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id (int32)id1 (int32)id2 (int32)func1 (string)func2 (string)label (bool)
0
13,988,825
8,660,836
" private void setNodekeyInJsonResponse(String service) throws Exception { String filename = this.baseDirectory + service + ".json"; Scanner s = new Scanner(new File(filename)); PrintWriter fw = new PrintWriter(new File(filename + ".new")); while (s.hasNextLine()) { fw.println(s.nextLine().replaceAll("NODEKEY", this.key)); } s.close(); fw.close(); (new File(filename + ".new")).renameTo(new File(filename)); } "
" public void transform(String style, String spec, OutputStream out) throws IOException { URL url = new URL(rootURL, spec); InputStream in = new PatchXMLSymbolsStream(new StripDoctypeStream(url.openStream())); transform(style, in, out); in.close(); } "
false
1
80,378
18,548,122
" public static void test(String args[]) { int trace; int bytes_read = 0; int last_contentLenght = 0; try { BufferedReader reader; URL url; url = new URL(args[0]); URLConnection istream = url.openConnection(); last_contentLenght = istream.getContentLength(); reader = new BufferedReader(new InputStreamReader(istream.getInputStream())); System.out.println(url.toString()); String line; trace = t2pNewTrace(); while ((line = reader.readLine()) != null) { bytes_read = bytes_read + line.length() + 1; t2pProcessLine(trace, line); } t2pHandleEventPairs(trace); t2pSort(trace, 0); t2pExportTrace(trace, new String("pngtest2.png"), 1000, 700, (float) 0, (float) 33); t2pExportTrace(trace, new String("pngtest3.png"), 1000, 700, (float) 2.3, (float) 2.44); System.out.println("Press any key to contiune read from stream !!!"); System.out.println(t2pGetProcessName(trace, 0)); System.in.read(); istream = url.openConnection(); if (last_contentLenght != istream.getContentLength()) { istream = url.openConnection(); istream.setRequestProperty("Range", "bytes=" + Integer.toString(bytes_read) + "-"); System.out.println(Integer.toString(istream.getContentLength())); reader = new BufferedReader(new InputStreamReader(istream.getInputStream())); while ((line = reader.readLine()) != null) { System.out.println(line); t2pProcessLine(trace, line); } } else System.out.println("File not changed !"); t2pDeleteTrace(trace); } catch (MalformedURLException e) { System.out.println("MalformedURLException !!!"); } catch (IOException e) { System.out.println("File not found " + args[0]); } ; } "
" private static String loadUrlToString(String a_url) throws IOException { URL l_url1 = new URL(a_url); BufferedReader br = new BufferedReader(new InputStreamReader(l_url1.openStream())); String l_content = ""; String l_ligne = null; l_content = br.readLine(); while ((l_ligne = br.readLine()) != null) { l_content += AA.SL + l_ligne; } return l_content; } "
true
2
21,354,223
7,421,563
" public String kodetu(String testusoila) { MessageDigest md = null; try { md = MessageDigest.getInstance("SHA"); md.update(testusoila.getBytes("UTF-8")); } catch (NoSuchAlgorithmException e) { new MezuLeiho("Ez da zifraketa algoritmoa aurkitu", "Ados", "Zifraketa Arazoa", JOptionPane.ERROR_MESSAGE); e.printStackTrace(); } catch (UnsupportedEncodingException e) { new MezuLeiho("Errorea kodetzerakoan", "Ados", "Kodeketa Errorea", JOptionPane.ERROR_MESSAGE); e.printStackTrace(); } byte raw[] = md.digest(); String hash = (new BASE64Encoder()).encode(raw); return hash; } "
" private StringBuffer encoder(String arg) { if (arg == null) { arg = ""; } MessageDigest md5 = null; try { md5 = MessageDigest.getInstance("MD5"); md5.update(arg.getBytes(SysConstant.charset)); } catch (Exception e) { e.printStackTrace(); } return toHex(md5.digest()); } "
true
3
15,826,299
19,728,871
" public static void printResponseHeaders(String address) { logger.info("Address: " + address); try { URL url = new URL(address); URLConnection conn = url.openConnection(); for (int i = 0; ; i++) { String headerName = conn.getHeaderFieldKey(i); String headerValue = conn.getHeaderField(i); if (headerName == null && headerValue == null) { break; } if (headerName == null) { logger.info(headerValue); continue; } logger.info(headerName + " " + headerValue); } } catch (Exception e) { logger.error("Exception Message: " + e.getMessage()); } } "
" public static String getEncodedPassword(String buff) { if (buff == null) return null; String t = new String(); try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(buff.getBytes()); byte[] r = md.digest(); for (int i = 0; i < r.length; i++) { t += toHexString(r[i]); } } catch (Exception e) { e.printStackTrace(); } return t; } "
false
4
9,938,081
11,517,213
" public void load(String fileName) { BufferedReader bufReader; loaded = false; vector.removeAllElements(); try { if (fileName.startsWith("http:")) { URL url = new URL(fileName); bufReader = new BufferedReader(new InputStreamReader(url.openStream())); } else bufReader = new BufferedReader(new FileReader(fileName)); String inputLine; while ((inputLine = bufReader.readLine()) != null) { if (listener != null) listener.handleLine(inputLine); else vector.add(inputLine); } bufReader.close(); loaded = true; } catch (IOException e) { errorMsg = e.getMessage(); } } "
" private static void copyFile(File sourceFile, File destFile) { try { 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(); } } } catch (Exception e) { throw new RuntimeException(e); } } "
false
5
18,220,543
17,366,812
" private MapProperties readProperties(URL url) { @SuppressWarnings("unchecked") MapProperties properties = new MapProperties(new LinkedHashMap()); InputStream is = null; try { is = url.openStream(); properties.load(is); } catch (IOException ex) { throw new RuntimeException(ex); } finally { StreamUtils.close(is); } return properties; } "
" public String tranportRemoteUnitToLocalTempFile(String urlStr) throws UnitTransportException { InputStream input = null; BufferedOutputStream bos = null; File tempUnit = null; try { URL url = null; int total = 0; try { url = new URL(urlStr); input = url.openStream(); URLConnection urlConnection; urlConnection = url.openConnection(); total = urlConnection.getContentLength(); } catch (IOException e) { throw new UnitTransportException(String.format("Can't get remote file [%s].", urlStr), e); } String unitName = urlStr.substring(urlStr.lastIndexOf('/') + 1); tempUnit = null; try { if (StringUtils.isNotEmpty(unitName)) tempUnit = new File(CommonUtil.getTempDir(), unitName); else tempUnit = File.createTempFile(CommonUtil.getTempDir(), "tempUnit"); File parent = tempUnit.getParentFile(); FileUtils.forceMkdir(parent); if (!tempUnit.exists()) FileUtils.touch(tempUnit); bos = new BufferedOutputStream(new FileOutputStream(tempUnit)); } catch (FileNotFoundException e) { throw new UnitTransportException(String.format("Can't find temp file [%s].", tempUnit.getAbsolutePath()), e); } catch (IOException e) { throw new UnitTransportException(String.format("Can't create temp file [%s].", tempUnit.getAbsolutePath()), e); } catch (DeployToolException e) { throw new UnitTransportException(String.format("Error when create temp file [%s].", tempUnit), e); } logger.info(String.format("Use [%s] for http unit [%s].", tempUnit.getAbsoluteFile(), urlStr)); int size = -1; try { size = IOUtils.copy(input, bos); bos.flush(); } catch (IOException e) { logger.info(String.format("Error when download [%s] to [%s].", urlStr, tempUnit)); } if (size != total) throw new UnitTransportException(String.format("The file size is not right when download http unit [%s]", urlStr)); } finally { if (input != null) IOUtils.closeQuietly(input); if (bos != null) IOUtils.closeQuietly(bos); } logger.info(String.format("Download unit to [%s].", tempUnit.getAbsolutePath())); return tempUnit.getAbsolutePath(); } "
false
6
22,328,849
17,334,846
" protected void doRestoreOrganize() throws Exception { Connection con = null; PreparedStatement ps = null; ResultSet result = null; String strDelQuery = "DELETE FROM " + Common.ORGANIZE_TABLE; String strSelQuery = "SELECT organize_id,organize_type_id,organize_name,organize_manager," + "organize_describe,work_type,show_order,position_x,position_y " + "FROM " + Common.ORGANIZE_B_TABLE + " " + "WHERE version_no = ?"; String strInsQuery = "INSERT INTO " + Common.ORGANIZE_TABLE + " " + "(organize_id,organize_type_id,organize_name,organize_manager," + "organize_describe,work_type,show_order,position_x,position_y) " + "VALUES (?,?,?,?,?,?,?,?,?)"; DBOperation dbo = factory.createDBOperation(POOL_NAME); try { try { con = dbo.getConnection(); con.setAutoCommit(false); ps = con.prepareStatement(strDelQuery); ps.executeUpdate(); ps = con.prepareStatement(strSelQuery); ps.setInt(1, this.versionNO); result = ps.executeQuery(); ps = con.prepareStatement(strInsQuery); while (result.next()) { ps.setString(1, result.getString("organize_id")); ps.setString(2, result.getString("organize_type_id")); ps.setString(3, result.getString("organize_name")); ps.setString(4, result.getString("organize_manager")); ps.setString(5, result.getString("organize_describe")); ps.setString(6, result.getString("work_type")); ps.setInt(7, result.getInt("show_order")); ps.setInt(8, result.getInt("position_x")); ps.setInt(9, result.getInt("position_y")); int resultCount = ps.executeUpdate(); if (resultCount != 1) { con.rollback(); throw new CesSystemException("Organize_backup.doRestoreOrganize(): ERROR Inserting data " + "in T_SYS_ORGANIZE INSERT !! resultCount = " + resultCount); } } con.commit(); } catch (SQLException se) { con.rollback(); throw new CesSystemException("Organize_backup.doRestoreOrganize(): SQLException: " + se); } finally { con.setAutoCommit(true); close(dbo, ps, result); } } catch (SQLException se) { throw new CesSystemException("Organize_backup.doRestoreOrganize(): SQLException while committing or rollback"); } } "
" static String encodeEmailAsUserId(String email) { try { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.update(email.toLowerCase().getBytes()); StringBuilder builder = new StringBuilder(); builder.append("1"); for (byte b : md5.digest()) { builder.append(String.format("%02d", new Object[] { Integer.valueOf(b & 0xFF) })); } return builder.toString().substring(0, 20); } catch (NoSuchAlgorithmException ex) { } return ""; } "
false
7
19,130,322
15,710,690
" private String sha1(String s) { String encrypt = s; try { MessageDigest sha = MessageDigest.getInstance("SHA-1"); sha.update(s.getBytes()); byte[] digest = sha.digest(); final StringBuffer buffer = new StringBuffer(); for (int i = 0; i < digest.length; ++i) { final byte b = digest[i]; final int value = (b & 0x7F) + (b < 0 ? 128 : 0); buffer.append(value < 16 ? "0" : ""); buffer.append(Integer.toHexString(value)); } encrypt = buffer.toString(); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } return encrypt; } "
" @SuppressWarnings("unused") private String getMD5(String value) { MessageDigest md5; try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { return ""; } md5.reset(); md5.update(value.getBytes()); byte[] messageDigest = md5.digest(); StringBuffer hexString = new StringBuffer(); for (int i = 0; i < messageDigest.length; i++) { hexString.append(Integer.toHexString(0xFF & messageDigest[i])); } String hashedPassword = hexString.toString(); return hashedPassword; } "
true
8
1,111,832
789,472
" private void storeFieldMap(WorkingContent c, Connection conn) throws SQLException { SQLDialect dialect = getDatabase().getSQLDialect(); if (TRANSACTIONS_ENABLED) { conn.setAutoCommit(false); } try { Object thisKey = c.getPrimaryKey(); deleteFieldContent(thisKey, conn); PreparedStatement ps = null; StructureItem nextItem; Map fieldMap = c.getFieldMap(); String type; Object value, siKey; for (Iterator i = c.getStructure().getStructureItems().iterator(); i.hasNext(); ) { nextItem = (StructureItem) i.next(); type = nextItem.getDataType().toUpperCase(); siKey = nextItem.getPrimaryKey(); value = fieldMap.get(nextItem.getName()); try { if (type.equals(StructureItem.DATE)) { ps = conn.prepareStatement(sqlConstants.get("INSERT_DATE_FIELD")); ps.setObject(1, thisKey); ps.setObject(2, siKey); dialect.setDate(ps, 3, (Date) value); ps.executeUpdate(); } else if (type.equals(StructureItem.INT) || type.equals(StructureItem.FLOAT) || type.equals(StructureItem.VARCHAR)) { ps = conn.prepareStatement(sqlConstants.get("INSERT_" + type + "_FIELD")); ps.setObject(1, thisKey); ps.setObject(2, siKey); if (value != null) { ps.setObject(3, value); } else { int sqlType = Types.INTEGER; if (type.equals(StructureItem.FLOAT)) { sqlType = Types.FLOAT; } else if (type.equals(StructureItem.VARCHAR)) { sqlType = Types.VARCHAR; } ps.setNull(3, sqlType); } ps.executeUpdate(); } else if (type.equals(StructureItem.TEXT)) { setTextField(c, siKey, (String) value, conn); } if (ps != null) { ps.close(); ps = null; } } finally { if (ps != null) ps.close(); } } if (TRANSACTIONS_ENABLED) { conn.commit(); } } catch (SQLException e) { if (TRANSACTIONS_ENABLED) { conn.rollback(); } throw e; } finally { if (TRANSACTIONS_ENABLED) { conn.setAutoCommit(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); } } "
true
9
7,046,481
18,317,332
" public InlineImageChunk(URL url) { super(); this.url = url; try { URLConnection urlConn = url.openConnection(); urlConn.setReadTimeout(15000); ImageInputStream iis = ImageIO.createImageInputStream(urlConn.getInputStream()); Iterator<ImageReader> readers = ImageIO.getImageReaders(iis); if (readers.hasNext()) { ImageReader reader = readers.next(); reader.setInput(iis, true); this.width = reader.getWidth(0); this.ascent = reader.getHeight(0); this.descent = 0; reader.dispose(); } else System.err.println("cannot read width and height of image " + url + " - no suitable reader!"); } catch (Exception exc) { System.err.println("cannot read width and height of image " + url + " due to exception:"); System.err.println(exc); exc.printStackTrace(System.err); } } "
" void execute(Connection conn, Component parent, String context, final ProgressMonitor progressMonitor, ProgressWrapper progressWrapper) throws Exception { int noOfComponents = m_components.length; Statement statement = null; StringBuffer pmNoteBuf = new StringBuffer(m_update ? "Updating " : "Creating "); pmNoteBuf.append(m_itemNameAbbrev); pmNoteBuf.append(" "); pmNoteBuf.append(m_itemNameValue); final String pmNote = pmNoteBuf.toString(); progressMonitor.setNote(pmNote); try { conn.setAutoCommit(false); int id = -1; if (m_update) { statement = conn.createStatement(); String sql = getUpdateSql(noOfComponents, m_id); statement.executeUpdate(sql); id = m_id; if (m_indexesChanged) deleteComponents(conn, id); } else { PreparedStatement pStmt = getInsertPrepStmt(conn, noOfComponents); pStmt.executeUpdate(); Integer res = DbCommon.getAutoGenId(parent, context, pStmt); if (res == null) return; id = res.intValue(); } if (!m_update || m_indexesChanged) { PreparedStatement insertCompPrepStmt = conn.prepareStatement(getInsertComponentPrepStmtSql()); for (int i = 0; i < noOfComponents; i++) { createComponent(progressMonitor, m_components, pmNote, id, i, insertCompPrepStmt); } } conn.commit(); m_itemTable.getPrimaryId().setVal(m_item, id); m_itemCache.updateCache(m_item, id); } catch (SQLException ex) { try { conn.rollback(); } catch (SQLException e) { e.printStackTrace(); } throw ex; } finally { if (statement != null) { statement.close(); } } } "
false
10
190,292
978,946
" private static void main(String[] args) { try { File f = new File("test.txt"); if (f.exists()) { throw new IOException(f + " already exists. I don't want to overwrite it."); } StraightStreamReader in; char[] cbuf = new char[0x1000]; int read; int totRead; FileOutputStream out = new FileOutputStream(f); for (int i = 0x00; i < 0x100; i++) { out.write(i); } out.close(); in = new StraightStreamReader(new FileInputStream(f)); for (int i = 0x00; i < 0x100; i++) { read = in.read(); if (read != i) { System.err.println("Error: " + i + " read as " + read); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = in.read(cbuf); if (totRead != 0x100) { System.err.println("Simple buffered read did not read the full amount: 0x" + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i]); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = 0; while (totRead <= 0x100 && (read = in.read(cbuf, totRead, 0x100 - totRead)) > 0) { totRead += read; } if (totRead != 0x100) { System.err.println("Not enough read. Bytes read: " + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i]); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = 0; while (totRead <= 0x100 && (read = in.read(cbuf, totRead + 0x123, 0x100 - totRead)) > 0) { totRead += read; } if (totRead != 0x100) { System.err.println("Not enough read. Bytes read: " + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i + 0x123] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i + 0x123]); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = 0; while (totRead <= 0x100 && (read = in.read(cbuf, totRead + 0x123, 7)) > 0) { totRead += read; } if (totRead != 0x100) { System.err.println("Not enough read. Bytes read: " + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i + 0x123] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i + 0x123]); } } in.close(); f.delete(); } catch (IOException x) { System.err.println(x.getMessage()); } } "
" public static void copyFile(File in, File out) throws IOException { FileChannel inChannel = new FileInputStream(in).getChannel(); FileChannel outChannel = new FileOutputStream(out).getChannel(); try { inChannel.transferTo(0, inChannel.size(), outChannel); } catch (IOException e) { throw e; } finally { if (inChannel != null) inChannel.close(); if (outChannel != null) outChannel.close(); } } "
true
11
19,653,581
9,312,243
" public List<SuspectFileProcessingStatus> retrieve() throws Exception { BufferedOutputStream bos = null; try { String listFilePath = GeneralUtils.generateAbsolutePath(getDownloadDirectoryPath(), getListName(), "/"); listFilePath = listFilePath.concat(".xml"); if (!new File(getDownloadDirectoryPath()).exists()) { FileUtils.forceMkdir(new File(getDownloadDirectoryPath())); } FileOutputStream listFileOutputStream = new FileOutputStream(listFilePath); bos = new BufferedOutputStream(listFileOutputStream); InputStream is = null; if (getUseProxy()) { is = URLUtils.getResponse(getUrl(), getUserName(), getPassword(), URLUtils.HTTP_GET_METHOD, getProxyHost(), getProxyPort()); IOUtils.copyLarge(is, bos); } else { URLUtils.getResponse(getUrl(), getUserName(), getPassword(), bos, null); } bos.flush(); bos.close(); File listFile = new File(listFilePath); if (!listFile.exists()) { throw new IllegalStateException("The list file did not get created"); } if (isLoggingInfo()) { logInfo("Downloaded list file : " + listFile); } List<SuspectFileProcessingStatus> sfpsList = new ArrayList<SuspectFileProcessingStatus>(); String loadType = GeneralConstants.LOAD_TYPE_FULL; String feedType = GeneralConstants.EMPTY_TOKEN; String listName = getListName(); String errorCode = ""; String description = ""; SuspectFileProcessingStatus sfps = getSuspectsLoaderService().storeFileIntoListIncomingDir(listFile, loadType, feedType, listName, errorCode, description); sfpsList.add(sfps); if (isLoggingInfo()) { logInfo("Retrieved list file with SuspectFileProcessingStatus: " + sfps); } return sfpsList; } finally { if (null != bos) { bos.close(); } } } "
" void shutdown(final boolean unexpected) { if (unexpected) { log.warn("S H U T D O W N --- received unexpected shutdown request."); } else { log.info("S H U T D O W N --- start regular shutdown."); } if (this.uncaughtException != null) { log.warn("Shutdown probably caused by the following Exception.", this.uncaughtException); } log.error("check if we need the controler listener infrastructure"); if (this.dumpDataAtEnd) { new PopulationWriter(this.population, this.network).write(this.controlerIO.getOutputFilename(FILENAME_POPULATION)); new NetworkWriter(this.network).write(this.controlerIO.getOutputFilename(FILENAME_NETWORK)); new ConfigWriter(this.config).write(this.controlerIO.getOutputFilename(FILENAME_CONFIG)); if (!unexpected && this.getConfig().vspExperimental().isWritingOutputEvents()) { File toFile = new File(this.controlerIO.getOutputFilename("output_events.xml.gz")); File fromFile = new File(this.controlerIO.getIterationFilename(this.getLastIteration(), "events.xml.gz")); IOUtils.copyFile(fromFile, toFile); } } if (unexpected) { log.info("S H U T D O W N --- unexpected shutdown request completed."); } else { log.info("S H U T D O W N --- regular shutdown completed."); } try { Runtime.getRuntime().removeShutdownHook(this.shutdownHook); } catch (IllegalStateException e) { log.info("Cannot remove shutdown hook. " + e.getMessage()); } this.shutdownHook = null; this.collectLogMessagesAppender = null; IOUtils.closeOutputDirLogging(); } "
true
12
369,572
4,761,833
" private void displayDiffResults() throws IOException { File outFile = File.createTempFile("diff", ".htm"); outFile.deleteOnExit(); FileOutputStream outStream = new FileOutputStream(outFile); BufferedWriter out = new BufferedWriter(new OutputStreamWriter(outStream)); out.write("<html><head><title>LOC Differences</title>\n" + SCRIPT + "</head>\n" + "<body bgcolor='#ffffff'>\n" + "<div onMouseOver=\"window.defaultStatus='Metrics'\">\n"); if (addedTable.length() > 0) { out.write("<table border><tr><th>Files Added:</th>" + "<th>Add</th><th>Type</th></tr>"); out.write(addedTable.toString()); out.write("</table><br><br>"); } if (modifiedTable.length() > 0) { out.write("<table border><tr><th>Files Modified:</th>" + "<th>Base</th><th>Del</th><th>Mod</th><th>Add</th>" + "<th>Total</th><th>Type</th></tr>"); out.write(modifiedTable.toString()); out.write("</table><br><br>"); } if (deletedTable.length() > 0) { out.write("<table border><tr><th>Files Deleted:</th>" + "<th>Del</th><th>Type</th></tr>"); out.write(deletedTable.toString()); out.write("</table><br><br>"); } out.write("<table name=METRICS BORDER>\n"); if (modifiedTable.length() > 0 || deletedTable.length() > 0) { out.write("<tr><td>Base:&nbsp;</td><td>"); out.write(Long.toString(base)); out.write("</td></tr>\n<tr><td>Deleted:&nbsp;</td><td>"); out.write(Long.toString(deleted)); out.write("</td></tr>\n<tr><td>Modified:&nbsp;</td><td>"); out.write(Long.toString(modified)); out.write("</td></tr>\n<tr><td>Added:&nbsp;</td><td>"); out.write(Long.toString(added)); out.write("</td></tr>\n<tr><td>New & Changed:&nbsp;</td><td>"); out.write(Long.toString(added + modified)); out.write("</td></tr>\n"); } out.write("<tr><td>Total:&nbsp;</td><td>"); out.write(Long.toString(total)); out.write("</td></tr>\n</table></div>"); redlinesOut.close(); out.flush(); InputStream redlines = new FileInputStream(redlinesTempFile); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = redlines.read(buffer)) != -1) outStream.write(buffer, 0, bytesRead); outStream.write("</BODY></HTML>".getBytes()); outStream.close(); Browser.launch(outFile.toURL().toString()); } "
" 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(); } "
true
13
2,285,441
16,987,999
" static synchronized Person lookup(PhoneNumber number, String siteName) { Vector<Person> foundPersons = new Vector<Person>(5); if (number.isFreeCall()) { Person p = new Person("", "FreeCall"); p.addNumber(number); foundPersons.add(p); } else if (number.isSIPNumber() || number.isQuickDial()) { Person p = new Person(); p.addNumber(number); foundPersons.add(p); } else if (ReverseLookup.rlsMap.containsKey(number.getCountryCode())) { nummer = number.getAreaNumber(); rls_list = ReverseLookup.rlsMap.get(number.getCountryCode()); Debug.info("Begin reverselookup for: " + nummer); if (nummer.startsWith(number.getCountryCode())) nummer = nummer.substring(number.getCountryCode().length()); city = ""; for (int i = 0; i < rls_list.size(); i++) { yield(); rls = rls_list.get(i); if (!siteName.equals("") && !siteName.equals(rls.getName())) { Debug.warning("This lookup should be done using a specific site, skipping"); continue; } prefix = rls.getPrefix(); ac_length = rls.getAreaCodeLength(); if (!nummer.startsWith(prefix)) nummer = prefix + nummer; urlstr = rls.getURL(); if (urlstr.contains("$AREACODE")) { urlstr = urlstr.replaceAll("\\$AREACODE", nummer.substring(prefix.length(), ac_length + prefix.length())); urlstr = urlstr.replaceAll("\\$NUMBER", nummer.substring(prefix.length() + ac_length)); } else if (urlstr.contains("$PFXAREACODE")) { urlstr = urlstr.replaceAll("\\$PFXAREACODE", nummer.substring(0, prefix.length() + ac_length)); urlstr = urlstr.replaceAll("\\$NUMBER", nummer.substring(prefix.length() + ac_length)); } else urlstr = urlstr.replaceAll("\\$NUMBER", nummer); Debug.info("Reverse lookup using: " + urlstr); url = null; data = new String[dataLength]; try { url = new URL(urlstr); if (url != null) { try { con = url.openConnection(); con.setConnectTimeout(5000); con.setReadTimeout(15000); con.addRequestProperty("User-Agent", userAgent); con.connect(); header = ""; charSet = ""; for (int j = 0; ; j++) { String headerName = con.getHeaderFieldKey(j); String headerValue = con.getHeaderField(j); if (headerName == null && headerValue == null) { break; } if ("content-type".equalsIgnoreCase(headerName)) { String[] split = headerValue.split(";", 2); for (int k = 0; k < split.length; k++) { if (split[k].trim().toLowerCase().startsWith("charset=")) { String[] charsetSplit = split[k].split("="); charSet = charsetSplit[1].trim(); } } } header += headerName + ": " + headerValue + " | "; } Debug.debug("Header of " + rls.getName() + ":" + header); Debug.debug("CHARSET : " + charSet); BufferedReader d; if (charSet.equals("")) { d = new BufferedReader(new InputStreamReader(con.getInputStream(), "ISO-8859-1")); } else { d = new BufferedReader(new InputStreamReader(con.getInputStream(), charSet)); } int lines = 0; while (null != ((str = d.readLine()))) { data[lines] = str; yield(); if (lines >= dataLength) { System.err.println("Result > " + dataLength + " Lines"); break; } lines++; } d.close(); Debug.info("Begin processing response from " + rls.getName()); for (int j = 0; j < rls.size(); j++) { yield(); firstname = ""; lastname = ""; company = ""; street = ""; zipcode = ""; city = ""; Person p = null; patterns = rls.getEntry(j); Pattern namePattern = null; Pattern streetPattern = null; Pattern cityPattern = null; Pattern zipcodePattern = null; Pattern firstnamePattern = null; Pattern lastnamePattern = null; Matcher nameMatcher = null; Matcher streetMatcher = null; Matcher cityMatcher = null; Matcher zipcodeMatcher = null; Matcher firstnameMatcher = null; Matcher lastnameMatcher = null; if (!patterns[ReverseLookupSite.NAME].equals("") && (patterns[ReverseLookupSite.FIRSTNAME].equals("") && patterns[ReverseLookupSite.LASTNAME].equals(""))) { namePattern = Pattern.compile(patterns[ReverseLookupSite.NAME]); } if (!patterns[ReverseLookupSite.STREET].equals("")) { streetPattern = Pattern.compile(patterns[ReverseLookupSite.STREET]); } if (!patterns[ReverseLookupSite.CITY].equals("")) { cityPattern = Pattern.compile(patterns[ReverseLookupSite.CITY]); } if (!patterns[ReverseLookupSite.ZIPCODE].equals("")) { zipcodePattern = Pattern.compile(patterns[ReverseLookupSite.ZIPCODE]); } if (!patterns[ReverseLookupSite.FIRSTNAME].equals("")) { firstnamePattern = Pattern.compile(patterns[ReverseLookupSite.FIRSTNAME]); } if (!patterns[ReverseLookupSite.LASTNAME].equals("")) { lastnamePattern = Pattern.compile(patterns[ReverseLookupSite.LASTNAME]); } for (int line = 0; line < dataLength; line++) { if (data[line] != null) { int spaceAlternative = 160; data[line] = data[line].replaceAll(new Character((char) spaceAlternative).toString(), " "); if (lastnamePattern != null) { lastnameMatcher = lastnamePattern.matcher(data[line]); if (lastnameMatcher.find()) { str = ""; for (int k = 1; k <= lastnameMatcher.groupCount(); k++) { if (lastnameMatcher.group(k) != null) str = str + lastnameMatcher.group(k).trim() + " "; } lastname = JFritzUtils.removeLeadingSpaces(HTMLUtil.stripEntities(str)); lastname = lastname.trim(); lastname = lastname.replaceAll(",", ""); lastname = lastname.replaceAll("%20", " "); lastname = JFritzUtils.replaceSpecialCharsUTF(lastname); lastname = JFritzUtils.removeLeadingSpaces(HTMLUtil.stripEntities(lastname)); lastname = JFritzUtils.removeDuplicateWhitespace(lastname); if ("lastname".equals(patterns[ReverseLookupSite.FIRSTOCCURANCE])) { p = new Person(); p.addNumber(number.getIntNumber(), "home"); foundPersons.add(p); } if (p != null) { p.setLastName(lastname); } } } yield(); if (firstnamePattern != null) { firstnameMatcher = firstnamePattern.matcher(data[line]); if (firstnameMatcher.find()) { str = ""; for (int k = 1; k <= firstnameMatcher.groupCount(); k++) { if (firstnameMatcher.group(k) != null) str = str + firstnameMatcher.group(k).trim() + " "; } firstname = JFritzUtils.removeLeadingSpaces(HTMLUtil.stripEntities(str)); firstname = firstname.trim(); firstname = firstname.replaceAll(",", ""); firstname = firstname.replaceAll("%20", " "); firstname = JFritzUtils.replaceSpecialCharsUTF(firstname); firstname = JFritzUtils.removeLeadingSpaces(HTMLUtil.stripEntities(firstname)); firstname = JFritzUtils.removeDuplicateWhitespace(firstname); if ("firstname".equals(patterns[ReverseLookupSite.FIRSTOCCURANCE])) { p = new Person(); p.addNumber(number.getIntNumber(), "home"); foundPersons.add(p); } if (p != null) { p.setFirstName(firstname); } } } yield(); if (namePattern != null) { nameMatcher = namePattern.matcher(data[line]); if (nameMatcher.find()) { str = ""; for (int k = 1; k <= nameMatcher.groupCount(); k++) { if (nameMatcher.group(k) != null) str = str + nameMatcher.group(k).trim() + " "; } String[] split; split = str.split(" ", 2); lastname = JFritzUtils.removeLeadingSpaces(HTMLUtil.stripEntities(split[0])); lastname = lastname.trim(); lastname = lastname.replaceAll(",", ""); lastname = lastname.replaceAll("%20", " "); lastname = JFritzUtils.replaceSpecialCharsUTF(lastname); lastname = JFritzUtils.removeLeadingSpaces(HTMLUtil.stripEntities(lastname)); lastname = JFritzUtils.removeDuplicateWhitespace(lastname); if (split[1].length() > 0) { firstname = HTMLUtil.stripEntities(split[1]); if ((firstname.indexOf(" ") > -1) && (firstname.indexOf(" u.") == -1)) { company = JFritzUtils.removeLeadingSpaces(firstname.substring(firstname.indexOf(" ")).trim()); firstname = JFritzUtils.removeLeadingSpaces(firstname.substring(0, firstname.indexOf(" ")).trim()); } else { firstname = JFritzUtils.removeLeadingSpaces(firstname.replaceAll(" u. ", " und ")); } } firstname = firstname.replaceAll("%20", " "); firstname = JFritzUtils.replaceSpecialCharsUTF(firstname); firstname = JFritzUtils.removeLeadingSpaces(HTMLUtil.stripEntities(firstname)); firstname = JFritzUtils.removeDuplicateWhitespace(firstname); firstname = firstname.trim(); company = company.replaceAll("%20", " "); company = JFritzUtils.replaceSpecialCharsUTF(company); company = JFritzUtils.removeLeadingSpaces(HTMLUtil.stripEntities(company)); company = JFritzUtils.removeDuplicateWhitespace(company); company = company.trim(); if ("name".equals(patterns[ReverseLookupSite.FIRSTOCCURANCE])) { p = new Person(); if (company.length() > 0) { p.addNumber(number.getIntNumber(), "business"); } else { p.addNumber(number.getIntNumber(), "home"); } foundPersons.add(p); } if (p != null) { p.setFirstName(firstname); p.setLastName(lastname); p.setCompany(company); } } } yield(); if (streetPattern != null) { streetMatcher = streetPattern.matcher(data[line]); if (streetMatcher.find()) { str = ""; for (int k = 1; k <= streetMatcher.groupCount(); k++) { if (streetMatcher.group(k) != null) str = str + streetMatcher.group(k).trim() + " "; } street = str.replaceAll("%20", " "); street = JFritzUtils.replaceSpecialCharsUTF(street); street = JFritzUtils.removeLeadingSpaces(HTMLUtil.stripEntities(street)); street = JFritzUtils.removeDuplicateWhitespace(street); street = street.trim(); if ("street".equals(patterns[ReverseLookupSite.FIRSTOCCURANCE])) { p = new Person(); p.addNumber(number.getIntNumber(), "home"); foundPersons.add(p); } if (p != null) { p.setStreet(street); } } } yield(); if (cityPattern != null) { cityMatcher = cityPattern.matcher(data[line]); if (cityMatcher.find()) { str = ""; for (int k = 1; k <= cityMatcher.groupCount(); k++) { if (cityMatcher.group(k) != null) str = str + cityMatcher.group(k).trim() + " "; } city = str.replaceAll("%20", " "); city = JFritzUtils.replaceSpecialCharsUTF(city); city = JFritzUtils.removeLeadingSpaces(HTMLUtil.stripEntities(city)); city = JFritzUtils.removeDuplicateWhitespace(city); city = city.trim(); if ("city".equals(patterns[ReverseLookupSite.FIRSTOCCURANCE])) { p = new Person(); p.addNumber(number.getIntNumber(), "home"); foundPersons.add(p); } if (p != null) { p.setCity(city); } } } yield(); if (zipcodePattern != null) { zipcodeMatcher = zipcodePattern.matcher(data[line]); if (zipcodeMatcher.find()) { str = ""; for (int k = 1; k <= zipcodeMatcher.groupCount(); k++) { if (zipcodeMatcher.group(k) != null) str = str + zipcodeMatcher.group(k).trim() + " "; } zipcode = str.replaceAll("%20", " "); zipcode = JFritzUtils.replaceSpecialCharsUTF(zipcode); zipcode = JFritzUtils.removeLeadingSpaces(HTMLUtil.stripEntities(zipcode)); zipcode = JFritzUtils.removeDuplicateWhitespace(zipcode); zipcode = zipcode.trim(); if ("zipcode".equals(patterns[ReverseLookupSite.FIRSTOCCURANCE])) { p = new Person(); p.addNumber(number.getIntNumber(), "home"); foundPersons.add(p); } if (p != null) { p.setPostalCode(zipcode); } } } } } if (!firstname.equals("") || !lastname.equals("") || !company.equals("")) break; } yield(); if (!firstname.equals("") || !lastname.equals("") || !company.equals("")) { if (city.equals("")) { if (number.getCountryCode().equals(ReverseLookup.GERMANY_CODE)) city = ReverseLookupGermany.getCity(nummer); else if (number.getCountryCode().equals(ReverseLookup.AUSTRIA_CODE)) city = ReverseLookupAustria.getCity(nummer); else if (number.getCountryCode().startsWith(ReverseLookup.USA_CODE)) city = ReverseLookupUnitedStates.getCity(nummer); else if (number.getCountryCode().startsWith(ReverseLookup.TURKEY_CODE)) city = ReverseLookupTurkey.getCity(nummer); } return foundPersons.get(0); } } catch (IOException e1) { Debug.error("Error while retrieving " + urlstr); } } } catch (MalformedURLException e) { Debug.error("URL invalid: " + urlstr); } } yield(); Debug.warning("No match for " + nummer + " found"); if (city.equals("")) { if (number.getCountryCode().equals(ReverseLookup.GERMANY_CODE)) city = ReverseLookupGermany.getCity(nummer); else if (number.getCountryCode().equals(ReverseLookup.AUSTRIA_CODE)) city = ReverseLookupAustria.getCity(nummer); else if (number.getCountryCode().startsWith(ReverseLookup.USA_CODE)) city = ReverseLookupUnitedStates.getCity(nummer); else if (number.getCountryCode().startsWith(ReverseLookup.TURKEY_CODE)) city = ReverseLookupTurkey.getCity(nummer); } Person p = new Person("", "", "", "", "", city, "", ""); p.addNumber(number.getAreaNumber(), "home"); return p; } else { Debug.warning("No reverse lookup sites for: " + number.getCountryCode()); Person p = new Person(); p.addNumber(number.getAreaNumber(), "home"); if (number.getCountryCode().equals(ReverseLookup.GERMANY_CODE)) city = ReverseLookupGermany.getCity(number.getIntNumber()); else if (number.getCountryCode().equals(ReverseLookup.AUSTRIA_CODE)) city = ReverseLookupAustria.getCity(number.getIntNumber()); else if (number.getCountryCode().startsWith(ReverseLookup.USA_CODE)) city = ReverseLookupUnitedStates.getCity(number.getIntNumber()); else if (number.getCountryCode().startsWith(ReverseLookup.TURKEY_CODE)) city = ReverseLookupTurkey.getCity(number.getIntNumber()); p.setCity(city); return p; } return new Person("not found", "Person"); } "
