label int64 0 1 | func1 stringlengths 173 53.1k | func2 stringlengths 173 53.1k | id int64 0 901k |
|---|---|---|---|
1 | public static boolean copyFile(File source, File dest) throws IOException { int answer = JOptionPane.YES_OPTION; if (dest.exists()) { answer = JOptionPane.showConfirmDialog(null, "File " + dest.getAbsolutePath() + "\n already exists. Overwrite?", "Warning", JOptionPane.YES_NO_OPTION); } if (answer == JOptionPane.NO_OPTION) return false; dest.createNewFile(); InputStream in = null; OutputStream out = null; try { in = new FileInputStream(source); out = new FileOutputStream(dest); byte[] buf = new byte[1024]; int len; while ((len = in.read(buf)) > 0) { out.write(buf, 0, len); } return true; } catch (Exception e) { return false; } finally { if (in != null) { in.close(); } if (out != null) { out.close(); } } } | public static void copyFile(File sourceFile, File destFile) throws IOException { if (!sourceFile.exists()) { return; } if (!destFile.exists()) { destFile.createNewFile(); } FileChannel source = null; FileChannel destination = null; source = new FileInputStream(sourceFile).getChannel(); destination = new FileOutputStream(destFile).getChannel(); if (destination != null && source != null) { destination.transferFrom(source, 0, source.size()); } if (source != null) { source.close(); } if (destination != null) { destination.close(); } } | 18,600 |
1 | public void convert(File file, String fromEncoding, String toEncoding) throws IOException { InputStream in = new FileInputStream(file); StringWriter cache = new StringWriter(); Reader reader = new InputStreamReader(in, fromEncoding); char[] buffer = new char[128]; int read; while ((read = reader.read(buffer)) > -1) { cache.write(buffer, 0, read); } reader.close(); in.close(); Log.warn(this, "read from file " + file + " (" + fromEncoding + "):" + cache); OutputStream out = new FileOutputStream(file); OutputStreamWriter writer = new OutputStreamWriter(out, toEncoding); writer.write(cache.toString()); cache.close(); writer.close(); out.close(); } | public static void copy(String from, String to) throws Exception { File inputFile = new File(from); File outputFile = new File(to); FileInputStream in = new FileInputStream(inputFile); FileOutputStream out = new FileOutputStream(outputFile); byte[] buffer = new byte[1024]; int len; while ((len = in.read(buffer)) != -1) out.write(buffer, 0, len); in.close(); out.close(); } | 18,601 |
0 | public static void downloadFromUrl(String url1, String fileName) { try { URL url = new URL(url1); File file = new File(fileName); URLConnection ucon = url.openConnection(); InputStream is = ucon.getInputStream(); BufferedInputStream bis = new BufferedInputStream(is); ByteArrayBuffer baf = new ByteArrayBuffer(50); int current = 0; while ((current = bis.read()) != -1) { baf.append((byte) current); } FileOutputStream fos = new FileOutputStream(file); fos.write(baf.toByteArray()); fos.close(); } catch (IOException e) { } } | public static String getMd5Digest(String pInput) { try { MessageDigest lDigest = MessageDigest.getInstance("MD5"); lDigest.update(pInput.getBytes()); BigInteger lHashInt = new BigInteger(1, lDigest.digest()); return String.format("%1$032x", lHashInt).toLowerCase(); } catch (NoSuchAlgorithmException lException) { throw new RuntimeException(lException); } } | 18,602 |
1 | public static boolean writeFileByChars(Reader pReader, File pFile, boolean pAppend) { boolean flag = false; try { FileWriter fw = new FileWriter(pFile, pAppend); IOUtils.copy(pReader, fw); fw.flush(); fw.close(); pReader.close(); flag = true; } catch (Exception e) { LOG.error("将字符流写入�?" + pFile.getName() + "出现异常�?", e); } return flag; } | public void doImport(File f, boolean checkHosp) throws Exception { connector.getConnection().setAutoCommit(false); File base = f.getParentFile(); ZipInputStream in = new ZipInputStream(new FileInputStream(f)); ZipEntry entry; while ((entry = in.getNextEntry()) != null) { String outFileName = entry.getName(); File outFile = new File(base, outFileName); OutputStream out = new FileOutputStream(outFile, false); byte[] buf = new byte[1024]; int len; while ((len = in.read(buf)) > 0) out.write(buf, 0, len); out.close(); } in.close(); importDirectory(base, checkHosp); connector.getConnection().commit(); } | 18,603 |
0 | public static void main(String[] args) throws Exception { InputStream in = null; try { in = new URL(args[0]).openStream(); IOUtils.copyBytes(in, System.out, 4096, false); } finally { IOUtils.closeStream(in); } } | public static boolean exec_applet(String fname, VarContainer vc, ActionContainer ac, ThingTypeContainer ttc, Output OUT, InputStream IN, boolean AT, Statement state, String[] arggies) { if (!urlpath.endsWith("/")) { urlpath = urlpath + '/'; } if (!urlpath.startsWith("http://")) { urlpath = "http://" + urlpath; } String url = urlpath; if (fname.startsWith("dusty_")) { url = url + "libraries/" + fname; } else { url = url + "users/" + fname; } StringBuffer src = new StringBuffer(2400); try { String s; BufferedReader br = new BufferedReader(new InputStreamReader(new URL(url).openStream())); while ((s = br.readLine()) != null) { src.append(s).append('\n'); } br.close(); } catch (Exception e) { OUT.println(new DSOut(DSOut.ERR_OUT, -1, "Dustyscript failed at reading the file'" + fname + "'\n\t...for 'use' statement"), vc, AT); return false; } fork(src, vc, ac, ttc, OUT, IN, AT, state, arggies); return true; } | 18,604 |
1 | protected void copy(URL url, File file) throws IOException { InputStream in = null; FileOutputStream out = null; try { in = url.openStream(); out = new FileOutputStream(file); IOUtils.copy(in, out); } finally { if (out != null) { out.close(); } if (in != null) { in.close(); } } } | public void write(URL exportUrl, OutputStream output) throws Exception { if (exportUrl == null || output == null) { throw new RuntimeException("null passed in for required parameters"); } MediaContent mc = new MediaContent(); mc.setUri(exportUrl.toString()); MediaSource ms = service.getMedia(mc); InputStream input = ms.getInputStream(); IOUtils.copy(input, output); } | 18,605 |
1 | public void doRender() throws IOException { File file = new File(fileName); if (!file.exists()) { logger.error("Static resource not found: " + fileName); isNotFound = true; return; } if (fileName.endsWith("xml") || fileName.endsWith("asp")) servletResponse.setContentType("text/xml"); else if (fileName.endsWith("css")) servletResponse.setContentType("text/css"); else if (fileName.endsWith("js")) servletResponse.setContentType("text/javascript"); InputStream in = null; try { in = new FileInputStream(file); IOUtils.copy(in, servletResponse.getOutputStream()); logger.debug("Static resource rendered: ".concat(fileName)); } catch (FileNotFoundException e) { logger.error("Static resource not found: " + fileName); isNotFound = true; } finally { IOUtils.closeQuietly(in); } } | 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(); } } | 18,606 |
1 | public void copyNIO(File in, File out) throws IOException { FileInputStream inStream = null; FileOutputStream outStream = null; FileChannel sourceChannel = null; FileChannel destinationChannel = null; try { inStream = new FileInputStream(in); outStream = new FileOutputStream(out); sourceChannel = inStream.getChannel(); destinationChannel = outStream.getChannel(); destinationChannel.transferFrom(sourceChannel, 0, sourceChannel.size()); } finally { if (sourceChannel != null) sourceChannel.close(); if (destinationChannel != null) destinationChannel.close(); if (inStream != null) inStream.close(); if (outStream != null) outStream.close(); } } | private static void copyContent(final File srcFile, final File dstFile, final boolean gzipContent) throws IOException { final File dstFolder = dstFile.getParentFile(); dstFolder.mkdirs(); if (!dstFolder.exists()) { throw new RuntimeException("Unable to create the folder " + dstFolder.getAbsolutePath()); } final InputStream in = new FileInputStream(srcFile); OutputStream out = new FileOutputStream(dstFile); if (gzipContent) { out = new GZIPOutputStream(out); } try { final byte[] buffer = new byte[1024]; int read; while ((read = in.read(buffer)) != -1) { out.write(buffer, 0, read); } } finally { in.close(); out.close(); } } | 18,607 |
0 | public File extractID3v2TagDataIntoFile(File outputFile) throws TagNotFoundException, IOException { int startByte = (int) ((MP3AudioHeader) audioHeader).getMp3StartByte(); if (startByte >= 0) { FileInputStream fis = new FileInputStream(file); FileChannel fc = fis.getChannel(); ByteBuffer bb = ByteBuffer.allocate(startByte); fc.read(bb); FileOutputStream out = new FileOutputStream(outputFile); out.write(bb.array()); out.close(); fc.close(); fis.close(); return outputFile; } throw new TagNotFoundException("There is no ID3v2Tag data in this file"); } | protected String readUrl(String urlString) throws IOException { URL url = new URL(urlString); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); String response = ""; String inputLine; while ((inputLine = in.readLine()) != null) response += inputLine; in.close(); return response; } | 18,608 |
0 | public long getMD5Hash(String str) { MessageDigest m = null; try { m = MessageDigest.getInstance("SHA-256"); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } m.update(str.getBytes(), 0, str.length()); return new BigInteger(1, m.digest()).longValue(); } | public static void BubbleSortDouble1(double[] num) { boolean flag = true; // set flag to true to begin first pass double temp; // holding variable while (flag) { flag = false; // set flag to false awaiting a possible swap for (int j = 0; j < num.length - 1; j++) { if (num[j] > num[j + 1]) // change to > for ascending sort { temp = num[j]; // swap elements num[j] = num[j + 1]; num[j + 1] = temp; flag = true; // shows a swap occurred } } } } | 18,609 |
0 | private PrecomputedAnimatedModel loadPrecomputedModel_(URL url) { if (precompCache.containsKey(url.toExternalForm())) { return (precompCache.get(url.toExternalForm()).copy()); } TextureLoader.getInstance().getTexture(""); List<SharedGroup> frames = new ArrayList<SharedGroup>(); Map<String, Animation> animations = new Hashtable<String, Animation>(); if (url.toExternalForm().endsWith(".amo")) { try { BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String objFileName = reader.readLine(); objFileName = url.toExternalForm().substring(0, url.toExternalForm().lastIndexOf("/")) + "/" + objFileName; frames = loadOBJFrames(objFileName); String line; while ((line = reader.readLine()) != null) { StringTokenizer tokenizer = new StringTokenizer(line); String animName = tokenizer.nextToken(); int from = Integer.valueOf(tokenizer.nextToken()); int to = Integer.valueOf(tokenizer.nextToken()); tokenizer.nextToken(); animations.put(animName, new Animation(animName, from, to)); } } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } else { frames = loadOBJFrames(url.toExternalForm()); } PrecomputedAnimatedModel precompModel = new PrecomputedAnimatedModel(frames, animations); precompCache.put(url.toExternalForm(), precompModel); return (precompModel); } | private boolean copy(File in, File out) { try { FileInputStream fis = new FileInputStream(in); FileOutputStream fos = new FileOutputStream(out); FileChannel readableChannel = fis.getChannel(); FileChannel writableChannel = fos.getChannel(); writableChannel.truncate(0); writableChannel.transferFrom(readableChannel, 0, readableChannel.size()); fis.close(); fos.close(); return true; } catch (IOException ioe) { guiBuilder.showError("Copy Error", "IOException during copy", ioe.getMessage()); return false; } } | 18,610 |
1 | @Override public void doExecute(String[] args) { if (args.length != 2) { printUsage(); } else { int fileNo = 0; try { fileNo = Integer.parseInt(args[1]) - 1; } catch (NumberFormatException e) { printUsage(); return; } if (fileNo < 0) { printUsage(); return; } StorageFile[] files = (StorageFile[]) ctx.getRemoteDir().listFiles(); try { StorageFile file = files[fileNo]; File outFile = getOutFile(file); FileOutputStream out = new FileOutputStream(outFile); InputStream in = file.openStream(); IOUtils.copy(in, out); IOUtils.closeQuietly(out); afterSave(outFile); if (outFile.exists()) { print("File written to: " + outFile.getAbsolutePath()); } } catch (IOException e) { printError("Failed to load file. " + e.getMessage()); } catch (Exception e) { printUsage(); return; } } } | 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(); } | 18,611 |
1 | public static String getMD5(String password) { try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(password.getBytes()); byte[] digest = md.digest(); String out = ""; for (int i = 0; i < digest.length; i++) { out += digest[i]; } return out; } catch (NoSuchAlgorithmException e) { System.err.println("Manca l'MD5 (piuttosto strano)"); } return ""; } | public static String getSHA1Digest(String inputStr) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md = null; byte[] sha1hash = null; md = MessageDigest.getInstance("SHA"); sha1hash = new byte[40]; md.update(inputStr.getBytes("iso-8859-1"), 0, inputStr.length()); sha1hash = md.digest(); return convertToHex(sha1hash); } | 18,612 |
0 | private void album(String albumTitle, String albumNbSong, URL url) { try { if (color == SWT.COLOR_WHITE) { color = SWT.COLOR_GRAY; } else { color = SWT.COLOR_WHITE; } url.openConnection(); InputStream is = url.openStream(); Image coverPicture = new Image(this.getDisplay(), is); Composite albumComposite = new Composite(main, SWT.NONE); albumComposite.setLayout(new FormLayout()); FormData data = new FormData(); data.left = new FormAttachment(0, 5); data.right = new FormAttachment(100, -5); if (prevCompo == null) { data.top = new FormAttachment(0, 0); } else { data.top = new FormAttachment(prevCompo, 0, SWT.BOTTOM); } albumComposite.setLayoutData(data); albumComposite.setBackground(Display.getDefault().getSystemColor(color)); Label cover = new Label(albumComposite, SWT.LEFT); cover.setText("cover"); cover.setImage(coverPicture); data = new FormData(75, 75); cover.setLayoutData(data); Label title = new Label(albumComposite, SWT.CENTER); title.setFont(new Font(this.getDisplay(), "Arial", 10, SWT.BOLD)); title.setText(albumTitle); data = new FormData(); data.bottom = new FormAttachment(50, -5); data.left = new FormAttachment(cover, 5); title.setBackground(Display.getDefault().getSystemColor(color)); title.setLayoutData(data); Label nbSong = new Label(albumComposite, SWT.LEFT | SWT.BOLD); nbSong.setFont(new Font(this.getDisplay(), "Arial", 8, SWT.ITALIC)); nbSong.setText("Release date : " + albumNbSong); data = new FormData(); data.top = new FormAttachment(50, 5); data.left = new FormAttachment(cover, 5); nbSong.setBackground(Display.getDefault().getSystemColor(color)); nbSong.setLayoutData(data); prevCompo = albumComposite; } catch (Exception e) { e.printStackTrace(); } } | private ArrayList execAtParentServer(ArrayList paramList) throws Exception { ArrayList outputList = null; String message = ""; try { HashMap serverUrlMap = InitXml.getInstance().getServerMap(); Iterator it = serverUrlMap.keySet().iterator(); while (it.hasNext()) { String server = (String) it.next(); String serverUrl = (String) serverUrlMap.get(server); serverUrl = serverUrl + Primer3Manager.servletName; URL url = new URL(serverUrl); URLConnection uc = url.openConnection(); uc.setDoOutput(true); OutputStream os = uc.getOutputStream(); StringBuffer buf = new StringBuffer(); buf.append("actionType=designparent"); for (int i = 0; i < paramList.size(); i++) { Primer3Param param = (Primer3Param) paramList.get(i); if (i == 0) { buf.append("&sequence=" + param.getSequence()); buf.append("&upstream_size" + upstreamSize); buf.append("&downstreamSize" + downstreamSize); buf.append("&MARGIN_LENGTH=" + marginLength); buf.append("&OVERLAP_LENGTH=" + overlapLength); buf.append("&MUST_XLATE_PRODUCT_MIN_SIZE=" + param.getPrimerProductMinSize()); buf.append("&MUST_XLATE_PRODUCT_MAX_SIZE=" + param.getPrimerProductMaxSize()); buf.append("&PRIMER_PRODUCT_OPT_SIZE=" + param.getPrimerProductOptSize()); buf.append("&PRIMER_MAX_END_STABILITY=" + param.getPrimerMaxEndStability()); buf.append("&PRIMER_MAX_MISPRIMING=" + param.getPrimerMaxMispriming()); buf.append("&PRIMER_PAIR_MAX_MISPRIMING=" + param.getPrimerPairMaxMispriming()); buf.append("&PRIMER_MIN_SIZE=" + param.getPrimerMinSize()); buf.append("&PRIMER_OPT_SIZE=" + param.getPrimerOptSize()); buf.append("&PRIMER_MAX_SIZE=" + param.getPrimerMaxSize()); buf.append("&PRIMER_MIN_TM=" + param.getPrimerMinTm()); buf.append("&PRIMER_OPT_TM=" + param.getPrimerOptTm()); buf.append("&PRIMER_MAX_TM=" + param.getPrimerMaxTm()); buf.append("&PRIMER_MAX_DIFF_TM=" + param.getPrimerMaxDiffTm()); buf.append("&PRIMER_MIN_GC=" + param.getPrimerMinGc()); buf.append("&PRIMER_OPT_GC_PERCENT=" + param.getPrimerOptGcPercent()); buf.append("&PRIMER_MAX_GC=" + param.getPrimerMaxGc()); buf.append("&PRIMER_SELF_ANY=" + param.getPrimerSelfAny()); buf.append("&PRIMER_SELF_END=" + param.getPrimerSelfEnd()); buf.append("&PRIMER_NUM_NS_ACCEPTED=" + param.getPrimerNumNsAccepted()); buf.append("&PRIMER_MAX_POLY_X=" + param.getPrimerMaxPolyX()); buf.append("&PRIMER_GC_CLAMP=" + param.getPrimerGcClamp()); } buf.append("&target=" + param.getPrimerSequenceId() + "," + (param.getTarget())[0] + "," + (param.getTarget())[1]); } PrintStream ps = new PrintStream(os); ps.print(buf.toString()); ps.close(); ObjectInputStream ois = new ObjectInputStream(uc.getInputStream()); outputList = (ArrayList) ois.readObject(); ois.close(); } } catch (IOException e1) { e1.printStackTrace(); } if ((outputList == null || outputList.size() == 0) && message != null && message.length() > 0) { throw new Exception(message); } return outputList; } | 18,613 |
0 | public InputStream getInputStream(IProgressMonitor monitor) throws IOException, CoreException { if (in == null && url != null) { if (connection == null) connection = url.openConnection(); if (monitor != null) { this.in = openStreamWithCancel(connection, monitor); } else { this.in = connection.getInputStream(); } if (in != null) { this.lastModified = connection.getLastModified(); } } return in; } | private static String getRegistrationClasses() { CentralRegistrationClass c = new CentralRegistrationClass(); String name = c.getClass().getCanonicalName().replace('.', '/').concat(".class"); try { Enumeration<URL> urlEnum = c.getClass().getClassLoader().getResources("META-INF/MANIFEST.MF"); while (urlEnum.hasMoreElements()) { URL url = urlEnum.nextElement(); String file = url.getFile(); JarURLConnection jarConnection = (JarURLConnection) url.openConnection(); Manifest mf = jarConnection.getManifest(); Attributes attrs = (Attributes) mf.getAttributes(name); if (attrs != null) { String classes = attrs.getValue("RegistrationClasses"); return classes; } } } catch (IOException ex) { ex.printStackTrace(); } return ""; } | 18,614 |
0 | protected void entryMatched(EntryMonitor monitor, Entry entry) { FTPClient ftpClient = new FTPClient(); try { Resource resource = entry.getResource(); if (!resource.isFile()) { return; } if (server.length() == 0) { return; } String passwordToUse = monitor.getRepository().getPageHandler().processTemplate(password, false); ftpClient.connect(server); if (user.length() > 0) { ftpClient.login(user, password); } int reply = ftpClient.getReplyCode(); if (!FTPReply.isPositiveCompletion(reply)) { ftpClient.disconnect(); monitor.handleError("FTP server refused connection:" + server, null); return; } ftpClient.setFileType(FTP.IMAGE_FILE_TYPE); ftpClient.enterLocalPassiveMode(); if (directory.length() > 0) { ftpClient.changeWorkingDirectory(directory); } String filename = monitor.getRepository().getEntryManager().replaceMacros(entry, fileTemplate); InputStream is = new BufferedInputStream(monitor.getRepository().getStorageManager().getFileInputStream(new File(resource.getPath()))); boolean ok = ftpClient.storeUniqueFile(filename, is); is.close(); if (ok) { monitor.logInfo("Wrote file:" + directory + " " + filename); } else { monitor.handleError("Failed to write file:" + directory + " " + filename, null); } } catch (Exception exc) { monitor.handleError("Error posting to FTP:" + server, exc); } finally { try { ftpClient.logout(); } catch (Exception exc) { } try { ftpClient.disconnect(); } catch (Exception exc) { } } } | public static void entering(String[] args) throws IOException, CodeCheckException { ClassWriter writer = new ClassWriter(); writer.readClass(new BufferedInputStream(new FileInputStream(args[0]))); int constantIndex = writer.getStringConstantIndex("Entering "); int fieldRefIndex = writer.getReferenceIndex(ClassWriter.CONSTANT_Fieldref, "java/lang/System", "out", "Ljava/io/PrintStream;"); int printlnRefIndex = writer.getReferenceIndex(ClassWriter.CONSTANT_Methodref, "java/io/PrintStream", "println", "(Ljava/lang/String;)V"); int printRefIndex = writer.getReferenceIndex(ClassWriter.CONSTANT_Methodref, "java/io/PrintStream", "print", "(Ljava/lang/String;)V"); for (Iterator i = writer.getMethods().iterator(); i.hasNext(); ) { MethodInfo method = (MethodInfo) i.next(); if (method.getName().equals("readConstant")) continue; CodeAttribute attribute = method.getCodeAttribute(); ArrayList instructions = new ArrayList(10); byte[] operands; operands = new byte[2]; NetByte.intToPair(fieldRefIndex, operands, 0); instructions.add(new Instruction(OpCode.getOpCodeByMnemonic("getstatic"), 0, operands, false)); instructions.add(new Instruction(OpCode.getOpCodeByMnemonic("dup"), 0, null, false)); instructions.add(Instruction.appropriateLdc(constantIndex, false)); operands = new byte[2]; NetByte.intToPair(printRefIndex, operands, 0); instructions.add(new Instruction(OpCode.getOpCodeByMnemonic("invokevirtual"), 0, operands, false)); instructions.add(Instruction.appropriateLdc(writer.getStringConstantIndex(method.getName()), false)); operands = new byte[2]; NetByte.intToPair(printlnRefIndex, operands, 0); instructions.add(new Instruction(OpCode.getOpCodeByMnemonic("invokevirtual"), 0, operands, false)); attribute.insertInstructions(0, 0, instructions); attribute.codeCheck(); } BufferedOutputStream outStream = new BufferedOutputStream(new FileOutputStream(args[1])); writer.writeClass(outStream); outStream.close(); } | 18,615 |
1 | private void copy(final File src, final File dstDir) { dstDir.mkdirs(); final File dst = new File(dstDir, src.getName()); BufferedReader reader = null; BufferedWriter writer = null; try { reader = new BufferedReader(new InputStreamReader(new FileInputStream(src), "ISO-8859-1")); writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(dst), "ISO-8859-1")); String read; while ((read = reader.readLine()) != null) { Line line = new Line(read); if (line.isComment()) continue; writer.write(read); writer.newLine(); } } catch (IOException e) { e.printStackTrace(); } finally { if (reader != null) try { reader.close(); } catch (IOException e) { } if (writer != null) { try { writer.flush(); } catch (IOException e) { } try { writer.close(); } catch (IOException e) { } } } } | protected void copyDependents() { for (File source : dependentFiles.keySet()) { try { if (!dependentFiles.get(source).exists()) { if (dependentFiles.get(source).isDirectory()) dependentFiles.get(source).mkdirs(); else dependentFiles.get(source).getParentFile().mkdirs(); } IOUtils.copyEverything(source, dependentFiles.get(source)); } catch (IOException e) { e.printStackTrace(); } } } | 18,616 |
0 | public static InputStream gunzip(final InputStream inputStream) throws IOException { Assert.notNull(inputStream, "inputStream"); GZIPInputStream gzipInputStream = new GZIPInputStream(inputStream); InputOutputStream inputOutputStream = new InputOutputStream(); IOUtils.copy(gzipInputStream, inputOutputStream); return inputOutputStream.getInputStream(); } | public static IChemModel readInChI(URL url) throws CDKException { IChemModel chemModel = new ChemModel(); try { IMoleculeSet moleculeSet = new MoleculeSet(); chemModel.setMoleculeSet(moleculeSet); StdInChIParser parser = new StdInChIParser(); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); String line; while ((line = in.readLine()) != null) { if (line.toLowerCase().startsWith("inchi=")) { IAtomContainer atc = parser.parseInchi(line); moleculeSet.addAtomContainer(atc); } } in.close(); } catch (Exception e) { e.printStackTrace(); throw new CDKException(e.getMessage()); } return chemModel; } | 18,617 |
