label int64 0 1 | func1 stringlengths 173 53.1k | func2 stringlengths 173 53.1k | id int64 0 901k |
|---|---|---|---|
0 | private List<File> ungzipFile(File directory, File compressedFile) throws IOException { List<File> files = new ArrayList<File>(); TarArchiveInputStream in = new TarArchiveInputStream(new GZIPInputStream(new FileInputStream(compressedFile))); try { TarArchiveEntry entry = in.getNextTarEntry(); while (entry != null) { if (entry.isDirectory()) { log.warn("TAR archive contains directories which are being ignored"); entry = in.getNextTarEntry(); continue; } String fn = new File(entry.getName()).getName(); if (fn.startsWith(".")) { log.warn("TAR archive contains a hidden file which is being ignored"); entry = in.getNextTarEntry(); continue; } File targetFile = new File(directory, fn); if (targetFile.exists()) { log.warn("TAR archive contains duplicate filenames, only the first is being extracted"); entry = in.getNextTarEntry(); continue; } files.add(targetFile); log.debug("Extracting file: " + entry.getName() + " to: " + targetFile.getAbsolutePath()); OutputStream fout = new BufferedOutputStream(new FileOutputStream(targetFile)); InputStream entryIn = new FileInputStream(entry.getFile()); IOUtils.copy(entryIn, fout); fout.close(); entryIn.close(); } } finally { in.close(); } return files; } | public static String generateMessageId(String plain) { byte[] cipher = new byte[35]; String messageId = null; try { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.update(plain.getBytes()); cipher = md5.digest(); StringBuffer sb = new StringBuffer(); for (int i = 0; i < cipher.length; i++) { String hex = Integer.toHexString(0xff & cipher[i]); if (hex.length() == 1) sb.append('0'); sb.append(hex); } StringBuffer pass = new StringBuffer(); pass.append(sb.substring(0, 6)); pass.append("H"); pass.append(sb.substring(6, 11)); pass.append("H"); pass.append(sb.substring(11, 21)); pass.append("H"); pass.append(sb.substring(21)); messageId = new String(pass); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } return messageId; } | 884,600 |
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!"); } | private void installBinaryFile(File source, File destination) { byte[] buffer = new byte[8192]; FileInputStream fis = null; FileOutputStream fos = null; try { fis = new FileInputStream(source); fos = new FileOutputStream(destination); int read; while ((read = fis.read(buffer)) != -1) { fos.write(buffer, 0, read); } } catch (FileNotFoundException e) { } catch (IOException e) { new ProjectCreateException(e, "Failed to read binary file: %1$s", source.getAbsolutePath()); } finally { if (fis != null) { try { fis.close(); } catch (IOException e) { } } if (fos != null) { try { fos.close(); } catch (IOException e) { } } } } | 884,601 |
0 | public static String getMD5Str(String str) { MessageDigest messageDigest = null; try { messageDigest = MessageDigest.getInstance("MD5"); messageDigest.reset(); messageDigest.update(str.getBytes("UTF-8")); } catch (NoSuchAlgorithmException e) { System.out.println("NoSuchAlgorithmException caught!"); System.exit(-1); } catch (UnsupportedEncodingException e) { e.printStackTrace(); } byte[] byteArray = messageDigest.digest(); StringBuffer md5StrBuff = new StringBuffer(); for (int i = 0; i < byteArray.length; i++) { if (Integer.toHexString(0xFF & byteArray[i]).length() == 1) md5StrBuff.append("0").append(Integer.toHexString(0xFF & byteArray[i])); else md5StrBuff.append(Integer.toHexString(0xFF & byteArray[i])); } return md5StrBuff.toString(); } | public static void BubbleSortInt2(int[] num) { int last_exchange; int right_border = num.length - 1; do { last_exchange = 0; for (int j = 0; j < num.length - 1; j++) { if (num[j] > num[j + 1]) { int temp = num[j]; num[j] = num[j + 1]; num[j + 1] = temp; last_exchange = j; } } right_border = last_exchange; } while (right_border > 0); } | 884,602 |
1 | public void zipUp() throws PersistenceException { ZipOutputStream out = null; try { if (!backup.exists()) backup.createNewFile(); out = new ZipOutputStream(new FileOutputStream(backup)); out.setLevel(Deflater.DEFAULT_COMPRESSION); for (String file : backupDirectory.list()) { logger.debug("Deflating: " + file); FileInputStream in = null; try { in = new FileInputStream(new File(backupDirectory, file)); out.putNextEntry(new ZipEntry(file)); IOUtils.copy(in, out); } finally { out.closeEntry(); if (null != in) in.close(); } } FileUtils.deleteDirectory(backupDirectory); } catch (Exception ex) { logger.error("Unable to ZIP the backup {" + backupDirectory.getAbsolutePath() + "}.", ex); throw new PersistenceException(ex); } finally { try { if (null != out) out.close(); } catch (IOException e) { logger.error("Unable to close ZIP output stream.", e); } } } | private static void doCopyFile(File srcFile, File destFile, boolean preserveFileDate) throws IOException { if (destFile.exists() && destFile.isDirectory()) { throw new IOException("Destination '" + destFile + "' exists but is a directory"); } FileInputStream input = new FileInputStream(srcFile); try { FileOutputStream output = new FileOutputStream(destFile); try { IOUtils.copy(input, output); } finally { IOUtils.closeQuietly(output); } } finally { IOUtils.closeQuietly(input); } if (srcFile.length() != destFile.length()) { throw new IOException("Failed to copy full contents from '" + srcFile + "' to '" + destFile + "'"); } if (preserveFileDate) { destFile.setLastModified(srcFile.lastModified()); } } | 884,603 |
1 | public void create_list() { try { String data = URLEncoder.encode("PHPSESSID", "UTF-8") + "=" + URLEncoder.encode(this.get_session(), "UTF-8"); URL url = new URL(URL_LOLA + FILE_CREATE_LIST); URLConnection conn = url.openConnection(); conn.setDoOutput(true); OutputStreamWriter wr = new OutputStreamWriter(conn.getOutputStream()); wr.write(data); wr.flush(); BufferedReader rd = new BufferedReader(new InputStreamReader(conn.getInputStream())); String line; line = rd.readLine(); wr.close(); rd.close(); System.out.println("Gene list saved in LOLA"); } catch (Exception e) { System.out.println("error in createList()"); e.printStackTrace(); } } | public 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(); } | 884,604 |
1 | public static Checksum checksum(File file, Checksum checksum) throws IOException { if (file.isDirectory()) { throw new IllegalArgumentException("Checksums can't be computed on directories"); } InputStream in = null; try { in = new CheckedInputStream(new FileInputStream(file), checksum); IOUtils.copy(in, new OutputStream() { @Override public void write(byte[] b, int off, int len) { } @Override public void write(int b) { } @Override public void write(byte[] b) throws IOException { } }); } finally { IOUtils.closeQuietly(in); } return checksum; } | private void copyTemplateFile(String sourceRoot, String targetRoot, String extension) throws Exception { String inputFileName = sourceRoot + extension; String outputFileName = targetRoot + extension; System.out.println("Copying resource file: " + outputFileName); File inputFile = new File(inputFileName); if (!inputFile.exists() || !inputFile.canRead()) { throw new Exception("Could not read from the file " + inputFileName); } File outputFile = new File(outputFileName); if (!outputFile.exists()) { if (!outputFile.createNewFile() || !outputFile.canWrite()) throw new Exception("Could not write to the file " + outputFileName); } FileReader in = new FileReader(inputFile); FileWriter out = new FileWriter(outputFile); try { char[] buffer = new char[1024]; int nread = 0; while ((nread = in.read(buffer)) != -1) { out.write(buffer, 0, nread); } } finally { in.close(); out.close(); } } | 884,605 |
0 | public static void copyFile(File from, File to) throws IOException { ensureFile(to); FileChannel srcChannel = new FileInputStream(from).getChannel(); FileChannel dstChannel = new FileOutputStream(to).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } | public final void conectar() throws IOException, FTPException { ftp = null; ftp = new FTPClient(); ftp.setRemoteHost(cfg.getFTPHost()); ftp.connect(); ftp.login(cfg.getFTPUser(), cfg.getFTPPass()); ftp.setProgressMonitor(pMonitor); ftp.setConnectMode(FTPConnectMode.PASV); ftp.setType(FTPTransferType.BINARY); } | 884,606 |
1 | public static boolean decodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.DECODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | public void command() { JFileChooser chooser = new JFileChooser(); chooser.setCurrentDirectory(new File(dir)); int returnVal = chooser.showOpenDialog(null); if (returnVal == JFileChooser.APPROVE_OPTION) { filename = chooser.getSelectedFile().getAbsolutePath(); String f2 = ""; for (int i = 0; i < filename.length(); ++i) { if (filename.charAt(i) != '\\') { f2 = f2 + filename.charAt(i); } else f2 = f2 + '/'; } filename = f2; if (filename.contains(dir)) { filename = filename.substring(dir.length()); } else { try { FileChannel srcFile = new FileInputStream(filename).getChannel(); FileChannel dstFile; filename = "ueditor_files/" + chooser.getSelectedFile().getName(); File newFile; if (!(newFile = new File(dir + filename)).createNewFile()) { dstFile = new FileInputStream(dir + filename).getChannel(); newFile = null; } else { dstFile = new FileOutputStream(newFile).getChannel(); } dstFile.transferFrom(srcFile, 0, srcFile.size()); srcFile.close(); dstFile.close(); System.out.println("file copyed to: " + dir + filename); } catch (Exception e) { e.printStackTrace(); label.setIcon(InputText.iconX); filename = null; for (Group g : groups) { g.updateValidity(true); } return; } } label.setIcon(InputText.iconV); for (Group g : groups) { g.updateValidity(true); } } } | 884,607 |
0 | 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 AudioFileFormat getAudioFileFormat(URL url) throws UnsupportedAudioFileException, IOException { InputStream stream = url.openStream(); AudioFileFormat format; try { format = getAudioFileFormat(new BufferedInputStream(stream)); } finally { stream.close(); } return format; } | 884,608 |
1 | public static boolean encodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.ENCODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | public static void copyFile(String fromFilePath, String toFilePath, boolean overwrite) throws IOException { File fromFile = new File(fromFilePath); File toFile = new File(toFilePath); if (!fromFile.exists()) throw new IOException("FileCopy: " + "no such source file: " + fromFilePath); if (!fromFile.isFile()) throw new IOException("FileCopy: " + "can't copy directory: " + fromFilePath); if (!fromFile.canRead()) throw new IOException("FileCopy: " + "source file is unreadable: " + fromFilePath); if (toFile.isDirectory()) toFile = new File(toFile, fromFile.getName()); if (toFile.exists()) { if (!overwrite) { throw new IOException(toFilePath + " already exists!"); } if (!toFile.canWrite()) { throw new IOException("FileCopy: destination file is unwriteable: " + toFilePath); } String parent = toFile.getParent(); if (parent == null) { parent = System.getProperty("user.dir"); } File dir = new File(parent); if (!dir.exists()) { throw new IOException("FileCopy: destination directory doesn't exist: " + parent); } if (dir.isFile()) { throw new IOException("FileCopy: destination is not a directory: " + parent); } if (!dir.canWrite()) { throw new IOException("FileCopy: destination directory is unwriteable: " + parent); } } FileInputStream from = null; FileOutputStream to = null; try { from = new FileInputStream(fromFile); to = new FileOutputStream(toFile); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = from.read(buffer)) != -1) to.write(buffer, 0, bytesRead); } finally { long lastModified = fromFile.lastModified(); toFile.setLastModified(lastModified); if (from != null) { try { from.close(); } catch (IOException e) { } } if (to != null) { try { to.close(); } catch (IOException e) { } } } } | 884,609 |
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 void zipDirectory(String dir, String zipfile) throws IOException, IllegalArgumentException { File d = new File(dir); if (!d.isDirectory()) throw new IllegalArgumentException("Not a directory: " + dir); String[] entries = d.list(); byte[] buffer = new byte[4096]; int bytesRead; ZipOutputStream out = new ZipOutputStream(new FileOutputStream(zipfile)); for (int i = 0; i < entries.length; i++) { File f = new File(d, entries[i]); if (f.isDirectory()) continue; FileInputStream in = new FileInputStream(f); ZipEntry entry = new ZipEntry(f.getPath()); out.putNextEntry(entry); while ((bytesRead = in.read(buffer)) != -1) out.write(buffer, 0, bytesRead); in.close(); } out.close(); } | 884,610 |
0 | private void makeConn(String filename1, String filename2) { String basename = "http://www.bestmm.com/"; String urlname = basename + filename1 + "/pic/" + filename2 + ".jpg"; URL url = null; try { url = new URL(urlname); } catch (MalformedURLException e) { System.err.println("URL Format Error!"); System.exit(1); } try { conn = (HttpURLConnection) url.openConnection(); } catch (IOException e) { System.err.println("Error IO"); System.exit(2); } } | private 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); } | 884,611 |
0 | 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 void init() throws IOException { if (this.inputStream == null) this.inputStream = new BufferedInputStream(url.openStream()); else { this.inputStream.close(); this.inputStream = new BufferedInputStream(url.openStream()); } } | 884,612 |
0 | public Configuration(URL url) { InputStream in = null; try { load(in = url.openStream()); } catch (Exception e) { throw new RuntimeException("Could not load configuration from " + url, e); } finally { if (in != null) { try { in.close(); } catch (IOException ignore) { } } } } | public static synchronized void repartition(File[] sourceFiles, File targetDirectory, String prefix, long maxUnitBases, long maxUnitEntries) throws Exception { if (!targetDirectory.exists()) { if (!targetDirectory.mkdirs()) throw new Exception("Could not create directory " + targetDirectory.getAbsolutePath()); } File tmpFile = new File(targetDirectory, "tmp.fasta"); FileOutputStream fos = new FileOutputStream(tmpFile); FileChannel fco = fos.getChannel(); for (File file : sourceFiles) { FileInputStream fis = new FileInputStream(file); FileChannel fci = fis.getChannel(); ByteBuffer buffer = ByteBuffer.allocate(64000); while (fci.read(buffer) > 0) { buffer.flip(); fco.write(buffer); buffer.clear(); } fci.close(); } fco.close(); FastaFile fastaFile = new FastaFile(tmpFile); fastaFile.split(targetDirectory, prefix, maxUnitBases, maxUnitEntries); tmpFile.delete(); } | 884,613 |
1 | public void delUser(User user) throws SQLException, IOException, ClassNotFoundException { String dbUserID; String stockSymbol; Statement stmt = con.createStatement(); try { con.setAutoCommit(false); dbUserID = user.getUserID(); if (getUser(dbUserID) != null) { ResultSet rs1 = stmt.executeQuery("SELECT userID, symbol " + "FROM UserStocks WHERE userID = '" + dbUserID + "'"); while (rs1.next()) { try { stockSymbol = rs1.getString("symbol"); delUserStocks(dbUserID, stockSymbol); } catch (SQLException ex) { throw new SQLException("Deletion of user stock holding failed: " + ex.getMessage()); } } try { stmt.executeUpdate("DELETE FROM Users WHERE " + "userID = '" + dbUserID + "'"); } catch (SQLException ex) { throw new SQLException("User deletion failed: " + ex.getMessage()); } } else throw new IOException("User not found in database - cannot delete."); try { con.commit(); } catch (SQLException ex) { throw new SQLException("Transaction commit failed: " + ex.getMessage()); } } catch (SQLException ex) { try { con.rollback(); } catch (SQLException sqx) { throw new SQLException("Transaction failed then rollback failed: " + sqx.getMessage()); } throw new SQLException("Transaction failed; was rolled back: " + ex.getMessage()); } stmt.close(); } | public ProgramProfilingSymbol deleteProfilingSymbol(int id) throws AdaptationException { ProgramProfilingSymbol profilingSymbol = null; Connection connection = null; Statement statement = null; ResultSet resultSet = null; try { String query = "SELECT * FROM ProgramProfilingSymbols " + "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 profiling " + "symbol failed."; log.error(msg); throw new AdaptationException(msg); } profilingSymbol = getProfilingSymbol(resultSet); query = "DELETE FROM ProgramProfilingSymbols " + "WHERE id = " + id; statement.executeUpdate(query); connection.commit(); } catch (SQLException ex) { try { connection.rollback(); } catch (Exception e) { } String msg = "SQLException in deleteProfilingSymbol"; 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 profilingSymbol; } | 884,614 |
1 | public boolean saveVideoXMLOnWebserver() { String text = ""; boolean erg = false; try { URL url = new URL("http://localhost:8080/virtPresenterVerwalter/videofile.jsp?id=" + this.getId()); HttpURLConnection http = (HttpURLConnection) url.openConnection(); BufferedReader in = new BufferedReader(new InputStreamReader(http.getInputStream())); String zeile = ""; while ((zeile = in.readLine()) != null) { text += zeile + "\n"; } in.close(); http.disconnect(); erg = saveVideoXMLOnWebserver(text); System.err.println("Job " + this.getId() + " erfolgreich bearbeitet!"); } catch (MalformedURLException e) { System.err.println("Job " + this.getId() + ": Konnte video.xml nicht erstellen. Verbindung konnte nicht aufgebaut werden."); return false; } catch (IOException e) { System.err.println("Job " + this.getId() + ": Konnte video.xml nicht erstellen. Konnte Daten nicht lesen/schreiben."); return false; } return erg; } | public static List<String> list() throws IOException { List<String> providers = new ArrayList<String>(); Enumeration<URL> urls = ClassLoader.getSystemResources("sentrick.classifiers"); while (urls.hasMoreElements()) { URL url = urls.nextElement(); String provider = null; BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); while ((provider = in.readLine()) != null) { provider = provider.trim(); if (provider.length() > 0) providers.add(provider); } in.close(); } return providers; } | 884,615 |
1 | private String hash(String message) { MessageDigest md = null; try { md = MessageDigest.getInstance("SHA1"); } catch (NoSuchAlgorithmException e) { throw new AssertionError("Can't find the SHA1 algorithm in the java.security package"); } String saltString = String.valueOf(12345); md.update(saltString.getBytes()); md.update(message.getBytes()); byte[] digestBytes = md.digest(); StringBuffer digestSB = new StringBuffer(); for (int i = 0; i < digestBytes.length; i++) { int lowNibble = digestBytes[i] & 0x0f; int highNibble = (digestBytes[i] >> 4) & 0x0f; digestSB.append(Integer.toHexString(highNibble)); digestSB.append(Integer.toHexString(lowNibble)); } String digestStr = digestSB.toString().trim(); return digestStr; } | private void getRandomGuid(boolean secure) { MessageDigest md5 = null; StringBuffer sbValueBeforeMD5 = new StringBuffer(); try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { throw new RuntimeException(e); } long time = System.currentTimeMillis(); long rand = 0; if (secure) { rand = secureRandom.nextLong(); } else { rand = random.nextLong(); } sbValueBeforeMD5.append(id); sbValueBeforeMD5.append(":"); sbValueBeforeMD5.append(Long.toString(time)); sbValueBeforeMD5.append(":"); sbValueBeforeMD5.append(Long.toString(rand)); String 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)); } guid = sb.toString(); } | 884,616 |
1 | public static void main(String[] args) throws Exception { String linesep = System.getProperty("line.separator"); FileOutputStream fos = new FileOutputStream(new File("lib-licenses.txt")); fos.write(new String("JCP contains the following libraries. Please read this for comments on copyright etc." + linesep + linesep).getBytes()); fos.write(new String("Chemistry Development Kit, master version as of " + new Date().toString() + " (http://cdk.sf.net)" + linesep).getBytes()); fos.write(new String("Copyright 1997-2009 The CDK Development Team" + linesep).getBytes()); fos.write(new String("License: LGPL v2 (http://www.gnu.org/licenses/old-licenses/gpl-2.0.html)" + linesep).getBytes()); fos.write(new String("Download: https://sourceforge.net/projects/cdk/files/" + linesep).getBytes()); fos.write(new String("Source available at: http://sourceforge.net/scm/?type=git&group_id=20024" + linesep + linesep).getBytes()); File[] files = new File(args[0]).listFiles(new JarFileFilter()); for (int i = 0; i < files.length; i++) { if (new File(files[i].getPath() + ".meta").exists()) { Map<String, Map<String, String>> metaprops = readProperties(new File(files[i].getPath() + ".meta")); Iterator<String> itsect = metaprops.keySet().iterator(); while (itsect.hasNext()) { String section = itsect.next(); fos.write(new String(metaprops.get(section).get("Library") + " " + metaprops.get(section).get("Version") + " (" + metaprops.get(section).get("Homepage") + ")" + linesep).getBytes()); fos.write(new String("Copyright " + metaprops.get(section).get("Copyright") + linesep).getBytes()); fos.write(new String("License: " + metaprops.get(section).get("License") + " (" + metaprops.get(section).get("LicenseURL") + ")" + linesep).getBytes()); fos.write(new String("Download: " + metaprops.get(section).get("Download") + linesep).getBytes()); fos.write(new String("Source available at: " + metaprops.get(section).get("SourceCode") + linesep + linesep).getBytes()); } } if (new File(files[i].getPath() + ".extra").exists()) { fos.write(new String("The author says:" + linesep).getBytes()); FileInputStream in = new FileInputStream(new File(files[i].getPath() + ".extra")); int len; byte[] buf = new byte[1024]; while ((len = in.read(buf)) > 0) { fos.write(buf, 0, len); } } fos.write(linesep.getBytes()); } fos.close(); } | private void copyFileToDir(MyFile file, MyFile to, wlPanel panel) throws IOException { Utilities.print("started copying " + file.getAbsolutePath() + "\n"); FileOutputStream fos = new FileOutputStream(new File(to.getAbsolutePath())); FileChannel foc = fos.getChannel(); FileInputStream fis = new FileInputStream(new File(file.getAbsolutePath())); FileChannel fic = fis.getChannel(); Date d1 = new Date(); long amount = foc.transferFrom(fic, rest, fic.size() - rest); fic.close(); foc.force(false); foc.close(); Date d2 = new Date(); long time = d2.getTime() - d1.getTime(); double secs = time / 1000.0; double rate = amount / secs; frame.getStatusArea().append(secs + "s " + "amount: " + Utilities.humanReadable(amount) + " rate: " + Utilities.humanReadable(rate) + "/s\n", "black"); panel.updateView(); } | 884,617 |