" private void copyFile(File sourceFile, File destFile) throws IOException { if (!sourceFile.exists()) { return; } if (!destFile.exists()) { destFile.createNewFile(); } FileChannel source = null; FileChannel destination = null; source = new FileInputStream(sourceFile).getChannel(); destination = new FileOutputStream(destFile).getChannel(); if (destination != null && source != null) { destination.transferFrom(source, 0, source.size()); } if (source != null) { source.close(); } if (destination != null) { destination.close(); } } "
false
14
13,041,693
116,038
" @Override public void vote(String urlString, Map<String, String> headData, Map<String, String> paramData) { HttpURLConnection httpConn = null; try { URL url = new URL(urlString); httpConn = (HttpURLConnection) url.openConnection(); String cookies = getCookies(httpConn); System.out.println(cookies); BufferedReader post = new BufferedReader(new InputStreamReader(httpConn.getInputStream(), "GB2312")); String text = null; while ((text = post.readLine()) != null) { System.out.println(text); } } catch (MalformedURLException e) { e.printStackTrace(); throw new VoteBeanException("网址不正确", e); } catch (IOException e) { e.printStackTrace(); throw new VoteBeanException("不能打开网址", e); } } "
" 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!"); } "
false
15
14,157,859
3,791,822
" static void copyFile(File file, File file1) throws IOException { byte abyte0[] = new byte[512]; FileInputStream fileinputstream = new FileInputStream(file); FileOutputStream fileoutputstream = new FileOutputStream(file1); int i; while ((i = fileinputstream.read(abyte0)) > 0) fileoutputstream.write(abyte0, 0, i); fileinputstream.close(); fileoutputstream.close(); } "
" public Void doInBackground() { setProgress(0); for (int i = 0; i < uploadFiles.size(); i++) { String filePath = uploadFiles.elementAt(i).getFilePath(); String fileName = uploadFiles.elementAt(i).getFileName(); String fileMsg = "Uploading file " + (i + 1) + "/" + uploadFiles.size() + "\n"; this.publish(fileMsg); try { File inFile = new File(filePath); FileInputStream in = new FileInputStream(inFile); byte[] inBytes = new byte[(int) chunkSize]; int count = 1; int maxCount = (int) (inFile.length() / chunkSize); if (inFile.length() % chunkSize > 0) { maxCount++; } int readCount = 0; readCount = in.read(inBytes); while (readCount > 0) { File splitFile = File.createTempFile("upl", null, null); String splitName = splitFile.getPath(); FileOutputStream out = new FileOutputStream(splitFile); out.write(inBytes, 0, readCount); out.close(); boolean chunkFinal = (count == maxCount); fileMsg = " - Sending chunk " + count + "/" + maxCount + ": "; this.publish(fileMsg); boolean uploadSuccess = false; int uploadTries = 0; while (!uploadSuccess && uploadTries <= 5) { uploadTries++; boolean uploadStatus = upload(splitName, fileName, count, chunkFinal); if (uploadStatus) { fileMsg = "OK\n"; this.publish(fileMsg); uploadSuccess = true; } else { fileMsg = "ERROR\n"; this.publish(fileMsg); uploadSuccess = false; } } if (!uploadSuccess) { fileMsg = "There was an error uploading your files. Please let the pipeline administrator know about this problem. Cut and paste the messages in this box, and supply them.\n"; this.publish(fileMsg); errorFlag = true; return null; } float thisProgress = (count * 100) / (maxCount); float completeProgress = (i * (100 / uploadFiles.size())); float totalProgress = completeProgress + (thisProgress / uploadFiles.size()); setProgress((int) totalProgress); splitFile.delete(); readCount = in.read(inBytes); count++; } } catch (Exception e) { this.publish(e.toString()); } } return null; } "
true
16
23,270,032
21,907,871
" public void checkin(Object _document) { this.document = (Document) _document; synchronized (url) { OutputStream outputStream = null; try { if ("file".equals(url.getProtocol())) { outputStream = new FileOutputStream(url.getFile()); } else { URLConnection connection = url.openConnection(); connection.setDoOutput(true); outputStream = connection.getOutputStream(); } new XMLOutputter(" ", true).output(this.document, outputStream); outputStream.flush(); outputStream.close(); } catch (IOException e) { e.printStackTrace(); } } } "
" public static void extractFile(String jarArchive, String fileToExtract, String destination) { FileWriter writer = null; ZipInputStream zipStream = null; try { FileInputStream inputStream = new FileInputStream(jarArchive); BufferedInputStream bufferedStream = new BufferedInputStream(inputStream); zipStream = new ZipInputStream(bufferedStream); writer = new FileWriter(new File(destination)); ZipEntry zipEntry = null; while ((zipEntry = zipStream.getNextEntry()) != null) { if (zipEntry.getName().equals(fileToExtract)) { int size = (int) zipEntry.getSize(); for (int i = 0; i < size; i++) { writer.write(zipStream.read()); } } } } catch (IOException e) { e.printStackTrace(); } finally { if (zipStream != null) try { zipStream.close(); } catch (IOException e) { e.printStackTrace(); } if (writer != null) try { writer.close(); } catch (IOException e) { e.printStackTrace(); } } } "
false
17
17,586,131
14,533,184
" protected void update(String sql, Object[] args) { Connection conn = null; PreparedStatement pstmt = null; try { conn = JdbcUtils.getConnection(); conn.setAutoCommit(false); pstmt = conn.prepareStatement(sql); this.setParameters(pstmt, args); pstmt.executeUpdate(); conn.commit(); conn.setAutoCommit(true); } catch (SQLException e) { try { if (conn != null) { conn.rollback(); conn.setAutoCommit(true); } } catch (SQLException ex) { ex.printStackTrace(); } throw new JdbcDaoException(e.getMessage(), e); } finally { JdbcUtils.free(pstmt, conn); } } "
" public boolean delete(int id) { boolean deletionOk = false; Connection conn = null; try { conn = db.getConnection(); conn.setAutoCommit(false); String sql = "DELETE FROM keyphrases WHERE website_id=?"; PreparedStatement ps = conn.prepareStatement(sql); ps.setInt(1, id); deletionOk = ps.executeUpdate() == 1; ps.close(); sql = "DELETE FROM websites WHERE id=?"; ps = conn.prepareStatement(sql); ps.setInt(1, id); boolean success = ps.executeUpdate() == 1; deletionOk = deletionOk && success; ps.close(); conn.commit(); conn.setAutoCommit(true); } catch (SQLException sqle) { try { conn.rollback(); conn.setAutoCommit(true); } catch (SQLException sex) { throw new OsseoFailure("SQL error: roll back failed. ", sex); } throw new OsseoFailure("SQL error: cannot remove website with id " + id + ".", sqle); } finally { db.putConnection(conn); } return deletionOk; } "
true
18
18,865,693
1,477,578
" private static void copyFile(File inputFile, File outputFile) throws IOException { FileReader in = new FileReader(inputFile); FileWriter out = new FileWriter(outputFile); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } "
" public static void copy(FileInputStream source, FileOutputStream dest) throws IOException { FileChannel in = null, out = null; try { in = source.getChannel(); out = dest.getChannel(); long size = in.size(); MappedByteBuffer buf = in.map(FileChannel.MapMode.READ_ONLY, 0, size); out.write(buf); } finally { if (in != null) in.close(); if (out != null) out.close(); } } "
true
19
5,506,807
10,176,882
" public void testPreparedStatement0009() throws Exception { Statement stmt = con.createStatement(); stmt.executeUpdate("create table #t0009 " + " (i integer not null, " + " s char(10) not null) "); con.setAutoCommit(false); PreparedStatement pstmt = con.prepareStatement("insert into #t0009 values (?, ?)"); int rowsToAdd = 8; final String theString = "abcdefghijklmnopqrstuvwxyz"; int count = 0; for (int i = 1; i <= rowsToAdd; i++) { pstmt.setInt(1, i); pstmt.setString(2, theString.substring(0, i)); count += pstmt.executeUpdate(); } pstmt.close(); assertEquals(count, rowsToAdd); con.rollback(); ResultSet rs = stmt.executeQuery("select s, i from #t0009"); assertNotNull(rs); count = 0; while (rs.next()) { count++; assertEquals(rs.getString(1).trim().length(), rs.getInt(2)); } assertEquals(count, 0); con.commit(); pstmt = con.prepareStatement("insert into #t0009 values (?, ?)"); rowsToAdd = 6; count = 0; for (int i = 1; i <= rowsToAdd; i++) { pstmt.setInt(1, i); pstmt.setString(2, theString.substring(0, i)); count += pstmt.executeUpdate(); } assertEquals(count, rowsToAdd); con.commit(); pstmt.close(); rs = stmt.executeQuery("select s, i from #t0009"); count = 0; while (rs.next()) { count++; assertEquals(rs.getString(1).trim().length(), rs.getInt(2)); } assertEquals(count, rowsToAdd); con.commit(); stmt.close(); con.setAutoCommit(true); } "
" @SuppressWarnings("unchecked") protected void processDownloadAction(HttpServletRequest request, HttpServletResponse response) throws Exception { File transformationFile = new File(xslBase, "file-info.xsl"); HashMap<String, Object> params = new HashMap<String, Object>(); params.putAll(request.getParameterMap()); params.put("{" + Definitions.CONFIGURATION_NAMESPACE + "}configuration", configuration); params.put("{" + Definitions.REQUEST_NAMESPACE + "}request", request); params.put("{" + Definitions.RESPONSE_NAMESPACE + "}response", response); params.put("{" + Definitions.SESSION_NAMESPACE + "}session", request.getSession()); params.put("{" + Definitions.INFOFUZE_NAMESPACE + "}development-mode", new Boolean(Config.getInstance().isDevelopmentMode())); Transformer transformer = new Transformer(); transformer.setTransformationFile(transformationFile); transformer.setParams(params); transformer.setTransformMode(TransformMode.NORMAL); transformer.setConfiguration(configuration); transformer.setErrorListener(new TransformationErrorListener(response)); transformer.setLogInfo(false); DataSourceIf dataSource = new NullSource(); Document fileInfoDoc = XmlUtils.getEmptyDOM(); DOMResult result = new DOMResult(fileInfoDoc); transformer.transform((Source) dataSource, result); Element documentElement = fileInfoDoc.getDocumentElement(); if (documentElement.getLocalName().equals("null")) { response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return; } InputStream is = null; try { XPath xpath = XPathFactory.newInstance().newXPath(); String sourceType = XPathUtils.getStringValue(xpath, "source-type", documentElement, null); String location = XPathUtils.getStringValue(xpath, "location", documentElement, null); String fileName = XPathUtils.getStringValue(xpath, "file-name", documentElement, null); String mimeType = XPathUtils.getStringValue(xpath, "mime-type", documentElement, null); String encoding = XPathUtils.getStringValue(xpath, "encoding", documentElement, null); if (StringUtils.equals(sourceType, "cifsSource")) { String domain = XPathUtils.getStringValue(xpath, "domain", documentElement, null); String userName = XPathUtils.getStringValue(xpath, "username", documentElement, null); String password = XPathUtils.getStringValue(xpath, "password", documentElement, null); URI uri = new URI(location); if (StringUtils.isNotBlank(userName)) { String userInfo = ""; if (StringUtils.isNotBlank(domain)) { userInfo = userInfo + domain + ";"; } userInfo = userInfo + userName; if (StringUtils.isNotBlank(password)) { userInfo = userInfo + ":" + password; } uri = new URI(uri.getScheme(), userInfo, uri.getHost(), uri.getPort(), uri.getPath(), uri.getQuery(), uri.getFragment()); } SmbFile smbFile = new SmbFile(uri.toURL()); is = new SmbFileInputStream(smbFile); } else if (StringUtils.equals(sourceType, "localFileSystemSource")) { File file = new File(location); is = new FileInputStream(file); } else { logger.error("Source type \"" + ((sourceType != null) ? sourceType : "") + "\" not supported"); response.sendError(HttpServletResponse.SC_INTERNAL_SERVER_ERROR); return; } if (StringUtils.isBlank(mimeType) && StringUtils.isBlank(encoding)) { response.setContentType(Definitions.MIMETYPE_BINARY); } else if (StringUtils.isBlank(encoding)) { response.setContentType(mimeType); } else { response.setContentType(mimeType + ";charset=" + encoding); } if (request.getParameterMap().containsKey(Definitions.REQUEST_PARAMNAME_DOWNLOAD)) { response.setHeader("Content-Disposition", "attachment; filename=" + fileName); } IOUtils.copy(new BufferedInputStream(is), response.getOutputStream()); } finally { if (is != null) { is.close(); } } } "
false
20
2,746,011
5,105,540
" @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 AudioInputStream getAudioInputStream(URL url) throws UnsupportedAudioFileException, IOException { if (TDebug.TraceAudioFileReader) { TDebug.out("MpegAudioFileReader.getAudioInputStream(URL): begin"); } long lFileLengthInBytes = AudioSystem.NOT_SPECIFIED; URLConnection conn = url.openConnection(); boolean isShout = false; int toRead = 4; byte[] head = new byte[toRead]; conn.setRequestProperty("Icy-Metadata", "1"); BufferedInputStream bInputStream = new BufferedInputStream(conn.getInputStream()); bInputStream.mark(toRead); int read = bInputStream.read(head, 0, toRead); if ((read > 2) && (((head[0] == 'I') | (head[0] == 'i')) && ((head[1] == 'C') | (head[1] == 'c')) && ((head[2] == 'Y') | (head[2] == 'y')))) isShout = true; bInputStream.reset(); InputStream inputStream = null; if (isShout == true) { IcyInputStream icyStream = new IcyInputStream(bInputStream); icyStream.addTagParseListener(IcyListener.getInstance()); inputStream = icyStream; } else { String metaint = conn.getHeaderField("icy-metaint"); if (metaint != null) { IcyInputStream icyStream = new IcyInputStream(bInputStream, metaint); icyStream.addTagParseListener(IcyListener.getInstance()); inputStream = icyStream; } else { inputStream = bInputStream; } } AudioInputStream audioInputStream = null; try { audioInputStream = getAudioInputStream(inputStream, lFileLengthInBytes); } catch (UnsupportedAudioFileException e) { inputStream.close(); throw e; } catch (IOException e) { inputStream.close(); throw e; } if (TDebug.TraceAudioFileReader) { TDebug.out("MpegAudioFileReader.getAudioInputStream(URL): end"); } return audioInputStream; } "
false
21
3,287,282
13,431,536
" public void googleImageSearch(String start) { try { String u = "http://images.google.com/images?q=" + custom + start; if (u.contains(" ")) { u = u.replace(" ", "+"); } URL url = new URL(u); HttpURLConnection httpcon = (HttpURLConnection) url.openConnection(); httpcon.addRequestProperty("User-Agent", "Mozilla/4.76"); BufferedReader readIn = new BufferedReader(new InputStreamReader(httpcon.getInputStream())); googleImages.clear(); String text = ""; String lin = ""; while ((lin = readIn.readLine()) != null) { text += lin; } readIn.close(); if (text.contains("\n")) { text = text.replace("\n", ""); } String[] array = text.split("\\Qhref=\"/imgres?imgurl=\\E"); for (String s : array) { if (s.startsWith("http://") || s.startsWith("https://") && s.contains("&amp;")) { String s1 = s.substring(0, s.indexOf("&amp;")); googleImages.add(s1); } } } catch (Exception ex4) { MusicBoxView.showErrorDialog(ex4); } jButton4.setEnabled(true); jButton2.setEnabled(true); getContentPane().remove(jLabel1); ImageIcon icon; try { icon = new ImageIcon(new URL(googleImages.elementAt(googleImageLocation))); int h = icon.getIconHeight(); int w = icon.getIconWidth(); jLabel1.setSize(w, h); jLabel1.setIcon(icon); add(jLabel1, BorderLayout.CENTER); } catch (MalformedURLException ex) { MusicBoxView.showErrorDialog(ex); jLabel1.setIcon(MusicBoxView.noImage); } add(jPanel1, BorderLayout.PAGE_END); pack(); } "
" @Override public int updateStatus(UserInfo userInfo, String status) throws Exception { OAuthConsumer consumer = SnsConstant.getOAuthConsumer(SnsConstant.SOHU); consumer.setTokenWithSecret(userInfo.getAccessToken(), userInfo.getAccessSecret()); try { URL url = new URL(SnsConstant.SOHU_UPDATE_STATUS_URL); HttpURLConnection request = (HttpURLConnection) url.openConnection(); request.setDoOutput(true); request.setRequestMethod("POST"); HttpParameters para = new HttpParameters(); para.put("status", StringUtils.utf8Encode(status).replaceAll("\\+", "%20")); consumer.setAdditionalParameters(para); consumer.sign(request); OutputStream ot = request.getOutputStream(); ot.write(("status=" + URLEncoder.encode(status, "utf-8")).replaceAll("\\+", "%20").getBytes()); ot.flush(); ot.close(); System.out.println("Sending request..."); request.connect(); System.out.println("Response: " + request.getResponseCode() + " " + request.getResponseMessage()); BufferedReader reader = new BufferedReader(new InputStreamReader(request.getInputStream())); String b = null; while ((b = reader.readLine()) != null) { System.out.println(b); } return SnsConstant.SOHU_UPDATE_STATUS_SUCC_WHAT; } catch (Exception e) { SnsConstant.SOHU_OPERATOR_FAIL_REASON = processException(e.getMessage()); return SnsConstant.SOHU_UPDATE_STATUS_FAIL_WHAT; } } "
false
22
16,744,397
18,315,736
" public void copyToZip(ZipOutputStream zout, String entryName) throws IOException { close(); ZipEntry entry = new ZipEntry(entryName); zout.putNextEntry(entry); if (!isEmpty() && this.tmpFile.exists()) { InputStream in = new FileInputStream(this.tmpFile); IOUtils.copyTo(in, zout); in.close(); } zout.flush(); zout.closeEntry(); delete(); } "
" private List<String> getTaxaList() { List<String> taxa = new Vector<String>(); String domain = m_domain.getStringValue(); String id = ""; if (domain.equalsIgnoreCase("Eukaryota")) id = "eukaryota"; try { URL url = new URL("http://www.ebi.ac.uk/genomes/" + id + ".details.txt"); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String link = ""; String key = ""; String name = ""; int counter = 0; String line = ""; reader.readLine(); while ((line = reader.readLine()) != null) { String[] st = line.split("\t"); ena_details ena = new ena_details(st[0], st[1], st[2], st[3], st[4]); ENADataHolder.instance().put(ena.desc, ena); taxa.add(ena.desc); } reader.close(); } catch (MalformedURLException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } return taxa; } "
false
23
18,269,744
10,140,251
" 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; } "
" protected String contentString() { String result = null; URL url; String encoding = null; try { url = url(); URLConnection connection = url.openConnection(); connection.setDoInput(true); connection.setDoOutput(false); connection.setUseCaches(false); for (Enumeration e = bindingKeys().objectEnumerator(); e.hasMoreElements(); ) { String key = (String) e.nextElement(); if (key.startsWith("?")) { connection.setRequestProperty(key.substring(1), valueForBinding(key).toString()); } } if (connection.getContentEncoding() != null) { encoding = connection.getContentEncoding(); } if (encoding == null) { encoding = (String) valueForBinding("encoding"); } if (encoding == null) { encoding = "UTF-8"; } InputStream stream = connection.getInputStream(); byte bytes[] = ERXFileUtilities.bytesFromInputStream(stream); stream.close(); result = new String(bytes, encoding); } catch (IOException ex) { throw NSForwardException._runtimeExceptionForThrowable(ex); } return result; } "
false
24
14,876,163
3,260,787
" public static void copyFile(File in, File out) throws IOException { FileChannel inChannel = new FileInputStream(in).getChannel(); FileChannel outChannel = new FileOutputStream(out).getChannel(); try { inChannel.transferTo(0, inChannel.size(), outChannel); } catch (IOException e) { throw e; } finally { if (inChannel != null) inChannel.close(); if (outChannel != null) outChannel.close(); } } "
" public CopyAllDataToOtherFolderResponse CopyAllDataToOtherFolder(DPWSContext context, CopyAllDataToOtherFolder CopyAllDataInps) throws DPWSException { CopyAllDataToOtherFolderResponse cpyRp = new CopyAllDataToOtherFolderResponseImpl(); int hany = 0; String errorMsg = null; try { if ((rootDir == null) || (rootDir.length() == (-1))) { errorMsg = LocalStorVerify.ISNT_ROOTFLD; } else { String sourceN = CopyAllDataInps.getSourceName(); String targetN = CopyAllDataInps.getTargetName(); if (LocalStorVerify.isValid(sourceN) && LocalStorVerify.isValid(targetN)) { String srcDir = rootDir + File.separator + sourceN; String trgDir = rootDir + File.separator + targetN; if (LocalStorVerify.isLength(srcDir) && LocalStorVerify.isLength(trgDir)) { for (File fs : new File(srcDir).listFiles()) { File ft = new File(trgDir + '\\' + fs.getName()); FileChannel in = null, out = null; try { in = new FileInputStream(fs).getChannel(); out = new FileOutputStream(ft).getChannel(); long size = in.size(); MappedByteBuffer buf = in.map(FileChannel.MapMode.READ_ONLY, 0, size); out.write(buf); } finally { if (in != null) in.close(); if (out != null) out.close(); hany++; } } } else { errorMsg = LocalStorVerify.FLD_TOOLNG; } } else { errorMsg = LocalStorVerify.ISNT_VALID; } } } catch (Throwable tr) { tr.printStackTrace(); errorMsg = tr.getMessage(); hany = (-1); } if (errorMsg != null) { } cpyRp.setNum(hany); return cpyRp; } "
true
25
14,313,659
10,109,343
" private int writeTraceFile(final File destination_file, final String trace_file_name, final String trace_file_path) { URL url = null; BufferedInputStream is = null; FileOutputStream fo = null; BufferedOutputStream os = null; int b = 0; if (destination_file == null) { return 0; } try { url = new URL("http://" + trace_file_path + "/" + trace_file_name); is = new BufferedInputStream(url.openStream()); fo = new FileOutputStream(destination_file); os = new BufferedOutputStream(fo); while ((b = is.read()) != -1) { os.write(b); } os.flush(); is.close(); os.close(); } catch (Exception e) { System.err.println(url.toString()); Utilities.unexpectedException(e, this, CONTACT); return 0; } return 1; } "
" public void readData() throws IOException { i = 0; j = 0; URL url = getClass().getResource("resources/tuneGridMaster.dat"); InputStream is = url.openStream(); InputStreamReader isr = new InputStreamReader(is); BufferedReader br = new BufferedReader(isr); s = br.readLine(); StringTokenizer st = new StringTokenizer(s); tune_x[i][j] = Double.parseDouble(st.nextToken()); gridmin = tune_x[i][j]; temp_prev = tune_x[i][j]; tune_y[i][j] = Double.parseDouble(st.nextToken()); kd[i][j] = Double.parseDouble(st.nextToken()); kfs[i][j] = Double.parseDouble(st.nextToken()); kfl[i][j] = Double.parseDouble(st.nextToken()); kdee[i][j] = Double.parseDouble(st.nextToken()); kdc[i][j] = Double.parseDouble(st.nextToken()); kfc[i][j] = Double.parseDouble(st.nextToken()); j++; int k = 0; 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; } tune_x[i][j] = temp_new; tune_y[i][j] = Double.parseDouble(st.nextToken()); kd[i][j] = Double.parseDouble(st.nextToken()); kfs[i][j] = Double.parseDouble(st.nextToken()); kfl[i][j] = Double.parseDouble(st.nextToken()); kdee[i][j] = Double.parseDouble(st.nextToken()); kdc[i][j] = Double.parseDouble(st.nextToken()); kfc[i][j] = Double.parseDouble(st.nextToken()); imax = i; jmax = j; j++; k++; } gridmax = tune_x[i][j - 1]; } "
false
26
13,745,376
10,567,003
" public IStatus runInUIThread(IProgressMonitor monitor) { monitor.beginTask(Strings.MSG_CONNECT_SERVER, 3); InputStream in = null; try { URL url = createOpenUrl(resource, pref); if (url != null) { URLConnection con = url.openConnection(); monitor.worked(1); monitor.setTaskName(Strings.MSG_WAIT_FOR_SERVER); con.connect(); in = con.getInputStream(); in.read(); monitor.worked(1); monitor.setTaskName(NLS.bind(Strings.MSG_OPEN_URL, url)); open(url, resource.getProject(), pref); monitor.worked(1); } } catch (ConnectException con) { if (count < 3) { ConnectAndOpenJob job = new ConnectAndOpenJob(resource, pref, ++count); job.schedule(1000L); } else { Activator.log(con); } } catch (Exception e) { Activator.log(e); } finally { Streams.close(in); monitor.done(); } return Status.OK_STATUS; } "
" private InputStream loadSource(String url) throws ClientProtocolException, IOException { HttpClient httpclient = new DefaultHttpClient(); httpclient.getParams().setParameter(HTTP.USER_AGENT, "Mozilla/4.0 (compatible; MSIE 7.0b; Windows NT 6.0)"); HttpGet httpget = new HttpGet(url); HttpResponse response = httpclient.execute(httpget); HttpEntity entity = response.getEntity(); return entity.getContent(); } "
false
27
22,075,089
20,623,710
" public static void executa(String arquivo, String filial, String ip) { String drive = arquivo.substring(0, 2); if (drive.indexOf(":") == -1) drive = ""; Properties p = Util.lerPropriedades(arquivo); String servidor = p.getProperty("servidor"); String impressora = p.getProperty("fila"); String arqRel = new String(drive + p.getProperty("arquivo")); String copias = p.getProperty("copias"); if (filial.equalsIgnoreCase(servidor)) { Socket s = null; int tentativas = 0; boolean conectado = false; while (!conectado) { try { tentativas++; System.out.println("Tentando conectar " + ip + " (" + tentativas + ")"); s = new Socket(ip, 7000); conectado = s.isConnected(); } catch (ConnectException ce) { System.err.println(ce.getMessage()); System.err.println(ce.getCause()); } catch (UnknownHostException uhe) { System.err.println(uhe.getMessage()); } catch (IOException ioe) { System.err.println(ioe.getMessage()); } } FileInputStream in = null; BufferedOutputStream out = null; try { in = new FileInputStream(new File(arqRel)); out = new BufferedOutputStream(new GZIPOutputStream(s.getOutputStream())); } catch (FileNotFoundException e3) { e3.printStackTrace(); } catch (IOException e3) { e3.printStackTrace(); } String arqtr = arqRel.substring(2); System.out.println("Proximo arquivo: " + arqRel + " ->" + arqtr); while (arqtr.length() < 30) arqtr += " "; while (impressora.length() < 30) impressora += " "; byte aux[] = new byte[30]; byte cop[] = new byte[2]; try { aux = arqtr.getBytes("UTF8"); out.write(aux); aux = impressora.getBytes("UTF8"); out.write(aux); cop = copias.getBytes("UTF8"); out.write(cop); out.flush(); } catch (UnsupportedEncodingException e2) { e2.printStackTrace(); } catch (IOException e2) { e2.printStackTrace(); } byte b[] = new byte[1024]; int nBytes; try { while ((nBytes = in.read(b)) != -1) out.write(b, 0, nBytes); out.flush(); out.close(); in.close(); s.close(); } catch (IOException e1) { e1.printStackTrace(); } System.out.println("Arquivo " + arqRel + " foi transmitido. \n\n"); try { Thread.sleep(1000); } catch (InterruptedException e) { e.printStackTrace(); } SimpleDateFormat dfArq = new SimpleDateFormat("yyyy-MM-dd"); SimpleDateFormat dfLog = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss"); String arqLog = "log" + filial + dfArq.format(new Date()) + ".txt"; PrintWriter pw = null; try { pw = new PrintWriter(new FileWriter(arqLog, true)); } catch (IOException e) { e.printStackTrace(); } pw.println("Arquivo: " + arquivo + " " + dfLog.format(new Date())); pw.flush(); pw.close(); File f = new File(arquivo); while (!f.delete()) { System.out.println("Erro apagando " + arquivo); } } } "
" 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(); } "
true
28
19,217,522
10,385,493
" 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; } "
" public void writeBack(File destinationFile, boolean makeCopy) throws IOException { if (makeCopy) { FileChannel sourceChannel = new java.io.FileInputStream(getFile()).getChannel(); FileChannel destinationChannel = new java.io.FileOutputStream(destinationFile).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), destinationChannel); sourceChannel.close(); destinationChannel.close(); } else { getFile().renameTo(destinationFile); } if (getExifTime() != null && getOriginalTime() != null && !getExifTime().equals(getOriginalTime())) { String adjustArgument = "-ts" + m_dfJhead.format(getExifTime()); ProcessBuilder pb = new ProcessBuilder(m_tm.getJheadCommand(), adjustArgument, destinationFile.getAbsolutePath()); pb.directory(destinationFile.getParentFile()); System.out.println(pb.command().get(0) + " " + pb.command().get(1) + " " + pb.command().get(2)); final Process p = pb.start(); try { p.waitFor(); } catch (InterruptedException e) { e.printStackTrace(); } } } "
true
29
7,681,426
11,717,079
" public void extractProfile(String parentDir, String fileName, String profileName) { try { byte[] buf = new byte[1024]; ZipInputStream zipinputstream = null; ZipEntry zipentry; if (createProfileDirectory(profileName, parentDir)) { debug("the profile directory created .starting the profile extraction"); String profilePath = parentDir + File.separator + fileName; zipinputstream = new ZipInputStream(new FileInputStream(profilePath)); zipentry = zipinputstream.getNextEntry(); while (zipentry != null) { String entryName = zipentry.getName(); int n; FileOutputStream fileoutputstream; File newFile = new File(entryName); String directory = newFile.getParent(); if (directory == null) { if (newFile.isDirectory()) break; } fileoutputstream = new FileOutputStream(parentDir + File.separator + profileName + File.separator + newFile.getName()); while ((n = zipinputstream.read(buf, 0, 1024)) > -1) fileoutputstream.write(buf, 0, n); fileoutputstream.close(); zipinputstream.closeEntry(); zipentry = zipinputstream.getNextEntry(); } zipinputstream.close(); debug("deleting the profile.zip file"); File newFile = new File(profilePath); if (newFile.delete()) { debug("the " + "[" + profilePath + "]" + " deleted successfully"); } else { debug("profile" + "[" + profilePath + "]" + "deletion fail"); throw new IllegalArgumentException("Error: deletion error!"); } } else { debug("error creating the profile directory"); } } catch (Exception e) { e.printStackTrace(); } } "
" void copyFile(File inputFile, File outputFile) { try { FileReader in; in = new FileReader(inputFile); FileWriter out = new FileWriter(outputFile); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } "
true
30
8,831,301
8,365,268
" public void run() { String s; s = ""; try { URL url = new URL("http://www.m-w.com/dictionary/" + word); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); String str; while (((str = in.readLine()) != null) && (!stopped)) { s = s + str; } in.close(); } catch (MalformedURLException e) { } catch (IOException e) { } Pattern pattern = Pattern.compile("Main Entry:.+?<br>(.+?)</td>", Pattern.CASE_INSENSITIVE | Pattern.DOTALL); Matcher matcher = pattern.matcher(s); java.io.StringWriter wr = new java.io.StringWriter(); HTMLDocument doc = null; HTMLEditorKit kit = (HTMLEditorKit) editor.getEditorKit(); try { doc = (HTMLDocument) editor.getDocument(); } catch (Exception e) { } System.out.println(wr); editor.setContentType("text/html"); if (matcher.find()) try { kit.insertHTML(doc, editor.getCaretPosition(), "<HR>" + matcher.group(1) + "<HR>", 0, 0, null); } catch (Exception e) { System.out.println(e.getMessage()); } else try { kit.insertHTML(doc, editor.getCaretPosition(), "<HR><FONT COLOR='RED'>NOT FOUND!!</FONT><HR>", 0, 0, null); } catch (Exception e) { System.out.println(e.getMessage()); } button.setEnabled(true); } "
" public static String[] readStats() throws Exception { URL url = null; BufferedReader reader = null; StringBuilder stringBuilder; try { url = new URL("http://localhost:" + port + webctx + "/shared/js/libOO/health_check.sjs"); HttpURLConnection connection = (HttpURLConnection) url.openConnection(); connection.setRequestMethod("GET"); connection.setReadTimeout(10 * 1000); connection.connect(); reader = new BufferedReader(new InputStreamReader(connection.getInputStream())); stringBuilder = new StringBuilder(); String line = null; while ((line = reader.readLine()) != null) { stringBuilder.append(line); } return stringBuilder.toString().split(","); } catch (Exception e) { e.printStackTrace(); throw e; } finally { if (reader != null) { try { reader.close(); } catch (IOException ioe) { ioe.printStackTrace(); } } } } "
true
31
308,643
21,172,450
" 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 unzip2(String strZipFile, String folder) throws IOException, ArchiveException { FileUtil.fileExists(strZipFile, true); final InputStream is = new FileInputStream(strZipFile); ArchiveInputStream in = new ArchiveStreamFactory().createArchiveInputStream("zip", is); ZipArchiveEntry entry = null; OutputStream out = null; while ((entry = (ZipArchiveEntry) in.getNextEntry()) != null) { File zipPath = new File(folder); File destinationFilePath = new File(zipPath, entry.getName()); destinationFilePath.getParentFile().mkdirs(); if (entry.isDirectory()) { continue; } else { out = new FileOutputStream(new File(folder, entry.getName())); IOUtils.copy(in, out); out.close(); } } in.close(); } "
true
32
11,322,573
3,224,152
" private void preprocessObjects(GeoObject[] objects) throws IOException { System.out.println("objects.length " + objects.length); for (int i = 0; i < objects.length; i++) { String fileName = objects[i].getPath(); int dotindex = fileName.lastIndexOf("."); dotindex = dotindex < 0 ? 0 : dotindex; String tmp = dotindex < 1 ? fileName : fileName.substring(0, dotindex + 3) + "w"; System.out.println("i: " + " world filename " + tmp); File worldFile = new File(tmp); if (worldFile.exists()) { BufferedReader worldFileReader = new BufferedReader(new InputStreamReader(new FileInputStream(worldFile))); if (staticDebugOn) debug("b4nextline: "); line = worldFileReader.readLine(); if (staticDebugOn) debug("line: " + line); if (line != null) { line = worldFileReader.readLine(); if (staticDebugOn) debug("line: " + line); tokenizer = new StringTokenizer(line, " \n\t\r\"", false); objects[i].setLon(Double.valueOf(tokenizer.nextToken()).doubleValue()); line = worldFileReader.readLine(); if (staticDebugOn) debug("line: " + line); tokenizer = new StringTokenizer(line, " \n\t\r\"", false); objects[i].setLat(Double.valueOf(tokenizer.nextToken()).doubleValue()); } } File file = new File(objects[i].getPath()); if (file.exists()) { System.out.println("object src file found "); int slashindex = fileName.lastIndexOf(java.io.File.separator); slashindex = slashindex < 0 ? 0 : slashindex; if (slashindex == 0) { slashindex = fileName.lastIndexOf("/"); slashindex = slashindex < 0 ? 0 : slashindex; } tmp = slashindex < 1 ? fileName : fileName.substring(slashindex + 1, fileName.length()); System.out.println("filename " + destinationDirectory + XPlat.fileSep + tmp); objects[i].setPath(tmp); file = new File(fileName); if (file.exists()) { DataInputStream dataIn = new DataInputStream(new BufferedInputStream(new FileInputStream(fileName))); DataOutputStream dataOut = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(destinationDirectory + XPlat.fileSep + tmp))); System.out.println("copying to " + destinationDirectory + XPlat.fileSep + tmp); for (; ; ) { try { dataOut.writeShort(dataIn.readShort()); } catch (EOFException e) { break; } catch (IOException e) { break; } } dataOut.close(); } } } } "