1 | private static void copy(File in, File out) throws IOException { if (!out.getParentFile().isDirectory()) out.getParentFile().mkdirs(); FileChannel ic = new FileInputStream(in).getChannel(); FileChannel oc = new FileOutputStream(out).getChannel(); ic.transferTo(0, ic.size(), oc); ic.close(); oc.close(); } | public void write(File file) throws Exception { if (getGEDCOMFile() != null) { size = getGEDCOMFile().length(); if (!getGEDCOMFile().renameTo(file)) { BufferedInputStream in = null; BufferedOutputStream out = null; try { in = new BufferedInputStream(new FileInputStream(getGEDCOMFile())); out = new BufferedOutputStream(new FileOutputStream(file)); IOUtils.copy(in, out); } finally { if (in != null) { try { in.close(); } catch (IOException e) { } } if (out != null) { try { out.close(); } catch (IOException e) { } } } } } else { throw new FileUploadException("Cannot write uploaded file to disk!"); } } | 18,618 |
0 | public Configuration(URL url) { InputStream in = null; try { load(in = url.openStream()); } catch (Exception e) { throw new RuntimeException("Could not load configuration from " + url, e); } finally { if (in != null) { try { in.close(); } catch (IOException ignore) { } } } } | private synchronized boolean saveU(URL url, String typeFlag, byte[] arrByte) { BufferedReader buffReader = null; BufferedOutputStream buffOS = null; URLConnection urlconnection = null; char flagChar = '0'; boolean flag = true; try { urlconnection = url.openConnection(); urlconnection.setDoOutput(true); urlconnection.setDoInput(true); urlconnection.setUseCaches(false); urlconnection.setRequestProperty("Content-type", "application/octet-stream"); buffOS = new BufferedOutputStream(urlconnection.getOutputStream()); buffOS.write((byte[]) typeFlag.getBytes()); buffOS.write(arrByte); buffOS.flush(); if (Config.DEBUG) System.out.println("Applet output file successfully! "); buffReader = new BufferedReader(new InputStreamReader(urlconnection.getInputStream())); StringBuffer stringBuff = new StringBuffer(); String serReturnMess = buffReader.readLine(); if (Config.DEBUG) System.out.println("Applet check status successfully! " + serReturnMess); flagChar = '2'; if (serReturnMess != null) { stringBuff.append(serReturnMess); serReturnMess = serReturnMess.substring(serReturnMess.indexOf(32)).trim() + '2'; flagChar = serReturnMess.charAt(0); } while ((serReturnMess = buffReader.readLine()) != null) { if (serReturnMess.length() <= 0) break; } } catch (Throwable e) { e.printStackTrace(); return false; } finally { try { if (buffOS != null) buffOS.close(); if (buffReader != null) buffReader.close(); } catch (Throwable e) { e.printStackTrace(); } if (flagChar == '2' || flagChar == '3') flag = true; else flag = false; } return flag; } | 18,619 |
0 | public void testStorageByteArray() throws Exception { TranslationResponseInMemory r = new TranslationResponseInMemory(2048, "UTF-8"); { OutputStream output = r.getOutputStream(); output.write("This is an example".getBytes("UTF-8")); output.write(" and another one.".getBytes("UTF-8")); assertEquals("This is an example and another one.", r.getText()); } { InputStream input = r.getInputStream(); StringWriter writer = new StringWriter(); try { IOUtils.copy(input, writer, "UTF-8"); } finally { input.close(); writer.close(); } assertEquals("This is an example and another one.", writer.toString()); } { OutputStream output = r.getOutputStream(); output.write(" and another line".getBytes("UTF-8")); assertEquals("This is an example and another one. and another line", r.getText()); } { Writer output = r.getWriter(); output.write(" and write some more"); assertEquals("This is an example and another one. and another line and write some more", r.getText()); } { r.addText(" and even more."); assertEquals("This is an example and another one. and another line and write some more and even more.", r.getText()); } assertFalse(r.hasEnded()); r.setEndState(ResponseStateOk.getInstance()); assertTrue(r.hasEnded()); try { r.getOutputStream(); fail("Previous line should throw IOException as result closed."); } catch (IOException e) { } try { r.getWriter(); fail("Previous line should throw IOException as result closed."); } catch (IOException e) { } } | public static void main(String args[]) { int i, j, l; short NUMNUMBERS = 256; short numbers[] = new short[NUMNUMBERS]; Darjeeling.print("START"); for (l = 0; l < 100; l++) { for (i = 0; i < NUMNUMBERS; i++) numbers[i] = (short) (NUMNUMBERS - 1 - i); for (i = 0; i < NUMNUMBERS; i++) { for (j = 0; j < NUMNUMBERS - i - 1; j++) if (numbers[j] > numbers[j + 1]) { short temp = numbers[j]; numbers[j] = numbers[j + 1]; numbers[j + 1] = temp; } } } Darjeeling.print("END"); } | 18,620 |
1 | public static void copy(final File src, final File dest) throws IOException { OutputStream stream = new FileOutputStream(dest); FileInputStream fis = new FileInputStream(src); byte[] buffer = new byte[16384]; while (fis.available() != 0) { int read = fis.read(buffer); stream.write(buffer, 0, read); } stream.flush(); } | private void stripOneFilex(File inFile, File outFile) throws IOException { StreamTokenizer reader = new StreamTokenizer(new FileReader(inFile)); BufferedWriter writer = new BufferedWriter(new FileWriter(outFile)); reader.slashSlashComments(false); reader.slashStarComments(false); reader.eolIsSignificant(true); int token; while ((token = reader.nextToken()) != StreamTokenizer.TT_EOF) { switch(token) { case StreamTokenizer.TT_NUMBER: throw new IllegalStateException("didn't expect TT_NUMBER: " + reader.nval); case StreamTokenizer.TT_WORD: System.out.print(reader.sval); writer.write("WORD:" + reader.sval, 0, reader.sval.length()); default: char outChar = (char) reader.ttype; System.out.print(outChar); writer.write(outChar); } } } | 18,621 |
0 | public static String md5Hash(String inString) throws TopicSpacesException { try { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.update(inString.getBytes()); byte[] array = md5.digest(); StringBuffer buf = new StringBuffer(); int len = array.length; for (int i = 0; i < len; i++) { int b = array[i] & 0xFF; buf.append(Integer.toHexString(b)); } return buf.toString(); } catch (Exception x) { throw new TopicSpacesException(x); } } | public static void buildPerMovieDiffBinary(String completePath, String slopeOneDataFolderName, String slopeOneDataFileName) { try { File inFile = new File(completePath + fSep + "SmartGRAPE" + fSep + slopeOneDataFolderName + fSep + slopeOneDataFileName); FileChannel inC = new FileInputStream(inFile).getChannel(); for (int i = 1; i <= 17770; i++) { File outFile = new File(completePath + fSep + "SmartGRAPE" + fSep + slopeOneDataFolderName + fSep + "Movie-" + i + "-SlopeOneData.txt"); FileChannel outC = new FileOutputStream(outFile).getChannel(); ByteBuffer buf = ByteBuffer.allocate(17770 * 10); for (int j = 1; j < i; j++) { ByteBuffer bbuf = ByteBuffer.allocate(12); inC.position((17769 * 17770 * 6) - ((17769 - (j - 1)) * (17770 - (j - 1)) * 6) + (i - j - 1) * 12); inC.read(bbuf); bbuf.flip(); buf.putShort(bbuf.getShort()); bbuf.getShort(); buf.putInt(bbuf.getInt()); buf.putFloat(-bbuf.getFloat()); } buf.putShort(new Integer(i).shortValue()); buf.putInt(0); buf.putFloat(0.0f); ByteBuffer remainingBuf = inC.map(FileChannel.MapMode.READ_ONLY, (17769 * 17770 * 6) - ((17769 - (i - 1)) * (17770 - (i - 1)) * 6), (17770 - i) * 12); while (remainingBuf.hasRemaining()) { remainingBuf.getShort(); buf.putShort(remainingBuf.getShort()); buf.putInt(remainingBuf.getInt()); buf.putFloat(remainingBuf.getFloat()); } buf.flip(); outC.write(buf); buf.clear(); outC.close(); } } catch (Exception e) { e.printStackTrace(); } } | 18,622 |
1 | public int delete(BusinessObject o) throws DAOException { int delete = 0; Account acc = (Account) o; try { PreparedStatement pst = connection.prepareStatement(XMLGetQuery.getQuery("DELETE_ACCOUNT")); pst.setInt(1, acc.getId()); delete = pst.executeUpdate(); if (delete <= 0) { connection.rollback(); throw new DAOException("Number of rows <= 0"); } else if (delete > 1) { connection.rollback(); throw new DAOException("Number of rows > 1"); } connection.commit(); } catch (SQLException e) { Log.write(e.getMessage()); throw new DAOException("A SQLException has occured"); } catch (NullPointerException npe) { Log.write(npe.getMessage()); throw new DAOException("Connection null"); } return delete; } | public static synchronized int registerVote(String IDVotazione, byte[] T1, byte[] sbT2, byte[] envelope, Config config) { if (IDVotazione == null) { LOGGER.error("registerVote::IDV null"); return C_addVote_BOH; } if (T1 == null) { LOGGER.error("registerVote::T1 null"); return C_addVote_BOH; } if (envelope == null) { LOGGER.error("registerVote::envelope null"); return C_addVote_BOH; } LOGGER.info("registering vote started"); Connection conn = null; PreparedStatement stmt = null; boolean autoCommitPresent = true; int ANSWER = C_addVote_BOH; try { ByteArrayInputStream tmpXMLStream = new ByteArrayInputStream(envelope); SAXReader tmpXMLReader = new SAXReader(); Document doc = tmpXMLReader.read(tmpXMLStream); if (LOGGER.isTraceEnabled()) LOGGER.trace(doc.asXML()); String sT1 = new String(Base64.encodeBase64(T1), "utf-8"); String ssbT2 = new String(Base64.encodeBase64(sbT2), "utf-8"); String sEnvelope = new String(Base64.encodeBase64(envelope), "utf-8"); LOGGER.trace("loading jdbc driver ..."); Class.forName("com.mysql.jdbc.Driver"); LOGGER.trace("... loaded"); conn = DriverManager.getConnection(config.getSconn()); autoCommitPresent = conn.getAutoCommit(); conn.setAutoCommit(false); String query = "" + " INSERT INTO votes(IDVotazione, T1, signByT2 , envelope) " + " VALUES (? , ? , ? , ? ) "; stmt = conn.prepareStatement(query); stmt.setString(1, IDVotazione); stmt.setString(2, sT1); stmt.setString(3, ssbT2); stmt.setString(4, sEnvelope); stmt.executeUpdate(); stmt.close(); LOGGER.debug("vote saved for references, now start the parsing"); query = "" + " INSERT INTO risposte (IDVotazione, T1, IDquestion , myrisposta,freetext) " + " VALUES (? , ? , ? , ? ,?) "; stmt = conn.prepareStatement(query); Element question, itemsElem, rispostaElem; List<Element> rispList; String id, rispostaText, risposta, freeText, questionType; Iterator<Element> questionIterator = doc.selectNodes("/poll/manifest/question").iterator(); while (questionIterator.hasNext()) { question = (Element) questionIterator.next(); risposta = freeText = ""; id = question.attributeValue("id"); itemsElem = question.element("items"); questionType = itemsElem == null ? "" : itemsElem.attributeValue("type"); rispostaElem = question.element("myrisposta"); rispostaText = rispostaElem == null ? "" : rispostaElem.getText(); if (rispostaText.equals(Votazione.C_TAG_WHITE_XML)) { risposta = C_TAG_WHITE; } else if (rispostaText.equals(Votazione.C_TAG_NULL_XML)) { risposta = C_TAG_NULL; } else { if (!rispostaText.equals("") && LOGGER.isDebugEnabled()) LOGGER.warn("Risposta text should be empty!: " + rispostaText); risposta = C_TAG_BUG; if (questionType.equals("selection")) { Element rispItem = rispostaElem.element("item"); String tmpRisposta = rispItem.attributeValue("index"); if (tmpRisposta != null) { risposta = tmpRisposta; if (risposta.equals("0")) freeText = rispItem.getText(); } } else if (questionType.equals("borda")) { rispList = rispostaElem.elements("item"); if (rispList != null) { risposta = ""; String index, tokens; for (Element rispItem : rispList) { index = rispItem.attributeValue("index"); tokens = rispItem.attributeValue("tokens"); if (index.equals("0")) freeText = rispItem.getText(); if (risposta.length() > 0) risposta += ","; risposta += index + ":" + tokens; } } } else if (questionType.equals("ordering")) { rispList = rispostaElem.elements("item"); if (rispList != null) { risposta = ""; String index, order; for (Element rispItem : rispList) { index = rispItem.attributeValue("index"); order = rispItem.attributeValue("order"); if (index == null) { continue; } if (index.equals("0")) freeText = rispItem.getText(); if (risposta.length() > 0) risposta += ","; risposta += index + ":" + order; } } } else if (questionType.equals("multiple")) { rispList = rispostaElem.elements("item"); if (rispList != null) { risposta = ""; String index; for (Element rispItem : rispList) { index = rispItem.attributeValue("index"); if (index.equals("0")) freeText = rispItem.getText(); if (risposta.length() > 0) risposta += ","; risposta += index; } } } else if (questionType.equals("free")) { freeText = rispostaElem.element("item").getText(); risposta = ""; } } if (LOGGER.isTraceEnabled()) { LOGGER.trace("ID_QUESTION: " + id); LOGGER.trace("question type: " + questionType); LOGGER.trace("risposta: " + risposta); LOGGER.trace("freetext: " + freeText); } if (risposta.equals(C_TAG_BUG)) { LOGGER.error("Invalid answer"); LOGGER.error("T1: " + sT1); LOGGER.error("ID_QUESTION: " + id); LOGGER.error("question type: " + questionType); } stmt.setString(1, IDVotazione); stmt.setString(2, sT1); stmt.setString(3, id); stmt.setString(4, risposta); stmt.setString(5, freeText); stmt.addBatch(); } stmt.executeBatch(); stmt.close(); conn.commit(); ANSWER = C_addVote_OK; LOGGER.info("registering vote end successfully"); } catch (SQLException e) { try { conn.rollback(); } catch (Exception ex) { } if (e.getErrorCode() == 1062) { ANSWER = C_addVote_DUPLICATE; LOGGER.error("error while registering vote (duplication)"); } else { ANSWER = C_addVote_BOH; LOGGER.error("error while registering vote", e); } } catch (UnsupportedEncodingException e) { try { conn.rollback(); } catch (Exception ex) { } LOGGER.error("encoding error", e); ANSWER = C_addVote_BOH; } catch (DocumentException e) { LOGGER.error("DocumentException", e); ANSWER = C_addVote_BOH; } catch (ClassNotFoundException e) { try { conn.rollback(); } catch (Exception ex) { } LOGGER.error("error while registering vote", e); ANSWER = C_addVote_BOH; } catch (Exception e) { try { conn.rollback(); } catch (Exception ex) { } LOGGER.error("Unexpected exception while registering vote", e); ANSWER = C_addVote_BOH; } finally { try { conn.setAutoCommit(autoCommitPresent); conn.close(); } catch (Exception e) { } ; } return ANSWER; } | 18,623 |
0 | private void update() throws IOException { FileOutputStream out = new FileOutputStream(combined); try { File[] _files = listJavascript(); List<File> files = new ArrayList<File>(Arrays.asList(_files)); files.add(0, new File(jsdir.getAbsolutePath() + "/leemba.js")); files.add(0, new File(jsdir.getAbsolutePath() + "/jquery.min.js")); for (File js : files) { FileInputStream fin = null; try { int count = 0; byte buf[] = new byte[16384]; fin = new FileInputStream(js); while ((count = fin.read(buf)) > 0) out.write(buf, 0, count); } catch (Throwable t) { log.error("Failed to read file: " + js.getAbsolutePath(), t); } finally { if (fin != null) fin.close(); } } } finally { out.close(); } } | protected InputSource defaultResolveEntity(String publicId, String systemId) throws SAXException { if (systemId == null) return null; if (systemId.indexOf("file:/") >= 0) { try { final InputSource is = new InputSource(new URL(systemId).openStream()); is.setSystemId(systemId); if (D.ON && log.finerable()) log.finer("Entity found " + systemId); return is; } catch (Exception ex) { if (D.ON && log.finerable()) log.finer("Unable to open " + systemId); } } final String PREFIX = "/metainfo/xml"; final org.zkoss.util.resource.Locator loader = Locators.getDefault(); URL url = null; int j = systemId.indexOf("://"); if (j > 0) { final String resId = PREFIX + systemId.substring(j + 2); url = loader.getResource(resId); } if (url == null) { j = systemId.lastIndexOf('/'); final String resId = j >= 0 ? PREFIX + systemId.substring(j) : PREFIX + '/' + systemId; url = loader.getResource(resId); } if (url != null) { if (D.ON && log.finerable()) log.finer("Entity resovled to " + url); try { final InputSource is = new InputSource(url.openStream()); is.setSystemId(url.toExternalForm()); return is; } catch (IOException ex) { throw new SAXException(ex); } } return null; } | 18,624 |
1 | public String get(String question) { try { System.out.println(url + question); URL urlonlineserver = new URL(url + question); BufferedReader in = new BufferedReader(new InputStreamReader(urlonlineserver.openStream())); String inputLine; String returnstring = ""; while ((inputLine = in.readLine()) != null) returnstring += inputLine; in.close(); return returnstring; } catch (IOException e) { return ""; } } | public static SubstanceSkin.ColorSchemes getColorSchemes(URL url) { List<SubstanceColorScheme> schemes = new ArrayList<SubstanceColorScheme>(); BufferedReader reader = null; Color ultraLight = null; Color extraLight = null; Color light = null; Color mid = null; Color dark = null; Color ultraDark = null; Color foreground = null; String name = null; ColorSchemeKind kind = null; boolean inColorSchemeBlock = false; try { reader = new BufferedReader(new InputStreamReader(url.openStream())); while (true) { String line = reader.readLine(); if (line == null) break; line = line.trim(); if (line.length() == 0) continue; if (line.startsWith("#")) { continue; } if (line.indexOf("{") >= 0) { if (inColorSchemeBlock) { throw new IllegalArgumentException("Already in color scheme definition"); } inColorSchemeBlock = true; name = line.substring(0, line.indexOf("{")).trim(); continue; } if (line.indexOf("}") >= 0) { if (!inColorSchemeBlock) { throw new IllegalArgumentException("Not in color scheme definition"); } inColorSchemeBlock = false; if ((name == null) || (kind == null) || (ultraLight == null) || (extraLight == null) || (light == null) || (mid == null) || (dark == null) || (ultraDark == null) || (foreground == null)) { throw new IllegalArgumentException("Incomplete specification"); } Color[] colors = new Color[] { ultraLight, extraLight, light, mid, dark, ultraDark, foreground }; if (kind == ColorSchemeKind.LIGHT) { schemes.add(getLightColorScheme(name, colors)); } else { schemes.add(getDarkColorScheme(name, colors)); } name = null; kind = null; ultraLight = null; extraLight = null; light = null; mid = null; dark = null; ultraDark = null; foreground = null; continue; } String[] split = line.split("="); if (split.length != 2) { throw new IllegalArgumentException("Unsupported format in line " + line); } String key = split[0].trim(); String value = split[1].trim(); if ("kind".equals(key)) { if (kind == null) { if ("Light".equals(value)) { kind = ColorSchemeKind.LIGHT; continue; } if ("Dark".equals(value)) { kind = ColorSchemeKind.DARK; continue; } throw new IllegalArgumentException("Unsupported format in line " + line); } throw new IllegalArgumentException("'kind' should only be defined once"); } if ("colorUltraLight".equals(key)) { if (ultraLight == null) { ultraLight = Color.decode(value); continue; } throw new IllegalArgumentException("'ultraLight' should only be defined once"); } if ("colorExtraLight".equals(key)) { if (extraLight == null) { extraLight = Color.decode(value); continue; } throw new IllegalArgumentException("'extraLight' should only be defined once"); } if ("colorLight".equals(key)) { if (light == null) { light = Color.decode(value); continue; } throw new IllegalArgumentException("'light' should only be defined once"); } if ("colorMid".equals(key)) { if (mid == null) { mid = Color.decode(value); continue; } throw new IllegalArgumentException("'mid' should only be defined once"); } if ("colorDark".equals(key)) { if (dark == null) { dark = Color.decode(value); continue; } throw new IllegalArgumentException("'dark' should only be defined once"); } if ("colorUltraDark".equals(key)) { if (ultraDark == null) { ultraDark = Color.decode(value); continue; } throw new IllegalArgumentException("'ultraDark' should only be defined once"); } if ("colorForeground".equals(key)) { if (foreground == null) { foreground = Color.decode(value); continue; } throw new IllegalArgumentException("'foreground' should only be defined once"); } throw new IllegalArgumentException("Unsupported format in line " + line); } ; } catch (IOException ioe) { throw new IllegalArgumentException(ioe); } finally { if (reader != null) { try { reader.close(); } catch (IOException ioe) { } } } return new SubstanceSkin.ColorSchemes(schemes); } | 18,625 |
0 | protected static JXStatusBar getStatusBar(final JXPanel jxPanel, final JTabbedPane mainTabbedPane) { JXStatusBar statusBar = new JXStatusBar(); try { ClassLoader cl = Thread.currentThread().getContextClassLoader(); Enumeration<URL> urls = cl.getResources("META-INF/MANIFEST.MF"); String substanceVer = null; String substanceBuildStamp = null; while (urls.hasMoreElements()) { InputStream is = urls.nextElement().openStream(); BufferedReader br = new BufferedReader(new InputStreamReader(is)); while (true) { String line = br.readLine(); if (line == null) break; int firstColonIndex = line.indexOf(":"); if (firstColonIndex < 0) continue; String name = line.substring(0, firstColonIndex).trim(); String val = line.substring(firstColonIndex + 1).trim(); if (name.compareTo("Substance-Version") == 0) substanceVer = val; if (name.compareTo("Substance-BuildStamp") == 0) substanceBuildStamp = val; } try { br.close(); } catch (IOException ioe) { } } if (substanceVer != null) { JLabel statusLabel = new JLabel(substanceVer + " [built on " + substanceBuildStamp + "]"); JXStatusBar.Constraint cStatusLabel = new JXStatusBar.Constraint(); cStatusLabel.setFixedWidth(300); statusBar.add(statusLabel, cStatusLabel); } } catch (IOException ioe) { } JXStatusBar.Constraint c2 = new JXStatusBar.Constraint(JXStatusBar.Constraint.ResizeBehavior.FILL); final JLabel tabLabel = new JLabel(""); statusBar.add(tabLabel, c2); mainTabbedPane.getModel().addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent e) { int selectedIndex = mainTabbedPane.getSelectedIndex(); if (selectedIndex < 0) tabLabel.setText("No selected tab"); else tabLabel.setText("Tab " + mainTabbedPane.getTitleAt(selectedIndex) + " selected"); } }); JPanel fontSizePanel = FontSizePanel.getPanel(); JXStatusBar.Constraint fontSizePanelConstraints = new JXStatusBar.Constraint(); fontSizePanelConstraints.setFixedWidth(270); statusBar.add(fontSizePanel, fontSizePanelConstraints); JPanel alphaPanel = new JPanel(new FlowLayout(FlowLayout.LEADING, 0, 0)); final JLabel alphaLabel = new JLabel("100%"); final JSlider alphaSlider = new JSlider(0, 100, 100); alphaSlider.setFocusable(false); alphaSlider.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent e) { int currValue = alphaSlider.getValue(); alphaLabel.setText(currValue + "%"); jxPanel.setAlpha(currValue / 100.0f); } }); alphaSlider.setToolTipText("Changes the global opacity. Is not Substance-specific"); alphaSlider.setPreferredSize(new Dimension(120, alphaSlider.getPreferredSize().height)); alphaPanel.add(alphaLabel); alphaPanel.add(alphaSlider); JXStatusBar.Constraint alphaPanelConstraints = new JXStatusBar.Constraint(); alphaPanelConstraints.setFixedWidth(160); statusBar.add(alphaPanel, alphaPanelConstraints); return statusBar; } | public static void copy(String fromFileName, String toFileName) throws IOException { File fromFile = new File(fromFileName); File toFile = new File(toFileName); if (!fromFile.exists()) throw new IOException("FileCopy: " + "no such source file: " + fromFileName); if (!fromFile.isFile()) throw new IOException("FileCopy: " + "can't copy directory: " + fromFileName); if (!fromFile.canRead()) throw new IOException("FileCopy: " + "source file is unreadable: " + fromFileName); if (toFile.isDirectory()) toFile = new File(toFile, fromFile.getName()); if (toFile.exists()) { if (!toFile.canWrite()) throw new IOException("FileCopy: " + "destination file is unwriteable: " + toFileName); System.out.print("Overwrite existing file " + toFile.getName() + "? (Y/N): "); System.out.flush(); BufferedReader in = new BufferedReader(new InputStreamReader(System.in)); String response = in.readLine(); if (!response.equals("Y") && !response.equals("y")) throw new IOException("FileCopy: " + "existing file was not overwritten."); } else { String parent = toFile.getParent(); if (parent == null) parent = System.getProperty("user.dir"); File dir = new File(parent); if (!dir.exists()) throw new IOException("FileCopy: " + "destination directory doesn't exist: " + parent); if (dir.isFile()) throw new IOException("FileCopy: " + "destination is not a directory: " + parent); if (!dir.canWrite()) throw new IOException("FileCopy: " + "destination directory is unwriteable: " + parent); } FileInputStream from = null; FileOutputStream to = null; try { from = new FileInputStream(fromFile); to = new FileOutputStream(toFile); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = from.read(buffer)) != -1) to.write(buffer, 0, bytesRead); } finally { if (from != null) try { from.close(); } catch (IOException e) { ; } if (to != null) try { to.close(); } catch (IOException e) { ; } } } | 18,626 |
