label int64 0 1 | func1 stringlengths 173 53.1k | func2 stringlengths 173 53.1k | id int64 0 901k |
|---|---|---|---|
0 | private String md5(String s) { StringBuffer hexString = null; try { MessageDigest digest = MessageDigest.getInstance("MD5"); digest.update(s.getBytes()); byte messageDigest[] = digest.digest(); hexString = new StringBuffer(); for (int i = 0; i < messageDigest.length; i++) { String hashPart = Integer.toHexString(0xFF & messageDigest[i]); if (hashPart.length() == 1) { hashPart = "0" + hashPart; } hexString.append(hashPart); } } catch (NoSuchAlgorithmException e) { Log.e(this.getClass().getSimpleName(), "MD5 algorithm not present"); } return hexString != null ? hexString.toString() : null; } | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | 14,100 |
0 | public RegionInfo(String name, int databaseID, int units, float xMin, float xMax, float yMin, float yMax, float zMin, float zMax, String imageURL) { this.name = name; this.databaseID = databaseID; this.units = units; this.xMin = xMin; this.xMax = xMax; this.yMin = yMin; this.yMax = yMax; this.zMin = zMin; this.zMax = zMax; try { MessageDigest digest = MessageDigest.getInstance("SHA-1"); digest.update(this.name.getBytes()); ByteArrayOutputStream baos = new ByteArrayOutputStream(); DataOutputStream daos = new DataOutputStream(baos); daos.writeInt(this.databaseID); daos.writeInt(this.units); daos.writeDouble(this.xMin); daos.writeDouble(this.xMax); daos.writeDouble(this.yMin); daos.writeDouble(this.yMax); daos.writeDouble(this.zMin); daos.writeDouble(this.zMax); daos.flush(); byte[] hashValue = digest.digest(baos.toByteArray()); int hashCode = 0; for (int i = 0; i < hashValue.length; i++) { hashCode += (int) hashValue[i] << (i % 4); } this.hashcode = hashCode; } catch (Exception e) { throw new IllegalArgumentException("Error occurred while generating hashcode for region " + this.name); } if (imageURL != null) { URL url = null; try { url = new URL(imageURL); } catch (MalformedURLException murle) { } if (url != null) { BufferedImage tmpImage = null; try { tmpImage = ImageIO.read(url); } catch (Exception e) { e.printStackTrace(); } mapImage = tmpImage; } else this.mapImage = null; } else this.mapImage = null; } | static JSONObject executeMethod(HttpClient httpClient, HttpMethod method, int timeout) throws HttpRequestFailureException, HttpException, IOException, HttpRequestTimeoutException { try { method.getParams().setSoTimeout(timeout * 1000); int status = -1; JSONObject result = null; for (int i = 0; i < RETRY; i++) { System.out.println("Execute method[" + method.getURI() + "](try " + (i + 1) + ")"); status = httpClient.executeMethod(method); if (status == HttpStatus.SC_OK) { InputStream inputStream = method.getResponseBodyAsStream(); ByteArrayOutputStream baos = new ByteArrayOutputStream(); IOUtils.copy(inputStream, baos); String response = new String(baos.toByteArray(), "UTF-8"); System.out.println(response); result = JSONObject.fromString(response); if (result.has("status")) { String lingrStatus = result.getString("status"); if ("ok".equals(lingrStatus)) { break; } else { try { Thread.sleep(1000); } catch (InterruptedException e) { } } } } else { throw new HttpRequestFailureException(status); } } return result; } catch (SocketTimeoutException e) { throw new HttpRequestTimeoutException(e); } finally { method.releaseConnection(); } } | 14,101 |
1 | public void copyFile(String oldPath, String newPath) { try { int bytesum = 0; int byteread = 0; File oldfile = new File(oldPath); if (oldfile.exists()) { InputStream inStream = new FileInputStream(oldPath); FileOutputStream fs = new FileOutputStream(newPath); byte[] buffer = new byte[1444]; while ((byteread = inStream.read(buffer)) != -1) { bytesum += byteread; fs.write(buffer, 0, byteread); } inStream.close(); fs.close(); } } catch (Exception e) { e.printStackTrace(); } } | private static void copySmallFile(File sourceFile, File targetFile) throws BusinessException { LOG.debug("Copying SMALL file '" + sourceFile.getAbsolutePath() + "' to '" + targetFile.getAbsolutePath() + "'."); FileChannel inChannel = null; FileChannel outChannel = null; try { inChannel = new FileInputStream(sourceFile).getChannel(); outChannel = new FileOutputStream(targetFile).getChannel(); inChannel.transferTo(0, inChannel.size(), outChannel); } catch (IOException e) { throw new BusinessException("Could not copy file from '" + sourceFile.getAbsolutePath() + "' to '" + targetFile.getAbsolutePath() + "'!", e); } finally { try { if (inChannel != null) inChannel.close(); } catch (IOException e) { LOG.error("Could not close input stream!", e); } try { if (outChannel != null) outChannel.close(); } catch (IOException e) { LOG.error("Could not close output stream!", e); } } } | 14,102 |
1 | static void createCompleteXML(File file) { FileInputStream fis = null; FileOutputStream fos = null; try { fis = new FileInputStream(errorFile); fos = new FileOutputStream(file); byte[] data = new byte[Integer.parseInt(BlueXStatics.prop.getProperty("allocationUnit"))]; int offset; while ((offset = fis.read(data)) != -1) fos.write(data, 0, offset); } catch (Exception e) { e.printStackTrace(); } finally { try { fis.close(); } catch (Exception e) { } try { fos.close(); } catch (Exception e) { } } FileWriter fw = null; try { fw = new FileWriter(file, true); fw.append("</detail>"); fw.append("\n</exception>"); fw.append("\n</log>"); } catch (Exception e) { e.printStackTrace(); } finally { try { fw.close(); } catch (Exception e) { } } } | public void insertStringInFile(String file, String textToInsert, long fromByte, long toByte) throws Exception { String tmpFile = file + ".tmp"; BufferedInputStream in = null; BufferedOutputStream out = null; long byteCount = 0; try { in = new BufferedInputStream(new FileInputStream(new File(file))); out = new BufferedOutputStream(new FileOutputStream(tmpFile)); long size = fromByte; byte[] buf = null; if (size == 0) { } else { buf = new byte[(int) size]; int length = -1; if ((length = in.read(buf)) != -1) { out.write(buf, 0, length); byteCount = byteCount + length; } else { String msg = "Failed to read the first '" + size + "' bytes of file '" + file + "'. This might be a programming error."; logger.warning(msg); throw new Exception(msg); } } buf = textToInsert.getBytes(); int length = buf.length; out.write(buf, 0, length); byteCount = byteCount + length; long skipLength = toByte - fromByte; long skippedBytes = in.skip(skipLength); if (skippedBytes == -1) { } else { buf = new byte[4096]; length = -1; while ((length = in.read(buf)) != -1) { out.write(buf, 0, length); byteCount = byteCount + length; } } in.close(); in = null; out.close(); out = null; File fileToDelete = new File(file); boolean wasDeleted = fileToDelete.delete(); if (!wasDeleted) { String msg = "Failed to delete the original file '" + file + "' to replace it with the modified file after text insertion."; logger.warning(msg); throw new Exception(msg); } File fileToRename = new File(tmpFile); boolean wasRenamed = fileToRename.renameTo(fileToDelete); if (!wasRenamed) { String msg = "Failed to rename tmp file '" + tmpFile + "' to the name of the original file '" + file + "'"; logger.warning(msg); throw new Exception(msg); } } catch (Exception e) { logger.log(Level.WARNING, "Failed to read/write file '" + file + "'.", e); throw e; } finally { if (in != null) { try { in.close(); } catch (IOException e) { logger.log(Level.FINEST, "Ignoring error closing input file '" + file + "'.", e); } } if (out != null) { try { out.close(); } catch (IOException e) { logger.log(Level.FINEST, "Ignoring error closing output file '" + tmpFile + "'.", e); } } } } | 14,103 |
0 | 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 Message[] expunge() throws MessagingException { Statement oStmt = null; CallableStatement oCall = null; PreparedStatement oUpdt = null; ResultSet oRSet; if (DebugFile.trace) { DebugFile.writeln("Begin DBFolder.expunge()"); DebugFile.incIdent(); } if (0 == (iOpenMode & READ_WRITE)) { if (DebugFile.trace) DebugFile.decIdent(); throw new javax.mail.FolderClosedException(this, "Folder is not open is READ_WRITE mode"); } if ((0 == (iOpenMode & MODE_MBOX)) && (0 == (iOpenMode & MODE_BLOB))) { if (DebugFile.trace) DebugFile.decIdent(); throw new javax.mail.FolderClosedException(this, "Folder is not open in MBOX nor BLOB mode"); } MboxFile oMBox = null; DBSubset oDeleted = new DBSubset(DB.k_mime_msgs, DB.gu_mimemsg + "," + DB.pg_message, DB.bo_deleted + "=1 AND " + DB.gu_category + "='" + oCatg.getString(DB.gu_category) + "'", 100); try { int iDeleted = oDeleted.load(getConnection()); File oFile = getFile(); if (oFile.exists() && iDeleted > 0) { oMBox = new MboxFile(oFile, MboxFile.READ_WRITE); int[] msgnums = new int[iDeleted]; for (int m = 0; m < iDeleted; m++) msgnums[m] = oDeleted.getInt(1, m); oMBox.purge(msgnums); oMBox.close(); } oStmt = oConn.createStatement(ResultSet.TYPE_FORWARD_ONLY, ResultSet.CONCUR_READ_ONLY); oRSet = oStmt.executeQuery("SELECT p." + DB.file_name + " FROM " + DB.k_mime_parts + " p," + DB.k_mime_msgs + " m WHERE p." + DB.gu_mimemsg + "=m." + DB.gu_mimemsg + " AND m." + DB.id_disposition + "='reference' AND m." + DB.bo_deleted + "=1 AND m." + DB.gu_category + "='" + oCatg.getString(DB.gu_category) + "'"); while (oRSet.next()) { String sFileName = oRSet.getString(1); if (!oRSet.wasNull()) { try { File oRef = new File(sFileName); oRef.delete(); } catch (SecurityException se) { if (DebugFile.trace) DebugFile.writeln("SecurityException " + sFileName + " " + se.getMessage()); } } } oRSet.close(); oRSet = null; oStmt.close(); oStmt = null; oFile = getFile(); oStmt = oConn.createStatement(); oStmt.executeUpdate("UPDATE " + DB.k_categories + " SET " + DB.len_size + "=" + String.valueOf(oFile.length()) + " WHERE " + DB.gu_category + "='" + getCategory().getString(DB.gu_category) + "'"); oStmt.close(); oStmt = null; if (oConn.getDataBaseProduct() == JDCConnection.DBMS_POSTGRESQL) { oStmt = oConn.createStatement(); for (int d = 0; d < iDeleted; d++) oStmt.executeQuery("SELECT k_sp_del_mime_msg('" + oDeleted.getString(0, d) + "')"); oStmt.close(); oStmt = null; } else { oCall = oConn.prepareCall("{ call k_sp_del_mime_msg(?) }"); for (int d = 0; d < iDeleted; d++) { oCall.setString(1, oDeleted.getString(0, d)); oCall.execute(); } oCall.close(); oCall = null; } if (oFile.exists() && iDeleted > 0) { BigDecimal oUnit = new BigDecimal(1); oStmt = oConn.createStatement(ResultSet.TYPE_FORWARD_ONLY, ResultSet.CONCUR_READ_ONLY); oRSet = oStmt.executeQuery("SELECT MAX(" + DB.pg_message + ") FROM " + DB.k_mime_msgs + " WHERE " + DB.gu_category + "='getCategory().getString(DB.gu_category)'"); oRSet.next(); BigDecimal oMaxPg = oRSet.getBigDecimal(1); if (oRSet.wasNull()) oMaxPg = new BigDecimal(0); oRSet.close(); oRSet = null; oStmt.close(); oStmt = null; oMaxPg = oMaxPg.add(oUnit); oStmt = oConn.createStatement(); oStmt.executeUpdate("UPDATE " + DB.k_mime_msgs + " SET " + DB.pg_message + "=" + DB.pg_message + "+" + oMaxPg.toString() + " WHERE " + DB.gu_category + "='" + getCategory().getString(DB.gu_category) + "'"); oStmt.close(); oStmt = null; DBSubset oMsgSet = new DBSubset(DB.k_mime_msgs, DB.gu_mimemsg + "," + DB.pg_message, DB.gu_category + "='" + getCategory().getString(DB.gu_category) + "' ORDER BY " + DB.pg_message, 1000); int iMsgCount = oMsgSet.load(oConn); oMBox = new MboxFile(oFile, MboxFile.READ_ONLY); long[] aPositions = oMBox.getMessagePositions(); oMBox.close(); if (iMsgCount != aPositions.length) { throw new IOException("DBFolder.expunge() Message count of " + String.valueOf(aPositions.length) + " at MBOX file " + oFile.getName() + " does not match message count at database index of " + String.valueOf(iMsgCount)); } oMaxPg = new BigDecimal(0); oUpdt = oConn.prepareStatement("UPDATE " + DB.k_mime_msgs + " SET " + DB.pg_message + "=?," + DB.nu_position + "=? WHERE " + DB.gu_mimemsg + "=?"); for (int m = 0; m < iMsgCount; m++) { oUpdt.setBigDecimal(1, oMaxPg); oUpdt.setBigDecimal(2, new BigDecimal(aPositions[m])); oUpdt.setString(3, oMsgSet.getString(0, m)); oUpdt.executeUpdate(); oMaxPg = oMaxPg.add(oUnit); } oUpdt.close(); } oConn.commit(); } catch (SQLException sqle) { try { if (oMBox != null) oMBox.close(); } catch (Exception e) { } try { if (oStmt != null) oStmt.close(); } catch (Exception e) { } try { if (oCall != null) oCall.close(); } catch (Exception e) { } try { if (oConn != null) oConn.rollback(); } catch (Exception e) { } throw new MessagingException(sqle.getMessage(), sqle); } catch (IOException sqle) { try { if (oMBox != null) oMBox.close(); } catch (Exception e) { } try { if (oStmt != null) oStmt.close(); } catch (Exception e) { } try { if (oCall != null) oCall.close(); } catch (Exception e) { } try { if (oConn != null) oConn.rollback(); } catch (Exception e) { } throw new MessagingException(sqle.getMessage(), sqle); } if (DebugFile.trace) { DebugFile.decIdent(); DebugFile.writeln("End DBFolder.expunge()"); } return null; } | 14,104 |
1 | public static void copy(Object arg1, Object arg2) { Writer writer = null; Reader reader = null; InputStream inStream = null; OutputStream outStream = null; try { if (arg2 instanceof Writer) { writer = (Writer) arg2; if (arg1 instanceof Reader) { reader = (Reader) arg1; copy(reader, writer); } else if (arg1 instanceof String) { reader = new FileReader(new File((String) arg1)); copy(reader, writer); } else if (arg1 instanceof File) { reader = new FileReader((File) arg1); copy(reader, writer); } else if (arg1 instanceof URL) { copy(((URL) arg1).openStream(), writer); } else if (arg1 instanceof InputStream) { reader = new InputStreamReader((InputStream) arg1); copy(reader, writer); } else if (arg1 instanceof RandomAccessFile) { copy((RandomAccessFile) arg1, writer); } else { throw new TypeError("Invalid first argument to copy()"); } } else if (arg2 instanceof OutputStream) { outStream = (OutputStream) arg2; if (arg1 instanceof Reader) { copy((Reader) arg1, new OutputStreamWriter(outStream)); } else if (arg1 instanceof String) { inStream = new FileInputStream(new File((String) arg1)); copy(inStream, outStream); } else if (arg1 instanceof File) { inStream = new FileInputStream((File) arg1); copy(inStream, outStream); } else if (arg1 instanceof URL) { copy(((URL) arg1).openStream(), outStream); } else if (arg1 instanceof InputStream) { copy((InputStream) arg1, outStream); } else if (arg1 instanceof RandomAccessFile) { copy((RandomAccessFile) arg1, outStream); } else { throw new TypeError("Invalid first argument to copy()"); } } else if (arg2 instanceof RandomAccessFile) { RandomAccessFile out = (RandomAccessFile) arg2; if (arg1 instanceof Reader) { copy((Reader) arg1, out); } else if (arg1 instanceof String) { inStream = new FileInputStream(new File((String) arg1)); copy(inStream, out); } else if (arg1 instanceof File) { inStream = new FileInputStream((File) arg1); copy(inStream, out); } else if (arg1 instanceof URL) { copy(((URL) arg1).openStream(), out); } else if (arg1 instanceof InputStream) { copy((InputStream) arg1, out); } else if (arg1 instanceof RandomAccessFile) { copy((RandomAccessFile) arg1, out); } else { throw new TypeError("Invalid first argument to copy()"); } } else if (arg2 instanceof File || arg2 instanceof String) { File outFile = null; if (arg2 instanceof File) { outFile = (File) arg2; } else { outFile = new File((String) arg2); } outStream = new FileOutputStream(outFile); if (arg1 instanceof Reader) { copy((Reader) arg1, new OutputStreamWriter(outStream)); } else if (arg1 instanceof String) { inStream = new FileInputStream(new File((String) arg1)); copy(inStream, outStream); } else if (arg1 instanceof File) { inStream = new FileInputStream((File) arg1); copy(inStream, outStream); } else if (arg1 instanceof URL) { copy(((URL) arg1).openStream(), outStream); } else if (arg1 instanceof InputStream) { copy((InputStream) arg1, outStream); } else if (arg1 instanceof RandomAccessFile) { copy((RandomAccessFile) arg1, outStream); } else { throw new TypeError("Invalid first argument to copy()"); } } else { throw new TypeError("Invalid second argument to copy()"); } } catch (IOException e) { throw new IOError(e.getMessage(), e); } } | public void testOptionalSections() throws Exception { final File implementationDirectory = this.getTestSourcesDirectory(); final File specificationDirectory = this.getTestSourcesDirectory(); IOUtils.copy(this.getClass().getResourceAsStream("ImplementationWithoutConstructorsSection.java.txt"), new FileOutputStream(new File(implementationDirectory, "Implementation.java"))); this.getTestTool().manageSources(this.getTestTool().getModules().getImplementation("Implementation"), implementationDirectory); IOUtils.copy(this.getClass().getResourceAsStream("ImplementationWithoutDefaultConstructorSection.java.txt"), new FileOutputStream(new File(implementationDirectory, "Implementation.java"))); this.getTestTool().manageSources(this.getTestTool().getModules().getImplementation("Implementation"), implementationDirectory); IOUtils.copy(this.getClass().getResourceAsStream("ImplementationWithoutDocumentationSection.java.txt"), new FileOutputStream(new File(implementationDirectory, "Implementation.java"))); this.getTestTool().manageSources(this.getTestTool().getModules().getImplementation("Implementation"), implementationDirectory); IOUtils.copy(this.getClass().getResourceAsStream("ImplementationWithoutLicenseSection.java.txt"), new FileOutputStream(new File(implementationDirectory, "Implementation.java"))); this.getTestTool().manageSources(this.getTestTool().getModules().getImplementation("Implementation"), implementationDirectory); IOUtils.copy(this.getClass().getResourceAsStream("SpecificationWithoutDocumentationSection.java.txt"), new FileOutputStream(new File(specificationDirectory, "Specification.java"))); this.getTestTool().manageSources(this.getTestTool().getModules().getSpecification("Specification"), specificationDirectory); IOUtils.copy(this.getClass().getResourceAsStream("SpecificationWithoutLicenseSection.java.txt"), new FileOutputStream(new File(specificationDirectory, "Specification.java"))); this.getTestTool().manageSources(this.getTestTool().getModules().getSpecification("Specification"), specificationDirectory); } | 14,105 |
1 | public static void nuovoAcquisto(int quantita, Date d, double price, int id) throws SQLException { MyDBConnection c = new MyDBConnection(); c.init(); Connection conn = c.getMyConnection(); PreparedStatement ps = conn.prepareStatement(insertAcquisto); ps.setInt(1, quantita); ps.setDate(2, d); ps.setDouble(3, price); ps.setInt(4, id); ps.executeUpdate(); double newPrice = price; int newQ = quantita; ResultSet rs = MyDBConnection.executeQuery(queryPrezzo.replace("?", "" + id), conn); if (rs.next()) { int oldQ = rs.getInt(1); double oldPrice = rs.getDouble(2); newQ = quantita + oldQ; newPrice = (oldPrice * oldQ + price * quantita) / newQ; updatePortafoglio(conn, newPrice, newQ, id); } else insertPortafoglio(conn, id, newPrice, newQ); try { conn.commit(); } catch (SQLException e) { conn.rollback(); throw new SQLException("Effettuato rollback dopo " + e.getMessage()); } finally { c.close(); } } | public void removeForwardAddress(final List<NewUser> forwardAddresses) { try { final List<Integer> usersToRemoveFromCache = new ArrayList<Integer>(); connection.setAutoCommit(false); new ProcessEnvelope().executeNull(new ExecuteProcessAbstractImpl(connection, false, false, true, true) { @Override public void executeProcessReturnNull() throws SQLException { psImpl = connImpl.prepareStatement(sqlCommands.getProperty("userForwardAddresses.delete")); Iterator<NewUser> iter = forwardAddresses.iterator(); Iterator<Integer> iter2; NewUser newUser; while (iter.hasNext()) { newUser = iter.next(); iter2 = newUser.forwardAddressIds.iterator(); while (iter2.hasNext()) { psImpl.setInt(1, iter2.next()); psImpl.executeUpdate(); } usersToRemoveFromCache.add(newUser.userId); } } }); connection.commit(); cmDB.removeUsers(usersToRemoveFromCache); } catch (SQLException sqle) { log.error(sqle); if (connection != null) { try { connection.rollback(); } catch (SQLException ex) { } } } finally { if (connection != null) { try { connection.setAutoCommit(true); } catch (SQLException ex) { } } } } | 14,106 |
1 | 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); } | protected void onSubmit() { super.onSubmit(); if (!this.hasError()) { final FileUpload upload = fileUploadField.getFileUpload(); if (upload != null) { try { StringWriter xmlSourceWriter = new StringWriter(); IOUtils.copy(upload.getInputStream(), xmlSourceWriter); processSubmittedDoap(xmlSourceWriter.toString()); } catch (IOException e) { setResponsePage(new ErrorReportPage(new UserReportableException("Unable to add doap using RDF supplied", DoapFormPage.class, e))); } } } } | 14,107 |
0 | public String getpage(String leurl) throws Exception { int data; StringBuffer lapage = new StringBuffer(); URL myurl = new URL(leurl); URLConnection conn = myurl.openConnection(); conn.connect(); if (!Pattern.matches("HTTP/... 2.. .*", conn.getHeaderField(0).toString())) { System.out.println(conn.getHeaderField(0).toString()); return lapage.toString(); } InputStream in = conn.getInputStream(); for (data = in.read(); data != -1; data = in.read()) lapage.append((char) data); return lapage.toString(); } | public static InputStream openRemoteFile(URL urlParam) throws KExceptionClass { InputStream result = null; try { result = urlParam.openStream(); } catch (IOException error) { String message = new String(); message = "No se puede abrir el recurso ["; message += urlParam.toString(); message += "]["; message += error.toString(); message += "]"; throw new KExceptionClass(message, error); } ; return (result); } | 14,108 |
0 | private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException { in.defaultReadObject(); OutputStream output = getOutputStream(); if (cachedContent != null) { output.write(cachedContent); } else { FileInputStream input = new FileInputStream(dfosFile); IOUtils.copy(input, output); dfosFile.delete(); dfosFile = null; } output.close(); cachedContent = null; } | public static String getHighlightBaseLib() throws Exception { StringBuffer highlightKey = new StringBuffer(); highlightKey.append("<c color=\"" + COLOR_BASELIB + "\">\n\t"); URL url = AbstractRunner.class.getResource("baselib.js"); if (url != null) { InputStream is = url.openStream(); InputStreamReader reader = new InputStreamReader(is, "UTF-8"); BufferedReader bfReader = new BufferedReader(reader); String tmp = null; do { tmp = bfReader.readLine(); if (tmp != null) { if (tmp.indexOf("function") > -1) { highlightKey.append("<w>" + (tmp.substring(tmp.indexOf("function") + 8, tmp.indexOf("(")).trim()) + "</w>\n\t"); } } } while (tmp != null); bfReader.close(); reader.close(); is.close(); } highlightKey.append("</c>"); return highlightKey.toString(); } | 14,109 |
1 | public String encrypt(String plaintext) throws Exception { MessageDigest md = null; try { md = MessageDigest.getInstance("SHA"); } catch (NoSuchAlgorithmException e) { throw new Exception(e.getMessage()); } try { md.update(plaintext.getBytes("UTF-8")); } catch (UnsupportedEncodingException e) { throw new Exception(e.getMessage()); } byte raw[] = md.digest(); String hash = (new BASE64Encoder()).encode(raw); return hash; } | public static String SHA(String s) { try { MessageDigest md = MessageDigest.getInstance("SHA"); md.update(s.getBytes(), 0, s.getBytes().length); byte[] hash = md.digest(); StringBuilder sb = new StringBuilder(); int msb; int lsb = 0; int i; for (i = 0; i < hash.length; i++) { msb = ((int) hash[i] & 0x000000FF) / 16; lsb = ((int) hash[i] & 0x000000FF) % 16; sb.append(hexChars[msb]); sb.append(hexChars[lsb]); } return sb.toString(); } catch (NoSuchAlgorithmException e) { return null; } } | 14,110 |
0 | private void displayDiffResults() throws IOException { File outFile = File.createTempFile("diff", ".htm"); outFile.deleteOnExit(); FileOutputStream outStream = new FileOutputStream(outFile); BufferedWriter out = new BufferedWriter(new OutputStreamWriter(outStream)); out.write("<html><head><title>LOC Differences</title>\n" + SCRIPT + "</head>\n" + "<body bgcolor='#ffffff'>\n" + "<div onMouseOver=\"window.defaultStatus='Metrics'\">\n"); if (addedTable.length() > 0) { out.write("<table border><tr><th>Files Added:</th>" + "<th>Add</th><th>Type</th></tr>"); out.write(addedTable.toString()); out.write("</table><br><br>"); } if (modifiedTable.length() > 0) { out.write("<table border><tr><th>Files Modified:</th>" + "<th>Base</th><th>Del</th><th>Mod</th><th>Add</th>" + "<th>Total</th><th>Type</th></tr>"); out.write(modifiedTable.toString()); out.write("</table><br><br>"); } if (deletedTable.length() > 0) { out.write("<table border><tr><th>Files Deleted:</th>" + "<th>Del</th><th>Type</th></tr>"); out.write(deletedTable.toString()); out.write("</table><br><br>"); } out.write("<table name=METRICS BORDER>\n"); if (modifiedTable.length() > 0 || deletedTable.length() > 0) { out.write("<tr><td>Base: </td><td>"); out.write(Long.toString(base)); out.write("</td></tr>\n<tr><td>Deleted: </td><td>"); out.write(Long.toString(deleted)); out.write("</td></tr>\n<tr><td>Modified: </td><td>"); out.write(Long.toString(modified)); out.write("</td></tr>\n<tr><td>Added: </td><td>"); out.write(Long.toString(added)); out.write("</td></tr>\n<tr><td>New & Changed: </td><td>"); out.write(Long.toString(added + modified)); out.write("</td></tr>\n"); } out.write("<tr><td>Total: </td><td>"); out.write(Long.toString(total)); out.write("</td></tr>\n</table></div>"); redlinesOut.close(); out.flush(); InputStream redlines = new FileInputStream(redlinesTempFile); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = redlines.read(buffer)) != -1) outStream.write(buffer, 0, bytesRead); outStream.write("</BODY></HTML>".getBytes()); outStream.close(); Browser.launch(outFile.toURL().toString()); } | public TreeMap getStrainMap() { TreeMap strainMap = new TreeMap(); String server = ""; try { Datasource[] ds = DatasourceManager.getDatasouce(alias, version, DatasourceManager.ALL_CONTAINS_GROUP); for (int i = 0; i < ds.length; i++) { if (ds[i].getDescription().startsWith(MOUSE_DBSNP)) { if (ds[i].getServer().length() == 0) { Connection con = ds[i].getConnection(); strainMap = Action.lineMode.regularSQL.GenotypeDataSearchAction.getStrainMap(con); break; } else { server = ds[i].getServer(); HashMap serverUrlMap = InitXml.getInstance().getServerMap(); String serverUrl = (String) serverUrlMap.get(server); URL url = new URL(serverUrl + servletName); URLConnection uc = url.openConnection(); uc.setDoOutput(true); OutputStream os = uc.getOutputStream(); StringBuffer buf = new StringBuffer(); buf.append("viewType=getstrains"); buf.append("&hHead=" + hHead); buf.append("&hCheck=" + version); PrintStream ps = new PrintStream(os); ps.print(buf.toString()); ps.close(); ObjectInputStream ois = new ObjectInputStream(uc.getInputStream()); strainMap = (TreeMap) ois.readObject(); ois.close(); } } } } catch (Exception e) { log.error("strain map", e); } return strainMap; } | 14,111 |
