el.getChildElements().get(0); el.removeChild(el2); coll.add(el2); } rssWriter.getMultiMap().put(cdkmol, coll); } rssWriter.write(soac); } else if (action.equals("getattachment")) { res.setContentType("application/zip"); outstream = res.getOutputStream(); DBSample sample = DBSamplePeer.retrieveByPK(new NumberKey(req.getParameter("sampleid"))); outstream.write(sample.getAttachment()); } else if (action.equals("createreport")) { res.setContentType("application/pdf"); outstream = res.getOutputStream(); boolean yearly = req.getParameter("style").equals("yearly"); int yearstart = Integer.parseInt(req.getParameter("yearstart")); int yearend = Integer.parseInt(req.getParameter("yearend")); int monthstart = 0; int monthend = 0; if (!yearly) { monthstart = Integer.parseInt(req.getParameter("monthstart")); monthend = Integer.parseInt(req.getParameter("monthend")); } int type = Integer.parseInt(req.getParameter("type")); JasperReport jasperReport = (JasperReport) JRLoader.loadObject(relativepath + "/reports/" + (yearly ? "yearly" : "monthly") + "_report_" + type + ".jasper"); Map parameters = new HashMap(); if (yearly) parameters.put("HEADER", "Report for years " + yearstart + " - " + yearend); else parameters.put("HEADER", "Report for " + monthstart + "/" + yearstart + " - " + monthend + "/" + yearend); DBConnection dbconn = TurbineDB.getConnection(); Connection conn = dbconn.getConnection(); Statement stmt = conn.createStatement(); ResultSet rs = null; if (type == 1) { rs = stmt.executeQuery("select YEAR(DATE) as YEAR, " + (yearly ? "" : " MONTH(DATE) as MONTH, ") + "AFFILIATION_1, AFFILIATION_2, MACHINE.NAME as NAME, count(*) as C, sum(WISHED_SPECTRUM like '%13C%' or WISHED_SPECTRUM like '%variable temperature%' or WISHED_SPECTRUM like '%ID sel. NOE%' or WISHED_SPECTRUM like '%solvent suppression%' or WISHED_SPECTRUM like '%standard spectrum%') as 1_D, sum(WISHED_SPECTRUM like '%H,H-COSY%' or WISHED_SPECTRUM like '%NOESY%' or WISHED_SPECTRUM like '%HMQC%' or WISHED_SPECTRUM like '%HMBC%') as 2_D, sum(OTHER_WISHED_SPECTRUM!='') as SPECIAL, sum(OTHER_NUCLEI!='') as HETERO, sum(PROCESS='self') as SELF, sum(PROCESS='robot') as ROBOT, sum(PROCESS='worker') as OPERATOR from (SAMPLE join TURBINE_USER using (USER_ID)) join MACHINE on MACHINE.MACHINE_ID=SAMPLE.MACHINE where YEAR(DATE)>=" + yearstart + " and YEAR(DATE)<=" + yearend + " and LOGIN_NAME<>'testuser' group by YEAR, " + (yearly ? "" : "MONTH, ") + "AFFILIATION_1, AFFILIATION_2, MACHINE.NAME"); } else if (type == 2) { rs = stmt.executeQuery("select YEAR(DATE) as YEAR, " + (yearly ? "" : " MONTH(DATE) as MONTH, ") + "MACHINE.NAME as NAME, count(*) as C, sum(WISHED_SPECTRUM like '%13C%' or WISHED_SPECTRUM like '%variable temperature%' or WISHED_SPECTRUM like '%ID sel. NOE%' or WISHED_SPECTRUM like '%solvent suppression%' or WISHED_SPECTRUM like '%standard spectrum%') as 1_D, sum(WISHED_SPECTRUM like '%H,H-COSY%' or WISHED_SPECTRUM like '%NOESY%' or WISHED_SPECTRUM like '%HMQC%' or WISHED_SPECTRUM like '%HMBC%') as 2_D, sum(OTHER_WISHED_SPECTRUM!='') as SPECIAL, sum(OTHER_NUCLEI!='') as HETERO, sum(PROCESS='self') as SELF, sum(PROCESS='robot') as ROBOT, sum(PROCESS='worker') as OPERATOR from (SAMPLE join TURBINE_USER using (USER_ID)) join MACHINE on MACHINE.MACHINE_ID=SAMPLE.MACHINE group by YEAR, " + (yearly ? "" : "MONTH, ") + "MACHINE.NAME"); } JasperPrint jasperPrint = JasperFillManager.fillReport(jasperReport, parameters, new JRResultSetDataSource(rs)); JasperExportManager.exportReportToPdfStream(jasperPrint, outstream); dbconn.close(); } else if (action.equals("exportcmlbyinchi")) { res.setContentType("text/xml"); out = res.getWriter(); String inchi = req.getParameter("inchi"); String spectrumtype = req.getParameter("spectrumtype"); Criteria crit = new Criteria(); crit.add(DBCanonicalNamePeer.NAME, inchi); crit.addJoin(DBCanonicalNamePeer.MOLECULE_ID, DBSpectrumPeer.MOLECULE_ID); crit.addJoin(DBSpectrumPeer.SPECTRUM_TYPE_ID, DBSpectrumTypePeer.SPECTRUM_TYPE_ID); crit.add(DBSpectrumTypePeer.NAME, spectrumtype); try { GeneralUtils.logToSql(crit.toString(), null); } catch (Exception ex) { } Vector spectra = DBSpectrumPeer.doSelect(crit); if (spectra.size() == 0) { out.write("No such molecule or spectrum"); } else { Element cmlElement = new Element("cml"); cmlElement.addAttribute(new Attribute("convention", "nmrshiftdb-convention")); cmlElement.setNamespaceURI("http://www.xml-cml.org/schema"); Element parent = ((DBSpectrum) spectra.get(0)).getDBMolecule().getCML(1); nu.xom.Node cmldoc = parent.getChild(0); ((Element) cmldoc).setNamespaceURI("http://www.xml-cml.org/schema"); parent.removeChildren(); cmlElement.appendChild(cmldoc); for (int k = 0; k < spectra.size(); k++) { Element parentspec = ((DBSpectrum) spectra.get(k)).getCmlSpect(); Node spectrumel = parentspec.getChild(0); parentspec.removeChildren(); cmlElement.appendChild(spectrumel); ((Element) spectrumel).setNamespaceURI("http://www.xml-cml.org/schema"); } out.write(cmlElement.toXML()); } } else if (action.equals("namelist")) { res.setContentType("application/zip"); outstream = res.getOutputStream(); ByteArrayOutputStream baos = new ByteArrayOutputStream(); ZipOutputStream zipout = new ZipOutputStream(baos); Criteria crit = new Criteria(); crit.addJoin(DBMoleculePeer.MOLECULE_ID, DBSpectrumPeer.MOLECULE_ID); crit.add(DBSpectrumPeer.REVIEW_FLAG, "true"); Vector v = DBMoleculePeer.doSelect(crit); for (int i = 0; i < v.size(); i++) { if (i % 500 == 0) { if (i != 0) { zipout.write(new String("<p>The list is continued <a href=\"nmrshiftdb.names." + i + ".html\">here</a></p></body></html>").getBytes()); zipout.closeEntry(); } zipout.putNextEntry(new ZipEntry("nmrshiftdb.names." + i + ".html")); zipout.write(new String("<html><body><h1>This is a list of strcutures in <a href=\"http://www.nmrshiftdb.org\">NMRShiftDB</a>, starting at " + i + ", Its main purpose is to be found by search engines</h1>").getBytes()); } DBMolecule mol = (DBMolecule) v.get(i); zipout.write(new String("<p><a href=\"" + mol.getEasylink(req) + "\">").getBytes()); Vector cannames = mol.getDBCanonicalNames(); for (int k = 0; k < cannames.size(); k++) { zipout.write(new String(((DBCanonicalName) cannames.get(k)).getName() + " ").getBytes()); } Vector chemnames = mol.getDBChemicalNames(); for (int k = 0; k < chemnames.size(); k++) { zipout.write(new String(((DBChemicalName) chemnames.get(k)).getName() + " ").getBytes()); } zipout.write(new String("</a>. Information we have got: NMR spectra").getBytes()); Vector spectra = mol.selectSpectra(); for (int k = 0; k < spectra.size(); k++) { zipout.write(new String(((DBSpectrum) spectra.get(k)).getDBSpectrumType().getName() + ", ").getBytes()); } if (mol.hasAny3d()) zipout.write(new String("3D coordinates, ").getBytes()); zipout.write(new String("File formats: CML, mol, png, jpeg").getBytes()); zipout.write(new String("</p>").getBytes()); } zipout.write(new String("</body></html>").getBytes()); zipout.closeEntry(); zipout.close(); InputStream is = new ByteArrayInputStream(baos.toByteArray()); byte[] buf = new byte[32 * 1024]; int nRead = 0; while ((nRead = is.read(buf)) != -1) { outstream.write(buf, 0, nRead); } } else if (action.equals("predictor")) { if (req.getParameter("symbol") == null) { res.setContentType("text/plain"); out = res.getWriter(); out.write("please give the symbol to create the predictor for in the request with symbol=X (e. g. symbol=C"); } res.setContentType("application/zip"); outstream = res.getOutputStream(); ByteArrayOutputStream baos = new ByteArrayOutputStream(); ZipOutputStream zipout = new ZipOutputStream(baos); String filename = "org/openscience/nmrshiftdb/PredictionTool.class"; zipout.putNextEntry(new ZipEntry(filename)); JarInputStream jip = new JarInputStream(new FileInputStream(ServletUtils.expandRelative(getServletConfig(), "/WEB-INF/lib/nmrshiftdb-lib.jar"))); JarEntry entry = jip.getNextJarEntry(); while (entry.getName().indexOf("PredictionTool.class") == -1) { entry = jip.getNextJarEntry(); } for (int i = 0; i < entry.getSize(); i++) { zipout.write(jip.read()); } zipout.closeEntry(); zipout.putNextEntry(new ZipEntry("nmrshiftdb.csv")); int i = 0; org.apache.turbine.util.db.pool.DBConnection conn = TurbineDB.getConnection(); HashMap mapsmap = new HashMap(); while (true) { Statement stmt = conn.createStatement(); ResultSet rs = stmt.executeQuery("select HOSE_CODE, VALUE, SYMBOL from HOSE_CODES where CONDITION_TYPE='m' and WITH_RINGS=0 and SYMBOL='" + req.getParameter("symbol") + "' limit " + (i * 1000) + ", 1000"); int m = 0; while (rs.next()) { String code = rs.getString(1); Double value = new Double(rs.getString(2)); String symbol = rs.getString(3); if (mapsmap.get(symbol) == null) { mapsmap.put(symbol, new HashMap()); } for (int spheres = 6; spheres > 0; spheres--) { StringBuffer hoseCodeBuffer = new StringBuffer(); StringTokenizer st = new StringTokenizer(code, "()/"); for (int k = 0; k < spheres; k++) { if (st.hasMoreTokens()) { String partcode = st.nextToken(); hoseCodeBuffer.append(partcode); } if (k == 0) { hoseCodeBuffer.append("("); } else if (k == 3) { hoseCodeBuffer.append(")"); } else { hoseCodeBuffer.append("/"); } } String hoseCode = hoseCodeBuffer.toString(); if (((HashMap) mapsmap.get(symbol)).get(hoseCode) == null) { ((HashMap) mapsmap.get(symbol)).put(hoseCode, new ArrayList()); } ((ArrayList) ((HashMap) mapsmap.get(symbol)).get(hoseCode)).add(value); } m++; } i++; stmt.close(); if (m == 0) break; } Set keySet = mapsmap.keySet(); Iterator it = keySet.iterator(); while (it.hasNext()) { String symbol = (String) it.next(); HashMap hosemap = ((HashMap) mapsmap.get(symbol)); Set keySet2 = hosemap.keySet(); Iterator it2 = keySet2.iterator(); while (it2.hasNext()) { String hoseCode = (String) it2.next(); ArrayList list = ((ArrayList) hosemap.get(hoseCode)); double[] values = new double[list.size()]; for (int k = 0; k < list.size(); k++) { values[k] = ((Double) list.get(k)).doubleValue(); } zipout.write(new String(symbol + "|" + hoseCode + "|" + Statistics.minimum(values) + "|" + Statistics.average(values) + "|" + Statistics.maximum(values) + "\r\n").getBytes()); } } zipout.closeEntry(); zipout.close(); InputStream is = new ByteArrayInputStream(baos.toByteArray()); byte[] buf = new byte[32 * 1024]; int nRead = 0; i = 0; while ((nRead = is.read(buf)) != -1) { outstream.write(buf, 0, nRead); } } else if (action.equals("exportspec") || action.equals("exportmol")) { if (spectrumId > -1) spectrum = DBSpectrumPeer.retrieveByPK(new NumberKey(spectrumId)); else spectrum = DBSpectrumPeer.retrieveByPK(new NumberKey(req.getParameter("spectrumid"))); export = new Export(spectrum); } else if (action.equals("exportmdl")) { res.setContentType("text/plain"); outstream = res.getOutputStream(); DBMolecule mol = DBMoleculePeer.retrieveByPK(new NumberKey(req.getParameter("moleculeid"))); outstream.write(mol.getStructureFile(Integer.parseInt(req.getParameter("coordsetid")), false).getBytes()); } else if (action.equals("exportlastinputs")) { format = action; } else if (action.equals("printpredict")) { res.setContentType("text/html"); out = res.getWriter(); HttpSession session = req.getSession(); VelocityContext context = PredictPortlet.getContext(session, true, true, new StringBuffer(), getServletConfig(), req, true); StringWriter w = new StringWriter(); Velocity.mergeTemplate("predictprint.vm", "ISO-8859-1", context, w); out.println(w.toString()); } else { res.setContentType("text/html"); out = res.getWriter(); out.println("No valid action"); } if (format == null) format = ""; if (format.equals("pdf") || format.equals("rtf")) { res.setContentType("application/" + format); out = res.getWriter(); } if (format.equals("docbook")) { res.setContentType("application/zip"); outstream = res.getOutputStream(); } if (format.equals("svg")) { res.setContentType("image/x-svg"); out = res.getWriter(); } if (format.equals("tiff")) { res.setContentType("image/tiff"); outstream = res.getOutputStream(); } if (format.equals("jpeg")) { res.setContentType("image/jpeg"); outstream = res.getOutputStream(); } if (format.equals("png")) { res.setContentType("image/png"); outstream = res.getOutputStream(); } if (format.equals("mdl") || format.equals("txt") || format.equals("cml") || format.equals("cmlboth") || format.indexOf("exsection") == 0) { res.setContentType("text/plain"); out = res.getWriter(); } if (format.equals("simplehtml") || format.equals("exportlastinputs")) { res.setContentType("text/html"); out = res.getWriter(); } if (action.equals("exportlastinputs")) { int numbertoexport = 4; if (req.getParameter("numbertoexport") != null) { try { numbertoexport = Integer.parseInt(req.getParameter("numbertoexport")); if (numbertoexport < 1 || numbertoexport > 20) throw new NumberFormatException("Number to small/large"); } catch (NumberFormatException ex) { out.println("The parameter <code>numbertoexport</code>must be an integer from 1 to 20"); } } NmrshiftdbUser user = null; try { user = NmrshiftdbUserPeer.getByName(req.getParameter("username")); } catch (NmrshiftdbException ex) { out.println("Seems <code>username</code> is not OK: " + ex.getMessage()); } if (user != null) { List l = NmrshiftdbUserPeer.executeQuery("SELECT LAST_DOWNLOAD_DATE FROM TURBINE_USER where LOGIN_NAME=\"" + user.getUserName() + "\";"); Date lastDownloadDate = ((Record) l.get(0)).getValue(1).asDate(); if (((new Date().getTime() - lastDownloadDate.getTime()) / 3600000) < 24) { out.println("Your last download was at " + lastDownloadDate + ". You may download your last inputs only once a day. Sorry for this, but we need to be carefull with resources. If you want to put your last inputs on your homepage best use some sort of cache (e. g. use wget for downlaod with crond and link to this static resource))!"); } else { NmrshiftdbUserPeer.executeStatement("UPDATE TURBINE_USER SET LAST_DOWNLOAD_DATE=NOW() where LOGIN_NAME=\"" + user.getUserName() + "\";"); Vector<String> parameters = new Vector<String>(); String query = "select distinct MOLECULE.MOLECULE_ID from MOLECULE, SPECTRUM where SPECTRUM.MOLECULE_ID = MOLECULE.MOLECULE_ID and SPECTRUM.REVIEW_FLAG =\"true\" and SPECTRUM.USER_ID=" + user.getUserId() + " order by MOLECULE.DATE desc;"; l = NmrshiftdbUserPeer.executeQuery(query); String url = javax.servlet.http.HttpUtils.getRequestURL(req).toString(); url = url.substring(0, url.length() - 17); for (int i = 0; i < numbertoexport; i++) { if (i == l.size()) break; DBMolecule mol = DBMoleculePeer.retrieveByPK(new NumberKey(((Record) l.get(i)).getValue(1).asInt())); parameters.add(new String("<a href=\"" + url + "/portal/pane0/Results?nmrshiftdbaction=showDetailsFromHome&molNumber=" + mol.getMoleculeId() + "\"><img src=\"" + javax.servlet.http.HttpUtils.getRequestURL(req).toString() + "?nmrshiftdbaction=exportmol&spectrumid=" + ((DBSpectrum) mol.getDBSpectrums().get(0)).getSpectrumId() + "&format=jpeg&size=150x150&backcolor=12632256\"></a>")); } VelocityContext context = new VelocityContext(); context.put("results", parameters); StringWriter w = new StringWriter(); Velocity.mergeTemplate("lateststructures.vm", "ISO-8859-1", context, w); out.println(w.toString()); } } } if (action.equals("exportspec")) { if (format.equals("txt")) { String lastsearchtype = req.getParameter("lastsearchtype"); if (lastsearchtype.equals(NmrshiftdbConstants.TOTALSPECTRUM) || lastsearchtype.equals(NmrshiftdbConstants.SUBSPECTRUM)) { List l = ParseUtils.parseSpectrumFromSpecFile(req.getParameter("lastsearchvalues")); spectrum.initSimilarity(l, lastsearchtype.equals(NmrshiftdbConstants.SUBSPECTRUM)); } Vector v = spectrum.getOptions(); DBMolecule mol = spectrum.getDBMolecule(); out.print(mol.getChemicalNamesAsOneString(false) + mol.getMolecularFormula(false) + "; " + mol.getMolecularWeight() + " Dalton\n\r"); out.print("\n\rAtom\t"); if (spectrum.getDBSpectrumType().getElementSymbol() == ("H")) out.print("Mult.\t"); out.print("Meas."); if (lastsearchtype.equals(NmrshiftdbConstants.TOTALSPECTRUM) || lastsearchtype.equals(NmrshiftdbConstants.SUBSPECTRUM)) { out.print("\tInput\tDiff"); } out.print("\n\r"); out.print("No.\t"); if (spectrum.getDBSpectrumType().getElementSymbol() == ("H")) out.print("\t"); out.print("Shift"); if (lastsearchtype.equals(NmrshiftdbConstants.TOTALSPECTRUM) || lastsearchtype.equals(NmrshiftdbConstants.SUBSPECTRUM)) { out.print("\tShift\tM-I"); } out.print("\n\r"); for (int i = 0; i < v.size(); i++) { out.print(((ValuesForVelocityBean) v.get(i)).getDisplayText() + "\t" + ((ValuesForVelocityBean) v.get(i)).getRange()); if (lastsearchtype.equals(NmrshiftdbConstants.TOTALSPECTRUM) || lastsearchtype.equals(NmrshiftdbConstants.SUBSPECTRUM)) { out.print("\t" + ((ValuesForVelocityBean) v.get(i)).getNameForElements() + "\t" + ((ValuesForVelocityBean) v.get(i)).getDelta()); } out.print("\n\r"); } } if (format.equals("simplehtml")) { String i1 = export.getImage(false, "jpeg", ServletUtils.expandRelative(this.getServletConfig(), "/nmrshiftdbhtml") + "/tmp/" + System.currentTimeMillis(), true); export.pictures[0] = new File(i1).getName(); String i2 = export.getImage(true, "jpeg", ServletUtils.expandRelative(this.getServletConfig(), "/nmrshiftdbhtml") + "/tmp/" + System.currentTimeMillis(), true); export.pictures[1] = new File(i2).getName(); String docbook = export.getHtml(); out.print(docbook); } if (format.equals("pdf") || format.equals("rtf")) { String svgSpec = export.getSpecSvg(400, 200); String svgspecfile = relativepath + "/tmp/" + System.currentTimeMillis() + "s.svg"; new FileOutputStream(svgspecfile).write(svgSpec.getBytes()); export.pictures[1] = svgspecfile; String molSvg = export.getMolSvg(true); String svgmolfile = relativepath + "/tmp/" + System.currentTimeMillis() + "m.svg"; new FileOutputStream(svgmolfile).write(molSvg.getBytes()); export.pictures[0] = svgmolfile; String docbook = export.getDocbook("pdf", "SVG"); TransformerFactory tFactory = TransformerFactory.newInstance(); Transformer transformer = tFactory.newTransformer(new StreamSource("file:" + GeneralUtils.getNmrshiftdbProperty("docbookxslpath", getServletConfig()) + "/fo/docbook.xsl")); ByteArrayOutputStream baos = new ByteArrayOutputStream(); transformer.transform(new StreamSource(new StringReader(docbook)), new StreamResult(baos)); FopFactory fopFactory = FopFactory.newInstance(); FOUserAgent foUserAgent = fopFactory.newFOUserAgent(); OutputStream out2 = new ByteArrayOutputStream(); Fop fop = fopFactory.newFop(format.equals("rtf") ? MimeConstants.MIME_RTF : MimeConstants.MIME_PDF, foUserAgent, out2); TransformerFactory factory = TransformerFactory.newInstance(); transformer = factory.newTransformer(); Source src = new StreamSource(new StringReader(baos.toString())); Result res2 = new SAXResult(fop.getDefaultHandler()); transformer.transform(src, res2); out.print(out2.toString()); } if (format.equals("docbook")) { String i1 = relativepath + "/tmp/" + System.currentTimeMillis() + ".svg"; new FileOutputStream(i1).write(export.getSpecSvg(300, 200).getBytes()); export.pictures[0] = new File(i1).getName(); String i2 = relativepath + "/tmp/" + System.currentTimeMillis() + ".svg"; new FileOutputStream(i2).write(export.getMolSvg(true).getBytes()); export.pictures[1] = new File(i2).getName(); String docbook = export.getDocbook("pdf", "SVG"); String docbookfile = relativepath + "/tmp/" + System.currentTimeMillis() + ".xml"; new FileOutputStream(docbookfile).write(docbook.getBytes()); ByteArrayOutputStream baos = export.makeZip(new String[] { docbookfile, i1, i2 }); outstream.write(baos.toByteArray()); } if (format.equals("svg")) { out.print(export.getSpecSvg(400, 200)); } if (format.equals("tiff") || format.equals("jpeg") || format.equals("png")) { InputStream is = new FileInputStream(export.getImage(false, format, relativepath + "/tmp/" + System.currentTimeMillis(), true)); byte[] buf = new byte[32 * 1024]; int nRead = 0; while ((nRead = is.read(buf)) != -1) { outstream.write(buf, 0, nRead); } } if (format.equals("cml")) { out.print(spectrum.getCmlSpect().toXML()); } if (format.equals("cmlboth")) { Element cmlElement = new Element("cml"); cmlElement.addAttribute(new Attribute("convention", "nmrshiftdb-convention")); cmlElement.setNamespaceURI("http://www.xml-cml.org/schema"); Element parent = spectrum.getDBMolecule().getCML(1, spectrum.getDBSpectrumType().getName().equals("1H")); nu.xom.Node cmldoc = parent.getChild(0); ((Element) cmldoc).setNamespaceURI("http://www.xml-cml.org/schema"); parent.removeChildren(); cmlElement.appendChild(cmldoc); Element parentspec = spectrum.getCmlSpect(); Node spectrumel = parentspec.getChild(0); parentspec.removeChildren(); cmlElement.appendChild(spectrumel); ((Element) spectrumel).setNamespaceURI("http://www.xml-cml.org/schema"); out.write(cmlElement.toXML()); } if (format.indexOf("exsection") == 0) { StringTokenizer st = new StringTokenizer(format, "-"); st.nextToken(); String template = st.nextToken(); Criteria crit = new Criteria(); crit.add(DBSpectrumPeer.USER_ID, spectrum.getUserId()); Vector v = spectrum.getDBMolecule().getDBSpectrums(crit); VelocityContext context = new VelocityContext(); context.put("spectra", v); context.put("molecule", spectrum.getDBMolecule()); StringWriter w = new StringWriter(); Velocity.mergeTemplate("exporttemplates/" + template, "ISO-8859-1", context, w); out.write(w.toString()); } } if (action.equals("exportmol")) { int width = -1; int height = -1; if (req.getParameter("size") != null) { StringTokenizer st = new StringTokenizer(req.getParameter("size"), "x"); width = Integer.parseInt(st.nextToken()); height = Integer.parseInt(st.nextToken()); } boolean shownumbers = true; if (req.getParameter("shownumbers") != null && req.getParameter("shownumbers").equals("false")) { shownumbers = false; } if (req.getParameter("backcolor") != null) { export.backColor = new Color(Integer.parseInt(req.getParameter("backcolor"))); } if (req.getParameter("markatom") != null) { export.selected = Integer.parseInt(req.getParameter("markatom")) - 1; } if (format.equals("svg")) { out.print(export.getMolSvg(true)); } if (format.equals("tiff") || format.equals("jpeg") || format.equals("png")) { InputStream is = new FileInputStream(export.getImage(true, format, relativepath + "/tmp/" + System.currentTimeMillis(), width, height, shownumbers, null)); byte[] buf = new byte[32 * 1024]; int nRead = 0; while ((nRead = is.read(buf)) != -1) { outstream.write(buf, 0, nRead); } } if (format.equals("mdl")) { out.println(spectrum.getDBMolecule().getStructureFile(1, false)); } if (format.equals("cml")) { out.println(spectrum.getDBMolecule().getCMLString(1)); } } if (out != null) out.flush(); else outstream.flush(); } catch (Exception ex) { ex.printStackTrace(); out.print(GeneralUtils.logError(ex, "NmrshiftdbServlet", null, true)); out.flush(); } } | 15,316 |
1 | public static void copy(String srcFileName, String destFileName) throws IOException { if (srcFileName == null) { throw new IllegalArgumentException("srcFileName is null"); } if (destFileName == null) { throw new IllegalArgumentException("destFileName is null"); } FileChannel src = null; FileChannel dest = null; try { src = new FileInputStream(srcFileName).getChannel(); dest = new FileOutputStream(destFileName).getChannel(); long n = src.size(); MappedByteBuffer buf = src.map(FileChannel.MapMode.READ_ONLY, 0, n); dest.write(buf); } finally { if (dest != null) { try { dest.close(); } catch (IOException e1) { } } if (src != null) { try { src.close(); } catch (IOException e1) { } } } } | public static void copy(FileInputStream from, FileOutputStream to) throws IOException { FileChannel fromChannel = from.getChannel(); FileChannel toChannel = to.getChannel(); copy(fromChannel, toChannel); fromChannel.close(); toChannel.close(); } | 15,317 |