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) { logger.error(Logger.SECURITY_FAILURE, "Problem encoding file to file", exc); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | public void testWriteThreadsNoCompression() throws Exception { Bootstrap bootstrap = new Bootstrap(); bootstrap.loadProfiles(CommandLineProcessorFactory.PROFILE.DB, CommandLineProcessorFactory.PROFILE.REST_CLIENT, CommandLineProcessorFactory.PROFILE.COLLECTOR); final LocalLogFileWriter writer = (LocalLogFileWriter) bootstrap.getBean(LogFileWriter.class); writer.init(); writer.setCompressionCodec(null); File fileInput = new File(baseDir, "testWriteOneFile/input"); fileInput.mkdirs(); File fileOutput = new File(baseDir, "testWriteOneFile/output"); fileOutput.mkdirs(); writer.setBaseDir(fileOutput); int fileCount = 100; int lineCount = 100; File[] inputFiles = createInput(fileInput, fileCount, lineCount); ExecutorService exec = Executors.newFixedThreadPool(fileCount); final CountDownLatch latch = new CountDownLatch(fileCount); for (int i = 0; i < fileCount; i++) { final File file = inputFiles[i]; final int count = i; exec.submit(new Callable<Boolean>() { @Override public Boolean call() throws Exception { FileStatus.FileTrackingStatus status = FileStatus.FileTrackingStatus.newBuilder().setFileDate(System.currentTimeMillis()).setDate(System.currentTimeMillis()).setAgentName("agent1").setFileName(file.getName()).setFileSize(file.length()).setLogType("type1").build(); BufferedReader reader = new BufferedReader(new FileReader(file)); try { String line = null; while ((line = reader.readLine()) != null) { writer.write(status, new ByteArrayInputStream((line + "\n").getBytes())); } } finally { IOUtils.closeQuietly(reader); } LOG.info("Thread[" + count + "] completed "); latch.countDown(); return true; } }); } latch.await(); exec.shutdown(); LOG.info("Shutdown thread service"); writer.close(); File[] outputFiles = fileOutput.listFiles(); assertNotNull(outputFiles); File testCombinedInput = new File(baseDir, "combinedInfile.txt"); testCombinedInput.createNewFile(); FileOutputStream testCombinedInputOutStream = new FileOutputStream(testCombinedInput); try { for (File file : inputFiles) { FileInputStream f1In = new FileInputStream(file); IOUtils.copy(f1In, testCombinedInputOutStream); } } finally { testCombinedInputOutStream.close(); } File testCombinedOutput = new File(baseDir, "combinedOutfile.txt"); testCombinedOutput.createNewFile(); FileOutputStream testCombinedOutOutStream = new FileOutputStream(testCombinedOutput); try { System.out.println("----------------- " + testCombinedOutput.getAbsolutePath()); for (File file : outputFiles) { FileInputStream f1In = new FileInputStream(file); IOUtils.copy(f1In, testCombinedOutOutStream); } } finally { testCombinedOutOutStream.close(); } FileUtils.contentEquals(testCombinedInput, testCombinedOutput); } | 18,627 |
1 | private static void readIzvestiyaArticles() throws IOException { CsvReader reader = new CsvReader(new InputStreamReader(IzvestiyaUtil.class.getClassLoader().getResourceAsStream("mathnet_izvestiya.csv")), ';'); reader.setTrimWhitespace(true); try { while (reader.readRecord()) { String id = reader.get(0); String filename = reader.get(1); StringTokenizer st = new StringTokenizer(filename, "-."); String name = st.nextToken(); String volume = st.nextToken(); String year = st.nextToken(); String extension = st.nextToken(); String filepath = String.format("%s/%s/%s-%s.%s", year, volume.length() == 1 ? "0" + volume : volume, name, volume, extension); id2filename.put(id, filepath); } } finally { reader.close(); } for (Map.Entry<String, String> entry : id2filename.entrySet()) { String filepath = String.format("%s/%s", INPUT_DIR, entry.getValue()); filepath = new File(filepath).exists() ? filepath : filepath.replace(".tex", ".TEX"); if (new File(filepath).exists()) { InputStream in = new FileInputStream(filepath); FileOutputStream out = new FileOutputStream(String.format("%s/%s.tex", OUTPUT_DIR, entry.getKey()), false); try { org.apache.commons.io.IOUtils.copy(in, out); } catch (Exception e) { org.apache.commons.io.IOUtils.closeQuietly(in); org.apache.commons.io.IOUtils.closeQuietly(out); } } else { logger.log(Level.INFO, "File with the path=" + filepath + " doesn't exist"); } } } | public Bitmap getImage() throws IOException { int recordBegin = 78 + 8 * mCount; Bitmap result = null; FileChannel channel = new FileInputStream(mFile).getChannel(); channel.position(mRecodeOffset[mPage]); ByteBuffer bodyBuffer; if (mPage + 1 < mCount) { int length = mRecodeOffset[mPage + 1] - mRecodeOffset[mPage]; bodyBuffer = channel.map(MapMode.READ_ONLY, mRecodeOffset[mPage], length); byte[] tmpCache = new byte[bodyBuffer.capacity()]; bodyBuffer.get(tmpCache); FileOutputStream o = new FileOutputStream("/sdcard/test.bmp"); o.write(tmpCache); o.flush(); o.getFD().sync(); o.close(); result = BitmapFactory.decodeByteArray(tmpCache, 0, length); } else { } channel.close(); return result; } | 18,628 |
1 | private void copyFile(File source, File target) throws IOException { FileChannel srcChannel = new FileInputStream(source).getChannel(); FileChannel dstChannel = new FileOutputStream(target).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } | @Override public void render(Output output) throws IOException { output.setStatus(headersFile.getStatusCode(), headersFile.getStatusMessage()); for (Entry<String, Set<String>> header : headersFile.getHeadersMap().entrySet()) { Set<String> values = header.getValue(); for (String value : values) { output.addHeader(header.getKey(), value); } } if (file != null) { InputStream inputStream = new FileInputStream(file); try { output.open(); OutputStream out = output.getOutputStream(); IOUtils.copy(inputStream, out); } finally { inputStream.close(); output.close(); } } } | 18,629 |
1 | public static void copyFile(File source, File dest) throws IOException { if (source.equals(dest)) return; FileChannel srcChannel = new FileInputStream(source).getChannel(); FileChannel dstChannel = new FileOutputStream(dest).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } | private File writeResourceToFile(String resource) throws IOException { File tmp = File.createTempFile("zfppt" + resource, null); InputStream res = Thread.currentThread().getContextClassLoader().getResourceAsStream(resource); OutputStream out = new FileOutputStream(tmp); IOUtils.copy(res, out); out.close(); return tmp; } | 18,630 |
0 | static void conditionalCopyFile(File dst, File src) throws IOException { if (dst.equals(src)) return; if (!dst.isFile() || dst.lastModified() < src.lastModified()) { System.out.println("Copying " + src); InputStream is = new FileInputStream(src); OutputStream os = new FileOutputStream(dst); byte[] buf = new byte[8192]; int len; while ((len = is.read(buf)) > 0) os.write(buf, 0, len); os.close(); is.close(); } } | public String md5(String string) throws GeneralSecurityException { MessageDigest algorithm = MessageDigest.getInstance("MD5"); algorithm.reset(); algorithm.update(string.getBytes()); byte messageDigest[] = algorithm.digest(); StringBuffer hexString = new StringBuffer(); for (int i = 0; i < messageDigest.length; i++) { hexString.append(Integer.toHexString(0xFF & messageDigest[i])); } return hexString.toString(); } | 18,631 |
0 | private MimeTypes() { try { final URL url = RES.getURL("types"); final InputStream is = url.openStream(); final BufferedReader br = new BufferedReader(new InputStreamReader(is)); String line = br.readLine(); while (line != null) { line = line.trim(); final int p = line.indexOf('#'); if (p >= 0) { line = line.substring(0, p).trim(); } if (line.length() > 0) { final StringTokenizer st = new StringTokenizer(line, " \t"); if (st.countTokens() > 1) { final String mime = st.nextToken(); while (st.hasMoreTokens()) { extnMap.put(st.nextToken(), mime); } } } line = br.readLine(); } br.close(); } catch (IOException e) { e.printStackTrace(); } canParse.add(TEXT_HTML); canParse.add(TEXT_CSS); } | @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); } } | 18,632 |
0 | public static void copyFile(final File sourceFile, final File destFile) throws IOException { if (destFile.getParentFile() != null && !destFile.getParentFile().mkdirs()) { LOG.error("GeneralHelper.copyFile(): Cannot create parent directories from " + destFile); } FileInputStream fIn = null; FileOutputStream fOut = null; FileChannel source = null; FileChannel destination = null; try { fIn = new FileInputStream(sourceFile); source = fIn.getChannel(); fOut = new FileOutputStream(destFile); destination = fOut.getChannel(); long transfered = 0; final long bytes = source.size(); while (transfered < bytes) { transfered += destination.transferFrom(source, 0, source.size()); destination.position(transfered); } } finally { if (source != null) { source.close(); } else if (fIn != null) { fIn.close(); } if (destination != null) { destination.close(); } else if (fOut != null) { fOut.close(); } } } | public void run() { try { if (LOGGER.isDebugEnabled()) { LOGGER.debug("Checking for updates at " + checkUrl); } URL url = new URL(checkUrl); HttpURLConnection connection = (HttpURLConnection) url.openConnection(); connection.connect(); if (connection.getResponseCode() == HttpURLConnection.HTTP_OK) { BufferedReader reader = new BufferedReader(new InputStreamReader(connection.getInputStream())); StringBuffer content = new StringBuffer(); String s = reader.readLine(); while (s != null) { content.append(s); s = reader.readLine(); } LOGGER.info("update-available", content.toString()); } else if (LOGGER.isDebugEnabled()) { LOGGER.debug("No update available (Response code " + connection.getResponseCode() + ")"); } } catch (Throwable e) { if (LOGGER.isDebugEnabled()) { LOGGER.debug("Update check failed", e); } } } | 18,633 |
1 | private String createCSVFile(String fileName) throws FileNotFoundException, IOException { String csvFile = fileName + ".csv"; BufferedReader buf = new BufferedReader(new FileReader(fileName)); BufferedWriter out = new BufferedWriter(new FileWriter(csvFile)); String line; while ((line = buf.readLine()) != null) out.write(line + "\n"); buf.close(); out.close(); return csvFile; } | 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(); } } | 18,634 |
1 | public static String md5(String word) { MessageDigest alg = null; try { alg = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException ex) { Logger.getLogger(ServletUtils.class.getName()).log(Level.SEVERE, null, ex); } alg.reset(); alg.update(word.getBytes()); byte[] digest = alg.digest(); StringBuilder hashedWord = new StringBuilder(); String hx; for (int i = 0; i < digest.length; i++) { hx = Integer.toHexString(0xFF & digest[i]); if (hx.length() == 1) { hx = "0" + hx; } hashedWord.append(hx); } return hashedWord.toString(); } | public RespID(PublicKey key) throws OCSPException { try { MessageDigest digest = MessageDigest.getInstance("SHA1"); ASN1InputStream aIn = new ASN1InputStream(key.getEncoded()); SubjectPublicKeyInfo info = SubjectPublicKeyInfo.getInstance(aIn.readObject()); digest.update(info.getPublicKeyData().getBytes()); ASN1OctetString keyHash = new DEROctetString(digest.digest()); this.id = new ResponderID(keyHash); } catch (Exception e) { throw new OCSPException("problem creating ID: " + e, e); } } | 18,635 |
1 | private void getRandomGUID(boolean secure) { MessageDigest md5 = null; StringBuffer sbValueBeforeMD5 = new StringBuffer(); try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { System.out.println("Error: " + e); } try { long time = System.currentTimeMillis(); long rand = 0; if (secure) { rand = mySecureRand.nextLong(); } else { rand = myRand.nextLong(); } sbValueBeforeMD5.append(s_id); sbValueBeforeMD5.append(":"); sbValueBeforeMD5.append(Long.toString(time)); sbValueBeforeMD5.append(":"); sbValueBeforeMD5.append(Long.toString(rand)); valueBeforeMD5 = sbValueBeforeMD5.toString(); md5.update(valueBeforeMD5.getBytes()); byte[] array = md5.digest(); StringBuffer sb = new StringBuffer(); for (int j = 0; j < array.length; ++j) { int b = array[j] & 0xFF; if (b < 0x10) sb.append('0'); sb.append(Integer.toHexString(b)); } valueAfterMD5 = sb.toString(); } catch (Exception e) { System.out.println("Error:" + e); } } | public static String md5(String value) throws NoSuchAlgorithmException { MessageDigest messageDigest = MessageDigest.getInstance("MD5"); try { messageDigest.update(value.getBytes("UTF-8")); } catch (UnsupportedEncodingException e) { messageDigest.update(value.getBytes()); } byte[] bytes = messageDigest.digest(); return byteArrayToHexString(bytes); } | 18,636 |
0 | private void inject(int x, int y) throws IOException { Tag source = data.getTag(); Log.event(Log.DEBUG_INFO, "source: " + source.getString()); if (source == Tag.ORGANISM) { String seed = data.readString(); data.readTag(Tag.STREAM); injectCodeTape(data.getIn(), seed, x, y); } else if (source == Tag.URL) { String url = data.readString(); String seed = url.substring(url.lastIndexOf('.') + 1); BufferedReader urlIn = null; try { urlIn = new BufferedReader(new InputStreamReader(new URL(url).openStream())); injectCodeTape(urlIn, seed, x, y); } finally { if (urlIn != null) urlIn.close(); } } else data.writeString("unknown organism source: " + source.getString()); } | public static boolean isODF(URL url) throws IOException { InputStream resStream = ODFUtil.findDataInputStream(url.openStream(), ODFUtil.MIMETYPE_FILE); if (null == resStream) { LOG.debug("mimetype stream not found in ODF package"); return false; } String mimetypeContent = IOUtils.toString(resStream); return mimetypeContent.startsWith(ODFUtil.MIMETYPE_START); } | 18,637 |
1 | public void extractImage(String input, OutputStream os, DjatokaDecodeParam params, IWriter w) throws DjatokaException { File in = null; if (input.equals(STDIN)) { try { in = File.createTempFile("tmp", ".jp2"); input = in.getAbsolutePath(); in.deleteOnExit(); IOUtils.copyFile(new File(STDIN), in); } catch (IOException e) { logger.error("Unable to process image from " + STDIN + ": " + e.getMessage()); throw new DjatokaException(e); } } BufferedImage bi = extractImpl.process(input, params); if (bi != null) { if (params.getScalingFactor() != 1.0 || params.getScalingDimensions() != null) bi = applyScaling(bi, params); if (params.getTransform() != null) bi = params.getTransform().run(bi); w.write(bi, os); } if (in != null) in.delete(); } | public boolean backupLastAuditSchema(File lastAuditSchema) { boolean isBkupFileOK = false; String writeTimestamp = DateFormatUtils.format(new java.util.Date(), configFile.getTimestampPattern()); File target = new File(configFile.getAuditSchemaFileDir() + File.separator + configFile.getAuditSchemaFileName() + ".bkup_" + writeTimestamp); FileChannel sourceChannel = null; FileChannel targetChannel = null; try { sourceChannel = new FileInputStream(lastAuditSchema).getChannel(); targetChannel = new FileOutputStream(target).getChannel(); targetChannel.transferFrom(sourceChannel, 0, sourceChannel.size()); } catch (IOException e) { logger.log(Level.SEVERE, "IO exception occurred while copying file", e); } finally { if ((target != null) && (target.exists()) && (target.length() > 0)) { isBkupFileOK = true; } try { if (sourceChannel != null) { sourceChannel.close(); } if (targetChannel != null) { targetChannel.close(); } } catch (IOException e) { logger.info("closing channels failed"); } } return isBkupFileOK; } | 18,638 |
0 | public Dbf(URL url) throws java.io.IOException, DbfFileException { if (DEBUG) System.out.println("---->uk.ac.leeds.ccg.dbffile.Dbf constructed. Will identify itself as " + DBC); URLConnection uc = url.openConnection(); InputStream in = uc.getInputStream(); EndianDataInputStream sfile = new EndianDataInputStream(in); init(sfile); } | public static void main(String args[]) { int i, j, l; short NUMNUMBERS = 256; short numbers[] = new short[NUMNUMBERS]; Darjeeling.print("START"); for (l = 0; l < 100; l++) { for (i = 0; i < NUMNUMBERS; i++) numbers[i] = (short) (NUMNUMBERS - 1 - i); for (i = 0; i < NUMNUMBERS; i++) { for (j = 0; j < NUMNUMBERS - i - 1; j++) if (numbers[j] > numbers[j + 1]) { short temp = numbers[j]; numbers[j] = numbers[j + 1]; numbers[j + 1] = temp; } } } Darjeeling.print("END"); } | 18,639 |
0 | protected InputStream acquireInputStream(String filename) throws IOException { Validate.notEmpty(filename); File f = new File(filename); if (f.exists()) { this.originalFilename = f.getName(); return new FileInputStream(f); } URL url = getClass().getClassLoader().getResource(filename); if (url == null) { if (!filename.startsWith("/")) { url = getClass().getClassLoader().getResource("/" + filename); if (url == null) { throw new IllegalArgumentException("File [" + filename + "] not found in classpath via " + getClass().getClassLoader().getClass()); } } } this.originalFilename = filename; return url.openStream(); } | private String getMD5(String data) { try { MessageDigest md5Algorithm = MessageDigest.getInstance("MD5"); md5Algorithm.update(data.getBytes(), 0, data.length()); byte[] digest = md5Algorithm.digest(); StringBuffer hexString = new StringBuffer(); String hexDigit = null; for (int i = 0; i < digest.length; i++) { hexDigit = Integer.toHexString(0xFF & digest[i]); if (hexDigit.length() < 2) { hexDigit = "0" + hexDigit; } hexString.append(hexDigit); } return hexString.toString(); } catch (NoSuchAlgorithmException ne) { return data; } } | 18,640 |
1 | public static synchronized String toMD5(String str) { Nulls.failIfNull(str, "Cannot create an MD5 encryption form a NULL string"); String hashword = null; try { MessageDigest md5 = MessageDigest.getInstance(MD5); md5.update(str.getBytes()); BigInteger hash = new BigInteger(1, md5.digest()); hashword = hash.toString(16); return Strings.padLeft(hashword, 32, "0"); } catch (NoSuchAlgorithmException ex) { ex.printStackTrace(); } return hashword; } | public void insertQuotation(final String sText, final Source aSource) throws ConfigHandlerError, com.sun.star.uno.Exception { final XTextDocument xTextDocument = (XTextDocument) this.docController.getXInterface(XTextDocument.class, this.docController.getXFrame().getController().getModel()); final XMultiServiceFactory xMultiServiceFactory = (XMultiServiceFactory) this.docController.getXInterface(XMultiServiceFactory.class, xTextDocument); final XText xText = xTextDocument.getText(); final XTextViewCursor xTextViewCursor = ((XTextViewCursorSupplier) this.docController.getXInterface(XTextViewCursorSupplier.class, this.docController.getXFrame().getController())).getViewCursor(); final XTextRange xTextRange = xTextViewCursor.getStart(); if (aSource.getSourceType() == SourceType.QUOTE || aSource.getSourceType() == SourceType.WEBQUOTE || aSource.getSourceType() == SourceType.WEBQUOTE) { final XPropertySet xQuoteProps = (XPropertySet) this.docController.getXInterface(XPropertySet.class, xTextViewCursor); if (this.docController.getTemplateController().isIndentation()) { xText.insertControlCharacter(xTextViewCursor, ControlCharacter.PARAGRAPH_BREAK, false); xQuoteProps.setPropertyValue("ParaStyleName", new String("Quotations")); } xQuoteProps.setPropertyValue("CharStyleName", new String("Citation")); final Object aBookmark = xMultiServiceFactory.createInstance("com.sun.star.text.Bookmark"); this.sourceUtils.setNameToObject(aBookmark, this.docController.getLanguageController().__("Quote: ") + aSource.getShortinfo()); final XTextContent xTextContent = (XTextContent) this.docController.getXInterface(XTextContent.class, aBookmark); xText.insertTextContent(xTextRange, xTextContent, false); this.sourceUtils.insertBibliographyEntry(xMultiServiceFactory, xTextRange, aSource, sText); if (this.docController.getTemplateController().isIndentation()) { xText.insertControlCharacter(xTextViewCursor, ControlCharacter.PARAGRAPH_BREAK, false); xQuoteProps.setPropertyValue("ParaStyleName", new String(this.docController.getLanguageController().__("Default"))); } xQuoteProps.setPropertyValue("CharStyleName", new String(this.docController.getLanguageController().__("Default"))); } else if (aSource.getSourceType() == SourceType.IMAGE || aSource.getSourceType() == SourceType.TABLE) { xText.insertControlCharacter(xTextRange, ControlCharacter.PARAGRAPH_BREAK, false); final XTextFrame xFrame = this.sourceUtils.getTextFrame(aSource.getShortinfo(), xMultiServiceFactory); xText.insertTextContent(xTextRange, xFrame, false); final XText xFrameText = xFrame.getText(); final XTextCursor xFrameCursor = xFrameText.createTextCursor(); final Size aNewSize = new Size(); XPropertySet xBaseFrameProps = null; final Size aPageTextAreaSize = this.sourceUtils.getPageTextAreaSize(xTextDocument, xTextViewCursor); if (aSource.getSourceType() == SourceType.IMAGE) { try { this.sourceUtils.setNameToObject(xFrame, this.docController.getLanguageController().__("Caption illustration: ") + aSource.getShortinfo()); final XNameContainer xBitmapContainer = (XNameContainer) this.docController.getXInterface(XNameContainer.class, xMultiServiceFactory.createInstance("com.sun.star.drawing.BitmapTable")); final XTextContent xImage = (XTextContent) this.docController.getXInterface(XTextContent.class, xMultiServiceFactory.createInstance("com.sun.star.text.TextGraphicObject")); this.sourceUtils.setNameToObject(xImage, this.docController.getLanguageController().__("Illustration: ") + aSource.getShortinfo()); final String graphicURL = this.docController.getPathUtils().getFileURLFromSystemPath(((Image) aSource).getFile().getPath(), ((Image) aSource).getFile().getPath()); xBaseFrameProps = (XPropertySet) this.docController.getXInterface(XPropertySet.class, xImage); xBaseFrameProps.setPropertyValue("AnchorType", com.sun.star.text.TextContentAnchorType.AT_PARAGRAPH); xBaseFrameProps.setPropertyValue("GraphicURL", graphicURL); final MessageDigest md = MessageDigest.getInstance("MD5"); md.update(graphicURL.getBytes(), 0, graphicURL.length()); final String internalName = new BigInteger(1, md.digest()).toString(16); xBitmapContainer.insertByName(internalName, graphicURL); final String internalURL = (String) (xBitmapContainer.getByName(internalName)); xBaseFrameProps.setPropertyValue("GraphicURL", internalURL); float imageRatio = (float) this.sourceUtils.getImageSize(((Image) aSource).getFile()).Height / (float) this.sourceUtils.getImageSize(((Image) aSource).getFile()).Width; final Size aUsedAreaSize = new Size(this.sourceUtils.getImageSize(((Image) aSource).getFile()).Width * 26, this.sourceUtils.getImageSize(((Image) aSource).getFile()).Height * 26); if (aUsedAreaSize.Width >= aPageTextAreaSize.Width) { aNewSize.Width = aPageTextAreaSize.Width; aNewSize.Height = (int) (aPageTextAreaSize.Width * imageRatio); } else { aNewSize.Width = aUsedAreaSize.Width; aNewSize.Height = aUsedAreaSize.Height; } xFrameText.insertTextContent(xFrameCursor, xImage, false); xBitmapContainer.removeByName(internalName); } catch (final NoSuchAlgorithmException e) { new ASTError(e).severe(); } this.sourceUtils.insertCaption(xFrame, aSource, this.docController.getLanguageController().__("Illustration"), xMultiServiceFactory); } else if (aSource.getSourceType() == SourceType.TABLE) { this.sourceUtils.setNameToObject(xFrame, this.docController.getLanguageController().__("Caption table: ") + aSource.getShortinfo()); xBaseFrameProps = this.sourceUtils.createTextEmbeddedObjectCalc(xMultiServiceFactory); this.sourceUtils.setNameToObject(xBaseFrameProps, this.docController.getLanguageController().__("Table: ") + aSource.getShortinfo()); xFrameText.insertTextContent(xFrameCursor, (XTextContent) this.docController.getXInterface(XTextContent.class, xBaseFrameProps), false); final XEmbeddedObjectSupplier2 xEmbeddedObjectSupplier = (XEmbeddedObjectSupplier2) this.docController.getXInterface(XEmbeddedObjectSupplier2.class, xBaseFrameProps); final XEmbeddedObject xEmbeddedObject = xEmbeddedObjectSupplier.getExtendedControlOverEmbeddedObject(); long nAspect = xEmbeddedObjectSupplier.getAspect(); final Size aVisualAreaSize = xEmbeddedObject.getVisualAreaSize(nAspect); final XComponent xComponent = xEmbeddedObjectSupplier.getEmbeddedObject(); XSpreadsheets xSpreadsheets = ((XSpreadsheetDocument) this.docController.getXInterface(XSpreadsheetDocument.class, xComponent)).getSheets(); final XIndexAccess xIndexAccess = (XIndexAccess) this.docController.getXInterface(XIndexAccess.class, xSpreadsheets); final XSpreadsheet xSpreadsheet = (XSpreadsheet) this.docController.getXInterface(XSpreadsheet.class, xIndexAccess.getByIndex(0)); final XSheetLinkable xSheetLinkable = (XSheetLinkable) this.docController.getXInterface(XSheetLinkable.class, xSpreadsheet); xSheetLinkable.link(this.docController.getPathUtils().getFileURLFromSystemPath(((Table) aSource).getFile().getPath(), ((Table) aSource).getFile().getPath()), "", "", "", com.sun.star.sheet.SheetLinkMode.NORMAL); final CellRangeAddress aUsedArea = this.sourceUtils.getUsedArea(xSpreadsheet); final Size aUsedAreaSize = this.sourceUtils.calcCellRangeSize(xSpreadsheets, aUsedArea); if ((aUsedAreaSize.Width != aVisualAreaSize.Width) || (aUsedAreaSize.Height != aVisualAreaSize.Height)) { aNewSize.Height = (aUsedAreaSize.Height > aPageTextAreaSize.Height) ? aPageTextAreaSize.Height : aUsedAreaSize.Height; aNewSize.Width = (aUsedAreaSize.Width > aPageTextAreaSize.Width) ? aPageTextAreaSize.Width : aUsedAreaSize.Width; xEmbeddedObject.setVisualAreaSize(nAspect, aNewSize); } this.sourceUtils.insertCaption(xFrame, aSource, this.docController.getLanguageController().__("Table"), xMultiServiceFactory); } xBaseFrameProps.setPropertyValue("Width", aNewSize.Width); xBaseFrameProps.setPropertyValue("Height", aNewSize.Height); final XShape xShape = (XShape) this.docController.getXInterface(XShape.class, xFrame); xShape.setSize(aNewSize); } final XTextFieldsSupplier xTextFieldsSupplier = (XTextFieldsSupplier) this.docController.getXInterface(XTextFieldsSupplier.class, xMultiServiceFactory); final XRefreshable xRefreshable = (XRefreshable) this.docController.getXInterface(XRefreshable.class, xTextFieldsSupplier.getTextFields()); xRefreshable.refresh(); } | 18,641 |