" private String transferWSDL(String usernameAndPassword) throws WiseConnectionException { String filePath = null; try { URL endpoint = new URL(wsdlURL); HttpURLConnection conn = (HttpURLConnection) endpoint.openConnection(); conn.setDoOutput(false); conn.setDoInput(true); conn.setUseCaches(false); conn.setRequestMethod("GET"); conn.setRequestProperty("Accept", "text/xml,application/xml,application/xhtml+xml,text/html;q=0.9,text/plain;q=0.8,image/png,*/*;q=0.5"); conn.setRequestProperty("Connection", "close"); if (this.password != null) { conn.setRequestProperty("Authorization", "Basic " + (new BASE64Encoder()).encode(usernameAndPassword.getBytes())); } InputStream is = null; if (conn.getResponseCode() == 200) { is = conn.getInputStream(); } else { is = conn.getErrorStream(); InputStreamReader isr = new InputStreamReader(is); StringWriter sw = new StringWriter(); char[] buf = new char[200]; int read = 0; while (read != -1) { read = isr.read(buf); sw.write(buf); } throw new WiseConnectionException("Remote server's response is an error: " + sw.toString()); } File file = new File(tmpDir, new StringBuffer("Wise").append(IDGenerator.nextVal()).append(".xml").toString()); OutputStream fos = new BufferedOutputStream(new FileOutputStream(file)); IOUtils.copyStream(fos, is); fos.close(); is.close(); filePath = file.getPath(); } catch (WiseConnectionException wce) { throw wce; } catch (Exception e) { logger.error("Failed to download wsdl from URL : " + wsdlURL); throw new WiseConnectionException("Wsdl download failed!", e); } return filePath; } "
true
33
13,569,337
11,394,767
" public static String getMD5HashFromString(String message) { String hashword = null; try { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.update(message.getBytes()); BigInteger hash = new BigInteger(1, md5.digest()); hashword = hash.toString(16); } catch (NoSuchAlgorithmException nsae) { } return hashword; } "
" public static byte[] gerarHash(String frase) { try { MessageDigest md = MessageDigest.getInstance("SHA-1"); md.update(frase.getBytes()); return md.digest(); } catch (NoSuchAlgorithmException e) { return null; } } "
true
34
254,039
16,016,623
" protected void doDownload(S3Bucket bucket, S3Object s3object) throws Exception { String key = s3object.getKey(); key = trimPrefix(key); String[] path = key.split("/"); String fileName = path[path.length - 1]; String dirPath = ""; for (int i = 0; i < path.length - 1; i++) { dirPath += path[i] + "/"; } File outputDir = new File(downloadFileOutputDir + "/" + dirPath); if (outputDir.exists() == false) { outputDir.mkdirs(); } File outputFile = new File(outputDir, fileName); long size = s3object.getContentLength(); if (outputFile.exists() && outputFile.length() == size) { return; } long startTime = System.currentTimeMillis(); log.info("Download start.S3 file=" + s3object.getKey() + " local file=" + outputFile.getAbsolutePath()); FileOutputStream fout = null; S3Object dataObject = null; try { fout = new FileOutputStream(outputFile); dataObject = s3.getObject(bucket, s3object.getKey()); InputStream is = dataObject.getDataInputStream(); IOUtils.copyStream(is, fout); downloadedFileList.add(key); long downloadTime = System.currentTimeMillis() - startTime; log.info("Download complete.Estimete time=" + downloadTime + "ms " + IOUtils.toBPSText(downloadTime, size)); } catch (Exception e) { log.error("Download fail. s3 file=" + key, e); outputFile.delete(); throw e; } finally { IOUtils.closeNoException(fout); if (dataObject != null) { dataObject.closeDataInputStream(); } } } "
" @Override protected ModelAndView handleRequestInternal(final HttpServletRequest request, final HttpServletResponse response) throws Exception { final String filename = ServletRequestUtils.getRequiredStringParameter(request, "id"); final File file = new File(path, filename + ".html"); logger.debug("Getting static content from: " + file.getPath()); final InputStream is = getServletContext().getResourceAsStream(file.getPath()); OutputStream out = null; if (is != null) { try { out = response.getOutputStream(); IOUtils.copy(is, out); } catch (IOException ioex) { logger.error(ioex); } finally { is.close(); if (out != null) { out.close(); } } } return null; } "
true
35
4,147,990
1,663,419
" public static void copyFile(File dst, File src, boolean append) throws FileNotFoundException, IOException { dst.createNewFile(); FileChannel in = new FileInputStream(src).getChannel(); FileChannel out = new FileOutputStream(dst).getChannel(); long startAt = 0; if (append) startAt = out.size(); in.transferTo(startAt, in.size(), out); out.close(); in.close(); } "
" private static void copyFile(File in, File out) throws IOException { FileChannel inChannel = new FileInputStream(in).getChannel(); FileChannel outChannel = new FileOutputStream(out).getChannel(); try { inChannel.transferTo(0, inChannel.size(), outChannel); } catch (IOException e) { throw e; } finally { if (inChannel != null) inChannel.close(); if (outChannel != null) outChannel.close(); } } "
true
36
16,603,670
12,576,210
" private String generateUniqueIdMD5(String workgroupIdString, String runIdString) { String passwordUnhashed = workgroupIdString + "-" + runIdString; MessageDigest m = null; try { m = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } m.update(passwordUnhashed.getBytes(), 0, passwordUnhashed.length()); String uniqueIdMD5 = new BigInteger(1, m.digest()).toString(16); return uniqueIdMD5; } "
" public static FTPClient createConnection(String hostname, int port, char[] username, char[] password, String workingDirectory, FileSystemOptions fileSystemOptions) throws FileSystemException { if (username == null) username = "anonymous".toCharArray(); if (password == null) password = "anonymous".toCharArray(); try { final FTPClient client = new FTPClient(); String key = FtpFileSystemConfigBuilder.getInstance().getEntryParser(fileSystemOptions); if (key != null) { FTPClientConfig config = new FTPClientConfig(key); String serverLanguageCode = FtpFileSystemConfigBuilder.getInstance().getServerLanguageCode(fileSystemOptions); if (serverLanguageCode != null) config.setServerLanguageCode(serverLanguageCode); String defaultDateFormat = FtpFileSystemConfigBuilder.getInstance().getDefaultDateFormat(fileSystemOptions); if (defaultDateFormat != null) config.setDefaultDateFormatStr(defaultDateFormat); String recentDateFormat = FtpFileSystemConfigBuilder.getInstance().getRecentDateFormat(fileSystemOptions); if (recentDateFormat != null) config.setRecentDateFormatStr(recentDateFormat); String serverTimeZoneId = FtpFileSystemConfigBuilder.getInstance().getServerTimeZoneId(fileSystemOptions); if (serverTimeZoneId != null) config.setServerTimeZoneId(serverTimeZoneId); String[] shortMonthNames = FtpFileSystemConfigBuilder.getInstance().getShortMonthNames(fileSystemOptions); if (shortMonthNames != null) { StringBuffer shortMonthNamesStr = new StringBuffer(40); for (int i = 0; i < shortMonthNames.length; i++) { if (shortMonthNamesStr.length() > 0) shortMonthNamesStr.append("|"); shortMonthNamesStr.append(shortMonthNames[i]); } config.setShortMonthNames(shortMonthNamesStr.toString()); } client.configure(config); } FTPFileEntryParserFactory myFactory = FtpFileSystemConfigBuilder.getInstance().getEntryParserFactory(fileSystemOptions); if (myFactory != null) client.setParserFactory(myFactory); try { client.connect(hostname, port); int reply = client.getReplyCode(); if (!FTPReply.isPositiveCompletion(reply)) throw new FileSystemException("vfs.provider.ftp/connect-rejected.error", hostname); if (!client.login(UserAuthenticatorUtils.toString(username), UserAuthenticatorUtils.toString(password))) throw new FileSystemException("vfs.provider.ftp/login.error", new Object[] { hostname, UserAuthenticatorUtils.toString(username) }, null); if (!client.setFileType(FTP.BINARY_FILE_TYPE)) throw new FileSystemException("vfs.provider.ftp/set-binary.error", hostname); Integer dataTimeout = FtpFileSystemConfigBuilder.getInstance().getDataTimeout(fileSystemOptions); if (dataTimeout != null) client.setDataTimeout(dataTimeout.intValue()); try { FtpFileSystemConfigBuilder.getInstance().setHomeDir(fileSystemOptions, client.printWorkingDirectory()); } catch (IOException ex) { throw new FileSystemException("Error obtaining working directory!"); } Boolean userDirIsRoot = FtpFileSystemConfigBuilder.getInstance().getUserDirIsRoot(fileSystemOptions); if (workingDirectory != null && (userDirIsRoot == null || !userDirIsRoot.booleanValue())) if (!client.changeWorkingDirectory(workingDirectory)) throw new FileSystemException("vfs.provider.ftp/change-work-directory.error", workingDirectory); Boolean passiveMode = FtpFileSystemConfigBuilder.getInstance().getPassiveMode(fileSystemOptions); if (passiveMode != null && passiveMode.booleanValue()) client.enterLocalPassiveMode(); } catch (final IOException e) { if (client.isConnected()) client.disconnect(); throw e; } return client; } catch (final Exception exc) { throw new FileSystemException("vfs.provider.ftp/connect.error", new Object[] { hostname }, exc); } } "
false
37
19,825,038
9,385,633
" public static byte[] post(String path, Map<String, String> params, String encode) throws Exception { StringBuilder parambuilder = new StringBuilder(""); if (params != null && !params.isEmpty()) { for (Map.Entry<String, String> entry : params.entrySet()) { parambuilder.append(entry.getKey()).append("=").append(URLEncoder.encode(entry.getValue(), encode)).append("&"); } parambuilder.deleteCharAt(parambuilder.length() - 1); } byte[] data = parambuilder.toString().getBytes(); URL url = new URL(path); HttpURLConnection conn = (HttpURLConnection) url.openConnection(); conn.setDoOutput(true); conn.setUseCaches(false); conn.setConnectTimeout(5 * 1000); conn.setRequestMethod("POST"); conn.setRequestProperty("Accept", "image/gif, image/jpeg, image/pjpeg, image/pjpeg, application/x-shockwave-flash, application/xaml+xml, application/vnd.ms-xpsdocument, application/x-ms-xbap, application/x-ms-application, application/vnd.ms-excel, application/vnd.ms-powerpoint, application/msword, */*"); conn.setRequestProperty("Accept-Language", "zh-CN"); conn.setRequestProperty("User-Agent", "Mozilla/4.0 (compatible; MSIE 8.0; Windows NT 5.2; Trident/4.0; .NET CLR 1.1.4322; .NET CLR 2.0.50727; .NET CLR 3.0.04506.30; .NET CLR 3.0.4506.2152; .NET CLR 3.5.30729)"); conn.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); conn.setRequestProperty("Content-Length", String.valueOf(data.length)); conn.setRequestProperty("Connection", "Keep-Alive"); DataOutputStream outStream = new DataOutputStream(conn.getOutputStream()); outStream.write(data); outStream.flush(); outStream.close(); if (conn.getResponseCode() == 200) { return StreamTool.readInputStream(conn.getInputStream()); } return null; } "
" protected void setRankOrder() { this.rankOrder = new int[values.length]; for (int i = 0; i < rankOrder.length; i++) { rankOrder[i] = i; assert (!Double.isNaN(values[i])); } for (int i = rankOrder.length - 1; i >= 0; i--) { boolean swapped = false; for (int j = 0; j < i; j++) if (values[rankOrder[j]] < values[rankOrder[j + 1]]) { int r = rankOrder[j]; rankOrder[j] = rankOrder[j + 1]; rankOrder[j + 1] = r; } } } "
false
38
810,724
22,207,815
" private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } "
" public static Checksum checksum(File file, Checksum checksum) throws IOException { if (file.isDirectory()) { throw new IllegalArgumentException("Checksums can't be computed on directories"); } InputStream in = null; try { in = new CheckedInputStream(new FileInputStream(file), checksum); IOUtils.copy(in, new NullOutputStream()); } finally { IOUtils.closeQuietly(in); } return checksum; } "
true
39
1,643,091
23,277,837
" private static void download(String urlString) throws IOException { URL url = new URL(urlString); url = handleRedirectUrl(url); URLConnection cn = url.openConnection(); Utils.setHeader(cn); long fileLength = cn.getContentLength(); Statics.getInstance().setFileLength(fileLength); long packageLength = fileLength / THREAD_COUNT; long leftLength = fileLength % THREAD_COUNT; String fileName = Utils.decodeURLFileName(url); RandomAccessFile file = new RandomAccessFile(fileName, "rw"); System.out.println("File: " + fileName + ", Size: " + Utils.calSize(fileLength)); CountDownLatch latch = new CountDownLatch(THREAD_COUNT + 1); long pos = 0; for (int i = 0; i < THREAD_COUNT; i++) { long endPos = pos + packageLength; if (leftLength > 0) { endPos++; leftLength--; } new Thread(new DownloadThread(latch, url, file, pos, endPos)).start(); pos = endPos; } new Thread(new MoniterThread(latch)).start(); try { latch.await(); } catch (InterruptedException e) { e.printStackTrace(); } } "
" private File download(String filename, URL url) { int size = -1; int received = 0; try { fireDownloadStarted(filename); File file = createFile(filename); BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(file)); System.out.println("下载资源:" + filename + ", url=" + url); // BufferedInputStream bis = new // BufferedInputStream(url.openStream()); InputStream bis = url.openStream(); byte[] buf = new byte[1024]; int count = 0; long lastUpdate = 0; size = bis.available(); while ((count = bis.read(buf)) != -1) { bos.write(buf, 0, count); received += count; long now = System.currentTimeMillis(); if (now - lastUpdate > 500) { fireDownloadUpdate(filename, size, received); lastUpdate = now; } } bos.close(); System.out.println("资源下载完毕:" + filename); fireDownloadCompleted(filename); return file; } catch (IOException e) { System.out.println("下载资源失败:" + filename + ", error=" + e.getMessage()); fireDownloadInterrupted(filename); if (!(e instanceof FileNotFoundException)) { e.printStackTrace(); } } return null; } "
false
40
1,214,975
21,172,450
" public static void writeToFile(InputStream input, File file, ProgressListener listener, long length) { OutputStream output = null; try { output = new CountingOutputStream(new FileOutputStream(file), listener, length); IOUtils.copy(input, output); } catch (IOException e) { throw new RuntimeException(e); } finally { IOUtils.closeQuietly(input); IOUtils.closeQuietly(output); } } "
" public static void unzip2(String strZipFile, String folder) throws IOException, ArchiveException { FileUtil.fileExists(strZipFile, true); final InputStream is = new FileInputStream(strZipFile); ArchiveInputStream in = new ArchiveStreamFactory().createArchiveInputStream("zip", is); ZipArchiveEntry entry = null; OutputStream out = null; while ((entry = (ZipArchiveEntry) in.getNextEntry()) != null) { File zipPath = new File(folder); File destinationFilePath = new File(zipPath, entry.getName()); destinationFilePath.getParentFile().mkdirs(); if (entry.isDirectory()) { continue; } else { out = new FileOutputStream(new File(folder, entry.getName())); IOUtils.copy(in, out); out.close(); } } in.close(); } "
true
41
9,070,085
17,832,320
" public String getMd5CodeOf16(String str) { StringBuffer buf = null; try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(str.getBytes()); byte b[] = md.digest(); int i; buf = new StringBuffer(""); for (int offset = 0; offset < b.length; offset++) { i = b[offset]; if (i < 0) i += 256; if (i < 16) buf.append("0"); buf.append(Integer.toHexString(i)); } } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } finally { return buf.toString().substring(8, 24); } } "
" public void run() { Pair p = null; try { while ((p = queue.pop()) != null) { GetMethod get = new GetMethod(p.getRemoteUri()); try { get.setFollowRedirects(true); get.setRequestHeader("Mariner-Application", "prerenderer"); get.setRequestHeader("Mariner-DeviceName", deviceName); int iGetResultCode = httpClient.executeMethod(get); if (iGetResultCode != 200) { throw new IOException("Got response code " + iGetResultCode + " for a request for " + p.getRemoteUri()); } InputStream is = get.getResponseBodyAsStream(); File localFile = new File(deviceFile, p.getLocalUri()); localFile.getParentFile().mkdirs(); OutputStream os = new FileOutputStream(localFile); IOUtils.copy(is, os); os.close(); } finally { get.releaseConnection(); } } } catch (Exception ex) { result = ex; } } "
false
42
10,445,018
19,295,210
" public String MD5(String text) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md; md = MessageDigest.getInstance("MD5"); byte[] md5hash = new byte[32]; md.update(text.getBytes("iso-8859-1"), 0, text.length()); md5hash = md.digest(); return convertToHex(md5hash); } "
" public static String generateHash(String value) { MessageDigest md5 = null; try { md5 = MessageDigest.getInstance("MD5"); md5.reset(); md5.update(value.getBytes()); } catch (NoSuchAlgorithmException e) { log.error("Could not find the requested hash method: " + e.getMessage()); } byte[] result = md5.digest(); StringBuffer hexString = new StringBuffer(); for (int i = 0; i < result.length; i++) { hexString.append(Integer.toHexString(0xFF & result[i])); } return hexString.toString(); } "
true
43
6,988,217
701,471
" public void testQueryForBinary() throws InvalidNodeTypeDefException, ParseException, Exception { JCRNodeSource source = (JCRNodeSource) resolveSource(BASE_URL + "images/photo.png"); assertNotNull(source); assertEquals(false, source.exists()); OutputStream os = source.getOutputStream(); assertNotNull(os); String content = "foo is a bar"; os.write(content.getBytes()); os.flush(); os.close(); QueryResultSource qResult = (QueryResultSource) resolveSource(BASE_URL + "images?/*[contains(local-name(), 'photo.png')]"); assertNotNull(qResult); Collection results = qResult.getChildren(); assertEquals(1, results.size()); Iterator it = results.iterator(); JCRNodeSource rSrc = (JCRNodeSource) it.next(); InputStream rSrcIn = rSrc.getInputStream(); ByteArrayOutputStream actualOut = new ByteArrayOutputStream(); IOUtils.copy(rSrcIn, actualOut); rSrcIn.close(); assertEquals(content, actualOut.toString()); actualOut.close(); rSrc.delete(); } "
" private boolean enregistreToi() { PrintWriter lEcrivain; String laDest = "./img_types/" + sonImage; if (!new File("./img_types").exists()) { new File("./img_types").mkdirs(); } try { FileChannel leFicSource = new FileInputStream(sonFichier).getChannel(); FileChannel leFicDest = new FileOutputStream(laDest).getChannel(); leFicSource.transferTo(0, leFicSource.size(), leFicDest); leFicSource.close(); leFicDest.close(); lEcrivain = new PrintWriter(new FileWriter(new File("bundll/types.jay"), true)); lEcrivain.println(sonNom); lEcrivain.println(sonImage); if (sonOptionRadio1.isSelected()) { lEcrivain.println("0:?"); } if (sonOptionRadio2.isSelected()) { lEcrivain.println("1:" + JOptionPane.showInputDialog(null, "Vous avez choisis de rendre ce terrain difficile � franchir.\nVeuillez en indiquer la raison.", "Demande de pr�cision", JOptionPane.INFORMATION_MESSAGE)); } if (sonOptionRadio3.isSelected()) { lEcrivain.println("2:?"); } lEcrivain.close(); return true; } catch (Exception lException) { return false; } } "
true
44
4,855,600
12,853,333
" public void schema(final Row row, TestResults testResults) throws Exception { String urlString = row.text(1); String schemaBase = null; if (row.cellExists(2)) { schemaBase = row.text(2); } try { StreamSource schemaSource; if (urlString.startsWith(CLASS_PREFIX)) { InputStream schema = XmlValidator.class.getClassLoader().getResourceAsStream(urlString.substring(CLASS_PREFIX.length())); schemaSource = new StreamSource(schema); } else { URL url = new URL(urlString); URLConnection urlConnection = url.openConnection(); urlConnection.connect(); InputStream inputStream = urlConnection.getInputStream(); schemaSource = new StreamSource(inputStream); } SchemaFactory factory = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI); if (schemaBase != null) { DefaultLSResourceResolver resolver = new DefaultLSResourceResolver(schemaBase); factory.setResourceResolver(resolver); } factory.newSchema(new URL(urlString)); Validator validator = factory.newSchema(schemaSource).newValidator(); StreamSource source = new StreamSource(new StringReader(xml)); validator.validate(source); row.pass(testResults); } catch (SAXException e) { Loggers.SERVICE_LOG.warn("schema error", e); throw new FitFailureException(e.getMessage()); } catch (IOException e) { Loggers.SERVICE_LOG.warn("schema error", e); throw new FitFailureException(e.getMessage()); } } "
" public static String getURLContent(String href) throws BuildException { URL url = null; String content; try { URL context = new URL("file:" + System.getProperty("user.dir") + "/"); url = new URL(context, href); InputStream is = url.openStream(); InputStreamReader isr = new InputStreamReader(is); StringBuffer stringBuffer = new StringBuffer(); char[] buffer = new char[1024]; int len; while ((len = isr.read(buffer, 0, 1024)) > 0) stringBuffer.append(buffer, 0, len); content = stringBuffer.toString(); isr.close(); } catch (Exception ex) { throw new BuildException("Cannot get content of URL " + href + ": " + ex); } return content; } "
false
45
1,989,226
11,961,013
" public void actualizar() throws SQLException, ClassNotFoundException, Exception { Connection conn = null; PreparedStatement ms = null; registroActualizado = false; try { conn = ToolsBD.getConn(); conn.setAutoCommit(false); Date fechaSystem = new Date(); DateFormat aaaammdd = new SimpleDateFormat("yyyyMMdd"); int fzafsis = Integer.parseInt(aaaammdd.format(fechaSystem)); DateFormat hhmmss = new SimpleDateFormat("HHmmss"); DateFormat sss = new SimpleDateFormat("S"); String ss = sss.format(fechaSystem); if (ss.length() > 2) { ss = ss.substring(0, 2); } int fzahsis = Integer.parseInt(hhmmss.format(fechaSystem) + ss); ms = conn.prepareStatement(SENTENCIA_UPDATE); if (fechaOficio != null && !fechaOficio.equals("")) { if (fechaOficio.matches("\\d{8}")) { ms.setInt(1, Integer.parseInt(fechaOficio)); } else { int fzafent = 0; try { fechaTest = dateF.parse(fechaOficio); Calendar cal = Calendar.getInstance(); cal.setTime(fechaTest); DateFormat date1 = new SimpleDateFormat("yyyyMMdd"); fzafent = Integer.parseInt(date1.format(fechaTest)); } catch (Exception e) { } ms.setInt(1, fzafent); } } else { ms.setInt(1, 0); } ms.setString(2, descripcion); ms.setInt(3, Integer.parseInt(anoSalida)); ms.setInt(4, Integer.parseInt(oficinaSalida)); ms.setInt(5, Integer.parseInt(numeroSalida)); ms.setString(6, nulo); ms.setString(7, motivosNulo); ms.setString(8, usuarioNulo); if (fechaNulo != null && !fechaNulo.equals("")) { int fzafent = 0; try { fechaTest = dateF.parse(fechaNulo); Calendar cal = Calendar.getInstance(); cal.setTime(fechaTest); DateFormat date1 = new SimpleDateFormat("yyyyMMdd"); fzafent = Integer.parseInt(date1.format(fechaTest)); } catch (Exception e) { } ms.setInt(9, fzafent); } else { ms.setInt(9, 0); } if (fechaEntrada != null && !fechaEntrada.equals("")) { int fzafent = 0; try { fechaTest = dateF.parse(fechaEntrada); Calendar cal = Calendar.getInstance(); cal.setTime(fechaTest); DateFormat date1 = new SimpleDateFormat("yyyyMMdd"); fzafent = Integer.parseInt(date1.format(fechaTest)); } catch (Exception e) { } ms.setInt(10, fzafent); } else { ms.setInt(10, 0); } ms.setString(11, descartadoEntrada); ms.setString(12, usuarioEntrada); ms.setString(13, motivosDescarteEntrada); ms.setInt(14, anoEntrada != null ? Integer.parseInt(anoEntrada) : 0); ms.setInt(15, oficinaEntrada != null ? Integer.parseInt(oficinaEntrada) : 0); ms.setInt(16, numeroEntrada != null ? Integer.parseInt(numeroEntrada) : 0); ms.setInt(17, anoOficio != null ? Integer.parseInt(anoOficio) : 0); ms.setInt(18, oficinaOficio != null ? Integer.parseInt(oficinaOficio) : 0); ms.setInt(19, numeroOficio != null ? Integer.parseInt(numeroOficio) : 0); int afectados = ms.executeUpdate(); if (afectados > 0) { registroActualizado = true; } else { registroActualizado = false; } conn.commit(); } catch (Exception ex) { System.out.println("Error inesperat, no s'ha desat el registre: " + ex.getMessage()); ex.printStackTrace(); registroActualizado = false; errores.put("", "Error inesperat, no s'ha desat el registre" + ": " + ex.getClass() + "->" + ex.getMessage()); try { if (conn != null) conn.rollback(); } catch (SQLException sqle) { throw new RemoteException("S'ha produït un error i no s'han pogut tornar enrere els canvis efectuats", sqle); } throw new RemoteException("Error inesperat, no s'ha actualitzat la taula de gestió dels ofici de remissió.", ex); } finally { ToolsBD.closeConn(conn, ms, null); } } "
" public static Builder fromURL(URL url) { try { InputStream in = null; try { in = url.openStream(); ByteArrayOutputStream baos = new ByteArrayOutputStream(); int read = -1; byte[] buf = new byte[4096]; while ((read = in.read(buf)) >= 0) { if (read > 0) { baos.write(buf, 0, read); } } StreamBuilder b = (StreamBuilder) fromMemory(baos.toByteArray()); try { b.setSystemId(url.toURI().toString()); } catch (URISyntaxException use) { b.setSystemId(url.toString()); } return b; } finally { if (in != null) { in.close(); } } } catch (IOException ex) { throw new XMLUnitException(ex); } } "
false
46
15,596,950
14,782,656
" private static ImageIcon tryLoadImageIconFromResource(String filename, String path, int width, int height) { ImageIcon icon = null; try { URL url = cl.getResource(path + pathSeparator + fixFilename(filename)); if (url != null && url.openStream() != null) { icon = new ImageIcon(url); } } catch (Exception e) { } if (icon == null) { return null; } if ((icon.getIconWidth() == width) && (icon.getIconHeight() == height)) { return icon; } else { return new ImageIcon(icon.getImage().getScaledInstance(width, height, java.awt.Image.SCALE_SMOOTH)); } } "
" private static Long statusSWGCraftTime() { long current = System.currentTimeMillis() / 1000L; if (current < (previousStatusCheck + SWGCraft.STATUS_CHECK_DELAY)) return previousStatusTime; URL url = null; try { synchronized (previousStatusTime) { if (current >= previousStatusCheck + SWGCraft.STATUS_CHECK_DELAY) { url = SWGCraft.getStatusTextURL(); String statusTime = ZReader.read(url.openStream()); previousStatusTime = Long.valueOf(statusTime); previousStatusCheck = current; } return previousStatusTime; } } catch (UnknownHostException e) { SWGCraft.showUnknownHostDialog(url, e); } catch (Throwable e) { SWGAide.printDebug("cmgr", 1, "SWGResourceManager:statusSWGCraftTime:", e.toString()); } return Long.valueOf(0); } "
false
47
249,428
6,166,363
" public boolean onStart() { log("Starting up, this may take a minute..."); gui = new ApeAtollGUI(); gui.setVisible(true); while (waitGUI) { sleep(100); } URLConnection url = null; BufferedReader in = null; BufferedWriter out = null; if (checkUpdates) { try { url = new URL("http://www.voltrex.be/rsbot/VoltrexApeAtollVERSION.txt").openConnection(); in = new BufferedReader(new InputStreamReader(url.getInputStream())); if (Double.parseDouble(in.readLine()) > properties.version()) { if (JOptionPane.showConfirmDialog(null, "Update found. Do you want to update?") == 0) { JOptionPane.showMessageDialog(null, "Please choose 'VoltrexApeAtoll.java' in your scripts/sources folder."); JFileChooser fc = new JFileChooser(); if (fc.showOpenDialog(null) == JFileChooser.APPROVE_OPTION) { url = new URL("http://www.voltrex.be/rsbot/VoltrexApeAtoll.java").openConnection(); in = new BufferedReader(new InputStreamReader(url.getInputStream())); out = new BufferedWriter(new FileWriter(fc.getSelectedFile().getPath())); String inp; while ((inp = in.readLine()) != null) { out.write(inp); out.newLine(); out.flush(); } log("Script successfully downloaded. Please recompile."); return false; } else log("Update canceled"); } else log("Update canceled"); } else log("You have the latest version."); if (in != null) in.close(); if (out != null) out.close(); } catch (IOException e) { log("Problem getting version. Please report this bug!"); } } try { BKG = ImageIO.read(new URL("http://i54.tinypic.com/2egcfaw.jpg")); } catch (final java.io.IOException e) { e.printStackTrace(); } try { final URL cursorURL = new URL("http://imgur.com/i7nMG.png"); final URL cursor80URL = new URL("http://imgur.com/8k9op.png"); normal = ImageIO.read(cursorURL); clicked = ImageIO.read(cursor80URL); } catch (MalformedURLException e) { log.info("Unable to buffer cursor."); } catch (IOException e) { log.info("Unable to open cursor image."); } scriptStartTime = System.currentTimeMillis(); mouse.setSpeed(MouseSpeed); camera.setPitch(true); log("You are using Voltrex Ape Atoll agility course."); return true; } "
" private static byte[] gerarHash(String frase) { try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(frase.getBytes()); return md.digest(); } catch (Exception e) { return null; } } "
false
48
6,751,999
18,761,618
" public static void main(String[] args) throws Exception { TripleDES tdes = new TripleDES(); StreamBlockReader reader = new StreamBlockReader(new FileInputStream("D:\\test.txt")); StreamBlockWriter writer = new StreamBlockWriter(new FileOutputStream("D:\\testTDESENC.txt")); SingleKey key = new SingleKey(new Block(128), ""); key = new SingleKey(new Block("01011101110000101001100111001011101000001110111101001001101101101101100000011101100100110000101100001110000001111101001101001101"), ""); Mode mode = new ECBTripleDESMode(tdes); tdes.encrypt(reader, writer, key, mode); } "
" private FileInputStream getPackageStream(String archivePath) throws IOException, PackageManagerException { final int lastSlashInName = filename.lastIndexOf("/"); final String newFileName = filename.substring(lastSlashInName); File packageFile = new File((new StringBuilder()).append(archivePath).append(newFileName).toString()); if (null != packageFile) return new FileInputStream(packageFile); if (null != packageURL) { final InputStream urlStream = new ConnectToServer(null).getInputStream(packageURL); packageFile = new File((new StringBuilder()).append(getName()).append(".deb").toString()); final OutputStream fileStream = new FileOutputStream(packageFile); final byte buffer[] = new byte[10240]; for (int read = 0; (read = urlStream.read(buffer)) > 0; ) fileStream.write(buffer, 0, read); urlStream.close(); fileStream.close(); return new FileInputStream(packageFile); } else { final String errorMessage = PreferenceStoreHolder.getPreferenceStoreByName("Screen").getPreferenceAsString("package.getPackageStream.packageURLIsNull", "No entry found for package.getPackageStream.packageURLIsNull"); if (pm != null) { pm.addWarning(errorMessage); logger.error(errorMessage); } else logger.error(errorMessage); throw new FileNotFoundException(); } } "
true
49
19,193,813
18,568,751
" public void writeTo(File f) throws IOException { if (state != STATE_OK) throw new IllegalStateException("Upload failed"); if (tempLocation == null) throw new IllegalStateException("File already saved"); if (f.isDirectory()) f = new File(f, filename); FileInputStream fis = new FileInputStream(tempLocation); FileOutputStream fos = new FileOutputStream(f); byte[] buf = new byte[BUFFER_SIZE]; try { int i = 0; while ((i = fis.read(buf)) != -1) fos.write(buf, 0, i); } finally { deleteTemporaryFile(); fis.close(); fos.close(); } } "
" public static Boolean decompress(File source, File destination) { FileOutputStream outputStream; ZipInputStream inputStream; try { outputStream = null; inputStream = new ZipInputStream(new FileInputStream(source)); int read; byte buffer[] = new byte[BUFFER_SIZE]; ZipEntry zipEntry; while ((zipEntry = inputStream.getNextEntry()) != null) { if (zipEntry.isDirectory()) new File(destination, zipEntry.getName()).mkdirs(); else { File fileEntry = new File(destination, zipEntry.getName()); fileEntry.getParentFile().mkdirs(); outputStream = new FileOutputStream(fileEntry); while ((read = inputStream.read(buffer, 0, BUFFER_SIZE)) != -1) { outputStream.write(buffer, 0, read); } outputStream.flush(); outputStream.close(); } } inputStream.close(); } catch (Exception oException) { return false; } return true; } "
true
50
418,257
21,900,384
" public BufferedWriter createOutputStream(String inFile, String outFile) throws IOException { int k_blockSize = 1024; int byteCount; char[] buf = new char[k_blockSize]; File ofp = new File(outFile); ZipOutputStream zos = new ZipOutputStream(new FileOutputStream(ofp)); zos.setMethod(ZipOutputStream.DEFLATED); OutputStreamWriter osw = new OutputStreamWriter(zos, "ISO-8859-1"); BufferedWriter bw = new BufferedWriter(osw); ZipEntry zot = null; File ifp = new File(inFile); ZipInputStream zis = new ZipInputStream(new FileInputStream(ifp)); InputStreamReader isr = new InputStreamReader(zis, "ISO-8859-1"); BufferedReader br = new BufferedReader(isr); ZipEntry zit = null; while ((zit = zis.getNextEntry()) != null) { if (zit.getName().equals("content.xml")) { continue; } zot = new ZipEntry(zit.getName()); zos.putNextEntry(zot); while ((byteCount = br.read(buf, 0, k_blockSize)) >= 0) bw.write(buf, 0, byteCount); bw.flush(); zos.closeEntry(); } zos.putNextEntry(new ZipEntry("content.xml")); bw.flush(); osw = new OutputStreamWriter(zos, "UTF8"); bw = new BufferedWriter(osw); return bw; } "
" @Override protected ActionForward executeAction(ActionMapping mapping, ActionForm form, User user, HttpServletRequest request, HttpServletResponse response) throws Exception { long resourceId = ServletRequestUtils.getLongParameter(request, "resourceId", 0L); String attributeIdentifier = request.getParameter("identifier"); if (resourceId != 0L && StringUtils.hasText(attributeIdentifier)) { try { BinaryAttribute binaryAttribute = resourceManager.readAttribute(resourceId, attributeIdentifier, user); response.addHeader("Content-Disposition", "attachment; filename=\"" + binaryAttribute.getName() + '"'); String contentType = binaryAttribute.getContentType(); if (contentType != null) { if ("application/x-zip-compressed".equalsIgnoreCase(contentType)) { response.setContentType("application/octet-stream"); } else { response.setContentType(contentType); } } else { response.setContentType("application/octet-stream"); } IOUtils.copy(binaryAttribute.getInputStream(), response.getOutputStream()); return null; } catch (DataRetrievalFailureException e) { addGlobalError(request, "errors.notFound"); } catch (Exception e) { addGlobalError(request, e); } } return mapping.getInputForward(); } "
true
51
10,793,825
2,247,987