1 | private final long test(final boolean applyFilter, final int executionCount) throws NoSuchAlgorithmException, NoSuchPaddingException, FileNotFoundException, IOException, RuleLoadingException { final boolean stripHtmlEnabled = true; final boolean injectSecretTokensEnabled = true; final boolean encryptQueryStringsEnabled = true; final boolean protectParamsAndFormsEnabled = true; final boolean applyExtraProtectionForDisabledFormFields = true; final boolean applyExtraProtectionForReadonlyFormFields = false; final boolean applyExtraProtectionForRequestParamValueCount = false; final ContentInjectionHelper helper = new ContentInjectionHelper(); final RuleFileLoader ruleFileLoaderModificationExcludes = new ClasspathZipRuleFileLoader(); ruleFileLoaderModificationExcludes.setPath(RuleParameter.MODIFICATION_EXCLUDES_DEFAULT.getValue()); final ContentModificationExcludeDefinitionContainer containerModExcludes = new ContentModificationExcludeDefinitionContainer(ruleFileLoaderModificationExcludes); containerModExcludes.parseDefinitions(); helper.setContentModificationExcludeDefinitions(containerModExcludes); final AttackHandler attackHandler = new AttackHandler(null, 123, 600000, 100000, 300000, 300000, null, "MOCK", false, false, 0, false, false, Pattern.compile("sjghggfakgfjagfgajgfjasgfs"), Pattern.compile("sjghggfakgfjagfgajgfjasgfs"), true, new AttackMailHandler()); final SessionCreationTracker sessionCreationTracker = new SessionCreationTracker(attackHandler, 0, 600000, 300000, 0, "", "", "", ""); final RequestWrapper request = new RequestWrapper(new RequestMock(), helper, sessionCreationTracker, "123.456.789.000", false, true, true); final RuleFileLoader ruleFileLoaderResponseModifications = new ClasspathZipRuleFileLoader(); ruleFileLoaderResponseModifications.setPath(RuleParameter.RESPONSE_MODIFICATIONS_DEFAULT.getValue()); final ResponseModificationDefinitionContainer container = new ResponseModificationDefinitionContainer(ruleFileLoaderResponseModifications); container.parseDefinitions(); final ResponseModificationDefinition[] responseModificationDefinitions = downCast(container.getAllEnabledRequestDefinitions()); final List<Pattern> tmpPatternsToExcludeCompleteTag = new ArrayList<Pattern>(responseModificationDefinitions.length); final List<Pattern> tmpPatternsToExcludeCompleteScript = new ArrayList<Pattern>(responseModificationDefinitions.length); final List<Pattern> tmpPatternsToExcludeLinksWithinScripts = new ArrayList<Pattern>(responseModificationDefinitions.length); final List<Pattern> tmpPatternsToExcludeLinksWithinTags = new ArrayList<Pattern>(responseModificationDefinitions.length); final List<Pattern> tmpPatternsToCaptureLinksWithinScripts = new ArrayList<Pattern>(responseModificationDefinitions.length); final List<Pattern> tmpPatternsToCaptureLinksWithinTags = new ArrayList<Pattern>(responseModificationDefinitions.length); final List<WordDictionary> tmpPrefiltersToExcludeCompleteTag = new ArrayList<WordDictionary>(responseModificationDefinitions.length); final List<WordDictionary> tmpPrefiltersToExcludeCompleteScript = new ArrayList<WordDictionary>(responseModificationDefinitions.length); final List<WordDictionary> tmpPrefiltersToExcludeLinksWithinScripts = new ArrayList<WordDictionary>(responseModificationDefinitions.length); final List<WordDictionary> tmpPrefiltersToExcludeLinksWithinTags = new ArrayList<WordDictionary>(responseModificationDefinitions.length); final List<WordDictionary> tmpPrefiltersToCaptureLinksWithinScripts = new ArrayList<WordDictionary>(responseModificationDefinitions.length); final List<WordDictionary> tmpPrefiltersToCaptureLinksWithinTags = new ArrayList<WordDictionary>(responseModificationDefinitions.length); final List<Integer[]> tmpGroupNumbersToCaptureLinksWithinScripts = new ArrayList<Integer[]>(responseModificationDefinitions.length); final List<Integer[]> tmpGroupNumbersToCaptureLinksWithinTags = new ArrayList<Integer[]>(responseModificationDefinitions.length); for (int i = 0; i < responseModificationDefinitions.length; i++) { final ResponseModificationDefinition responseModificationDefinition = responseModificationDefinitions[i]; if (responseModificationDefinition.isMatchesScripts()) { tmpPatternsToExcludeCompleteScript.add(responseModificationDefinition.getScriptExclusionPattern()); tmpPrefiltersToExcludeCompleteScript.add(responseModificationDefinition.getScriptExclusionPrefilter()); tmpPatternsToExcludeLinksWithinScripts.add(responseModificationDefinition.getUrlExclusionPattern()); tmpPrefiltersToExcludeLinksWithinScripts.add(responseModificationDefinition.getUrlExclusionPrefilter()); tmpPatternsToCaptureLinksWithinScripts.add(responseModificationDefinition.getUrlCapturingPattern()); tmpPrefiltersToCaptureLinksWithinScripts.add(responseModificationDefinition.getUrlCapturingPrefilter()); tmpGroupNumbersToCaptureLinksWithinScripts.add(ServerUtils.convertSimpleToObjectArray(responseModificationDefinition.getCapturingGroupNumbers())); } if (responseModificationDefinition.isMatchesTags()) { tmpPatternsToExcludeCompleteTag.add(responseModificationDefinition.getTagExclusionPattern()); tmpPrefiltersToExcludeCompleteTag.add(responseModificationDefinition.getTagExclusionPrefilter()); tmpPatternsToExcludeLinksWithinTags.add(responseModificationDefinition.getUrlExclusionPattern()); tmpPrefiltersToExcludeLinksWithinTags.add(responseModificationDefinition.getUrlExclusionPrefilter()); tmpPatternsToCaptureLinksWithinTags.add(responseModificationDefinition.getUrlCapturingPattern()); tmpPrefiltersToCaptureLinksWithinTags.add(responseModificationDefinition.getUrlCapturingPrefilter()); tmpGroupNumbersToCaptureLinksWithinTags.add(ServerUtils.convertSimpleToObjectArray(responseModificationDefinition.getCapturingGroupNumbers())); } } final Matcher[] matchersToExcludeCompleteTag = ServerUtils.convertListOfPatternToArrayOfMatcher(tmpPatternsToExcludeCompleteTag); final Matcher[] matchersToExcludeCompleteScript = ServerUtils.convertListOfPatternToArrayOfMatcher(tmpPatternsToExcludeCompleteScript); final Matcher[] matchersToExcludeLinksWithinScripts = ServerUtils.convertListOfPatternToArrayOfMatcher(tmpPatternsToExcludeLinksWithinScripts); final Matcher[] matchersToExcludeLinksWithinTags = ServerUtils.convertListOfPatternToArrayOfMatcher(tmpPatternsToExcludeLinksWithinTags); final Matcher[] matchersToCaptureLinksWithinScripts = ServerUtils.convertListOfPatternToArrayOfMatcher(tmpPatternsToCaptureLinksWithinScripts); final Matcher[] matchersToCaptureLinksWithinTags = ServerUtils.convertListOfPatternToArrayOfMatcher(tmpPatternsToCaptureLinksWithinTags); final WordDictionary[] prefiltersToExcludeCompleteTag = (WordDictionary[]) tmpPrefiltersToExcludeCompleteTag.toArray(new WordDictionary[0]); final WordDictionary[] prefiltersToExcludeCompleteScript = (WordDictionary[]) tmpPrefiltersToExcludeCompleteScript.toArray(new WordDictionary[0]); final WordDictionary[] prefiltersToExcludeLinksWithinScripts = (WordDictionary[]) tmpPrefiltersToExcludeLinksWithinScripts.toArray(new WordDictionary[0]); final WordDictionary[] prefiltersToExcludeLinksWithinTags = (WordDictionary[]) tmpPrefiltersToExcludeLinksWithinTags.toArray(new WordDictionary[0]); final WordDictionary[] prefiltersToCaptureLinksWithinScripts = (WordDictionary[]) tmpPrefiltersToCaptureLinksWithinScripts.toArray(new WordDictionary[0]); final WordDictionary[] prefiltersToCaptureLinksWithinTags = (WordDictionary[]) tmpPrefiltersToCaptureLinksWithinTags.toArray(new WordDictionary[0]); final int[][] groupNumbersToCaptureLinksWithinScripts = ServerUtils.convertArrayIntegerListTo2DimIntArray(tmpGroupNumbersToCaptureLinksWithinScripts); final int[][] groupNumbersToCaptureLinksWithinTags = ServerUtils.convertArrayIntegerListTo2DimIntArray(tmpGroupNumbersToCaptureLinksWithinTags); final Cipher cipher = CryptoUtils.getCipher(); final CryptoKeyAndSalt key = CryptoUtils.generateRandomCryptoKeyAndSalt(false); Cipher.getInstance("AES"); MessageDigest.getInstance("SHA-1"); final ResponseWrapper response = new ResponseWrapper(new ResponseMock(), request, attackHandler, helper, false, "___ENCRYPTED___", cipher, key, "___SEC-KEY___", "___SEC-VALUE___", "___PROT-KEY___", false, false, false, false, "123.456.789.000", new HashSet(), prefiltersToExcludeCompleteScript, matchersToExcludeCompleteScript, prefiltersToExcludeCompleteTag, matchersToExcludeCompleteTag, prefiltersToExcludeLinksWithinScripts, matchersToExcludeLinksWithinScripts, prefiltersToExcludeLinksWithinTags, matchersToExcludeLinksWithinTags, prefiltersToCaptureLinksWithinScripts, matchersToCaptureLinksWithinScripts, prefiltersToCaptureLinksWithinTags, matchersToCaptureLinksWithinTags, groupNumbersToCaptureLinksWithinScripts, groupNumbersToCaptureLinksWithinTags, true, false, true, true, true, true, true, true, true, true, true, false, false, true, "", "", (short) 3, true, false, false); final List durations = new ArrayList(); for (int i = 0; i < executionCount; i++) { final long start = System.currentTimeMillis(); Reader reader = null; Writer writer = null; try { reader = new BufferedReader(new FileReader(this.htmlFile)); writer = new FileWriter(this.outputFile); if (applyFilter) { writer = new ResponseFilterWriter(writer, true, "http://127.0.0.1/test/sample", "/test", "/test", "___SEC-KEY___", "___SEC-VALUE___", "___PROT-KEY___", cipher, key, helper, "___ENCRYPTED___", request, response, stripHtmlEnabled, injectSecretTokensEnabled, protectParamsAndFormsEnabled, encryptQueryStringsEnabled, applyExtraProtectionForDisabledFormFields, applyExtraProtectionForReadonlyFormFields, applyExtraProtectionForRequestParamValueCount, prefiltersToExcludeCompleteScript, matchersToExcludeCompleteScript, prefiltersToExcludeCompleteTag, matchersToExcludeCompleteTag, prefiltersToExcludeLinksWithinScripts, matchersToExcludeLinksWithinScripts, prefiltersToExcludeLinksWithinTags, matchersToExcludeLinksWithinTags, prefiltersToCaptureLinksWithinScripts, matchersToCaptureLinksWithinScripts, prefiltersToCaptureLinksWithinTags, matchersToCaptureLinksWithinTags, groupNumbersToCaptureLinksWithinScripts, groupNumbersToCaptureLinksWithinTags, true, true, false, true, true, true, true, true, true, true, true, false, false, true, "", "", (short) 3, true, false); writer = new BufferedWriter(writer); } char[] chars = new char[16 * 1024]; int read; while ((read = reader.read(chars)) != -1) { if (read > 0) { writer.write(chars, 0, read); } } durations.add(new Long(System.currentTimeMillis() - start)); } finally { if (reader != null) { try { reader.close(); } catch (IOException ignored) { } } if (writer != null) { try { writer.close(); } catch (IOException ignored) { } } } } long sum = 0; for (final Iterator iter = durations.iterator(); iter.hasNext(); ) { Long value = (Long) iter.next(); sum += value.longValue(); } return sum / durations.size(); } | private void forcedCopy(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(); } } } | 884,618 |
1 | private RemoteObject createRemoteObject(final VideoEntry videoEntry, final RemoteContainer container) throws RemoteException { MessageDigest instance; try { instance = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { throw new RemoteException(StatusCreator.newStatus("Error creating MD5", e)); } StringWriter sw = new StringWriter(); YouTubeMediaGroup mediaGroup = videoEntry.getMediaGroup(); if (mediaGroup != null) { if (mediaGroup.getDescription() != null) { sw.append(mediaGroup.getDescription().getPlainTextContent()); } List<MediaCategory> keywordsGroup = mediaGroup.getCategories(); StringBuilder sb = new StringBuilder(); if (keywordsGroup != null) { for (MediaCategory mediaCategory : keywordsGroup) { sb.append(mediaCategory.getContent()); } } } instance.update(sw.toString().getBytes()); RemoteObject remoteVideo = InfomngmntFactory.eINSTANCE.createRemoteObject(); remoteVideo.setHash(asHex(instance.digest())); remoteVideo.setId(SiteInspector.getId(videoEntry.getHtmlLink().getHref())); remoteVideo.setName(videoEntry.getTitle().getPlainText()); remoteVideo.setRepositoryTypeObjectId(KEY_VIDEO); remoteVideo.setWrappedObject(videoEntry); setInternalUrl(remoteVideo, container); return remoteVideo; } | public static String hashURL(String url) { if (url == null) { throw new IllegalArgumentException("URL may not be null. "); } String result = null; try { MessageDigest md = MessageDigest.getInstance("SHA-1"); if (md != null) { md.reset(); md.update(url.getBytes()); BigInteger hash = new BigInteger(1, md.digest()); result = hash.toString(16); } md = null; } catch (NoSuchAlgorithmException ex) { result = null; } return result; } | 884,619 |
1 | public static String encrypt(String senha) { try { MessageDigest digest = MessageDigest.getInstance("MD5"); digest.update(senha.getBytes()); BASE64Encoder encoder = new BASE64Encoder(); return encoder.encode(digest.digest()); } catch (NoSuchAlgorithmException ns) { ns.printStackTrace(); return senha; } } | private String calculateHash(String s) { if (s == null) { return null; } MessageDigest messageDigest; try { messageDigest = MessageDigest.getInstance("SHA"); } catch (NoSuchAlgorithmException e) { logger.error("Could not find a message digest algorithm."); return null; } messageDigest.update(s.getBytes()); byte[] hash = messageDigest.digest(); StringBuilder sb = new StringBuilder(); for (byte b : hash) { sb.append(String.format("%02x", b)); } return sb.toString(); } | 884,620 |
0 | public static HttpResponse query(DefaultHttpClient httpclient, Request request, Proxy proxy, Log log) throws ClientProtocolException, IOException, MojoExecutionException { log.debug("preparing " + request); if (proxy != null) { log.info("setting up " + proxy + " for request " + request); proxy.prepare(httpclient); } HttpRequestBase httpRequest = request.buildHttpRequestBase(httpclient, log); HttpHost targetHost = request.buildHttpHost(log); log.debug("HTTP " + request.getMethod() + " url=" + request.getFinalUrl()); long responseTime = System.currentTimeMillis(); HttpResponse response = httpclient.execute(targetHost, httpRequest); log.debug("received response (time=" + (System.currentTimeMillis() - responseTime) + "ms) for request [" + "HTTP " + request.getMethod() + " url=" + request.getFinalUrl() + "]"); return response; } | public InputSource resolveEntity(String pPublicId, String pSystemId) throws SAXException, IOException { getCisUtils().debug("Resolving entity publicId=" + pPublicId + ", systemId=" + pSystemId); final String res; if ("-//Sun Microsystems, Inc.//DTD Web Application 2.3//EN".equals(pPublicId)) { res = "resources/web-app_2_3.dtd"; } else { return null; } URL url = getClass().getResource(res); if (url == null) { throw new SAXException("Failed to locate resource: " + res); } InputSource isource = new InputSource(url.openStream()); isource.setSystemId(url.toExternalForm()); return isource; } | 884,621 |
0 | public boolean checkPassword(String password, String digest) { boolean passwordMatch = false; MessageDigest sha = null; try { sha = MessageDigest.getInstance("SHA-1"); if (digest.regionMatches(true, 0, "{SHA}", 0, 5)) { digest = digest.substring(5); } else if (digest.regionMatches(true, 0, "{SSHA}", 0, 6)) { digest = digest.substring(6); } byte[][] hs = split(Base64.decode(digest.getBytes()), 20); byte[] hash = hs[0]; byte[] salt = hs[1]; sha.reset(); sha.update(password.getBytes()); sha.update(salt); byte[] pwhash = sha.digest(); if (MessageDigest.isEqual(hash, pwhash)) { passwordMatch = true; } } catch (NoSuchAlgorithmException nsae) { CofaxToolsUtil.log("Algorithme SHA-1 non supporte a la verification du password" + nsae + id); } return passwordMatch; } | public void concatFiles() throws IOException { Writer writer = null; try { final File targetFile = new File(getTargetDirectory(), getTargetFile()); targetFile.getParentFile().mkdirs(); if (null != getEncoding()) { getLog().info("Writing aggregated file with encoding '" + getEncoding() + "'"); writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(targetFile), getEncoding())); } else { getLog().info("WARNING: writing aggregated file with system encoding"); writer = new FileWriter(targetFile); } for (File file : getFiles()) { Reader reader = null; try { if (null != getEncoding()) { getLog().info("Reading file " + file.getCanonicalPath() + " with encoding '" + getEncoding() + "'"); reader = new BufferedReader(new InputStreamReader(new FileInputStream(file), getEncoding())); } else { getLog().info("WARNING: Reading file " + file.getCanonicalPath() + " with system encoding"); reader = new FileReader(file); } IOUtils.copy(reader, writer); final String delimiter = getDelimiter(); if (delimiter != null) { writer.write(delimiter.toCharArray()); } } finally { IOUtils.closeQuietly(reader); } } } finally { IOUtils.closeQuietly(writer); } } | 884,622 |
0 | public void add(AddInterceptorChain chain, Entry entry, LDAPConstraints constraints) throws LDAPException { Connection con = (Connection) chain.getRequest().get(JdbcInsert.MYVD_DB_CON + this.dbInsertName); if (con == null) { throw new LDAPException("Operations Error", LDAPException.OPERATIONS_ERROR, "No Database Connection"); } try { con.setAutoCommit(false); HashMap<String, String> db2ldap = (HashMap<String, String>) chain.getRequest().get(JdbcInsert.MYVD_DB_DB2LDAP + this.dbInsertName); String uid = ((RDN) (new DN(entry.getEntry().getDN())).getRDNs().get(0)).getValue(); PreparedStatement ps = con.prepareStatement(this.insertSQL); for (int i = 0; i < this.fields.size(); i++) { String field = this.fields.get(i); if (field.equals(this.rdnField)) { ps.setString(i + 1, uid); } else { ps.setString(i + 1, entry.getEntry().getAttribute(db2ldap.get(field)).getStringValue()); } } ps.executeUpdate(); con.commit(); } catch (SQLException e) { try { con.rollback(); } catch (SQLException e1) { throw new LDAPException("Could not delete entry or rollback transaction", LDAPException.OPERATIONS_ERROR, e.toString(), e); } throw new LDAPException("Could not delete entry", LDAPException.OPERATIONS_ERROR, e.toString(), e); } } | 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); } | 884,623 |
1 | public void copy(File source, File destination) { try { FileInputStream fileInputStream = new FileInputStream(source); FileOutputStream fileOutputStream = new FileOutputStream(destination); FileChannel inputChannel = fileInputStream.getChannel(); FileChannel outputChannel = fileOutputStream.getChannel(); transfer(inputChannel, outputChannel, source.length(), 1024 * 1024 * 32, true, true); fileInputStream.close(); fileOutputStream.close(); } catch (Exception e) { e.printStackTrace(); } } | public static void copy_file(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) { ; } } } | 884,624 |
1 | public static String encode(String plaintext) { try { MessageDigest md = MessageDigest.getInstance("SHA"); md.update(plaintext.getBytes("UTF-8")); byte raw[] = md.digest(); String hash = (new BASE64Encoder()).encode(raw); return hash; } catch (Exception e) { e.printStackTrace(); throw new RuntimeException("Could not encrypt password for ISA db verification"); } } | public static String encryptPassword(String password) { try { MessageDigest md = MessageDigest.getInstance("SHA"); md.update(password.getBytes()); byte[] hash = md.digest(); StringBuilder hashStringBuf = new StringBuilder("{SHA}"); String byteString; int byteLength; for (int index = 0; index < hash.length; index++) { byteString = String.valueOf(hash[index] + 128); byteLength = byteString.length(); switch(byteLength) { case 1: byteString = "00" + byteString; break; case 2: byteString = "0" + byteString; break; } hashStringBuf.append(byteString); } return hashStringBuf.toString(); } catch (NoSuchAlgorithmException nsae) { log.error("Error getting password hash - " + nsae.getMessage()); return null; } } | 884,625 |
0 | private void publishMap(LWMap map) throws IOException { File savedMap = PublishUtil.saveMap(map); InputStream istream = new BufferedInputStream(new FileInputStream(savedMap)); OutputStream ostream = new BufferedOutputStream(new FileOutputStream(ActionUtil.selectFile("ConceptMap", "vue"))); int fileLength = (int) savedMap.length(); byte bytes[] = new byte[fileLength]; while (istream.read(bytes, 0, fileLength) != -1) ostream.write(bytes, 0, fileLength); istream.close(); ostream.close(); } | public long getLastModified() { if (lastModified == 0) { if (connection == null) try { connection = url.openConnection(); } catch (IOException e) { } if (connection != null) lastModified = connection.getLastModified(); } return lastModified; } | 884,626 |
