label int64 0 1 | func1 stringlengths 173 53.1k | func2 stringlengths 173 53.1k | id int64 0 901k |
|---|---|---|---|
0 | private void initialize(OAIRepository repo, String u, String v, String params) throws OAIException { oParent = repo; strVerb = v; strBaseURL = u; strParams = params; strResumptionToken = ""; iResumptionCount = 0; boolInitialized = false; boolValidResponse = false; iIndex = 1; iCount = -1; iCursor = -1; iRealCursor = -1; iCompleteListSize = -1; if (!strVerb.equals("ListIdentifiers") && !strVerb.equals("ListMetadataFormats") && !strVerb.equals("ListRecords") && !strVerb.equals("ListSets")) { throw new OAIException(OAIException.INVALID_VERB_ERR, "Invalid verb"); } if (strBaseURL.length() == 0) { throw new OAIException(OAIException.NO_BASE_URL_ERR, "No baseURL"); } if (params.length() > 0) { if (params.charAt(0) != '&') { params = "&" + params; } } try { URL url = new URL(strBaseURL + "?verb=" + strVerb + params); HttpURLConnection http = (HttpURLConnection) url.openConnection(); http = oParent.frndTrySend(http); DocumentBuilderFactory docFactory = DocumentBuilderFactory.newInstance(); docFactory.setNamespaceAware(true); if (oParent.getValidation() == OAIRepository.VALIDATION_VERY_STRICT) { docFactory.setValidating(true); } else { docFactory.setValidating(false); } DocumentBuilder docBuilder = docFactory.newDocumentBuilder(); try { xml = docBuilder.parse(http.getInputStream()); boolValidResponse = true; } catch (IllegalArgumentException iae) { throw new OAIException(OAIException.CRITICAL_ERR, iae.getMessage()); } catch (SAXException se) { if (oParent.getValidation() != OAIRepository.VALIDATION_LOOSE) { throw new OAIException(OAIException.XML_PARSE_ERR, se.getMessage() + " Try loose validation."); } else { try { http.disconnect(); url = new URL(strBaseURL + "?verb=" + strVerb + params); http = (HttpURLConnection) url.openConnection(); http = oParent.frndTrySend(http); xml = docBuilder.parse(priCreateDummyResponse(http.getInputStream())); } catch (SAXException se2) { throw new OAIException(OAIException.XML_PARSE_ERR, se2.getMessage()); } } } namespaceNode = xml.createElement(strVerb); namespaceNode.setAttribute("xmlns:oai", OAIRepository.XMLNS_OAI + strVerb); namespaceNode.setAttribute("xmlns:dc", OAIRepository.XMLNS_DC); PrefixResolverDefault prefixResolver = new PrefixResolverDefault(namespaceNode); XPath xpath = new XPath("//oai:" + strVerb + "/oai:" + priGetMainNodeName(), null, prefixResolver, XPath.SELECT, null); XPathContext xpathSupport = new XPathContext(); int ctxtNode = xpathSupport.getDTMHandleFromNode(xml); XObject list = xpath.execute(xpathSupport, ctxtNode, prefixResolver); Node node = list.nodeset().nextNode(); if (node == null) { namespaceNode.setAttribute("xmlns:oai", OAIRepository.XMLNS_OAI_2_0); prefixResolver = new PrefixResolverDefault(namespaceNode); xpath = new XPath("/oai:OAI-PMH", null, prefixResolver, XPath.SELECT, null); list = xpath.execute(xpathSupport, ctxtNode, prefixResolver); node = list.nodeset().nextNode(); if (node == null) { namespaceNode.setAttribute("xmlns:oai", OAIRepository.XMLNS_OAI_1_0 + strVerb); } else { xpath = new XPath("oai:OAI-PMH/oai:error", null, prefixResolver, XPath.SELECT, null); list = xpath.execute(xpathSupport, ctxtNode, prefixResolver); NodeList nl = list.nodelist(); if (nl.getLength() > 0) { oParent.frndSetErrors(nl); throw new OAIException(OAIException.OAI_ERR, oParent.getLastOAIError().getCode() + ": " + oParent.getLastOAIError().getReason()); } } } xpath = new XPath("//oai:" + strVerb + "/oai:" + priGetMainNodeName(), null, prefixResolver, XPath.SELECT, null); list = xpath.execute(xpathSupport, ctxtNode, prefixResolver); nodeList = list.nodelist(); boolInitialized = true; oParent.frndSetNamespaceNode(namespaceNode); xpath = new XPath("//oai:requestURL | //oai:request", null, prefixResolver, XPath.SELECT, null); node = xpath.execute(xpathSupport, ctxtNode, prefixResolver).nodeset().nextNode(); if (node != null) { oParent.frndSetRequest(node); } oParent.frndSetResponseDate(getResponseDate()); docFactory = null; docBuilder = null; url = null; prefixResolver = null; xpathSupport = null; xpath = null; } catch (TransformerException te) { throw new OAIException(OAIException.CRITICAL_ERR, te.getMessage()); } catch (MalformedURLException mue) { throw new OAIException(OAIException.CRITICAL_ERR, mue.getMessage()); } catch (FactoryConfigurationError fce) { throw new OAIException(OAIException.CRITICAL_ERR, fce.getMessage()); } catch (ParserConfigurationException pce) { throw new OAIException(OAIException.CRITICAL_ERR, pce.getMessage()); } catch (IOException ie) { throw new OAIException(OAIException.CRITICAL_ERR, ie.getMessage()); } } | public int procesar() { int mas = 0; String uriOntologia = "", source = "", uri = ""; String fichOrigenHTML = "", fichOrigenLN = ""; String ficheroOutOWL = ""; md5 firma = null; StringTokenV2 entra = null, entra2 = null, entra3 = null; FileInputStream lengNat = null; BufferedInputStream lengNat2 = null; DataInputStream entradaLenguajeNatural = null; FileWriter salOWL = null; BufferedWriter salOWL2 = null; PrintWriter salidaOWL = null; String sujeto = "", verbo = "", CD = "", CI = "", fraseOrigen = ""; StringTokenV2 token2; boolean bandera = false; OntClass c = null; OntClass cBak = null; String claseTrabajo = ""; String nombreClase = "", nombrePropiedad = "", variasPalabras = ""; int incre = 0, emergencia = 0; String lineaSalida = ""; String[] ontologia = new String[5]; ontologia[0] = "http://www.criado.info/owl/vertebrados_es.owl#"; ontologia[1] = "http://www.w3.org/2001/sw/WebOnt/guide-src/wine#"; ontologia[2] = "http://www.co-ode.org/ontologies/pizza/2005/10/18/pizza.owl#"; ontologia[3] = "http://www.w3.org/2001/sw/WebOnt/guide-src/food#"; ontologia[4] = "http://www.daml.org/2001/01/gedcom/gedcom#"; String[] ontologiaSource = new String[5]; ontologiaSource[0] = this.directorioMapeo + "\\" + "mapeo_vertebrados_es.xml"; ontologiaSource[1] = this.directorioMapeo + "\\" + "mapeo_wine_es.xml"; ontologiaSource[2] = this.directorioMapeo + "\\" + "mapeo_pizza_es.xml"; ontologiaSource[3] = this.directorioMapeo + "\\" + "mapeo_food_es.xml"; ontologiaSource[4] = this.directorioMapeo + "\\" + "mapeo_parentesco_es.xml"; mapeoIdiomas clasesOntologias; try { if ((entrada = entradaFichero.readLine()) != null) { if (entrada.trim().length() > 10) { entrada2 = new StringTokenV2(entrada.trim(), "\""); if (entrada2.isIncluidaSubcadena("<fichero ontologia=")) { ontologiaOrigen = entrada2.getToken(2); fichOrigenHTML = entrada2.getToken(4); fichOrigenLN = entrada2.getToken(6); if (ontologiaOrigen.equals("VERTEBRADOS")) { source = ontologiaSource[0]; uriOntologia = ontologia[0]; } if (ontologiaOrigen.equals("WINE")) { source = ontologiaSource[1]; uriOntologia = ontologia[1]; } if (ontologiaOrigen.equals("PIZZA")) { source = ontologiaSource[2]; uriOntologia = ontologia[2]; } if (ontologiaOrigen.equals("FOOD")) { source = ontologiaSource[3]; uriOntologia = ontologia[3]; } if (ontologiaOrigen.equals("PARENTESCOS")) { source = ontologiaSource[4]; uriOntologia = ontologia[4]; } firma = new md5(uriOntologia, false); clasesOntologias = new mapeoIdiomas(source); uri = ""; ficheroOutOWL = ""; entra2 = new StringTokenV2(fichOrigenHTML, "\\"); int numToken = entra2.getNumeroTokenTotales(); entra = new StringTokenV2(fichOrigenHTML, " "); if (entra.isIncluidaSubcadena(directorioLocal)) { entra = new StringTokenV2(entra.getQuitar(directorioLocal) + "", " "); uri = entra.getCambiar("\\", "/"); uri = entra.getQuitar(entra2.getToken(numToken)) + ""; entra3 = new StringTokenV2(entra2.getToken(numToken), "."); ficheroOutOWL = entra3.getToken(1) + "_" + firma.toString() + ".owl"; uri = urlPatron + uri + ficheroOutOWL; } entra3 = new StringTokenV2(fichOrigenHTML, "."); ficheroOutOWL = entra3.getToken(1) + "_" + firma.toString() + ".owl"; lineaSalida = "<vistasemantica origen=\"" + fichOrigenLN + "\" destino=\"" + uri + "\" />"; lengNat = new FileInputStream(fichOrigenLN); lengNat2 = new BufferedInputStream(lengNat); entradaLenguajeNatural = new DataInputStream(lengNat2); salOWL = new FileWriter(ficheroOutOWL); salOWL2 = new BufferedWriter(salOWL); salidaOWL = new PrintWriter(salOWL2); while ((entradaInstancias = entradaLenguajeNatural.readLine()) != null) { sujeto = ""; verbo = ""; CD = ""; CI = ""; fraseOrigen = ""; if (entradaInstancias.trim().length() > 10) { entrada2 = new StringTokenV2(entradaInstancias.trim(), "\""); if (entrada2.isIncluidaSubcadena("<oracion sujeto=")) { sujeto = entrada2.getToken(2).trim(); verbo = entrada2.getToken(4).trim(); CD = entrada2.getToken(6).trim(); CI = entrada2.getToken(8).trim(); fraseOrigen = entrada2.getToken(10).trim(); if (sujeto.length() > 0 & verbo.length() > 0 & CD.length() > 0) { bandera = false; c = null; cBak = null; nombreClase = clasesOntologias.getClaseInstancia(CD); if (nombreClase.length() > 0) { bandera = true; } if (bandera) { if (incre == 0) { salidaOWL.write(" <rdf:RDF " + "\n"); salidaOWL.write(" xmlns:j.0=\"" + uriOntologia + "\"" + "\n"); salidaOWL.write(" xmlns:protege=\"http://protege.stanford.edu/plugins/owl/protege#\"" + "\n"); salidaOWL.write(" xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\"" + "\n"); salidaOWL.write(" xmlns:xsd=\"http://www.w3.org/2001/XMLSchema#\"" + "\n"); salidaOWL.write(" xmlns:rdfs=\"http://www.w3.org/2000/01/rdf-schema#\"" + "\n"); salidaOWL.write(" xmlns:owl=\"http://www.w3.org/2002/07/owl#\" " + "\n"); salidaOWL.write(" xmlns=\"" + uri + "#\"" + "\n"); salidaOWL.write(" xml:base=\"" + uri + "\">" + "\n"); salidaOWL.write(" <owl:Ontology rdf:about=\"\">" + "\n"); salidaOWL.write(" <owl:imports rdf:resource=\"" + uriOntologia + "\"/>" + "\n"); salidaOWL.write(" </owl:Ontology>" + "\n"); salidaOWL.flush(); salida.write(lineaSalida + "\n"); salida.flush(); incre = 1; } salidaOWL.write(" <j.0:" + nombreClase + " rdf:ID=\"" + sujeto.toUpperCase() + "\"/>" + "\n"); salidaOWL.write(" <owl:AllDifferent>" + "\n"); salidaOWL.write(" <owl:distinctMembers rdf:parseType=\"Collection\">" + "\n"); salidaOWL.write(" <" + nombreClase + " rdf:about=\"#" + sujeto.toUpperCase() + "\"/>" + "\n"); salidaOWL.write(" </owl:distinctMembers>" + "\n"); salidaOWL.write(" </owl:AllDifferent>" + "\n"); salidaOWL.flush(); bandera = false; } } } } } salidaOWL.write(" </rdf:RDF>" + "\n" + "\n"); salidaOWL.write("<!-- Creado por [html2ws] http://www.luis.criado.org -->" + "\n"); salidaOWL.flush(); } } mas = 1; } else { salida.write("</listaVistasSemanticas>\n"); salida.flush(); salida.close(); bw2.close(); fw2.close(); salidaOWL.close(); entradaFichero.close(); ent2.close(); ent1.close(); mas = -1; } } catch (Exception e) { mas = -2; salida.write("No se encuentra: " + fichOrigen + "\n"); salida.flush(); } return mas; } | 12,200 |
0 | private void getRandomGUID(boolean secure) { MessageDigest md5 = null; StringBuffer sbValueBeforeMD5 = new StringBuffer(); try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { System.out.println("Error: " + e); } try { long time = System.currentTimeMillis(); long rand = 0L; 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 < 16) sb.append('0'); sb.append(Integer.toHexString(b)); } valueAfterMD5 = sb.toString(); } catch (Exception e) { System.out.println("Error:" + e); } } | public static EXISchema getEXISchema(String fileName, Class<?> cls, EXISchemaFactoryErrorHandler compilerErrorHandler) throws IOException, ClassNotFoundException, EXISchemaFactoryException { EXISchemaFactory schemaCompiler = new EXISchemaFactory(); schemaCompiler.setCompilerErrorHandler(compilerErrorHandler); InputSource inputSource = null; if (fileName != null) { URL url; if ((url = cls.getResource(fileName)) != null) { inputSource = new InputSource(url.openStream()); inputSource.setSystemId(url.toString()); } else throw new RuntimeException("File '" + fileName + "' not found."); } EXISchema compiled = schemaCompiler.compile(inputSource); InputStream serialized = serializeSchema(compiled); return loadSchema(serialized); } | 12,201 |
0 | public synchronized String encrypt(String plaintext) throws SystemUnavailableException { MessageDigest md = null; try { md = MessageDigest.getInstance("SHA"); } catch (NoSuchAlgorithmException e) { throw new SystemUnavailableException(e.getMessage()); } try { md.update(plaintext.getBytes("UTF-8")); } catch (UnsupportedEncodingException e) { throw new SystemUnavailableException(e.getMessage()); } byte raw[] = md.digest(); String hash = (new BASE64Encoder()).encode(raw); return hash; } | public ProgramSymbol deleteProgramSymbol(int id) throws AdaptationException { ProgramSymbol programSymbol = null; Connection connection = null; Statement statement = null; ResultSet resultSet = null; try { String query = "SELECT * FROM ProgramSymbols " + "WHERE id = " + id; connection = DriverManager.getConnection(CONN_STR); statement = connection.createStatement(); resultSet = statement.executeQuery(query); if (!resultSet.next()) { connection.rollback(); String msg = "Attempt to delete program symbol failed."; log.error(msg); throw new AdaptationException(msg); } programSymbol = getProgramSymbol(resultSet); query = "DELETE FROM ProgramSymbols " + "WHERE id = " + id; statement.executeUpdate(query); connection.commit(); } catch (SQLException ex) { try { connection.rollback(); } catch (Exception e) { } String msg = "SQLException in deleteProgramSymbol"; 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 programSymbol; } | 12,202 |
1 | public void actionPerformed(ActionEvent e) { if (path.compareTo("") != 0) { imageName = (path.substring(path.lastIndexOf(File.separator) + 1, path.length())); String name = imageName.substring(0, imageName.lastIndexOf('.')); String extension = imageName.substring(imageName.lastIndexOf('.') + 1, imageName.length()); File imageFile = new File(path); directoryPath = "images" + File.separator + imageName.substring(0, 1).toUpperCase(); File directory = new File(directoryPath); directory.mkdirs(); imagePath = "." + File.separator + "images" + File.separator + imageName.substring(0, 1).toUpperCase() + File.separator + imageName; File newFile = new File(imagePath); if (myImagesBehaviour.equals(TLanguage.getString("TIGManageGalleryDialog.REPLACE_IMAGE"))) { Vector<Vector<String>> aux = TIGDataBase.imageSearchByName(name); if (aux.size() != 0) { int idImage = TIGDataBase.imageKeySearchName(name); TIGDataBase.deleteAsociatedOfImage(idImage); } } if (myImagesBehaviour.equals(TLanguage.getString("TIGManageGalleryDialog.ADD_IMAGE"))) { int i = 1; while (newFile.exists()) { imagePath = "." + File.separator + "images" + File.separator + imageName.substring(0, 1).toUpperCase() + File.separator + imageName.substring(0, imageName.lastIndexOf('.')) + "_" + i + imageName.substring(imageName.lastIndexOf('.'), imageName.length()); name = name + "_" + i; newFile = new File(imagePath); i++; } } imagePathThumb = (imagePath.substring(0, imagePath.lastIndexOf("."))).concat("_th.jpg"); imageName = name + "." + extension; try { FileChannel srcChannel = new FileInputStream(path).getChannel(); FileChannel dstChannel = new FileOutputStream(imagePath).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (IOException exc) { System.out.println(exc.getMessage()); System.out.println(exc.toString()); } TIGDataBase.insertDB(theConcepts, imageName, imageName.substring(0, imageName.lastIndexOf('.'))); image = null; if (imageFile != null) { if (TFileUtils.isJAIRequired(imageFile)) { RenderedOp src = JAI.create("fileload", imageFile.getAbsolutePath()); BufferedImage bufferedImage = src.getAsBufferedImage(); image = new ImageIcon(bufferedImage); } else { image = new ImageIcon(imageFile.getAbsolutePath()); } if (image.getImageLoadStatus() == MediaTracker.ERRORED) { int choosenOption = JOptionPane.NO_OPTION; choosenOption = JOptionPane.showConfirmDialog(null, TLanguage.getString("TIGInsertImageAction.MESSAGE"), TLanguage.getString("TIGInsertImageAction.NAME"), JOptionPane.CLOSED_OPTION, JOptionPane.ERROR_MESSAGE); } else { createThumbnail(); } } } } | private static boolean genMovieRatingFile(String completePath, String masterFile, String CustLocationsFileName, String MovieRatingFileName) { try { File inFile1 = new File(completePath + fSep + "SmartGRAPE" + fSep + masterFile); FileChannel inC1 = new FileInputStream(inFile1).getChannel(); int fileSize1 = (int) inC1.size(); int totalNoDataRows = fileSize1 / 7; ByteBuffer mappedBuffer = inC1.map(FileChannel.MapMode.READ_ONLY, 0, fileSize1); System.out.println("Loaded master binary file"); File inFile2 = new File(completePath + fSep + "SmartGRAPE" + fSep + CustLocationsFileName); FileChannel inC2 = new FileInputStream(inFile2).getChannel(); int fileSize2 = (int) inC2.size(); System.out.println(fileSize2); File outFile = new File(completePath + fSep + "SmartGRAPE" + fSep + MovieRatingFileName); FileChannel outC = new FileOutputStream(outFile, true).getChannel(); for (int i = 0; i < 1; i++) { ByteBuffer locBuffer = inC2.map(FileChannel.MapMode.READ_ONLY, i * fileSize2, fileSize2); System.out.println("Loaded cust location file chunk: " + i); while (locBuffer.hasRemaining()) { int locationToRead = locBuffer.getInt(); mappedBuffer.position((locationToRead - 1) * 7); short movieName = mappedBuffer.getShort(); int customer = mappedBuffer.getInt(); byte rating = mappedBuffer.get(); ByteBuffer outBuf = ByteBuffer.allocate(3); outBuf.putShort(movieName); outBuf.put(rating); outBuf.flip(); outC.write(outBuf); } } mappedBuffer.clear(); inC1.close(); inC2.close(); outC.close(); return true; } catch (IOException e) { System.err.println(e); return false; } } | 12,203 |
0 | byte[] calculateDigest(String value) { try { MessageDigest mg = MessageDigest.getInstance("SHA1"); mg.update(value.getBytes()); return mg.digest(); } catch (Exception e) { throw Bark.unchecker(e); } } | @Override public void run() { handle.start(); handle.switchToIndeterminate(); FacebookJsonRestClient client = new FacebookJsonRestClient(API_KEY, SECRET); client.setIsDesktop(true); HttpURLConnection connection; List<String> cookies; try { String token = client.auth_createToken(); String post_url = "http://www.facebook.com/login.php"; String get_url = "http://www.facebook.com/login.php" + "?api_key=" + API_KEY + "&v=1.0" + "&auth_token=" + token; HttpURLConnection.setFollowRedirects(true); connection = (HttpURLConnection) new URL(get_url).openConnection(); connection.setRequestMethod("GET"); connection.setRequestProperty("User-Agent", "Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.9.2.3) Gecko/20100401"); connection.setRequestProperty("Host", "www.facebook.com"); connection.setRequestProperty("Accept-Charset", "UFT-8"); connection.connect(); cookies = connection.getHeaderFields().get("Set-Cookie"); connection = (HttpURLConnection) new URL(post_url).openConnection(); connection.setRequestMethod("POST"); connection.setRequestProperty("User-Agent", "Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.9.2.3) Gecko/20100401"); connection.setRequestProperty("Host", "www.facebook.com"); connection.setRequestProperty("Accept-Charset", "UFT-8"); if (cookies != null) { for (String cookie : cookies) { connection.addRequestProperty("Cookie", cookie.split(";", 2)[0]); } } String params = "api_key=" + API_KEY + "&auth_token=" + token + "&email=" + URLEncoder.encode(email, "UTF-8") + "&pass=" + URLEncoder.encode(pass, "UTF-8") + "&v=1.0"; connection.setRequestProperty("Content-Length", Integer.toString(params.length())); connection.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); connection.setDoOutput(true); connection.connect(); connection.getOutputStream().write(params.toString().getBytes("UTF-8")); connection.getOutputStream().close(); cookies = connection.getHeaderFields().get("Set-Cookie"); if (cookies == null) { ActionListener listener = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { String url = "http://www.chartsy.org/facebook/"; DesktopUtil.browseAndWarn(url, null); } }; NotifyUtil.show("Application Permission", "You need to grant permission first.", MessageType.WARNING, listener, false); connection.disconnect(); loggedIn = false; } else { sessionKey = client.auth_getSession(token); sessionSecret = client.getSessionSecret(); loggedIn = true; } connection.disconnect(); handle.finish(); } catch (FacebookException fex) { handle.finish(); NotifyUtil.error("Login Error", fex.getMessage(), fex, false); } catch (IOException ioex) { handle.finish(); NotifyUtil.error("Login Error", ioex.getMessage(), ioex, false); } } | 12,204 |
1 | public SpreadSheetFrame(FileManager owner, File file, Delimiter delim) { super(owner, file.getPath()); JPanel pane = new JPanel(new BorderLayout()); super.contentPane.add(pane); this.tableModel = new BigTableModel(file, delim); this.table = new JTable(tableModel); this.table.setAutoResizeMode(JTable.AUTO_RESIZE_OFF); this.tableModel.setTable(this.table); pane.add(new JScrollPane(this.table)); addInternalFrameListener(new InternalFrameAdapter() { @Override public void internalFrameClosed(InternalFrameEvent e) { tableModel.close(); } }); JMenu menu = new JMenu("Tools"); getJMenuBar().add(menu); menu.add(new AbstractAction("NCBI") { @Override public void actionPerformed(ActionEvent e) { try { Pattern delim = Pattern.compile("[ ]"); BufferedReader r = new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream("/home/lindenb/jeter.txt.gz")))); String line = null; URL url = new URL("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"); URLConnection conn = url.openConnection(); conn.setDoOutput(true); OutputStreamWriter wr = new OutputStreamWriter(conn.getOutputStream()); wr.write("db=snp&retmode=xml"); while ((line = r.readLine()) != null) { String tokens[] = delim.split(line, 2); if (!tokens[0].startsWith("rs")) continue; wr.write("&id=" + tokens[0].substring(2).trim()); } wr.flush(); r.close(); InputStream in = conn.getInputStream(); IOUtils.copyTo(in, System.err); in.close(); wr.close(); } catch (IOException err) { err.printStackTrace(); } } }); } | public static void concatFiles(List<File> sourceFiles, File destFile) throws IOException { FileOutputStream outFile = new FileOutputStream(destFile); FileChannel outChannel = outFile.getChannel(); for (File f : sourceFiles) { FileInputStream fis = new FileInputStream(f); FileChannel channel = fis.getChannel(); channel.transferTo(0, channel.size(), outChannel); channel.close(); fis.close(); } outChannel.close(); } | 12,205 |
0 | public UpdaterView(SingleFrameApplication app, String[] args) { super(app); if (args.length != 3) { System.out.println("Args must be passed."); System.exit(1); } else { currentVersion = Double.parseDouble(args[0]); currentDBVersion = Double.parseDouble(args[1]); dbAdmin = args[2].equals("true") ? true : false; } initComponents(); try { URL url = new URL(BASE_URL + "version.txt"); InputStream in = url.openStream(); BufferedInputStream buffIn = new BufferedInputStream(in); String tmp = ""; int data = buffIn.read(); while (data != -1) { tmp = tmp.concat(Character.toString((char) data)); data = buffIn.read(); } String[] versionEntries = tmp.split("\n"); if (versionEntries.length > 0) { String[] components = versionEntries[0].split(":"); if (dbAdmin || Double.parseDouble(components[4]) == currentDBVersion) { byteCount = Integer.parseInt(components[2]); lblCurrent.setText(new Double(currentVersion).toString()); lblLatest.setText(components[0]); latestVersionNum = Double.parseDouble(components[0]); lblNotes.setText("<html>" + components[1]); md5Hash = components[3]; latestDBVersion = Double.parseDouble(components[4]); upgradeURL = components[5]; progressBar.setMaximum(byteCount); if (dbAdmin && Double.parseDouble(components[4]) > currentDBVersion) { schemaUpdatesNeeded = true; schemaChanges.addFirst(latestDBVersion); double lastVersion = latestDBVersion; for (int i = 1; i < versionEntries.length; i++) { components = versionEntries[i].split(":"); double nextVers = Double.parseDouble(components[4]); if (nextVers != currentDBVersion) { if (lastVersion != nextVers) { schemaChanges.addFirst(nextVers); lastVersion = nextVers; } } else { schemaChanges.addFirst(currentDBVersion); break; } } } } else { for (int i = 1; i < versionEntries.length; i++) { components = versionEntries[i].split(":"); if (Double.parseDouble(components[4]) == currentDBVersion) { byteCount = Integer.parseInt(components[2]); lblCurrent.setText(new Double(currentVersion).toString()); lblLatest.setText(components[0]); latestVersionNum = Double.parseDouble(components[0]); lblNotes.setText("<html>" + components[1]); md5Hash = components[3]; latestDBVersion = Double.parseDouble(components[4]); upgradeURL = components[5]; progressBar.setMaximum(byteCount); schemaUpdatesNeeded = true; break; } } } } else { throw new InvalidUpdateFileFormatException("File Format is Wrong."); } if (latestVersionNum == currentVersion) { if (schemaUpdatesNeeded) { javax.swing.JOptionPane.showMessageDialog(super.getComponent(), "Updates are available but they require database changes. Please contact your system administrator to perform the upgrade.", "Myopa Updater", javax.swing.JOptionPane.INFORMATION_MESSAGE); } else { javax.swing.JOptionPane.showMessageDialog(super.getComponent(), "No Updates are available - your software is up to date!", "Myopa Updater", javax.swing.JOptionPane.INFORMATION_MESSAGE); } System.exit(0); } else { jButton1.setEnabled(true); } } catch (InvalidUpdateFileFormatException e) { } catch (MalformedURLException e) { System.out.println("EXCP " + e); } catch (IOException io) { System.out.println("IO" + io); } ResourceMap resourceMap = getResourceMap(); int messageTimeout = resourceMap.getInteger("StatusBar.messageTimeout"); messageTimer = new Timer(messageTimeout, new ActionListener() { public void actionPerformed(ActionEvent e) { statusMessageLabel.setText(""); } }); messageTimer.setRepeats(false); int busyAnimationRate = resourceMap.getInteger("StatusBar.busyAnimationRate"); for (int i = 0; i < busyIcons.length; i++) { busyIcons[i] = resourceMap.getIcon("StatusBar.busyIcons[" + i + "]"); } busyIconTimer = new Timer(busyAnimationRate, new ActionListener() { public void actionPerformed(ActionEvent e) { busyIconIndex = (busyIconIndex + 1) % busyIcons.length; statusAnimationLabel.setIcon(busyIcons[busyIconIndex]); } }); idleIcon = resourceMap.getIcon("StatusBar.idleIcon"); statusAnimationLabel.setIcon(idleIcon); progressBar.setVisible(false); TaskMonitor taskMonitor = new TaskMonitor(getApplication().getContext()); taskMonitor.addPropertyChangeListener(new java.beans.PropertyChangeListener() { public void propertyChange(java.beans.PropertyChangeEvent evt) { String propertyName = evt.getPropertyName(); if ("started".equals(propertyName)) { if (!busyIconTimer.isRunning()) { statusAnimationLabel.setIcon(busyIcons[0]); busyIconIndex = 0; busyIconTimer.start(); } progressBar.setVisible(true); progressBar.setIndeterminate(true); } else if ("done".equals(propertyName)) { busyIconTimer.stop(); statusAnimationLabel.setIcon(idleIcon); progressBar.setVisible(false); progressBar.setValue(0); } else if ("message".equals(propertyName)) { String text = (String) (evt.getNewValue()); statusMessageLabel.setText((text == null) ? "" : text); messageTimer.restart(); } else if ("progress".equals(propertyName)) { int value = (Integer) (evt.getNewValue()); progressBar.setVisible(true); progressBar.setIndeterminate(false); progressBar.setValue(value); } } }); } | private static byte[] finalizeStringHash(String loginHash) throws NoSuchAlgorithmException { MessageDigest md5Hasher; md5Hasher = MessageDigest.getInstance("MD5"); md5Hasher.update(loginHash.getBytes()); md5Hasher.update(LOGIN_FINAL_SALT); return md5Hasher.digest(); } | 12,206 |