0 | public static void main(String[] args) throws Exception { String infile = "C:\\copy.sql"; String outfile = "C:\\copy.txt"; FileInputStream fin = new FileInputStream(infile); FileOutputStream fout = new FileOutputStream(outfile); FileChannel fcin = fin.getChannel(); FileChannel fcout = fout.getChannel(); ByteBuffer buffer = ByteBuffer.allocate(1024); while (true) { buffer.clear(); int r = fcin.read(buffer); if (r == -1) { break; } buffer.flip(); fcout.write(buffer); } } | protected void onSubmit() { try { Connection conn = ((JdbcRequestCycle) getRequestCycle()).getConnection(); String sql = "insert into entry (author, accessibility) values(?,?)"; PreparedStatement pstmt = conn.prepareStatement(sql); pstmt.setInt(1, userId); pstmt.setInt(2, accessibility.getId()); pstmt.executeUpdate(); ResultSet insertedEntryIdRs = pstmt.getGeneratedKeys(); insertedEntryIdRs.next(); int insertedEntryId = insertedEntryIdRs.getInt(1); sql = "insert into revisions (title, entry, content, tags," + " revision_remark) values(?,?,?,?,?)"; PreparedStatement pstmt2 = conn.prepareStatement(sql); pstmt2.setString(1, getTitle()); pstmt2.setInt(2, insertedEntryId); pstmt2.setString(3, getContent()); pstmt2.setString(4, getTags()); pstmt2.setString(5, "newly added"); int insertCount = pstmt2.executeUpdate(); if (insertCount > 0) { info("Successfully added one new record."); } else { conn.rollback(); info("Addition of one new record failed."); } } catch (SQLException ex) { ex.printStackTrace(); } } | 14,112 |
1 | private void copyFile(File dir, File fileToAdd) { try { byte[] readBuffer = new byte[1024]; File file = new File(dir.getCanonicalPath() + File.separatorChar + fileToAdd.getName()); if (file.createNewFile()) { FileInputStream fis = new FileInputStream(fileToAdd); FileOutputStream fos = new FileOutputStream(file); int bytesRead; do { bytesRead = fis.read(readBuffer); fos.write(readBuffer, 0, bytesRead); } while (bytesRead == 0); fos.flush(); fos.close(); fis.close(); } else { logger.severe("unable to create file:" + file.getAbsolutePath()); } } catch (IOException ioe) { logger.severe("unable to create file:" + ioe); } } | private int mergeFiles(Merge merge) throws MojoExecutionException { String encoding = DEFAULT_ENCODING; if (merge.getEncoding() != null && merge.getEncoding().length() > 0) { encoding = merge.getEncoding(); } int numMergedFiles = 0; Writer ostream = null; FileOutputStream fos = null; try { fos = new FileOutputStream(merge.getTargetFile(), true); ostream = new OutputStreamWriter(fos, encoding); BufferedWriter output = new BufferedWriter(ostream); for (String orderingName : this.orderingNames) { List<File> files = this.orderedFiles.get(orderingName); if (files != null) { getLog().info("Appending: " + files.size() + " files that matched the name: " + orderingName + " to the target file: " + merge.getTargetFile().getAbsolutePath() + "..."); for (File file : files) { String fileName = file.getName(); getLog().info("Appending file: " + fileName + " to the target file: " + merge.getTargetFile().getAbsolutePath() + "..."); InputStream input = null; try { input = new FileInputStream(file); if (merge.getSeparator() != null && merge.getSeparator().trim().length() > 0) { String replaced = merge.getSeparator().trim(); replaced = replaced.replace("\n", ""); replaced = replaced.replace("\t", ""); replaced = replaced.replace("#{file.name}", fileName); replaced = replaced.replace("#{parent.name}", file.getParentFile() != null ? file.getParentFile().getName() : ""); replaced = replaced.replace("\\n", "\n"); replaced = replaced.replace("\\t", "\t"); getLog().debug("Appending separator: " + replaced); IOUtils.copy(new StringReader(replaced), output); } IOUtils.copy(input, output, encoding); } catch (IOException ioe) { throw new MojoExecutionException("Failed to append file: " + fileName + " to output file", ioe); } finally { IOUtils.closeQuietly(input); } numMergedFiles++; } } } output.flush(); } catch (IOException ioe) { throw new MojoExecutionException("Failed to open stream file to output file: " + merge.getTargetFile().getAbsolutePath(), ioe); } finally { if (fos != null) { IOUtils.closeQuietly(fos); } if (ostream != null) { IOUtils.closeQuietly(ostream); } } return numMergedFiles; } | 14,113 |
0 | public void parse(Project project, Object source, RootHandler handler) { AntXMLContext context = (AntXMLContext) Reflect.getField(handler, "context"); File buildFile = null; URL url = null; String buildFileName = null; if (source instanceof File) { buildFile = (File) source; buildFile = fu.normalize(buildFile.getAbsolutePath()); context.setBuildFile(buildFile); buildFileName = buildFile.toString(); } else if (source instanceof URL) { url = (URL) source; buildFileName = url.toString(); } else { throw new BuildException("Source " + source.getClass().getName() + " not supported by this plugin"); } InputStream inputStream = null; InputSource inputSource = null; try { XMLReader parser = JAXPUtils.getNamespaceXMLReader(); String uri = null; if (buildFile != null) { uri = fu.toURI(buildFile.getAbsolutePath()); inputStream = new FileInputStream(buildFile); } else { inputStream = url.openStream(); uri = url.toString(); } inputSource = new InputSource(inputStream); if (uri != null) { inputSource.setSystemId(uri); } project.log("parsing buildfile " + buildFileName + " with URI = " + uri, Project.MSG_VERBOSE); DefaultHandler hb = handler; parser.setContentHandler(hb); parser.setEntityResolver(hb); parser.setErrorHandler(hb); parser.setDTDHandler(hb); parser.parse(inputSource); } catch (SAXParseException exc) { Location location = new Location(exc.getSystemId(), exc.getLineNumber(), exc.getColumnNumber()); Throwable t = exc.getException(); if (t instanceof BuildException) { BuildException be = (BuildException) t; if (be.getLocation() == Location.UNKNOWN_LOCATION) { be.setLocation(location); } throw be; } throw new BuildException(exc.getMessage(), t, location); } catch (SAXException exc) { Throwable t = exc.getException(); if (t instanceof BuildException) { throw (BuildException) t; } throw new BuildException(exc.getMessage(), t); } catch (FileNotFoundException exc) { throw new BuildException(exc); } catch (UnsupportedEncodingException exc) { throw new BuildException("Encoding of project file " + buildFileName + " is invalid.", exc); } catch (IOException exc) { throw new BuildException("Error reading project file " + buildFileName + ": " + exc.getMessage(), exc); } finally { if (inputStream != null) { try { inputStream.close(); } catch (IOException ioe) { } } } } | public InputStream getResourceAsStream(String name) { try { URL url = getResource(name); System.out.println("Loading \"" + url + "\"..."); URLConnection urlConnection = url.openConnection(); if (urlConnection instanceof HttpURLConnection) { HttpURLConnection httpURLConnection = (HttpURLConnection) urlConnection; httpURLConnection.setFollowRedirects(true); httpURLConnection.setRequestMethod("GET"); int responseCode = httpURLConnection.getResponseCode(); System.out.println(httpURLConnection.getResponseMessage() + ", " + httpURLConnection.getContentLength() + " bytes" + ", " + new Date(httpURLConnection.getDate()) + ", " + new Date(httpURLConnection.getLastModified())); if (responseCode != HttpURLConnection.HTTP_OK) { return null; } } return urlConnection.getInputStream(); } catch (Exception ex) { ex.printStackTrace(); return null; } } | 14,114 |
1 | public static void main(String[] args) { Option optHelp = new Option("h", "help", false, "print this message"); Option optCerts = new Option("c", "cert", true, "use external semicolon separated X.509 certificate files"); optCerts.setArgName("certificates"); Option optPasswd = new Option("p", "password", true, "set password for opening PDF"); optPasswd.setArgName("password"); Option optExtract = new Option("e", "extract", true, "extract signed PDF revisions to given folder"); optExtract.setArgName("folder"); Option optListKs = new Option("lk", "list-keystore-types", false, "list keystore types provided by java"); Option optListCert = new Option("lc", "list-certificates", false, "list certificate aliases in a KeyStore"); Option optKsType = new Option("kt", "keystore-type", true, "use keystore type with given name"); optKsType.setArgName("keystore_type"); Option optKsFile = new Option("kf", "keystore-file", true, "use given keystore file"); optKsFile.setArgName("file"); Option optKsPass = new Option("kp", "keystore-password", true, "password for keystore file (look on -kf option)"); optKsPass.setArgName("password"); Option optFailFast = new Option("ff", "fail-fast", true, "flag which sets the Verifier to exit with error code on the first validation failure"); final Options options = new Options(); options.addOption(optHelp); options.addOption(optCerts); options.addOption(optPasswd); options.addOption(optExtract); options.addOption(optListKs); options.addOption(optListCert); options.addOption(optKsType); options.addOption(optKsFile); options.addOption(optKsPass); options.addOption(optFailFast); CommandLine line = null; try { CommandLineParser parser = new PosixParser(); line = parser.parse(options, args); } catch (ParseException exp) { System.err.println("Illegal command used: " + exp.getMessage()); System.exit(-1); } final boolean failFast = line.hasOption("ff"); final String[] tmpArgs = line.getArgs(); if (line.hasOption("h") || args == null || args.length == 0) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(70, "java -jar Verifier.jar [file1.pdf [file2.pdf ...]]", "JSignPdf Verifier is a command line tool for verifying signed PDF documents.", options, null, true); } else if (line.hasOption("lk")) { for (String tmpKsType : KeyStoreUtils.getKeyStores()) { System.out.println(tmpKsType); } } else if (line.hasOption("lc")) { for (String tmpCert : KeyStoreUtils.getCertAliases(line.getOptionValue("kt"), line.getOptionValue("kf"), line.getOptionValue("kp"))) { System.out.println(tmpCert); } } else { final VerifierLogic tmpLogic = new VerifierLogic(line.getOptionValue("kt"), line.getOptionValue("kf"), line.getOptionValue("kp")); tmpLogic.setFailFast(failFast); if (line.hasOption("c")) { String tmpCertFiles = line.getOptionValue("c"); for (String tmpCFile : tmpCertFiles.split(";")) { tmpLogic.addX509CertFile(tmpCFile); } } byte[] tmpPasswd = null; if (line.hasOption("p")) { tmpPasswd = line.getOptionValue("p").getBytes(); } String tmpExtractDir = null; if (line.hasOption("e")) { tmpExtractDir = new File(line.getOptionValue("e")).getPath(); } for (String tmpFilePath : tmpArgs) { System.out.println("Verifying " + tmpFilePath); final File tmpFile = new File(tmpFilePath); if (!tmpFile.canRead()) { System.err.println("Couln't read the file. Check the path and permissions."); if (failFast) { System.exit(-1); } continue; } final VerificationResult tmpResult = tmpLogic.verify(tmpFilePath, tmpPasswd); if (tmpResult.getException() != null) { tmpResult.getException().printStackTrace(); System.exit(-1); } else { System.out.println("Total revisions: " + tmpResult.getTotalRevisions()); for (SignatureVerification tmpSigVer : tmpResult.getVerifications()) { System.out.println(tmpSigVer.toString()); if (tmpExtractDir != null) { try { File tmpExFile = new File(tmpExtractDir + "/" + tmpFile.getName() + "_" + tmpSigVer.getRevision() + ".pdf"); System.out.println("Extracting to " + tmpExFile.getCanonicalPath()); FileOutputStream tmpFOS = new FileOutputStream(tmpExFile.getCanonicalPath()); InputStream tmpIS = tmpLogic.extractRevision(tmpFilePath, tmpPasswd, tmpSigVer.getName()); IOUtils.copy(tmpIS, tmpFOS); tmpIS.close(); tmpFOS.close(); } catch (IOException ioe) { ioe.printStackTrace(); } } } if (failFast && SignatureVerification.isError(tmpResult.getVerificationResultCode())) { System.exit(tmpResult.getVerificationResultCode()); } } } } } | public static void saveZipComponents(ZipComponents zipComponents, File zipFile) throws FileNotFoundException, IOException, Exception { ZipOutputStream zipOutStream = new ZipOutputStream(new FileOutputStream(zipFile)); for (ZipComponent comp : zipComponents.getComponents()) { ZipEntry newEntry = new ZipEntry(comp.getName()); zipOutStream.putNextEntry(newEntry); if (comp.isDirectory()) { } else { if (comp.getName().endsWith("document.xml") || comp.getName().endsWith("document.xml.rels")) { } InputStream inputStream = comp.getInputStream(); IOUtils.copy(inputStream, zipOutStream); inputStream.close(); } } zipOutStream.close(); } | 14,115 |
1 | public static String computeMD5(InputStream input) { InputStream digestStream = null; try { MessageDigest md5 = MessageDigest.getInstance("MD5"); digestStream = new DigestInputStream(input, md5); IOUtils.copy(digestStream, new NullOutputStream()); return new String(Base64.encodeBase64(md5.digest()), "UTF-8"); } catch (NoSuchAlgorithmException e) { throw new RuntimeException(e); } catch (IOException e) { throw new RuntimeException(e); } finally { IOUtils.closeQuietly(digestStream); } } | public final void deliver(final String from, final String recipient, final InputStream data) throws TooMuchDataException, IOException { System.out.println("FROM: " + from); System.out.println("TO: " + recipient); final File tmpDir = new File(System.getProperty("java.io.tmpdir")); final File file = new File(tmpDir, recipient); final FileWriter fw = new FileWriter(file); try { IOUtils.copy(data, fw); } finally { fw.close(); } } | 14,116 |
0 | private static void copierScriptChargement(File webInfDir, String initialDataChoice) { File chargementInitialDir = new File(webInfDir, "chargementInitial"); File fichierChargement = new File(chargementInitialDir, "ScriptChargementInitial.sql"); File fichierChargementAll = new File(chargementInitialDir, "ScriptChargementInitial-All.sql"); File fichierChargementTypesDocument = new File(chargementInitialDir, "ScriptChargementInitial-TypesDocument.sql"); File fichierChargementVide = new File(chargementInitialDir, "ScriptChargementInitial-Vide.sql"); if (fichierChargement.exists()) { fichierChargement.delete(); } File fichierUtilise = null; if ("all".equals(initialDataChoice)) { fichierUtilise = fichierChargementAll; } else if ("typesDocument".equals(initialDataChoice)) { fichierUtilise = fichierChargementTypesDocument; } else if ("empty".equals(initialDataChoice)) { fichierUtilise = fichierChargementVide; } if (fichierUtilise != null && fichierUtilise.exists()) { FileChannel source = null; FileChannel destination = null; try { source = new FileInputStream(fichierUtilise).getChannel(); destination = new FileOutputStream(fichierChargement).getChannel(); destination.transferFrom(source, 0, source.size()); } catch (Exception e) { throw new RuntimeException(e); } finally { if (source != null) { try { source.close(); } catch (Exception e) { e.printStackTrace(); } } if (destination != null) { try { destination.close(); } catch (Exception e) { e.printStackTrace(); } } } } } | private static void dumpUrl(URL url) throws IOException { BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String s = reader.readLine(); while (s != null) { System.out.println(s); s = reader.readLine(); } reader.close(); } | 14,117 |
0 | private void load() throws SQLException { Connection conn = null; Statement stmt = null; try { conn = FidoDataSource.getConnection(); conn.setAutoCommit(false); stmt = conn.createStatement(); ClearData.clearTables(stmt); stmt.executeUpdate("insert into Objects (ObjectId, Description) values (100, 'Person')"); stmt.executeUpdate("insert into Objects (ObjectId, Description) values (101, 'john')"); stmt.executeUpdate("insert into Objects (ObjectId, Description) values (200, 'Dog')"); stmt.executeUpdate("insert into Objects (ObjectId, Description) values (201, 'johns dog')"); stmt.executeQuery("select setval('objects_objectid_seq', 1000)"); stmt.executeUpdate("insert into ClassLinkTypes (LinkName, LinkType) values ('hasa', 2)"); stmt.executeUpdate("insert into ObjectLinks (ObjectId, LinkName, LinkToObject) values (100, 'isa', 1)"); stmt.executeUpdate("insert into ObjectLinks (ObjectId, LinkName, LinkToObject) values (101, 'instance', 100)"); stmt.executeUpdate("insert into ObjectLinks (ObjectId, LinkName, LinkToObject) values (200, 'isa', 1)"); stmt.executeUpdate("insert into ObjectLinks (ObjectId, LinkName, LinkToObject) values (201, 'instance', 200)"); stmt.executeUpdate("insert into ObjectLinks (ObjectId, LinkName, LinkToObject) values (101, 'hasa', 201)"); stmt.executeUpdate("insert into Dictionary (Word, SenseNumber, GrammarString, ObjectId) values ('LEFT-WALL', '1', 'QV+', 1)"); stmt.executeUpdate("insert into Dictionary (Word, SenseNumber, GrammarString, ObjectId) values ('does', '1', 'HV+', 1)"); stmt.executeUpdate("insert into Dictionary (Word, SenseNumber, GrammarString, ObjectId) values ('john', '1', 'S+ | DO-', 1)"); stmt.executeUpdate("insert into Dictionary (Word, SenseNumber, GrammarString, ObjectId) values ('a', '1', 'D+', 1)"); stmt.executeUpdate("insert into Dictionary (Word, SenseNumber, GrammarString, ObjectId) values ('dog', '1', '[D-] & (S+ | DO-)', 200)"); stmt.executeUpdate("insert into Dictionary (Word, SenseNumber, GrammarString, ObjectId) values ('have', '1', 'S- & HV- & QV- & DO+', 1)"); stmt.executeUpdate("insert into GrammarLinks (LinkName, LinkType) values ('S', 1)"); stmt.executeUpdate("insert into GrammarLinks (LinkName, LinkType) values ('DO', 3)"); stmt.executeUpdate("insert into GrammarLinks (LinkName, LinkType) values ('QV', 8)"); stmt.executeUpdate("insert into GrammarLinks (LinkName, LinkType) values ('D', 10)"); stmt.executeUpdate("insert into GrammarLinks (LinkName, LinkType) values ('HV', 16)"); stmt.executeUpdate("insert into Articles (ArticleName, Dereference) values ('a', 2)"); stmt.executeUpdate("insert into FrameSlots (SlotName) values ('actor')"); stmt.executeUpdate("insert into FrameSlots (SlotName) values ('object')"); stmt.executeUpdate("insert into Verbs (VerbName, Type, SubjectSlot, IndirectObjectSlot, PredicateNounSlot) values ('have', 1, 'actor', '', 'object')"); stmt.executeUpdate("insert into ProperNouns (Noun, SenseNumber, ObjectId) values ('john', 1, 101)"); stmt.executeQuery("select setval('instructions_instructionid_seq', 1)"); stmt.executeUpdate("insert into Instructions (Type, ExecuteString, FrameSlot, Operator, LinkName, ObjectId, AttributeName) " + "values (3, 'set_return_status true', null, 0, null, null, null)"); stmt.executeUpdate("insert into Instructions (Type, ExecuteString, FrameSlot, Operator, LinkName, ObjectId, AttributeName) " + "values (3, 'set_return_status false', null, 0, null, null, null)"); stmt.executeUpdate("insert into Instructions (Type, ExecuteString, FrameSlot, Operator, LinkName, ObjectId, AttributeName) " + "values (2, '', 'actor', 1, 'hasa', 200, null)"); stmt.executeUpdate("insert into InstructionGroups (InstructionId, Rank, GroupInstruction) " + "values (4, 1, 2)"); stmt.executeUpdate("insert into InstructionGroups (InstructionId, Rank, GroupInstruction) " + "values (4, 2, 3)"); stmt.executeQuery("select setval('transactions_transactionid_seq', 1)"); stmt.executeUpdate("insert into Transactions (InstructionId, Description) values (4, 'have - question')"); stmt.executeQuery("select setval('verbtransactions_verbid_seq', 1)"); stmt.executeUpdate("insert into VerbTransactions (VerbString, MoodType, TransactionId) values ('have', 3, 2)"); stmt.executeUpdate("insert into VerbConstraints (VerbId, FrameSlot, ObjectId) values (2, 'actor', 100)"); stmt.executeUpdate("insert into VerbConstraints (VerbId, FrameSlot, ObjectId) values (2, 'object', 200)"); stmt.executeUpdate("update SystemProperties set value = 'Tutorial 2 Data' where name = 'DB Data Version'"); conn.commit(); } catch (SQLException e) { if (conn != null) conn.rollback(); throw e; } finally { if (stmt != null) stmt.close(); if (conn != null) conn.close(); } } | public static File copyFileAs(String path, String newName) { File src = new File(path); File dest = new File(newName); try { if (!dest.exists()) { dest.createNewFile(); } FileChannel source = new FileInputStream(src).getChannel(); FileChannel destination = new FileOutputStream(dest).getChannel(); destination.transferFrom(source, 0, source.size()); source.close(); destination.close(); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } return dest; } | 14,118 |
1 | public static void copy(File src, File dest, boolean overwrite) throws IOException { if (!src.exists()) throw new IOException("File source does not exists"); if (dest.exists()) { if (!overwrite) throw new IOException("File destination already exists"); dest.delete(); } else { dest.createNewFile(); } InputStream is = new FileInputStream(src); OutputStream os = new FileOutputStream(dest); byte[] buffer = new byte[1024 * 4]; int len = 0; while ((len = is.read(buffer)) > 0) { os.write(buffer, 0, len); } os.close(); is.close(); } | public static void copyFile(final File in, final File out) throws IOException { final FileChannel inChannel = new FileInputStream(in).getChannel(); final FileChannel outChannel = new FileOutputStream(out).getChannel(); try { inChannel.transferTo(0, inChannel.size(), outChannel); } catch (final IOException e) { throw e; } finally { if (inChannel != null) { inChannel.close(); } if (outChannel != null) { outChannel.close(); } } } | 14,119 |
1 | private void chopFileDisk() throws IOException { File tempFile = new File("" + logFile + ".tmp"); BufferedInputStream bis = null; BufferedOutputStream bos = null; long startCopyPos; byte readBuffer[] = new byte[2048]; int readCount; long totalBytesRead = 0; if (reductionRatio > 0 && logFile.length() > 0) { startCopyPos = logFile.length() / reductionRatio; } else { startCopyPos = 0; } try { bis = new BufferedInputStream(new FileInputStream(logFile)); bos = new BufferedOutputStream(new FileOutputStream(tempFile)); do { readCount = bis.read(readBuffer, 0, readBuffer.length); if (readCount > 0) { totalBytesRead += readCount; if (totalBytesRead > startCopyPos) { bos.write(readBuffer, 0, readCount); } } } while (readCount > 0); } finally { if (bos != null) { try { bos.close(); } catch (IOException ex) { } } if (bis != null) { try { bis.close(); } catch (IOException ex) { } } } if (tempFile.isFile()) { if (!logFile.delete()) { throw new IOException("Error when attempting to delete the " + logFile + " file."); } if (!tempFile.renameTo(logFile)) { throw new IOException("Error when renaming the " + tempFile + " to " + logFile + "."); } } } | @SuppressWarnings("unchecked") private void doService(final HttpServletRequest request, final HttpServletResponse response) throws Exception { final String url = request.getRequestURL().toString(); if (url.endsWith("/favicon.ico")) { response.setStatus(HttpServletResponse.SC_NOT_FOUND); return; } if (url.contains("/delay")) { final String delay = StringUtils.substringBetween(url, "/delay", "/"); final int ms = Integer.parseInt(delay); if (LOG.isDebugEnabled()) { LOG.debug("Sleeping for " + ms + " before to deliver " + url); } Thread.sleep(ms); } final URL requestedUrl = new URL(url); final WebRequest webRequest = new WebRequest(requestedUrl); webRequest.setHttpMethod(HttpMethod.valueOf(request.getMethod())); for (final Enumeration<String> en = request.getHeaderNames(); en.hasMoreElements(); ) { final String headerName = en.nextElement(); final String headerValue = request.getHeader(headerName); webRequest.setAdditionalHeader(headerName, headerValue); } final List<NameValuePair> requestParameters = new ArrayList<NameValuePair>(); for (final Enumeration<String> paramNames = request.getParameterNames(); paramNames.hasMoreElements(); ) { final String name = paramNames.nextElement(); final String[] values = request.getParameterValues(name); for (final String value : values) { requestParameters.add(new NameValuePair(name, value)); } } if ("PUT".equals(request.getMethod()) && request.getContentLength() > 0) { final byte[] buffer = new byte[request.getContentLength()]; request.getInputStream().readLine(buffer, 0, buffer.length); webRequest.setRequestBody(new String(buffer)); } else { webRequest.setRequestParameters(requestParameters); } final WebResponse resp = MockConnection_.getResponse(webRequest); response.setStatus(resp.getStatusCode()); for (final NameValuePair responseHeader : resp.getResponseHeaders()) { response.addHeader(responseHeader.getName(), responseHeader.getValue()); } if (WriteContentAsBytes_) { IOUtils.copy(resp.getContentAsStream(), response.getOutputStream()); } else { final String newContent = getModifiedContent(resp.getContentAsString()); final String contentCharset = resp.getContentCharset(); response.setCharacterEncoding(contentCharset); response.getWriter().print(newContent); } response.flushBuffer(); } | 14,120 |