" public String getRec(String attribute, String url) { String arr[] = new String[3]; String[] subarr = new String[6]; String mdPrefix = ""; String mdPrefixValue = ""; String iden = ""; String idenValue = ""; String s = ""; String arguments = attribute.substring(attribute.indexOf("?") + 1); System.out.println("attributes" + arguments); java.util.StringTokenizer st = new java.util.StringTokenizer(arguments, "&"); int i = 0; int j = 0; int count = 0; int argCount = 0; java.util.Vector v1 = new java.util.Vector(1, 1); java.util.Vector v901 = new java.util.Vector(1, 1); java.util.Vector v902 = new java.util.Vector(1, 1); java.util.Vector v903 = new java.util.Vector(1, 1); java.util.Vector v904 = new java.util.Vector(1, 1); java.util.Vector v905 = new java.util.Vector(1, 1); java.util.Vector v906 = new java.util.Vector(1, 1); java.util.Vector v907 = new java.util.Vector(1, 1); java.util.Vector v908 = new java.util.Vector(1, 1); java.util.Vector v3 = new java.util.Vector(1, 1); java.util.Vector vData = new java.util.Vector(1, 1); java.util.Vector vSet = new java.util.Vector(1, 1); java.util.Vector v856 = new java.util.Vector(1, 1); Resdate dt = new Resdate(); try { while (st.hasMoreElements()) { arr[i] = st.nextElement().toString(); java.util.StringTokenizer subSt = new java.util.StringTokenizer(arr[i], "="); while (subSt.hasMoreElements()) { subarr[j] = subSt.nextElement().toString(); System.out.println(" arga are... " + subarr[j]); j++; } i++; count++; } } catch (Exception e) { e.printStackTrace(); } Namespace oains = Namespace.getNamespace("http://www.openarchives.org/OAI/2.0/"); Element root = new Element("OAI-PMH", oains); Namespace xsi = Namespace.getNamespace("xsi", "http://www.w3.org/2001/XMLSchema-instance"); Attribute schemaLocation = new Attribute("schemaLocation", "http://www.openarchives.org/OAI/2.0/ http://www.openarchives.org/OAI/2.0/OAI-PMH.xsd", xsi); root.setAttribute(schemaLocation); root.addNamespaceDeclaration(xsi); Document doc = new Document(root); Element responseDate = new Element("responseDate", oains); root.addContent(responseDate); responseDate.setText(dt.getDate()); Element request = new Element("request", oains); request.setAttribute("verb", "GetRecord"); int idenCount = 0, mdfCount = 0; for (int k = 2; k < j; k += 2) { System.out.println(" arg key " + subarr[k]); if (subarr[k].equals("metadataPrefix")) { mdPrefix = "metadataPrefix"; mdfCount++; mdPrefixValue = subarr[k + 1]; request.setAttribute(mdPrefix, mdPrefixValue); System.out.println(subarr[k] + "="); System.out.println(mdPrefixValue); argCount++; } else if (subarr[k].equals("identifier")) { iden = "identifier"; idenCount++; idenValue = subarr[k + 1]; request.setAttribute(iden, idenValue); System.out.println(subarr[k] + "="); System.out.println(idenValue); argCount++; } } request.setText(url); root.addContent(request); System.out.println("count" + argCount); if (mdfCount == 1 && idenCount == 1 && (mdPrefixValue.equals("marc21") || mdPrefixValue.equals("oai_dc") || mdPrefixValue.equals("mods"))) { try { v1 = ((ejb.bprocess.OAIPMH.ListGetRecordsHome) ejb.bprocess.util.HomeFactory.getInstance().getRemoteHome("ListGetRecords")).create().getRecord(idenValue, mdPrefixValue); } catch (Exception ex) { ex.printStackTrace(); } if (v1.size() == 0) { System.out.println("vector size is empty"); Errors e1 = new Errors(); Element errorXML = e1.describeError(3, attribute, url, "GetRecord"); root.addContent(errorXML); } else { Element GetRecord = new Element("GetRecord", oains); root.addContent(GetRecord); Element Record = new Element("record", oains); Element metadata = new Element("metadata", oains); Element head = new Element("header", oains); System.out.println("size i s " + v1.size()); for (int v = 0; v < v1.size(); v = v + 13) { vSet = (java.util.Vector) v1.elementAt(v + 1); Element ident = new Element("identifier", oains); ident.setText(idenValue); head.addContent(ident); Element dates = new Element("datestamp", oains); dates.setText(v1.elementAt(v).toString().substring(0, 10)); head.addContent(dates); for (int t = 0; t < vSet.size(); t++) { Element setSpec = new Element("setSpec", oains); System.out.println("set elem" + vSet.elementAt(t).toString()); setSpec.setText(vSet.elementAt(t).toString()); head.addContent(setSpec); } Element marcroot = new Element("record", "marc", "http://www.loc.gov/MARC21/slim"); Namespace xsimarc = Namespace.getNamespace("xsi", "http://www.w3.org/2001/XMLSchema-instance"); marcroot.addNamespaceDeclaration(xsimarc); Attribute schemaLocationmarc = new Attribute("schemaLocation", "http://www.loc.gov/MARC21/slim http://www.loc.gov/standards/marcxml/schema/MARC21slim.xsd", xsimarc); marcroot.setAttribute(schemaLocationmarc); marcroot.setAttribute("type", "Bibliographic"); v3 = (java.util.Vector) v1.elementAt(v + 10); java.util.Vector vL = (java.util.Vector) v3.elementAt(0); org.jdom.Element lead = new org.jdom.Element("leader", "marc", "http://www.loc.gov/MARC21/slim"); lead.setText(vL.elementAt(0).toString()); marcroot.addContent(lead); java.util.Vector vC = (java.util.Vector) v3.elementAt(1); for (int u = 0; u < vC.size(); u = u + 2) { org.jdom.Element ct = new org.jdom.Element("controlfield", "marc", "http://www.loc.gov/MARC21/slim"); ct.setAttribute("tag", vC.elementAt(u).toString()); ct.setText(vC.elementAt(u + 1).toString()); marcroot.addContent(ct); } v901 = (java.util.Vector) v1.elementAt(v + 2); for (int k = 0; k < v901.size(); k++) { org.jdom.Element datafield = new org.jdom.Element("datafield", "marc", "http://www.loc.gov/MARC21/slim"); datafield.setAttribute("tag", "901"); datafield.setAttribute("ind1", "0"); datafield.setAttribute("ind2", "0"); java.util.Vector vecSub = new java.util.Vector(1, 1); vecSub = (java.util.Vector) v901.elementAt(k); System.out.println("in getrec sub "); System.out.println("sub 901 size" + vecSub.size()); for (int k1 = 0; k1 < vecSub.size(); k1 = k1 + 2) { org.jdom.Element subfield = new org.jdom.Element("subfield", "marc", "http://www.loc.gov/MARC21/slim"); subfield.setAttribute("code", vecSub.elementAt(k1).toString()); subfield.setText(vecSub.elementAt(k1 + 1).toString()); datafield.addContent(subfield); } marcroot.addContent(datafield); } v902 = (java.util.Vector) v1.elementAt(v + 3); for (int l = 0; l < v902.size(); l++) { Element datafield1 = new Element("datafield", "marc", "http://www.loc.gov/MARC21/slim"); datafield1.setAttribute("tag", "902"); datafield1.setAttribute("ind1", "0"); datafield1.setAttribute("ind2", "0"); java.util.Vector vecSub1 = new java.util.Vector(1, 1); vecSub1 = (java.util.Vector) v902.elementAt(l); for (int b = 0; b < vecSub1.size(); b = b + 2) { Element subfield = new Element("subfield", "marc", "http://www.loc.gov/MARC21/slim"); subfield.setAttribute("code", vecSub1.elementAt(b).toString()); subfield.setText(vecSub1.elementAt(b + 1).toString()); datafield1.addContent(subfield); } marcroot.addContent(datafield1); } v903 = (java.util.Vector) v1.elementAt(v + 4); Element datafield1 = new Element("datafield", "marc", "http://www.loc.gov/MARC21/slim"); datafield1.setAttribute("tag", "903"); datafield1.setAttribute("ind1", "0"); datafield1.setAttribute("ind2", "0"); for (int l = 0; l < v903.size(); l++) { Element subfield = new Element("subfield", "marc", "http://www.loc.gov/MARC21/slim"); subfield.setAttribute("code", "a"); subfield.setText(v903.elementAt(l).toString()); datafield1.addContent(subfield); } marcroot.addContent(datafield1); v904 = (java.util.Vector) v1.elementAt(v + 5); Element datafield21 = new Element("datafield", "marc", "http://www.loc.gov/MARC21/slim"); datafield21.setAttribute("tag", "904"); datafield21.setAttribute("ind1", "0"); datafield21.setAttribute("ind2", "0"); for (int l = 0; l < v904.size(); l++) { Element subfield = new Element("subfield", "marc", "http://www.loc.gov/MARC21/slim"); subfield.setAttribute("code", "a"); subfield.setText(v904.elementAt(l).toString()); datafield21.addContent(subfield); } marcroot.addContent(datafield21); v905 = (java.util.Vector) v1.elementAt(v + 6); Element datafield31 = new Element("datafield", "marc", "http://www.loc.gov/MARC21/slim"); datafield31.setAttribute("tag", "905"); datafield31.setAttribute("ind1", "0"); datafield31.setAttribute("ind2", "0"); for (int l = 0; l < v905.size(); l++) { Element subfield = new Element("subfield", "marc", "http://www.loc.gov/MARC21/slim"); subfield.setAttribute("code", "a"); subfield.setText(v905.elementAt(l).toString()); datafield31.addContent(subfield); } marcroot.addContent(datafield31); v906 = (java.util.Vector) v1.elementAt(v + 7); Element datafield4 = new Element("datafield", "marc", "http://www.loc.gov/MARC21/slim"); datafield4.setAttribute("tag", "906"); datafield4.setAttribute("ind1", "0"); datafield4.setAttribute("ind2", "0"); for (int l = 0; l < v906.size(); l++) { Element subfield = new Element("subfield", "marc", "http://www.loc.gov/MARC21/slim"); subfield.setAttribute("code", "a"); subfield.setText(v906.elementAt(l).toString()); datafield4.addContent(subfield); } marcroot.addContent(datafield4); v907 = (java.util.Vector) v1.elementAt(v + 8); for (int l = 0; l < v907.size(); l++) { Element datafield5 = new Element("datafield", "marc", "http://www.loc.gov/MARC21/slim"); datafield5.setAttribute("tag", "907"); datafield5.setAttribute("ind1", "0"); datafield5.setAttribute("ind2", "0"); java.util.Vector vecSub1 = new java.util.Vector(1, 1); vecSub1 = (java.util.Vector) v907.elementAt(l); for (int b = 0; b < vecSub1.size(); b = b + 2) { Element subfield = new Element("subfield", "marc", "http://www.loc.gov/MARC21/slim"); subfield.setAttribute("code", vecSub1.elementAt(b).toString()); subfield.setText(vecSub1.elementAt(b + 1).toString()); datafield5.addContent(subfield); } marcroot.addContent(datafield5); } v908 = (java.util.Vector) v1.elementAt(v + 9); for (int l = 0; l < v908.size(); l++) { Element datafield6 = new Element("datafield", "marc", "http://www.loc.gov/MARC21/slim"); datafield6.setAttribute("tag", "908"); datafield6.setAttribute("ind1", "0"); datafield6.setAttribute("ind2", "0"); java.util.Vector vecSub1 = new java.util.Vector(1, 1); vecSub1 = (java.util.Vector) v908.elementAt(l); for (int b = 0; b < vecSub1.size(); b = b + 2) { Element subfield = new Element("subfield", "marc", "http://www.loc.gov/MARC21/slim"); subfield.setAttribute("code", vecSub1.elementAt(b).toString()); subfield.setText(vecSub1.elementAt(b + 1).toString()); datafield6.addContent(subfield); } marcroot.addContent(datafield6); } vData = (java.util.Vector) v1.elementAt(v + 11); for (int m = 0; m < vData.size(); m = m + 2) { Element datafield2 = new Element("datafield", "marc", "http://www.loc.gov/MARC21/slim"); datafield2.setAttribute("tag", vData.elementAt(m).toString()); datafield2.setAttribute("ind1", "0"); datafield2.setAttribute("ind2", "0"); java.util.Vector vSub = new java.util.Vector(1, 1); vSub = (java.util.Vector) vData.elementAt(m + 1); for (int n = 0; n < vSub.size(); n = n + 2) { Element subfield = new Element("subfield", "marc", "http://www.loc.gov/MARC21/slim"); subfield.setAttribute("code", vSub.elementAt(n).toString()); subfield.setText(vSub.elementAt(n + 1).toString()); datafield2.addContent(subfield); } marcroot.addContent(datafield2); } v856 = (java.util.Vector) v1.elementAt(v + 12); for (int l = 0; l < v856.size(); l = l + 2) { Element datafield3 = new Element("datafield", "marc", "http://www.loc.gov/MARC21/slim"); datafield3.setAttribute("tag", "856"); datafield3.setAttribute("ind1", "0"); datafield3.setAttribute("ind2", "0"); Element subfield1 = new Element("subfield", "marc", "http://www.loc.gov/MARC21/slim"); subfield1.setAttribute("code", v856.elementAt(l).toString()); subfield1.setText(v856.elementAt(l + 1).toString()); datafield3.addContent(subfield1); marcroot.addContent(datafield3); } if (mdPrefixValue.equals("oai_dc")) { try { Transformer transformer = TransformerFactory.newInstance().newTransformer(new StreamSource(ejb.bprocess.util.NewGenLibRoot.getRoot() + java.io.File.separator + "StyleSheets" + java.io.File.separator + "MARC21slim2OAIDC.xsl")); Document docmarc = new Document(marcroot); JDOMSource in = new JDOMSource(docmarc); JDOMResult out = new JDOMResult(); transformer.transform(in, out); Document doc2 = out.getDocument(); org.jdom.output.XMLOutputter out1 = new org.jdom.output.XMLOutputter(); out1.setTextTrim(true); out1.setIndent(" "); out1.setNewlines(true); String s1 = out1.outputString(doc2); System.out.println("dublin core is" + s1); Element dcroot1 = doc2.getRootElement(); Namespace xsi1 = Namespace.getNamespace("xsi", "http://www.w3.org/2001/XMLSchema-instance"); Namespace oainsdc = Namespace.getNamespace("http://www.openarchives.org/OAI/2.0/oai_dc/"); Element dcroot = new Element("dc", "oai_dc", "http://www.openarchives.org/OAI/2.0/oai_dc/"); Namespace dcns = Namespace.getNamespace("dc", "http://purl.org/dc/elements/1.1/"); dcroot.addNamespaceDeclaration(dcns); dcroot.addNamespaceDeclaration(xsi1); Attribute schemaLocationdc = new Attribute("schemaLocation", "http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd", xsi1); dcroot.setAttribute(schemaLocationdc); java.util.List dcList = doc2.getRootElement().getChildren(); for (int g = 0; g < dcList.size(); g++) { Element dcElem1 = (org.jdom.Element) dcList.get(g); Element dcElem = new Element(dcElem1.getName(), "dc", "http://purl.org/dc/elements/1.1/"); dcElem.setText(dcElem1.getText()); dcroot.addContent(dcElem); } metadata.addContent(dcroot); } catch (TransformerException e) { e.printStackTrace(); } } else if (mdPrefixValue.equals("mods")) { try { java.util.Properties systemSettings = System.getProperties(); java.util.prefs.Preferences prefs = java.util.prefs.Preferences.systemRoot(); if (prefs.getBoolean("useproxy", false)) { systemSettings.put("proxySet", "true"); systemSettings.put("proxyHost", prefs.get("proxyservername", "")); systemSettings.put("proxyPort", prefs.get("proxyport", "")); systemSettings.put("http.proxyHost", prefs.get("proxyservername", "")); systemSettings.put("http.proxyPort", prefs.get("proxyport", "")); } String urltext = ""; Transformer transformer = null; urltext = "http://www.loc.gov/standards/mods/v3/MARC21slim2MODS3.xsl"; java.net.URL url1 = new java.net.URL(urltext); java.net.URLConnection urlconn = url1.openConnection(); urlconn.setDoInput(true); transformer = TransformerFactory.newInstance().newTransformer(new StreamSource(urlconn.getInputStream())); Document docmarc = new Document(marcroot); JDOMSource in = new JDOMSource(docmarc); JDOMResult out = new JDOMResult(); transformer.transform(in, out); Document doc2 = out.getDocument(); org.jdom.output.XMLOutputter out1 = new org.jdom.output.XMLOutputter(); out1.setTextTrim(true); out1.setIndent(" "); out1.setNewlines(true); String s1 = out1.outputString(doc2); Namespace xsi1 = Namespace.getNamespace("xlink", "http://www.w3.org/1999/xlink"); Namespace oainsdc = Namespace.getNamespace("http://www.openarchives.org/OAI/2.0/oai_dc/"); Element mroot = new Element("mods", "http://www.loc.gov/mods/v3"); Namespace dcns = Namespace.getNamespace("http://www.loc.gov/mods/v3"); mroot.addNamespaceDeclaration(xsi1); Attribute schemaLocationdc = new Attribute("schemaLocation", "http://www.loc.gov/mods/v3 http://www.loc.gov/standards/mods/v3/mods-3-0.xsd", xsi1); mroot.setAttribute(schemaLocationdc); java.util.List dcList = doc2.getRootElement().getChildren(); for (int g = 0; g < dcList.size(); g++) { Element mElem1 = (org.jdom.Element) dcList.get(g); Element mElem = new Element(mElem1.getName(), "http://www.loc.gov/mods/v3"); if (mElem1.hasChildren()) { java.util.List mList1 = mElem1.getChildren(); for (int f = 0; f < mList1.size(); f++) { Element mElem2 = (org.jdom.Element) mList1.get(f); Element mElem3 = new Element(mElem2.getName(), "http://www.loc.gov/mods/v3"); if (mElem2.hasChildren()) { java.util.List mList2 = mElem2.getChildren(); for (int h = 0; h < mList2.size(); h++) { Element mElem4 = (org.jdom.Element) mList1.get(h); Element mElem5 = new Element(mElem4.getName(), "http://www.loc.gov/mods/v3"); mElem5.setText(mElem4.getText()); mElem3.addContent(mElem5); } } if (mElem2.hasChildren() == false) { mElem3.setText(mElem2.getText()); } mElem.addContent(mElem3); } } if (mElem1.hasChildren() == false) { mElem.setText(mElem1.getText()); } mroot.addContent(mElem); } metadata.addContent(mroot); } catch (Exception e) { e.printStackTrace(); } } if (mdPrefixValue.equals("marc21")) { metadata.addContent(marcroot); } else if (mdPrefixValue.equals("oai_dc")) { } } Record.addContent(head); Record.addContent(metadata); GetRecord.addContent(Record); } } else if (argCount <= 2) { if (idenCount < 1 && mdfCount < 1) { Errors e1 = new Errors(); Element errorXML = e1.describeError(2, "missing arguments: identifier,metadataprefix", url, "GetRecord"); root.addContent(errorXML); } else if (idenCount < 1) { Errors e1 = new Errors(); Element errorXML = e1.describeError(2, "missing argument: identifier", url, "GetRecord"); root.addContent(errorXML); } else if (mdfCount < 1) { Errors e1 = new Errors(); Element errorXML = e1.describeError(2, "missing argument: metadataprefix", url, "GetRecord"); root.addContent(errorXML); } else if (argCount > 2) { Errors e1 = new Errors(); Element errorXML = e1.describeError(2, "more number of arguments", url, "GetRecord"); root.addContent(errorXML); } else { System.out.println("no format"); Errors e1 = new Errors(); Element errorXML = e1.describeError(6, "", url, "GetRecord"); root.addContent(errorXML); } } XMLOutputter out = new XMLOutputter(); out.setIndent(" "); out.setNewlines(true); s = out.outputString(doc); return s; } "
" public static void main(String argv[]) { Matrix A, B, C, Z, O, I, R, S, X, SUB, M, T, SQ, DEF, SOL; int errorCount = 0; int warningCount = 0; double tmp, s; double[] columnwise = { 1., 2., 3., 4., 5., 6., 7., 8., 9., 10., 11., 12. }; double[] rowwise = { 1., 4., 7., 10., 2., 5., 8., 11., 3., 6., 9., 12. }; double[][] avals = { { 1., 4., 7., 10. }, { 2., 5., 8., 11. }, { 3., 6., 9., 12. } }; double[][] rankdef = avals; double[][] tvals = { { 1., 2., 3. }, { 4., 5., 6. }, { 7., 8., 9. }, { 10., 11., 12. } }; double[][] subavals = { { 5., 8., 11. }, { 6., 9., 12. } }; double[][] rvals = { { 1., 4., 7. }, { 2., 5., 8., 11. }, { 3., 6., 9., 12. } }; double[][] pvals = { { 4., 1., 1. }, { 1., 2., 3. }, { 1., 3., 6. } }; double[][] ivals = { { 1., 0., 0., 0. }, { 0., 1., 0., 0. }, { 0., 0., 1., 0. } }; double[][] evals = { { 0., 1., 0., 0. }, { 1., 0., 2.e-7, 0. }, { 0., -2.e-7, 0., 1. }, { 0., 0., 1., 0. } }; double[][] square = { { 166., 188., 210. }, { 188., 214., 240. }, { 210., 240., 270. } }; double[][] sqSolution = { { 13. }, { 15. } }; double[][] condmat = { { 1., 3. }, { 7., 9. } }; int rows = 3, cols = 4; int invalidld = 5; int raggedr = 0; int raggedc = 4; int validld = 3; int nonconformld = 4; int ib = 1, ie = 2, jb = 1, je = 3; int[] rowindexset = { 1, 2 }; int[] badrowindexset = { 1, 3 }; int[] columnindexset = { 1, 2, 3 }; int[] badcolumnindexset = { 1, 2, 4 }; double columnsummax = 33.; double rowsummax = 30.; double sumofdiagonals = 15; double sumofsquares = 650; print("\nTesting constructors and constructor-like methods...\n"); try { A = new Matrix(columnwise, invalidld); errorCount = try_failure(errorCount, "Catch invalid length in packed constructor... ", "exception not thrown for invalid input"); } catch (IllegalArgumentException e) { try_success("Catch invalid length in packed constructor... ", e.getMessage()); } try { A = new Matrix(rvals); tmp = A.get(raggedr, raggedc); } catch (IllegalArgumentException e) { try_success("Catch ragged input to default constructor... ", e.getMessage()); } catch (java.lang.ArrayIndexOutOfBoundsException e) { errorCount = try_failure(errorCount, "Catch ragged input to constructor... ", "exception not thrown in construction...ArrayIndexOutOfBoundsException thrown later"); } try { A = Matrix.constructWithCopy(rvals); tmp = A.get(raggedr, raggedc); } catch (IllegalArgumentException e) { try_success("Catch ragged input to constructWithCopy... ", e.getMessage()); } catch (java.lang.ArrayIndexOutOfBoundsException e) { errorCount = try_failure(errorCount, "Catch ragged input to constructWithCopy... ", "exception not thrown in construction...ArrayIndexOutOfBoundsException thrown later"); } A = new Matrix(columnwise, validld); B = new Matrix(avals); tmp = B.get(0, 0); avals[0][0] = 0.0; C = B.minus(A); avals[0][0] = tmp; B = Matrix.constructWithCopy(avals); tmp = B.get(0, 0); avals[0][0] = 0.0; if ((tmp - B.get(0, 0)) != 0.0) { errorCount = try_failure(errorCount, "constructWithCopy... ", "copy not effected... data visible outside"); } else { try_success("constructWithCopy... ", ""); } avals[0][0] = columnwise[0]; I = new Matrix(ivals); try { check(I, Matrix.identity(3, 4)); try_success("identity... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "identity... ", "identity Matrix not successfully created"); } print("\nTesting access methods...\n"); B = new Matrix(avals); if (B.getRowDimension() != rows) { errorCount = try_failure(errorCount, "getRowDimension... ", ""); } else { try_success("getRowDimension... ", ""); } if (B.getColumnDimension() != cols) { errorCount = try_failure(errorCount, "getColumnDimension... ", ""); } else { try_success("getColumnDimension... ", ""); } B = new Matrix(avals); double[][] barray = B.getArray(); if (barray != avals) { errorCount = try_failure(errorCount, "getArray... ", ""); } else { try_success("getArray... ", ""); } barray = B.getArrayCopy(); if (barray == avals) { errorCount = try_failure(errorCount, "getArrayCopy... ", "data not (deep) copied"); } try { check(barray, avals); try_success("getArrayCopy... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "getArrayCopy... ", "data not successfully (deep) copied"); } double[] bpacked = B.getColumnPackedCopy(); try { check(bpacked, columnwise); try_success("getColumnPackedCopy... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "getColumnPackedCopy... ", "data not successfully (deep) copied by columns"); } bpacked = B.getRowPackedCopy(); try { check(bpacked, rowwise); try_success("getRowPackedCopy... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "getRowPackedCopy... ", "data not successfully (deep) copied by rows"); } try { tmp = B.get(B.getRowDimension(), B.getColumnDimension() - 1); errorCount = try_failure(errorCount, "get(int,int)... ", "OutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { tmp = B.get(B.getRowDimension() - 1, B.getColumnDimension()); errorCount = try_failure(errorCount, "get(int,int)... ", "OutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("get(int,int)... OutofBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "get(int,int)... ", "OutOfBoundsException expected but not thrown"); } try { if (B.get(B.getRowDimension() - 1, B.getColumnDimension() - 1) != avals[B.getRowDimension() - 1][B.getColumnDimension() - 1]) { errorCount = try_failure(errorCount, "get(int,int)... ", "Matrix entry (i,j) not successfully retreived"); } else { try_success("get(int,int)... ", ""); } } catch (java.lang.ArrayIndexOutOfBoundsException e) { errorCount = try_failure(errorCount, "get(int,int)... ", "Unexpected ArrayIndexOutOfBoundsException"); } SUB = new Matrix(subavals); try { M = B.getMatrix(ib, ie + B.getRowDimension() + 1, jb, je); errorCount = try_failure(errorCount, "getMatrix(int,int,int,int)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { M = B.getMatrix(ib, ie, jb, je + B.getColumnDimension() + 1); errorCount = try_failure(errorCount, "getMatrix(int,int,int,int)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("getMatrix(int,int,int,int)... ArrayIndexOutOfBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "getMatrix(int,int,int,int)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } try { M = B.getMatrix(ib, ie, jb, je); try { check(SUB, M); try_success("getMatrix(int,int,int,int)... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "getMatrix(int,int,int,int)... ", "submatrix not successfully retreived"); } } catch (java.lang.ArrayIndexOutOfBoundsException e) { errorCount = try_failure(errorCount, "getMatrix(int,int,int,int)... ", "Unexpected ArrayIndexOutOfBoundsException"); } try { M = B.getMatrix(ib, ie, badcolumnindexset); errorCount = try_failure(errorCount, "getMatrix(int,int,int[])... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { M = B.getMatrix(ib, ie + B.getRowDimension() + 1, columnindexset); errorCount = try_failure(errorCount, "getMatrix(int,int,int[])... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("getMatrix(int,int,int[])... ArrayIndexOutOfBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "getMatrix(int,int,int[])... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } try { M = B.getMatrix(ib, ie, columnindexset); try { check(SUB, M); try_success("getMatrix(int,int,int[])... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "getMatrix(int,int,int[])... ", "submatrix not successfully retreived"); } } catch (java.lang.ArrayIndexOutOfBoundsException e) { errorCount = try_failure(errorCount, "getMatrix(int,int,int[])... ", "Unexpected ArrayIndexOutOfBoundsException"); } try { M = B.getMatrix(badrowindexset, jb, je); errorCount = try_failure(errorCount, "getMatrix(int[],int,int)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { M = B.getMatrix(rowindexset, jb, je + B.getColumnDimension() + 1); errorCount = try_failure(errorCount, "getMatrix(int[],int,int)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("getMatrix(int[],int,int)... ArrayIndexOutOfBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "getMatrix(int[],int,int)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } try { M = B.getMatrix(rowindexset, jb, je); try { check(SUB, M); try_success("getMatrix(int[],int,int)... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "getMatrix(int[],int,int)... ", "submatrix not successfully retreived"); } } catch (java.lang.ArrayIndexOutOfBoundsException e) { errorCount = try_failure(errorCount, "getMatrix(int[],int,int)... ", "Unexpected ArrayIndexOutOfBoundsException"); } try { M = B.getMatrix(badrowindexset, columnindexset); errorCount = try_failure(errorCount, "getMatrix(int[],int[])... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { M = B.getMatrix(rowindexset, badcolumnindexset); errorCount = try_failure(errorCount, "getMatrix(int[],int[])... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("getMatrix(int[],int[])... ArrayIndexOutOfBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "getMatrix(int[],int[])... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } try { M = B.getMatrix(rowindexset, columnindexset); try { check(SUB, M); try_success("getMatrix(int[],int[])... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "getMatrix(int[],int[])... ", "submatrix not successfully retreived"); } } catch (java.lang.ArrayIndexOutOfBoundsException e) { errorCount = try_failure(errorCount, "getMatrix(int[],int[])... ", "Unexpected ArrayIndexOutOfBoundsException"); } try { B.set(B.getRowDimension(), B.getColumnDimension() - 1, 0.); errorCount = try_failure(errorCount, "set(int,int,double)... ", "OutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { B.set(B.getRowDimension() - 1, B.getColumnDimension(), 0.); errorCount = try_failure(errorCount, "set(int,int,double)... ", "OutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("set(int,int,double)... OutofBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "set(int,int,double)... ", "OutOfBoundsException expected but not thrown"); } try { B.set(ib, jb, 0.); tmp = B.get(ib, jb); try { check(tmp, 0.); try_success("set(int,int,double)... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "set(int,int,double)... ", "Matrix element not successfully set"); } } catch (java.lang.ArrayIndexOutOfBoundsException e1) { errorCount = try_failure(errorCount, "set(int,int,double)... ", "Unexpected ArrayIndexOutOfBoundsException"); } M = new Matrix(2, 3, 0.); try { B.setMatrix(ib, ie + B.getRowDimension() + 1, jb, je, M); errorCount = try_failure(errorCount, "setMatrix(int,int,int,int,Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { B.setMatrix(ib, ie, jb, je + B.getColumnDimension() + 1, M); errorCount = try_failure(errorCount, "setMatrix(int,int,int,int,Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("setMatrix(int,int,int,int,Matrix)... ArrayIndexOutOfBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "setMatrix(int,int,int,int,Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } try { B.setMatrix(ib, ie, jb, je, M); try { check(M.minus(B.getMatrix(ib, ie, jb, je)), M); try_success("setMatrix(int,int,int,int,Matrix)... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "setMatrix(int,int,int,int,Matrix)... ", "submatrix not successfully set"); } B.setMatrix(ib, ie, jb, je, SUB); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { errorCount = try_failure(errorCount, "setMatrix(int,int,int,int,Matrix)... ", "Unexpected ArrayIndexOutOfBoundsException"); } try { B.setMatrix(ib, ie + B.getRowDimension() + 1, columnindexset, M); errorCount = try_failure(errorCount, "setMatrix(int,int,int[],Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { B.setMatrix(ib, ie, badcolumnindexset, M); errorCount = try_failure(errorCount, "setMatrix(int,int,int[],Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("setMatrix(int,int,int[],Matrix)... ArrayIndexOutOfBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "setMatrix(int,int,int[],Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } try { B.setMatrix(ib, ie, columnindexset, M); try { check(M.minus(B.getMatrix(ib, ie, columnindexset)), M); try_success("setMatrix(int,int,int[],Matrix)... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "setMatrix(int,int,int[],Matrix)... ", "submatrix not successfully set"); } B.setMatrix(ib, ie, jb, je, SUB); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { errorCount = try_failure(errorCount, "setMatrix(int,int,int[],Matrix)... ", "Unexpected ArrayIndexOutOfBoundsException"); } try { B.setMatrix(rowindexset, jb, je + B.getColumnDimension() + 1, M); errorCount = try_failure(errorCount, "setMatrix(int[],int,int,Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { B.setMatrix(badrowindexset, jb, je, M); errorCount = try_failure(errorCount, "setMatrix(int[],int,int,Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("setMatrix(int[],int,int,Matrix)... ArrayIndexOutOfBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "setMatrix(int[],int,int,Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } try { B.setMatrix(rowindexset, jb, je, M); try { check(M.minus(B.getMatrix(rowindexset, jb, je)), M); try_success("setMatrix(int[],int,int,Matrix)... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "setMatrix(int[],int,int,Matrix)... ", "submatrix not successfully set"); } B.setMatrix(ib, ie, jb, je, SUB); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { errorCount = try_failure(errorCount, "setMatrix(int[],int,int,Matrix)... ", "Unexpected ArrayIndexOutOfBoundsException"); } try { B.setMatrix(rowindexset, badcolumnindexset, M); errorCount = try_failure(errorCount, "setMatrix(int[],int[],Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e) { try { B.setMatrix(badrowindexset, columnindexset, M); errorCount = try_failure(errorCount, "setMatrix(int[],int[],Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } catch (java.lang.ArrayIndexOutOfBoundsException e1) { try_success("setMatrix(int[],int[],Matrix)... ArrayIndexOutOfBoundsException... ", ""); } } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "setMatrix(int[],int[],Matrix)... ", "ArrayIndexOutOfBoundsException expected but not thrown"); } try { B.setMatrix(rowindexset, columnindexset, M); try { check(M.minus(B.getMatrix(rowindexset, columnindexset)), M); try_success("setMatrix(int[],int[],Matrix)... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "setMatrix(int[],int[],Matrix)... ", "submatrix not successfully set"); } } catch (java.lang.ArrayIndexOutOfBoundsException e1) { errorCount = try_failure(errorCount, "setMatrix(int[],int[],Matrix)... ", "Unexpected ArrayIndexOutOfBoundsException"); } print("\nTesting array-like methods...\n"); S = new Matrix(columnwise, nonconformld); R = Matrix.random(A.getRowDimension(), A.getColumnDimension()); A = R; try { S = A.minus(S); errorCount = try_failure(errorCount, "minus conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("minus conformance check... ", ""); } if (A.minus(R).norm1() != 0.) { errorCount = try_failure(errorCount, "minus... ", "(difference of identical Matrices is nonzero,\nSubsequent use of minus should be suspect)"); } else { try_success("minus... ", ""); } A = R.copy(); A.minusEquals(R); Z = new Matrix(A.getRowDimension(), A.getColumnDimension()); try { A.minusEquals(S); errorCount = try_failure(errorCount, "minusEquals conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("minusEquals conformance check... ", ""); } if (A.minus(Z).norm1() != 0.) { errorCount = try_failure(errorCount, "minusEquals... ", "(difference of identical Matrices is nonzero,\nSubsequent use of minus should be suspect)"); } else { try_success("minusEquals... ", ""); } A = R.copy(); B = Matrix.random(A.getRowDimension(), A.getColumnDimension()); C = A.minus(B); try { S = A.plus(S); errorCount = try_failure(errorCount, "plus conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("plus conformance check... ", ""); } try { check(C.plus(B), A); try_success("plus... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "plus... ", "(C = A - B, but C + B != A)"); } C = A.minus(B); C.plusEquals(B); try { A.plusEquals(S); errorCount = try_failure(errorCount, "plusEquals conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("plusEquals conformance check... ", ""); } try { check(C, A); try_success("plusEquals... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "plusEquals... ", "(C = A - B, but C = C + B != A)"); } A = R.uminus(); try { check(A.plus(R), Z); try_success("uminus... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "uminus... ", "(-A + A != zeros)"); } A = R.copy(); O = new Matrix(A.getRowDimension(), A.getColumnDimension(), 1.0); C = A.arrayLeftDivide(R); try { S = A.arrayLeftDivide(S); errorCount = try_failure(errorCount, "arrayLeftDivide conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("arrayLeftDivide conformance check... ", ""); } try { check(C, O); try_success("arrayLeftDivide... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "arrayLeftDivide... ", "(M.\\M != ones)"); } try { A.arrayLeftDivideEquals(S); errorCount = try_failure(errorCount, "arrayLeftDivideEquals conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("arrayLeftDivideEquals conformance check... ", ""); } A.arrayLeftDivideEquals(R); try { check(A, O); try_success("arrayLeftDivideEquals... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "arrayLeftDivideEquals... ", "(M.\\M != ones)"); } A = R.copy(); try { A.arrayRightDivide(S); errorCount = try_failure(errorCount, "arrayRightDivide conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("arrayRightDivide conformance check... ", ""); } C = A.arrayRightDivide(R); try { check(C, O); try_success("arrayRightDivide... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "arrayRightDivide... ", "(M./M != ones)"); } try { A.arrayRightDivideEquals(S); errorCount = try_failure(errorCount, "arrayRightDivideEquals conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("arrayRightDivideEquals conformance check... ", ""); } A.arrayRightDivideEquals(R); try { check(A, O); try_success("arrayRightDivideEquals... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "arrayRightDivideEquals... ", "(M./M != ones)"); } A = R.copy(); B = Matrix.random(A.getRowDimension(), A.getColumnDimension()); try { S = A.arrayTimes(S); errorCount = try_failure(errorCount, "arrayTimes conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("arrayTimes conformance check... ", ""); } C = A.arrayTimes(B); try { check(C.arrayRightDivideEquals(B), A); try_success("arrayTimes... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "arrayTimes... ", "(A = R, C = A.*B, but C./B != A)"); } try { A.arrayTimesEquals(S); errorCount = try_failure(errorCount, "arrayTimesEquals conformance check... ", "nonconformance not raised"); } catch (IllegalArgumentException e) { try_success("arrayTimesEquals conformance check... ", ""); } A.arrayTimesEquals(B); try { check(A.arrayRightDivideEquals(B), R); try_success("arrayTimesEquals... ", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "arrayTimesEquals... ", "(A = R, A = A.*B, but A./B != R)"); } print("\nTesting I/O methods...\n"); try { DecimalFormat fmt = new DecimalFormat("0.0000E00"); fmt.setDecimalFormatSymbols(new DecimalFormatSymbols(Locale.US)); PrintWriter FILE = new PrintWriter(new FileOutputStream("JamaTestMatrix.out")); A.print(FILE, fmt, 10); FILE.close(); R = Matrix.read(new BufferedReader(new FileReader("JamaTestMatrix.out"))); if (A.minus(R).norm1() < .001) { try_success("print()/read()...", ""); } else { errorCount = try_failure(errorCount, "print()/read()...", "Matrix read from file does not match Matrix printed to file"); } } catch (java.io.IOException ioe) { warningCount = try_warning(warningCount, "print()/read()...", "unexpected I/O error, unable to run print/read test; check write permission in current directory and retry"); } catch (Exception e) { try { e.printStackTrace(System.out); warningCount = try_warning(warningCount, "print()/read()...", "Formatting error... will try JDK1.1 reformulation..."); DecimalFormat fmt = new DecimalFormat("0.0000"); PrintWriter FILE = new PrintWriter(new FileOutputStream("JamaTestMatrix.out")); A.print(FILE, fmt, 10); FILE.close(); R = Matrix.read(new BufferedReader(new FileReader("JamaTestMatrix.out"))); if (A.minus(R).norm1() < .001) { try_success("print()/read()...", ""); } else { errorCount = try_failure(errorCount, "print()/read() (2nd attempt) ...", "Matrix read from file does not match Matrix printed to file"); } } catch (java.io.IOException ioe) { warningCount = try_warning(warningCount, "print()/read()...", "unexpected I/O error, unable to run print/read test; check write permission in current directory and retry"); } } R = Matrix.random(A.getRowDimension(), A.getColumnDimension()); String tmpname = "TMPMATRIX.serial"; try { ObjectOutputStream out = new ObjectOutputStream(new FileOutputStream(tmpname)); out.writeObject(R); ObjectInputStream sin = new ObjectInputStream(new FileInputStream(tmpname)); A = (Matrix) sin.readObject(); try { check(A, R); try_success("writeObject(Matrix)/readObject(Matrix)...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "writeObject(Matrix)/readObject(Matrix)...", "Matrix not serialized correctly"); } } catch (java.io.IOException ioe) { warningCount = try_warning(warningCount, "writeObject()/readObject()...", "unexpected I/O error, unable to run serialization test; check write permission in current directory and retry"); } catch (Exception e) { errorCount = try_failure(errorCount, "writeObject(Matrix)/readObject(Matrix)...", "unexpected error in serialization test"); } print("\nTesting linear algebra methods...\n"); A = new Matrix(columnwise, 3); T = new Matrix(tvals); T = A.transpose(); try { check(A.transpose(), T); try_success("transpose...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "transpose()...", "transpose unsuccessful"); } A.transpose(); try { check(A.norm1(), columnsummax); try_success("norm1...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "norm1()...", "incorrect norm calculation"); } try { check(A.normInf(), rowsummax); try_success("normInf()...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "normInf()...", "incorrect norm calculation"); } try { check(A.normF(), Math.sqrt(sumofsquares)); try_success("normF...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "normF()...", "incorrect norm calculation"); } try { check(A.trace(), sumofdiagonals); try_success("trace()...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "trace()...", "incorrect trace calculation"); } try { check(A.getMatrix(0, A.getRowDimension() - 1, 0, A.getRowDimension() - 1).det(), 0.); try_success("det()...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "det()...", "incorrect determinant calculation"); } SQ = new Matrix(square); try { check(A.times(A.transpose()), SQ); try_success("times(Matrix)...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "times(Matrix)...", "incorrect Matrix-Matrix product calculation"); } try { check(A.times(0.), Z); try_success("times(double)...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "times(double)...", "incorrect Matrix-scalar product calculation"); } A = new Matrix(columnwise, 4); QRDecomposition QR = A.qr(); R = QR.getR(); try { check(A, QR.getQ().times(R)); try_success("QRDecomposition...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "QRDecomposition...", "incorrect QR decomposition calculation"); } SingularValueDecomposition SVD = A.svd(); try { check(A, SVD.getU().times(SVD.getS().times(SVD.getV().transpose()))); try_success("SingularValueDecomposition...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "SingularValueDecomposition...", "incorrect singular value decomposition calculation"); } DEF = new Matrix(rankdef); try { check(DEF.rank(), Math.min(DEF.getRowDimension(), DEF.getColumnDimension()) - 1); try_success("rank()...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "rank()...", "incorrect rank calculation"); } B = new Matrix(condmat); SVD = B.svd(); double[] singularvalues = SVD.getSingularValues(); try { check(B.cond(), singularvalues[0] / singularvalues[Math.min(B.getRowDimension(), B.getColumnDimension()) - 1]); try_success("cond()...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "cond()...", "incorrect condition number calculation"); } int n = A.getColumnDimension(); A = A.getMatrix(0, n - 1, 0, n - 1); A.set(0, 0, 0.); LUDecomposition LU = A.lu(); try { check(A.getMatrix(LU.getPivot(), 0, n - 1), LU.getL().times(LU.getU())); try_success("LUDecomposition...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "LUDecomposition...", "incorrect LU decomposition calculation"); } X = A.inverse(); try { check(A.times(X), Matrix.identity(3, 3)); try_success("inverse()...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "inverse()...", "incorrect inverse calculation"); } O = new Matrix(SUB.getRowDimension(), 1, 1.0); SOL = new Matrix(sqSolution); SQ = SUB.getMatrix(0, SUB.getRowDimension() - 1, 0, SUB.getRowDimension() - 1); try { check(SQ.solve(SOL), O); try_success("solve()...", ""); } catch (java.lang.IllegalArgumentException e1) { errorCount = try_failure(errorCount, "solve()...", e1.getMessage()); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "solve()...", e.getMessage()); } A = new Matrix(pvals); CholeskyDecomposition Chol = A.chol(); Matrix L = Chol.getL(); try { check(A, L.times(L.transpose())); try_success("CholeskyDecomposition...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "CholeskyDecomposition...", "incorrect Cholesky decomposition calculation"); } X = Chol.solve(Matrix.identity(3, 3)); try { check(A.times(X), Matrix.identity(3, 3)); try_success("CholeskyDecomposition solve()...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "CholeskyDecomposition solve()...", "incorrect Choleskydecomposition solve calculation"); } EigenvalueDecomposition Eig = A.eig(); Matrix D = Eig.getD(); Matrix V = Eig.getV(); try { check(A.times(V), V.times(D)); try_success("EigenvalueDecomposition (symmetric)...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "EigenvalueDecomposition (symmetric)...", "incorrect symmetric Eigenvalue decomposition calculation"); } A = new Matrix(evals); Eig = A.eig(); D = Eig.getD(); V = Eig.getV(); try { check(A.times(V), V.times(D)); try_success("EigenvalueDecomposition (nonsymmetric)...", ""); } catch (java.lang.RuntimeException e) { errorCount = try_failure(errorCount, "EigenvalueDecomposition (nonsymmetric)...", "incorrect nonsymmetric Eigenvalue decomposition calculation"); } print("\nTestMatrix completed.\n"); print("Total errors reported: " + Integer.toString(errorCount) + "\n"); print("Total warnings reported: " + Integer.toString(warningCount) + "\n"); } "
false
52
3,262,458
8,452,564
" @Override public void run() { while (run) { try { URL url = new URL("http://" + server.getIp() + "/" + tomcat.getName() + "/ui/pva/version.jsp?RT=" + System.currentTimeMillis()); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream(), Charset.forName("UTF-8"))); String inputLine; while ((inputLine = in.readLine()) != null) { if (inputLine.contains("currentversion")) { String s = inputLine.substring(inputLine.indexOf("=") + 1, inputLine.length()); tomcat.setDetailInfo(s.trim()); } } in.close(); tomcat.setIsAlive(true); } catch (Exception e) { tomcat.setIsAlive(false); } try { Thread.sleep(60000); } catch (InterruptedException e) { } } } "
" public void run() { try { HttpPost httpPostRequest = new HttpPost(Feesh.device_URL); List<NameValuePair> nameValuePairs = new ArrayList<NameValuePair>(); nameValuePairs.add(new BasicNameValuePair("c", "feed")); nameValuePairs.add(new BasicNameValuePair("amount", String.valueOf(foodAmount))); nameValuePairs.add(new BasicNameValuePair("type", String.valueOf(foodType))); httpPostRequest.setEntity(new UrlEncodedFormEntity(nameValuePairs)); HttpResponse httpResponse = (HttpResponse) new DefaultHttpClient().execute(httpPostRequest); HttpEntity entity = httpResponse.getEntity(); String resultString = ""; if (entity != null) { InputStream instream = entity.getContent(); resultString = convertStreamToString(instream); instream.close(); } Message msg_toast = new Message(); msg_toast.obj = resultString; toast_handler.sendMessage(msg_toast); } catch (UnsupportedEncodingException e) { e.printStackTrace(); } catch (ClientProtocolException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } "
false
53
17,267,601
20,336,463
" public void setBckImg(String newPath) { try { File inputFile = new File(getPath()); File outputFile = new File(newPath); if (!inputFile.getCanonicalPath().equals(outputFile.getCanonicalPath())) { FileInputStream in = new FileInputStream(inputFile); FileOutputStream out = null; try { out = new FileOutputStream(outputFile); } catch (FileNotFoundException ex1) { ex1.printStackTrace(); JOptionPane.showMessageDialog(null, ex1.getMessage().substring(0, Math.min(ex1.getMessage().length(), drawPanel.MAX_DIALOG_MSG_SZ)) + "-" + getClass(), "Set Bck Img", JOptionPane.ERROR_MESSAGE); } int c; if (out != null) { while ((c = in.read()) != -1) out.write(c); out.close(); } in.close(); } } catch (Exception ex) { ex.printStackTrace(); LogHandler.log(ex.getMessage(), Level.INFO, "LOG_MSG", isLoggingEnabled()); JOptionPane.showMessageDialog(null, ex.getMessage().substring(0, Math.min(ex.getMessage().length(), drawPanel.MAX_DIALOG_MSG_SZ)) + "-" + getClass(), "Set Bck Img", JOptionPane.ERROR_MESSAGE); } setPath(newPath); bckImg = new ImageIcon(getPath()); } "
" private static void prepare() { System.err.println("PREPARING-----------------------------------------"); deleteHome(); InputStream configStream = null; FileOutputStream tempStream = null; try { configStream = AllTests.class.getClassLoader().getResourceAsStream("net/sf/archimede/test/resources/repository.xml"); new File("temp").mkdir(); tempStream = new FileOutputStream(new File("temp/repository.xml")); IOUtils.copy(configStream, tempStream); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } finally { try { if (configStream != null) { configStream.close(); } } catch (IOException e) { e.printStackTrace(); } finally { if (tempStream != null) { try { tempStream.close(); } catch (IOException e) { e.printStackTrace(); } } } } String repositoryName = "jackrabbit.repository"; Properties jndiProperties = new Properties(); jndiProperties.put("java.naming.provider.url", "http://sf.net/projects/archimede#1"); jndiProperties.put("java.naming.factory.initial", "org.apache.jackrabbit.core.jndi.provider.DummyInitialContextFactory"); startupUtil = new StartupJcrUtil(REPOSITORY_HOME, "temp/repository.xml", repositoryName, jndiProperties); startupUtil.init(); } "
true
54
21,704,695
9,385,030
" public String hmacSHA256(String message, byte[] key) { MessageDigest sha256 = null; try { sha256 = MessageDigest.getInstance("SHA-256"); } catch (NoSuchAlgorithmException e) { throw new java.lang.AssertionError(this.getClass().getName() + ".hmacSHA256(): SHA-256 algorithm not found!"); } if (key.length > 64) { sha256.update(key); key = sha256.digest(); sha256.reset(); } byte block[] = new byte[64]; for (int i = 0; i < key.length; ++i) block[i] = key[i]; for (int i = key.length; i < block.length; ++i) block[i] = 0; for (int i = 0; i < 64; ++i) block[i] ^= 0x36; sha256.update(block); try { sha256.update(message.getBytes("UTF-8")); } catch (UnsupportedEncodingException e) { throw new java.lang.AssertionError("ITunesU.hmacSH256(): UTF-8 encoding not supported!"); } byte[] hash = sha256.digest(); sha256.reset(); for (int i = 0; i < 64; ++i) block[i] ^= (0x36 ^ 0x5c); sha256.update(block); sha256.update(hash); hash = sha256.digest(); char[] hexadecimals = new char[hash.length * 2]; for (int i = 0; i < hash.length; ++i) { for (int j = 0; j < 2; ++j) { int value = (hash[i] >> (4 - 4 * j)) & 0xf; char base = (value < 10) ? ('0') : ('a' - 10); hexadecimals[i * 2 + j] = (char) (base + value); } } return new String(hexadecimals); } "
" public static void main(String[] args) throws Exception { long start = System.currentTimeMillis(); XSLTBuddy buddy = new XSLTBuddy(); buddy.parseArgs(args); XSLTransformer transformer = new XSLTransformer(); if (buddy.templateDir != null) { transformer.setTemplateDir(buddy.templateDir); } FileReader xslReader = new FileReader(buddy.xsl); Templates xslTemplate = transformer.getXSLTemplate(buddy.xsl, xslReader); for (Enumeration e = buddy.params.keys(); e.hasMoreElements(); ) { String key = (String) e.nextElement(); transformer.addParam(key, buddy.params.get(key)); } Reader reader = null; if (buddy.src == null) { reader = new StringReader(XSLTBuddy.BLANK_XML); } else { reader = new FileReader(buddy.src); } if (buddy.out == null) { String result = transformer.doTransform(reader, xslTemplate, buddy.xsl); buddy.getLogger().info("\n\nXSLT Result:\n\n" + result + "\n"); } else { File file = new File(buddy.out); File dir = file.getParentFile(); if (dir != null) { dir.mkdirs(); } FileWriter writer = new FileWriter(buddy.out); transformer.doTransform(reader, xslTemplate, buddy.xsl, writer); writer.flush(); writer.close(); } buddy.getLogger().info("Transform done successfully in " + (System.currentTimeMillis() - start) + " milliseconds"); } "
false
55
18,513,921
430,971
" public static void copy(File src, File dst) { try { InputStream is = null; OutputStream os = null; try { is = new BufferedInputStream(new FileInputStream(src), BUFFER_SIZE); os = new BufferedOutputStream(new FileOutputStream(dst), BUFFER_SIZE); byte[] buffer = new byte[BUFFER_SIZE]; int len = 0; while ((len = is.read(buffer)) > 0) os.write(buffer, 0, len); } finally { if (null != is) is.close(); if (null != os) os.close(); } } catch (Exception e) { e.printStackTrace(); } } "
" public static void copyFile(File destFile, File src) throws IOException { File destDir = destFile.getParentFile(); File tempFile = new File(destFile + "_tmp"); destDir.mkdirs(); InputStream is = new FileInputStream(src); try { FileOutputStream os = new FileOutputStream(tempFile); try { byte[] buf = new byte[8192]; int len; while ((len = is.read(buf)) > 0) os.write(buf, 0, len); } finally { os.close(); } } finally { is.close(); } destFile.delete(); if (!tempFile.renameTo(destFile)) throw new IOException("Unable to rename " + tempFile + " to " + destFile); } "
true
56
15,982,225
23,285,410
" private static String getDigest(String srcStr, String alg) { Assert.notNull(srcStr); Assert.notNull(alg); try { MessageDigest alga = MessageDigest.getInstance(alg); alga.update(srcStr.getBytes()); byte[] digesta = alga.digest(); return byte2hex(digesta); } catch (Exception e) { throw new RuntimeException(e); } } "
" public void displayItems() throws IOException { URL url = new URL(SNIPPETS_FEED + "?bq=" + URLEncoder.encode(QUERY, "UTF-8") + "&key=" + DEVELOPER_KEY); HttpURLConnection httpConnection = (HttpURLConnection) url.openConnection(); InputStream inputStream = httpConnection.getInputStream(); int ch; while ((ch = inputStream.read()) > 0) { System.out.print((char) ch); } } "
false
57
7,398,604
820,905
" @Override public Collection<IAuthor> doImport() throws Exception { progress.initialize(2, "Ściągam autorów amerykańskich"); String url = "http://pl.wikipedia.org/wiki/Kategoria:Ameryka%C5%84scy_autorzy_fantastyki"; UrlResource resource = new UrlResource(url); InputStream urlInputStream = resource.getInputStream(); StringWriter writer = new StringWriter(); IOUtils.copy(urlInputStream, writer); progress.advance("Parsuję autorów amerykańskich"); DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); DocumentBuilder builder = factory.newDocumentBuilder(); String httpDoc = writer.toString(); httpDoc = httpDoc.replaceFirst("(?s)<!DOCTYPE.+?>\\n", ""); httpDoc = httpDoc.replaceAll("(?s)<script.+?</script>", ""); httpDoc = "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\" ?>\n" + httpDoc; ByteArrayInputStream byteInputStream = new ByteArrayInputStream(httpDoc.getBytes("UTF-8")); Document doc = builder.parse(byteInputStream); ArrayList<String> authorNames = new ArrayList<String>(); ArrayList<IAuthor> authors = new ArrayList<IAuthor>(); XPathFactory xpathFactory = XPathFactory.newInstance(); XPath xpath = xpathFactory.newXPath(); NodeList list = (NodeList) xpath.evaluate("//ul/li/div/div/a", doc, XPathConstants.NODESET); for (int i = 0; i < list.getLength(); i++) { String name = list.item(i).getTextContent(); if (StringUtils.isNotBlank(name)) { authorNames.add(name); } } list = (NodeList) xpath.evaluate("//td/ul/li/a", doc, XPathConstants.NODESET); for (int i = 0; i < list.getLength(); i++) { String name = list.item(i).getTextContent(); if (StringUtils.isNotBlank(name)) { authorNames.add(name); } } for (String name : authorNames) { int idx = name.lastIndexOf(' '); String fname = name.substring(0, idx).trim(); String lname = name.substring(idx + 1).trim(); authors.add(new Author(fname, lname)); } progress.advance("Wykonano"); return authors; } "
" 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!"); } "
true
58
19,584,493
4,076,629
" @Override public String toString() { if (byteArrayOutputStream == null) return "<Unparsed binary data: Content-Type=" + getHeader("Content-Type") + " >"; String charsetName = getCharsetName(); if (charsetName == null) charsetName = "ISO-8859-1"; try { if (unzip) { GZIPInputStream gzipInputStream = new GZIPInputStream(new ByteArrayInputStream(byteArrayOutputStream.toByteArray())); ByteArrayOutputStream unzippedResult = new ByteArrayOutputStream(); IOUtils.copy(gzipInputStream, unzippedResult); return unzippedResult.toString(charsetName); } else { return byteArrayOutputStream.toString(charsetName); } } catch (UnsupportedEncodingException e) { throw new OutputException(e); } catch (IOException e) { throw new OutputException(e); } } "
" public void uploadFile(String filename) throws RQLException { checkFtpClient(); OutputStream out = null; try { out = ftpClient.storeFileStream(filename); IOUtils.copy(new FileReader(filename), out); out.close(); ftpClient.completePendingCommand(); } catch (IOException ex) { throw new RQLException("Upload of local file with name " + filename + " via FTP to server " + server + " failed.", ex); } } "
true
59
1,888,878
7,665,877
" protected void copyFile(File source, File destination) throws ApplicationException { try { OutputStream out = new FileOutputStream(destination); DataInputStream in = new DataInputStream(new FileInputStream(source)); byte[] buf = new byte[8192]; for (int nread = in.read(buf); nread > 0; nread = in.read(buf)) { out.write(buf, 0, nread); } in.close(); out.close(); } catch (IOException e) { throw new ApplicationException("Can't copy file " + source + " to " + destination); } } "
" public SCFFile(URL url) throws IOException { URLConnection connection = url.openConnection(); byte[] content = new byte[connection.getContentLength()]; DataInputStream dis = new DataInputStream(connection.getInputStream()); dis.readFully(content); dis.close(); dis = new DataInputStream(new ByteArrayInputStream(content)); header = new SCFHeader(dis); if (!header.magicNumber.equals(".scf")) throw new RuntimeException(url + " is not an SCF file"); A = new int[header.samples]; C = new int[header.samples]; G = new int[header.samples]; T = new int[header.samples]; max = Integer.MIN_VALUE; dis.reset(); dis.skipBytes(header.samplesOffset); if (header.sampleSize == 1) { if (header.version < 3.00) { for (int i = 0; i < header.samples; ++i) { A[i] = dis.readUnsignedByte(); if (A[i] > max) max = A[i]; C[i] = dis.readUnsignedByte(); if (C[i] > max) max = C[i]; G[i] = dis.readUnsignedByte(); if (G[i] > max) max = G[i]; T[i] = dis.readUnsignedByte(); if (T[i] > max) max = T[i]; } } else { for (int i = 0; i < header.samples; ++i) { A[i] = dis.readUnsignedByte(); if (A[i] > max) max = A[i]; } for (int i = 0; i < header.samples; ++i) { C[i] = dis.readUnsignedByte(); if (C[i] > max) max = C[i]; } for (int i = 0; i < header.samples; ++i) { G[i] = dis.readUnsignedByte(); if (G[i] > max) max = G[i]; } for (int i = 0; i < header.samples; ++i) { T[i] = dis.readUnsignedByte(); if (T[i] > max) max = T[i]; } } } else if (header.sampleSize == 2) { if (header.version < 3.00) { for (int i = 0; i < header.samples; ++i) { A[i] = dis.readUnsignedShort(); if (A[i] > max) max = A[i]; C[i] = dis.readUnsignedShort(); if (C[i] > max) max = C[i]; G[i] = dis.readUnsignedShort(); if (G[i] > max) max = G[i]; T[i] = dis.readUnsignedShort(); if (T[i] > max) max = T[i]; } } else { for (int i = 0; i < header.samples; ++i) { A[i] = dis.readUnsignedShort(); if (A[i] > max) max = A[i]; } for (int i = 0; i < header.samples; ++i) { C[i] = dis.readUnsignedShort(); if (C[i] > max) max = C[i]; } for (int i = 0; i < header.samples; ++i) { G[i] = dis.readUnsignedShort(); if (G[i] > max) max = G[i]; } for (int i = 0; i < header.samples; ++i) { T[i] = dis.readUnsignedShort(); if (T[i] > max) max = T[i]; } } } centers = new int[header.bases]; byte[] buf = new byte[header.bases]; dis.reset(); dis.skipBytes(header.basesOffset); if (header.version < 3.00) { for (int i = 0; i < header.bases; ++i) { centers[i] = dis.readInt(); dis.skipBytes(4); buf[i] = dis.readByte(); dis.skipBytes(3); } } else { for (int i = 0; i < header.bases; ++i) centers[i] = dis.readInt(); dis.skipBytes(4 * header.bases); dis.readFully(buf); } sequence = new String(buf); dis.close(); } "
false
60
11,044,947
16,851,953
" public static void copyFile(File in, File out, boolean append) throws IOException { FileChannel inChannel = new FileInputStream(in).getChannel(); FileChannel outChannel = new FileOutputStream(out, append).getChannel(); try { inChannel.transferTo(0, inChannel.size(), outChannel); } catch (IOException e) { throw e; } finally { if (inChannel != null) inChannel.close(); if (outChannel != null) outChannel.close(); } } "
" @Test public void testTrainingDefault() 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); float desiredError = .001f; float mse = trainer.train(temp.getPath(), 500000, 1000, desiredError); assertTrue("" + mse, mse <= desiredError); } "
true
61
19,693,561
22,137,813
" public Model read(String uri, String base, String lang) { try { URL url = new URL(uri); return read(url.openStream(), base, lang); } catch (IOException e) { throw new OntologyException("I/O error while reading from uri " + uri); } } "
" 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; } "
false
62
601,908
12,678,589
" private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } "
" public static boolean 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; } "
true
63
18,293,811
7,303,337
" private static void copy(String from_name, String to_name) throws IOException { File from_file = new File(from_name); File to_file = new File(to_name); if (!from_file.exists()) abort("�������� ���� �� ���������" + from_file); if (!from_file.isFile()) abort("���������� ����������� ��������" + from_file); if (!from_file.canRead()) abort("�������� ���� ���������� ��� ������" + from_file); if (from_file.isDirectory()) to_file = new File(to_file, from_file.getName()); if (to_file.exists()) { if (!to_file.canWrite()) abort("�������� ���� ���������� ��� ������" + to_file); System.out.println("������������ ������� ����?" + to_file.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")) abort("������������ ���� �� ��� �����������"); } else { String parent = to_file.getParent(); if (parent == null) parent = System.getProperty("user.dir"); File dir = new File(parent); if (!dir.exists()) abort("������� ���������� �� ���������" + parent); if (!dir.isFile()) abort("�� �������� ���������" + parent); if (!dir.canWrite()) abort("������ �� ������" + parent); } FileInputStream from = null; FileOutputStream to = null; try { from = new FileInputStream(from_file); to = new FileOutputStream(to_file); byte[] buffer = new byte[4096]; int bytes_read; while ((bytes_read = from.read(buffer)) != -1) to.write(buffer, 0, bytes_read); } finally { if (from != null) try { from.close(); } catch (IOException e) { ; } if (to != null) try { to.close(); } catch (IOException e) { ; } } } "
" public static void downloadJars(IProject project, String repositoryUrl, String jarDirectory, String[] jars) { try { File tmpFile = null; for (String jar : jars) { try { tmpFile = File.createTempFile("tmpPlugin_", ".zip"); URL url = new URL(repositoryUrl + jarDirectory + jar); String destFilename = new File(url.getFile()).getName(); File destFile = new File(project.getLocation().append("lib").append(jarDirectory).toFile(), destFilename); InputStream inputStream = null; FileOutputStream outputStream = null; try { URLConnection urlConnection = url.openConnection(); inputStream = urlConnection.getInputStream(); outputStream = new FileOutputStream(tmpFile); IOUtils.copy(inputStream, outputStream); } finally { if (outputStream != null) { outputStream.close(); } if (inputStream != null) { inputStream.close(); } } FileUtils.copyFile(tmpFile, destFile); } finally { if (tmpFile != null) { tmpFile.delete(); } } } } catch (Exception ex) { ex.printStackTrace(); } } "
true
64
13,863,615
15,593,678
" protected String getLibJSCode() throws IOException { if (cachedLibJSCode == null) { InputStream is = getClass().getResourceAsStream(JS_LIB_FILE); StringWriter output = new StringWriter(); IOUtils.copy(is, output); cachedLibJSCode = output.toString(); } return cachedLibJSCode; } "
" private static void copyFile(File in, File out) throws Exception { final FileInputStream input = new FileInputStream(in); try { final FileOutputStream output = new FileOutputStream(out); try { final byte[] buf = new byte[4096]; int readBytes = 0; while ((readBytes = input.read(buf)) != -1) { output.write(buf, 0, readBytes); } } finally { output.close(); } } finally { input.close(); } } "
true
65
16,298,029
3,931,480
" public String md5(String password) { MessageDigest m = null; try { m = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException ex) { } m.update(password.getBytes(), 0, password.length()); return new BigInteger(1, m.digest()).toString(16); } "
" public final String encrypt(final String plaintext, final String salt) { if (plaintext == null) { throw new NullPointerException(); } if (salt == null) { throw new NullPointerException(); } try { final MessageDigest md = MessageDigest.getInstance("SHA"); md.update((plaintext + salt).getBytes("UTF-8")); return new BASE64Encoder().encode(md.digest()); } catch (NoSuchAlgorithmException e) { throw new EncryptionException(e); } catch (UnsupportedEncodingException e) { throw new EncryptionException(e); } } "
true
66
20,691,789
2,467,221
" public static void copyFile(File inputFile, File outputFile) throws IOException { FileChannel inChannel = null; FileChannel outChannel = null; try { inChannel = new FileInputStream(inputFile).getChannel(); outChannel = new FileOutputStream(outputFile).getChannel(); inChannel.transferTo(0, inChannel.size(), outChannel); } catch (IOException e) { throw e; } finally { try { if (inChannel != null) { inChannel.close(); } if (outChannel != null) { outChannel.close(); } } catch (IOException e) { throw e; } } } "
" void copyFile(File src, File dst) throws IOException { InputStream in = new FileInputStream(src); OutputStream out = new FileOutputStream(dst); byte[] buf = new byte[1024]; int len; while ((len = in.read(buf)) > 0) out.write(buf, 0, len); in.close(); out.close(); } "
true
67
2,232,619
7,577,030
" public void testStorageStringWriter() throws Exception { TranslationResponseInMemory r = new TranslationResponseInMemory(2048, "UTF-8"); { Writer w = r.getWriter(); w.write("This is an example"); w.write(" and another one."); w.flush(); assertEquals("This is an example and another one.", r.getText()); } { InputStream input = r.getInputStream(); StringWriter writer = new StringWriter(); try { IOUtils.copy(input, writer, "UTF-8"); } finally { input.close(); writer.close(); } assertEquals("This is an example and another one.", writer.toString()); } try { r.getOutputStream(); fail("Is not allowed as you already called getWriter()."); } catch (IOException e) { } { Writer output = r.getWriter(); output.write(" and another line"); output.write(" and write some more"); assertEquals("This is an example and another one. and another line and write some more", r.getText()); } { r.addText(" and some more."); assertEquals("This is an example and another one. and another line and write some more and some more.", r.getText()); } r.setEndState(ResponseStateOk.getInstance()); assertEquals(ResponseStateOk.getInstance(), r.getEndState()); try { r.getWriter(); fail("Previous line should throw IOException as result closed."); } catch (IOException e) { } } "
" private void zipFiles(File file, File[] fa) throws Exception { File f = new File(file, ALL_FILES_NAME); if (f.exists()) { f.delete(); f = new File(file, ALL_FILES_NAME); } ZipOutputStream zoutstrm = new ZipOutputStream(new FileOutputStream(f)); for (int i = 0; i < fa.length; i++) { ZipEntry zipEntry = new ZipEntry(fa[i].getName()); zoutstrm.putNextEntry(zipEntry); FileInputStream fr = new FileInputStream(fa[i]); byte[] buffer = new byte[1024]; int readCount = 0; while ((readCount = fr.read(buffer)) > 0) { zoutstrm.write(buffer, 0, readCount); } fr.close(); zoutstrm.closeEntry(); } zoutstrm.close(); log("created zip file: " + file.getName() + "/" + ALL_FILES_NAME); } "
true
68
7,066,835
1,966,262
" protected List<Datastream> getDatastreams(final DepositCollection pDeposit) throws IOException, SWORDException { List<Datastream> tDatastreams = new ArrayList<Datastream>(); LOG.debug("copying file"); String tZipTempFileName = super.getTempDir() + "uploaded-file.tmp"; IOUtils.copy(pDeposit.getFile(), new FileOutputStream(tZipTempFileName)); Datastream tDatastream = new LocalDatastream(super.getGenericFileName(pDeposit), this.getContentType(), tZipTempFileName); tDatastreams.add(tDatastream); tDatastreams.addAll(_zipFile.getFiles(tZipTempFileName)); return tDatastreams; } "
" 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; } "
true
69
17,217,414
17,984,312
" public void addEntry(InputStream jis, JarEntry entry) throws IOException, URISyntaxException { File target = new File(this.target.getPath() + entry.getName()).getAbsoluteFile(); if (!target.exists()) { target.createNewFile(); } if ((new File(this.source.toURI())).isDirectory()) { File sourceEntry = new File(this.source.getPath() + entry.getName()); FileInputStream fis = new FileInputStream(sourceEntry); byte[] classBytes = new byte[fis.available()]; fis.read(classBytes); (new FileOutputStream(target)).write(classBytes); } else { readwriteStreams(jis, (new FileOutputStream(target))); } } "
" public static void copyFile(File in, File out) throws IOException { FileChannel inChannel = new FileInputStream(in).getChannel(); FileChannel outChannel = new FileOutputStream(out).getChannel(); try { inChannel.transferTo(0, inChannel.size(), outChannel); } catch (IOException e) { throw e; } finally { if (inChannel != null) inChannel.close(); if (outChannel != null) outChannel.close(); } } "
true
70
7,396,680
5,856,886
" public static boolean copyMerge(FileSystem srcFS, Path srcDir, FileSystem dstFS, Path dstFile, boolean deleteSource, Configuration conf, String addString) throws IOException { dstFile = checkDest(srcDir.getName(), dstFS, dstFile, false); if (!srcFS.getFileStatus(srcDir).isDir()) return false; OutputStream out = dstFS.create(dstFile); try { FileStatus contents[] = srcFS.listStatus(srcDir); for (int i = 0; i < contents.length; i++) { if (!contents[i].isDir()) { InputStream in = srcFS.open(contents[i].getPath()); try { IOUtils.copyBytes(in, out, conf, false); if (addString != null) out.write(addString.getBytes("UTF-8")); } finally { in.close(); } } } } finally { out.close(); } if (deleteSource) { return srcFS.delete(srcDir, true); } else { return true; } } "
" public BufferedWriter createOutputStream(String inFile, String outFile) throws IOException { int k_blockSize = 1024; int byteCount; char[] buf = new char[k_blockSize]; File ofp = new File(outFile); ZipOutputStream zos = new ZipOutputStream(new FileOutputStream(ofp)); zos.setMethod(ZipOutputStream.DEFLATED); OutputStreamWriter osw = new OutputStreamWriter(zos, "ISO-8859-1"); BufferedWriter bw = new BufferedWriter(osw); ZipEntry zot = null; File ifp = new File(inFile); ZipInputStream zis = new ZipInputStream(new FileInputStream(ifp)); InputStreamReader isr = new InputStreamReader(zis, "ISO-8859-1"); BufferedReader br = new BufferedReader(isr); ZipEntry zit = null; while ((zit = zis.getNextEntry()) != null) { if (zit.getName().equals("content.xml")) { continue; } zot = new ZipEntry(zit.getName()); zos.putNextEntry(zot); while ((byteCount = br.read(buf, 0, k_blockSize)) >= 0) bw.write(buf, 0, byteCount); bw.flush(); zos.closeEntry(); } zos.putNextEntry(new ZipEntry("content.xml")); bw.flush(); osw = new OutputStreamWriter(zos, "UTF8"); bw = new BufferedWriter(osw); return bw; } "
true
71
6,908,554
20,669,450
" static void reopen(MJIEnv env, int objref) throws IOException { int fd = env.getIntField(objref, "fd"); long off = env.getLongField(objref, "off"); if (content.get(fd) == null) { int mode = env.getIntField(objref, "mode"); int fnRef = env.getReferenceField(objref, "fileName"); String fname = env.getStringObject(fnRef); if (mode == FD_READ) { FileInputStream fis = new FileInputStream(fname); FileChannel fc = fis.getChannel(); fc.position(off); content.set(fd, fis); } else if (mode == FD_WRITE) { FileOutputStream fos = new FileOutputStream(fname); FileChannel fc = fos.getChannel(); fc.position(off); content.set(fd, fos); } else { env.throwException("java.io.IOException", "illegal mode: " + mode); } } } "