1 | protected void removeMessage(ReplicationMessage message) { logger.info(String.format("remove replication message: %d", message.getId())); ConnectionProvider cp = null; Connection conn = null; PreparedStatement ps = null; try { SessionFactoryImplementor impl = (SessionFactoryImplementor) portalDao.getSessionFactory(); cp = impl.getConnectionProvider(); conn = cp.getConnection(); conn.setAutoCommit(false); ps = conn.prepareStatement("delete from light_replication_message where id=?"); ps.setLong(1, message.getId()); ps.executeUpdate(); conn.commit(); ps.close(); conn.close(); } catch (Exception e) { try { conn.rollback(); ps.close(); conn.close(); } catch (Exception se) { } } } | public void elimina(Pedido pe) throws errorSQL, errorConexionBD { System.out.println("GestorPedido.elimina()"); int id = pe.getId(); String sql; Statement stmt = null; try { gd.begin(); sql = "DELETE FROM pedido WHERE id=" + id; System.out.println("Ejecutando: " + sql); stmt = gd.getConexion().createStatement(); stmt.executeUpdate(sql); System.out.println("executeUpdate"); gd.commit(); System.out.println("commit"); stmt.close(); } catch (SQLException e) { gd.rollback(); throw new errorSQL(e.toString()); } catch (errorConexionBD e) { System.err.println("Error en GestorPedido.elimina(): " + e); } catch (errorSQL e) { System.err.println("Error en GestorPedido.elimina(): " + e); } } | 12,207 |
0 | public void setNewPassword(String password) { try { final MessageDigest digest = MessageDigest.getInstance("MD5"); digest.update(password.getBytes()); final String encrypted = "{MD5}" + new String(Base64Encoder.encode(digest.digest())); setUserPassword(encrypted.getBytes()); this.newPassword = password; firePropertyChange("newPassword", "", password); firePropertyChange("password", new byte[0], getUserPassword()); } catch (final NoSuchAlgorithmException e) { throw new RuntimeException("Can't encrypt user's password", e); } } | @Test public void testCopy_readerToWriter_nullOut() throws Exception { InputStream in = new ByteArrayInputStream(inData); in = new YellOnCloseInputStreamTest(in); Reader reader = new InputStreamReader(in, "US-ASCII"); try { IOUtils.copy(reader, (Writer) null); fail(); } catch (NullPointerException ex) { } } | 12,208 |
0 | public static String MD5ToString(String md5) { String hashword = null; try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(md5.getBytes()); BigInteger hash = new BigInteger(1, md.digest()); hashword = hash.toString(16); } catch (NoSuchAlgorithmException nsae) { } return hashword; } | public void render(Map model, HttpServletRequest request, HttpServletResponse response) throws Exception { response.setContentType(s_contentType); response.setHeader("Cache-control", "no-cache"); InputStream graphStream = getGraphStream(request); OutputStream out = getOutputStream(response); IOUtils.copy(graphStream, out); out.flush(); } | 12,209 |
1 | public static String encodePassword(String password) { try { MessageDigest messageDiegest = MessageDigest.getInstance("SHA-1"); messageDiegest.update(password.getBytes("UTF-8")); return Base64.encodeToString(messageDiegest.digest(), false); } catch (NoSuchAlgorithmException e) { log.error("Exception while encoding password"); throw new Error(e); } catch (UnsupportedEncodingException e) { log.error("Exception while encoding password"); throw new Error(e); } } | public static String MD5(String text) throws ProducteevSignatureException { try { MessageDigest md; md = MessageDigest.getInstance(ALGORITHM); byte[] md5hash; md.update(text.getBytes("utf-8"), 0, text.length()); md5hash = md.digest(); return convertToHex(md5hash); } catch (NoSuchAlgorithmException nsae) { throw new ProducteevSignatureException("No such algorithm : " + ALGORITHM, nsae); } catch (UnsupportedEncodingException e) { throw new ProducteevSignatureException("No such algorithm : " + ALGORITHM, e); } } | 12,210 |
0 | public static int unzipFile(File file_input, File dir_output) { ZipInputStream zip_in_stream; try { FileInputStream in = new FileInputStream(file_input); BufferedInputStream source = new BufferedInputStream(in); zip_in_stream = new ZipInputStream(source); } catch (IOException e) { return STATUS_IN_FAIL; } byte[] input_buffer = new byte[BUF_SIZE]; int len = 0; do { try { ZipEntry zip_entry = zip_in_stream.getNextEntry(); if (zip_entry == null) break; File output_file = new File(dir_output, zip_entry.getName()); FileOutputStream out = new FileOutputStream(output_file); BufferedOutputStream destination = new BufferedOutputStream(out, BUF_SIZE); while ((len = zip_in_stream.read(input_buffer, 0, BUF_SIZE)) != -1) destination.write(input_buffer, 0, len); destination.flush(); out.close(); } catch (IOException e) { return STATUS_GUNZIP_FAIL; } } while (true); try { zip_in_stream.close(); } catch (IOException e) { } return STATUS_OK; } | public static String hash(String str) { MessageDigest summer; try { summer = MessageDigest.getInstance("md5"); summer.update(str.getBytes()); } catch (NoSuchAlgorithmException ex) { return null; } BigInteger hash = new BigInteger(1, summer.digest()); String hashword = hash.toString(16); return hashword; } | 12,211 |
1 | void copyFile(File inputFile, File outputFile) { try { FileReader in; in = new FileReader(inputFile); FileWriter out = new FileWriter(outputFile); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } | @Test public void testGrantLicense() throws Exception { context.turnOffAuthorisationSystem(); Item item = Item.create(context); String defaultLicense = ConfigurationManager.getDefaultSubmissionLicense(); LicenseUtils.grantLicense(context, item, defaultLicense); StringWriter writer = new StringWriter(); IOUtils.copy(item.getBundles("LICENSE")[0].getBitstreams()[0].retrieve(), writer); String license = writer.toString(); assertThat("testGrantLicense 0", license, equalTo(defaultLicense)); context.restoreAuthSystemState(); } | 12,212 |
0 | @Override public AC3DModel loadModel(URL url, String skin) throws IOException, IncorrectFormatException, ParsingErrorException { boolean baseURLWasNull = setBaseURLFromModelURL(url); AC3DModel model = loadModel(url.openStream(), skin); if (baseURLWasNull) { popBaseURL(); } return (model); } | public void sendMessage(Message msg) { if (!blackList.contains(msg.getTo())) { Hashtable<String, String> content = msg.getContent(); Enumeration<String> keys = content.keys(); String key; String data = "to=" + msg.getTo() + "&from=" + msg.getFrom() + "&"; while (keys.hasMoreElements()) { key = (String) keys.nextElement(); data += key + "=" + content.get(key) + "&"; } URL url = null; try { logger.log(this, Level.FINER, "sending " + data + " to " + msg.getTo()); url = new URL("http://" + msg.getTo() + ":8080/webmsgservice?" + data); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); in.readLine(); in.close(); logger.log(this, Level.FINER, "message sent to " + msg.getTo()); } catch (MalformedURLException e) { blackList.add(msg.getTo()); logger.log(this, Level.WARNING, "an error occured during message sending (" + msg.getTo() + ") : " + e.getMessage()); e.printStackTrace(); } catch (IOException e) { logger.log(this, Level.WARNING, "an error occured during message sending (" + msg.getTo() + ") : " + e.getMessage()); blackList.add(msg.getTo()); } } else { logger.log(this, Level.FINE, "will not send message to " + msg.getTo() + " because black listed IP"); } } | 12,213 |
0 | public final Reader open(URL url) throws IOException { Reader ret = null; Charset cs = this.detectCodepage(url); if (cs != null) { ret = new InputStreamReader(new BufferedInputStream(url.openStream()), cs); } return ret; } | public synchronized DASMetaData fillInDASMetaData(URL url) throws DASException { try { con = (HttpURLConnection) url.openConnection(); dasRespVersion = con.getHeaderField("X-DAS-Version"); dasSchema = con.getHeaderField("X-DAS-SchemaName"); dasSchemaVersion = con.getHeaderField("X-DAS-SchemaVersion"); String dasStatusString = con.getHeaderField("X-DAS-Status"); if (dasStatusString == null) { throw new DASException("Temporary DAS Error"); } if (dasStatusString.indexOf(" ") != -1) { dasStatusString = dasStatusString.substring(0, dasStatusString.indexOf(" ")); } dasStatus = Integer.parseInt(dasStatusString); if (dasStatus != 200) { throw new DASException("Command cannot be executed: Error was " + Integer.toString(dasStatus)); } } catch (IOException e) { throw new DASException("Cannot connect to data source"); } if (dasSchema != null && dasSchemaVersion != null) { headers.put("X-DAS-Version", dasRespVersion); headers.put("X-DAS-SchemaName", dasSchema); headers.put("X-DAS-SchemaVersion", dasSchemaVersion); dasVersion = Float.parseFloat(dasRespVersion.substring(dasRespVersion.indexOf("/") + 1, dasRespVersion.length())); theMetaData = new DASMetaDataImpl(dasVersion, Float.parseFloat(dasSchemaVersion), dasSchema); } else { dasVersion = Float.parseFloat(dasRespVersion.substring(dasRespVersion.indexOf("/") + 1, dasRespVersion.length())); headers.put("X-DAS-Version", dasRespVersion); theMetaData = new DASMetaDataImpl(dasVersion); } String lengthStr = con.getHeaderField("content-length"); if (lengthStr != null) headers.put("content-length", lengthStr); theMetaData.setDASHeaders(headers); return theMetaData; } | 12,214 |
1 | public static void copyFile(File source, File destination) { if (!source.exists()) { return; } if ((destination.getParentFile() != null) && (!destination.getParentFile().exists())) { destination.getParentFile().mkdirs(); } try { FileChannel srcChannel = new FileInputStream(source).getChannel(); FileChannel dstChannel = new FileOutputStream(destination).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (IOException ioe) { Logger.error(FileUtil.class, ioe.getMessage(), ioe); } } | private void copyFile(String inputPath, String basis, String filename) throws GLMRessourceFileException { try { FileChannel inChannel = new FileInputStream(new File(inputPath)).getChannel(); File target = new File(basis, filename); FileChannel outChannel = new FileOutputStream(target).getChannel(); inChannel.transferTo(0, inChannel.size(), outChannel); inChannel.close(); outChannel.close(); } catch (Exception e) { throw new GLMRessourceFileException(7); } } | 12,215 |
0 | public void store(Component component, String componentName, int currentPilot) { try { PreparedStatement psta = jdbc.prepareStatement("UPDATE component_prop " + "SET size_height = ?, size_width = ?, pos_x = ?, pos_y = ? " + "WHERE pilot_id = ? " + "AND component_name = ?"); psta.setInt(1, component.getHeight()); psta.setInt(2, component.getWidth()); Point point = component.getLocation(); psta.setInt(3, point.x); psta.setInt(4, point.y); psta.setInt(5, currentPilot); psta.setString(6, componentName); int update = psta.executeUpdate(); if (update == 0) { psta = jdbc.prepareStatement("INSERT INTO component_prop " + "(size_height, size_width, pos_x, pos_y, pilot_id, component_name) " + "VALUES (?,?,?,?,?,?)"); psta.setInt(1, component.getHeight()); psta.setInt(2, component.getWidth()); psta.setInt(3, point.x); psta.setInt(4, point.y); psta.setInt(5, currentPilot); psta.setString(6, componentName); psta.executeUpdate(); } jdbc.commit(); } catch (SQLException e) { jdbc.rollback(); log.debug(e); } } | public static boolean copyFile(File sourceFile, File destFile) throws IOException { long flag = 0; if (!destFile.exists()) destFile.createNewFile(); FileChannel source = null; FileChannel destination = null; try { source = new FileInputStream(sourceFile).getChannel(); destination = new FileOutputStream(destFile).getChannel(); flag = destination.transferFrom(source, 0, source.size()); } catch (Exception e) { Logger.getLogger(FileUtils.class.getPackage().getName()).log(Level.WARNING, "ERROR: Problem copying file", e); } finally { if (source != null) source.close(); if (destination != null) destination.close(); } if (flag == 0) return false; else return true; } | 12,216 |
0 | private static boolean hasPackageInfo(URL url) { if (url == null) return false; BufferedReader br = null; try { br = new BufferedReader(new InputStreamReader(url.openStream())); String line; while ((line = br.readLine()) != null) { if (line.startsWith("Specification-Title: ") || line.startsWith("Specification-Version: ") || line.startsWith("Specification-Vendor: ") || line.startsWith("Implementation-Title: ") || line.startsWith("Implementation-Version: ") || line.startsWith("Implementation-Vendor: ")) return true; } } catch (IOException ioe) { } finally { if (br != null) try { br.close(); } catch (IOException e) { } } return false; } | public static String move_files(String sessionid, String keys, String absolutePathForTheDestinationTag) { String resultJsonString = "some problem existed inside the create_new_tag() function if you see this string"; try { Log.d("current running function name:", "move_files"); HttpClient httpclient = new DefaultHttpClient(); HttpPost httppost = new HttpPost("https://mt0-app.cloud.cm/rpc/json"); List<NameValuePair> nameValuePairs = new ArrayList<NameValuePair>(2); nameValuePairs.add(new BasicNameValuePair("c", "Storage")); nameValuePairs.add(new BasicNameValuePair("m", "move_file")); nameValuePairs.add(new BasicNameValuePair("absolute_new_parent_tag", absolutePathForTheDestinationTag)); nameValuePairs.add(new BasicNameValuePair("keys", keys)); httppost.setEntity(new UrlEncodedFormEntity(nameValuePairs)); httppost.setHeader("Cookie", "PHPSESSID=" + sessionid); HttpResponse response = httpclient.execute(httppost); resultJsonString = EntityUtils.toString(response.getEntity()); Log.d("jsonStringReturned:", resultJsonString); return resultJsonString; } catch (Exception e) { e.printStackTrace(); } return resultJsonString; } | 12,217 |
1 | public static String getPageSource(String url) throws ClientProtocolException, IOException { HttpClient client = new DefaultHttpClient(); HttpGet request = new HttpGet(url); HttpResponse response = client.execute(request); InputStream in = response.getEntity().getContent(); BufferedReader reader = new BufferedReader(new InputStreamReader(in)); StringBuilder source = new StringBuilder(); String line = null; while ((line = reader.readLine()) != null) source.append(line); in.close(); return source.toString(); } | 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(); } | 12,218 |
1 | protected void setupService(MessageContext msgContext) throws Exception { String realpath = msgContext.getStrProp(Constants.MC_REALPATH); String extension = (String) getOption(OPTION_JWS_FILE_EXTENSION); if (extension == null) extension = DEFAULT_JWS_FILE_EXTENSION; if ((realpath != null) && (realpath.endsWith(extension))) { String jwsFile = realpath; String rel = msgContext.getStrProp(Constants.MC_RELATIVE_PATH); File f2 = new File(jwsFile); if (!f2.exists()) { throw new FileNotFoundException(rel); } if (rel.charAt(0) == '/') { rel = rel.substring(1); } int lastSlash = rel.lastIndexOf('/'); String dir = null; if (lastSlash > 0) { dir = rel.substring(0, lastSlash); } String file = rel.substring(lastSlash + 1); String outdir = msgContext.getStrProp(Constants.MC_JWS_CLASSDIR); if (outdir == null) outdir = "."; if (dir != null) { outdir = outdir + File.separator + dir; } File outDirectory = new File(outdir); if (!outDirectory.exists()) { outDirectory.mkdirs(); } if (log.isDebugEnabled()) log.debug("jwsFile: " + jwsFile); String jFile = outdir + File.separator + file.substring(0, file.length() - extension.length() + 1) + "java"; String cFile = outdir + File.separator + file.substring(0, file.length() - extension.length() + 1) + "class"; if (log.isDebugEnabled()) { log.debug("jFile: " + jFile); log.debug("cFile: " + cFile); log.debug("outdir: " + outdir); } File f1 = new File(cFile); String clsName = null; if (clsName == null) clsName = f2.getName(); if (clsName != null && clsName.charAt(0) == '/') clsName = clsName.substring(1); clsName = clsName.substring(0, clsName.length() - extension.length()); clsName = clsName.replace('/', '.'); if (log.isDebugEnabled()) log.debug("ClsName: " + clsName); if (!f1.exists() || f2.lastModified() > f1.lastModified()) { log.debug(Messages.getMessage("compiling00", jwsFile)); log.debug(Messages.getMessage("copy00", jwsFile, jFile)); FileReader fr = new FileReader(jwsFile); FileWriter fw = new FileWriter(jFile); char[] buf = new char[4096]; int rc; while ((rc = fr.read(buf, 0, 4095)) >= 0) fw.write(buf, 0, rc); fw.close(); fr.close(); log.debug("javac " + jFile); Compiler compiler = CompilerFactory.getCompiler(); compiler.setClasspath(ClasspathUtils.getDefaultClasspath(msgContext)); compiler.setDestination(outdir); compiler.addFile(jFile); boolean result = compiler.compile(); (new File(jFile)).delete(); if (!result) { (new File(cFile)).delete(); Document doc = XMLUtils.newDocument(); Element root = doc.createElementNS("", "Errors"); StringBuffer message = new StringBuffer("Error compiling "); message.append(jFile); message.append(":\n"); List errors = compiler.getErrors(); int count = errors.size(); for (int i = 0; i < count; i++) { CompilerError error = (CompilerError) errors.get(i); if (i > 0) message.append("\n"); message.append("Line "); message.append(error.getStartLine()); message.append(", column "); message.append(error.getStartColumn()); message.append(": "); message.append(error.getMessage()); } root.appendChild(doc.createTextNode(message.toString())); throw new AxisFault("Server.compileError", Messages.getMessage("badCompile00", jFile), null, new Element[] { root }); } ClassUtils.removeClassLoader(clsName); soapServices.remove(clsName); } ClassLoader cl = ClassUtils.getClassLoader(clsName); if (cl == null) { cl = new JWSClassLoader(clsName, msgContext.getClassLoader(), cFile); } msgContext.setClassLoader(cl); SOAPService rpc = (SOAPService) soapServices.get(clsName); if (rpc == null) { rpc = new SOAPService(new RPCProvider()); rpc.setName(clsName); rpc.setOption(RPCProvider.OPTION_CLASSNAME, clsName); rpc.setEngine(msgContext.getAxisEngine()); String allowed = (String) getOption(RPCProvider.OPTION_ALLOWEDMETHODS); if (allowed == null) allowed = "*"; rpc.setOption(RPCProvider.OPTION_ALLOWEDMETHODS, allowed); String scope = (String) getOption(RPCProvider.OPTION_SCOPE); if (scope == null) scope = Scope.DEFAULT.getName(); rpc.setOption(RPCProvider.OPTION_SCOPE, scope); rpc.getInitializedServiceDesc(msgContext); soapServices.put(clsName, rpc); } rpc.setEngine(msgContext.getAxisEngine()); rpc.init(); msgContext.setService(rpc); } if (log.isDebugEnabled()) { log.debug("Exit: JWSHandler::invoke"); } } | void shutdown(final boolean unexpected) { if (unexpected) { log.warn("S H U T D O W N --- received unexpected shutdown request."); } else { log.info("S H U T D O W N --- start regular shutdown."); } if (this.uncaughtException != null) { log.warn("Shutdown probably caused by the following Exception.", this.uncaughtException); } log.error("check if we need the controler listener infrastructure"); if (this.dumpDataAtEnd) { new PopulationWriter(this.population, this.network).write(this.controlerIO.getOutputFilename(FILENAME_POPULATION)); new NetworkWriter(this.network).write(this.controlerIO.getOutputFilename(FILENAME_NETWORK)); new ConfigWriter(this.config).write(this.controlerIO.getOutputFilename(FILENAME_CONFIG)); if (!unexpected && this.getConfig().vspExperimental().isWritingOutputEvents()) { File toFile = new File(this.controlerIO.getOutputFilename("output_events.xml.gz")); File fromFile = new File(this.controlerIO.getIterationFilename(this.getLastIteration(), "events.xml.gz")); IOUtils.copyFile(fromFile, toFile); } } if (unexpected) { log.info("S H U T D O W N --- unexpected shutdown request completed."); } else { log.info("S H U T D O W N --- regular shutdown completed."); } try { Runtime.getRuntime().removeShutdownHook(this.shutdownHook); } catch (IllegalStateException e) { log.info("Cannot remove shutdown hook. " + e.getMessage()); } this.shutdownHook = null; this.collectLogMessagesAppender = null; IOUtils.closeOutputDirLogging(); } | 12,219 |
1 | private boolean enregistreToi() { PrintWriter lEcrivain; String laDest = "./img_types/" + sonImage; if (!new File("./img_types").exists()) { new File("./img_types").mkdirs(); } try { FileChannel leFicSource = new FileInputStream(sonFichier).getChannel(); FileChannel leFicDest = new FileOutputStream(laDest).getChannel(); leFicSource.transferTo(0, leFicSource.size(), leFicDest); leFicSource.close(); leFicDest.close(); lEcrivain = new PrintWriter(new FileWriter(new File("bundll/types.jay"), true)); lEcrivain.println(sonNom); lEcrivain.println(sonImage); if (sonOptionRadio1.isSelected()) { lEcrivain.println("0:?"); } if (sonOptionRadio2.isSelected()) { lEcrivain.println("1:" + JOptionPane.showInputDialog(null, "Vous avez choisis de rendre ce terrain difficile � franchir.\nVeuillez en indiquer la raison.", "Demande de pr�cision", JOptionPane.INFORMATION_MESSAGE)); } if (sonOptionRadio3.isSelected()) { lEcrivain.println("2:?"); } lEcrivain.close(); return true; } catch (Exception lException) { return false; } } | public void actionPerformed(ActionEvent e) { int returnVal = chooser.showSaveDialog(jd); if (returnVal == JFileChooser.APPROVE_OPTION) { File file = chooser.getSelectedFile(); String fileName = file.getPath(); String ext = StringUtil.getLowerExtension(fileName); if (!"png".equals(ext)) { fileName += ".png"; file = new File(fileName); } boolean doIt = true; if (file.exists()) { int i = JOptionPane.showConfirmDialog(jd, getMessage("warn_file_exist")); if (i != JOptionPane.YES_OPTION) doIt = false; } else if (!file.getParentFile().exists()) { doIt = file.getParentFile().mkdirs(); } if (doIt) { FileChannel src = null; FileChannel dest = null; try { src = new FileInputStream(imageURL.getPath()).getChannel(); dest = new FileOutputStream(fileName).getChannel(); src.transferTo(0, src.size(), dest); } catch (FileNotFoundException e1) { warn(jd, getMessage("err_no_source_file")); } catch (IOException e2) { warn(jd, getMessage("err_output_target")); } finally { try { if (src != null) src.close(); } catch (IOException e1) { } try { if (dest != null) dest.close(); } catch (IOException e1) { } src = null; dest = null; } } } } | 12,220 |
1 | public static void doVersionCheck(View view) { view.showWaitCursor(); try { URL url = new URL(jEdit.getProperty("version-check.url")); InputStream in = url.openStream(); BufferedReader bin = new BufferedReader(new InputStreamReader(in)); String line; String version = null; String build = null; while ((line = bin.readLine()) != null) { if (line.startsWith(".version")) version = line.substring(8).trim(); else if (line.startsWith(".build")) build = line.substring(6).trim(); } bin.close(); if (version != null && build != null) { if (jEdit.getBuild().compareTo(build) < 0) newVersionAvailable(view, version, url); else { GUIUtilities.message(view, "version-check" + ".up-to-date", new String[0]); } } } catch (IOException e) { String[] args = { jEdit.getProperty("version-check.url"), e.toString() }; GUIUtilities.error(view, "read-error", args); } view.hideWaitCursor(); } | private String checkForUpdate() { InputStream is = null; try { URL url = new URL(CHECK_UPDATES_URL); try { HttpURLConnection conn = (HttpURLConnection) url.openConnection(); conn.setRequestProperty("User-Agent", "TinyLaF"); Object content = conn.getContent(); if (!(content instanceof InputStream)) { return "An exception occured while checking for updates." + "\n\nException was: Content is no InputStream"; } is = (InputStream) content; } catch (IOException ex) { return "An exception occured while checking for updates." + "\n\nException was: " + ex.getClass().getName(); } } catch (MalformedURLException ex) { return "An exception occured while checking for updates." + "\n\nException was: " + ex.getClass().getName(); } try { BufferedReader in = new BufferedReader(new InputStreamReader(is)); StringBuffer buff = new StringBuffer(); String line; while ((line = in.readLine()) != null) { buff.append(line); } in.close(); return buff.toString(); } catch (IOException ex) { return "An exception occured while checking for updates." + "\n\nException was: " + ex.getClass().getName(); } } | 12,221 |