1 | public static String MD5(String text) throws NoSuchAlgorithmException, UnsupportedEncodingException { 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); } | public static String generate(String documentSelector) { if (documentSelector == null) { return null; } String date = Long.toString(System.currentTimeMillis()); try { MessageDigest md = MessageDigest.getInstance(HASH_ALGORITHM); md.update(documentSelector.getBytes()); md.update(date.getBytes()); byte[] digest = md.digest(); return toHexString(digest); } catch (NoSuchAlgorithmException e) { return null; } } | 15,318 |
1 | private static long saveAndClosePDFDocument(PDDocument document, OutputStreamProvider outProvider) throws IOException, COSVisitorException { File tempFile = null; InputStream in = null; OutputStream out = null; try { tempFile = File.createTempFile("temp", "pdf"); OutputStream tempFileOut = new FileOutputStream(tempFile); tempFileOut = new BufferedOutputStream(tempFileOut); document.save(tempFileOut); document.close(); tempFileOut.close(); long length = tempFile.length(); in = new BufferedInputStream(new FileInputStream(tempFile)); out = new BufferedOutputStream(outProvider.getOutputStream()); IOUtils.copy(in, out); return length; } finally { if (in != null) { IOUtils.closeQuietly(in); } if (out != null) { IOUtils.closeQuietly(out); } if (tempFile != null && !FileUtils.deleteQuietly(tempFile)) { tempFile.deleteOnExit(); } } } | public static boolean copyFile(File src, File des) { try { BufferedInputStream in = new BufferedInputStream(new FileInputStream(src)); BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(des)); int b; while ((b = in.read()) != -1) out.write(b); out.flush(); out.close(); in.close(); return true; } catch (IOException ie) { m_logCat.error("Copy file + " + src + " to " + des + " failed!", ie); return false; } } | 15,319 |
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 byte[] loadResource(String name) throws IOException { ClassPathResource cpr = new ClassPathResource(name); ByteArrayOutputStream baos = new ByteArrayOutputStream(); IOUtils.copy(cpr.getInputStream(), baos); return baos.toByteArray(); } | 15,320 |
0 | private File copyFile(String fileInClassPath, String systemPath) throws Exception { InputStream is = getClass().getResourceAsStream(fileInClassPath); OutputStream os = new FileOutputStream(systemPath); IOUtils.copy(is, os); is.close(); os.close(); return new File(systemPath); } | @MediumTest public void testUrlRewriteRules() throws Exception { ContentResolver resolver = getContext().getContentResolver(); GoogleHttpClient client = new GoogleHttpClient(resolver, "Test", false); Settings.Gservices.putString(resolver, "url:test", "http://foo.bar/ rewrite " + mServerUrl + "new/"); Settings.Gservices.putString(resolver, "digest", mServerUrl); try { HttpGet method = new HttpGet("http://foo.bar/path"); HttpResponse response = client.execute(method); String body = EntityUtils.toString(response.getEntity()); assertEquals("/new/path", body); } finally { client.close(); } } | 15,321 |
1 | public static String get(String u, String usr, String pwd) { String response = ""; logger.debug("Attempting to call: " + u); logger.debug("Creating Authenticator: usr=" + usr + ", pwd=" + pwd); Authenticator.setDefault(new CustomAuthenticator(usr, pwd)); try { URL url = new URL(u); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); StringBuffer sb = new StringBuffer(0); String str; while ((str = in.readLine()) != null) { sb.append(str); } in.close(); logger.debug("Response: " + sb.toString()); response = sb.toString(); } catch (MalformedURLException e) { logger.error(e); logger.trace(e, e); } catch (IOException e) { logger.error(e); logger.trace(e, e); } return response; } | public JythonWrapperAction(AActionBO.ActionDTO dto, URL url) throws IOException { super(dto); InputStream in = url.openStream(); InputStreamReader rin = new InputStreamReader(in); BufferedReader reader = new BufferedReader(rin); StringBuffer s = new StringBuffer(); String str; while ((str = reader.readLine()) != null) { s.append(str); s.append("\n"); } in.close(); script = s.toString(); } | 15,322 |
1 | public void doGet(HttpServletRequest req, HttpServletResponse resp) throws IOException { resp.setContentType("text/html"); resp.getWriter().println("Getting feed..."); String googleFeed = "http://news.google.com/news?ned=us&topic=h&output=rss"; String totalFeed = ""; try { URL url = new URL(googleFeed); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String line = null; while ((line = reader.readLine()) != null) { totalFeed += line; } reader.close(); parseFeedandPersist(totalFeed, resp); } catch (MalformedURLException e) { } catch (IOException e) { } } | private void getXMLData() { String result = null; URL url = null; URLConnection conn = null; BufferedReader rd = null; StringBuffer sb = new StringBuffer(); String line; try { url = new URL(this.url); conn = url.openConnection(); rd = new BufferedReader(new InputStreamReader(conn.getInputStream())); while ((line = rd.readLine()) != null) { sb.append(line + "\n"); } rd.close(); result = sb.toString(); } catch (MalformedURLException e) { log.error("URL was malformed: {}", url, e); } catch (IOException e) { log.error("IOException thrown: {}", url, e); } this.xmlString = result; } | 15,323 |
0 | public static void main(String[] args) { try { FTPClient p = new FTPClient(); p.connect("url"); p.login("login", "pass"); int sendCommand = p.sendCommand("SYST"); System.out.println("TryMe.main() - " + sendCommand + " (sendCommand)"); sendCommand = p.sendCommand("PWD"); System.out.println("TryMe.main() - " + sendCommand + " (sendCommand)"); sendCommand = p.sendCommand("NOOP"); System.out.println("TryMe.main() - " + sendCommand + " (sendCommand)"); sendCommand = p.sendCommand("PASV"); System.out.println("TryMe.main() - " + sendCommand + " (sendCommand)"); p.changeWorkingDirectory("/"); try { printDir(p, "/"); } catch (Exception e) { e.printStackTrace(); } p.logout(); p.disconnect(); } catch (UnknownHostException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } | private void addAllSpecialPages(Environment env, ZipOutputStream zipout, int progressStart, int progressLength) throws Exception, IOException { ResourceBundle messages = ResourceBundle.getBundle("ApplicationResources", locale); String tpl; int count = 0; int numberOfSpecialPages = 7; progress = Math.min(progressStart + (int) ((double) count * (double) progressLength / numberOfSpecialPages), 99); count++; String cssContent = wb.readRaw(virtualWiki, "StyleSheet"); addZipEntry(zipout, "css/vqwiki.css", cssContent); progress = Math.min(progressStart + (int) ((double) count * (double) progressLength / numberOfSpecialPages), 99); count++; tpl = getTemplateFilledWithContent("search"); addTopicEntry(zipout, tpl, "WikiSearch", "WikiSearch.html"); progress = Math.min(progressStart + (int) ((double) count * (double) progressLength / numberOfSpecialPages), 99); count++; zipout.putNextEntry(new ZipEntry("applets/export2html-applet.jar")); IOUtils.copy(new FileInputStream(ctx.getRealPath("/WEB-INF/classes/export2html/export2html-applet.jar")), zipout); zipout.closeEntry(); zipout.flush(); try { ByteArrayOutputStream bos = new ByteArrayOutputStream(); JarOutputStream indexjar = new JarOutputStream(bos); JarEntry jarEntry; File searchDir = new File(wb.getSearchEngine().getSearchIndexPath(virtualWiki)); String files[] = searchDir.list(); StringBuffer listOfAllFiles = new StringBuffer(); for (int i = 0; i < files.length; i++) { if (listOfAllFiles.length() > 0) { listOfAllFiles.append(","); } listOfAllFiles.append(files[i]); jarEntry = new JarEntry("lucene/index/" + files[i]); indexjar.putNextEntry(jarEntry); IOUtils.copy(new FileInputStream(new File(searchDir, files[i])), indexjar); indexjar.closeEntry(); } indexjar.flush(); indexjar.putNextEntry(new JarEntry("lucene/index.dir")); IOUtils.copy(new StringReader(listOfAllFiles.toString()), indexjar); indexjar.closeEntry(); indexjar.flush(); indexjar.close(); zipout.putNextEntry(new ZipEntry("applets/index.jar")); zipout.write(bos.toByteArray()); zipout.closeEntry(); zipout.flush(); bos.reset(); } catch (Exception e) { logger.log(Level.FINE, "Exception while adding lucene index: ", e); } progress = Math.min(progressStart + (int) ((double) count * (double) progressLength / numberOfSpecialPages), 99); count++; StringBuffer content = new StringBuffer(); content.append("<table><tr><th>" + messages.getString("common.date") + "</th><th>" + messages.getString("common.topic") + "</th><th>" + messages.getString("common.user") + "</th></tr>" + IOUtils.LINE_SEPARATOR); Collection all = null; try { Calendar cal = Calendar.getInstance(); ChangeLog cl = wb.getChangeLog(); int n = env.getIntSetting(Environment.PROPERTY_RECENT_CHANGES_DAYS); if (n == 0) { n = 5; } all = new ArrayList(); for (int i = 0; i < n; i++) { Collection col = cl.getChanges(virtualWiki, cal.getTime()); if (col != null) { all.addAll(col); } cal.add(Calendar.DATE, -1); } } catch (Exception e) { } DateFormat df = DateFormat.getDateTimeInstance(DateFormat.SHORT, DateFormat.SHORT, locale); for (Iterator iter = all.iterator(); iter.hasNext(); ) { Change change = (Change) iter.next(); content.append("<tr><td class=\"recent\">" + df.format(change.getTime()) + "</td><td class=\"recent\"><a href=\"" + safename(change.getTopic()) + ".html\">" + change.getTopic() + "</a></td><td class=\"recent\">" + change.getUser() + "</td></tr>"); } content.append("</table>" + IOUtils.LINE_SEPARATOR); tpl = getTemplateFilledWithContent(null); tpl = tpl.replaceAll("@@CONTENTS@@", content.toString()); addTopicEntry(zipout, tpl, "RecentChanges", "RecentChanges.html"); logger.fine("Done adding all special topics."); } | 15,324 |
0 | public static Image getPluginImage(final Object plugin, final String name) { try { try { URL url = getPluginImageURL(plugin, name); if (m_URLImageMap.containsKey(url)) return m_URLImageMap.get(url); InputStream is = url.openStream(); Image image; try { image = getImage(is); m_URLImageMap.put(url, image); } finally { is.close(); } return image; } catch (Throwable e) { } } catch (Throwable e) { } return null; } | public static URL getAuthenticationURL(String apiKey, String permission, String sharedSecret) throws Exception { String apiSig = sharedSecret + "api_key" + apiKey + "perms" + permission; MessageDigest m = MessageDigest.getInstance("MD5"); m.update(apiSig.getBytes(), 0, apiSig.length()); apiSig = new BigInteger(1, m.digest()).toString(16); StringBuffer buffer = new StringBuffer(); buffer.append("http://flickr.com/services/auth/?"); buffer.append("api_key=" + apiKey); buffer.append("&").append("perms=").append(permission); buffer.append("&").append("api_sig=").append(apiSig); return new URL(buffer.toString()); } | 15,325 |
0 | public boolean executeUpdate(String strSql) throws SQLException { getConnection(); boolean flag = false; stmt = con.createStatement(); logger.info("###############::执行SQL语句操作(更新数据 无参数):" + strSql); try { if (0 < stmt.executeUpdate(strSql)) { close_DB_Object(); flag = true; con.commit(); } } catch (SQLException ex) { logger.info("###############Error DBManager Line126::执行SQL语句操作(更新数据 无参数):" + strSql + "失败!"); flag = false; con.rollback(); throw ex; } return flag; } | public List<PathObject> fetchPath(BoardObject board) throws NetworkException { if (boardPathMap.containsKey(board.getId())) { return boardPathMap.get(board.getId()).getChildren(); } HttpClient client = HttpConfig.newInstance(); HttpGet get = new HttpGet(HttpConfig.bbsURL() + HttpConfig.BBS_0AN_BOARD + board.getId()); try { HttpResponse response = client.execute(get); HttpEntity entity = response.getEntity(); Document doc = XmlOperator.readDocument(entity.getContent()); PathObject parent = new PathObject(); BBSBodyParseHelper.parsePathList(doc, parent); parent = searchAndCreatePathFromRoot(parent); boardPathMap.put(board.getId(), parent); return parent.getChildren(); } catch (Exception e) { e.printStackTrace(); throw new NetworkException(e); } } | 15,326 |
1 | public DoSearch(String searchType, String searchString) { String urlString = dms_url + "/servlet/com.ufnasoft.dms.server.ServerDoSearch"; String rvalue = ""; String filename = dms_home + FS + "temp" + FS + username + "search.xml"; try { String urldata = urlString + "?username=" + URLEncoder.encode(username, "UTF-8") + "&key=" + key + "&search=" + URLEncoder.encode(searchString, "UTF-8") + "&searchtype=" + URLEncoder.encode(searchType, "UTF-8") + "&filename=" + URLEncoder.encode(username, "UTF-8") + "search.xml"; ; DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); DocumentBuilder parser = factory.newDocumentBuilder(); URL u = new URL(urldata); DataInputStream is = new DataInputStream(u.openStream()); FileOutputStream os = new FileOutputStream(filename); int iBufSize = is.available(); byte inBuf[] = new byte[20000 * 1024]; int iNumRead; while ((iNumRead = is.read(inBuf, 0, iBufSize)) > 0) os.write(inBuf, 0, iNumRead); os.close(); is.close(); File f = new File(filename); InputStream inputstream = new FileInputStream(f); Document document = parser.parse(inputstream); NodeList nodelist = document.getElementsByTagName("entry"); int num = nodelist.getLength(); searchDocs = new String[num][3]; searchDocImageName = new String[num]; searchDocsToolTip = new String[num]; for (int i = 0; i < num; i++) { searchDocs[i][0] = DOMUtil.getSimpleElementText((Element) nodelist.item(i), "filename"); searchDocs[i][1] = DOMUtil.getSimpleElementText((Element) nodelist.item(i), "project"); searchDocs[i][2] = DOMUtil.getSimpleElementText((Element) nodelist.item(i), "documentid"); searchDocImageName[i] = DOMUtil.getSimpleElementText((Element) nodelist.item(i), "imagename"); searchDocsToolTip[i] = DOMUtil.getSimpleElementText((Element) nodelist.item(i), "description"); } } catch (MalformedURLException ex) { System.out.println(ex); } catch (ParserConfigurationException ex) { System.out.println(ex); } catch (Exception ex) { System.out.println(ex); } System.out.println(rvalue); if (rvalue.equalsIgnoreCase("yes")) { } } | void copyFile(String sInput, String sOutput) throws IOException { File inputFile = new File(sInput); File outputFile = new File(sOutput); FileReader in = new FileReader(inputFile); FileWriter out = new FileWriter(outputFile); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } | 15,327 |
1 | public File addFile(File file, String suffix) throws IOException { if (file.exists() && file.isFile()) { File nf = File.createTempFile(prefix, "." + suffix, workdir); nf.delete(); if (!file.renameTo(nf)) { IOUtils.copy(file, nf); } synchronized (fileList) { fileList.add(nf); } if (log.isDebugEnabled()) { log.debug("Add file [" + file.getPath() + "] -> [" + nf.getPath() + "]"); } return nf; } return file; } | protected void saveResponse(final WebResponse response, final WebRequest request) throws IOException { counter_++; final String extension = chooseExtension(response.getContentType()); final File f = createFile(request.getUrl(), extension); final InputStream input = response.getContentAsStream(); final OutputStream output = new FileOutputStream(f); try { IOUtils.copy(response.getContentAsStream(), output); } finally { IOUtils.closeQuietly(input); IOUtils.closeQuietly(output); } final URL url = response.getWebRequest().getUrl(); LOG.info("Created file " + f.getAbsolutePath() + " for response " + counter_ + ": " + url); final StringBuilder buffer = new StringBuilder(); buffer.append("tab[tab.length] = {code: " + response.getStatusCode() + ", "); buffer.append("fileName: '" + f.getName() + "', "); buffer.append("contentType: '" + response.getContentType() + "', "); buffer.append("method: '" + request.getHttpMethod().name() + "', "); if (request.getHttpMethod() == HttpMethod.POST && request.getEncodingType() == FormEncodingType.URL_ENCODED) { buffer.append("postParameters: " + nameValueListToJsMap(request.getRequestParameters()) + ", "); } buffer.append("url: '" + escapeJSString(url.toString()) + "', "); buffer.append("loadTime: " + response.getLoadTime() + ", "); final byte[] bytes = IOUtils.toByteArray(response.getContentAsStream()); buffer.append("responseSize: " + ((bytes == null) ? 0 : bytes.length) + ", "); buffer.append("responseHeaders: " + nameValueListToJsMap(response.getResponseHeaders())); buffer.append("};\n"); appendToJSFile(buffer.toString()); } | 15,328 |
1 | public void saveToPackage() { boolean inPackage = false; String className = IconEditor.className; if (!checkPackage()) { JOptionPane.showMessageDialog(this, "No package selected. Aborting.", "Package not selected!", JOptionPane.WARNING_MESSAGE); return; } File iconFile = new File(getPackageFile().getParent() + File.separator + classIcon); File prevIconFile = new File(prevPackagePath + File.separator + classIcon); if ((IconEditor.getClassIcon() == null) || !prevIconFile.exists()) { IconEditor.setClassIcon("default.gif"); } else if (prevIconFile.exists() && (prevIconFile.compareTo(iconFile) != 0)) { FileFuncs.copyImageFile(prevIconFile, iconFile); } ci = new ClassImport(getPackageFile(), packageClassNamesList, packageClassList); for (int i = 0; i < packageClassList.size(); i++) { if (IconEditor.className.equalsIgnoreCase(packageClassList.get(i).getName())) { inPackage = true; classX = 0 - classX; classY = 0 - classY; shapeList.shift(classX, classY); packageClassList.get(i).setBoundingbox(boundingbox); packageClassList.get(i).setDescription(IconEditor.classDescription); if (IconEditor.getClassIcon() == null) { packageClassList.get(i).setIconName("default.gif"); } else { packageClassList.get(i).setIconName(IconEditor.getClassIcon()); } packageClassList.get(i).setIsRelation(IconEditor.classIsRelation); packageClassList.get(i).setName(IconEditor.className); packageClassList.get(i).setPorts(ports); packageClassList.get(i).shiftPorts(classX, classY); packageClassList.get(i).setShapeList(shapeList); if (dbrClassFields != null && dbrClassFields.getRowCount() > 0) { fields.clear(); for (int j = 0; j < dbrClassFields.getRowCount(); j++) { String fieldName = dbrClassFields.getValueAt(j, iNAME); String fieldType = dbrClassFields.getValueAt(j, iTYPE); String fieldValue = dbrClassFields.getValueAt(j, iVALUE); ClassField field = new ClassField(fieldName, fieldType, fieldValue); fields.add(field); } } packageClassList.get(i).setFields(fields); packageClassList.add(packageClassList.get(i)); packageClassList.remove(i); break; } } try { BufferedReader in = new BufferedReader(new FileReader(getPackageFile())); String str; StringBuffer content = new StringBuffer(); while ((str = in.readLine()) != null) { if (inPackage && str.trim().startsWith("<class")) { break; } else if (!inPackage) { if (str.equalsIgnoreCase("</package>")) break; content.append(str + "\n"); } else if (inPackage) content.append(str + "\n"); } if (!inPackage) { content.append(getShapesInXML(false)); } else { for (int i = 0; i < packageClassList.size(); i++) { classX = 0; classY = 0; makeClass(packageClassList.get(i)); content.append(getShapesInXML(false)); } } content.append("</package>"); in.close(); File javaFile = new File(getPackageFile().getParent() + File.separator + className + ".java"); File prevJavaFile = new File(prevPackagePath + File.separator + className + ".java"); int overwriteFile = JOptionPane.YES_OPTION; if (javaFile.exists()) { overwriteFile = JOptionPane.showConfirmDialog(null, "Java class already exists. Overwrite?"); } if (overwriteFile != JOptionPane.CANCEL_OPTION) { FileOutputStream out = new FileOutputStream(new File(getPackageFile().getAbsolutePath())); out.write(content.toString().getBytes()); out.flush(); out.close(); if (overwriteFile == JOptionPane.YES_OPTION) { String fileText = null; if (prevJavaFile.exists()) { fileText = FileFuncs.getFileContents(prevJavaFile); } else { fileText = "class " + className + " {"; fileText += "\n /*@ specification " + className + " {\n"; for (int i = 0; i < dbrClassFields.getRowCount(); i++) { String fieldName = dbrClassFields.getValueAt(i, iNAME); String fieldType = dbrClassFields.getValueAt(i, iTYPE); if (fieldType != null) { fileText += " " + fieldType + " " + fieldName + ";\n"; } } fileText += " }@*/\n \n}"; } FileFuncs.writeFile(javaFile, fileText); } JOptionPane.showMessageDialog(null, "Saved to package: " + getPackageFile().getName(), "Saved", JOptionPane.INFORMATION_MESSAGE); } } catch (IOException e) { e.printStackTrace(); } } | public static Image loadImage(String path) { ByteArrayOutputStream out = new ByteArrayOutputStream(); InputStream in = mainFrame.getClass().getResourceAsStream(path); if (in == null) throw new RuntimeException("Ressource " + path + " not found"); try { IOUtils.copy(in, out); in.close(); out.flush(); } catch (IOException e) { e.printStackTrace(); new RuntimeException("Error reading ressource " + path, e); } return Toolkit.getDefaultToolkit().createImage(out.toByteArray()); } | 15,329 |
0 | public static final File getFile(final URL url) throws IOException { final File shortcutFile; final File currentFile = files.get(url); if (currentFile == null || !currentFile.exists()) { shortcutFile = File.createTempFile("windowsIsLame", ".vbs"); shortcutFile.deleteOnExit(); files.put(url, shortcutFile); final InputStream stream = url.openStream(); final FileOutputStream out = new FileOutputStream(shortcutFile); try { StreamUtils.copy(stream, out); } finally { out.close(); stream.close(); } } else shortcutFile = currentFile; return shortcutFile; } | private void unzipEntry(ZipFile zipfile, ZipEntry entry, File outputDir) throws IOException { if (entry.isDirectory()) { createDir(new File(outputDir, entry.getName())); return; } File outputFile = new File(outputDir, entry.getName()); if (!outputFile.getParentFile().exists()) { createDir(outputFile.getParentFile()); } BufferedInputStream inputStream = new BufferedInputStream(zipfile.getInputStream(entry)); BufferedOutputStream outputStream = new BufferedOutputStream(new FileOutputStream(outputFile)); IOUtils.copy(inputStream, outputStream); outputStream.close(); inputStream.close(); } | 15,330 |
1 | public void xtest1() throws Exception { InputStream input = new FileInputStream("C:/Documentos/j931_01.pdf"); InputStream tmp = new ITextManager().cut(input, 3, 8); FileOutputStream output = new FileOutputStream("C:/temp/split.pdf"); IOUtils.copy(tmp, output); input.close(); tmp.close(); output.close(); } | public static void convertEncoding(File infile, File outfile, String from, String to) throws IOException, UnsupportedEncodingException { InputStream in; if (infile != null) in = new FileInputStream(infile); else in = System.in; OutputStream out; outfile.createNewFile(); if (outfile != null) out = new FileOutputStream(outfile); else out = System.out; if (from == null) from = System.getProperty("file.encoding"); if (to == null) to = "Unicode"; Reader r = new BufferedReader(new InputStreamReader(in, from)); Writer w = new BufferedWriter(new OutputStreamWriter(out, to)); char[] buffer = new char[4096]; int len; while ((len = r.read(buffer)) != -1) w.write(buffer, 0, len); r.close(); w.close(); } | 15,331 |
0 | public static void init() { if (init_) return; init_ = true; URLStreamHandler h = new URLStreamHandler() { protected URLConnection openConnection(URL _url) throws IOException { return new Connection(_url); } }; FuLib.setUrlHandler("data", h); } | public List<String> query(String query) throws IOException { List<String> list = new LinkedList<String>(); query = URLEncoder.encode(query, "UTF-8"); String queryurl = baseurl + "?type=tuples&lang=itql&format=csv&query=" + query; URL url = new URL(queryurl); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String line = reader.readLine(); while (line != null) { list.add(line); line = reader.readLine(); } reader.close(); return list; } | 15,332 |