0 | private void simulate() throws Exception { BufferedWriter out = null; out = new BufferedWriter(new FileWriter(outFile)); out.write("#Thread\tReputation\tAction\n"); out.flush(); System.out.println("Simulate..."); File file = new File(trsDemoSimulationfile); ObtainUserReputation obtainUserReputationRequest = new ObtainUserReputation(); ObtainUserReputationResponse obtainUserReputationResponse; RateUser rateUserRequest; RateUserResponse rateUserResponse; FileInputStream fis = new FileInputStream(file); BufferedReader br = new BufferedReader(new InputStreamReader(fis)); String call = br.readLine(); while (call != null) { rateUserRequest = generateRateUserRequest(call); try { rateUserResponse = trsPort.rateUser(rateUserRequest); System.out.println("----------------R A T I N G-------------------"); System.out.println("VBE: " + rateUserRequest.getVbeId()); System.out.println("VO: " + rateUserRequest.getVoId()); System.out.println("USER: " + rateUserRequest.getUserId()); System.out.println("SERVICE: " + rateUserRequest.getServiceId()); System.out.println("ACTION: " + rateUserRequest.getActionId()); System.out.println("OUTCOME: " + rateUserResponse.isOutcome()); System.out.println("----------------------------------------------"); assertEquals("The outcome field of the rateUser should be true: MESSAGE=" + rateUserResponse.getMessage(), true, rateUserResponse.isOutcome()); } catch (RemoteException e) { fail(e.getMessage()); } obtainUserReputationRequest.setIoi(null); obtainUserReputationRequest.setServiceId(null); obtainUserReputationRequest.setUserId(rateUserRequest.getUserId()); obtainUserReputationRequest.setVbeId(rateUserRequest.getVbeId()); obtainUserReputationRequest.setVoId(null); try { obtainUserReputationResponse = trsPort.obtainUserReputation(obtainUserReputationRequest); System.out.println("-----------R E P U T A T I O N----------------"); System.out.println("VBE: " + obtainUserReputationRequest.getVbeId()); System.out.println("VO: " + obtainUserReputationRequest.getVoId()); System.out.println("USER: " + obtainUserReputationRequest.getUserId()); System.out.println("SERVICE: " + obtainUserReputationRequest.getServiceId()); System.out.println("IOI: " + obtainUserReputationRequest.getIoi()); System.out.println("REPUTATION: " + obtainUserReputationResponse.getReputation()); System.out.println("----------------------------------------------"); assertEquals("The outcome field of the obtainUserReputation should be true: MESSAGE=" + obtainUserReputationResponse.getMessage(), true, obtainUserReputationResponse.isOutcome()); assertEquals(0.0, obtainUserReputationResponse.getReputation(), 1.0); } catch (RemoteException e) { fail(e.getMessage()); } obtainUserReputationRequest.setIoi(null); obtainUserReputationRequest.setServiceId(null); obtainUserReputationRequest.setUserId(rateUserRequest.getUserId()); obtainUserReputationRequest.setVbeId(rateUserRequest.getVbeId()); obtainUserReputationRequest.setVoId(rateUserRequest.getVoId()); try { obtainUserReputationResponse = trsPort.obtainUserReputation(obtainUserReputationRequest); System.out.println("-----------R E P U T A T I O N----------------"); System.out.println("VBE: " + obtainUserReputationRequest.getVbeId()); System.out.println("VO: " + obtainUserReputationRequest.getVoId()); System.out.println("USER: " + obtainUserReputationRequest.getUserId()); System.out.println("SERVICE: " + obtainUserReputationRequest.getServiceId()); System.out.println("IOI: " + obtainUserReputationRequest.getIoi()); System.out.println("REPUTATION: " + obtainUserReputationResponse.getReputation()); System.out.println("----------------------------------------------"); assertEquals("The outcome field of the obtainUserReputation should be true: MESSAGE=" + obtainUserReputationResponse.getMessage(), true, obtainUserReputationResponse.isOutcome()); assertEquals(0.0, obtainUserReputationResponse.getReputation(), 1.0); } catch (RemoteException e) { fail(e.getMessage()); } call = br.readLine(); } fis.close(); br.close(); out.flush(); out.close(); } | public byte[] pipeBytes() { byte ba[] = null; try { URL url = new URL(server); conn = (HttpURLConnection) url.openConnection(); InputStream is = conn.getInputStream(); ByteArrayOutputStream tout = new ByteArrayOutputStream(); int nmax = 10000; byte b[] = new byte[nmax + 1]; int nread = 0; while ((nread = is.read(b, 0, nmax)) >= 0) tout.write(b, 0, nread); ba = tout.toByteArray(); } catch (Exception ex) { System.err.println(ex); } return ba; } | 884,627 |
1 | public void testBeAbleToDownloadAndUpload() throws IOException { OutputStream outputStream = fileSystem.createOutputStream(_("hello"), OutputMode.OVERWRITE); outputStream.write(new byte[] { 1, 2, 3 }); outputStream.close(); InputStream inputStream = fileSystem.createInputStream(_("hello")); ByteArrayOutputStream buffer = new ByteArrayOutputStream(); IOUtils.copy(inputStream, buffer); inputStream.close(); ensure.that(buffer.toByteArray()).eq(new byte[] { 1, 2, 3 }); } | public void doFilter(ServletRequest request, ServletResponse response, FilterChain chain) throws IOException, ServletException { if (!(request instanceof HttpServletRequest)) { log.fatal("not a http request"); return; } HttpServletRequest httpRequest = (HttpServletRequest) request; String uri = httpRequest.getRequestURI(); int pathStartIdx = 0; String resourceName = null; pathStartIdx = uri.indexOf(path); if (pathStartIdx <= -1) { log.fatal("the url pattern must match: " + path + " found uri: " + uri); return; } resourceName = uri.substring(pathStartIdx + path.length()); int suffixIdx = uri.lastIndexOf('.'); if (suffixIdx <= -1) { log.fatal("no file suffix found for resource: " + uri); return; } String suffix = uri.substring(suffixIdx + 1).toLowerCase(); String mimeType = (String) mimeTypes.get(suffix); if (mimeType == null) { log.fatal("no mimeType found for resource: " + uri); log.fatal("valid mimeTypes are: " + mimeTypes.keySet()); return; } String themeName = getThemeName(); if (themeName == null) { themeName = this.themeName; } if (!themeName.startsWith("/")) { themeName = "/" + themeName; } InputStream is = null; is = ResourceFilter.class.getResourceAsStream(themeName + resourceName); if (is != null) { IOUtils.copy(is, response.getOutputStream()); response.setContentType(mimeType); response.flushBuffer(); IOUtils.closeQuietly(response.getOutputStream()); IOUtils.closeQuietly(is); } else { log.fatal("error loading resource: " + resourceName); } } | 884,628 |
0 | private void insert() throws SQLException, NamingException { Logger logger = getLogger(); if (logger.isDebugEnabled()) { logger.debug("enter - " + getClass().getName() + ".insert()"); } try { if (logger.isInfoEnabled()) { logger.info("insert(): Create new sequencer record for " + getName()); } Connection conn = null; PreparedStatement stmt = null; ResultSet rs = null; try { InitialContext ctx = new InitialContext(); DataSource ds = (DataSource) ctx.lookup(dataSourceName); conn = ds.getConnection(); conn.setReadOnly(false); stmt = conn.prepareStatement(INSERT_SEQ); stmt.setString(INS_NAME, getName()); stmt.setLong(INS_NEXT_KEY, defaultInterval * 2); stmt.setLong(INS_INTERVAL, defaultInterval); stmt.setLong(INS_UPDATE, System.currentTimeMillis()); try { if (stmt.executeUpdate() != 1) { nextId = -1L; logger.warn("insert(): Failed to create sequencer entry for " + getName() + " (no error message)"); } else if (logger.isInfoEnabled()) { nextId = defaultInterval; nextSeed = defaultInterval * 2; interval = defaultInterval; logger.info("insert(): First ID will be " + nextId); } } catch (SQLException e) { logger.warn("insert(): Error inserting row into database, possible concurrency issue: " + e.getMessage()); if (logger.isDebugEnabled()) { e.printStackTrace(); } nextId = -1L; } if (!conn.getAutoCommit()) { conn.commit(); } } finally { if (rs != null) { try { rs.close(); } catch (SQLException ignore) { } } if (stmt != null) { try { stmt.close(); } catch (SQLException ignore) { } } if (conn != null) { if (!conn.getAutoCommit()) { try { conn.rollback(); } catch (SQLException ignore) { } } try { conn.close(); } catch (SQLException ignore) { } } } } finally { if (logger.isDebugEnabled()) { logger.debug("exit - " + getClass().getName() + ".insert()"); } } } | private String getClassname(Bundle bundle) { URL urlEntry = bundle.getEntry("jdbcBundleInfo.xml"); InputStream in = null; try { in = urlEntry.openStream(); try { StringBuilder sb = new StringBuilder(); BufferedReader reader = new BufferedReader(new InputStreamReader(in)); String line; while ((line = reader.readLine()) != null) { if (!line.startsWith("<!DOCTYPE")) { sb.append(line); } } SAXBuilder builder = new SAXBuilder(false); Document doc = builder.build(new StringReader(sb.toString())); Element eRoot = doc.getRootElement(); if ("jdbcBundleInfo".equals(eRoot.getName())) { Attribute atri = eRoot.getAttribute("className"); if (atri != null) { return atri.getValue(); } } } catch (JDOMException e) { } } catch (IOException e) { } finally { if (in != null) { try { in.close(); } catch (IOException e) { } } } return null; } | 884,629 |
1 | public String hash(String plainTextPassword) { try { MessageDigest digest = MessageDigest.getInstance(digestAlgorithm); digest.update(plainTextPassword.getBytes(charset)); byte[] rawHash = digest.digest(); return new String(org.jboss.seam.util.Hex.encodeHex(rawHash)); } catch (NoSuchAlgorithmException e) { log.error("Digest algorithm #0 to calculate the password hash will not be supported.", digestAlgorithm); throw new RuntimeException(e); } catch (UnsupportedEncodingException e) { log.error("The Character Encoding #0 is not supported", charset); throw new RuntimeException(e); } } | public void setPassword(String plaintext) throws java.security.NoSuchAlgorithmException { StringBuffer encrypted = new StringBuffer(); java.security.MessageDigest digest = java.security.MessageDigest.getInstance("MD5"); digest.update(plaintext.getBytes()); byte[] digestArray = digest.digest(); for (int i = 0; i < digestArray.length; i++) { encrypted.append(byte2hex(digestArray[i])); } setEncryptedPassword(encrypted.toString()); } | 884,630 |
0 | public static String move_tags(String sessionid, String absolutePathForTheMovedTags, 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_tags"); 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_tag")); nameValuePairs.add(new BasicNameValuePair("absolute_new_parent_tag", absolutePathForTheDestinationTag)); nameValuePairs.add(new BasicNameValuePair("absolute_tags", absolutePathForTheMovedTags)); httppost.setEntity(new UrlEncodedFormEntity(nameValuePairs)); httppost.setHeader("Cookie", "PHPSESSID=" + sessionid); HttpResponse response = httpclient.execute(httppost); resultJsonString = EntityUtils.toString(response.getEntity()); return resultJsonString; } catch (Exception e) { e.printStackTrace(); } return resultJsonString; } | 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; } } | 884,631 |
1 | public static byte[] computeMD5(String s) { try { MessageDigest md = MessageDigest.getInstance("MD5"); md.reset(); md.update(s.getBytes()); return md.digest(); } catch (NoSuchAlgorithmException ex) { throw new RuntimeException(ex); } } | private static synchronized byte[] gerarHash(String frase) { try { MessageDigest md = MessageDigest.getInstance(algoritmo); md.update(frase.getBytes()); return md.digest(); } catch (NoSuchAlgorithmException e) { return null; } } | 884,632 |
1 | public static void copy(String pstrFileFrom, String pstrFileTo) { try { FileChannel srcChannel = new FileInputStream(pstrFileFrom).getChannel(); FileChannel dstChannel = new FileOutputStream(pstrFileTo).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (Exception e) { throw new RuntimeException(e); } } | public void testIsVersioned() throws ServiceException, IOException { JCRNodeSource emptySource = loadTestSource(); assertTrue(emptySource.isVersioned()); OutputStream sourceOut = emptySource.getOutputStream(); assertNotNull(sourceOut); InputStream contentIn = getClass().getResourceAsStream(CONTENT_FILE); try { IOUtils.copy(contentIn, sourceOut); sourceOut.flush(); } finally { sourceOut.close(); contentIn.close(); } assertTrue(emptySource.isVersioned()); } | 884,633 |
0 | public static ObjectID[] sortDecending(ObjectID[] oids) { for (int i = 1; i < oids.length; i++) { ObjectID iId = oids[i]; for (int j = 0; j < oids.length - i; j++) { if (oids[j].getTypePrefix() > oids[j + 1].getTypePrefix()) { ObjectID temp = oids[j]; oids[j] = oids[j + 1]; oids[j + 1] = temp; } } } return oids; } | public alto.io.Output openOutput() throws java.io.IOException { URL url = this.url; if (null != url) { URLConnection connection = url.openConnection(); connection.setDoOutput(true); if (connection instanceof alto.net.Connection) { ((alto.net.Connection) connection).setReference(this); } return new ReferenceOutputStream(this, connection); } HttpMessage container = this.write(); return new ReferenceOutputStream(this, container); } | 884,634 |
0 | public static void compress(final File zip, final Map<InputStream, String> entries, final IProgressMonitor monitor) throws IOException { if (zip == null || entries == null || CollectionUtils.isEmpty(entries.keySet())) throw new IllegalArgumentException("One ore more parameters are empty!"); if (zip.exists()) zip.delete(); else if (!zip.getParentFile().exists()) zip.getParentFile().mkdirs(); ZipOutputStream out = new ZipOutputStream(new BufferedOutputStream(new FileOutputStream(zip))); out.setLevel(Deflater.BEST_COMPRESSION); try { for (InputStream inputStream : entries.keySet()) { ZipEntry zipEntry = new ZipEntry(skipBeginningSlash(entries.get(inputStream))); out.putNextEntry(zipEntry); IOUtils.copy(inputStream, out); out.closeEntry(); inputStream.close(); if (monitor != null) monitor.worked(1); } } finally { IOUtils.closeQuietly(out); } } | @Override public void backup() { Connection connection = null; PreparedStatement prestm = null; try { if (logger.isInfoEnabled()) logger.info("backup table " + getOrigin() + " start..."); Class.forName(driver); connection = DriverManager.getConnection(url, username, password); String tableExistsResult = ""; prestm = connection.prepareStatement("show tables from " + schema + " like '" + getDestination() + "';"); ResultSet rs = prestm.executeQuery(); if (rs.next()) tableExistsResult = rs.getString(1); rs.close(); prestm.close(); if (StringUtils.isBlank(tableExistsResult)) { String createTableSql = ""; prestm = connection.prepareStatement("show create table " + getOrigin() + ";"); rs = prestm.executeQuery(); if (rs.next()) createTableSql = rs.getString(2); rs.close(); prestm.close(); createTableSql = createTableSql.replaceAll("`" + getOrigin() + "`", "`" + getDestination() + "`"); createTableSql = createTableSql.replaceAll("auto_increment", ""); createTableSql = createTableSql.replaceAll("AUTO_INCREMENT", ""); Matcher matcher = stripRelationTablePattern.matcher(createTableSql); if (matcher.find()) createTableSql = matcher.replaceAll(""); matcher = normalizePattern.matcher(createTableSql); if (matcher.find()) createTableSql = matcher.replaceAll("\n )"); Statement stm = connection.createStatement(); stm.execute(createTableSql); if (logger.isDebugEnabled()) logger.debug("table '" + getDestination() + "' created!"); } else if (logger.isDebugEnabled()) logger.debug("table '" + getDestination() + "' already exists"); Date date = new Date(); date.setTime(TimeUtil.addHours(date, -getHours()).getTimeInMillis()); date.setTime(TimeUtil.getTodayAtMidnight().getTimeInMillis()); if (logger.isInfoEnabled()) logger.info("backuping records before: " + date); long currentRows = 0L; prestm = connection.prepareStatement("select count(*) from " + getOrigin() + " where " + getCondition() + ""); java.sql.Date sqlDate = new java.sql.Date(date.getTime()); prestm.setDate(1, sqlDate); rs = prestm.executeQuery(); if (rs.next()) currentRows = rs.getLong(1); rs.close(); prestm.close(); if (currentRows > 0) { connection.setAutoCommit(false); prestm = connection.prepareStatement("INSERT INTO " + getDestination() + " SELECT * FROM " + getOrigin() + " WHERE " + getCondition()); prestm.setDate(1, sqlDate); int rows = prestm.executeUpdate(); prestm.close(); if (logger.isInfoEnabled()) logger.info(rows + " rows backupped"); prestm = connection.prepareStatement("DELETE FROM " + getOrigin() + " WHERE " + getCondition()); prestm.setDate(1, sqlDate); rows = prestm.executeUpdate(); prestm.close(); connection.commit(); if (logger.isInfoEnabled()) logger.info(rows + " rows deleted"); } else if (logger.isInfoEnabled()) logger.info("no backup need"); if (logger.isInfoEnabled()) logger.info("backup table " + getOrigin() + " end"); } catch (SQLException e) { logger.error(e, e); if (applicationContext != null) applicationContext.publishEvent(new TrapEvent(this, "dbcon", "Errore SQL durante il backup dei dati della tabella " + getOrigin(), e)); try { connection.rollback(); } catch (SQLException e1) { } } catch (Throwable e) { logger.error(e, e); if (applicationContext != null) applicationContext.publishEvent(new TrapEvent(this, "generic", "Errore generico durante il backup dei dati della tabella " + getOrigin(), e)); try { connection.rollback(); } catch (SQLException e1) { } } finally { try { if (prestm != null) prestm.close(); } catch (SQLException e) { } try { if (connection != null) connection.close(); } catch (SQLException e) { } } } | 884,635 |
1 | public static boolean encodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.ENCODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | private static boolean moveFiles(String sourceDir, String targetDir) { boolean isFinished = false; boolean fileMoved = false; File stagingDir = new File(sourceDir); if (!stagingDir.exists()) { System.out.println(getTimeStamp() + "ERROR - source directory does not exist."); return true; } if (stagingDir.listFiles() == null) { System.out.println(getTimeStamp() + "ERROR - Empty file list. Possible permission error on source directory " + sourceDir); return true; } File[] fileList = stagingDir.listFiles(); for (int x = 0; x < fileList.length; x++) { File f = fileList[x]; if (f.getName().startsWith(".")) { continue; } String targetFileName = targetDir + File.separator + f.getName(); String operation = "move"; boolean success = f.renameTo(new File(targetFileName)); if (success) { fileMoved = true; } else { operation = "mv"; try { Process process = Runtime.getRuntime().exec(new String[] { "mv", f.getCanonicalPath(), targetFileName }); process.waitFor(); process.destroy(); if (!new File(targetFileName).exists()) { success = false; } else { success = true; fileMoved = true; } } catch (Exception e) { success = false; } if (!success) { operation = "copy"; FileChannel in = null; FileChannel out = null; try { in = new FileInputStream(f).getChannel(); File outFile = new File(targetFileName); out = new FileOutputStream(outFile).getChannel(); in.transferTo(0, in.size(), out); in.close(); in = null; out.close(); out = null; f.delete(); success = true; } catch (Exception e) { success = false; } finally { if (in != null) { try { in.close(); } catch (Exception e) { } } if (out != null) { try { out.close(); } catch (Exception e) { } } } } } if (success) { System.out.println(getTimeStamp() + operation + " " + f.getAbsolutePath() + " to " + targetDir); fileMoved = true; } else { System.out.println(getTimeStamp() + "ERROR - " + operation + " " + f.getName() + " to " + targetFileName + " failed."); isFinished = true; } } if (fileMoved && !isFinished) { try { currentLastActivity = System.currentTimeMillis(); updateLastActivity(currentLastActivity); } catch (NumberFormatException e) { System.out.println(getTimeStamp() + "ERROR: NumberFormatException when trying to update lastActivity."); isFinished = true; } catch (IOException e) { System.out.println(getTimeStamp() + "ERROR: IOException when trying to update lastActivity. " + e.toString()); isFinished = true; } } return isFinished; } | 884,636 |
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 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); } | 884,637 |
0 | private List<Token> generateTokens(int tokenCount) throws XSServiceException { final List<Token> tokens = new ArrayList<Token>(tokenCount); final Random r = new Random(); String t = Long.toString(new Date().getTime()) + Integer.toString(r.nextInt()); final MessageDigest m; try { m = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { throw new XSServiceException("Error while creating tokens"); } for (int i = 0; i < tokenCount; ++i) { final Token token = new Token(); token.setValid(true); m.update(t.getBytes(), 0, t.length()); String md5 = new BigInteger(1, m.digest()).toString(16); while (md5.length() < 32) { md5 = String.valueOf(r.nextInt(9)) + md5; } t = md5.substring(0, 8) + "-" + md5.substring(8, 16) + "-" + md5.substring(16, 24) + "-" + md5.substring(24, 32); logger.debug("Generated token #" + (i + 1) + ": " + t); token.setTokenString(t); tokens.add(token); } return tokens; } | public static String readRss(String feed, int num) { InputStream stream = null; try { feed = appendParam(feed, "num", "" + num); System.out.println("feed=" + feed); URL url = new URL(feed); URLConnection connection = url.openConnection(); connection.setRequestProperty("User-Agent", RSS_USER_AGENT); stream = connection.getInputStream(); return CFileHelper.readInputStream(stream); } catch (Exception e) { throw new CException(e); } finally { CFileHelper.closeStream(stream); } } | 884,638 |
1 | public static void copyFile(String input, String output) { try { File inputFile = new File(input); File outputFile = new File(output); 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 (Exception e) { e.printStackTrace(); } } | public static void printResource(OutputStream os, String resourceName) throws IOException { InputStream is = null; try { is = ResourceLoader.loadResource(resourceName); if (is == null) { throw new IOException("Given resource not found!"); } IOUtils.copy(is, os); } finally { IOUtils.closeQuietly(is); } } | 884,639 |
0 | public ResourceBundle getResources() { if (resources == null) { String lang = userProps.getProperty("language"); lang = "en"; try { URL myurl = getResource("Resources_" + lang.trim() + ".properties"); InputStream in = myurl.openStream(); resources = new PropertyResourceBundle(in); in.close(); } catch (Exception ex) { System.err.println("Error loading Resources"); return null; } } return resources; } | 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); } } | 884,640 |