1 | private void backupFile(ZipOutputStream out, String base, String fn) throws IOException { String f = FileUtils.getAbsolutePath(fn); base = FileUtils.getAbsolutePath(base); if (!f.startsWith(base)) { Message.throwInternalError(f + " does not start with " + base); } f = f.substring(base.length()); f = correctFileName(f); out.putNextEntry(new ZipEntry(f)); InputStream in = FileUtils.openFileInputStream(fn); IOUtils.copyAndCloseInput(in, out); out.closeEntry(); } | private static void zip(ZipArchiveOutputStream zos, File efile, String base) throws IOException { if (efile.isDirectory()) { File[] lf = efile.listFiles(); base = base + File.separator + efile.getName(); for (File file : lf) { zip(zos, file, base); } } else { ZipArchiveEntry entry = new ZipArchiveEntry(efile, base + File.separator + efile.getName()); zos.setEncoding("utf-8"); zos.putArchiveEntry(entry); InputStream is = new FileInputStream(efile); IOUtils.copy(is, zos); is.close(); zos.closeArchiveEntry(); } } | 12,222 |
0 | public void run() { XmlFilesFilter filter = new XmlFilesFilter(); String pathTemp = Settings.get("vo_store.databaseMetaCollection"); String sectionName = pathTemp.substring(1, pathTemp.indexOf("/", 2)); String templateName = VOAccess.getElementByName(settingsDB, "TEMPLATE", sectionName); String schemaName = VOAccess.getElementByName(settingsDB, "SCHEMA", sectionName); byte[] buf = new byte[1024]; Hashtable templateElements = null; try { URL xmlTemplateUrl = new URL(httpURI + settingsDB + "/" + templateName); URL getDocPathsAndValuesXslUrl = new URL(httpURI + settingsDB + "/" + "getDocPathsValuesAndDisplays.xsl"); org.w3c.dom.Document curTemplateXml = VOAccess.readDocument(xmlTemplateUrl); DOMResult templateResult = new DOMResult(); InputStream tempInput = getDocPathsAndValuesXslUrl.openStream(); javax.xml.transform.sax.SAXSource tempXslSource = new javax.xml.transform.sax.SAXSource(new org.xml.sax.InputSource(tempInput)); Transformer trans = TransformerFactory.newInstance().newTransformer(tempXslSource); trans.setParameter("schemaUrl", httpURI + settingsDB + "/" + schemaName); trans.transform(new javax.xml.transform.dom.DOMSource(curTemplateXml), templateResult); tempInput.close(); templateElements = VOAccess.displaysToHashtable(templateResult); ((CollectionManagementService) CollectionsManager.getService(xmldbURI + rootDB, false, "CollectionManager")).createCollection(rootDB + pathTemp); } catch (Exception ex) { logger.error("Error parsing input document", ex); ex.printStackTrace(); } while (true) { File[] fileList = sourceMetaFilesDir.listFiles(filter); for (int i = 0; i < Math.min(fileList.length, 500); i++) { File newFile = fileList[i]; try { Document metaDoc = build.build(newFile); Element metaElm = metaDoc.getRootElement(); String dataFileName = metaElm.getChildText("Content"), previewFileName = metaElm.getChildText("Preview"); String objId = VOAccess.getUniqueId(); metaElm.getChild("Content").setText("videostore?type=doc&objId=" + objId); metaElm.getChild("Preview").setText("videostore?type=preview&objId=" + objId); boolean found = false; for (Iterator it = sourceDataFilesDirs.iterator(); it.hasNext() && !found; ) { String sourceDataFilesDir = (String) it.next(); File dataInput = new File(sourceDataFilesDir + "/" + dataFileName); if (dataInput.exists()) { found = true; BufferedInputStream inp = new BufferedInputStream(new FileInputStream(dataInput)); FileOutputStream outp = new FileOutputStream(new File(targetDataFilesDirs.get(curDirWriteTo) + "/" + objId + ".dat")); int read = inp.read(buf, 0, buf.length); while (read > 0) { outp.write(buf, 0, read); read = inp.read(buf, 0, buf.length); } inp.close(); outp.flush(); outp.close(); dataInput = new File(sourceDataFilesDir + "/" + previewFileName); inp = new BufferedInputStream(new FileInputStream(dataInput)); outp = new FileOutputStream(new File(targetDataFilesDirs.get(curDirWriteTo) + "/" + objId + ".jpg")); read = inp.read(buf, 0, buf.length); while (read > 0) { outp.write(buf, 0, read); read = inp.read(buf, 0, buf.length); } inp.close(); outp.flush(); outp.close(); curDirWriteTo++; if (curDirWriteTo >= targetDataFilesDirs.size()) { curDirWriteTo = 0; } } } if (!found) { newFile.renameTo(new File(newFile.getAbsolutePath() + ".not_found")); } else { String title = getValueByPath((String) templateElements.get("title"), metaDoc.getRootElement()); String description = getValueByPath((String) templateElements.get("description"), metaDoc.getRootElement()); String onlink = ""; if (null != templateElements.get("onlink")) { onlink = getValueByPath((String) templateElements.get("onlink"), metaDoc.getRootElement()); } String ncover = ""; if (null != templateElements.get("ncover")) { ncover = getValueByPath((String) templateElements.get("ncover"), metaDoc.getRootElement()); } String wcover = ""; if (null != templateElements.get("wcover")) { wcover = getValueByPath((String) templateElements.get("wcover"), metaDoc.getRootElement()); } String ecover = ""; if (null != templateElements.get("ecover")) { ecover = getValueByPath((String) templateElements.get("ecover"), metaDoc.getRootElement()); } String scover = ""; if (null != templateElements.get("scover")) { scover = getValueByPath((String) templateElements.get("scover"), metaDoc.getRootElement()); } String datefrom = ""; if (null != templateElements.get("datefrom")) { datefrom = getValueByPath((String) templateElements.get("datefrom"), metaDoc.getRootElement()); } String dateto = ""; if (null != templateElements.get("dateto")) { dateto = getValueByPath((String) templateElements.get("dateto"), metaDoc.getRootElement()); } String previewimg = ""; if (null != templateElements.get("previewimg")) { previewimg = getValueByPath((String) templateElements.get("previewimg"), metaDoc.getRootElement()); } String discRestr = "false"; String votingRestr = "false"; datefrom = VOAccess.parseDate(datefrom, "yyyy-MM-dd'T'HH:mm:ss", VO.defaultTimeFormat.toPattern()); dateto = VOAccess.parseDate(datefrom, "yyyy-MM-dd'T'HH:mm:ss", VO.defaultTimeFormat.toPattern()); Hashtable discussionFields = new Hashtable(); discussionFields.put("OBJECT_ID", objId); discussionFields.put("AUTHOR_ID", "auto"); discussionFields.put("AUTHOR_NAME", "auto"); discussionFields.put("OBJECT_SECTION", sectionName); discussionFields.put("OBJECT_PATH", pathTemp); discussionFields.put("FILE_PATH", ""); discussionFields.put("TITLE", title); discussionFields.put("DESCRIPTION", description); discussionFields.put("ONLINK", onlink); discussionFields.put("NCOVER", ncover); discussionFields.put("ECOVER", ecover); discussionFields.put("SCOVER", scover); discussionFields.put("WCOVER", wcover); discussionFields.put("PERIOD_START", datefrom); discussionFields.put("PERIOD_END", dateto); discussionFields.put("PREVIEW_IMG", previewimg); discussionFields.put("DISCUSSRESTRICTION", discRestr); discussionFields.put("VOTINGRESTRICTION", votingRestr); VOAccess.createDiscussionFile(discussionFields); VOAccess.updateLastItem(objId, sectionName); Collection col = CollectionsManager.getCollection(rootDB + pathTemp, true); XMLResource document = (XMLResource) col.createResource(objId + ".xml", XMLResource.RESOURCE_TYPE); document.setContent(outXml.outputString(metaElm)); col.storeResource(document); Indexer.index(objId); newFile.delete(); } } catch (Exception ex) { logger.error("Error parsing input document", ex); ex.printStackTrace(); newFile.renameTo(new File(newFile.getAbsolutePath() + ".bad")); } } try { this.sleep(600000); } catch (InterruptedException ex1) { ex1.printStackTrace(); } } } | public static String calculatesMD5(String plainText) throws NoSuchAlgorithmException { MessageDigest mdAlgorithm = MessageDigest.getInstance("MD5"); mdAlgorithm.update(plainText.getBytes()); byte[] digest = mdAlgorithm.digest(); StringBuffer hexString = new StringBuffer(); for (int i = 0; i < digest.length; i++) { plainText = Integer.toHexString(0xFF & digest[i]); if (plainText.length() < 2) { plainText = "0" + plainText; } hexString.append(plainText); } return hexString.toString(); } | 12,223 |
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 static boolean copyFileCover(String srcFileName, String descFileName, boolean coverlay) { File srcFile = new File(srcFileName); if (!srcFile.exists()) { System.out.println("�����ļ�ʧ�ܣ�Դ�ļ�" + srcFileName + "������!"); return false; } else if (!srcFile.isFile()) { System.out.println("�����ļ�ʧ�ܣ�" + srcFileName + "����һ���ļ�!"); return false; } File descFile = new File(descFileName); if (descFile.exists()) { if (coverlay) { System.out.println("Ŀ���ļ��Ѵ��ڣ���ɾ��!"); if (!FileOperateUtils.delFile(descFileName)) { System.out.println("ɾ��Ŀ���ļ�" + descFileName + "ʧ��!"); return false; } } else { System.out.println("�����ļ�ʧ�ܣ�Ŀ���ļ�" + descFileName + "�Ѵ���!"); return false; } } else { if (!descFile.getParentFile().exists()) { System.out.println("Ŀ���ļ����ڵ�Ŀ¼�����ڣ�����Ŀ¼!"); if (!descFile.getParentFile().mkdirs()) { System.out.println("����Ŀ���ļ����ڵ�Ŀ¼ʧ��!"); return false; } } } int readByte = 0; InputStream ins = null; OutputStream outs = null; try { ins = new FileInputStream(srcFile); outs = new FileOutputStream(descFile); byte[] buf = new byte[1024]; while ((readByte = ins.read(buf)) != -1) { outs.write(buf, 0, readByte); } System.out.println("���Ƶ����ļ�" + srcFileName + "��" + descFileName + "�ɹ�!"); return true; } catch (Exception e) { System.out.println("�����ļ�ʧ�ܣ�" + e.getMessage()); return false; } finally { if (outs != null) { try { outs.close(); } catch (IOException oute) { oute.printStackTrace(); } } if (ins != null) { try { ins.close(); } catch (IOException ine) { ine.printStackTrace(); } } } } | 12,224 |
1 | private File downloadPDB(String pdbId) { File tempFile = new File(path + "/" + pdbId + ".pdb.gz"); File pdbHome = new File(path); if (!pdbHome.canWrite()) { System.err.println("can not write to " + pdbHome); return null; } String ftp = String.format("ftp://ftp.ebi.ac.uk/pub/databases/msd/pdb_uncompressed/pdb%s.ent", pdbId.toLowerCase()); System.out.println("Fetching " + ftp); try { URL url = new URL(ftp); InputStream conn = url.openStream(); System.out.println("writing to " + tempFile); FileOutputStream outPut = new FileOutputStream(tempFile); GZIPOutputStream gzOutPut = new GZIPOutputStream(outPut); PrintWriter pw = new PrintWriter(gzOutPut); BufferedReader fileBuffer = new BufferedReader(new InputStreamReader(conn)); String line; while ((line = fileBuffer.readLine()) != null) { pw.println(line); } pw.flush(); pw.close(); outPut.close(); conn.close(); } catch (Exception e) { e.printStackTrace(); return null; } return tempFile; } | private void sendToServer(String fichaID, String respostas) throws FileNotFoundException, ParserConfigurationException, SAXException, IOException, URISyntaxException { ArrayList params = new ArrayList(); params.add(new BasicNameValuePair("xml", respostas)); params.add(new BasicNameValuePair("idForm", fichaID)); URI uri = URIUtils.createURI("http", "172.20.9.144", 8080, "/PSFServer/SaveAnswers", URLEncodedUtils.format(params, "UTF-8"), null); HttpPost request = new HttpPost(uri); request.setEntity(new UrlEncodedFormEntity(params, HTTP.UTF_8)); HttpClient client = new DefaultHttpClient(); HttpResponse httpResponse = client.execute(request); BufferedReader in = new BufferedReader(new InputStreamReader(httpResponse.getEntity().getContent())); StringBuffer sb = new StringBuffer(""); String line = ""; String NL = System.getProperty("line.separator"); while ((line = in.readLine()) != null) { sb.append(line + NL); } in.close(); String resposta = sb.toString(); if (resposta != null || resposta != "") { new DatabaseManager(this).getWritableDatabase().execSQL("delete from " + DatabaseManager.getTableDados()); } backToMain(); } | 12,225 |
0 | public static void compressAll(File dir, File file) throws IOException { if (!dir.isDirectory()) throw new IllegalArgumentException("Given file is no directory"); ZipOutputStream out = new ZipOutputStream(new FileOutputStream(file)); out.setLevel(0); String[] entries = dir.list(); byte[] buffer = new byte[4096]; int bytesRead; 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.getName()); out.putNextEntry(entry); while ((bytesRead = in.read(buffer)) != -1) out.write(buffer, 0, bytesRead); in.close(); } out.close(); } | public synchronized String encrypt(String plaintext) { MessageDigest md = null; try { md = MessageDigest.getInstance("SHA1"); } catch (NoSuchAlgorithmException noSuchAlgorithmException) { noSuchAlgorithmException.printStackTrace(); } try { md.update(plaintext.getBytes("UTF-8")); } catch (UnsupportedEncodingException unsupportedEncodingException) { unsupportedEncodingException.printStackTrace(); } byte raw[] = md.digest(); String hash = (new BASE64Encoder()).encode(raw); return hash; } | 12,226 |
0 | public static boolean isSameHttpContent(final String url, final File localFile, UsernamePasswordCredentials creds) throws IOException { if (localFile.isFile()) { long localContentLength = localFile.length(); long localLastModified = localFile.lastModified() / 1000; long contentLength = -1; long lastModified = -1; HttpClient httpclient = createHttpClient(creds); try { HttpHead httphead = new HttpHead(url); HttpResponse response = httpclient.execute(httphead); if (response != null) { StatusLine statusLine = response.getStatusLine(); int status = statusLine.getStatusCode() / 100; if (status == 2) { Header lastModifiedHeader = response.getFirstHeader("Last-Modified"); Header contentLengthHeader = response.getFirstHeader("Content-Length"); if (contentLengthHeader != null) { contentLength = Integer.parseInt(contentLengthHeader.getValue()); } if (lastModifiedHeader != null) { SimpleDateFormat formatter = new SimpleDateFormat("EEE, dd MMM yyyy HH:mm:ss zzz"); formatter.setDateFormatSymbols(new DateFormatSymbols(Locale.US)); try { lastModified = formatter.parse(lastModifiedHeader.getValue()).getTime() / 1000; } catch (ParseException e) { logger.error(e); } } } else { return true; } } } finally { httpclient.getConnectionManager().shutdown(); } if (logger.isDebugEnabled()) { logger.debug("local:" + localContentLength + " " + localLastModified); logger.debug("remote:" + contentLength + " " + lastModified); } if (contentLength != -1 && localContentLength != contentLength) return false; if (lastModified != -1 && lastModified != localLastModified) return false; if (contentLength == -1 && lastModified == -1) return false; return true; } return false; } | @Test public void testCopy() throws IOException { final byte[] input = { 0x00, 0x01, 0x7F, 0x03, 0x40 }; final byte[] verification = input.clone(); Assert.assertNotSame("Expecting verification to be a new array.", input, verification); final ByteArrayInputStream in = new ByteArrayInputStream(input); final ByteArrayOutputStream out = new ByteArrayOutputStream(); IOUtils.copy(in, out); final byte[] output = out.toByteArray(); Assert.assertTrue("Expecting input to be unchanged.", Arrays.equals(verification, input)); Assert.assertTrue("Expecting output to be like input.", Arrays.equals(verification, output)); Assert.assertNotSame("Expecting output to be a new array.", input, output); Assert.assertNotSame("Expecting output to be a new array.", verification, output); } | 12,227 |
0 | public GPSTrace loadGPSTrace(long reportID) { try { URL url = new URL(SERVER_URL + XML_PATH + "gps.xml"); System.out.println(url); DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); DocumentBuilder builder = factory.newDocumentBuilder(); document = builder.parse(url.openStream()); Element customerElement = document.getDocumentElement(); NodeList gps = customerElement.getElementsByTagName("gps"); trace = getGPSTrace(gps); } catch (SAXException sxe) { Exception x = sxe; if (sxe.getException() != null) x = sxe.getException(); x.printStackTrace(); } catch (ParserConfigurationException pce) { pce.printStackTrace(); } catch (IOException ioe) { ioe.printStackTrace(); } return trace; } | public RawTableData(int selectedId) { selectedProjectId = selectedId; String urlString = dms_url + "/servlet/com.ufnasoft.dms.server.ServerGetProjectDocuments"; String rvalue = ""; String filename = dms_home + FS + "temp" + FS + username + "documents.xml"; try { String urldata = urlString + "?username=" + URLEncoder.encode(username, "UTF-8") + "&key=" + URLEncoder.encode(key, "UTF-8") + "&projectid=" + selectedProjectId + "&filename=" + URLEncoder.encode(username, "UTF-8") + "documents.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("doc"); int num = nodelist.getLength(); rawTableData = new String[num][11]; imageNames = new String[num]; for (int i = 0; i < num; i++) { rawTableData[i][0] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "did")); rawTableData[i][1] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "t")); rawTableData[i][2] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "f")); rawTableData[i][3] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "d")); rawTableData[i][4] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "l")); String firstname = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "fn")); String lastname = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "ln")); rawTableData[i][5] = firstname + " " + lastname; rawTableData[i][6] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "dln")); rawTableData[i][7] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "rsid")); rawTableData[i][8] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "img")); imageNames[i] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "img")); rawTableData[i][9] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "ucin")); rawTableData[i][10] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "dtid")); } } catch (MalformedURLException ex) { System.out.println(ex); } catch (ParserConfigurationException ex) { System.out.println(ex); } catch (NullPointerException e) { } catch (Exception ex) { System.out.println(ex); } } | 12,228 |
0 | private final void copyTargetFileToSourceFile(File sourceFile, File targetFile) throws MJProcessorException { if (!targetFile.exists()) { targetFile.getParentFile().mkdirs(); try { if (!targetFile.exists()) { targetFile.createNewFile(); } } catch (IOException e) { throw new MJProcessorException(e.getMessage(), e); } } FileChannel in = null, out = null; try { in = new FileInputStream(sourceFile).getChannel(); out = new FileOutputStream(targetFile).getChannel(); long size = in.size(); MappedByteBuffer buf = in.map(FileChannel.MapMode.READ_ONLY, 0, size); out.write(buf); } catch (IOException e) { log.error(e); } finally { if (in != null) try { in.close(); } catch (IOException e) { log.error(e); } if (out != null) try { out.close(); } catch (IOException e) { log.error(e); } } } | 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(); } | 12,229 |
1 | public static String encryptMD5(String str) { try { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.update(str.getBytes()); byte[] hash = md5.digest(); md5.reset(); return Format.hashToHex(hash); } catch (java.security.NoSuchAlgorithmException nsae0) { return null; } } | private void getRandomGUID(boolean secure) throws NoSuchAlgorithmException { MessageDigest md5 = null; StringBuffer sbValueBeforeMD5 = new StringBuffer(); try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { System.out.println("Error: " + e); throw 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); } } | 12,230 |
0 | static String fetchURLComposeExternPackageList(String urlpath, String pkglisturlpath) { String link = pkglisturlpath + "package-list"; try { boolean relative = isRelativePath(urlpath); readPackageList((new URL(link)).openStream(), urlpath, relative); } catch (MalformedURLException exc) { return getText("doclet.MalformedURL", link); } catch (IOException exc) { return getText("doclet.URL_error", link); } return null; } | 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; } | 12,231 |
1 | public void testGetOldVersion() throws ServiceException, IOException, SAXException, ParserConfigurationException { JCRNodeSource emptySource = loadTestSource(); for (int i = 0; i < 3; i++) { OutputStream sourceOut = emptySource.getOutputStream(); InputStream contentIn = getClass().getResourceAsStream(CONTENT_FILE); try { IOUtils.copy(contentIn, sourceOut); sourceOut.flush(); } finally { sourceOut.close(); contentIn.close(); } } String testSourceUri = BASE_URL + "users/lars.trieloff?revision=1.1"; JCRNodeSource secondSource = (JCRNodeSource) resolveSource(testSourceUri); System.out.println("Read again at:" + secondSource.getSourceRevision()); InputStream expected = emptySource.getInputStream(); InputStream actual = secondSource.getInputStream(); assertTrue(isXmlEqual(expected, actual)); } | public boolean copier(String source, String nomFichierSource, java.io.File destination) { boolean resultat = false; OutputStream tmpOut; try { tmpOut = new BufferedOutputStream(new FileOutputStream(nomFichierSource + "001.tmp")); InputStream is = getClass().getResourceAsStream(source + nomFichierSource); int i; while ((i = is.read()) != -1) tmpOut.write(i); tmpOut.close(); is.close(); } catch (IOException ex) { ex.printStackTrace(); } FileChannel in = null; FileChannel out = null; try { in = new FileInputStream(new File(nomFichierSource + "001.tmp")).getChannel(); out = new FileOutputStream(destination).getChannel(); in.transferTo(0, in.size(), out); resultat = true; } catch (java.io.FileNotFoundException f) { } catch (java.io.IOException e) { } finally { if (in != null) { try { in.close(); } catch (IOException e) { } } if (out != null) { try { out.close(); } catch (IOException e) { } } } new File(nomFichierSource + "001.tmp").delete(); return (resultat); } | 12,232 |
0 | public static void bubbleSort(Drawable[] list) { boolean swapped; do { swapped = false; for (int i = 0; i < list.length - 1; ++i) { if (list[i].getSortValue() > list[i + 1].getSortValue()) { Drawable temp = list[i]; list[i] = list[i + 1]; list[i + 1] = temp; swapped = true; } } } while (swapped); } | @Override public void handle(String s, HttpServletRequest httpServletRequest, HttpServletResponse httpServletResponse, int i) throws IOException, ServletException { expected = new StringBuilder(); System.out.println("uri: " + httpServletRequest.getRequestURI()); System.out.println("queryString: " + (queryString = httpServletRequest.getQueryString())); System.out.println("method: " + httpServletRequest.getMethod()); ByteArrayOutputStream baos = new ByteArrayOutputStream(); IOUtils.copy(httpServletRequest.getInputStream(), baos); System.out.println("body: " + (body = baos.toString())); PrintWriter writer = httpServletResponse.getWriter(); writer.append("testsvar"); expected.append("testsvar"); Random r = new Random(); for (int j = 0; j < 10; j++) { int value = r.nextInt(Integer.MAX_VALUE); writer.append(value + ""); expected.append(value); } System.out.println(); writer.close(); httpServletResponse.setStatus(HttpServletResponse.SC_OK); } | 12,233 |
0 | @Override protected void copy(InputStream inputs, OutputStream outputs) throws IOException { if (outputs == null) { throw new NullPointerException(); } if (inputs == null) { throw new NullPointerException(); } ZipOutputStream zipoutputs = null; try { zipoutputs = new ZipOutputStream(outputs); zipoutputs.putNextEntry(new ZipEntry("default")); IOUtils.copy(inputs, zipoutputs); } catch (IOException e) { e.printStackTrace(); throw e; } finally { if (zipoutputs != null) { zipoutputs.close(); } if (inputs != null) { inputs.close(); } } } | private void fetch() throws IOException { if (getAttachmentUrl() != null && (!getAttachmentUrl().isEmpty())) { InputStream input = null; ByteArrayOutputStream output = null; try { URL url = new URL(getAttachmentUrl()); input = url.openStream(); output = new ByteArrayOutputStream(); int i; while ((i = input.read()) != -1) { output.write(i); } this.data = output.toByteArray(); } finally { if (input != null) { input.close(); } if (output != null) { output.close(); } } } } | 12,234 |
0 | public static NSImage getImage(URL url) { InputStream in = null; try { in = url.openStream(); } catch (IOException e) { Log.error(e.getMessage(), e); } ByteArrayOutputStream out = new ByteArrayOutputStream(); byte[] buff = new byte[10 * 1024]; int len; try { if (in != null) { while ((len = in.read(buff)) != -1) { out.write(buff, 0, len); } in.close(); } out.close(); } catch (IOException e) { Log.error(e.getMessage(), e); } NSData data = new NSData(out.toByteArray()); return new NSImage(data); } | public static String encode(String arg) { if (arg == null) { arg = ""; } MessageDigest md5 = null; try { md5 = MessageDigest.getInstance("MD5"); md5.update(arg.getBytes(JavaCenterHome.JCH_CHARSET)); } catch (Exception e) { e.printStackTrace(); } return toHex(md5.digest()); } | 12,235 |