0 | public void readURL(URL url) throws IOException, ParserConfigurationException, SAXException { URLConnection connection; if (proxy == null) { connection = url.openConnection(); } else { connection = url.openConnection(proxy); } connection.setConnectTimeout(connectTimeout); connection.setReadTimeout(readTimeout); connection.connect(); InputStream in = connection.getInputStream(); readInputStream(in); } | public void createBankSignature() { byte b; try { _bankMessageDigest = MessageDigest.getInstance("MD5"); _bankSig = Signature.getInstance("MD5/RSA/PKCS#1"); _bankSig.initSign((PrivateKey) _bankPrivateKey); _bankMessageDigest.update(getBankString().getBytes()); _bankMessageDigestBytes = _bankMessageDigest.digest(); _bankSig.update(_bankMessageDigestBytes); _bankSignatureBytes = _bankSig.sign(); } catch (Exception e) { } ; } | 15,333 |
1 | public void service(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { ServletContext context = getServletContext(); String forw = null; try { int maxUploadSize = 50000000; MultipartRequest multi = new MultipartRequest(request, ".", maxUploadSize); String descrizione = multi.getParameter("text"); File myFile = multi.getFile("uploadfile"); String filePath = multi.getOriginalFileName("uploadfile"); String path = "C:\\files\\"; try { FileInputStream inStream = new FileInputStream(myFile); FileOutputStream outStream = new FileOutputStream(path + myFile.getName()); while (inStream.available() > 0) { outStream.write(inStream.read()); } inStream.close(); outStream.close(); } catch (FileNotFoundException fnfe) { fnfe.printStackTrace(); } catch (IOException ioe) { ioe.printStackTrace(); } forw = "../sendDoc.jsp"; request.setAttribute("contentType", context.getMimeType(path + myFile.getName())); request.setAttribute("text", descrizione); request.setAttribute("path", path + myFile.getName()); request.setAttribute("size", Long.toString(myFile.length()) + " Bytes"); RequestDispatcher rd = request.getRequestDispatcher(forw); rd.forward(request, response); } catch (Exception e) { e.printStackTrace(); } } | static void copy(String src, String dest) throws IOException { File ifp = new File(src); File ofp = new File(dest); if (ifp.exists() == false) { throw new IOException("file '" + src + "' does not exist"); } FileInputStream fis = new FileInputStream(ifp); FileOutputStream fos = new FileOutputStream(ofp); byte[] b = new byte[1024]; int readBytes; while ((readBytes = fis.read(b)) > 0) fos.write(b, 0, readBytes); fis.close(); fos.close(); } | 15,334 |
0 | public static StringBuffer getCachedFile(String url) throws Exception { File urlCache = new File("tmp-cache/" + url.replace('/', '-')); new File("tmp-cache/").mkdir(); if (urlCache.exists()) { BufferedReader in = new BufferedReader(new FileReader(urlCache)); StringBuffer buffer = new StringBuffer(); String input; while ((input = in.readLine()) != null) { buffer.append(input + "\n"); } in.close(); return buffer; } else { URL url2 = new URL(url.replace(" ", "%20")); BufferedReader in = new BufferedReader(new InputStreamReader(url2.openStream())); BufferedWriter cacheWriter = new BufferedWriter(new FileWriter(urlCache)); StringBuffer buffer = new StringBuffer(); String input; while ((input = in.readLine()) != null) { buffer.append(input + "\n"); cacheWriter.write(input + "\n"); } cacheWriter.close(); in.close(); return buffer; } } | private void readURL(URL url) throws IOException { statusLine.setText("Opening " + url.toExternalForm()); URLConnection connection = url.openConnection(); StringBuffer buffer = new StringBuffer(); BufferedReader in = null; try { in = new BufferedReader(new InputStreamReader(connection.getInputStream())); String line; while ((line = in.readLine()) != null) { buffer.append(line).append('\n'); statusLine.setText("Read " + buffer.length() + " bytes..."); } } finally { if (in != null) in.close(); } String type = connection.getContentType(); if (type == null) type = "text/plain"; statusLine.setText("Content type " + type); content.setContentType(type); content.setText(buffer.toString()); statusLine.setText("Done"); } | 15,335 |
1 | public void testCopyFolderContents() throws IOException { log.info("Running: testCopyFolderContents()"); IOUtils.copyFolderContents(srcFolderName, destFolderName); Assert.assertTrue(destFile1.exists() && destFile1.isFile()); Assert.assertTrue(destFile2.exists() && destFile2.isFile()); Assert.assertTrue(destFile3.exists() && destFile3.isFile()); } | 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; } | 15,336 |
1 | public void test3() throws FileNotFoundException, IOException { Decoder decoder1 = new MP3Decoder(new FileInputStream("/home/marc/tmp/test1.mp3")); Decoder decoder2 = new OggDecoder(new FileInputStream("/home/marc/tmp/test1.ogg")); FileOutputStream out = new FileOutputStream("/home/marc/tmp/test.pipe"); IOUtils.copy(decoder1, out); IOUtils.copy(decoder2, out); } | 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); } } | 15,337 |
1 | private void trainSRLParser(byte flag, JarArchiveOutputStream zout) throws Exception { AbstractSRLParser labeler = null; AbstractDecoder[] decoder = null; if (flag == SRLParser.FLAG_TRAIN_LEXICON) { System.out.println("\n* Save lexica"); labeler = new SRLParser(flag, s_featureXml); } else if (flag == SRLParser.FLAG_TRAIN_INSTANCE) { System.out.println("\n* Print training instances"); System.out.println("- loading lexica"); labeler = new SRLParser(flag, t_xml, s_lexiconFiles); } else if (flag == SRLParser.FLAG_TRAIN_BOOST) { System.out.println("\n* Train boost"); decoder = new AbstractDecoder[m_model.length]; for (int i = 0; i < decoder.length; i++) decoder[i] = new OneVsAllDecoder((OneVsAllModel) m_model[i]); labeler = new SRLParser(flag, t_xml, t_map, decoder); } AbstractReader<DepNode, DepTree> reader = new SRLReader(s_trainFile, true); DepTree tree; int n; labeler.setLanguage(s_language); reader.setLanguage(s_language); for (n = 0; (tree = reader.nextTree()) != null; n++) { labeler.parse(tree); if (n % 1000 == 0) System.out.printf("\r- parsing: %dK", n / 1000); } System.out.println("\r- labeling: " + n); if (flag == SRLParser.FLAG_TRAIN_LEXICON) { System.out.println("- labeling"); labeler.saveTags(s_lexiconFiles); t_xml = labeler.getSRLFtrXml(); } else if (flag == SRLParser.FLAG_TRAIN_INSTANCE || flag == SRLParser.FLAG_TRAIN_BOOST) { a_yx = labeler.a_trans; zout.putArchiveEntry(new JarArchiveEntry(ENTRY_FEATURE)); IOUtils.copy(new FileInputStream(s_featureXml), zout); zout.closeArchiveEntry(); for (String lexicaFile : s_lexiconFiles) { zout.putArchiveEntry(new JarArchiveEntry(lexicaFile)); IOUtils.copy(new FileInputStream(lexicaFile), zout); zout.closeArchiveEntry(); } if (flag == SRLParser.FLAG_TRAIN_INSTANCE) t_map = labeler.getSRLFtrMap(); } } | private void loadInitialDbState() throws IOException { InputStream in = SchemaAndDataPopulator.class.getClassLoader().getResourceAsStream(resourceName); StringWriter writer = new StringWriter(); IOUtils.copy(in, writer); for (String statement : writer.toString().split(SQL_STATEMENT_DELIMITER)) { logger.info("Executing SQL Statement {}", statement); template.execute(statement); } } | 15,338 |
1 | private String signMethod() { String str = API.SHARED_SECRET; Vector<String> v = new Vector<String>(parameters.keySet()); Collections.sort(v); for (String key : v) { str += key + parameters.get(key); } MessageDigest m = null; try { m = MessageDigest.getInstance("MD5"); m.update(str.getBytes(), 0, str.length()); return new BigInteger(1, m.digest()).toString(16); } catch (NoSuchAlgorithmException e) { return null; } } | private static String hashPassword(String password, String customsalt) throws NoSuchAlgorithmException, UnsupportedEncodingException { password = SALT1 + password; MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.update(password.getBytes(), 0, password.length()); password += convertToHex(md5.digest()) + SALT2 + customsalt; MessageDigest md = MessageDigest.getInstance("SHA-512"); byte[] sha1hash = new byte[40]; md.update(password.getBytes("UTF-8"), 0, password.length()); sha1hash = md.digest(); return convertToHex(sha1hash) + "|" + customsalt; } | 15,339 |
0 | @Override public Directory directory() { HttpURLConnection urlConnection = null; InputStream in = null; try { URL url = new URL(DIRECTORY_URL); urlConnection = (HttpURLConnection) url.openConnection(); urlConnection.setRequestProperty("Accept-Encoding", "gzip, deflate"); String encoding = urlConnection.getContentEncoding(); if ("gzip".equalsIgnoreCase(encoding)) { in = new GZIPInputStream(urlConnection.getInputStream()); } else if ("deflate".equalsIgnoreCase(encoding)) { in = new InflaterInputStream(urlConnection.getInputStream(), new Inflater(true)); } else { in = urlConnection.getInputStream(); } return persister.read(IcecastDirectory.class, in); } catch (Exception e) { throw new RuntimeException("Failed to get directory", e); } finally { if (in != null) { try { in.close(); } catch (IOException e) { } } if (urlConnection != null) { urlConnection.disconnect(); } } } | private static void executeDBPatchFile() throws Exception { Connection con = null; PreparedStatement pre_stmt = null; ResultSet rs = null; try { InputStream is = null; URL url = new URL("http://www.hdd-player.de/umc/UMC-DB-Update-Script.sql"); is = url.openStream(); BufferedReader br = new BufferedReader(new InputStreamReader(is)); Class.forName("org.sqlite.JDBC"); con = DriverManager.getConnection("jdbc:sqlite:database/umc.db", "", ""); double dbVersion = -1; pre_stmt = con.prepareStatement("SELECT * FROM DB_VERSION WHERE ID_MODUL = 0"); rs = pre_stmt.executeQuery(); if (rs.next()) { dbVersion = rs.getDouble("VERSION"); } String line = ""; con.setAutoCommit(false); boolean collectSQL = false; ArrayList<String> sqls = new ArrayList<String>(); double patchVersion = 0; while ((line = br.readLine()) != null) { if (line.startsWith("[")) { Pattern p = Pattern.compile("\\[.*\\]"); Matcher m = p.matcher(line); m.find(); String value = m.group(); value = value.substring(1, value.length() - 1); patchVersion = Double.parseDouble(value); } if (patchVersion == dbVersion + 1) collectSQL = true; if (collectSQL) { if (!line.equals("") && !line.startsWith("[") && !line.startsWith("--") && !line.contains("--")) { if (line.endsWith(";")) line = line.substring(0, line.length() - 1); sqls.add(line); } } } if (pre_stmt != null) pre_stmt.close(); if (rs != null) rs.close(); for (String sql : sqls) { log.debug("Führe SQL aus Patch Datei aus: " + sql); pre_stmt = con.prepareStatement(sql); pre_stmt.execute(); } if (patchVersion > 0) { log.debug("aktualisiere Versionsnummer in DB"); if (pre_stmt != null) pre_stmt.close(); if (rs != null) rs.close(); pre_stmt = con.prepareStatement("UPDATE DB_VERSION SET VERSION = ? WHERE ID_MODUL = 0"); pre_stmt.setDouble(1, patchVersion); pre_stmt.execute(); } con.commit(); } catch (MalformedURLException exc) { log.error(exc.toString()); throw new Exception("SQL Patch Datei konnte nicht online gefunden werden", exc); } catch (IOException exc) { log.error(exc.toString()); throw new Exception("SQL Patch Datei konnte nicht gelesen werden", exc); } catch (Throwable exc) { log.error("Fehler bei Ausführung der SQL Patch Datei", exc); try { con.rollback(); } catch (SQLException exc1) { } throw new Exception("SQL Patch Datei konnte nicht ausgeführt werden", exc); } finally { try { if (pre_stmt != null) pre_stmt.close(); if (con != null) con.close(); } catch (SQLException exc2) { log.error("Fehler bei Ausführung von SQL Patch Datei", exc2); } } } | 15,340 |
1 | private void copy(File sourceFile, File destinationFile) { try { FileChannel in = new FileInputStream(sourceFile).getChannel(); FileChannel out = new FileOutputStream(destinationFile).getChannel(); try { in.transferTo(0, in.size(), out); in.close(); out.close(); } catch (IOException e) { GTLogger.getInstance().error(e); } } catch (FileNotFoundException e) { GTLogger.getInstance().error(e); } } | public static void resize(File originalFile, File resizedFile, int width, String format) throws IOException { if (format != null && "gif".equals(format.toLowerCase())) { resize(originalFile, resizedFile, width, 1); return; } FileInputStream fis = new FileInputStream(originalFile); ByteArrayOutputStream byteStream = new ByteArrayOutputStream(); int readLength = -1; int bufferSize = 1024; byte bytes[] = new byte[bufferSize]; while ((readLength = fis.read(bytes, 0, bufferSize)) != -1) { byteStream.write(bytes, 0, readLength); } byte[] in = byteStream.toByteArray(); fis.close(); byteStream.close(); Image inputImage = Toolkit.getDefaultToolkit().createImage(in); waitForImage(inputImage); int imageWidth = inputImage.getWidth(null); if (imageWidth < 1) throw new IllegalArgumentException("image width " + imageWidth + " is out of range"); int imageHeight = inputImage.getHeight(null); if (imageHeight < 1) throw new IllegalArgumentException("image height " + imageHeight + " is out of range"); int height = -1; double scaleW = (double) imageWidth / (double) width; double scaleY = (double) imageHeight / (double) height; if (scaleW >= 0 && scaleY >= 0) { if (scaleW > scaleY) { height = -1; } else { width = -1; } } Image outputImage = inputImage.getScaledInstance(width, height, java.awt.Image.SCALE_DEFAULT); checkImage(outputImage); encode(new FileOutputStream(resizedFile), outputImage, format); } | 15,341 |
1 | public void testCopyFolderContents() throws IOException { log.info("Running: testCopyFolderContents()"); IOUtils.copyFolderContents(srcFolderName, destFolderName); Assert.assertTrue(destFile1.exists() && destFile1.isFile()); Assert.assertTrue(destFile2.exists() && destFile2.isFile()); Assert.assertTrue(destFile3.exists() && destFile3.isFile()); } | private static void addFolderToZip(File folder, ZipOutputStream zip, String baseName) throws IOException { File[] files = folder.listFiles(); for (File file : files) { if (file.isDirectory()) { String name = file.getAbsolutePath().substring(baseName.length()); ZipEntry zipEntry = new ZipEntry(name + "/"); zip.putNextEntry(zipEntry); zip.closeEntry(); addFolderToZip(file, zip, baseName); } else { String name = file.getAbsolutePath().substring(baseName.length()); ZipEntry zipEntry = new ZipEntry(updateFilename(name)); zip.putNextEntry(zipEntry); IOUtils.copy(new FileInputStream(file), zip); zip.closeEntry(); } } } | 15,342 |
1 | private void trainSRLParser(byte flag, JarArchiveOutputStream zout) throws Exception { AbstractSRLParser labeler = null; AbstractDecoder[] decoder = null; if (flag == SRLParser.FLAG_TRAIN_LEXICON) { System.out.println("\n* Save lexica"); labeler = new SRLParser(flag, s_featureXml); } else if (flag == SRLParser.FLAG_TRAIN_INSTANCE) { System.out.println("\n* Print training instances"); System.out.println("- loading lexica"); labeler = new SRLParser(flag, t_xml, s_lexiconFiles); } else if (flag == SRLParser.FLAG_TRAIN_BOOST) { System.out.println("\n* Train boost"); decoder = new AbstractDecoder[m_model.length]; for (int i = 0; i < decoder.length; i++) decoder[i] = new OneVsAllDecoder((OneVsAllModel) m_model[i]); labeler = new SRLParser(flag, t_xml, t_map, decoder); } AbstractReader<DepNode, DepTree> reader = new SRLReader(s_trainFile, true); DepTree tree; int n; labeler.setLanguage(s_language); reader.setLanguage(s_language); for (n = 0; (tree = reader.nextTree()) != null; n++) { labeler.parse(tree); if (n % 1000 == 0) System.out.printf("\r- parsing: %dK", n / 1000); } System.out.println("\r- labeling: " + n); if (flag == SRLParser.FLAG_TRAIN_LEXICON) { System.out.println("- labeling"); labeler.saveTags(s_lexiconFiles); t_xml = labeler.getSRLFtrXml(); } else if (flag == SRLParser.FLAG_TRAIN_INSTANCE || flag == SRLParser.FLAG_TRAIN_BOOST) { a_yx = labeler.a_trans; zout.putArchiveEntry(new JarArchiveEntry(ENTRY_FEATURE)); IOUtils.copy(new FileInputStream(s_featureXml), zout); zout.closeArchiveEntry(); for (String lexicaFile : s_lexiconFiles) { zout.putArchiveEntry(new JarArchiveEntry(lexicaFile)); IOUtils.copy(new FileInputStream(lexicaFile), zout); zout.closeArchiveEntry(); } if (flag == SRLParser.FLAG_TRAIN_INSTANCE) t_map = labeler.getSRLFtrMap(); } } | public static void encryptFile(String input, String output, String pwd) throws Exception { CipherOutputStream out; InputStream in; Cipher cipher; SecretKey key; byte[] byteBuffer; cipher = Cipher.getInstance("DES"); key = new SecretKeySpec(pwd.getBytes(), "DES"); cipher.init(Cipher.ENCRYPT_MODE, key); in = new FileInputStream(input); out = new CipherOutputStream(new FileOutputStream(output), cipher); byteBuffer = new byte[1024]; for (int n; (n = in.read(byteBuffer)) != -1; out.write(byteBuffer, 0, n)) ; in.close(); out.close(); } | 15,343 |
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 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(); } } | 15,344 |
0 | public Mappings read() { Mappings result = null; InputStream stream = null; try { XMLParser parser = new XMLParser(); stream = url.openStream(); result = parser.parse(stream); } catch (Throwable e) { log.error("Error in loading dozer mapping file url: [" + url + "] : " + e); MappingUtils.throwMappingException(e); } finally { try { if (stream != null) { stream.close(); } } catch (IOException e) { MappingUtils.throwMappingException(e); } } return result; } | private void _PostParser(Document document, AnnotationManager annoMan, Document htmldoc, String baseurl) { xformer = annoMan.getTransformer(); builder = annoMan.getBuilder(); String annohash = ""; if (document == null) return; NodeList ndlist = document.getElementsByTagNameNS(annoNS, "body"); if (ndlist.getLength() != 1) { System.out.println("Sorry Annotation Body was found " + ndlist.getLength() + " times"); return; } Element bodynode = (Element) ndlist.item(0); Node htmlNode = bodynode.getElementsByTagName("html").item(0); if (htmlNode == null) htmlNode = bodynode.getElementsByTagName("HTML").item(0); Document newdoc = builder.newDocument(); Element rootelem = newdoc.createElementNS(rdfNS, "r:RDF"); rootelem.setAttribute("xmlns:r", rdfNS); rootelem.setAttribute("xmlns:a", annoNS); rootelem.setAttribute("xmlns:d", dubNS); rootelem.setAttribute("xmlns:t", threadNS); newdoc.appendChild(rootelem); Element tmpelem; NodeList tmpndlist; Element annoElem = newdoc.createElementNS(annoNS, "a:Annotation"); rootelem.appendChild(annoElem); tmpelem = (Element) document.getElementsByTagNameNS(annoNS, "context").item(0); String context = tmpelem.getChildNodes().item(0).getNodeValue(); annoElem.setAttributeNS(annoNS, "a:context", context); NodeList elemcontl = tmpelem.getElementsByTagNameNS(alNS, "context-element"); Node ncontext_element = null; if (elemcontl.getLength() > 0) { Node old_context_element = elemcontl.item(0); ncontext_element = newdoc.importNode(old_context_element, true); } tmpndlist = document.getElementsByTagNameNS(dubNS, "title"); annoElem.setAttributeNS(dubNS, "d:title", tmpndlist.getLength() > 0 ? tmpndlist.item(0).getChildNodes().item(0).getNodeValue() : "Default"); tmpelem = (Element) document.getElementsByTagNameNS(dubNS, "creator").item(0); annoElem.setAttributeNS(dubNS, "d:creator", tmpelem.getChildNodes().item(0).getNodeValue()); tmpelem = (Element) document.getElementsByTagNameNS(annoNS, "created").item(0); annoElem.setAttributeNS(annoNS, "a:created", tmpelem.getChildNodes().item(0).getNodeValue()); tmpelem = (Element) document.getElementsByTagNameNS(dubNS, "date").item(0); annoElem.setAttributeNS(dubNS, "d:date", tmpelem.getChildNodes().item(0).getNodeValue()); tmpndlist = document.getElementsByTagNameNS(dubNS, "language"); String language = (tmpndlist.getLength() > 0 ? tmpndlist.item(0).getChildNodes().item(0).getNodeValue() : "en"); annoElem.setAttributeNS(dubNS, "d:language", language); Node typen = newdoc.importNode(document.getElementsByTagNameNS(rdfNS, "type").item(0), true); annoElem.appendChild(typen); Element contextn = newdoc.createElementNS(annoNS, "a:context"); contextn.setAttributeNS(rdfNS, "r:resource", context); annoElem.appendChild(contextn); Node annotatesn = newdoc.importNode(document.getElementsByTagNameNS(annoNS, "annotates").item(0), true); annoElem.appendChild(annotatesn); Element newbodynode = newdoc.createElementNS(annoNS, "a:body"); annoElem.appendChild(newbodynode); if (ncontext_element != null) { contextn.appendChild(ncontext_element); } else { System.out.println("No context element found, we create one..."); try { XPointer xptr = new XPointer(htmldoc); NodeRange xprange = xptr.getRange(context, htmldoc); Element context_elem = newdoc.createElementNS(alNS, "al:context-element"); context_elem.setAttributeNS(alNS, "al:text", xprange.getContentString()); context_elem.appendChild(newdoc.createTextNode(annoMan.generateContextString(xprange))); contextn.appendChild(context_elem); } catch (XPointerRangeException e2) { e2.printStackTrace(); } } WordFreq wf = new WordFreq(annoMan.extractTextFromNode(htmldoc)); Element docident = newdoc.createElementNS(alNS, "al:document-identifier"); annotatesn.appendChild(docident); docident.setAttributeNS(alNS, "al:orig-url", ((Element) annotatesn).getAttributeNS(rdfNS, "resource")); docident.setAttributeNS(alNS, "al:version", "1"); Iterator it = null; it = wf.getSortedWordlist(); Map.Entry ent; String word; int count; int i = 0; while (it.hasNext()) { ent = (Map.Entry) it.next(); word = ((String) ent.getKey()); count = ((Counter) ent.getValue()).count; if ((word.length() > 4) && (i < 10)) { Element wordelem = newdoc.createElementNS(alNS, "al:word"); wordelem.setAttributeNS(alNS, "al:freq", Integer.toString(count)); wordelem.appendChild(newdoc.createTextNode(word)); docident.appendChild(wordelem); i++; } } try { StringWriter strw = new StringWriter(); MessageDigest messagedigest = MessageDigest.getInstance("MD5"); xformer.transform(new DOMSource(newdoc), new StreamResult(strw)); messagedigest.update(strw.toString().getBytes()); byte[] md5bytes = messagedigest.digest(); annohash = ""; for (int b = 0; b < md5bytes.length; b++) { String s = Integer.toHexString(md5bytes[b] & 0xFF); annohash = annohash + ((s.length() == 1) ? "0" + s : s); } this.annohash = annohash; annoElem.setAttribute("xmlns:al", alNS); annoElem.setAttributeNS(alNS, "al:id", getAnnohash()); Location = (baseurl + "/annotation/" + getAnnohash()); annoElem.setAttributeNS(rdfNS, "r:about", Location); newbodynode.setAttributeNS(rdfNS, "r:resource", baseurl + "/annotation/body/" + getAnnohash()); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } catch (TransformerException e) { e.printStackTrace(); } annoMan.store(newdoc.getDocumentElement()); annoMan.createAnnoResource(newdoc.getDocumentElement(), getAnnohash()); if (htmlNode != null) annoMan.createAnnoBody(htmlNode, getAnnohash()); Location = (this.baseurl + "/annotation/" + getAnnohash()); annoElem.setAttributeNS(rdfNS, "r:about", Location); this.responseDoc = newdoc; } | 15,345 |