0 | 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(); } | public HttpResponse executeHttp(final HttpUriRequest request, final int beginExpectedCode, final int endExpectedCode) throws ClientProtocolException, IOException, HttpException { final HttpResponse response = httpClient.execute(request); final int statusCode = response.getStatusLine().getStatusCode(); if (statusCode < beginExpectedCode || statusCode >= endExpectedCode) { throw newHttpException(request, response); } return response; } | 14,121 |
1 | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | private static void copy(File source, File target) throws IOException { FileChannel sourceChannel = new FileInputStream(source).getChannel(); FileChannel targetChannel = new FileOutputStream(target).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), targetChannel); sourceChannel.close(); targetChannel.close(); } | 14,122 |
1 | private Dataset(File f, Properties p, boolean ro) throws DatabaseException { folder = f; logger.debug("Opening dataset [" + ((ro) ? "readOnly" : "read/write") + " mode]"); readOnly = ro; logger = Logger.getLogger(Dataset.class); logger.debug("Opening environment: " + f); EnvironmentConfig envConfig = new EnvironmentConfig(); envConfig.setTransactional(false); envConfig.setAllowCreate(!readOnly); envConfig.setReadOnly(readOnly); env = new Environment(f, envConfig); File props = new File(folder, "dataset.properties"); if (!ro && p != null) { this.properties = p; try { FileOutputStream fos = new FileOutputStream(props); p.store(fos, null); fos.close(); } catch (IOException e) { logger.warn("Error saving dataset properties", e); } } else { if (props.exists()) { try { Properties pr = new Properties(); FileInputStream fis = new FileInputStream(props); pr.load(fis); fis.close(); this.properties = pr; } catch (IOException e) { logger.warn("Error reading dataset properties", e); } } } getPaths(); getNamespaces(); getTree(); pathDatabases = new HashMap(); frequencyDatabases = new HashMap(); lengthDatabases = new HashMap(); clustersDatabases = new HashMap(); pathMaps = new HashMap(); frequencyMaps = new HashMap(); lengthMaps = new HashMap(); clustersMaps = new HashMap(); } | 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"); } | 14,123 |
1 | public static void zipMapBos(DitaBoundedObjectSet mapBos, File outputZipFile, MapBosProcessorOptions options) throws Exception { log.debug("Determining zip file organization..."); BosVisitor visitor = new DxpFileOrganizingBosVisitor(); visitor.visit(mapBos); if (!options.isQuiet()) log.info("Creating DXP package \"" + outputZipFile.getAbsolutePath() + "\"..."); OutputStream outStream = new FileOutputStream(outputZipFile); ZipOutputStream zipOutStream = new ZipOutputStream(outStream); ZipEntry entry = null; URI rootMapUri = mapBos.getRoot().getEffectiveUri(); URI baseUri = null; try { baseUri = AddressingUtil.getParent(rootMapUri); } catch (URISyntaxException e) { throw new BosException("URI syntax exception getting parent URI: " + e.getMessage()); } Set<String> dirs = new HashSet<String>(); if (!options.isQuiet()) log.info("Constructing DXP package..."); for (BosMember member : mapBos.getMembers()) { if (!options.isQuiet()) log.info("Adding member " + member + " to zip..."); URI relativeUri = baseUri.relativize(member.getEffectiveUri()); File temp = new File(relativeUri.getPath()); String parentPath = temp.getParent(); if (parentPath != null && !"".equals(parentPath) && !parentPath.endsWith("/")) { parentPath += "/"; } log.debug("parentPath=\"" + parentPath + "\""); if (!"".equals(parentPath) && parentPath != null && !dirs.contains(parentPath)) { entry = new ZipEntry(parentPath); zipOutStream.putNextEntry(entry); zipOutStream.closeEntry(); dirs.add(parentPath); } entry = new ZipEntry(relativeUri.getPath()); zipOutStream.putNextEntry(entry); IOUtils.copy(member.getInputStream(), zipOutStream); zipOutStream.closeEntry(); } zipOutStream.close(); if (!options.isQuiet()) log.info("DXP package \"" + outputZipFile.getAbsolutePath() + "\" created."); } | private static void zip(ZipOutputStream aOutputStream, final File[] aFiles, final String sArchive, final URI aRootURI, final String sFilter) throws FileError { boolean closeStream = false; if (aOutputStream == null) try { aOutputStream = new ZipOutputStream(new FileOutputStream(sArchive)); closeStream = true; } catch (final FileNotFoundException e) { throw new FileError("Can't create ODF file!", e); } try { try { for (final File curFile : aFiles) { aOutputStream.putNextEntry(new ZipEntry(URLDecoder.decode(aRootURI.relativize(curFile.toURI()).toASCIIString(), "UTF-8"))); if (curFile.isDirectory()) { aOutputStream.closeEntry(); FileUtils.zip(aOutputStream, FileUtils.getFiles(curFile, sFilter), sArchive, aRootURI, sFilter); continue; } final FileInputStream inputStream = new FileInputStream(curFile); for (int i; (i = inputStream.read(FileUtils.BUFFER)) != -1; ) aOutputStream.write(FileUtils.BUFFER, 0, i); inputStream.close(); aOutputStream.closeEntry(); } } finally { if (closeStream && aOutputStream != null) aOutputStream.close(); } } catch (final IOException e) { throw new FileError("Can't zip file to archive!", e); } if (closeStream) DocumentController.getStaticLogger().fine(aFiles.length + " files and folders zipped as " + sArchive); } | 14,124 |
1 | public static final void copyFile(File source, File destination) throws IOException { FileChannel sourceChannel = new FileInputStream(source).getChannel(); FileChannel targetChannel = new FileOutputStream(destination).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), targetChannel); sourceChannel.close(); targetChannel.close(); } | @Test public void testCopy_inputStreamToWriter() throws Exception { InputStream in = new ByteArrayInputStream(inData); in = new YellOnCloseInputStreamTest(in); ByteArrayOutputStream baout = new ByteArrayOutputStream(); YellOnFlushAndCloseOutputStreamTest out = new YellOnFlushAndCloseOutputStreamTest(baout, true, true); Writer writer = new OutputStreamWriter(baout, "US-ASCII"); IOUtils.copy(in, writer); out.off(); writer.flush(); assertTrue("Not all bytes were read", in.available() == 0); assertEquals("Sizes differ", inData.length, baout.size()); assertTrue("Content differs", Arrays.equals(inData, baout.toByteArray())); } | 14,125 |
0 | public static void copyFile(String original, String destination) throws Exception { File original_file = new File(original); File destination_file = new File(destination); if (!original_file.exists()) throw new Exception("File with path " + original + " does not exist."); if (destination_file.exists()) throw new Exception("File with path " + destination + " already exists."); FileReader in = new FileReader(original_file); FileWriter out = new FileWriter(destination_file); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } | public static final synchronized String md5(final String data) { try { final MessageDigest md = MessageDigest.getInstance("MD5"); md.update(data.getBytes()); final byte[] b = md.digest(); return toHexString(b); } catch (final Exception e) { } return ""; } | 14,126 |
1 | 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); } } | public static void translateTableMetaData(String baseDir, String tableName, NameSpaceDefinition nsDefinition) throws Exception { setVosiNS(baseDir, "table", nsDefinition); String filename = baseDir + "table.xsl"; Scanner s = new Scanner(new File(filename)); PrintWriter fw = new PrintWriter(new File(baseDir + tableName + ".xsl")); while (s.hasNextLine()) { fw.println(s.nextLine().replaceAll("TABLENAME", tableName)); } s.close(); fw.close(); applyStyle(baseDir + "tables.xml", baseDir + tableName + ".json", baseDir + tableName + ".xsl"); } | 14,127 |
1 | public String getData() throws ValueFormatException, RepositoryException, IOException { InputStream is = getStream(); StringWriter sw = new StringWriter(); IOUtils.copy(is, sw, "UTF-8"); IOUtils.closeQuietly(is); return sw.toString(); } | private byte[] getBytes(String resource) throws IOException { InputStream is = HttpServletFileDownloadTest.class.getResourceAsStream(resource); ByteArrayOutputStream out = new ByteArrayOutputStream(); IOUtils.copy(is, out); IOUtils.closeQuietly(is); return out.toByteArray(); } | 14,128 |
1 | private void prepareQueryResultData(ZipEntryRef zer, String nodeDir, String reportDir, Set<ZipEntryRef> statusZers) throws Exception { String jobDir = nodeDir + File.separator + "job_" + zer.getUri(); if (!WorkDirectory.isWorkingDirectoryValid(jobDir)) { throw new Exception("Cannot acces to " + jobDir); } File f = new File(jobDir + File.separator + "result.xml"); if (!f.exists() || !f.isFile() || !f.canRead()) { throw new Exception("Cannot acces to result file " + f.getAbsolutePath()); } String fcopyName = reportDir + File.separator + zer.getName() + ".xml"; BufferedInputStream bis = new BufferedInputStream(new FileInputStream(f)); BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(fcopyName)); IOUtils.copy(bis, bos); bis.close(); bos.close(); zer.setUri(fcopyName); f = new File(jobDir + File.separator + "status.xml"); if (!f.exists() || !f.isFile() || !f.canRead()) { throw new Exception("Cannot acces to status file " + f.getAbsolutePath()); } fcopyName = reportDir + File.separator + zer.getName() + "_status.xml"; bis = new BufferedInputStream(new FileInputStream(f)); bos = new BufferedOutputStream(new FileOutputStream(fcopyName)); IOUtils.copy(bis, bos); bis.close(); bos.close(); statusZers.add(new ZipEntryRef(ZipEntryRef.SINGLE_FILE, zer.getName(), fcopyName, ZipEntryRef.WITH_REL)); } | public void imagesParserAssesmentItem(int file, int currentquestion, Resource resTemp) { NodeList nl = null; Node n = null; NamedNodeMap nnp = null; Node nsrc = null; URL url = null; String sFilename = ""; String sNewPath = ""; int index; String sOldPath = ""; try { if (file == 1) { nl = doc.getElementsByTagName("img"); } else { nl = doc_[currentquestion].getElementsByTagName("img"); } for (int i = 0; i < nl.getLength(); i++) { n = nl.item(i); nnp = n.getAttributes(); nsrc = nnp.getNamedItem("src"); String sTemp = nsrc.getTextContent(); url = new URL("file", "localhost", sTemp); sOldPath = url.getPath(); sOldPath = sOldPath.replace('/', File.separatorChar); int indexFirstSlash = sOldPath.indexOf(File.separatorChar); String sSourcePath = sOldPath.substring(indexFirstSlash + 1); index = sOldPath.lastIndexOf(File.separatorChar); sFilename = sOldPath.substring(index + 1); sNewPath = this.sTempLocation + sFilename; FileChannel in = null; FileChannel out = null; try { in = new FileInputStream(sSourcePath).getChannel(); out = new FileOutputStream(sNewPath).getChannel(); long size = in.size(); MappedByteBuffer buf = in.map(FileChannel.MapMode.READ_ONLY, 0, size); out.write(buf); } finally { if (in != null) in.close(); if (out != null) out.close(); } if (file == 1) { sXml = sXml.replace(nsrc.getTextContent(), sFilename); } else { sXml_[currentquestion] = sXml_[currentquestion].replace(nsrc.getTextContent(), sFilename); } lsImages.add(sFilename); resTemp.addFile(sFilename); } } catch (MalformedURLException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } | 14,129 |
1 | public void SendFile(File testfile) { try { SocketChannel sock = SocketChannel.open(new InetSocketAddress("127.0.0.1", 1234)); sock.configureBlocking(true); while (!sock.finishConnect()) { System.out.println("NOT connected!"); } System.out.println("CONNECTED!"); FileInputStream fis = new FileInputStream(testfile); FileChannel fic = fis.getChannel(); long len = fic.size(); Buffer.clear(); Buffer.putLong(len); Buffer.flip(); sock.write(Buffer); long cnt = 0; while (cnt < len) { Buffer.clear(); int add = fic.read(Buffer); cnt += add; Buffer.flip(); while (Buffer.hasRemaining()) { sock.write(Buffer); } } fic.close(); File tmpfile = getTmp().createNewFile("tmp", "tmp"); FileOutputStream fos = new FileOutputStream(tmpfile); FileChannel foc = fos.getChannel(); int mlen = -1; do { Buffer.clear(); mlen = sock.read(Buffer); Buffer.flip(); if (mlen > 0) { foc.write(Buffer); } } while (mlen > 0); foc.close(); } catch (IOException e) { e.printStackTrace(); } } | 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!"); } | 14,130 |
0 | private BundleURLClassPath createBundleURLClassPath(Bundle bundle, Version version, File bundleFile, File cache, boolean alreadyCached) throws Exception { String bundleClassPath = (String) bundle.getHeaders().get(Constants.BUNDLE_CLASSPATH); if (bundleClassPath == null) { bundleClassPath = "."; } ManifestEntry[] entries = ManifestEntry.parse(bundleClassPath); String[] classPaths = new String[0]; for (int i = 0; i < entries.length; i++) { String classPath = entries[i].getName(); if (classPath.startsWith("/")) { classPath = classPath.substring(1); } if (classPath.endsWith(".jar")) { try { File file = new File(cache, classPath); if (!alreadyCached) { file.getParentFile().mkdirs(); String url = new StringBuilder("jar:").append(bundleFile.toURI().toURL().toString()).append("!/").append(classPath).toString(); OutputStream os = new FileOutputStream(file); InputStream is = new URL(url).openStream(); IOUtil.copy(is, os); is.close(); os.close(); } else { if (!file.exists()) { throw new IOException(new StringBuilder("classpath ").append(classPath).append(" not found").toString()); } } } catch (IOException e) { FrameworkEvent frameworkEvent = new FrameworkEvent(FrameworkEvent.INFO, bundle, e); framework.postFrameworkEvent(frameworkEvent); continue; } } classPaths = (String[]) ArrayUtil.add(classPaths, classPath); } if (!alreadyCached) { String bundleNativeCode = (String) bundle.getHeaders().get(Constants.BUNDLE_NATIVECODE); if (bundleNativeCode != null) { entries = ManifestEntry.parse(bundleNativeCode); for (int i = 0; i < entries.length; i++) { ManifestEntry entry = entries[i]; String libPath = entry.getName(); String url = new StringBuilder("jar:").append(bundleFile.toURI().toURL().toString()).append("!/").append(libPath).toString(); File file = new File(cache, libPath); file.getParentFile().mkdirs(); OutputStream os = new FileOutputStream(file); InputStream is = new URL(url).openStream(); IOUtil.copy(is, os); is.close(); os.close(); } } } BundleURLClassPath urlClassPath = new BundleURLClassPathImpl(bundle, version, classPaths, cache); return urlClassPath; } | @SuppressWarnings("null") public static void copyFile(File src, File dst) throws IOException { if (!dst.getParentFile().exists()) { dst.getParentFile().mkdirs(); } dst.createNewFile(); FileChannel srcC = null; FileChannel dstC = null; try { srcC = new FileInputStream(src).getChannel(); dstC = new FileOutputStream(dst).getChannel(); dstC.transferFrom(srcC, 0, srcC.size()); } finally { try { if (dst != null) { dstC.close(); } } catch (Exception e) { e.printStackTrace(); } try { if (src != null) { srcC.close(); } } catch (Exception e) { e.printStackTrace(); } } } | 14,131 |
0 | public void testJTLM_publish911() throws Exception { EXISchema corpus = EXISchemaFactoryTestUtil.getEXISchema("/JTLM/schemas/TLMComposite.xsd", getClass(), m_compilerErrors); Assert.assertEquals(0, m_compilerErrors.getTotalCount()); GrammarCache grammarCache = new GrammarCache(corpus, GrammarOptions.STRICT_OPTIONS); AlignmentType alignment = AlignmentType.compress; Transmogrifier encoder = new Transmogrifier(); EXIDecoder decoder = new EXIDecoder(); Scanner scanner; InputSource inputSource; encoder.setAlignmentType(alignment); decoder.setAlignmentType(alignment); encoder.setEXISchema(grammarCache); ByteArrayOutputStream baos = new ByteArrayOutputStream(); encoder.setOutputStream(baos); URL url = resolveSystemIdAsURL("/JTLM/publish911.xml"); inputSource = new InputSource(url.toString()); inputSource.setByteStream(url.openStream()); byte[] bts; int n_events, n_texts; encoder.encode(inputSource); bts = baos.toByteArray(); decoder.setEXISchema(grammarCache); decoder.setInputStream(new ByteArrayInputStream(bts)); scanner = decoder.processHeader(); ArrayList<EXIEvent> exiEventList = new ArrayList<EXIEvent>(); EXIEvent exiEvent; n_events = 0; n_texts = 0; while ((exiEvent = scanner.nextEvent()) != null) { ++n_events; if (exiEvent.getEventVariety() == EXIEvent.EVENT_CH) { if (exiEvent.getCharacters().length() == 0) { --n_events; continue; } if (n_texts % 100 == 0) { final int n = n_texts / 100; Assert.assertEquals(JTLMTest.publish911_centennials[n], exiEvent.getCharacters().makeString()); } ++n_texts; } exiEventList.add(exiEvent); } Assert.assertEquals(96576, n_events); } | public static List<ServerInfo> getStartedServers() { List<ServerInfo> infos = new ArrayList<ServerInfo>(); try { StringBuilder request = new StringBuilder(); request.append(url).append("/").append(displayServlet); request.append("?ingame=1"); URL objUrl = new URL(request.toString()); URLConnection urlConnect = objUrl.openConnection(); InputStream in = urlConnect.getInputStream(); BufferedReader reader = new BufferedReader(new InputStreamReader(in)); while (reader.ready()) { String name = reader.readLine(); String ip = reader.readLine(); int port = Integer.valueOf(reader.readLine()); ServerInfo server = new ServerInfo(name, ip, port); server.nbPlayers = Integer.valueOf(reader.readLine()); infos.add(server); } in.close(); return infos; } catch (Exception e) { return infos; } } | 14,132 |
1 | public static void copyFile(File from, File to) throws IOException { ensureFile(to); FileChannel srcChannel = new FileInputStream(from).getChannel(); FileChannel dstChannel = new FileOutputStream(to).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } | public 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(); } } | 14,133 |
0 | private String generateServiceId(ObjectName mbeanName) { try { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.update(mbeanName.toString().getBytes()); StringBuffer hexString = new StringBuffer(); byte[] digest = md5.digest(); for (int i = 0; i < digest.length; i++) { hexString.append(Integer.toHexString(0xFF & digest[i])); } return hexString.toString().toUpperCase(); } catch (Exception ex) { RuntimeException runTimeEx = new RuntimeException("Unexpected error during MD5 hash creation, check your JRE"); runTimeEx.initCause(ex); throw runTimeEx; } } | private HttpURLConnection prepare(URL url, String method) { if (this.username != null && this.password != null) { this.headers.put("Authorization", "Basic " + Codec.encodeBASE64(this.username + ":" + this.password)); } try { HttpURLConnection connection = (HttpURLConnection) url.openConnection(); checkFileBody(connection); connection.setRequestMethod(method); for (String key : this.headers.keySet()) { connection.setRequestProperty(key, headers.get(key)); } return connection; } catch (Exception e) { throw new RuntimeException(e); } } | 14,134 |
0 | public void init() { try { UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); } catch (Throwable e) { } Container c = getContentPane(); c.setLayout(new BoxLayout(c, BoxLayout.Y_AXIS)); String[] lines = getAppletInfo().split("\n"); for (int i = 0; i < lines.length; i++) { c.add(new JLabel(lines[i])); } new Worker() { public Object construct() { Object result; try { if (getParameter("data") != null && getParameter("data").length() > 0) { NanoXMLDOMInput domi = new NanoXMLDOMInput(new UMLFigureFactory(), new StringReader(getParameter("data"))); result = domi.readObject(0); } else if (getParameter("datafile") != null) { InputStream in = null; try { URL url = new URL(getDocumentBase(), getParameter("datafile")); in = url.openConnection().getInputStream(); NanoXMLDOMInput domi = new NanoXMLDOMInput(new UMLFigureFactory(), in); result = domi.readObject(0); } finally { if (in != null) in.close(); } } else { result = null; } } catch (Throwable t) { result = t; } return result; } public void finished(Object result) { Container c = getContentPane(); c.setLayout(new BorderLayout()); c.removeAll(); initComponents(); if (result != null) { if (result instanceof Drawing) { setDrawing((Drawing) result); } else if (result instanceof Throwable) { getDrawing().add(new TextFigure(result.toString())); ((Throwable) result).printStackTrace(); } } boolean isLiveConnect; try { Class.forName("netscape.javascript.JSObject"); isLiveConnect = true; } catch (Throwable t) { isLiveConnect = false; } loadButton.setEnabled(isLiveConnect && getParameter("dataread") != null); saveButton.setEnabled(isLiveConnect && getParameter("datawrite") != null); if (isLiveConnect) { String methodName = getParameter("dataread"); if (methodName.indexOf('(') > 0) { methodName = methodName.substring(0, methodName.indexOf('(') - 1); } JSObject win = JSObject.getWindow(UMLLiveConnectApplet.this); Object data = win.call(methodName, new Object[0]); if (data instanceof String) { setData((String) data); } } c.validate(); } }.start(); } | public static String digest(String algorithm, String text) { MessageDigest mDigest = null; try { mDigest = MessageDigest.getInstance(algorithm); mDigest.update(text.getBytes(ENCODING)); } catch (NoSuchAlgorithmException nsae) { _log.error(nsae, nsae); } catch (UnsupportedEncodingException uee) { _log.error(uee, uee); } byte[] raw = mDigest.digest(); BASE64Encoder encoder = new BASE64Encoder(); return encoder.encode(raw); } | 14,135 |
1 | public void generate(FileObject outputDirectory, FileObject generatedOutputDirectory, List<Library> libraryModels, String tapdocXml) throws FileSystemException { if (!generatedOutputDirectory.exists()) { generatedOutputDirectory.createFolder(); } if (outputDirectory.exists()) { outputDirectory.createFolder(); } ZipUtils.extractZip(new ClasspathResource(classResolver, "/com/erinors/tapestry/tapdoc/service/xdoc/resources.zip"), outputDirectory); for (Library library : libraryModels) { String libraryName = library.getName(); String libraryLocation = library.getLocation(); generatedOutputDirectory.resolveFile(fileNameGenerator.getLibraryDirectory(libraryLocation)).createFolder(); try { String result = XsltUtils.xsltTransform(tapdocXml, getClass().getResourceAsStream("Library.xsl"), "libraryName", libraryName); FileObject index = generatedOutputDirectory.resolveFile(fileNameGenerator.getLibraryDirectory(libraryLocation)).resolveFile("index.xml"); Writer out = new OutputStreamWriter(index.getContent().getOutputStream(), "UTF-8"); out.write(result); out.close(); } catch (Exception e) { throw new RuntimeException(e); } for (Component component : library.getComponents()) { String componentName = component.getName(); System.out.println("Generating " + libraryName + ":" + componentName + "..."); Map<String, String> parameters = new HashMap<String, String>(); parameters.put("libraryName", libraryName); parameters.put("componentName", componentName); String result = XsltUtils.xsltTransform(tapdocXml, getClass().getResourceAsStream("Component.xsl"), parameters); Writer out = null; try { FileObject index = generatedOutputDirectory.resolveFile(fileNameGenerator.getComponentIndexFile(libraryLocation, componentName, true)); out = new OutputStreamWriter(index.getContent().getOutputStream(), "UTF-8"); out.write(result); out.close(); Resource specificationLocation = component.getSpecificationLocation(); if (specificationLocation.getRelativeResource(componentName + "_tapdoc/resource").getResourceURL() != null) { File srcResourcesDirectory = new File(specificationLocation.getRelativeResource(componentName + "_tapdoc/resource").getResourceURL().toURI()); FileObject dstResourcesFileObject = outputDirectory.resolveFile(fileNameGenerator.getComponentDirectory(libraryLocation, componentName)).resolveFile("resource"); if (srcResourcesDirectory.exists() && srcResourcesDirectory.isDirectory()) { File[] files = srcResourcesDirectory.listFiles(); if (files != null) { for (File resource : files) { if (resource.isFile() && !resource.isHidden()) { FileObject resourceFileObject = dstResourcesFileObject.resolveFile(resource.getName()); resourceFileObject.createFile(); InputStream inResource = null; OutputStream outResource = null; try { inResource = new FileInputStream(resource); outResource = resourceFileObject.getContent().getOutputStream(); IOUtils.copy(inResource, outResource); } finally { IOUtils.closeQuietly(inResource); IOUtils.closeQuietly(outResource); } } } } } } } catch (Exception e) { throw new RuntimeException(e); } finally { IOUtils.closeQuietly(out); } } } { Writer out = null; try { String result = XsltUtils.xsltTransform(tapdocXml, getClass().getResourceAsStream("Overview.xsl")); FileObject index = generatedOutputDirectory.resolveFile("index.xml"); out = new OutputStreamWriter(index.getContent().getOutputStream(), "UTF-8"); out.write(result); out.close(); } catch (Exception e) { throw new RuntimeException(e); } finally { IOUtils.closeQuietly(out); } } } | public static void main(String[] args) throws IOException, WrongFormatException, URISyntaxException { System.out.println(new URI("google.com.ua.css").toString()); Scanner scc = new Scanner(System.in); System.err.print(scc.nextLine().substring(1)); ServerSocket s = new ServerSocket(5354); while (true) { Socket client = s.accept(); InputStream iStream = client.getInputStream(); BufferedReader bf = new BufferedReader(new InputStreamReader(iStream)); String line = ""; while (!(line = bf.readLine()).equals("")) { System.out.println(line); } System.out.println("end of request"); new PrintWriter(client.getOutputStream()).println("hi"); bf.close(); } } | 14,136 |
1 | 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 downloadFile(HttpServletResponse response, String file) throws IOException { response.setContentType(FileUtils.getContentType(file)); response.setContentLength(FileUtils.getContentLength(file)); response.setHeader("Content-type", ResponseUtils.DOWNLOAD_CONTENT_TYPE); response.setHeader("Content-Disposition", "attachment; filename=\"" + FileUtils.getFileName(file) + "\""); response.setHeader("Content-Length", Integer.toString(FileUtils.getContentLength(file))); InputStream input = new FileInputStream(file); OutputStream output = response.getOutputStream(); IOUtils.copy(input, output, true); } | 14,137 |