0 | @Override public void login() { loginsuccessful = false; try { HttpParams params = new BasicHttpParams(); params.setParameter("http.useragent", "Mozilla/5.0 (Windows; U; Windows NT 6.1; en-GB; rv:1.9.2) Gecko/20100115 Firefox/3.6"); DefaultHttpClient httpclient = new DefaultHttpClient(params); NULogger.getLogger().info("Trying to log in to HotFile"); HttpPost httppost = new HttpPost("http://www.hotfile.com/login.php"); httppost.setHeader("Referer", "http://www.hotfile.com/"); httppost.setHeader("Cache-Control", "max-age=0"); httppost.setHeader("Origin", "http://www.hotfile.com/"); httppost.setHeader("Accept", "application/xml,application/xhtml+xml,text/html;q=0.9,text/plain;q=0.8,image/png,*/*;q=0.5"); List<NameValuePair> formparams = new ArrayList<NameValuePair>(); formparams.add(new BasicNameValuePair("returnto", "%2F")); formparams.add(new BasicNameValuePair("user", getUsername())); formparams.add(new BasicNameValuePair("pass", getPassword())); UrlEncodedFormEntity entity = new UrlEncodedFormEntity(formparams, "UTF-8"); httppost.setEntity(entity); HttpResponse httpresponse = httpclient.execute(httppost); if (httpresponse.getFirstHeader("Set-Cookie") == null) { NULogger.getLogger().info("HotFile Login not successful"); loginsuccessful = false; username = ""; password = ""; JOptionPane.showMessageDialog(NeembuuUploader.getInstance(), "<html><b>" + HOSTNAME + "</b> " + TranslationProvider.get("neembuuuploader.accounts.loginerror") + "</html>", HOSTNAME, JOptionPane.WARNING_MESSAGE); AccountsManager.getInstance().setVisible(true); } else { Iterator<Cookie> it = httpclient.getCookieStore().getCookies().iterator(); while (it.hasNext()) { hfcookie = it.next(); if (hfcookie.getName().equals("auth")) { NULogger.getLogger().log(Level.INFO, "hotfile login successful auth:{0}", hfcookie.getValue()); loginsuccessful = true; HostsPanel.getInstance().hotFileCheckBox.setEnabled(true); username = getUsername(); password = getPassword(); break; } } } } catch (Exception ex) { NULogger.getLogger().log(Level.SEVERE, "{0}: Error in Hotfile Login", getClass().getName()); } } | public static final String getContent(String address) { String content = ""; OutputStream out = null; URLConnection conn = null; InputStream in = null; try { URL url = new URL(address); out = new ByteArrayOutputStream(); conn = url.openConnection(); in = conn.getInputStream(); byte[] buffer = new byte[1024]; int numRead; while ((numRead = in.read(buffer)) != -1) { out.write(buffer, 0, numRead); } content = out.toString(); } catch (Exception exception) { exception.printStackTrace(); } finally { try { if (in != null) { in.close(); } if (out != null) { out.close(); } } catch (IOException ioe) { } } return content; } | 18,642 |
0 | private void prepareJobFile(ZipEntryRef zer, String nodeDir, String reportDir, Set<ZipEntryRef> statusZers) throws Exception { String jobDir = nodeDir + File.separator + "job_" + zer.getUri(); if (!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.JOB, zer.getName(), fcopyName)); } | void sortIds(int a[]) { ExecutionTimer t = new ExecutionTimer(); t.start(); for (int i = a.length; --i >= 0; ) { for (int j = 0; j < i; j++) { if (a[j] > a[j + 1]) { int T = a[j]; a[j] = a[j + 1]; a[j + 1] = T; } } } t.end(); TimerRecordFile timerFile = new TimerRecordFile("sort", "BufferSorting", "sortIds", t.duration()); } | 18,643 |
0 | public static String MD5(String text) throws ProducteevSignatureException { try { MessageDigest md; md = MessageDigest.getInstance(ALGORITHM); byte[] md5hash; md.update(text.getBytes("utf-8"), 0, text.length()); md5hash = md.digest(); return convertToHex(md5hash); } catch (NoSuchAlgorithmException nsae) { throw new ProducteevSignatureException("No such algorithm : " + ALGORITHM, nsae); } catch (UnsupportedEncodingException e) { throw new ProducteevSignatureException("No such algorithm : " + ALGORITHM, e); } } | private String getPage(String urlString) throws Exception { if (pageBuffer.containsKey(urlString)) return pageBuffer.get(urlString); URL url = new URL(urlString); HttpURLConnection connection = (HttpURLConnection) url.openConnection(); connection.connect(); BufferedReader in = null; StringBuilder page = new StringBuilder(); try { in = new BufferedReader(new InputStreamReader(connection.getInputStream())); String line; while ((line = in.readLine()) != null) { page.append(line); page.append("\n"); } } catch (IOException ioe) { logger.warn("Failed to read web page"); } finally { if (in != null) { in.close(); } } return page.toString(); } | 18,644 |
1 | public static void Sample2(String myField, String condition1, String condition2) throws SQLException { Connection connection = DriverManager.getConnection("jdbc:postgresql://localhost/test", "user", "password"); connection.setAutoCommit(false); Statement st = connection.createStatement(); String sql = "UPDATE myTable SET myField = '" + myField + "' WHERE myOtherField1 = '" + condition1 + "' AND myOtherField2 = '" + condition2 + "'"; int numChanged = st.executeUpdate(sql); // If more than 10 entries change, panic and rollback if(numChanged > 10) { connection.rollback(); } else { connection.commit(); } st.close(); connection.close(); } | public void add(Site site) throws Exception { DBOperation dbo = null; Connection connection = null; PreparedStatement preparedStatement = null; ResultSet resultSet = null; try { String sqlStr = "insert into t_ip_site (id,name,description,ascii_name,site_path,remark_number,increment_index,use_status,appserver_id) VALUES(?,?,?,?,?,?,?,?,?)"; dbo = createDBOperation(); connection = dbo.getConnection(); connection.setAutoCommit(false); preparedStatement = connection.prepareStatement(sqlStr); preparedStatement.setInt(1, site.getSiteID()); preparedStatement.setString(2, site.getName()); preparedStatement.setString(3, site.getDescription()); preparedStatement.setString(4, site.getAsciiName()); preparedStatement.setString(5, site.getPath()); preparedStatement.setInt(6, site.getRemarkNumber()); preparedStatement.setString(7, site.getIncrementIndex().trim()); preparedStatement.setString(8, String.valueOf(site.getUseStatus())); preparedStatement.setString(9, String.valueOf(site.getAppserverID())); preparedStatement.executeUpdate(); String[] path = new String[1]; path[0] = site.getPath(); selfDefineAdd(path, site, connection, preparedStatement); connection.commit(); int resID = site.getSiteID() + Const.SITE_TYPE_RES; String resName = site.getName(); int resTypeID = Const.RES_TYPE_ID; int operateTypeID = Const.OPERATE_TYPE_ID; String remark = ""; AuthorityManager am = new AuthorityManager(); am.createExtResource(Integer.toString(resID), resName, resTypeID, operateTypeID, remark); site.wirteFile(); } catch (SQLException ex) { connection.rollback(); log.error("����վ��ʧ��!", ex); throw ex; } finally { close(resultSet, null, preparedStatement, connection, dbo); } } | 18,645 |
1 | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | public void onUpload$btnFileUpload(UploadEvent ue) { BufferedInputStream in = null; BufferedOutputStream out = null; if (ue == null) { System.out.println("unable to upload file"); return; } else { System.out.println("fileUploaded()"); } try { Media m = ue.getMedia(); System.out.println("m.getContentType(): " + m.getContentType()); System.out.println("m.getFormat(): " + m.getFormat()); try { InputStream is = m.getStreamData(); in = new BufferedInputStream(is); File baseDir = new File(UPLOAD_PATH); if (!baseDir.exists()) { baseDir.mkdirs(); } final File file = new File(UPLOAD_PATH + m.getName()); OutputStream fout = new FileOutputStream(file); out = new BufferedOutputStream(fout); IOUtils.copy(in, out); if (m.getFormat().equals("zip") || m.getFormat().equals("x-gzip")) { final String filename = m.getName(); Messagebox.show("Archive file detected. Would you like to unzip this file?", "ALA Spatial Portal", Messagebox.YES + Messagebox.NO, Messagebox.QUESTION, new EventListener() { @Override public void onEvent(Event event) throws Exception { try { int response = ((Integer) event.getData()).intValue(); if (response == Messagebox.YES) { System.out.println("unzipping file to: " + UPLOAD_PATH); boolean success = Zipper.unzipFile(filename, new FileInputStream(file), UPLOAD_PATH, false); if (success) { Messagebox.show("File unzipped: '" + filename + "'"); } else { Messagebox.show("Unable to unzip '" + filename + "' "); } } else { System.out.println("leaving archive file alone"); } } catch (NumberFormatException nfe) { System.out.println("Not a valid response"); } } }); } else { Messagebox.show("File '" + m.getName() + "' successfully uploaded"); } } catch (IOException e) { System.out.println("IO Exception while saving file: "); e.printStackTrace(System.out); } catch (Exception e) { System.out.println("General Exception: "); e.printStackTrace(System.out); } finally { try { if (out != null) { out.close(); } if (in != null) { in.close(); } } catch (IOException e) { System.out.println("IO Exception while closing stream: "); e.printStackTrace(System.out); } } } catch (Exception e) { System.out.println("Error uploading file."); e.printStackTrace(System.out); } } | 18,646 |
1 | @Test public void testCopyOverSize() throws IOException { final InputStream in = new ByteArrayInputStream(TEST_DATA); final ByteArrayOutputStream out = new ByteArrayOutputStream(TEST_DATA.length); final int cpySize = ExtraIOUtils.copy(in, out, TEST_DATA.length + Long.SIZE); assertEquals("Mismatched copy size", TEST_DATA.length, cpySize); final byte[] outArray = out.toByteArray(); assertArrayEquals("Mismatched data", TEST_DATA, outArray); } | 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(); } } | 18,647 |
1 | private boolean hasPackageInfo(URL url) { if (url == null) return false; BufferedReader br = null; try { br = new BufferedReader(new InputStreamReader(url.openStream())); String line; while ((line = br.readLine()) != null) { if (line.startsWith("Specification-Title: ") || line.startsWith("Specification-Version: ") || line.startsWith("Specification-Vendor: ") || line.startsWith("Implementation-Title: ") || line.startsWith("Implementation-Version: ") || line.startsWith("Implementation-Vendor: ")) return true; } } catch (IOException ioe) { } finally { if (br != null) try { br.close(); } catch (IOException e) { } } return false; } | public static boolean reportException(Throwable ex, HashMap<String, String> suppl) { if (Activator.getDefault().getPreferenceStore().getBoolean(PreferenceConstants.P_CRASH_REPORTING)) { logger.debug("Report exception to devs..."); String data = "reportType=exception&" + "message=" + ex.getMessage(); data += "&build=" + Platform.getBundle("de.uni_mannheim.swt.codeconjurer").getHeaders().get("Bundle-Version"); int ln = 0; for (StackTraceElement el : ex.getStackTrace()) { data += "&st_line_" + ++ln + "=" + el.getClassName() + "#" + el.getMethodName() + "<" + el.getLineNumber() + ">"; } data += "&lines=" + ln; data += "&Suppl-Description=" + ex.toString(); data += "&Suppl-Server=" + Activator.getDefault().getPreferenceStore().getString(PreferenceConstants.P_SERVER); data += "&Suppl-User=" + Activator.getDefault().getPreferenceStore().getString(PreferenceConstants.P_USERNAME); if (suppl != null) { for (String key : suppl.keySet()) { data += "&Suppl-" + key + "=" + suppl.get(key); } } try { URL url = new URL("http://www.merobase.com:7777/org.code_conjurer.udc/CrashReport"); URLConnection conn = url.openConnection(); conn.setDoOutput(true); OutputStreamWriter writer = new OutputStreamWriter(conn.getOutputStream()); writer.write(data); writer.flush(); StringBuffer answer = new StringBuffer(); BufferedReader reader = new BufferedReader(new InputStreamReader(conn.getInputStream())); String line; while ((line = reader.readLine()) != null) { answer.append(line + "\r\n"); } writer.close(); reader.close(); logger.debug(answer.toString()); } catch (Exception e) { logger.debug("Could not report exception"); return false; } return true; } else { logger.debug("Reporting not wished!"); return false; } } | 18,648 |
0 | public PollSetMessage(String username, String question, String title, String[] choices) { this.username = username; MessageDigest m = null; try { m = MessageDigest.getInstance("SHA-1"); } catch (NoSuchAlgorithmException ex) { ex.printStackTrace(); } String id = username + String.valueOf(System.nanoTime()); m.update(id.getBytes(), 0, id.length()); voteId = new BigInteger(1, m.digest()).toString(16); this.question = question; this.title = title; this.choices = choices; } | public void addUrl(URL url) throws IOException, SAXException { InputStream inStream = url.openStream(); String path = url.getPath(); int slashInx = path.lastIndexOf('/'); String name = path.substring(slashInx + 1); Document doc = docBuild.parse(inStream); Element root = doc.getDocumentElement(); String rootTag = root.getTagName(); if (rootTag.equals("graphml")) { NodeList graphNodes = root.getElementsByTagName("graph"); for (int i = 0; i < graphNodes.getLength(); i++) { Element elem = (Element) graphNodes.item(i); String graphName = elem.getAttribute("id"); if (graphName == null) { graphName = name; } addStructure(new GraphSpec(graphName)); urlRefs.put(graphName, url); } } else if (rootTag.equals("tree")) { addStructure(new TreeSpec(name)); urlRefs.put(name, url); } else { throw new IllegalArgumentException("Format of " + url + " not understood."); } inStream.close(); } | 18,649 |
1 | public Parameters getParameters(HttpExchange http) throws IOException { ParametersImpl params = new ParametersImpl(); String query = null; if (http.getRequestMethod().equalsIgnoreCase("GET")) { query = http.getRequestURI().getRawQuery(); } else if (http.getRequestMethod().equalsIgnoreCase("POST")) { InputStream in = new MaxInputStream(http.getRequestBody()); if (in != null) { ByteArrayOutputStream bytes = new ByteArrayOutputStream(); IOUtils.copyTo(in, bytes); query = new String(bytes.toByteArray()); in.close(); } } else { throw new IOException("Method not supported " + http.getRequestMethod()); } if (query != null) { for (String s : query.split("[&]")) { s = s.replace('+', ' '); int eq = s.indexOf('='); if (eq > 0) { params.add(URLDecoder.decode(s.substring(0, eq), "UTF-8"), URLDecoder.decode(s.substring(eq + 1), "UTF-8")); } } } return params; } | public static int copy(File src, int amount, File dst) { final int BUFFER_SIZE = 1024; int amountToRead = amount; InputStream in = null; OutputStream out = null; try { in = new BufferedInputStream(new FileInputStream(src)); out = new BufferedOutputStream(new FileOutputStream(dst)); byte[] buf = new byte[BUFFER_SIZE]; while (amountToRead > 0) { int read = in.read(buf, 0, Math.min(BUFFER_SIZE, amountToRead)); if (read == -1) break; amountToRead -= read; out.write(buf, 0, read); } } catch (IOException e) { } finally { if (in != null) try { in.close(); } catch (IOException e) { } if (out != null) { try { out.flush(); } catch (IOException e) { } try { out.close(); } catch (IOException e) { } } } return amount - amountToRead; } | 18,650 |
0 | public String contentType() { if (_contentType != null) { return (String) _contentType; } String uti = null; URL url = url(); LOG.info("OKIOSIDManagedObject.contentType(): url = " + url + "\n"); if (url != null) { String contentType = null; try { contentType = url.openConnection().getContentType(); } catch (java.io.IOException e) { LOG.info("OKIOSIDManagedObject.contentType(): couldn't open URL connection!\n"); String urlString = url.getPath(); LOG.info("OKIOSIDManagedObject.contentType(): urlString = " + urlString + "\n"); if (urlString != null) { uti = UTType.preferredIdentifierForTag(UTType.FilenameExtensionTagClass, (NSPathUtilities.pathExtension(urlString)).toLowerCase(), null); } if (uti == null) { uti = UTType.Item; } return uti; } if (contentType != null) { LOG.info("OKIOSIDManagedObject.contentType(): contentType = " + contentType + "\n"); uti = UTType.preferredIdentifierForTag(UTType.MIMETypeTagClass, contentType, null); } if (uti == null) { uti = UTType.Item; } } else { uti = UTType.Item; } _contentType = uti; LOG.info("OKIOSIDManagedObject.contentType(): uti = " + uti + "\n"); return uti; } | 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(); } } | 18,651 |
0 | public void simulationEnded() { if (getParameter("ladderMatch") != null) { int[] scores = models.world.getScores(); if (models.simulator.getTick() < 100000) { for (int i = 0; i < scores.length; i++) { scores[i] = -1; } } StringBuffer args = new StringBuffer("ladder_result.php?matchid="); args.append(this.matchId); args.append("&hillid=").append(this.hillId); for (int i = 0; i < scores.length; i++) { args.append("&p").append(i).append('=').append(scores[i]); } try { URL url = new URL(getCodeBase(), args.toString()); URLConnection connection = url.openConnection(); System.err.println(((HttpURLConnection) connection).getResponseCode()); } catch (Exception e) { e.printStackTrace(); } } return; } | protected Object doExecute() throws Exception { if (args.size() == 1 && "-".equals(args.get(0))) { log.info("Printing STDIN"); cat(new BufferedReader(io.in), io); } else { for (String filename : args) { BufferedReader reader; try { URL url = new URL(filename); log.info("Printing URL: " + url); reader = new BufferedReader(new InputStreamReader(url.openStream())); } catch (MalformedURLException ignore) { File file = new File(filename); log.info("Printing file: " + file); reader = new BufferedReader(new FileReader(file)); } try { cat(reader, io); } finally { IOUtil.close(reader); } } } return SUCCESS; } | 18,652 |
0 | public void read(final URL url) throws IOException, DataFormatException { final URLConnection connection = url.openConnection(); final int fileSize = connection.getContentLength(); if (fileSize < 0) { throw new FileNotFoundException(url.getFile()); } final String mimeType = connection.getContentType(); decoder = FontRegistry.getFontProvider(mimeType); if (decoder == null) { throw new DataFormatException("Unsupported format"); } decoder.read(url); } | 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; } | 18,653 |
0 | public URL getResource(String path) throws MalformedURLException { if (!path.startsWith("/")) throw new MalformedURLException("Path '" + path + "' does not start with '/'"); URL url = new URL(myResourceBaseURL, path.substring(1)); InputStream is = null; try { is = url.openStream(); } catch (Throwable t) { url = null; } finally { if (is != null) { try { is.close(); } catch (Throwable t2) { } } } return url; } | private String getResourceAsString(final String name) throws IOException { final InputStream is = JiBXTestCase.class.getResourceAsStream(name); final ByteArrayOutputStream baos = new ByteArrayOutputStream(); IOUtils.copyAndClose(is, baos); return baos.toString(); } | 18,654 |
0 | private void announce(String trackerURL, byte[] hash, byte[] peerId, int port) { try { String strUrl = trackerURL + "?info_hash=" + URLEncoder.encode(new String(hash, Constants.BYTE_ENCODING), Constants.BYTE_ENCODING).replaceAll("\\+", "%20") + "&peer_id=" + URLEncoder.encode(new String(peerId, Constants.BYTE_ENCODING), Constants.BYTE_ENCODING).replaceAll("\\+", "%20") + "&port=" + port + "&uploaded=0&downloaded=0&left=0&numwant=50&no_peer_id=1&compact=1"; URL url = new URL(strUrl); URLConnection con = url.openConnection(); con.connect(); con.getContent(); } catch (Exception e) { e.printStackTrace(); } } | public static String encrypt(String algorithm, String[] input) { try { MessageDigest md = MessageDigest.getInstance(algorithm); md.reset(); for (int i = 0; i < input.length; i++) { if (input[i] != null) md.update(input[i].getBytes("UTF-8")); } byte[] messageDigest = md.digest(); StringBuffer hexString = new StringBuffer(); for (int i = 0; i < messageDigest.length; i++) { hexString.append(Integer.toHexString((0xf0 & messageDigest[i]) >> 4)); hexString.append(Integer.toHexString(0x0f & messageDigest[i])); } return hexString.toString(); } catch (NoSuchAlgorithmException e) { throw new RuntimeException(e); } catch (UnsupportedEncodingException e) { throw new RuntimeException(e); } catch (NullPointerException e) { return new StringBuffer().toString(); } } | 18,655 |
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; } | private void initialize() { if (!initialized) { if (context.getJavadocLinks() != null) { for (String url : context.getJavadocLinks()) { if (!url.endsWith("/")) { url += "/"; } StringWriter writer = new StringWriter(); try { IOUtils.copy(new URL(url + "package-list").openStream(), writer); } catch (Exception e) { e.printStackTrace(); continue; } StringTokenizer tokenizer2 = new StringTokenizer(writer.toString()); while (tokenizer2.hasMoreTokens()) { javadocByPackage.put(tokenizer2.nextToken(), url); } } } initialized = true; } } | 18,656 |