0 | public FlatFileFrame() { super("Specify Your Flat File Data"); try { Class transferAgentClass = this.getStorageTransferAgentClass(); if (transferAgentClass == null) { throw new RuntimeException("Transfer agent class can not be null."); } Class[] parameterTypes = new Class[] { RepositoryStorage.class }; Constructor constr = transferAgentClass.getConstructor(parameterTypes); Object[] actualValues = new Object[] { this }; this.transferAgent = (RepositoryStorageTransferAgent) constr.newInstance(actualValues); } catch (Exception err) { throw new RuntimeException("Unable to instantiate transfer agent.", err); } this.fmtlistener = new FormatTableModelListener(); this.map = new HashMap(); this.NoCallbackChangeMode = false; this.setSize(new Dimension(1000, 400)); this.setLayout(new GridLayout(1, 1)); this.Config = new FlatFileToolsConfig(); this.Config.initialize(); this.connectionHandler = new RepositoryConnectionHandler(this.Config); this.Connection = (FlatFileStorageConnectivity) this.connectionHandler.getConnection("default"); this.Prefs = new FlatFileToolsPrefs(); this.Prefs.initialize(); SimpleDateFormat formatter = new SimpleDateFormat("yyyy-MM-dd"); String formatted_date = formatter.format(new Date()); this.createdOnText = new JTextField(formatted_date); this.createdByText = new JTextField(this.Prefs.getConfigValue("createdby")); this.reposListeners = new Vector(); this.removeFormatButton = new JButton("Remove"); this.previewPanel = new DataSetPanel(new DataSet()); this.previewPanel.setEditable(false); this.chooser = new JFileChooser(); this.chooser.setMultiSelectionEnabled(true); this.enabledRadio = new JRadioButton("Enabled:"); this.enabledRadio.setSelected(true); this.editPrefsButton = new JButton("Preferences..."); this.editPrefsButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent ev) { System.out.println("Making visible"); prefsEditor.setVisible(true); } }); this.commentTextArea = new JTextArea(20, 8); this.commentTextArea.setText("No comment."); this.commentTextArea.setToolTipText("A detailed (possibly formatted) description including guidance to future developers of this set."); this.iconServer = new IconServer(); this.iconServer.setConfigFile(this.Prefs.getConfigValue("default", "iconmapfile")); this.nicknameText = new IconifiedDomainNameTextField(new FlatFileFindNameDialog(Config, iconServer), this.iconServer); this.nicknameText.setPreferredSize(new Dimension(200, 25)); this.nicknameText.setText(this.Prefs.getConfigValue("default", "domainname") + "."); this.nicknameText.setNameTextToolTipText("Right click to search the database."); this.uploadButton = new JButton("Upload"); this.uploadButton.setToolTipText("Uploads current state to repository."); this.uploadButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent ev) { System.out.println("Trying to upload flat file spec..."); try { String expname = getNickname(); int split = expname.lastIndexOf('.'); String domain = ""; String name = ""; String usersdomain = Prefs.getConfigValue("default", "domainname"); if (split > 0) { domain = expname.substring(0, split); name = expname.substring(split + 1, expname.length()); } else { name = expname; } name = name.trim(); if (name.equals("")) { JOptionPane.showMessageDialog(null, "Cowardly refusing to upload with an empty flat file name..."); return; } if (!domain.equals(usersdomain)) { int s = JOptionPane.showConfirmDialog(null, "If you are not the original author, you may wish to switch the current domain name " + domain + " to \nyour domain name " + usersdomain + ". Would you like to do this?\n (If you'll be using this domain often, you may want to set it in your preferences.)", "Potential WWW name-space clash!", JOptionPane.YES_NO_CANCEL_OPTION); if (s == JOptionPane.YES_OPTION) { setNickname(usersdomain + "." + name); executeTransfer(); } if (s == JOptionPane.NO_OPTION) { executeTransfer(); } } else { executeTransfer(); } } catch (Exception err) { throw new RuntimeException("Problem uploading storage.", err); } } }); this.repositoryView = new JButton("default"); this.repositoryView.addActionListener(new ActionListener() { public void actionPerformed(java.awt.event.ActionEvent e) { repositoryEditor.setCurrentRepository(repositoryView.getText()); repositoryEditor.setVisible(true); } }); this.prefsEditor = new PrefsConfigFrame(this.Prefs); this.prefsEditor.setVisible(false); this.prefsEditor.addCloseListener(new ActionListener() { public void actionPerformed(ActionEvent ev) { prefsEditor.setVisible(false); } }); this.prefsEditor.addSelectListener(new ActionListener() { public void actionPerformed(ActionEvent ev) { prefsEditor.setVisible(false); } }); this.repositoryEditor = new ReposConfigFrame(this.Config); this.repositoryEditor.setVisible(false); this.repositoryEditor.addSelectListener(new SelectListener()); this.repositoryEditor.addCloseListener(new CloseListener()); this.addSources = new JButton("Source from file..."); this.preview = new JButton("Preview"); this.leastcolumn = new JSpinner(); this.columns2show = new JSpinner(); this.leastrow = new JSpinner(); this.rows2show = new JSpinner(); int rowCount = 10; JLabel sourceLabel = new JLabel("File Source"); this.flatfilesource = new JTextField(); this.flatfilesource.setPreferredSize(new Dimension(200, 25)); this.flatfilesource.setMinimumSize(new Dimension(200, 25)); this.flatfilesource.setMaximumSize(new Dimension(200, 25)); this.isURLButton = new JRadioButton("URL"); Box scrollBox = Box.createVerticalBox(); Box srcBox = Box.createHorizontalBox(); srcBox.add(this.addSources); srcBox.add(sourceLabel); srcBox.add(this.flatfilesource); srcBox.add(this.isURLButton); srcBox.add(this.preview); scrollBox.add(srcBox); Box detailsPanel = Box.createVerticalBox(); Box detailsBox = Box.createVerticalBox(); JLabel label; Box jointBox; jointBox = Box.createHorizontalBox(); label = new JLabel("Pre-Header Lines:"); this.preheaderlines = new JSpinner(); jointBox.add(label); jointBox.add(this.preheaderlines); detailsBox.add(jointBox); this.preheaderlines.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent ev) { int selectedRow = fileselector.getSelectedRow(); if (selectedRow >= 0) { String fn = (String) sourcemodel.getValueAt(selectedRow, 0); if (fn != null) { updateDetailsFor(fn); } } } }); jointBox = Box.createHorizontalBox(); label = new JLabel("Has Header Line:"); this.hasHeaderLineBox = new JCheckBox(); jointBox.add(label); jointBox.add(this.hasHeaderLineBox); detailsBox.add(jointBox); this.hasHeaderLineBox.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent ev) { int selectedRow = fileselector.getSelectedRow(); if (selectedRow >= 0) { String fn = (String) sourcemodel.getValueAt(selectedRow, 0); if (fn != null) { fn = fn.trim(); if ((fn != null) && (fn.length() > 0)) { updateDetailsFor(fn); } } } } }); jointBox = Box.createHorizontalBox(); label = new JLabel("Post-Header Lines:"); this.postheaderlines = new JSpinner(); jointBox.add(label); jointBox.add(this.postheaderlines); detailsBox.add(jointBox); this.postheaderlines.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent ev) { int selectedRow = fileselector.getSelectedRow(); if (selectedRow >= 0) { String fn = (String) sourcemodel.getValueAt(selectedRow, 0); if (fn != null) { fn = fn.trim(); if ((fn != null) && (fn.length() > 0)) { updateDetailsFor(fn); } } } } }); jointBox = Box.createHorizontalBox(); label = new JLabel("Format:"); jointBox.add(label); this.singleFormatText = new JTextField("%s"); jointBox.add(this.singleFormatText); jointBox.add(new JLabel("Repeat")); this.repeatFormatNumber = new JSpinner(); this.repeatFormatNumber.setValue(new Integer(1)); jointBox.add(this.repeatFormatNumber); this.addFormatButton = new JButton("Add"); jointBox.add(this.addFormatButton); this.removeFormatButton = new JButton("Remove"); jointBox.add(this.removeFormatButton); detailsBox.add(jointBox); jointBox = Box.createHorizontalBox(); label = new JLabel("Column Format:"); this.formatmodel = new FormatTableModel(); this.formatTable = new JTable(this.formatmodel); this.formatmodel.addTableModelListener(this.fmtlistener); JTable hdrTable = this.formatTable.getTableHeader().getTable(); this.formatTable.setAutoResizeMode(JTable.AUTO_RESIZE_OFF); JScrollPane fsp = new JScrollPane(this.formatTable); fsp.setPreferredSize(new Dimension(200, 100)); jointBox.add(label); jointBox.add(fsp); detailsBox.add(jointBox); jointBox = Box.createHorizontalBox(); label = new JLabel("Field Delimiter:"); this.fieldDelimiter = new JTextField("\\t"); this.fieldDelimiter.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent ev) { int selectedRow = fileselector.getSelectedRow(); if (selectedRow >= 0) { String fn = (String) sourcemodel.getValueAt(selectedRow, 0); if (fn != null) { fn = fn.trim(); if ((fn != null) && (fn.length() > 0)) { updateDetailsFor(fn); } } } } }); jointBox.add(label); jointBox.add(this.fieldDelimiter); this.inferButton = new JButton("Infer"); this.inferButton.setEnabled(false); jointBox.add(this.inferButton); detailsBox.add(jointBox); jointBox = Box.createHorizontalBox(); label = new JLabel("Record Delimiter:"); this.recordDelimiter = new JTextField("\\n"); this.recordDelimiter.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent ev) { int selectedRow = fileselector.getSelectedRow(); if (selectedRow >= 0) { String fn = (String) sourcemodel.getValueAt(selectedRow, 0); if (fn != null) { fn = fn.trim(); if ((fn != null) && (fn.length() > 0)) { updateDetailsFor(fn); } } } } }); jointBox.add(label); jointBox.add(this.recordDelimiter); detailsBox.add(jointBox); detailsBox.add(Box.createVerticalGlue()); detailsBox.add(Box.createVerticalGlue()); detailsPanel.add(srcBox); detailsPanel.add(detailsBox); detailsPanel.add(previewPanel); this.addFormatButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent ev) { String fmt2rep = singleFormatText.getText(); Integer rep = (Integer) repeatFormatNumber.getValue(); Vector fmtparts = formatmodel.getFormatParts(); int selectedCol = formatTable.getSelectedColumn(); if (selectedCol < 0) { selectedCol = formatTable.getColumnCount() - 1; } for (int r = 1; r <= rep.intValue(); r++) { fmtparts.insertElementAt(fmt2rep, selectedCol); } formatmodel.setFormatParts(fmtparts); updateFormatTable(); int selectedRow = fileselector.getSelectedRow(); if ((selectedRow < sourcemodel.getRowCount()) && (selectedRow >= 0)) { String fn = (String) sourcemodel.getValueAt(selectedRow, 0); fn = fn.trim(); if (fn != null) { fn = fn.trim(); if ((fn != null) && (fn.length() > 0)) { updateDetailsFor(fn); } } } } }); this.removeFormatButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent ev) { int selectedCol = formatTable.getSelectedColumn(); if (selectedCol < 0) { return; } Vector parts = formatmodel.getFormatParts(); if (parts.size() == 1) { throw new RuntimeException("At least one format column is required."); } parts.removeElementAt(selectedCol); formatmodel.setFormatParts(parts); updateFormatTable(); int selectedRow = fileselector.getSelectedRow(); if ((selectedRow < sourcemodel.getRowCount()) && (selectedRow >= 0)) { String fn = (String) sourcemodel.getValueAt(selectedRow, 0); fn = fn.trim(); if (fn != null) { fn = fn.trim(); if ((fn != null) && (fn.length() > 0)) { updateDetailsFor(fn); } } } System.out.println("The new Column count after remove is " + formatmodel.getColumnCount()); } }); this.inferButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent ev) { int row = fileselector.getSelectedRow(); int col = 0; String filename = (String) sourcemodel.getValueAt(0, 0); Boolean isURL = (Boolean) sourcemodel.getValueAt(0, 1); BufferedReader br = null; File file = null; DataInputStream in = null; if (isURL.booleanValue()) { try { URL url2goto = new URL(filename); in = new DataInputStream(url2goto.openStream()); System.out.println("READY TO READ FROM URL:" + url2goto); } catch (Exception err) { throw new RuntimeException("Problem constructing URI for " + filename + ".", err); } } else { file = new File(filename); if (!file.exists()) { throw new RuntimeException("The file named '" + filename + "' does not exist."); } FileInputStream fstream = null; try { fstream = new FileInputStream(filename); in = new DataInputStream(fstream); } catch (Exception err) { throw new RuntimeException("Problem creating FileInputStream for " + filename + ".", err); } } br = new BufferedReader(new InputStreamReader(in)); JTable hdrTable = formatTable.getTableHeader().getTable(); try { String strLine; int line = 0; int ignorePreHdrLines = ((Integer) preheaderlines.getValue()).intValue(); int ignorePostHdrLines = ((Integer) postheaderlines.getValue()).intValue(); int numhdr = 0; boolean hasHeaderLine = false; if (hasHeaderLineBox.isSelected()) { hasHeaderLine = true; } if (hasHeaderLine) { numhdr = 1; } String FD = fieldDelimiter.getText(); while ((strLine = br.readLine()) != null) { if (line <= (ignorePreHdrLines + numhdr + ignorePostHdrLines)) { System.out.println(strLine); } else { String[] putative_cols = strLine.split(FD); System.out.println("The number of potential columns is " + putative_cols.length); String FMT = ""; while (formatTable.getColumnCount() > putative_cols.length) { TableColumn tcol = formatTable.getColumnModel().getColumn(0); formatTable.removeColumn(tcol); } for (int i = 0; i < putative_cols.length; i++) { String fmt = ""; try { Double dummy = new Double(putative_cols[i]); fmt = "%f"; } catch (Exception err) { fmt = "%s"; } FMT = FMT + fmt; formatTable.setValueAt(fmt, 0, i); } System.out.println("The potential format is " + FMT); formatmodel.setFormat(FMT); break; } line++; } in.close(); } catch (Exception err) { throw new RuntimeException("Problem reading single line from file.", err); } for (int j = 0; j < formatTable.getColumnCount(); j++) { hdrTable.getColumnModel().getColumn(j).setHeaderValue("" + (j + 1)); } formatTable.repaint(); } }); Box topbox = Box.createHorizontalBox(); topbox.add(detailsPanel); Box mainbox = Box.createVerticalBox(); Box setBox = Box.createHorizontalBox(); setBox.add(this.editPrefsButton); jointBox = Box.createHorizontalBox(); label = new JLabel("Created On:"); jointBox.add(label); this.createdOnText.setPreferredSize(new Dimension(50, 25)); jointBox.add(this.createdOnText); setBox.add(jointBox); jointBox = Box.createHorizontalBox(); label = new JLabel("Created By:"); jointBox.add(label); this.createdByText.setPreferredSize(new Dimension(50, 25)); jointBox.add(this.createdByText); setBox.add(jointBox); setBox.add(this.uploadButton); setBox.add(this.repositoryView); setBox.add(this.nicknameText); setBox.add(this.enabledRadio); mainbox.add(setBox); jointBox = Box.createHorizontalBox(); label = new JLabel("Comment:"); jointBox.add(label); jointBox.add(new JScrollPane(this.commentTextArea)); mainbox.add(jointBox); mainbox.add(topbox); mainbox.add(previewPanel); this.add(mainbox); this.addSources.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent ev) { int option = chooser.showOpenDialog(null); File[] files = null; if (option == JFileChooser.APPROVE_OPTION) { files = chooser.getSelectedFiles(); if (files.length > 10) { ((DefaultTableModel) sourcemodel).setRowCount(files.length); } else { ((DefaultTableModel) sourcemodel).setRowCount(10); } for (int i = 0; i < files.length; i++) { sourcemodel.setValueAt(files[i].getAbsolutePath(), i, 0); } } if (anyNonEmptySources()) { allowFormatParsing(true); } else { allowFormatParsing(false); } } }); this.preview.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent ev) { FlatFileDOM[] filespecs = new FlatFileDOM[map.size()]; int k = 0; for (int j = 0; j < sourcemodel.getRowCount(); j++) { String fn = (String) sourcemodel.getValueAt(j, 0); if (map.containsKey(fn)) { filespecs[k] = (FlatFileDOM) map.get(fn); k++; } } Vector hdrs = null; Vector types = null; for (int j = 0; j < filespecs.length; j++) { DataSetReader rdr = new DataSetReader(filespecs[j]); int rc = rdr.determineRowCount(); filespecs[j].setRowCount(rc); if (j == 0) { hdrs = rdr.getHeaders(); types = rdr.getTypes(); } System.out.println("The number of rows is=" + rc); } System.out.println("Creating flatfileset"); FlatFileSet dataset = new FlatFileSet(filespecs); System.out.println("Finished sorting!!!"); for (int j = 0; j < hdrs.size(); j++) { dataset.addColumn((String) hdrs.get(j), (Class) types.get(j)); } System.out.println("Number of headers is=" + hdrs.size()); System.out.println("The dataset rc is " + dataset.getRowCount()); System.out.println("The dataset cc is " + dataset.getColumnCount()); previewPanel.setDataSet(dataset); previewPanel.setVerticalScrollIntermittant(true); previewPanel.setHorizontalScrollIntermittant(true); previewPanel.setEditable(false); if (anyNonEmptySources()) { allowFormatParsing(true); } else { allowFormatParsing(false); } } }); allowFormatParsing(false); this.formatTable.repaint(); } | public static void writeInputStreamToFile(final InputStream stream, final File target) { long size = 0; FileOutputStream fileOut; try { fileOut = new FileOutputStream(target); size = IOUtils.copyLarge(stream, fileOut); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } if (log.isInfoEnabled()) { log.info("Wrote " + size + " bytes to " + target.getAbsolutePath()); } else { System.out.println("Wrote " + size + " bytes to " + target.getAbsolutePath()); } } | 15,346 |
0 | public boolean loadFile(String inpfile) { if (osmlContainer == null) return false; hApdx.clear(); try { BufferedReader in = null; if (inpfile.indexOf("http://") >= 0) { URL url = null; url = new URL(inpfile); URLConnection conn = url.openConnection(); conn.setUseCaches(false); InputStreamReader is = new InputStreamReader(conn.getInputStream()); in = new BufferedReader(is); } else { in = new BufferedReader(new FileReader(inpfile)); } String pline = null; while ((pline = in.readLine()) != null) { StringTokenizer tok = new StringTokenizer(pline, "\t\n\r"); if (tok.countTokens() < 2) continue; String name = tok.nextToken(); String apdx = tok.nextToken(); String note = ""; if (tok.countTokens() > 0) note = tok.nextToken(); if (name.length() == 0 || apdx.length() == 0) continue; OmicElementContainer element = (OmicElementContainer) OmicElementContainer.createContainer(); element.setName(name); element.setNote(note); element.addAppendix(apdx); String keys[] = commaPattern.split(apdx); for (int j = 0; j < keys.length; j++) { ArrayList v = (ArrayList) hApdx.get(keys[j]); if (v == null) v = new ArrayList(); v.add(element); hApdx.put(keys[j], v); } } in.close(); } catch (MalformedURLException mfe) { System.out.println("MalformedURLException"); return false; } catch (IOException ioe) { System.out.println("IOException"); return false; } System.out.println("appendix name list size " + hApdx.size()); if (bElementDirected) { int nCount = 0; ArrayList<OmicElementContainer> omicElementList = osmlContainer.getAllOmicElementContainers(); for (OmicElementContainer element : omicElementList) { String name = element.getName(); String apdx = element.getAppendix(); if (name.length() == 0) continue; String names[] = commaPattern.split(name); String apdxs[] = commaPattern.split(apdx); String list[] = new String[names.length + apdxs.length]; for (int j = 0; j < names.length; j++) list[j] = names[j]; for (int j = 0; j < apdxs.length; j++) list[j + names.length] = apdxs[j]; for (int j = 0; j < list.length; j++) { ArrayList v = (ArrayList) hApdx.get(list[j]); if (v == null) continue; for (int k = 0; k < v.size(); k++) { OmicElementContainer appendix = (OmicElementContainer) v.get(k); element.addAppendix(appendix.getName()); nCount++; } } } System.out.println("match appendix element " + nCount + " items"); } if (bFunctionDirected) { int nCount = 0; FunctionalClassContainer functions[] = osmlContainer.getFunctionalClassContainer("[@container=all]"); ArrayList vFunction = new ArrayList(); for (int i = 0; i < functions.length; i++) { if (!vFunction.contains(functions[i])) vFunction.add(functions[i]); } for (int i = 0; i < vFunction.size(); i++) { FunctionalClassContainer function = (FunctionalClassContainer) vFunction.get(i); String name = function.getName(); if (name.length() == 0) continue; String names[] = name.split(","); for (int j = 0; j < names.length; j++) { ArrayList v = (ArrayList) hApdx.get(names[j]); if (v == null) continue; for (int k = 0; k < v.size(); k++) { OmicElementContainer appendix = (OmicElementContainer) v.get(k); functions[i].addOmicElementContainer(appendix); nCount++; } } } System.out.println("match appendix function " + nCount + " items"); } return true; } | 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; } | 15,347 |
0 | public static String md5(String text) { MessageDigest msgDigest = null; try { msgDigest = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { throw new IllegalStateException("System doesn't support MD5 algorithm."); } try { msgDigest.update(text.getBytes("utf-8")); } catch (UnsupportedEncodingException e) { throw new IllegalStateException("System doesn't support your EncodingException."); } byte[] bytes = msgDigest.digest(); String md5Str = new String(encodeHex(bytes)); return md5Str; } | public void testFidelity() throws ParserException, IOException { Lexer lexer; Node node; int position; StringBuffer buffer; String string; char[] ref; char[] test; URL url = new URL("http://sourceforge.net"); lexer = new Lexer(url.openConnection()); position = 0; buffer = new StringBuffer(80000); while (null != (node = lexer.nextNode())) { string = node.toHtml(); if (position != node.getStartPosition()) fail("non-contiguous" + string); buffer.append(string); position = node.getEndPosition(); if (buffer.length() != position) fail("text length differed after encountering node " + string); } ref = lexer.getPage().getText().toCharArray(); test = new char[buffer.length()]; buffer.getChars(0, buffer.length(), test, 0); assertEquals("different amounts of text", ref.length, test.length); for (int i = 0; i < ref.length; i++) if (ref[i] != test[i]) fail("character differs at position " + i + ", expected <" + ref[i] + "> but was <" + test[i] + ">"); } | 15,348 |
0 | public static void main(String[] args) { try { { byte[] bytes1 = { (byte) 2, (byte) 2, (byte) 3, (byte) 0, (byte) 9 }; byte[] bytes2 = { (byte) 99, (byte) 2, (byte) 2, (byte) 3, (byte) 0, (byte) 9 }; System.out.println("Bytes 2,2,3,0,9 as Base64: " + encodeBytes(bytes1)); System.out.println("Bytes 2,2,3,0,9 w/ offset: " + encodeBytes(bytes2, 1, bytes2.length - 1)); byte[] dbytes = decode(encodeBytes(bytes1)); System.out.print(encodeBytes(bytes1) + " decoded: "); for (int i = 0; i < dbytes.length; i++) System.out.print(dbytes[i] + (i < dbytes.length - 1 ? "," : "\n")); } { java.io.FileInputStream fis = new java.io.FileInputStream("test.gif.b64"); Base64.InputStream b64is = new Base64.InputStream(fis, DECODE); byte[] bytes = new byte[0]; int b = -1; while ((b = b64is.read()) >= 0) { byte[] temp = new byte[bytes.length + 1]; System.arraycopy(bytes, 0, temp, 0, bytes.length); temp[bytes.length] = (byte) b; bytes = temp; } b64is.close(); javax.swing.ImageIcon iicon = new javax.swing.ImageIcon(bytes); javax.swing.JLabel jlabel = new javax.swing.JLabel("Read from test.gif.b64", iicon, 0); javax.swing.JFrame jframe = new javax.swing.JFrame(); jframe.getContentPane().add(jlabel); jframe.pack(); jframe.setVisible(true); java.io.FileOutputStream fos = new java.io.FileOutputStream("test.gif_out"); fos.write(bytes); fos.close(); fis = new java.io.FileInputStream("test.gif_out"); b64is = new Base64.InputStream(fis, ENCODE); byte[] ebytes = new byte[0]; b = -1; while ((b = b64is.read()) >= 0) { byte[] temp = new byte[ebytes.length + 1]; System.arraycopy(ebytes, 0, temp, 0, ebytes.length); temp[ebytes.length] = (byte) b; ebytes = temp; } b64is.close(); String s = new String(ebytes); javax.swing.JTextArea jta = new javax.swing.JTextArea(s); javax.swing.JScrollPane jsp = new javax.swing.JScrollPane(jta); jframe = new javax.swing.JFrame(); jframe.setTitle("Read from test.gif_out"); jframe.getContentPane().add(jsp); jframe.pack(); jframe.setVisible(true); fos = new java.io.FileOutputStream("test.gif.b64_out"); fos.write(ebytes); fis = new java.io.FileInputStream("test.gif.b64_out"); b64is = new Base64.InputStream(fis, DECODE); byte[] edbytes = new byte[0]; b = -1; while ((b = b64is.read()) >= 0) { byte[] temp = new byte[edbytes.length + 1]; System.arraycopy(edbytes, 0, temp, 0, edbytes.length); temp[edbytes.length] = (byte) b; edbytes = temp; } b64is.close(); iicon = new javax.swing.ImageIcon(edbytes); jlabel = new javax.swing.JLabel("Read from test.gif.b64_out", iicon, 0); jframe = new javax.swing.JFrame(); jframe.getContentPane().add(jlabel); jframe.pack(); jframe.setVisible(true); } { java.io.FileInputStream fis = new java.io.FileInputStream("test.gif_out"); byte[] rbytes = new byte[0]; int b = -1; while ((b = fis.read()) >= 0) { byte[] temp = new byte[rbytes.length + 1]; System.arraycopy(rbytes, 0, temp, 0, rbytes.length); temp[rbytes.length] = (byte) b; rbytes = temp; } fis.close(); java.io.FileOutputStream fos = new java.io.FileOutputStream("test.gif.b64_out2"); Base64.OutputStream b64os = new Base64.OutputStream(fos, ENCODE); b64os.write(rbytes); b64os.close(); fis = new java.io.FileInputStream("test.gif.b64_out2"); byte[] rebytes = new byte[0]; b = -1; while ((b = fis.read()) >= 0) { byte[] temp = new byte[rebytes.length + 1]; System.arraycopy(rebytes, 0, temp, 0, rebytes.length); temp[rebytes.length] = (byte) b; rebytes = temp; } fis.close(); String s = new String(rebytes); javax.swing.JTextArea jta = new javax.swing.JTextArea(s); javax.swing.JScrollPane jsp = new javax.swing.JScrollPane(jta); javax.swing.JFrame jframe = new javax.swing.JFrame(); jframe.setTitle("Read from test.gif.b64_out2"); jframe.getContentPane().add(jsp); jframe.pack(); jframe.setVisible(true); fos = new java.io.FileOutputStream("test.gif_out2"); b64os = new Base64.OutputStream(fos, DECODE); b64os.write(rebytes); b64os.close(); javax.swing.ImageIcon iicon = new javax.swing.ImageIcon("test.gif_out2"); javax.swing.JLabel jlabel = new javax.swing.JLabel("Read from test.gif_out2", iicon, 0); jframe = new javax.swing.JFrame(); jframe.getContentPane().add(jlabel); jframe.pack(); jframe.setVisible(true); } { java.io.FileInputStream fis = new java.io.FileInputStream("D:\\temp\\testencoding.txt"); Base64.InputStream b64is = new Base64.InputStream(fis, DECODE); java.io.FileOutputStream fos = new java.io.FileOutputStream("D:\\temp\\file.zip"); int b; while ((b = b64is.read()) >= 0) fos.write(b); fos.close(); b64is.close(); } } catch (Exception e) { e.printStackTrace(); } } | public final int sendMetaData(FileInputStream fis) throws Exception { try { UUID uuid = UUID.randomUUID(); HttpClient client = new SSLHttpClient(); StringBuilder builder = new StringBuilder(mServer).append("?cmd=meta").append("&id=" + uuid); HttpPost method = new HttpPost(builder.toString()); String fileName = uuid + ".metadata"; FileInputStreamPart part = new FileInputStreamPart("data", fileName, fis); MultipartEntity requestContent = new MultipartEntity(new Part[] { part }); method.setEntity(requestContent); HttpResponse response = client.execute(method); int code = response.getStatusLine().getStatusCode(); if (code == HttpStatus.SC_OK) { return 0; } else { return -1; } } catch (Exception e) { throw new Exception("send meta data", e); } } | 15,349 |