0 | public final String encrypt(String input) throws Exception { try { MessageDigest messageDigest = (MessageDigest) MessageDigest.getInstance(algorithm).clone(); messageDigest.reset(); messageDigest.update(input.getBytes()); String output = convert(messageDigest.digest()); return output; } catch (Throwable ex) { if (logger.isDebugEnabled()) { logger.debug("Fatal Error while digesting input string", ex); } } return input; } | public boolean reject(String surl, ProgressMonitor mon) throws IllegalArgumentException { DocumentBuilder builder = null; try { builder = DocumentBuilderFactory.newInstance().newDocumentBuilder(); URISplit split = URISplit.parse(surl); URL url = new URL(split.file); InputStream in = url.openStream(); InputSource source = new InputSource(in); Document document = builder.parse(source); in.close(); Node n = document.getDocumentElement(); String localName = n.getNodeName(); int i = localName.indexOf(":"); if (i > -1) { localName = localName.substring(i + 1); } if (localName.equals("Spase")) { return false; } else if (localName.equals("Eventlist")) { return false; } else if (localName.equals("VOTABLE")) { return false; } else { return true; } } catch (Exception ex) { Logger.getLogger(SpaseRecordDataSourceFactory.class.getName()).log(Level.SEVERE, null, ex); return true; } } | 14,138 |
0 | public void callBatch(final List<JsonRpcClient.Call> calls, final JsonRpcClient.BatchCallback callback) { HttpPost httpPost = new HttpPost(mRpcUrl); JSONObject requestJson = new JSONObject(); JSONArray callsJson = new JSONArray(); try { for (int i = 0; i < calls.size(); i++) { JsonRpcClient.Call call = calls.get(i); JSONObject callJson = new JSONObject(); callJson.put("method", call.getMethodName()); if (call.getParams() != null) { JSONObject callParams = (JSONObject) call.getParams(); @SuppressWarnings("unchecked") Iterator<String> keysIterator = callParams.keys(); String key; while (keysIterator.hasNext()) { key = keysIterator.next(); callJson.put(key, callParams.get(key)); } } callsJson.put(i, callJson); } requestJson.put("calls", callsJson); httpPost.setEntity(new StringEntity(requestJson.toString(), "UTF-8")); if (Log.isLoggable(TAG, Log.VERBOSE)) { Log.v(TAG, "POST request: " + requestJson.toString()); } } catch (JSONException e) { } catch (UnsupportedEncodingException e) { } try { HttpResponse httpResponse = mHttpClient.execute(httpPost); final int responseStatusCode = httpResponse.getStatusLine().getStatusCode(); if (200 <= responseStatusCode && responseStatusCode < 300) { BufferedReader reader = new BufferedReader(new InputStreamReader(httpResponse.getEntity().getContent(), "UTF-8"), 8 * 1024); StringBuilder sb = new StringBuilder(); String line; while ((line = reader.readLine()) != null) { sb.append(line).append("\n"); } if (Log.isLoggable(TAG, Log.VERBOSE)) { Log.v(TAG, "POST response: " + sb.toString()); } JSONTokener tokener = new JSONTokener(sb.toString()); JSONObject responseJson = new JSONObject(tokener); JSONArray resultsJson = responseJson.getJSONArray("results"); Object[] resultData = new Object[calls.size()]; for (int i = 0; i < calls.size(); i++) { JSONObject result = resultsJson.getJSONObject(i); if (result.has("error")) { callback.onError(i, new JsonRpcException((int) result.getInt("error"), calls.get(i).getMethodName(), result.getString("message"), null)); resultData[i] = null; } else { resultData[i] = result.get("data"); } } callback.onData(resultData); } else { callback.onError(-1, new JsonRpcException(-1, "Received HTTP status code other than HTTP 2xx: " + httpResponse.getStatusLine().getReasonPhrase())); } } catch (IOException e) { Log.e("JsonRpcJavaClient", e.getMessage()); e.printStackTrace(); } catch (JSONException e) { Log.e("JsonRpcJavaClient", "Error parsing server JSON response: " + e.getMessage()); e.printStackTrace(); } } | public void copy(File src, File dest) throws FileNotFoundException, IOException { FileInputStream srcStream = new FileInputStream(src); FileOutputStream destStream = new FileOutputStream(dest); FileChannel srcChannel = srcStream.getChannel(); FileChannel destChannel = destStream.getChannel(); srcChannel.transferTo(0, srcChannel.size(), destChannel); destChannel.close(); srcChannel.close(); destStream.close(); srcStream.close(); } | 14,139 |
1 | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | public DataRecord addRecord(InputStream input) throws DataStoreException { File temporary = null; try { temporary = newTemporaryFile(); DataIdentifier tempId = new DataIdentifier(temporary.getName()); usesIdentifier(tempId); long length = 0; MessageDigest digest = MessageDigest.getInstance(DIGEST); OutputStream output = new DigestOutputStream(new FileOutputStream(temporary), digest); try { length = IOUtils.copyLarge(input, output); } finally { output.close(); } DataIdentifier identifier = new DataIdentifier(digest.digest()); File file; synchronized (this) { usesIdentifier(identifier); file = getFile(identifier); System.out.println("new file name: " + file.getName()); File parent = file.getParentFile(); System.out.println("parent file: " + file.getParentFile().getName()); if (!parent.isDirectory()) { parent.mkdirs(); } if (!file.exists()) { temporary.renameTo(file); if (!file.exists()) { throw new IOException("Can not rename " + temporary.getAbsolutePath() + " to " + file.getAbsolutePath() + " (media read only?)"); } } else { long now = System.currentTimeMillis(); if (file.lastModified() < now) { file.setLastModified(now); } } if (!file.isFile()) { throw new IOException("Not a file: " + file); } if (file.length() != length) { throw new IOException(DIGEST + " collision: " + file); } } inUse.remove(tempId); return new FileDataRecord(identifier, file); } catch (NoSuchAlgorithmException e) { throw new DataStoreException(DIGEST + " not available", e); } catch (IOException e) { throw new DataStoreException("Could not add record", e); } finally { if (temporary != null) { temporary.delete(); } } } | 14,140 |
1 | public static void save(String from, String recipient, InputStream in, MimeMessage message) throws IOException, MessagingException, DocumentVideException { ConversationManager conversationManager = FGDSpringUtils.getConversationManager(); conversationManager.beginConversation(); FGDDelegate delegate = new FGDDelegate(); UtilisateurIFGD utilisateur = delegate.getUtilisateurParCourriel(from); if (utilisateur == null) { String responseEmailSubject = "Votre adresse ne correspond pas à celle d'un utilisateur d'IntelliGID"; String responseEmailMessage = "<h3>Pour sauvegarder un courriel, vous devez être un utilisateur d'IntelliGID et l'adresse de courrier électronique utilisée doit être celle apparaissant dans votre profil.</h3>"; String sender = recipient.endsWith("localhost") ? FGDSpringUtils.getExpediteurSupport() : recipient; Map<String, String> recipients = new HashMap<String, String>(); recipients.put(from, null); MailUtils.sendSimpleHTMLMessage(recipients, responseEmailSubject, responseEmailMessage, sender); return; } File tempFile = File.createTempFile("email", ".eml"); tempFile.deleteOnExit(); BufferedInputStream bis = new BufferedInputStream(in); BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(tempFile)); IOUtils.copy(bis, bos); IOUtils.closeQuietly(bis); IOUtils.closeQuietly(bos); if (message == null) { GestionnaireProprietesMimeMessageParser gestionnaire = new GestionnaireProprietesMimeMessageParser(); message = gestionnaire.asMimeMessage(new BufferedInputStream(new FileInputStream(tempFile))); } String subject; try { subject = message.getSubject().replace("Fwd:", "").trim(); } catch (MessagingException e) { subject = "Message sans sujet"; } File tempDir = new File(System.getProperty("java.io.tmpdir")); if (!tempDir.exists()) { tempDir.mkdirs(); } File emailFile = new File(tempDir, FilenameUtils.normalize(subject) + ".eml"); FileUtils.copyFile(tempFile, emailFile); FicheDocument ficheDocument = new FicheDocument(); ficheDocument.setFicheCompletee(false); ficheDocument.setDateCreationHorodatee(new Date()); ficheDocument.setUtilisateurSoumetteur(utilisateur); ficheDocument.getLangues().addAll(getLanguesDefaut()); ficheDocument.setCourriel(true); FileIOContenuFichierElectronique contenuFichier = new FileIOContenuFichierElectronique(emailFile, "multipart/alternative"); SupportDocument support = new SupportDocument(); support.setFicheDocument(ficheDocument); FichierElectroniqueUtils.setContenu(ficheDocument, support, contenuFichier, utilisateur); ficheDocument.setTitre(subject); delegate.sauvegarder(ficheDocument, utilisateur); String modifyEmail = "http://" + FGDSpringUtils.getServerHost() + ":" + FGDSpringUtils.getServerPort() + "/" + FGDSpringUtils.getApplicationName() + "/app/modifierDocument/id/" + ficheDocument.getId(); System.out.println(modifyEmail); String responseEmailSubject = "Veuillez compléter la fiche du courriel «" + subject + "»"; String responseEmailMessage = "<h3>Le courrier électronique a été sauvegardé, mais il est nécessaire de <a href=\"" + modifyEmail + "\">compléter sa fiche</a>.</h3>"; String sender = recipient.endsWith("localhost") ? FGDSpringUtils.getExpediteurSupport() : recipient; try { MailUtils.sendSimpleHTMLMessage(utilisateur, responseEmailSubject, responseEmailMessage, sender); } catch (Throwable e) { e.printStackTrace(); } conversationManager.commitTransaction(); tempFile.delete(); } | public void invoke(WorkflowContext arg0, ProgressMonitor arg1, Issues arg2) { File inputFile = new File(getInputFile()); File outputFile = new File(getOutputFile()); if (!getFileExtension(getInputFile()).equalsIgnoreCase(getFileExtension(getOutputFile())) || !getFileExtension(getInputFile()).equalsIgnoreCase(OO_CALC_EXTENSION)) { OpenOfficeConnection connection = new SocketOpenOfficeConnection(); OpenOfficeDocumentConverter converter = new OpenOfficeDocumentConverter(connection); converter.convert(inputFile, outputFile); connection.disconnect(); } else { FileChannel inputChannel = null; FileChannel outputChannel = null; try { inputChannel = new FileInputStream(inputFile).getChannel(); outputChannel = new FileOutputStream(outputFile).getChannel(); outputChannel.transferFrom(inputChannel, 0, inputChannel.size()); } catch (FileNotFoundException e) { arg2.addError("File not found: " + e.getMessage()); } catch (IOException e) { arg2.addError("Could not copy file: " + e.getMessage()); } finally { if (inputChannel != null) { try { inputChannel.close(); } catch (IOException e) { arg2.addError("Could not close input channel: " + e.getMessage()); } } if (outputChannel != null) { try { outputChannel.close(); } catch (IOException e) { arg2.addError("Could not close input channel: " + e.getMessage()); } } } } } | 14,141 |
0 | public HttpURLConnection openConnection(String url) throws IOException { if (isDebugMode()) System.out.println("open: " + url); URL u = new URL(url); HttpURLConnection urlConnection; if (proxy != null) urlConnection = (HttpURLConnection) u.openConnection(proxy); else urlConnection = (HttpURLConnection) u.openConnection(); urlConnection.setRequestProperty("User-Agent", userAgent); return urlConnection; } | private HashSet<String> loadSupportedAnnotationTypes(VannitationType baseVannitationType) { Enumeration<URL> urls = null; try { urls = this.getClass().getClassLoader().getResources("META-INF/" + baseVannitationType); } catch (IOException e) { throw new RuntimeException("Failed to load the annotations we support", e); } supportedAnnotationTypes.put(baseVannitationType, new HashSet<String>()); while (urls.hasMoreElements()) { URL url = urls.nextElement(); try { BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String line; while ((line = reader.readLine()) != null) { supportedAnnotationTypes.get(baseVannitationType).add(line.trim()); } reader.close(); } catch (Exception e) { throw new RuntimeException("Could not open " + url); } } return supportedAnnotationTypes.get(baseVannitationType); } | 14,142 |
1 | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | @Test public void shouldDownloadFileUsingPublicLink() throws Exception { String bucketName = "test-" + UUID.randomUUID(); Service service = new WebClientService(credentials); service.createBucket(bucketName); File file = folder.newFile("foo.txt"); FileUtils.writeStringToFile(file, UUID.randomUUID().toString()); service.createObject(bucketName, file.getName(), file, new NullProgressListener()); String publicUrl = service.getPublicUrl(bucketName, file.getName(), new DateTime().plusDays(5)); File saved = folder.newFile("saved.txt"); InputStream input = new URL(publicUrl).openConnection().getInputStream(); FileOutputStream output = new FileOutputStream(saved); IOUtils.copy(input, output); output.close(); assertThat("Corrupted download", Files.computeMD5(saved), equalTo(Files.computeMD5(file))); service.deleteObject(bucketName, file.getName()); service.deleteBucket(bucketName); } | 14,143 |
0 | public void adicionaCliente(ClienteBean cliente) { PreparedStatement pstmt = null; ResultSet rs = null; String sql = "insert into cliente(nome,cpf,telefone,cursoCargo,bloqueado,ativo,tipo) values(?,?,?,?,?,?,?)"; try { pstmt = connection.prepareStatement(sql, Statement.RETURN_GENERATED_KEYS); pstmt.setString(1, cliente.getNome()); pstmt.setString(2, cliente.getCPF()); pstmt.setString(3, cliente.getTelefone()); pstmt.setString(4, cliente.getCursoCargo()); pstmt.setString(5, cliente.getBloqueado()); pstmt.setString(6, cliente.getAtivo()); pstmt.setString(7, cliente.getTipo()); pstmt.executeUpdate(); rs = pstmt.getGeneratedKeys(); if (rs.next()) { cliente.setIdCliente(rs.getLong(1)); } connection.commit(); } catch (SQLException ex) { try { connection.rollback(); } catch (SQLException ex1) { throw new RuntimeException("Erro ao inserir cliente.", ex1); } throw new RuntimeException("Erro ao inserir cliente.", ex); } finally { try { if (rs != null) rs.close(); if (pstmt != null) pstmt.close(); } catch (SQLException ex) { throw new RuntimeException("Ocorreu um erro no banco de dados.", ex); } } } | public static BufferedInputStream getEventAttacchment(final String url) throws IOException { int slashIndex = url.lastIndexOf("/"); String encodedUrl = url.substring(0, slashIndex + 1) + URLEncoder.encode(url.substring(slashIndex + 1), "UTF-8"); String urlwithtoken = encodedUrl + "?ticket=" + getToken(); BufferedInputStream in = new BufferedInputStream(new URL(urlwithtoken).openStream()); return in; } | 14,144 |
0 | 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(); } } | private ByteArrayInputStream fetchUrl(String urlString, Exception[] outException) { URL url; try { url = new URL(urlString); InputStream is = null; int inc = 65536; int curr = 0; byte[] result = new byte[inc]; try { is = url.openStream(); int n; while ((n = is.read(result, curr, result.length - curr)) != -1) { curr += n; if (curr == result.length) { byte[] temp = new byte[curr + inc]; System.arraycopy(result, 0, temp, 0, curr); result = temp; } } return new ByteArrayInputStream(result, 0, curr); } finally { if (is != null) { try { is.close(); } catch (IOException e) { } } } } catch (Exception e) { outException[0] = e; } return null; } | 14,145 |
1 | public NamedList<Object> request(final SolrRequest request, ResponseParser processor) throws SolrServerException, IOException { HttpMethod method = null; InputStream is = null; SolrParams params = request.getParams(); Collection<ContentStream> streams = requestWriter.getContentStreams(request); String path = requestWriter.getPath(request); if (path == null || !path.startsWith("/")) { path = "/select"; } ResponseParser parser = request.getResponseParser(); if (parser == null) { parser = _parser; } ModifiableSolrParams wparams = new ModifiableSolrParams(); wparams.set(CommonParams.WT, parser.getWriterType()); wparams.set(CommonParams.VERSION, parser.getVersion()); if (params == null) { params = wparams; } else { params = new DefaultSolrParams(wparams, params); } if (_invariantParams != null) { params = new DefaultSolrParams(_invariantParams, params); } int tries = _maxRetries + 1; try { while (tries-- > 0) { try { if (SolrRequest.METHOD.GET == request.getMethod()) { if (streams != null) { throw new SolrException(SolrException.ErrorCode.BAD_REQUEST, "GET can't send streams!"); } method = new GetMethod(_baseURL + path + ClientUtils.toQueryString(params, false)); } else if (SolrRequest.METHOD.POST == request.getMethod()) { String url = _baseURL + path; boolean isMultipart = (streams != null && streams.size() > 1); if (streams == null || isMultipart) { PostMethod post = new PostMethod(url); post.getParams().setContentCharset("UTF-8"); if (!this.useMultiPartPost && !isMultipart) { post.addRequestHeader("Content-Type", "application/x-www-form-urlencoded; charset=UTF-8"); } List<Part> parts = new LinkedList<Part>(); Iterator<String> iter = params.getParameterNamesIterator(); while (iter.hasNext()) { String p = iter.next(); String[] vals = params.getParams(p); if (vals != null) { for (String v : vals) { if (this.useMultiPartPost || isMultipart) { parts.add(new StringPart(p, v, "UTF-8")); } else { post.addParameter(p, v); } } } } if (isMultipart) { int i = 0; for (ContentStream content : streams) { final ContentStream c = content; String charSet = null; String transferEncoding = null; parts.add(new PartBase(c.getName(), c.getContentType(), charSet, transferEncoding) { @Override protected long lengthOfData() throws IOException { return c.getSize(); } @Override protected void sendData(OutputStream out) throws IOException { Reader reader = c.getReader(); try { IOUtils.copy(reader, out); } finally { reader.close(); } } }); } } if (parts.size() > 0) { post.setRequestEntity(new MultipartRequestEntity(parts.toArray(new Part[parts.size()]), post.getParams())); } method = post; } else { String pstr = ClientUtils.toQueryString(params, false); PostMethod post = new PostMethod(url + pstr); final ContentStream[] contentStream = new ContentStream[1]; for (ContentStream content : streams) { contentStream[0] = content; break; } if (contentStream[0] instanceof RequestWriter.LazyContentStream) { post.setRequestEntity(new RequestEntity() { public long getContentLength() { return -1; } public String getContentType() { return contentStream[0].getContentType(); } public boolean isRepeatable() { return false; } public void writeRequest(OutputStream outputStream) throws IOException { ((RequestWriter.LazyContentStream) contentStream[0]).writeTo(outputStream); } }); } else { is = contentStream[0].getStream(); post.setRequestEntity(new InputStreamRequestEntity(is, contentStream[0].getContentType())); } method = post; } } else { throw new SolrServerException("Unsupported method: " + request.getMethod()); } } catch (NoHttpResponseException r) { method.releaseConnection(); method = null; if (is != null) { is.close(); } if ((tries < 1)) { throw r; } } } } catch (IOException ex) { throw new SolrServerException("error reading streams", ex); } method.setFollowRedirects(_followRedirects); method.addRequestHeader("User-Agent", AGENT); if (_allowCompression) { method.setRequestHeader(new Header("Accept-Encoding", "gzip,deflate")); } try { int statusCode = _httpClient.executeMethod(method); if (statusCode != HttpStatus.SC_OK) { StringBuilder msg = new StringBuilder(); msg.append(method.getStatusLine().getReasonPhrase()); msg.append("\n\n"); msg.append(method.getStatusText()); msg.append("\n\n"); msg.append("request: " + method.getURI()); throw new SolrException(statusCode, java.net.URLDecoder.decode(msg.toString(), "UTF-8")); } String charset = "UTF-8"; if (method instanceof HttpMethodBase) { charset = ((HttpMethodBase) method).getResponseCharSet(); } InputStream respBody = method.getResponseBodyAsStream(); if (_allowCompression) { Header contentEncodingHeader = method.getResponseHeader("Content-Encoding"); if (contentEncodingHeader != null) { String contentEncoding = contentEncodingHeader.getValue(); if (contentEncoding.contains("gzip")) { respBody = new GZIPInputStream(respBody); } else if (contentEncoding.contains("deflate")) { respBody = new InflaterInputStream(respBody); } } else { Header contentTypeHeader = method.getResponseHeader("Content-Type"); if (contentTypeHeader != null) { String contentType = contentTypeHeader.getValue(); if (contentType != null) { if (contentType.startsWith("application/x-gzip-compressed")) { respBody = new GZIPInputStream(respBody); } else if (contentType.startsWith("application/x-deflate")) { respBody = new InflaterInputStream(respBody); } } } } } return processor.processResponse(respBody, charset); } catch (HttpException e) { throw new SolrServerException(e); } catch (IOException e) { throw new SolrServerException(e); } finally { method.releaseConnection(); if (is != null) { is.close(); } } } | public void run() { LogPrinter.log(Level.FINEST, "Started Download at : {0, date, long}", new Date()); if (!PipeConnected) { throw new IllegalStateException("You should connect the pipe before with getInputStream()"); } InputStream ins = null; if (IsAlreadyDownloaded) { LogPrinter.log(Level.FINEST, "The file already Exists open and foward the byte"); try { ContentLength = (int) TheAskedFile.length(); ContentType = URLConnection.getFileNameMap().getContentTypeFor(TheAskedFile.getName()); ins = new FileInputStream(TheAskedFile); byte[] buffer = new byte[BUFFER_SIZE]; int read = ins.read(buffer); while (read >= 0) { Pipe.write(buffer, 0, read); read = ins.read(buffer); } } catch (IOException e) { e.printStackTrace(); } finally { if (ins != null) { try { ins.close(); } catch (IOException e) { } } } } else { LogPrinter.log(Level.FINEST, "the file does not exist locally so we try to download the thing"); File theDir = TheAskedFile.getParentFile(); if (!theDir.exists()) { theDir.mkdirs(); } for (URL url : ListFastest) { FileOutputStream fout = null; boolean OnError = false; long timestart = System.currentTimeMillis(); long bytecount = 0; try { URL newUrl = new URL(url.toString() + RequestedFile); LogPrinter.log(Level.FINEST, "the download URL = {0}", newUrl); URLConnection conn = newUrl.openConnection(); ContentType = conn.getContentType(); ContentLength = conn.getContentLength(); ins = conn.getInputStream(); fout = new FileOutputStream(TheAskedFile); byte[] buffer = new byte[BUFFER_SIZE]; int read = ins.read(buffer); while (read >= 0) { fout.write(buffer, 0, read); Pipe.write(buffer, 0, read); read = ins.read(buffer); bytecount += read; } Pipe.flush(); } catch (IOException e) { OnError = true; } finally { if (ins != null) { try { ins.close(); } catch (IOException e) { } } if (fout != null) { try { fout.close(); } catch (IOException e) { } } } long timeend = System.currentTimeMillis(); if (OnError) { continue; } else { long timetook = timeend - timestart; BigDecimal speed = new BigDecimal(bytecount).multiply(new BigDecimal(1000)).divide(new BigDecimal(timetook), MathContext.DECIMAL32); for (ReportCalculatedStatistique report : Listener) { report.reportUrlStat(url, speed, timetook); } break; } } } LogPrinter.log(Level.FINEST, "download finished at {0,date,long}", new Date()); if (Pipe != null) { try { Pipe.close(); } catch (IOException e) { e.printStackTrace(); } } } | 14,146 |
1 | @Test public void testCopy_readerToOutputStream_Encoding_nullEncoding() throws Exception { InputStream in = new ByteArrayInputStream(inData); in = new YellOnCloseInputStreamTest(in); Reader reader = new InputStreamReader(in, "US-ASCII"); ByteArrayOutputStream baout = new ByteArrayOutputStream(); OutputStream out = new YellOnFlushAndCloseOutputStreamTest(baout, false, true); IOUtils.copy(reader, out, null); assertEquals("Sizes differ", inData.length, baout.size()); assertTrue("Content differs", Arrays.equals(inData, baout.toByteArray())); } | public void close() { try { if (writer != null) { BufferedReader reader; writer.close(); writer = new BufferedWriter(new FileWriter(fileName)); for (int i = 0; i < headers.size(); i++) writer.write(headers.get(i) + ","); writer.write("\n"); reader = new BufferedReader(new FileReader(file)); while (reader.ready()) writer.write(reader.readLine() + "\n"); reader.close(); writer.close(); file.delete(); } } catch (java.io.IOException e) { throw new RuntimeException(e); } } | 14,147 |
0 | public static void BubbleSortLong2(long[] num) { int last_exchange; int right_border = num.length - 1; do { last_exchange = 0; for (int j = 0; j < num.length - 1; j++) { if (num[j] > num[j + 1]) { long temp = num[j]; num[j] = num[j + 1]; num[j + 1] = temp; last_exchange = j; } } right_border = last_exchange; } while (right_border > 0); } | private synchronized jdbcResultSet executeHTTP(String s) throws SQLException { byte result[]; try { URL url = new URL(sConnect); String p = StringConverter.unicodeToHexString(sUser); p += "+" + StringConverter.unicodeToHexString(sPassword); p += "+" + StringConverter.unicodeToHexString(s); URLConnection c = url.openConnection(); c.setDoOutput(true); OutputStream os = c.getOutputStream(); os.write(p.getBytes(ENCODING)); os.close(); c.connect(); InputStream is = (InputStream) c.getContent(); BufferedInputStream in = new BufferedInputStream(is); int len = c.getContentLength(); result = new byte[len]; for (int i = 0; i < len; i++) { int r = in.read(); result[i] = (byte) r; } } catch (Exception e) { throw Trace.error(Trace.CONNECTION_IS_BROKEN, e.getMessage()); } return new jdbcResultSet(new Result(result)); } | 14,148 |