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."); } | public static void unzip(File sourceZipFile, File unzipDestinationDirectory, FileFilter filter) throws IOException { unzipDestinationDirectory.mkdirs(); if (!unzipDestinationDirectory.exists()) { throw new IOException("Unable to create destination directory: " + unzipDestinationDirectory); } ZipFile zipFile; zipFile = new ZipFile(sourceZipFile, ZipFile.OPEN_READ); Enumeration<? extends ZipEntry> zipFileEntries = zipFile.entries(); while (zipFileEntries.hasMoreElements()) { ZipEntry entry = (ZipEntry) zipFileEntries.nextElement(); if (!entry.isDirectory()) { String currentEntry = entry.getName(); File destFile = new File(unzipDestinationDirectory, currentEntry); if (filter == null || filter.accept(destFile)) { File destinationParent = destFile.getParentFile(); destinationParent.mkdirs(); BufferedInputStream is = new BufferedInputStream(zipFile.getInputStream(entry)); FileOutputStream fos = new FileOutputStream(destFile); IOUtils.copyLarge(is, fos); fos.flush(); IOUtils.closeQuietly(fos); } } } zipFile.close(); } | 18,657 |
1 | public static void copyFile(File sourceFile, File destinationFile) throws IOException { if (!destinationFile.exists()) { destinationFile.createNewFile(); } FileChannel source = null; FileChannel destination = null; try { source = new FileInputStream(sourceFile).getChannel(); destination = new FileOutputStream(destinationFile).getChannel(); destination.transferFrom(source, 0, source.size()); } finally { if (source != null) { source.close(); } if (destination != null) { destination.close(); } } } | private void delay(HttpServletRequest request, HttpServletResponse response, FilterChain chain) throws IOException, ServletException { String url = request.getRequestURL().toString(); if (delayed.contains(url)) { delayed.remove(url); LOGGER.info(MessageFormat.format("Loading delayed resource at url = [{0}]", url)); chain.doFilter(request, response); } else { LOGGER.info("Returning resource = [LoaderApplication.swf]"); InputStream input = null; OutputStream output = null; try { input = getClass().getResourceAsStream("LoaderApplication.swf"); output = response.getOutputStream(); delayed.add(url); response.setHeader("Cache-Control", "no-cache"); IOUtils.copy(input, output); } finally { IOUtils.closeQuietly(output); IOUtils.closeQuietly(input); } } } | 18,658 |
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 upgradeSingleFileModelToDirectory(File modelFile) throws IOException { byte[] buf = new byte[8192]; int bytesRead = 0; File backupModelFile = new File(modelFile.getPath() + ".bak"); FileInputStream oldModelIn = new FileInputStream(modelFile); FileOutputStream backupModelOut = new FileOutputStream(backupModelFile); while ((bytesRead = oldModelIn.read(buf)) >= 0) { backupModelOut.write(buf, 0, bytesRead); } backupModelOut.close(); oldModelIn.close(); buf = null; modelFile.delete(); modelFile.mkdir(); BufferedReader oldModelsBuff = new BomStrippingInputStreamReader(new FileInputStream(backupModelFile), "UTF-8"); File metaDataFile = new File(modelFile, ConstantParameters.FILENAMEOFModelMetaData); BufferedWriter metaDataBuff = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(metaDataFile), "UTF-8")); for (int i = 0; i < 8; i++) { metaDataBuff.write(oldModelsBuff.readLine()); metaDataBuff.write('\n'); } metaDataBuff.close(); int classIndex = 1; BufferedWriter modelWriter = null; String line = null; while ((line = oldModelsBuff.readLine()) != null) { if (line.startsWith("Class=") && line.contains("numTraining=") && line.contains("numPos=")) { if (modelWriter != null) { modelWriter.close(); } File nextModel = new File(modelFile, String.format(ConstantParameters.FILENAMEOFPerClassModel, Integer.valueOf(classIndex++))); modelWriter = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(nextModel), "UTF-8")); } modelWriter.write(line); modelWriter.write('\n'); } if (modelWriter != null) { modelWriter.close(); } } | 18,659 |
0 | private void doUpload(UploadKind uploadKind, WriteKind writeKind) throws Exception { int n = 512 * 1024; AtomicInteger total = new AtomicInteger(0); ServerSocket ss = startSinkServer(total); URL url = new URL("http://localhost:" + ss.getLocalPort() + "/test1"); HttpURLConnection conn = (HttpURLConnection) url.openConnection(); conn.setDoOutput(true); conn.setRequestMethod("POST"); if (uploadKind == UploadKind.CHUNKED) { conn.setChunkedStreamingMode(-1); } else { conn.setFixedLengthStreamingMode(n); } OutputStream out = conn.getOutputStream(); if (writeKind == WriteKind.BYTE_BY_BYTE) { for (int i = 0; i < n; ++i) { out.write('x'); } } else { byte[] buf = new byte[writeKind == WriteKind.SMALL_BUFFERS ? 256 : 64 * 1024]; Arrays.fill(buf, (byte) 'x'); for (int i = 0; i < n; i += buf.length) { out.write(buf, 0, Math.min(buf.length, n - i)); } } out.close(); assertTrue(conn.getResponseCode() > 0); assertEquals(uploadKind == UploadKind.CHUNKED ? -1 : n, total.get()); } | @Override public User createUser(User bean) throws SitoolsException { checkUser(); if (!User.isValid(bean)) { throw new SitoolsException("CREATE_USER_MALFORMED"); } Connection cx = null; try { cx = ds.getConnection(); cx.setAutoCommit(false); PreparedStatement st = cx.prepareStatement(jdbcStoreResource.CREATE_USER); int i = 1; st.setString(i++, bean.getIdentifier()); st.setString(i++, bean.getFirstName()); st.setString(i++, bean.getLastName()); st.setString(i++, bean.getSecret()); st.setString(i++, bean.getEmail()); st.executeUpdate(); st.close(); createProperties(bean, cx); if (!cx.getAutoCommit()) { cx.commit(); } } catch (SQLException e) { try { cx.rollback(); } catch (SQLException e1) { e1.printStackTrace(); throw new SitoolsException("CREATE_USER ROLLBACK" + e1.getMessage(), e1); } e.printStackTrace(); throw new SitoolsException("CREATE_USER " + e.getMessage(), e); } finally { closeConnection(cx); } return getUserById(bean.getIdentifier()); } | 18,660 |
1 | public Integer execute(Connection con) throws SQLException { int updateCount = 0; boolean oldAutoCommitSetting = con.getAutoCommit(); Statement stmt = null; try { con.setAutoCommit(autoCommit); stmt = con.createStatement(); int statementCount = 0; for (String statement : sql) { try { updateCount += stmt.executeUpdate(statement); statementCount++; if (statementCount % commitRate == 0 && !autoCommit) { con.commit(); } } catch (SQLException ex) { if (!failOnError) { log.log(LogLevel.WARN, "%s. Failed to execute: %s.", ex.getMessage(), sql); } else { throw translate(statement, ex); } } } if (!autoCommit) { con.commit(); } return updateCount; } catch (SQLException ex) { if (!autoCommit) { con.rollback(); } throw ex; } finally { close(stmt); con.setAutoCommit(oldAutoCommitSetting); } } | private void alterarArtista(Artista artista) throws Exception { Connection conn = null; PreparedStatement ps = null; try { conn = C3P0Pool.getConnection(); String sql = "UPDATE artista SET nome = ?,sexo = ?,email = ?,obs = ?,telefone = ? where numeroinscricao = ?"; ps = conn.prepareStatement(sql); ps.setString(1, artista.getNome()); ps.setBoolean(2, artista.isSexo()); ps.setString(3, artista.getEmail()); ps.setString(4, artista.getObs()); ps.setString(5, artista.getTelefone()); ps.setInt(6, artista.getNumeroInscricao()); ps.executeUpdate(); alterarEndereco(conn, ps, artista); delObras(conn, ps, artista.getNumeroInscricao()); sql = "insert into obra VALUES (?,?,?,?,?,?)"; ps = conn.prepareStatement(sql); for (Obra obra : artista.getListaObras()) { salvarObra(conn, ps, obra, artista.getNumeroInscricao()); } conn.commit(); } catch (Exception e) { if (conn != null) conn.rollback(); throw e; } finally { close(conn, ps); } } | 18,661 |
0 | public static String digest(String str) { StringBuffer sb = new StringBuffer(); try { MessageDigest md5 = MessageDigest.getInstance("md5"); md5.update(str.getBytes("ISO8859-1")); byte[] array = md5.digest(); for (int x = 0; x < 16; x++) { if ((array[x] & 0xff) < 0x10) sb.append("0"); sb.append(Long.toString(array[x] & 0xff, 16)); } } catch (Exception e) { System.out.println(e); } return sb.toString(); } | private void parseXMLFile() { String u = WeatherApplication.SERVER + location + ".xml"; InputStream in = null; String str = null; try { URL url = new URL(u); HttpURLConnection con = (HttpURLConnection) url.openConnection(); in = url.openStream(); ParserToolXML prt = new ParserToolXML(in); if (prt.doc == null) { System.err.println(FILE_NOT_FOUND_MSG + u); return; } NodeList ndl = prt.doc.getElementsByTagName("weather"); for (int i = 0; i < ndl.getLength(); i++) { Forecast f = new Forecast(); str = prt.searchElementValue(ndl.item(i), "date"); f.setDate(str); str = prt.searchElementValue(ndl.item(i), "daycode"); f.setDaycode(Integer.parseInt(str.trim())); str = prt.searchElementValue(ndl.item(i), "nightcode"); f.setNightcode(Integer.parseInt(str.trim())); str = prt.searchElementValue(ndl.item(i), "maxtemp"); f.setDaytemp(Integer.parseInt(str.trim())); str = prt.searchElementValue(ndl.item(i), "mintemp"); f.setNighttemp(Integer.parseInt(str.trim())); str = prt.searchElementValue(ndl.item(i), "winddirectionday"); f.setDaywinddir(str); str = prt.searchElementValue(ndl.item(i), "windspeedday"); f.setDaywindspeed(Integer.parseInt(str.trim())); str = prt.searchElementValue(ndl.item(i), "winddirectionnight"); f.setNightwinddir(str); str = prt.searchElementValue(ndl.item(i), "windspeednight"); f.setNightwindspeed(Integer.parseInt(str.trim())); forecastlist.addElement(f); } } catch (MalformedURLException e) { System.err.println(MALFORMED_URL_MSG + u); System.err.println(e.getMessage()); e.printStackTrace(); } catch (IOException e) { } catch (NumberFormatException e) { System.err.println(FILE_CORRUPT_MSG + u); System.err.println("-" + str + "-"); System.err.println(e.getMessage()); e.printStackTrace(); } finally { if (in != null) { try { in.close(); } catch (IOException e) { System.err.println(COULD_NOT_CLOSE_FILE_MSG + u); e.printStackTrace(); } } } } | 18,662 |
1 | private String md5(String... args) throws FlickrException { try { StringBuilder sb = new StringBuilder(); for (String str : args) { sb.append(str); } MessageDigest md = MessageDigest.getInstance("MD5"); md.update(sb.toString().getBytes()); byte[] bytes = md.digest(); StringBuilder result = new StringBuilder(); for (byte b : bytes) { String hx = Integer.toHexString(0xFF & b); if (hx.length() == 1) { hx = "0" + hx; } result.append(hx); } return result.toString(); } catch (Exception ex) { throw new FlickrException(ex); } } | public static String getSHA1(String data) throws NoSuchAlgorithmException { String addr; data = data.toLowerCase(Locale.getDefault()); if (data.startsWith("mailto:")) { addr = data.substring(7); } else { addr = data; } MessageDigest md = MessageDigest.getInstance("SHA"); StringBuffer sb = new StringBuffer(); md.update(addr.getBytes()); byte[] digest = md.digest(); for (int i = 0; i < digest.length; i++) { String hex = Integer.toHexString(digest[i]); if (hex.length() == 1) { hex = "0" + hex; } hex = hex.substring(hex.length() - 2); sb.append(hex); } return sb.toString(); } | 18,663 |
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 protected void doPost(final HttpServletRequest req, final HttpServletResponse resp) throws ServletException, IOException { final String url = req.getParameter("url"); if (!isAllowed(url)) { resp.setStatus(HttpServletResponse.SC_FORBIDDEN); return; } final HttpClient client = new HttpClient(); client.getParams().setVersion(HttpVersion.HTTP_1_0); final PostMethod method = new PostMethod(url); method.getParams().setVersion(HttpVersion.HTTP_1_0); method.setFollowRedirects(false); final RequestEntity entity = new InputStreamRequestEntity(req.getInputStream()); method.setRequestEntity(entity); try { final int statusCode = client.executeMethod(method); if (statusCode != -1) { InputStream is = null; ServletOutputStream os = null; try { is = method.getResponseBodyAsStream(); try { os = resp.getOutputStream(); IOUtils.copy(is, os); } finally { if (os != null) { try { os.flush(); } catch (IOException ignored) { } } } } catch (IOException ioex) { final String message = ioex.getMessage(); if (!"chunked stream ended unexpectedly".equals(message)) { throw ioex; } } finally { IOUtils.closeQuietly(is); } } } finally { method.releaseConnection(); } } | 18,664 |
1 | private static void copyImage(String srcImg, String destImg) { try { FileChannel srcChannel = new FileInputStream(srcImg).getChannel(); FileChannel dstChannel = new FileOutputStream(destImg).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (Exception e) { e.printStackTrace(); } } | public static Document convertHtmlToXml(final InputStream htmlInputStream, final String classpathXsltResource, final String encoding) { Parser p = new Parser(); javax.xml.parsers.DocumentBuilder db; try { db = javax.xml.parsers.DocumentBuilderFactory.newInstance().newDocumentBuilder(); } catch (ParserConfigurationException e) { log.error("", e); throw new RuntimeException(); } Document document = db.newDocument(); InputStream is = htmlInputStream; if (log.isDebugEnabled()) { ByteArrayOutputStream baos; baos = new ByteArrayOutputStream(); try { IOUtils.copy(is, baos); } catch (IOException e) { log.error("Fail to make input stream copy.", e); } IOUtils.closeQuietly(is); ByteArrayInputStream byteArrayInputStream; byteArrayInputStream = new ByteArrayInputStream(baos.toByteArray()); try { IOUtils.toString(new ByteArrayInputStream(baos.toByteArray()), "UTF-8"); } catch (IOException e) { log.error("", e); } IOUtils.closeQuietly(byteArrayInputStream); is = new ByteArrayInputStream(baos.toByteArray()); } try { InputSource iSource = new InputSource(is); iSource.setEncoding(encoding); Source transformerSource = new SAXSource(p, iSource); Result result = new DOMResult(document); Transformer xslTransformer = getTransformerByName(classpathXsltResource, false); try { xslTransformer.transform(transformerSource, result); } catch (TransformerException e) { throw new RuntimeException(e); } } finally { try { is.close(); } catch (Exception e) { log.warn("", e); } } return document; } | 18,665 |
1 | public static void main(String[] args) { File directory = new File(args[0]); File[] files = directory.listFiles(); try { PrintWriter writer = new PrintWriter(new BufferedWriter(new FileWriter(args[1]))); for (int i = 0; i < files.length; i++) { BufferedReader reader = new BufferedReader(new FileReader(files[i])); while (reader.ready()) writer.println(reader.readLine()); reader.close(); } writer.flush(); writer.close(); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } | public IOCacheArray(final File file, int capacity, final IIOCacheArrayObjectMaker iomaker, int chunkSize, String name) { super(capacity, null, chunkSize, name); generator = new ICacheArrayObjectMaker() { FileOutputStream outStream; FileInputStream inStream; FileChannel outChannel; FileChannel inChannel; boolean inited = false; private synchronized void init() { if (!inited) { try { outStream = new FileOutputStream(file); inStream = new FileInputStream(file); outChannel = outStream.getChannel(); inChannel = inStream.getChannel(); } catch (FileNotFoundException foe) { Logging.errorln("IOCacheArray constuctor error: Could not open file " + file + ". Exception " + foe); Logging.errorln("outStream " + outStream + " inStream " + inStream + " outchan " + outChannel + " inchannel " + inChannel); } } inited = true; } public Object make(int itemIndex, int baseIndex, Object[] data) { init(); return iomaker.read(inChannel, itemIndex, baseIndex, data); } public boolean flush(int baseIndex, Object[] data) { init(); return iomaker.write(outChannel, baseIndex, data); } public CacheArrayBlockSummary summarize(int baseIndex, Object[] data) { init(); return iomaker.summarize(baseIndex, data); } }; } | 18,666 |
1 | public static void copyFile(File src, File dest, boolean force) throws IOException, InterruptedIOException { if (dest.exists()) { if (force) { dest.delete(); } else { throw new IOException("Cannot overwrite existing file!"); } } byte[] buffer = new byte[5 * 1024 * 1024]; int read = 0; InputStream in = null; OutputStream out = null; try { in = new BufferedInputStream(new FileInputStream(src)); out = new BufferedOutputStream(new FileOutputStream(dest)); while (true) { read = in.read(buffer); if (read == -1) { break; } out.write(buffer, 0, read); } } finally { buffer = null; if (in != null) { try { in.close(); } finally { if (out != null) { out.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(); } } | 18,667 |
0 | @Override protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { if (log.isTraceEnabled()) { log.trace("doGet(requestURI=" + request.getRequestURI() + ")"); } ServletConfig sc = getServletConfig(); String uriPrefix = request.getContextPath() + "/" + request.getServletPath(); String resUri = request.getRequestURI().substring(uriPrefix.length()); if (log.isTraceEnabled()) { log.trace("Request for resource '" + resUri + "'"); } boolean allowAccess = true; String prefixesSpec = sc.getInitParameter(PARAM_ALLOWED_PREFIXES); if (null != prefixesSpec && prefixesSpec.length() > 0) { String[] prefixes = prefixesSpec.split(";"); allowAccess = false; if (log.isTraceEnabled()) { log.trace("allowedPrefixes specified; checking access"); } for (String prefix : prefixes) { if (log.isTraceEnabled()) { log.trace("Checking resource URI '" + resUri + "' against allowed prefix '" + prefix + "'"); } if (resUri.startsWith(prefix)) { if (log.isTraceEnabled()) { log.trace("Found matching prefix for resource URI '" + resUri + "': '" + prefix + "'"); } allowAccess = true; break; } } } if (!allowAccess) { if (log.isWarnEnabled()) { log.warn("Requested for resource that does not match with" + " allowed prefixes: " + resUri); } response.sendError(HttpServletResponse.SC_FORBIDDEN); return; } String resPrefix = sc.getInitParameter(PARAM_RESOURCE_PREFIX); if (null != resPrefix && resPrefix.length() > 0) { if (log.isTraceEnabled()) { log.trace("resourcePrefix specified: " + resPrefix); } if (resPrefix.endsWith("/")) { resUri = resPrefix + resUri; } else { resUri = resPrefix + "/" + resUri; } } resUri = resUri.replaceAll("\\/\\/+", "/"); if (log.isTraceEnabled()) { log.trace("Qualified (prefixed) resource URI: " + resUri); } String baseClassName = sc.getInitParameter(PARAM_BASE_CLASS); if (null == baseClassName || 0 == baseClassName.length()) { if (log.isTraceEnabled()) { log.trace("No baseClass initialization parameter specified; using default: " + ResourceLoaderServlet.class.getName()); } baseClassName = ResourceLoaderServlet.class.getName(); } else { if (log.isTraceEnabled()) { log.trace("Using baseClass: " + baseClassName); } } Class baseClass; try { baseClass = Class.forName(baseClassName); } catch (ClassNotFoundException ex) { throw new ServletException("Base class '" + baseClassName + "' not found", ex); } URL resUrl = baseClass.getResource(resUri); if (null != resUrl) { if (log.isTraceEnabled()) { log.trace("Sending resource: " + resUrl); } URLConnection urlc = resUrl.openConnection(); response.setContentType(urlc.getContentType()); response.setContentLength(urlc.getContentLength()); response.setStatus(HttpServletResponse.SC_OK); final byte[] buf = new byte[255]; int r = 0; InputStream in = new BufferedInputStream(urlc.getInputStream()); OutputStream out = new BufferedOutputStream(response.getOutputStream()); do { r = in.read(buf, 0, 255); if (r > 0) { out.write(buf, 0, r); } } while (r > 0); in.close(); out.flush(); out.close(); } else { response.sendError(HttpServletResponse.SC_NOT_FOUND, "Resource not found"); } } | public void executeQuery(Connection connection, String query) { action = null; updateCount = 0; resultsAvailable = false; metaAvailable = false; planAvailable = false; if (connection == null) { ide.setStatus("not connected"); return; } cleanUp(); try { ide.setStatus("Executing query"); stmt = connection.createStatement(); if (query.toLowerCase().startsWith("select")) { result = stmt.executeQuery(query); resultsAvailable = true; action = "select"; } else if (query.toLowerCase().startsWith("update")) { updateCount = stmt.executeUpdate(query); action = "update"; } else if (query.toLowerCase().startsWith("delete")) { updateCount = stmt.executeUpdate(query); action = "delete"; } else if (query.toLowerCase().startsWith("insert")) { updateCount = stmt.executeUpdate(query); action = "insert"; } else if (query.toLowerCase().startsWith("commit")) { connection.commit(); action = "commit"; } else if (query.toLowerCase().startsWith("rollback")) { connection.rollback(); action = "rollback"; } else if (query.toLowerCase().startsWith("create")) { updateCount = stmt.executeUpdate(query); action = "create"; } else if (query.toLowerCase().startsWith("drop")) { updateCount = stmt.executeUpdate(query); action = "drop"; } else if (query.toLowerCase().startsWith("desc ")) { String objectName = query.substring(query.indexOf(' '), query.length()); query = "select * from (" + objectName + ") where rownum < 1"; descQuery(connection, query); } else if (query.toLowerCase().startsWith("explain plan for ")) { explainQuery(connection, query); } else { result = stmt.executeQuery(query); resultsAvailable = true; action = "select"; } ide.setStatus("executed query"); } catch (Exception e) { ide.setStatus(e.getMessage()); } } | 18,668 |
1 | private File prepareFileForUpload(File source, String s3key) throws IOException { File tmp = File.createTempFile("dirsync", ".tmp"); tmp.deleteOnExit(); InputStream in = null; OutputStream out = null; try { in = new FileInputStream(source); out = new DeflaterOutputStream(new CryptOutputStream(new FileOutputStream(tmp), cipher, getDataEncryptionKey())); IOUtils.copy(in, out); in.close(); out.close(); return tmp; } finally { IOUtils.closeQuietly(in); IOUtils.closeQuietly(out); } } | 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(); } } | 18,669 |
0 | public void addScanURL(final URL url) { if (url == null) throw new NullArgumentException(); try { url.openConnection().connect(); } catch (IOException e) { e.printStackTrace(); } urlList.add(url); } | protected String getPageText(final String url) { StringBuilder b = new StringBuilder(); BufferedReader reader = null; try { reader = new BufferedReader(new InputStreamReader(new URL(url).openStream())); String line = null; while ((line = reader.readLine()) != null) { b.append(line).append('\n'); } } catch (IOException ex) { ex.printStackTrace(); } finally { if (reader != null) { try { reader.close(); } catch (IOException ex) { ex.printStackTrace(); } } } return b.toString(); } | 18,670 |
0 | private void loadImage(URL url) { ImageData imageData; Image artworkImage = null; InputStream artworkStream = null; try { artworkStream = new BufferedInputStream(url.openStream()); imageData = new ImageLoader().load(artworkStream)[0]; Image tmpImage = new Image(getDisplay(), imageData); artworkImage = ImageUtilities.scaleImageTo(tmpImage, 128, 128); tmpImage.dispose(); } catch (Exception e) { } finally { if (artworkStream != null) { try { artworkStream.close(); } catch (IOException e) { e.printStackTrace(); } } } loadImage(artworkImage, url); } | 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(); } } | 18,671 |