1 | private Map<String, DomAttr> getAttributesFor(final BaseFrame frame) throws IOException { final Map<String, DomAttr> map = createAttributesCopyWithClonedAttribute(frame, "src"); final DomAttr srcAttr = map.get("src"); if (srcAttr == null) { return map; } final Page enclosedPage = frame.getEnclosedPage(); final String suffix = getFileExtension(enclosedPage); final File file = createFile(srcAttr.getValue(), "." + suffix); if (enclosedPage instanceof HtmlPage) { file.delete(); ((HtmlPage) enclosedPage).save(file); } else { final InputStream is = enclosedPage.getWebResponse().getContentAsStream(); final FileOutputStream fos = new FileOutputStream(file); IOUtils.copyLarge(is, fos); IOUtils.closeQuietly(is); IOUtils.closeQuietly(fos); } srcAttr.setValue(file.getParentFile().getName() + FILE_SEPARATOR + file.getName()); return map; } | public RepeatStatus execute(StepContribution contribution, ChunkContext chunkContext) throws Exception { ZipInputStream zis = new ZipInputStream(new BufferedInputStream(inputResource.getInputStream())); File targetDirectoryAsFile = new File(targetDirectory); if (!targetDirectoryAsFile.exists()) { FileUtils.forceMkdir(targetDirectoryAsFile); } File target = new File(targetDirectory, targetFile); BufferedOutputStream dest = null; while (zis.getNextEntry() != null) { if (!target.exists()) { target.createNewFile(); } FileOutputStream fos = new FileOutputStream(target); dest = new BufferedOutputStream(fos); IOUtils.copy(zis, dest); dest.flush(); dest.close(); } zis.close(); if (!target.exists()) { throw new IllegalStateException("Could not decompress anything from the archive!"); } return RepeatStatus.FINISHED; } | 15,350 |
0 | private static MimeType getMimeType(URL url) { String mimeTypeString = null; String charsetFromWebServer = null; String contentType = null; InputStream is = null; MimeType mimeTypeFromWebServer = null; MimeType mimeTypeFromFileSuffix = null; MimeType mimeTypeFromMagicNumbers = null; String fileSufix = null; if (url == null) return null; try { try { is = url.openConnection().getInputStream(); contentType = url.openConnection().getContentType(); } catch (IOException e) { } if (contentType != null) { StringTokenizer st = new StringTokenizer(contentType, ";"); if (st.hasMoreTokens()) mimeTypeString = st.nextToken().toLowerCase(); if (st.hasMoreTokens()) charsetFromWebServer = st.nextToken().toLowerCase(); if (charsetFromWebServer != null) { st = new StringTokenizer(charsetFromWebServer, "="); charsetFromWebServer = null; if (st.hasMoreTokens()) st.nextToken(); if (st.hasMoreTokens()) charsetFromWebServer = st.nextToken().toUpperCase(); } } mimeTypeFromWebServer = mimeString2mimeTypeMap.get(mimeTypeString); fileSufix = getFileSufix(url); mimeTypeFromFileSuffix = getMimeType(fileSufix); mimeTypeFromMagicNumbers = guessTypeUsingMagicNumbers(is, charsetFromWebServer); } finally { IOUtils.closeQuietly(is); } return decideBetweenThreeMimeTypes(mimeTypeFromWebServer, mimeTypeFromFileSuffix, mimeTypeFromMagicNumbers); } | public static List<ServerInfo> getStartedServers() { List<ServerInfo> infos = new ArrayList<ServerInfo>(); try { StringBuilder request = new StringBuilder(); request.append(url).append("/").append(displayServlet); request.append("?ingame=1"); URL objUrl = new URL(request.toString()); URLConnection urlConnect = objUrl.openConnection(); InputStream in = urlConnect.getInputStream(); BufferedReader reader = new BufferedReader(new InputStreamReader(in)); while (reader.ready()) { String name = reader.readLine(); String ip = reader.readLine(); int port = Integer.valueOf(reader.readLine()); ServerInfo server = new ServerInfo(name, ip, port); server.nbPlayers = Integer.valueOf(reader.readLine()); infos.add(server); } in.close(); return infos; } catch (Exception e) { return infos; } } | 15,351 |
1 | private void setInlineXML(Entry entry, DatastreamXMLMetadata ds) throws UnsupportedEncodingException, StreamIOException { String content; if (m_obj.hasContentModel(Models.SERVICE_DEPLOYMENT_3_0) && (ds.DatastreamID.equals("SERVICE-PROFILE") || ds.DatastreamID.equals("WSDL"))) { content = DOTranslationUtility.normalizeInlineXML(new String(ds.xmlContent, m_encoding), m_transContext); } else { content = new String(ds.xmlContent, m_encoding); } if (m_format.equals(ATOM_ZIP1_1)) { String name = ds.DSVersionID + ".xml"; try { m_zout.putNextEntry(new ZipEntry(name)); InputStream is = new ByteArrayInputStream(content.getBytes(m_encoding)); IOUtils.copy(is, m_zout); m_zout.closeEntry(); is.close(); } catch (IOException e) { throw new StreamIOException(e.getMessage(), e); } IRI iri = new IRI(name); entry.setSummary(ds.DSVersionID); entry.setContent(iri, ds.DSMIME); } else { entry.setContent(content, ds.DSMIME); } } | public void overwriteFileTest() throws Exception { File filefrom = new File("/tmp/from.txt"); File fileto = new File("/tmp/to.txt"); InputStream from = null; OutputStream to = null; try { from = new FileInputStream(filefrom); to = new FileOutputStream(fileto); byte[] buffer = new byte[4096]; int bytes_read; while ((bytes_read = from.read(buffer)) != -1) { to.write(buffer, 0, bytes_read); } } finally { if (from != null) { from.close(); } if (to != null) { to.close(); } } } | 15,352 |
0 | public boolean addTextGroup(String key, URL url) { if (_textGroups.contains(key)) return false; String s; Hashtable tg = new Hashtable(); String sGroupKey = "default"; String sGroup[]; Vector vGroup = new Vector(); int cntr; try { BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); while ((s = in.readLine()) != null) { if (s.startsWith("[")) { if (vGroup.size() > 0) { sGroup = new String[vGroup.size()]; for (cntr = 0; cntr < vGroup.size(); ++cntr) sGroup[cntr] = (String) vGroup.elementAt(cntr); tg.put(sGroupKey, sGroup); vGroup.removeAllElements(); } sGroupKey = s.substring(1, s.indexOf(']')); } else { vGroup.addElement(s); } } if (vGroup.size() > 0) { sGroup = new String[vGroup.size()]; for (cntr = 0; cntr < vGroup.size(); ++cntr) sGroup[cntr] = (String) vGroup.elementAt(cntr); tg.put(sGroupKey, sGroup); } in.close(); } catch (IOException ioe) { System.err.println("Error reading file for " + key); System.err.println(ioe.getMessage()); return false; } _textGroups.put(key, tg); return true; } | public boolean doUpload(int count) { String objFileName = Long.toString(new java.util.Date().getTime()) + Integer.toString(count); try { this.objectFileName[count] = objFileName + "_bak." + this.sourceFileExt[count]; File objFile = new File(this.contextPath + "/" + this.savePath, this.objectFileName[count]); if (objFile.exists()) { this.doUpload(count); } else { objFile.createNewFile(); } FileOutputStream fos = new FileOutputStream(objFile); BufferedOutputStream bos = new BufferedOutputStream(fos); int readLength = 0; int offset = 0; String str = ""; long readSize = 0L; while ((readLength = this.inStream.readLine(this.b, 0, this.b.length)) != -1) { str = new String(this.b, 0, readLength); if (str.indexOf("Content-Type:") != -1) { break; } } this.inStream.readLine(this.b, 0, this.b.length); while ((readLength = this.inStream.readLine(this.b, 0, b.length)) != -1) { str = new String(this.b, 0, readLength); if (this.b[0] == 45 && this.b[1] == 45 && this.b[2] == 45 && this.b[3] == 45 && this.b[4] == 45) { break; } bos.write(this.b, 0, readLength); readSize += readLength; if (readSize > this.size) { this.fileMessage[count] = "�ϴ��ļ������ļ���С�������ƣ�"; this.ok = false; break; } } if (this.ok) { bos.flush(); bos.close(); int fileLength = (int) (objFile.length()); byte[] bb = new byte[fileLength - 2]; FileInputStream fis = new FileInputStream(objFile); BufferedInputStream bis = new BufferedInputStream(fis); bis.read(bb, 0, (fileLength - 2)); fis.close(); bis.close(); this.objectFileName[count] = objFileName + "." + this.sourceFileExt[count]; File ok_file = new File(this.contextPath + "/" + this.savePath, this.objectFileName[count]); ok_file.createNewFile(); BufferedOutputStream bos_ok = new BufferedOutputStream(new FileOutputStream(ok_file)); bos_ok.write(bb); bos_ok.close(); objFile.delete(); this.fileMessage[count] = "OK"; return true; } else { bos.flush(); bos.close(); File delFile = new File(this.contextPath + "/" + this.savePath, this.objectFileName[count]); delFile.delete(); this.objectFileName[count] = "none"; return false; } } catch (Exception e) { this.objectFileName[count] = "none"; this.fileMessage[count] = e.toString(); return false; } } | 15,353 |
0 | public File extractID3v2TagDataIntoFile(File outputFile) throws TagNotFoundException, IOException { int startByte = (int) ((MP3AudioHeader) audioHeader).getMp3StartByte(); if (startByte >= 0) { FileInputStream fis = new FileInputStream(file); FileChannel fc = fis.getChannel(); ByteBuffer bb = ByteBuffer.allocate(startByte); fc.read(bb); FileOutputStream out = new FileOutputStream(outputFile); out.write(bb.array()); out.close(); fc.close(); fis.close(); return outputFile; } throw new TagNotFoundException("There is no ID3v2Tag data in this file"); } | public boolean renameTo(Folder f) throws MessagingException, StoreClosedException, NullPointerException { String[] aLabels = new String[] { "en", "es", "fr", "de", "it", "pt", "ca", "ja", "cn", "tw", "fi", "ru", "pl", "nl", "xx" }; PreparedStatement oUpdt = null; if (!((DBStore) getStore()).isConnected()) throw new StoreClosedException(getStore(), "Store is not connected"); if (oCatg.isNull(DB.gu_category)) throw new NullPointerException("Folder is closed"); try { oUpdt = getConnection().prepareStatement("DELETE FROM " + DB.k_cat_labels + " WHERE " + DB.gu_category + "=?"); oUpdt.setString(1, oCatg.getString(DB.gu_category)); oUpdt.executeUpdate(); oUpdt.close(); oUpdt.getConnection().prepareStatement("INSERT INTO " + DB.k_cat_labels + " (" + DB.gu_category + "," + DB.id_language + "," + DB.tr_category + "," + DB.url_category + ") VALUES (?,?,?,NULL)"); oUpdt.setString(1, oCatg.getString(DB.gu_category)); for (int l = 0; l < aLabels.length; l++) { oUpdt.setString(2, aLabels[l]); oUpdt.setString(3, f.getName().substring(0, 1).toUpperCase() + f.getName().substring(1).toLowerCase()); oUpdt.executeUpdate(); } oUpdt.close(); oUpdt = null; getConnection().commit(); } catch (SQLException sqle) { try { if (null != oUpdt) oUpdt.close(); } catch (SQLException ignore) { } try { getConnection().rollback(); } catch (SQLException ignore) { } throw new MessagingException(sqle.getMessage(), sqle); } return true; } | 15,354 |
0 | public void search() throws Exception { URL searchurl = new URL("" + "http://www.ncbi.nlm.nih.gov/blast/Blast.cgi" + "?CMD=Put" + "&DATABASE=" + this.database + "&PROGRAM=" + this.program + "&QUERY=" + this.sequence.seqString()); BufferedReader reader = new BufferedReader(new InputStreamReader(searchurl.openStream(), "UTF-8")); String line = ""; while ((line = reader.readLine()) != null) { if (line.contains("Request ID")) this.rid += line.substring(70, 81); } reader.close(); } | public static void copyFile(File in, File out) throws IOException { FileChannel sourceChannel = new FileInputStream(in).getChannel(); FileChannel destinationChannel = new FileOutputStream(out).getChannel(); destinationChannel.transferFrom(sourceChannel, 0, sourceChannel.size()); sourceChannel.close(); destinationChannel.close(); } | 15,355 |
1 | @Override public void save(String arxivId, InputStream inputStream, String encoding) { String filename = StringUtil.arxivid2filename(arxivId, "tex"); try { Writer writer = new OutputStreamWriter(new FileOutputStream(String.format("%s/%s", LATEX_DOCUMENT_DIR, filename)), encoding); IOUtils.copy(inputStream, writer, encoding); writer.flush(); writer.close(); inputStream.close(); } catch (IOException e) { logger.error("Failed to save the Latex source with id='{}'", arxivId, e); throw new RuntimeException(e); } } | public static boolean copyFile(File from, File tu) { final int BUFFER_SIZE = 4096; byte[] buffer = new byte[BUFFER_SIZE]; try { FileInputStream in = new FileInputStream(from); FileOutputStream out = new FileOutputStream(tu); int read; while ((read = in.read(buffer)) != -1) { out.write(buffer, 0, read); } in.close(); out.close(); } catch (IOException e) { return false; } return true; } | 15,356 |
0 | private void downloadFiles() throws SocketException, IOException { HashSet<String> files_set = new HashSet<String>(); boolean hasWildcarts = false; FTPClient client = new FTPClient(); for (String file : downloadFiles) { files_set.add(file); if (file.contains(WILDCARD_WORD) || file.contains(WILDCARD_DIGIT)) hasWildcarts = true; } client.connect(source.getHost()); client.login(username, password); FTPFile[] files = client.listFiles(source.getPath()); if (!hasWildcarts) { for (FTPFile file : files) { String filename = file.getName(); if (files_set.contains(filename)) { long file_size = file.getSize() / 1024; Calendar cal = file.getTimestamp(); URL source_file = new File(source + file.getName()).toURI().toURL(); DownloadQueue.add(new Download(projectName, parser.getParserID(), source_file, file_size, cal, target + file.getName())); } } } else { for (FTPFile file : files) { String filename = file.getName(); boolean match = false; for (String db_filename : downloadFiles) { db_filename = db_filename.replaceAll("\\" + WILDCARD_WORD, WILDCARD_WORD_PATTERN); db_filename = db_filename.replaceAll("\\" + WILDCARD_DIGIT, WILDCARD_DIGIT_PATTERN); Pattern p = Pattern.compile(db_filename); Matcher m = p.matcher(filename); match = m.matches(); } if (match) { long file_size = file.getSize() / 1024; Calendar cal = file.getTimestamp(); URL source_file = new File(source + file.getName()).toURI().toURL(); DownloadQueue.add(new Download(projectName, parser.getParserID(), source_file, file_size, cal, target + file.getName())); } } } } | private void getGUID(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); } } | 15,357 |
0 | public String sendRequest(HTTPHandler.RequestData requestData) throws HTTPHandlerException { try { final String urlString = requestData.getURLString(); final URL url = new URL(urlString); final String postString = requestData.getPostString(); m_pluginThreadContext.startTimer(); HttpURLConnection connection = (HttpURLConnection) url.openConnection(); final Iterator headersIterator = requestData.getHeaders().entrySet().iterator(); while (headersIterator.hasNext()) { final Map.Entry entry = (Map.Entry) headersIterator.next(); connection.setRequestProperty((String) entry.getKey(), (String) entry.getValue()); } final AuthorizationData authorizationData = requestData.getAuthorizationData(); if (authorizationData != null && authorizationData instanceof HTTPHandler.BasicAuthorizationData) { final HTTPHandler.BasicAuthorizationData basicAuthorizationData = (HTTPHandler.BasicAuthorizationData) authorizationData; connection.setRequestProperty("Authorization", "Basic " + Codecs.base64Encode(basicAuthorizationData.getUser() + ":" + basicAuthorizationData.getPassword())); } connection.setInstanceFollowRedirects(m_followRedirects); if (m_useCookies) { final String cookieString = m_cookieHandler.getCookieString(url, m_useCookiesVersionString); if (cookieString != null) { connection.setRequestProperty("Cookie", cookieString); } } connection.setUseCaches(false); if (postString != null) { connection.setRequestMethod("POST"); connection.setDoOutput(true); final BufferedOutputStream bos = new BufferedOutputStream(connection.getOutputStream()); final PrintWriter out = new PrintWriter(bos); out.write(postString); out.close(); } connection.connect(); final int responseCode = connection.getResponseCode(); if (m_timeToFirstByteIndex != null) { m_pluginThreadContext.getCurrentTestStatistics().addValue(m_timeToFirstByteIndex, System.currentTimeMillis() - m_pluginThreadContext.getStartTime()); } if (m_useCookies) { int headerIndex = 1; String headerKey = null; String headerValue = connection.getHeaderField(headerIndex); while (headerValue != null) { headerKey = connection.getHeaderFieldKey(headerIndex); if (headerKey != null && "Set-Cookie".equals(headerKey)) { m_cookieHandler.setCookies(headerValue, url); } headerValue = connection.getHeaderField(++headerIndex); } } if (responseCode == HttpURLConnection.HTTP_OK) { final InputStreamReader isr = new InputStreamReader(connection.getInputStream()); final BufferedReader in = new BufferedReader(isr); final StringWriter stringWriter = new StringWriter(512); char[] buffer = new char[512]; int charsRead = 0; if (!m_dontReadBody) { while ((charsRead = in.read(buffer, 0, buffer.length)) > 0) { stringWriter.write(buffer, 0, charsRead); } } in.close(); stringWriter.close(); m_pluginThreadContext.logMessage(urlString + " OK"); return stringWriter.toString(); } else if (responseCode == HttpURLConnection.HTTP_NOT_MODIFIED) { m_pluginThreadContext.logMessage(urlString + " was not modified"); } else if (responseCode == HttpURLConnection.HTTP_MOVED_PERM || responseCode == HttpURLConnection.HTTP_MOVED_TEMP || responseCode == 307) { m_pluginThreadContext.logMessage(urlString + " returned a redirect (" + responseCode + "). " + "Ensure the next URL is " + connection.getHeaderField("Location")); return null; } else { m_pluginThreadContext.logError("Unknown response code: " + responseCode + " for " + urlString); } return null; } catch (Exception e) { throw new HTTPHandlerException(e.getMessage(), e); } finally { m_pluginThreadContext.stopTimer(); } } | public void setPassword(String password) { MessageDigest md; try { md = MessageDigest.getInstance("SHA-256"); md.update(password.getBytes("UTF-8")); byte[] digest = md.digest(); String encodedPassword = Base64.encode(digest); this.password = encodedPassword; } catch (NoSuchAlgorithmException e) { logger.log(Level.SEVERE, "Password creation failed", e); throw new RuntimeException(e); } catch (UnsupportedEncodingException e) { logger.log(Level.SEVERE, "Password creation failed", e); throw new RuntimeException(e); } } | 15,358 |
1 | public Constructor run() throws Exception { String path = "META-INF/services/" + ComponentApplicationContext.class.getName(); ClassLoader loader = Thread.currentThread().getContextClassLoader(); final Enumeration<URL> urls; if (loader == null) { urls = ComponentApplicationContext.class.getClassLoader().getResources(path); } else { urls = loader.getResources(path); } while (urls.hasMoreElements()) { URL url = urls.nextElement(); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); try { String className = null; while ((className = reader.readLine()) != null) { final String name = className.trim(); if (!name.startsWith("#") && !name.startsWith(";") && !name.startsWith("//")) { final Class<?> cls; if (loader == null) { cls = Class.forName(name); } else { cls = Class.forName(name, true, loader); } int m = cls.getModifiers(); if (ComponentApplicationContext.class.isAssignableFrom(cls) && !Modifier.isAbstract(m) && !Modifier.isInterface(m)) { Constructor constructor = cls.getDeclaredConstructor(); if (!Modifier.isPublic(constructor.getModifiers())) { constructor.setAccessible(true); } return constructor; } else { throw new ClassCastException(cls.getName()); } } } } finally { reader.close(); } } throw new ComponentApplicationException("No " + "ComponentApplicationContext implementation " + "found."); } | public String getScore(int id) { String title = null; try { URL url = new URL(BASE_URL + id + ".html"); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String line; while ((line = reader.readLine()) != null) { if (line.contains("<title>")) { title = line.substring(line.indexOf("<title>") + 7, line.indexOf("</title>")); title = title.substring(0, title.indexOf("|")).trim(); break; } } reader.close(); } catch (IOException e) { e.printStackTrace(); } return title; } | 15,359 |
1 | public boolean backupLastAuditSchema(File lastAuditSchema) { boolean isBkupFileOK = false; String writeTimestamp = DateFormatUtils.format(new java.util.Date(), configFile.getTimestampPattern()); File target = new File(configFile.getAuditSchemaFileDir() + File.separator + configFile.getAuditSchemaFileName() + ".bkup_" + writeTimestamp); FileChannel sourceChannel = null; FileChannel targetChannel = null; try { sourceChannel = new FileInputStream(lastAuditSchema).getChannel(); targetChannel = new FileOutputStream(target).getChannel(); targetChannel.transferFrom(sourceChannel, 0, sourceChannel.size()); } catch (IOException e) { logger.log(Level.SEVERE, "IO exception occurred while copying file", e); } finally { if ((target != null) && (target.exists()) && (target.length() > 0)) { isBkupFileOK = true; } try { if (sourceChannel != null) { sourceChannel.close(); } if (targetChannel != null) { targetChannel.close(); } } catch (IOException e) { logger.warning("closing channels failed"); } } return isBkupFileOK; } | public static void write(File file, InputStream source) throws IOException { OutputStream outputStream = null; assert file != null : "file must not be null."; assert file.isFile() : "file must be a file."; assert file.canWrite() : "file must be writable."; assert source != null : "source must not be null."; try { outputStream = new BufferedOutputStream(new FileOutputStream(file)); IOUtils.copy(source, outputStream); outputStream.flush(); } finally { IOUtils.closeQuietly(outputStream); } } | 15,360 |
1 | public void run() { try { IOUtils.copy(is, os); os.flush(); } catch (IOException ioe) { logger.error("Unable to copy", ioe); } finally { IOUtils.closeQuietly(is); IOUtils.closeQuietly(os); } } | public void backupFile(File fromFile, File toFile) { 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); } catch (IOException e) { log.error(e.getMessage()); } finally { if (from != null) try { from.close(); } catch (IOException e) { log.error(e.getMessage()); } if (to != null) try { to.close(); } catch (IOException e) { log.error(e.getMessage()); } } } | 15,361 |