0 | public static String machineInfo() { StringBuilder machineInfo = new StringBuilder(); try { Enumeration networkInterfaces = NetworkInterface.getNetworkInterfaces(); while (networkInterfaces.hasMoreElements()) { NetworkInterface networkInterface = (NetworkInterface) networkInterfaces.nextElement(); if ("eth0".equals(networkInterface.getDisplayName())) { for (byte b : networkInterface.getHardwareAddress()) { StringTools.appendWithDelimiter(machineInfo, String.format("%02x", b).toUpperCase(), ":"); } machineInfo.append("\n"); break; } } } catch (IOException x) { System.out.println("LicenseTools.machineInfo: " + x.getMessage()); x.printStackTrace(); } if (machineInfo.length() == 0) { return null; } String info = machineInfo.toString(); try { MessageDigest messageDigest = MessageDigest.getInstance("MD5", "SUN"); messageDigest.update(info.getBytes()); byte[] md5 = messageDigest.digest(info.getBytes()); return new String(Base64.encodeBase64(md5)); } catch (Exception x) { System.out.println("LicenseTools.machineInfo: " + x.getMessage()); x.printStackTrace(); } return null; } | 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(); } } | 884,641 |
1 | public void readData() throws IOException { i = 0; j = 0; URL url = getClass().getResource("resources/Chrom_623_620.dat"); InputStream is = url.openStream(); InputStreamReader isr = new InputStreamReader(is); BufferedReader br = new BufferedReader(isr); s = br.readLine(); StringTokenizer st = new StringTokenizer(s); s = br.readLine(); st = new StringTokenizer(s); chrom_x[i][j] = Double.parseDouble(st.nextToken()); temp_prev = chrom_x[i][j]; chrom_y[i][j] = Double.parseDouble(st.nextToken()); gridmin = chrom_x[i][j]; gridmax = chrom_x[i][j]; sext1[i][j] = Double.parseDouble(st.nextToken()); sext2[i][j] = Double.parseDouble(st.nextToken()); sext3[i][j] = Double.parseDouble(st.nextToken()); sext4[i][j] = Double.parseDouble(st.nextToken()); j++; while ((s = br.readLine()) != null) { st = new StringTokenizer(s); temp_new = Double.parseDouble(st.nextToken()); if (temp_new != temp_prev) { temp_prev = temp_new; i++; j = 0; } chrom_x[i][j] = temp_new; chrom_y[i][j] = Double.parseDouble(st.nextToken()); sext1[i][j] = Double.parseDouble(st.nextToken()); sext2[i][j] = Double.parseDouble(st.nextToken()); sext3[i][j] = Double.parseDouble(st.nextToken()); sext4[i][j] = Double.parseDouble(st.nextToken()); imax = i; jmax = j; j++; if (chrom_x[i][j] <= gridmin) gridmin = chrom_x[i][j]; if (chrom_x[i][j] >= gridmax) gridmax = chrom_x[i][j]; } } | public static boolean reportException(Throwable ex, HashMap<String, String> suppl) { if (Activator.getDefault().getPreferenceStore().getBoolean(PreferenceConstants.P_CRASH_REPORTING)) { logger.debug("Report exception to devs..."); String data = "reportType=exception&" + "message=" + ex.getMessage(); data += "&build=" + Platform.getBundle("de.uni_mannheim.swt.codeconjurer").getHeaders().get("Bundle-Version"); int ln = 0; for (StackTraceElement el : ex.getStackTrace()) { data += "&st_line_" + ++ln + "=" + el.getClassName() + "#" + el.getMethodName() + "<" + el.getLineNumber() + ">"; } data += "&lines=" + ln; data += "&Suppl-Description=" + ex.toString(); data += "&Suppl-Server=" + Activator.getDefault().getPreferenceStore().getString(PreferenceConstants.P_SERVER); data += "&Suppl-User=" + Activator.getDefault().getPreferenceStore().getString(PreferenceConstants.P_USERNAME); if (suppl != null) { for (String key : suppl.keySet()) { data += "&Suppl-" + key + "=" + suppl.get(key); } } try { URL url = new URL("http://www.merobase.com:7777/org.code_conjurer.udc/CrashReport"); URLConnection conn = url.openConnection(); conn.setDoOutput(true); OutputStreamWriter writer = new OutputStreamWriter(conn.getOutputStream()); writer.write(data); writer.flush(); StringBuffer answer = new StringBuffer(); BufferedReader reader = new BufferedReader(new InputStreamReader(conn.getInputStream())); String line; while ((line = reader.readLine()) != null) { answer.append(line + "\r\n"); } writer.close(); reader.close(); logger.debug(answer.toString()); } catch (Exception e) { logger.debug("Could not report exception"); return false; } return true; } else { logger.debug("Reporting not wished!"); return false; } } | 884,642 |
1 | public static boolean decodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.DECODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | private void createWikiPages(WikiContext context) throws PluginException { OntologyWikiPageName owpn = new OntologyWikiPageName(omemo.getFormDataAlias().toUpperCase(), omemo.getFormDataVersionDate()); String wikiPageFullFileName = WikiPageName2FullFileName(context, owpn.toString()); String rdfFileNameWithPath = getWorkDir(context) + File.separator + owpn.toFileName(); FileOutputStream fos = null; FileInputStream fis = null; try { fos = new FileOutputStream(wikiPageFullFileName); fis = new FileInputStream(rdfFileNameWithPath); InfoExtractor infoe = new InfoExtractor(fis, omemo.getFormDataNS(), omemo.getFormDataOntLang()); infoe.writePage(getWorkDir(context), owpn, Omemo.checksWikiPageName); fis.close(); fos.close(); } catch (Exception e) { log.error("Can not read local rdf file or can not write wiki page"); throw new PluginException("Error creating wiki pages. See logs"); } } | 884,643 |
1 | public void copyFile(File s, File t) { try { FileChannel in = (new FileInputStream(s)).getChannel(); FileChannel out = (new FileOutputStream(t)).getChannel(); in.transferTo(0, s.length(), out); in.close(); out.close(); } catch (Exception e) { System.out.println(e); } } | protected void zipDirectory(File dir, File zipfile) throws IOException, IllegalArgumentException { if (!dir.isDirectory()) throw new IllegalArgumentException("Compress: not a directory: " + dir); String[] entries = dir.list(); byte[] buffer = new byte[4096]; int bytes_read; ZipOutputStream out = new ZipOutputStream(new FileOutputStream(zipfile)); for (int i = 0; i < entries.length; i++) { File f = new File(dir, entries[i]); if (f.isDirectory()) continue; FileInputStream in = new FileInputStream(f); ZipEntry entry = new ZipEntry(f.getPath()); out.putNextEntry(entry); while ((bytes_read = in.read(buffer)) != -1) out.write(buffer, 0, bytes_read); in.close(); } out.close(); } | 884,644 |
1 | public String obfuscateString(String string) { String obfuscatedString = null; try { MessageDigest md = MessageDigest.getInstance(ENCRYPTION_ALGORITHM); md.update(string.getBytes()); byte[] digest = md.digest(); obfuscatedString = new String(Base64.encode(digest)).replace(DELIM_PATH, '='); } catch (NoSuchAlgorithmException e) { StatusHandler.log("SHA not available", null); obfuscatedString = LABEL_FAILED_TO_OBFUSCATE; } return obfuscatedString; } | public byte[] getHash(String plaintext) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest digest = MessageDigest.getInstance("SHA-1"); digest.reset(); digest.update(salt.getBytes("UTF-8")); return digest.digest(plaintext.getBytes("UTF-8")); } | 884,645 |
0 | public static String md5(String s) { try { MessageDigest digest = MessageDigest.getInstance("MD5"); digest.update(s.getBytes()); byte[] md5sum = digest.digest(); BigInteger bigInt = new BigInteger(1, md5sum); String output = bigInt.toString(16); return prepad(output, 32, '0'); } catch (NoSuchAlgorithmException e) { System.err.println("No MD5 algorithm. we are sunk."); return s; } } | private boolean load(URL url) { try { URLConnection connection = url.openConnection(); parser = new PDFParser(connection.getInputStream()); } catch (IOException e) { e.printStackTrace(); return false; } return true; } | 884,646 |
1 | public synchronized void handleRequest(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { CacheEntry entry = null; Tenant tenant = null; if (!tenantInfo.getTenants().isEmpty()) { tenant = tenantInfo.getMatchingTenant(request); if (tenant == null) { tenant = tenantInfo.getTenants().get(0); } entry = tenantToCacheEntry.get(tenant.getName()); } else { entry = cacheEntry; } if (entry == null) { File tempDir = (File) servletContext.getAttribute("javax.servlet.context.tempdir"); tempDir = new File(tempDir, "pustefix-sitemap-cache"); if (!tempDir.exists()) { tempDir.mkdirs(); } entry = new CacheEntry(); entry.file = new File(tempDir, "sitemap" + (tenant == null ? "" : "-" + tenant.getName()) + ".xml"); try { String host = AbstractPustefixRequestHandler.getServerName(request); Document doc = getSearchEngineSitemap(tenant, host); Transformer trf = TransformerFactory.newInstance().newTransformer(); trf.setOutputProperty(OutputKeys.INDENT, "yes"); FileOutputStream out = new FileOutputStream(entry.file); MessageDigest digest; try { digest = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException x) { throw new RuntimeException("Can't create message digest", x); } DigestOutputStream digestOutput = new DigestOutputStream(out, digest); trf.transform(new DOMSource(doc), new StreamResult(digestOutput)); digestOutput.close(); byte[] digestBytes = digest.digest(); entry.etag = MD5Utils.byteToHex(digestBytes); } catch (Exception x) { throw new ServletException("Error creating sitemap", x); } } String reqETag = request.getHeader("If-None-Match"); if (reqETag != null) { if (entry.etag.equals(reqETag)) { response.setStatus(HttpServletResponse.SC_NOT_MODIFIED); response.flushBuffer(); return; } } long reqMod = request.getDateHeader("If-Modified-Since"); if (reqMod != -1) { if (entry.file.lastModified() < reqMod + 1000) { response.setStatus(HttpServletResponse.SC_NOT_MODIFIED); response.flushBuffer(); return; } } response.setContentType("application/xml"); response.setContentLength((int) entry.file.length()); response.setDateHeader("Last-Modified", entry.file.lastModified()); response.setHeader("ETag", entry.etag); OutputStream out = new BufferedOutputStream(response.getOutputStream()); InputStream in = new FileInputStream(entry.file); int bytes_read; byte[] buffer = new byte[8]; while ((bytes_read = in.read(buffer)) != -1) { out.write(buffer, 0, bytes_read); } out.flush(); in.close(); out.close(); } | public static void buildPerMovieDiffBinary(String completePath, String slopeOneDataFolderName, String slopeOneDataFileName) { try { File inFile = new File(completePath + fSep + "SmartGRAPE" + fSep + slopeOneDataFolderName + fSep + slopeOneDataFileName); FileChannel inC = new FileInputStream(inFile).getChannel(); for (int i = 1; i <= 17770; i++) { File outFile = new File(completePath + fSep + "SmartGRAPE" + fSep + slopeOneDataFolderName + fSep + "Movie-" + i + "-SlopeOneData.txt"); FileChannel outC = new FileOutputStream(outFile).getChannel(); ByteBuffer buf = ByteBuffer.allocate(17770 * 10); for (int j = 1; j < i; j++) { ByteBuffer bbuf = ByteBuffer.allocate(12); inC.position((17769 * 17770 * 6) - ((17769 - (j - 1)) * (17770 - (j - 1)) * 6) + (i - j - 1) * 12); inC.read(bbuf); bbuf.flip(); buf.putShort(bbuf.getShort()); bbuf.getShort(); buf.putInt(bbuf.getInt()); buf.putFloat(-bbuf.getFloat()); } buf.putShort(new Integer(i).shortValue()); buf.putInt(0); buf.putFloat(0.0f); ByteBuffer remainingBuf = inC.map(FileChannel.MapMode.READ_ONLY, (17769 * 17770 * 6) - ((17769 - (i - 1)) * (17770 - (i - 1)) * 6), (17770 - i) * 12); while (remainingBuf.hasRemaining()) { remainingBuf.getShort(); buf.putShort(remainingBuf.getShort()); buf.putInt(remainingBuf.getInt()); buf.putFloat(remainingBuf.getFloat()); } buf.flip(); outC.write(buf); buf.clear(); outC.close(); } } catch (Exception e) { e.printStackTrace(); } } | 884,647 |
1 | public static String encrypt(String plaintext) throws Exception { String algorithm = XML.get("security.algorithm"); if (algorithm == null) algorithm = "SHA-1"; MessageDigest md = MessageDigest.getInstance(algorithm); md.update(plaintext.getBytes("UTF-8")); return new BASE64Encoder().encode(md.digest()); } | public byte[] getCoded(String name, String pass) { byte[] digest = null; if (pass != null && 0 < pass.length()) { try { MessageDigest md = MessageDigest.getInstance("SHA-1"); md.update(name.getBytes()); md.update(pass.getBytes()); digest = md.digest(); } catch (Exception e) { e.printStackTrace(); digest = null; } } return digest; } | 884,648 |
1 | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | public void testReaderWriterF2() throws Exception { String inFile = "test_data/mri.png"; String outFile = "test_output/mri__smooth_testReaderWriter.mhd"; itkImageFileReaderF2_Pointer reader = itkImageFileReaderF2.itkImageFileReaderF2_New(); itkImageFileWriterF2_Pointer writer = itkImageFileWriterF2.itkImageFileWriterF2_New(); reader.SetFileName(inFile); writer.SetFileName(outFile); writer.SetInput(reader.GetOutput()); writer.Update(); } | 884,649 |
1 | public void test() throws Exception { StorageString s = new StorageString("UTF-8"); s.addText("Test"); try { s.getOutputStream(); fail("Should throw IOException as method not supported."); } catch (IOException e) { } try { s.getWriter(); fail("Should throw IOException as method not supported."); } catch (IOException e) { } s.addText("ing is important"); s.close(ResponseStateOk.getInstance()); assertEquals("Testing is important", s.getText()); InputStream input = s.getInputStream(); StringWriter writer = new StringWriter(); IOUtils.copy(input, writer, "UTF-8"); assertEquals("Testing is important", writer.toString()); } | public static boolean decodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.DECODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | 884,650 |
1 | void copyFileOnPeer(String path, RServerInfo peerserver, boolean allowoverwrite) throws IOException { RFile file = new RFile(path); OutputStream out = null; FileInputStream in = null; try { in = fileManager.openFileRead(path); out = localClient.openWrite(file, false, WriteMode.TRANSACTED, 1, peerserver, !allowoverwrite); IOUtils.copyLarge(in, out); out.close(); out = null; } finally { if (in != null) { try { in.close(); } catch (Throwable t) { } } if (out != null) { try { out.close(); } catch (Throwable t) { } } } } | public void testCodingBeyondContentLimitFromFile() throws Exception { ByteArrayOutputStream baos = new ByteArrayOutputStream(); WritableByteChannel channel = newChannel(baos); HttpParams params = new BasicHttpParams(); SessionOutputBuffer outbuf = new SessionOutputBufferImpl(1024, 128, params); HttpTransportMetricsImpl metrics = new HttpTransportMetricsImpl(); LengthDelimitedEncoder encoder = new LengthDelimitedEncoder(channel, outbuf, metrics, 16); File tmpFile = File.createTempFile("testFile", "txt"); FileOutputStream fout = new FileOutputStream(tmpFile); OutputStreamWriter wrtout = new OutputStreamWriter(fout); wrtout.write("stuff;"); wrtout.write("more stuff; and a lot more stuff"); wrtout.flush(); wrtout.close(); FileChannel fchannel = new FileInputStream(tmpFile).getChannel(); encoder.transfer(fchannel, 0, 20); String s = baos.toString("US-ASCII"); assertTrue(encoder.isCompleted()); assertEquals("stuff;more stuff", s); tmpFile.delete(); } | 884,651 |
0 | public boolean crear() { int result = 0; String sql = "insert into partida" + "(torneo_idTorneo, jugador_idJugadorNegras, jugador_idJugadorBlancas, registrado, fecha," + " movs, resultado, nombreBlancas, nombreNegras, eloBlancas, eloNegras, idApertura)" + "values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)"; try { connection = conexionBD.getConnection(); connection.setAutoCommit(false); ps = connection.prepareStatement(sql); populatePreparedStatement(unaPartida); result = ps.executeUpdate(); connection.commit(); } catch (SQLException ex) { ex.printStackTrace(); try { connection.rollback(); } catch (SQLException exe) { exe.printStackTrace(); } } finally { conexionBD.close(ps); conexionBD.close(connection); } return (result > 0); } | private boolean verifyAppId(String appid) { try { String urlstr = "http://" + appid + ".appspot.com"; URL url = new URL(urlstr); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); StringBuffer buf = new StringBuffer(); String line; while ((line = reader.readLine()) != null) { buf.append(line); } reader.close(); return buf.toString().contains("hyk-proxy"); } catch (Exception e) { } return false; } | 884,652 |
0 | public static URLConnection openRemoteDescriptionFile(String urlstr) throws MalformedURLException { URL url = new URL(urlstr); try { URLConnection conn = url.openConnection(); conn.connect(); return conn; } catch (Exception e) { Config conf = Config.getInstance(); SimpleSocketAddress localServAddr = conf.getLocalProxyServerAddress(); Proxy proxy = new Proxy(Type.HTTP, new InetSocketAddress(localServAddr.host, localServAddr.port)); URLConnection conn; try { conn = url.openConnection(proxy); conn.connect(); return conn; } catch (IOException e1) { logger.error("Failed to retrive desc file:" + url, e1); } } return null; } | public boolean verifySignature() { try { byte[] data = readFile(name + ".tmp1.bin"); if (data == null) return false; if (data[data.length - 0x104] != 'N' || data[data.length - 0x103] != 'G' || data[data.length - 0x102] != 'I' || data[data.length - 0x101] != 'S') return false; byte[] signature = new byte[0x100]; byte[] module = new byte[data.length - 0x104]; System.arraycopy(data, data.length - 0x100, signature, 0, 0x100); System.arraycopy(data, 0, module, 0, data.length - 0x104); BigIntegerEx power = new BigIntegerEx(BigIntegerEx.LITTLE_ENDIAN, new byte[] { 0x01, 0x00, 0x01, 0x00 }); BigIntegerEx mod = new BigIntegerEx(BigIntegerEx.LITTLE_ENDIAN, new byte[] { (byte) 0x6B, (byte) 0xCE, (byte) 0xF5, (byte) 0x2D, (byte) 0x2A, (byte) 0x7D, (byte) 0x7A, (byte) 0x67, (byte) 0x21, (byte) 0x21, (byte) 0x84, (byte) 0xC9, (byte) 0xBC, (byte) 0x25, (byte) 0xC7, (byte) 0xBC, (byte) 0xDF, (byte) 0x3D, (byte) 0x8F, (byte) 0xD9, (byte) 0x47, (byte) 0xBC, (byte) 0x45, (byte) 0x48, (byte) 0x8B, (byte) 0x22, (byte) 0x85, (byte) 0x3B, (byte) 0xC5, (byte) 0xC1, (byte) 0xF4, (byte) 0xF5, (byte) 0x3C, (byte) 0x0C, (byte) 0x49, (byte) 0xBB, (byte) 0x56, (byte) 0xE0, (byte) 0x3D, (byte) 0xBC, (byte) 0xA2, (byte) 0xD2, (byte) 0x35, (byte) 0xC1, (byte) 0xF0, (byte) 0x74, (byte) 0x2E, (byte) 0x15, (byte) 0x5A, (byte) 0x06, (byte) 0x8A, (byte) 0x68, (byte) 0x01, (byte) 0x9E, (byte) 0x60, (byte) 0x17, (byte) 0x70, (byte) 0x8B, (byte) 0xBD, (byte) 0xF8, (byte) 0xD5, (byte) 0xF9, (byte) 0x3A, (byte) 0xD3, (byte) 0x25, (byte) 0xB2, (byte) 0x66, (byte) 0x92, (byte) 0xBA, (byte) 0x43, (byte) 0x8A, (byte) 0x81, (byte) 0x52, (byte) 0x0F, (byte) 0x64, (byte) 0x98, (byte) 0xFF, (byte) 0x60, (byte) 0x37, (byte) 0xAF, (byte) 0xB4, (byte) 0x11, (byte) 0x8C, (byte) 0xF9, (byte) 0x2E, (byte) 0xC5, (byte) 0xEE, (byte) 0xCA, (byte) 0xB4, (byte) 0x41, (byte) 0x60, (byte) 0x3C, (byte) 0x7D, (byte) 0x02, (byte) 0xAF, (byte) 0xA1, (byte) 0x2B, (byte) 0x9B, (byte) 0x22, (byte) 0x4B, (byte) 0x3B, (byte) 0xFC, (byte) 0xD2, (byte) 0x5D, (byte) 0x73, (byte) 0xE9, (byte) 0x29, (byte) 0x34, (byte) 0x91, (byte) 0x85, (byte) 0x93, (byte) 0x4C, (byte) 0xBE, (byte) 0xBE, (byte) 0x73, (byte) 0xA9, (byte) 0xD2, (byte) 0x3B, (byte) 0x27, (byte) 0x7A, (byte) 0x47, (byte) 0x76, (byte) 0xEC, (byte) 0xB0, (byte) 0x28, (byte) 0xC9, (byte) 0xC1, (byte) 0xDA, (byte) 0xEE, (byte) 0xAA, (byte) 0xB3, (byte) 0x96, (byte) 0x9C, (byte) 0x1E, (byte) 0xF5, (byte) 0x6B, (byte) 0xF6, (byte) 0x64, (byte) 0xD8, (byte) 0x94, (byte) 0x2E, (byte) 0xF1, (byte) 0xF7, (byte) 0x14, (byte) 0x5F, (byte) 0xA0, (byte) 0xF1, (byte) 0xA3, (byte) 0xB9, (byte) 0xB1, (byte) 0xAA, (byte) 0x58, (byte) 0x97, (byte) 0xDC, (byte) 0x09, (byte) 0x17, (byte) 0x0C, (byte) 0x04, (byte) 0xD3, (byte) 0x8E, (byte) 0x02, (byte) 0x2C, (byte) 0x83, (byte) 0x8A, (byte) 0xD6, (byte) 0xAF, (byte) 0x7C, (byte) 0xFE, (byte) 0x83, (byte) 0x33, (byte) 0xC6, (byte) 0xA8, (byte) 0xC3, (byte) 0x84, (byte) 0xEF, (byte) 0x29, (byte) 0x06, (byte) 0xA9, (byte) 0xB7, (byte) 0x2D, (byte) 0x06, (byte) 0x0B, (byte) 0x0D, (byte) 0x6F, (byte) 0x70, (byte) 0x9E, (byte) 0x34, (byte) 0xA6, (byte) 0xC7, (byte) 0x31, (byte) 0xBE, (byte) 0x56, (byte) 0xDE, (byte) 0xDD, (byte) 0x02, (byte) 0x92, (byte) 0xF8, (byte) 0xA0, (byte) 0x58, (byte) 0x0B, (byte) 0xFC, (byte) 0xFA, (byte) 0xBA, (byte) 0x49, (byte) 0xB4, (byte) 0x48, (byte) 0xDB, (byte) 0xEC, (byte) 0x25, (byte) 0xF3, (byte) 0x18, (byte) 0x8F, (byte) 0x2D, (byte) 0xB3, (byte) 0xC0, (byte) 0xB8, (byte) 0xDD, (byte) 0xBC, (byte) 0xD6, (byte) 0xAA, (byte) 0xA6, (byte) 0xDB, (byte) 0x6F, (byte) 0x7D, (byte) 0x7D, (byte) 0x25, (byte) 0xA6, (byte) 0xCD, (byte) 0x39, (byte) 0x6D, (byte) 0xDA, (byte) 0x76, (byte) 0x0C, (byte) 0x79, (byte) 0xBF, (byte) 0x48, (byte) 0x25, (byte) 0xFC, (byte) 0x2D, (byte) 0xC5, (byte) 0xFA, (byte) 0x53, (byte) 0x9B, (byte) 0x4D, (byte) 0x60, (byte) 0xF4, (byte) 0xEF, (byte) 0xC7, (byte) 0xEA, (byte) 0xAC, (byte) 0xA1, (byte) 0x7B, (byte) 0x03, (byte) 0xF4, (byte) 0xAF, (byte) 0xC7 }); byte[] result = new BigIntegerEx(BigIntegerEx.LITTLE_ENDIAN, signature).modPow(power, mod).toByteArray(); byte[] digest; byte[] properResult = new byte[0x100]; for (int i = 0; i < properResult.length; i++) properResult[i] = (byte) 0xBB; MessageDigest md = MessageDigest.getInstance("SHA1"); md.update(module); md.update("MAIEV.MOD".getBytes()); digest = md.digest(); System.arraycopy(digest, 0, properResult, 0, digest.length); for (int i = 0; i < result.length; i++) if (result[i] != properResult[i]) return false; return true; } catch (Exception e) { System.out.println("Failed to verify signature: " + e.toString()); } return false; } | 884,653 |
1 | private static void copy(File source, File target) throws IOException { FileInputStream in = new FileInputStream(source); FileOutputStream out = new FileOutputStream(target); byte[] buffer = new byte[4096]; int no = 0; try { while ((no = in.read(buffer)) != -1) out.write(buffer, 0, no); } finally { in.close(); out.close(); } } | 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); } } | 884,654 |