1 | public static void rewrite(String[] args) throws IOException, CodeCheckException { ClassWriter writer = new ClassWriter(); writer.readClass(new FileInputStream(args[0])); for (Iterator i = writer.getMethods().iterator(); i.hasNext(); ) { MethodInfo method = (MethodInfo) i.next(); CodeAttribute attribute = method.getCodeAttribute(); int origStack = attribute.getMaxStack(); System.out.print(method.getName()); attribute.codeCheck(); System.out.println(" " + origStack + " " + attribute.getMaxStack()); } BufferedOutputStream outStream = new BufferedOutputStream(new FileOutputStream(args[1])); writer.writeClass(outStream); outStream.close(); } | private static void main(String[] args) { try { File f = new File("test.txt"); if (f.exists()) { throw new IOException(f + " already exists. I don't want to overwrite it."); } StraightStreamReader in; char[] cbuf = new char[0x1000]; int read; int totRead; FileOutputStream out = new FileOutputStream(f); for (int i = 0x00; i < 0x100; i++) { out.write(i); } out.close(); in = new StraightStreamReader(new FileInputStream(f)); for (int i = 0x00; i < 0x100; i++) { read = in.read(); if (read != i) { System.err.println("Error: " + i + " read as " + read); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = in.read(cbuf); if (totRead != 0x100) { System.err.println("Simple buffered read did not read the full amount: 0x" + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i]); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = 0; while (totRead <= 0x100 && (read = in.read(cbuf, totRead, 0x100 - totRead)) > 0) { totRead += read; } if (totRead != 0x100) { System.err.println("Not enough read. Bytes read: " + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i]); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = 0; while (totRead <= 0x100 && (read = in.read(cbuf, totRead + 0x123, 0x100 - totRead)) > 0) { totRead += read; } if (totRead != 0x100) { System.err.println("Not enough read. Bytes read: " + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i + 0x123] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i + 0x123]); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = 0; while (totRead <= 0x100 && (read = in.read(cbuf, totRead + 0x123, 7)) > 0) { totRead += read; } if (totRead != 0x100) { System.err.println("Not enough read. Bytes read: " + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i + 0x123] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i + 0x123]); } } in.close(); f.delete(); } catch (IOException x) { System.err.println(x.getMessage()); } } | 18,672 |
1 | public static void copyFile(File sourceFile, File destFile) throws IOException { if (!destFile.exists()) { destFile.createNewFile(); } FileChannel source = null; FileChannel destination = null; try { source = new FileInputStream(sourceFile).getChannel(); destination = new FileOutputStream(destFile).getChannel(); destination.transferFrom(source, 0, source.size()); } finally { if (source != null) { source.close(); } if (destination != null) { destination.close(); } } } | public static void fileCopy(File source, File dest) throws IOException { FileChannel in = null, out = null; try { in = new FileInputStream(source).getChannel(); out = new FileOutputStream(dest).getChannel(); long size = in.size(); MappedByteBuffer buf = in.map(FileChannel.MapMode.READ_ONLY, 0, size); out.write(buf); } finally { if (in != null) in.close(); if (out != null) out.close(); } } | 18,673 |
0 | public int read(String name) { status = STATUS_OK; try { name = name.trim().toLowerCase(); if ((name.indexOf("file:") >= 0) || (name.indexOf(":/") > 0)) { URL url = new URL(name); in = new BufferedInputStream(url.openStream()); } else { in = new BufferedInputStream(new FileInputStream(name)); } status = read(in); } catch (IOException e) { status = STATUS_OPEN_ERROR; } return status; } | public static List<ReactomeBean> getUrlData(URL url) throws IOException { List<ReactomeBean> beans = new ArrayList<ReactomeBean>(256); log.debug("Retreiving content for: " + url); StringBuffer content = new StringBuffer(4096); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); String str; while ((str = in.readLine()) != null) { if (str.startsWith("#")) { continue; } StringTokenizer stringTokenizer = new StringTokenizer(str, "\t"); String InteractionAc = stringTokenizer.nextToken(); String reactomeId = stringTokenizer.nextToken(); ReactomeBean reactomeBean = new ReactomeBean(); reactomeBean.setReactomeID(reactomeId); reactomeBean.setInteractionAC(InteractionAc); beans.add(reactomeBean); } in.close(); return beans; } | 18,674 |
1 | public static void main(String[] args) { String url = "jdbc:mysql://localhost/test"; String user = "root"; String password = "password"; String imageLocation = "C:\\Documents and Settings\\EddyM\\Desktop\\Nick\\01100002.tif"; String imageLocation2 = "C:\\Documents and Settings\\EddyM\\Desktop\\Nick\\011000022.tif"; try { Class.forName("com.mysql.jdbc.Driver"); } catch (ClassNotFoundException ex) { ex.printStackTrace(); } try { File f = new File(imageLocation); InputStream fis = new FileInputStream(f); Connection c = DriverManager.getConnection(url, user, password); ResultSet rs = c.createStatement().executeQuery("SELECT Image FROM ImageTable WHERE ImageID=12345678"); new File(imageLocation2).createNewFile(); rs.first(); System.out.println("GotFirst"); InputStream is = rs.getAsciiStream("Image"); System.out.println("gotStream"); FileOutputStream fos = new FileOutputStream(new File(imageLocation2)); int readInt; int i = 0; while (true) { readInt = is.read(); if (readInt == -1) { System.out.println("ReadInt == -1"); break; } i++; if (i % 1000000 == 0) System.out.println(i + " / " + is.available()); fos.write(readInt); } c.close(); } catch (SQLException ex) { ex.printStackTrace(); } catch (IOException ex) { ex.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!"); } | 18,675 |
0 | @Test public void testDocumentDownloadKnowledgeBase() throws IOException { if (uploadedKbDocumentID == null) { fail("Document Upload Test should run first"); } String downloadLink = GoogleDownloadLinkGenerator.generateTextDownloadLink(uploadedKbDocumentID); URL url = new URL(downloadLink); URLConnection urlConnection = url.openConnection(); urlConnection.connect(); InputStream input = url.openStream(); FileWriter fw = new FileWriter("tmpOutput.kb"); Reader reader = new InputStreamReader(input); BufferedReader bufferedReader = new BufferedReader(reader); String strLine = ""; int count = 0; while (count < 10000) { strLine = bufferedReader.readLine(); if (strLine != null && strLine != "") { fw.write(strLine); } count++; } } | protected void writePage(final CacheItem entry, final TranslationResponse response, ModifyTimes times) throws IOException { if (entry == null) { return; } Set<ResponseHeader> headers = new TreeSet<ResponseHeader>(); for (ResponseHeader h : entry.getHeaders()) { if (TranslationResponse.ETAG.equals(h.getName())) { if (!times.isFileLastModifiedKnown()) { headers.add(new ResponseHeaderImpl(h.getName(), doETagStripWeakMarker(h.getValues()))); } } else { headers.add(h); } } response.addHeaders(headers); if (!times.isFileLastModifiedKnown()) { response.setLastModified(entry.getLastModified()); } response.setTranslationCount(entry.getTranslationCount()); response.setFailCount(entry.getFailCount()); OutputStream output = response.getOutputStream(); try { InputStream input = entry.getContentAsStream(); try { IOUtils.copy(input, output); } finally { input.close(); } } finally { response.setEndState(ResponseStateOk.getInstance()); } } | 18,676 |
1 | public void gzipCompress(String file) { try { File inputFile = new File(file); FileInputStream fileinput = new FileInputStream(inputFile); File outputFile = new File(file.substring(0, file.length() - 1) + "z"); FileOutputStream stream = new FileOutputStream(outputFile); GZIPOutputStream gzipstream = new GZIPOutputStream(stream); BufferedInputStream bis = new BufferedInputStream(fileinput); int bytes_read = 0; byte[] buf = new byte[READ_BUFFER_SIZE]; while ((bytes_read = bis.read(buf, 0, BLOCK_SIZE)) != -1) { gzipstream.write(buf, 0, bytes_read); } bis.close(); inputFile.delete(); gzipstream.finish(); gzipstream.close(); } catch (FileNotFoundException fnfe) { System.out.println("Compressor: Cannot find file " + fnfe.getMessage()); } catch (SecurityException se) { System.out.println("Problem saving file " + se.getMessage()); } catch (IOException ioe) { System.out.println("Problem saving file " + ioe.getMessage()); } } | 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(); } } | 18,677 |
0 | public boolean backupFile(File oldFile, File newFile) { boolean isBkupFileOK = false; FileChannel sourceChannel = null; FileChannel targetChannel = null; try { sourceChannel = new FileInputStream(oldFile).getChannel(); targetChannel = new FileOutputStream(newFile).getChannel(); targetChannel.transferFrom(sourceChannel, 0, sourceChannel.size()); } catch (IOException e) { logger.log(Level.SEVERE, "IO exception occurred while copying config file", e); } finally { if ((newFile != null) && (newFile.exists()) && (newFile.length() > 0)) { isBkupFileOK = true; } try { if (sourceChannel != null) { sourceChannel.close(); } if (targetChannel != null) { targetChannel.close(); } } catch (IOException e) { logger.log(Level.INFO, "closing channels failed"); } } return isBkupFileOK; } | private void gerarFaturamento() { int opt = Funcoes.mensagemConfirma(null, "Confirma o faturamento?"); if (opt == JOptionPane.OK_OPTION) { StringBuilder insert = new StringBuilder(); insert.append("INSERT INTO RPFATURAMENTO "); insert.append("(CODEMP, CODFILIAL, CODPED, CODITPED, "); insert.append("QTDFATURADO, VLRFATURADO, QTDPENDENTE, "); insert.append("PERCCOMISFAT, VLRCOMISFAT, DTFATURADO ) "); insert.append("VALUES"); insert.append("(?,?,?,?,?,?,?,?,?,?)"); PreparedStatement ps; int parameterIndex; try { for (int i = 0; i < tab.getNumLinhas(); i++) { parameterIndex = 1; ps = con.prepareStatement(insert.toString()); ps.setInt(parameterIndex++, AplicativoRep.iCodEmp); ps.setInt(parameterIndex++, ListaCampos.getMasterFilial("RPFATURAMENTO")); ps.setInt(parameterIndex++, txtCodPed.getVlrInteger()); ps.setInt(parameterIndex++, (Integer) tab.getValor(i, ETabNota.ITEM.ordinal())); ps.setBigDecimal(parameterIndex++, (BigDecimal) tab.getValor(i, ETabNota.QTDFATURADA.ordinal())); ps.setBigDecimal(parameterIndex++, (BigDecimal) tab.getValor(i, ETabNota.VLRFATURADO.ordinal())); ps.setBigDecimal(parameterIndex++, (BigDecimal) tab.getValor(i, ETabNota.QDTPENDENTE.ordinal())); ps.setBigDecimal(parameterIndex++, (BigDecimal) tab.getValor(i, ETabNota.PERCCOMIS.ordinal())); ps.setBigDecimal(parameterIndex++, (BigDecimal) tab.getValor(i, ETabNota.VLRCOMIS.ordinal())); ps.setDate(parameterIndex++, Funcoes.dateToSQLDate(Calendar.getInstance().getTime())); ps.executeUpdate(); } gerarFaturamento.setEnabled(false); gerarComissao.setEnabled(true); Funcoes.mensagemInforma(null, "Faturamento criado para pedido " + txtCodPed.getVlrInteger()); con.commit(); } catch (Exception e) { e.printStackTrace(); Funcoes.mensagemErro(this, "Erro ao gerar faturamento!\n" + e.getMessage()); try { con.rollback(); } catch (SQLException e1) { e1.printStackTrace(); } } } } | 18,678 |
0 | public final void conectar() throws IOException, FTPException { ftp = null; ftp = new FTPClient(); ftp.setRemoteHost(cfg.getFTPHost()); ftp.connect(); ftp.login(cfg.getFTPUser(), cfg.getFTPPass()); ftp.setProgressMonitor(pMonitor); ftp.setConnectMode(FTPConnectMode.PASV); ftp.setType(FTPTransferType.BINARY); } | public static String generate(String username, String password) throws PersistenceException { String output = null; try { MessageDigest md = MessageDigest.getInstance("SHA-256"); md.reset(); md.update(username.getBytes()); md.update(password.getBytes()); byte[] rawhash = md.digest(); output = byteToBase64(rawhash); } catch (Exception e) { throw new PersistenceException("error, could not generate password"); } return output; } | 18,679 |
0 | @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())); } | private SpequlosResponse executeGet(String targetURL, String urlParameters) { URL url; HttpURLConnection connection = null; boolean succ = false; try { url = new URL(targetURL + "?" + urlParameters); connection = (HttpURLConnection) url.openConnection(); connection.setRequestMethod("GET"); connection.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); connection.setRequestProperty("Content-Length", "" + Integer.toString(urlParameters.getBytes().length)); connection.setRequestProperty("Content-Language", "en-US"); connection.setUseCaches(false); connection.setDoInput(true); connection.setDoOutput(true); InputStream is = connection.getInputStream(); BufferedReader rd = new BufferedReader(new InputStreamReader(is)); String line; StringBuffer log = new StringBuffer(); ArrayList<String> response = new ArrayList<String>(); while ((line = rd.readLine()) != null) { if (line.startsWith("<div class=\"qos\">")) { System.out.println("here is the line : " + line); String resp = line.split(">")[1].split("<")[0]; System.out.println("here is the splitted line : " + resp); if (!resp.startsWith("None")) { succ = true; String[] values = resp.split(" "); ArrayList<String> realvalues = new ArrayList<String>(); for (String s : values) { realvalues.add(s); } if (realvalues.size() == 5) { realvalues.add(2, realvalues.get(2) + " " + realvalues.get(3)); realvalues.remove(3); realvalues.remove(3); } for (String n : realvalues) { response.add(n); } } } else { log.append(line); log.append('\r'); } } rd.close(); SpequlosResponse speqresp = new SpequlosResponse(response, log.toString(), succ); return speqresp; } catch (Exception e) { e.printStackTrace(); String log = "Please check the availability of Spequlos server!<br />" + "URL:" + targetURL + "<br />" + "PARAMETERS:" + urlParameters + "<br />"; return new SpequlosResponse(null, log, succ); } finally { if (connection != null) connection.disconnect(); } } | 18,680 |
1 | @RequestMapping(value = "/verdocumentoFisico.html", method = RequestMethod.GET) public String editFile(ModelMap model, @RequestParam("id") int idAnexo) { Anexo anexo = anexoService.selectById(idAnexo); model.addAttribute("path", anexo.getAnexoCaminho()); try { InputStream is = new FileInputStream(new File(config.baseDir + "/arquivos_upload_direto/" + anexo.getAnexoCaminho())); FileOutputStream fos = new FileOutputStream(new File(config.baseDir + "/temp/" + anexo.getAnexoCaminho())); IOUtils.copy(is, fos); Runtime.getRuntime().exec("chmod 777 " + config.tempDir + anexo.getAnexoCaminho()); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } return "verdocumentoFisico"; } | private void appendAndDelete(FileOutputStream outstream, String file) throws FileNotFoundException, IOException { FileInputStream input = new FileInputStream(file); byte[] buffer = new byte[65536]; int l; while ((l = input.read(buffer)) != -1) outstream.write(buffer, 0, l); input.close(); new File(file).delete(); } | 18,681 |
1 | private void createSaveServiceProps() throws MojoExecutionException { saveServiceProps = new File(workDir, "saveservice.properties"); try { FileWriter out = new FileWriter(saveServiceProps); IOUtils.copy(Thread.currentThread().getContextClassLoader().getResourceAsStream("saveservice.properties"), out); out.flush(); out.close(); System.setProperty("saveservice_properties", File.separator + "target" + File.separator + "jmeter" + File.separator + "saveservice.properties"); } catch (IOException e) { throw new MojoExecutionException("Could not create temporary saveservice.properties", e); } } | public Object next() { if (!hasNext()) { throw new NoSuchElementException(); } this.currentGafFilePath = this.url; try { if (this.httpURL != null) { LOG.info("Reading URL :" + httpURL); InputStream is = this.httpURL.openStream(); int index = this.httpURL.toString().lastIndexOf('/'); String file = this.httpURL.toString().substring(index + 1); File downloadLocation = new File(GoConfigManager.getInstance().getGafUploadDir(), "tmp-" + file); OutputStream out = new FileOutputStream(downloadLocation); IOUtils.copy(is, out); out.close(); is = new FileInputStream(downloadLocation); if (url.endsWith(".gz")) { is = new GZIPInputStream(is); } this.currentGafFile = this.currentGafFilePath.substring(this.currentGafFilePath.lastIndexOf("/") + 1); this.httpURL = null; return is; } else { String file = files[counter++].getName(); this.currentGafFile = file; if (!this.currentGafFilePath.endsWith(file)) currentGafFilePath += file; LOG.info("Returning input stream for the file: " + file); _connect(); ftpClient.changeWorkingDirectory(path); InputStream is = ftpClient.retrieveFileStream(file); File downloadLocation = new File(GoConfigManager.getInstance().getGafUploadDir(), file); OutputStream out = new FileOutputStream(downloadLocation); IOUtils.copy(is, out); out.close(); System.out.println("Download complete....."); is = new FileInputStream(downloadLocation); if (file.endsWith(".gz")) { is = new GZIPInputStream(is); } return is; } } catch (IOException ex) { throw new RuntimeException(ex); } } | 18,682 |
0 | public static KUID createRandomID() { MessageDigestInput randomNumbers = new MessageDigestInput() { public void update(MessageDigest md) { byte[] random = new byte[LENGTH * 2]; GENERATOR.nextBytes(random); md.update(random); } }; MessageDigestInput properties = new MessageDigestInput() { public void update(MessageDigest md) { Properties props = System.getProperties(); try { for (Entry entry : props.entrySet()) { String key = (String) entry.getKey(); String value = (String) entry.getValue(); md.update(key.getBytes("UTF-8")); md.update(value.getBytes("UTF-8")); } } catch (UnsupportedEncodingException e) { throw new RuntimeException(e); } } }; MessageDigestInput millis = new MessageDigestInput() { public void update(MessageDigest md) { long millis = System.currentTimeMillis(); md.update((byte) ((millis >> 56L) & 0xFFL)); md.update((byte) ((millis >> 48L) & 0xFFL)); md.update((byte) ((millis >> 40L) & 0xFFL)); md.update((byte) ((millis >> 32L) & 0xFFL)); md.update((byte) ((millis >> 24L) & 0xFFL)); md.update((byte) ((millis >> 16L) & 0xFFL)); md.update((byte) ((millis >> 8L) & 0xFFL)); md.update((byte) ((millis) & 0xFFL)); } }; MessageDigestInput nanos = new MessageDigestInput() { public void update(MessageDigest md) { long nanos = System.nanoTime(); md.update((byte) ((nanos >> 56L) & 0xFFL)); md.update((byte) ((nanos >> 48L) & 0xFFL)); md.update((byte) ((nanos >> 40L) & 0xFFL)); md.update((byte) ((nanos >> 32L) & 0xFFL)); md.update((byte) ((nanos >> 24L) & 0xFFL)); md.update((byte) ((nanos >> 16L) & 0xFFL)); md.update((byte) ((nanos >> 8L) & 0xFFL)); md.update((byte) ((nanos) & 0xFFL)); } }; MessageDigestInput[] input = { properties, randomNumbers, millis, nanos }; Arrays.sort(input); try { MessageDigest md = MessageDigest.getInstance("SHA1"); for (MessageDigestInput mdi : input) { mdi.update(md); int hashCode = System.identityHashCode(mdi); md.update((byte) ((hashCode >> 24) & 0xFF)); md.update((byte) ((hashCode >> 16) & 0xFF)); md.update((byte) ((hashCode >> 8) & 0xFF)); md.update((byte) ((hashCode) & 0xFF)); md.update((byte) ((mdi.rnd >> 24) & 0xFF)); md.update((byte) ((mdi.rnd >> 16) & 0xFF)); md.update((byte) ((mdi.rnd >> 8) & 0xFF)); md.update((byte) ((mdi.rnd) & 0xFF)); } return new KUID(md.digest()); } catch (NoSuchAlgorithmException e) { throw new RuntimeException(e); } } | protected void shutdown(final boolean unexpected) { ControlerState oldState = this.state; this.state = ControlerState.Shutdown; if (oldState == ControlerState.Running) { if (unexpected) { log.warn("S H U T D O W N --- received unexpected shutdown request."); } else { log.info("S H U T D O W N --- start regular shutdown."); } if (this.uncaughtException != null) { log.warn("Shutdown probably caused by the following Exception.", this.uncaughtException); } this.controlerListenerManager.fireControlerShutdownEvent(unexpected); if (this.dumpDataAtEnd) { Knowledges kk; if (this.config.scenario().isUseKnowledges()) { kk = (this.getScenario()).getKnowledges(); } else { kk = this.getScenario().retrieveNotEnabledKnowledges(); } new PopulationWriter(this.population, this.network, kk).write(this.controlerIO.getOutputFilename(FILENAME_POPULATION)); new NetworkWriter(this.network).write(this.controlerIO.getOutputFilename(FILENAME_NETWORK)); new ConfigWriter(this.config).write(this.controlerIO.getOutputFilename(FILENAME_CONFIG)); ActivityFacilities facilities = this.getFacilities(); if (facilities != null) { new FacilitiesWriter((ActivityFacilitiesImpl) facilities).write(this.controlerIO.getOutputFilename("output_facilities.xml.gz")); } if (((NetworkFactoryImpl) this.network.getFactory()).isTimeVariant()) { new NetworkChangeEventsWriter().write(this.controlerIO.getOutputFilename("output_change_events.xml.gz"), ((NetworkImpl) this.network).getNetworkChangeEvents()); } if (this.config.scenario().isUseHouseholds()) { new HouseholdsWriterV10(this.scenarioData.getHouseholds()).writeFile(this.controlerIO.getOutputFilename(FILENAME_HOUSEHOLDS)); } if (this.config.scenario().isUseLanes()) { new LaneDefinitionsWriter20(this.scenarioData.getScenarioElement(LaneDefinitions20.class)).write(this.controlerIO.getOutputFilename(FILENAME_LANES)); } if (!unexpected && this.getConfig().vspExperimental().isWritingOutputEvents()) { File toFile = new File(this.controlerIO.getOutputFilename("output_events.xml.gz")); File fromFile = new File(this.controlerIO.getIterationFilename(this.getLastIteration(), "events.xml.gz")); IOUtils.copyFile(fromFile, toFile); } } if (unexpected) { log.info("S H U T D O W N --- unexpected shutdown request completed."); } else { log.info("S H U T D O W N --- regular shutdown completed."); } try { Runtime.getRuntime().removeShutdownHook(this.shutdownHook); } catch (IllegalStateException e) { log.info("Cannot remove shutdown hook. " + e.getMessage()); } this.shutdownHook = null; this.collectLogMessagesAppender = null; IOUtils.closeOutputDirLogging(); } } | 18,683 |