0 | static void copyFile(File file, File file1) throws IOException { byte abyte0[] = new byte[512]; FileInputStream fileinputstream = new FileInputStream(file); FileOutputStream fileoutputstream = new FileOutputStream(file1); int i; while ((i = fileinputstream.read(abyte0)) > 0) fileoutputstream.write(abyte0, 0, i); fileinputstream.close(); fileoutputstream.close(); } | private String[] sendRequest(String url, String requestString) throws ClickatellException, IOException { String response = null; MessageFormat responseFormat = new MessageFormat("{0}: {1}"); List idList = new LinkedList(); try { log_.debug("sendRequest: posting : " + requestString + " to " + url); URL requestURL = new URL(url); URLConnection urlConn = requestURL.openConnection(); urlConn.setDoInput(true); urlConn.setDoOutput(true); urlConn.setUseCaches(false); urlConn.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); PrintWriter pw = new PrintWriter(urlConn.getOutputStream()); pw.print(requestString); pw.flush(); pw.close(); InputStream is = urlConn.getInputStream(); BufferedReader responseReader = new BufferedReader(new InputStreamReader(is)); while ((response = responseReader.readLine()) != null) { Object[] objs = responseFormat.parse(response); if ("ERR".equalsIgnoreCase((String) objs[0])) { MessageFormat errorFormat = new MessageFormat("{0}: {1}, {2}"); Object[] errObjs = errorFormat.parse(response); String errorNo = (String) errObjs[1]; String description = (String) errObjs[2]; throw new ClickatellException("Clickatell error. Error " + errorNo + ", " + description, Integer.parseInt(errorNo)); } log_.debug("sendRequest: Got ID : " + ((String) objs[1])); idList.add(objs[1]); } responseReader.close(); } catch (ParseException ex) { throw new ClickatellException("Unexpected response from Clickatell. : " + response, ClickatellException.ERROR_UNKNOWN); } return (String[]) idList.toArray(new String[idList.size()]); } | 15,362 |
1 | private void getRandomGUID(boolean secure) { MessageDigest md5 = null; StringBuffer sbValueBeforeMD5 = new StringBuffer(); try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { } try { long time = System.currentTimeMillis(); long rand = 0; if (secure) { rand = mySecureRand.nextLong(); } else { rand = myRand.nextLong(); } sbValueBeforeMD5.append(s_id); sbValueBeforeMD5.append(":"); sbValueBeforeMD5.append(Long.toString(time)); sbValueBeforeMD5.append(":"); sbValueBeforeMD5.append(Long.toString(rand)); valueBeforeMD5 = sbValueBeforeMD5.toString(); md5.update(valueBeforeMD5.getBytes()); byte[] array = md5.digest(); StringBuffer sb = new StringBuffer(); for (int j = 0; j < array.length; ++j) { int b = array[j] & 0xFF; if (b < 0x10) sb.append('0'); sb.append(Integer.toHexString(b)); } valueAfterMD5 = sb.toString(); } catch (Exception e) { System.out.println("Error:" + e); } } | public static String MD5(String text) throws NoSuchAlgorithmException, UnsupportedEncodingException { 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); } | 15,363 |
0 | public static boolean loadTestProperties(Properties props, Class<?> callingClazz, Class<?> hierarchyRootClazz, String resourceBaseName) { if (!hierarchyRootClazz.isAssignableFrom(callingClazz)) { throw new IllegalArgumentException("Class " + callingClazz + " is not derived from " + hierarchyRootClazz); } if (null == resourceBaseName) { throw new NullPointerException("resourceBaseName is null"); } String fqcn = callingClazz.getName(); String uqcn = fqcn.substring(fqcn.lastIndexOf('.') + 1); String callingClassResource = uqcn + ".properties"; String globalCallingClassResource = "/" + callingClassResource; String baseClassResource = resourceBaseName + "-" + uqcn + ".properties"; String globalBaseClassResource = "/" + baseClassResource; String pkgResource = resourceBaseName + ".properties"; String globalResource = "/" + pkgResource; boolean loaded = false; final String[] resources = { baseClassResource, globalBaseClassResource, callingClassResource, globalCallingClassResource, pkgResource, globalResource }; List<URL> urls = new ArrayList<URL>(); Class<?> clazz = callingClazz; do { for (String res : resources) { URL url = clazz.getResource(res); if (null != url && !urls.contains(url)) { urls.add(url); } } if (hierarchyRootClazz.equals(clazz)) { clazz = null; } else { clazz = clazz.getSuperclass(); } } while (null != clazz); ListIterator<URL> it = urls.listIterator(urls.size()); while (it.hasPrevious()) { URL url = it.previous(); InputStream in = null; try { LOG.info("Loading test properties from resource: " + url); in = url.openStream(); props.load(in); loaded = true; } catch (IOException ex) { LOG.warn("Failed to load properties from resource: " + url, ex); } IOUtil.closeSilently(in); } return loaded; } | public static String ReadURLString(String str) throws IOException { try { URL url = new URL(str); InputStream is = url.openStream(); InputStreamReader isr = new InputStreamReader(is); BufferedReader in = new BufferedReader(isr); String inputLine; String line = ""; int i = 0; while ((inputLine = in.readLine()) != null) { line += inputLine + "\n"; } is.close(); isr.close(); in.close(); return line; } catch (Exception e) { e.printStackTrace(); } return ""; } | 15,364 |
0 | private void publishZip(LWMap map) { try { if (map.getFile() == null) { VueUtil.alert(VueResources.getString("dialog.mapsave.message"), VueResources.getString("dialog.mapsave.title")); return; } File savedCMap = PublishUtil.createZip(map, Publisher.resourceVector); InputStream istream = new BufferedInputStream(new FileInputStream(savedCMap)); OutputStream ostream = new BufferedOutputStream(new FileOutputStream(ActionUtil.selectFile("Export to Zip File", "zip"))); int fileLength = (int) savedCMap.length(); byte bytes[] = new byte[fileLength]; while (istream.read(bytes, 0, fileLength) != -1) ostream.write(bytes, 0, fileLength); istream.close(); ostream.close(); } catch (Exception ex) { System.out.println(ex); VueUtil.alert(VUE.getDialogParent(), VueResources.getString("dialog.export.message") + ex.getMessage(), VueResources.getString("dialog.export.title"), JOptionPane.ERROR_MESSAGE); ex.printStackTrace(); } } | private byte[] getBytesFromUrl(URL url) { ByteArrayOutputStream bais = new ByteArrayOutputStream(); InputStream is = null; try { is = url.openStream(); byte[] byteChunk = new byte[4096]; int n; while ((n = is.read(byteChunk)) > 0) { bais.write(byteChunk, 0, n); } } catch (IOException e) { System.err.printf("Failed while reading bytes from %s: %s", url.toExternalForm(), e.getMessage()); e.printStackTrace(); } finally { if (is != null) { try { is.close(); } catch (IOException e) { } } } return bais.toByteArray(); } | 15,365 |
0 | public void setInput(String input, Component caller, FFMpegProgressReceiver recv) throws IOException { inputMedium = null; if (input.contains("youtube")) { URL url = new URL(input); InputStreamReader read = new InputStreamReader(url.openStream()); BufferedReader in = new BufferedReader(read); String inputLine; String line = null; String vid = input.substring(input.indexOf("?v=") + 3); if (vid.indexOf("&") != -1) vid = vid.substring(0, vid.indexOf("&")); while ((inputLine = in.readLine()) != null) { if (inputLine.contains("\"t\": \"")) { line = inputLine.substring(inputLine.indexOf("\"t\": \"") + 6); line = line.substring(0, line.indexOf("\"")); break; } } in.close(); if (line == null) throw new IOException("Could not find flv-Video"); Downloader dl = new Downloader("http://www.youtube.com/get_video?video_id=" + vid + "&t=" + line, recv, lang); dl.start(); return; } Runtime rt = Runtime.getRuntime(); Process p = rt.exec(new String[] { path, "-i", input }); BufferedReader br = new BufferedReader(new InputStreamReader(p.getErrorStream())); String line; Codec videoCodec = null; Codec audioCodec = null; double duration = -1; String aspectRatio = null; String scala = null; String colorSpace = null; String rate = null; String mrate = null; String aRate = null; String aFreq = null; String aChannel = null; try { while ((line = br.readLine()) != null) { if (Constants.debug) System.out.println(line); if (line.contains("Duration:")) { int hours = Integer.parseInt(line.substring(12, 14)); int mins = Integer.parseInt(line.substring(15, 17)); double secs = Double.parseDouble(line.substring(18, line.indexOf(','))); duration = secs + 60 * mins + hours * 60 * 60; Pattern pat = Pattern.compile("[0-9]+ kb/s"); Matcher m = pat.matcher(line); if (m.find()) mrate = line.substring(m.start(), m.end()); } if (line.contains("Video:")) { String info = line.substring(24); String parts[] = info.split(", "); Pattern pat = Pattern.compile("Video: [a-zA-Z0-9]+,"); Matcher m = pat.matcher(line); String codec = ""; if (m.find()) codec = line.substring(m.start(), m.end()); videoCodec = supportedCodecs.getCodecByName(codec.replace("Video: ", "").replace(",", "")); colorSpace = parts[1]; pat = Pattern.compile("[0-9]+x[0-9]+"); m = pat.matcher(info); if (m.find()) scala = info.substring(m.start(), m.end()); pat = Pattern.compile("DAR [0-9]+:[0-9]+"); m = pat.matcher(info); if (m.find()) aspectRatio = info.substring(m.start(), m.end()).replace("DAR ", ""); else if (scala != null) aspectRatio = String.valueOf((double) (Math.round(((double) ConvertUtils.getWidthFromScala(scala) / (double) ConvertUtils.getHeightFromScala(scala)) * 100)) / 100); pat = Pattern.compile("[0-9]+ kb/s"); m = pat.matcher(info); if (m.find()) rate = info.substring(m.start(), m.end()); } else if (line.contains("Audio:")) { String info = line.substring(24); Pattern pat = Pattern.compile("Audio: [a-zA-Z0-9]+,"); Matcher m = pat.matcher(line); String codec = ""; if (m.find()) codec = line.substring(m.start(), m.end()).replace("Audio: ", "").replace(",", ""); if (codec.equals("mp3")) codec = "libmp3lame"; audioCodec = supportedCodecs.getCodecByName(codec); pat = Pattern.compile("[0-9]+ kb/s"); m = pat.matcher(info); if (m.find()) aRate = info.substring(m.start(), m.end()); pat = Pattern.compile("[0-9]+ Hz"); m = pat.matcher(info); if (m.find()) aFreq = info.substring(m.start(), m.end()); if (line.contains("5.1")) aChannel = "5.1"; else if (line.contains("2.1")) aChannel = "2.1"; else if (line.contains("stereo")) aChannel = "Stereo"; else if (line.contains("mono")) aChannel = "Mono"; } if (videoCodec != null && audioCodec != null && duration != -1) { if (rate == null && mrate != null && aRate != null) rate = String.valueOf(ConvertUtils.getRateFromRateString(mrate) - ConvertUtils.getRateFromRateString(aRate)) + " kb/s"; inputMedium = new InputMedium(audioCodec, videoCodec, input, duration, colorSpace, aspectRatio, scala, rate, mrate, aRate, aFreq, aChannel); break; } } if ((videoCodec != null || audioCodec != null) && duration != -1) inputMedium = new InputMedium(audioCodec, videoCodec, input, duration, colorSpace, aspectRatio, scala, rate, mrate, aRate, aFreq, aChannel); } catch (Exception exc) { if (caller != null) JOptionPane.showMessageDialog(caller, lang.inputerror + " Audiocodec? " + (audioCodec != null) + " Videocodec? " + (videoCodec != null), lang.error, JOptionPane.ERROR_MESSAGE); if (Constants.debug) System.out.println("Audiocodec: " + audioCodec + "\nVideocodec: " + videoCodec); if (Constants.debug) exc.printStackTrace(); throw new IOException("Input file error"); } if (inputMedium == null) { if (caller != null) JOptionPane.showMessageDialog(caller, lang.inputerror + " Audiocodec? " + (audioCodec != null) + " Videocodec? " + (videoCodec != null), lang.error, JOptionPane.ERROR_MESSAGE); if (Constants.debug) System.out.println("Audiocodec: " + audioCodec + "\nVideocodec: " + videoCodec); throw new IOException("Input file error"); } } | 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!"); } | 15,366 |
0 | public static String md5(String string) throws NoSuchAlgorithmException { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.reset(); md5.update(string.getBytes()); byte[] result = md5.digest(); StringBuffer hexString = new StringBuffer(); for (int i = 0; i < result.length; i++) { hexString.append(Integer.toHexString((result[i] & 0xFF) | 0x100).toLowerCase().substring(1, 3)); } return hexString.toString(); } | 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; } | 15,367 |
1 | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | public void trimAndWriteNewSff(OutputStream out) throws IOException { TrimParser trimmer = new TrimParser(); SffParser.parseSFF(untrimmedSffFile, trimmer); tempOut.close(); headerBuilder.withNoIndex().numberOfReads(numberOfTrimmedReads); SffWriter.writeCommonHeader(headerBuilder.build(), out); InputStream in = null; try { in = new FileInputStream(tempReadDataFile); IOUtils.copyLarge(in, out); } finally { IOUtil.closeAndIgnoreErrors(in); } } | 15,368 |
0 | public static String doGetWithBasicAuthentication(URL url, String username, String password, int timeout, Map<String, String> headers) throws Throwable { HttpURLConnection con = (HttpURLConnection) url.openConnection(); con.setRequestMethod("GET"); con.setDoInput(true); if (username != null || password != null) { byte[] encodedPassword = (username + ":" + password).getBytes(); BASE64Encoder encoder = new BASE64Encoder(); con.setRequestProperty("Authorization", "Basic " + encoder.encode(encodedPassword)); } if (headers != null) { for (Map.Entry<String, String> header : headers.entrySet()) { con.setRequestProperty(header.getKey(), header.getValue()); } } con.setConnectTimeout(timeout); InputStream is = con.getInputStream(); BufferedReader rd = new BufferedReader(new InputStreamReader(is)); String line; StringBuffer response = new StringBuffer(); while ((line = rd.readLine()) != null) { response.append(line); response.append('\n'); } rd.close(); is.close(); con.disconnect(); return response.toString(); } | @Override public void connect() throws Exception { if (client != null) { _logger.warn("Already connected."); return; } try { _logger.debug("About to connect to ftp server " + server + " port " + port); client = new FTPClient(); client.connect(server, port); if (!FTPReply.isPositiveCompletion(client.getReplyCode())) throw new Exception("Unable to connect to FTP server " + server + " port " + port + " got error [" + client.getReplyString() + "]"); _logger.info("Connected to ftp server " + server + " port " + port); _logger.debug(client.getReplyString()); if (!client.login(username, password)) throw new Exception("Invalid username / password combination for FTP server " + server + " port " + port); _logger.debug("Log in successful."); _logger.info("FTP server is [" + client.getSystemType() + "]"); if (passiveMode) { client.enterLocalPassiveMode(); _logger.info("Passive mode selected."); } else { client.enterLocalActiveMode(); _logger.info("Active mode selected."); } if (binaryMode) { client.setFileType(FTP.BINARY_FILE_TYPE); _logger.info("BINARY mode selected."); } else { client.setFileType(FTP.ASCII_FILE_TYPE); _logger.info("ASCII mode selected."); } if (client.changeWorkingDirectory(remoteRootDir)) { _logger.info("Changed directory to " + remoteRootDir); } else { throw new Exception("Cannot change directory to [" + remoteRootDir + "] on FTP server " + server + " port " + port); } } catch (Exception e) { _logger.error("Failed to connect to the FTP server " + server + " on port " + port, e); disconnect(); throw e; } } | 15,369 |
1 | public static void copyFile(String source, String destination, boolean overwrite) { File sourceFile = new File(source); try { File destinationFile = new File(destination); BufferedInputStream bis = new BufferedInputStream(new FileInputStream(sourceFile)); BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(destinationFile)); int temp = 0; while ((temp = bis.read()) != -1) bos.write(temp); bis.close(); bos.close(); } catch (Exception e) { } return; } | static void copy(String src, String dest) throws IOException { File ifp = new File(src); File ofp = new File(dest); if (ifp.exists() == false) { throw new IOException("file '" + src + "' does not exist"); } FileInputStream fis = new FileInputStream(ifp); FileOutputStream fos = new FileOutputStream(ofp); byte[] b = new byte[1024]; while (fis.read(b) > 0) fos.write(b); fis.close(); fos.close(); } | 15,370 |
0 | public Image storeImage(String title, String pathToImage, Map<String, Object> additionalProperties) { File collectionFolder = ProjectManager.getInstance().getFolder(PropertyHandler.getInstance().getProperty("_default_collection_name")); File imageFile = new File(pathToImage); String filename = ""; String format = ""; File copiedImageFile; while (true) { filename = "image" + UUID.randomUUID().hashCode(); if (!DbEntryProvider.INSTANCE.idExists(filename)) { Path path = new Path(pathToImage); format = path.getFileExtension(); copiedImageFile = new File(collectionFolder.getAbsolutePath() + File.separator + filename + "." + format); if (!copiedImageFile.exists()) break; } } try { copiedImageFile.createNewFile(); } catch (IOException e1) { ExceptionHandlingService.INSTANCE.handleException(e1); return null; } BufferedInputStream in = null; BufferedOutputStream out = null; try { in = new BufferedInputStream(new FileInputStream(imageFile), 4096); out = new BufferedOutputStream(new FileOutputStream(copiedImageFile), 4096); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } catch (FileNotFoundException e) { ExceptionHandlingService.INSTANCE.handleException(e); return null; } catch (IOException e) { ExceptionHandlingService.INSTANCE.handleException(e); return null; } Image image = new ImageImpl(); image.setId(filename); image.setFormat(format); image.setEntryDate(new Date()); image.setTitle(title); image.setAdditionalProperties(additionalProperties); boolean success = DbEntryProvider.INSTANCE.storeNewImage(image); if (success) return image; return null; } | public void invoke(MessageContext msgContext) throws AxisFault { log.debug("Enter: MD5AttachHandler::invoke"); try { Message msg = msgContext.getRequestMessage(); SOAPConstants soapConstants = msgContext.getSOAPConstants(); org.apache.axis.message.SOAPEnvelope env = (org.apache.axis.message.SOAPEnvelope) msg.getSOAPEnvelope(); org.apache.axis.message.SOAPBodyElement sbe = env.getFirstBody(); org.w3c.dom.Element sbElement = sbe.getAsDOM(); org.w3c.dom.Node n = sbElement.getFirstChild(); for (; n != null && !(n instanceof org.w3c.dom.Element); n = n.getNextSibling()) ; org.w3c.dom.Element paramElement = (org.w3c.dom.Element) n; String href = paramElement.getAttribute(soapConstants.getAttrHref()); org.apache.axis.Part ap = msg.getAttachmentsImpl().getAttachmentByReference(href); javax.activation.DataHandler dh = org.apache.axis.attachments.AttachmentUtils.getActivationDataHandler(ap); org.w3c.dom.Node timeNode = paramElement.getFirstChild(); long startTime = -1; if (timeNode != null && timeNode instanceof org.w3c.dom.Text) { String startTimeStr = ((org.w3c.dom.Text) timeNode).getData(); startTime = Long.parseLong(startTimeStr); } long receivedTime = System.currentTimeMillis(); long elapsedTime = -1; if (startTime > 0) elapsedTime = receivedTime - startTime; String elapsedTimeStr = elapsedTime + ""; java.security.MessageDigest md = java.security.MessageDigest.getInstance("MD5"); java.io.InputStream attachmentStream = dh.getInputStream(); int bread = 0; byte[] buf = new byte[64 * 1024]; do { bread = attachmentStream.read(buf); if (bread > 0) { md.update(buf, 0, bread); } } while (bread > -1); attachmentStream.close(); buf = null; String contentType = dh.getContentType(); if (contentType != null && contentType.length() != 0) { md.update(contentType.getBytes("US-ASCII")); } sbe = env.getFirstBody(); sbElement = sbe.getAsDOM(); n = sbElement.getFirstChild(); for (; n != null && !(n instanceof org.w3c.dom.Element); n = n.getNextSibling()) ; paramElement = (org.w3c.dom.Element) n; String MD5String = org.apache.axis.encoding.Base64.encode(md.digest()); String senddata = " elapsedTime=" + elapsedTimeStr + " MD5=" + MD5String; paramElement.appendChild(paramElement.getOwnerDocument().createTextNode(senddata)); sbe = new org.apache.axis.message.SOAPBodyElement(sbElement); env.clearBody(); env.addBodyElement(sbe); msg = new Message(env); msgContext.setResponseMessage(msg); } catch (Exception e) { log.error(Messages.getMessage("exception00"), e); throw AxisFault.makeFault(e); } log.debug("Exit: MD5AttachHandler::invoke"); } | 15,371 |
1 | public boolean copy(File src, File dest, byte[] b) { if (src.isDirectory()) { String[] ss = src.list(); for (int i = 0; i < ss.length; i++) if (!copy(new File(src, ss[i]), new File(dest, ss[i]), b)) return false; return true; } delete(dest); dest.getParentFile().mkdirs(); try { FileInputStream fis = new FileInputStream(src); try { FileOutputStream fos = new FileOutputStream(dest); try { int read; while ((read = fis.read(b)) != -1) fos.write(b, 0, read); } finally { try { fos.close(); } catch (IOException ignore) { } register(dest); } } finally { fis.close(); } if (log.isDebugEnabled()) log.debug("Success: M-COPY " + src + " -> " + dest); return true; } catch (IOException e) { log.error("Failed: M-COPY " + src + " -> " + dest, e); return false; } } | private void copyFile(String from, String to) throws Exception { URL monitorCallShellScriptUrl = Thread.currentThread().getContextClassLoader().getResource(from); File inScriptFile = null; try { inScriptFile = new File(monitorCallShellScriptUrl.toURI()); } catch (URISyntaxException e) { throw e; } File outScriptFile = new File(to); 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.setWorkingDirectory(workingDirectory); cmdExecutor.runCommand("chmod 777 " + to); } catch (Exception e) { throw e; } } | 15,372 |
1 | public static void unzipFile(File zipFile, File destFile, boolean removeSrcFile) throws Exception { ZipInputStream zipinputstream = new ZipInputStream(new FileInputStream(zipFile)); ZipEntry zipentry = zipinputstream.getNextEntry(); int BUFFER_SIZE = 4096; while (zipentry != null) { String entryName = zipentry.getName(); log.info("<<<<<< ZipUtility.unzipFile - Extracting: " + zipentry.getName()); File newFile = null; if (destFile.isDirectory()) newFile = new File(destFile, entryName); else newFile = destFile; if (zipentry.isDirectory() || entryName.endsWith(File.separator + ".")) { newFile.mkdirs(); } else { ByteBuffer buffer = ByteBuffer.allocate(BUFFER_SIZE); byte[] bufferArray = buffer.array(); FileUtilities.createDirectory(newFile.getParentFile()); FileChannel destinationChannel = new FileOutputStream(newFile).getChannel(); while (true) { buffer.clear(); int lim = zipinputstream.read(bufferArray); if (lim == -1) break; buffer.flip(); buffer.limit(lim); destinationChannel.write(buffer); } destinationChannel.close(); zipinputstream.closeEntry(); } zipentry = zipinputstream.getNextEntry(); } zipinputstream.close(); if (removeSrcFile) { if (zipFile.exists()) zipFile.delete(); } } | public void testAddFiles() throws Exception { File original = ZipPlugin.getFileInPlugin(new Path("testresources/test.zip")); File copy = new File(original.getParentFile(), "1test.zip"); InputStream in = null; OutputStream out = null; try { in = new FileInputStream(original); out = new FileOutputStream(copy); byte[] buf = new byte[1024]; int len; while ((len = in.read(buf)) > 0) out.write(buf, 0, len); } finally { Util.close(in); Util.close(out); } ArchiveFile archive = new ArchiveFile(ZipPlugin.createArchive(copy.getPath())); archive.addFiles(new String[] { ZipPlugin.getFileInPlugin(new Path("testresources/add.txt")).getPath() }, new NullProgressMonitor()); IArchive[] children = archive.getChildren(); boolean found = false; for (IArchive child : children) { if (child.getLabel(IArchive.NAME).equals("add.txt")) found = true; } assertTrue(found); copy.delete(); } | 15,373 |