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!"); } | private static void execute(String fileName) throws IOException, SQLException { InputStream input = DatabaseConstants.class.getResourceAsStream(fileName); StringWriter writer = new StringWriter(); IOUtils.copy(input, writer); String sql = writer.toString(); Statement statement = connection.createStatement(); statement.execute(sql); } | 884,655 |
1 | private void getRandomGUID(boolean secure) { MessageDigest md5 = null; StringBuffer sbValueBeforeMD5 = new StringBuffer(); try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { System.out.println("Error: " + e); } try { long time = System.currentTimeMillis(); long rand = 0; if (secure) { rand = mySecureRand.nextLong(); } else { rand = myRand.nextLong(); } sbValueBeforeMD5.append(s_id); sbValueBeforeMD5.append(":"); sbValueBeforeMD5.append(Long.toString(time)); sbValueBeforeMD5.append(":"); sbValueBeforeMD5.append(Long.toString(rand)); valueBeforeMD5 = sbValueBeforeMD5.toString(); md5.update(valueBeforeMD5.getBytes()); byte[] array = md5.digest(); StringBuffer sb = new StringBuffer(); for (int j = 0; j < array.length; ++j) { int b = array[j] & 0xFF; if (b < 0x10) sb.append('0'); sb.append(Integer.toHexString(b)); } valueAfterMD5 = sb.toString(); } catch (Exception e) { System.out.println("Error:" + e); } } | private String getEncryptedPassword() { String encrypted; char[] pwd = password.getPassword(); try { MessageDigest md = MessageDigest.getInstance("SHA-1"); md.update(new String(pwd).getBytes("UTF-8")); byte[] digested = md.digest(); encrypted = new String(Base64Coder.encode(digested)); } catch (Exception e) { encrypted = new String(pwd); } for (int i = 0; i < pwd.length; i++) pwd[i] = 0; return encrypted; } | 884,656 |
1 | public void delete(String language, String tag, int row) throws FidoDatabaseException { try { Connection conn = null; Statement stmt = null; try { String sql = "delete from LanguageMorphologies " + "where LanguageName = '" + language + "' and MorphologyTag = '" + tag + "' and " + " Rank = " + row; conn = fido.util.FidoDataSource.getConnection(); conn.setAutoCommit(false); stmt = conn.createStatement(); stmt.executeUpdate(sql); bumpAllRowsUp(stmt, language, tag, row); conn.commit(); } catch (SQLException e) { if (conn != null) conn.rollback(); throw e; } finally { if (stmt != null) stmt.close(); if (conn != null) conn.close(); } } catch (SQLException e) { throw new FidoDatabaseException(e); } } | public static synchronized int registerVote(String IDVotazione, byte[] T1, byte[] sbT2, byte[] envelope, Config config) { if (IDVotazione == null) { LOGGER.error("registerVote::IDV null"); return C_addVote_BOH; } if (T1 == null) { LOGGER.error("registerVote::T1 null"); return C_addVote_BOH; } if (envelope == null) { LOGGER.error("registerVote::envelope null"); return C_addVote_BOH; } LOGGER.info("registering vote started"); Connection conn = null; PreparedStatement stmt = null; boolean autoCommitPresent = true; int ANSWER = C_addVote_BOH; try { ByteArrayInputStream tmpXMLStream = new ByteArrayInputStream(envelope); SAXReader tmpXMLReader = new SAXReader(); Document doc = tmpXMLReader.read(tmpXMLStream); if (LOGGER.isTraceEnabled()) LOGGER.trace(doc.asXML()); String sT1 = new String(Base64.encodeBase64(T1), "utf-8"); String ssbT2 = new String(Base64.encodeBase64(sbT2), "utf-8"); String sEnvelope = new String(Base64.encodeBase64(envelope), "utf-8"); LOGGER.trace("loading jdbc driver ..."); Class.forName("com.mysql.jdbc.Driver"); LOGGER.trace("... loaded"); conn = DriverManager.getConnection(config.getSconn()); autoCommitPresent = conn.getAutoCommit(); conn.setAutoCommit(false); String query = "" + " INSERT INTO votes(IDVotazione, T1, signByT2 , envelope) " + " VALUES (? , ? , ? , ? ) "; stmt = conn.prepareStatement(query); stmt.setString(1, IDVotazione); stmt.setString(2, sT1); stmt.setString(3, ssbT2); stmt.setString(4, sEnvelope); stmt.executeUpdate(); stmt.close(); LOGGER.debug("vote saved for references, now start the parsing"); query = "" + " INSERT INTO risposte (IDVotazione, T1, IDquestion , myrisposta,freetext) " + " VALUES (? , ? , ? , ? ,?) "; stmt = conn.prepareStatement(query); Element question, itemsElem, rispostaElem; List<Element> rispList; String id, rispostaText, risposta, freeText, questionType; Iterator<Element> questionIterator = doc.selectNodes("/poll/manifest/question").iterator(); while (questionIterator.hasNext()) { question = (Element) questionIterator.next(); risposta = freeText = ""; id = question.attributeValue("id"); itemsElem = question.element("items"); questionType = itemsElem == null ? "" : itemsElem.attributeValue("type"); rispostaElem = question.element("myrisposta"); rispostaText = rispostaElem == null ? "" : rispostaElem.getText(); if (rispostaText.equals(Votazione.C_TAG_WHITE_XML)) { risposta = C_TAG_WHITE; } else if (rispostaText.equals(Votazione.C_TAG_NULL_XML)) { risposta = C_TAG_NULL; } else { if (!rispostaText.equals("") && LOGGER.isDebugEnabled()) LOGGER.warn("Risposta text should be empty!: " + rispostaText); risposta = C_TAG_BUG; if (questionType.equals("selection")) { Element rispItem = rispostaElem.element("item"); String tmpRisposta = rispItem.attributeValue("index"); if (tmpRisposta != null) { risposta = tmpRisposta; if (risposta.equals("0")) freeText = rispItem.getText(); } } else if (questionType.equals("borda")) { rispList = rispostaElem.elements("item"); if (rispList != null) { risposta = ""; String index, tokens; for (Element rispItem : rispList) { index = rispItem.attributeValue("index"); tokens = rispItem.attributeValue("tokens"); if (index.equals("0")) freeText = rispItem.getText(); if (risposta.length() > 0) risposta += ","; risposta += index + ":" + tokens; } } } else if (questionType.equals("ordering")) { rispList = rispostaElem.elements("item"); if (rispList != null) { risposta = ""; String index, order; for (Element rispItem : rispList) { index = rispItem.attributeValue("index"); order = rispItem.attributeValue("order"); if (index == null) { continue; } if (index.equals("0")) freeText = rispItem.getText(); if (risposta.length() > 0) risposta += ","; risposta += index + ":" + order; } } } else if (questionType.equals("multiple")) { rispList = rispostaElem.elements("item"); if (rispList != null) { risposta = ""; String index; for (Element rispItem : rispList) { index = rispItem.attributeValue("index"); if (index.equals("0")) freeText = rispItem.getText(); if (risposta.length() > 0) risposta += ","; risposta += index; } } } else if (questionType.equals("free")) { freeText = rispostaElem.element("item").getText(); risposta = ""; } } if (LOGGER.isTraceEnabled()) { LOGGER.trace("ID_QUESTION: " + id); LOGGER.trace("question type: " + questionType); LOGGER.trace("risposta: " + risposta); LOGGER.trace("freetext: " + freeText); } if (risposta.equals(C_TAG_BUG)) { LOGGER.error("Invalid answer"); LOGGER.error("T1: " + sT1); LOGGER.error("ID_QUESTION: " + id); LOGGER.error("question type: " + questionType); } stmt.setString(1, IDVotazione); stmt.setString(2, sT1); stmt.setString(3, id); stmt.setString(4, risposta); stmt.setString(5, freeText); stmt.addBatch(); } stmt.executeBatch(); stmt.close(); conn.commit(); ANSWER = C_addVote_OK; LOGGER.info("registering vote end successfully"); } catch (SQLException e) { try { conn.rollback(); } catch (Exception ex) { } if (e.getErrorCode() == 1062) { ANSWER = C_addVote_DUPLICATE; LOGGER.error("error while registering vote (duplication)"); } else { ANSWER = C_addVote_BOH; LOGGER.error("error while registering vote", e); } } catch (UnsupportedEncodingException e) { try { conn.rollback(); } catch (Exception ex) { } LOGGER.error("encoding error", e); ANSWER = C_addVote_BOH; } catch (DocumentException e) { LOGGER.error("DocumentException", e); ANSWER = C_addVote_BOH; } catch (ClassNotFoundException e) { try { conn.rollback(); } catch (Exception ex) { } LOGGER.error("error while registering vote", e); ANSWER = C_addVote_BOH; } catch (Exception e) { try { conn.rollback(); } catch (Exception ex) { } LOGGER.error("Unexpected exception while registering vote", e); ANSWER = C_addVote_BOH; } finally { try { conn.setAutoCommit(autoCommitPresent); conn.close(); } catch (Exception e) { } ; } return ANSWER; } | 884,657 |
0 | public void method31() { boolean flag = true; while (flag) { flag = false; for (int i = 0; i < anInt772 - 1; i++) if (anIntArray774[i] < anIntArray774[i + 1]) { int j = anIntArray774[i]; anIntArray774[i] = anIntArray774[i + 1]; anIntArray774[i + 1] = j; long l = aLongArray773[i]; aLongArray773[i] = aLongArray773[i + 1]; aLongArray773[i + 1] = l; flag = true; } } } | 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); } } | 884,658 |
0 | private void CopyTo(File dest) throws IOException { FileReader in = null; FileWriter out = null; int c; try { in = new FileReader(image); out = new FileWriter(dest); while ((c = in.read()) != -1) out.write(c); } finally { if (in != null) try { in.close(); } catch (Exception e) { } if (out != null) try { out.close(); } catch (Exception e) { } } } | public void testSimpleHttpPostsChunked() throws Exception { int reqNo = 20; Random rnd = new Random(); List testData = new ArrayList(reqNo); for (int i = 0; i < reqNo; i++) { int size = rnd.nextInt(20000); byte[] data = new byte[size]; rnd.nextBytes(data); testData.add(data); } this.server.registerHandler("*", new HttpRequestHandler() { public void handle(final HttpRequest request, final HttpResponse response, final HttpContext context) throws HttpException, IOException { if (request instanceof HttpEntityEnclosingRequest) { HttpEntity incoming = ((HttpEntityEnclosingRequest) request).getEntity(); byte[] data = EntityUtils.toByteArray(incoming); ByteArrayEntity outgoing = new ByteArrayEntity(data); outgoing.setChunked(true); response.setEntity(outgoing); } else { StringEntity outgoing = new StringEntity("No content"); response.setEntity(outgoing); } } }); this.server.start(); DefaultHttpClientConnection conn = new DefaultHttpClientConnection(); HttpHost host = new HttpHost("localhost", this.server.getPort()); try { for (int r = 0; r < reqNo; r++) { if (!conn.isOpen()) { Socket socket = new Socket(host.getHostName(), host.getPort()); conn.bind(socket, this.client.getParams()); } BasicHttpEntityEnclosingRequest post = new BasicHttpEntityEnclosingRequest("POST", "/"); byte[] data = (byte[]) testData.get(r); ByteArrayEntity outgoing = new ByteArrayEntity(data); outgoing.setChunked(true); post.setEntity(outgoing); HttpResponse response = this.client.execute(post, host, conn); byte[] received = EntityUtils.toByteArray(response.getEntity()); byte[] expected = (byte[]) testData.get(r); assertEquals(expected.length, received.length); for (int i = 0; i < expected.length; i++) { assertEquals(expected[i], received[i]); } if (!this.client.keepAlive(response)) { conn.close(); } } HttpConnectionMetrics cm = conn.getMetrics(); assertEquals(reqNo, cm.getRequestCount()); assertEquals(reqNo, cm.getResponseCount()); } finally { conn.close(); this.server.shutdown(); } } | 884,659 |
0 | public static String md5(String input) throws NoSuchAlgorithmException, UnsupportedEncodingException { StringBuffer result = new StringBuffer(); MessageDigest md = MessageDigest.getInstance("MD5"); md.update(input.getBytes("utf-8")); byte[] digest = md.digest(); for (byte b : digest) { result.append(String.format("%02X ", b & 0xff)); } return result.toString(); } | public static byte[] loadURLToBuffer(URL url, int maxLength) throws IOException { byte[] buf = new byte[maxLength]; byte[] data = null; int iCount = 0; BufferedInputStream in = new BufferedInputStream(url.openStream(), 20480); iCount = in.read(buf, 0, buf.length); if (iCount != -1) { data = new byte[iCount]; System.arraycopy(buf, 0, data, 0, iCount); } in.close(); return data; } | 884,660 |
0 | public void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { HttpSession session = request.getSession(false); if (session == null) { log.warn("HttpProxyServlet: no session"); response.setStatus(404); return; } User user = (User) session.getAttribute("user"); if (user == null) { log.warn("HttpProxyServlet: user not logged in"); response.setStatus(404); return; } String target = null; if (request.getPathInfo() != null && !request.getPathInfo().equals("")) { target = "http:/" + request.getPathInfo() + "?" + request.getQueryString(); log.info("HttpProxyServlet: target=" + target); } else { log.warn("HttpProxyServlet: missing pathInfo"); response.setStatus(404); return; } InputStream is = null; ServletOutputStream out = null; try { URL url = new URL(target); URLConnection uc = url.openConnection(); response.setContentType(uc.getContentType()); is = uc.getInputStream(); out = response.getOutputStream(); byte[] buf = new byte[4096]; int bytesRead; while ((bytesRead = is.read(buf)) != -1) { out.write(buf, 0, bytesRead); } } catch (MalformedURLException e) { log.warn("HttpProxyServlet: malformed URL"); response.setStatus(404); } catch (IOException e) { log.warn("HttpProxyServlet: I/O exception"); response.setStatus(404); } finally { if (is != null) { is.close(); } if (out != null) { out.close(); } } } | public static void copyResourceFileTo(String destFileName, String resourceFileName) { if (destFileName == null || resourceFileName == null) throw new IllegalArgumentException("Argument cannot be null."); try { FileInputStream in = null; FileOutputStream out = null; URL url = HelperMethods.class.getResource(resourceFileName); if (url == null) { System.out.println("URL " + resourceFileName + " cannot be created."); return; } String fileName = url.getFile(); fileName = fileName.replaceAll("%20", " "); File resourceFile = new File(fileName); if (!resourceFile.isFile()) { System.out.println(fileName + " cannot be opened."); return; } in = new FileInputStream(resourceFile); out = new FileOutputStream(new File(destFileName)); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } catch (IOException ex) { ex.printStackTrace(); } } | 884,661 |
1 | public static boolean encodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.ENCODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | public java.io.File gzip(java.io.File file) throws Exception { java.io.File tmp = null; InputStream is = null; OutputStream os = null; try { tmp = java.io.File.createTempFile(file.getName(), ".gz"); tmp.deleteOnExit(); is = new BufferedInputStream(new FileInputStream(file)); os = new GZIPOutputStream(new BufferedOutputStream(new FileOutputStream(tmp))); byte[] buf = new byte[4096]; int nread = -1; while ((nread = is.read(buf)) != -1) { os.write(buf, 0, nread); } os.flush(); } finally { os.close(); is.close(); } return tmp; } | 884,662 |
0 | public static String md5hash(String data) { MessageDigest digest; try { digest = java.security.MessageDigest.getInstance("MD5"); digest.update(data.getBytes()); return new BigInteger(1, digest.digest()).toString(16); } catch (NoSuchAlgorithmException e) { LOG.error(e); } return null; } | protected int sendData(String submitName, String submitValue) throws HttpException, IOException, SAXException { PostMethod postMethod = null; try { postMethod = new PostMethod(getDocumentBase().toString()); postMethod.getParams().setCookiePolicy(org.apache.commons.httpclient.cookie.CookiePolicy.IGNORE_COOKIES); postMethod.addRequestHeader("Cookie", getWikiPrefix() + "_session=" + getSession() + "; " + getWikiPrefix() + "UserID=" + getUserId() + "; " + getWikiPrefix() + "UserName=" + getUserName() + "; "); List<Part> parts = new ArrayList<Part>(); for (String s : new String[] { "wpSection", "wpEdittime", "wpScrolltop", "wpStarttime", "wpEditToken" }) { parts.add(new StringPart(s, StringEscapeUtils.unescapeJava(getNonNullParameter(s)))); } parts.add(new StringPart("action", "edit")); parts.add(new StringPart("wpTextbox1", getArticleContent())); parts.add(new StringPart("wpSummary", getSummary())); parts.add(new StringPart("wpAutoSummary", Digest.MD5.isImplemented() ? Digest.MD5.encrypt(getSummary()) : "")); parts.add(new StringPart(submitName, submitValue)); MultipartRequestEntity requestEntity = new MultipartRequestEntity(parts.toArray(new Part[parts.size()]), postMethod.getParams()); postMethod.setRequestEntity(requestEntity); int status = getHttpClient().executeMethod(postMethod); IOUtils.copyTo(postMethod.getResponseBodyAsStream(), System.err); return status; } catch (HttpException err) { throw err; } catch (IOException err) { throw err; } finally { if (postMethod != null) postMethod.releaseConnection(); } } | 884,663 |
1 | public static String encryptPassword(String password) { try { MessageDigest md = MessageDigest.getInstance("SHA"); md.update(password.getBytes()); byte[] hash = md.digest(); StringBuffer hashStringBuf = new StringBuffer(); String byteString; int byteLength; for (int index = 0; index < hash.length; index++) { byteString = String.valueOf(hash[index] + 128); byteLength = byteString.length(); switch(byteLength) { case 1: byteString = "00" + byteString; break; case 2: byteString = "0" + byteString; break; } hashStringBuf.append(byteString); } return hashStringBuf.toString(); } catch (NoSuchAlgorithmException nsae) { log.error("Error getting password hash - " + nsae.getMessage()); return null; } } | public static String getSSHADigest(String password, String salt) { String digest = null; MessageDigest sha = null; try { sha = MessageDigest.getInstance("SHA-1"); sha.reset(); sha.update(password.getBytes()); sha.update(salt.getBytes()); byte[] pwhash = sha.digest(); digest = "{SSHA}" + new String(Base64.encode(concatenate(pwhash, salt.getBytes()))); } catch (NoSuchAlgorithmException nsae) { CofaxToolsUtil.log("Algorithme SHA-1 non supporte a la creation du hashage" + nsae + id); } return digest; } | 884,664 |
0 | public void testScenario() throws Exception { String expression = "SELECT id, name, address, phone FROM " + TABLE + " where id > 2 and id < 12 order by id"; SQLQuery query = new SQLQuery(); query.setResourceID(mResourceID); query.addExpression(expression); TupleToWebRowSetCharArrays tupleToWebRowSet = new TupleToWebRowSetCharArrays(); tupleToWebRowSet.connectDataInput(query.getDataOutput()); DeliverToFTP deliverToFTP = new DeliverToFTP(); deliverToFTP.connectDataInput(tupleToWebRowSet.getResultOutput()); deliverToFTP.addFilename(FILE); deliverToFTP.addHost(mURL); PipelineWorkflow pipeline = new PipelineWorkflow(); pipeline.add(query); pipeline.add(tupleToWebRowSet); pipeline.add(deliverToFTP); mDRER.execute(pipeline, RequestExecutionType.SYNCHRONOUS); final URL url = new URL("ftp://" + mURL + "/" + FILE); final URLConnection connection = url.openConnection(); connection.setDoInput(true); connection.setDoOutput(false); InputStream is = connection.getInputStream(); WebRowSetToResultSet converter = new WebRowSetToResultSet(new InputStreamReader(is)); converter.setResultSetType(ResultSet.TYPE_FORWARD_ONLY); ResultSet rs = converter.getResultSet(); JDBCTestHelper.validateResultSet(mConnection, expression, rs, 1); rs.close(); } | @Override public void actionPerformed(ActionEvent e) { if (e.getSource() == btnClear) { passwordField.setText(""); } for (int i = 0; i < 10; i++) { if (e.getSource() == btnNumber[i]) { String password = new String((passwordField.getPassword())); passwordField.setText(password + i); } } if (e.getSource() == btnOK) { String password = new String((passwordField.getPassword())); ResultSet rs; Statement stmt; String sql; String result = ""; boolean checkPassword = false; sql = "select password from Senhas_De_Unica_Vez where login='" + login + "'" + " and key=" + key + " "; try { theConn = DatabaseConnection.getConnection(); stmt = theConn.createStatement(); rs = stmt.executeQuery(sql); while (rs.next()) { result = rs.getString("password"); } rs.close(); stmt.close(); try { MessageDigest messageDigest = MessageDigest.getInstance("SHA1"); messageDigest.update(password.getBytes()); BigInteger bigInt = new BigInteger(1, messageDigest.digest()); String output = bigInt.toString(16); if (output.compareTo(result) == 0) checkPassword = true; else checkPassword = false; } catch (NoSuchAlgorithmException exception) { exception.printStackTrace(); } } catch (Exception exception) { exception.printStackTrace(); } finally { try { if (theConn != null) theConn.close(); } catch (Exception exception) { } } if (checkPassword == true) { JOptionPane.showMessageDialog(null, "senha correta!"); sql = "delete from Senhas_De_Unica_Vez where login='" + login + "'" + " and key=" + key + " "; try { theConn = DatabaseConnection.getConnection(); stmt = theConn.createStatement(); stmt.executeUpdate(sql); stmt.close(); } catch (Exception exception) { exception.printStackTrace(); } finally { try { if (theConn != null) theConn.close(); } catch (Exception exception) { } } setVisible(false); setTries(0); Error.log(4003, "Senha de uso �nico verificada positivamente."); Error.log(4002, "Autentica��o etapa 3 encerrada."); ManagerWindow mw = new ManagerWindow(login); mw.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); } else { JOptionPane.showMessageDialog(null, "senha incorreta!"); int tries = getTries(); if (tries == 0) { Error.log(4004, "Primeiro erro da senha de uso �nico contabilizado."); } else if (tries == 1) { Error.log(4005, "Segundo erro da senha de uso �nico contabilizado."); } else if (tries == 2) { Error.log(4006, "Terceiro erro da senha de uso �nico contabilizado."); Error.log(4007, "Acesso do usuario " + login + " bloqueado pela autentica��o etapa 3."); Error.log(4002, "Autentica��o etapa 3 encerrada."); Error.log(1002, "Sistema encerrado."); setTries(++tries); System.exit(1); } setTries(++tries); } } } | 884,665 |