1 | private void doTask() { try { log("\n\n\n\n\n\n\n\n\n"); log(" ================================================="); log(" = Starting PSCafePOS ="); log(" ================================================="); log(" = An open source point of sale system ="); log(" = for educational organizations. ="); log(" ================================================="); log(" = General Information ="); log(" = http://pscafe.sourceforge.net ="); log(" = Free Product Support ="); log(" = http://www.sourceforge.net/projects/pscafe ="); log(" ================================================="); log(" = License Overview ="); log(" ================================================="); log(" = PSCafePOS is a POS System for Schools ="); log(" = Copyright (C) 2007 Charles Syperski ="); log(" = ="); log(" = This program is free software; you can ="); log(" = redistribute it and/or modify it under the ="); log(" = terms of the GNU General Public License as ="); log(" = published by the Free Software Foundation; ="); log(" = either version 2 of the License, or any later ="); log(" = version. ="); log(" = ="); log(" = This program is distributed in the hope that ="); log(" = it will be useful, but WITHOUT ANY WARRANTY; ="); log(" = without even the implied warranty of ="); log(" = MERCHANTABILITY or FITNESS FOR A PARTICULAR ="); log(" = PURPOSE. ="); log(" = ="); log(" = See the GNU General Public License for more ="); log(" = details. ="); log(" = ="); log(" = You should have received a copy of the GNU ="); log(" = General Public License along with this ="); log(" = program; if not, write to the ="); log(" = ="); log(" = Free Software Foundation, Inc. ="); log(" = 59 Temple Place, Suite 330 ="); log(" = Boston, MA 02111-1307 USA ="); log(" ================================================="); log(" = If you have any questions of comments please ="); log(" = let us know at http://pscafe.sourceforge.net ="); log(" ================================================="); pause(); File settings; if (blAltSettings) { System.out.println("\n + Alternative path specified at run time:"); System.out.println(" Path: " + strAltPath); settings = new File(strAltPath); } else { settings = new File("etc" + File.separatorChar + "settings.dbp"); } System.out.print("\n + Checking for existance of settings..."); boolean blGo = false; if (settings.exists() && settings.canRead()) { log("[OK]"); blGo = true; if (forceConfig) { System.out.print("\n + Running Config Wizard (at user request)..."); Process pp = Runtime.getRuntime().exec("java -cp . PSSettingWizard etc" + File.separatorChar + "settings.dbp"); InputStream stderr = pp.getErrorStream(); InputStream stdin = pp.getInputStream(); InputStreamReader isr = new InputStreamReader(stdin); BufferedReader br = new BufferedReader(isr); String ln = null; while ((ln = br.readLine()) != null) System.out.println(" " + ln); pp.waitFor(); } } else { log("[FAILED]"); settings = new File("etc" + File.separatorChar + "settings.dbp.firstrun"); System.out.print("\n + Checking if this is the first run... "); if (settings.exists() && settings.canRead()) { log("[FOUND]"); File toFile = new File("etc" + File.separatorChar + "settings.dbp"); FileInputStream from = null; FileOutputStream to = null; try { from = new FileInputStream(settings); to = new FileOutputStream(toFile); byte[] buffer = new byte[4096]; int bytes_read; while ((bytes_read = from.read(buffer)) != -1) { to.write(buffer, 0, bytes_read); } if (toFile.exists() && toFile.canRead()) { settings = null; settings = new File("etc" + File.separatorChar + "settings.dbp"); } System.out.print("\n + Running Settings Wizard... "); try { Process p = Runtime.getRuntime().exec("java PSSettingWizard etc" + File.separatorChar + "settings.dbp"); InputStream stderr = p.getErrorStream(); InputStream stdin = p.getInputStream(); InputStreamReader isr = new InputStreamReader(stdin); BufferedReader br = new BufferedReader(isr); String ln = null; while ((ln = br.readLine()) != null) System.out.println(" " + ln); p.waitFor(); log("[OK]"); if (p.exitValue() == 0) blGo = true; } catch (InterruptedException i) { System.err.println(i.getMessage()); } } catch (Exception ex) { System.err.println(ex.getMessage()); } finally { if (from != null) try { from.close(); } catch (IOException e) { ; } if (to != null) try { to.close(); } catch (IOException e) { ; } } } else { settings = null; settings = new File("etc" + File.separatorChar + "settings.dbp"); DBSettingsWriter writ = new DBSettingsWriter(); writ.writeFile(new DBSettings(), settings); blGo = true; } } if (blGo) { String cp = "."; try { File classpath = new File("lib"); File[] subFiles = classpath.listFiles(); for (int i = 0; i < subFiles.length; i++) { if (subFiles[i].isFile()) { cp += File.pathSeparatorChar + "lib" + File.separatorChar + subFiles[i].getName() + ""; } } } catch (Exception e) { System.err.println(e.getMessage()); } try { boolean blExecutePOS = false; System.out.print("\n + Checking runtime settings... "); DBSettings info = null; if (settings == null) settings = new File("etc" + File.separatorChar + "settings.dbp"); if (settings.exists() && settings.canRead()) { DBSettingsWriter writ = new DBSettingsWriter(); info = (DBSettings) writ.loadSettingsDB(settings); if (info != null) { blExecutePOS = true; } } if (blExecutePOS) { log("[OK]"); String strSSL = ""; String strSSLDebug = ""; if (info != null) { debug = info.get(DBSettings.MAIN_DEBUG).compareTo("1") == 0; if (debug) log(" * Debug Mode is ON"); else log(" * Debug Mode is OFF"); if (info.get(DBSettings.POS_SSLENABLED).compareTo("1") == 0) { strSSL = "-Djavax.net.ssl.keyStore=" + info.get(DBSettings.POS_SSLKEYSTORE) + " -Djavax.net.ssl.keyStorePassword=pscafe -Djavax.net.ssl.trustStore=" + info.get(DBSettings.POS_SSLTRUSTSTORE) + " -Djavax.net.ssl.trustStorePassword=pscafe"; log(" * Using SSL"); debug(" " + strSSL); if (info.get(DBSettings.POS_SSLDEBUG).compareTo("1") == 0) { strSSLDebug = "-Djavax.net.debug=all"; log(" * SSL Debugging enabled"); debug(" " + strSSLDebug); } } } String strPOSRun = "java -cp " + cp + " " + strSSL + " " + strSSLDebug + " POSDriver " + settings.getPath(); debug(strPOSRun); System.out.print("\n + Running PSCafePOS... "); Process pr = Runtime.getRuntime().exec(strPOSRun); System.out.print("[OK]\n\n"); InputStream stderr = pr.getErrorStream(); InputStream stdin = pr.getInputStream(); InputStreamReader isr = new InputStreamReader(stdin); InputStreamReader isre = new InputStreamReader(stderr); BufferedReader br = new BufferedReader(isr); BufferedReader bre = new BufferedReader(isre); String line = null; String lineError = null; log(" ================================================="); log(" = Output from PSCafePOS System ="); log(" ================================================="); while ((line = br.readLine()) != null || (lineError = bre.readLine()) != null) { if (line != null) System.out.println(" [PSCafePOS]" + line); if (lineError != null) System.out.println(" [ERR]" + lineError); } pr.waitFor(); log(" ================================================="); log(" = End output from PSCafePOS System ="); log(" = PSCafePOS has exited ="); log(" ================================================="); } else { log("[Failed]"); } } catch (Exception i) { log(i.getMessage()); i.printStackTrace(); } } } catch (Exception e) { log(e.getMessage()); } } | public byte process(ProcessorContext<PublishRequest> context) throws InterruptedException, ProcessorException { logger.info("MapTileChacheTask:process"); PublishRequest req = context.getItem().getEntity(); if (StringUtils.isEmpty(req.getBackMap())) return TaskState.STATE_TILE_CACHED; final PublicMapPost post; final GenericDAO<PublicMapPost> postDao = DAOFactory.createDAO(PublicMapPost.class); try { ReadOnlyTransaction.beginTransaction(); } catch (DatabaseException e) { logger.error("error", e); throw new ProcessorException(e); } int numCachedTiles = 0; try { List<MapTile> backTiles = new ArrayList<MapTile>(); post = postDao.findUniqueByCriteria(Expression.eq("guid", req.getPostGuid())); final LatLngRectangle bounds = new LatLngRectangle(new LatLngPoint(post.getSWLat(), post.getSWLon()), new LatLngPoint(post.getNELat(), post.getNELon())); final String backMapGuid = "gst"; final XFile dstDir = new XFile(new XFile(Configuration.getInstance().getPublicMapStorage().toString()), backMapGuid); dstDir.mkdir(); for (int z = Math.min(Tile.getOptimalZoom(bounds, 768), 9); z <= 17; z++) { final Tile tileStart = new Tile(bounds.getSouthWest().getLat(), bounds.getSouthWest().getLng(), z); final Tile tileEnd = new Tile(bounds.getNorthEast().getLat(), bounds.getNorthEast().getLng(), z); for (double y = tileEnd.getTileCoord().getY(); y <= tileStart.getTileCoord().getY(); y++) for (double x = tileStart.getTileCoord().getX(); x <= tileEnd.getTileCoord().getX(); x++) { NASAMapTile tile = new NASAMapTile((int) x, (int) y, z); XFile file = new XFile(dstDir, tile.toKeyString()); if (file.exists() && file.isFile()) continue; backTiles.add(tile); } } try { for (MapTile tile : backTiles) { InputStream in = null; OutputStream out = null; final URL url = new URL(tile.getPath()); try { final XFile outFile = new XFile(dstDir, tile.toKeyString()); final URLConnection conn = url.openConnection(); if (conn == null || !conn.getContentType().startsWith("image")) throw new IllegalAccessException("onearth.jpl.nasa.gov service returns non-image file, " + "content-type='" + conn.getContentType() + "'"); in = conn.getInputStream(); if (in != null) { out = new XFileOutputStream(outFile); IOUtils.copy(in, out); } else throw new IllegalStateException("opened stream is null"); } finally { if (out != null) { out.flush(); out.close(); } if (in != null) in.close(); } if (++numCachedTiles % 100 == 0) { logger.info(numCachedTiles + " tiles cached"); } } } catch (Throwable e) { logger.error("map tile caching has failed: ", e); throw new ProcessorException(e); } } catch (ProcessorException e) { logger.error("map tile caching has failed: ", e); throw e; } catch (Throwable e) { logger.error("map tile caching has failed: ", e); throw new ProcessorException(e); } finally { ReadOnlyTransaction.closeTransaction(); logger.info(numCachedTiles + " tiles cached"); } return TaskState.STATE_TILE_CACHED; } | 14,149 |
0 | private void saveAttachment(long messageId, Part attachment, boolean saveAsNew) throws IOException, MessagingException { long attachmentId = -1; Uri contentUri = null; int size = -1; File tempAttachmentFile = null; if ((!saveAsNew) && (attachment instanceof LocalAttachmentBodyPart)) { attachmentId = ((LocalAttachmentBodyPart) attachment).getAttachmentId(); } if (attachment.getBody() != null) { Body body = attachment.getBody(); if (body instanceof LocalAttachmentBody) { contentUri = ((LocalAttachmentBody) body).getContentUri(); } else { InputStream in = attachment.getBody().getInputStream(); tempAttachmentFile = File.createTempFile("att", null, mAttachmentsDir); FileOutputStream out = new FileOutputStream(tempAttachmentFile); size = IOUtils.copy(in, out); in.close(); out.close(); } } if (size == -1) { String disposition = attachment.getDisposition(); if (disposition != null) { String s = MimeUtility.getHeaderParameter(disposition, "size"); if (s != null) { size = Integer.parseInt(s); } } } if (size == -1) { size = 0; } String storeData = Utility.combine(attachment.getHeader(MimeHeader.HEADER_ANDROID_ATTACHMENT_STORE_DATA), ','); String name = MimeUtility.getHeaderParameter(attachment.getContentType(), "name"); String contentId = attachment.getContentId(); if (attachmentId == -1) { ContentValues cv = new ContentValues(); cv.put("message_id", messageId); cv.put("content_uri", contentUri != null ? contentUri.toString() : null); cv.put("store_data", storeData); cv.put("size", size); cv.put("name", name); cv.put("mime_type", attachment.getMimeType()); cv.put("content_id", contentId); attachmentId = mDb.insert("attachments", "message_id", cv); } else { ContentValues cv = new ContentValues(); cv.put("content_uri", contentUri != null ? contentUri.toString() : null); cv.put("size", size); cv.put("content_id", contentId); cv.put("message_id", messageId); mDb.update("attachments", cv, "id = ?", new String[] { Long.toString(attachmentId) }); } if (tempAttachmentFile != null) { File attachmentFile = new File(mAttachmentsDir, Long.toString(attachmentId)); tempAttachmentFile.renameTo(attachmentFile); attachment.setBody(new LocalAttachmentBody(contentUri, mContext)); ContentValues cv = new ContentValues(); cv.put("content_uri", contentUri != null ? contentUri.toString() : null); mDb.update("attachments", cv, "id = ?", new String[] { Long.toString(attachmentId) }); } if (attachment instanceof LocalAttachmentBodyPart) { ((LocalAttachmentBodyPart) attachment).setAttachmentId(attachmentId); } } | public JsonValue get(Url url) { try { URLConnection connection = new URL(url + "").openConnection(); return createItemFromResponse(url, connection); } catch (IOException e) { throw ItemscriptError.internalError(this, "get.IOException", e); } } | 14,150 |
0 | public static String remove_file(String sessionid, String key) { String resultJsonString = "some problem existed inside the create_new_tag() function if you see this string"; try { Log.d("current running function name:", "remove_file"); HttpClient httpclient = new DefaultHttpClient(); HttpPost httppost = new HttpPost("https://mt0-app.cloud.cm/rpc/json"); List<NameValuePair> nameValuePairs = new ArrayList<NameValuePair>(2); nameValuePairs.add(new BasicNameValuePair("c", "Storage")); nameValuePairs.add(new BasicNameValuePair("m", "remove_file")); nameValuePairs.add(new BasicNameValuePair("keys", key)); httppost.setEntity(new UrlEncodedFormEntity(nameValuePairs)); httppost.setHeader("Cookie", "PHPSESSID=" + sessionid); HttpResponse response = httpclient.execute(httppost); resultJsonString = EntityUtils.toString(response.getEntity()); Log.d("jsonStringReturned:", resultJsonString); return resultJsonString; } catch (Exception e) { e.printStackTrace(); } return resultJsonString; } | public static String encryptPass2(String pass) throws UnsupportedEncodingException { String passEncrypt; MessageDigest md5 = null; try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException ex) { } md5.update(pass.getBytes()); String dis = new String(md5.digest(), 10); passEncrypt = dis.toString(); return passEncrypt; } | 14,151 |
0 | public static String hash(String plainText) throws Exception { MessageDigest m = MessageDigest.getInstance("MD5"); m.update(plainText.getBytes(), 0, plainText.length()); String hash = new BigInteger(1, m.digest()).toString(16); if (hash.length() == 31) { hash = "0" + hash; } return hash; } | public void writeToFtp(String login, String password, String address, String directory, String filename) { String newline = System.getProperty("line.separator"); try { URL url = new URL("ftp://" + login + ":" + password + "@ftp." + address + directory + filename + ".html" + ";type=i"); URLConnection urlConn = url.openConnection(); urlConn.setDoOutput(true); OutputStreamWriter stream = new OutputStreamWriter(urlConn.getOutputStream()); stream.write("<html><title>" + title + "</title>" + newline); stream.write("<h1><b>" + title + "</b></h1>" + newline); stream.write("<h2>Table Of Contents:</h2><ul>" + newline); for (int k = 0; k < rings.size(); k++) { stream.write("<li><i><a href=\"#"); stream.write(readNoteTitle(k)); stream.write("\">"); stream.write(readNoteTitle(k)); stream.write("</a></i></li>" + newline); } stream.write("</ul><hr>" + newline + newline); for (int k = 0; k < rings.size(); k++) { stream.write("<h3><b>"); stream.write("<a name=\""); stream.write(readNoteTitle(k)); stream.write("\">"); stream.write(readNoteTitle(k) + "</a>"); stream.write("</b></h3>" + newline); stream.write(readNoteBody(k) + newline); } stream.write(newline + "<br><hr><a>This was created using Scribe, a free crutch editor.</a></html>"); stream.close(); } catch (IOException error) { System.out.println("There was an error: " + error); } } | 14,152 |
1 | public static void updateTableData(Connection dest, TableMetaData tableMetaData, Row r) throws Exception { PreparedStatement ps = null; try { dest.setAutoCommit(false); String sql = "UPDATE " + tableMetaData.getSchema() + "." + tableMetaData.getTableName() + " SET "; for (String columnName : tableMetaData.getColumnsNames()) { sql += columnName + " = ? ,"; } sql = sql.substring(0, sql.length() - 1); sql += " WHERE "; for (String pkColumnName : tableMetaData.getPkColumns()) { sql += pkColumnName + " = ? AND "; } sql = sql.substring(0, sql.length() - 4); System.out.println("UPDATE: " + sql); ps = dest.prepareStatement(sql); int param = 1; for (String columnName : tableMetaData.getColumnsNames()) { if (dest instanceof OracleConnection) { if (tableMetaData.getColumnsTypes().get(columnName).equalsIgnoreCase("BLOB")) { BLOB blob = new BLOB((OracleConnection) dest, (byte[]) r.getRowData().get(columnName)); ((OraclePreparedStatement) ps).setBLOB(param, blob); } else if (tableMetaData.getColumnsTypes().get(columnName).equalsIgnoreCase("CLOB")) { ((OraclePreparedStatement) ps).setStringForClob(param, (String) r.getRowData().get(columnName)); } else if (tableMetaData.getColumnsTypes().get(columnName).equalsIgnoreCase("LONG")) { ps.setBytes(param, (byte[]) r.getRowData().get(columnName)); } } else { ps.setObject(param, r.getRowData().get(columnName)); } param++; } for (String pkColumnName : tableMetaData.getPkColumns()) { ps.setObject(param, r.getRowData().get(pkColumnName)); param++; } if (ps.executeUpdate() != 1) { dest.rollback(); throw new Exception("Erro no update"); } ps.clearParameters(); dest.commit(); dest.setAutoCommit(true); } finally { if (ps != null) ps.close(); } } | public static void processAction(ActionRequest actionRequest, ActionResponse actionResponse) throws PortletException { log.debug("Start MemberPortletActionMethod.processAction()"); MemberProcessingActionRequest mp = null; try { ModuleManager moduleManager = ModuleManager.getInstance(PropertiesProvider.getConfigPath()); mp = new MemberProcessingActionRequest(actionRequest, moduleManager); String moduleName = RequestTools.getString(actionRequest, MemberConstants.MEMBER_MODULE_PARAM); String actionName = RequestTools.getString(actionRequest, MemberConstants.MEMBER_ACTION_PARAM); String subActionName = RequestTools.getString(actionRequest, MemberConstants.MEMBER_SUBACTION_PARAM).trim(); if (log.isDebugEnabled()) { Map parameterMap = actionRequest.getParameterMap(); if (!parameterMap.entrySet().isEmpty()) { log.debug("Action request parameter"); for (Object o : parameterMap.entrySet()) { Map.Entry entry = (Map.Entry) o; log.debug(" key: " + entry.getKey() + ", value: " + entry.getValue()); } } else { log.debug("Action request map is empty"); } log.debug(" Point #4.1 module '" + moduleName + "'"); log.debug(" Point #4.2 action '" + actionName + "'"); log.debug(" Point #4.3 subAction '" + subActionName + "'"); } if (mp.mod == null) { actionResponse.setRenderParameter(MemberConstants.ERROR_TEXT, "Point #4.2. Module '" + moduleName + "' not found"); return; } if (mp.mod.getType() != null && mp.mod.getType().getType() == ModuleTypeTypeType.LOOKUP_TYPE && (mp.getFromParam() == null || mp.getFromParam().length() == 0)) { actionResponse.setRenderParameter(MemberConstants.ERROR_TEXT, "Point #4.4. Module " + moduleName + " is lookup module"); return; } int actionType = ContentTypeActionType.valueOf(actionName).getType(); if (log.isDebugEnabled()) { log.debug("action name " + actionName); log.debug("ContentTypeActionType " + ContentTypeActionType.valueOf(actionName).toString()); log.debug("action type " + actionType); } mp.content = MemberServiceClass.getContent(mp.mod, actionType); if (mp.content == null) { actionResponse.setRenderParameter(MemberConstants.ERROR_TEXT, "Module: '" + moduleName + "', action '" + actionName + "', not found"); return; } if (log.isDebugEnabled()) { log.debug("Debug. Unmarshal sqlCache object"); synchronized (syncFile) { XmlTools.writeToFile(mp.content.getQueryArea().getSqlCache(), SiteUtils.getTempDir() + File.separatorChar + "member-content-site-start-0.xml", "windows-1251"); } } if (!MemberServiceClass.checkRole(actionRequest, mp.content)) { actionResponse.setRenderParameter(MemberConstants.ERROR_TEXT, "Access denied"); return; } if (log.isDebugEnabled()) { log.debug("Unmarshal sqlCache object"); synchronized (syncFile) { XmlTools.writeToFile(mp.content.getQueryArea().getSqlCache(), SiteUtils.getTempDir() + File.separatorChar + "member-content-site-start-2.xml", "windows-1251"); } } initRenderParameters(actionRequest.getParameterMap(), actionResponse); if ("commit".equalsIgnoreCase(subActionName)) { DatabaseAdapter dbDyn = null; PreparedStatement ps = null; try { dbDyn = mp.getDatabaseAdapter(); int i1; switch(actionType) { case ContentTypeActionType.INSERT_TYPE: if (log.isDebugEnabled()) log.debug("Start prepare data for inserting."); String validateStatus = mp.validateFields(dbDyn); if (log.isDebugEnabled()) log.debug("Validating status - " + validateStatus); if (validateStatus != null) { WebmillErrorPage.setErrorInfo(actionResponse, validateStatus, MemberConstants.ERROR_TEXT, null, "Continue", MemberConstants.ERROR_URL_NAME); return; } if (log.isDebugEnabled()) { log.debug("Unmarshal sqlCache object"); synchronized (syncFile) { XmlTools.writeToFile(mp.content.getQueryArea().getSqlCache(), SiteUtils.getTempDir() + File.separatorChar + "member-content-before-yesno.xml", "windows-1251"); } } if (log.isDebugEnabled()) log.debug("Start looking for field with type " + FieldsTypeJspTypeType.YES_1_NO_N.toString()); if (MemberServiceClass.hasYesNoField(actionRequest.getParameterMap(), mp.mod, mp.content)) { if (log.isDebugEnabled()) log.debug("Found field with type " + FieldsTypeJspTypeType.YES_1_NO_N.toString()); mp.process_Yes_1_No_N_Fields(dbDyn); } else { if (log.isDebugEnabled()) log.debug("Field with type " + FieldsTypeJspTypeType.YES_1_NO_N.toString() + " not found"); } String sql_ = MemberServiceClass.buildInsertSQL(mp.content, mp.getFromParam(), mp.mod, dbDyn, actionRequest.getServerName(), mp.getModuleManager(), mp.authSession); if (log.isDebugEnabled()) { log.debug("insert SQL:\n" + sql_ + "\n"); log.debug("Unmarshal sqlCache object"); synchronized (syncFile) { XmlTools.writeToFile(mp.content.getQueryArea().getSqlCache(), SiteUtils.getTempDir() + File.separatorChar + "member-content.xml", "windows-1251"); } } boolean checkStatus = false; switch(dbDyn.getFamaly()) { case DatabaseManager.MYSQL_FAMALY: break; default: checkStatus = mp.checkRestrict(); if (!checkStatus) throw new ServletException("check status of restrict failed"); break; } if (log.isDebugEnabled()) log.debug("check status - " + checkStatus); ps = dbDyn.prepareStatement(sql_); Object idNewRec = mp.bindInsert(dbDyn, ps); i1 = ps.executeUpdate(); if (log.isDebugEnabled()) log.debug("Number of inserter record - " + i1); DatabaseManager.close(ps); ps = null; if (log.isDebugEnabled()) { outputDebugOfInsertStatus(mp, dbDyn, idNewRec); } mp.prepareBigtextData(dbDyn, idNewRec, false); for (int i = 0; i < mp.mod.getRelateClassCount(); i++) { RelateClassType rc = mp.mod.getRelateClass(i); if (log.isDebugEnabled()) log.debug("#7.003.003 terminate class " + rc.getClassName()); CacheFactory.terminate(rc.getClassName(), null, Boolean.TRUE.equals(rc.getIsFullReinitCache())); } break; case ContentTypeActionType.CHANGE_TYPE: if (log.isDebugEnabled()) log.debug("Commit change page"); validateStatus = mp.validateFields(dbDyn); if (validateStatus != null) { WebmillErrorPage.setErrorInfo(actionResponse, validateStatus, MemberConstants.ERROR_TEXT, null, "Continue", MemberConstants.ERROR_URL_NAME); return; } if (MemberServiceClass.hasYesNoField(actionRequest.getParameterMap(), mp.mod, mp.content)) { if (log.isDebugEnabled()) log.debug("Found field with type " + FieldsTypeJspTypeType.YES_1_NO_N); mp.process_Yes_1_No_N_Fields(dbDyn); } Object idCurrRec; if (log.isDebugEnabled()) log.debug("PrimaryKeyType " + mp.content.getQueryArea().getPrimaryKeyType()); switch(mp.content.getQueryArea().getPrimaryKeyType().getType()) { case PrimaryKeyTypeType.NUMBER_TYPE: log.debug("PrimaryKeyType - 'number'"); idCurrRec = PortletService.getLong(actionRequest, mp.mod.getName() + '.' + mp.content.getQueryArea().getPrimaryKey()); break; case PrimaryKeyTypeType.STRING_TYPE: log.debug("PrimaryKeyType - 'string'"); idCurrRec = RequestTools.getString(actionRequest, mp.mod.getName() + '.' + mp.content.getQueryArea().getPrimaryKey()); break; default: throw new Exception("Change. Wrong type of primary key - " + mp.content.getQueryArea().getPrimaryKeyType()); } if (log.isDebugEnabled()) log.debug("mp.isSimpleField(): " + mp.isSimpleField()); if (mp.isSimpleField()) { log.debug("start build SQL"); sql_ = MemberServiceClass.buildUpdateSQL(dbDyn, mp.content, mp.getFromParam(), mp.mod, true, actionRequest.getParameterMap(), actionRequest.getRemoteUser(), actionRequest.getServerName(), mp.getModuleManager(), mp.authSession); if (log.isDebugEnabled()) log.debug("update SQL:" + sql_); ps = dbDyn.prepareStatement(sql_); mp.bindUpdate(dbDyn, ps, idCurrRec, true); i1 = ps.executeUpdate(); if (log.isDebugEnabled()) log.debug("Number of updated record - " + i1); } log.debug("prepare big text"); mp.prepareBigtextData(dbDyn, idCurrRec, true); if (mp.content.getQueryArea().getPrimaryKeyType().getType() != PrimaryKeyTypeType.NUMBER_TYPE) throw new Exception("PK of 'Bigtext' table must be a 'number' type"); log.debug("start sync cache data"); for (int i = 0; i < mp.mod.getRelateClassCount(); i++) { RelateClassType rc = mp.mod.getRelateClass(i); if (log.isDebugEnabled()) log.debug("#7.003.002 terminate class " + rc.getClassName() + ", id_rec " + idCurrRec); if (mp.content.getQueryArea().getPrimaryKeyType().getType() == PrimaryKeyTypeType.NUMBER_TYPE) { CacheFactory.terminate(rc.getClassName(), (Long) idCurrRec, Boolean.TRUE.equals(rc.getIsFullReinitCache())); } else { actionResponse.setRenderParameter(MemberConstants.ERROR_TEXT, "Change. Wrong type of primary key - " + mp.content.getQueryArea().getPrimaryKeyType()); return; } } break; case ContentTypeActionType.DELETE_TYPE: log.debug("Commit delete page<br>"); Object idRec; if (mp.content.getQueryArea().getPrimaryKeyType().getType() == PrimaryKeyTypeType.NUMBER_TYPE) { idRec = PortletService.getLong(actionRequest, mp.mod.getName() + '.' + mp.content.getQueryArea().getPrimaryKey()); } else if (mp.content.getQueryArea().getPrimaryKeyType().getType() == PrimaryKeyTypeType.STRING_TYPE) { idRec = RequestTools.getString(actionRequest, mp.mod.getName() + '.' + mp.content.getQueryArea().getPrimaryKey()); } else { actionResponse.setRenderParameter(MemberConstants.ERROR_TEXT, "Delete. Wrong type of primary key - " + mp.content.getQueryArea().getPrimaryKeyType()); return; } if (dbDyn.getFamaly() == DatabaseManager.MYSQL_FAMALY) mp.deleteBigtextData(dbDyn, idRec); sql_ = MemberServiceClass.buildDeleteSQL(dbDyn, mp.mod, mp.content, mp.getFromParam(), actionRequest.getParameterMap(), actionRequest.getRemoteUser(), actionRequest.getServerName(), moduleManager, mp.authSession); if (log.isDebugEnabled()) log.debug("delete SQL: " + sql_ + "<br>\n"); ps = dbDyn.prepareStatement(sql_); mp.bindDelete(ps); i1 = ps.executeUpdate(); if (log.isDebugEnabled()) log.debug("Number of deleted record - " + i1); if (idRec != null && (idRec instanceof Long)) { for (int i = 0; i < mp.mod.getRelateClassCount(); i++) { RelateClassType rc = mp.mod.getRelateClass(i); if (log.isDebugEnabled()) log.debug("#7.003.001 terminate class " + rc.getClassName() + ", id_rec " + idRec.toString()); CacheFactory.terminate(rc.getClassName(), (Long) idRec, Boolean.TRUE.equals(rc.getIsFullReinitCache())); } } break; default: actionResponse.setRenderParameter(MemberConstants.ERROR_TEXT, "Unknown type of action - " + actionName); return; } log.debug("do commit"); dbDyn.commit(); } catch (Exception e1) { try { dbDyn.rollback(); } catch (Exception e001) { log.info("error in rolback()"); } log.error("Error while processing this page", e1); if (dbDyn.testExceptionIndexUniqueKey(e1)) { WebmillErrorPage.setErrorInfo(actionResponse, "You input value already exists in DB. Try again with other value", MemberConstants.ERROR_TEXT, null, "Continue", MemberConstants.ERROR_URL_NAME); } else { WebmillErrorPage.setErrorInfo(actionResponse, "Error while processing request", MemberConstants.ERROR_TEXT, e1, "Continue", MemberConstants.ERROR_URL_NAME); } } finally { DatabaseManager.close(dbDyn, ps); } } } catch (Exception e) { final String es = "General processing error "; log.error(es, e); throw new PortletException(es, e); } finally { if (mp != null) { mp.destroy(); } } } | 14,153 |