1 | public static void copyFile(File src, File dst) throws IOException { FileChannel inChannel = new FileInputStream(src).getChannel(); FileChannel outChannel = new FileOutputStream(dst).getChannel(); try { inChannel.transferTo(0, inChannel.size(), outChannel); } finally { if (inChannel != null) inChannel.close(); if (outChannel != null) outChannel.close(); } } | public byte[] read(IFile input) { InputStream contents = null; try { ByteArrayOutputStream baos = new ByteArrayOutputStream(); contents = input.getContents(); IOUtils.copy(contents, baos); return baos.toByteArray(); } catch (IOException e) { Activator.logUnexpected(null, e); } catch (CoreException e) { Activator.logUnexpected(null, e); } finally { IOUtils.closeQuietly(contents); } return null; } | 12,236 |
0 | public static boolean encodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.ENCODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | public Configuration(URL url) { InputStream in = null; try { load(in = url.openStream()); } catch (Exception e) { throw new RuntimeException("Could not load configuration from " + url, e); } finally { if (in != null) { try { in.close(); } catch (IOException ignore) { } } } } | 12,237 |
0 | private static Document getDocument(URL url, String applicationVersion, boolean addHeader, int timeOut) throws IOException, ParserConfigurationException, SAXException { HttpURLConnection huc = (HttpURLConnection) url.openConnection(); huc.setConnectTimeout(1000 * timeOut); huc.setRequestMethod("GET"); if (addHeader) { huc.setRequestProperty("JavaPEG-Version", applicationVersion); } huc.connect(); int code = huc.getResponseCode(); if (code != HttpURLConnection.HTTP_OK) { throw new IOException("Invaild HTTP response: " + code); } DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); DocumentBuilder db = dbf.newDocumentBuilder(); return db.parse(huc.getInputStream()); } | public boolean loadResource(String resourcePath) { try { URL url = Thread.currentThread().getContextClassLoader().getResource(resourcePath); if (url == null) { logger.error("Cannot find the resource named: '" + resourcePath + "'. Failed to load the keyword list."); return false; } InputStreamReader isr = new InputStreamReader(url.openStream()); BufferedReader br = new BufferedReader(isr); String ligne = br.readLine(); while (ligne != null) { if (!contains(ligne.toUpperCase())) addLast(ligne.toUpperCase()); ligne = br.readLine(); } return true; } catch (IOException ioe) { logger.log(Level.ERROR, "Cannot load default SQL keywords file.", ioe); } return false; } | 12,238 |
0 | public static InputStream download_file(String sessionid, String key) { InputStream is = null; String urlString = "https://s2.cloud.cm/rpc/raw?c=Storage&m=download_file&key=" + key; try { String apple = ""; URL url = new URL(urlString); Log.d("current running function name:", "download_file"); HttpURLConnection conn = (HttpURLConnection) url.openConnection(); conn.setRequestProperty("Cookie", "PHPSESSID=" + sessionid); conn.setRequestMethod("POST"); conn.setDoInput(true); is = conn.getInputStream(); return is; } catch (Exception e) { e.printStackTrace(); Log.d("download problem", "download problem"); } return is; } | public static void copyFile(File src, File dest, boolean preserveFileDate) throws IOException { if (src.exists() && src.isDirectory()) { throw new IOException("source file exists but is a directory"); } if (dest.exists() && dest.isDirectory()) { dest = new File(dest, src.getName()); } if (!dest.exists()) { dest.createNewFile(); } FileChannel srcCH = null; FileChannel destCH = null; try { srcCH = new FileInputStream(src).getChannel(); destCH = new FileOutputStream(dest).getChannel(); destCH.transferFrom(srcCH, 0, srcCH.size()); } finally { closeQuietly(srcCH); closeQuietly(destCH); } if (src.length() != dest.length()) { throw new IOException("Failed to copy full contents from '" + src + "' to '" + dest + "'"); } if (preserveFileDate) { dest.setLastModified(src.lastModified()); } } | 12,239 |
1 | public long copyDirAllFilesToDirectory(String baseDirStr, String destDirStr) throws Exception { long plussQuotaSize = 0; if (baseDirStr.endsWith(sep)) { baseDirStr = baseDirStr.substring(0, baseDirStr.length() - 1); } if (destDirStr.endsWith(sep)) { destDirStr = destDirStr.substring(0, destDirStr.length() - 1); } FileUtils.getInstance().createDirectory(destDirStr); BufferedInputStream in = null; BufferedOutputStream out = null; byte dataBuff[] = new byte[bufferSize]; File baseDir = new File(baseDirStr); baseDir.mkdirs(); if (!baseDir.exists()) { createDirectory(baseDirStr); } if ((baseDir.exists()) && (baseDir.isDirectory())) { String[] entryList = baseDir.list(); if (entryList.length > 0) { for (int pos = 0; pos < entryList.length; pos++) { String entryName = entryList[pos]; String oldPathFileName = baseDirStr + sep + entryName; File entryFile = new File(oldPathFileName); if (entryFile.isFile()) { String newPathFileName = destDirStr + sep + entryName; File newFile = new File(newPathFileName); if (newFile.exists()) { plussQuotaSize -= newFile.length(); newFile.delete(); } in = new BufferedInputStream(new FileInputStream(oldPathFileName), bufferSize); out = new BufferedOutputStream(new FileOutputStream(newPathFileName), bufferSize); int readLen; while ((readLen = in.read(dataBuff)) > 0) { out.write(dataBuff, 0, readLen); plussQuotaSize += readLen; } out.flush(); in.close(); out.close(); } } } } else { throw new Exception("Base dir not exist ! baseDirStr = (" + baseDirStr + ")"); } return plussQuotaSize; } | 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; } | 12,240 |
1 | private static <T> Collection<T> loadFromServices(Class<T> interf) throws Exception { ClassLoader classLoader = DSServiceLoader.class.getClassLoader(); Enumeration<URL> e = classLoader.getResources("META-INF/services/" + interf.getName()); Collection<T> services = new ArrayList<T>(); while (e.hasMoreElements()) { URL url = e.nextElement(); InputStream is = url.openStream(); try { BufferedReader r = new BufferedReader(new InputStreamReader(is, "UTF-8")); while (true) { String line = r.readLine(); if (line == null) { break; } int comment = line.indexOf('#'); if (comment >= 0) { line = line.substring(0, comment); } String name = line.trim(); if (name.length() == 0) { continue; } Class<?> clz = Class.forName(name, true, classLoader); Class<? extends T> impl = clz.asSubclass(interf); Constructor<? extends T> ctor = impl.getConstructor(); T svc = ctor.newInstance(); services.add(svc); } } finally { is.close(); } } return services; } | public Point getCoordinates(String address, String city, String state, String country) { StringBuilder queryString = new StringBuilder(); StringBuilder urlString = new StringBuilder(); StringBuilder response = new StringBuilder(); if (address != null) { queryString.append(address.trim().replaceAll(" ", "+")); queryString.append("+"); } if (city != null) { queryString.append(city.trim().replaceAll(" ", "+")); queryString.append("+"); } if (state != null) { queryString.append(state.trim().replaceAll(" ", "+")); queryString.append("+"); } if (country != null) { queryString.append(country.replaceAll(" ", "+")); } urlString.append("http://maps.google.com/maps/geo?key="); urlString.append(key); urlString.append("&sensor=false&output=json&oe=utf8&q="); urlString.append(queryString.toString()); try { URL url = new URL(urlString.toString()); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String line; while ((line = reader.readLine()) != null) { response.append(line); } reader.close(); JSONObject root = (JSONObject) JSONValue.parse(response.toString()); JSONObject placemark = (JSONObject) ((JSONArray) root.get("Placemark")).get(0); JSONArray coordinates = (JSONArray) ((JSONObject) placemark.get("Point")).get("coordinates"); Point point = new Point(); point.setLatitude((Double) coordinates.get(1)); point.setLongitude((Double) coordinates.get(0)); return point; } catch (MalformedURLException ex) { return null; } catch (NullPointerException ex) { return null; } catch (IOException ex) { return null; } } | 12,241 |
1 | public String digestPassword(String password) { StringBuffer hexString = new StringBuffer(); try { MessageDigest algorithm = MessageDigest.getInstance("MD5"); algorithm.reset(); algorithm.update(password.getBytes()); byte[] messageDigest = algorithm.digest(); for (byte b : messageDigest) { hexString.append(Integer.toHexString(0xFF & b)); } } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } return hexString.toString(); } | public void loginMD5() throws Exception { GetMethod get = new GetMethod("http://login.yahoo.com/config/login?.src=www&.done=http://www.yahoo.com"); get.setRequestHeader("user-agent", "Mozilla/5.0 (Macintosh; U; PPC MacOS X; en-us) AppleWebKit/124 (KHTML, like Gecko) Safari/125.1"); client.executeMethod(get); parseResponse(get.getResponseBodyAsStream()); MessageDigest digest = MessageDigest.getInstance("MD5"); digest.update(password.getBytes("US-ASCII")); String hash1 = new String(digest.digest(), "US-ASCII"); String hash2 = hash1 + challenge; digest.update(hash2.getBytes("US-ASCII")); String hash = new String(digest.digest(), "US-ASCII"); NameValuePair[] pairs = { new NameValuePair("login", login), new NameValuePair("password", hash), new NameValuePair(".save", "1"), new NameValuePair(".tries", "1"), new NameValuePair(".src", "www"), new NameValuePair(".md5", "1"), new NameValuePair(".hash", "1"), new NameValuePair(".js", "1"), new NameValuePair(".last", ""), new NameValuePair(".promo", ""), new NameValuePair(".intl", "us"), new NameValuePair(".bypass", ""), new NameValuePair(".u", u), new NameValuePair(".v", "0"), new NameValuePair(".challenge", challenge), new NameValuePair(".yplus", ""), new NameValuePair(".emailCode", ""), new NameValuePair("pkg", ""), new NameValuePair("stepid", ""), new NameValuePair(".ev", ""), new NameValuePair("hasMsgr", "0"), new NameValuePair(".chkP", "Y"), new NameValuePair(".done", "http://www.yahoo.com"), new NameValuePair(".persistent", "y") }; get = new GetMethod("http://login.yahoo.com/config/login"); get.setRequestHeader("user-agent", "Mozilla/5.0 (Macintosh; U; PPC MacOS X; en-us) AppleWebKit/124 (KHTML, like Gecko) Safari/125.1"); get.addRequestHeader("Accept", "*/*"); get.addRequestHeader("Accept-Language", "en-us, ja;q=0.21, de-de;q=0.86, de;q=0.79, fr-fr;q=0.71, fr;q=0.64, nl-nl;q=0.57, nl;q=0.50, it-it;q=0.43, it;q=0.36, ja-jp;q=0.29, en;q=0.93, es-es;q=0.14, es;q=0.07"); get.setQueryString(pairs); client.executeMethod(get); get.getResponseBodyAsString(); } | 12,242 |
0 | private void save() { int[] selection = list.getSelectionIndices(); String dir = System.getProperty("user.dir"); for (int i = 0; i < selection.length; i++) { File src = files[selection[i]]; FileDialog dialog = new FileDialog(shell, SWT.SAVE); dialog.setFilterPath(dir); dialog.setFileName(src.getName()); String destination = dialog.open(); if (destination != null) { File dest = new File(destination); try { dest.createNewFile(); FileChannel srcC = new FileInputStream(src).getChannel(); FileChannel destC = new FileOutputStream(dest).getChannel(); destC.transferFrom(srcC, 0, srcC.size()); destC.close(); srcC.close(); updateSaved(selection[i], true); files[selection[i]] = dest; } catch (FileNotFoundException e) { IVC.showError("Error!", "" + e.getMessage(), ""); } catch (IOException e) { IVC.showError("Error!", "" + e.getMessage(), ""); } } } } | public Epg unmarshallFromUrl(URL url) throws IOException { BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String tmp = null; StringBuilder buffer = new StringBuilder(); while ((tmp = reader.readLine()) != null) { buffer.append(tmp); } return unmarshall(buffer.toString().getBytes()); } | 12,243 |
1 | private String generateUniqueIdMD5(Run run, HttpServletRequest request, String groupIdString) { String portalUrl = request.getScheme() + "://" + request.getServerName() + ":" + request.getServerPort(); String uniqueportalUrl = portalUrl + "run:" + run.getId().toString() + "group:" + groupIdString; MessageDigest m = null; try { m = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } m.update(uniqueportalUrl.getBytes(), 0, uniqueportalUrl.length()); String uniqueIdMD5 = new BigInteger(1, m.digest()).toString(16); return uniqueIdMD5; } | public String SHA1(String text) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md; md = MessageDigest.getInstance("SHA-1"); byte[] sha1hash = new byte[40]; md.update(text.getBytes("iso-8859-1"), 0, text.length()); sha1hash = md.digest(); return convertToHex(sha1hash); } | 12,244 |
0 | public void testDoPost() throws Exception { URL url = null; url = new URL("http://127.0.0.1:" + connector.getLocalPort() + "/test/dump/info?query=foo"); HttpURLConnection connection = (HttpURLConnection) url.openConnection(); connection.setRequestMethod("POST"); connection.setDoOutput(true); connection.setDoInput(true); connection.addRequestProperty(HttpHeaders.CONTENT_TYPE, MimeTypes.FORM_ENCODED); connection.addRequestProperty(HttpHeaders.CONTENT_LENGTH, "10"); connection.getOutputStream().write("abcd=1234\n".getBytes()); connection.getOutputStream().flush(); connection.connect(); String s0 = IO.toString(connection.getInputStream()); assertTrue(s0.startsWith("<html>")); assertTrue(s0.indexOf("<td>POST</td>") > 0); assertTrue(s0.indexOf("abcd: </th><td>1234") > 0); } | @Override public int onPut(Operation operation) { synchronized (MuleObexRequestHandler.connections) { MuleObexRequestHandler.connections++; if (logger.isDebugEnabled()) { logger.debug("Connection accepted, total number of connections: " + MuleObexRequestHandler.connections); } } int result = ResponseCodes.OBEX_HTTP_OK; try { headers = operation.getReceivedHeaders(); if (!this.maxFileSize.equals(ObexServer.UNLIMMITED_FILE_SIZE)) { Long fileSize = (Long) headers.getHeader(HeaderSet.LENGTH); if (fileSize == null) { result = ResponseCodes.OBEX_HTTP_LENGTH_REQUIRED; } if (fileSize > this.maxFileSize) { result = ResponseCodes.OBEX_HTTP_REQ_TOO_LARGE; } } if (result != ResponseCodes.OBEX_HTTP_OK) { InputStream in = operation.openInputStream(); ByteArrayOutputStream out = new ByteArrayOutputStream(); IOUtils.copy(in, out); in.close(); out.close(); data = out.toByteArray(); if (interrupted) { data = null; result = ResponseCodes.OBEX_HTTP_GONE; } } return result; } catch (IOException e) { return ResponseCodes.OBEX_HTTP_UNAVAILABLE; } finally { synchronized (this) { this.notify(); } synchronized (MuleObexRequestHandler.connections) { MuleObexRequestHandler.connections--; if (logger.isDebugEnabled()) { logger.debug("Connection closed, total number of connections: " + MuleObexRequestHandler.connections); } } } } | 12,245 |
1 | private void initUserExtensions(SeleniumConfiguration seleniumConfiguration) throws IOException { StringBuilder contents = new StringBuilder(); StringOutputStream s = new StringOutputStream(); IOUtils.copy(SeleniumConfiguration.class.getResourceAsStream("default-user-extensions.js"), s); contents.append(s.toString()); File providedUserExtensions = seleniumConfiguration.getFile(ConfigurationPropertyKeys.SELENIUM_USER_EXTENSIONS, seleniumConfiguration.getDirectoryConfiguration().getInput(), false); if (providedUserExtensions != null) { contents.append(FileUtils.readFileToString(providedUserExtensions, null)); } seleniumUserExtensions = new File(seleniumConfiguration.getDirectoryConfiguration().getInput(), "user-extensions.js"); FileUtils.forceMkdir(seleniumUserExtensions.getParentFile()); FileUtils.writeStringToFile(seleniumUserExtensions, contents.toString(), null); } | public void run() { saveWLHome(); for (final TabControl control : tabControls) { control.performOk(WLPropertyPage.this.getProject(), WLPropertyPage.this); } if (isEnabledJCLCopy()) { final File url = new File(WLPropertyPage.this.domainDirectory.getText()); File lib = new File(url, "lib"); File log4jLibrary = new File(lib, "log4j-1.2.13.jar"); if (!log4jLibrary.exists()) { InputStream srcFile = null; FileOutputStream fos = null; try { srcFile = toInputStream(new Path("jcl/log4j-1.2.13.jar")); fos = new FileOutputStream(log4jLibrary); IOUtils.copy(srcFile, fos); srcFile.close(); fos.flush(); fos.close(); srcFile = toInputStream(new Path("/jcl/commons-logging-1.0.4.jar")); File jcl = new File(lib, "commons-logging-1.0.4.jar"); fos = new FileOutputStream(jcl); IOUtils.copy(srcFile, fos); } catch (IOException e) { Logger.log(Logger.ERROR, "Could not copy JCL jars file to Bea WL", e); } finally { try { if (srcFile != null) { srcFile.close(); srcFile = null; } if (fos != null) { fos.flush(); fos.close(); fos = null; } } catch (IOException e) { } } } } if (isEnabledJSTLCopy()) { File url = new File(WLPropertyPage.this.domainDirectory.getText()); File lib = new File(url, "lib"); File jstlLibrary = new File(lib, "jstl.jar"); if (!jstlLibrary.exists()) { InputStream srcFile = null; FileOutputStream fos = null; try { srcFile = toInputStream(new Path("jstl/jstl.jar")); fos = new FileOutputStream(jstlLibrary); IOUtils.copy(srcFile, fos); } catch (IOException e) { Logger.log(Logger.ERROR, "Could not copy the JSTL 1.1 jar file to Bea WL", e); } finally { try { if (srcFile != null) { srcFile.close(); srcFile = null; } if (fos != null) { fos.flush(); fos.close(); fos = null; } } catch (final IOException e) { Logger.getLog().debug("I/O exception closing resources", e); } } } } } | 12,246 |
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; } | PackageFileImpl(PackageDirectoryImpl dir, String name, InputStream data) throws IOException { this.dir = dir; this.name = name; this.updates = dir.getUpdates(); ByteArrayOutputStream stream = new ByteArrayOutputStream(); IOUtils.copy(data, stream); updates.setNewData(getFullName(), stream.toByteArray()); stream.close(); } | 12,247 |
0 | public ODFSignatureService(TimeStampServiceValidator timeStampServiceValidator, RevocationDataService revocationDataService, SignatureFacet signatureFacet, InputStream documentInputStream, OutputStream documentOutputStream, TimeStampService timeStampService, String role, IdentityDTO identity, byte[] photo, DigestAlgo digestAlgo) throws Exception { super(digestAlgo); this.temporaryDataStorage = new HttpSessionTemporaryDataStorage(); this.documentOutputStream = documentOutputStream; this.tmpFile = File.createTempFile("eid-dss-", ".odf"); FileOutputStream fileOutputStream; fileOutputStream = new FileOutputStream(this.tmpFile); IOUtils.copy(documentInputStream, fileOutputStream); addSignatureFacet(new XAdESXLSignatureFacet(timeStampService, revocationDataService, getSignatureDigestAlgorithm())); addSignatureFacet(signatureFacet); XAdESSignatureFacet xadesSignatureFacet = super.getXAdESSignatureFacet(); xadesSignatureFacet.setRole(role); if (null != identity) { IdentitySignatureFacet identitySignatureFacet = new IdentitySignatureFacet(identity, photo, getSignatureDigestAlgorithm()); addSignatureFacet(identitySignatureFacet); } } | private void work(String[] args) throws Exception { String dictLocation = CONTENT_URL; String cpeContentDirName = CONTENT_DIR; String fn = dictLocation.substring(dictLocation.lastIndexOf("/") + 1); File destFile = new File(cpeContentDirName + File.separator + fn); URL url = new URL(dictLocation); URLConnection conn = url.openConnection(); conn.connect(); long lmodifiedRemote = conn.getLastModified(); boolean needToDownload = false; if (destFile.exists()) { System.out.println(destFile.getAbsolutePath() + " exists, check modification time"); long lmodifiedLocal = destFile.lastModified(); if (lmodifiedRemote > lmodifiedLocal) { System.out.println("Server file is newer, need to download"); needToDownload = true; } else { System.out.println("Local version is newer, no need to download"); } } else { System.out.println("Local version doesn't exist, need to download"); needToDownload = true; } if (needToDownload) { InputStream is = conn.getInputStream(); FileOutputStream fos = new FileOutputStream(destFile); byte[] buff = new byte[8192]; int read = 0; while ((read = is.read(buff)) > 0) { fos.write(buff, 0, read); } fos.flush(); fos.close(); is.close(); } } | 12,248 |
0 | private void listAndInstantiateServiceProviders() { final Enumeration<URL> resources = ClassLoaderHelper.getResources(SERVICES_FILE, ServiceManager.class); String name; try { while (resources.hasMoreElements()) { URL url = resources.nextElement(); InputStream stream = url.openStream(); try { BufferedReader reader = new BufferedReader(new InputStreamReader(stream), 100); name = reader.readLine(); while (name != null) { name = name.trim(); if (!name.startsWith("#")) { final ServiceProvider<?> serviceProvider = ClassLoaderHelper.instanceFromName(ServiceProvider.class, name, ServiceManager.class, "service provider"); @SuppressWarnings("unchecked") final Class<ServiceProvider<?>> serviceProviderClass = (Class<ServiceProvider<?>>) serviceProvider.getClass(); managedProviders.put(serviceProviderClass, new ServiceProviderWrapper(serviceProvider)); } name = reader.readLine(); } } finally { stream.close(); } } } catch (IOException e) { throw new SearchException("Unable to read " + SERVICES_FILE, e); } } | public static Element retrieveFromCache(String cacheName, Object key) { URL url = null; HttpURLConnection connection = null; InputStream is = null; OutputStream os = null; int result = 0; StringBuilder sb = null; Element cacheElement = null; try { url = new URL(EHCACHE_SERVER_BASE + "/" + cacheName + "/" + key); connection = (HttpURLConnection) url.openConnection(); connection.setRequestMethod("GET"); connection.connect(); is = connection.getInputStream(); byte[] response = new byte[4096]; result = is.read(response); while (result != -1) { sb.append(response); result = is.read(response); } if (is != null) { try { is.close(); } catch (Exception ignore) { } } if (connection != null) { connection.disconnect(); } cacheElement = new Element(key, sb.toString()); } catch (Exception e) { e.printStackTrace(); } finally { if (os != null) { try { os.close(); } catch (Exception ignore) { } } if (is != null) { try { is.close(); } catch (Exception ignore) { } } if (connection != null) { connection.disconnect(); } } return cacheElement; } | 12,249 |
0 | public static String getSHA1Digest(String inputStr) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md = null; byte[] sha1hash = null; md = MessageDigest.getInstance("SHA"); sha1hash = new byte[40]; md.update(inputStr.getBytes("iso-8859-1"), 0, inputStr.length()); sha1hash = md.digest(); return convertToHex(sha1hash); } | public static File[] splitFile(FileValidator validator, File source, long target_length, File todir, String prefix) { if (target_length == 0) return null; if (todir == null) { todir = new File(System.getProperty("java.io.tmpdir")); } if (prefix == null || prefix.equals("")) { prefix = source.getName(); } Vector result = new Vector(); FileOutputStream fos = null; FileInputStream fis = null; try { fis = new FileInputStream(source); byte[] bytes = new byte[CACHE_SIZE]; long current_target_size = 0; int current_target_nb = 1; int nbread = -1; try { File f = new File(todir, prefix + i18n.getString("targetname_suffix") + current_target_nb); if (!validator.verifyFile(f)) return null; result.add(f); fos = new FileOutputStream(f); while ((nbread = fis.read(bytes)) > -1) { if ((current_target_size + nbread) > target_length) { int limit = (int) (target_length - current_target_size); fos.write(bytes, 0, limit); fos.close(); current_target_nb++; current_target_size = 0; f = new File(todir, prefix + "_" + current_target_nb); if (!validator.verifyFile(f)) return null; result.add(f); fos = new FileOutputStream(f); fos.write(bytes, limit, nbread - limit); current_target_size += nbread - limit; } else { fos.write(bytes, 0, nbread); current_target_size += nbread; } } } catch (IOException ioe) { JOptionPane.showMessageDialog(null, ioe, i18n.getString("Failure"), JOptionPane.ERROR_MESSAGE); } finally { try { if (fos != null) fos.close(); } catch (IOException e) { } try { if (fis != null) fis.close(); } catch (IOException e) { } } } catch (Exception e) { JOptionPane.showMessageDialog(null, e, i18n.getString("Failure"), JOptionPane.ERROR_MESSAGE); } finally { try { if (fos != null) fos.close(); } catch (IOException e) { } } File[] fresult = null; if (result.size() > 0) { fresult = new File[result.size()]; fresult = (File[]) result.toArray(fresult); } return fresult; } | 12,250 |