0 | public static String getEncodedHex(String text) { MessageDigest md = null; String encodedString = null; try { md = MessageDigest.getInstance("MD5"); md.update(text.getBytes()); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } Hex hex = new Hex(); encodedString = new String(hex.encode(md.digest())); md.reset(); return encodedString; } | public boolean ponerRivalxRonda(int idJugadorDiv, int idRonda, int dato) { int intResult = 0; String sql = "UPDATE jugadorxdivxronda " + " SET idPareoRival = " + dato + " WHERE jugadorxDivision_idJugadorxDivision = " + idJugadorDiv + " AND ronda_numeroRonda = " + idRonda; try { connection = conexionBD.getConnection(); connection.setAutoCommit(false); ps = connection.prepareStatement(sql); intResult = ps.executeUpdate(); connection.commit(); } catch (SQLException ex) { ex.printStackTrace(); try { connection.rollback(); } catch (SQLException exe) { exe.printStackTrace(); } } finally { conexionBD.close(ps); conexionBD.close(connection); } return (intResult > 0); } | 884,666 |
0 | public File createTemporaryFile() throws IOException { URL url = clazz.getResource(resource); if (url == null) { throw new IOException("No resource available from '" + clazz.getName() + "' for '" + resource + "'"); } String extension = getExtension(resource); String prefix = "resource-temporary-file-creator"; File file = File.createTempFile(prefix, extension); InputStream input = url.openConnection().getInputStream(); FileOutputStream output = new FileOutputStream(file); com.volantis.synergetics.io.IOUtils.copyAndClose(input, output); return file; } | private boolean dependencyOutOfDate(ScriptCacheEntry entry) { if (entry != null) { for (Iterator i = entry.dependencies.keySet().iterator(); i.hasNext(); ) { URLConnection urlc = null; URL url = (URL) i.next(); try { urlc = url.openConnection(); urlc.setDoInput(false); urlc.setDoOutput(false); long dependentLastModified = urlc.getLastModified(); if (dependentLastModified > ((Long) entry.dependencies.get(url)).longValue()) { return true; } } catch (IOException ioe) { return true; } } } return false; } | 884,667 |
1 | public static String getUserPass(String user) throws NoSuchAlgorithmException { MessageDigest digest = MessageDigest.getInstance("MD5"); digest.update(user.getBytes()); byte[] hash = digest.digest(); System.out.println("Returning user pass:" + hash); return hash.toString(); } | public static String hash(String plaintext) { if (plaintext == null) { return ""; } MessageDigest md = null; try { md = MessageDigest.getInstance("SHA1"); md.update(plaintext.getBytes("UTF-8")); } catch (Exception e) { } return new String(Base64.encodeBase64(md.digest())); } | 884,668 |
0 | private void readArchives(final VideoArchiveSet vas) throws IOException { final BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); String line = null; try { while ((line = in.readLine()) != null) { if (line.startsWith("ARCHIVE")) { final StringTokenizer s = new StringTokenizer(line); s.nextToken(); final Integer tapeNumber = Integer.valueOf(s.nextToken()); final Timecode timeCode = new Timecode(s.nextToken()); final VideoArchive va = new VideoArchive(); va.setTimeCode(timeCode); va.setTapeNumber(tapeNumber); vas.addVideoArchive(va); archives.put(tapeNumber, va); } } } catch (IOException e) { throw e; } finally { in.close(); } if (archives.size() == 0) { log.warn("No lines with ARCHIVE were found in the current vif file, will try to look at another vif with same yearday, " + "ship and platform and try to get archives from there:"); String urlBase = url.getPath().toString().substring(0, url.getPath().toString().lastIndexOf("/")); File vifDir = new File(urlBase); File[] allYeardayFiles = vifDir.listFiles(); for (int i = 0; i < allYeardayFiles.length; i++) { if (allYeardayFiles[i].toString().endsWith(".vif")) { String filename = allYeardayFiles[i].toString().substring(allYeardayFiles[i].toString().lastIndexOf("/")); String fileLC = filename.toLowerCase(); String toLookFor = new String(new Character(vifMetadata.shipCode).toString() + new Character(vifMetadata.platformCode).toString()); String toLookForLC = toLookFor.toLowerCase(); if (fileLC.indexOf(toLookForLC) >= 0) { log.warn("Will try to read archives from file " + allYeardayFiles[i]); final BufferedReader tempIn = new BufferedReader(new FileReader(allYeardayFiles[i])); String tempLine = null; try { while ((tempLine = tempIn.readLine()) != null) { if (tempLine.startsWith("ARCHIVE")) { final StringTokenizer s = new StringTokenizer(tempLine); s.nextToken(); final Integer tapeNumber = Integer.valueOf(s.nextToken()); final Timecode timeCode = new Timecode(s.nextToken()); final VideoArchive va = new VideoArchive(); va.setTimeCode(timeCode); va.setTapeNumber(tapeNumber); vas.addVideoArchive(va); archives.put(tapeNumber, va); } } } catch (IOException e) { throw e; } finally { tempIn.close(); } } } if (archives.size() > 0) { log.warn("Found " + archives.size() + " archives in that vif so will use that"); break; } } if (archives.size() == 0) { log.warn("Still no archives were found in the file. Unable to process it."); } } } | public TempFileTextBody(InputStream is, String mimeCharset) throws IOException { this.mimeCharset = mimeCharset; TempPath tempPath = TempStorage.getInstance().getRootTempPath(); tempFile = tempPath.createTempFile("attachment", ".txt"); OutputStream out = tempFile.getOutputStream(); IOUtils.copy(is, out); out.close(); } | 884,669 |
1 | @RequestMapping(value = "/privatefiles/{file_name}") public void getFile(@PathVariable("file_name") String fileName, HttpServletResponse response, Principal principal) { try { Boolean validUser = false; final String currentUser = principal.getName(); Authentication auth = SecurityContextHolder.getContext().getAuthentication(); if (!auth.getPrincipal().equals(new String("anonymousUser"))) { MetabolightsUser metabolightsUser = (MetabolightsUser) auth.getPrincipal(); if (metabolightsUser != null && metabolightsUser.isCurator()) validUser = true; } if (currentUser != null) { Study study = studyService.getBiiStudy(fileName, true); Collection<User> users = study.getUsers(); Iterator<User> iter = users.iterator(); while (iter.hasNext()) { User user = iter.next(); if (user.getUserName().equals(currentUser)) { validUser = true; break; } } } if (!validUser) throw new RuntimeException(PropertyLookup.getMessage("Entry.notAuthorised")); try { InputStream is = new FileInputStream(privateFtpDirectory + fileName + ".zip"); response.setContentType("application/zip"); IOUtils.copy(is, response.getOutputStream()); } catch (Exception e) { throw new RuntimeException(PropertyLookup.getMessage("Entry.fileMissing")); } response.flushBuffer(); } catch (IOException ex) { logger.info("Error writing file to output stream. Filename was '" + fileName + "'"); throw new RuntimeException("IOError writing file to output stream"); } } | public static void importDB(String input, String output) { try { Class.forName("org.sqlite.JDBC"); String fileName = output + File.separator + G.databaseName; File dataBase = new File(fileName); if (!dataBase.exists()) { G.conn = DriverManager.getConnection("jdbc:sqlite:" + fileName); createTablesDB(); } else G.conn = DriverManager.getConnection("jdbc:sqlite:" + fileName); long tiempoInicio = System.currentTimeMillis(); String directoryPath = input + File.separator; File myDirectory = new File(directoryPath); String[] list = myDirectory.list(); File fileXML = new File(input + File.separator + G.imagesName); if (!fileXML.exists()) { JOptionPane.showMessageDialog(null, "No se encuentra el fichero XML", "Error", JOptionPane.ERROR_MESSAGE); } else { SAXBuilder builder = new SAXBuilder(false); Document docXML = builder.build(fileXML); Element root = docXML.getRootElement(); List images = root.getChildren("image"); Iterator j = images.iterator(); List<Element> globalLanguages = root.getChild("languages").getChildren("language"); Iterator<Element> langsI = globalLanguages.iterator(); HashMap<String, Integer> languageIDs = new HashMap<String, Integer>(); HashMap<String, Integer> typeIDs = new HashMap<String, Integer>(); Element e; int i = 0; int contTypes = 0; int contImages = 0; while (langsI.hasNext()) { e = langsI.next(); languageIDs.put(e.getText(), i); PreparedStatement stmt = G.conn.prepareStatement("INSERT OR IGNORE INTO language (id,name) VALUES (?,?)"); stmt.setInt(1, i); stmt.setString(2, e.getText()); stmt.executeUpdate(); stmt.close(); i++; } G.conn.setAutoCommit(false); while (j.hasNext()) { Element image = (Element) j.next(); String id = image.getAttributeValue("id"); List languages = image.getChildren("language"); Iterator k = languages.iterator(); if (exists(list, id)) { String pathSrc = directoryPath.concat(id); String pathDst = output + File.separator + id.substring(0, 1).toUpperCase() + File.separator; String folder = output + File.separator + id.substring(0, 1).toUpperCase(); String pathDstTmp = pathDst.concat(id); String idTmp = id; File testFile = new File(pathDstTmp); int cont = 1; while (testFile.exists()) { idTmp = id.substring(0, id.lastIndexOf('.')) + '_' + cont + id.substring(id.lastIndexOf('.'), id.length()); pathDstTmp = pathDst + idTmp; testFile = new File(pathDstTmp); cont++; } pathDst = pathDstTmp; id = idTmp; File newDirectoryFolder = new File(folder); if (!newDirectoryFolder.exists()) { newDirectoryFolder.mkdirs(); } try { FileChannel srcChannel = new FileInputStream(pathSrc).getChannel(); FileChannel dstChannel = new FileOutputStream(pathDst).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (IOException exc) { System.out.println(exc.toString()); } while (k.hasNext()) { Element languageElement = (Element) k.next(); String language = languageElement.getAttributeValue("id"); List words = languageElement.getChildren("word"); Iterator l = words.iterator(); while (l.hasNext()) { Element wordElement = (Element) l.next(); String type = wordElement.getAttributeValue("type"); if (!typeIDs.containsKey(type)) { typeIDs.put(type, contTypes); PreparedStatement stmt = G.conn.prepareStatement("INSERT OR IGNORE INTO type (id,name) VALUES (?,?)"); stmt.setInt(1, contTypes); stmt.setString(2, type); stmt.executeUpdate(); stmt.close(); contTypes++; } PreparedStatement stmt = G.conn.prepareStatement("INSERT OR IGNORE INTO main (word, idL, idT, name, nameNN) VALUES (?,?,?,?,?)"); stmt.setString(1, wordElement.getText().toLowerCase()); stmt.setInt(2, languageIDs.get(language)); stmt.setInt(3, typeIDs.get(type)); stmt.setString(4, id); stmt.setString(5, id); stmt.executeUpdate(); stmt.close(); if (contImages == 5000) { G.conn.commit(); contImages = 0; } else contImages++; } } } else { } } G.conn.setAutoCommit(true); G.conn.close(); long totalTiempo = System.currentTimeMillis() - tiempoInicio; System.out.println("El tiempo total es :" + totalTiempo / 1000 + " segundos"); } } catch (Exception e) { e.printStackTrace(); } } | 884,670 |
0 | void loadImage(Frame frame, URL url) throws Exception { URLConnection conn = url.openConnection(); String mimeType = conn.getContentType(); long length = conn.getContentLength(); InputStream is = conn.getInputStream(); loadImage(frame, is, length, mimeType); } | public static String getStringFromAFileAtURL(String anURL) { String htmlCode = "<html><body></body></html>"; try { URL url = new URL(anURL); URLConnection urlConnection = url.openConnection(); BufferedReader in = new BufferedReader(new InputStreamReader(urlConnection.getInputStream())); String inputLine = ""; htmlCode = ""; while ((inputLine = in.readLine()) != null) htmlCode += inputLine + "\n"; in.close(); } catch (Exception e) { logs.info("URLResolver : lien mort"); JOptionPane.showMessageDialog(null, "lien mort"); return "<html><body></body></html>"; } return checkXMLTagsLowerCase(htmlCode); } | 884,671 |
1 | void run(String[] args) { InputStream istream = System.in; System.out.println("TradeMaximizer " + version); String filename = parseArgs(args, false); if (filename != null) { System.out.println("Input from: " + filename); try { if (filename.startsWith("http:") || filename.startsWith("ftp:")) { URL url = new URL(filename); istream = url.openStream(); } else istream = new FileInputStream(filename); } catch (IOException ex) { fatalError(ex.toString()); } } List<String[]> wantLists = readWantLists(istream); if (wantLists == null) return; if (options.size() > 0) { System.out.print("Options:"); for (String option : options) System.out.print(" " + option); System.out.println(); } System.out.println(); try { MessageDigest digest = MessageDigest.getInstance("MD5"); for (String[] wset : wantLists) { for (String w : wset) { digest.update((byte) ' '); digest.update(w.getBytes()); } digest.update((byte) '\n'); } System.out.println("Input Checksum: " + toHexString(digest.digest())); } catch (NoSuchAlgorithmException ex) { } parseArgs(args, true); if (iterations > 1 && seed == -1) { seed = System.currentTimeMillis(); System.out.println("No explicit SEED, using " + seed); } if (!(metric instanceof MetricSumSquares) && priorityScheme != NO_PRIORITIES) System.out.println("Warning: using priorities with the non-default metric is normally worthless"); buildGraph(wantLists); if (showMissing && officialNames != null && officialNames.size() > 0) { for (String name : usedNames) officialNames.remove(name); List<String> missing = new ArrayList<String>(officialNames); Collections.sort(missing); for (String name : missing) { System.out.println("**** Missing want list for official name " + name); } System.out.println(); } if (showErrors && errors.size() > 0) { Collections.sort(errors); System.out.println("ERRORS:"); for (String error : errors) System.out.println(error); System.out.println(); } long startTime = System.currentTimeMillis(); graph.removeImpossibleEdges(); List<List<Graph.Vertex>> bestCycles = graph.findCycles(); int bestMetric = metric.calculate(bestCycles); if (iterations > 1) { System.out.println(metric); graph.saveMatches(); for (int i = 0; i < iterations - 1; i++) { graph.shuffle(); List<List<Graph.Vertex>> cycles = graph.findCycles(); int newMetric = metric.calculate(cycles); if (newMetric < bestMetric) { bestMetric = newMetric; bestCycles = cycles; graph.saveMatches(); System.out.println(metric); } else if (verbose) System.out.println("# " + metric); } System.out.println(); graph.restoreMatches(); } long stopTime = System.currentTimeMillis(); displayMatches(bestCycles); if (showElapsedTime) System.out.println("Elapsed time = " + (stopTime - startTime) + "ms"); } | public static synchronized String encrypt(String plaintext) throws Exception { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(plaintext.getBytes("UTF-8")); byte raw[] = md.digest(); return (new BASE64Encoder()).encode(raw); } | 884,672 |
0 | public static boolean downloadFile(String url, String destination) throws Exception { BufferedInputStream bi = null; BufferedOutputStream bo = null; File destfile; byte BUFFER[] = new byte[100]; java.net.URL fileurl; URLConnection conn; fileurl = new java.net.URL(url); conn = fileurl.openConnection(); long fullsize = conn.getContentLength(); long onepercent = fullsize / 100; MessageFrame.setTotalDownloadSize(fullsize); bi = new BufferedInputStream(conn.getInputStream()); destfile = new File(destination); if (!destfile.createNewFile()) { destfile.delete(); destfile.createNewFile(); } bo = new BufferedOutputStream(new FileOutputStream(destfile)); int read = 0; int sum = 0; long i = 0; while ((read = bi.read(BUFFER)) != -1) { bo.write(BUFFER, 0, read); sum += read; i += read; if (i > onepercent) { i = 0; MessageFrame.setDownloadProgress(sum); } } bi.close(); bo.close(); MessageFrame.setDownloadProgress(fullsize); return true; } | protected int sendData(String submitName, String submitValue) throws HttpException, IOException, SAXException { PostMethod postMethod = null; try { postMethod = new PostMethod(getDocumentBase().toString()); postMethod.getParams().setCookiePolicy(org.apache.commons.httpclient.cookie.CookiePolicy.IGNORE_COOKIES); postMethod.addRequestHeader("Cookie", getWikiPrefix() + "_session=" + getSession() + "; " + getWikiPrefix() + "UserID=" + getUserId() + "; " + getWikiPrefix() + "UserName=" + getUserName() + "; "); List<Part> parts = new ArrayList<Part>(); for (String s : new String[] { "wpSection", "wpEdittime", "wpScrolltop", "wpStarttime", "wpEditToken" }) { parts.add(new StringPart(s, StringEscapeUtils.unescapeJava(getNonNullParameter(s)))); } parts.add(new StringPart("action", "edit")); parts.add(new StringPart("wpTextbox1", getArticleContent())); parts.add(new StringPart("wpSummary", getSummary())); parts.add(new StringPart("wpAutoSummary", Digest.MD5.isImplemented() ? Digest.MD5.encrypt(getSummary()) : "")); parts.add(new StringPart(submitName, submitValue)); MultipartRequestEntity requestEntity = new MultipartRequestEntity(parts.toArray(new Part[parts.size()]), postMethod.getParams()); postMethod.setRequestEntity(requestEntity); int status = getHttpClient().executeMethod(postMethod); IOUtils.copyTo(postMethod.getResponseBodyAsStream(), System.err); return status; } catch (HttpException err) { throw err; } catch (IOException err) { throw err; } finally { if (postMethod != null) postMethod.releaseConnection(); } } | 884,673 |
0 | public void update(Site site) throws Exception { DBOperation dbo = null; Connection connection = null; PreparedStatement preparedStatement = null; ResultSet resultSet = null; String exp = site.getExtendParent(); String path = site.getPath(); try { String sqlStr = "update t_ip_site set id=?,name=?,description=?,ascii_name=?,remark_number=?,increment_index=?,use_status=?,appserver_id=? where id=?"; dbo = createDBOperation(); connection = dbo.getConnection(); connection.setAutoCommit(false); String[] selfDefinePath = getSelfDefinePath(path, exp, connection, preparedStatement, resultSet); selfDefineDelete(selfDefinePath, connection, preparedStatement); selfDefineAdd(selfDefinePath, site, connection, preparedStatement); preparedStatement = connection.prepareStatement(sqlStr); preparedStatement.setInt(1, site.getSiteID()); preparedStatement.setString(2, site.getName()); preparedStatement.setString(3, site.getDescription()); preparedStatement.setString(4, site.getAsciiName()); preparedStatement.setInt(5, site.getRemarkNumber()); preparedStatement.setString(6, site.getIncrementIndex().trim()); preparedStatement.setString(7, String.valueOf(site.getUseStatus())); preparedStatement.setString(8, String.valueOf(site.getAppserverID())); preparedStatement.setInt(9, site.getSiteID()); preparedStatement.executeUpdate(); connection.commit(); int resID = site.getSiteID() + Const.SITE_TYPE_RES; StructResource sr = new StructResource(); sr.setResourceID(Integer.toString(resID)); sr.setOperateID(Integer.toString(1)); sr.setOperateTypeID(Const.OPERATE_TYPE_ID); sr.setTypeID(Const.RES_TYPE_ID); StructAuth sa = new AuthorityManager().getExternalAuthority(sr); int authID = sa.getAuthID(); if (authID == 0) { String resName = site.getName(); int resTypeID = Const.RES_TYPE_ID; int operateTypeID = Const.OPERATE_TYPE_ID; String remark = ""; AuthorityManager am = new AuthorityManager(); am.createExtResource(Integer.toString(resID), resName, resTypeID, operateTypeID, remark); } site.wirteFile(); } catch (SQLException ex) { connection.rollback(); log.error("����վ������ʧ��!", ex); throw ex; } finally { close(resultSet, null, preparedStatement, connection, dbo); } } | public static String generateSig(Map<String, String> params, String secret) { SortedSet<String> keys = new TreeSet<String>(params.keySet()); keys.remove(FacebookParam.SIGNATURE.toString()); String str = ""; for (String key : keys) { str += key + "=" + params.get(key); } str += secret; try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(str.getBytes("UTF-8")); StringBuilder result = new StringBuilder(); for (byte b : md.digest()) { result.append(Integer.toHexString((b & 0xf0) >>> 4)); result.append(Integer.toHexString(b & 0x0f)); } return result.toString(); } catch (Exception e) { throw new RuntimeException(e); } } | 884,674 |
0 | public LinkedList<NameValuePair> getQuestion() { InputStream is = null; String result = ""; LinkedList<NameValuePair> question = new LinkedList<NameValuePair>(); try { HttpClient httpclient = new DefaultHttpClient(); HttpPost httppost = new HttpPost(domain); httppost.setEntity(new UrlEncodedFormEntity(library)); HttpResponse response = httpclient.execute(httppost); HttpEntity entity = response.getEntity(); is = entity.getContent(); } catch (Exception e) { Log.e("log_tag", "Error in http connection " + e.toString()); } try { BufferedReader reader = new BufferedReader(new InputStreamReader(is, "iso-8859-1"), 8); StringBuilder sb = new StringBuilder(); String line = null; while ((line = reader.readLine()) != null) { sb.append(line); } is.close(); result = sb.toString(); if (result.equals("null,")) { return null; } } catch (Exception e) { Log.e("log_tag", "Error converting result " + e.toString()); } try { JSONObject json = new JSONObject(result); JSONArray data = json.getJSONArray("data"); JSONObject quest = data.getJSONObject(0); question.add(new BasicNameValuePair("q", quest.getString("q"))); question.add(new BasicNameValuePair("a", quest.getString("a"))); question.add(new BasicNameValuePair("b", quest.getString("b"))); question.add(new BasicNameValuePair("c", quest.getString("c"))); question.add(new BasicNameValuePair("d", quest.getString("d"))); question.add(new BasicNameValuePair("correct", quest.getString("correct"))); return question; } catch (JSONException e) { Log.e("log_tag", "Error parsing data " + e.toString()); } return null; } | public static String login() throws Exception { if (sid == null) { String login = ROLAPClientAux.loadProperties().getProperty("user"); String password = ROLAPClientAux.loadProperties().getProperty("password"); MessageDigest md = MessageDigest.getInstance("MD5"); md.update(password.getBytes()); String password2 = asHexString(md.digest()); String query = "/server/login?user=" + login + "&extern_password=" + password + "&password=" + password2; Vector<String> res = ROLAPClientAux.sendRequest(query); String vals[] = res.get(0).split(";"); sid = vals[0]; } return sid; } | 884,675 |