1 | protected static URL[] createUrls(URL jarUrls[]) { ArrayList<URL> additionalUrls = new ArrayList<URL>(Arrays.asList(jarUrls)); for (URL ju : jarUrls) { try { JarFile jar = new JarFile(ju.getFile()); Enumeration<JarEntry> entries = jar.entries(); while (entries.hasMoreElements()) { JarEntry j = entries.nextElement(); if (j.isDirectory()) continue; if (j.getName().startsWith("lib/") && j.getName().endsWith(".jar")) { URL url = new URL("jar:" + ju.getProtocol() + ":" + ju.getFile() + "!/" + j.getName()); InputStream is = url.openStream(); File tmpFile = File.createTempFile("SCDeploy", ".jar"); FileOutputStream fos = new FileOutputStream(tmpFile); IOUtils.copy(is, fos); is.close(); fos.close(); additionalUrls.add(new URL("file://" + tmpFile.getAbsolutePath())); } } } catch (IOException e) { } } return additionalUrls.toArray(new URL[] {}); } | public void doPost(HttpServletRequest req, HttpServletResponse res) throws ServletException, IOException { PrintWriter out = null; ServletOutputStream outstream = null; try { String action = req.getParameter("nmrshiftdbaction"); String relativepath = ServletUtils.expandRelative(this.getServletConfig(), "/WEB-INF"); TurbineConfig tc = new TurbineConfig(relativepath + "..", relativepath + getServletConfig().getInitParameter("properties")); tc.init(); int spectrumId = -1; DBSpectrum spectrum = null; Export export = null; String format = req.getParameter("format"); if (action.equals("test")) { try { res.setContentType("text/plain"); out = res.getWriter(); List l = DBSpectrumPeer.executeQuery("select SPECTRUM_ID from SPECTRUM limit 1"); if (l.size() > 0) spectrumId = ((Record) l.get(0)).getValue(1).asInt(); out.write("success"); } catch (Exception ex) { out.write("failure"); } } else if (action.equals("rss")) { int numbertoexport = 10; out = res.getWriter(); if (req.getParameter("numbertoexport") != null) { try { numbertoexport = Integer.parseInt(req.getParameter("numbertoexport")); if (numbertoexport < 1 || numbertoexport > 20) throw new NumberFormatException("Number to small/large"); } catch (NumberFormatException ex) { out.println("The parameter <code>numbertoexport</code>must be an integer from 1 to 20"); } } res.setContentType("text/xml"); RssWriter rssWriter = new RssWriter(); rssWriter.setWriter(res.getWriter()); AtomContainerSet soac = new AtomContainerSet(); String query = "select distinct MOLECULE.MOLECULE_ID from MOLECULE, SPECTRUM where SPECTRUM.MOLECULE_ID = MOLECULE.MOLECULE_ID and SPECTRUM.REVIEW_FLAG =\"true\" order by MOLECULE.DATE desc;"; List l = NmrshiftdbUserPeer.executeQuery(query); for (int i = 0; i < numbertoexport; i++) { if (i == l.size()) break; DBMolecule mol = DBMoleculePeer.retrieveByPK(new NumberKey(((Record) l.get(i)).getValue(1).asInt())); IMolecule cdkmol = mol.getAsCDKMoleculeAsEntered(1); soac.addAtomContainer(cdkmol); rssWriter.getLinkmap().put(cdkmol, mol.getEasylink(req)); rssWriter.getDatemap().put(cdkmol, mol.getDate()); rssWriter.getTitlemap().put(cdkmol, mol.getChemicalNamesAsOneStringWithFallback()); rssWriter.getCreatormap().put(cdkmol, mol.getNmrshiftdbUser().getUserName()); rssWriter.setCreator(GeneralUtils.getAdminEmail(getServletConfig())); Vector v = mol.getDBCanonicalNames(); for (int k = 0; k < v.size(); k++) { DBCanonicalName canonName = (DBCanonicalName) v.get(k); if (canonName.getDBCanonicalNameType().getCanonicalNameType() == "INChI") { rssWriter.getInchimap().put(cdkmol, canonName.getName()); break; } } rssWriter.setTitle("NMRShiftDB"); rssWriter.setLink("http://www.nmrshiftdb.org"); rssWriter.setDescription("NMRShiftDB is an open-source, open-access, open-submission, open-content web database for chemical structures and their nuclear magnetic resonance data"); rssWriter.setPublisher("NMRShiftDB.org"); rssWriter.setImagelink("http://www.nmrshiftdb.org/images/nmrshift-logo.gif"); rssWriter.setAbout("http://www.nmrshiftdb.org/NmrshiftdbServlet?nmrshiftdbaction=rss"); Collection coll = new ArrayList(); Vector spectra = mol.selectSpectra(null); for (int k = 0; k < spectra.size(); k++) { Element el = ((DBSpectrum) spectra.get(k)).getCmlSpect(); Element el2 = el.getChildElements().get(0); el.removeChild(el2); coll.add(el2); } rssWriter.getMultiMap().put(cdkmol, coll); } rssWriter.write(soac); } else if (action.equals("getattachment")) { res.setContentType("application/zip"); outstream = res.getOutputStream(); DBSample sample = DBSamplePeer.retrieveByPK(new NumberKey(req.getParameter("sampleid"))); outstream.write(sample.getAttachment()); } else if (action.equals("createreport")) { res.setContentType("application/pdf"); outstream = res.getOutputStream(); boolean yearly = req.getParameter("style").equals("yearly"); int yearstart = Integer.parseInt(req.getParameter("yearstart")); int yearend = Integer.parseInt(req.getParameter("yearend")); int monthstart = 0; int monthend = 0; if (!yearly) { monthstart = Integer.parseInt(req.getParameter("monthstart")); monthend = Integer.parseInt(req.getParameter("monthend")); } int type = Integer.parseInt(req.getParameter("type")); JasperReport jasperReport = (JasperReport) JRLoader.loadObject(relativepath + "/reports/" + (yearly ? "yearly" : "monthly") + "_report_" + type + ".jasper"); Map parameters = new HashMap(); if (yearly) parameters.put("HEADER", "Report for years " + yearstart + " - " + yearend); else parameters.put("HEADER", "Report for " + monthstart + "/" + yearstart + " - " + monthend + "/" + yearend); DBConnection dbconn = TurbineDB.getConnection(); Connection conn = dbconn.getConnection(); Statement stmt = conn.createStatement(); ResultSet rs = null; if (type == 1) { rs = stmt.executeQuery("select YEAR(DATE) as YEAR, " + (yearly ? "" : " MONTH(DATE) as MONTH, ") + "AFFILIATION_1, AFFILIATION_2, MACHINE.NAME as NAME, count(*) as C, sum(WISHED_SPECTRUM like '%13C%' or WISHED_SPECTRUM like '%variable temperature%' or WISHED_SPECTRUM like '%ID sel. NOE%' or WISHED_SPECTRUM like '%solvent suppression%' or WISHED_SPECTRUM like '%standard spectrum%') as 1_D, sum(WISHED_SPECTRUM like '%H,H-COSY%' or WISHED_SPECTRUM like '%NOESY%' or WISHED_SPECTRUM like '%HMQC%' or WISHED_SPECTRUM like '%HMBC%') as 2_D, sum(OTHER_WISHED_SPECTRUM!='') as SPECIAL, sum(OTHER_NUCLEI!='') as HETERO, sum(PROCESS='self') as SELF, sum(PROCESS='robot') as ROBOT, sum(PROCESS='worker') as OPERATOR from (SAMPLE join TURBINE_USER using (USER_ID)) join MACHINE on MACHINE.MACHINE_ID=SAMPLE.MACHINE where YEAR(DATE)>=" + yearstart + " and YEAR(DATE)<=" + yearend + " and LOGIN_NAME<>'testuser' group by YEAR, " + (yearly ? "" : "MONTH, ") + "AFFILIATION_1, AFFILIATION_2, MACHINE.NAME"); } else if (type == 2) { rs = stmt.executeQuery("select YEAR(DATE) as YEAR, " + (yearly ? "" : " MONTH(DATE) as MONTH, ") + "MACHINE.NAME as NAME, count(*) as C, sum(WISHED_SPECTRUM like '%13C%' or WISHED_SPECTRUM like '%variable temperature%' or WISHED_SPECTRUM like '%ID sel. NOE%' or WISHED_SPECTRUM like '%solvent suppression%' or WISHED_SPECTRUM like '%standard spectrum%') as 1_D, sum(WISHED_SPECTRUM like '%H,H-COSY%' or WISHED_SPECTRUM like '%NOESY%' or WISHED_SPECTRUM like '%HMQC%' or WISHED_SPECTRUM like '%HMBC%') as 2_D, sum(OTHER_WISHED_SPECTRUM!='') as SPECIAL, sum(OTHER_NUCLEI!='') as HETERO, sum(PROCESS='self') as SELF, sum(PROCESS='robot') as ROBOT, sum(PROCESS='worker') as OPERATOR from (SAMPLE join TURBINE_USER using (USER_ID)) join MACHINE on MACHINE.MACHINE_ID=SAMPLE.MACHINE group by YEAR, " + (yearly ? "" : "MONTH, ") + "MACHINE.NAME"); } JasperPrint jasperPrint = JasperFillManager.fillReport(jasperReport, parameters, new JRResultSetDataSource(rs)); JasperExportManager.exportReportToPdfStream(jasperPrint, outstream); dbconn.close(); } else if (action.equals("exportcmlbyinchi")) { res.setContentType("text/xml"); out = res.getWriter(); String inchi = req.getParameter("inchi"); String spectrumtype = req.getParameter("spectrumtype"); Criteria crit = new Criteria(); crit.add(DBCanonicalNamePeer.NAME, inchi); crit.addJoin(DBCanonicalNamePeer.MOLECULE_ID, DBSpectrumPeer.MOLECULE_ID); crit.addJoin(DBSpectrumPeer.SPECTRUM_TYPE_ID, DBSpectrumTypePeer.SPECTRUM_TYPE_ID); crit.add(DBSpectrumTypePeer.NAME, spectrumtype); try { GeneralUtils.logToSql(crit.toString(), null); } catch (Exception ex) { } Vector spectra = DBSpectrumPeer.doSelect(crit); if (spectra.size() == 0) { out.write("No such molecule or spectrum"); } else { Element cmlElement = new Element("cml"); cmlElement.addAttribute(new Attribute("convention", "nmrshiftdb-convention")); cmlElement.setNamespaceURI("http://www.xml-cml.org/schema"); Element parent = ((DBSpectrum) spectra.get(0)).getDBMolecule().getCML(1); nu.xom.Node cmldoc = parent.getChild(0); ((Element) cmldoc).setNamespaceURI("http://www.xml-cml.org/schema"); parent.removeChildren(); cmlElement.appendChild(cmldoc); for (int k = 0; k < spectra.size(); k++) { Element parentspec = ((DBSpectrum) spectra.get(k)).getCmlSpect(); Node spectrumel = parentspec.getChild(0); parentspec.removeChildren(); cmlElement.appendChild(spectrumel); ((Element) spectrumel).setNamespaceURI("http://www.xml-cml.org/schema"); } out.write(cmlElement.toXML()); } } else if (action.equals("namelist")) { res.setContentType("application/zip"); outstream = res.getOutputStream(); ByteArrayOutputStream baos = new ByteArrayOutputStream(); ZipOutputStream zipout = new ZipOutputStream(baos); Criteria crit = new Criteria(); crit.addJoin(DBMoleculePeer.MOLECULE_ID, DBSpectrumPeer.MOLECULE_ID); crit.add(DBSpectrumPeer.REVIEW_FLAG, "true"); Vector v = DBMoleculePeer.doSelect(crit); for (int i = 0; i < v.size(); i++) { if (i % 500 == 0) { if (i != 0) { zipout.write(new String("<p>The list is continued <a href=\"nmrshiftdb.names." + i + ".html\">here</a></p></body></html>").getBytes()); zipout.closeEntry(); } zipout.putNextEntry(new ZipEntry("nmrshiftdb.names." + i + ".html")); zipout.write(new String("<html><body><h1>This is a list of strcutures in <a href=\"http://www.nmrshiftdb.org\">NMRShiftDB</a>, starting at " + i + ", Its main purpose is to be found by search engines</h1>").getBytes()); } DBMolecule mol = (DBMolecule) v.get(i); zipout.write(new String("<p><a href=\"" + mol.getEasylink(req) + "\">").getBytes()); Vector cannames = mol.getDBCanonicalNames(); for (int k = 0; k < cannames.size(); k++) { zipout.write(new String(((DBCanonicalName) cannames.get(k)).getName() + " ").getBytes()); } Vector chemnames = mol.getDBChemicalNames(); for (int k = 0; k < chemnames.size(); k++) { zipout.write(new String(((DBChemicalName) chemnames.get(k)).getName() + " ").getBytes()); } zipout.write(new String("</a>. Information we have got: NMR spectra").getBytes()); Vector spectra = mol.selectSpectra(); for (int k = 0; k < spectra.size(); k++) { zipout.write(new String(((DBSpectrum) spectra.get(k)).getDBSpectrumType().getName() + ", ").getBytes()); } if (mol.hasAny3d()) zipout.write(new String("3D coordinates, ").getBytes()); zipout.write(new String("File formats: CML, mol, png, jpeg").getBytes()); zipout.write(new String("</p>").getBytes()); } zipout.write(new String("</body></html>").getBytes()); zipout.closeEntry(); zipout.close(); InputStream is = new ByteArrayInputStream(baos.toByteArray()); byte[] buf = new byte[32 * 1024]; int nRead = 0; while ((nRead = is.read(buf)) != -1) { outstream.write(buf, 0, nRead); } } else if (action.equals("predictor")) { if (req.getParameter("symbol") == null) { res.setContentType("text/plain"); out = res.getWriter(); out.write("please give the symbol to create the predictor for in the request with symbol=X (e. g. symbol=C"); } res.setContentType("application/zip"); outstream = res.getOutputStream(); ByteArrayOutputStream baos = new ByteArrayOutputStream(); ZipOutputStream zipout = new ZipOutputStream(baos); String filename = "org/openscience/nmrshiftdb/PredictionTool.class"; zipout.putNextEntry(new ZipEntry(filename)); JarInputStream jip = new JarInputStream(new FileInputStream(ServletUtils.expandRelative(getServletConfig(), "/WEB-INF/lib/nmrshiftdb-lib.jar"))); JarEntry entry = jip.getNextJarEntry(); while (entry.getName().indexOf("PredictionTool.class") == -1) { entry = jip.getNextJarEntry(); } for (int i = 0; i < entry.getSize(); i++) { zipout.write(jip.read()); } zipout.closeEntry(); zipout.putNextEntry(new ZipEntry("nmrshiftdb.csv")); int i = 0; org.apache.turbine.util.db.pool.DBConnection conn = TurbineDB.getConnection(); HashMap mapsmap = new HashMap(); while (true) { Statement stmt = conn.createStatement(); ResultSet rs = stmt.executeQuery("select HOSE_CODE, VALUE, SYMBOL from HOSE_CODES where CONDITION_TYPE='m' and WITH_RINGS=0 and SYMBOL='" + req.getParameter("symbol") + "' limit " + (i * 1000) + ", 1000"); int m = 0; while (rs.next()) { String code = rs.getString(1); Double value = new Double(rs.getString(2)); String symbol = rs.getString(3); if (mapsmap.get(symbol) == null) { mapsmap.put(symbol, new HashMap()); } for (int spheres = 6; spheres > 0; spheres--) { StringBuffer hoseCodeBuffer = new StringBuffer(); StringTokenizer st = new StringTokenizer(code, "()/"); for (int k = 0; k < spheres; k++) { if (st.hasMoreTokens()) { String partcode = st.nextToken(); hoseCodeBuffer.append(partcode); } if (k == 0) { hoseCodeBuffer.append("("); } else if (k == 3) { hoseCodeBuffer.append(")"); } else { hoseCodeBuffer.append("/"); } } String hoseCode = hoseCodeBuffer.toString(); if (((HashMap) mapsmap.get(symbol)).get(hoseCode) == null) { ((HashMap) mapsmap.get(symbol)).put(hoseCode, new ArrayList()); } ((ArrayList) ((HashMap) mapsmap.get(symbol)).get(hoseCode)).add(value); } m++; } i++; stmt.close(); if (m == 0) break; } Set keySet = mapsmap.keySet(); Iterator it = keySet.iterator(); while (it.hasNext()) { String symbol = (String) it.next(); HashMap hosemap = ((HashMap) mapsmap.get(symbol)); Set keySet2 = hosemap.keySet(); Iterator it2 = keySet2.iterator(); while (it2.hasNext()) { String hoseCode = (String) it2.next(); ArrayList list = ((ArrayList) hosemap.get(hoseCode)); double[] values = new double[list.size()]; for (int k = 0; k < list.size(); k++) { values[k] = ((Double) list.get(k)).doubleValue(); } zipout.write(new String(symbol + "|" + hoseCode + "|" + Statistics.minimum(values) + "|" + Statistics.average(values) + "|" + Statistics.maximum(values) + "\r\n").getBytes()); } } zipout.closeEntry(); zipout.close(); InputStream is = new ByteArrayInputStream(baos.toByteArray()); byte[] buf = new byte[32 * 1024]; int nRead = 0; i = 0; while ((nRead = is.read(buf)) != -1) { outstream.write(buf, 0, nRead); } } else if (action.equals("exportspec") || action.equals("exportmol")) { if (spectrumId > -1) spectrum = DBSpectrumPeer.retrieveByPK(new NumberKey(spectrumId)); else spectrum = DBSpectrumPeer.retrieveByPK(new NumberKey(req.getParameter("spectrumid"))); export = new Export(spectrum); } else if (action.equals("exportmdl")) { res.setContentType("text/plain"); outstream = res.getOutputStream(); DBMolecule mol = DBMoleculePeer.retrieveByPK(new NumberKey(req.getParameter("moleculeid"))); outstream.write(mol.getStructureFile(Integer.parseInt(req.getParameter("coordsetid")), false).getBytes()); } else if (action.equals("exportlastinputs")) { format = action; } else if (action.equals("printpredict")) { res.setContentType("text/html"); out = res.getWriter(); HttpSession session = req.getSession(); VelocityContext context = PredictPortlet.getContext(session, true, true, new StringBuffer(), getServletConfig(), req, true); StringWriter w = new StringWriter(); Velocity.mergeTemplate("predictprint.vm", "ISO-8859-1", context, w); out.println(w.toString()); } else { res.setContentType("text/html"); out = res.getWriter(); out.println("No valid action"); } if (format == null) format = ""; if (format.equals("pdf") || format.equals("rtf")) { res.setContentType("application/" + format); out = res.getWriter(); } if (format.equals("docbook")) { res.setContentType("application/zip"); outstream = res.getOutputStream(); } if (format.equals("svg")) { res.setContentType("image/x-svg"); out = res.getWriter(); } if (format.equals("tiff")) { res.setContentType("image/tiff"); outstream = res.getOutputStream(); } if (format.equals("jpeg")) { res.setContentType("image/jpeg"); outstream = res.getOutputStream(); } if (format.equals("png")) { res.setContentType("image/png"); outstream = res.getOutputStream(); } if (format.equals("mdl") || format.equals("txt") || format.equals("cml") || format.equals("cmlboth") || format.indexOf("exsection") == 0) { res.setContentType("text/plain"); out = res.getWriter(); } if (format.equals("simplehtml") || format.equals("exportlastinputs")) { res.setContentType("text/html"); out = res.getWriter(); } if (action.equals("exportlastinputs")) { int numbertoexport = 4; if (req.getParameter("numbertoexport") != null) { try { numbertoexport = Integer.parseInt(req.getParameter("numbertoexport")); if (numbertoexport < 1 || numbertoexport > 20) throw new NumberFormatException("Number to small/large"); } catch (NumberFormatException ex) { out.println("The parameter <code>numbertoexport</code>must be an integer from 1 to 20"); } } NmrshiftdbUser user = null; try { user = NmrshiftdbUserPeer.getByName(req.getParameter("username")); } catch (NmrshiftdbException ex) { out.println("Seems <code>username</code> is not OK: " + ex.getMessage()); } if (user != null) { List l = NmrshiftdbUserPeer.executeQuery("SELECT LAST_DOWNLOAD_DATE FROM TURBINE_USER where LOGIN_NAME=\"" + user.getUserName() + "\";"); Date lastDownloadDate = ((Record) l.get(0)).getValue(1).asDate(); if (((new Date().getTime() - lastDownloadDate.getTime()) / 3600000) < 24) { out.println("Your last download was at " + lastDownloadDate + ". You may download your last inputs only once a day. Sorry for this, but we need to be carefull with resources. If you want to put your last inputs on your homepage best use some sort of cache (e. g. use wget for downlaod with crond and link to this static resource))!"); } else { NmrshiftdbUserPeer.executeStatement("UPDATE TURBINE_USER SET LAST_DOWNLOAD_DATE=NOW() where LOGIN_NAME=\"" + user.getUserName() + "\";"); Vector<String> parameters = new Vector<String>(); String query = "select distinct MOLECULE.MOLECULE_ID from MOLECULE, SPECTRUM where SPECTRUM.MOLECULE_ID = MOLECULE.MOLECULE_ID and SPECTRUM.REVIEW_FLAG =\"true\" and SPECTRUM.USER_ID=" + user.getUserId() + " order by MOLECULE.DATE desc;"; l = NmrshiftdbUserPeer.executeQuery(query); String url = javax.servlet.http.HttpUtils.getRequestURL(req).toString(); url = url.substring(0, url.length() - 17); for (int i = 0; i < numbertoexport; i++) { if (i == l.size()) break; DBMolecule mol = DBMoleculePeer.retrieveByPK(new NumberKey(((Record) l.get(i)).getValue(1).asInt())); parameters.add(new String("<a href=\"" + url + "/portal/pane0/Results?nmrshiftdbaction=showDetailsFromHome&molNumber=" + mol.getMoleculeId() + "\"><img src=\"" + javax.servlet.http.HttpUtils.getRequestURL(req).toString() + "?nmrshiftdbaction=exportmol&spectrumid=" + ((DBSpectrum) mol.getDBSpectrums().get(0)).getSpectrumId() + "&format=jpeg&size=150x150&backcolor=12632256\"></a>")); } VelocityContext context = new VelocityContext(); context.put("results", parameters); StringWriter w = new StringWriter(); Velocity.mergeTemplate("lateststructures.vm", "ISO-8859-1", context, w); out.println(w.toString()); } } } if (action.equals("exportspec")) { if (format.equals("txt")) { String lastsearchtype = req.getParameter("lastsearchtype"); if (lastsearchtype.equals(NmrshiftdbConstants.TOTALSPECTRUM) || lastsearchtype.equals(NmrshiftdbConstants.SUBSPECTRUM)) { List l = ParseUtils.parseSpectrumFromSpecFile(req.getParameter("lastsearchvalues")); spectrum.initSimilarity(l, lastsearchtype.equals(NmrshiftdbConstants.SUBSPECTRUM)); } Vector v = spectrum.getOptions(); DBMolecule mol = spectrum.getDBMolecule(); out.print(mol.getChemicalNamesAsOneString(false) + mol.getMolecularFormula(false) + "; " + mol.getMolecularWeight() + " Dalton\n\r"); out.print("\n\rAtom\t"); if (spectrum.getDBSpectrumType().getElementSymbol() == ("H")) out.print("Mult.\t"); out.print("Meas."); if (lastsearchtype.equals(NmrshiftdbConstants.TOTALSPECTRUM) || lastsearchtype.equals(NmrshiftdbConstants.SUBSPECTRUM)) { out.print("\tInput\tDiff"); } out.print("\n\r"); out.print("No.\t"); if (spectrum.getDBSpectrumType().getElementSymbol() == ("H")) out.print("\t"); out.print("Shift"); if (lastsearchtype.equals(NmrshiftdbConstants.TOTALSPECTRUM) || lastsearchtype.equals(NmrshiftdbConstants.SUBSPECTRUM)) { out.print("\tShift\tM-I"); } out.print("\n\r"); for (int i = 0; i < v.size(); i++) { out.print(((ValuesForVelocityBean) v.get(i)).getDisplayText() + "\t" + ((ValuesForVelocityBean) v.get(i)).getRange()); if (lastsearchtype.equals(NmrshiftdbConstants.TOTALSPECTRUM) || lastsearchtype.equals(NmrshiftdbConstants.SUBSPECTRUM)) { out.print("\t" + ((ValuesForVelocityBean) v.get(i)).getNameForElements() + "\t" + ((ValuesForVelocityBean) v.get(i)).getDelta()); } out.print("\n\r"); } } if (format.equals("simplehtml")) { String i1 = export.getImage(false, "jpeg", ServletUtils.expandRelative(this.getServletConfig(), "/nmrshiftdbhtml") + "/tmp/" + System.currentTimeMillis(), true); export.pictures[0] = new File(i1).getName(); String i2 = export.getImage(true, "jpeg", ServletUtils.expandRelative(this.getServletConfig(), "/nmrshiftdbhtml") + "/tmp/" + System.currentTimeMillis(), true); export.pictures[1] = new File(i2).getName(); String docbook = export.getHtml(); out.print(docbook); } if (format.equals("pdf") || format.equals("rtf")) { String svgSpec = export.getSpecSvg(400, 200); String svgspecfile = relativepath + "/tmp/" + System.currentTimeMillis() + "s.svg"; new FileOutputStream(svgspecfile).write(svgSpec.getBytes()); export.pictures[1] = svgspecfile; String molSvg = export.getMolSvg(true); String svgmolfile = relativepath + "/tmp/" + System.currentTimeMillis() + "m.svg"; new FileOutputStream(svgmolfile).write(molSvg.getBytes()); export.pictures[0] = svgmolfile; String docbook = export.getDocbook("pdf", "SVG"); TransformerFactory tFactory = TransformerFactory.newInstance(); Transformer transformer = tFactory.newTransformer(new StreamSource("file:" + GeneralUtils.getNmrshiftdbProperty("docbookxslpath", getServletConfig()) + "/fo/docbook.xsl")); ByteArrayOutputStream baos = new ByteArrayOutputStream(); transformer.transform(new StreamSource(new StringReader(docbook)), new StreamResult(baos)); FopFactory fopFactory = FopFactory.newInstance(); FOUserAgent foUserAgent = fopFactory.newFOUserAgent(); OutputStream out2 = new ByteArrayOutputStream(); Fop fop = fopFactory.newFop(format.equals("rtf") ? MimeConstants.MIME_RTF : MimeConstants.MIME_PDF, foUserAgent, out2); TransformerFactory factory = TransformerFactory.newInstance(); transformer = factory.newTransformer(); Source src = new StreamSource(new StringReader(baos.toString())); Result res2 = new SAXResult(fop.getDefaultHandler()); transformer.transform(src, res2); out.print(out2.toString()); } if (format.equals("docbook")) { String i1 = relativepath + "/tmp/" + System.currentTimeMillis() + ".svg"; new FileOutputStream(i1).write(export.getSpecSvg(300, 200).getBytes()); export.pictures[0] = new File(i1).getName(); String i2 = relativepath + "/tmp/" + System.currentTimeMillis() + ".svg"; new FileOutputStream(i2).write(export.getMolSvg(true).getBytes()); export.pictures[1] = new File(i2).getName(); String docbook = export.getDocbook("pdf", "SVG"); String docbookfile = relativepath + "/tmp/" + System.currentTimeMillis() + ".xml"; new FileOutputStream(docbookfile).write(docbook.getBytes()); ByteArrayOutputStream baos = export.makeZip(new String[] { docbookfile, i1, i2 }); outstream.write(baos.toByteArray()); } if (format.equals("svg")) { out.print(export.getSpecSvg(400, 200)); } if (format.equals("tiff") || format.equals("jpeg") || format.equals("png")) { InputStream is = new FileInputStream(export.getImage(false, format, relativepath + "/tmp/" + System.currentTimeMillis(), true)); byte[] buf = new byte[32 * 1024]; int nRead = 0; while ((nRead = is.read(buf)) != -1) { outstream.write(buf, 0, nRead); } } if (format.equals("cml")) { out.print(spectrum.getCmlSpect().toXML()); } if (format.equals("cmlboth")) { Element cmlElement = new Element("cml"); cmlElement.addAttribute(new Attribute("convention", "nmrshiftdb-convention")); cmlElement.setNamespaceURI("http://www.xml-cml.org/schema"); Element parent = spectrum.getDBMolecule().getCML(1, spectrum.getDBSpectrumType().getName().equals("1H")); nu.xom.Node cmldoc = parent.getChild(0); ((Element) cmldoc).setNamespaceURI("http://www.xml-cml.org/schema"); parent.removeChildren(); cmlElement.appendChild(cmldoc); Element parentspec = spectrum.getCmlSpect(); Node spectrumel = parentspec.getChild(0); parentspec.removeChildren(); cmlElement.appendChild(spectrumel); ((Element) spectrumel).setNamespaceURI("http://www.xml-cml.org/schema"); out.write(cmlElement.toXML()); } if (format.indexOf("exsection") == 0) { StringTokenizer st = new StringTokenizer(format, "-"); st.nextToken(); String template = st.nextToken(); Criteria crit = new Criteria(); crit.add(DBSpectrumPeer.USER_ID, spectrum.getUserId()); Vector v = spectrum.getDBMolecule().getDBSpectrums(crit); VelocityContext context = new VelocityContext(); context.put("spectra", v); context.put("molecule", spectrum.getDBMolecule()); StringWriter w = new StringWriter(); Velocity.mergeTemplate("exporttemplates/" + template, "ISO-8859-1", context, w); out.write(w.toString()); } } if (action.equals("exportmol")) { int width = -1; int height = -1; if (req.getParameter("size") != null) { StringTokenizer st = new StringTokenizer(req.getParameter("size"), "x"); width = Integer.parseInt(st.nextToken()); height = Integer.parseInt(st.nextToken()); } boolean shownumbers = true; if (req.getParameter("shownumbers") != null && req.getParameter("shownumbers").equals("false")) { shownumbers = false; } if (req.getParameter("backcolor") != null) { export.backColor = new Color(Integer.parseInt(req.getParameter("backcolor"))); } if (req.getParameter("markatom") != null) { export.selected = Integer.parseInt(req.getParameter("markatom")) - 1; } if (format.equals("svg")) { out.print(export.getMolSvg(true)); } if (format.equals("tiff") || format.equals("jpeg") || format.equals("png")) { InputStream is = new FileInputStream(export.getImage(true, format, relativepath + "/tmp/" + System.currentTimeMillis(), width, height, shownumbers, null)); byte[] buf = new byte[32 * 1024]; int nRead = 0; while ((nRead = is.read(buf)) != -1) { outstream.write(buf, 0, nRead); } } if (format.equals("mdl")) { out.println(spectrum.getDBMolecule().getStructureFile(1, false)); } if (format.equals("cml")) { out.println(spectrum.getDBMolecule().getCMLString(1)); } } if (out != null) out.flush(); else outstream.flush(); } catch (Exception ex) { ex.printStackTrace(); out.print(GeneralUtils.logError(ex, "NmrshiftdbServlet", null, true)); out.flush(); } } | 18,684 |