0 | public static byte[] generateAuthId(String userName, String password) { byte[] ret = new byte[16]; try { MessageDigest messageDigest = MessageDigest.getInstance("MD5"); String str = userName + password; messageDigest.update(str.getBytes()); ret = messageDigest.digest(); } catch (NoSuchAlgorithmException ex) { ex.printStackTrace(); } return ret; } | public void testJDBCSavepoints() throws Exception { String sql; String msg; int i; PreparedStatement ps; ResultSet rs; Savepoint sp1; Savepoint sp2; Savepoint sp3; Savepoint sp4; Savepoint sp5; Savepoint sp6; Savepoint sp7; int rowcount = 0; sql = "drop table t if exists"; stmt.executeUpdate(sql); sql = "create table t(id int, fn varchar, ln varchar, zip int)"; stmt.executeUpdate(sql); conn1.setAutoCommit(true); conn1.setAutoCommit(false); sql = "insert into t values(?,?,?,?)"; ps = conn1.prepareStatement(sql); ps.setString(2, "Mary"); ps.setString(3, "Peterson-Clancy"); i = 0; for (; i < 10; i++) { ps.setInt(1, i); ps.setInt(4, i); ps.executeUpdate(); } sp1 = conn1.setSavepoint("savepoint1"); for (; i < 20; i++) { ps.setInt(1, i); ps.setInt(4, i); ps.executeUpdate(); } sp2 = conn1.setSavepoint("savepoint2"); for (; i < 30; i++) { ps.setInt(1, i); ps.setInt(4, i); ps.executeUpdate(); } sp3 = conn1.setSavepoint("savepoint3"); for (; i < 40; i++) { ps.setInt(1, i); ps.setInt(4, i); ps.executeUpdate(); } sp4 = conn1.setSavepoint("savepoint4"); for (; i < 50; i++) { ps.setInt(1, i); ps.setInt(4, i); ps.executeUpdate(); } sp5 = conn1.setSavepoint("savepoint5"); sp6 = conn1.setSavepoint("savepoint6"); sp7 = conn1.setSavepoint("savepoint7"); rs = stmt.executeQuery("select count(*) from t"); rs.next(); rowcount = rs.getInt(1); rs.close(); msg = "select count(*) from t value"; try { assertEquals(msg, 50, rowcount); } catch (Exception e) { } conn2.setAutoCommit(false); conn2.setSavepoint("savepoint1"); conn2.setSavepoint("savepoint2"); msg = "savepoint released succesfully on non-originating connection"; try { conn2.releaseSavepoint(sp2); assertTrue(msg, false); } catch (Exception e) { } try { conn2.rollback(sp1); msg = "succesful rollback to savepoint on " + "non-originating connection"; assertTrue(msg, false); } catch (Exception e) { } msg = "direct execution of <release savepoint> statement failed to " + "release JDBC-created SQL-savepoint with identical savepoint name"; try { conn2.createStatement().executeUpdate("release savepoint \"savepoint2\""); } catch (Exception e) { try { assertTrue(msg, false); } catch (Exception e2) { } } msg = "direct execution of <rollback to savepoint> statement failed to " + "roll back to existing JDBC-created SQL-savepoint with identical " + "savepoint name"; try { conn2.createStatement().executeUpdate("rollback to savepoint \"savepoint1\""); } catch (Exception e) { e.printStackTrace(); try { assertTrue(msg, false); } catch (Exception e2) { } } conn1.releaseSavepoint(sp6); msg = "savepoint released succesfully > 1 times"; try { conn1.releaseSavepoint(sp6); assertTrue(msg, false); } catch (Exception e) { } msg = "savepoint released successfully after preceding savepoint released"; try { conn1.releaseSavepoint(sp7); assertTrue(msg, false); } catch (Exception e) { } msg = "preceding same-point savepoint destroyed by following savepoint release"; try { conn1.releaseSavepoint(sp5); } catch (Exception e) { try { assertTrue(msg, false); } catch (Exception e2) { } } conn1.rollback(sp4); rs = stmt.executeQuery("select count(*) from t"); rs.next(); rowcount = rs.getInt(1); rs.close(); msg = "select * rowcount after 50 inserts - 10 rolled back:"; try { assertEquals(msg, 40, rowcount); } catch (Exception e) { } msg = "savepoint rolled back succesfully > 1 times"; try { conn1.rollback(sp4); assertTrue(msg, false); } catch (Exception e) { } conn1.rollback(sp3); rs = stmt.executeQuery("select count(*) from t"); rs.next(); rowcount = rs.getInt(1); rs.close(); msg = "select count(*) after 50 inserts - 20 rolled back:"; try { assertEquals(msg, 30, rowcount); } catch (Exception e) { } msg = "savepoint released succesfully after use in rollback"; try { conn1.releaseSavepoint(sp3); assertTrue(msg, false); } catch (Exception e) { } conn1.rollback(sp1); msg = "savepoint rolled back without raising an exception after " + "rollback to a preceeding savepoint"; try { conn1.rollback(sp2); assertTrue(msg, false); } catch (Exception e) { } conn1.rollback(); msg = "savepoint released succesfully when it should have been " + "destroyed by a full rollback"; try { conn1.releaseSavepoint(sp1); assertTrue(msg, false); } catch (Exception e) { } conn1.setAutoCommit(false); sp1 = conn1.setSavepoint("savepoint1"); conn1.rollback(); conn1.setAutoCommit(false); conn1.createStatement().executeUpdate("savepoint \"savepoint1\""); conn1.setAutoCommit(false); sp1 = conn1.setSavepoint("savepoint1"); conn1.createStatement().executeUpdate("savepoint \"savepoint1\""); conn1.setAutoCommit(false); sp1 = conn1.setSavepoint("savepoint1"); conn1.createStatement().executeUpdate("savepoint \"savepoint1\""); } | 12,251 |
1 | public static void main(String[] args) throws IOException { File fileIn = new File("D:\\zz_c\\study2\\src\\study\\io\\A.java"); InputStream fin = new FileInputStream(fileIn); PipedInputStream pin = new PipedInputStream(); PipedOutputStream pout = new PipedOutputStream(); pout.connect(pin); IoRead i = new IoRead(); i.setIn(pin); File fileOU1 = new File("D:\\zz_c\\study2\\src\\study\\io\\A1.java"); File fileOU2 = new File("D:\\zz_c\\study2\\src\\study\\io\\A2.java"); File fileOU3 = new File("D:\\zz_c\\study2\\src\\study\\io\\A3.java"); i.addOut(new BufferedOutputStream(new FileOutputStream(fileOU1))); i.addOut(new BufferedOutputStream(new FileOutputStream(fileOU2))); i.addOut(new BufferedOutputStream(new FileOutputStream(fileOU3))); PipedInputStream pin2 = new PipedInputStream(); PipedOutputStream pout2 = new PipedOutputStream(); i.addOut(pout2); pout2.connect(pin2); i.start(); int read; try { read = fin.read(); while (read != -1) { pout.write(read); read = fin.read(); } fin.close(); pout.close(); } catch (IOException e) { e.printStackTrace(); } int c = pin2.read(); while (c != -1) { System.out.print((char) c); c = pin2.read(); } pin2.close(); } | public ModelAndView handleRequest(HttpServletRequest request, HttpServletResponse response) throws Exception { HttpClientInfo clientInfo = HttpUtil.parseClientInfo((HttpServletRequest) request); if (request.getParameter("_debug_") != null) { StringBuffer buffer = new StringBuffer(); Enumeration iter = request.getHeaderNames(); while (iter.hasMoreElements()) { String name = (String) iter.nextElement(); buffer.append(name + "=" + request.getHeader(name)).append("\n"); } buffer.append("\n"); iter = request.getParameterNames(); while (iter.hasMoreElements()) { String name = (String) iter.nextElement(); String value = request.getParameter(name); if (!"ISO-8859-1".equalsIgnoreCase(clientInfo.getPreferCharset())) value = new String(value.getBytes("ISO-8859-1"), clientInfo.getPreferCharset()); buffer.append(name).append("=").append(value).append("\n"); } response.setContentType("text/plain; charset=UTF-8"); response.setCharacterEncoding("UTF-8"); response.getWriter().write(buffer.toString()); return null; } Object resultObj = handleRequest(request); if (resultObj == null) { String requestException = (String) request.getAttribute("XSMP.handleRequest.Exception"); if (requestException != null) response.sendError(500, requestException); else response.setContentLength(0); } else { if (resultObj instanceof DataHandler) { response.setContentType(((DataHandler) resultObj).getContentType()); response.setContentLength(((DataHandler) resultObj).getInputStream().available()); IOUtils.copy(((DataHandler) resultObj).getInputStream(), response.getOutputStream()); } else { String temp = resultObj.toString(); if (temp.startsWith("<") && temp.endsWith(">")) response.setContentType("text/html; charset=" + clientInfo.getPreferCharset()); else response.setContentType("text/plain; charset=" + clientInfo.getPreferCharset()); byte[] buffer = temp.getBytes(clientInfo.getPreferCharset()); response.setContentLength(buffer.length); response.getOutputStream().write(buffer); } } return null; } | 12,252 |
0 | public static String validateSession(String sessionid, String servicekey, HttpServletRequest request) { if (sessionid == null) { return "error"; } String loginapp = SSOFilter.getLoginapp(); String u = SSOUtil.addParameter(loginapp + "/api/validatesessionid", "sessionid", sessionid); u = SSOUtil.addParameter(u, "servicekey", servicekey); u = SSOUtil.addParameter(u, "ip", request.getRemoteHost()); u = SSOUtil.addParameter(u, "url", encodeUrl(request.getRequestURI())); u = SSOUtil.addParameter(u, "useragent", request.getHeader("User-Agent")); String response = "error"; try { URL url = new URL(u); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String line; while ((line = reader.readLine()) != null) { response = line.trim(); } reader.close(); } catch (MalformedURLException e) { } catch (IOException e) { } if ("error".equals(response)) { return "error"; } else { return response; } } | public static void copyFile(File file, String pathExport) throws IOException { File out = new File(pathExport); FileChannel sourceChannel = new FileInputStream(file).getChannel(); FileChannel destinationChannel = new FileOutputStream(out).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), destinationChannel); sourceChannel.close(); destinationChannel.close(); } | 12,253 |
0 | void bsort(int a[], int lo, int hi) throws Exception { for (int j = hi; j > lo; j--) { for (int i = lo; i < j; i++) { if (a[i] > a[i + 1]) { int T = a[i]; a[i] = a[i + 1]; a[i + 1] = T; pause(); } } } } | public static void doVersionCheck(View view) { view.showWaitCursor(); try { URL url = new URL(jEdit.getProperty("version-check.url")); InputStream in = url.openStream(); BufferedReader bin = new BufferedReader(new InputStreamReader(in)); String line; String version = null; String build = null; while ((line = bin.readLine()) != null) { if (line.startsWith(".version")) version = line.substring(8).trim(); else if (line.startsWith(".build")) build = line.substring(6).trim(); } bin.close(); if (version != null && build != null) { if (jEdit.getBuild().compareTo(build) < 0) newVersionAvailable(view, version, url); else { GUIUtilities.message(view, "version-check" + ".up-to-date", new String[0]); } } } catch (IOException e) { String[] args = { jEdit.getProperty("version-check.url"), e.toString() }; GUIUtilities.error(view, "read-error", args); } view.hideWaitCursor(); } | 12,254 |
1 | public void copyAffix(MailAffix affix, long mailId1, long mailId2) throws Exception { File file = new File(this.getResDir(mailId1) + affix.getAttachAlias()); if (file.exists()) { File file2 = new File(this.getResDir(mailId2) + affix.getAttachAlias()); if (!file2.exists()) { file2.createNewFile(); BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(file2)); BufferedInputStream in = new BufferedInputStream(new FileInputStream(file)); int read; while ((read = in.read()) != -1) { out.write(read); } out.flush(); in.close(); out.close(); } } else { log.debug(file.getAbsolutePath() + file.getName() + "�����ڣ������ļ�ʧ�ܣ���������"); } } | public static void copyFile(final File source, final File dest) throws IOException { FileChannel in = null, out = null; try { in = new FileInputStream(source).getChannel(); out = new FileOutputStream(dest).getChannel(); long size = in.size(); MappedByteBuffer buf = in.map(FileChannel.MapMode.READ_ONLY, 0, size); out.write(buf); } finally { if (in != null) { in.close(); } if (out != null) { out.close(); } } } | 12,255 |
0 | public static void copyResourceToFile(Class owningClass, String resourceName, File destinationDir) { final byte[] resourceBytes = readResource(owningClass, resourceName); final ByteArrayInputStream inputStream = new ByteArrayInputStream(resourceBytes); final File destinationFile = new File(destinationDir, resourceName); final FileOutputStream fileOutputStream; try { fileOutputStream = new FileOutputStream(destinationFile); } catch (FileNotFoundException e) { throw new RuntimeException(e); } try { IOUtils.copy(inputStream, fileOutputStream); } catch (IOException e) { throw new RuntimeException(e); } } | public void run() { logger.info("downloading '" + url.toString() + "' to: " + dstFile.getAbsolutePath()); Preferences prefs = Preferences.userRoot().node("gvsig.downloader"); int timeout = prefs.getInt("timeout", 60000); DataOutputStream dos; try { DataInputStream is; OutputStreamWriter os = null; HttpURLConnection connection = null; if (url.getProtocol().equals("https")) { disableHttsValidation(); } connection = (HttpURLConnection) url.openConnection(); connection.setConnectTimeout(timeout); if (data != null) { connection.setRequestProperty("SOAPAction", "post"); connection.setRequestMethod("POST"); connection.setDoOutput(true); connection.setRequestProperty("Content-Type", "text/xml; charset=UTF-8"); os = new OutputStreamWriter(connection.getOutputStream()); os.write(data); os.flush(); is = new DataInputStream(connection.getInputStream()); } else { is = new DataInputStream(url.openStream()); } dos = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(dstFile))); byte[] buffer = new byte[1024 * 4]; long readed = 0; for (int i = is.read(buffer); !Utilities.getCanceled(groupID) && i > 0; i = is.read(buffer)) { dos.write(buffer, 0, i); readed += i; } if (os != null) { os.close(); } dos.close(); is.close(); is = null; dos = null; if (Utilities.getCanceled(groupID)) { logger.warning("[RemoteServices] '" + url + "' CANCELED."); dstFile.delete(); dstFile = null; } else { Utilities.addDownloadedURL(url, dstFile.getAbsolutePath()); } } catch (Exception e) { e.printStackTrace(); Utilities.downloadException = e; } } | 12,256 |
1 | public void testCommitRollback() throws Exception { Statement stmt = con.createStatement(); assertNotNull(stmt); assertTrue(con.getAutoCommit()); stmt.execute("CREATE TABLE #TESTCOMMIT (id int primary key)"); con.setAutoCommit(false); assertFalse(con.getAutoCommit()); assertEquals(1, stmt.executeUpdate("INSERT INTO #TESTCOMMIT VALUES (1)")); con.commit(); assertEquals(1, stmt.executeUpdate("INSERT INTO #TESTCOMMIT VALUES (2)")); assertEquals(1, stmt.executeUpdate("INSERT INTO #TESTCOMMIT VALUES (3)")); con.rollback(); assertEquals(1, stmt.executeUpdate("INSERT INTO #TESTCOMMIT VALUES (4)")); con.setAutoCommit(true); ResultSet rs = stmt.executeQuery("SELECT COUNT(*) FROM #TESTCOMMIT"); rs.next(); assertEquals("commit", 2, rs.getInt(1)); stmt.close(); } | public SysSequences getSeqs(String tableName) throws SQLException { SysSequences seq = new SysSequences(); if (tableName == null || tableName.trim().equals("")) return null; Connection conn = null; try { conn = ConnectUtil.getConnect(); conn.setAutoCommit(false); PreparedStatement ps = conn.prepareStatement("update ss_sys_sequences set next_value=next_value+step_value where table_name='" + tableName + "'"); ps.executeUpdate(); ps.close(); ps = conn.prepareStatement("select * from ss_sys_sequences where table_name='" + tableName + "'"); ResultSet rs = ps.executeQuery(); while (rs.next()) { long nextValue = rs.getLong(2); long stepValue = rs.getLong(3); seq.setTableName(tableName); seq.setNextValue(nextValue - stepValue + 1); seq.setStepValue(stepValue); } rs.close(); ps.close(); if (seq.getTableName() == null) { ps = conn.prepareStatement("insert into ss_sys_sequences values('" + tableName + "'," + (Constants.DEFAULT_CURR_VALUE + Constants.DEFAULT_STEP_VALUE) + "," + Constants.DEFAULT_STEP_VALUE + ")"); ps.executeUpdate(); ps.close(); seq.setTableName(tableName); seq.setNextValue(Constants.DEFAULT_CURR_VALUE + 1); seq.setStepValue(Constants.DEFAULT_STEP_VALUE); } conn.commit(); } catch (Exception e) { conn.rollback(); e.printStackTrace(); } finally { try { conn.setAutoCommit(true); } catch (Exception e) { } ConnectUtil.closeConn(conn); } return seq; } | 12,257 |
0 | public void get(final String remoteFilePath, final String remoteFileName, final String localName) { final FTPClient ftp = new FTPClient(); final FTPMessageCollector listener = new FTPMessageCollector(); try { final String localDirName = localName.substring(0, localName.lastIndexOf(File.separator)); System.out.println("ftp:"); System.out.println(" remoteDir " + remoteFilePath); System.out.println(" localDir " + localDirName); final File localDir = new File(localDirName); if (!localDir.exists()) { System.out.println(" create Dir " + localDirName); localDir.mkdir(); } ftp.setTimeout(10000); ftp.setRemoteHost(host); ftp.setMessageListener(listener); } catch (final UnknownHostException e) { showConnectError(); return; } catch (final Exception e) { e.printStackTrace(); } final TileInfoManager tileInfoMgr = TileInfoManager.getInstance(); final Job downloadJob = new Job(Messages.job_name_ftpDownload) { @Override protected IStatus run(final IProgressMonitor monitor) { try { showTileInfo(remoteFileName, -1); System.out.println(" connect " + host); ftp.connect(); showTileInfo(remoteFileName, -2); System.out.println(" login " + user + " " + password); ftp.login(user, password); System.out.println(" set passive mode"); ftp.setConnectMode(FTPConnectMode.PASV); System.out.println(" set type binary"); ftp.setType(FTPTransferType.BINARY); showTileInfo(remoteFileName, -3); System.out.println(" chdir " + remoteFilePath); ftp.chdir(remoteFilePath); ftp.setProgressMonitor(new FTPProgressMonitor() { public void bytesTransferred(final long count) { tileInfoMgr.updateSRTMTileInfo(TileEventId.SRTM_DATA_LOADING_MONITOR, remoteFileName, count); } }); showTileInfo(remoteFileName, -4); System.out.println(" get " + remoteFileName + " -> " + localName + " ..."); ftp.get(localName, remoteFileName); System.out.println(" quit"); ftp.quit(); } catch (final UnknownHostException e) { return new Status(IStatus.ERROR, TourbookPlugin.PLUGIN_ID, IStatus.ERROR, NLS.bind(Messages.error_message_cannotConnectToServer, host), e); } catch (final SocketTimeoutException e) { return new Status(IStatus.ERROR, TourbookPlugin.PLUGIN_ID, IStatus.ERROR, NLS.bind(Messages.error_message_timeoutWhenConnectingToServer, host), e); } catch (final Exception e) { e.printStackTrace(); tileInfoMgr.updateSRTMTileInfo(TileEventId.SRTM_DATA_ERROR_LOADING, remoteFileName, 0); } finally { tileInfoMgr.updateSRTMTileInfo(TileEventId.SRTM_DATA_END_LOADING, remoteFileName, 0); } return Status.OK_STATUS; } }; downloadJob.schedule(); try { downloadJob.join(); } catch (final InterruptedException e) { e.printStackTrace(); } } | public static boolean decodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.DECODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | 12,258 |
0 | public static void copy(String fromFileName, String toFileName) throws IOException { File fromFile = new File(fromFileName); File toFile = new File(toFileName); if (!fromFile.exists()) throw new IOException("FileCopy: " + "no such source file: " + fromFileName); if (!fromFile.isFile()) throw new IOException("FileCopy: " + "can't copy directory: " + fromFileName); if (!fromFile.canRead()) throw new IOException("FileCopy: " + "source file is unreadable: " + fromFileName); if (toFile.isDirectory()) toFile = new File(toFile, fromFile.getName()); if (toFile.exists()) { if (!toFile.canWrite()) throw new IOException("FileCopy: " + "destination file is unwriteable: " + toFileName); System.out.print("Overwrite existing file " + toFile.getName() + "? (Y/N): "); System.out.flush(); BufferedReader in = new BufferedReader(new InputStreamReader(System.in)); String response = in.readLine(); if (!response.equals("Y") && !response.equals("y")) throw new IOException("FileCopy: " + "existing file was not overwritten."); } else { String parent = toFile.getParent(); if (parent == null) parent = System.getProperty("user.dir"); File dir = new File(parent); if (!dir.exists()) throw new IOException("FileCopy: " + "destination directory doesn't exist: " + parent); if (dir.isFile()) throw new IOException("FileCopy: " + "destination is not a directory: " + parent); if (!dir.canWrite()) throw new IOException("FileCopy: " + "destination directory is unwriteable: " + parent); } FileInputStream from = null; FileOutputStream to = null; try { from = new FileInputStream(fromFile); to = new FileOutputStream(toFile); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = from.read(buffer)) != -1) to.write(buffer, 0, bytesRead); } finally { if (from != null) try { from.close(); } catch (IOException e) { ; } if (to != null) try { to.close(); } catch (IOException e) { ; } } } | public static String hashPassword(String password) { String hashStr = null; try { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.update(password.getBytes(Charset.defaultCharset())); BigInteger hash = new BigInteger(1, md5.digest()); hashStr = hash.toString(16); } catch (NoSuchAlgorithmException e) { return password; } StringBuilder buffer = new StringBuilder(hashStr); while (buffer.length() < 32) { buffer.insert(0, '0'); } return buffer.toString(); } | 12,259 |
1 | public static String md5Encode16(String s) { try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(s.getBytes("utf-8")); byte b[] = md.digest(); int i; StringBuilder buf = new StringBuilder(""); for (int offset = 0; offset < b.length; offset++) { i = b[offset]; if (i < 0) i += 256; if (i < 16) buf.append("0"); buf.append(Integer.toHexString(i)); } return buf.toString().substring(8, 24); } catch (NoSuchAlgorithmException e) { throw new IllegalArgumentException(e); } catch (UnsupportedEncodingException e) { throw new IllegalArgumentException(e); } } | public String encodePassword(String rawPass, Object salt) { MessageDigest sha; try { sha = MessageDigest.getInstance("SHA"); } catch (java.security.NoSuchAlgorithmException e) { throw new LdapDataAccessException("No SHA implementation available!"); } sha.update(rawPass.getBytes()); if (salt != null) { Assert.isInstanceOf(byte[].class, salt, "Salt value must be a byte array"); sha.update((byte[]) salt); } byte[] hash = combineHashAndSalt(sha.digest(), (byte[]) salt); return (salt == null ? SHA_PREFIX : SSHA_PREFIX) + new String(Base64.encodeBase64(hash)); } | 12,260 |
1 | public static void copyFiles(String strPath, String dstPath) throws IOException { File src = new File(strPath); File dest = new File(dstPath); if (src.isDirectory()) { dest.mkdirs(); String list[] = src.list(); for (int i = 0; i < list.length; i++) { if (list[i].lastIndexOf(SVN) != -1) { if (!SVN.equalsIgnoreCase(list[i].substring(list[i].length() - 4, list[i].length()))) { String dest1 = dest.getAbsolutePath() + "\\" + list[i]; String src1 = src.getAbsolutePath() + "\\" + list[i]; copyFiles(src1, dest1); } } else { String dest1 = dest.getAbsolutePath() + "\\" + list[i]; String src1 = src.getAbsolutePath() + "\\" + list[i]; copyFiles(src1, dest1); } } } else { FileInputStream fin = new FileInputStream(src); FileOutputStream fout = new FileOutputStream(dest); int c; while ((c = fin.read()) >= 0) fout.write(c); fin.close(); fout.close(); } } | public static void copyFile(File source, File dest) throws IOException { FileChannel in = null, out = null; try { in = new FileInputStream(source).getChannel(); out = new FileOutputStream(dest).getChannel(); in.transferTo(0, in.size(), out); } catch (Exception e) { log.error(e, e); } finally { if (in != null) in.close(); if (out != null) out.close(); } } | 12,261 |
0 | protected final void connectFtp() throws IOException { try { if (!this.ftpClient.isConnected()) { this.ftpClient.connect(getHost(), getPort()); getLog().write(Level.INFO, String.format(getMessages().getString("FtpSuccessfullyConnected"), getHost())); int reply = this.ftpClient.getReplyCode(); if (!FTPReply.isPositiveCompletion(reply)) { this.ftpClient.disconnect(); throw new IOException(String.format(getMessages().getString("FtpErrorConnectingRefused"), getHost())); } if (getUsername() != null) { if (!this.ftpClient.login(getUsername(), getPassword())) { this.ftpClient.logout(); disconnectFtp(); throw new IOException(String.format(getMessages().getString("FtpErrorAuthorizing"), getHost())); } } this.ftpClient.setFileType(FTP.BINARY_FILE_TYPE); this.ftpClient.enterLocalPassiveMode(); getLog().write(Level.INFO, String.format(getMessages().getString("FtpSuccessfullyAuthorized"), getHost())); } } catch (IOException ex) { disconnectFtp(); throw new IOException(String.format(getMessages().getString("FtpErrorConnecting"), getHost(), ex.toString())); } } | public static Chunk updateLastSend(Chunk c) throws Exception { DBConnectionManager dbm = null; Connection conn = null; PreparedStatement stmt = null; Chunk ret = null; String SQL = "UPDATE CHUNK SET SENT=? WHERE FILEHASH=? AND STARTOFF=? AND LENGTH=?"; log.debug("update chunk last sent for chunk " + c.getHash() + " startoff " + c.getStartOffset()); try { dbm = DBConnectionManager.getInstance(); conn = dbm.getConnection("satmule"); stmt = conn.prepareStatement(SQL); stmt.setDate(1, new java.sql.Date(c.getLastSend().getTime())); stmt.setString(2, c.getHash()); stmt.setLong(3, c.getStartOffset()); stmt.setLong(4, c.getSize()); stmt.executeUpdate(); conn.commit(); stmt.close(); dbm.freeConnection("satmule", conn); } catch (Exception e) { log.error("Error while updating chunk " + c.getHash() + "offset:" + c.getStartOffset() + "SQL error: " + SQL, e); Exception excep; if (dbm == null) excep = new Exception("Could not obtain pool object DbConnectionManager"); else if (conn == null) excep = new Exception("The Db connection pool could not obtain a database connection"); else { conn.rollback(); excep = new Exception("SQL Error : " + SQL + " error: " + e); dbm.freeConnection("satmule", conn); } throw excep; } return ret; } | 12,262 |
1 | private static File[] getWsdls(File dirfile) throws Exception { File[] allfiles = dirfile.listFiles(); List<File> files = new ArrayList<File>(); if (allfiles != null) { MessageDigest md = MessageDigest.getInstance("MD5"); String outputDir = argMap.get(OUTPUT_DIR); for (File file : allfiles) { if (file.getName().endsWith(WSDL_SUFFIX)) { files.add(file); } if (file.getName().endsWith(WSDL_SUFFIX) || file.getName().endsWith(XSD_SUFFIX)) { md.update(FileUtil.getBytes(file)); } } computedHash = md.digest(); hashFile = new File(outputDir + File.separator + argMap.get(BASE_PACKAGE).replace('.', File.separatorChar) + File.separator + "hash.md5"); if (hashFile.exists()) { byte[] readHash = FileUtil.getBytes(hashFile); if (Arrays.equals(readHash, computedHash)) { System.out.println("Skipping generation, files not changed."); files.clear(); } } } File[] filesarr = new File[files.size()]; files.toArray(filesarr); return filesarr; } | private static String md5Encode(String pass) { String string; try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(pass.getBytes()); byte[] result = md.digest(); string = bytes2hexStr(result); } catch (NoSuchAlgorithmException e) { throw new RuntimeException("La libreria java.security no implemente MD5"); } return string; } | 12,263 |