1 | @Transient private String md5sum(String text) { try { MessageDigest md = MessageDigest.getInstance("MD5"); md.reset(); md.update(text.getBytes()); byte messageDigest[] = md.digest(); return bufferToHex(messageDigest, 0, messageDigest.length); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } return null; } | private boolean keysMatch(String keyNMinusOne, String keyN) { boolean match = false; try { MessageDigest digest = MessageDigest.getInstance("SHA-1"); digest.reset(); digest.update(keyNMinusOne.getBytes()); byte[] hashedBytes = digest.digest(); String encodedHashedKey = new String(com.Ostermiller.util.Base64.encode(hashedBytes)); match = encodedHashedKey.equals(keyN); } catch (NoSuchAlgorithmException e) { } return match; } | 884,676 |
1 | private void compress(File target, Set<File> files) throws CacheOperationException, ConfigurationException { ZipOutputStream zipOutput = null; try { zipOutput = new ZipOutputStream(new BufferedOutputStream(new FileOutputStream(target))); for (File file : files) { BufferedInputStream fileInput = null; File cachePathName = new File(cacheFolder, file.getPath()); try { if (!cachePathName.exists()) { throw new CacheOperationException("Expected to add file ''{0}'' to export archive ''{1}'' (Account : {2}) but it " + "has gone missing (cause unknown). This can indicate implementation or deployment " + "error. Aborting export operation as a safety precaution.", cachePathName.getPath(), target.getAbsolutePath(), account.getOid()); } fileInput = new BufferedInputStream(new FileInputStream(cachePathName)); ZipEntry entry = new ZipEntry(file.getPath()); entry.setSize(cachePathName.length()); entry.setTime(cachePathName.lastModified()); zipOutput.putNextEntry(entry); cacheLog.debug("Added new export zip entry ''{0}''.", file.getPath()); int count, total = 0; int buffer = 2048; byte[] data = new byte[buffer]; while ((count = fileInput.read(data, 0, buffer)) != -1) { zipOutput.write(data, 0, count); total += count; } zipOutput.flush(); if (total != cachePathName.length()) { throw new CacheOperationException("Only wrote {0} out of {1} bytes when archiving file ''{2}'' (Account : {3}). " + "This could have occured either due implementation error or file I/O error. " + "Aborting archive operation to prevent a potentially corrupt export archive to " + "be created.", total, cachePathName.length(), cachePathName.getPath(), account.getOid()); } else { cacheLog.debug("Wrote {0} out of {1} bytes to zip entry ''{2}''", total, cachePathName.length(), file.getPath()); } } catch (SecurityException e) { throw new ConfigurationException("Security manager has denied r/w access when attempting to read file ''{0}'' and " + "write it to archive ''{1}'' (Account : {2}) : {3}", e, cachePathName.getPath(), target, account.getOid(), e.getMessage()); } catch (IllegalArgumentException e) { throw new CacheOperationException("Error creating ZIP archive for account ID = {0} : {1}", e, account.getOid(), e.getMessage()); } catch (FileNotFoundException e) { throw new CacheOperationException("Attempted to include file ''{0}'' in export archive but it has gone missing " + "(Account : {1}). Possible implementation error in local file cache. Aborting " + "export operation as a precaution ({2})", e, cachePathName.getPath(), account.getOid(), e.getMessage()); } catch (ZipException e) { throw new CacheOperationException("Error writing export archive for account ID = {0} : {1}", e, account.getOid(), e.getMessage()); } catch (IOException e) { throw new CacheOperationException("I/O error while creating export archive for account ID = {0}. " + "Operation aborted ({1})", e, account.getOid(), e.getMessage()); } finally { if (zipOutput != null) { try { zipOutput.closeEntry(); } catch (Throwable t) { cacheLog.warn("Unable to close zip entry for file ''{0}'' in export archive ''{1}'' " + "(Account : {2}) : {3}.", t, file.getPath(), target.getAbsolutePath(), account.getOid(), t.getMessage()); } } if (fileInput != null) { try { fileInput.close(); } catch (Throwable t) { cacheLog.warn("Failed to close input stream from file ''{0}'' being added " + "to export archive (Account : {1}) : {2}", t, cachePathName.getPath(), account.getOid(), t.getMessage()); } } } } } catch (FileNotFoundException e) { throw new CacheOperationException("Unable to create target export archive ''{0}'' for account {1) : {2}", e, target, account.getOid(), e.getMessage()); } finally { try { if (zipOutput != null) { zipOutput.close(); } } catch (Throwable t) { cacheLog.warn("Failed to close the stream to export archive ''{0}'' : {1}.", t, target, t.getMessage()); } } } | public void command() { JFileChooser chooser = new JFileChooser(); chooser.setCurrentDirectory(new File(dir)); int returnVal = chooser.showOpenDialog(null); if (returnVal == JFileChooser.APPROVE_OPTION) { filename = chooser.getSelectedFile().getAbsolutePath(); String f2 = ""; for (int i = 0; i < filename.length(); ++i) { if (filename.charAt(i) != '\\') { f2 = f2 + filename.charAt(i); } else f2 = f2 + '/'; } filename = f2; if (filename.contains(dir)) { filename = filename.substring(dir.length()); } else { try { FileChannel srcFile = new FileInputStream(filename).getChannel(); FileChannel dstFile; filename = "ueditor_files/" + chooser.getSelectedFile().getName(); File newFile; if (!(newFile = new File(dir + filename)).createNewFile()) { dstFile = new FileInputStream(dir + filename).getChannel(); newFile = null; } else { dstFile = new FileOutputStream(newFile).getChannel(); } dstFile.transferFrom(srcFile, 0, srcFile.size()); srcFile.close(); dstFile.close(); System.out.println("file copyed to: " + dir + filename); } catch (Exception e) { e.printStackTrace(); label.setIcon(InputText.iconX); filename = null; for (Group g : groups) { g.updateValidity(true); } return; } } label.setIcon(InputText.iconV); for (Group g : groups) { g.updateValidity(true); } } } | 884,677 |
1 | public static void copy(File source, File target) { FileChannel in = null; FileChannel out = null; try { in = new FileInputStream(source).getChannel(); out = new FileOutputStream(target).getChannel(); ByteBuffer buffer = ByteBuffer.allocateDirect(BUFFER); while (in.read(buffer) != -1) { buffer.flip(); while (buffer.hasRemaining()) { out.write(buffer); } buffer.clear(); } } catch (IOException ex) { throw new RuntimeException(ex); } finally { close(in); close(out); } } | public boolean backupFile(File oldFile, File newFile) { boolean isBkupFileOK = false; FileChannel sourceChannel = null; FileChannel targetChannel = null; try { sourceChannel = new FileInputStream(oldFile).getChannel(); targetChannel = new FileOutputStream(newFile).getChannel(); targetChannel.transferFrom(sourceChannel, 0, sourceChannel.size()); } catch (IOException e) { logger.log(Level.SEVERE, "IO exception occurred while copying file", e); } finally { if ((newFile != null) && (newFile.exists()) && (newFile.length() > 0)) { isBkupFileOK = true; } try { if (sourceChannel != null) { sourceChannel.close(); } if (targetChannel != null) { targetChannel.close(); } } catch (IOException e) { logger.info("closing channels failed"); } } return isBkupFileOK; } | 884,678 |
1 | public JSONObject getTargetGraph(HttpSession session, JSONObject json) throws JSONException { StringBuffer out = new StringBuffer(); Graph tgt = null; MappingManager manager = (MappingManager) session.getAttribute(RuncibleConstants.MAPPING_MANAGER.key()); try { tgt = manager.getTargetGraph(); if (tgt != null) { FlexGraphViewFactory factory = new FlexGraphViewFactory(); factory.setColorScheme(ColorSchemes.ORANGES); factory.visit(tgt); GraphView view = factory.getGraphView(); GraphViewRenderer renderer = new FlexGraphViewRenderer(); renderer.setGraphView(view); InputStream xmlStream = renderer.renderGraphView(); StringWriter writer = new StringWriter(); IOUtils.copy(xmlStream, writer); writer.close(); System.out.println(writer.toString()); out.append(writer.toString()); } else { out.append("No target graph loaded."); } } catch (Exception e) { return JSONUtils.SimpleJSONError("Cannot load target graph: " + e.getMessage()); } return JSONUtils.SimpleJSONResponse(out.toString()); } | 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!"); } | 884,679 |
0 | private void createScript(File scriptsLocation, String relativePath, String scriptContent) { Writer fileWriter = null; try { File scriptFile = new File(scriptsLocation.getAbsolutePath() + "/" + relativePath); scriptFile.getParentFile().mkdirs(); fileWriter = new FileWriter(scriptFile); IOUtils.copy(new StringReader(scriptContent), fileWriter); } catch (IOException e) { throw new UnitilsException(e); } finally { IOUtils.closeQuietly(fileWriter); } } | public int addLocationInfo(int id, double lattitude, double longitude) { int ret = 0; Connection conn = null; PreparedStatement psmt = null; try { String sql = "insert into kddb.location_info (user_id, latitude, longitude) values(?, ?, ?)"; conn = getConnection(); psmt = conn.prepareStatement(sql); psmt.setInt(1, id); psmt.setDouble(2, lattitude); psmt.setDouble(3, longitude); ret = psmt.executeUpdate(); if (ret == 1) { conn.commit(); } else { conn.rollback(); } } catch (SQLException ex) { log.error("[addLocationInfo]", ex); } finally { endProsess(conn, psmt, null, null); } return ret; } | 884,680 |
1 | private void copyFile(File in, File out) throws Exception { FileChannel sourceChannel = new FileInputStream(in).getChannel(); FileChannel destinationChannel = new FileOutputStream(out).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), destinationChannel); sourceChannel.close(); destinationChannel.close(); } | public void actionPerformed(ActionEvent ev) { if (fileChooser == null) { fileChooser = new JFileChooser(); ExtensionFileFilter fileFilter = new ExtensionFileFilter("Device profile (*.jar, *.zip)"); fileFilter.addExtension("jar"); fileFilter.addExtension("zip"); fileChooser.setFileFilter(fileFilter); } if (fileChooser.showOpenDialog(SwingSelectDevicePanel.this) == JFileChooser.APPROVE_OPTION) { String manifestDeviceName = null; URL[] urls = new URL[1]; ArrayList descriptorEntries = new ArrayList(); JarFile jar = null; try { jar = new JarFile(fileChooser.getSelectedFile()); Manifest manifest = jar.getManifest(); if (manifest != null) { Attributes attrs = manifest.getMainAttributes(); manifestDeviceName = attrs.getValue("Device-Name"); } for (Enumeration en = jar.entries(); en.hasMoreElements(); ) { String entry = ((JarEntry) en.nextElement()).getName(); if ((entry.toLowerCase().endsWith(".xml") || entry.toLowerCase().endsWith("device.txt")) && !entry.toLowerCase().startsWith("meta-inf")) { descriptorEntries.add(entry); } } urls[0] = fileChooser.getSelectedFile().toURL(); } catch (IOException e) { Message.error("Error reading file: " + fileChooser.getSelectedFile().getName() + ", " + Message.getCauseMessage(e), e); return; } finally { if (jar != null) { try { jar.close(); } catch (IOException ignore) { } } } if (descriptorEntries.size() == 0) { Message.error("Cannot find any device profile in file: " + fileChooser.getSelectedFile().getName()); return; } if (descriptorEntries.size() > 1) { manifestDeviceName = null; } ClassLoader classLoader = Common.createExtensionsClassLoader(urls); HashMap devices = new HashMap(); for (Iterator it = descriptorEntries.iterator(); it.hasNext(); ) { String entryName = (String) it.next(); try { devices.put(entryName, DeviceImpl.create(emulatorContext, classLoader, entryName, J2SEDevice.class)); } catch (IOException e) { Message.error("Error parsing device profile, " + Message.getCauseMessage(e), e); return; } } for (Enumeration en = lsDevicesModel.elements(); en.hasMoreElements(); ) { DeviceEntry entry = (DeviceEntry) en.nextElement(); if (devices.containsKey(entry.getDescriptorLocation())) { devices.remove(entry.getDescriptorLocation()); } } if (devices.size() == 0) { Message.info("Device profile already added"); return; } try { File deviceFile = new File(Config.getConfigPath(), fileChooser.getSelectedFile().getName()); if (deviceFile.exists()) { deviceFile = File.createTempFile("device", ".jar", Config.getConfigPath()); } IOUtils.copyFile(fileChooser.getSelectedFile(), deviceFile); DeviceEntry entry = null; for (Iterator it = devices.keySet().iterator(); it.hasNext(); ) { String descriptorLocation = (String) it.next(); Device device = (Device) devices.get(descriptorLocation); if (manifestDeviceName != null) { entry = new DeviceEntry(manifestDeviceName, deviceFile.getName(), descriptorLocation, false); } else { entry = new DeviceEntry(device.getName(), deviceFile.getName(), descriptorLocation, false); } lsDevicesModel.addElement(entry); Config.addDeviceEntry(entry); } lsDevices.setSelectedValue(entry, true); } catch (IOException e) { Message.error("Error adding device profile, " + Message.getCauseMessage(e), e); return; } } } | 884,681 |
1 | public void save() { final JFileChooser fc = new JFileChooser(); fc.setFileFilter(new FileFilter() { public String getDescription() { return "PDF File"; } public boolean accept(File f) { return f.isDirectory() || f.getName().toLowerCase().endsWith(".pdf"); } }); if (fc.showSaveDialog(this) != JFileChooser.APPROVE_OPTION) { return; } File targetFile = fc.getSelectedFile(); if (!targetFile.getName().toLowerCase().endsWith(".pdf")) { targetFile = new File(targetFile.getParentFile(), targetFile.getName() + ".pdf"); } if (targetFile.exists()) { if (JOptionPane.showConfirmDialog(this, "Do you want to overwrite the file?") != JOptionPane.YES_OPTION) { return; } } try { final InputStream is = new FileInputStream(filename); try { final OutputStream os = new FileOutputStream(targetFile); try { final byte[] buffer = new byte[32768]; for (int read; (read = is.read(buffer)) != -1; ) { os.write(buffer, 0, read); } } finally { os.close(); } } finally { is.close(); } } catch (IOException e) { e.printStackTrace(); } } | public static int convertImage(InputStream is, OutputStream os, String command) throws IOException, InterruptedException { if (logger.isInfoEnabled()) { logger.info(command); } Process p = Runtime.getRuntime().exec(command); ByteArrayOutputStream errOut = new ByteArrayOutputStream(); StreamGobbler errGobbler = new StreamGobbler(p.getErrorStream(), errOut, "Convert Thread (err gobbler): " + command); errGobbler.start(); StreamGobbler outGobbler = new StreamGobbler(new BufferedInputStream(is), p.getOutputStream(), "Convert Thread (out gobbler): " + command); outGobbler.start(); try { IOUtils.copy(p.getInputStream(), os); os.flush(); if (p.waitFor() != 0) { logger.error("Unable to convert, stderr: " + new String(errOut.toByteArray(), "UTF-8")); } return p.exitValue(); } finally { IOUtils.closeQuietly(os); } } | 884,682 |
0 | @Test public void pk() throws Exception { Connection conn = s.getConnection(); conn.setAutoCommit(false); PreparedStatement ps = conn.prepareStatement("insert into t_test(t_name,t_cname,t_data,t_date,t_double) values(?,?,?,?,?)"); for (int i = 10; i < 20; ++i) { ps.setString(1, "name-" + i); ps.setString(2, "cname-" + i); ps.setBlob(3, null); ps.setTimestamp(4, new Timestamp(System.currentTimeMillis())); ps.setNull(5, java.sql.Types.DOUBLE); ps.executeUpdate(); } conn.rollback(); conn.setAutoCommit(true); ps.close(); conn.close(); } | JSONResponse execute() throws ServerException, RtmApiException, IOException { HttpClient httpclient = new DefaultHttpClient(); URI uri; try { uri = new URI(this.request.getUrl()); HttpPost httppost = new HttpPost(uri); HttpResponse response = httpclient.execute(httppost); InputStream is = response.getEntity().getContent(); try { StringBuilder sb = new StringBuilder(); BufferedReader r = new BufferedReader(new InputStreamReader(new DoneHandlerInputStream(is))); for (String line = r.readLine(); line != null; line = r.readLine()) { sb.append(line); } return new JSONResponse(sb.toString()); } finally { is.close(); } } catch (URISyntaxException e) { throw new RtmApiException(e.getMessage()); } catch (ClientProtocolException e) { throw new RtmApiException(e.getMessage()); } } | 884,683 |
0 | public void greatestIncrease(int maxIterations) { double[] increase = new double[numModels]; int[] id = new int[numModels]; Model md = new Model(); double oldPerf = 1; for (int i = 0; i < numModels; i++) { md.addModel(models[i], false); increase[i] = oldPerf - md.getLoss(); id[i] = i; oldPerf = md.getLoss(); } for (int i = 0; i < numModels; i++) { for (int j = 0; j < numModels - 1 - i; j++) { if (increase[j] < increase[j + 1]) { double increasetemp = increase[j]; int temp = id[j]; increase[j] = increase[j + 1]; id[j] = id[j + 1]; increase[j + 1] = increasetemp; id[j + 1] = temp; } } } for (int i = 0; i < maxIterations; i++) { addToEnsemble(models[id[i]]); if (report) ensemble.report(models[id[i]].getName(), allSets); updateBestModel(); } } | private FTPClient getClient() throws SocketException, IOException { FTPClient ftp = new FTPClient(); ftp.addProtocolCommandListener(new PrintCommandListener(new PrintWriter(System.out))); ftp.setDefaultPort(getPort()); ftp.connect(getIp()); int reply = ftp.getReplyCode(); if (!FTPReply.isPositiveCompletion(reply)) { log.warn("FTP server refused connection: {}", getIp()); ftp.disconnect(); return null; } if (!ftp.login(getUsername(), getPassword())) { log.warn("FTP server refused login: {}, user: {}", getIp(), getUsername()); ftp.logout(); ftp.disconnect(); return null; } ftp.setControlEncoding(getEncoding()); ftp.setFileType(FTP.BINARY_FILE_TYPE); ftp.enterLocalPassiveMode(); return ftp; } | 884,684 |
0 | protected Set<String> moduleNamesFromReader(URL url) throws IOException { BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); Set<String> names = new HashSet<String>(); String line; while ((line = reader.readLine()) != null) { line = line.trim(); Matcher m = nonCommentPattern.matcher(line); if (m.find()) { names.add(m.group().trim()); } } return names; } | @Override protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException { PrintWriter writer = null; InputStream is = null; FileOutputStream fos = null; try { writer = response.getWriter(); } catch (IOException ex) { log(OctetStreamReader.class.getName() + "has thrown an exception: " + ex.getMessage()); } String filename = request.getHeader("X-File-Name"); try { is = request.getInputStream(); fos = new FileOutputStream(new File(targetPath + filename)); IOUtils.copy(is, fos); response.setStatus(HttpServletResponse.SC_OK); writer.print("{success: true}"); } catch (FileNotFoundException ex) { response.setStatus(HttpServletResponse.SC_INTERNAL_SERVER_ERROR); writer.print("{success: false}"); log(OctetStreamReader.class.getName() + "has thrown an exception: " + ex.getMessage()); } catch (IOException ex) { response.setStatus(HttpServletResponse.SC_INTERNAL_SERVER_ERROR); writer.print("{success: false}"); log(OctetStreamReader.class.getName() + "has thrown an exception: " + ex.getMessage()); } finally { try { fos.close(); is.close(); } catch (IOException ignored) { } } writer.flush(); writer.close(); } | 884,685 |
1 | private void doDecrypt(boolean createOutput) throws IOException { FileInputStream input = null; FileOutputStream output = null; File tempOutput = null; try { input = new FileInputStream(infile); String cipherBaseFilename = basename(infile); byte[] magic = new byte[MAGIC.length]; input.read(magic); for (int i = 0; i < MAGIC.length; i++) { if (MAGIC[i] != magic[i]) throw new IOException("Not a BORK file (bad magic number)"); } short version = readShort(input); if (version / 1000 > VERSION / 1000) throw new IOException("File created by an incompatible future version: " + version + " > " + VERSION); String cipherName = readString(input); Cipher cipher = createCipher(cipherName, createSessionKey(password, cipherBaseFilename)); CipherInputStream decryptedInput = new CipherInputStream(input, cipher); long headerCrc = Unsigned.promote(readInt(decryptedInput)); decryptedInput.resetCRC(); outfile = new File(outputDir, readString(decryptedInput)); if (!createOutput || outfile.exists()) { skipped = true; return; } tempOutput = File.createTempFile("bork", null, outputDir); tempOutput.deleteOnExit(); byte[] buffer = new byte[BUFFER_SIZE]; output = new FileOutputStream(tempOutput); int bytesRead; while ((bytesRead = decryptedInput.read(buffer)) != -1) output.write(buffer, 0, bytesRead); output.close(); output = null; if (headerCrc != decryptedInput.getCRC()) { outfile = null; throw new IOException("CRC mismatch: password is probably incorrect"); } if (!tempOutput.renameTo(outfile)) throw new IOException("Failed to rename temp output file " + tempOutput + " to " + outfile); outfile.setLastModified(infile.lastModified()); } finally { close(input); close(output); if (tempOutput != null) tempOutput.delete(); } } | private void copy(File inputFile, File outputFile) { BufferedReader reader = null; BufferedWriter writer = null; try { reader = new BufferedReader(new InputStreamReader(new FileInputStream(inputFile), "UTF-8")); writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(outputFile), "UTF-8")); while (reader.ready()) { writer.write(reader.readLine()); writer.write(System.getProperty("line.separator")); } } catch (IOException e) { } finally { try { if (reader != null) reader.close(); if (writer != null) writer.close(); } catch (IOException e1) { } } } | 884,686 |