0 | public static String md5Encrypt(final String txt) { String enTxt = txt; MessageDigest md = null; try { md = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { logger.error("Error:", e); } if (null != md) { byte[] md5hash = new byte[32]; try { md.update(txt.getBytes("UTF-8"), 0, txt.length()); } catch (UnsupportedEncodingException e) { logger.error("Error:", e); } md5hash = md.digest(); StringBuffer md5StrBuff = new StringBuffer(); for (int i = 0; i < md5hash.length; i++) { if (Integer.toHexString(0xFF & md5hash[i]).length() == 1) { md5StrBuff.append("0").append(Integer.toHexString(0xFF & md5hash[i])); } else { md5StrBuff.append(Integer.toHexString(0xFF & md5hash[i])); } } enTxt = md5StrBuff.toString(); } return enTxt; } | public void run() { try { Socket socket = getSocket(); System.out.println("opening socket to " + address + " on " + port); InputStream in = socket.getInputStream(); for (; ; ) { FileTransferHeader header = FileTransferHeader.readHeader(in); if (header == null) break; System.out.println("header: " + header); String[] parts = header.getFilename().getSegments(); String filename; if (parts.length > 0) filename = "dl-" + parts[parts.length - 1]; else filename = "dl-" + session.getScreenname(); System.out.println("writing to file " + filename); long sum = 0; if (new File(filename).exists()) { FileInputStream fis = new FileInputStream(filename); byte[] block = new byte[10]; for (int i = 0; i < block.length; ) { int count = fis.read(block); if (count == -1) break; i += count; } FileTransferChecksum summer = new FileTransferChecksum(); summer.update(block, 0, 10); sum = summer.getValue(); } FileChannel fileChannel = new FileOutputStream(filename).getChannel(); FileTransferHeader outHeader = new FileTransferHeader(header); outHeader.setHeaderType(FileTransferHeader.HEADERTYPE_ACK); outHeader.setIcbmMessageId(cookie); outHeader.setBytesReceived(0); outHeader.setReceivedChecksum(sum); OutputStream socketOut = socket.getOutputStream(); System.out.println("sending header: " + outHeader); outHeader.write(socketOut); for (int i = 0; i < header.getFileSize(); ) { long transferred = fileChannel.transferFrom(Channels.newChannel(in), 0, header.getFileSize() - i); System.out.println("transferred " + transferred); if (transferred == -1) return; i += transferred; } System.out.println("finished transfer!"); fileChannel.close(); FileTransferHeader doneHeader = new FileTransferHeader(header); doneHeader.setHeaderType(FileTransferHeader.HEADERTYPE_RECEIVED); doneHeader.setFlags(doneHeader.getFlags() | FileTransferHeader.FLAG_DONE); doneHeader.setBytesReceived(doneHeader.getBytesReceived() + 1); doneHeader.setIcbmMessageId(cookie); doneHeader.setFilesLeft(doneHeader.getFilesLeft() - 1); doneHeader.write(socketOut); if (doneHeader.getFilesLeft() - 1 <= 0) { socket.close(); break; } } } catch (IOException e) { e.printStackTrace(); return; } } | 14,154 |
1 | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | @Override public void copyTo(ManagedFile other) throws ManagedIOException { try { if (other.getType() == ManagedFileType.FILE) { IOUtils.copy(this.getContent().getInputStream(), other.getContent().getOutputStream()); } else { ManagedFile newFile = other.retrive(this.getPath()); newFile.createFile(); IOUtils.copy(this.getContent().getInputStream(), newFile.getContent().getOutputStream()); } } catch (IOException ioe) { throw ManagedIOException.manage(ioe); } } | 14,155 |
1 | public static String sendGetRequest(String endpoint, String requestParameters) { if (endpoint == null) return null; String result = null; if (endpoint.startsWith("http://")) { try { StringBuffer data = new StringBuffer(); String urlStr = endpoint; if (requestParameters != null && requestParameters.length() > 0) { urlStr += "?" + requestParameters; } URL url = new URL(urlStr); URLConnection conn = url.openConnection(); BufferedReader rd = new BufferedReader(new InputStreamReader(conn.getInputStream())); StringBuffer sb = new StringBuffer(); String line; while ((line = rd.readLine()) != null) { sb.append(line); } rd.close(); result = sb.toString(); } catch (Exception e) { Logger.getLogger(HTTPClient.class.getClass().getName()).log(Level.FINE, "Could not connect to URL, is the service online?"); } } return result; } | public String getWebPage(String url) { String content = ""; URL urlObj = null; try { urlObj = new URL(url); } catch (MalformedURLException urlEx) { urlEx.printStackTrace(); throw new Error("URL creation failed."); } try { BufferedReader reader = new BufferedReader(new InputStreamReader(urlObj.openStream())); String line; while ((line = reader.readLine()) != null) { content += line; } } catch (IOException e) { e.printStackTrace(); throw new Error("Page retrieval failed."); } return content; } | 14,156 |
1 | private void copy(File fromFile, File toFile) throws IOException { String fromFileName = fromFile.getName(); File tmpFile = new File(fromFileName); String toFileName = toFile.getName(); if (!tmpFile.exists()) throw new IOException("FileCopy: " + "no such source file: " + fromFileName); if (!tmpFile.isFile()) throw new IOException("FileCopy: " + "can't copy directory: " + fromFileName); if (!tmpFile.canRead()) throw new IOException("FileCopy: " + "source file is unreadable: " + fromFileName); FileInputStream from = null; FileOutputStream to = null; try { from = new FileInputStream(tmpFile); File toF = new File(toFile.getCanonicalPath()); if (!toF.exists()) ; toF.createNewFile(); if (!SBCMain.DEBUG_MODE) to = new FileOutputStream(toFile); else to = new FileOutputStream(toF); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = from.read(buffer)) != -1) to.write(buffer, 0, bytesRead); } finally { if (from != null) try { from.close(); } catch (IOException e) { ; } if (to != null) try { to.close(); } catch (IOException e) { ; } } } | private void packageDestZip(File tmpFile) throws FileNotFoundException, IOException { log("Creating launch profile package " + destfile); ZipOutputStream out = new ZipOutputStream(new BufferedOutputStream(new FileOutputStream(destfile))); ZipEntry e = new ZipEntry(RESOURCE_JAR_FILENAME); e.setMethod(ZipEntry.STORED); e.setSize(tmpFile.length()); e.setCompressedSize(tmpFile.length()); e.setCrc(calcChecksum(tmpFile, new CRC32())); out.putNextEntry(e); InputStream in = new BufferedInputStream(new FileInputStream(tmpFile)); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.closeEntry(); out.finish(); out.close(); } | 14,157 |
0 | public void testServletTesterClient() throws Exception { String base_url = tester.createSocketConnector(true); URL url = new URL(base_url + "/context/hello/info"); String result = IO.toString(url.openStream()); assertEquals("<h1>Hello Servlet</h1>", result); } | @Override public String encryptPassword(String password) throws JetspeedSecurityException { if (securePasswords == false) { return password; } if (password == null) { return null; } try { if ("SHA-512".equals(passwordsAlgorithm)) { password = password + JetspeedResources.getString("aipo.encrypt_key"); MessageDigest md = MessageDigest.getInstance(passwordsAlgorithm); md.reset(); md.update(password.getBytes()); byte[] hash = md.digest(); StringBuffer sb = new StringBuffer(); for (int i = 0; i < hash.length; i++) { sb.append(Integer.toHexString((hash[i] >> 4) & 0x0F)); sb.append(Integer.toHexString(hash[i] & 0x0F)); } return sb.toString(); } else { MessageDigest md = MessageDigest.getInstance(passwordsAlgorithm); byte[] digest = md.digest(password.getBytes(ALEipConstants.DEF_CONTENT_ENCODING)); ByteArrayOutputStream bas = new ByteArrayOutputStream(digest.length + digest.length / 3 + 1); OutputStream encodedStream = MimeUtility.encode(bas, "base64"); encodedStream.write(digest); encodedStream.flush(); encodedStream.close(); return bas.toString(); } } catch (Exception e) { logger.error("Unable to encrypt password." + e.getMessage(), e); return null; } } | 14,158 |
1 | 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; } } | public ActualTask(TEditor editor, TIGDataBase dataBase, String directoryPath) { File myDirectory = new File(directoryPath); int i; Vector images = new Vector(); images = dataBase.allImageSearch(); lengthOfTask = images.size() * 2; String directory = directoryPath + "Images" + myDirectory.separator; File newDirectoryFolder = new File(directory); newDirectoryFolder.mkdirs(); try { DocumentBuilderFactory domFactory = DocumentBuilderFactory.newInstance(); DocumentBuilder domBuilder = domFactory.newDocumentBuilder(); doc = domBuilder.newDocument(); } catch (Exception exc) { System.out.println(exc.getMessage()); System.out.println(exc.toString()); } Element dbElement = doc.createElement("dataBase"); for (i = 0; ((i < images.size()) && !stop); i++) { current = i; String element = (String) images.elementAt(i); String pathSrc = "Images" + File.separator + element.substring(0, 1).toUpperCase() + File.separator + element; String name = pathSrc.substring(pathSrc.lastIndexOf(myDirectory.separator) + 1, pathSrc.length()); String pathDst = directory + name; try { FileChannel srcChannel = new FileInputStream(pathSrc).getChannel(); FileChannel dstChannel = new FileOutputStream(pathDst).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (IOException exc) { System.out.println(exc.getMessage()); System.out.println(exc.toString()); } Vector keyWords = new Vector(); keyWords = dataBase.asociatedConceptSearch((String) images.elementAt(i)); Element imageElement = doc.createElement("image"); Element imageNameElement = doc.createElement("name"); imageNameElement.appendChild(doc.createTextNode(name)); imageElement.appendChild(imageNameElement); for (int j = 0; j < keyWords.size(); j++) { Element keyWordElement = doc.createElement("keyWord"); keyWordElement.appendChild(doc.createTextNode((String) keyWords.elementAt(j))); imageElement.appendChild(keyWordElement); } dbElement.appendChild(imageElement); } try { doc.appendChild(dbElement); File dst = new File(directory.concat("Images")); BufferedWriter bufferWriter = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(dst), "UTF-8")); TransformerFactory transformerFactory = TransformerFactory.newInstance(); Transformer transformer = transformerFactory.newTransformer(); DOMSource source = new DOMSource(doc); StreamResult result = new StreamResult(bufferWriter); transformer.transform(source, result); bufferWriter.close(); } catch (Exception exc) { System.out.println(exc.getMessage()); System.out.println(exc.toString()); } current = lengthOfTask; } | 14,159 |
0 | public static String read(URL url) throws Exception { String filename = Integer.toString(url.toString().hashCode()); boolean cached = false; File dir = new File(Config.CACHE_PATH); for (File file : dir.listFiles()) { if (!file.isFile()) continue; if (file.getName().equals(filename)) { filename = file.getName(); cached = true; break; } } File file = new File(Config.CACHE_PATH, filename); if (Config.USE_CACHE && cached) return read(file); System.out.println(">> CACHE HIT FAILED."); InputStream in = null; try { in = url.openStream(); } catch (Exception e) { System.out.println(">> OPEN STREAM FAILED: " + url.toString()); return null; } String content = read(in); save(file, content); return content; } | String openUrlAsString(String address, int maxLines) { StringBuffer sb; try { URL url = new URL(address); InputStream in = url.openStream(); BufferedReader br = new BufferedReader(new InputStreamReader(in)); sb = new StringBuffer(); int count = 0; String line; while ((line = br.readLine()) != null && count++ < maxLines) sb.append(line + "\n"); in.close(); } catch (IOException e) { sb = null; } return sb != null ? new String(sb) : null; } | 14,160 |
1 | public static SimpleDataTable loadDataFromFile(URL urlMetadata, URL urlData) throws IOException { BufferedReader in = new BufferedReader(new InputStreamReader(urlMetadata.openStream())); List<String> columnNamesList = new ArrayList<String>(); String[] lineParts = null; String line; in.readLine(); while ((line = in.readLine()) != null) { lineParts = line.split(","); columnNamesList.add(lineParts[0]); } String[] columnNamesArray = new String[columnNamesList.size()]; int index = 0; for (String s : columnNamesList) { columnNamesArray[index] = s; index++; } SimpleDataTable table = new SimpleDataTable("tabulka s daty", columnNamesArray); in = new BufferedReader(new InputStreamReader(urlData.openStream())); lineParts = null; line = null; SimpleDataTableRow tableRow; double[] rowData; while ((line = in.readLine()) != null) { lineParts = line.split(","); rowData = new double[columnNamesList.size()]; for (int i = 0; i < columnNamesArray.length; i++) { rowData[i] = Double.parseDouble(lineParts[i + 1]); } tableRow = new SimpleDataTableRow(rowData, lineParts[0]); table.add(tableRow); } return table; } | public boolean import_status(String filename) { int pieceId; int i, j, col, row; int rotation; int number; boolean byurl = false; e2piece temppiece; String lineread; StringTokenizer tok; BufferedReader entree; try { if (byurl == true) { URL url = new URL(baseURL, filename); InputStream in = url.openStream(); entree = new BufferedReader(new InputStreamReader(in)); } else { entree = new BufferedReader(new FileReader(filename)); } pieceId = 0; for (i = 0; i < board.colnb; i++) { for (j = 0; j < board.rownb; j++) { unplace_piece_at(i, j); } } while (true) { lineread = entree.readLine(); if (lineread == null) { break; } tok = new StringTokenizer(lineread, " "); pieceId = Integer.parseInt(tok.nextToken()); col = Integer.parseInt(tok.nextToken()) - 1; row = Integer.parseInt(tok.nextToken()) - 1; rotation = Integer.parseInt(tok.nextToken()); place_piece_at(pieceId, col, row, 0); temppiece = board.get_piece_at(col, row); temppiece.reset_rotation(); temppiece.rotate(rotation); } return true; } catch (IOException err) { return false; } } | 14,161 |
0 | 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 InputStream getUrlInputStream(final java.net.URL url) throws java.io.IOException, java.lang.InstantiationException { final java.net.URLConnection conn = url.openConnection(); conn.connect(); final InputStream input = url.openStream(); if (input == null) { throw new java.lang.InstantiationException("Url " + url + " does not provide data."); } return input; } | 14,162 |
1 | public static void copyFile(File inputFile, File outputFile) throws IOException { FileChannel srcChannel = new FileInputStream(inputFile).getChannel(); FileChannel dstChannel = new FileOutputStream(outputFile).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } | public static void copyURLToFile(URL source, File destination) throws IOException { InputStream input = source.openStream(); try { FileOutputStream output = openOutputStream(destination); try { IOUtils.copy(input, output); } finally { IOUtils.closeQuietly(output); } } finally { IOUtils.closeQuietly(input); } } | 14,163 |
0 | public static String[] bubbleSort(String[] unsortedString, boolean ascending) { if (unsortedString.length < 2) return unsortedString; String[] sortedString = new String[unsortedString.length]; for (int i = 0; i < unsortedString.length; i++) { sortedString[i] = unsortedString[i]; } if (ascending) { for (int i = 0; i < sortedString.length - 1; i++) { for (int j = 1; j < sortedString.length - 1 - i; j++) if (sortedString[j + 1].compareToIgnoreCase(sortedString[j]) < 0) { String swap = sortedString[j]; sortedString[j] = sortedString[j + 1]; sortedString[j + 1] = swap; } } } else { for (int i = sortedString.length - 2; i >= 0; i--) { for (int j = sortedString.length - 2 - i; j >= 0; j--) if (sortedString[j + 1].compareToIgnoreCase(sortedString[j]) > 0) { String swap = sortedString[j]; sortedString[j] = sortedString[j + 1]; sortedString[j + 1] = swap; } } } return sortedString; } | protected PersistenceUnitInfo getPersistenceUnitInfo() { if (this.persistenceUnitInfo == null) { this.persistenceUnitInfo = new PersistenceUnitInfo() { private List<ClassTransformer> transformers; private List<String> managedClasses; private List<String> mappingFileNames; private ClassLoader classLoader; public String getPersistenceUnitName() { return "jomc-standalone"; } public String getPersistenceProviderClassName() { return getPersistenceProvider().getClass().getName(); } public PersistenceUnitTransactionType getTransactionType() { return PersistenceUnitTransactionType.JTA; } public DataSource getJtaDataSource() { try { return (DataSource) getContext().lookup(getEnvironment().getJtaDataSourceJndiName()); } catch (final NamingException e) { getLogger().fatal(e); throw new RuntimeException(e); } } public DataSource getNonJtaDataSource() { return null; } public List<String> getMappingFileNames() { try { if (this.mappingFileNames == null) { this.mappingFileNames = new LinkedList<String>(); final DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setNamespaceAware(true); factory.setValidating(false); final DocumentBuilder documentBuilder = factory.newDocumentBuilder(); for (final Enumeration<URL> e = this.getNewTempClassLoader().getResources("META-INF/persistence.xml"); e.hasMoreElements(); ) { final URL url = e.nextElement(); final InputStream in = url.openStream(); final Document doc = documentBuilder.parse(in); in.close(); final NodeList persistenceUnits = doc.getElementsByTagNameNS(PERSISTENCE_NS, "persistence-unit"); for (int i = persistenceUnits.getLength() - 1; i >= 0; i--) { final Element persistenceUnit = (Element) persistenceUnits.item(i); final NodeList mappingFiles = persistenceUnit.getElementsByTagNameNS(PERSISTENCE_NS, "mapping-file"); for (int j = mappingFiles.getLength() - 1; j >= 0; j--) { final Element mappingFile = (Element) mappingFiles.item(j); this.mappingFileNames.add(mappingFile.getFirstChild().getNodeValue()); } } } } return this.mappingFileNames; } catch (final SAXException e) { getLogger().fatal(e); throw new RuntimeException(e); } catch (final IOException e) { getLogger().fatal(e); throw new RuntimeException(e); } catch (final ParserConfigurationException e) { getLogger().fatal(e); throw new RuntimeException(e); } } public List<URL> getJarFileUrls() { try { final List<URL> jarFileUrls = new LinkedList<URL>(); for (final Enumeration<URL> unitUrls = this.getClassLoader().getResources("META-INF/persistence.xml"); unitUrls.hasMoreElements(); ) { final URL unitUrl = unitUrls.nextElement(); final String externalForm = unitUrl.toExternalForm(); final String jarUrl = externalForm.substring(0, externalForm.indexOf("META-INF")); jarFileUrls.add(new URL(jarUrl)); } return jarFileUrls; } catch (final IOException e) { getLogger().fatal(e); throw new RuntimeException(e.getMessage(), e); } } public URL getPersistenceUnitRootUrl() { return getEnvironment().getJpaRootUrl(); } public List<String> getManagedClassNames() { try { if (this.managedClasses == null) { this.managedClasses = new LinkedList<String>(); final DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setNamespaceAware(true); factory.setValidating(false); final DocumentBuilder documentBuilder = factory.newDocumentBuilder(); for (final Enumeration<URL> e = this.getNewTempClassLoader().getResources("META-INF/persistence.xml"); e.hasMoreElements(); ) { final URL url = e.nextElement(); final InputStream in = url.openStream(); final Document doc = documentBuilder.parse(in); in.close(); final NodeList persistenceUnits = doc.getElementsByTagNameNS(PERSISTENCE_NS, "persistence-unit"); for (int i = persistenceUnits.getLength() - 1; i >= 0; i--) { final Element persistenceUnit = (Element) persistenceUnits.item(i); final NodeList classes = persistenceUnit.getElementsByTagNameNS(PERSISTENCE_NS, "class"); for (int j = classes.getLength() - 1; j >= 0; j--) { final Element clazz = (Element) classes.item(j); this.managedClasses.add(clazz.getFirstChild().getNodeValue()); } } } } return this.managedClasses; } catch (final SAXException e) { getLogger().fatal(e); throw new RuntimeException(e); } catch (final IOException e) { getLogger().fatal(e); throw new RuntimeException(e); } catch (final ParserConfigurationException e) { getLogger().fatal(e); throw new RuntimeException(e); } } public boolean excludeUnlistedClasses() { return false; } public Properties getProperties() { return getEnvironment().getProperties(); } public ClassLoader getClassLoader() { if (this.classLoader == null) { this.classLoader = this.getClass().getClassLoader(); if (this.classLoader == null) { this.classLoader = ClassLoader.getSystemClassLoader(); } this.classLoader = new URLClassLoader(new URL[] { getEnvironment().getJpaRootUrl() }, this.classLoader); } return this.classLoader; } public void addTransformer(final ClassTransformer transformer) { if (this.transformers == null) { this.transformers = new LinkedList<ClassTransformer>(); } this.transformers.add(transformer); } public ClassLoader getNewTempClassLoader() { final List<URL> jarFileUrls = this.getJarFileUrls(); jarFileUrls.add(getEnvironment().getJpaRootUrl()); return new URLClassLoader(jarFileUrls.toArray(new URL[jarFileUrls.size()])); } }; } return this.persistenceUnitInfo; } | 14,164 |
0 | public static void initStaticStuff() { Enumeration<URL> urls = null; try { urls = Play.class.getClassLoader().getResources("play.static"); } catch (Exception e) { } while (urls != null && urls.hasMoreElements()) { URL url = urls.nextElement(); try { BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream(), "utf-8")); String line = null; while ((line = reader.readLine()) != null) { try { Class.forName(line); } catch (Exception e) { System.out.println("! Cannot init static : " + line); } } } catch (Exception ex) { Logger.error(ex, "Cannot load %s", url); } } } | public static void main(String[] args) throws IOException { long readfilelen = 0; BufferedRandomAccessFile brafReadFile, brafWriteFile; brafReadFile = new BufferedRandomAccessFile("C:\\WINNT\\Fonts\\STKAITI.TTF"); readfilelen = brafReadFile.initfilelen; brafWriteFile = new BufferedRandomAccessFile(".\\STKAITI.001", "rw", 10); byte buf[] = new byte[1024]; int readcount; long start = System.currentTimeMillis(); while ((readcount = brafReadFile.read(buf)) != -1) { brafWriteFile.write(buf, 0, readcount); } brafWriteFile.close(); brafReadFile.close(); System.out.println("BufferedRandomAccessFile Copy & Write File: " + brafReadFile.filename + " FileSize: " + java.lang.Integer.toString((int) readfilelen >> 1024) + " (KB) " + "Spend: " + (double) (System.currentTimeMillis() - start) / 1000 + "(s)"); java.io.FileInputStream fdin = new java.io.FileInputStream("C:\\WINNT\\Fonts\\STKAITI.TTF"); java.io.BufferedInputStream bis = new java.io.BufferedInputStream(fdin, 1024); java.io.DataInputStream dis = new java.io.DataInputStream(bis); java.io.FileOutputStream fdout = new java.io.FileOutputStream(".\\STKAITI.002"); java.io.BufferedOutputStream bos = new java.io.BufferedOutputStream(fdout, 1024); java.io.DataOutputStream dos = new java.io.DataOutputStream(bos); start = System.currentTimeMillis(); for (int i = 0; i < readfilelen; i++) { dos.write(dis.readByte()); } dos.close(); dis.close(); System.out.println("DataBufferedios Copy & Write File: " + brafReadFile.filename + " FileSize: " + java.lang.Integer.toString((int) readfilelen >> 1024) + " (KB) " + "Spend: " + (double) (System.currentTimeMillis() - start) / 1000 + "(s)"); } | 14,165 |
0 | public InputStream sendReceive(String trackerURL) throws TorrentException { try { URL url = new URL(trackerURL); URLConnection conn = url.openConnection(); conn.setDoOutput(true); in = conn.getInputStream(); } catch (MalformedURLException e) { throw new TorrentException(e); } catch (IOException e) { throw new TorrentException(e); } return in; } | public byte[] loadRaw(String ontologyUrl) throws IOException { URL url = new URL(ontologyUrl); InputStream is = url.openStream(); final int BUFFER_SIZE = 1024; byte[] buffer = new byte[BUFFER_SIZE]; ByteArrayOutputStream ontologyBytes = new ByteArrayOutputStream(); for (; ; ) { int bytesRead = is.read(buffer); if (bytesRead <= 0) break; ontologyBytes.write(buffer, 0, bytesRead); } return ontologyBytes.toByteArray(); } | 14,166 |