0 | public void testSetRequestProperty() throws Exception { MockHTTPServer httpServer = new MockHTTPServer("HTTP Server for User-Specified Request Property", 2); httpServer.start(); synchronized (bound) { if (!httpServer.started) { bound.wait(5000); } } HttpURLConnection urlConnection = (HttpURLConnection) new URL("http://localhost:" + httpServer.port()).openConnection(); assertEquals(0, urlConnection.getRequestProperties().size()); final String PROPERTY1 = "Accept"; final String PROPERTY2 = "Connection"; urlConnection.setRequestProperty(PROPERTY1, null); urlConnection.setRequestProperty(PROPERTY1, null); urlConnection.setRequestProperty(PROPERTY2, "keep-alive"); assertEquals(2, urlConnection.getRequestProperties().size()); assertNull(urlConnection.getRequestProperty(PROPERTY1)); assertEquals("keep-alive", urlConnection.getRequestProperty(PROPERTY2)); urlConnection.setRequestProperty(PROPERTY1, "/"); urlConnection.setRequestProperty(PROPERTY2, null); assertEquals("/", urlConnection.getRequestProperty(PROPERTY1)); assertNull(urlConnection.getRequestProperty(PROPERTY2)); } | 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!"); } | 12,264 |
1 | protected static void copyOrMove(File sourceLocation, File targetLocation, boolean move) throws IOException { String[] children; int i; InputStream in; OutputStream out; byte[] buf; int len; if (sourceLocation.isDirectory()) { if (!targetLocation.exists()) targetLocation.mkdir(); children = sourceLocation.list(); for (i = 0; i < children.length; i++) { copyOrMove(new File(sourceLocation, children[i]), new File(targetLocation, children[i]), move); } if (move) sourceLocation.delete(); } else { in = new FileInputStream(sourceLocation); if (targetLocation.isDirectory()) out = new FileOutputStream(targetLocation.getAbsolutePath() + File.separator + sourceLocation.getName()); else out = new FileOutputStream(targetLocation); buf = new byte[1024]; while ((len = in.read(buf)) > 0) out.write(buf, 0, len); in.close(); out.close(); if (move) sourceLocation.delete(); } } | private void sendData(HttpServletResponse response, MediaBean mediaBean) throws IOException { if (logger.isInfoEnabled()) logger.info("sendData[" + mediaBean + "]"); response.setContentLength(mediaBean.getContentLength()); response.setContentType(mediaBean.getContentType()); response.addHeader("Last-Modified", mediaBean.getLastMod()); response.addHeader("Cache-Control", "must-revalidate"); response.addHeader("content-disposition", "attachment, filename=" + (new Date()).getTime() + "_" + mediaBean.getFileName()); byte[] content = mediaBean.getContent(); InputStream is = null; OutputStream os = null; try { os = response.getOutputStream(); is = new ByteArrayInputStream(content); IOUtils.copy(is, os); } catch (IOException e) { logger.error(e, e); } finally { if (is != null) try { is.close(); } catch (IOException e) { } if (os != null) try { os.close(); } catch (IOException e) { } } } | 12,265 |
1 | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | public static void extract(final File destDir, final Collection<ZipEntryInfo> entryInfos) throws IOException { if (destDir == null || CollectionUtils.isEmpty(entryInfos)) throw new IllegalArgumentException("One or parameter is null or empty!"); if (!destDir.exists()) destDir.mkdirs(); for (ZipEntryInfo entryInfo : entryInfos) { ZipEntry entry = entryInfo.getZipEntry(); InputStream in = entryInfo.getInputStream(); File entryDest = new File(destDir, entry.getName()); entryDest.getParentFile().mkdirs(); if (!entry.isDirectory()) { OutputStream out = new FileOutputStream(new File(destDir, entry.getName())); try { IOUtils.copy(in, out); out.flush(); } finally { IOUtils.closeQuietly(in); IOUtils.closeQuietly(out); } } } } | 12,266 |
0 | public static String encrypt(String plaintext) throws NoSuchAlgorithmException { MessageDigest md; try { md = MessageDigest.getInstance("SHA"); } catch (NoSuchAlgorithmException e) { logger.error("unable to encrypt password" + e.getMessage()); throw new NoSuchAlgorithmException(e.getMessage()); } try { md.update(plaintext.getBytes("UTF-8")); } catch (UnsupportedEncodingException e) { logger.error("unable to encrypt password" + e.getMessage()); throw new NoSuchAlgorithmException(e.getMessage()); } byte raw[] = md.digest(); return (new BASE64Encoder()).encode(raw); } | public VersionInfo getVersionInfo(String url) { try { XmlContentHandler handler = new XmlContentHandler(); XMLReader myReader = XMLReaderFactory.createXMLReader(); myReader.setContentHandler(handler); myReader.parse(new InputSource(new URL(url).openStream())); return handler.getVersionInfo(); } catch (SAXException e) { if (debug) { println("SAXException was thrown!"); e.printStackTrace(); } } catch (MalformedURLException e) { if (debug) { println("MalformedURLException was thrown!"); e.printStackTrace(); } } catch (IOException e) { if (debug) { println("IOException was thrown!"); e.printStackTrace(); } } return null; } | 12,267 |
0 | public String getProxy(String userName, String password) throws Exception { URL url = new URL(httpURL); HttpURLConnection conn = (HttpURLConnection) url.openConnection(); conn.setDoOutput(true); conn.setRequestMethod("POST"); ObjectOutputStream outputToServlet = new ObjectOutputStream(conn.getOutputStream()); outputToServlet.writeObject(userName); outputToServlet.writeObject(password); outputToServlet.flush(); outputToServlet.close(); ObjectInputStream inputFromServlet = new ObjectInputStream(conn.getInputStream()); return inputFromServlet.readObject() + ""; } | private byte[] szyfrujKlucz(byte[] kluczSesyjny) { byte[] zaszyfrowanyKlucz = null; byte[] klucz = null; try { MessageDigest skrot = MessageDigest.getInstance("SHA-1"); skrot.update(haslo.getBytes()); byte[] skrotHasla = skrot.digest(); Object kluczDoKlucza = MARS_Algorithm.makeKey(skrotHasla); int resztaKlucza = this.dlugoscKlucza % ROZMIAR_BLOKU; if (resztaKlucza == 0) { klucz = kluczSesyjny; zaszyfrowanyKlucz = new byte[this.dlugoscKlucza]; } else { int liczbaBlokow = this.dlugoscKlucza / ROZMIAR_BLOKU + 1; int nowyRozmiar = liczbaBlokow * ROZMIAR_BLOKU; zaszyfrowanyKlucz = new byte[nowyRozmiar]; klucz = new byte[nowyRozmiar]; byte roznica = (byte) (ROZMIAR_BLOKU - resztaKlucza); System.arraycopy(kluczSesyjny, 0, klucz, 0, kluczSesyjny.length); for (int i = kluczSesyjny.length; i < nowyRozmiar; i++) klucz[i] = (byte) roznica; } byte[] szyfrogram = null; int liczbaBlokow = klucz.length / ROZMIAR_BLOKU; int offset = 0; for (offset = 0; offset < liczbaBlokow; offset++) { szyfrogram = MARS_Algorithm.blockEncrypt(klucz, offset * ROZMIAR_BLOKU, kluczDoKlucza); System.arraycopy(szyfrogram, 0, zaszyfrowanyKlucz, offset * ROZMIAR_BLOKU, szyfrogram.length); } } catch (InvalidKeyException ex) { Logger.getLogger(SzyfrowaniePliku.class.getName()).log(Level.SEVERE, null, ex); } catch (NoSuchAlgorithmException ex) { ex.printStackTrace(); } return zaszyfrowanyKlucz; } | 12,268 |
1 | public static String getMD5(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 SHA1(String text) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md; md = MessageDigest.getInstance("SHA-1"); byte[] sha1hash = new byte[40]; md.update(text.getBytes("iso-8859-1"), 0, text.length()); sha1hash = md.digest(); return convertToHex(sha1hash); } | 12,269 |
1 | public static String getMD5Str(String source) { String s = null; char hexDigits[] = { '0', '1', '2', '3', '4', '5', '6', '7', '8', '9', 'a', 'b', 'c', 'd', 'e', 'f' }; try { java.security.MessageDigest md = java.security.MessageDigest.getInstance("MD5"); md.update(source.getBytes()); byte tmp[] = md.digest(); char str[] = new char[16 * 2]; int k = 0; for (int i = 0; i < 16; i++) { byte byte0 = tmp[i]; str[k++] = hexDigits[byte0 >>> 4 & 0xf]; str[k++] = hexDigits[byte0 & 0xf]; } s = new String(str); } catch (Exception e) { e.printStackTrace(); } return s; } | 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) { } ; } | 12,270 |
1 | public static String backupFile(File source) { File backup = new File(source.getParent() + "/~" + source.getName()); try { BufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream(source))); BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(backup))); return FileUtil.backupFile(reader, writer, source.getAbsolutePath()); } catch (FileNotFoundException fe) { String msg = "Failed to find file for backup [" + source.getAbsolutePath() + "]."; _log.error(msg, fe); throw new InvalidImplementationException(msg, fe); } } | 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) { } } } } | 12,271 |
1 | public void SplitFile(File in, File out0, File out1, long pos) throws IOException { FileInputStream fis = new FileInputStream(in); FileOutputStream fos = new FileOutputStream(out0); FileChannel fic = fis.getChannel(); FileChannel foc = fos.getChannel(); foc.transferFrom(fic, 0, pos); foc.close(); fos = new FileOutputStream(out1); foc = fos.getChannel(); foc.transferFrom(fic, 0, fic.size() - pos); foc.close(); fic.close(); } | private void removeSessionId(InputStream inputStream, Output output) throws IOException { String jsessionid = RewriteUtils.getSessionId(target); boolean textContentType = ResourceUtils.isTextContentType(httpClientResponse.getHeader(HttpHeaders.CONTENT_TYPE), target.getDriver().getConfiguration().getParsableContentTypes()); if (jsessionid == null || !textContentType) { IOUtils.copy(inputStream, output.getOutputStream()); } else { String charset = httpClientResponse.getContentCharset(); if (charset == null) { charset = "ISO-8859-1"; } String content = IOUtils.toString(inputStream, charset); content = removeSessionId(jsessionid, content); if (output.getHeader(HttpHeaders.CONTENT_LENGTH) != null) { output.setHeader(HttpHeaders.CONTENT_LENGTH, Integer.toString(content.length())); } OutputStream outputStream = output.getOutputStream(); IOUtils.write(content, outputStream, charset); } inputStream.close(); } | 12,272 |
0 | public static Bitmap loadBitmap(String token, String id, final String type) { String imageUrl = XMLfunctions.URL; imageUrl = imageUrl.replace("{0}", token); imageUrl = imageUrl.replace("{1}", id); InputStream imageStream = null; try { HttpGet httpRequest = new HttpGet(new URL(imageUrl).toURI()); HttpResponse response = (HttpResponse) new DefaultHttpClient().execute(httpRequest); httpRequest = null; BufferedHttpEntity bufHttpEntity = new BufferedHttpEntity(response.getEntity()); response = null; imageStream = bufHttpEntity.getContent(); bufHttpEntity = null; if (imageStream != null) { final BitmapFactory.Options options = new BitmapFactory.Options(); if (type.equals("image")) { options.inSampleSize = 2; } return BitmapFactory.decodeStream(imageStream, null, options); } else { } } catch (IOException e) { } catch (URISyntaxException e) { } finally { if (imageStream != null) closeStream(imageStream); } return null; } | @Deprecated public static void getAndProcessContents(String videoPageURL, int bufsize, String charset, Closure<String> process) throws IOException { URL url = null; HttpURLConnection connection = null; InputStream is = null; InputStreamReader isr = null; BufferedReader br = null; try { url = new URL(videoPageURL); connection = (HttpURLConnection) url.openConnection(); is = connection.getInputStream(); isr = new InputStreamReader(is, charset); br = new BufferedReader(isr); for (String line = br.readLine(); line != null; line = br.readLine()) { process.exec(line); } } finally { Closeables.closeQuietly(br); Closeables.closeQuietly(isr); Closeables.closeQuietly(is); HttpUtils.disconnect(connection); } } | 12,273 |
1 | public static String getMD5(String s) throws NoSuchAlgorithmException { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.reset(); md5.update(s.getBytes()); byte[] result = md5.digest(); StringBuilder hexString = new StringBuilder(); for (int i = 0; i < result.length; i++) { hexString.append(String.format("%02x", 0xFF & result[i])); } return hexString.toString(); } | @Test public void testHandleMessageInvalidSignature() throws Exception { KeyPair keyPair = MiscTestUtils.generateKeyPair(); DateTime notBefore = new DateTime(); DateTime notAfter = notBefore.plusYears(1); X509Certificate certificate = MiscTestUtils.generateCertificate(keyPair.getPublic(), "CN=Test", notBefore, notAfter, null, keyPair.getPrivate(), true, 0, null, null); ServletConfig mockServletConfig = EasyMock.createMock(ServletConfig.class); Map<String, String> httpHeaders = new HashMap<String, String>(); HttpSession mockHttpSession = EasyMock.createMock(HttpSession.class); HttpServletRequest mockServletRequest = EasyMock.createMock(HttpServletRequest.class); EasyMock.expect(mockServletConfig.getInitParameter("AuditService")).andStubReturn(null); EasyMock.expect(mockServletConfig.getInitParameter("AuditServiceClass")).andStubReturn(AuditTestService.class.getName()); EasyMock.expect(mockServletConfig.getInitParameter("SignatureService")).andStubReturn(null); EasyMock.expect(mockServletConfig.getInitParameter("SignatureServiceClass")).andStubReturn(SignatureTestService.class.getName()); EasyMock.expect(mockServletRequest.getRemoteAddr()).andStubReturn("remote-address"); MessageDigest messageDigest = MessageDigest.getInstance("SHA1"); byte[] document = "hello world".getBytes(); byte[] digestValue = messageDigest.digest(document); EasyMock.expect(mockHttpSession.getAttribute(SignatureDataMessageHandler.DIGEST_VALUE_SESSION_ATTRIBUTE)).andStubReturn(digestValue); EasyMock.expect(mockHttpSession.getAttribute(SignatureDataMessageHandler.DIGEST_ALGO_SESSION_ATTRIBUTE)).andStubReturn("SHA-1"); SignatureDataMessage message = new SignatureDataMessage(); message.certificateChain = new LinkedList<X509Certificate>(); message.certificateChain.add(certificate); Signature signature = Signature.getInstance("SHA1withRSA"); signature.initSign(keyPair.getPrivate()); signature.update("foobar-document".getBytes()); byte[] signatureValue = signature.sign(); message.signatureValue = signatureValue; EasyMock.replay(mockServletConfig, mockHttpSession, mockServletRequest); AppletServiceServlet.injectInitParams(mockServletConfig, this.testedInstance); this.testedInstance.init(mockServletConfig); try { this.testedInstance.handleMessage(message, httpHeaders, mockServletRequest, mockHttpSession); fail(); } catch (ServletException e) { LOG.debug("expected exception: " + e.getMessage()); EasyMock.verify(mockServletConfig, mockHttpSession, mockServletRequest); assertNull(SignatureTestService.getSignatureValue()); assertEquals("remote-address", AuditTestService.getAuditSignatureRemoteAddress()); assertEquals(certificate, AuditTestService.getAuditSignatureClientCertificate()); } } | 12,274 |
0 | private String clientLogin(AuthInfo authInfo) throws AuthoricationRequiredException { logger.fine("clientLogin."); try { String url = "https://www.google.com/accounts/ClientLogin"; HttpPost httpPost = new HttpPost(url); ArrayList<NameValuePair> params = new ArrayList<NameValuePair>(); params.add(new BasicNameValuePair("accountType", "HOSTED_OR_GOOGLE")); params.add(new BasicNameValuePair("Email", authInfo.getEmail())); params.add(new BasicNameValuePair("Passwd", new String(authInfo.getPassword()))); params.add(new BasicNameValuePair("service", "ah")); params.add(new BasicNameValuePair("source", "client.kotan-server.appspot.com")); httpPost.setEntity(new UrlEncodedFormEntity(params, "UTF-8")); HttpResponse response = clientManager.httpClient.execute(httpPost); HttpEntity entity = response.getEntity(); if (response.getStatusLine().getStatusCode() != HttpStatus.SC_OK) { entity.consumeContent(); throw new AuthoricationRequiredException(EntityUtils.toString(entity)); } BufferedReader reader = new BufferedReader(new InputStreamReader(entity.getContent())); while (true) { String line = reader.readLine(); if (line == null) break; if (line.startsWith("Auth=")) { return line.substring("Auth=".length()); } } reader.close(); throw new AuthoricationRequiredException("Login failure."); } catch (IOException e) { throw new AuthoricationRequiredException(e); } } | public static String submitURLRequest(String url) throws HttpException, IOException, URISyntaxException { HttpClient httpclient = new DefaultHttpClient(); InputStream stream = null; user_agents = new LinkedList<String>(); user_agents.add("Mozilla/5.0 (Windows; U; Windows NT 6.1; en-US; rv:1.9.2.2) Gecko/20100316 Firefox/3.6.2"); String response_text = ""; URI uri = new URI(url); HttpGet post = new HttpGet(uri); int MAX = user_agents.size() - 1; int index = (int) Math.round(((double) Math.random() * (MAX))); String agent = user_agents.get(index); httpclient.getParams().setParameter(CoreProtocolPNames.USER_AGENT, agent); httpclient.getParams().setParameter("User-Agent", agent); httpclient.getParams().setParameter(ClientPNames.COOKIE_POLICY, CookiePolicy.ACCEPT_NONE); HttpResponse response = httpclient.execute(post); HttpEntity entity = response.getEntity(); if (entity != null) { stream = entity.getContent(); response_text = convertStreamToString(stream); } httpclient.getConnectionManager().shutdown(); if (stream != null) { stream.close(); } return response_text; } | 12,275 |
0 | public void openJadFile(URL url) { try { setStatusBar("Loading..."); jad.clear(); jad.load(url.openStream()); loadFromJad(url); } catch (FileNotFoundException ex) { System.err.println("Cannot found " + url.getPath()); } catch (NullPointerException ex) { ex.printStackTrace(); System.err.println("Cannot open jad " + url.getPath()); } catch (IllegalArgumentException ex) { ex.printStackTrace(); System.err.println("Cannot open jad " + url.getPath()); } catch (IOException ex) { ex.printStackTrace(); System.err.println("Cannot open jad " + url.getPath()); } } | protected BufferedReader getDataReader() { BufferedReader in = null; PrintWriter out = null; try { String line; URL url = new URL(this.catalog.getCatalogURL()); Debug.output("Catalog URL:" + url.toString()); in = new BufferedReader(new InputStreamReader(url.openStream())); File dir = (File) SessionHandler.getServletContext().getAttribute("javax.servlet.context.tempdir"); File temp = new File(dir, TEMP); Debug.output("Temp file:" + temp.toString()); out = new PrintWriter(new BufferedWriter(new FileWriter(temp))); while ((line = in.readLine()) != null) { out.println(line); } Debug.output("Temp file size:" + temp.length()); return new BufferedReader(new FileReader(temp)); } catch (IOException e) { throw new SeismoException(e); } finally { Util.close(in); Util.close(out); } } | 12,276 |
0 | public static byte[] ComputeForText(String ThisString) throws Exception { byte[] Result; MessageDigest MD5Hasher; MD5Hasher = MessageDigest.getInstance("MD5"); MD5Hasher.update(ThisString.replaceAll("\r", "").getBytes("iso-8859-1")); Result = MD5Hasher.digest(); return Result; } | public void readMESHDescriptorFileIntoFiles(String outfiledir) { String inputLine, ins; String filename = getMESHdescriptorfilename(); String uid = ""; String name = ""; String description = ""; String element_of = ""; Vector treenr = new Vector(); Vector related = new Vector(); Vector synonyms = new Vector(); Vector actions = new Vector(); Vector chemicals = new Vector(); Vector allCASchemicals = new Vector(); Set CAS = new TreeSet(); Map treenr2uid = new TreeMap(); Map uid2name = new TreeMap(); String cut1, cut2; try { BufferedReader in = new BufferedReader(new FileReader(filename)); String outfile = outfiledir + "\\mesh"; BufferedWriter out_concept = new BufferedWriter(new FileWriter(outfile + "_concept.txt")); BufferedWriter out_concept_name = new BufferedWriter(new FileWriter(outfile + "_concept_name.txt")); BufferedWriter out_relation = new BufferedWriter(new FileWriter(outfile + "_relation.txt")); BufferedWriter cas_mapping = new BufferedWriter(new FileWriter(outfile + "to_cas_mapping.txt")); BufferedWriter ec_mapping = new BufferedWriter(new FileWriter(outfile + "to_ec_mapping.txt")); Connection db = tools.openDB("kb"); String query = "SELECT hierarchy_complete,uid FROM mesh_tree, mesh_graph_uid_name WHERE term=name"; ResultSet rs = tools.executeQuery(db, query); while (rs.next()) { String db_treenr = rs.getString("hierarchy_complete"); String db_uid = rs.getString("uid"); treenr2uid.put(db_treenr, db_uid); } db.close(); System.out.println("Reading in the DUIDs ..."); BufferedReader in_for_mapping = new BufferedReader(new FileReader(filename)); inputLine = getNextLine(in_for_mapping); boolean leave = false; while ((in_for_mapping != null) && (inputLine != null)) { if (inputLine.startsWith("<DescriptorRecord DescriptorClass")) { inputLine = getNextLine(in_for_mapping); cut1 = "<DescriptorUI>"; cut2 = "</DescriptorUI>"; String mesh_uid = inputLine.substring(cut1.length(), inputLine.indexOf(cut2)); if (mesh_uid.compareTo("D041441") == 0) leave = true; inputLine = getNextLine(in_for_mapping); inputLine = getNextLine(in_for_mapping); cut1 = "<String>"; cut2 = "</String>"; String mesh_name = inputLine.substring(cut1.length(), inputLine.indexOf(cut2)); uid2name.put(mesh_uid, mesh_name); } inputLine = getNextLine(in_for_mapping); } in_for_mapping.close(); BufferedReader in_ec_numbers = new BufferedReader(new FileReader("e:\\projects\\ondex\\ec_concept_acc.txt")); Set ec_numbers = new TreeSet(); String ec_line = in_ec_numbers.readLine(); while (in_ec_numbers.ready()) { StringTokenizer st = new StringTokenizer(ec_line); st.nextToken(); ec_numbers.add(st.nextToken()); ec_line = in_ec_numbers.readLine(); } in_ec_numbers.close(); tools.printDate(); inputLine = getNextLine(in); while (inputLine != null) { if (inputLine.startsWith("<DescriptorRecord DescriptorClass")) { treenr.clear(); related.clear(); synonyms.clear(); actions.clear(); chemicals.clear(); boolean id_ready = false; boolean line_read = false; while ((inputLine != null) && (!inputLine.startsWith("</DescriptorRecord>"))) { line_read = false; if ((inputLine.startsWith("<DescriptorUI>")) && (!id_ready)) { cut1 = "<DescriptorUI>"; cut2 = "</DescriptorUI>"; uid = inputLine.substring(cut1.length(), inputLine.indexOf(cut2)); inputLine = getNextLine(in); inputLine = getNextLine(in); cut1 = "<String>"; cut2 = "</String>"; name = inputLine.substring(cut1.length(), inputLine.indexOf(cut2)); id_ready = true; } if (inputLine.compareTo("<SeeRelatedList>") == 0) { while ((inputLine != null) && (inputLine.indexOf("</SeeRelatedList>") == -1)) { if (inputLine.startsWith("<DescriptorUI>")) { cut1 = "<DescriptorUI>"; cut2 = "</DescriptorUI>"; String id = inputLine.substring(cut1.length(), inputLine.indexOf(cut2)); related.add(id); } inputLine = getNextLine(in); line_read = true; } } if (inputLine.compareTo("<TreeNumberList>") == 0) { while ((inputLine != null) && (inputLine.indexOf("</TreeNumberList>") == -1)) { if (inputLine.startsWith("<TreeNumber>")) { cut1 = "<TreeNumber>"; cut2 = "</TreeNumber>"; String id = inputLine.substring(cut1.length(), inputLine.indexOf(cut2)); treenr.add(id); } inputLine = getNextLine(in); line_read = true; } } if (inputLine.startsWith("<Concept PreferredConceptYN")) { boolean prefConcept = false; if (inputLine.compareTo("<Concept PreferredConceptYN=\"Y\">") == 0) prefConcept = true; while ((inputLine != null) && (inputLine.indexOf("</Concept>") == -1)) { if (inputLine.startsWith("<CASN1Name>") && prefConcept) { cut1 = "<CASN1Name>"; cut2 = "</CASN1Name>"; String casn1 = inputLine.substring(cut1.length(), inputLine.indexOf(cut2)); String chem_name = casn1; String chem_description = ""; if (casn1.length() > chem_name.length() + 2) chem_description = casn1.substring(chem_name.length() + 2, casn1.length()); String reg_number = ""; inputLine = getNextLine(in); if (inputLine.startsWith("<RegistryNumber>")) { cut1 = "<RegistryNumber>"; cut2 = "</RegistryNumber>"; reg_number = inputLine.substring(cut1.length(), inputLine.indexOf(cut2)); } Vector chemical = new Vector(); String type = ""; if (reg_number.startsWith("EC")) { type = "EC"; reg_number = reg_number.substring(3, reg_number.length()); } else { type = "CAS"; } chemical.add(type); chemical.add(reg_number); chemical.add(chem_name); chemical.add(chem_description); chemicals.add(chemical); if (type.compareTo("CAS") == 0) { if (!CAS.contains(reg_number)) { CAS.add(reg_number); allCASchemicals.add(chemical); } } } if (inputLine.startsWith("<ScopeNote>") && prefConcept) { cut1 = "<ScopeNote>"; description = inputLine.substring(cut1.length(), inputLine.length()); } if (inputLine.startsWith("<TermUI>")) { inputLine = getNextLine(in); cut1 = "<String>"; cut2 = "</String>"; String syn = inputLine.substring(cut1.length(), inputLine.indexOf(cut2)); if (syn.indexOf("&") != -1) { String syn1 = syn.substring(0, syn.indexOf("&")); String syn2 = syn.substring(syn.indexOf("amp;") + 4, syn.length()); syn = syn1 + " & " + syn2; } if (name.compareTo(syn) != 0) synonyms.add(syn); } if (inputLine.startsWith("<PharmacologicalAction>")) { inputLine = getNextLine(in); inputLine = getNextLine(in); cut1 = "<DescriptorUI>"; cut2 = "</DescriptorUI>"; String act_ui = inputLine.substring(cut1.length(), inputLine.indexOf(cut2)); actions.add(act_ui); } inputLine = getNextLine(in); line_read = true; } } if (!line_read) inputLine = getNextLine(in); } String pos_tag = ""; element_of = "MESHD"; String is_primary = "0"; out_concept.write(uid + "\t" + pos_tag + "\t" + description + "\t" + element_of + "\t"); out_concept.write(is_primary + "\n"); String name_stemmed = ""; String name_tagged = ""; element_of = "MESHD"; String is_unique = "0"; int is_preferred = 1; String original_name = name; String is_not_substring = "0"; out_concept_name.write(uid + "\t" + name + "\t" + name_stemmed + "\t"); out_concept_name.write(name_tagged + "\t" + element_of + "\t"); out_concept_name.write(is_unique + "\t" + is_preferred + "\t"); out_concept_name.write(original_name + "\t" + is_not_substring + "\n"); is_preferred = 0; for (int i = 0; i < synonyms.size(); i++) { name = (String) synonyms.get(i); original_name = name; out_concept_name.write(uid + "\t" + name + "\t" + name_stemmed + "\t"); out_concept_name.write(name_tagged + "\t" + element_of + "\t"); out_concept_name.write(is_unique + "\t" + is_preferred + "\t"); out_concept_name.write(original_name + "\t" + is_not_substring + "\n"); } String rel_type = "is_r"; element_of = "MESHD"; String from_name = name; for (int i = 0; i < related.size(); i++) { String to_uid = (String) related.get(i); String to_name = (String) uid2name.get(to_uid); out_relation.write(uid + "\t" + to_uid + "\t"); out_relation.write(rel_type + "\t" + element_of + "\t"); out_relation.write(from_name + "\t" + to_name + "\n"); } rel_type = "is_a"; element_of = "MESHD"; related.clear(); for (int i = 0; i < treenr.size(); i++) { String tnr = (String) treenr.get(i); if (tnr.length() > 3) tnr = tnr.substring(0, tnr.lastIndexOf(".")); String rel_uid = (String) treenr2uid.get(tnr); if (rel_uid != null) related.add(rel_uid); else System.out.println(uid + ": No DUI found for " + tnr); } for (int i = 0; i < related.size(); i++) { String to_uid = (String) related.get(i); String to_name = (String) uid2name.get(to_uid); out_relation.write(uid + "\t" + to_uid + "\t"); out_relation.write(rel_type + "\t" + element_of + "\t"); out_relation.write(from_name + "\t" + to_name + "\n"); } if (related.size() == 0) System.out.println(uid + ": No is_a relations"); rel_type = "act"; element_of = "MESHD"; for (int i = 0; i < actions.size(); i++) { String to_uid = (String) actions.get(i); String to_name = (String) uid2name.get(to_uid); out_relation.write(uid + "\t" + to_uid + "\t"); out_relation.write(rel_type + "\t" + element_of + "\t"); out_relation.write(from_name + "\t" + to_name + "\n"); } String method = "IMPM"; String score = "1.0"; for (int i = 0; i < chemicals.size(); i++) { Vector chemical = (Vector) chemicals.get(i); String type = (String) chemical.get(0); String chem = (String) chemical.get(1); if (!ec_numbers.contains(chem) && (type.compareTo("EC") == 0)) { if (chem.compareTo("1.14.