" private void auth() throws IOException { authorized = false; seqNumber = 0; DatagramSocket ds = new DatagramSocket(); ds.setSoTimeout(UDPHID_DEFAULT_TIMEOUT); ds.connect(addr, port); DatagramPacket p = new DatagramPacket(buffer.array(), buffer.capacity()); for (int i = 0; i < UDPHID_DEFAULT_ATTEMPTS; i++) { buffer.clear(); buffer.put((byte) REQ_CHALLENGE); buffer.put(htons((short) UDPHID_PROTO)); buffer.put(name.getBytes()); ds.send(new DatagramPacket(buffer.array(), buffer.position())); buffer.clear(); try { ds.receive(p); } catch (SocketTimeoutException e) { continue; } switch(buffer.get()) { case ANS_CHALLENGE: break; case ANS_FAILURE: throw new IOException("REQ_FAILURE"); default: throw new IOException("invalid packet"); } byte challenge_id = buffer.get(); int challenge_len = (int) buffer.get(); byte[] challenge = new byte[challenge_len]; buffer.get(challenge, 0, p.getLength() - buffer.position()); byte[] response; try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(challenge_id); md.update(password.getBytes(), 0, password.length()); md.update(challenge, 0, challenge.length); response = md.digest(); } catch (NoSuchAlgorithmException e) { throw new IOException("NoSuchAlgorithmException: " + e.toString()); } buffer.clear(); buffer.put((byte) REQ_RESPONSE); buffer.put(challenge_id); buffer.put((byte) response.length); buffer.put(response); buffer.put(login.getBytes()); ds.send(new DatagramPacket(buffer.array(), buffer.position())); buffer.clear(); try { ds.receive(p); } catch (SocketTimeoutException e) { continue; } switch(buffer.get()) { case ANS_SUCCESS: int sidLength = buffer.get(); sid = new byte[sidLength]; buffer.get(sid, 0, sidLength); authorized = true; return; case ANS_FAILURE: throw new IOException("access deny"); default: throw new IOException("invalid packet"); } } throw new IOException("operation time out"); } "
false
72
1,966,263
18,600,188
" 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 copyFile(String fileName, String messageID, boolean isError) { try { File inputFile = new File(fileName); File outputFile = null; if (isError) { outputFile = new File(provider.getErrorDataLocation(folderName) + messageID + ".xml"); } else { outputFile = new File(provider.getDataProcessedLocation(folderName) + messageID + ".xml"); } FileReader in = new FileReader(inputFile); FileWriter out = new FileWriter(outputFile); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } catch (Exception e) { } } "
true
73
8,330,064
12,524,253
" @Test public void testWriteAndReadBigger() throws Exception { JCFSFileServer server = new JCFSFileServer(defaultTcpPort, defaultTcpAddress, defaultUdpPort, defaultUdpAddress, dir, 0, 0); JCFS.configureDiscovery(defaultUdpAddress, defaultUdpPort); try { server.start(); RFile file = new RFile("testreadwrite.txt"); RFileOutputStream out = new RFileOutputStream(file); String body = ""; int size = 50 * 1024; for (int i = 0; i < size; i++) { body = body + "a"; } out.write(body.getBytes("utf-8")); out.close(); File expected = new File(dir, "testreadwrite.txt"); assertTrue(expected.isFile()); assertEquals(body.length(), expected.length()); RFileInputStream in = new RFileInputStream(file); byte[] buffer = new byte[body.length()]; int readCount = in.read(buffer); in.close(); assertEquals(body.length(), readCount); String resultRead = new String(buffer, "utf-8"); assertEquals(body, resultRead); } finally { server.stop(); } } "
" public DialogSongList(JFrame frame) { super(frame, "Menu_SongList", "songList"); setMinimumSize(new Dimension(400, 200)); JPanel panel, spanel; Container contentPane; (contentPane = getContentPane()).add(songSelector = new SongSelector(configKey, null, true)); songSelector.setSelectionAction(new Runnable() { public void run() { final Item<URL, MidiFileInfo> item = songSelector.getSelectedInfo(); if (item != null) { try { selection = new File(item.getKey().toURI()); author.setEnabled(true); title.setEnabled(true); difficulty.setEnabled(true); save.setEnabled(true); final MidiFileInfo info = item.getValue(); author.setText(info.getAuthor()); title.setText(info.getTitle()); Util.selectKey(difficulty, info.getDifficulty()); return; } catch (Exception e) { } } selection = null; author.setEnabled(false); title.setEnabled(false); difficulty.setEnabled(false); save.setEnabled(false); } }); contentPane.add(panel = new JPanel(), BorderLayout.SOUTH); panel.setLayout(new BorderLayout()); JScrollPane scrollPane; panel.add(scrollPane = new JScrollPane(spanel = new JPanel()), BorderLayout.NORTH); scrollPane.setPreferredSize(new Dimension(0, 60)); Util.addLabeledComponent(spanel, "Lbl_Author", author = new JTextField(10)); Util.addLabeledComponent(spanel, "Lbl_Title", title = new JTextField(14)); Util.addLabeledComponent(spanel, "Lbl_Difficulty", difficulty = new JComboBox()); difficulty.addItem(new Item<Byte, String>((byte) -1, "")); for (Map.Entry<Byte, String> entry : SongSelector.DIFFICULTIES.entrySet()) { final String value = entry.getValue(); difficulty.addItem(new Item<Byte, String>(entry.getKey(), Util.getMsg(value, value), value)); } spanel.add(save = new JButton()); Util.updateButtonText(save, "Save"); save.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { final File selected = MidiSong.setMidiFileInfo(selection, author.getText(), title.getText(), getAsByte(difficulty)); SongSelector.refresh(); try { songSelector.setSelected(selected == null ? null : selected.toURI().toURL()); } catch (MalformedURLException ex) { } } }); author.setEnabled(false); title.setEnabled(false); difficulty.setEnabled(false); save.setEnabled(false); JButton button; panel.add(spanel = new JPanel(), BorderLayout.WEST); spanel.add(button = new JButton()); Util.updateButtonText(button, "Import"); button.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { final File inputFile = KeyboardHero.midiFile(); try { if (inputFile == null) return; final File dir = (new File(Util.DATA_FOLDER + MidiSong.MIDI_FILES_DIR)); if (dir.exists()) { if (!dir.isDirectory()) { Util.error(Util.getMsg("Err_MidiFilesDirNotDirectory"), dir.getParent()); return; } } else if (!dir.mkdirs()) { Util.error(Util.getMsg("Err_CouldntMkDir"), dir.getParent()); return; } File outputFile = new File(dir.getPath() + File.separator + inputFile.getName()); if (!outputFile.exists() || KeyboardHero.confirm("Que_FileExistsOverwrite")) { final FileChannel inChannel = new FileInputStream(inputFile).getChannel(); inChannel.transferTo(0, inChannel.size(), new FileOutputStream(outputFile).getChannel()); } } catch (Exception ex) { Util.getMsg(Util.getMsg("Err_CouldntImportSong"), ex.toString()); } SongSelector.refresh(); } }); spanel.add(button = new JButton()); Util.updateButtonText(button, "Delete"); button.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { if (KeyboardHero.confirm(Util.getMsg("Que_SureToDelete"))) { try { new File(songSelector.getSelectedFile().toURI()).delete(); } catch (Exception ex) { Util.error(Util.getMsg("Err_CouldntDeleteFile"), ex.toString()); } SongSelector.refresh(); } } }); panel.add(spanel = new JPanel(), BorderLayout.CENTER); spanel.setLayout(new FlowLayout()); spanel.add(button = new JButton()); Util.updateButtonText(button, "Close"); button.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { close(); } }); spanel.add(button = new JButton()); Util.updateButtonText(button, "Play"); button.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { Game.newGame(songSelector.getSelectedFile()); close(); } }); panel.add(spanel = new JPanel(), BorderLayout.EAST); spanel.add(button = new JButton()); Util.updateButtonText(button, "Refresh"); button.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { SongSelector.refresh(); } }); getRootPane().setDefaultButton(button); instance = this; } "
true
74
4,376,758
22,249,465
" public void setKey(String key) { MessageDigest md5; byte[] mdKey = new byte[32]; try { md5 = MessageDigest.getInstance("MD5"); md5.update(key.getBytes()); byte[] digest = md5.digest(); System.arraycopy(digest, 0, mdKey, 0, 16); System.arraycopy(digest, 0, mdKey, 16, 16); } catch (Exception e) { System.out.println("MD5 not implemented, can't generate key out of string!"); System.exit(1); } setKey(mdKey); } "
" public static String getWebPage(URL urlObj) { try { String content = ""; InputStreamReader is = new InputStreamReader(urlObj.openStream()); BufferedReader reader = new BufferedReader(is); String line; while ((line = reader.readLine()) != null) { content += line; } return content; } catch (IOException e) { throw new Error("The page " + quote(urlObj.toString()) + "could not be retrieved." + "\nThis is could be caused by a number of things:" + "\n" + "\n - the computer hosting the web page you want is down, or has returned an error" + "\n - your computer does not have Internet access" + "\n - the heat death of the universe has occurred, taking down all web servers with it"); } } "
false
75
105,319
16,341,721
" private String MD5Sum(String input) { String hashtext = null; try { MessageDigest md = MessageDigest.getInstance("MD5"); md.reset(); md.update(input.getBytes()); byte[] digest = md.digest(); BigInteger bigInt = new BigInteger(1, digest); hashtext = bigInt.toString(16); while (hashtext.length() < 32) { hashtext = "0" + hashtext; } } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } return hashtext; } "
" public boolean isPasswordCorrect(String attempt) { try { MessageDigest digest = MessageDigest.getInstance(attempt); digest.update(salt); digest.update(attempt.getBytes("UTF-8")); byte[] attemptHash = digest.digest(); return attemptHash.equals(hash); } catch (UnsupportedEncodingException ex) { Logger.getLogger(UserRecord.class.getName()).log(Level.SEVERE, null, ex); return false; } catch (NoSuchAlgorithmException ex) { Logger.getLogger(UserRecord.class.getName()).log(Level.SEVERE, null, ex); return false; } } "
true
76
7,839,811
4,056,440
" public static String md5(String input) { byte[] temp; try { MessageDigest messageDigest; messageDigest = MessageDigest.getInstance("MD5"); messageDigest.update(input.getBytes()); temp = messageDigest.digest(); } catch (Exception e) { return null; } return MyUtils.byte2HexStr(temp); } "
" public final String hashPassword(final String password) { try { if (salt == null) { salt = new byte[16]; SecureRandom sr = SecureRandom.getInstance("SHA1PRNG"); sr.setSeed(System.currentTimeMillis()); sr.nextBytes(salt); } MessageDigest md = MessageDigest.getInstance("SHA"); md.update(salt); md.update(password.getBytes("UTF-8")); byte[] hash = md.digest(); for (int i = 0; i < (1999); i++) { md.reset(); hash = md.digest(hash); } return byteToString(hash, 60); } catch (Exception exception) { log.error(exception); return null; } } "
true
77
4,207,693
5,713,525
" private synchronized boolean saveU(URL url, String typeFlag, byte[] arrByte) { BufferedReader buffReader = null; BufferedOutputStream buffOS = null; URLConnection urlconnection = null; char flagChar = '0'; boolean flag = true; try { urlconnection = url.openConnection(); urlconnection.setDoOutput(true); urlconnection.setDoInput(true); urlconnection.setUseCaches(false); urlconnection.setRequestProperty("Content-type", "application/octet-stream"); buffOS = new BufferedOutputStream(urlconnection.getOutputStream()); buffOS.write((byte[]) typeFlag.getBytes()); buffOS.write(arrByte); buffOS.flush(); if (Config.DEBUG) System.out.println("Applet output file successfully! "); buffReader = new BufferedReader(new InputStreamReader(urlconnection.getInputStream())); StringBuffer stringBuff = new StringBuffer(); String serReturnMess = buffReader.readLine(); if (Config.DEBUG) System.out.println("Applet check status successfully! " + serReturnMess); flagChar = '2'; if (serReturnMess != null) { stringBuff.append(serReturnMess); serReturnMess = serReturnMess.substring(serReturnMess.indexOf(32)).trim() + '2'; flagChar = serReturnMess.charAt(0); } while ((serReturnMess = buffReader.readLine()) != null) { if (serReturnMess.length() <= 0) break; } } catch (Throwable e) { e.printStackTrace(); return false; } finally { try { if (buffOS != null) buffOS.close(); if (buffReader != null) buffReader.close(); } catch (Throwable e) { e.printStackTrace(); } if (flagChar == '2' || flagChar == '3') flag = true; else flag = false; } return flag; } "
" private byte[] getFileFromFtp(String remote) throws Exception { ftp = new FTPClient(); int reply; ftp.connect(ftpServer); reply = ftp.getReplyCode(); if (!FTPReply.isPositiveCompletion(reply)) { ftp.disconnect(); throw new Exception("FTP server refused connection."); } if (!ftp.login(ftpUsername, ftpPassword)) { ftp.logout(); throw new Exception("Cann't login to ftp."); } ftp.enterLocalPassiveMode(); ByteArrayOutputStream baos = new ByteArrayOutputStream(); ftp.retrieveFile(remote, baos); ftp.logout(); if (ftp.isConnected()) { try { ftp.disconnect(); } catch (IOException f) { } } return baos.toByteArray(); } "
false
78
12,678,588
952,242
" public static boolean encodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.ENCODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } "
" public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } "
true
79
21,395,181
22,135,738
" @Test public void test20_badSmtp() throws Exception { Db db = DbConnection.defaultCieDbRW(); try { db.begin(); oldSmtp = Config.getProperty(db, "com.entelience.mail.MailHelper.hostName", "localhost"); oldSupport = Config.getProperty(db, "com.entelience.esis.feature.SupportNotifier", false); Config.setProperty(db, "com.entelience.mail.MailHelper.hostName", "127.0.10.1", 1); Config.setProperty(db, "com.entelience.esis.feature.SupportNotifier", "true", 1); PreparedStatement pst = db.prepareStatement("DELETE FROM t_client_errors"); db.executeUpdate(pst); db.commit(); } catch (Exception e) { db.rollback(); } finally { db.safeClose(); } } "
" protected void sort(double[] a) throws Exception { for (int i = a.length - 1; i >= 0; i--) { boolean swapped = false; for (int j = 0; j < i; j++) { if (a[j] > a[j + 1]) { double d = a[j]; a[j] = a[j + 1]; a[j + 1] = d; swapped = true; } } if (!swapped) return; } } "
false
80
19,338,729
19,898,737
" public static InputStream call(String serviceUrl, Map parameters) throws IOException, RestException { StringBuffer urlString = new StringBuffer(serviceUrl); String query = RestClient.buildQueryString(parameters); HttpURLConnection conn; if ((urlString.length() + query.length() + 1) > MAX_URI_LENGTH_FOR_GET) { URL url = new URL(urlString.toString()); conn = (HttpURLConnection) url.openConnection(); conn.setRequestProperty("User-Agent", USER_AGENT_STRING); conn.setRequestMethod("POST"); conn.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); conn.setDoOutput(true); conn.getOutputStream().write(query.getBytes()); } else { if (query.length() > 0) { urlString.append("?").append(query); } URL url = new URL(urlString.toString()); conn = (HttpURLConnection) url.openConnection(); conn.setRequestProperty("User-Agent", USER_AGENT_STRING); conn.setRequestMethod("GET"); } int responseCode = conn.getResponseCode(); if (HttpURLConnection.HTTP_OK != responseCode) { ByteArrayOutputStream errorBuffer = new ByteArrayOutputStream(); int read; byte[] readBuffer = new byte[ERROR_READ_BUFFER_SIZE]; InputStream errorStream = conn.getErrorStream(); while (-1 != (read = errorStream.read(readBuffer))) { errorBuffer.write(readBuffer, 0, read); } throw new RestException("Request failed, HTTP " + responseCode + ": " + conn.getResponseMessage(), errorBuffer.toByteArray()); } return conn.getInputStream(); } "
" private void updateSystem() throws IOException { String stringUrl="http://code.google.com/p/senai-pe-cronos/downloads/list"; try { url = new URL(stringUrl); } catch (MalformedURLException ex) { ex.printStackTrace(); } InputStream is = url.openStream(); InputStreamReader isr = new InputStreamReader(is); BufferedReader br = new BufferedReader(isr); String linha = br.readLine(); while (linha != null) { linha = br.readLine(); if(linha.contains("/files/updateCronos-0-")){ String[] s=linha.split("-"); String[] v=s[4].split(".exe"); versao=v[0]; println("----"+versao); break; } } stringUrl="http://senai-pe-cronos.googlecode.com/files/updateCronos-0-"+versao+".exe"; UpdateCronos update=new UpdateCronos(); try { url = new URL(stringUrl); } catch (MalformedURLException ex) { ex.printStackTrace(); } System.out.println("versão:"+versao); if(Integer.parseInt(versao)>version){ File f = update.gravaArquivoDeURL(url,System.getProperty("user.dir"),String.valueOf(version),versao); if(update.isS()) { Runtime.getRuntime().exec(location+"\\update.exe"); System.exit(0); } } } "
false
81
16,845,107
7,321,949
" public boolean copyFile(File destinationFolder, File fromFile) { boolean result = false; String toFileName = destinationFolder.getAbsolutePath() + "/" + fromFile.getName(); File toFile = new File(toFileName); FileInputStream from = null; FileOutputStream to = null; try { from = new FileInputStream(fromFile); to = new FileOutputStream(toFile); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = from.read(buffer)) != -1) to.write(buffer, 0, bytesRead); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } finally { if (from != null) { try { from.close(); } catch (IOException e2) { e2.printStackTrace(); } if (to != null) { try { to.close(); result = true; } catch (IOException e3) { e3.printStackTrace(); } } } } return result; } "
" private boolean saveLOBDataToFileSystem() { if ("".equals(m_attachmentPathRoot)) { log.severe("no attachmentPath defined"); return false; } if (m_items == null || m_items.size() == 0) { setBinaryData(null); return true; } final DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); try { final DocumentBuilder builder = factory.newDocumentBuilder(); final Document document = builder.newDocument(); final Element root = document.createElement("attachments"); document.appendChild(root); document.setXmlStandalone(true); for (int i = 0; i < m_items.size(); i++) { log.fine(m_items.get(i).toString()); File entryFile = m_items.get(i).getFile(); final String path = entryFile.getAbsolutePath(); log.fine(path + " - " + m_attachmentPathRoot); if (!path.startsWith(m_attachmentPathRoot)) { log.fine("move file: " + path); FileChannel in = null; FileChannel out = null; try { final File destFolder = new File(m_attachmentPathRoot + File.separator + getAttachmentPathSnippet()); if (!destFolder.exists()) { if (!destFolder.mkdirs()) { log.warning("unable to create folder: " + destFolder.getPath()); } } final File destFile = new File(m_attachmentPathRoot + File.separator + getAttachmentPathSnippet() + File.separator + entryFile.getName()); in = new FileInputStream(entryFile).getChannel(); out = new FileOutputStream(destFile).getChannel(); in.transferTo(0, in.size(), out); in.close(); out.close(); if (entryFile.exists()) { if (!entryFile.delete()) { entryFile.deleteOnExit(); } } entryFile = destFile; } catch (IOException e) { e.printStackTrace(); log.severe("unable to copy file " + entryFile.getAbsolutePath() + " to " + m_attachmentPathRoot + File.separator + getAttachmentPathSnippet() + File.separator + entryFile.getName()); } finally { if (in != null && in.isOpen()) { in.close(); } if (out != null && out.isOpen()) { out.close(); } } } final Element entry = document.createElement("entry"); entry.setAttribute("name", getEntryName(i)); String filePathToStore = entryFile.getAbsolutePath(); filePathToStore = filePathToStore.replaceFirst(m_attachmentPathRoot.replaceAll("\\\\", "\\\\\\\\"), ATTACHMENT_FOLDER_PLACEHOLDER); log.fine(filePathToStore); entry.setAttribute("file", filePathToStore); root.appendChild(entry); } final Source source = new DOMSource(document); final ByteArrayOutputStream bos = new ByteArrayOutputStream(); final Result result = new StreamResult(bos); final Transformer xformer = TransformerFactory.newInstance().newTransformer(); xformer.transform(source, result); final byte[] xmlData = bos.toByteArray(); log.fine(bos.toString()); setBinaryData(xmlData); return true; } catch (Exception e) { log.log(Level.SEVERE, "saveLOBData", e); } setBinaryData(null); return false; } "
true
82
8,661,929
2,446,253
" 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; } "
" private int renumberOrderBy(long tableID) throws SnapInException { int count = 0; Connection con = null; Statement stmt = null; ResultSet rs = null; try { con = getDataSource().getConnection(); con.setAutoCommit(false); stmt = con.createStatement(); StringBuffer query = new StringBuffer(); query.append("SELECT ").append(DatabaseConstants.TableFieldName_JV_FIELDBEHAVIOR_ID).append(" FROM ").append(DatabaseConstants.TableName_JV_FIELDBEHAVIOR).append(" WHERE ").append(DatabaseConstants.TableFieldName_JV_FIELDBEHAVIOR_TABLEID).append(" = ").append(tableID).append(" ORDER BY ").append(DatabaseConstants.TableFieldName_JV_FIELDBEHAVIOR_ORDERBY); Vector rowIDVector = new Vector(); rs = stmt.executeQuery(query.toString()); while (rs.next()) { count++; rowIDVector.add(rs.getLong(DatabaseConstants.TableFieldName_JV_FIELDBEHAVIOR_ID) + ""); } StringBuffer updateString = new StringBuffer(); updateString.append("UPDATE ").append(DatabaseConstants.TableName_JV_FIELDBEHAVIOR).append(" SET ").append(DatabaseConstants.TableFieldName_JV_FIELDBEHAVIOR_ORDERBY).append(" = ? WHERE ").append(DatabaseConstants.TableFieldName_JV_FIELDBEHAVIOR_ID).append(" = ?"); PreparedStatement pstmt = con.prepareStatement(updateString.toString()); int orderByValue = ORDERBY_BY_DELTA_VALUE; Enumeration en = rowIDVector.elements(); while (en.hasMoreElements()) { pstmt.setInt(1, orderByValue); pstmt.setString(2, en.nextElement().toString()); orderByValue += ORDERBY_BY_DELTA_VALUE; pstmt.executeUpdate(); } con.setAutoCommit(true); if (pstmt != null) { pstmt.close(); } } catch (java.sql.SQLException e) { if (con == null) { logger.error("java.sql.SQLException", e); } else { try { logger.error("Transaction is being rolled back."); con.rollback(); con.setAutoCommit(true); } catch (java.sql.SQLException e2) { logger.error("java.sql.SQLException", e2); } } } catch (Exception e) { logger.error("Error occured during RenumberOrderBy", e); } finally { getDataSourceHelper().releaseResources(con, stmt, rs); } return count; } "
true
83
21,293,476
716,032
" public void addGames(List<Game> games) throws StadiumException, SQLException { Connection conn = ConnectionManager.getManager().getConnection(); conn.setAutoCommit(false); PreparedStatement stm = null; ResultSet rs = null; try { for (Game game : games) { stm = conn.prepareStatement(Statements.SELECT_STADIUM); stm.setString(1, game.getStadiumName()); stm.setString(2, game.getStadiumCity()); rs = stm.executeQuery(); int stadiumId = -1; while (rs.next()) { stadiumId = rs.getInt("stadiumID"); } if (stadiumId == -1) throw new StadiumException("No such stadium"); stm = conn.prepareStatement(Statements.INSERT_GAME); stm.setInt(1, stadiumId); stm.setDate(2, game.getGameDate()); stm.setTime(3, game.getGameTime()); stm.setString(4, game.getTeamA()); stm.setString(5, game.getTeamB()); stm.executeUpdate(); int gameId = getMaxId(); List<SectorPrice> sectorPrices = game.getSectorPrices(); for (SectorPrice price : sectorPrices) { stm = conn.prepareStatement(Statements.INSERT_TICKET_PRICE); stm.setInt(1, gameId); stm.setInt(2, price.getSectorId()); stm.setInt(3, price.getPrice()); stm.executeUpdate(); } } } catch (SQLException e) { conn.rollback(); throw e; } finally { rs.close(); stm.close(); } conn.commit(); conn.setAutoCommit(true); } "
" public void getZipFiles(String filename) { try { String destinationname = "c:\\mods\\peu\\"; byte[] buf = new byte[1024]; ZipInputStream zipinputstream = null; ZipEntry zipentry; zipinputstream = new ZipInputStream(new FileInputStream(filename)); zipentry = zipinputstream.getNextEntry(); while (zipentry != null) { String entryName = zipentry.getName(); System.out.println("entryname " + entryName); int n; FileOutputStream fileoutputstream; File newFile = new File(entryName); String directory = newFile.getParent(); if (directory == null) { if (newFile.isDirectory()) break; } fileoutputstream = new FileOutputStream(destinationname + entryName); while ((n = zipinputstream.read(buf, 0, 1024)) > -1) fileoutputstream.write(buf, 0, n); fileoutputstream.close(); zipinputstream.closeEntry(); zipentry = zipinputstream.getNextEntry(); } zipinputstream.close(); } catch (Exception e) { e.printStackTrace(); } } "
false
84
1,244,216
3,078,767
" public String postEvent(EventDocument eventDoc, Map attachments) { if (eventDoc == null || eventDoc.getEvent() == null) return null; if (queue == null) { sendEvent(eventDoc, attachments); return eventDoc.getEvent().getEventId(); } if (attachments != null) { Iterator iter = attachments.entrySet().iterator(); while (iter.hasNext()) { Map.Entry entry = (Map.Entry) iter.next(); if (entry.getValue() instanceof DataHandler) { File file = new File(attachmentStorge + "/" + GuidUtil.generate() + entry.getKey()); try { IOUtils.copy(((DataHandler) entry.getValue()).getInputStream(), new FileOutputStream(file)); entry.setValue(file); } catch (IOException err) { err.printStackTrace(); } } } } InternalEventObject eventObj = new InternalEventObject(); eventObj.setEventDocument(eventDoc); eventObj.setAttachments(attachments); eventObj.setSessionContext(SessionContextUtil.getCurrentContext()); eventDoc.getEvent().setEventId(GuidUtil.generate()); getQueue().post(eventObj); return eventDoc.getEvent().getEventId(); } "
" public static void copyFile(File source, File dest) throws IOException { FileChannel in = null, out = null; try { in = new FileInputStream(source).getChannel(); out = new FileOutputStream(dest).getChannel(); in.transferTo(0, in.size(), out); } catch (FileNotFoundException fnfe) { Log.debug(fnfe); } finally { if (in != null) in.close(); if (out != null) out.close(); } } "
true
85
22,328,848
4,411,141
" protected void doRestoreOrganizeTypeRelation() throws Exception { Connection con = null; PreparedStatement ps = null; ResultSet result = null; String strDelQuery = "DELETE FROM " + Common.ORGANIZE_TYPE_RELATION_TABLE; String strSelQuery = "SELECT parent_organize_type,child_organize_type " + "FROM " + Common.ORGANIZE_TYPE_RELATION_B_TABLE + " " + "WHERE version_no = ?"; String strInsQuery = "INSERT INTO " + Common.ORGANIZE_TYPE_RELATION_TABLE + " " + "(parent_organize_type,child_organize_type) " + "VALUES (?,?)"; DBOperation dbo = factory.createDBOperation(POOL_NAME); try { try { con = dbo.getConnection(); con.setAutoCommit(false); ps = con.prepareStatement(strDelQuery); ps.executeUpdate(); ps = con.prepareStatement(strSelQuery); ps.setInt(1, this.versionNO); result = ps.executeQuery(); ps = con.prepareStatement(strInsQuery); while (result.next()) { ps.setString(1, result.getString("parent_organize_type")); ps.setString(2, result.getString("child_organize_type")); int resultCount = ps.executeUpdate(); if (resultCount != 1) { con.rollback(); throw new CesSystemException("Organize_backup.doRestoreOrganizeTypeRelation(): ERROR Inserting data " + "in T_SYS_ORGANIZE_TYPE_RELATION INSERT !! resultCount = " + resultCount); } } con.commit(); } catch (SQLException se) { con.rollback(); throw new CesSystemException("Organize_backup.doRestoreOrganizeTypeRelation(): SQLException: " + se); } finally { con.setAutoCommit(true); close(dbo, ps, result); } } catch (SQLException se) { throw new CesSystemException("Organize_backup.doRestoreOrganizeTypeRelation(): SQLException while committing or rollback"); } } "
" private void addDocToDB(String action, DataSource database) { String typeOfDoc = findTypeOfDoc(action).trim().toLowerCase(); Connection con = null; try { con = database.getConnection(); con.setAutoCommit(false); checkDupDoc(typeOfDoc, con); String add = "insert into " + typeOfDoc + " values( ?, ?, ?, ?, ?, ?, ? )"; PreparedStatement prepStatement = con.prepareStatement(add); prepStatement.setString(1, selectedCourse.getCourseId()); prepStatement.setString(2, selectedCourse.getAdmin()); prepStatement.setTimestamp(3, getTimeStamp()); prepStatement.setString(4, getLink()); prepStatement.setString(5, homePage.getUser()); prepStatement.setString(6, getText()); prepStatement.setString(7, getTitle()); prepStatement.executeUpdate(); prepStatement.close(); con.commit(); } catch (Exception e) { sqlError = true; e.printStackTrace(); if (con != null) try { con.rollback(); } catch (Exception logOrIgnore) { } try { throw e; } catch (Exception e1) { e1.printStackTrace(); } } finally { if (con != null) try { con.close(); } catch (Exception logOrIgnore) { } } } "
true
86
17,001,260
8,364,547
" public static void getGPX(String gpxURL, String fName) { try { URL url = new URL(gpxURL); HttpURLConnection urlConnection = (HttpURLConnection) url.openConnection(); urlConnection.setRequestMethod("GET"); urlConnection.setDoOutput(true); urlConnection.connect(); File storage = mContext.getExternalFilesDir(null); File file = new File(storage, fName); FileOutputStream os = new FileOutputStream(file); InputStream is = urlConnection.getInputStream(); byte[] buffer = new byte[1024]; int bufferLength = 0; while ((bufferLength = is.read(buffer)) > 0) { os.write(buffer, 0, bufferLength); } os.close(); } catch (MalformedURLException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } "
" @Override public void executeInterruptible() { encodingTerminated = false; File destinationFile = null; try { Runtime runtime = Runtime.getRuntime(); IconAndFileListElement element; while ((element = getNextFileElement()) != null) { File origFile = element.getFile(); destinationFile = new File(encodeFileCard.getDestinationFolder().getValue(), origFile.getName()); if (!destinationFile.getParentFile().exists()) { destinationFile.getParentFile().mkdirs(); } actualFileLabel.setText(origFile.getName()); actualFileModel.setMaximum((int) origFile.length()); actualFileModel.setValue(0); int bitrate; synchronized (bitratePattern) { Matcher bitrateMatcher = bitratePattern.matcher(encodeFileCard.getBitrate().getValue()); bitrateMatcher.find(); bitrate = Integer.parseInt(bitrateMatcher.group(1)); } List<String> command = new LinkedList<String>(); command.add(encoderFile.getCanonicalPath()); command.add("--mp3input"); command.add("-m"); command.add("j"); String sampleFreq = Settings.getSetting("encode.sample.freq"); if (Util.isNotEmpty(sampleFreq)) { command.add("--resample"); command.add(sampleFreq); } QualityElement quality = (QualityElement) ((JComboBox) encodeFileCard.getQuality().getValueComponent()).getSelectedItem(); command.add("-q"); command.add(Integer.toString(quality.getValue())); command.add("-b"); command.add(Integer.toString(bitrate)); command.add("--cbr"); command.add("-"); command.add(destinationFile.getCanonicalPath()); if (LOG.isDebugEnabled()) { StringBuilder commandLine = new StringBuilder(); boolean first = true; for (String part : command) { if (!first) commandLine.append(" "); commandLine.append(part); first = false; } LOG.debug("Command line: " + commandLine.toString()); } encodingProcess = runtime.exec(command.toArray(new String[0])); lastPosition = 0l; InputStream fileStream = null; try { fileStream = new PositionNotifierInputStream(new FileInputStream(origFile), origFile.length(), 2048, this); IOUtils.copy(fileStream, encodingProcess.getOutputStream()); encodingProcess.getOutputStream().close(); } finally { IOUtils.closeQuietly(fileStream); if (LOG.isDebugEnabled()) { InputStream processOut = null; try { processOut = encodingProcess.getInputStream(); StringWriter sw = new StringWriter(); IOUtils.copy(processOut, sw); LOG.debug("Process output stream:\n" + sw); IOUtils.closeQuietly(processOut); processOut = encodingProcess.getErrorStream(); sw = new StringWriter(); IOUtils.copy(processOut, sw); LOG.debug("Process error stream:\n" + sw); } finally { IOUtils.closeQuietly(processOut); } } } int result = encodingProcess.waitFor(); encodingProcess = null; if (result != 0) { LOG.warn("Encoder process returned error code " + result); } if (Boolean.parseBoolean(encodeFileCard.getCopyTag().getValue())) { MP3File mp3Input = new MP3File(origFile); MP3File mp3Output = new MP3File(destinationFile); boolean write = false; if (mp3Input.hasID3v2tag()) { ID3v2Tag id3v2Tag = new ID3v2Tag(); for (ID3v2Frame frame : mp3Input.getID3v2tag().getAllframes()) { id3v2Tag.addFrame(frame); } mp3Output.setID3v2tag(id3v2Tag); write = true; } if (mp3Input.hasID3v11tag()) { mp3Output.setID3v11tag(mp3Input.getID3v11tag()); write = true; } if (write) mp3Output.write(); } } actualFileLabel.setText(Messages.getString("operations.file.encode.execute.actualfile.terminated")); actualFileModel.setValue(actualFileModel.getMaximum()); } catch (Exception e) { LOG.error("Cannot encode files", e); if (!(e instanceof IOException && encodingTerminated)) MainWindowInterface.showError(e); if (destinationFile != null) destinationFile.delete(); } } "
false
87
11,594,590
4,860,089
" public <T extends FetionResponse> T executeAction(FetionAction<T> fetionAction) throws IOException { URL url = new URL(fetionAction.getProtocol().name().toLowerCase() + "://" + fetionUrl + fetionAction.getRequestData()); URLConnection connection = url.openConnection(); InputStream in = connection.getInputStream(); byte[] buffer = new byte[10240]; ByteArrayOutputStream bout = new ByteArrayOutputStream(); int read = 0; while ((read = in.read(buffer)) > 0) { bout.write(buffer, 0, read); } return fetionAction.processResponse(parseRawResponse(bout.toByteArray())); } "
" public int[] sort() { int i, tmp; int[] newIndex = new int[nrows]; for (i = 0; i < nrows; i++) { newIndex[i] = i; } boolean change = true; if (this.ascending) { if (data[0][column] instanceof Comparable) { while (change) { change = false; for (i = 0; i < nrows - 1; i++) { if (((Comparable) data[newIndex[i]][column]).compareTo((Comparable) data[newIndex[i + 1]][column]) > 0) { tmp = newIndex[i]; newIndex[i] = newIndex[i + 1]; newIndex[i + 1] = tmp; change = true; } } } return newIndex; } if (data[0][column] instanceof String || data[0][column] instanceof ClassLabel) { while (change) { change = false; for (i = 0; i < nrows - 1; i++) { if ((data[newIndex[i]][column].toString()).compareTo(data[newIndex[i + 1]][column].toString()) > 0) { tmp = newIndex[i]; newIndex[i] = newIndex[i + 1]; newIndex[i + 1] = tmp; change = true; } } } } return newIndex; } if (!this.ascending) { if (data[0][column] instanceof Comparable) { while (change) { change = false; for (i = 0; i < nrows - 1; i++) { if (((Comparable) data[newIndex[i]][column]).compareTo((Comparable) data[newIndex[i + 1]][column]) < 0) { tmp = newIndex[i]; newIndex[i] = newIndex[i + 1]; newIndex[i + 1] = tmp; change = true; } } } return newIndex; } if (data[0][column] instanceof String || data[0][column] instanceof ClassLabel) { while (change) { change = false; for (i = 0; i < nrows - 1; i++) { if ((data[newIndex[i]][column].toString()).compareTo(data[newIndex[i + 1]][column].toString()) < 0) { tmp = newIndex[i]; newIndex[i] = newIndex[i + 1]; newIndex[i + 1] = tmp; change = true; } } } } return newIndex; } else return newIndex; } "