1 | public boolean excuteBackup(String backupOrginlDrctry, String targetFileNm, String archiveFormat) throws JobExecutionException { File targetFile = new File(targetFileNm); File srcFile = new File(backupOrginlDrctry); if (!srcFile.exists()) { log.error("백업원본디렉토리[" + srcFile.getAbsolutePath() + "]가 존재하지 않습니다."); throw new JobExecutionException("백업원본디렉토리[" + srcFile.getAbsolutePath() + "]가 존재하지 않습니다."); } if (srcFile.isFile()) { log.error("백업원본디렉토리[" + srcFile.getAbsolutePath() + "]가 파일입니다. 디렉토리명을 지정해야 합니다. "); throw new JobExecutionException("백업원본디렉토리[" + srcFile.getAbsolutePath() + "]가 파일입니다. 디렉토리명을 지정해야 합니다. "); } boolean result = false; FileInputStream finput = null; FileOutputStream fosOutput = null; ArchiveOutputStream aosOutput = null; ArchiveEntry entry = null; try { log.debug("charter set : " + Charset.defaultCharset().name()); fosOutput = new FileOutputStream(targetFile); aosOutput = new ArchiveStreamFactory().createArchiveOutputStream(archiveFormat, fosOutput); if (ArchiveStreamFactory.TAR.equals(archiveFormat)) { ((TarArchiveOutputStream) aosOutput).setLongFileMode(TarArchiveOutputStream.LONGFILE_GNU); } File[] fileArr = srcFile.listFiles(); ArrayList list = EgovFileTool.getSubFilesByAll(fileArr); for (int i = 0; i < list.size(); i++) { File sfile = new File((String) list.get(i)); finput = new FileInputStream(sfile); if (ArchiveStreamFactory.TAR.equals(archiveFormat)) { entry = new TarArchiveEntry(sfile, new String(sfile.getAbsolutePath().getBytes(Charset.defaultCharset().name()), "8859_1")); ((TarArchiveEntry) entry).setSize(sfile.length()); } else { entry = new ZipArchiveEntry(sfile.getAbsolutePath()); ((ZipArchiveEntry) entry).setSize(sfile.length()); } aosOutput.putArchiveEntry(entry); IOUtils.copy(finput, aosOutput); aosOutput.closeArchiveEntry(); finput.close(); result = true; } aosOutput.close(); } catch (Exception e) { log.error("백업화일생성중 에러가 발생했습니다. 에러 : " + e.getMessage()); log.debug(e); result = false; throw new JobExecutionException("백업화일생성중 에러가 발생했습니다.", e); } finally { try { if (finput != null) finput.close(); } catch (Exception e2) { log.error("IGNORE:", e2); } try { if (aosOutput != null) aosOutput.close(); } catch (Exception e2) { log.error("IGNORE:", e2); } try { if (fosOutput != null) fosOutput.close(); } catch (Exception e2) { log.error("IGNORE:", e2); } try { if (result == false) targetFile.delete(); } catch (Exception e2) { log.error("IGNORE:", e2); } } return result; } | protected List<Datastream> getDatastreams(final DepositCollection pDeposit) throws IOException, SWORDException { List<Datastream> tDatastreams = new ArrayList<Datastream>(); LOG.debug("copying file"); String tZipTempFileName = super.getTempDir() + "uploaded-file.tmp"; IOUtils.copy(pDeposit.getFile(), new FileOutputStream(tZipTempFileName)); Datastream tDatastream = new LocalDatastream(super.getGenericFileName(pDeposit), this.getContentType(), tZipTempFileName); tDatastreams.add(tDatastream); tDatastreams.addAll(_zipFile.getFiles(tZipTempFileName)); return tDatastreams; } | 15,374 |
1 | public static void generateCode(File flowFile, String packagePath, File destDir, File scriptRootFolder) throws IOException { InputStream javaSrcIn = generateCode(flowFile, packagePath, scriptRootFolder); File outputFolder = new File(destDir, packagePath.replace('.', File.separatorChar)); String fileName = flowFile.getName(); fileName = fileName.substring(0, fileName.lastIndexOf(".") + 1) + Consts.FILE_EXTENSION_GROOVY; File outputFile = new File(outputFolder, fileName); OutputStream javaSrcOut = new FileOutputStream(outputFile); IOUtils.copyBufferedStream(javaSrcIn, javaSrcOut); javaSrcIn.close(); javaSrcOut.close(); } | 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(); } } | 15,375 |
0 | public void testDecode1000BinaryStore() throws Exception { EXISchema corpus = EXISchemaFactoryTestUtil.getEXISchema("/DataStore/DataStore.xsd", getClass(), m_compilerErrors); Assert.assertEquals(0, m_compilerErrors.getTotalCount()); GrammarCache grammarCache = new GrammarCache(corpus, GrammarOptions.STRICT_OPTIONS); String[] base64Values100 = { "R0lGODdhWALCov////T09M7Ozqampn19fVZWVi0tLQUFBSxYAsJAA/8Iutz+MMpJq7046827/2Ao\n", "/9j/4BBKRklGAQEBASwBLP/hGlZFeGlmTU0qF5ZOSUtPTiBDT1JQT1JBVElPTk5J", "R0lGODlhHh73KSkpOTk5QkJCSkpKUlJSWlpaY2Nja2trc3Nze3t7hISEjIyMlJSUnJycpaWlra2t\n" + "tbW1vb29xsbGzs7O1tbW3t7e5+fn7+/v//////////8=", "/9j/4BBKRklGAQEBAf/bQwYEBQYFBAYGBQYHBwYIChAKCgkJChQODwwQFxQYGBc=", "R0lGODlhHh73M2aZzP8zMzNmM5kzzDP/M2YzZmZmmWbM", "/9j/4BBKRklGAQEBAf/bQwYEBQYFBAYGBQYHBwYIChAKCgkJChQODwwQFxQYGBcUFhYaHSUfGhsj\n" + "HBYWICwgIyYnKSopGR8tMC0oMCUoKSj/20M=", "R0lGODdhWAK+ov////j4+NTU1JOTk0tLSx8fHwkJCSxYAr5AA/8IMkzjrEEmahy23SpC", "R0lGODdh4QIpAncJIf4aU29mdHdhcmU6IE1pY3Jvc29mdCBPZmZpY2Us4QIpAof//////8z//5n/\n", "R0lGODdhWAK+ov////v7++fn58DAwI6Ojl5eXjExMQMDAyxYAr5AA/8Iutz+MMpJq7046827/2Ao\n" + "jmRpnmiqPsKxvg==", "R0lGODdh4QIpAncJIf4aU29mdHdhcmU6IE1pY3Jvc29mdCBPZmZpY2Us4QIpAob//////8z//5n/\nzP//zMw=" }; AlignmentType alignment = AlignmentType.bitPacked; Transmogrifier encoder = new Transmogrifier(); encoder.setEXISchema(grammarCache); encoder.setAlignmentType(alignment); ByteArrayOutputStream baos = new ByteArrayOutputStream(); encoder.setOutputStream(baos); URL url = resolveSystemIdAsURL("/DataStore/instance/1000BinaryStore.xml"); encoder.encode(new InputSource(url.openStream())); byte[] bts = baos.toByteArray(); Scanner scanner; int n_texts; EXIDecoder decoder = new EXIDecoder(999); decoder.setEXISchema(grammarCache); decoder.setAlignmentType(alignment); decoder.setInputStream(new ByteArrayInputStream(bts)); scanner = decoder.processHeader(); EXIEvent exiEvent; n_texts = 0; while ((exiEvent = scanner.nextEvent()) != null) { if (exiEvent.getEventVariety() == EXIEvent.EVENT_CH) { if (++n_texts % 100 == 0) { String expected = base64Values100[(n_texts / 100) - 1]; String val = exiEvent.getCharacters().makeString(); Assert.assertEquals(expected, val); } } } Assert.assertEquals(1000, n_texts); } | 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; } | 15,376 |
0 | public static synchronized String encrypt(String plaintext) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md = null; md = MessageDigest.getInstance("SHA"); md.update(plaintext.getBytes("UTF-8")); byte raw[] = md.digest(); String hash = (new BASE64Encoder()).encode(raw); return hash; } | public LineIterator iterator() { LineIterator ret; final String charsetname; final Charset charset; final CharsetDecoder charsetDecoder; synchronized (this) { charsetname = this.charsetname; charset = this.charset; charsetDecoder = this.charsetDecoder; } try { if (charsetDecoder != null) ret = new LineIterator(this, url.openStream(), returnNullUponEof, charsetDecoder); else if (charset != null) ret = new LineIterator(this, url.openStream(), returnNullUponEof, charset); else if (charsetname != null) ret = new LineIterator(this, url.openStream(), returnNullUponEof, Charset.forName(charsetname)); else ret = new LineIterator(this, url.openStream(), returnNullUponEof, (Charset) null); synchronized (openedIterators) { openedIterators.add(ret); } return ret; } catch (IOException e) { throw new IllegalStateException(e); } } | 15,377 |
1 | 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); } | 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!"); } | 15,378 |
0 | private void addJarToPackages(URL jarurl, File jarfile, boolean cache) { try { boolean caching = this.jarfiles != null; URLConnection jarconn = null; boolean localfile = true; if (jarfile == null) { jarconn = jarurl.openConnection(); if (jarconn.getURL().getProtocol().equals("file")) { String jarfilename = jarurl.getFile(); jarfilename = jarfilename.replace('/', File.separatorChar); jarfile = new File(jarfilename); } else { localfile = false; } } if (localfile && !jarfile.exists()) { return; } Hashtable zipPackages = null; long mtime = 0; String jarcanon = null; JarXEntry entry = null; boolean brandNew = false; if (caching) { if (localfile) { mtime = jarfile.lastModified(); jarcanon = jarfile.getCanonicalPath(); } else { mtime = jarconn.getLastModified(); jarcanon = jarurl.toString(); } entry = (JarXEntry) this.jarfiles.get(jarcanon); if ((entry == null || !(new File(entry.cachefile).exists())) && cache) { message("processing new jar, '" + jarcanon + "'"); String jarname; if (localfile) { jarname = jarfile.getName(); } else { jarname = jarurl.getFile(); int slash = jarname.lastIndexOf('/'); if (slash != -1) jarname = jarname.substring(slash + 1); } jarname = jarname.substring(0, jarname.length() - 4); entry = new JarXEntry(jarname); this.jarfiles.put(jarcanon, entry); brandNew = true; } if (mtime != 0 && entry != null && entry.mtime == mtime) { zipPackages = readCacheFile(entry, jarcanon); } } if (zipPackages == null) { caching = caching && cache; if (caching) { this.indexModified = true; if (entry.mtime != 0) { message("processing modified jar, '" + jarcanon + "'"); } entry.mtime = mtime; } InputStream jarin; if (jarconn == null) { jarin = new BufferedInputStream(new FileInputStream(jarfile)); } else { jarin = jarconn.getInputStream(); } zipPackages = getZipPackages(jarin); if (caching) { writeCacheFile(entry, jarcanon, zipPackages, brandNew); } } addPackages(zipPackages, jarcanon); } catch (IOException ioe) { ioe.printStackTrace(); warning("skipping bad jar, '" + (jarfile != null ? jarfile.toString() : jarurl.toString()) + "'"); } } | public Project deleteProject(int projectID) throws AdaptationException { Project project = null; Connection connection = null; Statement statement = null; ResultSet resultSet = null; try { String query = "SELECT * FROM Projects WHERE id = " + projectID; connection = DriverManager.getConnection(CONN_STR); statement = connection.createStatement(); resultSet = statement.executeQuery(query); if (!resultSet.next()) { connection.rollback(); String msg = "Attempt to delete project failed."; log.error(msg); throw new AdaptationException(msg); } project = getProject(resultSet); query = "DELETE FROM Projects WHERE id = " + projectID; statement.executeUpdate(query); connection.commit(); } catch (SQLException ex) { try { connection.rollback(); } catch (Exception e) { } String msg = "SQLException in deleteProject"; log.error(msg, ex); throw new AdaptationException(msg, ex); } finally { try { resultSet.close(); } catch (Exception ex) { } try { statement.close(); } catch (Exception ex) { } try { connection.close(); } catch (Exception ex) { } } return project; } | 15,379 |
0 | public void doNew(Vector userId, String shareFlag, String folderId) throws AddrException { DBOperation dbo = null; Connection connection = null; PreparedStatement ps = null; ResultSet rset = null; String sql = "insert into " + SHARE_TABLE + " values(?,?,?)"; try { dbo = createDBOperation(); connection = dbo.getConnection(); connection.setAutoCommit(false); for (int i = 0; i < userId.size(); i++) { String user = (String) userId.elementAt(i); ps = connection.prepareStatement(sql); ps.setInt(1, Integer.parseInt(folderId)); ps.setInt(2, Integer.parseInt(user)); ps.setString(3, shareFlag); int resultCount = ps.executeUpdate(); if (resultCount != 1) { throw new Exception("error"); } } connection.commit(); } catch (Exception ex) { if (connection != null) { try { connection.rollback(); } catch (SQLException e) { e.printStackTrace(); } } logger.error("���������ļ�����Ϣʧ��, " + ex.getMessage()); throw new AddrException("���������ļ�����Ϣʧ��,һ�������ļ���ֻ�ܹ����ͬһ�û�һ��!"); } finally { close(rset, null, ps, connection, dbo); } } | public void run(IProgressMonitor runnerMonitor) throws CoreException { try { Map<String, File> projectFiles = new HashMap<String, File>(); IPath basePath = new Path("/"); for (File nextLocation : filesToZip) { projectFiles.putAll(getFilesToZip(nextLocation, basePath, fileFilter)); } if (projectFiles.isEmpty()) { PlatformActivator.logDebug("Zip file (" + zipFileName + ") not created because there were no files to zip"); return; } IPath resultsPath = PlatformActivator.getDefault().getResultsPath(); File copyRoot = resultsPath.toFile(); copyRoot.mkdirs(); IPath zipFilePath = resultsPath.append(new Path(finalZip)); String zipFileName = zipFilePath.toPortableString(); ZipOutputStream out = new ZipOutputStream(new FileOutputStream(zipFileName)); try { out.setLevel(Deflater.DEFAULT_COMPRESSION); for (String filePath : projectFiles.keySet()) { File nextFile = projectFiles.get(filePath); FileInputStream fin = new FileInputStream(nextFile); try { out.putNextEntry(new ZipEntry(filePath)); try { byte[] bin = new byte[4096]; int bread = fin.read(bin, 0, 4096); while (bread != -1) { out.write(bin, 0, bread); bread = fin.read(bin, 0, 4096); } } finally { out.closeEntry(); } } finally { fin.close(); } } } finally { out.close(); } } catch (FileNotFoundException e) { Status error = new Status(Status.ERROR, PlatformActivator.PLUGIN_ID, Status.ERROR, e.getLocalizedMessage(), e); throw new CoreException(error); } catch (IOException e) { Status error = new Status(Status.ERROR, PlatformActivator.PLUGIN_ID, Status.ERROR, e.getLocalizedMessage(), e); throw new CoreException(error); } } | 15,380 |
0 | public void testReleaseOnEntityWriteTo() throws Exception { HttpParams params = defaultParams.copy(); ConnManagerParams.setMaxTotalConnections(params, 1); ConnManagerParams.setMaxConnectionsPerRoute(params, new ConnPerRouteBean(1)); ThreadSafeClientConnManager mgr = createTSCCM(params, null); assertEquals(0, mgr.getConnectionsInPool()); DefaultHttpClient client = new DefaultHttpClient(mgr, params); HttpGet httpget = new HttpGet("/random/20000"); HttpHost target = getServerHttp(); HttpResponse response = client.execute(target, httpget); ClientConnectionRequest connreq = mgr.requestConnection(new HttpRoute(target), null); try { connreq.getConnection(250, TimeUnit.MILLISECONDS); fail("ConnectionPoolTimeoutException should have been thrown"); } catch (ConnectionPoolTimeoutException expected) { } HttpEntity e = response.getEntity(); assertNotNull(e); ByteArrayOutputStream outsteam = new ByteArrayOutputStream(); e.writeTo(outsteam); assertEquals(1, mgr.getConnectionsInPool()); connreq = mgr.requestConnection(new HttpRoute(target), null); ManagedClientConnection conn = connreq.getConnection(250, TimeUnit.MILLISECONDS); mgr.releaseConnection(conn, -1, null); mgr.shutdown(); } | public static void doVersionCheck(View view) { view.showWaitCursor(); try { URL url = new URL(jEdit.getProperty("version-check.url")); InputStream in = url.openStream(); BufferedReader bin = new BufferedReader(new InputStreamReader(in)); String line; String develBuild = null; String stableBuild = null; while ((line = bin.readLine()) != null) { if (line.startsWith(".build")) develBuild = line.substring(6).trim(); else if (line.startsWith(".stablebuild")) stableBuild = line.substring(12).trim(); } bin.close(); if (develBuild != null && stableBuild != null) { doVersionCheck(view, stableBuild, develBuild); } } catch (IOException e) { String[] args = { jEdit.getProperty("version-check.url"), e.toString() }; GUIUtilities.error(view, "read-error", args); } view.hideWaitCursor(); } | 15,381 |
0 | private void btnOkActionPerformed(java.awt.event.ActionEvent evt) { try { int id = 0; String sql = "SELECT MAX(ID) as MAX_ID from CORE_USER_GROUPS"; PreparedStatement pStmt = Database.getMyConnection().prepareStatement(sql); ResultSet rs = pStmt.executeQuery(); if (rs.next()) { id = rs.getInt("MAX_ID") + 1; } else { id = 1; } Database.close(pStmt); sql = "INSERT INTO CORE_USER_GROUPS" + " (ID, GRP_NAME, GRP_DESC, DATE_INITIAL, DATE_FINAL, IND_STATUS)" + " VALUES (?, ?, ?, ?, ?, ?)"; pStmt = Database.getMyConnection().prepareStatement(sql); pStmt.setInt(1, id); pStmt.setString(2, txtGrpName.getText()); pStmt.setString(3, txtGrpDesc.getText()); pStmt.setDate(4, Utils.getTodaySql()); pStmt.setDate(5, Date.valueOf("9999-12-31")); pStmt.setString(6, "A"); pStmt.executeUpdate(); Database.getMyConnection().commit(); Database.close(pStmt); MessageBox.ok("New group added successfully", this); rs = getGroups(); tblGroups.setModel(new GroupsTableModel(rs)); Database.close(rs); } catch (SQLException e) { log.error("Failed with update operation \n" + e.getMessage()); MessageBox.ok("Failed to create the new group in the database", this); try { Database.getMyConnection().rollback(); } catch (Exception inner) { } ; } catch (IllegalArgumentException e) { log.error("Illegal argument for the DATE_FINAL \n" + e.getMessage()); MessageBox.ok("Failed to create the new group in the database", this); try { Database.getMyConnection().rollback(); } catch (Exception inner) { } ; } finally { txtGrpName.setEnabled(false); txtGrpDesc.setEnabled(false); btnOk.setEnabled(false); btnCancel.requestFocus(); } } | public static void copyFile(File sourceFile, File destFile) throws IOException { if (!destFile.exists()) { destFile.createNewFile(); } FileChannel source = null; FileChannel destination = null; try { source = new FileInputStream(sourceFile).getChannel(); destination = new FileOutputStream(destFile).getChannel(); destination.transferFrom(source, 0, source.size()); } finally { if (source != null) { source.close(); } if (destination != null) { destination.close(); } } } | 15,382 |
1 | public static void copyTo(java.io.File source, java.io.File dest) throws Exception { java.io.FileInputStream inputStream = null; java.nio.channels.FileChannel sourceChannel = null; java.io.FileOutputStream outputStream = null; java.nio.channels.FileChannel destChannel = null; long size = source.length(); long bufferSize = 1024; long count = 0; if (size < bufferSize) bufferSize = size; Exception exception = null; try { if (dest.exists() == false) dest.createNewFile(); inputStream = new java.io.FileInputStream(source); sourceChannel = inputStream.getChannel(); outputStream = new java.io.FileOutputStream(dest); destChannel = outputStream.getChannel(); while (count < size) count += sourceChannel.transferTo(count, bufferSize, destChannel); } catch (Exception e) { exception = e; } finally { closeFileChannel(sourceChannel); closeFileChannel(destChannel); } if (exception != null) throw exception; } | public static void fileCopy(File sourceFile, File destFile) throws IOException { FileChannel source = null; FileChannel destination = null; FileInputStream fis = null; FileOutputStream fos = null; try { fis = new FileInputStream(sourceFile); fos = new FileOutputStream(destFile); source = fis.getChannel(); destination = fos.getChannel(); destination.transferFrom(source, 0, source.size()); } finally { fis.close(); fos.close(); if (source != null) { source.close(); } if (destination != null) { destination.close(); } } } | 15,383 |
1 | public static void copy(File source, File sink) throws IOException { if (source == null) throw new NullPointerException("Source file must not be null"); if (sink == null) throw new NullPointerException("Target file must not be null"); if (!source.exists()) throw new IOException("Source file " + source.getPath() + " does not exist"); if (!source.isFile()) throw new IOException("Source file " + source.getPath() + " is not a regular file"); if (!source.canRead()) throw new IOException("Source file " + source.getPath() + " can not be read (missing acces right)"); if (!sink.exists()) throw new IOException("Target file " + sink.getPath() + " does not exist"); if (!sink.isFile()) throw new IOException("Target file " + sink.getPath() + " is not a regular file"); if (!sink.canWrite()) throw new IOException("Target file " + sink.getPath() + " is write protected"); InputStream input = null; OutputStream output = null; try { input = new FileInputStream(source); output = new FileOutputStream(sink); byte[] buffer = new byte[1024]; while (input.available() > 0) { int bread = input.read(buffer); if (bread > 0) output.write(buffer, 0, bread); } } finally { if (input != null) try { input.close(); } catch (IOException x) { } if (output != null) try { output.close(); } catch (IOException x) { } } } | public boolean backupFile(File oldFile, File newFile) { boolean isBkupFileOK = false; FileChannel sourceChannel = null; FileChannel targetChannel = null; try { sourceChannel = new FileInputStream(oldFile).getChannel(); targetChannel = new FileOutputStream(newFile).getChannel(); targetChannel.transferFrom(sourceChannel, 0, sourceChannel.size()); } catch (IOException e) { logger.log(Level.SEVERE, "IO exception occurred while copying file", e); } finally { if ((newFile != null) && (newFile.exists()) && (newFile.length() > 0)) { isBkupFileOK = true; } try { if (sourceChannel != null) { sourceChannel.close(); } if (targetChannel != null) { targetChannel.close(); } } catch (IOException e) { logger.info("closing channels failed"); } } return isBkupFileOK; } | 15,384 |
1 | public static void encryptFile(String input, String output, String pwd) throws Exception { CipherOutputStream out; InputStream in; Cipher cipher; SecretKey key; byte[] byteBuffer; cipher = Cipher.getInstance("DES"); key = new SecretKeySpec(pwd.getBytes(), "DES"); cipher.init(Cipher.ENCRYPT_MODE, key); in = new FileInputStream(input); out = new CipherOutputStream(new FileOutputStream(output), cipher); byteBuffer = new byte[1024]; for (int n; (n = in.read(byteBuffer)) != -1; out.write(byteBuffer, 0, n)) ; in.close(); out.close(); } | private void buildBundle() { if (targetProject == null) { MessageDialog.openError(getShell(), "Error", "No target SPAB project selected!"); return; } if (projectProcessDirSelector.getText().trim().length() == 0) { MessageDialog.openError(getShell(), "Error", "No process directory selected for project " + targetProject.getName() + "!"); return; } deleteBundleFile(); try { File projectDir = targetProject.getLocation().toFile(); File projectProcessesDir = new File(projectDir, projectProcessDirSelector.getText()); boolean bpmoCopied = IOUtils.copyProcessFilesSecure(getBPMOFile(), projectProcessesDir); boolean sbpelCopied = IOUtils.copyProcessFilesSecure(getSBPELFile(), projectProcessesDir); boolean xmlCopied = IOUtils.copyProcessFilesSecure(getBPEL4SWSFile(), projectProcessesDir); bundleFile = IOUtils.archiveBundle(projectDir, Activator.getDefault().getStateLocation().toFile()); if (bpmoCopied) { new File(projectProcessesDir, getBPMOFile().getName()).delete(); } if (sbpelCopied) { new File(projectProcessesDir, getSBPELFile().getName()).delete(); } if (xmlCopied) { new File(projectProcessesDir, getBPEL4SWSFile().getName()).delete(); } } catch (Throwable anyError) { LogManager.logError(anyError); MessageDialog.openError(getShell(), "Error", "Error building SPAB :\n" + anyError.getMessage()); updateBundleUI(); return; } bpmoFile = getBPMOFile(); sbpelFile = getSBPELFile(); xmlFile = getBPEL4SWSFile(); updateBundleUI(); getWizard().getContainer().updateButtons(); } | 15,385 |
0 | protected Drawing loadDrawing(ProgressIndicator progress) throws IOException { Drawing drawing = createDrawing(); if (getParameter("datafile") != null) { URL url = new URL(getDocumentBase(), getParameter("datafile")); URLConnection uc = url.openConnection(); if (uc instanceof HttpURLConnection) { ((HttpURLConnection) uc).setUseCaches(false); } int contentLength = uc.getContentLength(); InputStream in = uc.getInputStream(); try { if (contentLength != -1) { in = new BoundedRangeInputStream(in); ((BoundedRangeInputStream) in).setMaximum(contentLength + 1); progress.setProgressModel((BoundedRangeModel) in); progress.setIndeterminate(false); } BufferedInputStream bin = new BufferedInputStream(in); bin.mark(512); IOException formatException = null; for (InputFormat format : drawing.getInputFormats()) { try { bin.reset(); } catch (IOException e) { uc = url.openConnection(); in = uc.getInputStream(); in = new BoundedRangeInputStream(in); ((BoundedRangeInputStream) in).setMaximum(contentLength + 1); progress.setProgressModel((BoundedRangeModel) in); bin = new BufferedInputStream(in); bin.mark(512); } try { bin.reset(); format.read(bin, drawing, true); formatException = null; break; } catch (IOException e) { formatException = e; } } if (formatException != null) { throw formatException; } } finally { in.close(); } } return drawing; } | private static Manifest getManifest() throws IOException { Stack manifests = new Stack(); for (Enumeration e = Run.class.getClassLoader().getResources(MANIFEST); e.hasMoreElements(); ) manifests.add(e.nextElement()); while (!manifests.isEmpty()) { URL url = (URL) manifests.pop(); InputStream in = url.openStream(); Manifest mf = new Manifest(in); in.close(); if (mf.getMainAttributes().getValue(MAIN_CLASS) != null) return mf; } throw new Error("No " + MANIFEST + " with " + MAIN_CLASS + " found"); } | 15,386 |