-") == 0) chem = "1.14.-.-"; else System.out.println("MISSING EC: " + chem); } String id = type + ":" + chem; String entry = uid + "\t" + id + "\t" + method + "\t" + score + "\n"; if (type.compareTo("CAS") == 0) cas_mapping.write(entry); else ec_mapping.write(entry); } } else inputLine = getNextLine(in); } System.out.println("End import descriptors"); tools.printDate(); in.close(); out_concept.close(); out_concept_name.close(); out_relation.close(); cas_mapping.close(); ec_mapping.close(); outfile = outfiledir + "\\cas"; out_concept = new BufferedWriter(new FileWriter(outfile + "_concept.txt")); out_concept_name = new BufferedWriter(new FileWriter(outfile + "_concept_name.txt")); BufferedWriter out_concept_acc = new BufferedWriter(new FileWriter(outfile + "_concept_acc.txt")); for (int i = 0; i < allCASchemicals.size(); i++) { Vector chemical = (Vector) allCASchemicals.get(i); String cas_id = "CAS:" + (String) chemical.get(1); String cas_name = (String) chemical.get(2); String cas_pos_tag = ""; String cas_description = (String) chemical.get(3); String cas_element_of = "CAS"; String cas_is_primary = "0"; out_concept.write(cas_id + "\t" + cas_pos_tag + "\t" + cas_description + "\t"); out_concept.write(cas_element_of + "\t" + cas_is_primary + "\n"); String cas_name_stemmed = ""; String cas_name_tagged = ""; String cas_is_unique = "0"; String cas_is_preferred = "0"; String cas_original_name = cas_name; String cas_is_not_substring = "0"; out_concept_name.write(cas_id + "\t" + cas_name + "\t" + cas_name_stemmed + "\t"); out_concept_name.write(cas_name_tagged + "\t" + cas_element_of + "\t"); out_concept_name.write(cas_is_unique + "\t" + cas_is_preferred + "\t"); out_concept_name.write(cas_original_name + "\t" + cas_is_not_substring + "\n"); out_concept_acc.write(cas_id + "\t" + (String) chemical.get(1) + "\t"); out_concept_acc.write(cas_element_of + "\n"); } out_concept.close(); out_concept_name.close(); out_concept_acc.close(); } catch (Exception e) { settings.writeLog("Error while reading MESH descriptor file: " + e.getMessage()); } } | 12,277 |
0 | public void actionPerformed(ActionEvent e) { if (saveForWebChooser == null) { ExtensionFileFilter fileFilter = new ExtensionFileFilter("HTML files"); fileFilter.addExtension("html"); saveForWebChooser = new JFileChooser(); saveForWebChooser.setFileFilter(fileFilter); saveForWebChooser.setDialogTitle("Save for Web..."); saveForWebChooser.setCurrentDirectory(new File(Config.getRecentDirectory("recentSaveForWebDirectory"))); } if (saveForWebChooser.showSaveDialog(Main.this) == JFileChooser.APPROVE_OPTION) { Config.setRecentDirectory("recentSaveForWebDirectory", saveForWebChooser.getCurrentDirectory().getAbsolutePath()); File pathFile = saveForWebChooser.getSelectedFile().getParentFile(); String name = saveForWebChooser.getSelectedFile().getName(); if (!name.toLowerCase().endsWith(".html") && name.indexOf('.') == -1) { name = name + ".html"; } String resource = MIDletClassLoader.getClassResourceName(this.getClass().getName()); URL url = this.getClass().getClassLoader().getResource(resource); String path = url.getPath(); int prefix = path.indexOf(':'); String mainJarFileName = path.substring(prefix + 1, path.length() - resource.length()); File appletJarDir = new File(new File(mainJarFileName).getParent(), "lib"); File appletJarFile = new File(appletJarDir, "microemu-javase-applet.jar"); if (!appletJarFile.exists()) { appletJarFile = null; } if (appletJarFile == null) { } if (appletJarFile == null) { ExtensionFileFilter fileFilter = new ExtensionFileFilter("JAR packages"); fileFilter.addExtension("jar"); JFileChooser appletChooser = new JFileChooser(); appletChooser.setFileFilter(fileFilter); appletChooser.setDialogTitle("Select MicroEmulator applet jar package..."); appletChooser.setCurrentDirectory(new File(Config.getRecentDirectory("recentAppletJarDirectory"))); if (appletChooser.showOpenDialog(Main.this) == JFileChooser.APPROVE_OPTION) { Config.setRecentDirectory("recentAppletJarDirectory", appletChooser.getCurrentDirectory().getAbsolutePath()); appletJarFile = appletChooser.getSelectedFile(); } else { return; } } JadMidletEntry jadMidletEntry; Iterator it = common.jad.getMidletEntries().iterator(); if (it.hasNext()) { jadMidletEntry = (JadMidletEntry) it.next(); } else { Message.error("MIDlet Suite has no entries"); return; } String midletInput = common.jad.getJarURL(); DeviceEntry deviceInput = selectDevicePanel.getSelectedDeviceEntry(); if (deviceInput != null && deviceInput.getDescriptorLocation().equals(DeviceImpl.DEFAULT_LOCATION)) { deviceInput = null; } File htmlOutputFile = new File(pathFile, name); if (!allowOverride(htmlOutputFile)) { return; } File appletPackageOutputFile = new File(pathFile, "microemu-javase-applet.jar"); if (!allowOverride(appletPackageOutputFile)) { return; } File midletOutputFile = new File(pathFile, midletInput.substring(midletInput.lastIndexOf("/") + 1)); if (!allowOverride(midletOutputFile)) { return; } File deviceOutputFile = null; String deviceDescriptorLocation = null; if (deviceInput != null) { deviceOutputFile = new File(pathFile, deviceInput.getFileName()); if (!allowOverride(deviceOutputFile)) { return; } deviceDescriptorLocation = deviceInput.getDescriptorLocation(); } try { AppletProducer.createHtml(htmlOutputFile, (DeviceImpl) DeviceFactory.getDevice(), jadMidletEntry.getClassName(), midletOutputFile, appletPackageOutputFile, deviceOutputFile); AppletProducer.createMidlet(new URL(midletInput), midletOutputFile); IOUtils.copyFile(appletJarFile, appletPackageOutputFile); if (deviceInput != null) { IOUtils.copyFile(new File(Config.getConfigPath(), deviceInput.getFileName()), deviceOutputFile); } } catch (IOException ex) { Logger.error(ex); } } } | public static String upload_file(String sessionid, String localFilePath, String remoteTagPath) { String jsonstring = "If you see this message, there is some problem inside the function:upload_file()"; String srcPath = localFilePath; String uploadUrl = "https://s2.cloud.cm/rpc/json/?session_id=" + sessionid + "&c=Storage&m=upload_file&tag=" + remoteTagPath; String end = "\r\n"; String twoHyphens = "--"; String boundary = "******"; try { URL url = new URL(uploadUrl); HttpURLConnection httpURLConnection = (HttpURLConnection) url.openConnection(); httpURLConnection.setDoInput(true); httpURLConnection.setDoOutput(true); httpURLConnection.setUseCaches(false); httpURLConnection.setRequestMethod("POST"); httpURLConnection.setRequestProperty("Connection", "Keep-Alive"); httpURLConnection.setRequestProperty("Charset", "UTF-8"); httpURLConnection.setRequestProperty("Content-Type", "multipart/form-data;boundary=" + boundary); DataOutputStream dos = new DataOutputStream(httpURLConnection.getOutputStream()); dos.writeBytes(twoHyphens + boundary + end); dos.writeBytes("Content-Disposition: form-data; name=\"file\"; filename=\"" + srcPath.substring(srcPath.lastIndexOf("/") + 1) + "\"" + end); dos.writeBytes(end); FileInputStream fis = new FileInputStream(srcPath); byte[] buffer = new byte[8192]; int count = 0; while ((count = fis.read(buffer)) != -1) { dos.write(buffer, 0, count); } fis.close(); dos.writeBytes(end); dos.writeBytes(twoHyphens + boundary + twoHyphens + end); dos.flush(); InputStream is = httpURLConnection.getInputStream(); InputStreamReader isr = new InputStreamReader(is, "utf-8"); BufferedReader br = new BufferedReader(isr); jsonstring = br.readLine(); dos.close(); is.close(); return jsonstring; } catch (Exception e) { e.printStackTrace(); } return jsonstring; } | 12,278 |
1 | public ActualTask(TEditor editor, TIGDataBase dataBase, String directoryPath, Vector images) { int i; lengthOfTask = images.size(); Element dataBaseXML = new Element("dataBase"); for (i = 0; ((i < images.size()) && !stop && !cancel); i++) { Vector imagen = new Vector(2); imagen = (Vector) images.elementAt(i); String element = (String) imagen.elementAt(0); current = i; String pathSrc = System.getProperty("user.dir") + File.separator + "images" + File.separator + element.substring(0, 1).toUpperCase() + File.separator + element; String name = pathSrc.substring(pathSrc.lastIndexOf(File.separator) + 1, pathSrc.length()); String pathDst = directoryPath + name; try { FileChannel srcChannel = new FileInputStream(pathSrc).getChannel(); FileChannel dstChannel = new FileOutputStream(pathDst).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (IOException exc) { System.out.println(exc.getMessage()); System.out.println(exc.toString()); } Vector<String> keyWords = new Vector<String>(); keyWords = TIGDataBase.asociatedConceptSearch(element); Element image = new Element("image"); image.setAttribute("name", name); if (keyWords.size() != 0) { for (int k = 0; k < keyWords.size(); k++) { Element category = new Element("category"); category.setText(keyWords.get(k).trim()); image.addContent(category); } } dataBaseXML.addContent(image); } Document doc = new Document(dataBaseXML); try { XMLOutputter out = new XMLOutputter(); FileOutputStream f = new FileOutputStream(directoryPath + "images.xml"); out.output(doc, f); f.flush(); f.close(); } catch (Exception e) { e.printStackTrace(); } current = lengthOfTask; } | @Test public void testCopy_inputStreamToWriter_nullIn() throws Exception { ByteArrayOutputStream baout = new ByteArrayOutputStream(); OutputStream out = new YellOnFlushAndCloseOutputStreamTest(baout, true, true); Writer writer = new OutputStreamWriter(baout, "US-ASCII"); try { IOUtils.copy((InputStream) null, writer); fail(); } catch (NullPointerException ex) { } } | 12,279 |
0 | public String readFile(String filename) throws IOException { FTPClient ftpClient = new FTPClient(); ftpClient.connect(server, port); ftpClient.login(USERNAME, PASSWORD); ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); boolean success = ftpClient.retrieveFile(filename, outputStream); ftpClient.disconnect(); if (!success) { throw new IOException("Retrieve file failed: " + filename); } return outputStream.toString(); } | public static void copyClassPathResource(String classPathResourceName, String fileSystemDirectoryName) { InputStream resourceInputStream = null; OutputStream fileOutputStream = null; try { resourceInputStream = FileUtils.class.getResourceAsStream(classPathResourceName); String fileName = StringUtils.substringAfterLast(classPathResourceName, "/"); File fileSystemDirectory = new File(fileSystemDirectoryName); fileSystemDirectory.mkdirs(); fileOutputStream = new FileOutputStream(fileSystemDirectoryName + "/" + fileName); IOUtils.copy(resourceInputStream, fileOutputStream); } catch (IOException e) { throw new UnitilsException(e); } finally { closeQuietly(resourceInputStream); closeQuietly(fileOutputStream); } } | 12,280 |
1 | private void doConvert(HttpServletResponse response, ConversionRequestResolver rr, EGE ege, ConversionsPath cpath) throws FileUploadException, IOException, RequestResolvingException, EGEException, FileNotFoundException, ConverterException, ZipException { InputStream is = null; OutputStream os = null; if (ServletFileUpload.isMultipartContent(rr.getRequest())) { ServletFileUpload upload = new ServletFileUpload(); FileItemIterator iter = upload.getItemIterator(rr.getRequest()); while (iter.hasNext()) { FileItemStream item = iter.next(); if (!item.isFormField()) { is = item.openStream(); applyConversionsProperties(rr.getConversionProperties(), cpath); DataBuffer buffer = new DataBuffer(0, EGEConstants.BUFFER_TEMP_PATH); String alloc = buffer.allocate(is); InputStream ins = buffer.getDataAsStream(alloc); is.close(); try { ValidationResult vRes = ege.performValidation(ins, cpath.getInputDataType()); if (vRes.getStatus().equals(ValidationResult.Status.FATAL)) { ValidationServlet valServ = new ValidationServlet(); valServ.printValidationResult(response, vRes); try { ins.close(); } finally { buffer.removeData(alloc, true); } return; } } catch (ValidatorException vex) { LOGGER.warn(vex.getMessage()); } finally { try { ins.close(); } catch (Exception ex) { } } File zipFile = null; FileOutputStream fos = null; String newTemp = UUID.randomUUID().toString(); IOResolver ior = EGEConfigurationManager.getInstance().getStandardIOResolver(); File buffDir = new File(buffer.getDataDir(alloc)); zipFile = new File(EGEConstants.BUFFER_TEMP_PATH + File.separator + newTemp + EZP_EXT); fos = new FileOutputStream(zipFile); ior.compressData(buffDir, fos); ins = new FileInputStream(zipFile); File szipFile = new File(EGEConstants.BUFFER_TEMP_PATH + File.separator + newTemp + ZIP_EXT); fos = new FileOutputStream(szipFile); try { try { ege.performConversion(ins, fos, cpath); } finally { fos.close(); } boolean isComplex = EGEIOUtils.isComplexZip(szipFile); response.setContentType(APPLICATION_OCTET_STREAM); String fN = item.getName().substring(0, item.getName().lastIndexOf(".")); if (isComplex) { String fileExt; if (cpath.getOutputDataType().getMimeType().equals(APPLICATION_MSWORD)) { fileExt = DOCX_EXT; } else { fileExt = ZIP_EXT; } response.setHeader("Content-Disposition", "attachment; filename=\"" + fN + fileExt + "\""); FileInputStream fis = new FileInputStream(szipFile); os = response.getOutputStream(); try { EGEIOUtils.copyStream(fis, os); } finally { fis.close(); } } else { String fileExt = getMimeExtensionProvider().getFileExtension(cpath.getOutputDataType().getMimeType()); response.setHeader("Content-Disposition", "attachment; filename=\"" + fN + fileExt + "\""); os = response.getOutputStream(); EGEIOUtils.unzipSingleFile(new ZipFile(szipFile), os); } } finally { ins.close(); if (os != null) { os.flush(); os.close(); } buffer.clear(true); szipFile.delete(); if (zipFile != null) { zipFile.delete(); } } } } } else { response.sendError(HttpServletResponse.SC_BAD_REQUEST); return; } } | static void copyFile(File in, File outDir, String outFileName) throws IOException { FileChannel inChannel = new FileInputStream(in).getChannel(); outDir.mkdirs(); File outFile = new File(outDir, outFileName); FileChannel outChannel = new FileOutputStream(outFile).getChannel(); try { inChannel.transferTo(0, inChannel.size(), outChannel); } catch (IOException e) { throw e; } finally { if (inChannel != null) { inChannel.close(); } if (outChannel != null) { outChannel.close(); } } } | 12,281 |
0 | private void refreshJOGL(final File installDir) { try { Class subAppletClass = Class.forName(subAppletClassName); } catch (ClassNotFoundException cnfe) { displayError("Start failed : class not found : " + subAppletClassName); } if (!installDir.exists()) { installDir.mkdirs(); } String libURLName = nativeLibsJarNames[osType]; URL nativeLibURL; URLConnection urlConnection; String path = getCodeBase().toExternalForm() + libURLName; try { nativeLibURL = new URL(path); urlConnection = nativeLibURL.openConnection(); } catch (Exception e) { e.printStackTrace(); displayError("Couldn't access the native lib URL : " + path); return; } long lastModified = urlConnection.getLastModified(); File localNativeFile = new File(installDir, nativeLibsFileNames[osType]); boolean needsRefresh = (!localNativeFile.exists()) || localNativeFile.lastModified() != lastModified; if (needsRefresh) { displayMessage("Updating local version of the native libraries"); File localJarFile = new File(installDir, nativeLibsJarNames[osType]); try { saveNativesJarLocally(localJarFile, urlConnection); } catch (IOException ioe) { ioe.printStackTrace(); displayError("Unable to install the native file locally"); return; } InputStream is = null; BufferedOutputStream out = null; try { JarFile jf = new JarFile(localJarFile); JarEntry nativeLibEntry = findNativeEntry(jf); if (nativeLibEntry == null) { displayError("native library not found in jar file"); } else { is = jf.getInputStream(nativeLibEntry); int totalLength = (int) nativeLibEntry.getSize(); try { out = new BufferedOutputStream(new FileOutputStream(localNativeFile)); } catch (FileNotFoundException ex) { ex.printStackTrace(); return; } byte[] buffer = new byte[1024]; int sum = 0; int len; try { while ((len = is.read(buffer)) > 0) { out.write(buffer, 0, len); sum += len; int percent = (100 * sum / totalLength); displayMessage("Installing native files"); progressBar.setValue(percent); } displayMessage("Download complete"); } catch (IOException ioe) { ioe.printStackTrace(); displayMessage("An error has occured during native library download"); return; } finally { if (out != null) { try { out.close(); } catch (IOException ignore) { } } } if (checkNativeCertificates(nativeLibEntry.getCertificates())) { localNativeFile.setLastModified(lastModified); loadNativesAndStart(localNativeFile); } else { displayError("The native librairies aren't properly signed"); } } } catch (IOException e) { e.printStackTrace(); } finally { if (is != null) { try { is.close(); } catch (IOException ignore) { } } } } else { loadNativesAndStart(localNativeFile); } } | protected InputStream callApiMethod(String apiUrl, int expected) { try { URL url = new URL(apiUrl); HttpURLConnection request = (HttpURLConnection) url.openConnection(); for (String headerName : requestHeaders.keySet()) { request.setRequestProperty(headerName, requestHeaders.get(headerName)); } request.connect(); if (request.getResponseCode() != expected) { Error error = readResponse(Error.class, getWrappedInputStream(request.getErrorStream(), GZIP_ENCODING.equalsIgnoreCase(request.getContentEncoding()))); throw createBingSearchApiClientException(error); } else { return getWrappedInputStream(request.getInputStream(), GZIP_ENCODING.equalsIgnoreCase(request.getContentEncoding())); } } catch (IOException e) { throw new BingSearchException(e); } } | 12,282 |
1 | private static void copyFile(File sourceFile, File destFile) throws IOException { if (!destFile.exists()) { destFile.createNewFile(); } FileChannel source = null; FileChannel destination = null; try { source = new FileInputStream(sourceFile).getChannel(); destination = new FileOutputStream(destFile).getChannel(); destination.transferFrom(source, 0, source.size()); } finally { if (source != null) { source.close(); } if (destination != null) { destination.close(); } } } | public void postProcess() throws StopWriterVisitorException { dbfWriter.postProcess(); try { short originalEncoding = dbf.getDbaseHeader().getLanguageID(); File dbfFile = fTemp; FileChannel fcinDbf = new FileInputStream(dbfFile).getChannel(); FileChannel fcoutDbf = new FileOutputStream(file).getChannel(); DriverUtilities.copy(fcinDbf, fcoutDbf); fTemp.delete(); close(); RandomAccessFile fo = new RandomAccessFile(file, "rw"); fo.seek(29); fo.writeByte(originalEncoding); fo.close(); open(file); } catch (FileNotFoundException e) { throw new StopWriterVisitorException(getName(), e); } catch (IOException e) { throw new StopWriterVisitorException(getName(), e); } catch (CloseDriverException e) { throw new StopWriterVisitorException(getName(), e); } catch (OpenDriverException e) { throw new StopWriterVisitorException(getName(), e); } } | 12,283 |
1 | public ActionForward uploadFile(ActionMapping mapping, ActionForm actForm, HttpServletRequest request, HttpServletResponse in_response) { ActionMessages errors = new ActionMessages(); ActionMessages messages = new ActionMessages(); String returnPage = "submitPocketSampleInformationPage"; UploadForm form = (UploadForm) actForm; Integer shippingId = null; try { eHTPXXLSParser parser = new eHTPXXLSParser(); String proposalCode; String proposalNumber; String proposalName; String uploadedFileName; String realXLSPath; if (request != null) { proposalCode = (String) request.getSession().getAttribute(Constants.PROPOSAL_CODE); proposalNumber = String.valueOf(request.getSession().getAttribute(Constants.PROPOSAL_NUMBER)); proposalName = proposalCode + proposalNumber.toString(); uploadedFileName = form.getRequestFile().getFileName(); String fileName = proposalName + "_" + uploadedFileName; realXLSPath = request.getRealPath("\\tmp\\") + "\\" + fileName; FormFile f = form.getRequestFile(); InputStream in = f.getInputStream(); File outputFile = new File(realXLSPath); if (outputFile.exists()) outputFile.delete(); FileOutputStream out = new FileOutputStream(outputFile); while (in.available() != 0) { out.write(in.read()); out.flush(); } out.flush(); out.close(); } else { proposalCode = "ehtpx"; proposalNumber = "1"; proposalName = proposalCode + proposalNumber.toString(); uploadedFileName = "ispyb-template41.xls"; realXLSPath = "D:\\" + uploadedFileName; } FileInputStream inFile = new FileInputStream(realXLSPath); parser.retrieveShippingId(realXLSPath); shippingId = parser.getShippingId(); String requestShippingId = form.getShippingId(); if (requestShippingId != null && !requestShippingId.equals("")) { shippingId = new Integer(requestShippingId); } ClientLogger.getInstance().debug("uploadFile for shippingId " + shippingId); if (shippingId != null) { Log.debug(" ---[uploadFile] Upload for Existing Shipment (DewarTRacking): Deleting Samples from Shipment :"); double nbSamplesContainers = DBAccess_EJB.DeleteAllSamplesAndContainersForShipping(shippingId); if (nbSamplesContainers > 0) parser.getValidationWarnings().add(new XlsUploadException("Shipment contained Samples and/or Containers", "Previous Samples and/or Containers have been deleted and replaced by new ones.")); else parser.getValidationWarnings().add(new XlsUploadException("Shipment contained no Samples and no Containers", "Samples and Containers have been added.")); } Hashtable<String, Hashtable<String, Integer>> listProteinAcronym_SampleName = new Hashtable<String, Hashtable<String, Integer>>(); ProposalFacadeLocal proposal = ProposalFacadeUtil.getLocalHome().create(); ProteinFacadeLocal protein = ProteinFacadeUtil.getLocalHome().create(); CrystalFacadeLocal crystal = CrystalFacadeUtil.getLocalHome().create(); ProposalLightValue targetProposal = (ProposalLightValue) (((ArrayList) proposal.findByCodeAndNumber(proposalCode, new Integer(proposalNumber))).get(0)); ArrayList listProteins = (ArrayList) protein.findByProposalId(targetProposal.getProposalId()); for (int p = 0; p < listProteins.size(); p++) { ProteinValue prot = (ProteinValue) listProteins.get(p); Hashtable<String, Integer> listSampleName = new Hashtable<String, Integer>(); CrystalLightValue listCrystals[] = prot.getCrystals(); for (int c = 0; c < listCrystals.length; c++) { CrystalLightValue _xtal = (CrystalLightValue) listCrystals[c]; CrystalValue xtal = crystal.findByPrimaryKey(_xtal.getPrimaryKey()); BlsampleLightValue listSamples[] = xtal.getBlsamples(); for (int s = 0; s < listSamples.length; s++) { BlsampleLightValue sample = listSamples[s]; listSampleName.put(sample.getName(), sample.getBlSampleId()); } } listProteinAcronym_SampleName.put(prot.getAcronym(), listSampleName); } parser.validate(inFile, listProteinAcronym_SampleName, targetProposal.getProposalId()); List listErrors = parser.getValidationErrors(); List listWarnings = parser.getValidationWarnings(); if (listErrors.size() == 0) { parser.open(realXLSPath); if (parser.getCrystals().size() == 0) { parser.getValidationErrors().add(new XlsUploadException("No crystals have been found", "Empty shipment")); } } Iterator errIt = listErrors.iterator(); while (errIt.hasNext()) { XlsUploadException xlsEx = (XlsUploadException) errIt.next(); errors.add(ActionMessages.GLOBAL_MESSAGE, new ActionMessage("message.free", xlsEx.getMessage() + " ---> " + xlsEx.getSuggestedFix())); } try { saveErrors(request, errors); } catch (Exception e) { } Iterator warnIt = listWarnings.iterator(); while (warnIt.hasNext()) { XlsUploadException xlsEx = (XlsUploadException) warnIt.next(); messages.add(ActionMessages.GLOBAL_MESSAGE, new ActionMessage("message.free", xlsEx.getMessage() + " ---> " + xlsEx.getSuggestedFix())); } try { saveMessages(request, messages); } catch (Exception e) { } if (listErrors.size() > 0) { resetCounts(shippingId); return mapping.findForward("submitPocketSampleInformationPage"); } if (listWarnings.size() > 0) returnPage = "submitPocketSampleInformationPage"; String crystalDetailsXML; XtalDetails xtalDetailsWebService = new XtalDetails(); CrystalDetailsBuilder cDE = new CrystalDetailsBuilder(); CrystalDetailsElement cd = cDE.createCrystalDetailsElement(proposalName, parser.getCrystals()); cDE.validateJAXBObject(cd); crystalDetailsXML = cDE.marshallJaxBObjToString(cd); xtalDetailsWebService.submitCrystalDetails(crystalDetailsXML); String diffractionPlan; DiffractionPlan diffractionPlanWebService = new DiffractionPlan(); DiffractionPlanBuilder dPB = new DiffractionPlanBuilder(); Iterator it = parser.getDiffractionPlans().iterator(); while (it.hasNext()) { DiffractionPlanElement dpe = (DiffractionPlanElement) it.next(); dpe.setProjectUUID(proposalName); diffractionPlan = dPB.marshallJaxBObjToString(dpe); diffractionPlanWebService.submitDiffractionPlan(diffractionPlan); } String crystalShipping; Shipping shippingWebService = new Shipping(); CrystalShippingBuilder cSB = new CrystalShippingBuilder(); Person person = cSB.createPerson("XLS Upload", null, "ISPyB", null, null, "ISPyB", null, "ispyb@esrf.fr", "0000", "0000", null, null); Laboratory laboratory = cSB.createLaboratory("Generic Laboratory", "ISPyB Lab", "Sandwich", "Somewhere", "UK", "ISPyB", "ispyb.esrf.fr", person); DeliveryAgent deliveryAgent = parser.getDeliveryAgent(); CrystalShipping cs = cSB.createCrystalShipping(proposalName, laboratory, deliveryAgent, parser.getDewars()); String shippingName; shippingName = uploadedFileName.substring(0, ((uploadedFileName.toLowerCase().lastIndexOf(".xls")) > 0) ? uploadedFileName.toLowerCase().lastIndexOf(".xls") : 0); if (shippingName.equalsIgnoreCase("")) shippingName = uploadedFileName.substring(0, ((uploadedFileName.toLowerCase().lastIndexOf(".xlt")) > 0) ? uploadedFileName.toLowerCase().lastIndexOf(".xlt") : 0); cs.setName(shippingName); crystalShipping = cSB.marshallJaxBObjToString(cs); shippingWebService.submitCrystalShipping(crystalShipping, (ArrayList) parser.getDiffractionPlans(), shippingId); ServerLogger.Log4Stat("XLS_UPLOAD", proposalName, uploadedFileName); } catch (XlsUploadException e) { resetCounts(shippingId); errors.add(ActionMessages.GLOBAL_MESSAGE, new ActionMessage("errors.detail", e.getMessage())); ClientLogger.getInstance().error(e.toString()); saveErrors(request, errors); return mapping.findForward("error"); } catch (Exception e) { resetCounts(shippingId); errors.add(ActionMessages.GLOBAL_MESSAGE, new ActionMessage("errors.detail", e.toString())); ClientLogger.getInstance().error(e.toString()); e.printStackTrace(); saveErrors(request, errors); return mapping.findForward("error"); } setCounts(shippingId); return mapping.findForward(returnPage); } | PackageFileImpl(PackageDirectoryImpl dir, String name, InputStream data) throws IOException { this.dir = dir; this.name = name; this.updates = dir.getUpdates(); ByteArrayOutputStream stream = new ByteArrayOutputStream(); IOUtils.copy(data, stream); updates.setNewData(getFullName(), stream.toByteArray()); stream.close(); } | 12,284 |