1 | public static String md5(String text) { String encrypted = ""; try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(text.getBytes()); encrypted = hex(md.digest()); } catch (NoSuchAlgorithmException nsaEx) { } return encrypted; } | public static String shaEncrypt(final String txt) { String enTxt = txt; MessageDigest md = null; try { md = MessageDigest.getInstance("SHA-1"); } catch (NoSuchAlgorithmException e) { logger.error("Error:", e); } if (null != md) { byte[] shahash = new byte[32]; try { md.update(txt.getBytes("UTF-8"), 0, txt.length()); } catch (UnsupportedEncodingException e) { logger.error("Error:", e); } shahash = md.digest(); StringBuffer md5StrBuff = new StringBuffer(); for (int i = 0; i < shahash.length; i++) { if (Integer.toHexString(0xFF & shahash[i]).length() == 1) { md5StrBuff.append("0").append(Integer.toHexString(0xFF & shahash[i])); } else { md5StrBuff.append(Integer.toHexString(0xFF & shahash[i])); } } enTxt = md5StrBuff.toString(); } return enTxt; } | 884,687 |
1 | private void copyFile(File in, File out) throws IOException { FileChannel sourceChannel = new FileInputStream(in).getChannel(); FileChannel destinationChannel = new FileOutputStream(out).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), destinationChannel); sourceChannel.close(); destinationChannel.close(); } | private String copyTutorial() throws IOException { File inputFile = new File(getFilenameForOriginalTutorial()); File outputFile = new File(getFilenameForCopiedTutorial()); FileReader in = new FileReader(inputFile); FileWriter out = new FileWriter(outputFile); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); return getFilenameForCopiedTutorial(); } | 884,688 |
1 | protected String readFileUsingHttp(String fileUrlName) { String response = ""; try { URL url = new URL(fileUrlName); URLConnection connection = url.openConnection(); HttpURLConnection httpConn = (HttpURLConnection) connection; httpConn.setRequestProperty("Content-Type", "text/html"); httpConn.setRequestProperty("Content-Length", "0"); httpConn.setRequestMethod("GET"); httpConn.setDoOutput(true); httpConn.setDoInput(true); httpConn.setAllowUserInteraction(false); InputStreamReader isr = new InputStreamReader(httpConn.getInputStream()); BufferedReader in = new BufferedReader(isr); String inputLine = ""; while ((inputLine = in.readLine()) != null) { response += inputLine + "\n"; } if (response.endsWith("\n")) { response = response.substring(0, response.length() - 1); } in.close(); } catch (Exception x) { x.printStackTrace(); } return response; } | protected Set<String> moduleNamesFromReader(URL url) throws IOException { BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); Set<String> names = new HashSet<String>(); String line; while ((line = reader.readLine()) != null) { line = line.trim(); Matcher m = nonCommentPattern.matcher(line); if (m.find()) { names.add(m.group().trim()); } } return names; } | 884,689 |
0 | public static void copyFile(String fromFilePath, String toFilePath, boolean overwrite) throws IOException { File fromFile = new File(fromFilePath); File toFile = new File(toFilePath); if (!fromFile.exists()) throw new IOException("FileCopy: " + "no such source file: " + fromFilePath); if (!fromFile.isFile()) throw new IOException("FileCopy: " + "can't copy directory: " + fromFilePath); if (!fromFile.canRead()) throw new IOException("FileCopy: " + "source file is unreadable: " + fromFilePath); if (toFile.isDirectory()) toFile = new File(toFile, fromFile.getName()); if (toFile.exists()) { if (!overwrite) { throw new IOException(toFilePath + " already exists!"); } if (!toFile.canWrite()) { throw new IOException("FileCopy: destination file is unwriteable: " + toFilePath); } String parent = toFile.getParent(); if (parent == null) { parent = System.getProperty("user.dir"); } File dir = new File(parent); if (!dir.exists()) { throw new IOException("FileCopy: destination directory doesn't exist: " + parent); } if (dir.isFile()) { throw new IOException("FileCopy: destination is not a directory: " + parent); } if (!dir.canWrite()) { throw new IOException("FileCopy: destination directory is unwriteable: " + parent); } } FileInputStream from = null; FileOutputStream to = null; try { from = new FileInputStream(fromFile); to = new FileOutputStream(toFile); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = from.read(buffer)) != -1) to.write(buffer, 0, bytesRead); } finally { long lastModified = fromFile.lastModified(); toFile.setLastModified(lastModified); if (from != null) { try { from.close(); } catch (IOException e) { } } if (to != null) { try { to.close(); } catch (IOException e) { } } } } | public static String hashURL(String url) { if (url == null) { throw new IllegalArgumentException("URL may not be null. "); } String result = null; try { MessageDigest md = MessageDigest.getInstance("SHA-1"); if (md != null) { md.reset(); md.update(url.getBytes()); BigInteger hash = new BigInteger(1, md.digest()); result = hash.toString(16); } md = null; } catch (NoSuchAlgorithmException ex) { result = null; } return result; } | 884,690 |
1 | public static void copy(String a, String b) throws IOException { File inputFile = new File(a); File outputFile = new File(b); FileReader in = new FileReader(inputFile); FileWriter out = new FileWriter(outputFile); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } | private boolean copy(File in, File out) { try { FileInputStream fis = new FileInputStream(in); FileOutputStream fos = new FileOutputStream(out); FileChannel readableChannel = fis.getChannel(); FileChannel writableChannel = fos.getChannel(); writableChannel.truncate(0); writableChannel.transferFrom(readableChannel, 0, readableChannel.size()); fis.close(); fos.close(); return true; } catch (IOException ioe) { System.out.println("Copy Error: IOException during copy\r\n" + ioe.getMessage()); return false; } } | 884,691 |
0 | public InputStream getResourceAsStream(String name) { try { URL url = getResource(name); System.out.println("Loading \"" + url + "\"..."); URLConnection urlConnection = url.openConnection(); if (urlConnection instanceof HttpURLConnection) { HttpURLConnection httpURLConnection = (HttpURLConnection) urlConnection; httpURLConnection.setFollowRedirects(true); httpURLConnection.setRequestMethod("GET"); int responseCode = httpURLConnection.getResponseCode(); System.out.println(httpURLConnection.getResponseMessage() + ", " + httpURLConnection.getContentLength() + " bytes" + ", " + new Date(httpURLConnection.getDate()) + ", " + new Date(httpURLConnection.getLastModified())); if (responseCode != HttpURLConnection.HTTP_OK) { return null; } } return urlConnection.getInputStream(); } catch (Exception ex) { ex.printStackTrace(); return null; } } | private static void fileUpload() throws Exception { DefaultHttpClient httpclient = new DefaultHttpClient(); HttpPost httppost = new HttpPost(postURL); file = new File("h:\\Rock Lee.jpg"); MultipartEntity mpEntity = new MultipartEntity(HttpMultipartMode.BROWSER_COMPATIBLE); ContentBody cbFile = new FileBody(file); mpEntity.addPart("file", cbFile); httppost.setEntity(mpEntity); System.out.println("executing request " + httppost.getRequestLine()); System.out.println("Now uploading your file into bayfiles.com"); HttpResponse response = httpclient.execute(httppost); HttpEntity resEntity = response.getEntity(); System.out.println(response.getStatusLine()); if (resEntity != null) { uploadresponse = EntityUtils.toString(resEntity); } System.out.println("Upload response : " + uploadresponse); downloadlink = parseResponse(uploadresponse, "\"downloadUrl\":\"", "\""); downloadlink = downloadlink.replaceAll("\\\\", ""); deletelink = parseResponse(uploadresponse, "\"deleteUrl\":\"", "\""); deletelink = deletelink.replaceAll("\\\\", ""); System.out.println("Download link : " + downloadlink); System.out.println("Delete link : " + deletelink); } | 884,692 |
1 | public static String sendRequest(String urlstring) { URL url; String line; Log.i("DVBMonitor", "Please wait while receiving data from dvb..."); try { url = new URL(urlstring); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); if ((line = in.readLine()) != null) { return line; } else { return null; } } catch (Exception ex) { Log.e("DVBMonitor", ex.toString() + " while sending request to dvb"); return null; } } | protected String getRequestContent(String urlText, String method) throws Exception { URL url = new URL(urlText); HttpURLConnection urlcon = (HttpURLConnection) url.openConnection(); urlcon.setRequestProperty("Referer", REFERER_STR); urlcon.setRequestMethod(method); urlcon.setUseCaches(false); urlcon.connect(); BufferedReader reader = new BufferedReader(new InputStreamReader(urlcon.getInputStream())); String line = reader.readLine(); reader.close(); urlcon.disconnect(); return line; } | 884,693 |
0 | public static Image getPluginImage(Object plugin, String name) { try { URL url = getPluginImageURL(plugin, name); InputStream is = url.openStream(); Image image; try { image = getImage(is); } finally { is.close(); } return image; } catch (Throwable e) { } return null; } | public static boolean download(String url, File file) { HttpURLConnection conn = null; BufferedInputStream in = null; BufferedOutputStream out = null; try { conn = (HttpURLConnection) new URL(url).openConnection(); conn.connect(); if (conn.getResponseCode() == 200) { System.out.println("length:" + conn.getContentLength()); in = new BufferedInputStream(conn.getInputStream()); out = new BufferedOutputStream(new FileOutputStream(file)); byte[] b = new byte[1024 << 10]; int i = 0; while ((i = in.read(b)) > -1) { if (i > 0) out.write(b, 0, i); } return true; } else { System.out.println(conn.getResponseCode() + ":" + url); } } catch (Exception e) { e.printStackTrace(); } finally { if (in != null) try { in.close(); } catch (IOException e) { e.printStackTrace(); } if (out != null) try { out.close(); } catch (IOException e) { e.printStackTrace(); } if (conn != null) conn.disconnect(); } return false; } | 884,694 |
1 | private void processData(InputStream raw) { String fileName = remoteName; if (localName != null) { fileName = localName; } try { FileOutputStream fos = new FileOutputStream(new File(fileName), true); IOUtils.copy(raw, fos); LOG.info("ok"); } catch (IOException e) { LOG.error("error writing file", e); } } | public void copy(File source, File dest) throws IOException { System.out.println("copy " + source + " -> " + dest); FileInputStream in = new FileInputStream(source); try { FileOutputStream out = new FileOutputStream(dest); try { byte[] buf = new byte[1024]; int len = 0; while ((len = in.read(buf)) > 0) out.write(buf, 0, len); } finally { out.close(); } } finally { in.close(); } } | 884,695 |
1 | protected void doDownload(S3Bucket bucket, S3Object s3object) throws Exception { String key = s3object.getKey(); key = trimPrefix(key); String[] path = key.split("/"); String fileName = path[path.length - 1]; String dirPath = ""; for (int i = 0; i < path.length - 1; i++) { dirPath += path[i] + "/"; } File outputDir = new File(downloadFileOutputDir + "/" + dirPath); if (outputDir.exists() == false) { outputDir.mkdirs(); } File outputFile = new File(outputDir, fileName); long size = s3object.getContentLength(); if (outputFile.exists() && outputFile.length() == size) { return; } long startTime = System.currentTimeMillis(); log.info("Download start.S3 file=" + s3object.getKey() + " local file=" + outputFile.getAbsolutePath()); FileOutputStream fout = null; S3Object dataObject = null; try { fout = new FileOutputStream(outputFile); dataObject = s3.getObject(bucket, s3object.getKey()); InputStream is = dataObject.getDataInputStream(); IOUtils.copyStream(is, fout); downloadedFileList.add(key); long downloadTime = System.currentTimeMillis() - startTime; log.info("Download complete.Estimete time=" + downloadTime + "ms " + IOUtils.toBPSText(downloadTime, size)); } catch (Exception e) { log.error("Download fail. s3 file=" + key, e); outputFile.delete(); throw e; } finally { IOUtils.closeNoException(fout); if (dataObject != null) { dataObject.closeDataInputStream(); } } } | public static 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; } | 884,696 |
0 | protected InputStream callApiGet(String apiUrl, int expected) { try { URL url = new URL(apiUrl); HttpURLConnection request = (HttpURLConnection) url.openConnection(); if (ApplicationConstants.CONNECT_TIMEOUT > -1) { request.setConnectTimeout(ApplicationConstants.CONNECT_TIMEOUT); } if (ApplicationConstants.READ_TIMEOUT > -1) { request.setReadTimeout(ApplicationConstants.READ_TIMEOUT); } for (String headerName : requestHeaders.keySet()) { request.setRequestProperty(headerName, requestHeaders.get(headerName)); } request.connect(); if (request.getResponseCode() != expected) { throw new BingMapsException(convertStreamToString(request.getErrorStream())); } else { return getWrappedInputStream(request.getInputStream(), GZIP_ENCODING.equalsIgnoreCase(request.getContentEncoding())); } } catch (IOException e) { throw new BingMapsException(e); } } | public static final boolean zipUpdate(String zipfile, String name, String oldname, byte[] contents, boolean delete) { try { File temp = File.createTempFile("atf", ".zip"); InputStream in = new BufferedInputStream(new FileInputStream(zipfile)); OutputStream os = new BufferedOutputStream(new FileOutputStream(temp)); ZipInputStream zin = new ZipInputStream(in); ZipOutputStream zout = new ZipOutputStream(os); ZipEntry e; ZipEntry e2; byte buffer[] = new byte[TEMP_FILE_BUFFER_SIZE]; int bytesRead; boolean found = false; boolean rename = false; String oname = name; if (oldname != null) { name = oldname; rename = true; } while ((e = zin.getNextEntry()) != null) { if (!e.isDirectory()) { String ename = e.getName(); if (delete && ename.equals(name)) continue; e2 = new ZipEntry(rename ? oname : ename); zout.putNextEntry(e2); if (ename.equals(name)) { found = true; zout.write(contents); } else { while ((bytesRead = zin.read(buffer)) != -1) zout.write(buffer, 0, bytesRead); } zout.closeEntry(); } } if (!found && !delete) { e = new ZipEntry(name); zout.putNextEntry(e); zout.write(contents); zout.closeEntry(); } zin.close(); zout.close(); File fp = new File(zipfile); fp.delete(); MLUtil.copyFile(temp, fp); temp.delete(); return (true); } catch (FileNotFoundException e) { MLUtil.runtimeError(e, "updateZip " + zipfile + " " + name); } catch (IOException e) { MLUtil.runtimeError(e, "updateZip " + zipfile + " " + name); } return (false); } | 884,697 |
1 | boolean copyFileStructure(File oldFile, File newFile) { if (oldFile == null || newFile == null) return false; File searchFile = newFile; do { if (oldFile.equals(searchFile)) return false; searchFile = searchFile.getParentFile(); } while (searchFile != null); if (oldFile.isDirectory()) { if (progressDialog != null) { progressDialog.setDetailFile(oldFile, ProgressDialog.COPY); } if (simulateOnly) { } else { if (!newFile.mkdirs()) return false; } File[] subFiles = oldFile.listFiles(); if (subFiles != null) { if (progressDialog != null) { progressDialog.addWorkUnits(subFiles.length); } for (int i = 0; i < subFiles.length; i++) { File oldSubFile = subFiles[i]; File newSubFile = new File(newFile, oldSubFile.getName()); if (!copyFileStructure(oldSubFile, newSubFile)) return false; if (progressDialog != null) { progressDialog.addProgress(1); if (progressDialog.isCancelled()) return false; } } } } else { if (simulateOnly) { } else { FileReader in = null; FileWriter out = null; try { in = new FileReader(oldFile); out = new FileWriter(newFile); int count; while ((count = in.read()) != -1) out.write(count); } catch (FileNotFoundException e) { return false; } catch (IOException e) { return false; } finally { try { if (in != null) in.close(); if (out != null) out.close(); } catch (IOException e) { return false; } } } } return true; } | @Test public void testTrainingQuickprop() throws IOException { File temp = File.createTempFile("fannj_", ".tmp"); temp.deleteOnExit(); IOUtils.copy(this.getClass().getResourceAsStream("xor.data"), new FileOutputStream(temp)); List<Layer> layers = new ArrayList<Layer>(); layers.add(Layer.create(2)); layers.add(Layer.create(3, ActivationFunction.FANN_SIGMOID_SYMMETRIC)); layers.add(Layer.create(1, ActivationFunction.FANN_SIGMOID_SYMMETRIC)); Fann fann = new Fann(layers); Trainer trainer = new Trainer(fann); trainer.setTrainingAlgorithm(TrainingAlgorithm.FANN_TRAIN_QUICKPROP); float desiredError = .001f; float mse = trainer.train(temp.getPath(), 500000, 1000, desiredError); assertTrue("" + mse, mse <= desiredError); } | 884,698 |
1 | @Override public CasAssembly build() { try { prepareForBuild(); File casWorkingDirectory = casFile.getParentFile(); DefaultCasFileReadIndexToContigLookup read2contigMap = new DefaultCasFileReadIndexToContigLookup(); AbstractDefaultCasFileLookup readIdLookup = new DefaultReadCasFileLookup(casWorkingDirectory); CasParser.parseOnlyMetaData(casFile, MultipleWrapper.createMultipleWrapper(CasFileVisitor.class, read2contigMap, readIdLookup)); ReadWriteDirectoryFileServer consedOut = DirectoryFileServer.createReadWriteDirectoryFileServer(commandLine.getOptionValue("o")); long startTime = DateTimeUtils.currentTimeMillis(); int numberOfCasContigs = read2contigMap.getNumberOfContigs(); for (long i = 0; i < numberOfCasContigs; i++) { File outputDir = consedOut.createNewDir("" + i); Command aCommand = new Command(new File("fakeCommand")); aCommand.setOption("-casId", "" + i); aCommand.setOption("-cas", commandLine.getOptionValue("cas")); aCommand.setOption("-o", outputDir.getAbsolutePath()); aCommand.setOption("-tempDir", tempDir.getAbsolutePath()); aCommand.setOption("-prefix", "temp"); if (commandLine.hasOption("useIllumina")) { aCommand.addFlag("-useIllumina"); } if (commandLine.hasOption("useClosureTrimming")) { aCommand.addFlag("-useClosureTrimming"); } if (commandLine.hasOption("trim")) { aCommand.setOption("-trim", commandLine.getOptionValue("trim")); } if (commandLine.hasOption("trimMap")) { aCommand.setOption("-trimMap", commandLine.getOptionValue("trimMap")); } if (commandLine.hasOption("chromat_dir")) { aCommand.setOption("-chromat_dir", commandLine.getOptionValue("chromat_dir")); } submitSingleCasAssemblyConversion(aCommand); } waitForAllAssembliesToFinish(); int numContigs = 0; int numReads = 0; for (int i = 0; i < numberOfCasContigs; i++) { File countMap = consedOut.getFile(i + "/temp.counts"); Scanner scanner = new Scanner(countMap); if (!scanner.hasNextInt()) { throw new IllegalStateException("single assembly conversion # " + i + " did not complete"); } numContigs += scanner.nextInt(); numReads += scanner.nextInt(); scanner.close(); } System.out.println("num contigs =" + numContigs); System.out.println("num reads =" + numReads); consedOut.createNewDir("edit_dir"); consedOut.createNewDir("phd_dir"); String prefix = commandLine.hasOption("prefix") ? commandLine.getOptionValue("prefix") : DEFAULT_PREFIX; OutputStream masterAceOut = new FileOutputStream(consedOut.createNewFile("edit_dir/" + prefix + ".ace.1")); OutputStream masterPhdOut = new FileOutputStream(consedOut.createNewFile("phd_dir/" + prefix + ".phd.ball")); OutputStream masterConsensusOut = new FileOutputStream(consedOut.createNewFile(prefix + ".consensus.fasta")); OutputStream logOut = new FileOutputStream(consedOut.createNewFile(prefix + ".log")); try { masterAceOut.write(String.format("AS %d %d%n", numContigs, numReads).getBytes()); for (int i = 0; i < numberOfCasContigs; i++) { InputStream aceIn = consedOut.getFileAsStream(i + "/temp.ace"); IOUtils.copy(aceIn, masterAceOut); InputStream phdIn = consedOut.getFileAsStream(i + "/temp.phd"); IOUtils.copy(phdIn, masterPhdOut); InputStream consensusIn = consedOut.getFileAsStream(i + "/temp.consensus.fasta"); IOUtils.copy(consensusIn, masterConsensusOut); IOUtil.closeAndIgnoreErrors(aceIn, phdIn, consensusIn); File tempDir = consedOut.getFile(i + ""); IOUtil.recursiveDelete(tempDir); } consedOut.createNewSymLink("../phd_dir/" + prefix + ".phd.ball", "edit_dir/phd.ball"); if (commandLine.hasOption("chromat_dir")) { consedOut.createNewDir("chromat_dir"); File originalChromatDir = new File(commandLine.getOptionValue("chromat_dir")); for (File chromat : originalChromatDir.listFiles(new FilenameFilter() { @Override public boolean accept(File dir, String name) { return name.endsWith(".scf"); } })) { File newChromatFile = consedOut.createNewFile("chromat_dir/" + FilenameUtils.getBaseName(chromat.getName())); FileOutputStream newChromat = new FileOutputStream(newChromatFile); InputStream in = new FileInputStream(chromat); IOUtils.copy(in, newChromat); IOUtil.closeAndIgnoreErrors(in, newChromat); } } System.out.println("finished making casAssemblies"); for (File traceFile : readIdLookup.getFiles()) { final String name = traceFile.getName(); String extension = FilenameUtils.getExtension(name); if (name.contains("fastq")) { if (!consedOut.contains("solexa_dir")) { consedOut.createNewDir("solexa_dir"); } if (consedOut.contains("solexa_dir/" + name)) { IOUtil.delete(consedOut.getFile("solexa_dir/" + name)); } consedOut.createNewSymLink(traceFile.getAbsolutePath(), "solexa_dir/" + name); } else if ("sff".equals(extension)) { if (!consedOut.contains("sff_dir")) { consedOut.createNewDir("sff_dir"); } if (consedOut.contains("sff_dir/" + name)) { IOUtil.delete(consedOut.getFile("sff_dir/" + name)); } consedOut.createNewSymLink(traceFile.getAbsolutePath(), "sff_dir/" + name); } } long endTime = DateTimeUtils.currentTimeMillis(); logOut.write(String.format("took %s%n", new Period(endTime - startTime)).getBytes()); } finally { IOUtil.closeAndIgnoreErrors(masterAceOut, masterPhdOut, masterConsensusOut, logOut); } } catch (Exception e) { handleException(e); } finally { cleanup(); } return null; } | public static void copyFile(File in, File out) throws FileNotFoundException, IOException { FileChannel sourceChannel = null; FileChannel destinationChannel = null; try { sourceChannel = new FileInputStream(in).getChannel(); destinationChannel = new FileOutputStream(out).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), destinationChannel); } finally { try { sourceChannel.close(); } catch (Exception ex) { } try { destinationChannel.close(); } catch (Exception ex) { } } } | 884,699 |
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