0 | public String ask(String s) { System.out.println("asking ---> " + s); try { String result = null; URL url = new URL("http://www.google.com/search?hl=en&rls=GGLR,GGLR:2005-50,GGLR:en&sa=X&oi=spell&resnum=0&ct=result&cd=1&q=" + URLEncoder.encode(s, "UTF-8")); URLConnection connection = url.openConnection(); connection.setRequestProperty("User-Agent", "Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1)"); connection.setDoOutput(false); BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream(), "UTF-8")); String inputLine; while ((inputLine = in.readLine()) != null) { int textPos = inputLine.indexOf("Web definitions for "); if (textPos >= 0) { int ltrPos = inputLine.indexOf("<font size=-1>", textPos + 18); if (ltrPos >= 0) { int closePos = inputLine.indexOf("<", ltrPos + 14); if (closePos >= 0) { result = inputLine.substring(ltrPos + 14, closePos); } } } else { int ltrPos = inputLine.indexOf("— Location: "); if (ltrPos >= 0) { int closePos = inputLine.indexOf("<br", ltrPos + 18); if (closePos >= 0) { result = inputLine.substring(ltrPos + 18, closePos); } } } } in.close(); if (result != null) { result = result.replaceAll("<b>", ""); result = result.replaceAll("</b>", ""); result = result.replaceAll("("|')", "'"); System.out.println("result ---> " + result); } else { System.out.println("result ---> none!"); String ss = s.toUpperCase(); if (ss.startsWith("WHAT IS ")) { String toSearch = ss.substring(8).trim(); try { String str = getResultStr("http://www.google.com/search?hl=en&q=define%3A" + toSearch); str = cutAfter(str, "on the Web"); str = cutAfter(str, "<li>"); str = getBefore(str, "<br>"); result = str.replaceAll("\n", ""); } catch (Exception ee) { } } } return result; } catch (Exception e) { e.printStackTrace(); } return null; } | public static void main(String[] args) { if (args.length != 3) { System.out.println("Usage: HexStrToBin enc/dec <infileName> <outfilename>"); System.exit(1); } try { ByteArrayOutputStream os = new ByteArrayOutputStream(); InputStream in = new FileInputStream(args[1]); int len = 0; byte buf[] = new byte[1024]; while ((len = in.read(buf)) > 0) os.write(buf, 0, len); in.close(); os.close(); byte[] data = null; if (args[0].equals("dec")) data = decode(os.toString()); else { String strData = encode(os.toByteArray()); data = strData.getBytes(); } FileOutputStream fos = new FileOutputStream(args[2]); fos.write(data); fos.close(); } catch (Exception e) { e.printStackTrace(); } } | 14,167 |
1 | public void execute() { File sourceFile = new File(oarfilePath); File destinationFile = new File(deploymentDirectory + File.separator + sourceFile.getName()); try { FileInputStream fis = new FileInputStream(sourceFile); FileOutputStream fos = new FileOutputStream(destinationFile); byte[] readArray = new byte[2048]; while (fis.read(readArray) != -1) { fos.write(readArray); } fis.close(); fos.flush(); fos.close(); } catch (IOException ioe) { logger.severe("failed to copy the file:" + ioe); } } | 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); } } } | 14,168 |
1 | 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(); } } | private void regattaBackup() { SwingWorker sw = new SwingWorker() { Regatta lRegatta = fRegatta; public Object construct() { String fullName = lRegatta.getSaveDirectory() + lRegatta.getSaveName(); System.out.println(MessageFormat.format(res.getString("MainMessageBackingUp"), new Object[] { fullName + BAK })); try { FileInputStream fis = new FileInputStream(new File(fullName)); FileOutputStream fos = new FileOutputStream(new File(fullName + BAK)); int bufsize = 1024; byte[] buffer = new byte[bufsize]; int n = 0; while ((n = fis.read(buffer, 0, bufsize)) >= 0) fos.write(buffer, 0, n); fos.flush(); fos.close(); } catch (java.io.IOException ex) { Util.showError(ex, true); } return null; } }; sw.start(); } | 14,169 |
0 | public static File[] splitFile(FileValidator validator, File source, long target_length, File todir, String prefix) { if (target_length == 0) return null; if (todir == null) { todir = new File(System.getProperty("java.io.tmpdir")); } if (prefix == null || prefix.equals("")) { prefix = source.getName(); } Vector result = new Vector(); FileOutputStream fos = null; FileInputStream fis = null; try { fis = new FileInputStream(source); byte[] bytes = new byte[CACHE_SIZE]; long current_target_size = 0; int current_target_nb = 1; int nbread = -1; try { File f = new File(todir, prefix + i18n.getString("targetname_suffix") + current_target_nb); if (!validator.verifyFile(f)) return null; result.add(f); fos = new FileOutputStream(f); while ((nbread = fis.read(bytes)) > -1) { if ((current_target_size + nbread) > target_length) { int limit = (int) (target_length - current_target_size); fos.write(bytes, 0, limit); fos.close(); current_target_nb++; current_target_size = 0; f = new File(todir, prefix + "_" + current_target_nb); if (!validator.verifyFile(f)) return null; result.add(f); fos = new FileOutputStream(f); fos.write(bytes, limit, nbread - limit); current_target_size += nbread - limit; } else { fos.write(bytes, 0, nbread); current_target_size += nbread; } } } catch (IOException ioe) { JOptionPane.showMessageDialog(null, ioe, i18n.getString("Failure"), JOptionPane.ERROR_MESSAGE); } finally { try { if (fos != null) fos.close(); } catch (IOException e) { } try { if (fis != null) fis.close(); } catch (IOException e) { } } } catch (Exception e) { JOptionPane.showMessageDialog(null, e, i18n.getString("Failure"), JOptionPane.ERROR_MESSAGE); } finally { try { if (fos != null) fos.close(); } catch (IOException e) { } } File[] fresult = null; if (result.size() > 0) { fresult = new File[result.size()]; fresult = (File[]) result.toArray(fresult); } return fresult; } | protected HttpResponse executeRequest(AbstractHttpRequest request) throws ConnectionException, RequestCancelledException { try { HttpResponse response = getHttpClient().execute(request); if (!response.is2xxSuccess()) { throw new ConnectionException(); } return response; } catch (IOException ex) { throw new ConnectionException(); } catch (TimeoutException ex) { throw new ConnectionException(); } } | 14,170 |
0 | public static File getFileFromURL(URL url) { File tempFile; BufferedInputStream in = null; BufferedOutputStream out = null; try { String tempDir = System.getProperty("java.io.tmpdir", "."); tempFile = File.createTempFile("xxindex", ".tmp", new File(tempDir)); tempFile.deleteOnExit(); InputStream is = url.openStream(); in = new BufferedInputStream(is); FileOutputStream fos = new FileOutputStream(tempFile); out = new BufferedOutputStream(fos); byte[] b = new byte[1]; while (in.read(b) >= 0) { out.write(b); } logger.debug(url + " written to local file " + tempFile.getAbsolutePath()); } catch (IOException e) { throw new IllegalStateException("Could not create local file for URL: " + url, e); } finally { try { if (in != null) { in.close(); } if (out != null) { out.close(); } } catch (IOException e) { } } return tempFile; } | public static void copyFile(File src, File dst) throws IOException { FileInputStream fis = null; FileOutputStream fos = null; fis = new FileInputStream(src); fos = new FileOutputStream(dst); byte[] buffer = new byte[16384]; int read = 0; while ((read = fis.read(buffer)) != -1) { fos.write(buffer, 0, read); } fis.close(); fos.flush(); fos.close(); } | 14,171 |
0 | public void run() { if (data.length() > 0) { String method = getMethod(); String action = getAction(); URL url; try { URL actionURL; URL baseURL = hdoc.getBase(); if (action == null) { String file = baseURL.getFile(); actionURL = new URL(baseURL.getProtocol(), baseURL.getHost(), baseURL.getPort(), file); } else actionURL = new URL(baseURL, action); URLConnection connection; if ("post".equalsIgnoreCase(method)) { url = actionURL; connection = url.openConnection(); ((HttpURLConnection) connection).setFollowRedirects(false); XRendererSupport.setCookies(url, connection); connection.setRequestProperty("Accept-Language", "en-us"); connection.setRequestProperty("User-Agent", XRendererSupport.getContext().getUserAgent()); postData(connection, data); XRendererSupport.getContext().getLogger().message(this, "Posted data: {" + data + "}"); } else { url = new URL(actionURL + "?" + data); connection = url.openConnection(); XRendererSupport.setCookies(url, connection); } connection.connect(); in = connection.getInputStream(); URL base = connection.getURL(); XRendererSupport.getCookies(base, connection); XRendererSupport.getContext().getLogger().message(this, "Stream got ok."); JEditorPane c = (JEditorPane) getContainer(); HTMLEditorKit kit = (HTMLEditorKit) c.getEditorKit(); newDoc = (HTMLDocument) kit.createDefaultDocument(); newDoc.putProperty(Document.StreamDescriptionProperty, base); SwingUtilities.invokeLater(new Runnable() { public void run() { XRendererSupport.getContext().getLogger().message(this, "loading..."); loadDocument(); XRendererSupport.getContext().getLogger().message(this, "document loaded..."); } }); } catch (MalformedURLException m) { } catch (IOException e) { } } } | public static Bitmap loadBitmap(String token, String id, final String type) { String imageUrl = XMLfunctions.URL; imageUrl = imageUrl.replace("{0}", token); imageUrl = imageUrl.replace("{1}", id); InputStream imageStream = null; try { HttpGet httpRequest = new HttpGet(new URL(imageUrl).toURI()); HttpResponse response = (HttpResponse) new DefaultHttpClient().execute(httpRequest); httpRequest = null; BufferedHttpEntity bufHttpEntity = new BufferedHttpEntity(response.getEntity()); response = null; imageStream = bufHttpEntity.getContent(); bufHttpEntity = null; if (imageStream != null) { final BitmapFactory.Options options = new BitmapFactory.Options(); if (type.equals("image")) { options.inSampleSize = 2; } return BitmapFactory.decodeStream(imageStream, null, options); } else { } } catch (IOException e) { } catch (URISyntaxException e) { } finally { if (imageStream != null) closeStream(imageStream); } return null; } | 14,172 |
1 | public static void main(String[] args) { String str = "vbnjm7pexhlmof3kapi_key76bbc056cf516a844af25a763b2b8426auth_tokenff8080812374bd3f0123b60363a5230acomment_text你frob118edb4cb78b439207c2329b76395f9fmethodyupoo.photos.comments.addphoto_idff80808123922c950123b6066c946a3f"; MessageDigest md = null; String s = new String("你"); try { md = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); throw new RuntimeException(e.getMessage()); } md.reset(); try { md.update(str.getBytes("UTF-8")); System.out.println(new BigInteger(1, md.digest()).toString(16)); System.out.println(new BigInteger(1, s.getBytes("UTF-8")).toString(16)); } catch (UnsupportedEncodingException e) { e.printStackTrace(); } } | private String hashString(String key) { MessageDigest digest; try { digest = java.security.MessageDigest.getInstance("MD5"); digest.update(key.getBytes()); byte[] hash = digest.digest(); BigInteger bi = new BigInteger(1, hash); return String.format("%0" + (hash.length << 1) + "X", bi) + KERNEL_VERSION; } catch (NoSuchAlgorithmException e) { e.printStackTrace(); return "" + key.hashCode(); } } | 14,173 |
0 | public static void zipMapBos(DitaBoundedObjectSet mapBos, File outputZipFile, MapBosProcessorOptions options) throws Exception { log.debug("Determining zip file organization..."); BosVisitor visitor = new DxpFileOrganizingBosVisitor(); visitor.visit(mapBos); if (!options.isQuiet()) log.info("Creating DXP package \"" + outputZipFile.getAbsolutePath() + "\"..."); OutputStream outStream = new FileOutputStream(outputZipFile); ZipOutputStream zipOutStream = new ZipOutputStream(outStream); ZipEntry entry = null; URI rootMapUri = mapBos.getRoot().getEffectiveUri(); URI baseUri = null; try { baseUri = AddressingUtil.getParent(rootMapUri); } catch (URISyntaxException e) { throw new BosException("URI syntax exception getting parent URI: " + e.getMessage()); } Set<String> dirs = new HashSet<String>(); if (!options.isQuiet()) log.info("Constructing DXP package..."); for (BosMember member : mapBos.getMembers()) { if (!options.isQuiet()) log.info("Adding member " + member + " to zip..."); URI relativeUri = baseUri.relativize(member.getEffectiveUri()); File temp = new File(relativeUri.getPath()); String parentPath = temp.getParent(); if (parentPath != null && !"".equals(parentPath) && !parentPath.endsWith("/")) { parentPath += "/"; } log.debug("parentPath=\"" + parentPath + "\""); if (!"".equals(parentPath) && parentPath != null && !dirs.contains(parentPath)) { entry = new ZipEntry(parentPath); zipOutStream.putNextEntry(entry); zipOutStream.closeEntry(); dirs.add(parentPath); } entry = new ZipEntry(relativeUri.getPath()); zipOutStream.putNextEntry(entry); IOUtils.copy(member.getInputStream(), zipOutStream); zipOutStream.closeEntry(); } zipOutStream.close(); if (!options.isQuiet()) log.info("DXP package \"" + outputZipFile.getAbsolutePath() + "\" created."); } | public void addUser(String strUserName, String strPass, boolean isEncrypt) throws Exception { Connection con = null; PreparedStatement pstmt = null; try { con = DbForumFactory.getConnection(); con.setAutoCommit(false); int userID = DbSequenceManager.nextID(DbSequenceManager.USER); pstmt = con.prepareStatement(INSERT_USER); pstmt.setString(1, strUserName); if (isEncrypt) { pstmt.setString(2, SecurityUtil.md5ByHex(strPass)); } else { pstmt.setString(2, strPass); } pstmt.setString(3, ""); pstmt.setString(4, ""); pstmt.setString(5, ""); pstmt.setString(6, ""); pstmt.setString(7, ""); pstmt.setInt(8, userID); pstmt.executeUpdate(); pstmt.clearParameters(); pstmt = con.prepareStatement(INSERT_USERPROPS); pstmt.setString(1, ""); pstmt.setString(2, ""); pstmt.setString(3, ""); pstmt.setInt(4, 0); pstmt.setString(5, ""); pstmt.setInt(6, 0); pstmt.setInt(7, 0); pstmt.setString(8, ""); pstmt.setString(9, ""); pstmt.setString(10, ""); pstmt.setInt(11, 0); pstmt.setInt(12, 0); pstmt.setInt(13, 0); pstmt.setInt(14, 0); pstmt.setString(15, ""); pstmt.setString(16, ""); pstmt.setString(17, ""); pstmt.setString(18, ""); pstmt.setString(19, ""); pstmt.setString(20, ""); pstmt.setString(21, ""); pstmt.setString(22, ""); pstmt.setString(23, ""); pstmt.setInt(24, 0); pstmt.setInt(25, 0); pstmt.setInt(26, userID); pstmt.executeUpdate(); pstmt.clearParameters(); pstmt = con.prepareStatement(INSTER_USERGROUP); pstmt.setInt(1, 4); pstmt.setInt(2, userID); pstmt.setInt(3, 0); pstmt.executeUpdate(); con.commit(); } catch (Exception e) { try { con.rollback(); } catch (SQLException e1) { } log.error("insert user Error: " + e.toString()); } finally { DbForumFactory.closeDB(null, pstmt, null, con); } } | 14,174 |
1 | public static boolean encodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.ENCODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | public static void copyURLToFile(URL source, File destination) throws IOException { InputStream input = source.openStream(); try { FileOutputStream output = openOutputStream(destination); try { IOUtils.copy(input, output); } finally { IOUtils.closeQuietly(output); } } finally { IOUtils.closeQuietly(input); } } | 14,175 |
1 | public boolean copyDirectoryTree(File srcPath, File dstPath) { try { if (srcPath.isDirectory()) { if (!dstPath.exists()) dstPath.mkdir(); String files[] = srcPath.list(); for (int i = 0; i < files.length; i++) copyDirectoryTree(new File(srcPath, files[i]), new File(dstPath, files[i])); } else { if (!srcPath.exists()) { errMsgLog += "copyDirectoryTree I/O error from '" + srcPath + "' does not exist.\n"; lastErrMsgLog = errMsgLog; return (false); } else { InputStream in = new FileInputStream(srcPath); OutputStream out = new FileOutputStream(dstPath); byte[] buf = new byte[10240]; int len; while ((len = in.read(buf)) > 0) out.write(buf, 0, len); in.close(); out.close(); } } return (true); } catch (Exception e) { errMsgLog += "copyDirectoryTree I/O error from '" + srcPath.getName() + "' to '" + dstPath.getName() + "\n " + e + "\n"; lastErrMsgLog = errMsgLog; return (false); } } | 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(); } } | 14,176 |
1 | public void run() { LOG.debug(this); String[] parts = createCmdArray(getCommand()); Runtime runtime = Runtime.getRuntime(); try { Process process = runtime.exec(parts); if (isBlocking()) { process.waitFor(); StringWriter out = new StringWriter(); IOUtils.copy(process.getInputStream(), out); String stdout = out.toString().replaceFirst("\\s+$", ""); if (StringUtils.isNotBlank(stdout)) { LOG.info("Process stdout:\n" + stdout); } StringWriter err = new StringWriter(); IOUtils.copy(process.getErrorStream(), err); String stderr = err.toString().replaceFirst("\\s+$", ""); if (StringUtils.isNotBlank(stderr)) { LOG.error("Process stderr:\n" + stderr); } } } catch (IOException ioe) { LOG.error(String.format("Could not exec [%s]", getCommand()), ioe); } catch (InterruptedException ie) { LOG.error(String.format("Interrupted [%s]", getCommand()), ie); } } | private void forcedCopy(File sourceFile, File destFile) throws IOException { if (!destFile.exists()) { destFile.createNewFile(); } FileChannel source = null; FileChannel destination = null; try { source = new FileInputStream(sourceFile).getChannel(); destination = new FileOutputStream(destFile).getChannel(); destination.transferFrom(source, 0, source.size()); } finally { if (source != null) { source.close(); } if (destination != null) { destination.close(); } } } | 14,177 |
1 | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | @Override @RemoteMethod public boolean encrypt(int idAnexo) { try { Anexo anexo = anexoService.selectById(idAnexo); aes.init(Cipher.ENCRYPT_MODE, aeskeySpec); FileInputStream fis = new FileInputStream(config.baseDir + "/arquivos_upload_direto/" + anexo.getAnexoCaminho()); CipherOutputStream cos = new CipherOutputStream(new FileOutputStream(config.baseDir + "/arquivos_upload_direto/encrypt/" + anexo.getAnexoCaminho()), aes); IOUtils.copy(fis, cos); cos.close(); fis.close(); } catch (Exception e) { e.printStackTrace(); return false; } return true; } | 14,178 |
1 | public long copyDirAllFilesToDirectoryRecursive(String baseDirStr, String destDirStr, boolean copyOutputsRtIDsDirs) throws Exception { long plussQuotaSize = 0; if (baseDirStr.endsWith(sep)) { baseDirStr = baseDirStr.substring(0, baseDirStr.length() - 1); } if (destDirStr.endsWith(sep)) { destDirStr = destDirStr.substring(0, destDirStr.length() - 1); } FileUtils.getInstance().createDirectory(destDirStr); BufferedInputStream in = null; BufferedOutputStream out = null; byte dataBuff[] = new byte[bufferSize]; File baseDir = new File(baseDirStr); baseDir.mkdirs(); if (!baseDir.exists()) { createDirectory(baseDirStr); } if ((baseDir.exists()) && (baseDir.isDirectory())) { String[] entryList = baseDir.list(); if (entryList.length > 0) { for (int pos = 0; pos < entryList.length; pos++) { String entryName = entryList[pos]; String oldPathFileName = baseDirStr + sep + entryName; File entryFile = new File(oldPathFileName); if (entryFile.isFile()) { String newPathFileName = destDirStr + sep + entryName; File newFile = new File(newPathFileName); if (newFile.exists()) { plussQuotaSize -= newFile.length(); newFile.delete(); } in = new BufferedInputStream(new FileInputStream(oldPathFileName), bufferSize); out = new BufferedOutputStream(new FileOutputStream(newPathFileName), bufferSize); int readLen; while ((readLen = in.read(dataBuff)) > 0) { out.write(dataBuff, 0, readLen); plussQuotaSize += readLen; } out.flush(); in.close(); out.close(); } if (entryFile.isDirectory()) { boolean enableCopyDir = false; if (copyOutputsRtIDsDirs) { enableCopyDir = true; } else { if (entryFile.getParentFile().getName().equals("outputs")) { enableCopyDir = false; } else { enableCopyDir = true; } } if (enableCopyDir) { plussQuotaSize += this.copyDirAllFilesToDirectoryRecursive(baseDirStr + sep + entryName, destDirStr + sep + entryName, copyOutputsRtIDsDirs); } } } } } else { throw new Exception("Base dir not exist ! baseDirStr = (" + baseDirStr + ")"); } return plussQuotaSize; } | public static void ExtraeArchivoJAR(String Archivo, String DirJAR, String DirDestino) { FileInputStream entrada = null; FileOutputStream salida = null; try { File f = new File(DirDestino + separador + Archivo); try { f.createNewFile(); } catch (Exception sad) { sad.printStackTrace(); } InputStream source = OP_Proced.class.getResourceAsStream(DirJAR + "/" + Archivo); BufferedInputStream in = new BufferedInputStream(source); FileOutputStream out = new FileOutputStream(f); int ch; while ((ch = in.read()) != -1) out.write(ch); in.close(); out.close(); } catch (IOException ex) { System.out.println(ex); } finally { if (entrada != null) { try { entrada.close(); } catch (IOException ex) { ex.printStackTrace(); } } if (salida != null) { try { salida.close(); } catch (IOException ex) { ex.printStackTrace(); } } } } | 14,179 |
0 | public static long copy(File src, File dest) throws UtilException { FileChannel srcFc = null; FileChannel destFc = null; try { srcFc = new FileInputStream(src).getChannel(); destFc = new FileOutputStream(dest).getChannel(); long srcLength = srcFc.size(); srcFc.transferTo(0, srcLength, destFc); return srcLength; } catch (IOException e) { throw new UtilException(e); } finally { try { if (srcFc != null) srcFc.close(); srcFc = null; } catch (IOException e) { } try { if (destFc != null) destFc.close(); destFc = null; } catch (IOException e) { } } } | public void testFidelity() throws ParserException, IOException { Lexer lexer; Node node; int position; StringBuffer buffer; String string; char[] ref; char[] test; URL url = new URL("http://sourceforge.net"); lexer = new Lexer(url.openConnection()); position = 0; buffer = new StringBuffer(80000); while (null != (node = lexer.nextNode())) { string = node.toHtml(); if (position != node.getStartPosition()) fail("non-contiguous" + string); buffer.append(string); position = node.getEndPosition(); if (buffer.length() != position) fail("text length differed after encountering node " + string); } ref = lexer.getPage().getText().toCharArray(); test = new char[buffer.length()]; buffer.getChars(0, buffer.length(), test, 0); assertEquals("different amounts of text", ref.length, test.length); for (int i = 0; i < ref.length; i++) if (ref[i] != test[i]) fail("character differs at position " + i + ", expected <" + ref[i] + "> but was <" + test[i] + ">"); } | 14,180 |
1 | private void loadServers() { try { URL url = new URL(VirtualDeckConfig.SERVERS_URL); cmbServer.addItem("Local"); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); String str; if (in.readLine().equals("[list]")) { while ((str = in.readLine()) != null) { String[] host_line = str.split(";"); Host h = new Host(); h.setIp(host_line[0]); h.setPort(Integer.parseInt(host_line[1])); h.setName(host_line[2]); getServers().add(h); cmbServer.addItem(h.getName()); } } in.close(); } catch (MalformedURLException e) { } catch (IOException e) { } } | public static ArrayList<String> remoteCall(Map<String, String> dataDict) { ArrayList<String> result = new ArrayList<String>(); String encodedData = ""; for (String key : dataDict.keySet()) { String encodedSegment = ""; String value = dataDict.get(key); if (value == null) continue; try { encodedSegment = key + "=" + URLEncoder.encode(value, "UTF-8"); } catch (UnsupportedEncodingException e) { e.printStackTrace(); } if (encodedData.length() > 0) { encodedData += "&"; } encodedData += encodedSegment; } try { URL url = new URL(baseURL + encodedData); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String line; while ((line = reader.readLine()) != null) { result.add(line); System.out.println("GOT: " + line); } reader.close(); result.remove(0); if (result.size() != 0) { if (!result.get(result.size() - 1).equals("DONE")) { result.clear(); } else { result.remove(result.size() - 1); } } } catch (MalformedURLException e) { } catch (IOException e) { } return result; } | 14,181 |
1 | public static boolean copyFile(String source, String destination, boolean replace) { File sourceFile = new File(source); File destinationFile = new File(destination); if (sourceFile.isDirectory() || destinationFile.isDirectory()) return false; if (destinationFile.isFile() && !replace) return false; if (!sourceFile.isFile()) return false; if (replace) destinationFile.delete(); try { File dir = destinationFile.getParentFile(); while (dir != null && !dir.exists()) { dir.mkdir(); } DataOutputStream outStream = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(destinationFile), 10240)); DataInputStream inStream = new DataInputStream(new BufferedInputStream(new FileInputStream(sourceFile), 10240)); try { while (inStream.available() > 0) { outStream.write(inStream.readUnsignedByte()); } } catch (EOFException eof) { } inStream.close(); outStream.close(); } catch (IOException ex) { throw new FailedException("Failed to copy file " + sourceFile.getAbsolutePath() + " to " + destinationFile.getAbsolutePath(), ex).setFile(destinationFile.getAbsolutePath()); } return true; } | @Override public void fileUpload(UploadEvent uploadEvent) { FileOutputStream tmpOutStream = null; try { tmpUpload = File.createTempFile("projectImport", ".xml"); tmpOutStream = new FileOutputStream(tmpUpload); IOUtils.copy(uploadEvent.getInputStream(), tmpOutStream); panel.setGeneralMessage("Project file " + uploadEvent.getFileName() + " uploaded and ready for import."); } catch (Exception e) { panel.setGeneralMessage("Could not upload file: " + e); } finally { if (tmpOutStream != null) { IOUtils.closeQuietly(tmpOutStream); } } } | 14,182 |
0 | public static String md5Encode(String s) { try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(s.getBytes()); return toHexString(md.digest()); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); return s; } } | public static URLConnection openRemoteDescriptionFile(String urlstr) throws MalformedURLException { URL url = new URL(urlstr); try { URLConnection conn = url.openConnection(); conn.connect(); return conn; } catch (Exception e) { Config conf = Config.getInstance(); SimpleSocketAddress localServAddr = conf.getLocalProxyServerAddress(); Proxy proxy = new Proxy(Type.HTTP, new InetSocketAddress(localServAddr.host, localServAddr.port)); URLConnection conn; try { conn = url.openConnection(proxy); conn.connect(); return conn; } catch (IOException e1) { logger.error("Failed to retrive desc file:" + url, e1); } } return null; } | 14,183 |