false
88
1,637,147
547,576
" protected PredicateAnnotationRecord generatePredicateAnnotationRecord(PredicateAnnotationRecord par, String miDescriptor) { String annotClass = par.annotation.getType().substring(1, par.annotation.getType().length() - 1).replace('/', '.'); String methodName = getMethodName(par); String hashKey = annotClass + CLASS_SIG_SEPARATOR_STRING + methodName; PredicateAnnotationRecord gr = _generatedPredicateRecords.get(hashKey); if (gr != null) { _sharedAddData.cacheInfo.incCombinePredicateCacheHit(); return gr; } else { _sharedAddData.cacheInfo.incCombinePredicateCacheMiss(); } String predicateClass = ((_predicatePackage.length() > 0) ? (_predicatePackage + ".") : "") + annotClass + "Pred"; ClassFile predicateCF = null; File clonedFile = new File(_predicatePackageDir, annotClass.replace('.', '/') + "Pred.class"); if (clonedFile.exists() && clonedFile.isFile() && clonedFile.canRead()) { try { predicateCF = new ClassFile(new FileInputStream(clonedFile)); } catch (IOException ioe) { throw new ThreadCheckException("Could not open predicate class file, source=" + clonedFile, ioe); } } else { ByteArrayOutputStream baos = new ByteArrayOutputStream(); try { _templatePredicateClassFile.write(baos); predicateCF = new ClassFile(new ByteArrayInputStream(baos.toByteArray())); } catch (IOException ioe) { throw new ThreadCheckException("Could not open predicate template class file", ioe); } } clonedFile.getParentFile().mkdirs(); final ArrayList<String> paramNames = new ArrayList<String>(); final HashMap<String, String> paramTypes = new HashMap<String, String>(); performCombineTreeWalk(par, new ILambda.Ternary<Object, String, String, AAnnotationsAttributeInfo.Annotation.AMemberValue>() { public Object apply(String param1, String param2, AAnnotationsAttributeInfo.Annotation.AMemberValue param3) { paramNames.add(param1); paramTypes.put(param1, param2); return null; } }, ""); ArrayList<PredicateAnnotationRecord> memberPARs = new ArrayList<PredicateAnnotationRecord>(); for (String key : par.combinedPredicates.keySet()) { for (PredicateAnnotationRecord memberPAR : par.combinedPredicates.get(key)) { if ((memberPAR.predicateClass != null) && (memberPAR.predicateMI != null)) { memberPARs.add(memberPAR); } else { memberPARs.add(generatePredicateAnnotationRecord(memberPAR, miDescriptor)); } } } AUTFPoolInfo predicateClassNameItem = new ASCIIPoolInfo(predicateClass.replace('.', '/'), predicateCF.getConstantPool()); int[] l = predicateCF.addConstantPoolItems(new APoolInfo[] { predicateClassNameItem }); predicateClassNameItem = predicateCF.getConstantPoolItem(l[0]).execute(CheckUTFVisitor.singleton(), null); ClassPoolInfo predicateClassItem = new ClassPoolInfo(predicateClassNameItem, predicateCF.getConstantPool()); l = predicateCF.addConstantPoolItems(new APoolInfo[] { predicateClassItem }); predicateClassItem = predicateCF.getConstantPoolItem(l[0]).execute(CheckClassVisitor.singleton(), null); predicateCF.setThisClass(predicateClassItem); StringBuilder sb = new StringBuilder(); sb.append("(Ljava/lang/Object;"); if (par.passArguments) { sb.append("[Ljava/lang/Object;"); } for (String key : paramNames) { sb.append(paramTypes.get(key)); } sb.append(")Z"); String methodDesc = sb.toString(); MethodInfo templateMI = null; MethodInfo predicateMI = null; for (MethodInfo mi : predicateCF.getMethods()) { if ((mi.getName().toString().equals(methodName)) && (mi.getDescriptor().toString().equals(methodDesc))) { predicateMI = mi; break; } else if ((mi.getName().toString().equals("template")) && (mi.getDescriptor().toString().startsWith("(")) && (mi.getDescriptor().toString().endsWith(")Z"))) { templateMI = mi; } } if ((templateMI == null) && (predicateMI == null)) { throw new ThreadCheckException("Could not find template predicate method in class file"); } if (predicateMI == null) { AUTFPoolInfo namecpi = new ASCIIPoolInfo(methodName, predicateCF.getConstantPool()); l = predicateCF.addConstantPoolItems(new APoolInfo[] { namecpi }); namecpi = predicateCF.getConstantPoolItem(l[0]).execute(CheckUTFVisitor.singleton(), null); AUTFPoolInfo descpi = new ASCIIPoolInfo(methodDesc, predicateCF.getConstantPool()); l = predicateCF.addConstantPoolItems(new APoolInfo[] { descpi }); descpi = predicateCF.getConstantPoolItem(l[0]).execute(CheckUTFVisitor.singleton(), null); ArrayList<AAttributeInfo> list = new ArrayList<AAttributeInfo>(); for (AAttributeInfo a : templateMI.getAttributes()) { try { AAttributeInfo clonedA = (AAttributeInfo) a.clone(); list.add(clonedA); } catch (CloneNotSupportedException e) { throw new InstrumentorException("Could not clone method attributes"); } } predicateMI = new MethodInfo(templateMI.getAccessFlags(), namecpi, descpi, list.toArray(new AAttributeInfo[] {})); predicateCF.getMethods().add(predicateMI); CodeAttributeInfo.CodeProperties props = predicateMI.getCodeAttributeInfo().getProperties(); props.maxLocals += paramTypes.size() + 1 + (par.passArguments ? 1 : 0); InstructionList il = new InstructionList(predicateMI.getCodeAttributeInfo().getCode()); if ((par.combineMode == Combine.Mode.OR) || (par.combineMode == Combine.Mode.XOR) || (par.combineMode == Combine.Mode.IMPLIES)) { il.insertInstr(new GenericInstruction(Opcode.ICONST_0), predicateMI.getCodeAttributeInfo()); } else { il.insertInstr(new GenericInstruction(Opcode.ICONST_1), predicateMI.getCodeAttributeInfo()); } boolean res; res = il.advanceIndex(); assert res == true; int accumVarIndex = props.maxLocals - 1; AInstruction loadAccumInstr; AInstruction storeAccumInstr; if (accumVarIndex < 256) { loadAccumInstr = new GenericInstruction(Opcode.ILOAD, (byte) accumVarIndex); storeAccumInstr = new GenericInstruction(Opcode.ISTORE, (byte) accumVarIndex); } else { byte[] bytes = new byte[] { Opcode.ILOAD, 0, 0 }; Types.bytesFromShort((short) accumVarIndex, bytes, 1); loadAccumInstr = new WideInstruction(bytes); bytes[0] = Opcode.ISTORE; storeAccumInstr = new WideInstruction(bytes); } il.insertInstr(storeAccumInstr, predicateMI.getCodeAttributeInfo()); res = il.advanceIndex(); assert res == true; int maxStack = 0; int paramIndex = 1; int lvIndex = 1; if (par.passArguments) { lvIndex += 1; } int memberCount = 0; for (PredicateAnnotationRecord memberPAR : memberPARs) { ++memberCount; il.insertInstr(new GenericInstruction(Opcode.ALOAD_0), predicateMI.getCodeAttributeInfo()); res = il.advanceIndex(); assert res == true; int curStack = 1; if (memberPAR.passArguments) { if (par.passArguments) { il.insertInstr(new GenericInstruction(Opcode.ALOAD_1), predicateMI.getCodeAttributeInfo()); res = il.advanceIndex(); assert res == true; curStack += 1; } } for (int paramNameIndex = 0; paramNameIndex < memberPAR.paramNames.size(); ++paramNameIndex) { String t = memberPAR.paramTypes.get(memberPAR.paramNames.get(paramNameIndex)); if (t.length() == 0) { throw new ThreadCheckException("Length of parameter type no. " + paramIndex + " string is 0 in " + predicateMI.getName() + " in class " + predicateCF.getThisClassName()); } byte opcode; int nextLVIndex = lvIndex; switch(t.charAt(0)) { case 'I': case 'B': case 'C': case 'S': case 'Z': opcode = Opcode.ILOAD; nextLVIndex += 1; curStack += 1; break; case 'F': opcode = Opcode.FLOAD; nextLVIndex += 1; curStack += 1; break; case '[': case 'L': opcode = Opcode.ALOAD; nextLVIndex += 1; curStack += 1; break; case 'J': opcode = Opcode.LLOAD; nextLVIndex += 2; curStack += 2; break; case 'D': opcode = Opcode.DLOAD; nextLVIndex += 2; curStack += 2; break; default: throw new ThreadCheckException("Parameter type no. " + paramIndex + ", " + t + ", is unknown in " + predicateMI.getName() + " in class " + predicateCF.getThisClassName()); } AInstruction load = Opcode.getShortestLoadStoreInstruction(opcode, (short) lvIndex); il.insertInstr(load, predicateMI.getCodeAttributeInfo()); res = il.advanceIndex(); assert res == true; ++paramIndex; lvIndex = nextLVIndex; } if (curStack > maxStack) { maxStack = curStack; } ReferenceInstruction predicateCallInstr = new ReferenceInstruction(Opcode.INVOKESTATIC, (short) 0); int predicateCallIndex = predicateCF.addMethodToConstantPool(memberPAR.predicateClass.replace('.', '/'), memberPAR.predicateMI.getName().toString(), memberPAR.predicateMI.getDescriptor().toString()); predicateCallInstr.setReference(predicateCallIndex); il.insertInstr(predicateCallInstr, predicateMI.getCodeAttributeInfo()); res = il.advanceIndex(); assert res == true; if ((par.combineMode == Combine.Mode.NOT) || ((par.combineMode == Combine.Mode.IMPLIES) && (memberCount == 1))) { il.insertInstr(new GenericInstruction(Opcode.ICONST_1), predicateMI.getCodeAttributeInfo()); res = il.advanceIndex(); assert res == true; il.insertInstr(new GenericInstruction(Opcode.SWAP), predicateMI.getCodeAttributeInfo()); res = il.advanceIndex(); assert res == true; il.insertInstr(new GenericInstruction(Opcode.ISUB), predicateMI.getCodeAttributeInfo()); res = il.advanceIndex(); assert res == true; } il.insertInstr(loadAccumInstr, predicateMI.getCodeAttributeInfo()); res = il.advanceIndex(); assert res == true; if (par.combineMode == Combine.Mode.OR) { il.insertInstr(new GenericInstruction(Opcode.IOR), predicateMI.getCodeAttributeInfo()); } else if ((par.combineMode == Combine.Mode.AND) || (par.combineMode == Combine.Mode.NOT)) { il.insertInstr(new GenericInstruction(Opcode.IAND), predicateMI.getCodeAttributeInfo()); } else if (par.combineMode == Combine.Mode.XOR) { il.insertInstr(new GenericInstruction(Opcode.IADD), predicateMI.getCodeAttributeInfo()); } else if (par.combineMode == Combine.Mode.IMPLIES) { il.insertInstr(new GenericInstruction(Opcode.IOR), predicateMI.getCodeAttributeInfo()); } else { assert false; } res = il.advanceIndex(); assert res == true; il.insertInstr(storeAccumInstr, predicateMI.getCodeAttributeInfo()); res = il.advanceIndex(); assert res == true; } if (par.combineMode == Combine.Mode.XOR) { il.insertInstr(loadAccumInstr, predicateMI.getCodeAttributeInfo()); res = il.advanceIndex(); assert res == true; il.insertInstr(new GenericInstruction(Opcode.ICONST_1), predicateMI.getCodeAttributeInfo()); res = il.advanceIndex(); assert res == true; il.insertInstr(new GenericInstruction(Opcode.ICONST_0), predicateMI.getCodeAttributeInfo()); res = il.advanceIndex(); assert res == true; WideBranchInstruction br2 = new WideBranchInstruction(Opcode.GOTO_W, il.getIndex() + 1); il.insertInstr(br2, predicateMI.getCodeAttributeInfo()); res = il.advanceIndex(); assert res == true; int jumpIndex = il.getIndex(); il.insertInstr(new GenericInstruction(Opcode.ICONST_1), predicateMI.getCodeAttributeInfo()); res = il.advanceIndex(); assert res == true; res = il.rewindIndex(3); assert res == true; BranchInstruction br1 = new BranchInstruction(Opcode.IF_ICMPEQ, jumpIndex); il.insertInstr(br1, predicateMI.getCodeAttributeInfo()); res = il.advanceIndex(4); assert res == true; } else { il.insertInstr(loadAccumInstr, predicateMI.getCodeAttributeInfo()); res = il.advanceIndex(); assert res == true; } il.deleteInstr(predicateMI.getCodeAttributeInfo()); predicateMI.getCodeAttributeInfo().setCode(il.getCode()); props.maxStack = Math.max(maxStack, 2); predicateMI.getCodeAttributeInfo().setProperties(props.maxStack, props.maxLocals); try { FileOutputStream fos = new FileOutputStream(clonedFile); predicateCF.write(fos); fos.close(); } catch (IOException e) { throw new ThreadCheckException("Could not write cloned predicate class file, target=" + clonedFile); } } gr = new PredicateAnnotationRecord(par.annotation, predicateClass, predicateMI, paramNames, paramTypes, new ArrayList<AAnnotationsAttributeInfo.Annotation.AMemberValue>(), par.passArguments, null, new HashMap<String, ArrayList<PredicateAnnotationRecord>>()); _generatedPredicateRecords.put(hashKey, gr); return gr; } "
" public static void main(String argv[]) { System.out.println("Starting URL tests"); System.out.println("Test 1: Simple URL test"); try { URL url = new URL("http", "www.fsf.org", 80, "/"); if (!url.getProtocol().equals("http") || !url.getHost().equals("www.fsf.org") || url.getPort() != 80 || !url.getFile().equals("/")) System.out.println("FAILED: Simple URL test"); System.out.println("URL is: " + url.toString()); URLConnection uc = url.openConnection(); if (uc instanceof HttpURLConnection) System.out.println("Got the expected connection type"); HttpURLConnection hc = (HttpURLConnection) uc; hc.connect(); System.out.flush(); System.out.println("Dumping response headers"); for (int i = 0; ; i++) { String key = hc.getHeaderFieldKey(i); if (key == null) break; System.out.println(key + ": " + hc.getHeaderField(i)); } System.out.flush(); System.out.println("Dumping contents"); BufferedReader br = new BufferedReader(new InputStreamReader(hc.getInputStream())); for (String str = br.readLine(); str != null; str = br.readLine()) { System.out.println(str); } System.out.flush(); hc.disconnect(); System.out.println("Content Type: " + hc.getContentType()); System.out.println("Content Encoding: " + hc.getContentEncoding()); System.out.println("Content Length: " + hc.getContentLength()); System.out.println("Date: " + hc.getDate()); System.out.println("Expiration: " + hc.getExpiration()); System.out.println("Last Modified: " + hc.getLastModified()); System.out.println("PASSED: Simple URL test"); } catch (IOException e) { System.out.println("FAILED: Simple URL test: " + e); } System.out.println("Test 2: URL parsing test"); try { URL url = new URL("http://www.urbanophile.com/arenn/trans/trans.html#mis"); if (!url.toString().equals("http://www.urbanophile.com/arenn/trans/trans.html#mis")) System.out.println("FAILED: Parse URL test: " + url.toString()); else { System.out.println("Parsed ok: " + url.toString()); url = new URL("http://www.foo.com:8080/#"); if (!url.toString().equals("http://www.foo.com:8080/#")) System.out.println("FAILED: Parse URL test: " + url.toString()); else { System.out.println("Parsed ok: " + url.toString()); url = new URL("http://www.bar.com/test:file/"); if (!url.toString().equals("http://www.bar.com/test:file/")) System.out.println("FAILED: Parse URL test: " + url.toString()); else { System.out.println("Parsed ok: " + url.toString()); url = new URL("http://www.gnu.org"); if (!url.toString().equals("http://www.gnu.org/")) System.out.println("FAILED: Parse URL test: " + url.toString()); else { System.out.println("Parsed ok: " + url.toString()); url = new URL("HTTP://www.fsf.org/"); if (!url.toString().equals("http://www.fsf.org/")) System.out.println("FAILED: Parse URL test: " + url.toString()); else { System.out.println("Parsed ok: " + url.toString()); System.out.println("PASSED: URL parse test"); } } } } } } catch (IOException e) { System.out.println("FAILED: URL parsing test: " + e); } System.out.println("Test 3: getContent test"); try { URL url = new URL("http://localhost/~arenn/services.txt"); Object obj = url.getContent(); System.out.println("Object type is: " + obj.getClass().getName()); if (obj instanceof InputStream) { System.out.println("Got InputStream, so dumping contents"); BufferedReader br = new BufferedReader(new InputStreamReader((InputStream) obj)); for (String str = br.readLine(); str != null; str = br.readLine()) System.out.println(str); br.close(); } else { System.out.println("FAILED: Object is not an InputStream"); } System.out.println("PASSED: getContent test"); } catch (IOException e) { System.out.println("FAILED: getContent test: " + e); } System.out.println("URL test complete"); } "
false
89
189,777
21,224,683
" 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 delete(String user) throws FidoDatabaseException { try { Connection conn = null; Statement stmt = null; try { conn = fido.util.FidoDataSource.getConnection(); conn.setAutoCommit(false); stmt = conn.createStatement(); stmt.executeUpdate("delete from Principals where PrincipalId = '" + user + "'"); stmt.executeUpdate("delete from Roles where PrincipalId = '" + user + "'"); 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); } } "
false
90
5,935,063
19,462,026
" public String generateKey(Message msg) { String text = msg.getDefaultMessage(); String meaning = msg.getMeaning(); if (text == null) { return null; } MessageDigest md5; try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { throw new RuntimeException("Error initializing MD5", e); } try { md5.update(text.getBytes("UTF-8")); if (meaning != null) { md5.update(meaning.getBytes("UTF-8")); } } catch (UnsupportedEncodingException e) { throw new RuntimeException("UTF-8 unsupported", e); } return StringUtils.toHexString(md5.digest()); } "
" public void copy(final File source, final File dest) throws IOException { final FileInputStream in = new FileInputStream(source); try { final FileOutputStream out = new FileOutputStream(dest); try { final FileChannel inChannel = in.getChannel(); final FileChannel outChannel = out.getChannel(); inChannel.transferTo(0, inChannel.size(), outChannel); } finally { out.close(); } } finally { in.close(); } } "
false
91
13,626,014
23,247,146
" public void createPartControl(Composite parent) { FormToolkit toolkit; toolkit = new FormToolkit(parent.getDisplay()); form = toolkit.createForm(parent); form.setText("Apple Inc."); toolkit.decorateFormHeading(form); form.getBody().setLayout(new GridLayout()); chart = createChart(); final DateAxis dateAxis = new DateAxis(); viewer = new GraphicalViewerImpl(); viewer.setRootEditPart(new ScalableRootEditPart()); viewer.setEditPartFactory(new ChartEditPartFactory(dateAxis)); viewer.createControl(form.getBody()); viewer.setContents(chart); viewer.setEditDomain(new EditDomain()); viewer.addSelectionChangedListener(new ISelectionChangedListener() { public void selectionChanged(SelectionChangedEvent event) { System.err.println("selectionChanged " + event.getSelection()); } }); viewer.addSelectionChangedListener(new ISelectionChangedListener() { public void selectionChanged(SelectionChangedEvent event) { deleteAction.update(); } }); ActionRegistry actionRegistry = new ActionRegistry(); createActions(actionRegistry); ContextMenuProvider cmProvider = new BlockContextMenuProvider(viewer, actionRegistry); viewer.setContextMenu(cmProvider); getSite().setSelectionProvider(viewer); deleteAction.setSelectionProvider(viewer); viewer.getEditDomain().getCommandStack().addCommandStackEventListener(new CommandStackEventListener() { public void stackChanged(CommandStackEvent event) { undoAction.setEnabled(viewer.getEditDomain().getCommandStack().canUndo()); redoAction.setEnabled(viewer.getEditDomain().getCommandStack().canRedo()); } }); Data data = Data.getData(); chart.setInput(data); DateRange dateRange = new DateRange(0, 50); dateAxis.setDates(data.date); dateAxis.setSelectedRange(dateRange); slider = new Slider(form.getBody(), SWT.NONE); slider.setMinimum(0); slider.setMaximum(data.close.length - 1); slider.setSelection(dateRange.start); slider.setThumb(dateRange.length); slider.addListener(SWT.Selection, new Listener() { public void handleEvent(Event event) { DateRange r = new DateRange(slider.getSelection(), slider.getThumb()); dateAxis.setSelectedRange(r); } }); final Scale spinner = new Scale(form.getBody(), SWT.NONE); spinner.setMinimum(5); spinner.setMaximum(data.close.length - 1); spinner.setSelection(dateRange.length); spinner.addListener(SWT.Selection, new Listener() { public void handleEvent(Event event) { slider.setThumb(spinner.getSelection()); DateRange r = new DateRange(slider.getSelection(), slider.getThumb()); dateAxis.setSelectedRange(r); } }); GridDataFactory.defaultsFor(viewer.getControl()).grab(true, true).align(GridData.FILL, GridData.FILL).applyTo(viewer.getControl()); GridDataFactory.defaultsFor(slider).grab(true, false).align(GridData.FILL, GridData.FILL).grab(true, false).applyTo(slider); GridDataFactory.defaultsFor(spinner).grab(true, false).align(GridData.FILL, GridData.FILL).grab(true, false).applyTo(spinner); getSite().getWorkbenchWindow().getSelectionService().addSelectionListener(this); } "
" @Override public synchronized HttpURLConnection getTileUrlConnection(int zoom, int tilex, int tiley) throws IOException { HttpURLConnection conn = null; try { String url = getTileUrl(zoom, tilex, tiley); conn = (HttpURLConnection) new URL(url).openConnection(); } catch (IOException e) { throw e; } catch (Exception e) { log.error("", e); throw new IOException(e); } try { i.set("conn", conn); i.eval("addHeaders(conn);"); } catch (EvalError e) { String msg = e.getMessage(); if (!AH_ERROR.equals(msg)) { log.error(e.getClass() + ": " + e.getMessage(), e); throw new IOException(e); } } return conn; } "
false
92
1,663,419
22,642,186
" private static void copyFile(File in, File out) throws IOException { FileChannel inChannel = new FileInputStream(in).getChannel(); FileChannel outChannel = new FileOutputStream(out).getChannel(); try { inChannel.transferTo(0, inChannel.size(), outChannel); } catch (IOException e) { throw e; } finally { if (inChannel != null) inChannel.close(); if (outChannel != null) outChannel.close(); } } "
" @Override protected int run(CmdLineParser parser) { final List<String> args = parser.getRemainingArgs(); if (args.isEmpty()) { System.err.println("summarysort :: WORKDIR not given."); return 3; } if (args.size() == 1) { System.err.println("summarysort :: INPATH not given."); return 3; } final String outS = (String) parser.getOptionValue(outputDirOpt); final Path wrkDir = new Path(args.get(0)), in = new Path(args.get(1)), out = outS == null ? null : new Path(outS); final boolean verbose = parser.getBoolean(verboseOpt); final Configuration conf = getConf(); final Timer t = new Timer(); try { @SuppressWarnings("deprecation") final int maxReduceTasks = new JobClient(new JobConf(conf)).getClusterStatus().getMaxReduceTasks(); conf.setInt("mapred.reduce.tasks", Math.max(1, maxReduceTasks * 9 / 10)); final Job job = sortOne(conf, in, wrkDir, "summarysort", ""); System.out.printf("summarysort :: Waiting for job completion...\n"); t.start(); if (!job.waitForCompletion(verbose)) { System.err.println("summarysort :: Job failed."); return 4; } System.out.printf("summarysort :: Job complete in %d.%03d s.\n", t.stopS(), t.fms()); } catch (IOException e) { System.err.printf("summarysort :: Hadoop error: %s\n", e); return 4; } catch (ClassNotFoundException e) { throw new RuntimeException(e); } catch (InterruptedException e) { throw new RuntimeException(e); } if (out != null) try { System.out.println("summarysort :: Merging output..."); t.start(); final FileSystem srcFS = wrkDir.getFileSystem(conf); final FileSystem dstFS = out.getFileSystem(conf); final OutputStream outs = dstFS.create(out); final FileStatus[] parts = srcFS.globStatus(new Path(wrkDir, in.getName() + "-[0-9][0-9][0-9][0-9][0-9][0-9]*")); { int i = 0; final Timer t2 = new Timer(); for (final FileStatus part : parts) { t2.start(); final InputStream ins = srcFS.open(part.getPath()); IOUtils.copyBytes(ins, outs, conf, false); ins.close(); System.out.printf("summarysort :: Merged part %d in %d.%03d s.\n", ++i, t2.stopS(), t2.fms()); } } for (final FileStatus part : parts) srcFS.delete(part.getPath(), false); outs.write(BlockCompressedStreamConstants.EMPTY_GZIP_BLOCK); outs.close(); System.out.printf("summarysort :: Merging complete in %d.%03d s.\n", t.stopS(), t.fms()); } catch (IOException e) { System.err.printf("summarysort :: Output merging failed: %s\n", e); return 5; } return 0; } "
true
93
17,267,680
11,103,449
" private String transferWSDL(String wsdlURL, String userPassword) throws WiseConnectionException { String filePath = null; try { URL endpoint = new URL(wsdlURL); HttpURLConnection conn = (HttpURLConnection) endpoint.openConnection(); conn.setDoOutput(false); conn.setDoInput(true); conn.setUseCaches(false); conn.setRequestMethod("GET"); conn.setRequestProperty("Accept", "text/xml,application/xml,application/xhtml+xml,text/html;q=0.9,text/plain;q=0.8,image/png,*/*;q=0.5"); conn.setRequestProperty("Connection", "close"); if (userPassword != null) { conn.setRequestProperty("Authorization", "Basic " + (new BASE64Encoder()).encode(userPassword.getBytes())); } InputStream is = null; if (conn.getResponseCode() == 200) { is = conn.getInputStream(); } else { is = conn.getErrorStream(); InputStreamReader isr = new InputStreamReader(is); StringWriter sw = new StringWriter(); char[] buf = new char[200]; int read = 0; while (read != -1) { read = isr.read(buf); sw.write(buf); } throw new WiseConnectionException("Remote server's response is an error: " + sw.toString()); } File file = new File(tmpDeployDir, new StringBuffer("Wise").append(IDGenerator.nextVal()).append(".xml").toString()); OutputStream fos = new BufferedOutputStream(new FileOutputStream(file)); IOUtils.copyStream(fos, is); fos.close(); is.close(); filePath = file.getPath(); } catch (WiseConnectionException wce) { throw wce; } catch (Exception e) { throw new WiseConnectionException("Wsdl download failed!", e); } return filePath; } "
" @Override public void run() { try { IOUtils.copy(_is, processOutStr); } catch (final IOException ioe) { proc.destroy(); } finally { IOUtils.closeQuietly(_is); IOUtils.closeQuietly(processOutStr); } } "
true
94
11,245,902
11,334,494
" public static void uploadFile(File in, String out, String host, int port, String path, String login, String password, boolean renameIfExist) throws IOException { FTPClient ftp = null; try { m_logCat.info("Uploading " + in + " to " + host + ":" + port + " at " + path); ftp = new FTPClient(); int reply; ftp.connect(host, port); m_logCat.info("Connected to " + host + "... Trying to authenticate"); reply = ftp.getReplyCode(); if (!FTPReply.isPositiveCompletion(reply)) { ftp.disconnect(); m_logCat.error("FTP server " + host + " refused connection."); throw new IOException("Cannot connect to the FTP Server: connection refused."); } if (!ftp.login(login, password)) { ftp.logout(); throw new IOException("Cannot connect to the FTP Server: login / password is invalid!"); } ftp.setFileType(FTP.BINARY_FILE_TYPE); if (!ftp.changeWorkingDirectory(path)) { m_logCat.warn("Remote working directory: " + path + "does not exist on the FTP Server ..."); m_logCat.info("Trying to create remote directory: " + path); if (!ftp.makeDirectory(path)) { m_logCat.error("Failed to create remote directory: " + path); throw new IOException("Failed to store " + in + " in the remote directory: " + path); } if (!ftp.changeWorkingDirectory(path)) { m_logCat.error("Failed to change directory. Unexpected error"); throw new IOException("Failed to change to remote directory : " + path); } } if (out == null) { out = in.getName(); if (out.startsWith("/")) { out = out.substring(1); } } if (renameIfExist) { String[] files = ftp.listNames(); String f = in + out; for (int i = 0; i < files.length; i++) { if (files[i].equals(out)) { m_logCat.debug("Found existing file on the server: " + out); boolean rename_ok = false; String bak = "_bak"; int j = 0; String newExt = null; while (!rename_ok) { if (j == 0) newExt = bak; else newExt = bak + j; if (ftp.rename(out, out + newExt)) { m_logCat.info(out + " renamed to " + out + newExt); rename_ok = true; } else { m_logCat.warn("Renaming to " + out + newExt + " has failed!, trying again ..."); j++; } } break; } } } InputStream input = new FileInputStream(in); m_logCat.info("Starting transfert of " + in); ftp.storeFile(out, input); m_logCat.info(in + " uploaded successfully"); input.close(); ftp.logout(); } catch (FTPConnectionClosedException e) { m_logCat.error("Server closed connection.", e); } finally { if (ftp.isConnected()) { try { ftp.disconnect(); } catch (IOException f) { } } } } "
" public void store(Component component, String componentName, int currentPilot) { try { PreparedStatement psta = jdbc.prepareStatement("UPDATE component_prop " + "SET size_height = ?, size_width = ?, pos_x = ?, pos_y = ? " + "WHERE pilot_id = ? " + "AND component_name = ?"); psta.setInt(1, component.getHeight()); psta.setInt(2, component.getWidth()); Point point = component.getLocation(); psta.setInt(3, point.x); psta.setInt(4, point.y); psta.setInt(5, currentPilot); psta.setString(6, componentName); int update = psta.executeUpdate(); if (update == 0) { psta = jdbc.prepareStatement("INSERT INTO component_prop " + "(size_height, size_width, pos_x, pos_y, pilot_id, component_name) " + "VALUES (?,?,?,?,?,?)"); psta.setInt(1, component.getHeight()); psta.setInt(2, component.getWidth()); psta.setInt(3, point.x); psta.setInt(4, point.y); psta.setInt(5, currentPilot); psta.setString(6, componentName); psta.executeUpdate(); } jdbc.commit(); } catch (SQLException e) { jdbc.rollback(); log.debug(e); } } "
false
95
7,344,728
15,286,502
" public static String hash(String plainText) throws Exception { MessageDigest m = MessageDigest.getInstance("MD5"); m.update(plainText.getBytes(), 0, plainText.length()); String hash = new BigInteger(1, m.digest()).toString(16); if (hash.length() == 31) { hash = "0" + hash; } return hash; } "
" public static String md5(String senha) { MessageDigest md = null; try { md = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { System.out.println("Ocorreu NoSuchAlgorithmException"); } md.update(senha.getBytes()); byte[] xx = md.digest(); String n2 = null; StringBuffer resposta = new StringBuffer(); for (int i = 0; i < xx.length; i++) { n2 = Integer.toHexString(0XFF & ((int) (xx[i]))); if (n2.length() < 2) { n2 = "0" + n2; } resposta.append(n2); } return resposta.toString(); } "
true
96
13,521,323
346,058
" public static void copyFile(final String inFile, final String outFile) { FileChannel in = null; FileChannel out = null; try { in = new FileInputStream(inFile).getChannel(); out = new FileOutputStream(outFile).getChannel(); in.transferTo(0, in.size(), out); } catch (final Exception e) { } finally { if (in != null) { try { in.close(); } catch (final Exception e) { } } if (out != null) { try { out.close(); } catch (final Exception e) { } } } } "
" private 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!"); } "
true
97
708,766
557,734
" private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } "
" public void constructAssociationView() { String className; String methodName; String field; boolean foundRead = false; boolean foundWrite = false; boolean classWritten = false; try { AssocView = new BufferedWriter(new FileWriter("InfoFiles/AssociationView.txt")); FileInputStream fstreamPC = new FileInputStream("InfoFiles/PrincipleClassGroup.txt"); DataInputStream inPC = new DataInputStream(fstreamPC); BufferedReader PC = new BufferedReader(new InputStreamReader(inPC)); while ((field = PC.readLine()) != null) { className = field; AssocView.write(className); AssocView.newLine(); classWritten = true; while ((methodName = PC.readLine()) != null) { if (methodName.contentEquals("EndOfClass")) break; AssocView.write("StartOfMethod"); AssocView.newLine(); AssocView.write(methodName); AssocView.newLine(); for (int i = 0; i < readFileCount && foundRead == false; i++) { if (methodName.compareTo(readArray[i]) == 0) { foundRead = true; for (int j = 1; readArray[i + j].compareTo("EndOfMethod") != 0; j++) { if (readArray[i + j].indexOf(".") > 0) { field = readArray[i + j].substring(0, readArray[i + j].indexOf(".")); if (isPrincipleClass(field) == true) { AssocView.write(readArray[i + j]); AssocView.newLine(); } } } } } for (int i = 0; i < writeFileCount && foundWrite == false; i++) { if (methodName.compareTo(writeArray[i]) == 0) { foundWrite = true; for (int j = 1; writeArray[i + j].compareTo("EndOfMethod") != 0; j++) { if (writeArray[i + j].indexOf(".") > 0) { field = writeArray[i + j].substring(0, writeArray[i + j].indexOf(".")); if (isPrincipleClass(field) == true) { AssocView.write(writeArray[i + j]); AssocView.newLine(); } } } } } AssocView.write("EndOfMethod"); AssocView.newLine(); foundRead = false; foundWrite = false; } if (classWritten == true) { AssocView.write("EndOfClass"); AssocView.newLine(); classWritten = false; } } PC.close(); AssocView.close(); } catch (IOException e) { e.printStackTrace(); } } "
true
98
7,346,958
16,005,909
" public static String SHA1(String text) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md; md = MessageDigest.getInstance("SHA-1"); byte[] sha1hash = new byte[40]; md.update(text.getBytes("iso-8859-1"), 0, text.length()); sha1hash = md.digest(); return convertToHex(sha1hash); } "
" public static byte[] hash(String identifier) { if (function.equals("SHA-1")) { try { MessageDigest md = MessageDigest.getInstance(function); md.reset(); byte[] code = md.digest(identifier.getBytes()); byte[] value = new byte[KEY_LENGTH / 8]; int shrink = code.length / value.length; int bitCount = 1; for (int j = 0; j < code.length * 8; j++) { int currBit = ((code[j / 8] & (1 << (j % 8))) >> j % 8); if (currBit == 1) bitCount++; if (((j + 1) % shrink) == 0) { int shrinkBit = (bitCount % 2 == 0) ? 0 : 1; value[j / shrink / 8] |= (shrinkBit << ((j / shrink) % 8)); bitCount = 1; } } return value; } catch (Exception e) { e.printStackTrace(); } } if (function.equals("CRC32")) { CRC32 crc32 = new CRC32(); crc32.reset(); crc32.update(identifier.getBytes()); long code = crc32.getValue(); code &= (0xffffffffffffffffL >>> (64 - KEY_LENGTH)); byte[] value = new byte[KEY_LENGTH / 8]; for (int i = 0; i < value.length; i++) { value[value.length - i - 1] = (byte) ((code >> 8 * i) & 0xff); } return value; } if (function.equals("Java")) { int code = identifier.hashCode(); code &= (0xffffffff >>> (32 - KEY_LENGTH)); byte[] value = new byte[KEY_LENGTH / 8]; for (int i = 0; i < value.length; i++) { value[value.length - i - 1] = (byte) ((code >> 8 * i) & 0xff); } return value; } return null; } "
true
99
8,023,601
10,896,362
" protected static List<Pattern> getBotPatterns() { List<Pattern> patterns = new ArrayList<Pattern>(); try { Enumeration<URL> urls = AbstractPustefixRequestHandler.class.getClassLoader().getResources("META-INF/org/pustefixframework/http/bot-user-agents.txt"); while (urls.hasMoreElements()) { URL url = urls.nextElement(); InputStream in = url.openStream(); BufferedReader reader = new BufferedReader(new InputStreamReader(in, "utf8")); String line; while ((line = reader.readLine()) != null) { line = line.trim(); if (!line.startsWith("#")) { Pattern pattern = Pattern.compile(line); patterns.add(pattern); } } in.close(); } } catch (IOException e) { throw new RuntimeException("Error reading bot user-agent configuration", e); } return patterns; } "
" private HttpResponse executePutPost(HttpEntityEnclosingRequestBase request, String content) { try { if (LOG.isTraceEnabled()) { LOG.trace("Content: {}", content); } StringEntity e = new StringEntity(content, "UTF-8"); e.setContentType("application/json"); request.setEntity(e); return executeRequest(request); } catch (Exception e) { throw Exceptions.propagate(e); } } "
false
End of preview (truncated to 100 rows)