1 | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | public String copyImages(Document doc, String sXML, String newPath, String tagName, String itemName) { NodeList nl = null; Node n = null; NamedNodeMap nnp = null; Node nsrc = null; URL url = null; String sFilename = ""; String sNewPath = ""; int index; String sOldPath = ""; try { nl = doc.getElementsByTagName(tagName); for (int i = 0; i < nl.getLength(); i++) { n = nl.item(i); nnp = n.getAttributes(); nsrc = nnp.getNamedItem(itemName); String sTemp = nsrc.getTextContent(); url = new URL("file", "localhost", sTemp); sOldPath = url.getPath(); sOldPath = sOldPath.replace('/', File.separatorChar); int indexFirstSlash = sOldPath.indexOf(File.separatorChar); String sSourcePath; if (itemName.equals("data")) sSourcePath = sOldPath; else sSourcePath = sOldPath.substring(indexFirstSlash + 1); index = sOldPath.lastIndexOf(File.separatorChar); sFilename = sOldPath.substring(index + 1); sNewPath = newPath + 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(); } sXML = sXML.replace(nsrc.getTextContent(), sFilename); } } catch (MalformedURLException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } return sXML; } | 15,387 |
0 | public void setBckImg(String newPath) { try { File inputFile = new File(getPath()); File outputFile = new File(newPath); if (!inputFile.getCanonicalPath().equals(outputFile.getCanonicalPath())) { FileInputStream in = new FileInputStream(inputFile); FileOutputStream out = null; try { out = new FileOutputStream(outputFile); } catch (FileNotFoundException ex1) { ex1.printStackTrace(); JOptionPane.showMessageDialog(null, ex1.getMessage().substring(0, Math.min(ex1.getMessage().length(), drawPanel.MAX_DIALOG_MSG_SZ)) + "-" + getClass(), "Set Bck Img", JOptionPane.ERROR_MESSAGE); } int c; if (out != null) { while ((c = in.read()) != -1) out.write(c); out.close(); } in.close(); } } catch (Exception ex) { ex.printStackTrace(); LogHandler.log(ex.getMessage(), Level.INFO, "LOG_MSG", isLoggingEnabled()); JOptionPane.showMessageDialog(null, ex.getMessage().substring(0, Math.min(ex.getMessage().length(), drawPanel.MAX_DIALOG_MSG_SZ)) + "-" + getClass(), "Set Bck Img", JOptionPane.ERROR_MESSAGE); } setPath(newPath); bckImg = new ImageIcon(getPath()); } | public int getDBVersion() throws MigrationException { int dbVersion; PreparedStatement ps; try { Connection conn = getConnection(); ps = conn.prepareStatement("SELECT version FROM " + getTablename()); try { ResultSet rs = ps.executeQuery(); try { if (rs.next()) { dbVersion = rs.getInt(1); if (rs.next()) { throw new MigrationException("Too many version in table: " + getTablename()); } } else { ps.close(); ps = conn.prepareStatement("INSERT INTO " + getTablename() + " (version) VALUES (?)"); ps.setInt(1, 1); try { ps.executeUpdate(); } finally { ps.close(); } dbVersion = 1; } } finally { rs.close(); } } finally { ps.close(); } } catch (SQLException e) { logger.log(Level.WARNING, "Could not access " + tablename + ": " + e); dbVersion = 0; Connection conn = getConnection(); try { if (!conn.getAutoCommit()) { conn.rollback(); } conn.setAutoCommit(false); } catch (SQLException e1) { throw new MigrationException("Could not reset transaction state", e1); } } return dbVersion; } | 15,388 |
1 | public String stringOfUrl(String addr) throws IOException { ByteArrayOutputStream output = new ByteArrayOutputStream(); URL url = new URL(addr); IOUtils.copy(url.openStream(), output); return output.toString(); } | protected void zipDirectory(File dir, File zipfile) throws IOException, IllegalArgumentException { if (!dir.isDirectory()) throw new IllegalArgumentException("Compress: not a directory: " + dir); String[] entries = dir.list(); byte[] buffer = new byte[4096]; int bytes_read; ZipOutputStream out = new ZipOutputStream(new FileOutputStream(zipfile)); for (int i = 0; i < entries.length; i++) { File f = new File(dir, entries[i]); if (f.isDirectory()) continue; FileInputStream in = new FileInputStream(f); ZipEntry entry = new ZipEntry(f.getPath()); out.putNextEntry(entry); while ((bytes_read = in.read(buffer)) != -1) out.write(buffer, 0, bytes_read); in.close(); } out.close(); } | 15,389 |
0 | private void innerJob(String inFrom, String inTo, String line, Map<String, Match> result) throws UnsupportedEncodingException, IOException { String subline = line.substring(line.indexOf(inTo) + inTo.length()); String tempStr = subline.substring(subline.indexOf(inFrom) + inFrom.length(), subline.indexOf(inTo)); String inURL = "http://goal.2010worldcup.163.com/data/match/general/" + tempStr.substring(tempStr.indexOf("/") + 1) + ".xml"; URL url = new URL(inURL); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream(), "utf-8")); String inLine = null; String scoreFrom = "score=\""; String homeTo = "\" side=\"Home"; String awayTo = "\" side=\"Away"; String goalInclud = "Stat"; String playerFrom = "playerId=\""; String playerTo = "\" position="; String timeFrom = "time=\""; String timeTo = "\" period"; String teamFinish = "</Team>"; boolean homeStart = false; boolean awayStart = false; while ((inLine = reader.readLine()) != null) { if (inLine.indexOf(teamFinish) != -1) { homeStart = false; awayStart = false; } if (inLine.indexOf(homeTo) != -1) { result.get(key).setHomeScore(inLine.substring(inLine.indexOf(scoreFrom) + scoreFrom.length(), inLine.indexOf(homeTo))); homeStart = true; } if (homeStart && inLine.indexOf(goalInclud) != -1) { MatchEvent me = new MatchEvent(); me.setPlayerName(getPlayerName(inLine.substring(inLine.indexOf(playerFrom) + playerFrom.length(), inLine.indexOf(playerTo)))); me.setTime(inLine.substring(inLine.indexOf(timeFrom) + timeFrom.length(), inLine.indexOf(timeTo))); result.get(key).getHomeEvents().add(me); } if (inLine.indexOf(awayTo) != -1) { result.get(key).setAwayScore(inLine.substring(inLine.indexOf(scoreFrom) + scoreFrom.length(), inLine.indexOf(awayTo))); awayStart = true; } if (awayStart && inLine.indexOf(goalInclud) != -1) { MatchEvent me = new MatchEvent(); me.setPlayerName(getPlayerName(inLine.substring(inLine.indexOf(playerFrom) + playerFrom.length(), inLine.indexOf(playerTo)))); me.setTime(inLine.substring(inLine.indexOf(timeFrom) + timeFrom.length(), inLine.indexOf(timeTo))); result.get(key).getAwayEvents().add(me); } } reader.close(); } | public static String calcolaMd5(String messaggio) { MessageDigest md; try { md = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { throw new RuntimeException(e); } md.reset(); md.update(messaggio.getBytes()); byte[] impronta = md.digest(); return new String(impronta); } | 15,390 |
0 | @Override public void save(String arxivId, InputStream inputStream, String encoding) { String filename = StringUtil.arxivid2filename(arxivId, "tex"); try { Writer writer = new OutputStreamWriter(new FileOutputStream(String.format("%s/%s", LATEX_DOCUMENT_DIR, filename)), encoding); IOUtils.copy(inputStream, writer, encoding); writer.flush(); writer.close(); inputStream.close(); } catch (IOException e) { logger.error("Failed to save the Latex source with id='{}'", arxivId, e); throw new RuntimeException(e); } } | public void run(IProgressMonitor monitor) throws InvocationTargetException, InterruptedException { int remainingWorkUnits = 10; monitor.beginTask("New Modulo Project Creation", remainingWorkUnits); IWorkspace ws = ResourcesPlugin.getWorkspace(); newProject = fMainPage.getProjectHandle(); IProjectDescription description = ws.newProjectDescription(newProject.getName()); String[] natures = { JavaCore.NATURE_ID, ModuloLauncherPlugin.NATURE_ID }; description.setNatureIds(natures); ICommand command = description.newCommand(); command.setBuilderName(JavaCore.BUILDER_ID); ICommand[] commands = { command }; description.setBuildSpec(commands); IJavaProject jproject = JavaCore.create(newProject); ModuloProject modProj = new ModuloProject(); modProj.setJavaProject(jproject); try { newProject.create(description, new SubProgressMonitor(monitor, 1)); newProject.open(new SubProgressMonitor(monitor, 1)); IFolder srcFolder = newProject.getFolder("src"); IFolder javaFolder = srcFolder.getFolder("java"); IFolder buildFolder = newProject.getFolder("build"); IFolder classesFolder = buildFolder.getFolder("classes"); modProj.createFolder(srcFolder); modProj.createFolder(javaFolder); modProj.createFolder(buildFolder); modProj.createFolder(classesFolder); IPath buildPath = newProject.getFolder("build/classes").getFullPath(); jproject.setOutputLocation(buildPath, new SubProgressMonitor(monitor, 1)); IClasspathEntry[] entries = new IClasspathEntry[] { JavaCore.newSourceEntry(newProject.getFolder("src/java").getFullPath()), JavaCore.newContainerEntry(new Path(JavaRuntime.JRE_CONTAINER)), JavaCore.newContainerEntry(new Path(ModuloClasspathContainer.CONTAINER_ID)) }; jproject.setRawClasspath(entries, new SubProgressMonitor(monitor, 1)); ModuleDefinition definition = new ModuleDefinition(); definition.setId(fModuloPage.getPackageName()); definition.setVersion(new VersionNumber(1, 0, 0)); definition.setMetaName(fModuloPage.getModuleName()); definition.setMetaDescription("The " + fModuloPage.getModuleName() + " Module."); definition.setModuleClassName(fModuloPage.getPackageName() + "." + fModuloPage.getModuleClassName()); if (fModuloPage.isConfigSelectioned()) definition.setConfigurationClassName(fModuloPage.getPackageName() + "." + fModuloPage.getConfigClassName()); if (fModuloPage.isStatSelectioned()) definition.setStatisticsClassName(fModuloPage.getPackageName() + "." + fModuloPage.getStatClassName()); modProj.setDefinition(definition); modProj.createPackage(); modProj.createModuleXML(); modProj.createMainClass(); if (fModuloPage.isConfigSelectioned()) modProj.createConfigClass(); if (fModuloPage.isStatSelectioned()) modProj.createStatClass(); modProj.createModuleProperties(); modProj.createMessagesProperties(); IFolder binFolder = newProject.getFolder("bin"); binFolder.delete(true, new SubProgressMonitor(monitor, 1)); } catch (CoreException e) { e.printStackTrace(); } finally { monitor.done(); } } | 15,391 |
0 | public static void main(String[] args) throws Exception { URI uri = new URI("file:/c:/foo.xyz"); System.err.println(uri); uri = new URI("bin.file:/c:/foo.xyz"); System.err.println(uri); uri = new URI("bin.http://c:/foo.xyz"); System.err.println(uri); uri = new URI("bin.http://c:/foo.xyz?x[3:5]"); System.err.println(uri); uri = new File("C:\\Documents and Settings\\jbf\\My Documents\\foo.jy").toURI(); System.err.println(uri); uri = new File("/home/jbf/my%file.txt").toURI(); System.err.println(uri); System.err.println(uri.toURL()); URL url = uri.toURL(); InputStream in = url.openStream(); int ch = in.read(); while (ch != -1) { System.err.print((char) ch); ch = in.read(); } } | public void createResource(String resourceUri, boolean publish, User user) throws IOException { PermissionAPI perAPI = APILocator.getPermissionAPI(); Logger.debug(this.getClass(), "createResource"); resourceUri = stripMapping(resourceUri); String hostName = getHostname(resourceUri); String path = getPath(resourceUri); String folderName = getFolderName(path); String fileName = getFileName(path); fileName = deleteSpecialCharacter(fileName); if (fileName.startsWith(".")) { return; } Host host = HostFactory.getHostByHostName(hostName); Folder folder = FolderFactory.getFolderByPath(folderName, host); boolean hasPermission = perAPI.doesUserHavePermission(folder, PERMISSION_WRITE, user, false); if (hasPermission) { if (!checkFolderFilter(folder, fileName)) { throw new IOException("The file doesn't comply the folder's filter"); } if (host.getInode() != 0 && folder.getInode() != 0) { File file = new File(); file.setTitle(fileName); file.setFileName(fileName); file.setShowOnMenu(false); file.setLive(publish); file.setWorking(true); file.setDeleted(false); file.setLocked(false); file.setModDate(new Date()); String mimeType = FileFactory.getMimeType(fileName); file.setMimeType(mimeType); String author = user.getFullName(); file.setAuthor(author); file.setModUser(author); file.setSortOrder(0); file.setShowOnMenu(false); try { Identifier identifier = null; if (!isResource(resourceUri)) { WebAssetFactory.createAsset(file, user.getUserId(), folder, publish); identifier = IdentifierCache.getIdentifierFromIdentifierCache(file); } else { File actualFile = FileFactory.getFileByURI(path, host, false); identifier = IdentifierCache.getIdentifierFromIdentifierCache(actualFile); WebAssetFactory.createAsset(file, user.getUserId(), folder, identifier, false, false); WebAssetFactory.publishAsset(file); String assetsPath = FileFactory.getRealAssetsRootPath(); new java.io.File(assetsPath).mkdir(); java.io.File workingIOFile = FileFactory.getAssetIOFile(file); DotResourceCache vc = CacheLocator.getVeloctyResourceCache(); vc.remove(ResourceManager.RESOURCE_TEMPLATE + workingIOFile.getPath()); if (file != null && file.getInode() > 0) { byte[] currentData = new byte[0]; FileInputStream is = new FileInputStream(workingIOFile); int size = is.available(); currentData = new byte[size]; is.read(currentData); java.io.File newVersionFile = FileFactory.getAssetIOFile(file); vc.remove(ResourceManager.RESOURCE_TEMPLATE + newVersionFile.getPath()); FileChannel channelTo = new FileOutputStream(newVersionFile).getChannel(); ByteBuffer currentDataBuffer = ByteBuffer.allocate(currentData.length); currentDataBuffer.put(currentData); currentDataBuffer.position(0); channelTo.write(currentDataBuffer); channelTo.force(false); channelTo.close(); } java.util.List<Tree> parentTrees = TreeFactory.getTreesByChild(file); for (Tree tree : parentTrees) { Tree newTree = TreeFactory.getTree(tree.getParent(), file.getInode()); if (newTree.getChild() == 0) { newTree.setParent(tree.getParent()); newTree.setChild(file.getInode()); newTree.setRelationType(tree.getRelationType()); newTree.setTreeOrder(0); TreeFactory.saveTree(newTree); } } } List<Permission> permissions = perAPI.getPermissions(folder); for (Permission permission : permissions) { Permission filePermission = new Permission(); filePermission.setPermission(permission.getPermission()); filePermission.setRoleId(permission.getRoleId()); filePermission.setInode(identifier.getInode()); perAPI.save(filePermission); } } catch (Exception ex) { Logger.debug(this, ex.toString()); } } } else { throw new IOException("You don't have access to add that folder/host"); } } | 15,392 |
0 | private String getTextResponse(String address) throws Exception { URL url = new URL(address); HttpURLConnection con = (HttpURLConnection) url.openConnection(); con.setUseCaches(false); BufferedReader in = null; try { con.connect(); assertEquals(HttpURLConnection.HTTP_OK, con.getResponseCode()); in = new BufferedReader(new InputStreamReader(con.getInputStream())); StringBuilder builder = new StringBuilder(); String inputLine = null; while ((inputLine = in.readLine()) != null) { builder.append(inputLine); } return builder.toString(); } finally { if (in != null) { in.close(); } con.disconnect(); } } | 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); } } | 15,393 |
0 | private Concept fetchDataNeeded(String conceptUri) { if (cache.size() > MAX_CACHE) cache.clear(); if (cache.containsKey(conceptUri)) return this.cache.get(conceptUri); try { URL url = new URL(conceptUri); HttpURLConnection connection = (HttpURLConnection) url.openConnection(); connection.setInstanceFollowRedirects(true); connection.setRequestProperty("Accept", "application/rdf+xml"); if (connection.getResponseCode() == HttpURLConnection.HTTP_OK && connection.getContentType().contains("application/rdf+xml")) { InputStream is = connection.getInputStream(); HashMap<String, String> parameters = new HashMap<String, String>(); parameters.put("uri", conceptUri); Transformer tf = this.templates.getDAOTransformer(keyTemplates, parameters); DOMResult outputTarget = new DOMResult(); tf.transform(new StreamSource(is), outputTarget); Concept concept = ConceptXMLBind.getInstance().restoreConcept(outputTarget.getNode()); this.cache.put(conceptUri, concept); return concept; } else { logger.error("Unable to get a representation of the resource: " + connection.getResponseCode() + " => " + connection.getContentType()); throw new RuntimeException("Unable to get a representation of the resource"); } } catch (Exception e) { logger.error("Unable to fetch data for concept " + conceptUri, e); throw new RuntimeException(e); } } | public static void writeURLToFile(String url, String path) throws MalformedURLException, IOException { java.io.BufferedInputStream in = new java.io.BufferedInputStream(new java.net.URL(url).openStream()); java.io.FileOutputStream fos = new java.io.FileOutputStream(path); java.io.BufferedOutputStream bout = new BufferedOutputStream(fos, 1024); byte data[] = new byte[1024]; int count; while ((count = in.read(data, 0, 1024)) != -1) { ; bout.write(data, 0, count); } bout.close(); in.close(); } | 15,394 |
1 | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | private void copyIntoFile(String resource, File output) throws IOException { FileOutputStream out = null; InputStream in = null; try { out = FileUtils.openOutputStream(output); in = GroovyInstanceTest.class.getResourceAsStream(resource); IOUtils.copy(in, out); } finally { IOUtils.closeQuietly(out); IOUtils.closeQuietly(in); } } | 15,395 |
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; } | private JButton getButtonImagen() { if (buttonImagen == null) { buttonImagen = new JButton(); buttonImagen.setText(Messages.getString("gui.AdministracionResorces.6")); buttonImagen.setIcon(new ImageIcon(getClass().getResource("/es/unizar/cps/tecnoDiscap/data/icons/view_sidetree.png"))); buttonImagen.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent e) { JFileChooser fc = new JFileChooser(); fc.addChoosableFileFilter(new ImageFilter()); fc.setAccessory(new ImagePreview(fc)); int returnVal = fc.showDialog(AdministracionResorces.this, Messages.getString("gui.AdministracionResorces.8")); if (returnVal == JFileChooser.APPROVE_OPTION) { File file = fc.getSelectedFile(); String rutaGlobal = System.getProperty("user.dir") + "/" + rutaDatos + "imagenes/" + file.getName(); String rutaRelativa = rutaDatos + "imagenes/" + file.getName(); try { FileInputStream fis = new FileInputStream(file); FileOutputStream fos = new FileOutputStream(rutaGlobal, true); FileChannel canalFuente = fis.getChannel(); FileChannel canalDestino = fos.getChannel(); canalFuente.transferTo(0, canalFuente.size(), canalDestino); fis.close(); fos.close(); imagen.setImagenURL(rutaRelativa); gui.getEntrenamientoIzquierdaLabel().setIcon(gui.getProcesadorDatos().escalaImageIcon(((Imagen) gui.getComboBoxImagenesIzquierda().getSelectedItem()).getImagenURL())); gui.getEntrenamientoDerechaLabel().setIcon(gui.getProcesadorDatos().escalaImageIcon(((Imagen) gui.getComboBoxImagenesDerecha().getSelectedItem()).getImagenURL())); buttonImagen.setIcon(new ImageIcon(getClass().getResource("/es/unizar/cps/tecnoDiscap/data/icons/view_sidetreeOK.png"))); labelImagenPreview.setIcon(gui.getProcesadorDatos().escalaImageIcon(imagen.getImagenURL())); } catch (IOException ex) { ex.printStackTrace(); } } else { } } }); } return buttonImagen; } | 15,396 |
1 | private static void copySmallFile(File sourceFile, File targetFile) throws BusinessException { LOG.debug("Copying SMALL file '" + sourceFile.getAbsolutePath() + "' to '" + targetFile.getAbsolutePath() + "'."); FileChannel inChannel = null; FileChannel outChannel = null; try { inChannel = new FileInputStream(sourceFile).getChannel(); outChannel = new FileOutputStream(targetFile).getChannel(); inChannel.transferTo(0, inChannel.size(), outChannel); } catch (IOException e) { throw new BusinessException("Could not copy file from '" + sourceFile.getAbsolutePath() + "' to '" + targetFile.getAbsolutePath() + "'!", e); } finally { try { if (inChannel != null) inChannel.close(); } catch (IOException e) { LOG.error("Could not close input stream!", e); } try { if (outChannel != null) outChannel.close(); } catch (IOException e) { LOG.error("Could not close output stream!", e); } } } | protected void writeToResponse(InputStream stream, HttpServletResponse response) throws IOException { OutputStream output = response.getOutputStream(); try { IOUtils.copy(stream, output); } finally { try { stream.close(); } finally { output.close(); } } } | 15,397 |
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 void importCertFile(File file) throws IOException { File kd; File cd; synchronized (this) { kd = keysDir; cd = certsDir; } if (!cd.isDirectory()) { kd.mkdirs(); cd.mkdirs(); } String newName = file.getName(); File dest = new File(cd, newName); FileChannel sourceChannel = null; FileChannel destinationChannel = null; try { sourceChannel = new FileInputStream(file).getChannel(); destinationChannel = new FileOutputStream(dest).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), destinationChannel); } finally { if (sourceChannel != null) { try { sourceChannel.close(); } catch (IOException e) { } } if (destinationChannel != null) { try { destinationChannel.close(); } catch (IOException e) { } } } } | 15,398 |
1 | @SuppressWarnings("null") public static void copyFile(File src, File dst) throws IOException { if (!dst.getParentFile().exists()) { dst.getParentFile().mkdirs(); } dst.createNewFile(); FileChannel srcC = null; FileChannel dstC = null; try { srcC = new FileInputStream(src).getChannel(); dstC = new FileOutputStream(dst).getChannel(); dstC.transferFrom(srcC, 0, srcC.size()); } finally { try { if (dst != null) { dstC.close(); } } catch (Exception e) { e.printStackTrace(); } try { if (src != null) { srcC.close(); } } catch (Exception e) { e.printStackTrace(); } } } | public void upgradeSingleFileModelToDirectory(File modelFile) throws IOException { byte[] buf = new byte[8192]; int bytesRead = 0; File backupModelFile = new File(modelFile.getPath() + ".bak"); FileInputStream oldModelIn = new FileInputStream(modelFile); FileOutputStream backupModelOut = new FileOutputStream(backupModelFile); while ((bytesRead = oldModelIn.read(buf)) >= 0) { backupModelOut.write(buf, 0, bytesRead); } backupModelOut.close(); oldModelIn.close(); buf = null; modelFile.delete(); modelFile.mkdir(); BufferedReader oldModelsBuff = new BomStrippingInputStreamReader(new FileInputStream(backupModelFile), "UTF-8"); File metaDataFile = new File(modelFile, ConstantParameters.FILENAMEOFModelMetaData); BufferedWriter metaDataBuff = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(metaDataFile), "UTF-8")); for (int i = 0; i < 8; i++) { metaDataBuff.write(oldModelsBuff.readLine()); metaDataBuff.write('\n'); } metaDataBuff.close(); int classIndex = 1; BufferedWriter modelWriter = null; String line = null; while ((line = oldModelsBuff.readLine()) != null) { if (line.startsWith("Class=") && line.contains("numTraining=") && line.contains("numPos=")) { if (modelWriter != null) { modelWriter.close(); } File nextModel = new File(modelFile, String.format(ConstantParameters.FILENAMEOFPerClassModel, Integer.valueOf(classIndex++))); modelWriter = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(nextModel), "UTF-8")); } modelWriter.write(line); modelWriter.write('\n'); } if (modelWriter != null) { modelWriter.close(); } } | 15,399 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.