1 | public static void copyFile(String sourceName, String destName) throws IOException { FileChannel sourceChannel = null; FileChannel destChannel = null; try { sourceChannel = new FileInputStream(sourceName).getChannel(); destChannel = new FileOutputStream(destName).getChannel(); destChannel.transferFrom(sourceChannel, 0, sourceChannel.size()); } catch (IOException exception) { throw exception; } finally { if (sourceChannel != null) { try { sourceChannel.close(); } catch (IOException ex) { } } if (destChannel != null) { try { destChannel.close(); } catch (IOException ex) { } } } } | private void handleFile(File file, HttpServletRequest request, HttpServletResponse response) throws Exception { String filename = file.getName(); long filesize = file.length(); String mimeType = getMimeType(filename); response.setContentType(mimeType); if (filesize > getDownloadThreshhold()) { response.setHeader("Content-Disposition", "attachment; filename=" + filename); } response.setContentLength((int) filesize); ServletOutputStream out = response.getOutputStream(); IOUtils.copy(new FileInputStream(file), out); out.flush(); } | 14,184 |
0 | public boolean isWebServerAvaliable(String url) { long inicial = new Date().getTime(); HttpURLConnection connection = null; try { URL urlBase = urlBase = new URL(url); getLog().info("Verificando se WebServer esta no ar: " + urlBase.toString()); connection = (HttpURLConnection) urlBase.openConnection(); connection.connect(); } catch (Exception e) { return false; } finally { try { getLog().info("Resposta do WebServer: " + connection.getResponseCode()); } catch (IOException e) { e.printStackTrace(); return false; } long tfinal = new Date().getTime(); getLog().info("Tempo esperado: " + ((tfinal - inicial) / 1000) + " segundos!"); } return true; } | public static Test suite() throws Exception { java.net.URL url = ClassLoader.getSystemResource("host0.jndi.properties"); java.util.Properties host0JndiProps = new java.util.Properties(); host0JndiProps.load(url.openStream()); java.util.Properties systemProps = System.getProperties(); systemProps.putAll(host0JndiProps); System.setProperties(systemProps); TestSuite suite = new TestSuite(); suite.addTest(new TestSuite(T06OTSInterpositionUnitTestCase.class)); TestSetup wrapper = new JBossTestSetup(suite) { protected void setUp() throws Exception { super.setUp(); deploy("dtmpassthrough2ots.jar"); } protected void tearDown() throws Exception { undeploy("dtmpassthrough2ots.jar"); super.tearDown(); } }; return wrapper; } | 14,185 |
0 | public void testRegisterFactory() throws Exception { try { new URL("classpath:/"); fail("MalformedURLException expected"); } catch (MalformedURLException e) { assertTrue(true); } ClasspathURLConnection.registerFactory(); URL url = new URL("classpath:/dummy.txt"); try { url.openStream(); fail("IOException expected"); } catch (IOException e) { assertTrue(true); } ClasspathURLConnection.registerFactory(); url = new URL("classpath:/net/sf/alster/xsl/alster.xml"); InputStream in = url.openStream(); assertEquals('<', in.read()); in.close(); } | private static void copyFile(File sourceFile, File targetFile) throws FileSaveException { try { FileInputStream inputStream = new FileInputStream(sourceFile); FileOutputStream outputStream = new FileOutputStream(targetFile); FileChannel readableChannel = inputStream.getChannel(); FileChannel writableChannel = outputStream.getChannel(); writableChannel.truncate(0); writableChannel.transferFrom(readableChannel, 0, readableChannel.size()); inputStream.close(); outputStream.close(); } catch (IOException ioException) { String exceptionMessage = "An error occurred when copying from the file \"" + sourceFile.getAbsolutePath() + "\" to the file \"" + targetFile.getAbsolutePath() + "\"."; throw new FileSaveException(exceptionMessage, ioException); } } | 14,186 |
1 | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | @Override public void messageReceived(ChannelHandlerContext ctx, MessageEvent e) throws Exception { Object msg = e.getMessage(); if (!(msg instanceof HttpMessage) && !(msg instanceof HttpChunk)) { ctx.sendUpstream(e); return; } HttpMessage currentMessage = this.currentMessage; File localFile = this.file; if (currentMessage == null) { HttpMessage m = (HttpMessage) msg; if (m.isChunked()) { final String localName = UUID.randomUUID().toString(); List<String> encodings = m.getHeaders(HttpHeaders.Names.TRANSFER_ENCODING); encodings.remove(HttpHeaders.Values.CHUNKED); if (encodings.isEmpty()) { m.removeHeader(HttpHeaders.Names.TRANSFER_ENCODING); } this.currentMessage = m; this.file = new File(Play.tmpDir, localName); this.out = new FileOutputStream(file, true); } else { ctx.sendUpstream(e); } } else { final HttpChunk chunk = (HttpChunk) msg; if (maxContentLength != -1 && (localFile.length() > (maxContentLength - chunk.getContent().readableBytes()))) { currentMessage.setHeader(HttpHeaders.Names.WARNING, "play.netty.content.length.exceeded"); } else { IOUtils.copyLarge(new ChannelBufferInputStream(chunk.getContent()), this.out); if (chunk.isLast()) { this.out.flush(); this.out.close(); currentMessage.setHeader(HttpHeaders.Names.CONTENT_LENGTH, String.valueOf(localFile.length())); currentMessage.setContent(new FileChannelBuffer(localFile)); this.out = null; this.currentMessage = null; this.file = null; Channels.fireMessageReceived(ctx, currentMessage, e.getRemoteAddress()); } } } } | 14,187 |
1 | public static String[] retrieveFasta(String id) throws Exception { URL url = new URL("http://www.uniprot.org/uniprot/" + id + ".fasta"); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String header = reader.readLine(); StringBuffer seq = new StringBuffer(); String line = ""; while ((line = reader.readLine()) != null) { seq.append(line); } reader.close(); String[] first = header.split("OS="); return new String[] { id, first[0].split("\\s")[1], first[1].split("GN=")[0], seq.toString() }; } | private static BundleInfo[] getBundleInfoArray(String location) throws IOException { URL url = new URL(location + BUNDLE_LIST_FILE); BufferedReader br = null; List<BundleInfo> list = new ArrayList<BundleInfo>(); try { br = new BufferedReader(new InputStreamReader(url.openStream())); while (true) { String line = br.readLine(); if (line == null) { break; } int pos1 = line.indexOf('='); if (pos1 < 0) { continue; } BundleInfo info = new BundleInfo(); info.bundleSymbolicName = line.substring(0, pos1); info.location = line.substring(pos1 + 1); list.add(info); } if (!setBundleInfoName(location + BUNDLE_NAME_LIST_FILE + "_" + Locale.getDefault().getLanguage(), list)) { setBundleInfoName(location + BUNDLE_NAME_LIST_FILE, list); } return list.toArray(BUNDLE_INFO_EMPTY_ARRAY); } finally { if (br != null) { br.close(); } } } | 14,188 |
1 | private void writeJar() { try { File outJar = new File(currentProjectDir + DEPLOYDIR + fileSeparator + currentProjectName + ".jar"); jarSize = (int) outJar.length(); File tempJar = File.createTempFile("hipergps" + currentProjectName, ".jar"); tempJar.deleteOnExit(); File preJar = new File(currentProjectDir + "/res/wtj2me.jar"); JarInputStream preJarInStream = new JarInputStream(new FileInputStream(preJar)); Manifest mFest = preJarInStream.getManifest(); java.util.jar.Attributes atts = mFest.getMainAttributes(); if (hiperGeoId != null) { atts.putValue("hiperGeoId", hiperGeoId); } jad.updateAttributes(atts); JarOutputStream jarOutStream = new JarOutputStream(new FileOutputStream(tempJar), mFest); byte[] buffer = new byte[WalkingtoolsInformation.BUFFERSIZE]; JarEntry jarEntry = null; while ((jarEntry = preJarInStream.getNextJarEntry()) != null) { if (jarEntry.getName().contains("net/") || jarEntry.getName().contains("org/")) { try { jarOutStream.putNextEntry(jarEntry); } catch (ZipException ze) { continue; } int read; while ((read = preJarInStream.read(buffer)) != -1) { jarOutStream.write(buffer, 0, read); } jarOutStream.closeEntry(); } } File[] icons = { new File(currentProjectDir + WalkingtoolsInformation.IMAGEDIR + fileSeparator + "icon_" + WalkingtoolsInformation.MEDIAUUID + ".png"), new File(currentProjectDir + WalkingtoolsInformation.IMAGEDIR + fileSeparator + "loaderIcon_" + WalkingtoolsInformation.MEDIAUUID + ".png"), new File(currentProjectDir + WalkingtoolsInformation.IMAGEDIR + fileSeparator + "mygps_" + WalkingtoolsInformation.MEDIAUUID + ".png") }; for (int i = 0; i < icons.length; i++) { jarEntry = new JarEntry("img/" + icons[i].getName()); try { jarOutStream.putNextEntry(jarEntry); } catch (ZipException ze) { continue; } FileInputStream in = new FileInputStream(icons[i]); while (true) { int read = in.read(buffer, 0, buffer.length); if (read <= 0) { break; } jarOutStream.write(buffer, 0, read); } in.close(); } for (int i = 0; i < imageFiles.size(); i++) { jarEntry = new JarEntry("img/" + imageFiles.get(i).getName()); try { jarOutStream.putNextEntry(jarEntry); } catch (ZipException ze) { continue; } FileInputStream in = new FileInputStream(imageFiles.get(i)); while (true) { int read = in.read(buffer, 0, buffer.length); if (read <= 0) { break; } jarOutStream.write(buffer, 0, read); } in.close(); } for (int i = 0; i < audioFiles.size(); i++) { jarEntry = new JarEntry("audio/" + audioFiles.get(i).getName()); try { jarOutStream.putNextEntry(jarEntry); } catch (ZipException ze) { continue; } FileInputStream in = new FileInputStream(audioFiles.get(i)); while (true) { int read = in.read(buffer, 0, buffer.length); if (read <= 0) { break; } jarOutStream.write(buffer, 0, read); } in.close(); } File gpx = new File(currentProjectDir + WalkingtoolsInformation.GPXDIR + "/hipergps.gpx"); jarEntry = new JarEntry("gpx/" + gpx.getName()); jarOutStream.putNextEntry(jarEntry); FileInputStream in = new FileInputStream(gpx); while (true) { int read = in.read(buffer, 0, buffer.length); if (read <= 0) { break; } jarOutStream.write(buffer, 0, read); } in.close(); jarOutStream.flush(); jarOutStream.close(); jarSize = (int) tempJar.length(); preJarInStream = new JarInputStream(new FileInputStream(tempJar)); mFest = preJarInStream.getManifest(); atts = mFest.getMainAttributes(); atts.putValue("MIDlet-Jar-Size", "" + jarSize + 1); jarOutStream = new JarOutputStream(new FileOutputStream(outJar), mFest); while ((jarEntry = preJarInStream.getNextJarEntry()) != null) { try { jarOutStream.putNextEntry(jarEntry); } catch (ZipException ze) { continue; } int read; while ((read = preJarInStream.read(buffer)) != -1) { jarOutStream.write(buffer, 0, read); } jarOutStream.closeEntry(); } jarOutStream.flush(); preJarInStream.close(); jarOutStream.close(); } catch (FileNotFoundException ex) { ex.printStackTrace(); } catch (IOException ioe) { ioe.printStackTrace(); } } | 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(); } } | 14,189 |
0 | public static String md(String passwd) { MessageDigest md5 = null; String digest = passwd; try { md5 = MessageDigest.getInstance("MD5"); md5.update(passwd.getBytes()); byte[] digestData = md5.digest(); digest = byteArrayToHex(digestData); } catch (NoSuchAlgorithmException e) { LOG.warn("MD5 not supported. Using plain string as password!"); } catch (Exception e) { LOG.warn("Digest creation failed. Using plain string as password!"); } return digest; } | public static void doVersionCheck(View view) { view.showWaitCursor(); try { URL url = new URL(jEdit.getProperty("version-check.url")); InputStream in = url.openStream(); BufferedReader bin = new BufferedReader(new InputStreamReader(in)); String line; String develBuild = null; String stableBuild = null; while ((line = bin.readLine()) != null) { if (line.startsWith(".build")) develBuild = line.substring(6).trim(); else if (line.startsWith(".stablebuild")) stableBuild = line.substring(12).trim(); } bin.close(); if (develBuild != null && stableBuild != null) { doVersionCheck(view, stableBuild, develBuild); } } catch (IOException e) { String[] args = { jEdit.getProperty("version-check.url"), e.toString() }; GUIUtilities.error(view, "read-error", args); } view.hideWaitCursor(); } | 14,190 |
0 | public synchronized void deleteDocument(final String file) throws IOException { SQLException ex = null; try { PreparedStatement findFileStmt = con.prepareStatement("SELECT ID AS \"ID\" FROM File_ WHERE Name = ?"); findFileStmt.setString(1, file); ResultSet rs = findFileStmt.executeQuery(); if (null != rs && rs.next()) { int fileId = rs.getInt("ID"); rs.close(); rs = null; PreparedStatement deleteTokensStmt = con.prepareStatement("DELETE FROM Token_ WHERE FieldID IN ( SELECT ID FROM Field_ WHERE FileID = ? )"); deleteTokensStmt.setInt(1, fileId); deleteTokensStmt.executeUpdate(); PreparedStatement deleteFieldsStmt = con.prepareStatement("DELETE FROM Field_ WHERE FileID = ?"); deleteFieldsStmt.setInt(1, fileId); deleteFieldsStmt.executeUpdate(); PreparedStatement deleteFileStmt = con.prepareStatement("DELETE FROM File_ WHERE ID = ?"); deleteFileStmt.setInt(1, fileId); deleteFileStmt.executeUpdate(); deleteFileStmt.close(); deleteFileStmt = null; deleteFieldsStmt.close(); deleteFieldsStmt = null; deleteTokensStmt.close(); deleteTokensStmt = null; } findFileStmt.close(); findFileStmt = null; } catch (SQLException e) { e.printStackTrace(); ex = e; try { this.con.rollback(); } catch (SQLException e2) { } } finally { try { this.con.setAutoCommit(true); } catch (SQLException e2) { } } if (null != ex) throw new IOException(ex.getMessage()); } | public static String generateHash(String string, String algoritmo) { try { MessageDigest md = MessageDigest.getInstance(algoritmo); md.update(string.getBytes()); byte[] result = md.digest(); int firstPart; int lastPart; StringBuilder sBuilder = new StringBuilder(); for (int i = 0; i < result.length; i++) { firstPart = ((result[i] >> 4) & 0xf) << 4; lastPart = result[i] & 0xf; if (firstPart == 0) sBuilder.append("0"); sBuilder.append(Integer.toHexString(firstPart | lastPart)); } return sBuilder.toString(); } catch (NoSuchAlgorithmException ex) { return null; } } | 14,191 |
1 | private void CopyTo(File dest) throws IOException { FileReader in = null; FileWriter out = null; int c; try { in = new FileReader(image); out = new FileWriter(dest); while ((c = in.read()) != -1) out.write(c); } finally { if (in != null) try { in.close(); } catch (Exception e) { } if (out != null) try { out.close(); } catch (Exception e) { } } } | public static PortalConfig install(File xml, File dir) throws IOException, ConfigurationException { if (!dir.exists()) { log.info("Creating directory {}", dir); dir.mkdirs(); } if (!xml.exists()) { log.info("Installing default configuration to {}", xml); OutputStream output = new FileOutputStream(xml); try { InputStream input = ResourceLoader.open("res://" + PORTAL_CONFIG_XML); try { IOUtils.copy(input, output); } finally { input.close(); } } finally { output.close(); } } return create(xml, dir); } | 14,192 |
0 | private static HttpURLConnection getConnection(URL url) throws IOException { HttpURLConnection conn = (HttpURLConnection) url.openConnection(); conn.setRequestMethod("GET"); conn.setDoInput(true); conn.setDoOutput(true); conn.setRequestProperty("Accept", "application/zip;text/html"); return conn; } | private static void copier(FichierElectronique source, FichierElectronique cible) throws IOException { cible.setNom(source.getNom()); cible.setTaille(source.getTaille()); cible.setTypeMime(source.getTypeMime()); cible.setSoumetteur(source.getSoumetteur()); cible.setDateDerniereModification(source.getDateDerniereModification()); cible.setEmprunteur(source.getEmprunteur()); cible.setDateEmprunt(source.getDateEmprunt()); cible.setNumeroVersion(source.getNumeroVersion()); InputStream inputStream = source.getInputStream(); OutputStream outputStream = cible.getOutputStream(); try { IOUtils.copy(inputStream, outputStream); } finally { try { inputStream.close(); } finally { outputStream.close(); } if (source instanceof FichierElectroniqueDefaut) { FichierElectroniqueDefaut fichierElectroniqueTemporaire = (FichierElectroniqueDefaut) source; fichierElectroniqueTemporaire.deleteTemp(); } } } | 14,193 |
0 | @Override public void run() { handle.start(); handle.switchToIndeterminate(); FacebookJsonRestClient client = new FacebookJsonRestClient(API_KEY, SECRET); client.setIsDesktop(true); HttpURLConnection connection; List<String> cookies; try { String token = client.auth_createToken(); String post_url = "http://www.facebook.com/login.php"; String get_url = "http://www.facebook.com/login.php" + "?api_key=" + API_KEY + "&v=1.0" + "&auth_token=" + token; HttpURLConnection.setFollowRedirects(true); connection = (HttpURLConnection) new URL(get_url).openConnection(); connection.setRequestMethod("GET"); connection.setRequestProperty("User-Agent", "Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.9.2.3) Gecko/20100401"); connection.setRequestProperty("Host", "www.facebook.com"); connection.setRequestProperty("Accept-Charset", "UFT-8"); connection.connect(); cookies = connection.getHeaderFields().get("Set-Cookie"); connection = (HttpURLConnection) new URL(post_url).openConnection(); connection.setRequestMethod("POST"); connection.setRequestProperty("User-Agent", "Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.9.2.3) Gecko/20100401"); connection.setRequestProperty("Host", "www.facebook.com"); connection.setRequestProperty("Accept-Charset", "UFT-8"); if (cookies != null) { for (String cookie : cookies) { connection.addRequestProperty("Cookie", cookie.split(";", 2)[0]); } } String params = "api_key=" + API_KEY + "&auth_token=" + token + "&email=" + URLEncoder.encode(email, "UTF-8") + "&pass=" + URLEncoder.encode(pass, "UTF-8") + "&v=1.0"; connection.setRequestProperty("Content-Length", Integer.toString(params.length())); connection.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); connection.setDoOutput(true); connection.connect(); connection.getOutputStream().write(params.toString().getBytes("UTF-8")); connection.getOutputStream().close(); cookies = connection.getHeaderFields().get("Set-Cookie"); if (cookies == null) { ActionListener listener = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { String url = "http://www.chartsy.org/facebook/"; DesktopUtil.browseAndWarn(url, null); } }; NotifyUtil.show("Application Permission", "You need to grant permission first.", MessageType.WARNING, listener, false); connection.disconnect(); loggedIn = false; } else { sessionKey = client.auth_getSession(token); sessionSecret = client.getSessionSecret(); loggedIn = true; } connection.disconnect(); handle.finish(); } catch (FacebookException fex) { handle.finish(); NotifyUtil.error("Login Error", fex.getMessage(), fex, false); } catch (IOException ioex) { handle.finish(); NotifyUtil.error("Login Error", ioex.getMessage(), ioex, false); } } | private void testURL(String urlStr) throws MalformedURLException, IOException { HttpURLConnection conn = null; try { URL url = new URL(urlStr); conn = (HttpURLConnection) url.openConnection(); int code = conn.getResponseCode(); assertEquals(HttpURLConnection.HTTP_OK, code); } finally { if (conn != null) { conn.disconnect(); } } } | 14,194 |
1 | private String hashMD5(String strToHash) throws Exception { try { byte[] bHash = new byte[strToHash.length() * 2]; MessageDigest md = MessageDigest.getInstance("MD5"); md.update(strToHash.getBytes("UTF-16LE")); bHash = md.digest(); StringBuffer hexString = new StringBuffer(); for (byte element : bHash) { String strTemp = Integer.toHexString(element); hexString.append(strTemp.replaceAll("f", "")); } return hexString.toString(); } catch (NoSuchAlgorithmException duu) { throw new Exception("NoSuchAlgorithmException: " + duu.getMessage()); } } | public static String encryptPassword(String password) { String hash = null; try { MessageDigest md = null; md = MessageDigest.getInstance("SHA"); md.update(password.getBytes("UTF-8")); byte raw[] = md.digest(); hash = Base64.encode(raw, false); } catch (Exception e) { } return hash; } | 14,195 |
1 | public void run() { LOG.debug(this); String[] parts = createCmdArray(getCommand()); Runtime runtime = Runtime.getRuntime(); try { Process process = runtime.exec(parts); if (isBlocking()) { process.waitFor(); StringWriter out = new StringWriter(); IOUtils.copy(process.getInputStream(), out); String stdout = out.toString().replaceFirst("\\s+$", ""); if (StringUtils.isNotBlank(stdout)) { LOG.info("Process stdout:\n" + stdout); } StringWriter err = new StringWriter(); IOUtils.copy(process.getErrorStream(), err); String stderr = err.toString().replaceFirst("\\s+$", ""); if (StringUtils.isNotBlank(stderr)) { LOG.error("Process stderr:\n" + stderr); } } } catch (IOException ioe) { LOG.error(String.format("Could not exec [%s]", getCommand()), ioe); } catch (InterruptedException ie) { LOG.error(String.format("Interrupted [%s]", getCommand()), ie); } } | 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!"); } | 14,196 |
1 | private String fetchLocalPage(String page) throws IOException { final String fullUrl = HOST + page; LOG.debug("Fetching local page: " + fullUrl); URL url = new URL(fullUrl); URLConnection connection = url.openConnection(); StringBuilder sb = new StringBuilder(); BufferedReader input = null; try { input = new BufferedReader(new InputStreamReader(connection.getInputStream())); String line = null; while ((line = input.readLine()) != null) { sb.append(line).append("\n"); } } finally { if (input != null) try { input.close(); } catch (IOException e) { LOG.error("Could not close reader!", e); } } return sb.toString(); } | @Override public void doFilter(ServletRequest req, ServletResponse res, FilterChain chain) throws IOException, ServletException { HttpServletRequest request = (HttpServletRequest) req; HttpServletResponse response = (HttpServletResponse) res; ImagesService imgService = ImagesServiceFactory.getImagesService(); InputStream stream = request.getInputStream(); ArrayList<Byte> bytes = new ArrayList<Byte>(); int b = 0; while ((b = stream.read()) != -1) { bytes.add((byte) b); } byte img[] = new byte[bytes.size()]; for (int i = 0; i < bytes.size(); i++) { img[i] = bytes.get(i); } BlobstoreService blobstoreService = BlobstoreServiceFactory.getBlobstoreService(); String urlBlobstore = blobstoreService.createUploadUrl("/blobstore-servlet?action=upload"); URL url = new URL("http://localhost:8888" + urlBlobstore); HttpURLConnection connection = (HttpURLConnection) url.openConnection(); connection.setDoInput(true); connection.setDoOutput(true); connection.setRequestMethod("POST"); connection.setRequestProperty("Content-Type", "multipart/form-data;boundary=29772313"); OutputStream out = connection.getOutputStream(); out.write(img); out.flush(); out.close(); System.out.println(connection.getResponseCode()); System.out.println(connection.getResponseMessage()); BufferedReader rd = new BufferedReader(new InputStreamReader(connection.getInputStream())); String responseText = ""; String line; while ((line = rd.readLine()) != null) { responseText += line; } out.close(); rd.close(); response.sendRedirect("/blobstore-servlet?action=getPhoto&" + responseText); } | 14,197 |
0 | private static void copyFile(String fromFile, String toFile) throws Exception { FileInputStream from = null; FileOutputStream to = null; try { from = new FileInputStream(fromFile); to = new FileOutputStream(toFile); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = from.read(buffer)) != -1) to.write(buffer, 0, bytesRead); } finally { if (from != null) try { from.close(); } catch (IOException e) { ; } if (to != null) try { to.close(); } catch (IOException e) { ; } } } | private void downloadPage(final URL url, final File file) { try { long size = 0; final byte[] buffer = new byte[BotUtil.BUFFER_SIZE]; final File tempFile = new File(file.getParentFile(), "temp.tmp"); int length; int lastUpdate = 0; FileOutputStream fos = new FileOutputStream(tempFile); final InputStream is = url.openStream(); do { length = is.read(buffer); if (length >= 0) { fos.write(buffer, 0, length); size += length; } if (lastUpdate > UPDATE_TIME) { report(0, (int) (size / Format.MEMORY_MEG), "Downloading... " + Format.formatMemory(size)); lastUpdate = 0; } lastUpdate++; } while (length >= 0); fos.close(); if (url.toString().toLowerCase().endsWith(".gz")) { final FileInputStream fis = new FileInputStream(tempFile); final GZIPInputStream gis = new GZIPInputStream(fis); fos = new FileOutputStream(file); size = 0; lastUpdate = 0; do { length = gis.read(buffer); if (length >= 0) { fos.write(buffer, 0, length); size += length; } if (lastUpdate > UPDATE_TIME) { report(0, (int) (size / Format.MEMORY_MEG), "Uncompressing... " + Format.formatMemory(size)); lastUpdate = 0; } lastUpdate++; } while (length >= 0); fos.close(); fis.close(); gis.close(); tempFile.delete(); } else { file.delete(); tempFile.renameTo(file); } } catch (final IOException e) { throw new AnalystError(e); } } | 14,198 |
0 | public Source resolve(String href, String base) throws TransformerException { if (href.endsWith(".txt")) { try { URL url = new URL(new URL(base), href); java.io.InputStream in = url.openConnection().getInputStream(); java.io.InputStreamReader reader = new java.io.InputStreamReader(in, "iso-8859-1"); StringBuffer sb = new StringBuffer(); while (true) { int c = reader.read(); if (c < 0) break; sb.append((char) c); } com.icl.saxon.expr.TextFragmentValue tree = new com.icl.saxon.expr.TextFragmentValue(sb.toString(), url.toString(), (com.icl.saxon.Controller) transformer); return tree.getFirst(); } catch (Exception err) { throw new TransformerException(err); } } else { return null; } } | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | 14,199 |
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