Dataset Card for "code_x_glue_cc_clone_detection_big_clone_bench"

Dataset Summary

CodeXGLUE Clone-detection-BigCloneBench dataset, available at https://github.com/microsoft/CodeXGLUE/tree/main/Code-Code/Clone-detection-BigCloneBench

Given two codes as the input, the task is to do binary classification (0/1), where 1 stands for semantic equivalence and 0 for others. Models are evaluated by F1 score. The dataset we use is BigCloneBench and filtered following the paper Detecting Code Clones with Graph Neural Network and Flow-Augmented Abstract Syntax Tree.

Supported Tasks and Leaderboards

  • semantic-similarity-classification: The dataset can be used to train a model for classifying if two given java methods are cloens of each other.

Languages

  • Java programming language

Dataset Structure

Data Instances

An example of 'test' looks as follows.

{
    "func1": "    @Test(expected = GadgetException.class)\n    public void malformedGadgetSpecIsCachedAndThrows() throws Exception {\n        HttpRequest request = createCacheableRequest();\n        expect(pipeline.execute(request)).andReturn(new HttpResponse(\"malformed junk\")).once();\n        replay(pipeline);\n        try {\n            specFactory.getGadgetSpec(createContext(SPEC_URL, false));\n            fail(\"No exception thrown on bad parse\");\n        } catch (GadgetException e) {\n        }\n        specFactory.getGadgetSpec(createContext(SPEC_URL, false));\n    }\n", 
    "func2": "    public InputStream getInputStream() throws TGBrowserException {\n        try {\n            if (!this.isFolder()) {\n                URL url = new URL(this.url);\n                InputStream stream = url.openStream();\n                return stream;\n            }\n        } catch (Throwable throwable) {\n            throw new TGBrowserException(throwable);\n        }\n        return null;\n    }\n", 
    "id": 0, 
    "id1": 2381663, 
    "id2": 4458076, 
    "label": false
}

Data Fields

In the following each data field in go is explained for each config. The data fields are the same among all splits.

default

field name type description
id int32 Index of the sample
id1 int32 The first function id
id2 int32 The second function id
func1 string The full text of the first function
func2 string The full text of the second function
label bool 1 is the functions are not equivalent, 0 otherwise

Data Splits

name train validation test
default 901028 415416 415416

Dataset Creation

Curation Rationale

[More Information Needed]

Source Data

Initial Data Collection and Normalization

Data was mined from the IJaDataset 2.0 dataset. [More Information Needed]

Who are the source language producers?

[More Information Needed]

Annotations

Annotation process

Data was manually labeled by three judges by automatically identifying potential clones using search heuristics. [More Information Needed]

Who are the annotators?

[More Information Needed]

Personal and Sensitive Information

[More Information Needed]

Considerations for Using the Data

Social Impact of Dataset

[More Information Needed]

Discussion of Biases

Most of the clones are type 1 and 2 with type 3 and especially type 4 being rare.

[More Information Needed]

Other Known Limitations

[More Information Needed]

Additional Information

Dataset Curators

https://github.com/microsoft, https://github.com/madlag

Licensing Information

Computational Use of Data Agreement (C-UDA) License.

Citation Information

@inproceedings{svajlenko2014towards,
  title={Towards a big data curated benchmark of inter-project code clones},
  author={Svajlenko, Jeffrey and Islam, Judith F and Keivanloo, Iman and Roy, Chanchal K and Mia, Mohammad Mamun},
  booktitle={2014 IEEE International Conference on Software Maintenance and Evolution},
  pages={476--480},
  year={2014},
  organization={IEEE}
}

@inproceedings{wang2020detecting,
  title={Detecting Code Clones with Graph Neural Network and Flow-Augmented Abstract Syntax Tree},
  author={Wang, Wenhan and Li, Ge and Ma, Bo and Xia, Xin and Jin, Zhi},
  booktitle={2020 IEEE 27th International Conference on Software Analysis, Evolution and Reengineering (SANER)},
  pages={261--271},
  year={2020},
  organization={IEEE}
}

Contributions

Thanks to @madlag (and partly also @ncoop57) for adding this dataset.

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