1 | public void copyToCurrentDir(File _copyFile, String _fileName) throws IOException { File outputFile = new File(getCurrentPath() + File.separator + _fileName); FileReader in; FileWriter out; if (!outputFile.exists()) { outputFile.createNewFile(); } in = new FileReader(_copyFile); out = new FileWriter(outputFile); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); reList(); } | private void doPOST(HttpURLConnection connection, InputStream inputXML) throws MessageServiceException { try { OutputStream requestStream = new BufferedOutputStream(connection.getOutputStream()); IOUtils.copyAndClose(inputXML, requestStream); connection.connect(); } catch (IOException e) { throw new MessageServiceException(e.getMessage(), e); } } | 12,285 |
1 | private void copyResource(String resource, File targetDir) { InputStream is = FragmentFileSetTest.class.getResourceAsStream(resource); Assume.assumeNotNull(is); int i = resource.lastIndexOf("/"); String filename; if (i == -1) { filename = resource; } else { filename = resource.substring(i + 1); } try { FileOutputStream fos = new FileOutputStream(new File(targetDir, filename)); IOUtils.copy(is, fos); fos.close(); } catch (IOException e) { e.printStackTrace(); Assert.fail(e.getMessage()); } } | public static final void copyFile(File source, File destination) throws IOException { FileChannel sourceChannel = new FileInputStream(source).getChannel(); FileChannel targetChannel = new FileOutputStream(destination).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), targetChannel); sourceChannel.close(); targetChannel.close(); } | 12,286 |
1 | private static void main(String[] args) { try { File f = new File("test.txt"); if (f.exists()) { throw new IOException(f + " already exists. I don't want to overwrite it."); } StraightStreamReader in; char[] cbuf = new char[0x1000]; int read; int totRead; FileOutputStream out = new FileOutputStream(f); for (int i = 0x00; i < 0x100; i++) { out.write(i); } out.close(); in = new StraightStreamReader(new FileInputStream(f)); for (int i = 0x00; i < 0x100; i++) { read = in.read(); if (read != i) { System.err.println("Error: " + i + " read as " + read); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = in.read(cbuf); if (totRead != 0x100) { System.err.println("Simple buffered read did not read the full amount: 0x" + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i]); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = 0; while (totRead <= 0x100 && (read = in.read(cbuf, totRead, 0x100 - totRead)) > 0) { totRead += read; } if (totRead != 0x100) { System.err.println("Not enough read. Bytes read: " + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i]); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = 0; while (totRead <= 0x100 && (read = in.read(cbuf, totRead + 0x123, 0x100 - totRead)) > 0) { totRead += read; } if (totRead != 0x100) { System.err.println("Not enough read. Bytes read: " + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i + 0x123] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i + 0x123]); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = 0; while (totRead <= 0x100 && (read = in.read(cbuf, totRead + 0x123, 7)) > 0) { totRead += read; } if (totRead != 0x100) { System.err.println("Not enough read. Bytes read: " + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i + 0x123] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i + 0x123]); } } in.close(); f.delete(); } catch (IOException x) { System.err.println(x.getMessage()); } } | public static void copyFile(File src, String srcEncoding, File dest, String destEncoding) throws IOException { InputStreamReader in = new InputStreamReader(new FileInputStream(src), srcEncoding); OutputStreamWriter out = new OutputStreamWriter(new RobustFileOutputStream(dest), destEncoding); int c; while ((c = in.read()) != -1) out.write(c); out.flush(); in.close(); out.close(); } | 12,287 |
0 | static void invalidSlave(String msg, Socket sock) throws IOException { BufferedReader _sinp = null; PrintWriter _sout = null; try { _sout = new PrintWriter(sock.getOutputStream(), true); _sinp = new BufferedReader(new InputStreamReader(sock.getInputStream())); _sout.println(msg); logger.info("NEW< " + msg); String txt = SocketSlaveListener.readLine(_sinp, 30); String sname = ""; String spass = ""; String shash = ""; try { String[] items = txt.split(" "); sname = items[1].trim(); spass = items[2].trim(); shash = items[3].trim(); } catch (Exception e) { throw new IOException("Slave Inititalization Faailed"); } String pass = sname + spass + _pass; MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.reset(); md5.update(pass.getBytes()); String hash = SocketSlaveListener.hash2hex(md5.digest()).toLowerCase(); if (!hash.equals(shash)) { throw new IOException("Slave Inititalization Faailed"); } } catch (Exception e) { } throw new IOException("Slave Inititalization Faailed"); } | @Test public void test_lookupType_FullSearch_TwoWords() throws Exception { URL url = new URL(baseUrl + "/lookupType/deep+core"); HttpURLConnection connection = (HttpURLConnection) url.openConnection(); connection.setRequestMethod("GET"); connection.setRequestProperty("Accept", "application/json"); assertThat(connection.getResponseCode(), equalTo(200)); assertThat(getResponse(connection), equalTo("[{\"itemTypeID\":11395,\"itemCategoryID\":16,\"name\":\"Deep Core Mining\",\"icon\":\"50_11\"},{\"itemTypeID\":12108,\"itemCategoryID\":7,\"name\":\"Deep Core Mining Laser I\",\"icon\":\"35_01\",\"metaLevel\":0},{\"itemTypeID\":12109,\"itemCategoryID\":9,\"name\":\"Deep Core Mining Laser I Blueprint\",\"icon\":\"12_08\"},{\"itemTypeID\":18068,\"itemCategoryID\":7,\"name\":\"Modulated Deep Core Miner II\",\"icon\":\"35_01\",\"metaLevel\":5},{\"itemTypeID\":18069,\"itemCategoryID\":9,\"name\":\"Modulated Deep Core Miner II Blueprint\",\"icon\":\"12_08\"},{\"itemTypeID\":24305,\"itemCategoryID\":7,\"name\":\"Modulated Deep Core Strip Miner II\",\"icon\":\"49_05\",\"metaLevel\":5},{\"itemTypeID\":24306,\"itemCategoryID\":9,\"name\":\"Modulated Deep Core Strip Miner II Blueprint\",\"icon\":\"12_08\"},{\"itemTypeID\":28748,\"itemCategoryID\":7,\"name\":\"ORE Deep Core Mining Laser\",\"icon\":\"35_01\",\"metaLevel\":6}]")); assertThat(connection.getHeaderField("Content-Type"), equalTo("application/json; charset=utf-8")); } | 12,288 |
0 | 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) { } } | protected void unZip() throws PersistenceException { boolean newZip = false; try { if (null == backup) { mode = (String) context.get(Context.MODE); if (null == mode) mode = Context.MODE_NAME_RESTORE; backupDirectory = (File) context.get(Context.BACKUP_DIRECTORY); logger.debug("Got backup directory {" + backupDirectory.getAbsolutePath() + "}"); if (!backupDirectory.exists() && mode.equals(Context.MODE_NAME_BACKUP)) { newZip = true; backupDirectory.mkdirs(); } else if (!backupDirectory.exists()) { throw new PersistenceException("Backup directory {" + backupDirectory.getAbsolutePath() + "} does not exist."); } backup = new File(backupDirectory + "/" + getBackupName() + ".zip"); logger.debug("Got zip file {" + backup.getAbsolutePath() + "}"); } File _explodedDirectory = File.createTempFile("exploded-" + backup.getName() + "-", ".zip"); _explodedDirectory.mkdirs(); _explodedDirectory.delete(); backupDirectory = new File(_explodedDirectory.getParentFile(), _explodedDirectory.getName()); backupDirectory.mkdirs(); logger.debug("Created exploded directory {" + backupDirectory.getAbsolutePath() + "}"); if (!backup.exists() && mode.equals(Context.MODE_NAME_BACKUP)) { newZip = true; backup.createNewFile(); } else if (!backup.exists()) { throw new PersistenceException("Backup file {" + backup.getAbsolutePath() + "} does not exist."); } if (newZip) return; ZipFile zip = new ZipFile(backup); Enumeration zipFileEntries = zip.entries(); while (zipFileEntries.hasMoreElements()) { ZipEntry entry = (ZipEntry) zipFileEntries.nextElement(); String currentEntry = entry.getName(); logger.debug("Inflating: " + entry); File destFile = new File(backupDirectory, currentEntry); File destinationParent = destFile.getParentFile(); destinationParent.mkdirs(); if (!entry.isDirectory()) { InputStream in = null; OutputStream out = null; try { in = zip.getInputStream(entry); out = new FileOutputStream(destFile); IOUtils.copy(in, out); } finally { if (null != out) out.close(); if (null != in) in.close(); } } } } catch (IOException e) { logger.error("Unable to unzip {" + backup + "}", e); throw new PersistenceException(e); } } | 12,289 |
0 | private void addConfigurationResource(final String fileName, final boolean ensureLoaded) { try { final ClassLoader cl = this.getClass().getClassLoader(); final Properties p = new Properties(); final URL url = cl.getResource(fileName); if (url == null) { throw new NakedObjectRuntimeException("Failed to load configuration resource: " + fileName); } p.load(url.openStream()); configuration.add(p); } catch (Exception e) { if (ensureLoaded) { throw new NakedObjectRuntimeException(e); } LOG.debug("Resource: " + fileName + " not found, but not needed"); } } | public static void copyFile(final File sourceFile, final File destFile) throws IOException { if (!destFile.exists()) { destFile.createNewFile(); } FileInputStream inStream = null; FileOutputStream outStream = null; FileChannel source = null; FileChannel destination = null; try { source = (inStream = new FileInputStream(sourceFile)).getChannel(); destination = (outStream = new FileOutputStream(destFile)).getChannel(); destination.transferFrom(source, 0, source.size()); } finally { closeIO(source); closeIO(inStream); closeIO(destination); closeIO(outStream); } } | 12,290 |
1 | public static boolean copy(File source, File target) { try { if (!source.exists()) return false; target.getParentFile().mkdirs(); InputStream input = new FileInputStream(source); OutputStream output = new FileOutputStream(target); byte[] buf = new byte[1024]; int len; while ((len = input.read(buf)) > 0) output.write(buf, 0, len); input.close(); output.close(); return true; } catch (Exception exc) { exc.printStackTrace(); return false; } } | public static boolean copyFile(File from, File to) { try { FileChannel fromChannel = new FileInputStream(from).getChannel(); FileChannel toChannel = new FileOutputStream(to).getChannel(); toChannel.transferFrom(fromChannel, 0, fromChannel.size()); fromChannel.close(); toChannel.close(); } catch (IOException e) { log.error("failed to copy " + from.getAbsolutePath() + " to " + to.getAbsolutePath() + ": caught exception", e); return false; } return true; } | 12,291 |
1 | private static void prepare() { System.err.println("PREPARING-----------------------------------------"); deleteHome(); InputStream configStream = null; FileOutputStream tempStream = null; try { configStream = AllTests.class.getClassLoader().getResourceAsStream("net/sf/archimede/test/resources/repository.xml"); new File("temp").mkdir(); tempStream = new FileOutputStream(new File("temp/repository.xml")); IOUtils.copy(configStream, tempStream); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } finally { try { if (configStream != null) { configStream.close(); } } catch (IOException e) { e.printStackTrace(); } finally { if (tempStream != null) { try { tempStream.close(); } catch (IOException e) { e.printStackTrace(); } } } } String repositoryName = "jackrabbit.repository"; Properties jndiProperties = new Properties(); jndiProperties.put("java.naming.provider.url", "http://sf.net/projects/archimede#1"); jndiProperties.put("java.naming.factory.initial", "org.apache.jackrabbit.core.jndi.provider.DummyInitialContextFactory"); startupUtil = new StartupJcrUtil(REPOSITORY_HOME, "temp/repository.xml", repositoryName, jndiProperties); startupUtil.init(); } | public String stringOfUrl(String addr) throws IOException { ByteArrayOutputStream output = new ByteArrayOutputStream(); URL url = new URL(addr); IOUtils.copy(url.openStream(), output); return output.toString(); } | 12,292 |
0 | private static String getDocumentAt(String urlString) { StringBuffer html_text = new StringBuffer(); try { URL url = new URL(urlString); URLConnection conn = url.openConnection(); BufferedReader reader = new BufferedReader(new InputStreamReader(conn.getInputStream())); String line = null; while ((line = reader.readLine()) != null) html_text.append(line + "\n"); reader.close(); } catch (MalformedURLException e) { System.out.println("����URL: " + urlString); } catch (IOException e) { e.printStackTrace(); } return html_text.toString(); } | protected void syncMessages(Message message) { if (message.getEvent() == Event.CONNECT || message.getEvent() == Event.SYNC_DONE) return; logger.info(String.format("remove stale replication messages: %s", message.toString())); String className = ""; long classId = 0; if (message.getBody() instanceof Entity) { Entity entity = (Entity) message.getBody(); className = entity.getClass().getName(); classId = entity.getId(); } ConnectionProvider cp = null; Connection conn = null; PreparedStatement ps = null; try { SessionFactoryImplementor impl = (SessionFactoryImplementor) portalDao.getSessionFactory(); cp = impl.getConnectionProvider(); conn = cp.getConnection(); conn.setAutoCommit(false); ps = conn.prepareStatement("delete from light_replication_message where event=? and className=? and classId=?"); ps.setString(1, message.getEvent().toString()); ps.setString(2, className); ps.setLong(3, classId); ps.executeUpdate(); conn.commit(); ps.close(); conn.close(); } catch (Exception e) { try { conn.rollback(); ps.close(); conn.close(); } catch (Exception se) { } } } | 12,293 |
0 | @Override public void onCreate(Bundle icicle) { super.onCreate(icicle); TextView tv = new TextView(this); try { URL url = new URL(""); SAXParserFactory spf = SAXParserFactory.newInstance(); SAXParser sp = spf.newSAXParser(); XMLReader xr = sp.getXMLReader(); ExampleHandler myExampleHandler = new ExampleHandler(); xr.setContentHandler(myExampleHandler); xr.parse(new InputSource(url.openStream())); ParsedExampleDataSet parsedExampleDataSet = myExampleHandler.getParsedData(); tv.setText(parsedExampleDataSet.toString()); } catch (Exception e) { tv.setText("Error: " + e.getMessage()); Log.e(MY_DEBUG_TAG, "WeatherQueryError", e); } this.setContentView(tv); } | public void store(Component component, String componentName, int currentPilot) { try { PreparedStatement psta = jdbc.prepareStatement("UPDATE component_prop " + "SET size_height = ?, size_width = ?, pos_x = ?, pos_y = ? " + "WHERE pilot_id = ? " + "AND component_name = ?"); psta.setInt(1, component.getHeight()); psta.setInt(2, component.getWidth()); Point point = component.getLocation(); psta.setInt(3, point.x); psta.setInt(4, point.y); psta.setInt(5, currentPilot); psta.setString(6, componentName); int update = psta.executeUpdate(); if (update == 0) { psta = jdbc.prepareStatement("INSERT INTO component_prop " + "(size_height, size_width, pos_x, pos_y, pilot_id, component_name) " + "VALUES (?,?,?,?,?,?)"); psta.setInt(1, component.getHeight()); psta.setInt(2, component.getWidth()); psta.setInt(3, point.x); psta.setInt(4, point.y); psta.setInt(5, currentPilot); psta.setString(6, componentName); psta.executeUpdate(); } jdbc.commit(); } catch (SQLException e) { jdbc.rollback(); log.debug(e); } } | 12,294 |
1 | private String getXml(String url) throws Exception { HttpClient httpclient = new DefaultHttpClient(); HttpGet httpget = new HttpGet(url); HttpResponse response = httpclient.execute(httpget); HttpEntity entity = response.getEntity(); String results = null; if (entity != null) { long len = entity.getContentLength(); if (len != -1 && len < 2048) { results = EntityUtils.toString(entity); } else { } } return (results); } | public static Vector getVectorForm(String u, String usr, String pwd) { Vector response = new Vector(); 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())); String str; while ((str = in.readLine()) != null) { response.add(str); } in.close(); logger.debug("Response: " + response.toString()); } catch (MalformedURLException e) { logger.error(e); logger.trace(e, e); } catch (IOException e) { logger.error(e); logger.trace(e, e); } return response; } | 12,295 |
0 | public static int best(int r, int n, int s) { if ((n <= 0) || (r < 0) || (r > n) || (s < 0)) return 0; int[] rolls = new int[n]; for (int i = 0; i < n; i++) rolls[i] = d(s); boolean found; do { found = false; for (int x = 0; x < n - 1; x++) { if (rolls[x] < rolls[x + 1]) { int t = rolls[x]; rolls[x] = rolls[x + 1]; rolls[x + 1] = t; found = true; } } } while (found); int sum = 0; for (int i = 0; i < r; i++) sum += rolls[i]; return sum; } | private static MappedObject sendHttpRequestToUrl(URL url, String method) throws Exception { try { HttpURLConnection connection = (HttpURLConnection) url.openConnection(); connection.setRequestMethod(method); connection.connect(); InputStream is = connection.getInputStream(); BufferedReader reader = new BufferedReader(new InputStreamReader(is)); StringBuilder buffer = new StringBuilder(); String line = null; while ((line = reader.readLine()) != null) { buffer.append(line); } System.out.println("Read: " + buffer.toString()); connection.disconnect(); JAXBContext context = JAXBContext.newInstance(MappedObject.class); Unmarshaller unmarshaller = context.createUnmarshaller(); MappedObject mapped = (MappedObject) unmarshaller.unmarshal(new StringReader(buffer.toString())); return mapped; } catch (IOException e) { e.printStackTrace(); } throw new Exception("Could not establish connection to " + url.toExternalForm()); } | 12,296 |
0 | private String fetchHTML(String s) { String str; StringBuffer sb = new StringBuffer(); try { URL url = new URL(s); InputStream is = url.openStream(); InputStreamReader isr = new InputStreamReader(is); BufferedReader br = new BufferedReader(isr); while ((str = br.readLine()) != null) { sb.append(str); } } catch (MalformedURLException e) { } catch (IOException e) { } return sb.toString(); } | public void deployDir(File srcDir, String destDir) { File[] dirFiles = srcDir.listFiles(); for (int k = 0; dirFiles != null && k < dirFiles.length; k++) { if (!dirFiles[k].getName().startsWith(".")) { if (dirFiles[k].isFile()) { File deployFile = new File(destDir + File.separator + dirFiles[k].getName()); if (dirFiles[k].lastModified() != deployFile.lastModified() || dirFiles[k].length() != deployFile.length()) { IOUtils.copy(dirFiles[k], deployFile); } } else if (dirFiles[k].isDirectory()) { String newDestDir = destDir + File.separator + dirFiles[k].getName(); deployDir(dirFiles[k], newDestDir); } } } } | 12,297 |
1 | private static void copyFile(String from, String to) throws IOException { FileReader in = new FileReader(from); FileWriter out = new FileWriter(to); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } | private long generateUnixInstallShell(File unixShellFile, String instTemplate, File instClassFile) throws IOException { FileOutputStream byteWriter = new FileOutputStream(unixShellFile); InputStream is = getClass().getResourceAsStream("/" + instTemplate); InputStreamReader isr = new InputStreamReader(is); LineNumberReader reader = new LineNumberReader(isr); String content = ""; String installClassStartStr = "000000000000"; NumberFormat nf = NumberFormat.getInstance(Locale.US); nf.setGroupingUsed(false); nf.setMinimumIntegerDigits(installClassStartStr.length()); int installClassStartPos = 0; long installClassOffset = 0; System.out.println(VAGlobals.i18n("VAArchiver_GenerateInstallShell")); String line = reader.readLine(); while ((line != null) && (!line.startsWith("# InstallClassStart"))) { content += line + "\n"; line = reader.readLine(); } content += "InstallClassStart=" + installClassStartStr + "\n"; installClassStartPos = content.length() - 1 - 1 - installClassStartStr.length(); line = reader.readLine(); while ((line != null) && (!line.startsWith("# InstallClassSize"))) { content += line + "\n"; line = reader.readLine(); } content += new String("InstallClassSize=" + instClassFile.length() + "\n"); line = reader.readLine(); while ((line != null) && (!line.startsWith("# InstallClassName"))) { content += line + "\n"; line = reader.readLine(); } content += new String("InstallClassName=" + instClassName_ + "\n"); line = reader.readLine(); while ((line != null) && (!line.startsWith("# Install class"))) { content += line + "\n"; line = reader.readLine(); } if (line != null) content += line + "\n"; byteWriter.write(content.substring(0, installClassStartPos + 1).getBytes()); byteWriter.write(nf.format(content.length()).getBytes()); byteWriter.write(content.substring(installClassStartPos + 1 + installClassStartStr.length()).getBytes()); installClassOffset = content.length(); content = null; FileInputStream classStream = new FileInputStream(instClassFile); byte[] buf = new byte[2048]; int read = classStream.read(buf); while (read > 0) { byteWriter.write(buf, 0, read); read = classStream.read(buf); } classStream.close(); reader.close(); byteWriter.close(); return installClassOffset; } | 12,298 |
1 | private void backupOriginalFile(String myFile) { Date date = new Date(); SimpleDateFormat format = new SimpleDateFormat("yyyy-MM-dd_S"); String datePortion = format.format(date); try { FileInputStream fis = new FileInputStream(myFile); FileOutputStream fos = new FileOutputStream(myFile + "-" + datePortion + "_UserID" + ".html"); FileChannel fcin = fis.getChannel(); FileChannel fcout = fos.getChannel(); fcin.transferTo(0, fcin.size(), fcout); fcin.close(); fcout.close(); fis.close(); fos.close(); System.out.println("**** Backup of file made."); } catch (Exception e) { System.out.println(e); } } | public static void copyFile(File source, File dest) throws IOException { FileChannel in = null, out = null; try { in = new FileInputStream(source).getChannel(); out = new FileOutputStream(dest).getChannel(); 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(); } } | 12,299 |
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