1 | public static String getPasswordHash(String password) { MessageDigest md; try { md = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { throw new IllegalArgumentException(e); } md.update(password.getBytes()); byte[] digest = md.digest(); BigInteger i = new BigInteger(1, digest); String hash = i.toString(16); while (hash.length() < 32) { hash = "0" + hash; } return hash; } | public static String MD5(String text) { byte[] md5hash = new byte[32]; try { MessageDigest md; md = MessageDigest.getInstance("MD5"); md.update(text.getBytes("iso-8859-1"), 0, text.length()); md5hash = md.digest(); } catch (Exception e) { e.printStackTrace(); } return convertToHex(md5hash); } | 18,685 |
1 | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | public static void upload(FTPDetails ftpDetails) { FTPClient ftp = new FTPClient(); try { String host = ftpDetails.getHost(); logger.info("Connecting to ftp host: " + host); ftp.connect(host); logger.info("Received reply from ftp :" + ftp.getReplyString()); ftp.login(ftpDetails.getUserName(), ftpDetails.getPassword()); ftp.setFileType(FTP.BINARY_FILE_TYPE); ftp.makeDirectory(ftpDetails.getRemoterDirectory()); logger.info("Created directory :" + ftpDetails.getRemoterDirectory()); ftp.changeWorkingDirectory(ftpDetails.getRemoterDirectory()); BufferedInputStream ftpInput = new BufferedInputStream(new FileInputStream(new File(ftpDetails.getLocalFilePath()))); OutputStream storeFileStream = ftp.storeFileStream(ftpDetails.getRemoteFileName()); IOUtils.copy(ftpInput, storeFileStream); logger.info("Copied file : " + ftpDetails.getLocalFilePath() + " >>> " + host + ":/" + ftpDetails.getRemoterDirectory() + "/" + ftpDetails.getRemoteFileName()); ftpInput.close(); storeFileStream.close(); ftp.logout(); ftp.disconnect(); logger.info("Logged out. "); } catch (Exception e) { throw new RuntimeException(e); } } | 18,686 |
0 | public void reload() throws SAXException, IOException { if (url != null) { java.io.InputStream is = url.openStream(); configDoc = builder.parse(is); is.close(); System.out.println("XML config file read correctly from " + url); } else { configDoc = builder.parse(configFile); System.out.println("XML config file read correctly from " + configFile); } } | List<String> HttpGet(URL url) throws IOException { List<String> responseList = new ArrayList<String>(); Logger.getInstance().logInfo("HTTP GET: " + url, null, null); URLConnection con = url.openConnection(); con.setAllowUserInteraction(false); BufferedReader in = new BufferedReader(new InputStreamReader(con.getInputStream())); String inputLine; while ((inputLine = in.readLine()) != null) responseList.add(inputLine); in.close(); return responseList; } | 18,687 |
1 | public static byte[] readHTTPFile(String url, StringBuffer contentType, StringBuffer encoding) { try { URL u = new URL(url); URLConnection urlConn = u.openConnection(); urlConn.setReadTimeout(10 * 1000); urlConn.setConnectTimeout(10 * 1000); urlConn.setDoInput(true); urlConn.setDoOutput(false); String status = urlConn.getHeaderField(null).toLowerCase(); String location = urlConn.getHeaderField("Location"); String cookie = urlConn.getHeaderField("Set-Cookie"); int times = 0; while ((status.indexOf("http/1.1 3") >= 0 || status.indexOf("http/1.0 3") >= 0) && !HelperStd.isEmpty(location)) { if (!HelperStd.isEmpty(urlConn.getHeaderField("Set-Cookie"))) cookie = urlConn.getHeaderField("Set-Cookie"); u = new URL(location); urlConn = u.openConnection(); urlConn.setReadTimeout(10 * 1000); urlConn.setConnectTimeout(10 * 1000); urlConn.setDoInput(true); urlConn.setDoOutput(false); urlConn.setRequestProperty("Cookie", cookie); status = urlConn.getHeaderField(null).toLowerCase(); location = urlConn.getHeaderField("Location"); times++; if (times > 10) break; } System.out.println(urlConn.getHeaderField(null) + ":" + urlConn.getContentLength() + ":" + u); if (contentType != null) contentType.append(urlConn.getContentType()); if (encoding != null) { String enc = null, ct = urlConn.getContentType(); if (ct != null && ct.indexOf("charset=") > 0) { int a = ct.indexOf("charset=") + "charset=".length(); enc = ct.substring(a); } if (enc == null) enc = urlConn.getContentEncoding(); if (enc == null) enc = "ISO-8859-1"; encoding.append(enc); } BufferedInputStream in = new BufferedInputStream(urlConn.getInputStream()); ByteArrayOutputStream bout = new ByteArrayOutputStream(); byte[] b = new byte[1024]; int read = 0; while (read != -1) { read = in.read(b); if (read > 0) bout.write(b, 0, read); } in.close(); System.out.println(bout.size()); return bout.toByteArray(); } catch (Exception e) { e.printStackTrace(); System.out.println("readHTTPFile:" + e.getMessage() + "," + url); } return new byte[0]; } | public static void main(String[] args) { StringBuffer htmlPage; htmlPage = new StringBuffer(); double min = 99999.99; double max = 0; double value = 0; try { URL url = new URL("http://search.ebay.com/" + args[0]); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); String line; while ((line = in.readLine()) != null) { htmlPage.append(line); htmlPage.append("\n"); } } catch (Exception ex) { ex.printStackTrace(); } Pattern p = Pattern.compile("\\$([\\d\\.]+)", Pattern.CASE_INSENSITIVE); Matcher m = p.matcher(htmlPage); while (m.find()) { if (m.start(0) < m.end(0)) { value = Double.parseDouble(m.group(1)); if (value < min) { min = value; } if (value > max) { max = value; } } } if (min == 99999.99) { min = 0; } System.out.println(args[0] + "," + min + "," + max); System.exit(0); } | 18,688 |
1 | private String unzip(TupleInput input) { boolean zipped = input.readBoolean(); if (!zipped) { return input.readString(); } int len = input.readInt(); try { byte array[] = new byte[len]; input.read(array); GZIPInputStream in = new GZIPInputStream(new ByteArrayInputStream(array)); ByteArrayOutputStream out = new ByteArrayOutputStream(); IOUtils.copyTo(in, out); in.close(); out.close(); return new String(out.toByteArray()); } catch (IOException err) { throw new RuntimeException(err); } } | public void copyFile(String source_name, String dest_name) throws IOException { File source_file = new File(source_name); File destination_file = new File(dest_name); Reader source = null; Writer destination = null; char[] buffer; int bytes_read; try { if (!source_file.exists() || !source_file.isFile()) throw new FileCopyException("FileCopy: no such source file: " + source_name); if (!source_file.canRead()) throw new FileCopyException("FileCopy: source file " + "is unreadable: " + source_name); if (destination_file.exists()) { if (destination_file.isFile()) { DataInputStream in = new DataInputStream(System.in); String response; if (!destination_file.canWrite()) throw new FileCopyException("FileCopy: destination " + "file is unwriteable: " + dest_name); } else { throw new FileCopyException("FileCopy: destination " + "is not a file: " + dest_name); } } else { File parentdir = parent(destination_file); if (!parentdir.exists()) throw new FileCopyException("FileCopy: destination " + "directory doesn't exist: " + dest_name); if (!parentdir.canWrite()) throw new FileCopyException("FileCopy: destination " + "directory is unwriteable: " + dest_name); } source = new BufferedReader(new FileReader(source_file)); destination = new BufferedWriter(new FileWriter(destination_file)); buffer = new char[1024]; while (true) { bytes_read = source.read(buffer, 0, 1024); if (bytes_read == -1) break; destination.write(buffer, 0, bytes_read); } } finally { if (source != null) { try { source.close(); } catch (IOException e) { ; } } if (destination != null) { try { destination.close(); } catch (IOException e) { ; } } } } | 18,689 |
0 | public static void gunzip(File gzippedFile, File destinationFile) throws IOException { int buffer = 2048; FileInputStream in = new FileInputStream(gzippedFile); GZIPInputStream zipin = new GZIPInputStream(in); byte[] data = new byte[buffer]; FileOutputStream out = new FileOutputStream(destinationFile); int length; while ((length = zipin.read(data, 0, buffer)) != -1) out.write(data, 0, length); out.close(); zipin.close(); } | private Document parseResponse(String url) throws IOException, MalformedURLException, ParserConfigurationException, SAXException { DocumentBuilder db = DocumentBuilderFactory.newInstance().newDocumentBuilder(); InputStream stream = null; try { stream = new URL(url).openStream(); return db.parse(stream); } finally { PetstoreUtil.closeIgnoringException(stream); } } | 18,690 |
0 | public static void copyFile(File source, File destination) { if (!source.exists()) { return; } if ((destination.getParentFile() != null) && (!destination.getParentFile().exists())) { destination.getParentFile().mkdirs(); } try { FileChannel srcChannel = new FileInputStream(source).getChannel(); FileChannel dstChannel = new FileOutputStream(destination).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (IOException ioe) { ioe.printStackTrace(); } } | public static String md5encrypt(String toEncrypt) { if (toEncrypt == null) { throw new IllegalArgumentException("null is not a valid password to encrypt"); } try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(toEncrypt.getBytes()); byte[] hash = md.digest(); return new String(dumpBytes(hash)); } catch (NoSuchAlgorithmException nsae) { return toEncrypt; } } | 18,691 |
1 | private String SHA1(String text) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md; md = MessageDigest.getInstance("SHA-1"); byte[] sha1hash = new byte[40]; md.update(text.getBytes("iso-8859-1"), 0, text.length()); sha1hash = md.digest(); return convertToHex(sha1hash); } | public boolean check(Object credentials) { String password = (credentials instanceof String) ? (String) credentials : credentials.toString(); try { MessageDigest md = MessageDigest.getInstance("MD5"); byte[] ha1; if (credentials instanceof Credential.MD5) { ha1 = ((Credential.MD5) credentials).getDigest(); } else { md.update(username.getBytes(StringUtil.__ISO_8859_1)); md.update((byte) ':'); md.update(realm.getBytes(StringUtil.__ISO_8859_1)); md.update((byte) ':'); md.update(password.getBytes(StringUtil.__ISO_8859_1)); ha1 = md.digest(); } md.reset(); md.update(method.getBytes(StringUtil.__ISO_8859_1)); md.update((byte) ':'); md.update(uri.getBytes(StringUtil.__ISO_8859_1)); byte[] ha2 = md.digest(); md.update(TypeUtil.toString(ha1, 16).getBytes(StringUtil.__ISO_8859_1)); md.update((byte) ':'); md.update(nonce.getBytes(StringUtil.__ISO_8859_1)); md.update((byte) ':'); md.update(nc.getBytes(StringUtil.__ISO_8859_1)); md.update((byte) ':'); md.update(cnonce.getBytes(StringUtil.__ISO_8859_1)); md.update((byte) ':'); md.update(qop.getBytes(StringUtil.__ISO_8859_1)); md.update((byte) ':'); md.update(TypeUtil.toString(ha2, 16).getBytes(StringUtil.__ISO_8859_1)); byte[] digest = md.digest(); return (TypeUtil.toString(digest, 16).equalsIgnoreCase(response)); } catch (Exception e) { Log.warn(e); } return false; } | 18,692 |
1 | public BufferedWriter createOutputStream(String inFile, String outFile) throws IOException { int k_blockSize = 1024; int byteCount; char[] buf = new char[k_blockSize]; File ofp = new File(outFile); ZipOutputStream zos = new ZipOutputStream(new FileOutputStream(ofp)); zos.setMethod(ZipOutputStream.DEFLATED); OutputStreamWriter osw = new OutputStreamWriter(zos, "ISO-8859-1"); BufferedWriter bw = new BufferedWriter(osw); ZipEntry zot = null; File ifp = new File(inFile); ZipInputStream zis = new ZipInputStream(new FileInputStream(ifp)); InputStreamReader isr = new InputStreamReader(zis, "ISO-8859-1"); BufferedReader br = new BufferedReader(isr); ZipEntry zit = null; while ((zit = zis.getNextEntry()) != null) { if (zit.getName().equals("content.xml")) { continue; } zot = new ZipEntry(zit.getName()); zos.putNextEntry(zot); while ((byteCount = br.read(buf, 0, k_blockSize)) >= 0) bw.write(buf, 0, byteCount); bw.flush(); zos.closeEntry(); } zos.putNextEntry(new ZipEntry("content.xml")); bw.flush(); osw = new OutputStreamWriter(zos, "UTF8"); bw = new BufferedWriter(osw); return bw; } | 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(); } } | 18,693 |
1 | public void test3() throws FileNotFoundException, IOException { Decoder decoder1 = new MP3Decoder(new FileInputStream("/home/marc/tmp/test1.mp3")); Decoder decoder2 = new OggDecoder(new FileInputStream("/home/marc/tmp/test1.ogg")); FileOutputStream out = new FileOutputStream("/home/marc/tmp/test.pipe"); IOUtils.copy(decoder1, out); IOUtils.copy(decoder2, out); } | private static void copyFile(String src, String dest) throws IOException { File destFile = new File(dest); if (destFile.exists()) { destFile.delete(); } FileChannel srcChannel = new FileInputStream(src).getChannel(); FileChannel dstChannel = new FileOutputStream(dest).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } | 18,694 |
0 | public JarClassLoader(ClassLoader parent) { super(parent); initLogger(); hmClass = new HashMap<String, Class<?>>(); lstJarFile = new ArrayList<JarFileInfo>(); hsDeleteOnExit = new HashSet<File>(); String sUrlTopJar = null; pd = getClass().getProtectionDomain(); CodeSource cs = pd.getCodeSource(); URL urlTopJar = cs.getLocation(); String protocol = urlTopJar.getProtocol(); JarFileInfo jarFileInfo = null; if ("http".equals(protocol) || "https".equals(protocol)) { try { urlTopJar = new URL("jar:" + urlTopJar + "!/"); JarURLConnection jarCon = (JarURLConnection) urlTopJar.openConnection(); JarFile jarFile = jarCon.getJarFile(); jarFileInfo = new JarFileInfo(jarFile, jarFile.getName(), null, null); logInfo(LogArea.JAR, "Loading from top JAR: '%s' PROTOCOL: '%s'", urlTopJar, protocol); } catch (Exception e) { logError(LogArea.JAR, "Failure to load HTTP JAR: %s %s", urlTopJar, e.toString()); return; } } if ("file".equals(protocol)) { try { sUrlTopJar = URLDecoder.decode(urlTopJar.getFile(), "UTF-8"); } catch (UnsupportedEncodingException e) { logError(LogArea.JAR, "Failure to decode URL: %s %s", urlTopJar, e.toString()); return; } File fileJar = new File(sUrlTopJar); if (fileJar.isDirectory()) { logInfo(LogArea.JAR, "Loading from exploded directory: %s", sUrlTopJar); return; } try { jarFileInfo = new JarFileInfo(new JarFile(fileJar), fileJar.getName(), null, null); logInfo(LogArea.JAR, "Loading from top JAR: '%s' PROTOCOL: '%s'", sUrlTopJar, protocol); } catch (IOException e) { logError(LogArea.JAR, "Not a JAR: %s %s", sUrlTopJar, e.toString()); return; } } try { if (jarFileInfo == null) { throw new IOException(String.format("Unknown protocol %s", protocol)); } loadJar(jarFileInfo); } catch (IOException e) { logError(LogArea.JAR, "Not valid URL: %s %s", urlTopJar, e.toString()); return; } checkShading(); Runtime.getRuntime().addShutdownHook(new Thread() { public void run() { shutdown(); } }); } | private void publishCMap(LWMap map) throws IOException { try { File savedCMap = PublishUtil.createIMSCP(Publisher.resourceVector); InputStream istream = new BufferedInputStream(new FileInputStream(savedCMap)); OutputStream ostream = new BufferedOutputStream(new FileOutputStream(ActionUtil.selectFile("IMSCP", "zip"))); int fileLength = (int) savedCMap.length(); byte bytes[] = new byte[fileLength]; while (istream.read(bytes, 0, fileLength) != -1) ostream.write(bytes, 0, fileLength); istream.close(); ostream.close(); } catch (IOException ex) { throw ex; } catch (Exception ex) { System.out.println(ex); VueUtil.alert(VUE.getDialogParent(), VueResources.getString("dialog.export.message") + ex.getMessage(), VueResources.getString("dialog.export.title"), JOptionPane.ERROR_MESSAGE); } } | 18,695 |
0 | public static void createZipFromDataset(String localResourceId, File dataset, File metadata) { CommunicationLogger.warning("System entered ZipFactory"); try { String tmpDir = System.getProperty("java.io.tmpdir"); String outFilename = tmpDir + "/" + localResourceId + ".zip"; CommunicationLogger.warning("File name: " + outFilename); ZipOutputStream out = new ZipOutputStream(new FileOutputStream(outFilename)); byte[] buf = new byte[1024]; FileInputStream in = new FileInputStream(dataset); out.putNextEntry(new ZipEntry(dataset.getName())); int len; while ((len = in.read(buf)) > 0) out.write(buf, 0, len); in = new FileInputStream(metadata); out.putNextEntry(new ZipEntry(metadata.getName())); while ((len = in.read(buf)) > 0) out.write(buf, 0, len); out.closeEntry(); in.close(); out.close(); } catch (IOException e) { System.out.println("IO EXCEPTION: " + e.getMessage()); } } | @Override protected Set<DataRecord> retrieveRecords(DataTemplate template) { String query = template.getQuery(); if (query == null) { query = topic; } String select = prefix + " SELECT ?resource WHERE { { ?resource rdf:type " + "<http://dbpedia.org/class/yago/" + StringUtils.toCamelCase(query) + "> } UNION { ?resource skos:subject <http://dbpedia.org/resource/Category:" + query.replaceAll(" ", "_") + "> } }"; Document doc = null; HashSet<DataRecord> recs = new HashSet<DataRecord>(); try { URL url = new URL(queryBase + URLEncoder.encode(select, "UTF-8")); InputStream inStream = url.openStream(); doc = docBuild.parse(inStream); HashSet<String> resourceNames = new HashSet<String>(); Element table = doc.getDocumentElement(); NodeList rows = table.getElementsByTagName("tr"); for (int i = 0; i < rows.getLength(); i++) { Element row = (Element) rows.item(i); NodeList cols = row.getElementsByTagName("td"); if (cols.getLength() > 0) { Element elem = (Element) cols.item(0); String resource = ((Text) elem.getFirstChild()).getData(); resourceNames.add(resource); } } inStream.close(); for (String resource : resourceNames) { MultiValueMap<String> resRecord = queryResource(resource); if (resource != null) { DataRecord rec = parseResource(resRecord, template); if (rec != null) { recs.add(rec); } } } } catch (IOException exc) { exc.printStackTrace(); } catch (SAXException exc) { exc.printStackTrace(); } return recs; } | 18,696 |
1 | public static LicenseKey parseKey(String key) throws InvalidLicenseKeyException { final String f_key = key.trim(); StringTokenizer st = new StringTokenizer(f_key, FIELD_SEPERATOR); int tc = st.countTokens(); int tc_name = tc - 9; try { final String product = st.nextToken(); final String type = st.nextToken(); final String loadStr = st.nextToken(); final int load = Integer.parseInt(loadStr); final String lowMajorVersionStr = st.nextToken(); final int lowMajorVersion = Integer.parseInt(lowMajorVersionStr); final String lowMinorVersionStr = st.nextToken(); final double lowMinorVersion = Double.parseDouble("0." + lowMinorVersionStr); final String highMajorVersionStr = st.nextToken(); final int highMajorVersion = Integer.parseInt(highMajorVersionStr); final String highMinorVersionStr = st.nextToken(); final double highMinorVersion = Double.parseDouble("0." + highMinorVersionStr); String regName = ""; for (int i = 0; i < tc_name; i++) regName += (i == 0 ? st.nextToken() : FIELD_SEPERATOR + st.nextToken()); final String randomHexStr = st.nextToken(); final String md5Str = st.nextToken(); String subKey = f_key.substring(0, f_key.indexOf(md5Str) - 1); byte[] md5; MessageDigest md = null; md = MessageDigest.getInstance("MD5"); md.update(subKey.getBytes()); md.update(FIELD_SEPERATOR.getBytes()); md.update(zuonicsPassword.getBytes()); md5 = md.digest(); String testKey = subKey + FIELD_SEPERATOR; for (int i = 0; i < md5.length; i++) testKey += Integer.toHexString(md5[i]).toUpperCase(); if (!testKey.equals(f_key)) throw new InvalidLicenseKeyException("doesn't hash"); final String f_regName = regName; return new LicenseKey() { public String getProduct() { return product; } public String getType() { return type; } public int getLoad() { return load; } public String getRegName() { return f_regName; } public double getlowVersion() { return lowMajorVersion + lowMinorVersion; } public double getHighVersion() { return highMajorVersion + highMinorVersion; } public String getRandomHexStr() { return randomHexStr; } public String getMD5HexStr() { return md5Str; } public String toString() { return f_key; } public boolean equals(Object obj) { if (obj.toString().equals(toString())) return true; return false; } }; } catch (Exception e) { throw new InvalidLicenseKeyException(e.getMessage()); } } | public String calculateProjectMD5(String scenarioName) throws Exception { Scenario s = ScenariosManager.getInstance().getScenario(scenarioName); s.loadParametersAndValues(); String scenarioMD5 = calculateScenarioMD5(s); Map<ProjectComponent, String> map = getProjectMD5(new ProjectComponent[] { ProjectComponent.resources, ProjectComponent.classes, ProjectComponent.suts, ProjectComponent.libs }); map.put(ProjectComponent.currentScenario, scenarioMD5); MessageDigest md = MessageDigest.getInstance("MD5"); Iterator<String> iter = map.values().iterator(); while (iter.hasNext()) { md.update(iter.next().getBytes()); } byte[] hash = md.digest(); BigInteger result = new BigInteger(hash); String rc = result.toString(16); return rc; } | 18,697 |
1 | private void copy(File sourceFile, File destinationFile) { try { FileChannel in = new FileInputStream(sourceFile).getChannel(); FileChannel out = new FileOutputStream(destinationFile).getChannel(); try { in.transferTo(0, in.size(), out); in.close(); out.close(); } catch (IOException e) { GTLogger.getInstance().error(e); } } catch (FileNotFoundException e) { GTLogger.getInstance().error(e); } } | public static boolean copyFile(String fromfile, String tofile) { File from = new File(fromfile); File to = new File(tofile); if (!from.exists()) return false; if (to.exists()) { log.error(tofile + "exists already"); return false; } BufferedInputStream in = null; BufferedOutputStream out = null; FileInputStream fis = null; FileOutputStream ois = null; boolean flag = true; try { to.createNewFile(); fis = new FileInputStream(from); ois = new FileOutputStream(to); in = new BufferedInputStream(fis); out = new BufferedOutputStream(ois); byte[] buf = new byte[2048]; int readBytes = 0; while ((readBytes = in.read(buf, 0, buf.length)) != -1) { out.write(buf, 0, readBytes); } } catch (IOException e) { log.error(e); flag = false; } finally { try { if (in != null) in.close(); if (out != null) out.close(); } catch (IOException e) { log.error(e); flag = false; } } return flag; } | 18,698 |
0 | public static String getSHADigest(String input) { if (input == null) return null; MessageDigest sha = null; try { sha = MessageDigest.getInstance("SHA-1"); } catch (java.security.NoSuchAlgorithmException nsae) { throw new RuntimeException(nsae); } if (sha == null) throw new RuntimeException("No message digest"); sha.update(input.getBytes()); byte[] data = sha.digest(); StringBuffer buf = new StringBuffer(data.length * 2); for (int i = 0; i < data.length; i++) { int value = data[i] & 0xff; buf.append(hexDigit(value >> 4)); buf.append(hexDigit(value)); } return buf.toString(); } | public static void copyFile(File src, File dest, boolean force) throws IOException, InterruptedIOException { if (dest.exists()) { if (force) { dest.delete(); } else { throw new IOException("Cannot overwrite existing file!"); } } byte[] buffer = new byte[5 * 1024 * 1024]; int read = 0; InputStream in = null; OutputStream out = null; try { in = new BufferedInputStream(new FileInputStream(src)); out = new BufferedOutputStream(new FileOutputStream(dest)); while (true) { read = in.read(buffer); if (read == -1) { break; } out.write(buffer, 0, read); } } finally { buffer = null; if (in != null) { try { in.close(); } finally { if (out != null) { out.close(); } } } } } | 18,699 |
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